\n Overcoming the natural recalcitrance of lignocellulosic biomass is necessary in order to efficiently convert biomass into biofuels or biomaterials and many times this requires some type of chemical pretreatment and/or biological treatment. While bulk chemical analysis is the traditional method of determining the impact a treatment has on biomass, the chemistry on the surface of the sample can differ from the bulk chemistry. Specifically, enzymes and microorganisms bind to the surface of the biomass and their efficiency could be greatly impacted by the chemistry of the surface. Therefore, it is important to study and understand the chemistry of the biomass at the surface. Time\u2010of\u2010flight secondary ion mass spectrometry (ToF\u2010\n
\n Overcoming the natural recalcitrance of lignocellulosic biomass is necessary in order to efficiently convert biomass into biofuels or biomaterials and many times this requires some type of chemical pretreatment and/or biological treatment. While bulk chemical analysis is the traditional method of determining the impact a treatment has on biomass, the chemistry on the surface of the sample can differ from the bulk chemistry. Specifically, enzymes and microorganisms bind to the surface of the biomass and their efficiency could be greatly impacted by the chemistry of the surface. Therefore, it is important to study and understand the chemistry of the biomass at the surface. Time\u2010of\u2010flight secondary ion mass spectrometry (ToF\u2010\n
Improving access to the carbohydrate content of lignocellulose is key to reducing recalcitrance for microbial deconstruction and conversion to fuels and chemicals.
Improving access to the carbohydrate content of lignocellulose is key to reducing recalcitrance for microbial deconstruction and conversion to fuels and chemicals.
Future production of renewable transportation fuels such as ethanol must rely on abundant nonfood plant sources also known as lignocellulosic biomass. However, a major historical barrier to low-cost production of ethanol from biomass is the low ethanol yields and titers that result from fermentation of biomass solids at high solids when compared with simple sugar fermentations. Here, we show that combining a cosolvent-enhanced lignocellulosic fractionation (CELF) pretreatment process with subsequent simultaneous saccharification and fermentation (SSF) can achieve similar high ethanol yields and titers that match that of separate pure glucose fermentations. We demonstrate a strategy whereby direct fermentation of biomass to ethanol is now limited by the microbe rather than by the process.
", "abstract": "Future production of renewable transportation fuels such as ethanol must rely on abundant nonfood plant sources also known as lignocellulosic biomass. However, a major historical barrier to low-cost production of ethanol from biomass is the low ethanol yields and titers that result from fermentation of biomass solids at high solids when compared with simple sugar fermentations. Here, we show that combining a cosolvent-enhanced lignocellulosic fractionation (CELF) pretreatment process with subsequent simultaneous saccharification and fermentation (SSF) can achieve similar high ethanol yields and titers that match that of separate pure glucose fermentations. We demonstrate a strategy whereby direct fermentation of biomass to ethanol is now limited by the microbe rather than by the process.
", "date": "2017-10-15", "issue": "44", "identifier": "https://www.osti.gov/biblio/1399640", "bibliographicCitation": "https://doi.org/10.1073/pnas.1704652114", "topic": [ "Unknown" ], "journal_name": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "114", "publisher_information": "Proceedings of the National Academy of Sciences", "country_publication_code": "US", "creator": [ { "name": "Thanh Yen [Department of Bioengineering,Bourns College of Engineering,University of California,Riverside,CA 92507,,Center for Environmental Research and Technology (CE-CERT),Bourns College of Engineering,University of California,Riverside,CA 92507,] Nguyen", "primaryContact": true }, { "name": "Charles M. [Center for Environmental Research and Technology (CE-CERT),Bourns College of Engineering,University of California,Riverside,CA 92507,,Department of Chemical and Environmental Engineering,Bourns College of Engineering,University of California,Riverside,CA 92507,,BioEnergy Science Center (BESC),Oak Ridge National Laboratory,Oak Ridge,TN 37831] (ORCID:0000000250470815) Cai", "primaryContact": false }, { "name": "Rajeev [Center for Environmental Research and Technology (CE-CERT),Bourns College of Engineering,University of California,Riverside,CA 92507,,BioEnergy Science Center (BESC),Oak Ridge National Laboratory,Oak Ridge,TN 37831] Kumar", "primaryContact": false }, { "name": "Charles E. [Department of Bioengineering,Bourns College of Engineering,University of California,Riverside,CA 92507,,Center for Environmental Research and Technology (CE-CERT),Bourns College of Engineering,University of California,Riverside,CA 92507,,Department of Chemical and Environmental Engineering,Bourns College of Engineering,University of California,Riverside,CA 92507,,BioEnergy Science Center (BESC),Oak Ridge National Laboratory,Oak Ridge,TN 37831] Wyman", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/1399640", "active": false }, { "brc": "CBI", "title": "Strengths, challenges, and opportunities for hydrothermal pretreatment in lignocellulosic biorefineries", "description": "Pretreatment prior to or during biological conversion is required to achieve high sugar yields essential to economic production of fuels and chemicals from low cost, abundant lignocellulosic biomass. Aqueous thermochemical pretreatments achieve this performance objective from pretreatment coupled with subsequent enzymatic hydrolysis, but chemical pretreatment can also suffer from additional costs for exotic materials of construction, the need to recover or neutralize the chemicals, introduction of compounds that inhibit downstream operations, and waste disposal, as well as for the chemicals themselves. The simplicity of hydrothermal pretreatment with just hot water offers the potential to greatly improve the cost of the entire conversion process if sugar degradation during pretreatment, production of un-fermentable oligomers, and the amount of expensive enzymes needed to obtain satisfactory yields from hydrothermally pretreated solids can be reduced. Biorefinery economics would also benefit if value could be generated from lignin and other components that are currently fated to be burned for power. However, achieving these goals will no doubt require development of advanced hydrothermal pretreatment configurations. For example, passing water through a stationary bed of lignocellulosic biomass in a flowthrough configuration achieves very high yields of hemicellulose sugars, removes more than 75% of the lignin for potential valorization, and improves sugar release from the pretreated solids with lower enzyme loadings. Unfortunately, the large quantities of water needed to achieve this performance result in very dilute sugars, high energy costs for pretreatment and product recover, and large amounts of oligomers. Furthermore, improving our understanding of hydrothermal pretreatment fundamentals is needed to gain insights into R&D opportunities to improve performance, and help identify novel configurations that lower capital and operating costs and achieve higher yields.", "abstract": "Pretreatment prior to or during biological conversion is required to achieve high sugar yields essential to economic production of fuels and chemicals from low cost, abundant lignocellulosic biomass. Aqueous thermochemical pretreatments achieve this performance objective from pretreatment coupled with subsequent enzymatic hydrolysis, but chemical pretreatment can also suffer from additional costs for exotic materials of construction, the need to recover or neutralize the chemicals, introduction of compounds that inhibit downstream operations, and waste disposal, as well as for the chemicals themselves. The simplicity of hydrothermal pretreatment with just hot water offers the potential to greatly improve the cost of the entire conversion process if sugar degradation during pretreatment, production of un-fermentable oligomers, and the amount of expensive enzymes needed to obtain satisfactory yields from hydrothermally pretreated solids can be reduced. Biorefinery economics would also benefit if value could be generated from lignin and other components that are currently fated to be burned for power. However, achieving these goals will no doubt require development of advanced hydrothermal pretreatment configurations. For example, passing water through a stationary bed of lignocellulosic biomass in a flowthrough configuration achieves very high yields of hemicellulose sugars, removes more than 75% of the lignin for potential valorization, and improves sugar release from the pretreated solids with lower enzyme loadings. Unfortunately, the large quantities of water needed to achieve this performance result in very dilute sugars, high energy costs for pretreatment and product recover, and large amounts of oligomers. Furthermore, improving our understanding of hydrothermal pretreatment fundamentals is needed to gain insights into R&D opportunities to improve performance, and help identify novel configurations that lower capital and operating costs and achieve higher yields.", "date": "2017-10-10", "issue": "1", "identifier": "https://www.osti.gov/biblio/1405277", "bibliographicCitation": "https://doi.org/10.1002/bbb.1825", "keywords": [ "09 BIOMASS FUELS", "biomass", "hydrothermal pretreatment", "lignin", "sugars", "water" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Biofuels, Bioproducts & Biorefining", "volume": "12", "publisher_information": "Wiley", "country_publication_code": "US", "creator": [ { "name": "Bin [Washington State Univ.,Richland,WA (United States)] (ORCID:0000000316868800) Yang", "primaryContact": true }, { "name": "Ling [National Renewable Energy Lab. (NREL),Golden,CO (United States)] Tao", "primaryContact": false }, { "name": "Charles E. [Univ. of California,Riverside,CA (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Wyman", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Bioenergy Technologies Office (EE-3B)" } } ], "dataset_url": "https://www.osti.gov/biblio/1405277", "active": false, "has_related_ids": [ "NREL/JA--5100-70374" ] }, { "brc": "CBI", "title": "The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project", "description": "Considerable progress has been made in ecological and evolutionary genetics with studies demonstrating how genes underlying plant and microbial traits can influence adaptation and even \u2018extend\u2019 to influence community structure and ecosystem level processes. The progress in this area is limited to model systems with deep genetic and genomic resources that often have negligible ecological impact or interest. Therefore, important linkages between genetic adaptations and their consequences at organismal and ecological scales are often lacking. We introduce the Sphagnome Project, which incorporates genomics into a long-running history of Sphagnum research that has documented unparalleled contributions to peatland ecology, carbon sequestration, biogeochemistry, microbiome research, niche construction, and ecosystem engineering. The Sphagnome Project encompasses a genus-level sequencing effort that represents a new type of model system driven not only by genetic tractability, but by ecologically relevant questions and hypotheses.", "abstract": "Considerable progress has been made in ecological and evolutionary genetics with studies demonstrating how genes underlying plant and microbial traits can influence adaptation and even \u2018extend\u2019 to influence community structure and ecosystem level processes. The progress in this area is limited to model systems with deep genetic and genomic resources that often have negligible ecological impact or interest. Therefore, important linkages between genetic adaptations and their consequences at organismal and ecological scales are often lacking. We introduce the Sphagnome Project, which incorporates genomics into a long-running history of Sphagnum research that has documented unparalleled contributions to peatland ecology, carbon sequestration, biogeochemistry, microbiome research, niche construction, and ecosystem engineering. The Sphagnome Project encompasses a genus-level sequencing effort that represents a new type of model system driven not only by genetic tractability, but by ecologically relevant questions and hypotheses.", "date": "2017-10-26", "issue": "NA", "identifier": "https://www.osti.gov/biblio/1407984", "bibliographicCitation": "https://doi.org/10.1111/nph.14860", "keywords": [ "54 ENVIRONMENTAL SCIENCES", "60 APPLIED LIFE SCIENCES", "Sphagnome", "Sphagnum", "ecological genomics", "ecosystem engineering", "evolutionary genetics", "genome sequencing", "niche construction", "peatlands" ], "topic": [ "Environmental Science & Sustainability", "Plant Biology" ], "journal_name": "New Phytologist", "volume": "NA", "publisher_information": "Wiley", "country_publication_code": "US", "creator": [ { "name": "David J. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Biosciences Division,Climate Change Science Inst.] (ORCID:0000000247949913) Weston", "primaryContact": true }, { "name": "Merritt R. [Univ. of Guelph,ON (Canada). Dept. of Integrative Biology] Turetsky", "primaryContact": false }, { "name": "Matthew G. [Texas Tech Univ.,Lubbock,TX (United States). Dept. of Biological Sciences] Johnson", "primaryContact": false }, { "name": "Gustaf [Swedish Univ. of Agricultural Sciences (SLU),Uppsala (Sweden). Dept. of Ecology] Granath", "primaryContact": false }, { "name": "Zo\u00eb [Univ. of Western Ontario,London,ON (Canada). Dept. of Biology] Lindo", "primaryContact": false }, { "name": "Lisa R. [Queen Mary Univ. of London (United Kingdom). School of Geography] Belyea", "primaryContact": false }, { "name": "Steven K. [Union College,Schenectady,NY (United States). Dept. of Biological Sciences] Rice", "primaryContact": false }, { "name": "David T. [Univ. of New Mexico,Albuquerque,NM (United States). Dept. of Biology] Hanson", "primaryContact": false }, { "name": "Katharina A. M. [Univ. of Maryland Center of Environmental Science,Frostburg,MD (United States). Applachian Lab.] Engelhardt", "primaryContact": false }, { "name": "Jeremy [HudsonAlpha Inst. of Biotechnology,Huntsville,AL (United States); USDOE Joint Genome Institute (JGI),Walnut Creek,CA (United States)] Schmutz", "primaryContact": false }, { "name": "Ellen [Umea Univ. (Sweden). Dept. of Ecology and Environmental Science] Dorrepaal", "primaryContact": false }, { "name": "Eug\u00e9nie S. [Univ. of Alaska,Fairbanks,AK (United States). Inst. of Arctic Biology] Euskirchen", "primaryContact": false }, { "name": "Hans K. [Norwegian Univ. of Science and Technology,Trondheim (Norway). NTNU Univ. Museum] Sten\u00f8ien", "primaryContact": false }, { "name": "P\u00e9ter [Univ. of Zurich (Switzerland). Dept. of Systematic and Evolutionary Botany] Sz\u00f6v\u00e9nyi", "primaryContact": false }, { "name": "Michelle [Duke Univ.,Durham,NC (United States). Dept. of Biology] Jackson", "primaryContact": false }, { "name": "Bryan T. [Duke Univ.,Durham,NC (United States). Dept. of Biology] Piatkowski", "primaryContact": false }, { "name": "Wellington [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Biosciences Division] (ORCID:0000000202009856) Muchero", "primaryContact": false }, { "name": "Richard J. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Climate Change Science Inst.,Environmental Sciences Division] (ORCID:0000000202389828) Norby", "primaryContact": false }, { "name": "Joel E. [Georgia Inst. of Technology,Atlanta,GA (United States). Schools of Biology and Earth and Atmospheric Sciences] Kostka", "primaryContact": false }, { "name": "Jennifer B. [Georgia Inst. of Technology,Atlanta,GA (United States). Schools of Biology and Earth and Atmospheric Sciences] Glass", "primaryContact": false }, { "name": "H\u00e5kan [Uppsala Univ. (Sweden). Dept. of Ecology and Genetics] Rydin", "primaryContact": false }, { "name": "Juul [Wageningen Univ. (Netherlands). Plant Ecology and Nature Conservation Group,Dept. of Environmental Sciences] Limpens", "primaryContact": false }, { "name": "Eeva-Stiina [Univ. of Eastern Finland,Joensuu (Finland). School of Forest Sciences] Tuittila", "primaryContact": false }, { "name": "Kristian K. [Max Planck Inst. for Evolutionary Biology,Plon (Germany)] Ullrich", "primaryContact": false }, { "name": "Alyssa [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Biosciences Division] Carrell", "primaryContact": false }, { "name": "Brian W. [Florida Atlantic Univ.,Davie,FL (United States). Dept. of Biological Sciences] Benscoter", "primaryContact": false }, { "name": "Jin-Gui [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Biosciences Division] (ORCID:0000000217524201) Chen", "primaryContact": false }, { "name": "Tobi A. [Univ. of Guelph,ON (Canada). Dept. of Integrative Biology] Oke", "primaryContact": false }, { "name": "Mats B. [Swedish Univ. of Agricultural Sciences (SLU),Umea (Sweden). Dept. of Forest Ecology and Management] Nilsson", "primaryContact": false }, { "name": "Priya [Univ. of Tennessee,Knoxville,TN (United States). Dept of Plant Sciences] Ranjan", "primaryContact": false }, { "name": "Daniel [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Biosciences Division] (ORCID:0000000298228251) Jacobson", "primaryContact": false }, { "name": "Erik A. [Northern Research Station,Hougton,MI (United States). U.S. Forest Service] Lilleskov", "primaryContact": false }, { "name": "R. S. [Queen Mary Univ.,London (United Kingdom). School of Biological and Chemical Sciences] Clymo", "primaryContact": false }, { "name": "A. Jonathan [Duke Univ.,Durham,NC (United States). Dept. of Biology] Shaw", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1407984", "active": false }, { "brc": "CBI", "title": "Insights into cell wall structure of Sida hermaphrodita and its influence on recalcitrance", "description": "Not Available", "abstract": "Not Available", "date": "2017-06-30", "issue": "C", "identifier": "https://www.osti.gov/biblio/1413774", "bibliographicCitation": "https://doi.org/10.1016/j.carbpol.2017.03.062", "topic": [ "Unknown" ], "journal_name": "Carbohydrate Polymers", "volume": "168", "publisher_information": "Elsevier", "country_publication_code": "GB", "creator": [ { "name": "Tatjana Damm", "primaryContact": true }, { "name": "Sivakumar Pattathil", "primaryContact": false }, { "name": "Markus G\u00fcnl", "primaryContact": false }, { "name": "Nicolai David Jablonowski", "primaryContact": false }, { "name": "Malcolm O'Neill", "primaryContact": false }, { "name": "Katharina Susanne Gr\u00fcn", "primaryContact": false }, { "name": "Philipp Michael Grande", "primaryContact": false }, { "name": "Walter Leitner", "primaryContact": false }, { "name": "Ulrich Schurr", "primaryContact": false }, { "name": "Bj\u00f6rn Usadel", "primaryContact": false }, { "name": "Holger Klose", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/1413774", "active": false }, { "brc": "CBI", "title": "Extremely thermophilic energy metabolisms: biotechnological prospects", "description": "Not Available", "abstract": "Not Available", "date": "2017-05-31", "issue": "C", "identifier": "https://www.osti.gov/biblio/1416770", "bibliographicCitation": "https://doi.org/10.1016/j.copbio.2017.02.016", "topic": [ "Unknown" ], "journal_name": "Current Opinion in Biotechnology", "volume": "45", "publisher_information": "Elsevier", "country_publication_code": "GB", "creator": [ { "name": "Christopher T. Straub", "primaryContact": true }, { "name": "Benjamin M. Zeldes", "primaryContact": false }, { "name": "Gerrit J. Schut", "primaryContact": false }, { "name": "Michael WW Adams", "primaryContact": false }, { "name": "Robert M. Kelly", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Advanced Research Projects Agency - Energy (ARPA-E)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1416770", "active": false }, { "brc": "CBI", "title": "Lignocellulose deconstruction in the biosphere", "description": "Microorganisms have evolved different and yet complementary mechanisms to degrade biomass in the biosphere. The chemical biology of lignocellulose deconstruction is a complex and intricate process that appears to vary in response to specific ecosystems. These microorganisms rely on simple to complex arrangements of glycoside hydrolases to conduct most of these polysaccharide depolymerization reactions and also, as discovered more recently, oxidative mechanisms via lytic polysaccharide monooxygenases or non-enzymatic Fenton reactions which are used to enhance deconstruction. It is now clear that these deconstruction mechanisms are often more efficient in the presence of the microorganisms. In general, a major fraction of the total plant biomass deconstruction in the biosphere results from the action of various microorganisms, primarily aerobic bacteria and fungi, as well as a variety of anaerobic bacteria. Beyond carbon recycling, specialized microorganisms interact with plants to manage nitrogen in the biosphere. Understanding the interplay between these organisms within or across ecosystems is crucial to further our grasp of chemical recycling in the biosphere and also enables optimization of the burgeoning plant-based bioeconomy.", "abstract": "Microorganisms have evolved different and yet complementary mechanisms to degrade biomass in the biosphere. The chemical biology of lignocellulose deconstruction is a complex and intricate process that appears to vary in response to specific ecosystems. These microorganisms rely on simple to complex arrangements of glycoside hydrolases to conduct most of these polysaccharide depolymerization reactions and also, as discovered more recently, oxidative mechanisms via lytic polysaccharide monooxygenases or non-enzymatic Fenton reactions which are used to enhance deconstruction. It is now clear that these deconstruction mechanisms are often more efficient in the presence of the microorganisms. In general, a major fraction of the total plant biomass deconstruction in the biosphere results from the action of various microorganisms, primarily aerobic bacteria and fungi, as well as a variety of anaerobic bacteria. Beyond carbon recycling, specialized microorganisms interact with plants to manage nitrogen in the biosphere. Understanding the interplay between these organisms within or across ecosystems is crucial to further our grasp of chemical recycling in the biosphere and also enables optimization of the burgeoning plant-based bioeconomy.", "date": "2017-11-01", "issue": "C", "identifier": "https://www.osti.gov/biblio/1417727", "bibliographicCitation": "https://doi.org/10.1016/j.cbpa.2017.10.013", "keywords": [ "09 BIOMASS FUELS", "deconstruction", "depolymerization", "lignocellulose" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Current Opinion in Chemical Biology", "volume": "41", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Yannick J. [National Renewable Energy Laboratory (NREL),Golden,CO (United States)] Bomble", "primaryContact": true }, { "name": "Chien-Yuan [National Renewable Energy Laboratory (NREL),Golden,CO (United States)] Lin", "primaryContact": false }, { "name": "Antonella [National Renewable Energy Laboratory (NREL),Golden,CO (United States)] Amore", "primaryContact": false }, { "name": "Hui [National Renewable Energy Laboratory (NREL),Golden,CO (United States)] Wei", "primaryContact": false }, { "name": "Evert K. [National Renewable Energy Laboratory (NREL),Golden,CO (United States)] Holwerda", "primaryContact": false }, { "name": "Peter N. [National Renewable Energy Laboratory (NREL),Golden,CO (United States)] Ciesielski", "primaryContact": false }, { "name": "Bryon S. [National Renewable Energy Laboratory (NREL),Golden,CO (United States)] Donohoe", "primaryContact": false }, { "name": "Stephen R. [National Renewable Energy Laboratory (NREL),Golden,CO (United States)] Decker", "primaryContact": false }, { "name": "Lee R. [Dartmouth College,Hanover,NH (United States)] Lynd", "primaryContact": false }, { "name": "Michael E. [National Renewable Energy Laboratory (NREL),Golden,CO (United States)] Himmel", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Basic Energy Sciences (BES)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Office of Biological and Environmental Research" } } ], "dataset_url": "https://www.osti.gov/biblio/1417727", "active": false, "has_related_ids": [ "NREL/JA--2700-68493" ] }, { "brc": "CBI", "title": "Analyzing Xyloglucan Endotransglycosylases by Incorporating Synthetic Oligosaccharides into Plant Cell Walls", "description": "\n The plant cell wall is a cellular exoskeleton consisting predominantly of a complex polysaccharide network that defines the shape of cells. During growth, this network can be loosened through the action of xyloglucan endotransglycosylases (XETs), glycoside hydrolases that \u201ccut and paste\u201d xyloglucan polysaccharides through a transglycosylation process. We have analyzed cohorts of XETs in different plant species to evaluate the substrate specificities of xyloglucan acceptors by using a set of synthetic oligosaccharides obtained by automated glycan assembly. The ability of XETs to incorporate the oligosaccharides into polysaccharides printed as microarrays and into stem sections of\n
\n The plant cell wall is a cellular exoskeleton consisting predominantly of a complex polysaccharide network that defines the shape of cells. During growth, this network can be loosened through the action of xyloglucan endotransglycosylases (XETs), glycoside hydrolases that \u201ccut and paste\u201d xyloglucan polysaccharides through a transglycosylation process. We have analyzed cohorts of XETs in different plant species to evaluate the substrate specificities of xyloglucan acceptors by using a set of synthetic oligosaccharides obtained by automated glycan assembly. The ability of XETs to incorporate the oligosaccharides into polysaccharides printed as microarrays and into stem sections of\n
\n Currently, major biofuel crops are also food crops that demand fertile soils and good\u2010quality water. Jerusalem artichoke (\n
\n Currently, major biofuel crops are also food crops that demand fertile soils and good\u2010quality water. Jerusalem artichoke (\n
\n A reduction in the lignin content in transgenic plants induces the ectopic expression of defense genes, but the importance of altered lignin composition in such phenomena remains unclear. \n Two Arabidopsis lines with similar lignin contents, but strikingly different lignin compositions, exhibited different quantitative and qualitative transcriptional responses. Plants with lignin composed primarily of guaiacyl units overexpressed genes responsive to oomycete and bacterial pathogen attack, whereas plants with lignin composed primarily of syringyl units expressed a far greater number of defense genes, including some associated with\n Several of the defense genes were differentially induced by water\u2010soluble extracts from cell walls of plants of the two lines. Glycome profiling, fractionation and enzymatic digestion studies indicated that the different lignin compositions led to differential extractability of a range of heterogeneous oligosaccharide epitopes, with elicitor activity originating from different cell wall polymers. Alteration of lignin composition affects interactions with plant cell wall matrix polysaccharides to alter the sequestration of multiple latent defense signal molecules with an impact on biotic stress responses.\n
\n
\n A reduction in the lignin content in transgenic plants induces the ectopic expression of defense genes, but the importance of altered lignin composition in such phenomena remains unclear. \n Two Arabidopsis lines with similar lignin contents, but strikingly different lignin compositions, exhibited different quantitative and qualitative transcriptional responses. Plants with lignin composed primarily of guaiacyl units overexpressed genes responsive to oomycete and bacterial pathogen attack, whereas plants with lignin composed primarily of syringyl units expressed a far greater number of defense genes, including some associated with\n Several of the defense genes were differentially induced by water\u2010soluble extracts from cell walls of plants of the two lines. Glycome profiling, fractionation and enzymatic digestion studies indicated that the different lignin compositions led to differential extractability of a range of heterogeneous oligosaccharide epitopes, with elicitor activity originating from different cell wall polymers. Alteration of lignin composition affects interactions with plant cell wall matrix polysaccharides to alter the sequestration of multiple latent defense signal molecules with an impact on biotic stress responses.\n
\n
\n Cell wall recalcitrance is the major challenge to improving saccharification efficiency in converting lignocellulose into biofuels. However, information regarding the transcriptional regulation of secondary cell wall biogenesis remains poor in switchgrass (\n
\n Cell wall recalcitrance is the major challenge to improving saccharification efficiency in converting lignocellulose into biofuels. However, information regarding the transcriptional regulation of secondary cell wall biogenesis remains poor in switchgrass (\n
\n Screening the genetic diversity of 45\n
\n Screening the genetic diversity of 45\n
The formation of lignin-like structures by the degradation primarily of plant polysaccharides has been observed after the severe thermochemical acidic pretreatment of lignocellulosic biomass.
", "abstract": "The formation of lignin-like structures by the degradation primarily of plant polysaccharides has been observed after the severe thermochemical acidic pretreatment of lignocellulosic biomass.
", "date": "2018-04-09", "issue": "10", "identifier": "https://www.osti.gov/biblio/1474538", "bibliographicCitation": "https://doi.org/10.1039/C8GC00353J", "keywords": [ "09 BIOMASS FUELS" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Green Chemistry", "volume": "20", "publisher_information": "Royal Society of Chemistry", "country_publication_code": "US", "creator": [ { "name": "Somnath D. [Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:0000000207583937) Shinde", "primaryContact": true }, { "name": "Xianzhi [Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:0000000343033403) Meng", "primaryContact": false }, { "name": "Rajeev [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Bourns College of Engineering,Riverside,CA (United States)] (ORCID:0000000175230108) Kumar", "primaryContact": false }, { "name": "Arthur J. [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:000000023536554X) Ragauskas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1474538", "active": false }, { "brc": "CBI", "title": "Functional Analysis of the Glucan Degradation Locus in Caldicellulosiruptor bescii Reveals Essential Roles of Component Glycoside Hydrolases in Plant Biomass Deconstruction", "description": "We present that the ability to hydrolyze microcrystalline cellulose is an uncommon feature in the microbial world, but it can be exploited for conversion of lignocellulosic feedstocks into biobased fuels and chemicals. Understanding the physiological and biochemical mechanisms by which microorganisms deconstruct cellulosic material is key to achieving this objective. The glucan degradation locus (GDL) in the genomes of extremely thermophilic Caldicellulosiruptor species encodes polysaccharide lyases (PLs), unique cellulose binding proteins (tapirins), and putative posttranslational modifying enzymes, in addition to multidomain, multifunctional glycoside hydrolases (GHs), thereby representing an alternative paradigm for plant biomass degradation compared to fungal or cellulosomal systems. To examine the individual and collective in vivoroles of the glycolytic enzymes, the six GH genes in the GDL of Caldicellulosiruptor bescii were systematically deleted, and the extents to which the resulting mutant strains could solubilize microcrystalline cellulose (Avicel) and plant biomass (switchgrass or poplar) were examined. Three of the GDL enzymes, Athe_1867 (CelA) (GH9-CBM3-CBM3-CBM3-GH48), Athe_1859 (GH5-CBM3-CBM3-GH44), and Athe_1857 (GH10-CBM3-CBM3-GH48), acted synergisticallyCellulose solvent-based fractionation technologies can prove to be economical to enhance lignocellulosic biomass microbial conversion to fuels and chemicals.
", "abstract": "Cellulose solvent-based fractionation technologies can prove to be economical to enhance lignocellulosic biomass microbial conversion to fuels and chemicals.
", "date": "2018-12-31", "issue": "1", "identifier": "https://www.osti.gov/biblio/1476948", "bibliographicCitation": "https://doi.org/10.1039/C8SE00287H", "topic": [ "Unknown" ], "journal_name": "Sustainable Energy & Fuels", "volume": "3", "publisher_information": "Royal Society of Chemistry (RSC)", "country_publication_code": "GB", "creator": [ { "name": "Behzad [Department of Chemical Engineering,Isfahan University of Technology,Isfahan 84156-83111,Iran] (ORCID:0000000227388653) Satari", "primaryContact": true }, { "name": "Keikhosro [Department of Chemical Engineering,Isfahan University of Technology,Isfahan 84156-83111,Iran,Industrial Biotechnology Group] (ORCID:000000019030956X) Karimi", "primaryContact": false }, { "name": "Rajeev [Center for Environmental Research and Technology (CE-CERT),Bourns College of Engineering,University of California Riverside (UCR),Riverside,USA] (ORCID:0000000175230108) Kumar", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/1476948", "active": false }, { "brc": "CBI", "title": "Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing", "description": "Switchgrass (Panicum virgatum L.) is an important bioenergy crop widely used for lignocellulosic research. While extensive transcriptomic analyses have been conducted on this species using short read-based sequencing techniques, very little has been reliably derived regarding alternatively spliced (AS) transcripts. Here, we present an analysis of transcriptomes of six switchgrass tissue types pooled together, sequenced using Pacific Biosciences (PacBio) single-molecular long-read technology. Our analysis identified 105,419 unique transcripts covering 43,570 known genes and 8795 previously unknown genes. 45,168 are novel transcripts of known genes. A total of 60,096 AS transcripts are identified, 45,628 being novel. We have also predicted 1549 transcripts of genes involved in cell wall construction and remodeling, 639 being novel transcripts of known cell wall genes. Most of the predicted transcripts are validated against Illumina-based short reads. Specifically, 96% of the splice junction sites in all the unique transcripts are validated by at least five Illumina reads. Comparisons between genes derived from our identified transcripts and the current genome annotation revealed that among the gene set predicted by both analyses, 16,640 have different exon-intron structures. Overall, substantial amount of new information is derived from the PacBio RNA data regarding both the transcriptome and the genome of switchgrass.", "abstract": "Switchgrass (Panicum virgatum L.) is an important bioenergy crop widely used for lignocellulosic research. While extensive transcriptomic analyses have been conducted on this species using short read-based sequencing techniques, very little has been reliably derived regarding alternatively spliced (AS) transcripts. Here, we present an analysis of transcriptomes of six switchgrass tissue types pooled together, sequenced using Pacific Biosciences (PacBio) single-molecular long-read technology. Our analysis identified 105,419 unique transcripts covering 43,570 known genes and 8795 previously unknown genes. 45,168 are novel transcripts of known genes. A total of 60,096 AS transcripts are identified, 45,628 being novel. We have also predicted 1549 transcripts of genes involved in cell wall construction and remodeling, 639 being novel transcripts of known cell wall genes. Most of the predicted transcripts are validated against Illumina-based short reads. Specifically, 96% of the splice junction sites in all the unique transcripts are validated by at least five Illumina reads. Comparisons between genes derived from our identified transcripts and the current genome annotation revealed that among the gene set predicted by both analyses, 16,640 have different exon-intron structures. Overall, substantial amount of new information is derived from the PacBio RNA data regarding both the transcriptome and the genome of switchgrass.", "date": "2018-06-19", "issue": "1", "identifier": "https://www.osti.gov/biblio/1477307", "bibliographicCitation": "https://doi.org/10.1186/s13068-018-1167-z", "keywords": [ "09 BIOMASS FUELS", "Alternative splicing", "PacBio sequencing", "Plant cell wall", "Switchgrass", "Transcriptomic analysis" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Biotechnology for Biofuels", "volume": "11", "publisher_information": "BioMed Central", "country_publication_code": "US", "creator": [ { "name": "Chunman [Jilin Univ.,Changchun (China); Univ. of Georgia,Athens,GA (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Zuo", "primaryContact": true }, { "name": "Matthew [USDOE Joint Genome Institute (JGI),Walnut Creek,CA (United States)] Blow", "primaryContact": false }, { "name": "Avinash [HudsonAlpha Institute for Biotechnology,Huntsville,AL (United States)] Sreedasyam", "primaryContact": false }, { "name": "Rita C. [USDOE Joint Genome Institute (JGI),Walnut Creek,CA (United States)] Kuo", "primaryContact": false }, { "name": "Govindarajan Kunde [USDOE Joint Genome Institute (JGI),Walnut Creek,CA (United States)] Ramamoorthy", "primaryContact": false }, { "name": "Ivone [Noble Research Institute,LLC,Ardmore,OK (United States)] Torres-Jerez", "primaryContact": false }, { "name": "Guifen [Noble Research Institute,LLC,Ardmore,OK (United States)] Li", "primaryContact": false }, { "name": "Mei [USDOE Joint Genome Institute (JGI),Walnut Creek,CA (United States)] Wang", "primaryContact": false }, { "name": "David [USDOE Joint Genome Institute (JGI),Walnut Creek,CA (United States)] Dilworth", "primaryContact": false }, { "name": "Kerrie [USDOE Joint Genome Institute (JGI),Walnut Creek,CA (United States)] Barry", "primaryContact": false }, { "name": "Michael [Noble Research Institute,LLC,Ardmore,OK (United States)] Udvardi", "primaryContact": false }, { "name": "Jeremy [USDOE Joint Genome Institute (JGI),Walnut Creek,CA (United States); HudsonAlpha Institute for Biotechnology,Huntsville,AL (United States)] Schmutz", "primaryContact": false }, { "name": "Yuhong [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Noble Research Institute,LLC,Ardmore,OK (United States)] Tang", "primaryContact": false }, { "name": "Ying [Jilin Univ.,Changchun (China); Univ. of Georgia,Athens,GA (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Xu", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1477307", "active": false }, { "brc": "CBI", "title": "Recent Advances in the Transcriptional Regulation of Secondary Cell Wall Biosynthesis in the Woody Plants", "description": "Not Available", "abstract": "Not Available", "date": "2018-10-22", "identifier": "https://www.osti.gov/biblio/1478538", "bibliographicCitation": "https://doi.org/10.3389/fpls.2018.01535", "keywords": [ "09 BIOMASS FUELS", "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Biomass & Feedstock", "Microbiology" ], "journal_name": "Frontiers in Plant Science", "volume": "9", "publisher_information": "Frontiers Media SA", "country_publication_code": "Switzerland", "creator": [ { "name": "Jin Zhang", "primaryContact": true }, { "name": "Meng Xie", "primaryContact": false }, { "name": "Gerald A. Tuskan", "primaryContact": false }, { "name": "Wellington Muchero", "primaryContact": false }, { "name": "Jin-Gui Chen", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1478538", "active": false }, { "brc": "CBI", "title": "Overexpression of a serine hydroxymethyltransferase increases biomass production and reduces recalcitrance in the bioenergy crop\r\n Populus", "description": "Cell wall recalcitrance is the major obstacle for plant biomass conversion to biofuels.
", "abstract": "Cell wall recalcitrance is the major obstacle for plant biomass conversion to biofuels.
", "date": "2018-12-31", "issue": "1", "identifier": "https://www.osti.gov/biblio/1480552", "bibliographicCitation": "https://doi.org/10.1039/C8SE00471D", "keywords": [ "09 BIOMASS FUELS" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Sustainable Energy & Fuels", "volume": "3", "publisher_information": "Royal Society of Chemistry", "country_publication_code": "GB", "creator": [ { "name": "Jin [BioEnergy Science Center and Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,USA,Center for Bioenergy Innovation] (ORCID:0000000283975078) Zhang", "primaryContact": true }, { "name": "Mi [BioEnergy Science Center and Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,USA] (ORCID:0000000175231266) Li", "primaryContact": false }, { "name": "Anthony C. [BioEnergy Science Center and Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,USA] Bryan", "primaryContact": false }, { "name": "Chang Geun [BioEnergy Science Center and Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,USA,Center for Bioenergy Innovation] (ORCID:0000000261792414) Yoo", "primaryContact": false }, { "name": "William [ArborGen Inc.,Ridgeville,USA] Rottmann", "primaryContact": false }, { "name": "Kimberly A. [ArborGen Inc.,Ridgeville,USA] Winkeler", "primaryContact": false }, { "name": "Cassandra M. [ArborGen Inc.,Ridgeville,USA] Collins", "primaryContact": false }, { "name": "Vasanth [U.S. Department of Energy Joint Genome Institute,Walnut Creek,USA] (ORCID:0000000299835707) Singan", "primaryContact": false }, { "name": "Erika A. [U.S. Department of Energy Joint Genome Institute,Walnut Creek,USA] (ORCID:0000000322497225) Lindquist", "primaryContact": false }, { "name": "Sara S. [BioEnergy Science Center and Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,USA,Center for Bioenergy Innovation] (ORCID:0000000281235439) Jawdy", "primaryContact": false }, { "name": "Lee E. [BioEnergy Science Center and Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,USA,Center for Bioenergy Innovation] (ORCID:0000000312117532) Gunter", "primaryContact": false }, { "name": "Nancy L. [BioEnergy Science Center and Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,USA,Center for Bioenergy Innovation] (ORCID:0000000302907987) Engle", "primaryContact": false }, { "name": "Xiaohan [BioEnergy Science Center and Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,USA,Center for Bioenergy Innovation] (ORCID:0000000152074210) Yang", "primaryContact": false }, { "name": "Kerrie [U.S. Department of Energy Joint Genome Institute,Walnut Creek,USA] (ORCID:0000000289996785) Barry", "primaryContact": false }, { "name": "Timothy J. [BioEnergy Science Center and Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,USA,Center for Bioenergy Innovation] (ORCID:0000000295406622) Tschaplinski", "primaryContact": false }, { "name": "Jeremy [U.S. Department of Energy Joint Genome Institute,Walnut Creek,USA,HudsonAlpha Institute for Biotechnology,Huntsville] (ORCID:0000000180629172) Schmutz", "primaryContact": false }, { "name": "Yunqiao [BioEnergy Science Center and Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,USA,Center for Bioenergy Innovation] (ORCID:0000000325541447) Pu", "primaryContact": false }, { "name": "Arthur J. [BioEnergy Science Center and Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,USA,Center for Bioenergy Innovation] (ORCID:000000023536554X) Ragauskas", "primaryContact": false }, { "name": "Gerald A. [BioEnergy Science Center and Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,USA,Center for Bioenergy Innovation] (ORCID:0000000301061289) Tuskan", "primaryContact": false }, { "name": "Wellington [BioEnergy Science Center and Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,USA,Center for Bioenergy Innovation] (ORCID:0000000202009856) Muchero", "primaryContact": false }, { "name": "Jin-Gui [BioEnergy Science Center and Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,USA,Center for Bioenergy Innovation] (ORCID:0000000217524201) Chen", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1480552", "active": false }, { "brc": "CBI", "title": "High Throughput Screening Technologies in Biomass Characterization", "description": "Not Available", "abstract": "Not Available", "date": "2018-11-26", "identifier": "https://www.osti.gov/biblio/1483426", "bibliographicCitation": "https://doi.org/10.3389/fenrg.2018.00120", "keywords": [ "09 BIOMASS FUELS", "biomass compositional analysis", "biomass conversion", "biomass recalcitrance", "biomass recalcitrance", "biomass compositional analysis", "high throughput analysis", "neural networks", "biomass conversion", "high throughput analysis", "neural networks" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Frontiers in Energy Research", "volume": "6", "publisher_information": "Frontiers Research Foundation", "country_publication_code": "Switzerland", "creator": [ { "name": "Stephen R. Decker", "primaryContact": true }, { "name": "Anne E. Harman-Ware", "primaryContact": false }, { "name": "Renee M. Happs", "primaryContact": false }, { "name": "Edward J. Wolfrum", "primaryContact": false }, { "name": "Gerald A. Tuskan", "primaryContact": false }, { "name": "David Kainer", "primaryContact": false }, { "name": "Gbekeloluwa B. Oguntimein", "primaryContact": false }, { "name": "Miguel Rodriguez", "primaryContact": false }, { "name": "Deborah Weighill", "primaryContact": false }, { "name": "Piet Jones", "primaryContact": false }, { "name": "Daniel Jacobson", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "DOE Office of Science" } }, { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Bioenergy Technologies Office (EE-3B)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1483426", "active": false, "has_related_ids": [ "NREL/JA-2700-72729" ] }, { "brc": "CBI", "title": "Editorial: Advancements in Biomass Recalcitrance: The Use of Lignin for the Production of Fuels and Chemicals", "description": "The valorization of lignin has become a dominant translational research theme in biorefining in the last few years (Ragauskas et al., 2014). Historically, lignin has been sourced from kraft and sulfite pulping operations, and each of these sources provides some natural limitations to their usage. Commercially, this type of lignin has been used as a dispersant, dust suppression agent, surfactant, binder, and emulsifiers; however, most of these applications are low-value, and the markets are saturated (Gargulak and Lebo, 2000). The general limitation of these lignins is due to the presence of sulfur, extensive cross-linking, difficult process ability, purity, and low-molecular-weight profiles in the case of kraft lignin.", "abstract": "The valorization of lignin has become a dominant translational research theme in biorefining in the last few years (Ragauskas et al., 2014). Historically, lignin has been sourced from kraft and sulfite pulping operations, and each of these sources provides some natural limitations to their usage. Commercially, this type of lignin has been used as a dispersant, dust suppression agent, surfactant, binder, and emulsifiers; however, most of these applications are low-value, and the markets are saturated (Gargulak and Lebo, 2000). The general limitation of these lignins is due to the presence of sulfur, extensive cross-linking, difficult process ability, purity, and low-molecular-weight profiles in the case of kraft lignin.", "date": "2018-11-07", "identifier": "https://www.osti.gov/biblio/1484101", "bibliographicCitation": "https://doi.org/10.3389/fenrg.2018.00118", "keywords": [ "09 BIOMASS FUELS", "biorefinery", "characterization", "lignin valorization", "lignocellulosic biomass", "recalcitrance" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Frontiers in Energy Research", "volume": "6", "publisher_information": "Frontiers Research Foundation", "country_publication_code": "US", "creator": [ { "name": "Arthur J. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation. Biosciences Division. UT-ORNL Joint Inst. for Biological Science; Univ. of Tennessee,Knoxville,TN (United States). Dept. of Chemical and Biomolecular Engineering,Forestry,Wildlife,and Fisheries. Center for Renewable Carbon] Ragauskas", "primaryContact": true }, { "name": "Chang Geun [State Univ. of New York College of Environmental Science and Forestry (SUNY-ESF),Syracuse,NY (United States). Dept. of Paper and Bioprocess Engineering] Yoo", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1484101", "active": false }, { "brc": "CBI", "title": "Hardwood Tree Genomics: Unlocking Woody Plant Biology", "description": "Not Available", "abstract": "Not Available", "date": "2018-12-16", "identifier": "https://www.osti.gov/biblio/1487165", "bibliographicCitation": "https://doi.org/10.3389/fpls.2018.01799", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "adaptive traits", "comparative genomics", "evolutionary ecology", "quantitative genetics", "somatic mutations", "tree habit" ], "topic": [ "Microbiology" ], "journal_name": "Frontiers in Plant Science", "volume": "9", "publisher_information": "Frontiers Research Foundation", "country_publication_code": "Switzerland", "creator": [ { "name": "Gerald A. Tuskan", "primaryContact": true }, { "name": "Andrew T. Groover", "primaryContact": false }, { "name": "Jeremy Schmutz", "primaryContact": false }, { "name": "Stephen Paul DiFazio", "primaryContact": false }, { "name": "Alexander Myburg", "primaryContact": false }, { "name": "Dario Grattapaglia", "primaryContact": false }, { "name": "Lawrence B. Smart", "primaryContact": false }, { "name": "Tongming Yin", "primaryContact": false }, { "name": "Jean-Marc Aury", "primaryContact": false }, { "name": "Antoine Kremer", "primaryContact": false }, { "name": "Thibault Leroy", "primaryContact": false }, { "name": "Gregoire Le Provost", "primaryContact": false }, { "name": "Christophe Plomion", "primaryContact": false }, { "name": "John E. Carlson", "primaryContact": false }, { "name": "Jennifer Randall", "primaryContact": false }, { "name": "Jared Westbrook", "primaryContact": false }, { "name": "Jane Grimwood", "primaryContact": false }, { "name": "Wellington Muchero", "primaryContact": false }, { "name": "Daniel Jacobson", "primaryContact": false }, { "name": "Joshua K. Michener", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDA" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1487165", "active": false }, { "brc": "CBI", "title": "Characterization of fractional cuts of co-solvent enhanced lignocellulosic fractionation lignin isolated by sequential precipitation", "description": "We report that lignin valorization is significantly hindered by the intrinsic heterogeneity of its complex structures and variability of biomass feedstocks. Fractionation of lignin can overcome these challenges by producing functionally distinct lignin cuts that can be further tailored to end products. Herein, lignin was extracted and depolymerized from poplar by the co-solvent enhanced lignocellulosic fractionation method with renewable THF to obtain CELF lignin. Several solvents were screened to separate soluble and insoluble fractions from the parent CELF lignin. The ethanol soluble portion was then fractionated into different molecular weight cuts via sequential precipitation of the lignin by reducing the concentration of THF. The physicochemical structures of different CELF lignin cuts were elucidated by GPC and NMR techniques. In conclusio, these results suggest that CELF lignin cuts with lower molecular weight contain progressively higher phenolic and carboxylic acid OH groups, which can be more suitable as green antioxidants than the parent lignin.", "abstract": "We report that lignin valorization is significantly hindered by the intrinsic heterogeneity of its complex structures and variability of biomass feedstocks. Fractionation of lignin can overcome these challenges by producing functionally distinct lignin cuts that can be further tailored to end products. Herein, lignin was extracted and depolymerized from poplar by the co-solvent enhanced lignocellulosic fractionation method with renewable THF to obtain CELF lignin. Several solvents were screened to separate soluble and insoluble fractions from the parent CELF lignin. The ethanol soluble portion was then fractionated into different molecular weight cuts via sequential precipitation of the lignin by reducing the concentration of THF. The physicochemical structures of different CELF lignin cuts were elucidated by GPC and NMR techniques. In conclusio, these results suggest that CELF lignin cuts with lower molecular weight contain progressively higher phenolic and carboxylic acid OH groups, which can be more suitable as green antioxidants than the parent lignin.", "date": "2018-09-26", "issue": "C", "identifier": "https://www.osti.gov/biblio/1489560", "bibliographicCitation": "https://doi.org/10.1016/j.biortech.2018.09.130", "keywords": [ "09 BIOMASS FUELS", "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "59 BASIC BIOLOGICAL SCIENCES", "Co-solvent enhanced lignocellulosic fractionation", "Lignin valorization", "Molecular weight distribution", "Sequential precipitation" ], "topic": [ "Biomass & Feedstock", "Chemistry", "Microbiology" ], "journal_name": "Bioresource Technology", "volume": "272", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Xianzhi [Univ. of Tennessee,Knoxville,TN (United States)] Meng", "primaryContact": true }, { "name": "Aakash [Univ. of California,Riverside,CA (United States)] Parikh", "primaryContact": false }, { "name": "Bhogeswararao [Univ. of California,Riverside,CA (United States)] Seemala", "primaryContact": false }, { "name": "Rajeev [Univ. of California,Riverside,CA (United States)] Kumar", "primaryContact": false }, { "name": "Yunqiao Joseph [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000325541447) Pu", "primaryContact": false }, { "name": "Charles E. [Univ. of California,Riverside,CA (United States)] Wyman", "primaryContact": false }, { "name": "Charles M. [Univ. of California,Riverside,CA (United States)] Cai", "primaryContact": false }, { "name": "Arthur J. [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:000000023536554X) Ragauskas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Bioenergy Technologies Office (EE-3B)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1489560", "active": false }, { "brc": "CBI", "title": "Complete Genome Sequences of Two Megasphaera elsdenii Strains, NCIMB 702410 and ATCC 25940", "description": "\n Here, we report the complete genome sequences of two\n
\n Here, we report the complete genome sequences of two\n
\n Genetic improvement through breeding is one of the key approaches to increasing biomass supply. This paper documents the breeding progress to date for four perennial biomass crops (PBCs) that have high output\u2013input energy ratios: namely\n
\n Genetic improvement through breeding is one of the key approaches to increasing biomass supply. This paper documents the breeding progress to date for four perennial biomass crops (PBCs) that have high output\u2013input energy ratios: namely\n
\n Switchgrass (\n
\n Switchgrass (\n
\n Microbial conversion of aromatic compounds is an emerging and promising strategy for valorization of the plant biopolymer lignin. A critical and often rate-limiting reaction in aromatic catabolism is\n
\n Microbial conversion of aromatic compounds is an emerging and promising strategy for valorization of the plant biopolymer lignin. A critical and often rate-limiting reaction in aromatic catabolism is\n
Deep eutectic solvents (DESs) have gained increasing attention due to their application-friendly properties, including universal solvating capabilities and wide tunability. Additionally, ease of synthesis and broad availability from inexpensive chemical components could render DESs more versatile solvents for biomass pretreatment, as compared with traditional ionic liquids. Because the long-term success of the biorefinery depends on the development of sustainable processes to convert lignocellulosics into biofuels, DESs derived from renewable sources such as lignin are highly desirable. We herein present our innovative process that integrates the use of low-recalcitrant engineered biomass with its pretreatment using lignin-derived DESs. The promising results described by near-theoretical sugar yield demonstrate the effectiveness of the integrated process, opening up opportunities toward a sustainable and circular bioeconomy.
", "abstract": "Deep eutectic solvents (DESs) have gained increasing attention due to their application-friendly properties, including universal solvating capabilities and wide tunability. Additionally, ease of synthesis and broad availability from inexpensive chemical components could render DESs more versatile solvents for biomass pretreatment, as compared with traditional ionic liquids. Because the long-term success of the biorefinery depends on the development of sustainable processes to convert lignocellulosics into biofuels, DESs derived from renewable sources such as lignin are highly desirable. We herein present our innovative process that integrates the use of low-recalcitrant engineered biomass with its pretreatment using lignin-derived DESs. The promising results described by near-theoretical sugar yield demonstrate the effectiveness of the integrated process, opening up opportunities toward a sustainable and circular bioeconomy.
", "date": "2019-06-23", "issue": "28", "identifier": "https://www.osti.gov/biblio/1529169", "bibliographicCitation": "https://doi.org/10.1073/pnas.1904636116", "keywords": [ "09 BIOMASS FUELS", "bioenergy", "cinnamyl alcohol dehydrogenase", "green solvent", "lignocellulosic biomass" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "116", "publisher_information": "Proceedings of the National Academy of Sciences", "country_publication_code": "US", "creator": [ { "name": "Kwang Ho [Clean Energy Research Center,Korea Institute of Science and Technology,Seoul 02702,Republic of Korea,,Department of Wood Science,University of British Columbia,Vancouver,BC,V6T 1Z4,Canada,] (ORCID:0000000339431927) Kim", "primaryContact": true }, { "name": "Aymerick [Feedstocks Division,Joint BioEnergy Institute,Emeryville,CA 94608,,Environmental Genomics and Systems Biology Division,Lawrence Berkeley National Laboratory,Berkeley,CA 94720,] Eudes", "primaryContact": false }, { "name": "Keunhong [Department of Chemistry,Korea Military Academy,Seoul 01805,Republic of Korea,] Jeong", "primaryContact": false }, { "name": "Chang Geun [Department of Paper and Bioprocess Engineering,State University of New York College of Environmental Science and Forestry,Syracuse,NY 13210,] Yoo", "primaryContact": false }, { "name": "Chang Soo [Clean Energy Research Center,Korea Institute of Science and Technology,Seoul 02702,Republic of Korea,] Kim", "primaryContact": false }, { "name": "Arthur [Center for Bioenergy Innovation,University of Tennessee\u2013Oak Ridge National Laboratory Joint Institute for Biological Science,Oak Ridge,TN 37831,,Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,TN 37831,,Department of Chemical and Biomolecular Engineering,University of Tennessee,Knoxville,TN 37996,,Center for Renewable Carbon,Department of Forestry,Wildlife,and Fisheries,University of Tennessee,Institute of Agriculture,Knoxville,TN 37996] (ORCID:000000023536554X) Ragauskas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1529169", "active": false }, { "brc": "CBI", "title": "Predicting the Longitudinally and Radially Varying Gut Microbiota Composition Using Multi-Scale Microbial Metabolic Modeling", "description": "Background: The gut microbiota is a heterogeneous group of microbes that is spatially distributed along various sections of the intestines and across the mucosa and lumen in each section. Understanding the dynamics between the spatially differential microbial populations and the driving forces for the observed spatial organization will provide valuable insights into important questions such as the nature of colonization of the infant gut and different types of inflammatory bowel disease localized in different regions of the intestines. However, in most studies, the microbiota is sampled only at a single site (often feces) or from a particular anatomical site of the intestines. Differential oxygen availability is putatively a key factor shaping the spatial organization. Results: To test this hypothesis, we constructed a community genome-scale metabolic model consisting of representative organisms for the major phyla present in the human gut microbiome. By solving step-wise optimization problems embedded in a dynamic framework to predict community metabolism and integrate the mucosally-adherent with the luminal microbiome between consecutive sections along the intestines, we were able to capture (i) the essential features of the spatially differential composition of obligate anaerobes vs. facultative anaerobes and aerobes determined experimentally, and (ii) the accumulation of microbial biomass in the lumen. Sensitivity analysis suggests that the spatial organization depends primarily on the oxygen-per-microbe availability in each region. Oxygen availability is reduced relative to the ~100-fold increase in mucosal microbial density along the intestines, causing the switch between aerobes and anaerobes. Conclusion: The proposed integrated dynamic framework is able to predict spatially differential gut microbiota composition using microbial genome-scale metabolic models and test hypotheses regarding the dynamics of the gut microbiota. It can potentially become a valuable tool for exploring therapeutic strategies for site-specific perturbation of the gut microbiota and the associated metabolic activities.
", "abstract": "Background: The gut microbiota is a heterogeneous group of microbes that is spatially distributed along various sections of the intestines and across the mucosa and lumen in each section. Understanding the dynamics between the spatially differential microbial populations and the driving forces for the observed spatial organization will provide valuable insights into important questions such as the nature of colonization of the infant gut and different types of inflammatory bowel disease localized in different regions of the intestines. However, in most studies, the microbiota is sampled only at a single site (often feces) or from a particular anatomical site of the intestines. Differential oxygen availability is putatively a key factor shaping the spatial organization. Results: To test this hypothesis, we constructed a community genome-scale metabolic model consisting of representative organisms for the major phyla present in the human gut microbiome. By solving step-wise optimization problems embedded in a dynamic framework to predict community metabolism and integrate the mucosally-adherent with the luminal microbiome between consecutive sections along the intestines, we were able to capture (i) the essential features of the spatially differential composition of obligate anaerobes vs. facultative anaerobes and aerobes determined experimentally, and (ii) the accumulation of microbial biomass in the lumen. Sensitivity analysis suggests that the spatial organization depends primarily on the oxygen-per-microbe availability in each region. Oxygen availability is reduced relative to the ~100-fold increase in mucosal microbial density along the intestines, causing the switch between aerobes and anaerobes. Conclusion: The proposed integrated dynamic framework is able to predict spatially differential gut microbiota composition using microbial genome-scale metabolic models and test hypotheses regarding the dynamics of the gut microbiota. It can potentially become a valuable tool for exploring therapeutic strategies for site-specific perturbation of the gut microbiota and the associated metabolic activities.
", "date": "2019-06-25", "issue": "7", "identifier": "https://www.osti.gov/biblio/1529648", "bibliographicCitation": "https://doi.org/10.3390/pr7070394", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "Engineering", "genome-scale metabolic model", "gut microbiome", "multi-scale modeling", "spatial heterogeneity" ], "topic": [ "Microbiology" ], "journal_name": "Processes", "volume": "7", "publisher_information": "Multidisciplinary Digital Publishing Institute (MDPI)", "country_publication_code": "Switzerland", "creator": [ { "name": "Chan", "primaryContact": true }, { "name": "Friedman", "primaryContact": false }, { "name": "Wu", "primaryContact": false }, { "name": "Maranas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC)" } } ], "dataset_url": "https://www.osti.gov/biblio/1529648", "active": false }, { "brc": "CBI", "title": "Comparison of Multi-Objective Evolutionary Algorithms to Solve the Modular Cell Design Problem for Novel Biocatalysis", "description": "A large space of chemicals with broad industrial and consumer applications could be synthesized by engineered microbial biocatalysts. However, the current strain optimization process is prohibitively laborious and costly to produce one target chemical and often requires new engineering efforts to produce new molecules. To tackle this challenge, modular cell design based on a chassis strain that can be combined with different product synthesis pathway modules has recently been proposed. This approach seeks to minimize unexpected failure and avoid task repetition, leading to a more robust and faster strain engineering process. In our previous study, we mathematically formulated the modular cell design problem based on the multi-objective optimization framework. In this study, we evaluated a library of state-of-the-art multi-objective evolutionary algorithms (MOEAs) to identify the most effective method to solve the modular cell design problem. Using the best MOEA, we found better solutions for modular cells compatible with many product synthesis modules. Furthermore, the best performing algorithm could provide better and more diverse design options that might help increase the likelihood of successful experimental implementation. We identified key parameter configurations to overcome the difficulty associated with multi-objective optimization problems with many competing design objectives. Interestingly, we found that MOEA performance with a real application problem, e.g., the modular strain design problem, does not always correlate with artificial benchmarks. Overall, MOEAs provide powerful tools to solve the modular cell design problem for novel biocatalysis.
", "abstract": "A large space of chemicals with broad industrial and consumer applications could be synthesized by engineered microbial biocatalysts. However, the current strain optimization process is prohibitively laborious and costly to produce one target chemical and often requires new engineering efforts to produce new molecules. To tackle this challenge, modular cell design based on a chassis strain that can be combined with different product synthesis pathway modules has recently been proposed. This approach seeks to minimize unexpected failure and avoid task repetition, leading to a more robust and faster strain engineering process. In our previous study, we mathematically formulated the modular cell design problem based on the multi-objective optimization framework. In this study, we evaluated a library of state-of-the-art multi-objective evolutionary algorithms (MOEAs) to identify the most effective method to solve the modular cell design problem. Using the best MOEA, we found better solutions for modular cells compatible with many product synthesis modules. Furthermore, the best performing algorithm could provide better and more diverse design options that might help increase the likelihood of successful experimental implementation. We identified key parameter configurations to overcome the difficulty associated with multi-objective optimization problems with many competing design objectives. Interestingly, we found that MOEA performance with a real application problem, e.g., the modular strain design problem, does not always correlate with artificial benchmarks. Overall, MOEAs provide powerful tools to solve the modular cell design problem for novel biocatalysis.
", "date": "2019-06-10", "issue": "6", "identifier": "https://www.osti.gov/biblio/1529693", "bibliographicCitation": "https://doi.org/10.3390/pr7060361", "topic": [ "Unknown" ], "journal_name": "Processes", "volume": "7", "publisher_information": "MDPI AG", "country_publication_code": "Switzerland", "creator": [ { "name": "Sergio (ORCID:000000023998986X) Garcia", "primaryContact": true }, { "name": "Cong T. (ORCID:000000028362725X) Trinh", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/1529693", "active": false }, { "brc": "CBI", "title": "The unexpected malleability of lignin", "description": "Here, Curcumin, an aromatic diarylheptanoid, is a principal component of turmeric (Curcuma longa), commonly used in Asian cooking, giving curry its orange colour. Introducing two enzymes into Arabidopsis thaliana caused incorporation of curcumin into its lignin polymer, enhancing sugar release from the cell wall and turning it yellow.", "abstract": "Here, Curcumin, an aromatic diarylheptanoid, is a principal component of turmeric (Curcuma longa), commonly used in Asian cooking, giving curry its orange colour. Introducing two enzymes into Arabidopsis thaliana caused incorporation of curcumin into its lignin polymer, enhancing sugar release from the cell wall and turning it yellow.", "date": "2019-01-27", "issue": "2", "identifier": "https://www.osti.gov/biblio/1530102", "bibliographicCitation": "https://doi.org/10.1038/s41477-019-0360-9", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "Nature Plants", "volume": "5", "publisher_information": "Nature Publishing Group", "country_publication_code": "US", "creator": [ { "name": "Gerald A. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000301061289) Tuskan", "primaryContact": true } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1530102", "active": false }, { "brc": "CBI", "title": "Plant Host-Associated Mechanisms for Microbial Selection", "description": "Not Available", "abstract": "Not Available", "date": "2019-07-02", "identifier": "https://www.osti.gov/biblio/1530904", "bibliographicCitation": "https://doi.org/10.3389/fpls.2019.00862", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "Frontiers in Plant Science", "volume": "10", "publisher_information": "Frontiers Media SA", "country_publication_code": "Switzerland", "creator": [ { "name": "Piet Jones", "primaryContact": true }, { "name": "Benjamin J. Garcia", "primaryContact": false }, { "name": "Anna Furches", "primaryContact": false }, { "name": "Gerald A. Tuskan", "primaryContact": false }, { "name": "Daniel Jacobson", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1530904", "active": false }, { "brc": "CBI", "title": "Wavelet-Based Genomic Signal Processing for Centromere Identification and Hypothesis Generation", "description": "Various \u2018omics data types have been generated for Populus trichocarpa, each providing a layer of information which can be represented as a density signal across a chromosome. We make use of genome sequence data, variants data across a population as well as methylation data across 10 different tissues, combined with wavelet-based signal processing to perform a comprehensive analysis of the signature of the centromere in these different data signals, and successfully identify putative centromeric regions in P. trichocarpa from these signals. Furthermore, using SNP (single nucleotide polymorphism) correlations across a natural population of P. trichocarpa, we find evidence for the co-evolution of the centromeric histone CENH3 with the sequence of the newly identified centromeric regions, and identify a new CENH3 candidate in P. trichocarpa.", "abstract": "Various \u2018omics data types have been generated for Populus trichocarpa, each providing a layer of information which can be represented as a density signal across a chromosome. We make use of genome sequence data, variants data across a population as well as methylation data across 10 different tissues, combined with wavelet-based signal processing to perform a comprehensive analysis of the signature of the centromere in these different data signals, and successfully identify putative centromeric regions in P. trichocarpa from these signals. Furthermore, using SNP (single nucleotide polymorphism) correlations across a natural population of P. trichocarpa, we find evidence for the co-evolution of the centromeric histone CENH3 with the sequence of the newly identified centromeric regions, and identify a new CENH3 candidate in P. trichocarpa.", "date": "2019-05-30", "issue": "N/a", "identifier": "https://www.osti.gov/biblio/1542248", "bibliographicCitation": "https://doi.org/10.3389/fgene.2019.00487", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "CENH3", "DNA methylation", "Populus trichocarpacentromeres", "SNP density", "co-evolution", "data integration", "wavelet transform" ], "topic": [ "Microbiology" ], "journal_name": "Frontiers in Genetics", "volume": "10", "publisher_information": "Frontiers", "country_publication_code": "US", "creator": [ { "name": "Deborah [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000349795871) Weighill", "primaryContact": true }, { "name": "David [West Virginia Univ.,Morgantown,WV (United States)] Macaya-Sanz", "primaryContact": false }, { "name": "Stephen Paul [West Virginia Univ.,Morgantown,WV (United States)] DiFazio", "primaryContact": false }, { "name": "Wayne [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:000000034771998X) Joubert", "primaryContact": false }, { "name": "Manesh B. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Shah", "primaryContact": false }, { "name": "Jeremy [USDOE Joint Genome Institute (JGI),Walnut Creek,CA (United States); HudsonAlpha Institute for Biotechnology,Huntsville,AL (United States)] Schmutz", "primaryContact": false }, { "name": "Avinash [HudsonAlpha Institute for Biotechnology,Huntsville,AL (United States)] Sreedasyam", "primaryContact": false }, { "name": "Gerald A. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000301061289) Tuskan", "primaryContact": false }, { "name": "Daniel A. [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000298228251) Jacobson", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1542248", "active": false }, { "brc": "CBI", "title": "Genetic variation of biomass recalcitrance in a natural Salix viminalis (L.) population", "description": "Background
Salix spp. are high-productivity crops potentially used for lignocellulosic biofuels such as bioethanol. In general, pretreatment is needed to facilitate the enzymatic depolymerization process. Biomass resistance to degradation, i.e., biomass recalcitrance, is a trait which can be assessed by measuring the sugar released after combined pretreatment and enzymatic hydrolysis. We have examined genetic parameters of enzymatic sugar release and other traits related to biorefinery use in a population of 286 natural Salix viminalis clones. Moreover, we have evaluated phenotypic and genetic correlations between these traits and performed a genomewide association mapping analysis using a set of 19,411 markers.
Results
Sugar release (glucose and xylose) after pretreatment and enzymatic saccharification proved highly variable with large genetic and phenotypic variations, and chip heritability estimates (h2) of 0.23-0.29. Lignin syringyl/guaiacyl (S/G) ratio and wood density were the most heritable traits (h2 = 0.42 and 0.59, respectively). Sugar release traits were positively correlated, phenotypically and genetically, with biomass yield and lignin S/G ratio. Association mapping revealed seven marker-trait associations below a suggestive significance threshold, including one marker associated with glucose release.
Conclusions
We identified lignin S/G ratio and shoot diameter as heritable traits that could be relatively easily evaluated by breeders, making them suitable proxy traits for developing low-recalcitrance varieties. One marker below the implied threshold for marker associations was identified for sugar release, meriting further investigation while also highlighting the difficulties in employing genomewide association mapping for complex traits.
", "abstract": "Background
Salix spp. are high-productivity crops potentially used for lignocellulosic biofuels such as bioethanol. In general, pretreatment is needed to facilitate the enzymatic depolymerization process. Biomass resistance to degradation, i.e., biomass recalcitrance, is a trait which can be assessed by measuring the sugar released after combined pretreatment and enzymatic hydrolysis. We have examined genetic parameters of enzymatic sugar release and other traits related to biorefinery use in a population of 286 natural Salix viminalis clones. Moreover, we have evaluated phenotypic and genetic correlations between these traits and performed a genomewide association mapping analysis using a set of 19,411 markers.
Results
Sugar release (glucose and xylose) after pretreatment and enzymatic saccharification proved highly variable with large genetic and phenotypic variations, and chip heritability estimates (h2) of 0.23-0.29. Lignin syringyl/guaiacyl (S/G) ratio and wood density were the most heritable traits (h2 = 0.42 and 0.59, respectively). Sugar release traits were positively correlated, phenotypically and genetically, with biomass yield and lignin S/G ratio. Association mapping revealed seven marker-trait associations below a suggestive significance threshold, including one marker associated with glucose release.
Conclusions
We identified lignin S/G ratio and shoot diameter as heritable traits that could be relatively easily evaluated by breeders, making them suitable proxy traits for developing low-recalcitrance varieties. One marker below the implied threshold for marker associations was identified for sugar release, meriting further investigation while also highlighting the difficulties in employing genomewide association mapping for complex traits.
", "date": "2019-06-02", "issue": "1", "identifier": "https://www.osti.gov/biblio/1542755", "bibliographicCitation": "https://doi.org/10.1186/s13068-019-1479-7", "keywords": [ "09 BIOMASS FUELS", "Salix viminalis", "bioenergy crops", "biomass recalcitrance", "enzymatic saccharification", "genetic parameters", "genomewide association study", "lignocellulosic biofuels", "plant breeding" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Biotechnology for Biofuels", "volume": "12", "publisher_information": "BioMed Central", "country_publication_code": "US", "creator": [ { "name": "Jonas A. [Swedish Univ. of Agricultural Sciences,Uppsala (Sweden)] Ohlsson", "primaryContact": true }, { "name": "Henrik R. [Swedish Univ. of Agricultural Sciences,Uppsala (Sweden)] Hallingb\u00e4ck", "primaryContact": false }, { "name": "Mohamed [Swedish Univ. of Agricultural Sciences,Uppsala (Sweden)] Jebrane", "primaryContact": false }, { "name": "Anne E. [National Renewable Energy Lab. (NREL),Golden,CO (United States)] Harman-Ware", "primaryContact": false }, { "name": "Todd [National Renewable Energy Lab. (NREL),Golden,CO (United States)] Shollenberger", "primaryContact": false }, { "name": "Stephen R. [National Renewable Energy Lab. (NREL),Golden,CO (United States)] Decker", "primaryContact": false }, { "name": "Mats [Swedish Univ. of Agricultural Sciences,Uppsala (Sweden)] Sandgren", "primaryContact": false }, { "name": "Ann-Christin [Swedish Univ. of Agricultural Sciences,Uppsala (Sweden)] (ORCID:0000000252417161) R\u00f6nnberg-W\u00e4stljung", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23), Center for Bioenergy Innovation (CBI)" } } ], "dataset_url": "https://www.osti.gov/biblio/1542755", "active": false, "has_related_ids": [ "NREL/JA--2700-73918" ] }, { "brc": "CBI", "title": "Investigating the correlation of biomass recalcitrance with pyrolysis oil using poplar as the feedstock", "description": "Pyrolysis of five poplar samples with differing degrees of recalcitrance was performed; the correlations between the poplar enzymatic hydrolysis glucose yields and the physicochemical properties of pyrolysis product were studied in this work. Sugar release of five poplar samples varied from 48.1 to 112.3 mg/g for glucose, and 12.0 to 32.4 mg/g for xylose. The yield of pyrolysis products was calculated and the molecular weight distribution of pyrolysis oils was measured by GPC, ranging from 268 to 289 g/mol for its weight-average molecular weight. GC\u2013MS analysis of the bio-oil exhibited a strong correlation between biomass recalcitrance and guaiacyl-type structures in bio-oils. The correlation between biomass recalcitrance and the ratio of syringyl-to-guaiacyl-type-related structures was also assessed. The results from quantitative 31P NMR indicated some correlation between biomass recalcitrance and the guaiacyl hydroxyl groups in bio-oils. These conclusions illustrate correlations and differences between converting biomass to biofuels via the biological and thermal platform.", "abstract": "Pyrolysis of five poplar samples with differing degrees of recalcitrance was performed; the correlations between the poplar enzymatic hydrolysis glucose yields and the physicochemical properties of pyrolysis product were studied in this work. Sugar release of five poplar samples varied from 48.1 to 112.3 mg/g for glucose, and 12.0 to 32.4 mg/g for xylose. The yield of pyrolysis products was calculated and the molecular weight distribution of pyrolysis oils was measured by GPC, ranging from 268 to 289 g/mol for its weight-average molecular weight. GC\u2013MS analysis of the bio-oil exhibited a strong correlation between biomass recalcitrance and guaiacyl-type structures in bio-oils. The correlation between biomass recalcitrance and the ratio of syringyl-to-guaiacyl-type-related structures was also assessed. The results from quantitative 31P NMR indicated some correlation between biomass recalcitrance and the guaiacyl hydroxyl groups in bio-oils. These conclusions illustrate correlations and differences between converting biomass to biofuels via the biological and thermal platform.", "date": "2019-05-31", "issue": "C", "identifier": "https://www.osti.gov/biblio/1543197", "bibliographicCitation": "https://doi.org/10.1016/j.biortech.2019.121589", "keywords": [ "09 BIOMASS FUELS", "Bio-oil", "Biomass recalcitrance", "GC\u2013MS", "Lignin", "NMR", "Populus", "Pyrolysis" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Bioresource Technology", "volume": "289", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Kongyu [Zhejiang Univ.,Hangzhou (China); Univ. of Tennessee,Knoxville,TN (United States)] Lu", "primaryContact": true }, { "name": "Naijia [Univ. of Tennessee,Knoxville,TN (United States)] Hao", "primaryContact": false }, { "name": "Xianzhi [Univ. of Tennessee,Knoxville,TN (United States)] Meng", "primaryContact": false }, { "name": "Zhongyang [Zhejiang Univ.,Hangzhou (China)] Luo", "primaryContact": false }, { "name": "Gerald A. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000301061289) Tuskan", "primaryContact": false }, { "name": "Arthur J. [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:000000023536554X) Ragauskas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "China Scholarship Council" } }, { "fundingOrganization": { "organizationName": "National Basic Research Program of China" } }, { "fundingOrganization": { "organizationName": "National Natural Science Foundation of China" } }, { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1543197", "active": false }, { "brc": "CBI", "title": "4-Coumarate 3-hydroxylase in the lignin biosynthesis pathway is a cytosolic ascorbate peroxidase", "description": "Lignin biosynthesis is evolutionarily conserved among higher plants and features a critical 3-hydroxylation reaction involving phenolic esters. Yet, increasing evidence questions the involvement of a single pathway to lignin formation in vascular plants. In this work we describe an enzyme catalyzing the direct 3-hydroxylation of 4-coumarate to caffeate in lignin biosynthesis as a bifunctional peroxidase that oxidizes both ascorbate and 4-coumarate at comparable rates. A combination of biochemical and genetic evidence in the model plants Brachypodium distachyon and Arabidopsis thaliana supports a role for this coumarate 3-hydroxylase (C3H) in the early steps of lignin biosynthesis. The subsequent efficient O-methylation of caffeate to ferulate in grasses is substantiated by in vivo biochemical assays. Our results identify C3H as the only non-membrane bound hydroxylase in the lignin pathway and revise the currently accepted models of lignin biosynthesis, suggesting new gene targets to improve forage and bioenergy crops.", "abstract": "Lignin biosynthesis is evolutionarily conserved among higher plants and features a critical 3-hydroxylation reaction involving phenolic esters. Yet, increasing evidence questions the involvement of a single pathway to lignin formation in vascular plants. In this work we describe an enzyme catalyzing the direct 3-hydroxylation of 4-coumarate to caffeate in lignin biosynthesis as a bifunctional peroxidase that oxidizes both ascorbate and 4-coumarate at comparable rates. A combination of biochemical and genetic evidence in the model plants Brachypodium distachyon and Arabidopsis thaliana supports a role for this coumarate 3-hydroxylase (C3H) in the early steps of lignin biosynthesis. The subsequent efficient O-methylation of caffeate to ferulate in grasses is substantiated by in vivo biochemical assays. Our results identify C3H as the only non-membrane bound hydroxylase in the lignin pathway and revise the currently accepted models of lignin biosynthesis, suggesting new gene targets to improve forage and bioenergy crops.", "date": "2019-04-29", "issue": "1", "identifier": "https://www.osti.gov/biblio/1545188", "bibliographicCitation": "https://doi.org/10.1038/s41467-019-10082-7", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "Nature Communications", "volume": "10", "publisher_information": "Nature Publishing Group", "country_publication_code": "US", "creator": [ { "name": "Jaime [Univ. of North Texas,Denton,TX (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:000000029545312X) Barros", "primaryContact": true }, { "name": "Luis [Univ. of North Texas,Denton,TX (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Escamilla-Trevino", "primaryContact": false }, { "name": "Luhua [Univ. of North Texas,Denton,TX (United States)] Song", "primaryContact": false }, { "name": "Xiaolan [Univ. of North Texas,Denton,TX (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Rao", "primaryContact": false }, { "name": "Juan Carlos [Univ. of North Texas,Denton,TX (United States)] Serrani-Yarce", "primaryContact": false }, { "name": "Maite Docampo [Univ. of North Texas,Denton,TX (United States)] (ORCID:0000000152053989) Palacios", "primaryContact": false }, { "name": "Nancy [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000302907987) Engle", "primaryContact": false }, { "name": "Feroza K. [Univ. of North Texas,Denton,TX (United States)] Choudhury", "primaryContact": false }, { "name": "Timothy J. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000295406622) Tschaplinski", "primaryContact": false }, { "name": "Barney J. [Univ. of North Texas,Denton,TX (United States)] Venables", "primaryContact": false }, { "name": "Ron [Univ. of North Texas,Denton,TX (United States)] Mittler", "primaryContact": false }, { "name": "Richard A. [Univ. of North Texas,Denton,TX (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000183939408) Dixon", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1545188", "active": false }, { "brc": "CBI", "title": "Complete Genome Sequence of Salinisphaera sp. Strain LB1, a Moderately Halo-Acidophilic Bacterium Isolated from Lake Brown, Western Australia", "description": "Salinisphaera sp. strain LB1 was isolated from Lake Brown, Western Australia, surface water enriched at pH 4.0 and with 5% (wt/vol) NaCl. We discuss the complete genome sequence in this report.
", "abstract": "Salinisphaera sp. strain LB1 was isolated from Lake Brown, Western Australia, surface water enriched at pH 4.0 and with 5% (wt/vol) NaCl. We discuss the complete genome sequence in this report.
", "date": "2018-10-03", "issue": "13", "identifier": "https://www.osti.gov/biblio/1545196", "bibliographicCitation": "https://doi.org/10.1128/MRA.01047-18", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "Microbiology Resource Announcements", "volume": "7", "publisher_information": "SSPA - American Society for Microbiology", "country_publication_code": "US", "creator": [ { "name": "Kaela B. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] O\u2019Dell", "primaryContact": true }, { "name": "E. Anne [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Hatmaker", "primaryContact": false }, { "name": "Adam M. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000158235329) Guss", "primaryContact": false }, { "name": "Melanie R. [Missouri Univ. of Science and Technology,Rolla,MO (United States)] (ORCID:0000000190542687) Mormile", "primaryContact": false }, { "name": "David A. [Univ. of Arizona,Tucson,AZ (United States)] Baltrus", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1545196", "active": false }, { "brc": "CBI", "title": "Association mapping, transcriptomics, and transient expression identify candidate genes mediating plant\u2013pathogen interactions in a tree", "description": "Invasive microbes causing diseases such as sudden oak death negatively affect ecosystems and economies around the world. The deployment of resistant genotypes for combating introduced diseases typically relies on breeding programs that can take decades to complete. To reflect how this process can be accelerated, we employed a genome-wide association mapping of ca. 1,000 resequenced Populus trichocarpa trees individually challenged with Sphaerulina musiva, an invasive fungal pathogen. Among crucial associations, three loci associated with resistance were identified and predicted to encode one putative membrane-bound L-type receptor-like kinase and two receptor-like proteins. A susceptibility-associated locus was predicted to encode a putative G-type D-mannose\u2013binding receptor-like kinase. Multiple lines of evidence, including allele analysis, transcriptomics, binding assays, and overexpression, support the hypothesized function of these candidate genes in the P. trichocarpa response to S. musiva.", "abstract": "Invasive microbes causing diseases such as sudden oak death negatively affect ecosystems and economies around the world. The deployment of resistant genotypes for combating introduced diseases typically relies on breeding programs that can take decades to complete. To reflect how this process can be accelerated, we employed a genome-wide association mapping of ca. 1,000 resequenced Populus trichocarpa trees individually challenged with Sphaerulina musiva, an invasive fungal pathogen. Among crucial associations, three loci associated with resistance were identified and predicted to encode one putative membrane-bound L-type receptor-like kinase and two receptor-like proteins. A susceptibility-associated locus was predicted to encode a putative G-type D-mannose\u2013binding receptor-like kinase. Multiple lines of evidence, including allele analysis, transcriptomics, binding assays, and overexpression, support the hypothesized function of these candidate genes in the P. trichocarpa response to S. musiva.", "date": "2018-10-17", "issue": "45", "identifier": "https://www.osti.gov/biblio/1545198", "bibliographicCitation": "https://doi.org/10.1073/pnas.1804428115", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "Populus trichocarpa", "association mapping", "disease resistance", "invasive disease", "septoria canker" ], "topic": [ "Microbiology" ], "journal_name": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "115", "publisher_information": "National Academy of Sciences", "country_publication_code": "US", "creator": [ { "name": "Wellington [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000202009856) Muchero", "primaryContact": true }, { "name": "Kelsey L. [Oregon State University,Corvallis,OR (United States)] Sondreli", "primaryContact": false }, { "name": "Jin-Gui [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000217524201) Chen", "primaryContact": false }, { "name": "Breeanna R. [University of Georgia,Athens,GA (United States)] Urbanowicz", "primaryContact": false }, { "name": "Jin [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000283975078) Zhang", "primaryContact": false }, { "name": "Vasanth [US Department of Energy,Walnut Creek,CA (United States)] Singan", "primaryContact": false }, { "name": "Yongil [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000269255410) Yang", "primaryContact": false }, { "name": "Robert S. [North Dakota State University,Fargo,ND (United States)] Brueggeman", "primaryContact": false }, { "name": "Juan [North Dakota State University,Fargo,ND (United States)] Franco-Coronado", "primaryContact": false }, { "name": "Nivi [North Dakota State University,Fargo,ND (United States)] Abraham", "primaryContact": false }, { "name": "Jeong-Yeh [University of Georgia,Athens,GA (United States)] Yang", "primaryContact": false }, { "name": "Kelley W. [University of Georgia,Athens,GA (United States)] (ORCID:000000031768582X) Moremen", "primaryContact": false }, { "name": "Alexandra J. [Oregon State University,Corvallis,OR (United States)] Weisberg", "primaryContact": false }, { "name": "Jeff H. [Oregon State University,Corvallis,OR (United States)] (ORCID:0000000218330695) Chang", "primaryContact": false }, { "name": "Erika [US Department of Energy,Walnut Creek,CA (United States)] Lindquist", "primaryContact": false }, { "name": "Kerrie [US Department of Energy,Walnut Creek,CA (United States)] Barry", "primaryContact": false }, { "name": "Priya [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000203571939) Ranjan", "primaryContact": false }, { "name": "Sara [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000281235439) Jawdy", "primaryContact": false }, { "name": "Jeremy [US Department of Energy,Walnut Creek,CA (United States); HudsonAlpha Institute for Biotechnology,Huntsville,AL (United States)] Schmutz", "primaryContact": false }, { "name": "Gerald A. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); US Department of Energy,Walnut Creek,CA (United States)] (ORCID:0000000301061289) Tuskan", "primaryContact": false }, { "name": "Jared M. [Oregon State University,Corvallis,OR (United States); North Dakota State University,Fargo,ND (United States)] (ORCID:0000000333034269) LeBoldus", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Institutes of Health (NIH)" } }, { "fundingOrganization": { "organizationName": "US Department of Agriculture" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Basic Energy Sciences (BES)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1545198", "active": false }, { "brc": "CBI", "title": "Cellulolytic enzyme-aided extraction of hemicellulose from switchgrass and its characteristics", "description": "The isolation of biomass components with their intact structure is integral for understanding the characteristics of biomass. Compared to other major biomass components such as cellulose and lignin, hemicellulose remains a challenging component to be isolated from the plant cell wall without significant depolymerization and modification. Here, a novel cellulolytic enzyme-aided hemicellulose (CEH) isolation method was developed to isolate hemicellulose with a near-native branched structure from switchgrass. The structural characteristics of CEH were investigated and compared with hemicelluloses isolated by conventional alkaline extracted hemicellulose (AEH) and DMSO extracted hemicellulose (DMSOH) methods. Gel permeation chromatography (GPC) analysis indicated that CEH had a weight-average molecular weight of 44 kDa, which was comparable to that of AEH (43 kDa) but higher than that of DMSOH (37 kDa). The chemical composition analysis revealed that CEH retained a higher proportion of glucuronic acid compared to AEH and DMSOH. The 2D 13C\u20131H heteronuclear single quantum coherence (HSQC) NMR spectra containing the \u03b2-(1,4)-linked-D-xylan backbone, non-reducing-end peaks and both \u03b1- and \u03b2-reducing-end peaks in CEH were comparable to the spectra of the commercial beechwood xylan. CEH showed a highly branched hemicellulose structure, which retained methoxyl groups, O-acetyl groups, and 4-O-methyl-glucuronic acid attached to the xylan backbone.", "abstract": "The isolation of biomass components with their intact structure is integral for understanding the characteristics of biomass. Compared to other major biomass components such as cellulose and lignin, hemicellulose remains a challenging component to be isolated from the plant cell wall without significant depolymerization and modification. Here, a novel cellulolytic enzyme-aided hemicellulose (CEH) isolation method was developed to isolate hemicellulose with a near-native branched structure from switchgrass. The structural characteristics of CEH were investigated and compared with hemicelluloses isolated by conventional alkaline extracted hemicellulose (AEH) and DMSO extracted hemicellulose (DMSOH) methods. Gel permeation chromatography (GPC) analysis indicated that CEH had a weight-average molecular weight of 44 kDa, which was comparable to that of AEH (43 kDa) but higher than that of DMSOH (37 kDa). The chemical composition analysis revealed that CEH retained a higher proportion of glucuronic acid compared to AEH and DMSOH. The 2D 13C\u20131H heteronuclear single quantum coherence (HSQC) NMR spectra containing the \u03b2-(1,4)-linked-D-xylan backbone, non-reducing-end peaks and both \u03b1- and \u03b2-reducing-end peaks in CEH were comparable to the spectra of the commercial beechwood xylan. CEH showed a highly branched hemicellulose structure, which retained methoxyl groups, O-acetyl groups, and 4-O-methyl-glucuronic acid attached to the xylan backbone.", "date": "2019-06-12", "issue": "14", "identifier": "https://www.osti.gov/biblio/1545200", "bibliographicCitation": "https://doi.org/10.1039/c9gc00252a", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "Cellulase", "Glucuronic acid", "Glucuronoarabinoxylan", "Hemicellulose", "Structural properties" ], "topic": [ "Microbiology" ], "journal_name": "Green Chemistry", "volume": "21", "publisher_information": "Royal Society of Chemistry", "country_publication_code": "US", "creator": [ { "name": "Jinhua [Donghua Univ.,Shanghai (China); Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:0000000162676426) Ding", "primaryContact": true }, { "name": "Chang Geun [State Univ. of New York (SUNY),Syracuse,NY (United States)] (ORCID:0000000261792414) Yoo", "primaryContact": false }, { "name": "Yunqiao [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000325541447) Pu", "primaryContact": false }, { "name": "Xianzhi [Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:0000000343033403) Meng", "primaryContact": false }, { "name": "Samarthya [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000294951880) Bhagia", "primaryContact": false }, { "name": "Chongwen [Donghua Univ.,Shanghai (China); Key Lab. of Textile Science & Technology (China)] Yu", "primaryContact": false }, { "name": "Arthur J. [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:000000023536554X) Ragauskas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1545200", "active": false }, { "brc": "CBI", "title": "Mediation of plant\u2013mycorrhizal interaction by a lectin receptor-like kinase", "description": "The molecular mechanisms underlying mycorrhizal symbioses, the most ubiquitous and impactful mutualistic plant\u2013microbial interaction in nature, are largely unknown. Through genetic mapping, resequencing and molecular validation, we demonstrate that a G-type lectin receptor-like kinase (lecRLK) mediates the symbiotic interaction between Populus and the ectomycorrhizal fungus Laccaria bicolor. Furthermore, this finding uncovers an important molecular step in the establishment of symbiotic plant\u2013fungal associations and provides a molecular target for engineering beneficial mycorrhizal relationships.", "abstract": "The molecular mechanisms underlying mycorrhizal symbioses, the most ubiquitous and impactful mutualistic plant\u2013microbial interaction in nature, are largely unknown. Through genetic mapping, resequencing and molecular validation, we demonstrate that a G-type lectin receptor-like kinase (lecRLK) mediates the symbiotic interaction between Populus and the ectomycorrhizal fungus Laccaria bicolor. Furthermore, this finding uncovers an important molecular step in the establishment of symbiotic plant\u2013fungal associations and provides a molecular target for engineering beneficial mycorrhizal relationships.", "date": "2019-07-07", "issue": "7", "identifier": "https://www.osti.gov/biblio/1545248", "bibliographicCitation": "https://doi.org/10.1038/s41477-019-0469-x", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "Nature Plants", "volume": "5", "publisher_information": "Nature Publishing Group", "country_publication_code": "US", "creator": [ { "name": "Jessy [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000303682054) Labb\u00e9", "primaryContact": true }, { "name": "Wellington [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Muchero", "primaryContact": false }, { "name": "Olaf [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Czarnecki", "primaryContact": false }, { "name": "Juan [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Wang", "primaryContact": false }, { "name": "Xiaoping [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Wang", "primaryContact": false }, { "name": "Anthony C. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Bryan", "primaryContact": false }, { "name": "Kaijie [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Zheng", "primaryContact": false }, { "name": "Yongil [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Yang", "primaryContact": false }, { "name": "Meng [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000302473701) Xie", "primaryContact": false }, { "name": "Jin [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000283975078) Zhang", "primaryContact": false }, { "name": "Dongfang [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000177026645) Wang", "primaryContact": false }, { "name": "Peter [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Meidl", "primaryContact": false }, { "name": "Hemeng [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Wang", "primaryContact": false }, { "name": "Jennifer L. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Morrell-Falvey", "primaryContact": false }, { "name": "Kevin R. [Univ. of Wisconsin-Madison,Madison,WI (United States)] (ORCID:0000000301732871) Cope", "primaryContact": false }, { "name": "Lucas G. S. [Univ. of Wisconsin-Madison,Madison,WI (United States)] Maia", "primaryContact": false }, { "name": "Jean -Michel [Univ. of Wisconsin-Madison,Madison,WI (United States)] An\u00e9", "primaryContact": false }, { "name": "Ritesh [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Mewalal", "primaryContact": false }, { "name": "Sara S. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Jawdy", "primaryContact": false }, { "name": "Lee E. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Gunter", "primaryContact": false }, { "name": "Wendy [USDOE Joint Genome Institute (JGI),Walnut Creek,CA (United States)] Schackwitz", "primaryContact": false }, { "name": "Joel [USDOE Joint Genome Institute (JGI),Walnut Creek,CA (United States)] (ORCID:0000000195116441) Martin", "primaryContact": false }, { "name": "Fran\u00e7ois [Institut National de la Recherche Agronomique et Univ. de Lorraine,Champenoux (France)] Le Tacon", "primaryContact": false }, { "name": "Ting [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Li", "primaryContact": false }, { "name": "Zhihao [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Zhang", "primaryContact": false }, { "name": "Priya [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Ranjan", "primaryContact": false }, { "name": "Erika [USDOE Joint Genome Institute (JGI),Walnut Creek,CA (United States)] Lindquist", "primaryContact": false }, { "name": "Xiaohan [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000152074210) Yang", "primaryContact": false }, { "name": "Daniel A. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000298228251) Jacobson", "primaryContact": false }, { "name": "Timothy J. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000295406622) Tschaplinski", "primaryContact": false }, { "name": "Kerrie [USDOE Joint Genome Institute (JGI),Walnut Creek,CA (United States)] Barry", "primaryContact": false }, { "name": "Jeremy [USDOE Joint Genome Institute (JGI),Walnut Creek,CA (United States); HudsonAlpha Institute for Biotechnology,Huntsville,AL (United States)] (ORCID:0000000180629172) Schmutz", "primaryContact": false }, { "name": "Jin -Gui [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000217524201) Chen", "primaryContact": false }, { "name": "Gerald A. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Tuskan", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1545248", "active": false }, { "brc": "CBI", "title": "RElative QUantitation Inferred by Evaluating Mixtures (REQUIEM)", "description": "Motivated by the lack of easily implementable and generally applicable strategies to increase and assess data accuracy, we devised a novel label-free approach, termed REQUIEM, to address challenges in relative quantitation. For comparing the relative amounts of analytes in two samples, a mixture is prepared from aliquots of the samples, and the samples and the mixture are analyzed in parallel according to the intended workflow. Processing of the resulting data using the REQUIEM algorithm yields unbiased analyte fold-changes and associated statistics, allowing several types of errors to be diagnosed or eliminated. Extensive simulations and analysis of carefully prepared standard samples demonstrated the rigorous foundations of REQUIEM. We applied REQUIEM to several real-world analytical techniques and workflows, notably to tandem mass spectrometry analysis by using isomeric oligosaccharides as test analytes. Finally, we conclude that REQUIEM can reveal inaccuracies in the data that are difficult to identify by using traditional approaches.", "abstract": "Motivated by the lack of easily implementable and generally applicable strategies to increase and assess data accuracy, we devised a novel label-free approach, termed REQUIEM, to address challenges in relative quantitation. For comparing the relative amounts of analytes in two samples, a mixture is prepared from aliquots of the samples, and the samples and the mixture are analyzed in parallel according to the intended workflow. Processing of the resulting data using the REQUIEM algorithm yields unbiased analyte fold-changes and associated statistics, allowing several types of errors to be diagnosed or eliminated. Extensive simulations and analysis of carefully prepared standard samples demonstrated the rigorous foundations of REQUIEM. We applied REQUIEM to several real-world analytical techniques and workflows, notably to tandem mass spectrometry analysis by using isomeric oligosaccharides as test analytes. Finally, we conclude that REQUIEM can reveal inaccuracies in the data that are difficult to identify by using traditional approaches.", "date": "2017-10-03", "issue": "C", "identifier": "https://www.osti.gov/biblio/1546758", "bibliographicCitation": "https://doi.org/10.1016/j.aca.2017.09.023", "keywords": [ "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "Accuracy", "Mass spectrometry", "Precision", "RNA-Seq", "Relative quantitation" ], "topic": [ "Chemistry" ], "journal_name": "Analytica Chimica Acta", "volume": "993", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Sami T. [Complex Carbohydrate Research Center,Athens,GA (United States); None] (ORCID:0000000271500665) Tuomivaara", "primaryContact": true }, { "name": "Paul [Univ. of Georgia,Athens,GA (United States). Dept. of Statistics] Schliekelman", "primaryContact": false }, { "name": "Alison V. [Complex Carbohydrate Research Center,Athens,GA (United States); Univ. of Georgia,Athens,GA (United States). Dept. of Biochemistry and Molecular Biology] Nairn", "primaryContact": false }, { "name": "Kelley W. [Complex Carbohydrate Research Center,Athens,GA (United States); Univ. of Georgia,Athens,GA (United States). Dept. of Biochemistry and Molecular Biology] Moremen", "primaryContact": false }, { "name": "William S. [Complex Carbohydrate Research Center,Athens,GA (United States); Univ. of Georgia,Athens,GA (United States). Dept. of Biochemistry and Molecular Biology] (ORCID:0000000308833237) York", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1546758", "active": false }, { "brc": "CBI", "title": "Population-level approaches reveal novel aspects of lignin biosynthesis, content, composition and structure", "description": "Not Available", "abstract": "Not Available", "date": "2019-03-31", "issue": "C", "identifier": "https://www.osti.gov/biblio/1547584", "bibliographicCitation": "https://doi.org/10.1016/j.copbio.2019.02.017", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "Current Opinion in Biotechnology", "volume": "56", "publisher_information": "Elsevier", "country_publication_code": "GB", "creator": [ { "name": "Gerald A. Tuskan", "primaryContact": true }, { "name": "Wellington Muchero", "primaryContact": false }, { "name": "Timothy J. Tschaplinski", "primaryContact": false }, { "name": "Arthur J. Ragauskas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1547584", "active": false }, { "brc": "CBI", "title": "A Multifunctional Cosolvent Pair Reveals Molecular Principles of Biomass Deconstruction", "description": "The complex structure of plant cell walls resists chemical or biological degradation, challenging the breakdown of lignocellulosic biomass into renewable chemical precursors that could form the basis of future production of green chemicals and transportation fuels. In this report, experimental and computational results reveal that the effect of the tetrahydrofuran (THF)\u2013water cosolvents on the structure of lignin and on its interactions with cellulose in the cell wall drives multiple synergistic mechanisms leading to the efficient breakdown and fractionation of biomass into valuable chemical precursors. Molecular simulations reflect that THF\u2013water is an excellent \u201ctheta\u201d solvent, such that lignin dissociates from itself and from cellulose and expands to form a random coil. The expansion of the lignin molecules exposes interunit linkages, rendering them more susceptible to depolymerization by acid-catalyzed cleavage of aryl-ether bonds. Nanoscale infrared sensors confirm cosolvent-mediated molecular rearrangement of lignin in the cell wall of micrometer-thick hardwood slices and track the disappearance of lignin. At bulk scale, adding dilute acid to the cosolvent mixture liberates the majority of the hemicellulose and lignin from biomass, allowing unfettered access of cellulolytic enzymes to the remaining cellulose-rich material, allowing them to sustain high rates of hydrolysis to glucose without enzyme deactivation. Through this multiscale analysis, synergistic mechanisms for biomass deconstruction are confirmed, portending a paradigm shift toward first-principles design and evaluation of other cosolvent methods to realize low cost fuels and bioproducts.", "abstract": "The complex structure of plant cell walls resists chemical or biological degradation, challenging the breakdown of lignocellulosic biomass into renewable chemical precursors that could form the basis of future production of green chemicals and transportation fuels. In this report, experimental and computational results reveal that the effect of the tetrahydrofuran (THF)\u2013water cosolvents on the structure of lignin and on its interactions with cellulose in the cell wall drives multiple synergistic mechanisms leading to the efficient breakdown and fractionation of biomass into valuable chemical precursors. Molecular simulations reflect that THF\u2013water is an excellent \u201ctheta\u201d solvent, such that lignin dissociates from itself and from cellulose and expands to form a random coil. The expansion of the lignin molecules exposes interunit linkages, rendering them more susceptible to depolymerization by acid-catalyzed cleavage of aryl-ether bonds. Nanoscale infrared sensors confirm cosolvent-mediated molecular rearrangement of lignin in the cell wall of micrometer-thick hardwood slices and track the disappearance of lignin. At bulk scale, adding dilute acid to the cosolvent mixture liberates the majority of the hemicellulose and lignin from biomass, allowing unfettered access of cellulolytic enzymes to the remaining cellulose-rich material, allowing them to sustain high rates of hydrolysis to glucose without enzyme deactivation. Through this multiscale analysis, synergistic mechanisms for biomass deconstruction are confirmed, portending a paradigm shift toward first-principles design and evaluation of other cosolvent methods to realize low cost fuels and bioproducts.", "date": "2019-07-14", "issue": "32", "identifier": "https://www.osti.gov/biblio/1558519", "bibliographicCitation": "https://doi.org/10.1021/jacs.8b10242", "keywords": [ "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY" ], "topic": [ "Chemistry" ], "journal_name": "Journal of the American Chemical Society", "volume": "141", "publisher_information": "American Chemical Society (ACS)", "country_publication_code": "US", "creator": [ { "name": "Abhishek S. [Univ. of California,Riverside,CA (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). BioEnergy Science Center (BESC)] Patri", "primaryContact": true }, { "name": "Barmak [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). UT/ORNL Center for Molecular Biophysics; Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Joint Inst. for Biological Sciences] (ORCID:0000000305689866) Mostofian", "primaryContact": false }, { "name": "Yunqiao [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). BioEnergy Science Center (BESC); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Joint Inst. for Biological Sciences] (ORCID:0000000325541447) Pu", "primaryContact": false }, { "name": "Nicholas [Univ. of Central Florida,Orlando,FL (United States). NanoScience Technology Center] Ciaffone", "primaryContact": false }, { "name": "Mikhael [Univ. of Central Florida,Orlando,FL (United States). NanoScience Technology Center] Soliman", "primaryContact": false }, { "name": "Micholas Dean [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). UT/ORNL Center for Molecular Biophysics; Univ. of Tennessee,Knoxville,TN (United States). Dept. of Biochemistry] (ORCID:0000000207777539) Smith", "primaryContact": false }, { "name": "Rajeev [Univ. of California,Riverside,CA (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). BioEnergy Science Center (BESC); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] Kumar", "primaryContact": false }, { "name": "Xiaolin [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). UT/ORNL Center for Molecular Biophysics; The Ohio State Univ.,Columbus,OH (United States). College of Pharmacy] (ORCID:0000000273963225) Cheng", "primaryContact": false }, { "name": "Charles E. [Univ. of California,Riverside,CA (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). BioEnergy Science Center (BESC); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] Wyman", "primaryContact": false }, { "name": "Laurene [Univ. of Central Florida,Orlando,FL (United States). NanoScience Technology Center] Tetard", "primaryContact": false }, { "name": "Arthur J. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). BioEnergy Science Center (BESC); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Joint Inst. for Biological Sciences; Univ. of Tennessee,Knoxville,TN (United States). Dept. of Chemical and Biomolecular Engineering; Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] (ORCID:000000023536554X) Ragauskas", "primaryContact": false }, { "name": "Jeremy C. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). UT/ORNL Center for Molecular Biophysics; Univ. of Tennessee,Knoxville,TN (United States). Dept. of Biochemistry] (ORCID:0000000229783227) Smith", "primaryContact": false }, { "name": "Loukas [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). UT/ORNL Center for Molecular Biophysics; Univ. of Tennessee,Knoxville,TN (United States). Dept. of Biochemistry] (ORCID:000000018569060X) Petridis", "primaryContact": false }, { "name": "Charles M. [Univ. of California,Riverside,CA (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). BioEnergy Science Center (BESC); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] (ORCID:0000000250470815) Cai", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1558519", "active": false }, { "brc": "CBI", "title": "Multi-Phenotype Association Decomposition: Unraveling Complex Gene-Phenotype Relationships", "description": "Various patterns of multi-phenotype associations (MPAs) exist in the results of Genome Wide Association Studies (GWAS) involving different topologies of single nucleotide polymorphism (SNP)-phenotype associations. These can provide interesting information about the different impacts of a gene on closely related phenotypes or disparate phenotypes (pleiotropy). In this work we present MPA Decomposition, a new network-based approach which decomposes the results of a multi-phenotype GWAS study into three bipartite networks, which, when used together, unravel the multi-phenotype signatures of genes on a genome-wide scale. The decomposition involves the construction of a phenotype powerset space, and subsequent mapping of genes into this new space. Clustering of genes in this powerset space groups genes based on their detailed MPA signatures. We show that this method allows us to find multiple different MPA and pleiotropic signatures within individual genes and to classify and cluster genes based on these SNP-phenotype association topologies. We demonstrate the use of this approach on a GWAS analysis of a large population of 882 Populus trichocarpa genotypes using untargeted metabolomics phenotypes. This method should prove invaluable in the interpretation of large GWAS datasets and aid in future synthetic biology efforts designed to optimize phenotypes of interest.", "abstract": "Various patterns of multi-phenotype associations (MPAs) exist in the results of Genome Wide Association Studies (GWAS) involving different topologies of single nucleotide polymorphism (SNP)-phenotype associations. These can provide interesting information about the different impacts of a gene on closely related phenotypes or disparate phenotypes (pleiotropy). In this work we present MPA Decomposition, a new network-based approach which decomposes the results of a multi-phenotype GWAS study into three bipartite networks, which, when used together, unravel the multi-phenotype signatures of genes on a genome-wide scale. The decomposition involves the construction of a phenotype powerset space, and subsequent mapping of genes into this new space. Clustering of genes in this powerset space groups genes based on their detailed MPA signatures. We show that this method allows us to find multiple different MPA and pleiotropic signatures within individual genes and to classify and cluster genes based on these SNP-phenotype association topologies. We demonstrate the use of this approach on a GWAS analysis of a large population of 882 Populus trichocarpa genotypes using untargeted metabolomics phenotypes. This method should prove invaluable in the interpretation of large GWAS datasets and aid in future synthetic biology efforts designed to optimize phenotypes of interest.", "date": "2019-05-09", "issue": "n/a", "identifier": "https://www.osti.gov/biblio/1559645", "bibliographicCitation": "https://doi.org/10.3389/fgene.2019.00417", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "Frontiers in Genetics", "volume": "10", "country_publication_code": "US", "creator": [ { "name": "Deborah A. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000349795871) Weighill", "primaryContact": true }, { "name": "Piet C. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Jones", "primaryContact": false }, { "name": "Carissa R. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Bleker", "primaryContact": false }, { "name": "Priya [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Ranjan", "primaryContact": false }, { "name": "Manesh B. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Shah", "primaryContact": false }, { "name": "Nan [Univ. of Tennessee,Knoxville,TN (United States)] Zhao", "primaryContact": false }, { "name": "Madhavi Z. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000266772180) Martin", "primaryContact": false }, { "name": "Stephen [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Difazio", "primaryContact": false }, { "name": "David [West Virginia Univ.,Morgantown,WV (United States)] Macaya-Sanz", "primaryContact": false }, { "name": "Jeremy [USDOE Joint Genome Institute (JGI),Walnut Creek,CA (United States)] Schmutz", "primaryContact": false }, { "name": "Avinash [Hudson Alpha Inst. of Biotechnology,Huntsville,AL (United States)] Sreedasyam", "primaryContact": false }, { "name": "Timothy J. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000295406622) Tschaplinski", "primaryContact": false }, { "name": "Gerald A. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000301061289) Tuskan", "primaryContact": false }, { "name": "Daniel A. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000298228251) Jacobson", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1559645", "active": false }, { "brc": "CBI", "title": "Target highlights in CASP13: Experimental target structures through the eyes of their authors", "description": "The functional and biological significance of selected CASP13 targets are described by the authors of the structures. The structural biologists discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP13 experiment.", "abstract": "The functional and biological significance of selected CASP13 targets are described by the authors of the structures. The structural biologists discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP13 experiment.", "date": "2019-08-22", "issue": "12", "identifier": "https://www.osti.gov/biblio/1559927", "bibliographicCitation": "https://doi.org/10.1002/prot.25805", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "CASP", "X-ray crystallography", "cryo-EM", "protein structure prediction" ], "topic": [ "Microbiology" ], "journal_name": "Proteins", "volume": "87", "publisher_information": "Wiley", "country_publication_code": "US", "creator": [ { "name": "Rosalba [BSC\u2010CNS Barcelona Supercomputing Center,Barcelona (Spain)] (ORCID:0000000294812557) Lepore", "primaryContact": true }, { "name": "Andriy [Univ. of California,Davis,CA (United States)] (ORCID:0000000150667178) Kryshtafovych", "primaryContact": false }, { "name": "Markus [National Renewable Energy Lab. (NREL),Golden,CO (United States)] Alahuhta", "primaryContact": false }, { "name": "Harshul A. [Max Planck Inst. for Developmental Biology,T\u00fcbingen (Germany)] Veraszto", "primaryContact": false }, { "name": "Yannick J. [National Renewable Energy Lab. (NREL),Golden,CO (United States)] Bomble", "primaryContact": false }, { "name": "Joshua C. [Univ. of Oxford (United Kingdom); Univ. of Bristol (United Kingdom)] Bufton", "primaryContact": false }, { "name": "Alex N. [Univ. of Oxford (United Kingdom)] Bullock", "primaryContact": false }, { "name": "Cody [Univ. of Windsor,ON (Canada)] Caba", "primaryContact": false }, { "name": "Hongnan [Univ. of Houston,TX (United States); Univ. of Wisconsin,Madison,WI (United States)] Cao", "primaryContact": false }, { "name": "Owen R. [Newcastle Univ.,Newcastle upon Tyne (United Kingdom)] Davies", "primaryContact": false }, { "name": "Ambroise [Univ. of Auckland (Australia); Univ. Grenoble Alpes (France)] Desfosses", "primaryContact": false }, { "name": "Matthew [Nutrition and Health,Zurich (Switzerland)] Dunne", "primaryContact": false }, { "name": "Krzysztof [Univ. of California,Davis,CA (United States)] (ORCID:000000028061412X) Fidelis", "primaryContact": false }, { "name": "Celia W. [Univ. of California,Irvine,CA (United States)] Goulding", "primaryContact": false }, { "name": "Manickam [Newcastle Univ.,Newcastle upon Tyne (United Kingdom)] Gurusaran", "primaryContact": false }, { "name": "Irina [Univ. Grenoble Alpes (France)] Gutsche", "primaryContact": false }, { "name": "Christopher J. [Univ. of Birmingham (United Kingdom)] Harding", "primaryContact": false }, { "name": "Marcus D. [Max Planck Inst. for Developmental Biology,T\u00fcbingen (Germany)] Hartmann", "primaryContact": false }, { "name": "Christopher S. [Univ. of California,Santa Barbara,CA (United States)] (ORCID:0000000222166445) Hayes", "primaryContact": false }, { "name": "Andrzej [Midwest Center for Structural Genomics,Argonne,IL (United States); Univ. of Chicago,IL (United States)] Joachimiak", "primaryContact": false }, { "name": "Petr G. [Univ. of Texas Medical Branch,Galveston,TX (United States)] Leiman", "primaryContact": false }, { "name": "Peter [Univ. of Toronto,ON (Canada)] Loppnau", "primaryContact": false }, { "name": "Andrew L. [Univ. of Birmingham (United Kingdom)] Lovering", "primaryContact": false }, { "name": "Vladimir V. [National Renewable Energy Lab. (NREL),Golden,CO (United States)] Lunin", "primaryContact": false }, { "name": "Karolina [Midwest Center for Structural Genomics,Argonne,IL (United States)] Michalska", "primaryContact": false }, { "name": "Ignacio [Univ. of Chicago,IL (United States)] Mir\u2010Sanchis", "primaryContact": false }, { "name": "Alok [Univ. of Auckland (Australia)] Mitra", "primaryContact": false }, { "name": "John [Univ. of Maryland,Rockville,MD (United States)] Moult", "primaryContact": false }, { "name": "George N. [Univ. of Houston,TX (United States); Univ. of Wisconsin,Madison,WI (United States)] Phillips Jr", "primaryContact": false }, { "name": "Daniel M. [Univ. of Oxford (United Kingdom)] Pinkas", "primaryContact": false }, { "name": "Phoebe A. [Univ. of Chicago,IL (United States)] Rice", "primaryContact": false }, { "name": "Yufeng [Univ. of Windsor,ON (Canada); Univ. of Toronto,ON (Canada)] Tong", "primaryContact": false }, { "name": "Maya [Univ. College London (United Kingdom)] Topf", "primaryContact": false }, { "name": "Jonathan D. [Michigan State Univ.,East Lansing,MI (United States)] Walton", "primaryContact": false }, { "name": "Torsten [Univ. of Basel (Switzerland)] (ORCID:000000032715335X) Schwede", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1559927", "active": false, "has_related_ids": [ "NREL/JA-2700-74703" ] }, { "brc": "CBI", "title": "Co-expression networks for plant biology: why and how", "description": "Not Available", "abstract": "Not Available", "date": "2019-08-21", "issue": "10", "identifier": "https://www.osti.gov/biblio/1560912", "bibliographicCitation": "https://doi.org/10.1093/abbs/gmz080", "topic": [ "Unknown" ], "journal_name": "Acta Biochimica et Biophysica Sinica", "volume": "51", "publisher_information": "China Science Publishing & Media Ltd.", "country_publication_code": "Country unknown/Code not available", "creator": [ { "name": "Xiaolan Rao", "primaryContact": true }, { "name": "Richard A. Dixon", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1560912", "active": false }, { "brc": "CBI", "title": "Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis", "description": "A microbe\u2019s ecological niche and biotechnological utility are confirmed by its specific set of co-evolved metabolic pathways. The acquisition of new pathways, through horizontal gene transfer or genetic engineering, can have unpredictable consequences. In this work, we show that two different pathways for coumarate catabolism failed to function when initially transferred into Escherichia coli. Using laboratory evolution, we elucidated the factors limiting activity of the newly acquired pathways and the modifications required to overcome these limitations. Both pathways required host mutations to enable effective growth with coumarate, but the necessary mutations differed. In one case, a pathway intermediate inhibited purine nucleotide biosynthesis, and this inhibition was relieved by single amino acid replacements in IMP dehydrogenase. A strain that natively contains this coumarate catabolism pathway, Acinetobacter baumannii, is resistant to inhibition by the relevant intermediate, indicating that natural pathway transfers have faced and overcome similar challenges. Molecular dynamics simulation of the wild type and a representative single-residue mutant provide insight into the structural and dynamic changes that relieve inhibition. These results reflect how deleterious interactions can limit pathway transfer, that these interactions can be traced to specific molecular interactions between host and pathway, and how evolution or engineering can alleviate these limitations.", "abstract": "A microbe\u2019s ecological niche and biotechnological utility are confirmed by its specific set of co-evolved metabolic pathways. The acquisition of new pathways, through horizontal gene transfer or genetic engineering, can have unpredictable consequences. In this work, we show that two different pathways for coumarate catabolism failed to function when initially transferred into Escherichia coli. Using laboratory evolution, we elucidated the factors limiting activity of the newly acquired pathways and the modifications required to overcome these limitations. Both pathways required host mutations to enable effective growth with coumarate, but the necessary mutations differed. In one case, a pathway intermediate inhibited purine nucleotide biosynthesis, and this inhibition was relieved by single amino acid replacements in IMP dehydrogenase. A strain that natively contains this coumarate catabolism pathway, Acinetobacter baumannii, is resistant to inhibition by the relevant intermediate, indicating that natural pathway transfers have faced and overcome similar challenges. Molecular dynamics simulation of the wild type and a representative single-residue mutant provide insight into the structural and dynamic changes that relieve inhibition. These results reflect how deleterious interactions can limit pathway transfer, that these interactions can be traced to specific molecular interactions between host and pathway, and how evolution or engineering can alleviate these limitations.", "date": "2019-09-17", "issue": "6", "identifier": "https://www.osti.gov/biblio/1570140", "bibliographicCitation": "https://doi.org/10.1111/MMI.14393", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "IMPDH", "biosystem design", "lignin catabolism", "molecular dynamics", "pathway optimization" ], "topic": [ "Microbiology" ], "journal_name": "Molecular Microbiology", "volume": "112", "publisher_information": "Wiley", "country_publication_code": "US", "creator": [ { "name": "Dan [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000347904448) Close", "primaryContact": true }, { "name": "Conner J. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Univ. of Tennessee,Knoxville,TN (United States)] Cooper", "primaryContact": false }, { "name": "Xingyou [Brandeis Univ.,Waltham,MA (United States)] Wang", "primaryContact": false }, { "name": "Payal [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Univ. of Tennessee,Knoxville,TN (United States)] Chirania", "primaryContact": false }, { "name": "Madhulika [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Gupta", "primaryContact": false }, { "name": "John R. [Univ. of Tennessee,Knoxville,TN (United States)] Ossyra", "primaryContact": false }, { "name": "Richard J. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000185510138) Giannone", "primaryContact": false }, { "name": "Nancy L. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000302907987) Engle", "primaryContact": false }, { "name": "Timothy J. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000295406622) Tschaplinski", "primaryContact": false }, { "name": "Jeremy C. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:0000000229783227) Smith", "primaryContact": false }, { "name": "Lizbeth [Brandeis Univ.,Waltham,MA (United States)] Hedstrom", "primaryContact": false }, { "name": "Jerry M. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:0000000231039333) Parks", "primaryContact": false }, { "name": "Josh [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000323028180) Michener", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1570140", "active": false }, { "brc": "CBI", "title": "Near-equilibrium glycolysis supports metabolic homeostasis and energy yield", "description": "Glycolysis plays a central role in producing ATP and biomass. Its control principles, however, remain incompletely understood. In this work, we create a method that combines 2H and 13C tracers to determine glycolytic thermodynamics. With this method, we show that, in conditions and organisms with relatively slow fluxes, multiple steps in glycolysis are near to equilibrium, reflecting spare enzyme capacity. In Escherichia coli, nitrogen or phosphorus upshift rapidly increases the thermodynamic driving force, deploying the spare enzyme capacity to increase flux. Similarly, respiration inhibition in mammalian cells rapidly increases both glycolytic flux and the thermodynamic driving force. The thermodynamic shift allows flux to increase with only small metabolite concentration changes. Finally, we find that the cellulose-degrading anaerobe Clostridium cellulolyticum exhibits slow, near-equilibrium glycolysis due to the use of pyrophosphate rather than ATP for fructose-bisphosphate production, resulting in enhanced per-glucose ATP yield. Thus, near-equilibrium steps of glycolysis promote both rapid flux adaptation and energy efficiency.", "abstract": "Glycolysis plays a central role in producing ATP and biomass. Its control principles, however, remain incompletely understood. In this work, we create a method that combines 2H and 13C tracers to determine glycolytic thermodynamics. With this method, we show that, in conditions and organisms with relatively slow fluxes, multiple steps in glycolysis are near to equilibrium, reflecting spare enzyme capacity. In Escherichia coli, nitrogen or phosphorus upshift rapidly increases the thermodynamic driving force, deploying the spare enzyme capacity to increase flux. Similarly, respiration inhibition in mammalian cells rapidly increases both glycolytic flux and the thermodynamic driving force. The thermodynamic shift allows flux to increase with only small metabolite concentration changes. Finally, we find that the cellulose-degrading anaerobe Clostridium cellulolyticum exhibits slow, near-equilibrium glycolysis due to the use of pyrophosphate rather than ATP for fructose-bisphosphate production, resulting in enhanced per-glucose ATP yield. Thus, near-equilibrium steps of glycolysis promote both rapid flux adaptation and energy efficiency.", "date": "2019-09-22", "issue": "10", "identifier": "https://www.osti.gov/biblio/1570470", "bibliographicCitation": "https://doi.org/10.1038/s41589-019-0364-9", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "Nature Chemical Biology", "volume": "15", "publisher_information": "Nature Publishing Group", "country_publication_code": "US", "creator": [ { "name": "Junyoung O. [Univ. of California,Los Angeles,CA (United States); Princeton Univ.,NJ (United States); CABBI] (ORCID:0000000198698993) Park", "primaryContact": true }, { "name": "Lukas B. [Princeton Univ.,NJ (United States)] Tanner", "primaryContact": false }, { "name": "Monica H. [Princeton Univ.,NJ (United States)] Wei", "primaryContact": false }, { "name": "Daven B. [Univ. of Wisconsin,Madison,WI (United States)] (ORCID:0000000280813436) Khana", "primaryContact": false }, { "name": "Tyler B. [Univ. of Wisconsin,Madison,WI (United States)] Jacobson", "primaryContact": false }, { "name": "Zheyun [Princeton Univ.,NJ (United States)] Zhang", "primaryContact": false }, { "name": "Sara A. [Princeton Univ.,NJ (United States)] (ORCID:0000000234845461) Rubin", "primaryContact": false }, { "name": "Sophia Hsin-Jung [Princeton Univ.,NJ (United States)] Li", "primaryContact": false }, { "name": "Meytal B. [Princeton Univ.,NJ (United States); ExxonMobil Research and Engineering Company,Annandale,NJ (United States)] Higgins", "primaryContact": false }, { "name": "David M. [Univ. of Wisconsin,Madison,WI (United States)] Stevenson", "primaryContact": false }, { "name": "Daniel [Univ. of Wisconsin,Madison,WI (United States)] (ORCID:0000000235683070) Amador-Noguez", "primaryContact": false }, { "name": "Joshua D. [Princeton Univ.,NJ (United States)] (ORCID:0000000212474727) Rabinowitz", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1570470", "active": false }, { "brc": "CBI", "title": "Passive membrane transport of lignin-related compounds", "description": "Lignin is an significant aromatic polymer found in plant secondary cell walls. Recently, lignin has attracted renewed interest as a feedstock for bio-based chemicals via catalytic and biological approaches and has emerged as a target for genetic engineering to improve lignocellulose digestibility by altering its composition. In lignin biosynthesis and microbial conversion, small phenolic lignin precursors or degradation products cross membrane bilayers through an unidentified translocation mechanism prior to incorporation into lignin polymers (synthesis) or catabolism (bioconversion), with both passive and transporter-assisted mechanisms postulated. To test the passive permeation potential of these phenolics, we performed molecular dynamics simulations for 69 monomeric and dimeric lignin-related phenolics with 3 model membranes to determine the membrane partitioning and permeability coefficients for each compound. The findings support an accessible passive permeation mechanism for most compounds, including monolignols, dimeric phenolics, and the flavonoid, tricin. Computed lignin partition coefficients are consistent with concentration enrichment near lipid carbonyl groups, and permeability coefficients are sufficient to keep pace with cellular metabolism. Interactions between methoxy and hydroxy groups are found to reduce membrane partitioning and improve permeability. Only carboxylate-modified or glycosylated lignin phenolics are predicted to require transporters for membrane translocation. Overall, the results suggest that most lignin-related compounds can passively traverse plant and microbial membranes on timescales commensurate with required biological activities, with any potential transport regulation mechanism in lignin synthesis, catabolism, or bioconversion requiring compound functionalization.
", "abstract": "Lignin is an significant aromatic polymer found in plant secondary cell walls. Recently, lignin has attracted renewed interest as a feedstock for bio-based chemicals via catalytic and biological approaches and has emerged as a target for genetic engineering to improve lignocellulose digestibility by altering its composition. In lignin biosynthesis and microbial conversion, small phenolic lignin precursors or degradation products cross membrane bilayers through an unidentified translocation mechanism prior to incorporation into lignin polymers (synthesis) or catabolism (bioconversion), with both passive and transporter-assisted mechanisms postulated. To test the passive permeation potential of these phenolics, we performed molecular dynamics simulations for 69 monomeric and dimeric lignin-related phenolics with 3 model membranes to determine the membrane partitioning and permeability coefficients for each compound. The findings support an accessible passive permeation mechanism for most compounds, including monolignols, dimeric phenolics, and the flavonoid, tricin. Computed lignin partition coefficients are consistent with concentration enrichment near lipid carbonyl groups, and permeability coefficients are sufficient to keep pace with cellular metabolism. Interactions between methoxy and hydroxy groups are found to reduce membrane partitioning and improve permeability. Only carboxylate-modified or glycosylated lignin phenolics are predicted to require transporters for membrane translocation. Overall, the results suggest that most lignin-related compounds can passively traverse plant and microbial membranes on timescales commensurate with required biological activities, with any potential transport regulation mechanism in lignin synthesis, catabolism, or bioconversion requiring compound functionalization.
", "date": "2019-10-27", "issue": "46", "identifier": "https://www.osti.gov/biblio/1574194", "bibliographicCitation": "https://doi.org/10.1073/pnas.1904643116", "keywords": [ "09 BIOMASS FUELS", "BCPL", "biological funneling", "free energy calculation", "lignin biosynthesis", "lignin permeability", "molecular dynamics" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "116", "publisher_information": "National Academy of Sciences", "country_publication_code": "US", "creator": [ { "name": "Josh V. [National Renewable Energy Lab. (NREL),Golden,CO (United States)] (ORCID:0000000331396469) Vermaas", "primaryContact": true }, { "name": "Richard A. [Univ. of North Texas,Denton,TX (United States)] (ORCID:0000000183939408) Dixon", "primaryContact": false }, { "name": "Fang [Univ. of North Texas,Denton,TX (United States)] Chen", "primaryContact": false }, { "name": "Shawn D. [Univ. of British Columbia,Vancouver,BC (Canada)] Mansfield", "primaryContact": false }, { "name": "Wout [Ghent Univ. (Belgium)] Boerjan", "primaryContact": false }, { "name": "John [Univ. of Wisconsin,Madison,WI (United States)] (ORCID:0000000260934521) Ralph", "primaryContact": false }, { "name": "Michael F. [National Renewable Energy Lab. (NREL),Golden,CO (United States)] Crowley", "primaryContact": false }, { "name": "Gregg T. [National Renewable Energy Lab. (NREL),Golden,CO (United States)] (ORCID:000000023480212X) Beckham", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Bioenergy Technologies Office (EE-3B)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1574194", "active": false, "has_related_ids": [ "NREL/JA--2700-74621" ] }, { "brc": "CBI", "title": "Technoeconomic and life-cycle analysis of single-step catalytic conversion of wet ethanol into fungible fuel blendstocks", "description": "Technoeconomic and life-cycle analyses are presented for catalytic conversion of ethanol to fungible hydrocarbon fuel blendstocks, informed by advances in catalyst and process development. Whereas prior work toward this end focused on 3-step processes featuring dehydration, oligomerization, and hydrogenation, the consolidated alcohol dehydration and oligomerization (CADO) approach described here results in 1-step conversion of wet ethanol vapor (40 wt% in water) to hydrocarbons and water over a metal-modified zeolite catalyst. A development project increased liquid hydrocarbon yields from 36% of theoretical to >80%, reduced catalyst cost by an order of magnitude, scaled up the process by 300-fold, and reduced projected costs of ethanol conversion 12-fold. Current CADO products conform most closely to gasoline blendstocks, but can be blended with jet fuel at low levels today, and could potentially be blended at higher levels in the future. Operating plus annualized capital costs for conversion of wet ethanol to fungible blendstocks are estimated at $2.00/GJ for CADO today and $1.44/GJ in the future, similar to the unit energy cost of producing anhydrous ethanol from wet ethanol ($1.46/GJ). Including the cost of ethanol from either corn or future cellulosic biomass but not production incentives, projected minimum selling prices for fungible blendstocks produced via CADO are competitive with conventional jet fuel when oil is $100 per barrel but not at $60 per barrel. However, with existing production incentives, the projected minimum blendstock selling price is competitive with oil at $60 per barrel. Life-cycle greenhouse gas emission reductions for CADO-derived hydrocarbon blendstocks closely follow those for the ethanol feedstock.
", "abstract": "Technoeconomic and life-cycle analyses are presented for catalytic conversion of ethanol to fungible hydrocarbon fuel blendstocks, informed by advances in catalyst and process development. Whereas prior work toward this end focused on 3-step processes featuring dehydration, oligomerization, and hydrogenation, the consolidated alcohol dehydration and oligomerization (CADO) approach described here results in 1-step conversion of wet ethanol vapor (40 wt% in water) to hydrocarbons and water over a metal-modified zeolite catalyst. A development project increased liquid hydrocarbon yields from 36% of theoretical to >80%, reduced catalyst cost by an order of magnitude, scaled up the process by 300-fold, and reduced projected costs of ethanol conversion 12-fold. Current CADO products conform most closely to gasoline blendstocks, but can be blended with jet fuel at low levels today, and could potentially be blended at higher levels in the future. Operating plus annualized capital costs for conversion of wet ethanol to fungible blendstocks are estimated at $2.00/GJ for CADO today and $1.44/GJ in the future, similar to the unit energy cost of producing anhydrous ethanol from wet ethanol ($1.46/GJ). Including the cost of ethanol from either corn or future cellulosic biomass but not production incentives, projected minimum selling prices for fungible blendstocks produced via CADO are competitive with conventional jet fuel when oil is $100 per barrel but not at $60 per barrel. However, with existing production incentives, the projected minimum blendstock selling price is competitive with oil at $60 per barrel. Life-cycle greenhouse gas emission reductions for CADO-derived hydrocarbon blendstocks closely follow those for the ethanol feedstock.
", "date": "2019-11-24", "identifier": "https://www.osti.gov/biblio/1575808", "bibliographicCitation": "https://doi.org/10.1073/pnas.1821684116", "keywords": [ "09 BIOMASS FUELS", "Low-carbon fungible fuel blendstocks", "ethanol", "heterogeneous catalysis", "low-carbon fungible fuel blendstocks" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "2018", "publisher_information": "National Academy of Sciences", "country_publication_code": "US", "creator": [ { "name": "John R. Hannon", "primaryContact": true }, { "name": "Lee R. Lynd", "primaryContact": false }, { "name": "Onofre Andrade", "primaryContact": false }, { "name": "Pahola Thathiana Benavides", "primaryContact": false }, { "name": "Gregg T. (ORCID:000000023480212X) Beckham", "primaryContact": false }, { "name": "Mary J. Biddy", "primaryContact": false }, { "name": "Nathan Brown", "primaryContact": false }, { "name": "Mateus F. Chagas", "primaryContact": false }, { "name": "Brian H. (ORCID:0000000274083609) Davison", "primaryContact": false }, { "name": "Thomas Foust", "primaryContact": false }, { "name": "Tassia L. Junqueira", "primaryContact": false }, { "name": "Mark S. Laser", "primaryContact": false }, { "name": "Zhenglong Li", "primaryContact": false }, { "name": "Tom Richard", "primaryContact": false }, { "name": "Ling Tao", "primaryContact": false }, { "name": "Gerald A. Tuskan", "primaryContact": false }, { "name": "Michael Wang", "primaryContact": false }, { "name": "Jeremy (ORCID:0000000215428144) Woods", "primaryContact": false }, { "name": "Charles E. Wyman", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Bioenergy Technologies Office" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Bioenergy Technologies Office (EE-3B)" } } ], "dataset_url": "https://www.osti.gov/biblio/1575808", "active": false }, { "brc": "CBI", "title": "Comparative genomics can provide new insights into the evolutionary mechanisms and gene function in CAM plants", "description": "Crassulacean acid metabolism (CAM) photosynthesis is an important biological innovation enabling plant adaptation to hot and dry environments. CAM plants feature high water-use efficiency, with potential for sustainable crop production under water-limited conditions. A deep understanding of CAM-related gene function and molecular evolution of CAM plants is critical for exploiting the potential of engineering CAM into C3 crops to enhance crop production on semi-arid or marginal agricultural lands. With the newly emerging genomics resources for multiple CAM species, progress has been made in comparative genomics studies on the molecular basis and subsequently on the evolution of CAM. Here, recent advances in CAM comparative genomics research in constitutive and facultative CAM plants are reviewed, with a focus on the analyses of DNA/protein sequences and gene expression to provide new insights into the path and driving force of CAM evolution and to identify candidate genes involved in CAM-related biological processes. Potential applications of new computational and experimental technologies (e.g. CRISPR/Cas-mediated genome-editing technology) to the comparative and evolutionary genomics research on CAM plants are offered.
", "abstract": "Crassulacean acid metabolism (CAM) photosynthesis is an important biological innovation enabling plant adaptation to hot and dry environments. CAM plants feature high water-use efficiency, with potential for sustainable crop production under water-limited conditions. A deep understanding of CAM-related gene function and molecular evolution of CAM plants is critical for exploiting the potential of engineering CAM into C3 crops to enhance crop production on semi-arid or marginal agricultural lands. With the newly emerging genomics resources for multiple CAM species, progress has been made in comparative genomics studies on the molecular basis and subsequently on the evolution of CAM. Here, recent advances in CAM comparative genomics research in constitutive and facultative CAM plants are reviewed, with a focus on the analyses of DNA/protein sequences and gene expression to provide new insights into the path and driving force of CAM evolution and to identify candidate genes involved in CAM-related biological processes. Potential applications of new computational and experimental technologies (e.g. CRISPR/Cas-mediated genome-editing technology) to the comparative and evolutionary genomics research on CAM plants are offered.
", "date": "2019-09-06", "issue": "22", "identifier": "https://www.osti.gov/biblio/1576659", "bibliographicCitation": "https://doi.org/10.1093/jxb/erz408", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "comparative genomics", "crassulacean acid metabolism", "drought stress", "evolution", "gene function", "genome editing", "photosynthesis" ], "topic": [ "Microbiology" ], "journal_name": "Journal of Experimental Botany", "volume": "70", "publisher_information": "Oxford University Press", "country_publication_code": "GB", "creator": [ { "name": "Xiaohan [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,TN,USA,The Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,USA] (ORCID:0000000152074210) Yang", "primaryContact": true }, { "name": "Degao [Department of Genetics,Cell Biology and Development and Center for Precision Plant Genomics,University of Minnesota,Saint Paul,MN,USA] Liu", "primaryContact": false }, { "name": "Timothy J. [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,TN,USA,The Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,USA] (ORCID:0000000295406622) Tschaplinski", "primaryContact": false }, { "name": "Gerald A. [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,TN,USA,The Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,USA] (ORCID:0000000301061289) Tuskan", "primaryContact": false }, { "name": "ed.,David [University of Wyoming,USA] Williams", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1576659", "active": false }, { "brc": "CBI", "title": "A High-Performance Computing Implementation of Iterative Random Forest for the Creation of Predictive Expression Networks", "description": "As time progresses and technology improves, biological data sets are continuously increasing in size. New methods and new implementations of existing methods are needed to keep pace with this increase. In this paper, we present a high-performance computing (HPC)-capable implementation of Iterative Random Forest (iRF). This new implementation enables the explainable-AI eQTL analysis of SNP sets with over a million SNPs. Using this implementation, we also present a new method, iRF Leave One Out Prediction (iRF-LOOP), for the creation of Predictive Expression Networks on the order of 40,000 genes or more. We compare the new implementation of iRF with the previous R version and analyze its time to completion on two of the world\u2019s fastest supercomputers, Summit and Titan. We also show iRF-LOOP\u2019s ability to capture biologically significant results when creating Predictive Expression Networks. This new implementation of iRF will enable the analysis of biological data sets at scales that were previously not possible.
", "abstract": "As time progresses and technology improves, biological data sets are continuously increasing in size. New methods and new implementations of existing methods are needed to keep pace with this increase. In this paper, we present a high-performance computing (HPC)-capable implementation of Iterative Random Forest (iRF). This new implementation enables the explainable-AI eQTL analysis of SNP sets with over a million SNPs. Using this implementation, we also present a new method, iRF Leave One Out Prediction (iRF-LOOP), for the creation of Predictive Expression Networks on the order of 40,000 genes or more. We compare the new implementation of iRF with the previous R version and analyze its time to completion on two of the world\u2019s fastest supercomputers, Summit and Titan. We also show iRF-LOOP\u2019s ability to capture biologically significant results when creating Predictive Expression Networks. This new implementation of iRF will enable the analysis of biological data sets at scales that were previously not possible.
", "date": "2019-12-01", "issue": "12", "identifier": "https://www.osti.gov/biblio/1576840", "bibliographicCitation": "https://doi.org/10.3390/genes10120996", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "Gene Expression Networks", "Iterative Random Forest", "Random Forest", "X-AI-based eQTL", "high-performance\r\ncomputing" ], "topic": [ "Microbiology" ], "journal_name": "Genes", "volume": "10", "publisher_information": "MDPI", "country_publication_code": "Switzerland", "creator": [ { "name": "Ashley Cliff", "primaryContact": true }, { "name": "Jonathon Romero", "primaryContact": false }, { "name": "David Kainer", "primaryContact": false }, { "name": "Angelica Walker", "primaryContact": false }, { "name": "Anna Furches", "primaryContact": false }, { "name": "Daniel (ORCID:0000000298228251) Jacobson", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1576840", "active": false }, { "brc": "CBI", "title": "Catalytic Mechanism of Aryl-Ether Bond Cleavage in Lignin by LigF and LigG", "description": "Given the abundance of lignin in nature, multiple enzyme systems have been discovered to cleave the \u03b2-O-4 bonds, the most prevalent intermonomer linkage. In particular, stereospecific cleavage of lignin oligomers by glutathione S-transferases (GSTs) has been reported in several sphingomonads. Here in this paper, we apply quantum mechanics/molecular mechanics simulations to study the mechanism of two glutathione-dependent enzymes in the \u03b2-aryl ether catabolic pathway of Sphingomonas sp. SYK-6, namely, LigF, a \u03b2-etherase, and LigG, a lyase. For LigF, the free-energy landscape supports a SN2 reaction mechanism, with the monoaromatic leaving group being promptly neutralized upon release. Specific interactions with conserved residues are responsible for stereoselectivity and for activation of the cofactor as a nucleophile. A glutathione conjugate is also released by LigF and serves the substrate of LigG, undergoing a SN2-like reaction, in which Cys15 acts as the nucleophile, to yield the second monoaromatic product. The simulations suggest that the electron-donating substituent at the para-position found in lignin-derived aromatics and the interaction with Tyr217 are essential for reactivity in LigG. Overall, this work deepens the understanding of the stereospecific enzymatic mechanisms in the \u03b2-aryl ether cleavage pathway and reveals key structural features underpinning the ligninolytic activity detected in several sphingomonad GSTs.", "abstract": "Given the abundance of lignin in nature, multiple enzyme systems have been discovered to cleave the \u03b2-O-4 bonds, the most prevalent intermonomer linkage. In particular, stereospecific cleavage of lignin oligomers by glutathione S-transferases (GSTs) has been reported in several sphingomonads. Here in this paper, we apply quantum mechanics/molecular mechanics simulations to study the mechanism of two glutathione-dependent enzymes in the \u03b2-aryl ether catabolic pathway of Sphingomonas sp. SYK-6, namely, LigF, a \u03b2-etherase, and LigG, a lyase. For LigF, the free-energy landscape supports a SN2 reaction mechanism, with the monoaromatic leaving group being promptly neutralized upon release. Specific interactions with conserved residues are responsible for stereoselectivity and for activation of the cofactor as a nucleophile. A glutathione conjugate is also released by LigF and serves the substrate of LigG, undergoing a SN2-like reaction, in which Cys15 acts as the nucleophile, to yield the second monoaromatic product. The simulations suggest that the electron-donating substituent at the para-position found in lignin-derived aromatics and the interaction with Tyr217 are essential for reactivity in LigG. Overall, this work deepens the understanding of the stereospecific enzymatic mechanisms in the \u03b2-aryl ether cleavage pathway and reveals key structural features underpinning the ligninolytic activity detected in several sphingomonad GSTs.", "date": "2019-11-04", "issue": "48", "identifier": "https://www.osti.gov/biblio/1578254", "bibliographicCitation": "https://doi.org/10.1021/acs.jpcb.9b06243", "keywords": [ "09 BIOMASS FUELS", "BCPL", "enzyme", "lignin", "mechanism", "molecular modeling", "qmmm" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Journal of Physical Chemistry. B", "volume": "123", "publisher_information": "American Chemical Society", "country_publication_code": "US", "creator": [ { "name": "Erica Teixeira [National Renewable Energy Lab. (NREL),Golden,CO (United States). National Bioenergy Center; Univ. of Campinas (UNICAMP),Sao Paulo (Brazil). Inst. of Chemistry and Center for Computing in Engineering and Sciences] Prates", "primaryContact": true }, { "name": "Michael F. [National Renewable Energy Lab. (NREL),Golden,CO (United States). Biosciences Center] (ORCID:0000000151639398) Crowley", "primaryContact": false }, { "name": "Munir S. [Univ. of Campinas (UNICAMP),Sao Paulo (Brazil). Inst. of Chemistry and Center for Computing in Engineering and Sciences] (ORCID:0000000174851228) Skaf", "primaryContact": false }, { "name": "Gregg T. [National Renewable Energy Lab. (NREL),Golden,CO (United States). National Bioenergy Center] (ORCID:000000023480212X) Beckham", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "S\u00e3o Paulo Research Foundation (FAPESP)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Bioenergy Technologies Office (EE-3B)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1578254", "active": false, "has_related_ids": [ "NREL/JA--2700-75435" ] }, { "brc": "CBI", "title": "Synthetic fungal multifunctional cellulases for enhanced biomass conversion", "description": "Synthetic multifunctional enzymes exhibit superior performance to their non-multifunctional enzyme components and exhibit novel cellulose deconstruction mechanisms.
", "abstract": "Synthetic multifunctional enzymes exhibit superior performance to their non-multifunctional enzyme components and exhibit novel cellulose deconstruction mechanisms.
", "date": "2020-01-26", "issue": "2", "identifier": "https://www.osti.gov/biblio/1579978", "bibliographicCitation": "https://doi.org/10.1039/C9GC03062J", "keywords": [ "09 BIOMASS FUELS", "BCPL", "cellulases", "multifunctional enzymes" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Green Chemistry", "volume": "22", "publisher_information": "Royal Society of Chemistry", "country_publication_code": "GB", "creator": [ { "name": "Roman [Biosciences Center,National Renewable Energy Lab,Golden,USA] (ORCID:0000000283524234) Brunecky", "primaryContact": true }, { "name": "Venkataramanan [Biosciences Center,National Renewable Energy Lab,Golden,USA] (ORCID:0000000156569528) Subramanian", "primaryContact": false }, { "name": "John M. [Biosciences Center,National Renewable Energy Lab,Golden,USA] Yarbrough", "primaryContact": false }, { "name": "Bryon S. [Biosciences Center,National Renewable Energy Lab,Golden,USA] Donohoe", "primaryContact": false }, { "name": "Todd B. [Biosciences Center,National Renewable Energy Lab,Golden,USA] Vinzant", "primaryContact": false }, { "name": "Todd A. [Biosciences Center,National Renewable Energy Lab,Golden,USA] Vanderwall", "primaryContact": false }, { "name": "Brandon C. [Biosciences Center,National Renewable Energy Lab,Golden,USA] Knott", "primaryContact": false }, { "name": "Yogesh B. [Life Sciences Division,Institute of Advanced Study in Science and Technology (IASST),Guwahati,India] Chaudhari", "primaryContact": false }, { "name": "Yannick J. [Biosciences Center,National Renewable Energy Lab,Golden,USA] Bomble", "primaryContact": false }, { "name": "Michael E. [Biosciences Center,National Renewable Energy Lab,Golden,USA] Himmel", "primaryContact": false }, { "name": "Stephen R. [Biosciences Center,National Renewable Energy Lab,Golden,USA] (ORCID:0000000170029034) Decker", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Bioenergy Technologies Office (EE-3B)" } } ], "dataset_url": "https://www.osti.gov/biblio/1579978", "active": false, "has_related_ids": [ "NREL/JA--2700-75366" ] }, { "brc": "CBI", "title": "Assessment of yield gaps on global grazed\u2010only permanent pasture using climate binning", "description": "To meet rising demands for agricultural products, existing agricultural lands must either produce more or expand in area. Yield gaps (YGs)\u2014the difference between current and potential yield of agricultural systems\u2014indicate the ability to increase output while holding land area constant. Here, we assess YGs in global grazed\u2010only permanent pasture lands using a climate binning approach. We create a snapshot of circa 2000 empirical yields for meat and milk production from cattle, sheep, and goats by sorting pastures into climate bins defined by total annual precipitation and growing degree\u2010days. We then estimate YGs from intra\u2010bin yield comparisons. We evaluate YG patterns across three FAO definitions of grazed livestock agroecosystems (arid, humid, and temperate), and groups of animal production systems that vary in animal types and animal products. For all subcategories of grazed\u2010only permanent pasture assessed, we find potential to increase productivity several\u2010fold over current levels. However, because productivity of grazed pasture systems is generally low, even large relative increases in yield translated to small absolute gains in global protein production. In our dataset, milk\u2010focused production systems were found to be seven times as productive as meat\u2010focused production systems regardless of animal type, while cattle were four times as productive as sheep and goats regardless of animal output type. Sustainable intensification of pasture is most promising for local development, where large relative increases in production can substantially increase incomes or \u201cspare\u201d large amounts of land for other uses. Our results motivate the need for further studies to target agroecological and economic limitations on productivity to improve YG estimates and identify sustainable pathways toward intensification.
", "abstract": "To meet rising demands for agricultural products, existing agricultural lands must either produce more or expand in area. Yield gaps (YGs)\u2014the difference between current and potential yield of agricultural systems\u2014indicate the ability to increase output while holding land area constant. Here, we assess YGs in global grazed\u2010only permanent pasture lands using a climate binning approach. We create a snapshot of circa 2000 empirical yields for meat and milk production from cattle, sheep, and goats by sorting pastures into climate bins defined by total annual precipitation and growing degree\u2010days. We then estimate YGs from intra\u2010bin yield comparisons. We evaluate YG patterns across three FAO definitions of grazed livestock agroecosystems (arid, humid, and temperate), and groups of animal production systems that vary in animal types and animal products. For all subcategories of grazed\u2010only permanent pasture assessed, we find potential to increase productivity several\u2010fold over current levels. However, because productivity of grazed pasture systems is generally low, even large relative increases in yield translated to small absolute gains in global protein production. In our dataset, milk\u2010focused production systems were found to be seven times as productive as meat\u2010focused production systems regardless of animal type, while cattle were four times as productive as sheep and goats regardless of animal output type. Sustainable intensification of pasture is most promising for local development, where large relative increases in production can substantially increase incomes or \u201cspare\u201d large amounts of land for other uses. Our results motivate the need for further studies to target agroecological and economic limitations on productivity to improve YG estimates and identify sustainable pathways toward intensification.
", "date": "2019-12-31", "issue": "3", "identifier": "https://www.osti.gov/biblio/1581018", "bibliographicCitation": "https://doi.org/10.1111/gcb.14925", "topic": [ "Unknown" ], "journal_name": "Global Change Biology", "volume": "26", "publisher_information": "Wiley-Blackwell", "country_publication_code": "GB", "creator": [ { "name": "Leonardo A. [School of Agricultural Engineering (FEAGRI) University of Campinas Campinas Brazil,Department of Crop Production Ecology Swedish University of Agricultural Sciences Uppsala Sweden] Monteiro", "primaryContact": true }, { "name": "Andrew M. [Thayer School of Engineering Dartmouth College Hanover NH USA] Allee", "primaryContact": false }, { "name": "Eleanor E. [School of Agricultural Engineering (FEAGRI) University of Campinas Campinas Brazil,Earth Systems Research Center University of New Hampshire Durham NH USA] (ORCID:0000000292726276) Campbell", "primaryContact": false }, { "name": "Lee R. [Thayer School of Engineering Dartmouth College Hanover NH USA,Interdisciplinary Center of Energy Planning (NIPE) University of Campinas (UNICAMP) Campinas Brazil] Lynd", "primaryContact": false }, { "name": "Johnny R. [School of Agricultural Engineering (FEAGRI) University of Campinas Campinas Brazil] Soares", "primaryContact": false }, { "name": "Deepak [School of Agricultural Engineering (FEAGRI) University of Campinas Campinas Brazil,Carl R. Woese Institute for Genomic Biology University of Illinois Urbana Urbana IL USA] (ORCID:0000000240773919) Jaiswal", "primaryContact": false }, { "name": "Julianne [School of Agricultural Engineering (FEAGRI) University of Campinas Campinas Brazil] de Castro Oliveira", "primaryContact": false }, { "name": "Murilo [School of Agricultural Engineering (FEAGRI) University of Campinas Campinas Brazil] dos Santos Vianna", "primaryContact": false }, { "name": "Ashley E. [Department of Mechanical Engineering Massachusetts Institute of Technology Cambridge MA USA] Morishige", "primaryContact": false }, { "name": "Gleyce K. D. A. [School of Agricultural Engineering (FEAGRI) University of Campinas Campinas Brazil] Figueiredo", "primaryContact": false }, { "name": "Rubens A. C. [Interdisciplinary Center of Energy Planning (NIPE) University of Campinas (UNICAMP) Campinas Brazil] Lamparelli", "primaryContact": false }, { "name": "Nathaniel D. [Department of Ecosystem Science and Sustainability Colorado State University Fort Collins CO USA] Mueller", "primaryContact": false }, { "name": "James [Institute on the Environment University of Minnesota St. Paul MN USA] Gerber", "primaryContact": false }, { "name": "Luis A. B. [Interdisciplinary Center of Energy Planning (NIPE) University of Campinas (UNICAMP) Campinas Brazil] Cortez", "primaryContact": false }, { "name": "John J. [School of Agricultural Engineering (FEAGRI) University of Campinas Campinas Brazil,Department of Chemical and Biological Engineering Colorado State University Fort Collins CO USA] Sheehan", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/1581018", "active": false }, { "brc": "CBI", "title": "Molecular weight distribution of raw and catalytic fast pyrolysis oils: comparison of analytical methodologies", "description": "Comprehensive analysis of the molecular weight distribution of raw and catalytic fast pyrolysis oils remains a key technical hurdle to understanding oil quality and multiple methods may be necessary to accurately represent all components present.
", "abstract": "Comprehensive analysis of the molecular weight distribution of raw and catalytic fast pyrolysis oils remains a key technical hurdle to understanding oil quality and multiple methods may be necessary to accurately represent all components present.
", "date": "2020-01-21", "issue": "7", "identifier": "https://www.osti.gov/biblio/1593173", "bibliographicCitation": "https://doi.org/10.1039/C9RA09726K", "keywords": [ "09 BIOMASS FUELS", "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "CCTPL", "catalysis", "gel permeation chromatography", "light 12 scattering", "molecular weight", "pyrolysis" ], "topic": [ "Biomass & Feedstock", "Chemistry" ], "journal_name": "RSC Advances", "volume": "10", "publisher_information": "Royal Society of Chemistry (RSC)", "country_publication_code": "GB", "creator": [ { "name": "Anne E. [Biosciences Center,National Renewable Energy Laboratory,Golden,USA] Harman-Ware", "primaryContact": true }, { "name": "Kellene [National Bioenergy Center,National Renewable Energy Laboratory,Golden,USA] Orton", "primaryContact": false }, { "name": "Chris [Wyatt Technology Corporation,Goleta,USA] Deng", "primaryContact": false }, { "name": "Sophia [Wyatt Technology Corporation,Goleta,USA] Kenrick", "primaryContact": false }, { "name": "Daniel [National Bioenergy Center,National Renewable Energy Laboratory,Golden,USA] Carpenter", "primaryContact": false }, { "name": "Jack R. [National Bioenergy Center,National Renewable Energy Laboratory,Golden,USA] (ORCID:0000000330418742) Ferrell", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Bioenergy Technologies Office (EE-3B)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1593173", "active": false, "has_related_ids": [ "NREL/JA-5100-75507" ] }, { "brc": "CBI", "title": "Conversion of phosphoenolpyruvate to pyruvate in Thermoanaerobacterium saccharolyticum", "description": "Not Available", "abstract": "Not Available", "date": "2020-05-31", "issue": "C", "identifier": "https://www.osti.gov/biblio/1593471", "bibliographicCitation": "https://doi.org/10.1016/j.mec.2020.e00122", "keywords": [ "Thermoanaerobacterium saccharolyticum", "09 BIOMASS FUELS", "Consolidated bioprocessing", "Ethanol", "Pyruvate", "Pyruvate kinase", "Pyruvate phosphate dikinase" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Metabolic Engineering Communications", "volume": "10", "publisher_information": "Elsevier", "country_publication_code": "Netherlands", "creator": [ { "name": "Jingxuan Cui", "primaryContact": true }, { "name": "Marybeth I. Maloney", "primaryContact": false }, { "name": "Daniel G. Olson", "primaryContact": false }, { "name": "Lee R. Lynd", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division" } } ], "dataset_url": "https://www.osti.gov/biblio/1593471", "active": false }, { "brc": "CBI", "title": "Nanomechanics and Raman Spectroscopy of in Situ Native Carbohydrate Storage Granules for Enhancing Starch Quality and Lignocellulosic Biomass Production", "description": "Not Available", "abstract": "Not Available", "date": "2020-02-05", "issue": "6", "identifier": "https://www.osti.gov/biblio/1598065", "bibliographicCitation": "https://doi.org/10.1021/acsomega.9b02849", "keywords": [ "09 BIOMASS FUELS" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "ACS Omega", "volume": "5", "publisher_information": "American Chemical Society (ACS)", "country_publication_code": "US", "creator": [ { "name": "Rubye H. [Computational Sciences and Engineering Division,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37830,United States] Farahi", "primaryContact": true }, { "name": "Aude L. [Aix Marseille University,CNRS,Centrale Marseille,Institut Fresnel,Marseille 13397,France] (ORCID:0000000173907832) Lereu", "primaryContact": false }, { "name": "Anne M. [Aix Marseille University,CNRS,CINaM,Marseille 13288,France] (ORCID:0000000202051341) Charrier", "primaryContact": false }, { "name": "Udaya C. [BioEnergy Science Center,Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37830,United States] Kalluri", "primaryContact": false }, { "name": "Brian H. [BioEnergy Science Center,Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37830,United States,Department of Chemical and Biomolecular Engineering,University of Tennessee,Knoxville,Tennessee 37996,United States] Davison", "primaryContact": false }, { "name": "Ali [Computational Sciences and Engineering Division,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37830,United States,BioEnergy Science Center,Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37830,United States,Department of Chemical and Biomolecular Engineering,University of Tennessee,Knoxville,Tennessee 37996,United States,Department of Physics,University of Tennessee,Knoxville,Tennessee 37996,United States] (ORCID:0000000247364157) Passian", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1598065", "active": false }, { "brc": "CBI", "title": "Targeting Root Ion Uptake Kinetics to Increase Plant Productivity and Nutrient Use Efficiency", "description": "Not Available", "abstract": "Not Available", "date": "2020-02-05", "issue": "4", "identifier": "https://www.osti.gov/biblio/1598086", "bibliographicCitation": "https://doi.org/10.1104/pp.19.01496", "topic": [ "Unknown" ], "journal_name": "Plant Physiology (Bethesda)", "volume": "182", "publisher_information": "Oxford University Press", "country_publication_code": "US", "creator": [ { "name": "Marcus [Noble Research Institute,LLC,Ardmore,Oklahoma 73401] (ORCID:0000000323498967) Griffiths", "primaryContact": true }, { "name": "Larry M. [Noble Research Institute,LLC,Ardmore,Oklahoma 73401] (ORCID:0000000219959479) York", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/1598086", "active": false }, { "brc": "CBI", "title": "Towards renewable flavors, fragrances, and beyond", "description": "Esters demand a large space of unique molecules with broad range of applications as flavors, fragrances, pharmaceuticals, cosmetics, green solvents, and advanced biofuels. Global demand of natural esters in food, household cleaner, personal care, and perfume industries is increasing while the ester supply from natural sources has been limited. Development of novel microbial cell factories for ester production from renewable feedstocks can potentially provide an alternative and sustainable source of natural esters and hence help fulfill growing demand. In this work, we highlight recent advances in microbial production of esters and provide perspectives for improving its economic feasibility. As the field matures, microbial ester production platforms will enable renewable and sustainable production of flavors, fragrances, and open new market opportunities beyond what nature can offer.", "abstract": "Esters demand a large space of unique molecules with broad range of applications as flavors, fragrances, pharmaceuticals, cosmetics, green solvents, and advanced biofuels. Global demand of natural esters in food, household cleaner, personal care, and perfume industries is increasing while the ester supply from natural sources has been limited. Development of novel microbial cell factories for ester production from renewable feedstocks can potentially provide an alternative and sustainable source of natural esters and hence help fulfill growing demand. In this work, we highlight recent advances in microbial production of esters and provide perspectives for improving its economic feasibility. As the field matures, microbial ester production platforms will enable renewable and sustainable production of flavors, fragrances, and open new market opportunities beyond what nature can offer.", "date": "2020-02-24", "issue": "C", "identifier": "https://www.osti.gov/biblio/1598473", "bibliographicCitation": "https://doi.org/10.1016/j.copbio.2019.12.017", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "Clostridium thermocellum", "Natural esters", "flavors", "advanced biofuels", "consolidated bioprocessing", "cosmetics", "fragrances", "green solvents", "microbial manufacturing platform", "modular cell engineering", "pharmaceuticals" ], "topic": [ "Microbiology" ], "journal_name": "Current Opinion in Biotechnology", "volume": "61", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Jong-Won [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); University of Tennessee Knoxville] Lee", "primaryContact": true }, { "name": "Cong T. [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Trinh", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1598473", "active": false }, { "brc": "CBI", "title": "Exceptional solvent tolerance in Yarrowia lipolytica is enhanced by sterols", "description": "Green organic solvents such as ionic liquids (ILs) have versatile use yet are inhibitory to microbes even at low concentrations of 0.5\u20131.0% (v/v) ILs. We discovered the oleaginous yeast Yarrowia lipolytica can grow in 10% (v/v) of 1-ethyl-3-methylimidazolium acetate ([EMIM][OAc]), which makes it more tolerant than most engineered microorganisms and naturally screened isolates. However, the underlying mechanism of IL tolerance in Y. lipolytica is not understood. Through adaptive laboratory evolution, in combination with physiological characterization and omics analysis, we shed light on the underlying mechanism of how Y. lipolytica restructures its membrane to tolerate different types of ILs at high levels up to 18% ILs. Particularly, we discovered that sterols play a key role for exceptional IL tolerance in Y. lipolytica.", "abstract": "Green organic solvents such as ionic liquids (ILs) have versatile use yet are inhibitory to microbes even at low concentrations of 0.5\u20131.0% (v/v) ILs. We discovered the oleaginous yeast Yarrowia lipolytica can grow in 10% (v/v) of 1-ethyl-3-methylimidazolium acetate ([EMIM][OAc]), which makes it more tolerant than most engineered microorganisms and naturally screened isolates. However, the underlying mechanism of IL tolerance in Y. lipolytica is not understood. Through adaptive laboratory evolution, in combination with physiological characterization and omics analysis, we shed light on the underlying mechanism of how Y. lipolytica restructures its membrane to tolerate different types of ILs at high levels up to 18% ILs. Particularly, we discovered that sterols play a key role for exceptional IL tolerance in Y. lipolytica.", "date": "2019-03-14", "issue": "C", "identifier": "https://www.osti.gov/biblio/1598475", "bibliographicCitation": "https://doi.org/10.1016/j.ymben.2019.03.003", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "Adaptive laboratory evolution", "Glycerophospholipids", "Ionic liquid", "Lipidomics", "Metabolomics", "Sterol transcription factor", "Sterols", "Stress responsive metabolism", "Yarrowia lipolytica" ], "topic": [ "Microbiology" ], "journal_name": "Metabolic Engineering", "volume": "54", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Caleb [Univ. of Tennessee,Knoxville,TN (United States); University of Tennessee Knoxville] Walker", "primaryContact": true }, { "name": "Seunghyun [Univ. of Tennessee,Knoxville,TN (United States)] Ryu", "primaryContact": false }, { "name": "Cong T. [Univ. of Tennessee,Knoxville,TN (United States)] Trinh", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23). Biological Systems Science Division" } } ], "dataset_url": "https://www.osti.gov/biblio/1598475", "active": false }, { "brc": "CBI", "title": "Modular design: Implementing proven engineering principles in biotechnology", "description": "Modular design resides at the foundation of contemporary engineering, enabling rapid, efficient, and reproducible construction and maintenance of complex systems across applications. Remarkably, modularity has recently been discovered as a governing principle in natural biological systems from genes to proteins to complex networks within a cell and organism communities. The convergent knowledge of natural and engineered modular systems provides a key to drive modern biotechnology to address emergent challenges associated with health, food, energy, and the environment. Here, we first present the theory and application of modular design in traditional engineering fields. We further discuss the significance and impact of modular architectures on systems biology and biotechnology. Next, we focus on the very recent theoretical and experimental advances in modular cell engineering that seeks to enable rapid and systematic development of microbial catalysts capable of efficiently synthesizing a large space of useful chemicals. We conclude with an outlook towards theoretical and practical opportunities for a more systematic and effective application of modular engineering in biotechnology.", "abstract": "Modular design resides at the foundation of contemporary engineering, enabling rapid, efficient, and reproducible construction and maintenance of complex systems across applications. Remarkably, modularity has recently been discovered as a governing principle in natural biological systems from genes to proteins to complex networks within a cell and organism communities. The convergent knowledge of natural and engineered modular systems provides a key to drive modern biotechnology to address emergent challenges associated with health, food, energy, and the environment. Here, we first present the theory and application of modular design in traditional engineering fields. We further discuss the significance and impact of modular architectures on systems biology and biotechnology. Next, we focus on the very recent theoretical and experimental advances in modular cell engineering that seeks to enable rapid and systematic development of microbial catalysts capable of efficiently synthesizing a large space of useful chemicals. We conclude with an outlook towards theoretical and practical opportunities for a more systematic and effective application of modular engineering in biotechnology.", "date": "2019-06-06", "issue": "7", "identifier": "https://www.osti.gov/biblio/1598476", "bibliographicCitation": "https://doi.org/10.1016/j.biotechadv.2019.06.002", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "Evolvability", "Industrialization of biology", "Metabolic engineering", "Microbial biocatalysis", "ModCell", "Modular cell", "Modular cell engineering", "Modular design", "Modularity", "Networks", "Pareto optimality", "Robustness", "Synthetic biology", "Systems biology" ], "topic": [ "Microbiology" ], "journal_name": "Biotechnology Advances", "volume": "37", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Sergio [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); University of Tennessee Knoxville] Garcia", "primaryContact": true }, { "name": "Cong T. [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Trinh", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1598476", "active": false }, { "brc": "CBI", "title": "Glycosylation of hyperthermostable designer cellulosome components yields enhanced stability and cellulose hydrolysis", "description": "Biomass deconstruction remains integral for enabling second-generation biofuel production at scale. However, several steps necessary to achieve significant solubilization of biomass, notably harsh pretreatment conditions, impose economic barriers to commercialization. By employing hyperthermostable cellulase machinery, biomass deconstruction can be made more efficient, leading to milder pretreatment conditions and ultimately lower production costs. The hyperthermophilic bacterium Caldicellulosiruptor bescii produces extremely active hyperthermostable cellulases, including the hyperactive multifunctional cellulase CbCel9A/Cel48A. Recombinant CbCel9A/Cel48A components have been previously produced in Escherichia coli and integrated into synthetic hyperthermophilic designer cellulosome complexes. Since then, glycosylation has been shown to be vital for the high activity and stability of CbCel9A/Cel48A. Here, we studied the impact of glycosylation on a hyperthermostable designer cellulosome system in which two of the cellulosomal components, the scaffoldin and the GH9 domain of CbCel9A/Cel48A, were glycosylated as a consequence of employing Ca. bescii as an expression host. Inclusion of the glycosylated components yielded an active cellulosome system that exhibited long-term stability at 75 degrees C. The resulting glycosylated designer cellulosomes showed significantly greater synergistic activity compared to the enzymatic components alone, as well as higher thermostability than the analogous nonglycosylated designer cellulosomes. These results indicate that glycosylation can be used as an essential engineering tool to improve the properties of designer cellulosomes. Additionally, Ca. bescii was shown to be an attractive candidate for production of glycosylated designer cellulosome components, which may further promote the viability of this bacterium both as a cellulase expression host and as a potential consolidated bioprocessing platform organism.", "abstract": "Biomass deconstruction remains integral for enabling second-generation biofuel production at scale. However, several steps necessary to achieve significant solubilization of biomass, notably harsh pretreatment conditions, impose economic barriers to commercialization. By employing hyperthermostable cellulase machinery, biomass deconstruction can be made more efficient, leading to milder pretreatment conditions and ultimately lower production costs. The hyperthermophilic bacterium Caldicellulosiruptor bescii produces extremely active hyperthermostable cellulases, including the hyperactive multifunctional cellulase CbCel9A/Cel48A. Recombinant CbCel9A/Cel48A components have been previously produced in Escherichia coli and integrated into synthetic hyperthermophilic designer cellulosome complexes. Since then, glycosylation has been shown to be vital for the high activity and stability of CbCel9A/Cel48A. Here, we studied the impact of glycosylation on a hyperthermostable designer cellulosome system in which two of the cellulosomal components, the scaffoldin and the GH9 domain of CbCel9A/Cel48A, were glycosylated as a consequence of employing Ca. bescii as an expression host. Inclusion of the glycosylated components yielded an active cellulosome system that exhibited long-term stability at 75 degrees C. The resulting glycosylated designer cellulosomes showed significantly greater synergistic activity compared to the enzymatic components alone, as well as higher thermostability than the analogous nonglycosylated designer cellulosomes. These results indicate that glycosylation can be used as an essential engineering tool to improve the properties of designer cellulosomes. Additionally, Ca. bescii was shown to be an attractive candidate for production of glycosylated designer cellulosome components, which may further promote the viability of this bacterium both as a cellulase expression host and as a potential consolidated bioprocessing platform organism.", "date": "2020-02-16", "issue": "20", "identifier": "https://www.osti.gov/biblio/1602688", "bibliographicCitation": "https://doi.org/10.1111/febs.15251", "keywords": [ "09 BIOMASS FUELS", "Caldicellulosiruptor bescii", "cellulase", "cellulosome", "expression host", "glycosylation", "scaffoldin", "thermostability" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Federation of European Biochemical Societies (FEBS) Journal", "volume": "287", "publisher_information": "Federation of European Biochemical Societies", "country_publication_code": "US", "creator": [ { "name": "Amaranta [Weizmann Inst. of Science,Rehovot (Israel)] (ORCID:0000000185167296) Kahn", "primaryContact": true }, { "name": "Sarah [Weizmann Inst. of Science,Rehovot (Israel); Univ. of the Negev (Israel)] Morais", "primaryContact": false }, { "name": "Daehwan [National Renewable Energy Lab. (NREL),Golden,CO (United States)] Chung", "primaryContact": false }, { "name": "Nicholas [National Renewable Energy Lab. (NREL),Golden,CO (United States)] (ORCID:0000000246550038) Sarai", "primaryContact": false }, { "name": "Neal [National Renewable Energy Lab. (NREL),Golden,CO (United States)] Hengge", "primaryContact": false }, { "name": "Audrey [Weizmann Inst. of Science,Rehovot (Israel)] Kahn", "primaryContact": false }, { "name": "Michael E. [National Renewable Energy Lab. (NREL),Golden,CO (United States)] Himmel", "primaryContact": false }, { "name": "Edward A. [Weizmann Inst. of Science,Rehovot (Israel)] Bayer", "primaryContact": false }, { "name": "Yannick J. [National Renewable Energy Lab. (NREL),Golden,CO (United States)] (ORCID:0000000176248000) Bomble", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1602688", "active": false, "has_related_ids": [ "NREL/JA-2700-76211" ] }, { "brc": "CBI", "title": "Occurrence of Thermophilic Microorganisms in Different Full Scale Biogas Plants", "description": "In recent years, various substrates have been tested to increase the sustainable production of biomethane. The effect of these substrates on methanogenesis has been investigated mainly in small volume fermenters and were, for the most part, focused on studying the diversity of mesophilic microorganisms. However, studies of thermophilic communities in large scale operating mesophilic biogas plants do not yet exist. Methods: Microbiological, biochemical, biophysical methods, and statistical analysis were used to track thermophilic communities in mesophilic anaerobic digesters. Results: The diversity of the main thermophile genera in eight biogas plants located in the Czech Republic using different input substrates was investigated. In total, 19 thermophilic genera were detected after 16S rRNA gene sequencing. The highest percentage (40.8%) of thermophiles was found in the Modrice biogas plant where the input substrate was primary sludge and biological sludge (50/50, w/w %). The smallest percentage (1.87%) of thermophiles was found in the Cej\u010d biogas plant with the input substrate being maize silage and liquid pig manure (80/20, w/w %). Conclusions: The composition of the anaerobic consortia in anaerobic digesters is an important factor for the biogas plant operator. The present study can help characterizing the impact of input feeds on the composition of microbial communities in these plants.", "abstract": "In recent years, various substrates have been tested to increase the sustainable production of biomethane. The effect of these substrates on methanogenesis has been investigated mainly in small volume fermenters and were, for the most part, focused on studying the diversity of mesophilic microorganisms. However, studies of thermophilic communities in large scale operating mesophilic biogas plants do not yet exist. Methods: Microbiological, biochemical, biophysical methods, and statistical analysis were used to track thermophilic communities in mesophilic anaerobic digesters. Results: The diversity of the main thermophile genera in eight biogas plants located in the Czech Republic using different input substrates was investigated. In total, 19 thermophilic genera were detected after 16S rRNA gene sequencing. The highest percentage (40.8%) of thermophiles was found in the Modrice biogas plant where the input substrate was primary sludge and biological sludge (50/50, w/w %). The smallest percentage (1.87%) of thermophiles was found in the Cej\u010d biogas plant with the input substrate being maize silage and liquid pig manure (80/20, w/w %). Conclusions: The composition of the anaerobic consortia in anaerobic digesters is an important factor for the biogas plant operator. The present study can help characterizing the impact of input feeds on the composition of microbial communities in these plants.", "date": "2019-12-30", "issue": "1", "identifier": "https://www.osti.gov/biblio/1603254", "bibliographicCitation": "https://doi.org/10.3390/ijms21010283", "keywords": [ "09 BIOMASS FUELS", "Illumina sequencing", "anaerobic digesters", "biogas", "renewable energy", "thermophilic microorganisms" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "International Journal of Molecular Sciences (Online)", "volume": "21", "publisher_information": "MDPI", "country_publication_code": "US", "creator": [ { "name": "Ivan [Masaryk Univ. (Czech Republic)] (ORCID:0000000224359726) Kushkevych", "primaryContact": true }, { "name": "Jiri [Masaryk Univ. (Czech Republic)] Cejnar", "primaryContact": false }, { "name": "Monika [Masaryk Univ. (Czech Republic)] Vitezova", "primaryContact": false }, { "name": "Tomas [Mendel Univ. (Czech Republic). Dept. of Agricultural,Food and Environmental Engineering,Faculty of AgriSciences] Vitez", "primaryContact": false }, { "name": "Dani [Univ. of Veterinary and Pharmaceutical Sciences (Czech Republic)] (ORCID:0000000224359726) Dordevic", "primaryContact": false }, { "name": "Yannick J [National Renewable Energy Laboratory (NREL),Golden,CO (United States)] Bomble", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1603254", "active": false, "has_related_ids": [ "NREL-JA--2700-75825" ] }, { "brc": "CBI", "title": "Biodesign Research to Advance the Principles and Applications of Biosystems Design", "description": "Over the course of civilization, humans have increasingly expanded their freedom to live a better life. In comparison with the primitive society, our modern society has many more choices of life-supporting resources, such as year-round food supply, permanent shelters, diverse energy sources, and effective preventive and curing medicine. However, our society is currently still heavily relying on the resources provided by Mother Nature, which cannot meet the future global needs in terms of both quantity and quality under the pressure of population growth, natural resource reduction, and environmental deterioration. For example, the food sources originating from plants, animals, or microbes do not have the nutrition balance for optimal human health. Climate change and environmental deterioration threaten the food security. Increasingly, infectious diseases (e.g., HIV/AIDS), genetic diseases (e.g., cancer), and improper lifestyle-related disorders (e.g., obesity) become more prevalent and remain challenging to be prevented, controlled, and cured. Conventional medical technologies and modern medicine development are also meeting the ceiling. Antibiotic resistance is threatening the health of humans, animals, and environment. As the human lifespan continues to increase, aging-related diseases, disorders, and poor life quality are becoming global challenges. Plants, animals, and microbes in nature have evolved as part of our Earth ecosystem, not for benefiting humans. Even though humans have put forth tremendous efforts to domesticate plants, animals, and microbes based on random/induced mutations, hybridization, and limited genetic modifications via biological engineering, the improved food and industrial crop plants, animals, and microbial strains are still far from optimized for meeting the human needs. In other words, natural evolution and domestication in plants, animals, and microbes are tinkering processes and therefore cannot meet the ever-exploding population on the one hand and the unending appetite for living better quality life on the other. One promising strategy for solving these global challenges is to employ revolutionary biosystems design (also called biodesign), which is defined as predictable modification of existing organisms or creation of new organisms using rational engineering or automated design based on the theory and principles of biosystems design.", "abstract": "Over the course of civilization, humans have increasingly expanded their freedom to live a better life. In comparison with the primitive society, our modern society has many more choices of life-supporting resources, such as year-round food supply, permanent shelters, diverse energy sources, and effective preventive and curing medicine. However, our society is currently still heavily relying on the resources provided by Mother Nature, which cannot meet the future global needs in terms of both quantity and quality under the pressure of population growth, natural resource reduction, and environmental deterioration. For example, the food sources originating from plants, animals, or microbes do not have the nutrition balance for optimal human health. Climate change and environmental deterioration threaten the food security. Increasingly, infectious diseases (e.g., HIV/AIDS), genetic diseases (e.g., cancer), and improper lifestyle-related disorders (e.g., obesity) become more prevalent and remain challenging to be prevented, controlled, and cured. Conventional medical technologies and modern medicine development are also meeting the ceiling. Antibiotic resistance is threatening the health of humans, animals, and environment. As the human lifespan continues to increase, aging-related diseases, disorders, and poor life quality are becoming global challenges. Plants, animals, and microbes in nature have evolved as part of our Earth ecosystem, not for benefiting humans. Even though humans have put forth tremendous efforts to domesticate plants, animals, and microbes based on random/induced mutations, hybridization, and limited genetic modifications via biological engineering, the improved food and industrial crop plants, animals, and microbial strains are still far from optimized for meeting the human needs. In other words, natural evolution and domestication in plants, animals, and microbes are tinkering processes and therefore cannot meet the ever-exploding population on the one hand and the unending appetite for living better quality life on the other. One promising strategy for solving these global challenges is to employ revolutionary biosystems design (also called biodesign), which is defined as predictable modification of existing organisms or creation of new organisms using rational engineering or automated design based on the theory and principles of biosystems design.", "date": "2019-11-21", "issue": "NA", "identifier": "https://www.osti.gov/biblio/1606789", "bibliographicCitation": "https://doi.org/10.34133/2019/9680853", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "BioDesign Research", "volume": "2019", "publisher_information": "AAAS", "country_publication_code": "US", "creator": [ { "name": "Xiaohan [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Biosciences Division and The Center for Bioenergy Innovation] (ORCID:0000000152074210) Yang", "primaryContact": true }, { "name": "Lei S. [Stanford Univ.,CA (United States)] Qi", "primaryContact": false }, { "name": "Alfonso [Univ. of Warwick,Coventry (United Kingdom). Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences; Univ. Paris-Saclay,Evry (France); Univ. of Valencia-CSIC,Paterna (Spain). Inst. for Integrative Systems Biology (I2SysBio)] Jaramillo", "primaryContact": false }, { "name": "Zong-Ming [Univ. of Tennessee,Knoxville,TN (United States); Nanjing Agricultural Univ.,Jiangsu Province (China)] Cheng", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "Biotechnology and Biological Sciences Research Council (BBSRC)" } }, { "fundingOrganization": { "organizationName": "Engineering and Physical Sciences Research Council (EPSRC)" } }, { "fundingOrganization": { "organizationName": "Li Ka\r\nShing Foundation" } }, { "fundingOrganization": { "organizationName": "Tennessee Agricultural Experiment Station" } }, { "fundingOrganization": { "organizationName": "USDOD" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1606789", "active": false }, { "brc": "CBI", "title": "Structural changes of lignins in natural Populus variants during different pretreatments", "description": "In the present study, three leading pretreatment technologies including dilute acid (DA), liquid hot water (LHW), and organosolv pretreatments (OS) were applied on two Populus natural variants with different recalcitrance. The structural features of the isolated lignins were analyzed accordingly. All the studied pretreatments reduced the molecular weights of the lignins. Aliphatic OH was reduced while phenolic OH was increased in all pretreated lignins. HSQC analysis revealed that pretreatment influenced the lignin composition and relative distribution of inter-unit linkages. The lignin S/G ratio was found to increase during DA pretreatment, while it was decreased after LHW and OS pretreatment. LHW pretreatment also resulted in much less cleavage of \u03b2-O-4 linkage than the other two pretreatments. These results could offer guidelines on appropriate selection of biomass and pretreatment technology in the future biorefinery process.", "abstract": "In the present study, three leading pretreatment technologies including dilute acid (DA), liquid hot water (LHW), and organosolv pretreatments (OS) were applied on two Populus natural variants with different recalcitrance. The structural features of the isolated lignins were analyzed accordingly. All the studied pretreatments reduced the molecular weights of the lignins. Aliphatic OH was reduced while phenolic OH was increased in all pretreated lignins. HSQC analysis revealed that pretreatment influenced the lignin composition and relative distribution of inter-unit linkages. The lignin S/G ratio was found to increase during DA pretreatment, while it was decreased after LHW and OS pretreatment. LHW pretreatment also resulted in much less cleavage of \u03b2-O-4 linkage than the other two pretreatments. These results could offer guidelines on appropriate selection of biomass and pretreatment technology in the future biorefinery process.", "date": "2019-12-31", "issue": "C", "identifier": "https://www.osti.gov/biblio/1606831", "bibliographicCitation": "https://doi.org/10.1016/j.biortech.2019.122240", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "Lignin", "Natural Populus variants", "Pretreatment", "Recalcitrance", "S/G ratio" ], "topic": [ "Microbiology" ], "journal_name": "Bioresource Technology", "volume": "295", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Haitao [Hubei Univ. of Technology,Wuhan (China). Hubei Provincial Key Lab. of Green Materials for Light Industry; Hubei Univ. of Technology,Wuhan (China). Collaborative Innovation Center of Green Light-weight Materials and Processing] Yang", "primaryContact": true }, { "name": "Chang Geun [State Univ. of New York (SUNY),Albany,NY (United States)] Yoo", "primaryContact": false }, { "name": "Xianzhi [Univ. of Tennessee,Knoxville,TN (United States)] Meng", "primaryContact": false }, { "name": "Yunqiao Joseph [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). BioEnergy Science Center (BESC)] (ORCID:0000000325541447) Pu", "primaryContact": false }, { "name": "Wellington [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). BioEnergy Science Center (BESC)] (ORCID:0000000202009856) Muchero", "primaryContact": false }, { "name": "Gerald A. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). BioEnergy Science Center (BESC)] (ORCID:0000000301061289) Tuskan", "primaryContact": false }, { "name": "Timothy [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). BioEnergy Science Center (BESC)] (ORCID:0000000295406622) Tschaplinski", "primaryContact": false }, { "name": "Arthur J. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). BioEnergy Science Center (BESC)] (ORCID:000000023536554X) Ragauskas", "primaryContact": false }, { "name": "Lan [Univ. of Tennessee,Knoxville,TN (United States)] Yao", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1606831", "active": false }, { "brc": "CBI", "title": "Can exascale computing and explainable artificial intelligence applied to plant biology deliver on the United Nations sustainable development goals?", "description": "Human population growth and accelerated climate change necessitate agricultural improvements using designer crop ideotypes (idealized plants that can grow in niche environments). Diverse and highly skilled research groups must integrate efforts to bridge the gaps needed to achieve international goals toward sustainable agriculture. Given the scale of global agricultural needs and the breadth of multiple types of omics data needed to optimize these efforts, explainable artificial intelligence (AI with a decipherable decision making process that provides a meaningful explanation to humans) and exascale computing (computers that can perform 1018 floating-point operations per second, or exaflops) are crucial. Accurate phenotyping and daily-resolution climatype associations are equally important for refining ideotype production to specific environments at various levels of granularity. In this article, we review advances toward tackling technological hurdles to solve multiple United Nations Sustainable Development Goals and discuss a vision to overcome gaps between research and policy.", "abstract": "Human population growth and accelerated climate change necessitate agricultural improvements using designer crop ideotypes (idealized plants that can grow in niche environments). Diverse and highly skilled research groups must integrate efforts to bridge the gaps needed to achieve international goals toward sustainable agriculture. Given the scale of global agricultural needs and the breadth of multiple types of omics data needed to optimize these efforts, explainable artificial intelligence (AI with a decipherable decision making process that provides a meaningful explanation to humans) and exascale computing (computers that can perform 1018 floating-point operations per second, or exaflops) are crucial. Accurate phenotyping and daily-resolution climatype associations are equally important for refining ideotype production to specific environments at various levels of granularity. In this article, we review advances toward tackling technological hurdles to solve multiple United Nations Sustainable Development Goals and discuss a vision to overcome gaps between research and policy.", "date": "2020-02-17", "issue": "C", "identifier": "https://www.osti.gov/biblio/1607410", "bibliographicCitation": "https://doi.org/10.1016/j.copbio.2020.01.010", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "Current Opinion in Biotechnology", "volume": "61", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Jared [USDOE Bioenergy Research Centers (BRC) (United States). The Center for Bioenergy Innovation (CBI); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000348611188) Streich", "primaryContact": true }, { "name": "Jonathon [USDOE Bioenergy Research Centers (BRC) (United States). The Center for Bioenergy Innovation (CBI); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:0000000152491946) Romero", "primaryContact": false }, { "name": "Jo\u00e3o Gabriel Felipe Machado [USDOE Bioenergy Research Centers (BRC) (United States). The Center for Bioenergy Innovation (CBI); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000310230363) Gazolla", "primaryContact": false }, { "name": "David [USDOE Bioenergy Research Centers (BRC) (United States). The Center for Bioenergy Innovation (CBI); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Kainer", "primaryContact": false }, { "name": "Ashley [USDOE Bioenergy Research Centers (BRC) (United States). The Center for Bioenergy Innovation (CBI); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Univ. of Tennessee,Knoxville,TN (United States)] Cliff", "primaryContact": false }, { "name": "Erica Teixeira [USDOE Bioenergy Research Centers (BRC) (United States). The Center for Bioenergy Innovation (CBI); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Prates", "primaryContact": false }, { "name": "James B. [Lawrence Berkeley National Lab. (LBNL),Berkeley,CA (United States)] Brown", "primaryContact": false }, { "name": "Sacha [Univ. of Cambridge (United Kingdom)] (ORCID:0000000219805365) Khoury", "primaryContact": false }, { "name": "Gerald A. [USDOE Bioenergy Research Centers (BRC) (United States). The Center for Bioenergy Innovation (CBI); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000301061289) Tuskan", "primaryContact": false }, { "name": "Michael [USDOE Bioenergy Research Centers (BRC) (United States). The Center for Bioenergy Innovation (CBI); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000222047569) Garvin", "primaryContact": false }, { "name": "Daniel [USDOE Bioenergy Research Centers (BRC) (United States). The Center for Bioenergy Innovation (CBI); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:0000000298228251) Jacobson", "primaryContact": false }, { "name": "Antoine L. [Univ. of Tuscia,Viterbo (Italy)] Harfouche", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "EU 7th Framework Programme" } }, { "fundingOrganization": { "organizationName": "USDOE Laboratory Directed Research and Development (LDRD) Program" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1607410", "active": false }, { "brc": "CBI", "title": "Identification of Key Enzymes for Pectin Synthesis in Seed Mucilage", "description": "Pectin is a vital component of the plant cell wall, and provides the molecular glue that maintains cell-cell adhesion, among other functions. As the most complex wall polysaccharide, pectin is composed of several covalently-linked domains, such as homogalacturonan (HG) and rhamnogalacturonan I (RG I). Pectin has widespread uses in the food industry and has emerging biomedical applications, but its synthesis remains poorly understood. For instance, the enzymes that catalyze RG I elongation remain unknown. Recently, a co-expression and sequence-based MUCILAGE-RELATED (MUCI) reverse genetic screen uncovered hemicellulose biosynthetic enzymes in the Arabidopsis thaliana seed coat. Here, we use an extension of this strategy to identify MUCI70 as the founding member of a glycosyltransferase family essential for the accumulation of seed mucilage, a gelatinous wall rich in unbranched RG I. Detailed biochemical and histological characterization of two muci70 mutants and two gaut11 mutants identified MUCI70 and GAUT11 as required for two distinct RG I domains in seed mucilage. We demonstrate that, unlike MUCI70, GAUT11 catalyzes HG elongation in vitro, and is thus likely required for the synthesis of an HG region important for RG I elongation. Analysis of a muci70 gaut11 double mutant confirmed that MUCI70 and GAUT11 are indispensable for the production and release of the bulk of mucilage RG I, and for shaping the surface morphology of seeds. In addition, we uncover relationships between pectin and hemicelluloses and show that xylan is essential for the elongation of at least one RG I domain.", "abstract": "Pectin is a vital component of the plant cell wall, and provides the molecular glue that maintains cell-cell adhesion, among other functions. As the most complex wall polysaccharide, pectin is composed of several covalently-linked domains, such as homogalacturonan (HG) and rhamnogalacturonan I (RG I). Pectin has widespread uses in the food industry and has emerging biomedical applications, but its synthesis remains poorly understood. For instance, the enzymes that catalyze RG I elongation remain unknown. Recently, a co-expression and sequence-based MUCILAGE-RELATED (MUCI) reverse genetic screen uncovered hemicellulose biosynthetic enzymes in the Arabidopsis thaliana seed coat. Here, we use an extension of this strategy to identify MUCI70 as the founding member of a glycosyltransferase family essential for the accumulation of seed mucilage, a gelatinous wall rich in unbranched RG I. Detailed biochemical and histological characterization of two muci70 mutants and two gaut11 mutants identified MUCI70 and GAUT11 as required for two distinct RG I domains in seed mucilage. We demonstrate that, unlike MUCI70, GAUT11 catalyzes HG elongation in vitro, and is thus likely required for the synthesis of an HG region important for RG I elongation. Analysis of a muci70 gaut11 double mutant confirmed that MUCI70 and GAUT11 are indispensable for the production and release of the bulk of mucilage RG I, and for shaping the surface morphology of seeds. In addition, we uncover relationships between pectin and hemicelluloses and show that xylan is essential for the elongation of at least one RG I domain.", "date": "2018-10-12", "issue": "3", "identifier": "https://www.osti.gov/biblio/1612316", "bibliographicCitation": "https://doi.org/10.1104/pp.18.00584", "keywords": [ "54 ENVIRONMENTAL SCIENCES", "plant sciences" ], "topic": [ "Environmental Science & Sustainability" ], "journal_name": "Plant Physiology (Bethesda)", "volume": "178", "publisher_information": "American Society of Plant Biologists", "country_publication_code": "US", "creator": [ { "name": "C\u0103t\u0103lin [Forschungszentrum J\u00fclich (Germany); Aachen Univ. (Germany); DOE/OSTI] (ORCID:000000019105014X) Voiniciuc", "primaryContact": true }, { "name": "Kristen A. [Univ. of Georgia,Athens,GA (United States)] (ORCID:0000000217502029) Engle", "primaryContact": false }, { "name": "Markus [Forschungszentrum J\u00fclich (Germany)] G\u00fcnl", "primaryContact": false }, { "name": "Sabine [Forschungszentrum J\u00fclich (Germany)] (ORCID:0000000286409063) Dieluweit", "primaryContact": false }, { "name": "Maximilian Heinrich-Wilhelm [Forschungszentrum J\u00fclich (Germany); Aachen Univ. (Germany)] Schmidt", "primaryContact": false }, { "name": "Jeong-Yeh [Univ. of Georgia,Athens,GA (United States)] (ORCID:0000000178981337) Yang", "primaryContact": false }, { "name": "Kelley W. [Univ. of Georgia,Athens,GA (United States)] Moremen", "primaryContact": false }, { "name": "Debra [Univ. of Georgia,Athens,GA (United States)] Mohnen", "primaryContact": false }, { "name": "Bj\u00f6rn [Forschungszentrum J\u00fclich (Germany); Aachen Univ. (Germany)] (ORCID:0000000309218041) Usadel", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "Deutsche Forschungsgemeinschaft" } }, { "fundingOrganization": { "organizationName": "Ministry of Innovation, Science and Research of North-Rhine Westphalia" } }, { "fundingOrganization": { "organizationName": "National Institutes of Health (NIH)" } }, { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "Natural Sciences and Engineering Research Council of Canada (NERSC)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC)" } } ], "dataset_url": "https://www.osti.gov/biblio/1612316", "active": false }, { "brc": "CBI", "title": "Data Integration in Poplar: \u2018Omics Layers and Integration Strategies", "description": "Populus trichocarpa is an important biofuel feedstock that has been the target of extensive research and is emerging as a model organism for plants, especially woody perennials. This research has generated several large \u2018omics datasets. However, only few studies in Populus have attempted to integrate various data types. This review will summarize various \u2018omics data layers, focusing on their application in Populus species. Subsequently, network and signal processing techniques for the integration and analysis of these data types will be discussed, with particular reference to examples in Populus.", "abstract": "Populus trichocarpa is an important biofuel feedstock that has been the target of extensive research and is emerging as a model organism for plants, especially woody perennials. This research has generated several large \u2018omics datasets. However, only few studies in Populus have attempted to integrate various data types. This review will summarize various \u2018omics data layers, focusing on their application in Populus species. Subsequently, network and signal processing techniques for the integration and analysis of these data types will be discussed, with particular reference to examples in Populus.", "date": "2019-09-24", "issue": "na", "identifier": "https://www.osti.gov/biblio/1616837", "bibliographicCitation": "https://doi.org/10.3389/fgene.2019.00874", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "Populus", "data integration", "multi-omic data", "networks", "signal processing", "wavelet transform" ], "topic": [ "Microbiology" ], "journal_name": "Frontiers in Genetics", "volume": "10", "publisher_information": "Frontiers", "country_publication_code": "US", "creator": [ { "name": "Deborah A. [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Harvard Univ.,Boston,MA (United States)] (ORCID:0000000349795871) Weighill", "primaryContact": true }, { "name": "Timothy J. [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000295406622) Tschaplinski", "primaryContact": false }, { "name": "Gerald A. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000301061289) Tuskan", "primaryContact": false }, { "name": "Daniel A. [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000298228251) Jacobson", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1616837", "active": false }, { "brc": "CBI", "title": "Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave", "description": "Not Available", "abstract": "Not Available", "date": "2018-08-05", "issue": "1", "identifier": "https://www.osti.gov/biblio/1618568", "bibliographicCitation": "https://doi.org/10.1186/s12864-018-4964-7", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "Circadian rhythm", "Comparative genomics", "Crassulacean acid metabolism", "Photosynthesis", "Positive selection", "Transcriptome" ], "topic": [ "Microbiology" ], "journal_name": "BMC Genomics", "volume": "19", "publisher_information": "Springer Science + Business Media", "country_publication_code": "GB", "creator": [ { "name": "Hengfu Yin", "primaryContact": true }, { "name": "Hao-Bo Guo", "primaryContact": false }, { "name": "David J. Weston", "primaryContact": false }, { "name": "Anne M. Borland", "primaryContact": false }, { "name": "Priya Ranjan", "primaryContact": false }, { "name": "Paul E. Abraham", "primaryContact": false }, { "name": "Sara S. Jawdy", "primaryContact": false }, { "name": "James Wachira", "primaryContact": false }, { "name": "Gerald A. Tuskan", "primaryContact": false }, { "name": "Timothy J. Tschaplinski", "primaryContact": false }, { "name": "Stan D. Wullschleger", "primaryContact": false }, { "name": "Hong Guo", "primaryContact": false }, { "name": "Robert L. Hettich", "primaryContact": false }, { "name": "Stephen M. Gross", "primaryContact": false }, { "name": "Zhong Wang", "primaryContact": false }, { "name": "Axel Visel", "primaryContact": false }, { "name": "Xiaohan Yang", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/1618568", "active": false }, { "brc": "CBI", "title": "Determination of glycoside hydrolase specificities during hydrolysis of plant cell walls using glycome profiling", "description": "Not Available", "abstract": "Not Available", "date": "2017-02-01", "issue": "1", "identifier": "https://www.osti.gov/biblio/1618668", "bibliographicCitation": "https://doi.org/10.1186/s13068-017-0703-6", "keywords": [ "09 BIOMASS FUELS", "Enzyme specificity", "Glycome profiling", "Glycoside hydrolase", "Nanostructure-initiator mass spectrometry", "Xylanase", "Xyloglucanase" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Biotechnology for Biofuels", "volume": "10", "publisher_information": "Springer Science + Business Media", "country_publication_code": "Netherlands", "creator": [ { "name": "Johnnie A. Walker", "primaryContact": true }, { "name": "Sivakumar Pattathil", "primaryContact": false }, { "name": "Lai F. Bergeman", "primaryContact": false }, { "name": "Emily T. Beebe", "primaryContact": false }, { "name": "Kai Deng", "primaryContact": false }, { "name": "Maryam Mirzai", "primaryContact": false }, { "name": "Trent R. Northen", "primaryContact": false }, { "name": "Michael G. Hahn", "primaryContact": false }, { "name": "Brian G. Fox", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1618668", "active": false }, { "brc": "CBI", "title": "Overexpression of a Domain of Unknown Function 266-containing protein results in high cellulose content, reduced recalcitrance, and enhanced plant growth in the bioenergy crop Populus", "description": "Not Available", "abstract": "Not Available", "date": "2017-03-22", "issue": "1", "identifier": "https://www.osti.gov/biblio/1618674", "bibliographicCitation": "https://doi.org/10.1186/s13068-017-0760-x", "keywords": [ "09 BIOMASS FUELS", "60 APPLIED LIFE SCIENCES", "DUF266", "Populus", "bioenergy", "biofuel", "biomass", "cell wall", "cellulose", "recalcitrance", "sugar release" ], "topic": [ "Biomass & Feedstock", "Plant Biology" ], "journal_name": "Biotechnology for Biofuels", "volume": "10", "publisher_information": "Springer Science + Business Media", "country_publication_code": "Netherlands", "creator": [ { "name": "Yongil Yang", "primaryContact": true }, { "name": "Chang Geun Yoo", "primaryContact": false }, { "name": "Hao-Bo Guo", "primaryContact": false }, { "name": "William Rottmann", "primaryContact": false }, { "name": "Kimberly A. Winkeler", "primaryContact": false }, { "name": "Cassandra M. Collins", "primaryContact": false }, { "name": "Lee E. Gunter", "primaryContact": false }, { "name": "Sara S. Jawdy", "primaryContact": false }, { "name": "Xiaohan Yang", "primaryContact": false }, { "name": "Hong Guo", "primaryContact": false }, { "name": "Yunqiao Pu", "primaryContact": false }, { "name": "Arthur J. Ragauskas", "primaryContact": false }, { "name": "Gerald A. 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(ORCID:000000017708786X) Hettich", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1618720", "active": false }, { "brc": "CBI", "title": "An iterative computational design approach to increase the thermal endurance of a mesophilic enzyme", "description": "Not Available", "abstract": "Not Available", "date": "2018-07-08", "issue": "1", "identifier": "https://www.osti.gov/biblio/1618725", "bibliographicCitation": "https://doi.org/10.1186/s13068-018-1178-9", "keywords": [ "09 BIOMASS FUELS", "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "97 MATHEMATICS AND COMPUTING", "biofuels", "computational protein design", "pyruvate decarboxylase", "thermal stability" ], "topic": [ "Biomass & Feedstock", "Chemistry", "Computational Biology & Modeling" ], "journal_name": "Biotechnology for Biofuels", "volume": "11", "publisher_information": "Springer Science + Business Media", "country_publication_code": "Netherlands", "creator": [ { "name": "Deanne W. Sammond", "primaryContact": true }, { "name": "Noah Kastelowitz", "primaryContact": false }, { "name": "Bryon S. Donohoe", "primaryContact": false }, { "name": "Markus Alahuhta", "primaryContact": false }, { "name": "Vladimir V. Lunin", "primaryContact": false }, { "name": "Daehwan Chung", "primaryContact": false }, { "name": "Nicholas S. Sarai", "primaryContact": false }, { "name": "Hang Yin", "primaryContact": false }, { "name": "Ashutosh Mittal", "primaryContact": false }, { "name": "Michael E. Himmel", "primaryContact": false }, { "name": "Adam M. Guss", "primaryContact": false }, { "name": "Yannick J. Bomble", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Inst. of Health (NIH)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1618725", "active": false, "has_related_ids": [ "NREL/JA--5100-71815" ] }, { "brc": "CBI", "title": "Expressing the Thermoanaerobacterium saccharolyticum pforA in engineered Clostridium thermocellum improves ethanol production", "description": "Not Available", "abstract": "Not Available", "date": "2018-09-05", "issue": "1", "identifier": "https://www.osti.gov/biblio/1618728", "bibliographicCitation": "https://doi.org/10.1186/s13068-018-1245-2", "keywords": [ "Biotechnology & Applied Microbiology", "Clostridium thermocellum", "Consolidated bioprocessing", "Energy & Fuels", "Ethanol", "Isobutanol", "Pyruvate ferredoxin oxidoreductase", "Thermoanaerobacterium saccharolyticum" ], "topic": [ "Unknown" ], "journal_name": "Biotechnology for Biofuels", "volume": "11", "publisher_information": "Springer Science + Business Media", "country_publication_code": "Netherlands", "creator": [ { "name": "Shuen Hon", "primaryContact": true }, { "name": "Evert K. Holwerda", "primaryContact": false }, { "name": "Robert S. Worthen", "primaryContact": false }, { "name": "Marybeth I. Maloney", "primaryContact": false }, { "name": "Liang Tian", "primaryContact": false }, { "name": "Jingxuan Cui", "primaryContact": false }, { "name": "Paul P. Lin", "primaryContact": false }, { "name": "Lee R. Lynd", "primaryContact": false }, { "name": "Daniel G. Olson", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "DOE Center for Bioenergy Innovation" } }, { "fundingOrganization": { "organizationName": "DOE Joint Genome Institute" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER), DOE BioEnergy Science Center" } } ], "dataset_url": "https://www.osti.gov/biblio/1618728", "active": false }, { "brc": "CBI", "title": "Development and characterization of stable anaerobic thermophilic methanogenic microbiomes fermenting switchgrass at decreasing residence times", "description": "Not Available", "abstract": "Not Available", "date": "2018-09-05", "issue": "1", "identifier": "https://www.osti.gov/biblio/1618731", "bibliographicCitation": "https://doi.org/10.1186/s13068-018-1238-1", "keywords": [ "09 BIOMASS FUELS", "Anaerobic", "Clostridium clariflavum", "Lignocellulose", "Metagenomics", "Methanogenic", "Microbial communities", "Solubilization", "Thermophilic" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Biotechnology for Biofuels", "volume": "11", "publisher_information": "Springer Science + Business Media", "country_publication_code": "Netherlands", "creator": [ { "name": "Xiaoyu (ORCID:0000000230389374) Liang", "primaryContact": true }, { "name": "Jason M. Whitham", "primaryContact": false }, { "name": "Evert K. Holwerda", "primaryContact": false }, { "name": "Xiongjun Shao", "primaryContact": false }, { "name": "Liang Tian", "primaryContact": false }, { "name": "Yu-Wei Wu", "primaryContact": false }, { "name": "Vincent Lombard", "primaryContact": false }, { "name": "Bernard Henrissat", "primaryContact": false }, { "name": "Dawn M. Klingeman", "primaryContact": false }, { "name": "Zamin K. Yang", "primaryContact": false }, { "name": "Mircea Podar", "primaryContact": false }, { "name": "Tom L. Richard", "primaryContact": false }, { "name": "James G. Elkins", "primaryContact": false }, { "name": "Steven D. Brown", "primaryContact": false }, { "name": "Lee R. Lynd", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1618731", "active": false }, { "brc": "CBI", "title": "High activity CAZyme cassette for improving biomass degradation in thermophiles", "description": "Not Available", "abstract": "Not Available", "date": "2018-01-31", "issue": "1", "identifier": "https://www.osti.gov/biblio/1618733", "bibliographicCitation": "https://doi.org/10.1186/s13068-018-1014-2", "keywords": [ "09 BIOMASS FUELS", "Caldicellulosiruptor bescii", "anaerobe", "biofuels", "biomass", "biomass degrading enzymes", "cellulose", "thermophile" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Biotechnology for Biofuels", "volume": "11", "publisher_information": "Springer Science + Business Media", "country_publication_code": "Netherlands", "creator": [ { "name": "Roman Brunecky", "primaryContact": true }, { "name": "Daehwan Chung", "primaryContact": false }, { "name": "Nicholas S. Sarai", "primaryContact": false }, { "name": "Neal Hengge", "primaryContact": false }, { "name": "Jordan F. Russell", "primaryContact": false }, { "name": "Jenna Young", "primaryContact": false }, { "name": "Ashutosh Mittal", "primaryContact": false }, { "name": "Patthra Pason", "primaryContact": false }, { "name": "Todd Vander Wall", "primaryContact": false }, { "name": "William Michener", "primaryContact": false }, { "name": "Todd Shollenberger", "primaryContact": false }, { "name": "Janet Westpheling", "primaryContact": false }, { "name": "Michael E. Himmel", "primaryContact": false }, { "name": "Yannick J. (ORCID:0000000176248000) Bomble", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "King Mongkut\u2019s Univ. of Technology Thonburi (KMUTT), Bangkok (Thailand)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1618733", "active": false, "has_related_ids": [ "NREL/JA-2700-70440" ] }, { "brc": "CBI", "title": "Fractionation and characterization of lignin streams from unique high-lignin content endocarp feedstocks", "description": "Not Available", "abstract": "Not Available", "date": "2018-11-07", "issue": "1", "identifier": "https://www.osti.gov/biblio/1618740", "bibliographicCitation": "https://doi.org/10.1186/s13068-018-1305-7", "keywords": [ "09 BIOMASS FUELS", "Biofuel", "Biorefinery", "Deep eutectic solvent", "Endocarp", "Lignin", "Pretreatment" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Biotechnology for Biofuels", "volume": "11", "publisher_information": "Springer Science + Business Media", "country_publication_code": "Netherlands", "creator": [ { "name": "Wenqi Li", "primaryContact": true }, { "name": "Kirtley Amos", "primaryContact": false }, { "name": "Mi Li", "primaryContact": false }, { "name": "Yunqiao Pu", "primaryContact": false }, { "name": "Seth Debolt", "primaryContact": false }, { "name": "Arthur J. Ragauskas", "primaryContact": false }, { "name": "Jian (ORCID:0000000330224446) Shi", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/1618740", "active": false }, { "brc": "CBI", "title": "Multiple levers for overcoming the recalcitrance of lignocellulosic biomass", "description": "Not Available", "abstract": "Not Available", "date": "2019-01-16", "issue": "1", "identifier": "https://www.osti.gov/biblio/1618748", "bibliographicCitation": "https://doi.org/10.1186/s13068-019-1353-7", "keywords": [ "09 BIOMASS FUELS", "CELF", "Caldicellulosiruptor bescii", "Clostridium thermocellum", "Populus natural variants", "biomass deconstruction", "cotreatment", "fungal cellulase", "recalcitrance", "transgenic switchgrass" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Biotechnology for Biofuels", "volume": "12", "publisher_information": "Springer Science + Business Media", "country_publication_code": "Netherlands", "creator": [ { "name": "Evert K. Holwerda", "primaryContact": true }, { "name": "Robert S. Worthen", "primaryContact": false }, { "name": "Ninad Kothari", "primaryContact": false }, { "name": "Ronald C. Lasky", "primaryContact": false }, { "name": "Brian H. Davison", "primaryContact": false }, { "name": "Chunxiang Fu", "primaryContact": false }, { "name": "Zeng-Yu Wang", "primaryContact": false }, { "name": "Richard A. Dixon", "primaryContact": false }, { "name": "Ajaya K. Biswal", "primaryContact": false }, { "name": "Debra Mohnen", "primaryContact": false }, { "name": "Richard S. Nelson", "primaryContact": false }, { "name": "Holly L. Baxter", "primaryContact": false }, { "name": "Mitra Mazarei", "primaryContact": false }, { "name": "Jr.,C. Neal Stewart", "primaryContact": false }, { "name": "Wellington Muchero", "primaryContact": false }, { "name": "Gerald A. Tuskan", "primaryContact": false }, { "name": "Charles M. Cai", "primaryContact": false }, { "name": "Erica E. Gjersing", "primaryContact": false }, { "name": "Mark F. Davis", "primaryContact": false }, { "name": "Michael E. Himmel", "primaryContact": false }, { "name": "Charles E. Wyman", "primaryContact": false }, { "name": "Paul Gilna", "primaryContact": false }, { "name": "Lee R. Lynd", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1618748", "active": false, "has_related_ids": [ "NREL/JA--2700-73226" ] }, { "brc": "CBI", "title": "Desirable plant cell wall traits for higher-quality miscanthus lignocellulosic biomass", "description": "Not Available", "abstract": "Not Available", "date": "2019-04-14", "issue": "1", "identifier": "https://www.osti.gov/biblio/1618751", "bibliographicCitation": "https://doi.org/10.1186/s13068-019-1426-7", "keywords": [ "Bioenergy", "Biomass", "Biotechnology & Applied Microbiology", "Carbohydrate", "Cell wall", "Energy & Fuels", "Glycan", "Lignin", "Lignocellulose", "Miscanthus", "Recalcitrance" ], "topic": [ "Unknown" ], "journal_name": "Biotechnology for Biofuels", "volume": "12", "publisher_information": "Springer Science + Business Media", "country_publication_code": "Netherlands", "creator": [ { "name": "Ricardo M. F. (ORCID:000000025426412X) da Costa", "primaryContact": true }, { "name": "Sivakumar Pattathil", "primaryContact": false }, { "name": "Utku Avci", "primaryContact": false }, { "name": "Ana Winters", "primaryContact": false }, { "name": "Michael G. Hahn", "primaryContact": false }, { "name": "Maurice (ORCID:000000031990589X) Bosch", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC)" } } ], "dataset_url": "https://www.osti.gov/biblio/1618751", "active": false }, { "brc": "CBI", "title": "CELF significantly reduces milling requirements and improves soaking effectiveness for maximum sugar recovery of Alamo switchgrass over dilute sulfuric acid pretreatment", "description": "Not Available", "abstract": "Not Available", "date": "2019-07-09", "issue": "1", "identifier": "https://www.osti.gov/biblio/1618756", "bibliographicCitation": "https://doi.org/10.1186/s13068-019-1515-7", "keywords": [ "09 BIOMASS FUELS", "Biomass", "Biotechnology & Applied Microbiology", "Dilute acid", "Energy & Fuels", "Enzymatic hydrolysis", "Pretreatment", "Size reduction", "Soaking", "Tetrahydrofuran" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Biotechnology for Biofuels", "volume": "12", "publisher_information": "Springer Science + Business Media", "country_publication_code": "Netherlands", "creator": [ { "name": "Abhishek S. Patri", "primaryContact": true }, { "name": "Laura McAlister", "primaryContact": false }, { "name": "Charles M. Cai", "primaryContact": false }, { "name": "Rajeev Kumar", "primaryContact": false }, { "name": "Charles E. (ORCID:0000000279852841) Wyman", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC)" } } ], "dataset_url": "https://www.osti.gov/biblio/1618756", "active": false }, { "brc": "CBI", "title": "Microbial biosynthesis of lactate esters", "description": "Green organic solvents such as lactate esters have broad industrial applications and favorable environmental profiles. Thus, manufacturing and use of these biodegradable solvents from renewable feedstocks help benefit the environment. However, to date, the direct microbial biosynthesis of lactate esters from fermentable sugars has not yet been demonstrated.
\n\n In this study, we present a microbial conversion platform for direct biosynthesis of lactate esters from fermentable sugars. First, we designed a pyruvate-to-lactate ester module, consisting of a lactate dehydrogenase (\n
\n We have successfully established the biosynthesis pathway of lactate esters from fermentable sugars and demonstrated for the first time the direct fermentative production of lactate esters from glucose using an\n
Green organic solvents such as lactate esters have broad industrial applications and favorable environmental profiles. Thus, manufacturing and use of these biodegradable solvents from renewable feedstocks help benefit the environment. However, to date, the direct microbial biosynthesis of lactate esters from fermentable sugars has not yet been demonstrated.
\n\n In this study, we present a microbial conversion platform for direct biosynthesis of lactate esters from fermentable sugars. First, we designed a pyruvate-to-lactate ester module, consisting of a lactate dehydrogenase (\n
\n We have successfully established the biosynthesis pathway of lactate esters from fermentable sugars and demonstrated for the first time the direct fermentative production of lactate esters from glucose using an\n
\n Esters are versatile chemicals and potential drop-in biofuels. To develop a sustainable production platform, microbial ester biosynthesis using alcohol acetyltransferases (AATs) has been studied for decades. Volatility of esters endows high-temperature fermentation with advantageous downstream product separation. However, due to the limited thermostability of AATs known, the ester biosynthesis has largely relied on use of mesophilic microbes. Therefore, developing thermostable AATs is important for ester production directly from lignocellulosic biomass by the thermophilic consolidated bioprocessing (CBP) microbes, e.g.,\n
\n In this study, we engineered a thermostable chloramphenicol acetyltransferase from\n
This study highlights that CAT is a potential thermostable AAT that can be harnessed to develop the thermophilic CBP microbial platform for biosynthesis of designer bioesters directly from lignocellulosic biomass.
\n\n Esters are versatile chemicals and potential drop-in biofuels. To develop a sustainable production platform, microbial ester biosynthesis using alcohol acetyltransferases (AATs) has been studied for decades. Volatility of esters endows high-temperature fermentation with advantageous downstream product separation. However, due to the limited thermostability of AATs known, the ester biosynthesis has largely relied on use of mesophilic microbes. Therefore, developing thermostable AATs is important for ester production directly from lignocellulosic biomass by the thermophilic consolidated bioprocessing (CBP) microbes, e.g.,\n
\n In this study, we engineered a thermostable chloramphenicol acetyltransferase from\n
This study highlights that CAT is a potential thermostable AAT that can be harnessed to develop the thermophilic CBP microbial platform for biosynthesis of designer bioesters directly from lignocellulosic biomass.
\nIn this work, three pretreatments under investigation at the DOE Bioenergy Research Centers (BRCs) were subjected to a side-by-side comparison to assess their performance on model bioenergy hardwoods (a eucalyptus and a hybrid poplar). These include co-solvent-enhanced lignocellulosic fractionation (CELF), pretreatment with an ionic liquid using potentially biomass-derived components (cholinium lysinate or [Ch][Lys]), and two-stage Cu-catalyzed alkaline hydrogen peroxide pretreatment (Cu-AHP). For each of the feedstocks, the pretreatments were assessed for their impact on lignin and xylan solubilization and enzymatic hydrolysis yields as a function of enzyme loading. Lignins recovered from the pretreatments were characterized for polysaccharide content, molar mass distributions, \u03b2-aryl ether content, and response to depolymerization by thioacidolysis.
\n\n All three pretreatments resulted in significant solubilization of lignin and xylan, with the CELF pretreatment solubilizing the majority of both biopolymer categories. Enzymatic hydrolysis yields were shown to exhibit a strong, positive correlation with the lignin solubilized for the low enzyme loadings. The pretreatment-derived solubles in the [Ch][Lys]-pretreated biomass were presumed to contribute to inhibition of enzymatic hydrolysis in the eucalyptus as a substantial fraction of the pretreatment liquor was carried forward into hydrolysis for this pretreatment. The pretreatment-solubilized lignins exhibited significant differences in polysaccharide content, molar mass distributions, aromatic monomer yield by thioacidolysis, and \u03b2-aryl ether content. Key trends include a substantially higher polysaccharide content in the lignins recovered from the [Ch][Lys] pretreatment and high \u03b2-aryl ether contents and aromatic monomer yields from the Cu-AHP pretreatment. For all lignins, the\n 13\n C NMR-determined \u03b2-aryl ether content was shown to be correlated with the monomer yield with a second-order functionality.\n
\nOverall, it was demonstrated that the three pretreatments highlighted in this study demonstrated uniquely different functionalities in reducing biomass recalcitrance and achieving higher enzymatic hydrolysis yields for the hybrid poplar while yielding a lignin-rich stream that may be suitable for valorization. Furthermore, modification of lignin during pretreatment, particularly cleavage of \u03b2-aryl ether bonds, is shown to be detrimental to subsequent depolymerization.
\nIn this work, three pretreatments under investigation at the DOE Bioenergy Research Centers (BRCs) were subjected to a side-by-side comparison to assess their performance on model bioenergy hardwoods (a eucalyptus and a hybrid poplar). These include co-solvent-enhanced lignocellulosic fractionation (CELF), pretreatment with an ionic liquid using potentially biomass-derived components (cholinium lysinate or [Ch][Lys]), and two-stage Cu-catalyzed alkaline hydrogen peroxide pretreatment (Cu-AHP). For each of the feedstocks, the pretreatments were assessed for their impact on lignin and xylan solubilization and enzymatic hydrolysis yields as a function of enzyme loading. Lignins recovered from the pretreatments were characterized for polysaccharide content, molar mass distributions, \u03b2-aryl ether content, and response to depolymerization by thioacidolysis.
\n\n All three pretreatments resulted in significant solubilization of lignin and xylan, with the CELF pretreatment solubilizing the majority of both biopolymer categories. Enzymatic hydrolysis yields were shown to exhibit a strong, positive correlation with the lignin solubilized for the low enzyme loadings. The pretreatment-derived solubles in the [Ch][Lys]-pretreated biomass were presumed to contribute to inhibition of enzymatic hydrolysis in the eucalyptus as a substantial fraction of the pretreatment liquor was carried forward into hydrolysis for this pretreatment. The pretreatment-solubilized lignins exhibited significant differences in polysaccharide content, molar mass distributions, aromatic monomer yield by thioacidolysis, and \u03b2-aryl ether content. Key trends include a substantially higher polysaccharide content in the lignins recovered from the [Ch][Lys] pretreatment and high \u03b2-aryl ether contents and aromatic monomer yields from the Cu-AHP pretreatment. For all lignins, the\n 13\n C NMR-determined \u03b2-aryl ether content was shown to be correlated with the monomer yield with a second-order functionality.\n
\nOverall, it was demonstrated that the three pretreatments highlighted in this study demonstrated uniquely different functionalities in reducing biomass recalcitrance and achieving higher enzymatic hydrolysis yields for the hybrid poplar while yielding a lignin-rich stream that may be suitable for valorization. Furthermore, modification of lignin during pretreatment, particularly cleavage of \u03b2-aryl ether bonds, is shown to be detrimental to subsequent depolymerization.
\n\n Insights into the evolution of plant cell walls have important implications for comprehending these diverse and abundant biological structures. In order to understand the evolving structure\u2013function relationships of the plant cell wall, it is imperative to trace the origin of its different components. The present study is focused on plant 1,4\u2010\u03b2\u2010xylan, tracing its evolutionary origin by genome and transcriptome mining followed by phylogenetic analysis, utilizing a large selection of plants and algae. It substantiates the findings by heterologous expression and biochemical characterization of a charophyte alga xylan synthase. \n Of the 12 known gene classes involved in 1,4\u2010\u03b2\u2010xylan formation,\n These data suggest that plant 1,4\u2010\u03b2\u2010xylan originated in charophytes and shed light on the origin of one of the key cell wall innovations to occur in charophyte algae, facilitating terrestrialization and emergence of polysaccharide\u2010based plant cell walls.\n
\n
\n Insights into the evolution of plant cell walls have important implications for comprehending these diverse and abundant biological structures. In order to understand the evolving structure\u2013function relationships of the plant cell wall, it is imperative to trace the origin of its different components. The present study is focused on plant 1,4\u2010\u03b2\u2010xylan, tracing its evolutionary origin by genome and transcriptome mining followed by phylogenetic analysis, utilizing a large selection of plants and algae. It substantiates the findings by heterologous expression and biochemical characterization of a charophyte alga xylan synthase. \n Of the 12 known gene classes involved in 1,4\u2010\u03b2\u2010xylan formation,\n These data suggest that plant 1,4\u2010\u03b2\u2010xylan originated in charophytes and shed light on the origin of one of the key cell wall innovations to occur in charophyte algae, facilitating terrestrialization and emergence of polysaccharide\u2010based plant cell walls.\n
\n
\r\n A particularly promising approach to deconstructing and fractionating lignocellulosic biomass to produce green renewable fuels and high-value chemicals pretreats the biomass with organic solvents in aqueous solution. Here, neutron scattering and molecular-dynamics simulations reveal the temperature-dependent morphological changes in poplar wood biomass during tetrahydrofuran (THF):water pretreatment and provide a mechanism by which the solvent components drive efficient biomass breakdown. Whereas lignin dissociates over a wide temperature range (>25 \u00b0C) cellulose disruption occurs only above 150 \u00b0C. Neutron scattering with contrast variation provides direct evidence for the formation of THF-rich nanoclusters (R\r\n g\r\n \u223c 0.5 nm) on the nonpolar cellulose surfaces and on hydrophobic lignin, and equivalent water-rich nanoclusters on polar cellulose surfaces. The disassembly of the amphiphilic biomass is thus enabled through the local demixing of highly functional cosolvents, THF and water, which preferentially solvate specific biomass surfaces so as to match the local solute polarity. A multiscale description of the efficiency of THF:water pretreatment is provided: matching polarity at the atomic scale prevents lignin aggregation and disrupts cellulose, leading to improvements in deconstruction at the macroscopic scale.\r\n
", "abstract": "\r\n A particularly promising approach to deconstructing and fractionating lignocellulosic biomass to produce green renewable fuels and high-value chemicals pretreats the biomass with organic solvents in aqueous solution. Here, neutron scattering and molecular-dynamics simulations reveal the temperature-dependent morphological changes in poplar wood biomass during tetrahydrofuran (THF):water pretreatment and provide a mechanism by which the solvent components drive efficient biomass breakdown. Whereas lignin dissociates over a wide temperature range (>25 \u00b0C) cellulose disruption occurs only above 150 \u00b0C. Neutron scattering with contrast variation provides direct evidence for the formation of THF-rich nanoclusters (R\r\n g\r\n \u223c 0.5 nm) on the nonpolar cellulose surfaces and on hydrophobic lignin, and equivalent water-rich nanoclusters on polar cellulose surfaces. The disassembly of the amphiphilic biomass is thus enabled through the local demixing of highly functional cosolvents, THF and water, which preferentially solvate specific biomass surfaces so as to match the local solute polarity. A multiscale description of the efficiency of THF:water pretreatment is provided: matching polarity at the atomic scale prevents lignin aggregation and disrupts cellulose, leading to improvements in deconstruction at the macroscopic scale.\r\n
", "date": "2020-07-06", "issue": "29", "identifier": "https://www.osti.gov/biblio/1637572", "bibliographicCitation": "https://doi.org/10.1073/pnas.1922883117", "keywords": [ "09 BIOMASS FUELS", "biomass", "pretreatment", "solvents" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "117", "publisher_information": "National Academy of Sciences", "country_publication_code": "US", "creator": [ { "name": "Sai Venkatesh Pingali", "primaryContact": true }, { "name": "Micholas Dean Smith", "primaryContact": false }, { "name": "Shih-Hsien Liu", "primaryContact": false }, { "name": "Takat B. (ORCID:0000000331917770) Rawal", "primaryContact": false }, { "name": "Yunqiao Pu", "primaryContact": false }, { "name": "Riddhi Shah", "primaryContact": false }, { "name": "Barbara R. (ORCID:0000000225742567) Evans", "primaryContact": false }, { "name": "Volker S. Urban", "primaryContact": false }, { "name": "Brian H. (ORCID:0000000274083609) Davison", "primaryContact": false }, { "name": "Charles M. (ORCID:0000000250470815) Cai", "primaryContact": false }, { "name": "Arthur J. (ORCID:000000023536554X) Ragauskas", "primaryContact": false }, { "name": "Hugh M. O\u2019Neill", "primaryContact": false }, { "name": "Jeremy C. Smith", "primaryContact": false }, { "name": "Loukas Petridis", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1637572", "active": false }, { "brc": "CBI", "title": "Plant Biosystems Design for a Carbon-Neutral Bioeconomy", "description": "\r\n Our society faces multiple daunting challenges including finding sustainable solutions towards climate change mitigation; efficient production of food, biofuels, and biomaterials; maximizing land-use efficiency; and enabling a sustainable bioeconomy. Plants can provide environmentally and economically sustainable solutions to these challenges due to their inherent capabilities for photosynthetic capture of atmospheric CO\r\n 2\r\n , allocation of carbon to various organs and partitioning into various chemical forms, including contributions to total soil carbon. In order to enhance crop productivity and optimize chemistry simultaneously in the above- and belowground plant tissues, transformative biosystems design strategies are needed. Concerted research efforts will be required for accelerating the development of plant cultivars, genotypes, or varieties that are cooptimized in the contexts of biomass-derived fuels and/or materials aboveground and enhanced carbon sequestration belowground. Here, we briefly discuss significant knowledge gaps in our process understanding and the potential of synthetic biology in enabling advancements along the fundamental to applied research arc. Ultimately, a convergence of perspectives from academic, industrial, government, and consumer sectors will be needed to realize the potential merits of plant biosystems design for a carbon neutral bioeconomy.\r\n
", "abstract": "\r\n Our society faces multiple daunting challenges including finding sustainable solutions towards climate change mitigation; efficient production of food, biofuels, and biomaterials; maximizing land-use efficiency; and enabling a sustainable bioeconomy. Plants can provide environmentally and economically sustainable solutions to these challenges due to their inherent capabilities for photosynthetic capture of atmospheric CO\r\n 2\r\n , allocation of carbon to various organs and partitioning into various chemical forms, including contributions to total soil carbon. In order to enhance crop productivity and optimize chemistry simultaneously in the above- and belowground plant tissues, transformative biosystems design strategies are needed. Concerted research efforts will be required for accelerating the development of plant cultivars, genotypes, or varieties that are cooptimized in the contexts of biomass-derived fuels and/or materials aboveground and enhanced carbon sequestration belowground. Here, we briefly discuss significant knowledge gaps in our process understanding and the potential of synthetic biology in enabling advancements along the fundamental to applied research arc. Ultimately, a convergence of perspectives from academic, industrial, government, and consumer sectors will be needed to realize the potential merits of plant biosystems design for a carbon neutral bioeconomy.\r\n
", "date": "2020-06-10", "identifier": "https://www.osti.gov/biblio/1639132", "bibliographicCitation": "https://doi.org/10.34133/2020/7914051", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "BioDesign Research", "volume": "2020", "publisher_information": "American Association for the Advancement of Science (AAAS)", "country_publication_code": "India", "creator": [ { "name": "Udaya C. [Biosciences Division,Oak Ridge National Laboratory,PO Box 2008,Oak Ridge,TN 37831-6422,USA] (ORCID:0000000259638370) Kalluri", "primaryContact": true }, { "name": "Xiaohan [Biosciences Division,Oak Ridge National Laboratory,PO Box 2008,Oak Ridge,TN 37831-6422,USA] (ORCID:0000000152074210) Yang", "primaryContact": false }, { "name": "Stan D. [Environmental Sciences Division,Oak Ridge National Laboratory,PO Box 2008,Oak Ridge,TN 37831-6422,USA] (ORCID:0000000298690446) Wullschleger", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1639132", "active": false }, { "brc": "CBI", "title": "Prime Editing Technology and Its Prospects for Future Applications in Plant Biology Research", "description": "Many applications in plant biology requires editing genomes accurately including correcting point mutations, incorporation of single-nucleotide polymorphisms (SNPs), and introduction of multinucleotide insertion/deletions (indels) into a predetermined position in the genome. These types of modifications are possible using existing genome-editing technologies such as the CRISPR-Cas systems, which require induction of double-stranded breaks in the target DNA site and the supply of a donor DNA molecule that contains the desired edit sequence. However, low frequency of homologous recombination in plants and difficulty of delivering the donor DNA molecules make this process extremely inefficient. Another kind of technology known as base editing can perform precise editing; however, only certain types of modifications can be obtained, e.g., C/G-to-T/A and A/T-to-G/C. Recently, a new type of genome-editing technology, referred to as \u201cprime editing,\u201d has been developed, which can achieve various types of editing such as any base-to-base conversion, including both transitions (C\u2192T, G\u2192A, A\u2192G, and T\u2192C) and transversion mutations (C\u2192A, C\u2192G, G\u2192C, G\u2192T, A\u2192C, A\u2192T, T\u2192A, and T\u2192G), as well as small indels without the requirement for inducing double-stranded break in the DNA. Because prime editing has wide flexibility to achieve different types of edits in the genome, it holds a great potential for developing superior crops for various purposes, such as increasing yield, providing resistance to various abiotic and biotic stresses, and improving quality of plant product. In this review, we describe the prime editing technology and discuss its limitations and potential applications in plant biology research.
", "abstract": "Many applications in plant biology requires editing genomes accurately including correcting point mutations, incorporation of single-nucleotide polymorphisms (SNPs), and introduction of multinucleotide insertion/deletions (indels) into a predetermined position in the genome. These types of modifications are possible using existing genome-editing technologies such as the CRISPR-Cas systems, which require induction of double-stranded breaks in the target DNA site and the supply of a donor DNA molecule that contains the desired edit sequence. However, low frequency of homologous recombination in plants and difficulty of delivering the donor DNA molecules make this process extremely inefficient. Another kind of technology known as base editing can perform precise editing; however, only certain types of modifications can be obtained, e.g., C/G-to-T/A and A/T-to-G/C. Recently, a new type of genome-editing technology, referred to as \u201cprime editing,\u201d has been developed, which can achieve various types of editing such as any base-to-base conversion, including both transitions (C\u2192T, G\u2192A, A\u2192G, and T\u2192C) and transversion mutations (C\u2192A, C\u2192G, G\u2192C, G\u2192T, A\u2192C, A\u2192T, T\u2192A, and T\u2192G), as well as small indels without the requirement for inducing double-stranded break in the DNA. Because prime editing has wide flexibility to achieve different types of edits in the genome, it holds a great potential for developing superior crops for various purposes, such as increasing yield, providing resistance to various abiotic and biotic stresses, and improving quality of plant product. In this review, we describe the prime editing technology and discuss its limitations and potential applications in plant biology research.
", "date": "2020-06-25", "identifier": "https://www.osti.gov/biblio/1639134", "bibliographicCitation": "https://doi.org/10.34133/2020/9350905", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "BioDesign Research", "volume": "2020", "publisher_information": "AAAS", "country_publication_code": "India", "creator": [ { "name": "Md. Mahmudul [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge TN 37831,USA,Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA,Department of Genetics and Plant Breeding,Patuakhali Science and Technology University,Dumki,Patuakhali 8602,Bangladesh] Hassan", "primaryContact": true }, { "name": "Guoliang [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge TN 37831,USA,Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA] Yuan", "primaryContact": false }, { "name": "Jin-Gui [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge TN 37831,USA,Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA] (ORCID:0000000217524201) Chen", "primaryContact": false }, { "name": "Gerald A. [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge TN 37831,USA,Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA] Tuskan", "primaryContact": false }, { "name": "Xiaohan [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge TN 37831,USA,Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA] (ORCID:0000000152074210) Yang", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1639134", "active": false }, { "brc": "CBI", "title": "Characterization of the Clostridium thermocellum AdhE, NfnAB, ferredoxin and Pfor proteins for their ability to support high titer ethanol production in Thermoanaerobacterium saccharolyticum", "description": "Not Available", "abstract": "Not Available", "date": "2018-12-31", "issue": "C", "identifier": "https://www.osti.gov/biblio/1642283", "bibliographicCitation": "https://doi.org/10.1016/j.ymben.2018.09.006", "topic": [ "Unknown" ], "journal_name": "Metabolic Engineering", "volume": "51", "publisher_information": "Elsevier", "country_publication_code": "Belgium", "creator": [ { "name": "Jingxuan (ORCID:0000000187384948) Cui", "primaryContact": true }, { "name": "Daniel G. Olson", "primaryContact": false }, { "name": "Lee R. Lynd", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/1642283", "active": false }, { "brc": "CBI", "title": "Reconfiguring Plant Metabolism for Biodegradable Plastic Production", "description": "For decades, plants have been the subject of genetic engineering to synthesize novel, value-added compounds. Polyhydroxyalkanoates (PHAs), a large class of biodegradable biopolymers naturally synthesized in eubacteria, are among the novel products that have been introduced to make use of plant acetyl-CoA metabolic pathways. It was hoped that renewable PHA production would help address environmental issues associated with the accumulation of nondegradable plastic wastes. However, after three decades of effort synthesizing PHAs, and in particular the simplest form polyhydroxybutyrate (PHB), and seeking to improve their production in plants, it has proven very difficult to reach a commercially profitable rate in a normally growing plant. This seems to be due to the growth defects associated with PHA production and accumulation in plant cells. Here, we review major breakthroughs that have been made in plant-based PHA synthesis using traditional genetic engineering approaches and discuss challenges that have been encountered. Then, from the point of view of plant synthetic biology, we provide perspectives on reprograming plant acetyl-CoA pathways for PHA production, with the goal of maximizing PHA yield while minimizing growth inhibition. Specifically, we suggest genetic elements that can be considered in genetic circuit design, approaches for nuclear genome and plastome modification, and the use of multiomics and mathematical modeling in understanding and restructuring plant metabolic pathways.
", "abstract": "For decades, plants have been the subject of genetic engineering to synthesize novel, value-added compounds. Polyhydroxyalkanoates (PHAs), a large class of biodegradable biopolymers naturally synthesized in eubacteria, are among the novel products that have been introduced to make use of plant acetyl-CoA metabolic pathways. It was hoped that renewable PHA production would help address environmental issues associated with the accumulation of nondegradable plastic wastes. However, after three decades of effort synthesizing PHAs, and in particular the simplest form polyhydroxybutyrate (PHB), and seeking to improve their production in plants, it has proven very difficult to reach a commercially profitable rate in a normally growing plant. This seems to be due to the growth defects associated with PHA production and accumulation in plant cells. Here, we review major breakthroughs that have been made in plant-based PHA synthesis using traditional genetic engineering approaches and discuss challenges that have been encountered. Then, from the point of view of plant synthetic biology, we provide perspectives on reprograming plant acetyl-CoA pathways for PHA production, with the goal of maximizing PHA yield while minimizing growth inhibition. Specifically, we suggest genetic elements that can be considered in genetic circuit design, approaches for nuclear genome and plastome modification, and the use of multiomics and mathematical modeling in understanding and restructuring plant metabolic pathways.
", "date": "2020-08-04", "identifier": "https://www.osti.gov/biblio/1645173", "bibliographicCitation": "https://doi.org/10.34133/2020/9078303", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "BioDesign Research", "volume": "2020", "publisher_information": "AAAS", "country_publication_code": "India", "creator": [ { "name": "Haiwei [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA] (ORCID:0000000330636555) Lu", "primaryContact": true }, { "name": "Guoliang [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA,The Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA] (ORCID:0000000265628769) Yuan", "primaryContact": false }, { "name": "Steven H. [Department of Forest Ecosystems and Society,Oregon State University,Corvallis,OR 97331,USA] (ORCID:0000000196703082) Strauss", "primaryContact": false }, { "name": "Timothy J. [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA,The Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA] Tschaplinski", "primaryContact": false }, { "name": "Gerald A. [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA,The Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA] Tuskan", "primaryContact": false }, { "name": "Jin-Gui [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA,The Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA] (ORCID:0000000217524201) Chen", "primaryContact": false }, { "name": "Xiaohan [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA,The Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA] (ORCID:0000000152074210) Yang", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1645173", "active": false }, { "brc": "CBI", "title": "Observation of Potential Contaminants in Processed Biomass Using Fourier Transform Infrared Spectroscopy", "description": "With rapidly increased interests in biomass, diverse chemical and biological processes have been applied for biomass utilization. Fourier transform infrared (FTIR) analysis has been used for characterizing different types of biomass and their products, including natural and processed biomass. During biomass treatments, some solvents and/or catalysts can be retained and contaminate biomass. In addition, contaminants can be generated by the decomposition of biomass components. Herein, we report FTIR analyses of a series of contaminants, such as various solvents, chemicals, enzymes, and possibly formed degradation by-products in the biomass conversion process along with poplar biomass. This information helps to prevent misunderstanding the FTIR analysis results of the processed biomass.
", "abstract": "With rapidly increased interests in biomass, diverse chemical and biological processes have been applied for biomass utilization. Fourier transform infrared (FTIR) analysis has been used for characterizing different types of biomass and their products, including natural and processed biomass. During biomass treatments, some solvents and/or catalysts can be retained and contaminate biomass. In addition, contaminants can be generated by the decomposition of biomass components. Herein, we report FTIR analyses of a series of contaminants, such as various solvents, chemicals, enzymes, and possibly formed degradation by-products in the biomass conversion process along with poplar biomass. This information helps to prevent misunderstanding the FTIR analysis results of the processed biomass.
", "date": "2020-06-23", "issue": "12", "identifier": "https://www.osti.gov/biblio/1646526", "bibliographicCitation": "https://doi.org/10.3390/app10124345", "keywords": [ "09 BIOMASS FUELS", "FTIR", "by-products", "contaminants", "poplar" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Applied Sciences", "volume": "10", "publisher_information": "MDPI AG", "country_publication_code": "Switzerland", "creator": [ { "name": "Jingshun Zhuang", "primaryContact": true }, { "name": "Mi Li", "primaryContact": false }, { "name": "Yunqiao Pu", "primaryContact": false }, { "name": "Arthur (ORCID:000000023536554X) Ragauskas", "primaryContact": false }, { "name": "Chang (ORCID:0000000261792414) Yoo", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Nuclear Energy (NE)" } } ], "dataset_url": "https://www.osti.gov/biblio/1646526", "active": false }, { "brc": "CBI", "title": "Choosing pasture maps: An assessment of pasture land classification definitions and a case study of Brazil", "description": "Not Available", "abstract": "Not Available", "date": "2020-11-30", "issue": "C", "identifier": "https://www.osti.gov/biblio/1647107", "bibliographicCitation": "https://doi.org/10.1016/j.jag.2020.102205", "topic": [ "Unknown" ], "journal_name": "International Journal of Applied Earth Observation and Geoinformation", "volume": "93", "publisher_information": "Elsevier", "country_publication_code": "Netherlands", "creator": [ { "name": "Julianne Oliveira", "primaryContact": true }, { "name": "Eleanor E. Campbell", "primaryContact": false }, { "name": "Rubens A. C. Lamparelli", "primaryContact": false }, { "name": "Gleyce K. D. A. Figueiredo", "primaryContact": false }, { "name": "Johnny R. Soares", "primaryContact": false }, { "name": "Deepak Jaiswal", "primaryContact": false }, { "name": "Leonardo A. Monteiro", "primaryContact": false }, { "name": "Murilo S. Vianna", "primaryContact": false }, { "name": "Lee R. Lynd", "primaryContact": false }, { "name": "John J. Sheehan", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/1647107", "active": false }, { "brc": "CBI", "title": "Effects of CELF Pretreatment Severity on Lignin Structure and the Lignin-Based Polyurethane Properties", "description": "Conversion of technical lignin into performance biopolymers such as polyurethane offers environmental and economic advantages when combined with production of biofuels from biomass sugars, presenting significant interest toward studying the role of pretreatment on lignin structure and functionality. Co-solvent enhanced lignocellulosic fractionation (CELF) pretreatment, employing acidic aqueous tetrahydrofuran (THF) mixtures, was developed to effectively break down the lignin-carbohydrate matrix and promote extraction of lignin from lignocellulosic biomass with desirable purity and yield. In this study, we report the effects of CELF pretreatment reaction severity on the molecular structure of CELF-extracted lignin and its impact toward the mechanical properties of the resulting lignin-based polyurethanes. Reaction temperature was found to play the most significant role, compared to reaction time and acidity, in manipulating structural features such as molecular weight, functionality and intra-polymer structure. At the severe reaction conditions at 180°C, the order of reactivity for primary lignin interlinkages characterized by semiquantitative HSQC NMR analysis were found to be β-ether > phenylcoumaran (β−5′) > resinol (β−β′) facilitating a high degree of depolymerization and yielding a high frequency of free phenolics and reduced aliphatic hydroxyl groups. All side-chain interlinkages were depleted converting guaiacyl subunits into condensed forms, while still retaining uncondensed syringyl subunits. Under the mild 150°C temperature reaction, CELF lignin had higher molecular weight and retained more β-ether interlinkages. The results from CELF lignin-based polyurethane synthesis indicated that the tensile properties depended on the miscibility of CELF lignin with other components and low molecular weight cuts improved the dispersion of lignin in the polyurethane network. Pre-mixing of CELF with poly(ethylene glycol) (PEG) reduced the brittleness and improved the ductility of the CELF lignin-PEG polyurethanes.", "abstract": "Conversion of technical lignin into performance biopolymers such as polyurethane offers environmental and economic advantages when combined with production of biofuels from biomass sugars, presenting significant interest toward studying the role of pretreatment on lignin structure and functionality. Co-solvent enhanced lignocellulosic fractionation (CELF) pretreatment, employing acidic aqueous tetrahydrofuran (THF) mixtures, was developed to effectively break down the lignin-carbohydrate matrix and promote extraction of lignin from lignocellulosic biomass with desirable purity and yield. In this study, we report the effects of CELF pretreatment reaction severity on the molecular structure of CELF-extracted lignin and its impact toward the mechanical properties of the resulting lignin-based polyurethanes. Reaction temperature was found to play the most significant role, compared to reaction time and acidity, in manipulating structural features such as molecular weight, functionality and intra-polymer structure. At the severe reaction conditions at 180°C, the order of reactivity for primary lignin interlinkages characterized by semiquantitative HSQC NMR analysis were found to be β-ether > phenylcoumaran (β−5′) > resinol (β−β′) facilitating a high degree of depolymerization and yielding a high frequency of free phenolics and reduced aliphatic hydroxyl groups. All side-chain interlinkages were depleted converting guaiacyl subunits into condensed forms, while still retaining uncondensed syringyl subunits. Under the mild 150°C temperature reaction, CELF lignin had higher molecular weight and retained more β-ether interlinkages. The results from CELF lignin-based polyurethane synthesis indicated that the tensile properties depended on the miscibility of CELF lignin with other components and low molecular weight cuts improved the dispersion of lignin in the polyurethane network. Pre-mixing of CELF with poly(ethylene glycol) (PEG) reduced the brittleness and improved the ductility of the CELF lignin-PEG polyurethanes.", "date": "2020-07-07", "issue": "1", "identifier": "https://www.osti.gov/biblio/1649027", "bibliographicCitation": "https://doi.org/10.3389/fenrg.2020.00149", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "Frontiers in Energy Research", "volume": "8", "publisher_information": "Frontiers Research Foundation", "country_publication_code": "US", "creator": [ { "name": "Yunyan [Univ. of Tennessee,Knoxville,TN (United States)] Wang", "primaryContact": true }, { "name": "Priya [Univ. of California,Riverside,CA (United States)] Sengupta", "primaryContact": false }, { "name": "Brent [Univ. of California,Riverside,CA (United States)] Scheidemantle", "primaryContact": false }, { "name": "Yunqiao Joseph [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000325541447) Pu", "primaryContact": false }, { "name": "Charles E. [Univ. of California,Riverside,CA (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Wyman", "primaryContact": false }, { "name": "Charles M. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Univ. of California,Riverside,CA (United States)] Cai", "primaryContact": false }, { "name": "Arthur J. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:000000023536554X) Ragauskas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/1649027", "active": false }, { "brc": "CBI", "title": "Transgenic Poplar Designed for Biofuels", "description": "Members of the genus Populus (i.e., cottonwood, hybrid poplar) represent a promising source of lignocellulosic biomass for biofuels. However, one of the major factors negatively affecting poplar\u2019s efficient conversion to biofuel is the inherent recalcitrance to enzymatic saccharification due to cell wall components such as lignin. To this effect, there have been efforts to modify gene expression to reduce biomass recalcitrance by changing cell wall properties. Furthermore, we review recent genetic modifications of poplar that led to change cell wall properties and the resulting effects on subsequent pretreatment efficacy and saccharification. Although genetic engineering\u2019s impacts on cell wall properties are not fully predictable, recent studies have shown promising improvement in the biological conversion of transgenic poplar to biofuels.", "abstract": "Members of the genus Populus (i.e., cottonwood, hybrid poplar) represent a promising source of lignocellulosic biomass for biofuels. However, one of the major factors negatively affecting poplar\u2019s efficient conversion to biofuel is the inherent recalcitrance to enzymatic saccharification due to cell wall components such as lignin. To this effect, there have been efforts to modify gene expression to reduce biomass recalcitrance by changing cell wall properties. Furthermore, we review recent genetic modifications of poplar that led to change cell wall properties and the resulting effects on subsequent pretreatment efficacy and saccharification. Although genetic engineering\u2019s impacts on cell wall properties are not fully predictable, recent studies have shown promising improvement in the biological conversion of transgenic poplar to biofuels.", "date": "2020-05-28", "issue": "9", "identifier": "https://www.osti.gov/biblio/1649088", "bibliographicCitation": "https://doi.org/10.1016/j.tplants.2020.03.008", "keywords": [ "09 BIOMASS FUELS", "Cell wall chemistry", "Cellulose", "Gene", "Lignin", "Recalcitrance", "Saccharification", "Transgenic poplar" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Trends in Plant Science", "volume": "25", "publisher_information": "Cell Press", "country_publication_code": "US", "creator": [ { "name": "Nathan D. [University of Tennessee,Knoxville,TN (United States)] Bryant", "primaryContact": true }, { "name": "Yunqiao Joseph [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000325541447) Pu", "primaryContact": false }, { "name": "Timothy J. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000295406622) Tschaplinski", "primaryContact": false }, { "name": "Gerald A. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000301061289) Tuskan", "primaryContact": false }, { "name": "Wellington [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000202009856) Muchero", "primaryContact": false }, { "name": "Udaya C. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000259638370) Kalluri", "primaryContact": false }, { "name": "Chang Geun [State University of New York College of Environmental Science and Forestry,Syracuse,NY (United States)] Yoo", "primaryContact": false }, { "name": "Arthur J. [University of Tennessee,Knoxville,TN (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); University of Tennessee Institute of Agriculture,Knoxville,TN (United States)] (ORCID:000000023536554X) Ragauskas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1649088", "active": false }, { "brc": "CBI", "title": "The critical role of lignin in lignocellulosic biomass conversion and recent pretreatment strategies: A comprehensive review", "description": "Heterogeneity and rigidity of lignocellulose causing resistance to its deconstruction have provided technical and economic challenges in the current biomass conversion processes. Lignin has been considered as a crucial recalcitrance component in biomass utilization. An in-depth understanding of lignin properties and their influences on biomass conversion can provide clues to improve biomass utilization. Also, utilization of lignin can significantly increase the economic viability of biorefinery. Recent lignin-targeting pretreatments have aimed not only to overcome recalcitrance for biomass conversion but also to selectively fractionate lignin for lignin valorization. Numerous studies have been conducted in biomass characteristics and conversion technologies, and the role of lignin is critical for lignin valorization and biomass pretreatment development. In this review, we provide a comprehensive review of lignin-related biomass characteristics, the impact of lignin on the biological conversion of biomass, and recent lignin-targeting pretreatment strategies. The desired lignin properties in biorefinery and future pretreatment directions are also discussed.", "abstract": "Heterogeneity and rigidity of lignocellulose causing resistance to its deconstruction have provided technical and economic challenges in the current biomass conversion processes. Lignin has been considered as a crucial recalcitrance component in biomass utilization. An in-depth understanding of lignin properties and their influences on biomass conversion can provide clues to improve biomass utilization. Also, utilization of lignin can significantly increase the economic viability of biorefinery. Recent lignin-targeting pretreatments have aimed not only to overcome recalcitrance for biomass conversion but also to selectively fractionate lignin for lignin valorization. Numerous studies have been conducted in biomass characteristics and conversion technologies, and the role of lignin is critical for lignin valorization and biomass pretreatment development. In this review, we provide a comprehensive review of lignin-related biomass characteristics, the impact of lignin on the biological conversion of biomass, and recent lignin-targeting pretreatment strategies. The desired lignin properties in biorefinery and future pretreatment directions are also discussed.", "date": "2020-03-31", "issue": "1", "identifier": "https://www.osti.gov/biblio/1649140", "bibliographicCitation": "https://doi.org/10.1016/j.biortech.2020.122784", "keywords": [ "09 BIOMASS FUELS", "biorefinery", "lignin characteristics", "lignin inhibition", "lignin valorization", "recalcitrance" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Bioresource Technology", "volume": "301", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Chang Geun [State Univ. of New York (SUNY),Syracuse,NY (United States). College of Environmental Science and Forestry,Dept. of Paper and Bioprocess Engineering] Yoo", "primaryContact": true }, { "name": "Xianzhi [Univ. of Tennessee,Knoxville,TN (United States). Dept. of Chemical and Biomolecular Engineering] Meng", "primaryContact": false }, { "name": "Yunqiao Joseph [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Biosciences Division and Center for Bioenergy Innovation (CBI),Joint Inst. for Biological Sciences] (ORCID:0000000325541447) Pu", "primaryContact": false }, { "name": "Arthur J. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Biosciences Division and Center for Bioenergy Innovation (CBI),Joint Inst. for Biological Sciences; Univ. of Tennessee,Knoxville,TN (United States). Dept. of Chemical and Biomolecular Engineering and Dept. of Forestry,Wildlife and Fisheries,Center of Renewable Carbon] (ORCID:000000023536554X) Ragauskas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1649140", "active": false }, { "brc": "CBI", "title": "Engineering biosynthetic enzymes for industrial natural product synthesis", "description": "This review describes examples of the broadening industrial relevance of engineered secondary metabolism enzymes, natural products and analogs being made with these enzymes, and technology improvements that have enabled their development since 1999.", "abstract": "This review describes examples of the broadening industrial relevance of engineered secondary metabolism enzymes, natural products and analogs being made with these enzymes, and technology improvements that have enabled their development since 1999.", "date": "2020-05-03", "issue": "8", "identifier": "https://www.osti.gov/biblio/1649565", "bibliographicCitation": "https://doi.org/10.1039/c9np00071b", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "Natural Product Reports", "volume": "37", "publisher_information": "Royal Society of Chemistry", "country_publication_code": "US", "creator": [ { "name": "Stephanie [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000157122568) Galanie", "primaryContact": true }, { "name": "David [Codexis,Inc.,Redwood City,CA (United States)] (ORCID:0000000162681399) Entwistle", "primaryContact": false }, { "name": "James [Inscripta,Inc.,Pleasonton,CA (United States)] Lalonde", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1649565", "active": false }, { "brc": "CBI", "title": "Plant Hosts Modify Belowground Microbial Community Response to Extreme Drought", "description": "Drought stress negatively impacts microbial activity, yet the magnitude of stress responses is likely dependent on a diversity of belowground interactions. Populus trichocarpa individuals and no-plant bulk soils were exposed to extended drought (~0.03% gravimetric water content [GWC] after 12 days), rewet, and a 12-day \u201crecovery\u201d period to determine the effects of plant presence in mediating soil microbiome stability to water stress. Plant metabolomic analyses indicated that drought exposure increased host investment in C and N metabolic pathways (amino acids, fatty acids, phenolic glycosides) regardless of recovery. Several metabolites positively correlated with root-associated microbial alpha-diversity, but not those of soil communities. Soil bacterial community composition shifted with P. trichocarpa presence and with drought relative to irrigated controls, whereas soil fungal composition shifted only with plant presence. However, root fungal communities strongly shifted with drought, whereas root bacterial communities changed to a lesser degree. The proportion of bacterial water-stress opportunistic operational taxonomic units (OTUs) (enriched counts in drought) was high (~11%) at the end of drying phases and maintained after rewet and recovery phases in bulk soils, but it declined over time in soils with plants present. For root fungi, opportunistic OTUs were high at the end of recovery in drought treatments (~17% abundance), although relatively not responsive in soils, particularly planted soils (<0.5% abundance for sensitive or opportunistic). These data indicate that plants modulate soil and root-associated microbial drought responses via tight plant-microbe linkages during extreme drought scenarios, but trajectories after extreme drought vary with plant habitat and microbial functional groups.", "abstract": "Drought stress negatively impacts microbial activity, yet the magnitude of stress responses is likely dependent on a diversity of belowground interactions. Populus trichocarpa individuals and no-plant bulk soils were exposed to extended drought (~0.03% gravimetric water content [GWC] after 12 days), rewet, and a 12-day \u201crecovery\u201d period to determine the effects of plant presence in mediating soil microbiome stability to water stress. Plant metabolomic analyses indicated that drought exposure increased host investment in C and N metabolic pathways (amino acids, fatty acids, phenolic glycosides) regardless of recovery. Several metabolites positively correlated with root-associated microbial alpha-diversity, but not those of soil communities. Soil bacterial community composition shifted with P. trichocarpa presence and with drought relative to irrigated controls, whereas soil fungal composition shifted only with plant presence. However, root fungal communities strongly shifted with drought, whereas root bacterial communities changed to a lesser degree. The proportion of bacterial water-stress opportunistic operational taxonomic units (OTUs) (enriched counts in drought) was high (~11%) at the end of drying phases and maintained after rewet and recovery phases in bulk soils, but it declined over time in soils with plants present. For root fungi, opportunistic OTUs were high at the end of recovery in drought treatments (~17% abundance), although relatively not responsive in soils, particularly planted soils (<0.5% abundance for sensitive or opportunistic). These data indicate that plants modulate soil and root-associated microbial drought responses via tight plant-microbe linkages during extreme drought scenarios, but trajectories after extreme drought vary with plant habitat and microbial functional groups.", "date": "2020-06-29", "issue": "3", "identifier": "https://www.osti.gov/biblio/1649570", "bibliographicCitation": "https://doi.org/10.1128/msystems.00092-20", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "mSystems", "volume": "5", "publisher_information": "American Society for Microbiology", "country_publication_code": "US", "creator": [ { "name": "Allison M. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000198453558) Veach", "primaryContact": true }, { "name": "Huaihai [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000221211822) Chen", "primaryContact": false }, { "name": "Zamin Koo [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Yang", "primaryContact": false }, { "name": "Nancy L. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000302907987) Engle", "primaryContact": false }, { "name": "Timothy [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000295406622) Tschaplinski", "primaryContact": false }, { "name": "Christopher Warren [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000187592448) Schadt", "primaryContact": false }, { "name": "Melissa [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:000000018329366X) Cregger", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1649570", "active": false }, { "brc": "CBI", "title": "Robust paths to net greenhouse gas mitigation and negative emissions via advanced biofuels", "description": "Biofuel and bioenergy systems are integral to most climate stabilization scenarios for displacement of transport sector fossil fuel use and for producing negative emissions via carbon capture and storage (CCS). However, the net greenhouse gas mitigation benefit of such pathways is controversial due to concerns around ecosystem carbon losses from land use change and foregone sequestration benefits from alternative land uses. Here, we couple bottom-up ecosystem simulation with models of cellulosic biofuel production and CCS in order to track ecosystem and supply chain carbon flows for current and future biofuel systems, with comparison to competing land-based biological mitigation schemes. Analyzing three contrasting US case study sites, we show that on land transitioning out of crops or pasture, switchgrass cultivation for cellulosic ethanol production has per-hectare mitigation potential comparable to reforestation and severalfold greater than grassland restoration. In contrast, harvesting and converting existing secondary forest at those sites incurs large initial carbon debt requiring long payback periods. We also highlight how plausible future improvements in energy crop yields and biorefining technology together with CCS would achieve mitigation potential 4 and 15 times greater than forest and grassland restoration, respectively. Finally, we show that recent estimates of induced land use change are small relative to the opportunities for improving system performance that we quantify here. While climate and other ecosystem service benefits cannot be taken for granted from cellulosic biofuel deployment, our scenarios illustrate how conventional and carbon-negative biofuel systems could make a near-term, robust, and distinctive contribution to the climate challenge.
", "abstract": "Biofuel and bioenergy systems are integral to most climate stabilization scenarios for displacement of transport sector fossil fuel use and for producing negative emissions via carbon capture and storage (CCS). However, the net greenhouse gas mitigation benefit of such pathways is controversial due to concerns around ecosystem carbon losses from land use change and foregone sequestration benefits from alternative land uses. Here, we couple bottom-up ecosystem simulation with models of cellulosic biofuel production and CCS in order to track ecosystem and supply chain carbon flows for current and future biofuel systems, with comparison to competing land-based biological mitigation schemes. Analyzing three contrasting US case study sites, we show that on land transitioning out of crops or pasture, switchgrass cultivation for cellulosic ethanol production has per-hectare mitigation potential comparable to reforestation and severalfold greater than grassland restoration. In contrast, harvesting and converting existing secondary forest at those sites incurs large initial carbon debt requiring long payback periods. We also highlight how plausible future improvements in energy crop yields and biorefining technology together with CCS would achieve mitigation potential 4 and 15 times greater than forest and grassland restoration, respectively. Finally, we show that recent estimates of induced land use change are small relative to the opportunities for improving system performance that we quantify here. While climate and other ecosystem service benefits cannot be taken for granted from cellulosic biofuel deployment, our scenarios illustrate how conventional and carbon-negative biofuel systems could make a near-term, robust, and distinctive contribution to the climate challenge.
", "date": "2020-08-23", "issue": "36", "identifier": "https://www.osti.gov/biblio/1650388", "bibliographicCitation": "https://doi.org/10.1073/pnas.1920877117", "keywords": [ "54 ENVIRONMENTAL SCIENCES", "BECCS", "biofuels", "ecosystem modeling", "life cycle assessment", "negative emissions" ], "topic": [ "Environmental Science & Sustainability" ], "journal_name": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "117", "publisher_information": "National Academy of Sciences", "country_publication_code": "US", "creator": [ { "name": "John L. (ORCID:0000000344518947) Field", "primaryContact": true }, { "name": "Tom L. Richard", "primaryContact": false }, { "name": "Erica A. H. (ORCID:0000000334972011) Smithwick", "primaryContact": false }, { "name": "Hao Cai", "primaryContact": false }, { "name": "Mark S. Laser", "primaryContact": false }, { "name": "David S. (ORCID:000000017228053X) LeBauer", "primaryContact": false }, { "name": "Stephen P. (ORCID:0000000285017164) Long", "primaryContact": false }, { "name": "Keith Paustian", "primaryContact": false }, { "name": "Zhangcai (ORCID:0000000194144854) Qin", "primaryContact": false }, { "name": "John J. (ORCID:0000000349536634) Sheehan", "primaryContact": false }, { "name": "Pete (ORCID:0000000237841124) Smith", "primaryContact": false }, { "name": "Michael Q. Wang", "primaryContact": false }, { "name": "Lee R. (ORCID:000000025642668X) Lynd", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "Energy Biosciences Institute" } }, { "fundingOrganization": { "organizationName": "Link Foundation" } }, { "fundingOrganization": { "organizationName": "National Institute of Food and Agriculture (NIFA)" } }, { "fundingOrganization": { "organizationName": "Sao Paulo Research Foundation (FAPESP)" } }, { "fundingOrganization": { "organizationName": "USDA" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1650388", "active": false }, { "brc": "CBI", "title": "21st\u2010century biogeochemical modeling: Challenges for Century\u2010based models and where do we go from here?", "description": "Not Available", "abstract": "Not Available", "date": "2020-08-24", "identifier": "https://www.osti.gov/biblio/1650409", "bibliographicCitation": "https://doi.org/10.1111/gcbb.12730", "keywords": [ "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "59 BASIC BIOLOGICAL SCIENCES", "Bioenergy", "Biogeochemical modeling", "Drought", "N2O", "Plant age dynamics", "Soil", "bioenergy", "biogeochemical modeling", "drought", "plant age dynamics", "soil" ], "topic": [ "Chemistry", "Microbiology" ], "journal_name": "Global Change Biology. Bioenergy", "publisher_information": "Wiley", "country_publication_code": "GB", "creator": [ { "name": "Danielle [Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois at Champaign\u2010Urbana Urbana IL USA; Department of Forest,Rangeland,and Fire Sciences University of Idaho Moscow ID USA] (ORCID:0000000314143080) Berardi", "primaryContact": true }, { "name": "Edward [Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois at Champaign\u2010Urbana Urbana IL USA; Department of Biology West Virginia University Morgantown WV USA] Brzostek", "primaryContact": false }, { "name": "Elena [Institute for Sustainability,Energy and Environment University of Illinois at Champaign\u2010Urbana Urbana IL USA] Blanc\u2010Betes", "primaryContact": false }, { "name": "Brian [Center for Bioenergy Innovation Oak Ridge National Laboratory Oak Ridge TN USA] Davison", "primaryContact": false }, { "name": "Evan H. [Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois at Champaign\u2010Urbana Urbana IL USA; Institute for Sustainability,Energy and Environment University of Illinois at Champaign\u2010Urbana Urbana IL USA] (ORCID:0000000334006286) DeLucia", "primaryContact": false }, { "name": "Melannie D. [Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois at Champaign\u2010Urbana Urbana IL USA; Natural Resource Ecology Laboratory Colorado State University Fort Collins CO USA] Hartman", "primaryContact": false }, { "name": "Jeffrey [Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois at Champaign\u2010Urbana Urbana IL USA; Department of Forest,Rangeland,and Fire Sciences University of Idaho Moscow ID USA] Kent", "primaryContact": false }, { "name": "William J. [Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois at Champaign\u2010Urbana Urbana IL USA; Natural Resource Ecology Laboratory Colorado State University Fort Collins CO USA] Parton", "primaryContact": false }, { "name": "Debasish [Biosystems,Engineering,and Soil Science University of Tennessee Knoxville TN USA] (ORCID:000000019425675X) Saha", "primaryContact": false }, { "name": "Tara W. [Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois at Champaign\u2010Urbana Urbana IL USA; Department of Forest,Rangeland,and Fire Sciences University of Idaho Moscow ID USA] (ORCID:0000000344221510) Hudiburg", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1650409", "active": false }, { "brc": "CBI", "title": "Natural deep eutectic solvent mediated extrusion for continuous high-solid pretreatment of lignocellulosic biomass", "description": "Several deep eutectic solvents (DESs) have been demonstrated to be highly effective for lignocellulosic biomass pretreatment, combining the advantages of simple synthesis, relatively low chemical cost and better biocompatibility. However, low biomass loading that is usually involved with DES pretreatment hinders its practical use. Here, a twin-screw extruder was used for pretreating biomass sorghum bagasse at solid loadings up to 50%, mediated by a neutral-pH DES, choline chloride : glycerol (ChCl : Gly). This continuous extrusion process led to high glucose and xylose yields of >85% from enzymatic saccharification of the pretreated sorghum. A combination of microscopic, spectroscopic, and X-ray diffraction analyses demonstrate a high degree of defibration and disruption of the biomass cell wall structures; however, little or no change in chemical compositions. Further results from gel permeation chromatographic (GPC) and nuclear magnetic resonance (NMR) spectroscopic analyses indicate that ChCl : Gly-mediated extrusion preserved the basic lignin structural characteristics with no significant differences between extruded biomass at a solid loading of 30% and 50%. This study demonstrates the potential of DES-mediated extrusion as a highly effective continuous high-solid biomass pretreatment technology for industrially relevant applications.", "abstract": "Several deep eutectic solvents (DESs) have been demonstrated to be highly effective for lignocellulosic biomass pretreatment, combining the advantages of simple synthesis, relatively low chemical cost and better biocompatibility. However, low biomass loading that is usually involved with DES pretreatment hinders its practical use. Here, a twin-screw extruder was used for pretreating biomass sorghum bagasse at solid loadings up to 50%, mediated by a neutral-pH DES, choline chloride : glycerol (ChCl : Gly). This continuous extrusion process led to high glucose and xylose yields of >85% from enzymatic saccharification of the pretreated sorghum. A combination of microscopic, spectroscopic, and X-ray diffraction analyses demonstrate a high degree of defibration and disruption of the biomass cell wall structures; however, little or no change in chemical compositions. Further results from gel permeation chromatographic (GPC) and nuclear magnetic resonance (NMR) spectroscopic analyses indicate that ChCl : Gly-mediated extrusion preserved the basic lignin structural characteristics with no significant differences between extruded biomass at a solid loading of 30% and 50%. This study demonstrates the potential of DES-mediated extrusion as a highly effective continuous high-solid biomass pretreatment technology for industrially relevant applications.", "date": "2020-07-06", "issue": "16", "identifier": "https://www.osti.gov/biblio/1651282", "bibliographicCitation": "https://doi.org/10.1039/d0gc01560a", "keywords": [ "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY" ], "topic": [ "Chemistry" ], "journal_name": "Green Chemistry", "volume": "22", "publisher_information": "Royal Society of Chemistry", "country_publication_code": "US", "creator": [ { "name": "Binling [Chinese Academy of Tropical Agricultural Sciences,Haikou (China). Haikou Experimental Station; Univ. of Kentucky,Lexington,KY (United States). Biosystems and Agricultural Engineering] (ORCID:0000000309967608) Ai", "primaryContact": true }, { "name": "Wenqi [Univ. of Kentucky,Lexington,KY (United States). Biosystems and Agricultural Engineering] (ORCID:0000000312466919) Li", "primaryContact": false }, { "name": "Joseph [Univ. of Kentucky,Lexington,KY (United States). Biosystems and Agricultural Engineering] (ORCID:0000000194996563) Woomer", "primaryContact": false }, { "name": "Mi [Univ. of Tennessee,Knoxville,TN (United States). Dept. of Forestry,Wildlife,and Fisheries,Center for Renewable Carbon] Li", "primaryContact": false }, { "name": "Yunqiao [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Joint Institute for Biological Sciences (JICS),Center for BioEnergy Innovation,Biosciences Division] (ORCID:0000000325541447) Pu", "primaryContact": false }, { "name": "Zhanwu [Chinese Academy of Tropical Agricultural Sciences,Haikou (China). Haikou Experimental Station] Sheng", "primaryContact": false }, { "name": "Lili [Chinese Academy of Tropical Agricultural Sciences,Haikou (China). Haikou Experimental Station] Zheng", "primaryContact": false }, { "name": "Akinbode [Univ. of Kentucky,Lexington,KY (United States). Biosystems and Agricultural Engineering] Adedeji", "primaryContact": false }, { "name": "Arthur J. [Univ. of Tennessee,Knoxville,TN (United States). Dept. of Forestry,Wildlife,and Fisheries,Center for Renewable Carbon and Dept. of Chemical and Biomolecular Engineering; Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Joint Institute for Biological Sciences (JICS),Center for BioEnergy Innovation,Biosciences Division] (ORCID:000000023536554X) Ragauskas", "primaryContact": false }, { "name": "Jian [Univ. of Kentucky,Lexington,KY (United States). Biosystems and Agricultural Engineering] (ORCID:0000000330224446) Shi", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "Central Public-interest Scientific Institution Basal Research Fund for Chinese Academy of Tropical Agricultural Sciences" } }, { "fundingOrganization": { "organizationName": "Chinese Scholarship Council" } }, { "fundingOrganization": { "organizationName": "National Natural Science Foundation of China (NNSFC)" } }, { "fundingOrganization": { "organizationName": "USDA" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1651282", "active": false }, { "brc": "CBI", "title": "A biomass pretreatment using cellulose-derived solvent Cyrene", "description": "Despite only recently becoming available in the quantities required for solvent usage, the cellulose-derived solvent, named Cyrene, has gained significant attention in green chemistry in recent years. To fulfill the sustainability criteria of future biorefineries, a novel renewable biomass pretreatment using Cyrene and water was developed for the first time. Results showed that Cyrene has high potential as a green pretreatment solvent in terms of lignin fractionation/recovery and sugar release in the follow-up enzymatic hydrolysis. The mechanism of this pretreatment was revealed by investigating the structural characteristics of pretreated biomass, and the recovered lignin was also fully characterized to assess its valorization potential. Results indicated that Cyrene pretreatment could be performed at a mild condition (120 \u00b0C) to reduce the lignin condensation and the cleavage of \u03b2-O-4 linkages without compromising lignin removal and the following sugar platform. The successful utilization of this cellulose-derived solvent in pretreatment will further contribute to the realization of a \u201cclosed-loop\u201d biorefinery process.", "abstract": "Despite only recently becoming available in the quantities required for solvent usage, the cellulose-derived solvent, named Cyrene, has gained significant attention in green chemistry in recent years. To fulfill the sustainability criteria of future biorefineries, a novel renewable biomass pretreatment using Cyrene and water was developed for the first time. Results showed that Cyrene has high potential as a green pretreatment solvent in terms of lignin fractionation/recovery and sugar release in the follow-up enzymatic hydrolysis. The mechanism of this pretreatment was revealed by investigating the structural characteristics of pretreated biomass, and the recovered lignin was also fully characterized to assess its valorization potential. Results indicated that Cyrene pretreatment could be performed at a mild condition (120 \u00b0C) to reduce the lignin condensation and the cleavage of \u03b2-O-4 linkages without compromising lignin removal and the following sugar platform. The successful utilization of this cellulose-derived solvent in pretreatment will further contribute to the realization of a \u201cclosed-loop\u201d biorefinery process.", "date": "2020-04-06", "issue": "9", "identifier": "https://www.osti.gov/biblio/1651291", "bibliographicCitation": "https://doi.org/10.1039/D0GC00661K", "keywords": [ "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY" ], "topic": [ "Chemistry" ], "journal_name": "Green Chemistry", "volume": "22", "publisher_information": "Royal Society of Chemistry", "country_publication_code": "US", "creator": [ { "name": "Xianzhi [Univ. of Tennessee,Knoxville,TN (United States)] Meng", "primaryContact": true }, { "name": "Yunqiao Joseph [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000325541447) Pu", "primaryContact": false }, { "name": "Mi [Univ. of Tennessee,Knoxville,TN (United States)] Li", "primaryContact": false }, { "name": "Arthur J. [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:000000023536554X) Ragauskas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1651291", "active": false }, { "brc": "CBI", "title": "Adaptive laboratory evolution of Pseudomonas putida KT2440 improves p-coumaric and ferulic acid catabolism and tolerance", "description": "Not Available", "abstract": "Not Available", "date": "2020-11-30", "issue": "C", "identifier": "https://www.osti.gov/biblio/1658976", "bibliographicCitation": "https://doi.org/10.1016/j.mec.2020.e00143", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "Microbial lignin conversion", "Pseudomonas putida KT2440", "adaptive laboratory evolution", "hydroxycinnamic acids", "microbial lignin conversion" ], "topic": [ "Microbiology" ], "journal_name": "Metabolic Engineering Communications", "volume": "11", "publisher_information": "Elsevier", "country_publication_code": "Netherlands", "creator": [ { "name": "Elsayed T. Mohamed", "primaryContact": true }, { "name": "Allison Z. Werner", "primaryContact": false }, { "name": "Davinia Salvach\u00faa", "primaryContact": false }, { "name": "Christine A. Singer", "primaryContact": false }, { "name": "Kiki Szostkiewicz", "primaryContact": false }, { "name": "Manuel Rafael Jim\u00e9nez-D\u00edaz", "primaryContact": false }, { "name": "Thomas Eng", "primaryContact": false }, { "name": "Mohammad S. Radi", "primaryContact": false }, { "name": "Blake A. Simmons", "primaryContact": false }, { "name": "Aindrila Mukhopadhyay", "primaryContact": false }, { "name": "Markus J. Herrg\u00e5rd", "primaryContact": false }, { "name": "Steven W. Singer", "primaryContact": false }, { "name": "Gregg T. Beckham", "primaryContact": false }, { "name": "Adam M. Feist", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "The Novo Nordisk Foundation" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1658976", "active": false, "has_related_ids": [ "NREL/JA--2800-77969" ] }, { "brc": "CBI", "title": "Biomass Recalcitrance in Willow Under Two Biological Conversion Paradigms: Enzymatic Hydrolysis and Anaerobic Digestion", "description": "Biomass recalcitrance, the inherent resistance of plants towards deconstruction, negatively affects the viability of biorefineries. This trait is not only dictated by the properties of the biomass but also by the conversion system used and its interactions with specific features of the biomass. Here, biomass recalcitrance to anaerobic digestion (AD) was assessed using a biomethanation potential (BMP) assay. Plant material (n = 94) was selected from a large population of natural Salix viminalis accessions, previously evaluated for biomass recalcitrance using hydrothermal pretreatment-enzymatic hydrolysis. Correlations between yields from the two biological conversion systems were evaluated, as well as the influence of biomass compositional features, analyzed by pyrolysis-molecular beam mass spectrometry (py-MBMS), and other biomass physical properties on conversion performance. BMP values averaged 198.0 Nml CH4/g biomass after 94 days, ranging from 28.6 to 245.9. S lignin and carbohydrate-derived spectral features were positively correlated with performance under both systems, whereas G lignin, p-coumaric acid, and ferulic acid-derived ions were negatively correlated with yields and rates. Most spectral features were more strongly correlated with enzymatic hydrolysis yields compared to methane production. For early-stage methane production and rate, recalcitrance factors were similar compared to enzymatic hydrolysis, with weaker correlations observed at later timepoints. The results suggest that although variation in methane potential was considerably lower than enzymatic hydrolysis yields, a reduced recalcitrance under this system will still be of importance to improve early conversion rates. Spectral features of low methane-producing samples indicate the presence of inhibitory substances, warranting further study.", "abstract": "Biomass recalcitrance, the inherent resistance of plants towards deconstruction, negatively affects the viability of biorefineries. This trait is not only dictated by the properties of the biomass but also by the conversion system used and its interactions with specific features of the biomass. Here, biomass recalcitrance to anaerobic digestion (AD) was assessed using a biomethanation potential (BMP) assay. Plant material (n = 94) was selected from a large population of natural Salix viminalis accessions, previously evaluated for biomass recalcitrance using hydrothermal pretreatment-enzymatic hydrolysis. Correlations between yields from the two biological conversion systems were evaluated, as well as the influence of biomass compositional features, analyzed by pyrolysis-molecular beam mass spectrometry (py-MBMS), and other biomass physical properties on conversion performance. BMP values averaged 198.0 Nml CH4/g biomass after 94 days, ranging from 28.6 to 245.9. S lignin and carbohydrate-derived spectral features were positively correlated with performance under both systems, whereas G lignin, p-coumaric acid, and ferulic acid-derived ions were negatively correlated with yields and rates. Most spectral features were more strongly correlated with enzymatic hydrolysis yields compared to methane production. For early-stage methane production and rate, recalcitrance factors were similar compared to enzymatic hydrolysis, with weaker correlations observed at later timepoints. The results suggest that although variation in methane potential was considerably lower than enzymatic hydrolysis yields, a reduced recalcitrance under this system will still be of importance to improve early conversion rates. Spectral features of low methane-producing samples indicate the presence of inhibitory substances, warranting further study.", "date": "2019-12-06", "identifier": "https://www.osti.gov/biblio/1659772", "bibliographicCitation": "https://doi.org/10.1007/s12155-019-10079-6", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "Salix viminalis", "anaerobic digestion", "analytical pyrolysis", "biomass recalcitrance", "biomethanation potential", "enzymatic hydrolysis" ], "topic": [ "Microbiology" ], "journal_name": "BioEnergy Research", "volume": "13", "publisher_information": "Springer", "country_publication_code": "US", "creator": [ { "name": "Anne [National Renewable Energy Lab. (NREL),Golden,CO (United States). Biosciences Center,Center for Bioenergy Innovation] Ware", "primaryContact": true }, { "name": "Jonas A. [Swedish Univ. of Agricultural Sciences,Uppsala (Sweden)] Ohlsson", "primaryContact": false }, { "name": "Mats [Swedish Univ. of Agricultural Sciences,Uppsala (Sweden)] Sandgren", "primaryContact": false }, { "name": "Anna [Swedish Univ. of Agricultural Sciences,Uppsala (Sweden)] Schnurer", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "Swedish Research Council" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1659772", "active": false, "has_related_ids": [ "NREL/JA--2700-74548" ] }, { "brc": "CBI", "title": "High-Throughput Switchgrass Phenotyping and Biomass Modeling by UAV", "description": "Not Available", "abstract": "Not Available", "date": "2020-10-19", "identifier": "https://www.osti.gov/biblio/1678775", "bibliographicCitation": "https://doi.org/10.3389/fpls.2020.574073", "keywords": [ "09 BIOMASS FUELS", "59 BASIC BIOLOGICAL SCIENCES", "LiDAR", "Nitrogen", "biomass", "phenotype", "spectral index" ], "topic": [ "Biomass & Feedstock", "Microbiology" ], "journal_name": "Frontiers in Plant Science", "volume": "11", "publisher_information": "Frontiers Media SA", "country_publication_code": "Switzerland", "creator": [ { "name": "Fei Li", "primaryContact": true }, { "name": "Cristiano Piasecki", "primaryContact": false }, { "name": "Reginald J. Millwood", "primaryContact": false }, { "name": "Benjamin Wolfe", "primaryContact": false }, { "name": "Mitra Mazarei", "primaryContact": false }, { "name": "Jr.,C. Neal Stewart", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1678775", "active": false }, { "brc": "CBI", "title": "Thermodynamic analysis of the pathway for ethanol production from cellobiose in Clostridium thermocellum", "description": "Not Available", "abstract": "Not Available", "date": "2019-08-31", "issue": "C", "identifier": "https://www.osti.gov/biblio/1694035", "bibliographicCitation": "https://doi.org/10.1016/j.ymben.2019.06.006", "topic": [ "Unknown" ], "journal_name": "Metabolic Engineering", "volume": "55", "publisher_information": "Elsevier", "country_publication_code": "Belgium", "creator": [ { "name": "Satyakam Dash", "primaryContact": true }, { "name": "Daniel G. Olson", "primaryContact": false }, { "name": "Siu Hung Joshua Chan", "primaryContact": false }, { "name": "Daniel Amador-Noguez", "primaryContact": false }, { "name": "Lee R. Lynd", "primaryContact": false }, { "name": "Costas D. Maranas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/1694035", "active": false }, { "brc": "CBI", "title": "The effect of switchgrass plant cell wall properties on its deconstruction by thermochemical pretreatments coupled with fungal enzymatic hydrolysis or Clostridium thermocellum consolidated bioprocessing", "description": "A combination of thermochemical pretreatment and biological digestion technologies is usually required to overcome lignocellulosic recalcitrance and accomplish effective biomass deconstruction. In this study, we aimed to understand switchgrass breakdown by hydrothermal, dilute acid, dilute alkali, and co-solvent enhanced lignocellulosic fractionation (CELF) pretreatments followed by application of traditional fungal enzymatic hydrolysis (EH) and Clostridium thermocellum consolidated bioprocessing (CBP) to the resulting solids. Unpretreated and pretreated switchgrass and their EH and CBP residues were characterized by a suite of analytical techniques to understand structural changes that occurred during deconstruction. CELF pretreated solids showed the highest accessibility and digestibility by both EH and CBP followed by dilute alkali and then dilute acid/hydrothermal pretreated solids. Lignin removal from biomass had a more positive impact on substrate accessibility and digestibility than did xylan removal, while xyloglucan removal by pretreatment appeared essential for cellulose digestion by fungal enzymes. The extent of CBP digestion of cellulose and non-cellulosic glycans was larger than that by EH. Unlike dilute alkali pretreatment, cellulose crystallinity increased for acid-based pretreatments in the following order: hydrothermal, dilute acid, and CELF. Acid-based pretreatments also substantially reduced cellulose degree of polymerization. All thermochemical and biological digestion approaches increased syringyl to guaiacyl lignin (S/G) ratio and reduced \u03b2-O-4 lignin interunit linkage and hydroxycinnamates content from levels in unpretreated switchgrass. The substantial increase in S/G ratio after hydrothermal and dilute alkali preatreatments suggested that high temperatures or alkali removed a large portion of G lignin from switchgrass.", "abstract": "A combination of thermochemical pretreatment and biological digestion technologies is usually required to overcome lignocellulosic recalcitrance and accomplish effective biomass deconstruction. In this study, we aimed to understand switchgrass breakdown by hydrothermal, dilute acid, dilute alkali, and co-solvent enhanced lignocellulosic fractionation (CELF) pretreatments followed by application of traditional fungal enzymatic hydrolysis (EH) and Clostridium thermocellum consolidated bioprocessing (CBP) to the resulting solids. Unpretreated and pretreated switchgrass and their EH and CBP residues were characterized by a suite of analytical techniques to understand structural changes that occurred during deconstruction. CELF pretreated solids showed the highest accessibility and digestibility by both EH and CBP followed by dilute alkali and then dilute acid/hydrothermal pretreated solids. Lignin removal from biomass had a more positive impact on substrate accessibility and digestibility than did xylan removal, while xyloglucan removal by pretreatment appeared essential for cellulose digestion by fungal enzymes. The extent of CBP digestion of cellulose and non-cellulosic glycans was larger than that by EH. Unlike dilute alkali pretreatment, cellulose crystallinity increased for acid-based pretreatments in the following order: hydrothermal, dilute acid, and CELF. Acid-based pretreatments also substantially reduced cellulose degree of polymerization. All thermochemical and biological digestion approaches increased syringyl to guaiacyl lignin (S/G) ratio and reduced \u03b2-O-4 lignin interunit linkage and hydroxycinnamates content from levels in unpretreated switchgrass. The substantial increase in S/G ratio after hydrothermal and dilute alkali preatreatments suggested that high temperatures or alkali removed a large portion of G lignin from switchgrass.", "date": "2020-10-27", "issue": "N/A", "identifier": "https://www.osti.gov/biblio/1706247", "bibliographicCitation": "https://doi.org/10.1039/d0gc02546a", "keywords": [ "09 BIOMASS FUELS", "Clostridium thermocellum", "bioethanol", "consolidated bioprocessing", "enzymatic hydrolysis", "fungal enzymes", "lignocellulosic biomass", "pretreatment", "switchgrass" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Green Chemistry", "volume": "N/A", "publisher_information": "Royal Society of Chemistry", "country_publication_code": "US", "creator": [ { "name": "Ninad [Univ. of California,Riverside,CA (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000238480818) Kothari", "primaryContact": true }, { "name": "Samarthya [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000294951880) Bhagia", "primaryContact": false }, { "name": "Yunqiao Joseph [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000325541447) Pu", "primaryContact": false }, { "name": "Chang Geun [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); State Univ. of New York (SUNY),Syracuse,NY (United States)] (ORCID:0000000261792414) Yoo", "primaryContact": false }, { "name": "Mi [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000175231266) Li", "primaryContact": false }, { "name": "Sivasankari [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Univ. of Georgia,Athens,GA (United States)] Venketachalam", "primaryContact": false }, { "name": "Sivakumar [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Univ. of Georgia,Athens,GA (United States)] Pattathil", "primaryContact": false }, { "name": "Rajeev [Univ. of California,Riverside,CA (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000175230108) Kumar", "primaryContact": false }, { "name": "Charles M. [Univ. of California,Riverside,CA (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Cai", "primaryContact": false }, { "name": "Michael G. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Univ. of Georgia,Athens,GA (United States)] (ORCID:0000000321365191) Hahn", "primaryContact": false }, { "name": "Arthur J. [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:000000023536554X) Ragauskas", "primaryContact": false }, { "name": "Charles E. [Univ. of California,Riverside,CA (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000279852841) Wyman", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1706247", "active": false }, { "brc": "CBI", "title": "Metabolic Fluxes of Nitrogen and Pyrophosphate in Chemostat Cultures of Clostridium thermocellum and Thermoanaerobacterium saccharolyticum", "description": "\n This study discusses the fate of pyrophosphate in the metabolism of two thermophilic anaerobes that lack a soluble irreversible pyrophosphatase as present in\n
\n This study discusses the fate of pyrophosphate in the metabolism of two thermophilic anaerobes that lack a soluble irreversible pyrophosphatase as present in\n
With these guidelines, we aim to unite the lignin-first biorefining research field around best practices for performing or reporting feedstock analysis, reactor design, catalyst performance, and product yields.
", "abstract": "With these guidelines, we aim to unite the lignin-first biorefining research field around best practices for performing or reporting feedstock analysis, reactor design, catalyst performance, and product yields.
", "date": "2021-01-25", "issue": "1", "identifier": "https://www.osti.gov/biblio/1712788", "bibliographicCitation": "https://doi.org/10.1039/D0EE02870C", "keywords": [ "09 BIOMASS FUELS", "birefining", "lignin" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Energy & Environmental Science", "volume": "14", "publisher_information": "Royal Society of Chemistry", "country_publication_code": "GB", "creator": [ { "name": "Mahdi M. [Department of Chemical Engineering and Department of Chemistry & Biochemistry,University of California,Santa Barbara,USA] (ORCID:0000000244121985) Abu-Omar", "primaryContact": true }, { "name": "Katalin [Stratingh Institute for Chemistry,University of Groningen,9747 AG Groningen,The Netherlands] (ORCID:0000000280464248) Barta", "primaryContact": false }, { "name": "Gregg T. [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,Golden,USA,Center for Bioenergy Innovation,Oak Ridge] (ORCID:000000023480212X) Beckham", "primaryContact": false }, { "name": "Jeremy S. [Laboratory of Sustainable and Catalytic Processing,Institute of Chemical Sciences and Engineering,\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL),CH-1015 Lausanne,Switzerland] (ORCID:0000000209670583) Luterbacher", "primaryContact": false }, { "name": "John [U.S. Department of Energy Great Lakes Bioenergy Research Center,University of Wisconsin-Madison,Madison,USA] (ORCID:0000000260934521) Ralph", "primaryContact": false }, { "name": "Roberto [Department of Chemical Engineering,Imperial College London,London SW7 2AZ,UK] (ORCID:0000000271754972) Rinaldi", "primaryContact": false }, { "name": "Yuriy [Department of Chemical Engineering,MIT,Cambridge,USA] (ORCID:0000000200254233) Rom\u00e1n-Leshkov", "primaryContact": false }, { "name": "Joseph S. M. [Department of Organic Chemistry,Stockholm University,SE-106 91 Stockholm,Sweden] (ORCID:0000000187355397) Samec", "primaryContact": false }, { "name": "Bert F. [Center for Sustainable Catalysis and Engineering,KU Leuven,3001 Leuven,Belgium] (ORCID:0000000196571710) Sels", "primaryContact": false }, { "name": "Feng [State Key Laboratory of Catalysis,Dalian National Laboratory for Clean Energy,Dalian Institute of Chemical Physics,Chinese Academy of Sciences,Dalian] (ORCID:0000000291678743) Wang", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "European Research Council (ERC)" } }, { "fundingOrganization": { "organizationName": "National Natural Science Foundation of China (NNSFC)" } }, { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Bioenergy Technologies Office" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1712788", "active": false, "has_related_ids": [ "NREL/JA--2A00-78122" ] }, { "brc": "CBI", "title": "Recent Advances in the Application of Functionalized Lignin in Value-Added Polymeric Materials", "description": "The quest for converting lignin into high-value products has been continuously pursued in the past few decades. In its native form, lignin is a group of heterogeneous polymers comprised of phenylpropanoids. The major commercial lignin streams, including Kraft lignin, lignosulfonates, soda lignin and organosolv lignin, are produced from industrial processes including the paper and pulping industry and emerging lignocellulosic biorefineries. Although lignin has been viewed as a low-cost and renewable feedstock to replace petroleum-based materials, its utilization in polymeric materials has been suppressed due to the low reactivity and inherent physicochemical properties of lignin. Hence, various lignin modification strategies have been developed to overcome these problems. Herein, we review recent progress made in the utilization of functionalized lignins in commodity polymers including thermoset resins, blends/composites, grafted functionalized copolymers and carbon fiber precursors. In the synthesis of thermoset resins such as polyurethane, phenol-formaldehyde and epoxy, they are covalently incorporated into the polymer matrix, and the discussion is focused on chemical modifications improving the reactivity of technical lignins. In blends/composites, functionalization of technical lignins is based upon tuning the intermolecular forces between polymer components. In addition, grafted functional polymers have expanded the utilization of lignin-based copolymers to biomedical materials and value-added additives. Different modification approaches have also been applied to facilitate the application of lignin as carbon fiber precursors, heavy metal adsorbents and nanoparticles. These emerging fields will create new opportunities in cost-effectively integrating the lignin valorization into lignocellulosic biorefineries.
", "abstract": "The quest for converting lignin into high-value products has been continuously pursued in the past few decades. In its native form, lignin is a group of heterogeneous polymers comprised of phenylpropanoids. The major commercial lignin streams, including Kraft lignin, lignosulfonates, soda lignin and organosolv lignin, are produced from industrial processes including the paper and pulping industry and emerging lignocellulosic biorefineries. Although lignin has been viewed as a low-cost and renewable feedstock to replace petroleum-based materials, its utilization in polymeric materials has been suppressed due to the low reactivity and inherent physicochemical properties of lignin. Hence, various lignin modification strategies have been developed to overcome these problems. Herein, we review recent progress made in the utilization of functionalized lignins in commodity polymers including thermoset resins, blends/composites, grafted functionalized copolymers and carbon fiber precursors. In the synthesis of thermoset resins such as polyurethane, phenol-formaldehyde and epoxy, they are covalently incorporated into the polymer matrix, and the discussion is focused on chemical modifications improving the reactivity of technical lignins. In blends/composites, functionalization of technical lignins is based upon tuning the intermolecular forces between polymer components. In addition, grafted functional polymers have expanded the utilization of lignin-based copolymers to biomedical materials and value-added additives. Different modification approaches have also been applied to facilitate the application of lignin as carbon fiber precursors, heavy metal adsorbents and nanoparticles. These emerging fields will create new opportunities in cost-effectively integrating the lignin valorization into lignocellulosic biorefineries.
", "date": "2020-10-02", "issue": "10", "identifier": "https://www.osti.gov/biblio/1714399", "bibliographicCitation": "https://doi.org/10.3390/polym12102277", "keywords": [ "36 MATERIALS SCIENCE", "adsorbents", "carbon fiber", "composites", "copolymers", "functionalization", "lignin", "nanoparticles", "resins", "thermoplastics" ], "topic": [ "Materials Science & Bioproducts" ], "journal_name": "Polymers", "volume": "12", "publisher_information": "MDPI AG", "country_publication_code": "Switzerland", "creator": [ { "name": "Yun-Yan (ORCID:0000000208664640) Wang", "primaryContact": true }, { "name": "Xianzhi Meng", "primaryContact": false }, { "name": "Yunqiao Pu", "primaryContact": false }, { "name": "Arthur (ORCID:000000023536554X) J. Ragauskas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Advanced Research Projects Agency - Energy (ARPA-E)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1714399", "active": false }, { "brc": "CBI", "title": "High-Throughput Functional Genomics for Energy Production", "description": "Functional genomics remains a foundational field for establishing genotype-phenotype relationships that enable strain engineering. High-throughput (HTP) methods accelerate the Design-Build-Test-Learn cycle that currently drives synthetic biology towards a forward engineering future. Trackable mutagenesis techniques including transposon insertion sequencing and CRISPR-Cas-mediated genome editing allow for rapid fitness profiling of a collection, or library, of mutants to discover beneficial mutations. Due to the relative speed of these experiments compared to adaptive evolution experiments, iterative rounds of mutagenesis can be implemented for next-generation metabolic engineering efforts to design complex production and tolerance phenotypes. Further, the expansion of these mutagenesis techniques to novel bacteria are opening up industrial microbes that show promise for establishing a bio-based economy.", "abstract": "Functional genomics remains a foundational field for establishing genotype-phenotype relationships that enable strain engineering. High-throughput (HTP) methods accelerate the Design-Build-Test-Learn cycle that currently drives synthetic biology towards a forward engineering future. Trackable mutagenesis techniques including transposon insertion sequencing and CRISPR-Cas-mediated genome editing allow for rapid fitness profiling of a collection, or library, of mutants to discover beneficial mutations. Due to the relative speed of these experiments compared to adaptive evolution experiments, iterative rounds of mutagenesis can be implemented for next-generation metabolic engineering efforts to design complex production and tolerance phenotypes. Further, the expansion of these mutagenesis techniques to novel bacteria are opening up industrial microbes that show promise for establishing a bio-based economy.", "date": "2020-11-01", "identifier": "https://www.osti.gov/biblio/1721731", "bibliographicCitation": "https://doi.org/10.1016/j.copbio.2020.09.010", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "genomic methods", "high-throughput", "microbial systems" ], "topic": [ "Microbiology" ], "journal_name": "Current Opinion in Biotechnology", "volume": "67", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Jacob A. [Univ. of Colorado,Boulder,CO (United States)] Fenster", "primaryContact": true }, { "name": "Carrie A. [Univ. of Colorado,Boulder,CO (United States); National Renewable Energy Lab. (NREL),Golden,CO (United States)] Eckert", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1721731", "active": false, "has_related_ids": [ "NREL/JA--2700-77739" ] }, { "brc": "CBI", "title": "Characterization of alkylguaiacol-degrading cytochromes P450 for the biocatalytic valorization of lignin", "description": "Upgrading lignin, an underutilized component of biomass, is essential for the sustainability of biorefineries. Biocatalysis has considerable potential for upgrading lignin, but our lack of knowledge of relevant enzymes and pathways has limited its application. Herein, we describe a microbial pathway responsible for catabolizing alkylguaiacols, a major component of several industrial lignin streams. Catabolism is initiated by a cytochrome P450, with related P450s catalyzing the O-demethylation of different lignin-derived guaiacols and subsequent catabolism depending on the substitution pattern of the guaiacol. Importantly, the alkylguaiacol catabolic pathway enables bacterial growth on corn stover lignin produced by reductive catalytic fractionation. Overall, these insights greatly facilitate the engineering of P450s and bacteria to biocatalytically upgrade lignin.", "abstract": "Upgrading lignin, an underutilized component of biomass, is essential for the sustainability of biorefineries. Biocatalysis has considerable potential for upgrading lignin, but our lack of knowledge of relevant enzymes and pathways has limited its application. Herein, we describe a microbial pathway responsible for catabolizing alkylguaiacols, a major component of several industrial lignin streams. Catabolism is initiated by a cytochrome P450, with related P450s catalyzing the O-demethylation of different lignin-derived guaiacols and subsequent catabolism depending on the substitution pattern of the guaiacol. Importantly, the alkylguaiacol catabolic pathway enables bacterial growth on corn stover lignin produced by reductive catalytic fractionation. Overall, these insights greatly facilitate the engineering of P450s and bacteria to biocatalytically upgrade lignin.", "date": "2020-09-27", "issue": "41", "identifier": "https://www.osti.gov/biblio/1726039", "bibliographicCitation": "https://doi.org/10.1073/pnas.1916349117", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "O-demethylase", "biocatalysis", "cytochrome P450", "guaiacol", "lignin valorization" ], "topic": [ "Microbiology" ], "journal_name": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "117", "publisher_information": "National Academy of Sciences", "country_publication_code": "US", "creator": [ { "name": "Morgan M. [Univ. of British Columbia,Vancouver,BC (Canada)] (ORCID:0000000302637315) Fetherolf", "primaryContact": true }, { "name": "David J. [Univ. of British Columbia,Vancouver,BC (Canada)] (ORCID:000000022382709X) Levy-Booth", "primaryContact": false }, { "name": "Laura E. [Univ. of British Columbia,Vancouver,BC (Canada)] (ORCID:0000000283038439) Navas", "primaryContact": false }, { "name": "Jie [Univ. of British Columbia,Vancouver,BC (Canada)] (ORCID:0000000211443830) Liu", "primaryContact": false }, { "name": "Jason C. [Univ. of British Columbia,Vancouver,BC (Canada)] (ORCID:000000025627273X) Grigg", "primaryContact": false }, { "name": "Andrew [Univ. of British Columbia,Vancouver,BC (Canada)] (ORCID:0000000300808803) Wilson", "primaryContact": false }, { "name": "Rui [National Renewable Energy Lab. (NREL),Golden,CO (United States)] Katahira", "primaryContact": false }, { "name": "Gregg T. [National Renewable Energy Lab. (NREL),Golden,CO (United States)] (ORCID:000000023480212X) Beckham", "primaryContact": false }, { "name": "William W. [Univ. of British Columbia,Vancouver,BC (Canada)] (ORCID:000000026509746X) Mohn", "primaryContact": false }, { "name": "Lindsay D. [Univ. of British Columbia,Vancouver,BC (Canada)] (ORCID:0000000267748158) Eltis", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Bioenergy Technologies Office (EE-3B)" } } ], "dataset_url": "https://www.osti.gov/biblio/1726039", "active": false, "has_related_ids": [ "NREL/JA--2800-77914" ] }, { "brc": "CBI", "title": "Modeled economic potential for Eucalyptus spp. production for jet fuel additives in the United States", "description": "Feedstock price and availability remain a barrier to adoption of cellulosic biofuels. Eucalyptus spp., can produce an energy-dense terpene suitable for high-density synthetic hydrocarbon-type fuel (grade JP-10) production in addition to cellulosic-based feedstock for traditional jet fuels (e.g., grade Jet A) and gasoline. This study modeled economic potential for Eucalyptus to fulfill US fuel markets. Cold-tolerant Eucalyptus was simulated in an annual coppice system for maximized leaf production. Results of the lowest simulated price ($110 t-1) show that within 10 years, there is potential to produce 204 million L yr-1 of fuel, including 51 million L yr-1 of JP-10-type fuel, 75 million L yr-1 of Jet A type fuel, and 77 million L yr-1 of gasoline. These quantities of fuel could be valued at approximately $500 million (USD), with feedstock costs totaling approximately $100 million (USD). Longer-term markets (to 20 years) or higher priced (to $220 t-1) scenarios show potential for more production. Furthermore, research to determine potential for genetic improvement, delivered fuel costs, and biorefinery siting near existing infrastructure is recommended.", "abstract": "Feedstock price and availability remain a barrier to adoption of cellulosic biofuels. Eucalyptus spp., can produce an energy-dense terpene suitable for high-density synthetic hydrocarbon-type fuel (grade JP-10) production in addition to cellulosic-based feedstock for traditional jet fuels (e.g., grade Jet A) and gasoline. This study modeled economic potential for Eucalyptus to fulfill US fuel markets. Cold-tolerant Eucalyptus was simulated in an annual coppice system for maximized leaf production. Results of the lowest simulated price ($110 t-1) show that within 10 years, there is potential to produce 204 million L yr-1 of fuel, including 51 million L yr-1 of JP-10-type fuel, 75 million L yr-1 of Jet A type fuel, and 77 million L yr-1 of gasoline. These quantities of fuel could be valued at approximately $500 million (USD), with feedstock costs totaling approximately $100 million (USD). Longer-term markets (to 20 years) or higher priced (to $220 t-1) scenarios show potential for more production. Furthermore, research to determine potential for genetic improvement, delivered fuel costs, and biorefinery siting near existing infrastructure is recommended.", "date": "2020-11-17", "issue": "1", "identifier": "https://www.osti.gov/biblio/1731037", "bibliographicCitation": "https://doi.org/10.1016/j.biombioe.2020.105807", "keywords": [ "09 BIOMASS FUELS", "Aviation biofuels", "Bioenergy crops", "Mallee eucalypts", "Oil mallee", "Short-rotation annual coppice" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Biomass and Bioenergy", "volume": "143", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Maggie R. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000181319328) Davis", "primaryContact": true }, { "name": "David [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000172714676) Kainer", "primaryContact": false }, { "name": "Gerald A. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000301061289) Tuskan", "primaryContact": false }, { "name": "Matthew H. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000281537154) Langholtz", "primaryContact": false }, { "name": "Chad M. [Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:0000000173085058) Hellwinckel", "primaryContact": false }, { "name": "Magen [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Shedden", "primaryContact": false }, { "name": "Laurence [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000312709626) Eaton", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/1731037", "active": false }, { "brc": "CBI", "title": "Lectin Receptor-Like Kinases: The Sensor and Mediator at the Plant Cell Surface", "description": "Lectin receptor-like kinases (LecRLKs), a plant-specific receptor-like kinase (RLK) sub-family, have been recently found to play crucial roles in plant development and responses to abiotic and biotic stresses. In this review, we first describe the classification and structures of Lectin RLKs. Then we focus on the analysis of functions of LecRLKs in various biological processes and discuss the status of LecRLKs from the ligands they recognize, substrate they target, signaling pathways they are involved in, to the overall regulation of growth-defense tradeoffs. LecRLKs and the signaling components they interact with constitute recognition and protection systems at the plant cell surface contributing to the detection of environmental changes monitoring plant fitness.
", "abstract": "Lectin receptor-like kinases (LecRLKs), a plant-specific receptor-like kinase (RLK) sub-family, have been recently found to play crucial roles in plant development and responses to abiotic and biotic stresses. In this review, we first describe the classification and structures of Lectin RLKs. Then we focus on the analysis of functions of LecRLKs in various biological processes and discuss the status of LecRLKs from the ligands they recognize, substrate they target, signaling pathways they are involved in, to the overall regulation of growth-defense tradeoffs. LecRLKs and the signaling components they interact with constitute recognition and protection systems at the plant cell surface contributing to the detection of environmental changes monitoring plant fitness.
", "date": "2020-12-09", "identifier": "https://www.osti.gov/biblio/1734950", "bibliographicCitation": "https://doi.org/10.3389/fpls.2020.596301", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "abiotic stress", "biotic stress", "lectin", "lectin receptor-like kinase", "plant defense", "plant development", "receptor-like kinase" ], "topic": [ "Microbiology" ], "journal_name": "Frontiers in Plant Science", "volume": "11", "publisher_information": "Frontiers Research Foundation", "country_publication_code": "Switzerland", "creator": [ { "name": "Yali Sun", "primaryContact": true }, { "name": "Zhenzhen Qiao", "primaryContact": false }, { "name": "Wellington Muchero", "primaryContact": false }, { "name": "Jin-Gui Chen", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/1734950", "active": false }, { "brc": "CBI", "title": "Lignin-derived electrochemical energy materials and systems", "description": "Electrochemical energy storage systems such as supercapacitors, rechargeable batteries and fuel cells have been proven the most effective technologies for energy conversion, storage, and management at different scales. Although a large number of electrochemical energy technologies have been developed in the past and they will continue to be optimized in terms of cost, lifetime, and performance, there is a substantial growing demand for advanced electrochemical energy systems. To deploy these advanced systems, the electrode and electrolyte materials with higher performance, longer life, and lower cost, must be developed. Lignin is the second most abundant natural polymer after cellulose, a byproduct from emerging cellulosic biorefineries, and a waste product from pulp and paper industries. Numerous researches have successfully demonstrated that lignin from different sources can be used as precursors or feedstocks for preparing high-performance electrochemical energy materials and components such as electrodes, electrolytes, membrane separators, and additives. Moreover, techno-economic analyses indicate that it is possible to prepare cost-effective carbons from lignin at engineering scales, compared to current carbon products. These facts suggest that scalable conversion of lignin into high-value energy materials will offer a promising pathway to not only promote the utilization and valorization of lignin but also boost the development of the advanced electrochemical energy systems. This review presents state of the arts of renewable energy materials derived from various lignin and their applications in electrochemical energy systems with emphasis on supercapacitors, rechargeable batteries, and fuel cells. Meanwhile, this article also aims to carve out the critical barriers for lignin-derived high-performance materials for energy applications, intending to identify viable approaches for synthesis of sustainable new energy materials.", "abstract": "Electrochemical energy storage systems such as supercapacitors, rechargeable batteries and fuel cells have been proven the most effective technologies for energy conversion, storage, and management at different scales. Although a large number of electrochemical energy technologies have been developed in the past and they will continue to be optimized in terms of cost, lifetime, and performance, there is a substantial growing demand for advanced electrochemical energy systems. To deploy these advanced systems, the electrode and electrolyte materials with higher performance, longer life, and lower cost, must be developed. Lignin is the second most abundant natural polymer after cellulose, a byproduct from emerging cellulosic biorefineries, and a waste product from pulp and paper industries. Numerous researches have successfully demonstrated that lignin from different sources can be used as precursors or feedstocks for preparing high-performance electrochemical energy materials and components such as electrodes, electrolytes, membrane separators, and additives. Moreover, techno-economic analyses indicate that it is possible to prepare cost-effective carbons from lignin at engineering scales, compared to current carbon products. These facts suggest that scalable conversion of lignin into high-value energy materials will offer a promising pathway to not only promote the utilization and valorization of lignin but also boost the development of the advanced electrochemical energy systems. This review presents state of the arts of renewable energy materials derived from various lignin and their applications in electrochemical energy systems with emphasis on supercapacitors, rechargeable batteries, and fuel cells. Meanwhile, this article also aims to carve out the critical barriers for lignin-derived high-performance materials for energy applications, intending to identify viable approaches for synthesis of sustainable new energy materials.", "date": "2020-01-23", "issue": "3", "identifier": "https://www.osti.gov/biblio/1737405", "bibliographicCitation": "https://doi.org/10.1002/bbb.2083", "keywords": [ "09 BIOMASS FUELS", "biomass utilization", "electrochemical systems", "energy storage", "large-scale production", "lignin valorization", "renewable materials" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Biofuels, Bioproducts & Biorefining", "volume": "14", "publisher_information": "Wiley", "country_publication_code": "US", "creator": [ { "name": "Xiaoyu [Washington State Univ.,Richland,WA (United States); Beihang Univ.,Beijing (China)] (ORCID:0000000183813338) Wu", "primaryContact": true }, { "name": "Junhua [Idaho National Lab. (INL),Idaho Falls,ID (United States)] Jiang", "primaryContact": false }, { "name": "Chongmin [Pacific Northwest National Lab. (PNNL),Richland,WA (United States)] (ORCID:0000000333270958) Wang", "primaryContact": false }, { "name": "Jian [Pacific Northwest National Lab. (PNNL),Richland,WA (United States)] (ORCID:0000000153297408) Liu", "primaryContact": false }, { "name": "Yunqiao [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Pu", "primaryContact": false }, { "name": "Arthur [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:000000023536554X) Ragauskas", "primaryContact": false }, { "name": "Songmei [Beihang Univ.,Beijing (China)] Li", "primaryContact": false }, { "name": "Bin [Washington State Univ.,Richland,WA (United States); Pacific Northwest National Lab. (PNNL),Richland,WA (United States); Aalto Univ.,(Finland)] (ORCID:0000000316868800) Yang", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1737405", "active": false, "has_related_ids": [ "PNNL-SA--144600" ] }, { "brc": "CBI", "title": "Microbe to Microbiome: A Paradigm Shift in the Application of Microorganisms for Sustainable Agriculture", "description": "Light, water and healthy soil are three essential natural resources required for agricultural productivity. Industrialization of agriculture has resulted in intensification of cropping practices using enormous amounts of chemical pesticides and fertilizers that damage these natural resources. Therefore, there is a need to embrace agriculture practices that do not depend on greater use of fertilizers and water to meet the growing demand of global food requirements. Plants and soil harbor millions of microorganisms, which collectively form a microbial community known as the microbiome. An effective microbiome can offer benefits to its host, including plant growth promotion, nutrient use efficiency, and control of pests and phytopathogens. Therefore, there is an immediate need to bring functional potential of plant-associated microbiome and its innovation into crop production. In addition to that, new scientific methodologies that can track the nutrient flux through the plant, its resident microbiome and surrounding soil, will offer new opportunities for the design of more efficient microbial consortia design. It is now increasingly acknowledged that the diversity of a microbial inoculum is as important as its plant growth promoting ability. Not surprisingly, outcomes from such plant and soil microbiome studies have resulted in a paradigm shift away from single, specific soil microbes to a more holistic microbiome approach for enhancing crop productivity and the restoration of soil health. Herein, we have reviewed this paradigm shift and discussed various aspects of benign microbiome-based approaches for sustainable agriculture.
", "abstract": "Light, water and healthy soil are three essential natural resources required for agricultural productivity. Industrialization of agriculture has resulted in intensification of cropping practices using enormous amounts of chemical pesticides and fertilizers that damage these natural resources. Therefore, there is a need to embrace agriculture practices that do not depend on greater use of fertilizers and water to meet the growing demand of global food requirements. Plants and soil harbor millions of microorganisms, which collectively form a microbial community known as the microbiome. An effective microbiome can offer benefits to its host, including plant growth promotion, nutrient use efficiency, and control of pests and phytopathogens. Therefore, there is an immediate need to bring functional potential of plant-associated microbiome and its innovation into crop production. In addition to that, new scientific methodologies that can track the nutrient flux through the plant, its resident microbiome and surrounding soil, will offer new opportunities for the design of more efficient microbial consortia design. It is now increasingly acknowledged that the diversity of a microbial inoculum is as important as its plant growth promoting ability. Not surprisingly, outcomes from such plant and soil microbiome studies have resulted in a paradigm shift away from single, specific soil microbes to a more holistic microbiome approach for enhancing crop productivity and the restoration of soil health. Herein, we have reviewed this paradigm shift and discussed various aspects of benign microbiome-based approaches for sustainable agriculture.
", "date": "2020-12-20", "identifier": "https://www.osti.gov/biblio/1737691", "bibliographicCitation": "https://doi.org/10.3389/fmicb.2020.622926", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "cover crop", "microbial consortia", "mycorrhiza", "rhizobacteria", "rhizosphere" ], "topic": [ "Microbiology" ], "journal_name": "Frontiers in Microbiology", "volume": "11", "publisher_information": "Frontiers Research Foundation", "country_publication_code": "Switzerland", "creator": [ { "name": "Prasun Ray", "primaryContact": true }, { "name": "Venkatachalam Lakshmanan", "primaryContact": false }, { "name": "Jessy L. Labb\u00e9", "primaryContact": false }, { "name": "Kelly D. Craven", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1737691", "active": false }, { "brc": "CBI", "title": "Water-Dependent Blending of Pectin Films: The Mechanics of Conjoined Biopolymers", "description": "Biodegradable pectin polymers have been recommended for a variety of biomedical applications, ranging from the delivery of oral drugs to the repair of injured visceral organs. A promising approach to regulate pectin biostability is the blending of pectin films. To investigate the development of conjoined films, we examined the physical properties of high-methoxyl pectin polymer-polymer (homopolymer) interactions at the adhesive interface. Pectin polymers were tested in glass phase (10\u201313% w/w water content) and gel phase (38\u201341% w/w water content). The tensile strength of polymer-polymer adhesion was measured after variable development time and compressive force. Regardless of pretest parameters, the adhesive strength of two glass phase films was negligible. In contrast, adhesion testing of two gel phase films resulted in significant tensile adhesion strength (p < 0.01). Adhesion was also observed between glass phase and gel phase films\u2014likely reflecting the diffusion of water from the gel phase to the glass phase films. In studies of the interaction between two gel phase films, the polymer-polymer adhesive strength increased linearly with increasing compressive force (range 10\u201380 N) (R2 = 0.956). In contrast, adhesive strength increased logarithmically with time (range 10\u201310,000 s) (R2 = 0.913); most of the adhesive strength was observed within minutes of contact. Fracture mechanics demonstrated that the adhesion of two gel phase films resulted in a conjoined film with distinctive physical properties including increased extensibility, decreased stiffness and a 30% increase in the work of cohesion relative to native polymers (p < 0.01). Scanning electron microscopy of the conjoined films demonstrated cross-grain adhesion at the interface between the adhesive homopolymers. These structural and functional data suggest that blended pectin films have emergent physical properties resulting from the cross-grain intermingling of interfacial pectin chains.", "abstract": "Biodegradable pectin polymers have been recommended for a variety of biomedical applications, ranging from the delivery of oral drugs to the repair of injured visceral organs. A promising approach to regulate pectin biostability is the blending of pectin films. To investigate the development of conjoined films, we examined the physical properties of high-methoxyl pectin polymer-polymer (homopolymer) interactions at the adhesive interface. Pectin polymers were tested in glass phase (10\u201313% w/w water content) and gel phase (38\u201341% w/w water content). The tensile strength of polymer-polymer adhesion was measured after variable development time and compressive force. Regardless of pretest parameters, the adhesive strength of two glass phase films was negligible. In contrast, adhesion testing of two gel phase films resulted in significant tensile adhesion strength (p < 0.01). Adhesion was also observed between glass phase and gel phase films\u2014likely reflecting the diffusion of water from the gel phase to the glass phase films. In studies of the interaction between two gel phase films, the polymer-polymer adhesive strength increased linearly with increasing compressive force (range 10\u201380 N) (R2 = 0.956). In contrast, adhesive strength increased logarithmically with time (range 10\u201310,000 s) (R2 = 0.913); most of the adhesive strength was observed within minutes of contact. Fracture mechanics demonstrated that the adhesion of two gel phase films resulted in a conjoined film with distinctive physical properties including increased extensibility, decreased stiffness and a 30% increase in the work of cohesion relative to native polymers (p < 0.01). Scanning electron microscopy of the conjoined films demonstrated cross-grain adhesion at the interface between the adhesive homopolymers. These structural and functional data suggest that blended pectin films have emergent physical properties resulting from the cross-grain intermingling of interfacial pectin chains.", "date": "2020-04-29", "issue": "9", "identifier": "https://www.osti.gov/biblio/1756330", "bibliographicCitation": "https://doi.org/10.3390/molecules25092108", "keywords": [ "62 RADIOLOGY AND NUCLEAR MEDICINE", "fracture mechanics", "homopolymer adhesion", "pectin", "polysaccharide", "scanning electron microscopy" ], "topic": [ "Unknown" ], "journal_name": "Molecules", "volume": "25", "publisher_information": "MDPI", "country_publication_code": "US", "creator": [ { "name": "Yifan [Brigham and Women's Hospital (Harvard Medical School),Boston,MA (United States)] Zheng", "primaryContact": true }, { "name": "Aidan [Brigham and Women's Hospital (Harvard Medical School),Boston,MA (United States)] Pierce", "primaryContact": false }, { "name": "Willi L. [Brigham and Women's Hospital (Harvard Medical School),Boston,MA (United States); Univ. of Heidelberg (Germany)] Wagner", "primaryContact": false }, { "name": "Henrik V. [Lawrence Berkeley National Lab. (LBNL),Berkeley,CA (United States). Joint BioEnergy Institute and Environmental Genomics and Systems Biology Division] (ORCID:0000000267023560) Scheller", "primaryContact": false }, { "name": "Debra [Univ. of Georgia,Athens,GA (United States). Complex Carbohydrate Research Center] Mohnen", "primaryContact": false }, { "name": "Maximilian [Univ. Medical Center of the Johannes Gutenberg Univ.,Mainz (Germany)] Ackermann", "primaryContact": false }, { "name": "Steven J. [Brigham and Women's Hospital (Harvard Medical School),Boston,MA (United States)] Mentzer", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "German Research Foundation (DFG)" } }, { "fundingOrganization": { "organizationName": "National Institutes of Health (NIH)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC)" } } ], "dataset_url": "https://www.osti.gov/biblio/1756330", "active": false }, { "brc": "CBI", "title": "A rapid thioacidolysis method for biomass lignin composition and tricin analysis", "description": "\n Biomass composition varies from plant to plant and greatly affects biomass utilization. Lignin is a heterogeneous phenolic polymer derived mainly from\n
In combination with gas chromatography\u2013mass spectrometry (GC\u2013MS) and liquid chromatography\u2013mass spectrometry (LC\u2013MS), the modified thioacidolysis method can be used to simultaneously characterize the lignin composition and tricin content using 2\u20135\u00a0mg of dry samples. The modified method eliminates the solvent extraction and drastically improves the throughput; 80 samples can be processed in one day per person. Our results indicate that there is no significant difference in the determination of lignin S/G ratio and tricin content between the original and modified methods.
\nA modified thioacidolysis protocol was established. The results demonstrate that the modified method can be used for rapid, high-throughput, and reliable lignin composition and tricin content analyses for screening transgenic plants for cell wall modifications or in large-scale genome-wide association studies (GWAS).
\n\n Biomass composition varies from plant to plant and greatly affects biomass utilization. Lignin is a heterogeneous phenolic polymer derived mainly from\n
In combination with gas chromatography\u2013mass spectrometry (GC\u2013MS) and liquid chromatography\u2013mass spectrometry (LC\u2013MS), the modified thioacidolysis method can be used to simultaneously characterize the lignin composition and tricin content using 2\u20135\u00a0mg of dry samples. The modified method eliminates the solvent extraction and drastically improves the throughput; 80 samples can be processed in one day per person. Our results indicate that there is no significant difference in the determination of lignin S/G ratio and tricin content between the original and modified methods.
\nA modified thioacidolysis protocol was established. The results demonstrate that the modified method can be used for rapid, high-throughput, and reliable lignin composition and tricin content analyses for screening transgenic plants for cell wall modifications or in large-scale genome-wide association studies (GWAS).
\nNon-model microorganisms often possess complex phenotypes that could be important for the future of biofuel and chemical production. They have received significant interest the last several years, but advancement is still slow due to the lack of a robust genetic toolbox in most organisms. Typically, \u201cdomestication\u201d of a new non-model microorganism has been done on an ad hoc basis, and historically, it can take years to develop transformation and basic genetic tools. Here, we review the barriers and solutions to rapid development of genetic transformation tools in new hosts, with a major focus on Restriction-Modification systems, which are a well-known and significant barrier to efficient transformation. We further explore the tools and approaches used for efficient gene deletion, DNA insertion, and heterologous gene expression. Finally, more advanced and high-throughput tools are now being developed in diverse non-model microbes, paving the way for rapid and multiplexed genome engineering for biotechnology.
", "abstract": "Non-model microorganisms often possess complex phenotypes that could be important for the future of biofuel and chemical production. They have received significant interest the last several years, but advancement is still slow due to the lack of a robust genetic toolbox in most organisms. Typically, \u201cdomestication\u201d of a new non-model microorganism has been done on an ad hoc basis, and historically, it can take years to develop transformation and basic genetic tools. Here, we review the barriers and solutions to rapid development of genetic transformation tools in new hosts, with a major focus on Restriction-Modification systems, which are a well-known and significant barrier to efficient transformation. We further explore the tools and approaches used for efficient gene deletion, DNA insertion, and heterologous gene expression. Finally, more advanced and high-throughput tools are now being developed in diverse non-model microbes, paving the way for rapid and multiplexed genome engineering for biotechnology.
", "date": "2021-01-24", "issue": "1", "identifier": "https://www.osti.gov/biblio/1762511", "bibliographicCitation": "https://doi.org/10.1186/s13068-020-01872-z", "keywords": [ "09 BIOMASS FUELS", "Genetic tools", "Genetics", "Metabolic engineering", "Non-model microbes", "Synthetic biology", "Transformation" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Biotechnology for Biofuels", "volume": "14", "publisher_information": "Springer Science + Business Media", "country_publication_code": "Netherlands", "creator": [ { "name": "Lauren A. Riley", "primaryContact": true }, { "name": "Adam M. (ORCID:0000000158235329) Guss", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Transportation Office. Bioenergy Technologies Office" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1762511", "active": false }, { "brc": "CBI", "title": "Computational biophysical characterization of the SARS-CoV-2 spike protein binding with the ACE2 receptor and implications for infectivity", "description": "Not Available", "abstract": "Not Available", "date": "2019-12-31", "issue": "C", "identifier": "https://www.osti.gov/biblio/1762536", "bibliographicCitation": "https://doi.org/10.1016/j.csbj.2020.09.019", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "ATR1", "Biophysics", "COVID 19", "Human ACE2", "SARS CoV-2" ], "topic": [ "Microbiology" ], "journal_name": "Computational and Structural Biotechnology Journal", "volume": "18", "publisher_information": "Elsevier", "country_publication_code": "Sweden", "creator": [ { "name": "Ratul Chowdhury", "primaryContact": true }, { "name": "Veda Sheersh Boorla", "primaryContact": false }, { "name": "Costas D. Maranas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1762536", "active": false }, { "brc": "CBI", "title": "Double bonus: surfactant-assisted biomass pelleting benefits both the pelleting process and subsequent enzymatic saccharification of the pretreated pellets", "description": "Pelleting overcomes the utilization limitation of lignocellulosic biomass due to its low density and related processing costs. Efficiently combining biomass pelleting and enzymatic saccharification is a challenge for applying biomass with low density in a biorefinery. In this study, we propose a novel biomass processing approach involving the addition of surfactant during pelleting and using the pellets for pretreatment and enzymatic saccharification. Here, we investigated the effects of polyethylene glycol (PEG) 6000 assisted pelleting on pelleting specific energy consumption and friction, and on subsequent pretreatment as well as on enzymatic saccharification of the pretreated pellets. The results showed that PEG 6000 assisted pelleting decreased the total pelleting specific energy consumption by about 14% for wheat straw and 18% for pine, and reduced the maximum friction during ejection of pellets by about 34% for wheat straw and 29% for pine. PEG 6000 assisted pelleting enhanced subsequent enzymatic sugar yield effectively for both acid and alkaline pretreated wheat straw and pine, especially for acid-treated pine pellets, where a 256% increase in glucose yield was obtained. The results suggest that PEG 6000 decreases the cleavage of \u03b2-O-4' linkages during pretreatment and thus hinders the formation of phenolic hydroxyl groups, contributing to the enhanced sugar yield in enzymatic saccharification. As surfactants were found to have beneficial effects on both biomass pelleting and the sugar yield obtained from the enzymatic saccharification of the pretreated pellets, it would be advantageous to add surfactants during pelletizing when the pellets are intended for application in a biorefinery.", "abstract": "Pelleting overcomes the utilization limitation of lignocellulosic biomass due to its low density and related processing costs. Efficiently combining biomass pelleting and enzymatic saccharification is a challenge for applying biomass with low density in a biorefinery. In this study, we propose a novel biomass processing approach involving the addition of surfactant during pelleting and using the pellets for pretreatment and enzymatic saccharification. Here, we investigated the effects of polyethylene glycol (PEG) 6000 assisted pelleting on pelleting specific energy consumption and friction, and on subsequent pretreatment as well as on enzymatic saccharification of the pretreated pellets. The results showed that PEG 6000 assisted pelleting decreased the total pelleting specific energy consumption by about 14% for wheat straw and 18% for pine, and reduced the maximum friction during ejection of pellets by about 34% for wheat straw and 29% for pine. PEG 6000 assisted pelleting enhanced subsequent enzymatic sugar yield effectively for both acid and alkaline pretreated wheat straw and pine, especially for acid-treated pine pellets, where a 256% increase in glucose yield was obtained. The results suggest that PEG 6000 decreases the cleavage of \u03b2-O-4' linkages during pretreatment and thus hinders the formation of phenolic hydroxyl groups, contributing to the enhanced sugar yield in enzymatic saccharification. As surfactants were found to have beneficial effects on both biomass pelleting and the sugar yield obtained from the enzymatic saccharification of the pretreated pellets, it would be advantageous to add surfactants during pelletizing when the pellets are intended for application in a biorefinery.", "date": "2021-01-12", "issue": "TBD", "identifier": "https://www.osti.gov/biblio/1763454", "bibliographicCitation": "https://doi.org/10.1039/d0gc03855e", "keywords": [ "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY" ], "topic": [ "Chemistry" ], "journal_name": "Green Chemistry", "volume": "TBD", "publisher_information": "Royal Society of Chemistry", "country_publication_code": "US", "creator": [ { "name": "Chunxiao [Univ. of Copenhagen (Denmark); Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:0000000327916572) Gong", "primaryContact": true }, { "name": "Nathan [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Bryant", "primaryContact": false }, { "name": "Xianzhi [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000343033403) Meng", "primaryContact": false }, { "name": "Samarthya [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000294951880) Bhagia", "primaryContact": false }, { "name": "Yunqiao [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000325541447) Pu", "primaryContact": false }, { "name": "Donglin [Univ. of Copenhagen (Denmark)] Xin", "primaryContact": false }, { "name": "Christian [Univ. of Copenhagen (Denmark)] (ORCID:000000027496297X) Bender Koch", "primaryContact": false }, { "name": "Claus [Univ. of Copenhagen (Denmark)] Felby", "primaryContact": false }, { "name": "Lisbeth Garbrecht [Univ. of Copenhagen (Denmark)] (ORCID:0000000196857460) Thygesen", "primaryContact": false }, { "name": "Arthur [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:000000023536554X) Ragauskas", "primaryContact": false }, { "name": "Sune Tjalfe [Univ. of Copenhagen (Denmark)] (ORCID:0000000189089977) Thomsen", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "Chinese Scholarship Council (CSC)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1763454", "active": false }, { "brc": "CBI", "title": "Building kinetic models for metabolic engineering", "description": "Kinetic formalisms of metabolism link metabolic fluxes to enzyme levels, metabolite concentrations and their allosteric regulatory interactions. Though they require the identification of physiologically relevant values for numerous parameters, kinetic formalisms uniquely establish a mechanistic link across heterogeneous omics datasets and provide an overarching vantage point to effectively inform metabolic engineering strategies. Advances in computational power, gene annotation coverage, and formalism standardization have led to significant progress over the past few years. However, careful interpretation of model predictions, limited metabolic flux datasets, and assessment of parameter sensitivity remain as challenges. In this study we highlight fundamental considerations which influence model quality and prediction, advances in methodologies, and success stories of deploying kinetic models to guide metabolic engineering.", "abstract": "Kinetic formalisms of metabolism link metabolic fluxes to enzyme levels, metabolite concentrations and their allosteric regulatory interactions. Though they require the identification of physiologically relevant values for numerous parameters, kinetic formalisms uniquely establish a mechanistic link across heterogeneous omics datasets and provide an overarching vantage point to effectively inform metabolic engineering strategies. Advances in computational power, gene annotation coverage, and formalism standardization have led to significant progress over the past few years. However, careful interpretation of model predictions, limited metabolic flux datasets, and assessment of parameter sensitivity remain as challenges. In this study we highlight fundamental considerations which influence model quality and prediction, advances in methodologies, and success stories of deploying kinetic models to guide metabolic engineering.", "date": "2020-12-23", "identifier": "https://www.osti.gov/biblio/1764394", "bibliographicCitation": "https://doi.org/10.1016/j.copbio.2020.11.010", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "Current Opinion in Biotechnology", "volume": "67", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Charles J. [Pennsylvania State Univ.,University Park,PA (United States); Penn State] (ORCID:0000000314944566) Foster", "primaryContact": true }, { "name": "Lin [Pennsylvania State Univ.,University Park,PA (United States)] (ORCID:0000000294555570) Wang", "primaryContact": false }, { "name": "Hoang V. [Pennsylvania State Univ.,University Park,PA (United States)] (ORCID:000000023861357X) Dinh", "primaryContact": false }, { "name": "Patrick F. [Pennsylvania State Univ.,University Park,PA (United States)] (ORCID:0000000255609986) Suthers", "primaryContact": false }, { "name": "Costas D. [Pennsylvania State Univ.,University Park,PA (United States)] Maranas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1764394", "active": false }, { "brc": "CBI", "title": "Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law formalisms", "description": "Understanding the governing principles behind organisms\u2019 metabolism and growth underpins their effective deployment as bioproduction chassis. A central objective of metabolic modeling is predicting how metabolism and growth are affected by both external environmental factors and internal genotypic perturbations. The fundamental concepts of reaction stoichiometry, thermodynamics, and mass action kinetics have emerged as the foundational principles of many modeling frameworks designed to describe how and why organisms allocate resources towards both growth and bioproduction. Furthermore, this review focuses on the latest algorithmic advancements that have integrated these foundational principles into increasingly sophisticated quantitative frameworks.", "abstract": "Understanding the governing principles behind organisms\u2019 metabolism and growth underpins their effective deployment as bioproduction chassis. A central objective of metabolic modeling is predicting how metabolism and growth are affected by both external environmental factors and internal genotypic perturbations. The fundamental concepts of reaction stoichiometry, thermodynamics, and mass action kinetics have emerged as the foundational principles of many modeling frameworks designed to describe how and why organisms allocate resources towards both growth and bioproduction. Furthermore, this review focuses on the latest algorithmic advancements that have integrated these foundational principles into increasingly sophisticated quantitative frameworks.", "date": "2020-12-09", "identifier": "https://www.osti.gov/biblio/1764395", "bibliographicCitation": "https://doi.org/10.1016/j.ymben.2020.11.013", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "Metabolic Engineering", "volume": "63", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Patrick F. [Pennsylvania State Univ.,University Park,PA (United States); The Pennsylvania State University] (ORCID:0000000255609986) Suthers", "primaryContact": true }, { "name": "Charles J. [Pennsylvania State Univ.,University Park,PA (United States)] (ORCID:0000000314944566) Foster", "primaryContact": false }, { "name": "Debolina [Pennsylvania State Univ.,University Park,PA (United States)] Sarkar", "primaryContact": false }, { "name": "Lin [Pennsylvania State Univ.,University Park,PA (United States)] (ORCID:0000000294555570) Wang", "primaryContact": false }, { "name": "Costas D. [Pennsylvania State Univ.,University Park,PA (United States)] Maranas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1764395", "active": false }, { "brc": "CBI", "title": "Coupling of Flavonoid Initiation Sites with Monolignols Studied by Density Functional Theory", "description": "Lignin recalcitrance presents a challenge for the development of a bioeconomy that employs lignocellulosic feedstocks. The efficiency of lignin deconstruction is improved by a reduction of molecular weight, and given the discovery that flavones serve as initiation sites in lignin biosynthesis, these molecular weight reductions could potentially be achieved with plant metabolic engineering to over-express flavonoids. Upon increasing the flavonoid content in lignin, the bond strengths and properties of flavonoid-monolignol linkages become increasingly important. To that end, the current work applies density functional theory calculations to elucidate the bond dissociation enthalpies (BDEs) of flavonoid-monolignol linkages, including dimers with oxidized monolignols. Specifically, the dimer bond strengths and monomer hydrogen abstraction energies for the flavonoids tricin, chrysoeriol, luteolin, apigenin, catechin, epicatechin, epigallocatechin, and epigallocatechin gallate are calculated, when coupled to seven natural and engineered monolignols. Results indicate that 4'-O-\u00df linkage strengths between flavonoids and monolignols are of comparable strength to inter-monolignol \u00df-O-4 linkages, with average flavonoid-monolignol BDEs of 70.7 kcal/mol relative to ~69.3 kcal/mol in analogous canonical monolignols. Epigallocatechin yielded the lowest 4'-O-\u00df bond strength of 52.3 kcal/mol when coupled to an oxidized monolignol, while the flavones overall produced lower average BDEs, relative to the flavanols. Substituents at the 3'-C and 5'-C positions on flavonoids affected the dimer linkage strengths to a greater extent than glycosylation or substituents further from the linkage. Erythro and threo stereochemistry across the flavonoid-monolignol linkage library exhibited only small energetic differences and no pronounced correlations. Taken together, the predictions from this work support the concept that higher concentrations of flavonoid initiation sites in lignin may afford linkage properties conducive to more facile lignin depolymerization.", "abstract": "Lignin recalcitrance presents a challenge for the development of a bioeconomy that employs lignocellulosic feedstocks. The efficiency of lignin deconstruction is improved by a reduction of molecular weight, and given the discovery that flavones serve as initiation sites in lignin biosynthesis, these molecular weight reductions could potentially be achieved with plant metabolic engineering to over-express flavonoids. Upon increasing the flavonoid content in lignin, the bond strengths and properties of flavonoid-monolignol linkages become increasingly important. To that end, the current work applies density functional theory calculations to elucidate the bond dissociation enthalpies (BDEs) of flavonoid-monolignol linkages, including dimers with oxidized monolignols. Specifically, the dimer bond strengths and monomer hydrogen abstraction energies for the flavonoids tricin, chrysoeriol, luteolin, apigenin, catechin, epicatechin, epigallocatechin, and epigallocatechin gallate are calculated, when coupled to seven natural and engineered monolignols. Results indicate that 4'-O-\u00df linkage strengths between flavonoids and monolignols are of comparable strength to inter-monolignol \u00df-O-4 linkages, with average flavonoid-monolignol BDEs of 70.7 kcal/mol relative to ~69.3 kcal/mol in analogous canonical monolignols. Epigallocatechin yielded the lowest 4'-O-\u00df bond strength of 52.3 kcal/mol when coupled to an oxidized monolignol, while the flavones overall produced lower average BDEs, relative to the flavanols. Substituents at the 3'-C and 5'-C positions on flavonoids affected the dimer linkage strengths to a greater extent than glycosylation or substituents further from the linkage. Erythro and threo stereochemistry across the flavonoid-monolignol linkage library exhibited only small energetic differences and no pronounced correlations. Taken together, the predictions from this work support the concept that higher concentrations of flavonoid initiation sites in lignin may afford linkage properties conducive to more facile lignin depolymerization.", "date": "2021-01-18", "issue": "4", "identifier": "https://www.osti.gov/biblio/1765613", "bibliographicCitation": "https://doi.org/10.1021/acssuschemeng.0c04240", "keywords": [ "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "bond dissociation enthalpy", "catechin", "epicatechin", "flavanols", "flavone", "flavonoids", "lignin valorization", "tricin" ], "topic": [ "Chemistry" ], "journal_name": "ACS Sustainable Chemistry & Engineering", "volume": "9", "publisher_information": "American Chemical Society (ACS)", "country_publication_code": "US", "creator": [ { "name": "Laura [National Renewable Energy Lab. (NREL),Golden,CO (United States)] Berstis", "primaryContact": true }, { "name": "Thomas [US Dept. of Agriculture (USDA),Auburn,AL (United States)] (ORCID:0000000339092152) Elder", "primaryContact": false }, { "name": "Richard [Univ. of North Texas,Denton,TX (United States)] (ORCID:0000000183939408) Dixon", "primaryContact": false }, { "name": "Michael [National Renewable Energy Lab. (NREL),Golden,CO (United States)] (ORCID:0000000151639398) Crowley", "primaryContact": false }, { "name": "Gregg T. [National Renewable Energy Lab. (NREL),Golden,CO (United States)] (ORCID:000000023480212X) Beckham", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE)" } } ], "dataset_url": "https://www.osti.gov/biblio/1765613", "active": false, "has_related_ids": [ "NREL-JA--2800-78130" ] }, { "brc": "CBI", "title": "Targeting hydroxycinnamoyl CoA: shikimate hydroxycinnamoyl transferase for lignin modification in Brachypodium distachyon", "description": "\n Hydroxycinnamoyl CoA: shikimate hydroxycinnamoyl transferase (HCT) is a central enzyme of the so-called \u201cesters\u201d pathway to monolignols. As originally envisioned, HCT functions twice in this pathway, to form coumaroyl shikimate and then, in the \u201creverse\u201d direction, to convert caffeoyl shikimate to caffeoyl CoA. The discovery of a caffeoyl shikimate esterase (CSE) that forms caffeic acid directly from caffeoyl shikimate calls into question the need for the reverse HCT reaction in lignin biosynthesis. Loss of function of HCT gives severe growth phenotypes in several dicot plants, but less so in some monocots, questioning whether this enzyme, and therefore the shikimate shunt, plays the same role in both monocots and dicots. The model grass\n
\n The kinetic properties of recombinant\n
\n Down-regulation of HCT1, or co-down-regulation of both\n
\n Hydroxycinnamoyl CoA: shikimate hydroxycinnamoyl transferase (HCT) is a central enzyme of the so-called \u201cesters\u201d pathway to monolignols. As originally envisioned, HCT functions twice in this pathway, to form coumaroyl shikimate and then, in the \u201creverse\u201d direction, to convert caffeoyl shikimate to caffeoyl CoA. The discovery of a caffeoyl shikimate esterase (CSE) that forms caffeic acid directly from caffeoyl shikimate calls into question the need for the reverse HCT reaction in lignin biosynthesis. Loss of function of HCT gives severe growth phenotypes in several dicot plants, but less so in some monocots, questioning whether this enzyme, and therefore the shikimate shunt, plays the same role in both monocots and dicots. The model grass\n
\n The kinetic properties of recombinant\n
\n Down-regulation of HCT1, or co-down-regulation of both\n
Multiple analytical methods have been developed to determine the ratios of aromatic lignin units, particularly the syringyl/guaiacyl (S/G) ratio, of lignin biopolymers in plant cell walls. Chemical degradation methods such as thioacidolysis produce aromatic lignin units that are released from certain linkages and may induce chemical changes rendering it difficult to distinguish and determine the source of specific aromatic lignin units released, as is the case with nitrobenzene oxidation methodology. NMR methods provide powerful tools used to analyze cell walls for lignin composition and linkage information. Pyrolysis-mass spectrometry methods are also widely used, particularly as high-throughput methodologies. However, the different techniques used to analyze aromatic lignin unit ratios frequently yield different results within and across particular studies, making it difficult to interpret and compare results. This also makes it difficult to obtain meaningful insights relating these measurements to other characteristics of plant cell walls that may impact biomass sustainability and conversion metrics for the production of bio-derived fuels and chemicals.
\nThe authors compared the S/G lignin unit ratios obtained from thioacidolysis, pyrolysis-molecular beam mass spectrometry (py-MBMS), HSQC liquid-state NMR and solid-state (ss) NMR methodologies of pine, several genotypes of poplar, and corn stover biomass. An underutilized approach to deconvolute ssNMR spectra was implemented to derive S/G ratios. The S/G ratios obtained for the samples did not agree across the different methods, but trends were similar with the most agreement among the py-MBMS, HSQC NMR and deconvoluted ssNMR methods. The relationship between S/G, thioacidolysis yields, and linkage analysis determined by HSQC is also addressed.
\nThis work demonstrates that different methods using chemical, thermal, and non-destructive NMR techniques to determine native lignin S/G ratios in plant cell walls may yield different results depending on species and linkage abundances. Spectral deconvolution can be applied to many hardwoods with lignin dominated by S and G units, but the results may not be reliable for some woody and grassy species of more diverse lignin composition. HSQC may be a better method for analyzing lignin in those species given the wealth of information provided on additional aromatic moieties and bond linkages. Additionally, trends or correlations in lignin characteristics such as S/G ratios and lignin linkages within the same species such as poplar may not necessarily exhibit the same trends or correlations made across different biomass types. Careful consideration is required when choosing a method to measure S/G ratios and the benefits and shortcomings of each method discussed here are summarized.
\nMultiple analytical methods have been developed to determine the ratios of aromatic lignin units, particularly the syringyl/guaiacyl (S/G) ratio, of lignin biopolymers in plant cell walls. Chemical degradation methods such as thioacidolysis produce aromatic lignin units that are released from certain linkages and may induce chemical changes rendering it difficult to distinguish and determine the source of specific aromatic lignin units released, as is the case with nitrobenzene oxidation methodology. NMR methods provide powerful tools used to analyze cell walls for lignin composition and linkage information. Pyrolysis-mass spectrometry methods are also widely used, particularly as high-throughput methodologies. However, the different techniques used to analyze aromatic lignin unit ratios frequently yield different results within and across particular studies, making it difficult to interpret and compare results. This also makes it difficult to obtain meaningful insights relating these measurements to other characteristics of plant cell walls that may impact biomass sustainability and conversion metrics for the production of bio-derived fuels and chemicals.
\nThe authors compared the S/G lignin unit ratios obtained from thioacidolysis, pyrolysis-molecular beam mass spectrometry (py-MBMS), HSQC liquid-state NMR and solid-state (ss) NMR methodologies of pine, several genotypes of poplar, and corn stover biomass. An underutilized approach to deconvolute ssNMR spectra was implemented to derive S/G ratios. The S/G ratios obtained for the samples did not agree across the different methods, but trends were similar with the most agreement among the py-MBMS, HSQC NMR and deconvoluted ssNMR methods. The relationship between S/G, thioacidolysis yields, and linkage analysis determined by HSQC is also addressed.
\nThis work demonstrates that different methods using chemical, thermal, and non-destructive NMR techniques to determine native lignin S/G ratios in plant cell walls may yield different results depending on species and linkage abundances. Spectral deconvolution can be applied to many hardwoods with lignin dominated by S and G units, but the results may not be reliable for some woody and grassy species of more diverse lignin composition. HSQC may be a better method for analyzing lignin in those species given the wealth of information provided on additional aromatic moieties and bond linkages. Additionally, trends or correlations in lignin characteristics such as S/G ratios and lignin linkages within the same species such as poplar may not necessarily exhibit the same trends or correlations made across different biomass types. Careful consideration is required when choosing a method to measure S/G ratios and the benefits and shortcomings of each method discussed here are summarized.
\n\n A major challenge for sustainable food, fuel, and fiber production is simultaneous genetic improvement of yield, biomass quality, and resilience to episodic environmental stress and climate change. For\n
\n A major challenge for sustainable food, fuel, and fiber production is simultaneous genetic improvement of yield, biomass quality, and resilience to episodic environmental stress and climate change. For\n
The ability to deconstruct plant biomass without conventional pretreatment has made members of the genus Caldicellulosiruptor the target of investigation for the consolidated processing of plant lignocellulosic biomass to biofuels and bioproducts. To investigate the synergy of enzymes involved and to further improve the ability of C. bescii to degrade cellulose, we introduced CAZymes that act synergistically with the C. bescii exoproteome in vivo and in vitro. We recently demonstrated that the Acidothermus cellulolyticus E1 endo-1,4-\u03b2-D-glucanase (GH5) with a family 2 carbohydrate-binding module (CBM) increased the activity of C. bescii exoproteome on biomass, presumably acting in concert with CelA. The \u03b2-glucanase, GuxA, from A. cellulolyticus is a multi-domain enzyme with strong processive exoglucanase activity, and the cellobiose phosphorylase from Thermotoga maritima catalyzes cellulose degradation acting synergistically with cellobiohydrolases and endoglucanases. We identified new chromosomal insertion sites to co-express these enzymes and the resulting strain showed a significant increase in the enzymatic activity of the exoproteome.
", "abstract": "The ability to deconstruct plant biomass without conventional pretreatment has made members of the genus Caldicellulosiruptor the target of investigation for the consolidated processing of plant lignocellulosic biomass to biofuels and bioproducts. To investigate the synergy of enzymes involved and to further improve the ability of C. bescii to degrade cellulose, we introduced CAZymes that act synergistically with the C. bescii exoproteome in vivo and in vitro. We recently demonstrated that the Acidothermus cellulolyticus E1 endo-1,4-\u03b2-D-glucanase (GH5) with a family 2 carbohydrate-binding module (CBM) increased the activity of C. bescii exoproteome on biomass, presumably acting in concert with CelA. The \u03b2-glucanase, GuxA, from A. cellulolyticus is a multi-domain enzyme with strong processive exoglucanase activity, and the cellobiose phosphorylase from Thermotoga maritima catalyzes cellulose degradation acting synergistically with cellobiohydrolases and endoglucanases. We identified new chromosomal insertion sites to co-express these enzymes and the resulting strain showed a significant increase in the enzymatic activity of the exoproteome.
", "date": "2019-04-30", "issue": "5", "identifier": "https://www.osti.gov/biblio/1772499", "bibliographicCitation": "https://doi.org/10.1007/s10295-019-02150-0", "keywords": [ "09 BIOMASS FUELS", "Caldicellulosiruptor", "biochemicals", "bioenergy", "biofuels", "biomass deconstruction", "cellobiose phosphorylase", "consolidated bioprocessing", "gene integration", "glucanase" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Journal of Industrial Microbiology and Biotechnology", "volume": "46", "publisher_information": "Oxford University Press", "country_publication_code": "DE", "creator": [ { "name": "Sun-Ki [0000 0004 1936 738X grid.213876.9 Department of Genetics University of Georgia 30602 Athens GA USA,0000 0001 0789 9563 grid.254224.7 Department of Food Science and Technology Chung-Ang University 17546 Anseong Gyeonggi Republic of Korea,0000 0004 0446 2659 grid.135519.a The BioEnergy Science Center and the Center for BioEnergy Innovation Oak Ridge National Laboratory 37831 Oak Ridge TN USA] Kim", "primaryContact": true }, { "name": "Daehwan [0000 0001 2199 3636 grid.419357.d Biosciences Center,National Renewable Energy Laboratory Golden CO USA,0000 0004 0446 2659 grid.135519.a The BioEnergy Science Center and the Center for BioEnergy Innovation Oak Ridge National Laboratory 37831 Oak Ridge TN USA] Chung", "primaryContact": false }, { "name": "Michael E. [0000 0001 2199 3636 grid.419357.d Biosciences Center,National Renewable Energy Laboratory Golden CO USA,0000 0004 0446 2659 grid.135519.a The BioEnergy Science Center and the Center for BioEnergy Innovation Oak Ridge National Laboratory 37831 Oak Ridge TN USA] Himmel", "primaryContact": false }, { "name": "Yannick J. [0000 0001 2199 3636 grid.419357.d Biosciences Center,National Renewable Energy Laboratory Golden CO USA,0000 0004 0446 2659 grid.135519.a The BioEnergy Science Center and the Center for BioEnergy Innovation Oak Ridge National Laboratory 37831 Oak Ridge TN USA] Bomble", "primaryContact": false }, { "name": "Janet [0000 0004 1936 738X grid.213876.9 Department of Genetics University of Georgia 30602 Athens GA USA,0000 0004 0446 2659 grid.135519.a The BioEnergy Science Center and the Center for BioEnergy Innovation Oak Ridge National Laboratory 37831 Oak Ridge TN USA] Westpheling", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1772499", "active": false, "has_related_ids": [ "NREL/JA--2700-73412" ] }, { "brc": "CBI", "title": "Cross-national analysis of food security drivers: comparing results based on the Food Insecurity Experience Scale and Global Food Security Index", "description": "\n The second UN Sustainable Development Goal establishes food security as a priority for governments, multilateral organizations, and NGOs. These institutions track national-level food security performance with an array of metrics and weigh intervention options considering the leverage of many possible drivers. We studied the relationships between several candidate drivers and two response variables based on prominent measures of national food security: the 2019 Global Food Security Index (GFSI) and the Food Insecurity Experience Scale\u2019s (FIES) estimate of the percentage of a nation\u2019s population experiencing food security or mild food insecurity (FI\n
\n The second UN Sustainable Development Goal establishes food security as a priority for governments, multilateral organizations, and NGOs. These institutions track national-level food security performance with an array of metrics and weigh intervention options considering the leverage of many possible drivers. We studied the relationships between several candidate drivers and two response variables based on prominent measures of national food security: the 2019 Global Food Security Index (GFSI) and the Food Insecurity Experience Scale\u2019s (FIES) estimate of the percentage of a nation\u2019s population experiencing food security or mild food insecurity (FI\n
\n Software product line engineering is a best practice for managing reuse in families of software systems that is increasingly being applied to novel and emerging domains. In this work we investigate the use of software product line engineering in one of these new domains, synthetic biology. In synthetic biology living organisms are programmed to perform new functions or improve existing functions. These programs are designed and constructed using small building blocks made out of DNA. We conjecture that there are families of products that consist of common and variable DNA parts, and we can leverage product line engineering to help synthetic biologists build, evolve, and reuse DNA parts. In this paper we perform an investigation of domain engineering that leverages an open-source repository of more than 45,000 reusable DNA parts. We show the feasibility of these new types of product line models by identifying features and related artifacts in up to 93.5% of products, and that there is indeed both commonality and variability. We then construct feature models for four commonly engineered functions leading to product lines ranging from 10 to 7.5 \u00d7 10\n 20\n products. In a case study we demonstrate how we can use the feature models to help guide new experimentation in aspects of application engineering. Finally, in an empirical study we demonstrate the effectiveness and efficiency of automated reverse engineering on both complete and incomplete sets of products. In the process of these studies, we highlight key challenges and uncovered limitations of existing SPL techniques and tools which provide a roadmap for making SPL engineering applicable to new and emerging domains.\n
", "abstract": "\n Software product line engineering is a best practice for managing reuse in families of software systems that is increasingly being applied to novel and emerging domains. In this work we investigate the use of software product line engineering in one of these new domains, synthetic biology. In synthetic biology living organisms are programmed to perform new functions or improve existing functions. These programs are designed and constructed using small building blocks made out of DNA. We conjecture that there are families of products that consist of common and variable DNA parts, and we can leverage product line engineering to help synthetic biologists build, evolve, and reuse DNA parts. In this paper we perform an investigation of domain engineering that leverages an open-source repository of more than 45,000 reusable DNA parts. We show the feasibility of these new types of product line models by identifying features and related artifacts in up to 93.5% of products, and that there is indeed both commonality and variability. We then construct feature models for four commonly engineered functions leading to product lines ranging from 10 to 7.5 \u00d7 10\n 20\n products. In a case study we demonstrate how we can use the feature models to help guide new experimentation in aspects of application engineering. Finally, in an empirical study we demonstrate the effectiveness and efficiency of automated reverse engineering on both complete and incomplete sets of products. In the process of these studies, we highlight key challenges and uncovered limitations of existing SPL techniques and tools which provide a roadmap for making SPL engineering applicable to new and emerging domains.\n
", "date": "2021-03-24", "issue": "3", "identifier": "https://www.osti.gov/biblio/1772687", "bibliographicCitation": "https://doi.org/10.1007/s10664-021-09940-0", "keywords": [ "97 MATHEMATICS AND COMPUTING", "BioBricks", "Reverse engineering", "Software product lines", "Synthetic biology" ], "topic": [ "Computational Biology & Modeling" ], "journal_name": "Empirical Software Engineering", "volume": "26", "publisher_information": "Springer Science + Business Media", "country_publication_code": "Netherlands", "creator": [ { "name": "Mikaela (ORCID:0000000306207830) Cashman", "primaryContact": true }, { "name": "Justin (ORCID:0000000219272036) Firestone", "primaryContact": false }, { "name": "Myra B. (ORCID:0000000324432425) Cohen", "primaryContact": false }, { "name": "Thammasak Thianniwet", "primaryContact": false }, { "name": "Wei (ORCID:0000000338261276) Niu", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Inst. of Justice (NIJ)" } }, { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR)" } } ], "dataset_url": "https://www.osti.gov/biblio/1772687", "active": false }, { "brc": "CBI", "title": "A four-gene operon in Bacillus cereus produces two rare spore-decorating sugars", "description": "Not Available", "abstract": "Not Available", "date": "2017-02-28", "issue": "18", "identifier": "https://www.osti.gov/biblio/1772833", "bibliographicCitation": "https://doi.org/10.1074/jbc.M117.777417", "topic": [ "Unknown" ], "journal_name": "Journal of Biological Chemistry", "volume": "292", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Zi Li", "primaryContact": true }, { "name": "Thiya Mukherjee", "primaryContact": false }, { "name": "Kyle Bowler", "primaryContact": false }, { "name": "Sholeh Namdari", "primaryContact": false }, { "name": "Zachary Snow", "primaryContact": false }, { "name": "Sarah Prestridge", "primaryContact": false }, { "name": "Alexandra Carlton", "primaryContact": false }, { "name": "Maor Bar-Peled", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/1772833", "active": false }, { "brc": "CBI", "title": "Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass", "description": "Long-term climate change and periodic environmental extremes threaten food and fuel security and global crop productivity. Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience, these approaches require sufficient knowledge of the genes that underlie productivity and adaptation\u2014knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass (Panicum virgatum). Analysis of biomass and survival among 732\u00a0resequenced genotypes, which were grown across 10\u00a0common gardens that span 1,800\u00a0km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate\u2013gene\u2013biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene\u2013trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy.", "abstract": "Long-term climate change and periodic environmental extremes threaten food and fuel security and global crop productivity. Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience, these approaches require sufficient knowledge of the genes that underlie productivity and adaptation\u2014knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass (Panicum virgatum). Analysis of biomass and survival among 732\u00a0resequenced genotypes, which were grown across 10\u00a0common gardens that span 1,800\u00a0km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate\u2013gene\u2013biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene\u2013trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy.", "date": "2021-01-26", "issue": "7846", "identifier": "https://www.osti.gov/biblio/1773844", "bibliographicCitation": "https://doi.org/10.1038/s41586-020-03127-1", "keywords": [ "09 BIOMASS FUELS", "Panicum virgatum", "climate adaptation", "switchgrass" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Nature (London)", "volume": "590", "publisher_information": "Nature Publishing Group", "country_publication_code": "US", "creator": [ { "name": "John T. [HudsonAlpha Inst. for Biotechnology,Huntsville,AL (United States); University of Texas at Austin] (ORCID:0000000289381166) Lovell", "primaryContact": true }, { "name": "Alice H. [Univ. of Texas,Austin,TX (United States)] MacQueen", "primaryContact": false }, { "name": "Sujan [HudsonAlpha Inst. for Biotechnology,Huntsville,AL (United States)] Mamidi", "primaryContact": false }, { "name": "Jason [Univ. of Texas,Austin,TX (United States)] Bonnette", "primaryContact": false }, { "name": "Jerry [HudsonAlpha Inst. for Biotechnology,Huntsville,AL (United States)] (ORCID:0000000279433997) Jenkins", "primaryContact": false }, { "name": "Joseph D. [Univ. of Texas,Austin,TX (United States)] (ORCID:0000000285575086) Napier", "primaryContact": false }, { "name": "Avinash [HudsonAlpha Inst. for Biotechnology,Huntsville,AL (United States)] (ORCID:0000000173367012) Sreedasyam", "primaryContact": false }, { "name": "Adam [HudsonAlpha Inst. for Biotechnology,Huntsville,AL (United States)] Healey", "primaryContact": false }, { "name": "Adam [Lawrence Berkeley National Lab. (LBNL),Berkeley,CA (United States); Univ. of California,Berkeley,CA (United States)] Session", "primaryContact": false }, { "name": "Shengqiang [Lawrence Berkeley National Lab. (LBNL),Berkeley,CA (United States)] (ORCID:0000000243368994) Shu", "primaryContact": false }, { "name": "Kerrie [Lawrence Berkeley National Lab. (LBNL),Berkeley,CA (United States)] Barry", "primaryContact": false }, { "name": "Stacy [Rutgers Univ.,New Brunswick,NJ (United States)] Bonos", "primaryContact": false }, { "name": "LoriBeth [HudsonAlpha Inst. for Biotechnology,Huntsville,AL (United States)] Boston", "primaryContact": false }, { "name": "Christopher [Lawrence Berkeley National Lab. (LBNL),Berkeley,CA (United States)] Daum", "primaryContact": false }, { "name": "Shweta [Lawrence Berkeley National Lab. (LBNL),Berkeley,CA (United States)] Deshpande", "primaryContact": false }, { "name": "Aren [Lawrence Berkeley National Lab. (LBNL),Berkeley,CA (United States)] Ewing", "primaryContact": false }, { "name": "Paul P. [HudsonAlpha Inst. for Biotechnology,Huntsville,AL (United States)] Grabowski", "primaryContact": false }, { "name": "Taslima [Univ. of Texas,Austin,TX (United States)] Haque", "primaryContact": false }, { "name": "Melanie [US Dept. of Agriculture (USDA),Griffin,GA (United States)] Harrison", "primaryContact": false }, { "name": "Jiming [Michigan State Univ.,East Lansing,MI (United States)] (ORCID:0000000264356140) Jiang", "primaryContact": false }, { "name": "Dave [Univ. of Arizona,Tucson,AZ (United States)] (ORCID:0000000230923629) Kudrna", "primaryContact": false }, { "name": "Anna [Lawrence Berkeley National Lab. (LBNL),Berkeley,CA (United States)] Lipzen", "primaryContact": false }, { "name": "Thomas H. [Univ. of Georgia,Athens,GA (United States)] (ORCID:0000000156819662) Pendergast", "primaryContact": false }, { "name": "Chris [HudsonAlpha Inst. for Biotechnology,Huntsville,AL (United States)] Plott", "primaryContact": false }, { "name": "Peng [Univ. of Georgia,Athens,GA (United States)] Qi", "primaryContact": false }, { "name": "Christopher A. [Clemson Univ.,SC (United States)] (ORCID:0000000227804274) Saski", "primaryContact": false }, { "name": "Eugene V. [Univ. of Texas,Austin,TX (United States); Marshall Univ.,Huntington,WV (United States)] (ORCID:0000000326897410) Shakirov", "primaryContact": false }, { "name": "David [HudsonAlpha Inst. for Biotechnology,Huntsville,AL (United States)] Sims", "primaryContact": false }, { "name": "Manoj [Jawaharlal Nehru Univ.,New Delhi (India)] Sharma", "primaryContact": false }, { "name": "Rita [Jawaharlal Nehru Univ.,New Delhi (India)] Sharma", "primaryContact": false }, { "name": "Ada [HudsonAlpha Inst. for Biotechnology,Huntsville,AL (United States)] Stewart", "primaryContact": false }, { "name": "Vasanth R. [Lawrence Berkeley National Lab. (LBNL),Berkeley,CA (United States)] (ORCID:0000000299835707) Singan", "primaryContact": false }, { "name": "Yuhong [Noble Research Inst. LLC,Ardmore,OK (United States)] Tang", "primaryContact": false }, { "name": "Sandra [Univ. of Nebraska,Lincoln,NE (United States)] Thibivillier", "primaryContact": false }, { "name": "Jenell [HudsonAlpha Inst. for Biotechnology,Huntsville,AL (United States)] Webber", "primaryContact": false }, { "name": "Xiaoyu [Univ. of Texas,Austin,TX (United States)] Weng", "primaryContact": false }, { "name": "Melissa [HudsonAlpha Inst. for Biotechnology,Huntsville,AL (United States)] Williams", "primaryContact": false }, { "name": "Guohong Albert [Lawrence Berkeley National Lab. (LBNL),Berkeley,CA (United States)] Wu", "primaryContact": false }, { "name": "Yuko [Lawrence Berkeley National Lab. (LBNL),Berkeley,CA (United States)] Yoshinaga", "primaryContact": false }, { "name": "Matthew [Lawrence Berkeley National Lab. (LBNL),Berkeley,CA (United States)] Zane", "primaryContact": false }, { "name": "Li [Univ. of Texas,Austin,TX (United States)] Zhang", "primaryContact": false }, { "name": "Jiyi [Noble Research Inst. LLC,Ardmore,OK (United States)] Zhang", "primaryContact": false }, { "name": "Kathrine D. [Univ. of Texas,Austin,TX (United States)] Behrman", "primaryContact": false }, { "name": "Arvid R. [South Dakota State Univ.,Brookings,SD (United States)] Boe", "primaryContact": false }, { "name": "Philip A. [US Dept. of Agriculture (USDA),Temple,TX (United States)] Fay", "primaryContact": false }, { "name": "Felix B. [Univ. of Missouri,Columbia,MO (United States)] (ORCID:0000000308256855) Fritschi", "primaryContact": false }, { "name": "Julie D. [Argonne National Lab. (ANL),Argonne,IL (United States)] (ORCID:0000000170694560) Jastrow", "primaryContact": false }, { "name": "John [US Dept. of Agriculture (USDA),Kingsville,TX (United States)] Lloyd-Reilley", "primaryContact": false }, { "name": "Juan Manuel [Antonio Narro Agrarian Autonomous Univ.,Saltillo (Mexico)] Mart\u00ednez-Reyna", "primaryContact": false }, { "name": "Roser [Argonne National Lab. (ANL),Argonne,IL (United States)] Matamala", "primaryContact": false }, { "name": "Robert B. [US Dept. of Agriculture (USDA),Lincoln,NE (United States)] Mitchell", "primaryContact": false }, { "name": "Francis M. [Texas A & M Univ.,Overton,TX (United States)] Rouquette", "primaryContact": false }, { "name": "Pamela [Univ. of California,Davis,CA (United States); Joint BioEnergy Institute (JBEI),Emeryville,CA (United States)] (ORCID:0000000241071345) Ronald", "primaryContact": false }, { "name": "Malay [Noble Research Inst. LLC,Ardmore,OK (United States)] Saha", "primaryContact": false }, { "name": "Christian M. [US Dept. of Agriculture (USDA),Albany,CA (United States)] Tobias", "primaryContact": false }, { "name": "Michael [Noble Research Inst. LLC,Ardmore,OK (United States)] (ORCID:0000000198500828) Udvardi", "primaryContact": false }, { "name": "Rod A. [Univ. of Arizona,Tucson,AZ (United States)] (ORCID:0000000166336226) Wing", "primaryContact": false }, { "name": "Yanqi [Oklahoma State Univ.,Stillwater,OK (United States)] (ORCID:0000000308026881) Wu", "primaryContact": false }, { "name": "Laura E. [Univ. of Oklahoma,Norman,OK (United States); Washington State Univ.,Pullman,WA (United States)] (ORCID:0000000186107551) Bartley", "primaryContact": false }, { "name": "Michael [US Dept. of Agriculture (USDA),Madison,WI (United States); Univ. of Wisconsin,Madison,WI (United States)] Casler", "primaryContact": false }, { "name": "Katrien M. [Univ. of Georgia,Athens,GA (United States); USDOE Center for Bioenergy Innovation,Oak Ridge,TN (United States)] Devos", "primaryContact": false }, { "name": "David B. [Michigan State Univ.,East Lansing,MI (United States)] Lowry", "primaryContact": false }, { "name": "Daniel S. [Lawrence Berkeley National Lab. (LBNL),Berkeley,CA (United States); Univ. of California,Berkeley,CA (United States); Center for Advanced Bioenergy and Bioproducts Innovation (CABBI),Berkeley,CA (United States); Chan-Zuckerberg Biohub,San Francisco,CA (United States)] (ORCID:0000000287042224) Rokhsar", "primaryContact": false }, { "name": "Jane [HudsonAlpha Inst. for Biotechnology,Huntsville,AL (United States)] (ORCID:0000000283568325) Grimwood", "primaryContact": false }, { "name": "Thomas E. [Univ. of Texas,Austin,TX (United States)] (ORCID:0000000195509288) Juenger", "primaryContact": false }, { "name": "Jeremy [HudsonAlpha Inst. for Biotechnology,Huntsville,AL (United States); Lawrence Berkeley National Lab. (LBNL),Berkeley,CA (United States)] (ORCID:0000000180629172) Schmutz", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division" } } ], "dataset_url": "https://www.osti.gov/biblio/1773844", "active": false }, { "brc": "CBI", "title": "Revisiting \u201cAdditional Carbon\u201d: Tracking Atmosphere\u2013Ecosystem Carbon Exchange to Establish Mitigation and Negative Emissions From Bio-Based Systems", "description": "Climate stabilization plans rely heavily on advanced bioenergy and bioproducts for substitution of fossil-based energy sources and materials, and increasingly, for negative emissions via the direct sequestration of biogenic carbon. Yet, there remain persistent, largely unresolved critiques of bioenergy assessment methodology, particularly in the areas of land use and biogenic carbon accounting. The concept of \u201cadditional carbon\u201d calls for evaluating the climate performance of bio-based systems by whether feedstock production creates measurable new local agro-ecosystem uptake of carbon from the atmosphere. This concept is challenging to operationalize for first-generation biofuels, and has largely been advanced as a negative critique. However, carbon additionality is more straightforward to establish\u2014and less critical to overall system mitigation performance\u2014in advanced bioenergy systems. In this Perspective, I review the additional carbon critique, and why it is analytically challenging to address in first-generation biofuel systems based on conventional food crops with large existing markets. Next, I make a case that carbon additionality (1) is more readily achievable with cellulosic feedstocks, (2) is more directly observable for dedicated biomass crops, and (3) is not a strict requirement for achieving net mitigation in carbon-negative bio-based systems. I end by discussing how centering atmosphere\u2013ecosystem carbon exchanges in bio-based system assessment could create new opportunities for enterprise-scale performance monitoring and verification, augmenting and diversifying the current reliance on model-based life-cycle assessment approaches.
", "abstract": "Climate stabilization plans rely heavily on advanced bioenergy and bioproducts for substitution of fossil-based energy sources and materials, and increasingly, for negative emissions via the direct sequestration of biogenic carbon. Yet, there remain persistent, largely unresolved critiques of bioenergy assessment methodology, particularly in the areas of land use and biogenic carbon accounting. The concept of \u201cadditional carbon\u201d calls for evaluating the climate performance of bio-based systems by whether feedstock production creates measurable new local agro-ecosystem uptake of carbon from the atmosphere. This concept is challenging to operationalize for first-generation biofuels, and has largely been advanced as a negative critique. However, carbon additionality is more straightforward to establish\u2014and less critical to overall system mitigation performance\u2014in advanced bioenergy systems. In this Perspective, I review the additional carbon critique, and why it is analytically challenging to address in first-generation biofuel systems based on conventional food crops with large existing markets. Next, I make a case that carbon additionality (1) is more readily achievable with cellulosic feedstocks, (2) is more directly observable for dedicated biomass crops, and (3) is not a strict requirement for achieving net mitigation in carbon-negative bio-based systems. I end by discussing how centering atmosphere\u2013ecosystem carbon exchanges in bio-based system assessment could create new opportunities for enterprise-scale performance monitoring and verification, augmenting and diversifying the current reliance on model-based life-cycle assessment approaches.
", "date": "2021-04-12", "identifier": "https://www.osti.gov/biblio/1776983", "bibliographicCitation": "https://doi.org/10.3389/fclim.2021.603239", "keywords": [ "54 ENVIRONMENTAL SCIENCES", "BECCS", "additional carbon", "biofuels", "biogenic carbon", "bioproducts", "life-cycle assessment", "mitigation", "negative emissions" ], "topic": [ "Environmental Science & Sustainability" ], "journal_name": "Frontiers in Climate", "volume": "3", "publisher_information": "Frontiers Media SA", "country_publication_code": "Country unknown/Code not available", "creator": [ { "name": "John L. Field", "primaryContact": true } ], "funding": [ { "fundingOrganization": { "organizationName": "NIFA" } }, { "fundingOrganization": { "organizationName": "USDA" } }, { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1776983", "active": false }, { "brc": "CBI", "title": "Machine Learning-Based Classification of Lignocellulosic Biomass from Pyrolysis-Molecular Beam Mass Spectrometry Data", "description": "High-throughput analysis of biomass is necessary to ensure consistent and uniform feedstocks for agricultural and bioenergy applications and is needed to inform genomics and systems biology models. Pyrolysis followed by mass spectrometry such as molecular beam mass spectrometry (py-MBMS) analyses are becoming increasingly popular for the rapid analysis of biomass cell wall composition and typically require the use of different data analysis tools depending on the need and application. Here, the authors report the py-MBMS analysis of several types of lignocellulosic biomass to gain an understanding of spectral patterns and variation with associated biomass composition and use machine learning approaches to classify, differentiate, and predict biomass types on the basis of py-MBMS spectra. Py-MBMS spectra were also corrected for instrumental variance using generalized linear modeling (GLM) based on the use of select ions relative abundances as spike-in controls. Machine learning classification algorithms e.g., random forest, k-nearest neighbor, decision tree, Gaussian Na\u00efve Bayes, gradient boosting, and multilayer perceptron classifiers were used. The k-nearest neighbors (k-NN) classifier generally performed the best for classifications using raw spectral data, and the decision tree classifier performed the worst. After normalization of spectra to account for instrumental variance, all the classifiers had comparable and generally acceptable performance for predicting the biomass types, although the k-NN and decision tree classifiers were not as accurate for prediction of specific sample types. Gaussian Na\u00efve Bayes (GNB) and extreme gradient boosting (XGB) classifiers performed better than the k-NN and the decision tree classifiers for the prediction of biomass mixtures. The data analysis workflow reported here could be applied and extended for comparison of biomass samples of varying types, species, phenotypes, and/or genotypes or subjected to different treatments, environments, etc. to further elucidate the sources of spectral variance, patterns, and to infer compositional information based on spectral analysis, particularly for analysis of data without a priori knowledge of the feedstock composition or identity.
", "abstract": "High-throughput analysis of biomass is necessary to ensure consistent and uniform feedstocks for agricultural and bioenergy applications and is needed to inform genomics and systems biology models. Pyrolysis followed by mass spectrometry such as molecular beam mass spectrometry (py-MBMS) analyses are becoming increasingly popular for the rapid analysis of biomass cell wall composition and typically require the use of different data analysis tools depending on the need and application. Here, the authors report the py-MBMS analysis of several types of lignocellulosic biomass to gain an understanding of spectral patterns and variation with associated biomass composition and use machine learning approaches to classify, differentiate, and predict biomass types on the basis of py-MBMS spectra. Py-MBMS spectra were also corrected for instrumental variance using generalized linear modeling (GLM) based on the use of select ions relative abundances as spike-in controls. Machine learning classification algorithms e.g., random forest, k-nearest neighbor, decision tree, Gaussian Na\u00efve Bayes, gradient boosting, and multilayer perceptron classifiers were used. The k-nearest neighbors (k-NN) classifier generally performed the best for classifications using raw spectral data, and the decision tree classifier performed the worst. After normalization of spectra to account for instrumental variance, all the classifiers had comparable and generally acceptable performance for predicting the biomass types, although the k-NN and decision tree classifiers were not as accurate for prediction of specific sample types. Gaussian Na\u00efve Bayes (GNB) and extreme gradient boosting (XGB) classifiers performed better than the k-NN and the decision tree classifiers for the prediction of biomass mixtures. The data analysis workflow reported here could be applied and extended for comparison of biomass samples of varying types, species, phenotypes, and/or genotypes or subjected to different treatments, environments, etc. to further elucidate the sources of spectral variance, patterns, and to infer compositional information based on spectral analysis, particularly for analysis of data without a priori knowledge of the feedstock composition or identity.
", "date": "2021-04-14", "issue": "8", "identifier": "https://www.osti.gov/biblio/1777643", "bibliographicCitation": "https://doi.org/10.3390/ijms22084107", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "Gaussian Na\u00efve Bayes", "bioenergy", "biomass", "biomass analysis", "biomaterials", "biopolymers", "classifiers", "cork", "decision tree", "gradient boosting", "molecular beam mass spectrometry", "multilayer perceptron", "pyrolysis", "random\r\nforest", "suberin" ], "topic": [ "Microbiology" ], "journal_name": "International Journal of Molecular Sciences (Online)", "volume": "22", "publisher_information": "MDPI AG", "country_publication_code": "Switzerland", "creator": [ { "name": "Ambarish Nag", "primaryContact": true }, { "name": "Alida Gerritsen", "primaryContact": false }, { "name": "Crissa Doeppke", "primaryContact": false }, { "name": "Anne E. Harman-Ware", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Transportation Office. Bioenergy Technologies Office" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1777643", "active": false, "has_related_ids": [ "NREL/JA--2800-79514" ] }, { "brc": "CBI", "title": "Engineering promiscuity of chloramphenicol acetyltransferase for microbial designer ester biosynthesis", "description": "Not Available", "abstract": "Not Available", "date": "2021-06-30", "issue": "C", "identifier": "https://www.osti.gov/biblio/1778546", "bibliographicCitation": "https://doi.org/10.1016/j.ymben.2021.04.005", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "60 APPLIED LIFE SCIENCES", "Clostridium thermocellum", "Escherichia coli", "Ester biosynthesis", "alcohol acyltransferase", "chloramphenicol acetyltransferase", "enzyme thermostability" ], "topic": [ "Microbiology", "Plant Biology" ], "journal_name": "Metabolic Engineering", "volume": "66", "publisher_information": "Elsevier", "country_publication_code": "Belgium", "creator": [ { "name": "Hyeongmin Seo", "primaryContact": true }, { "name": "Jong-Won Lee", "primaryContact": false }, { "name": "Richard J. Giannone", "primaryContact": false }, { "name": "Noah J. (ORCID:0000000240935615) Dunlap", "primaryContact": false }, { "name": "Cong T. (ORCID:000000028362725X) Trinh", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1778546", "active": false }, { "brc": "CBI", "title": "K-FIT: An accelerated kinetic parameterization algorithm using steady-state fluxomic data", "description": "Not Available", "abstract": "Not Available", "date": "2020-08-31", "issue": "C", "identifier": "https://www.osti.gov/biblio/1779370", "bibliographicCitation": "https://doi.org/10.1016/j.ymben.2020.03.001", "topic": [ "Unknown" ], "journal_name": "Metabolic Engineering", "volume": "61", "publisher_information": "Elsevier", "country_publication_code": "Belgium", "creator": [ { "name": "Saratram Gopalakrishnan", "primaryContact": true }, { "name": "Satyakam Dash", "primaryContact": false }, { "name": "Costas Maranas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/1779370", "active": false }, { "brc": "CBI", "title": "Development of a thermophilic coculture for corn fiber conversion to ethanol", "description": "\n The fiber in corn kernels, currently unutilized in the corn to ethanol process, represents an opportunity for introduction of cellulose conversion technology. We report here that\n
\n The fiber in corn kernels, currently unutilized in the corn to ethanol process, represents an opportunity for introduction of cellulose conversion technology. We report here that\n
\n The\n
\n Of the 2772 completed microbial genomes downloaded from GenBank only 665 genomes had an annotated\n
\n The coupling of the largest RNase P RNA database and associated structure class identification with the P Finder algorithm is both sensitive and rapid, yielding high quality results to aid researchers annotating either genomic or metagenomic data. It is the only algorithm to date that can identify challenging RNAse P classes such as C-type and the minimal T-type RNase P RNAs. P Finder is written in C# and has a user-friendly GUI that can run on multiple 64-bit windows platforms (Windows Vista/7/8/10). P Finder is free available for download at\n
\n The\n
\n Of the 2772 completed microbial genomes downloaded from GenBank only 665 genomes had an annotated\n
\n The coupling of the largest RNase P RNA database and associated structure class identification with the P Finder algorithm is both sensitive and rapid, yielding high quality results to aid researchers annotating either genomic or metagenomic data. It is the only algorithm to date that can identify challenging RNAse P classes such as C-type and the minimal T-type RNase P RNAs. P Finder is written in C# and has a user-friendly GUI that can run on multiple 64-bit windows platforms (Windows Vista/7/8/10). P Finder is free available for download at\n
As a major component of plant secondary cell walls, lignin provides structural integrity and rigidity, and contributes to primary defense by providing a physical barrier to pathogen ingress. Genetic modification of lignin biosynthesis has been adopted to reduce the recalcitrance of lignified cell walls to improve biofuel production, tree pulping properties and forage digestibility. However, lignin\u2010modification is often, but unpredictably, associated with dwarf phenotypes. Hypotheses suggested to explain this include: collapsed vessels leading to defects in water and solute transport; accumulation of molecule(s) that are inhibitory to plant growth or deficiency of metabolites that are critical for plant growth; activation of defense pathways linked to cell wall integrity sensing. However, there is still no commonly accepted underlying mechanism for the growth defects. Here, we discuss recent data on transcriptional reprogramming in plants with modified lignin content and their corresponding suppressor mutants, and evaluate growth\u2010defense trade\u2010offs as a factor underlying the growth phenotypes. New approaches will be necessary to estimate how gross changes in transcriptional reprogramming may quantitatively affect growth. Better understanding of the basis for yield drag following cell wall engineering is important for the biotechnological exploitation of plants as factories for fuels and chemicals.
", "abstract": "As a major component of plant secondary cell walls, lignin provides structural integrity and rigidity, and contributes to primary defense by providing a physical barrier to pathogen ingress. Genetic modification of lignin biosynthesis has been adopted to reduce the recalcitrance of lignified cell walls to improve biofuel production, tree pulping properties and forage digestibility. However, lignin\u2010modification is often, but unpredictably, associated with dwarf phenotypes. Hypotheses suggested to explain this include: collapsed vessels leading to defects in water and solute transport; accumulation of molecule(s) that are inhibitory to plant growth or deficiency of metabolites that are critical for plant growth; activation of defense pathways linked to cell wall integrity sensing. However, there is still no commonly accepted underlying mechanism for the growth defects. Here, we discuss recent data on transcriptional reprogramming in plants with modified lignin content and their corresponding suppressor mutants, and evaluate growth\u2010defense trade\u2010offs as a factor underlying the growth phenotypes. New approaches will be necessary to estimate how gross changes in transcriptional reprogramming may quantitatively affect growth. Better understanding of the basis for yield drag following cell wall engineering is important for the biotechnological exploitation of plants as factories for fuels and chemicals.
", "date": "2021-05-03", "issue": "1", "identifier": "https://www.osti.gov/biblio/1781272", "bibliographicCitation": "https://doi.org/10.1111/nph.17383", "topic": [ "Unknown" ], "journal_name": "New Phytologist", "volume": "231", "publisher_information": "Wiley-Blackwell", "country_publication_code": "GB", "creator": [ { "name": "Chan Man [BioDiscovery Institute and Department of Biological Sciences University of North Texas 1155 Union Circle #311428 Denton TX 76203 USA,Center for Bioenergy Innovation (CBI) Oak Ridge National Laboratory Oak Ridge TN 37831 USA] (ORCID:0000000211980564) Ha", "primaryContact": true }, { "name": "Xiaolan [College of Life Sciences Hubei University No. 28 Nanli Road Hong\u2010shan District,Wuchang,Wuhan Hubei Province 430068 China] Rao", "primaryContact": false }, { "name": "Garima [BioDiscovery Institute and Department of Biological Sciences University of North Texas 1155 Union Circle #311428 Denton TX 76203 USA] Saxena", "primaryContact": false }, { "name": "Richard A. [BioDiscovery Institute and Department of Biological Sciences University of North Texas 1155 Union Circle #311428 Denton TX 76203 USA,Center for Bioenergy Innovation (CBI) Oak Ridge National Laboratory Oak Ridge TN 37831 USA] (ORCID:0000000183939408) Dixon", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/1781272", "active": false }, { "brc": "CBI", "title": "Structural and functional analysis of lignostilbene dioxygenases from Sphingobium sp. SYK-6", "description": "Not Available", "abstract": "Not Available", "date": "2020-12-31", "issue": "C", "identifier": "https://www.osti.gov/biblio/1782872", "bibliographicCitation": "https://doi.org/10.1016/j.jbc.2021.100758", "keywords": [ "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "59 BASIC BIOLOGICAL SCIENCES", "aromatic catabolism", "bacterial catabolism", "carotenoid cleavage oxygenase", "lignin degradation", "lignostilbene" ], "topic": [ "Chemistry", "Microbiology" ], "journal_name": "Journal of Biological Chemistry", "volume": "296", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Eugene Kuatsjah", "primaryContact": true }, { "name": "Anson C. K. Chan", "primaryContact": false }, { "name": "Rui Katahira", "primaryContact": false }, { "name": "Stefan J. Haugen", "primaryContact": false }, { "name": "Gregg T. Beckham", "primaryContact": false }, { "name": "Michael E. P. (ORCID:0000000325890014) Murphy", "primaryContact": false }, { "name": "Lindsay D. (ORCID:0000000267748158) Eltis", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Bioenergy Technologies Office (EE-3B)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1782872", "active": false, "has_related_ids": [ "NREL/JA--2800-80099" ] }, { "brc": "CBI", "title": "Polyurethanes Based on Unmodified and Refined Technical Lignins: Correlation between Molecular Structure and Material Properties", "description": "The structural complexity and robust intermolecular interactions have challenged the incorporation of technical lignin into value-added polymeric materials for decades. To study the correlation between lignin molecular structure and material properties of lignin-based polyurethanes, we applied co-solvent enhanced lignocellulosic fractionation pretreatment followed by sequential precipitation to produce three distinct lignin preparations with narrowly distributed (molecular weight dispersity <2) and comparatively low molecular weight (<1500 g/mol) from poplar biomass. Structural characterization indicated that these lignin preparations differed in average molecular chain length and stiffness as well as hydroxyl group distribution. Secondary hydroxyl group providers such as aliphatic diols and polyethers were incorporated as building blocks into the lignin-based polyurethanes to provide additional hydrogen capacity to improve the dispersion of lignin in the polyurethane network. The selected aliphatic diols and polyethers interacted with lignin molecules at different levels of strength depending on their molecular structure, and their impacts were ultimately reflected in the mechanical and thermal properties of the resulting lignin-based polyurethanes. The copolymerization of technical lignin with tailored structure and secondary hydroxyl providers could provide new strategies in formulating lignin-based/containing polyurethanes for various functional applications.", "abstract": "The structural complexity and robust intermolecular interactions have challenged the incorporation of technical lignin into value-added polymeric materials for decades. To study the correlation between lignin molecular structure and material properties of lignin-based polyurethanes, we applied co-solvent enhanced lignocellulosic fractionation pretreatment followed by sequential precipitation to produce three distinct lignin preparations with narrowly distributed (molecular weight dispersity <2) and comparatively low molecular weight (<1500 g/mol) from poplar biomass. Structural characterization indicated that these lignin preparations differed in average molecular chain length and stiffness as well as hydroxyl group distribution. Secondary hydroxyl group providers such as aliphatic diols and polyethers were incorporated as building blocks into the lignin-based polyurethanes to provide additional hydrogen capacity to improve the dispersion of lignin in the polyurethane network. The selected aliphatic diols and polyethers interacted with lignin molecules at different levels of strength depending on their molecular structure, and their impacts were ultimately reflected in the mechanical and thermal properties of the resulting lignin-based polyurethanes. The copolymerization of technical lignin with tailored structure and secondary hydroxyl providers could provide new strategies in formulating lignin-based/containing polyurethanes for various functional applications.", "date": "2021-04-25", "issue": "5", "identifier": "https://www.osti.gov/biblio/1784105", "bibliographicCitation": "https://doi.org/10.1021/acs.biomac.1c00223", "keywords": [ "36 MATERIALS SCIENCE" ], "topic": [ "Materials Science & Bioproducts" ], "journal_name": "Biomacromolecules", "volume": "22", "publisher_information": "American Chemical Society", "country_publication_code": "US", "creator": [ { "name": "Yun-Yan [Univ. of Tennessee,Knoxville,TN (United States). Center for Renewable Carbon,Dept. of Forestry,Wildlife,and Fisheries] Wang", "primaryContact": true }, { "name": "Brent [Univ. of California,Riverside,CA (United States). Center for Environmental Research and Technology (CE-CERT),Bourns College of Engineering; Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). The Center for Bioenergy Innovation (CBI); Univ. of California,Riverside,CA (United States)] Scheidemantle", "primaryContact": false }, { "name": "Charles E. [Univ. of California,Riverside,CA (United States). Center for Environmental Research and Technology (CE-CERT),Bourns College of Engineering; Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). The Center for Bioenergy Innovation (CBI); Univ. of California,Riverside,CA (United States); Univ. of California,Riverside,CA (United States). Dept. of Chemical and Environmental Engineering] Wyman", "primaryContact": false }, { "name": "Charles M. [Univ. of California,Riverside,CA (United States). Center for Environmental Research and Technology (CE-CERT),Bourns College of Engineering; Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). The Center for Bioenergy Innovation (CBI); Univ. of California,Riverside,CA (United States); Univ. of California,Riverside,CA (United States). Dept. of Chemical and Environmental Engineering] (ORCID:0000000250470815) Cai", "primaryContact": false }, { "name": "Arthur J. [Univ. of Tennessee,Knoxville,TN (United States). Center for Renewable Carbon,Dept. of Forestry,Wildlife,and Fisheries; Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). The Center for Bioenergy Innovation (CBI); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Joint Institute for Biological Science; Univ. of Tennessee,Knoxville,TN (United States). Dept. of Chemical and Biomolecular Engineering] (ORCID:000000023536554X) Ragauskas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1784105", "active": false }, { "brc": "CBI", "title": "Emerging Strategies for Modifying Lignin Chemistry to Enhance Biological Lignin Valorization", "description": "Biological lignin valorization represents a promising approach contributing to sustainable and economic biorefineries. Here, the low level of valuable lignin\u2013derived products remains a major challenge hindering the implementation of microbial lignin conversion. Lignin's properties play a significant role in determining the efficiency of lignin bioconversion. To date, despite significant progress in the development of biomass pretreatment, lignin fractionation, and fermentation over the last few decades, little efforts have gone into identifying the ideal lignin substrates for an efficient microbial metabolism. In this Minireview, emerging and state\u2013of\u2013the\u2013art strategies for biomass pretreatment and lignin fractionation are summarized to elaborate their roles in modifying lignin structure for bioconversion. Fermentation strategies aimed at enhancing lignin depolymerization for microbial utilization are systematically reviewed as well. With an improved understanding of the ideal lignin structure elucidated by comprehensive metabolic pathways and/or big data analysis, modifying lignin chemistry could be more directional and effective. Ultimately, together with the progress of fermentation process optimization, biological lignin valorization will become more competitive in biorefineries.", "abstract": "Biological lignin valorization represents a promising approach contributing to sustainable and economic biorefineries. Here, the low level of valuable lignin\u2013derived products remains a major challenge hindering the implementation of microbial lignin conversion. Lignin's properties play a significant role in determining the efficiency of lignin bioconversion. To date, despite significant progress in the development of biomass pretreatment, lignin fractionation, and fermentation over the last few decades, little efforts have gone into identifying the ideal lignin substrates for an efficient microbial metabolism. In this Minireview, emerging and state\u2013of\u2013the\u2013art strategies for biomass pretreatment and lignin fractionation are summarized to elaborate their roles in modifying lignin structure for bioconversion. Fermentation strategies aimed at enhancing lignin depolymerization for microbial utilization are systematically reviewed as well. With an improved understanding of the ideal lignin structure elucidated by comprehensive metabolic pathways and/or big data analysis, modifying lignin chemistry could be more directional and effective. Ultimately, together with the progress of fermentation process optimization, biological lignin valorization will become more competitive in biorefineries.", "date": "2020-08-03", "issue": "20", "identifier": "https://www.osti.gov/biblio/1784146", "bibliographicCitation": "https://doi.org/10.1002/cssc.202001401", "keywords": [ "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "59 BASIC BIOLOGICAL SCIENCES", "biocatalysis", "biomass valorization", "fermentation", "lignin", "structure elucidation" ], "topic": [ "Chemistry", "Microbiology" ], "journal_name": "ChemSusChem", "volume": "13", "publisher_information": "ChemPubSoc Europe", "country_publication_code": "US", "creator": [ { "name": "Zhi\u2010Min [Inner Mongolia Univ.,Hohhot (China); Univ. of Tennessee,Knoxville,TN (United States)] Zhao", "primaryContact": true }, { "name": "Zhi\u2010Hua [Texas A & M Univ.,College Station,TX (United States)] Liu", "primaryContact": false }, { "name": "Yunqiao Joseph [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000325541447) Pu", "primaryContact": false }, { "name": "Xianzhi [Univ. of Tennessee,Knoxville,TN (United States)] Meng", "primaryContact": false }, { "name": "Jifei [Inner Mongolia Univ.,Hohhot (China)] Xu", "primaryContact": false }, { "name": "Joshua S. [Texas A & M Univ.,College Station,TX (United States)] Yuan", "primaryContact": false }, { "name": "Arthur J. [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Univ. of Tennessee Institute of Agriculture,Knoxville,TN (United States)] (ORCID:000000023536554X) Ragauskas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "Center for Bioenergy Innovation (CBI)" } }, { "fundingOrganization": { "organizationName": "National Natural Science Foundation of China" } }, { "fundingOrganization": { "organizationName": "Natural Science Foundation of Inner Mongolia" } }, { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Office of Sustainable Transportation. Bioenergy Technologies Office (BETO)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1784146", "active": false }, { "brc": "CBI", "title": "Elucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modeling", "description": "\n Marine nitrogen-fixing microorganisms are an important source of fixed nitrogen in oceanic ecosystems. The colonial cyanobacterium\n
\n Marine nitrogen-fixing microorganisms are an important source of fixed nitrogen in oceanic ecosystems. The colonial cyanobacterium\n
\n We report the draft genome sequences of five native nitrogen-fixing bacteria associated with roots of switchgrass isolated from the Tallgrass Prairies of Oklahoma. Nitrogen-fixing genes, including the\n
\n We report the draft genome sequences of five native nitrogen-fixing bacteria associated with roots of switchgrass isolated from the Tallgrass Prairies of Oklahoma. Nitrogen-fixing genes, including the\n
Sex dimorphism and gene expression were studied in developing catkins in 159 F 2 individuals from the bioenergy crop Salix purpurea , and potential mechanisms and pathways for regulating sex development were explored. Differential expression, eQTL, bisulfite sequencing, and network analysis were used to characterize sex dimorphism, detect candidate master regulator genes, and identify pathways through which the sex determination region (SDR) may mediate sex dimorphism. Eleven genes are presented as candidates for master regulators of sex, supported by gene expression and network analyses. These include genes putatively involved in hormone signaling, epigenetic modification, and regulation of transcription. eQTL analysis revealed a suite of transcription factors and genes involved in secondary metabolism and floral development that were predicted to be under direct control of the sex determination region. Furthermore, data from bisulfite sequencing and small RNA sequencing revealed strong differences in expression between males and females that would implicate both of these processes in sex dimorphism pathways. These data indicate that the mechanism of sex determination in Salix purpurea is likely different from that observed in the related genus Populus. This further demonstrates the dynamic nature of SDRs in plants, which involves a multitude of mechanisms of sex determination and a high rate of turnover.
", "abstract": "Sex dimorphism and gene expression were studied in developing catkins in 159 F 2 individuals from the bioenergy crop Salix purpurea , and potential mechanisms and pathways for regulating sex development were explored. Differential expression, eQTL, bisulfite sequencing, and network analysis were used to characterize sex dimorphism, detect candidate master regulator genes, and identify pathways through which the sex determination region (SDR) may mediate sex dimorphism. Eleven genes are presented as candidates for master regulators of sex, supported by gene expression and network analyses. These include genes putatively involved in hormone signaling, epigenetic modification, and regulation of transcription. eQTL analysis revealed a suite of transcription factors and genes involved in secondary metabolism and floral development that were predicted to be under direct control of the sex determination region. Furthermore, data from bisulfite sequencing and small RNA sequencing revealed strong differences in expression between males and females that would implicate both of these processes in sex dimorphism pathways. These data indicate that the mechanism of sex determination in Salix purpurea is likely different from that observed in the related genus Populus. This further demonstrates the dynamic nature of SDRs in plants, which involves a multitude of mechanisms of sex determination and a high rate of turnover.
", "date": "2021-07-31", "issue": "1", "identifier": "https://www.osti.gov/biblio/1811559", "bibliographicCitation": "https://doi.org/10.1038/s41438-021-00606-y", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "Flowering", "Plant hybridization" ], "topic": [ "Microbiology" ], "journal_name": "Horticulture Research", "volume": "8", "publisher_information": "Oxford University Press", "country_publication_code": "GB", "creator": [ { "name": "Brennan (ORCID:0000000248960030) Hyden", "primaryContact": true }, { "name": "Craig H. Carlson", "primaryContact": false }, { "name": "Fred E. (ORCID:0000000187818689) Gouker", "primaryContact": false }, { "name": "Jeremy Schmutz", "primaryContact": false }, { "name": "Kerrie Barry", "primaryContact": false }, { "name": "Anna Lipzen", "primaryContact": false }, { "name": "Aditi Sharma", "primaryContact": false }, { "name": "Laura Sandor", "primaryContact": false }, { "name": "Gerald A. Tuskan", "primaryContact": false }, { "name": "Guanqiao Feng", "primaryContact": false }, { "name": "Matthew S. Olson", "primaryContact": false }, { "name": "Stephen P. DiFazio", "primaryContact": false }, { "name": "Lawrence B. (ORCID:0000000278127736) Smart", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1811559", "active": false }, { "brc": "CBI", "title": "Redefining marginal land for bioenergy crop production", "description": "\n Marginal land has received wide attention for its potential to produce bioenergy feedstocks while minimizing diversion of productive agricultural land from food crop production. However, there has been no consensus in the literature on how to define or identify land that is marginal for food crops and beneficial for bioenergy crops. Studies have used different definitions to quantify the amount of such land available; these have largely been based on assumed biophysical thresholds for soil quality and productivity that are unchanging over space and time. We discuss the limitations of these definitions and the rationale for considering economic returns and environmental outcomes in classifying land as marginal. We then propose the concept of \u201csocially\u201d marginal which is defined as land that is earning close to zero returns\n
\n Marginal land has received wide attention for its potential to produce bioenergy feedstocks while minimizing diversion of productive agricultural land from food crop production. However, there has been no consensus in the literature on how to define or identify land that is marginal for food crops and beneficial for bioenergy crops. Studies have used different definitions to quantify the amount of such land available; these have largely been based on assumed biophysical thresholds for soil quality and productivity that are unchanging over space and time. We discuss the limitations of these definitions and the rationale for considering economic returns and environmental outcomes in classifying land as marginal. We then propose the concept of \u201csocially\u201d marginal which is defined as land that is earning close to zero returns\n
\n Soil\u2010borne microbes can establish compatible relationships with host plants, providing a large variety of nutritive and protective compounds in exchange for photosynthesized sugars. However, the molecular mechanisms mediating the establishment of these beneficial relationships remain unclear. Our previous genetic mapping and whole\u2010genome resequencing studies identified a gene deletion event of a\n
\n Soil\u2010borne microbes can establish compatible relationships with host plants, providing a large variety of nutritive and protective compounds in exchange for photosynthesized sugars. However, the molecular mechanisms mediating the establishment of these beneficial relationships remain unclear. Our previous genetic mapping and whole\u2010genome resequencing studies identified a gene deletion event of a\n
\n
\n
\n Green fluorescent protein (GFP) has been widely used for monitoring gene expression and protein localization in diverse organisms. However, highly sensitive imaging equipment, like fluorescence microscope, is usually required for the visualization of GFP, limitings its application to fixed locations in samples. A reporter that can be visualized in real-time regardless the shape, size and location of the target samples will increase the flexibility and efficiency of research work. Here, we report the application of a GFP-like protein, called eYGFPuv, in both transient expression and stable transformation, in two herbaceous plant species (\n
\n Green fluorescent protein (GFP) has been widely used for monitoring gene expression and protein localization in diverse organisms. However, highly sensitive imaging equipment, like fluorescence microscope, is usually required for the visualization of GFP, limitings its application to fixed locations in samples. A reporter that can be visualized in real-time regardless the shape, size and location of the target samples will increase the flexibility and efficiency of research work. Here, we report the application of a GFP-like protein, called eYGFPuv, in both transient expression and stable transformation, in two herbaceous plant species (\n
Roots are central to the function of natural and agricultural ecosystems by driving plant acquisition of soil resources and influencing the carbon cycle. Root characteristics like length, diameter and volume are critical to measure to understand plant and soil functions. RhizoVision Explorer is an open-source software designed to enable researchers interested in roots by providing an easy-to-use interface, fast image processing and reliable measurements. The default broken roots mode is intended for roots sampled from pots and soil cores, washed and typically scanned on a flatbed scanner, and provides measurements like length, diameter and volume. The optional whole root mode for complete root systems or root crowns provides additional measurements such as angles, root depth and convex hull. Both modes support providing measurements grouped by defined diameter ranges, the inclusion of multiple regions of interest and batch analysis. RhizoVision Explorer was successfully validated against ground truth data using a new copper wire image set. In comparison, the current reference software, the commercial WinRhizo\u2122, drastically underestimated volume when wires of different diameters were in the same image. Additionally, measurements were compared with WinRhizo\u2122 and IJ_Rhizo using a simulated root image set, showing general agreement in software measurements, except for root volume. Finally, scanned root image sets acquired in different labs for the crop, herbaceous and tree species were used to compare results from RhizoVision Explorer with WinRhizo\u2122. The two software showed general agreement, except that WinRhizo\u2122 substantially underestimated root volume relative to RhizoVision Explorer. In the current context of rapidly growing interest in root science, RhizoVision Explorer intends to become a reference software, improve the overall accuracy and replicability of root trait measurements and provide a foundation for collaborative improvement and reliable access to all.
", "abstract": "Roots are central to the function of natural and agricultural ecosystems by driving plant acquisition of soil resources and influencing the carbon cycle. Root characteristics like length, diameter and volume are critical to measure to understand plant and soil functions. RhizoVision Explorer is an open-source software designed to enable researchers interested in roots by providing an easy-to-use interface, fast image processing and reliable measurements. The default broken roots mode is intended for roots sampled from pots and soil cores, washed and typically scanned on a flatbed scanner, and provides measurements like length, diameter and volume. The optional whole root mode for complete root systems or root crowns provides additional measurements such as angles, root depth and convex hull. Both modes support providing measurements grouped by defined diameter ranges, the inclusion of multiple regions of interest and batch analysis. RhizoVision Explorer was successfully validated against ground truth data using a new copper wire image set. In comparison, the current reference software, the commercial WinRhizo\u2122, drastically underestimated volume when wires of different diameters were in the same image. Additionally, measurements were compared with WinRhizo\u2122 and IJ_Rhizo using a simulated root image set, showing general agreement in software measurements, except for root volume. Finally, scanned root image sets acquired in different labs for the crop, herbaceous and tree species were used to compare results from RhizoVision Explorer with WinRhizo\u2122. The two software showed general agreement, except that WinRhizo\u2122 substantially underestimated root volume relative to RhizoVision Explorer. In the current context of rapidly growing interest in root science, RhizoVision Explorer intends to become a reference software, improve the overall accuracy and replicability of root trait measurements and provide a foundation for collaborative improvement and reliable access to all.
", "date": "2021-09-12", "issue": "6", "identifier": "https://www.osti.gov/biblio/1830875", "bibliographicCitation": "https://doi.org/10.1093/aobpla/plab056", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "Ground truth", "phenomics", "phenotyping", "rhizosphere", "root system architecture", "traits" ], "topic": [ "Microbiology" ], "journal_name": "AoB Plants", "volume": "13", "publisher_information": "Oxford University Press; Annals of Botany Company", "country_publication_code": "GB", "creator": [ { "name": "Anand [Noble Research Institute,LLC,Ardmore,OK 73401,USA] Seethepalli", "primaryContact": true }, { "name": "Kundan [Noble Research Institute,LLC,Ardmore,OK 73401,USA] Dhakal", "primaryContact": false }, { "name": "Marcus [Noble Research Institute,LLC,Ardmore,OK 73401,USA] Griffiths", "primaryContact": false }, { "name": "Haichao [Noble Research Institute,LLC,Ardmore,OK 73401,USA] Guo", "primaryContact": false }, { "name": "Gregoire T. [Theoretical and Experimental Ecology Station,CNRS,09200 Moulis,France] Freschet", "primaryContact": false }, { "name": "Larry M. [Noble Research Institute,LLC,Ardmore,OK 73401,USA,Biosciences Division and Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,TN 37830,USA] York", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1830875", "active": false }, { "brc": "CBI", "title": "Plant-Based Biosensors for Detecting CRISPR-Mediated Genome Engineering", "description": "Not Available", "abstract": "Not Available", "date": "2021-12-07", "issue": "12", "identifier": "https://www.osti.gov/biblio/1834653", "bibliographicCitation": "https://doi.org/10.1021/acssynbio.1c00455", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "CRISPR", "biosensor", "biotechnology", "detection", "genetics", "genome editing", "imaging probes", "plants", "sensors", "transient gene expression" ], "topic": [ "Microbiology" ], "journal_name": "ACS Synthetic Biology", "volume": "10", "publisher_information": "American Chemical Society", "country_publication_code": "US", "creator": [ { "name": "Guoliang [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States,The Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States] (ORCID:0000000265628769) Yuan", "primaryContact": true }, { "name": "Md. Mahmudul [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States,The Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States,Department of Genetics and Plant Breeding,Patuakhali Science and Technology University,Dumki,Patuakhali 8602,Bangladesh] Hassan", "primaryContact": false }, { "name": "Tao [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States,The Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States] (ORCID:0000000293820731) Yao", "primaryContact": false }, { "name": "Haiwei [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States] Lu", "primaryContact": false }, { "name": "Michael Melesse [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States] Vergara", "primaryContact": false }, { "name": "Jesse L. [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States] Labb\u00e9", "primaryContact": false }, { "name": "Wellington [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States,The Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States] Muchero", "primaryContact": false }, { "name": "Changtian [Department of Plant Science and Landscape Architecture,University of Maryland,College Park,Maryland 20742,United States] Pan", "primaryContact": false }, { "name": "Jin-Gui [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States,The Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States] Chen", "primaryContact": false }, { "name": "Gerald A. [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States,The Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States] Tuskan", "primaryContact": false }, { "name": "Yiping [Department of Plant Science and Landscape Architecture,University of Maryland,College Park,Maryland 20742,United States,Institute for Bioscience and Biotechnology Research,University of Maryland,Rockville,Maryland 20850,United States] Qi", "primaryContact": false }, { "name": "Paul E. [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States] Abraham", "primaryContact": false }, { "name": "Xiaohan [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States,The Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States] (ORCID:0000000152074210) Yang", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1834653", "active": false }, { "brc": "CBI", "title": "Biological Parts for Plant Biodesign to Enhance Land-Based Carbon Dioxide Removal", "description": "A grand challenge facing society is climate change caused mainly by rising CO2 concentration in Earth\u2019s atmosphere. Terrestrial plants are linchpins in global carbon cycling, with a unique capability of capturing CO2 via photosynthesis and translocating captured carbon to stems, roots, and soils for long-term storage. However, many researchers postulate that existing land plants cannot meet the ambitious requirement for CO2 removal to mitigate climate change in the future due to low photosynthetic efficiency, limited carbon allocation for long-term storage, and low suitability for the bioeconomy. To address these limitations, there is an urgent need for genetic improvement of existing plants or construction of novel plant systems through biosystems design (or biodesign). Here, we summarize validated biological parts (e.g., protein-encoding genes and noncoding RNAs) for biological engineering of carbon dioxide removal (CDR) traits in terrestrial plants to accelerate land-based decarbonization in bioenergy plantations and agricultural settings and promote a vibrant bioeconomy. Specifically, we first summarize the framework of plant-based CDR (e.g., CO2 capture, translocation, storage, and conversion to value-added products). Then, we highlight some representative biological parts, with experimental evidence, in this framework. Finally, we discuss challenges and strategies for the identification and curation of biological parts for CDR engineering in plants.", "abstract": "A grand challenge facing society is climate change caused mainly by rising CO2 concentration in Earth\u2019s atmosphere. Terrestrial plants are linchpins in global carbon cycling, with a unique capability of capturing CO2 via photosynthesis and translocating captured carbon to stems, roots, and soils for long-term storage. However, many researchers postulate that existing land plants cannot meet the ambitious requirement for CO2 removal to mitigate climate change in the future due to low photosynthetic efficiency, limited carbon allocation for long-term storage, and low suitability for the bioeconomy. To address these limitations, there is an urgent need for genetic improvement of existing plants or construction of novel plant systems through biosystems design (or biodesign). Here, we summarize validated biological parts (e.g., protein-encoding genes and noncoding RNAs) for biological engineering of carbon dioxide removal (CDR) traits in terrestrial plants to accelerate land-based decarbonization in bioenergy plantations and agricultural settings and promote a vibrant bioeconomy. Specifically, we first summarize the framework of plant-based CDR (e.g., CO2 capture, translocation, storage, and conversion to value-added products). Then, we highlight some representative biological parts, with experimental evidence, in this framework. Finally, we discuss challenges and strategies for the identification and curation of biological parts for CDR engineering in plants.", "date": "2021-11-28", "identifier": "https://www.osti.gov/biblio/1836428", "bibliographicCitation": "https://doi.org/10.34133/2021/9798714", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "BioDesign Research", "volume": "2021", "publisher_information": "AAAS", "country_publication_code": "US", "creator": [ { "name": "Xiaohan [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation] (ORCID:0000000152074210) Yang", "primaryContact": true }, { "name": "Degao [University of Minnesota,St. Paul] Liu", "primaryContact": false }, { "name": "Haiwei [Central Community College \u2013 Hastings] Lu", "primaryContact": false }, { "name": "David [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation] (ORCID:0000000247949913) Weston", "primaryContact": false }, { "name": "Jay [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation] (ORCID:0000000217524201) Chen", "primaryContact": false }, { "name": "Wellington [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation] (ORCID:0000000202009856) Muchero", "primaryContact": false }, { "name": "Stanton [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation] Martin", "primaryContact": false }, { "name": "Yang [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000160454969) Liu", "primaryContact": false }, { "name": "Md Mahmudul [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation] (ORCID:0000000333998121) Hassan", "primaryContact": false }, { "name": "Guoliang [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation] Yuan", "primaryContact": false }, { "name": "Udaya C. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation] (ORCID:0000000259638370) Kalluri", "primaryContact": false }, { "name": "Timothy [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation] (ORCID:0000000295406622) Tschaplinski", "primaryContact": false }, { "name": "Julie [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Mitchell", "primaryContact": false }, { "name": "Stan [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Climate Change Science Inst.] (ORCID:0000000298690446) Wullschleger", "primaryContact": false }, { "name": "Gerald A. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation] (ORCID:0000000301061289) Tuskan", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1836428", "active": false }, { "brc": "CBI", "title": "Novel computational and experimental approaches for investigating the thermodynamics of metabolic networks", "description": "Not Available", "abstract": "Not Available", "date": "2022-03-31", "issue": "C", "identifier": "https://www.osti.gov/biblio/1837796", "bibliographicCitation": "https://doi.org/10.1016/j.mib.2021.11.007", "keywords": [ "09 BIOMASS FUELS", "59 BASIC BIOLOGICAL SCIENCES", "60 APPLIED LIFE SCIENCES" ], "topic": [ "Biomass & Feedstock", "Microbiology", "Plant Biology" ], "journal_name": "Current Opinion in Microbiology", "volume": "66", "publisher_information": "Elsevier", "country_publication_code": "GB", "creator": [ { "name": "Daven B. (ORCID:0000000280813436) Khana", "primaryContact": true }, { "name": "Melanie M. (ORCID:0000000237551979) Callaghan", "primaryContact": false }, { "name": "Daniel (ORCID:0000000235683070) Amador-Noguez", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1837796", "active": false }, { "brc": "CBI", "title": "Novel Mutant Alleles Reveal a Role of the Extra-Large G Protein in Rice Grain Filling, Panicle Architecture, Plant Growth, and Disease Resistance", "description": "\n Plant growth and grain filling are the key agronomical traits for grain weight and yield of rice. The continuous improvement in rice yield is required for a future sustainable global economy and food security. The heterotrimeric G protein complex containing a canonical \u03b1 subunit (RGA1) couples extracellular signals perceived by receptors to modulate cell function including plant development and grain weight. We hypothesized that, besides RGA1, three atypical, extra-large GTP-binding protein (XLG) subunits also regulate panicle architecture, plant growth, development, grain weight, and disease resistance. Here, we identified a role of XLGs in agronomic traits and stress tolerance by genetically ablating all three rice XLGs individually and in combination using the CRISPR/Cas9 genome editing in rice. For this study, eight (three single, two double, and three triple) null mutants were selected. Three XLG proteins combinatorically regulate seed filling, because loss confers a decrease in grain weight from 14% with loss of one XLG and loss of three to 32% decrease in grain weight. Null mutations in\n
\n Plant growth and grain filling are the key agronomical traits for grain weight and yield of rice. The continuous improvement in rice yield is required for a future sustainable global economy and food security. The heterotrimeric G protein complex containing a canonical \u03b1 subunit (RGA1) couples extracellular signals perceived by receptors to modulate cell function including plant development and grain weight. We hypothesized that, besides RGA1, three atypical, extra-large GTP-binding protein (XLG) subunits also regulate panicle architecture, plant growth, development, grain weight, and disease resistance. Here, we identified a role of XLGs in agronomic traits and stress tolerance by genetically ablating all three rice XLGs individually and in combination using the CRISPR/Cas9 genome editing in rice. For this study, eight (three single, two double, and three triple) null mutants were selected. Three XLG proteins combinatorically regulate seed filling, because loss confers a decrease in grain weight from 14% with loss of one XLG and loss of three to 32% decrease in grain weight. Null mutations in\n
Bioenergy production often focuses on the aboveground feedstock production for conversion to fuel and other materials. However, the belowground component is crucial for soil carbon sequestration, greenhouse gas fluxes, and ecosystem function. Roots maximize feedstock production on marginal lands by acquiring soil resources and mediating soil ecosystem processes through interactions with the microbial community. This belowground world is challenging to observe and quantify; however, there are unprecedented opportunities using current methodologies to bring roots, microbes, and soil into focus. These opportunities allow not only breeding for increased feedstock production but breeding for increased soil health and carbon sequestration as well. A recent workshop hosted by the USDOE Bioenergy Research Centers highlighted these challenges and opportunities while creating a roadmap for increased collaboration and data interoperability through standardization of methodologies and data using F.A.I.R. principles. This article provides a background on the need for belowground research in bioenergy cropping systems, a primer on root system properties of major U.S. bioenergy crops, and an overview of the roles of root chemistry, exudation, and microbial interactions on sustainability. Crucially, we outline how to adopt standardized measures and databases to meet the most pressing methodological needs to accelerate root, soil, and microbial research to meet the pressing societal challenges of the century.
", "abstract": "Bioenergy production often focuses on the aboveground feedstock production for conversion to fuel and other materials. However, the belowground component is crucial for soil carbon sequestration, greenhouse gas fluxes, and ecosystem function. Roots maximize feedstock production on marginal lands by acquiring soil resources and mediating soil ecosystem processes through interactions with the microbial community. This belowground world is challenging to observe and quantify; however, there are unprecedented opportunities using current methodologies to bring roots, microbes, and soil into focus. These opportunities allow not only breeding for increased feedstock production but breeding for increased soil health and carbon sequestration as well. A recent workshop hosted by the USDOE Bioenergy Research Centers highlighted these challenges and opportunities while creating a roadmap for increased collaboration and data interoperability through standardization of methodologies and data using F.A.I.R. principles. This article provides a background on the need for belowground research in bioenergy cropping systems, a primer on root system properties of major U.S. bioenergy crops, and an overview of the roles of root chemistry, exudation, and microbial interactions on sustainability. Crucially, we outline how to adopt standardized measures and databases to meet the most pressing methodological needs to accelerate root, soil, and microbial research to meet the pressing societal challenges of the century.
", "date": "2022-02-10", "issue": "1", "identifier": "https://www.osti.gov/biblio/1844820", "bibliographicCitation": "https://doi.org/10.1002/ppj2.20028", "keywords": [ "09 BIOMASS FUELS" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Plant Phenome Journal", "volume": "5", "publisher_information": "Wiley Blackwell (John Wiley & Sons)", "country_publication_code": "US", "creator": [ { "name": "Larry M. [Center for Bioenergy Innovation (CBI) Oak Ridge National Laboratory Oak Ridge TN 37831 USA,Biosciences Division Oak Ridge National Laboratory Oak Ridge TN 37831 USA] (ORCID:0000000219959479) York", "primaryContact": true }, { "name": "Jonathan R. [Center for Bioenergy Innovation (CBI) Oak Ridge National Laboratory Oak Ridge TN 37831 USA,Dep. of Natural Sciences Univ. of Maryland Eastern Shore Princess Anne MD 21853 USA] (ORCID:0000000293687926) Cumming", "primaryContact": false }, { "name": "Adrianna [Great Lakes Bioenergy Research Center (GLBRC) Michigan State Univ. East Lansing MI 48824 USA] (ORCID:0000000277939329) Trusiak", "primaryContact": false }, { "name": "Gregory [Great Lakes Bioenergy Research Center (GLBRC) Michigan State Univ. East Lansing MI 48824 USA,Dep. of Plant,Soil and Microbial Sciences Michigan State Univ. East Lansing MI 48824 USA] (ORCID:0000000272628978) Bonito", "primaryContact": false }, { "name": "Adam C. [Center for Advanced Bioenergy and Bioproducts Innovation (CABBI) Univ. of Illinois at Urbana\u2010Champaign Urbana IL 61801 USA,Institute for Sustainability,Energy,and Environment Univ. of Illinois at Urbana\u2010Champaign Urbana IL 61801 USA] (ORCID:0000000338179352) von Haden", "primaryContact": false }, { "name": "Udaya C. [Center for Bioenergy Innovation (CBI) Oak Ridge National Laboratory Oak Ridge TN 37831 USA,Biosciences Division Oak Ridge National Laboratory Oak Ridge TN 37831 USA] (ORCID:0000000259638370) Kalluri", "primaryContact": false }, { "name": "Lisa K. [Great Lakes Bioenergy Research Center (GLBRC) Michigan State Univ. East Lansing MI 48824 USA,Dep. of Plant,Soil and Microbial Sciences Michigan State Univ. East Lansing MI 48824 USA] (ORCID:0000000305146503) Tiemann", "primaryContact": false }, { "name": "Peter F. [Environmental Genomics and Systems Biology Lawrence Berkeley National Lab Berkeley CA 94720 USA] (ORCID:0000000235542008) Andeer", "primaryContact": false }, { "name": "Elena [Center for Advanced Bioenergy and Bioproducts Innovation (CABBI) Univ. of Illinois at Urbana\u2010Champaign Urbana IL 61801 USA,Institute for Sustainability,Energy,and Environment Univ. of Illinois at Urbana\u2010Champaign Urbana IL 61801 USA] (ORCID:0000000220494613) Blanc\u2010Betes", "primaryContact": false }, { "name": "Jonathan H. [Environmental Genomics and Systems Biology Lawrence Berkeley National Lab Berkeley CA 94720 USA,Joint BioEnergy Institute Emeryville CA 94608 USA] (ORCID:0000000254283224) Diab", "primaryContact": false }, { "name": "Alonso [Center for Advanced Bioenergy and Bioproducts Innovation (CABBI) Univ. of Illinois at Urbana\u2010Champaign Urbana IL 61801 USA,Dep. of Natural Resources &,Environmental Sciences Univ. of Illinois at Urbana\u2010Champaign Urbana IL 61801 USA] (ORCID:0000000177431149) Favela", "primaryContact": false }, { "name": "Amandine [Center for Advanced Bioenergy and Bioproducts Innovation (CABBI) Univ. of Illinois at Urbana\u2010Champaign Urbana IL 61801 USA,Institute for Sustainability,Energy,and Environment Univ. of Illinois at Urbana\u2010Champaign Urbana IL 61801 USA] (ORCID:000000018687294X) Germon", "primaryContact": false }, { "name": "Nuria [Center for Advanced Bioenergy and Bioproducts Innovation (CABBI) Univ. of Illinois at Urbana\u2010Champaign Urbana IL 61801 USA,Institute for Sustainability,Energy,and Environment Univ. of Illinois at Urbana\u2010Champaign Urbana IL 61801 USA] (ORCID:0000000347843585) Gomez\u2010Casanovas", "primaryContact": false }, { "name": "Charles A. [Center for Advanced Bioenergy and Bioproducts Innovation (CABBI) Univ. of Illinois at Urbana\u2010Champaign Urbana IL 61801 USA,Program in Ecology,Evolution,and Conservation Biology Univ. of Illinois at Urbana\u2010Champaign Urbana IL 61801 USA] (ORCID:0000000166697160) Hyde", "primaryContact": false }, { "name": "Angela D. [Center for Advanced Bioenergy and Bioproducts Innovation (CABBI) Univ. of Illinois at Urbana\u2010Champaign Urbana IL 61801 USA,Dep. of Natural Resources &,Environmental Sciences Univ. of Illinois at Urbana\u2010Champaign Urbana IL 61801 USA,Program in Ecology,Evolution,and Conservation Biology Univ. of Illinois at Urbana\u2010Champaign Urbana IL 61801 USA] (ORCID:0000000318372382) Kent", "primaryContact": false }, { "name": "Dae Kwan [Great Lakes Bioenergy Research Center (GLBRC) Michigan State Univ. East Lansing MI 48824 USA,DOE Plant Research Lab Michigan State Univ. East Lansing MI 48824 USA] (ORCID:0000000297205138) Ko", "primaryContact": false }, { "name": "Austin [Great Lakes Bioenergy Research Center Texas A&,M College Station TX 77843 USA,Dep. of Biochemistry Texas A&,M College Station TX 77843 USA] (ORCID:000000030083637X) Lamb", "primaryContact": false }, { "name": "Ali M. [Center for Bioenergy Innovation Univ. of Georgia Athens GA 30602 USA,Dep. of Crop and Soil Sciences and Institute of Plant Breeding Genetics and Genomics Univ. of Georgia Athens GA 30602 USA] (ORCID:0000000317101142) Missaoui", "primaryContact": false }, { "name": "Trent R. [Environmental Genomics and Systems Biology Lawrence Berkeley National Lab Berkeley CA 94720 USA,Joint BioEnergy Institute Emeryville CA 94608 USA,The DOE Joint Genome Institute Lawrence Berkeley National Lab Berkeley CA 94720 USA] (ORCID:0000000184043259) Northen", "primaryContact": false }, { "name": "Yunqiao [Center for Bioenergy Innovation (CBI) Oak Ridge National Laboratory Oak Ridge TN 37831 USA,Biosciences Division Oak Ridge National Laboratory Oak Ridge TN 37831 USA] (ORCID:0000000325541447) Pu", "primaryContact": false }, { "name": "Arthur J. [Center for Bioenergy Innovation (CBI) Oak Ridge National Laboratory Oak Ridge TN 37831 USA,Dep. of Chemical &,Biomolecular Engineering Univ. of Tennessee Knoxville TN 37996 USA,Dep. of Forestry,Wildlife,and Fisheries,Center for Renewable Carbon Univ. of Tennessee Institute of Agriculture Knoxville TN 37996 USA] (ORCID:0000000314206678) Ragauskas", "primaryContact": false }, { "name": "Sierra [Center for Advanced Bioenergy and Bioproducts Innovation (CABBI) Univ. of Illinois at Urbana\u2010Champaign Urbana IL 61801 USA,Dep. of Natural Resources &,Environmental Sciences Univ. of Illinois at Urbana\u2010Champaign Urbana IL 61801 USA] Raglin", "primaryContact": false }, { "name": "Henrik V. [Environmental Genomics and Systems Biology Lawrence Berkeley National Lab Berkeley CA 94720 USA,Joint BioEnergy Institute Emeryville CA 94608 USA,Dep. of Plant and Microbial Biology Univ. of California Berkeley Berkeley CA 94720 USA] (ORCID:0000000267023560) Scheller", "primaryContact": false }, { "name": "Lorenzo [Joint BioEnergy Institute Emeryville CA 94608 USA,Dep. of Plant and Microbial Biology Univ. of California Berkeley Berkeley CA 94720 USA] (ORCID:0000000206244693) Washington", "primaryContact": false }, { "name": "Wendy H. [Center for Advanced Bioenergy and Bioproducts Innovation (CABBI) Univ. of Illinois at Urbana\u2010Champaign Urbana IL 61801 USA,Institute for Sustainability,Energy,and Environment Univ. of Illinois at Urbana\u2010Champaign Urbana IL 61801 USA,Dep. of Plant Biology Dep. of Geology Univ. of Illinois at Urbana\u2010Champaign Urbana IL 61801 USA] (ORCID:0000000221044796) Yang", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1844820", "active": false }, { "brc": "CBI", "title": "Strikingly high amount of tricin-lignin observed from vanilla (Vanilla planifolia) aerial roots", "description": "Lignin has attracted tremendous interest as a renewable resource for biofuels, biomaterials, and chemicals especially in the era of bio-based refineries. The structural studies of lignin play an essential role in both understanding the nature and biosynthesis of these polymers and optimizing their valorization values. In this study, we have investigated the structures of lignin from different tissues\u2014aerial roots, nodes, internodes, and seeds, from vanilla (Vanilla planifolia) by using gel permeation chromatography (GPC), heteronuclear single-quantum coherence (HSQC) nuclear magnetic resonance (NMR), and 31P NMR. An unusual tricin-lignin was observed in the aerial roots of vanilla with an strikingly high level of tricin unit, whereas the lignin from the nodes and internodes displayed traditional S/G type lignin with only 4\u201310% tricin abundance. The aerial roots lignin is primarily composed of \u03b2-O-4' alkyl-aryl ether substructures (96% of linkages) in comparison to 65 and 73% in the nodes and internodes lignin, respectively. Additionally, thioacidolysis quantification results showed that lignin from aerial roots has 29.1 mg g-1 tricin, about 3- to 5-fold higher than the lignins isolated from nodes (10.1 mg g-1) and internodes (6.9 mg g-1). This communication of a particularly high level of tricin-lignin in vanilla plant has important impacts including: (1) the presence of the high amount of tricin as part of lignin from aerial roots could play a vital role for the valorization of lignin, even tricin itself, as a feedstock for value-added chemicals and commodities; and (2) it could open new ways to scientists to design and engineer the structure of tricin-lignin, or lignin in general, to confer plants with new or improved properties due to the plasticity of lignification.", "abstract": "Lignin has attracted tremendous interest as a renewable resource for biofuels, biomaterials, and chemicals especially in the era of bio-based refineries. The structural studies of lignin play an essential role in both understanding the nature and biosynthesis of these polymers and optimizing their valorization values. In this study, we have investigated the structures of lignin from different tissues\u2014aerial roots, nodes, internodes, and seeds, from vanilla (Vanilla planifolia) by using gel permeation chromatography (GPC), heteronuclear single-quantum coherence (HSQC) nuclear magnetic resonance (NMR), and 31P NMR. An unusual tricin-lignin was observed in the aerial roots of vanilla with an strikingly high level of tricin unit, whereas the lignin from the nodes and internodes displayed traditional S/G type lignin with only 4\u201310% tricin abundance. The aerial roots lignin is primarily composed of \u03b2-O-4' alkyl-aryl ether substructures (96% of linkages) in comparison to 65 and 73% in the nodes and internodes lignin, respectively. Additionally, thioacidolysis quantification results showed that lignin from aerial roots has 29.1 mg g-1 tricin, about 3- to 5-fold higher than the lignins isolated from nodes (10.1 mg g-1) and internodes (6.9 mg g-1). This communication of a particularly high level of tricin-lignin in vanilla plant has important impacts including: (1) the presence of the high amount of tricin as part of lignin from aerial roots could play a vital role for the valorization of lignin, even tricin itself, as a feedstock for value-added chemicals and commodities; and (2) it could open new ways to scientists to design and engineer the structure of tricin-lignin, or lignin in general, to confer plants with new or improved properties due to the plasticity of lignification.", "date": "2021-12-08", "issue": "1", "identifier": "https://www.osti.gov/biblio/1844862", "bibliographicCitation": "https://doi.org/10.1039/d1gc03625d", "keywords": [ "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY" ], "topic": [ "Chemistry" ], "journal_name": "Green Chemistry", "volume": "24", "publisher_information": "Royal Society of Chemistry", "country_publication_code": "US", "creator": [ { "name": "Mi [Univ. of Tennessee,Knoxville,TN (United States). Center for Renewable Carbon] (ORCID:0000000175231266) Li", "primaryContact": true }, { "name": "Yunqiao [UT-ORNL Joint Inst. for Biological Sciences,Oak Ridge,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] (ORCID:0000000325541447) Pu", "primaryContact": false }, { "name": "Xianzhi [Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:0000000343033403) Meng", "primaryContact": false }, { "name": "Fang [Univ. of North Texas,Denton,TX (United States). BioDiscovery Inst.] Chen", "primaryContact": false }, { "name": "Richard A. [Univ. of North Texas,Denton,TX (United States). BioDiscovery Inst.] Dixon", "primaryContact": false }, { "name": "Arthur J. [Univ. of Tennessee,Knoxville,TN (United States). Center for Renewable Carbon; UT-ORNL Joint Inst. for Biological Sciences,Oak Ridge,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI); Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:000000023536554X) Ragauskas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Laboratory Directed Research and Development (LDRD) Program" } } ], "dataset_url": "https://www.osti.gov/biblio/1844862", "active": false }, { "brc": "CBI", "title": "Opportunities and challenges for flow-through hydrothermal pretreatment in advanced biorefineries", "description": "Hydrothermal pretreatment (HTP) using only water offers great potential to reduce the overall cost of the bioconversion process. However, traditional HTP performed in a batch has limitations in removing lignin and often needs to be performed under severe conditions to achieve reasonable pretreatment effects. Additionally, lignin left in the pretreated residue at these conditions is also highly condensed, thus possessing an even more adverse impact on the hydrolysis process, which requires high enzyme loadings. To address these technical challenges, HTP performed in a flow-through configuration was developed to simultaneously achieve near-complete hemicellulose recovery, high lignin removal and high sugar release. Despite facing challenges such as potentially large water usage, flow-through HTP still represents one of the most cost-effective and eco-friendly pretreatment methods. This review mainly covers the latest cutting-edge innovations of flow-through HTP along with structural and compositional changes of cellulose, hemicellulose, and lignin before and after pretreatment.", "abstract": "Hydrothermal pretreatment (HTP) using only water offers great potential to reduce the overall cost of the bioconversion process. However, traditional HTP performed in a batch has limitations in removing lignin and often needs to be performed under severe conditions to achieve reasonable pretreatment effects. Additionally, lignin left in the pretreated residue at these conditions is also highly condensed, thus possessing an even more adverse impact on the hydrolysis process, which requires high enzyme loadings. To address these technical challenges, HTP performed in a flow-through configuration was developed to simultaneously achieve near-complete hemicellulose recovery, high lignin removal and high sugar release. Despite facing challenges such as potentially large water usage, flow-through HTP still represents one of the most cost-effective and eco-friendly pretreatment methods. This review mainly covers the latest cutting-edge innovations of flow-through HTP along with structural and compositional changes of cellulose, hemicellulose, and lignin before and after pretreatment.", "date": "2021-09-27", "issue": "1", "identifier": "https://www.osti.gov/biblio/1844863", "bibliographicCitation": "https://doi.org/10.1016/j.biortech.2021.126061", "keywords": [ "09 BIOMASS FUELS", "Biomass pretreatment", "flow-through hydrothermal pretreatment", "lignin valorization" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Bioresource Technology", "volume": "343", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Xianzhi [Univ. of Tennessee,Knoxville,TN (United States)] Meng", "primaryContact": true }, { "name": "Chang Geun [State Univ. of New York (SUNY),Syracuse,NY (United States)] Yoo", "primaryContact": false }, { "name": "Yunqiao [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000325541447) Pu", "primaryContact": false }, { "name": "Arthur J. [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI); Univ. of Tennessee,Knoxville,TN (United States). Inst. of Agriculture,Center of Renewable Carbon] (ORCID:000000023536554X) Ragauskas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1844863", "active": false }, { "brc": "CBI", "title": "Valorisation of technical lignin in rigid polyurethane foam: A critical evaluation on trends, guidelines and future perspectives", "description": "Lignin is one of the most abundant aromatic natural polymers. Produced as a by-product from the biomass refinery industries, lignin remains largely underutilised in high-value industrial applications. The incorporation of lignin in rigid polyurethane foam (RPUF) has been the focus of much research, due to its potential to replace fossil fuel-based components of RPUF. However, the overall sustainability of RPUF depends on numerous factors including processability, cost-effectiveness, and retention of performance throughout the service life. To date, the incorporation of lignin has been explored either as filler particles (through direct incorporation) or as a blendable liquid polyol introduced after chemical modifications (such as oxyalkylation, functionalisation, or depolymerisation). However, the production of lignin incorporated foam with high performance through cost-effective processing is still an ongoing challenge. Herein, this review critically appraises the progress on the effective incorporation of lignin in RPUF. Firstly, this review briefly covers the essential raw materials, formulation, important properties, and sustainability aspects of RPUF for industrial applications. Secondly, it provides insights on the key parameters of lignin of relevance to incorporation into RPUF. Thirdly, it benchmarks the reported studies on incorporation of lignin in RPUF systems by evaluating their important properties and proposes potential strategies for addressing the key challenges in the incorporation of lignin in RPUF. By bridging the gaps that exist in the literature on the utilisation of lignin in RPUF this account will serve as a resource for both beginners and professionals in the polyurethane and biorefinery industries towards the successful development of lignin incorporated RPUF for industrial applications", "abstract": "Lignin is one of the most abundant aromatic natural polymers. Produced as a by-product from the biomass refinery industries, lignin remains largely underutilised in high-value industrial applications. The incorporation of lignin in rigid polyurethane foam (RPUF) has been the focus of much research, due to its potential to replace fossil fuel-based components of RPUF. However, the overall sustainability of RPUF depends on numerous factors including processability, cost-effectiveness, and retention of performance throughout the service life. To date, the incorporation of lignin has been explored either as filler particles (through direct incorporation) or as a blendable liquid polyol introduced after chemical modifications (such as oxyalkylation, functionalisation, or depolymerisation). However, the production of lignin incorporated foam with high performance through cost-effective processing is still an ongoing challenge. Herein, this review critically appraises the progress on the effective incorporation of lignin in RPUF. Firstly, this review briefly covers the essential raw materials, formulation, important properties, and sustainability aspects of RPUF for industrial applications. Secondly, it provides insights on the key parameters of lignin of relevance to incorporation into RPUF. Thirdly, it benchmarks the reported studies on incorporation of lignin in RPUF systems by evaluating their important properties and proposes potential strategies for addressing the key challenges in the incorporation of lignin in RPUF. By bridging the gaps that exist in the literature on the utilisation of lignin in RPUF this account will serve as a resource for both beginners and professionals in the polyurethane and biorefinery industries towards the successful development of lignin incorporated RPUF for industrial applications", "date": "2021-10-11", "issue": "22", "identifier": "https://www.osti.gov/biblio/1844864", "bibliographicCitation": "https://doi.org/10.1039/d1gc02744a", "keywords": [ "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "lignin", "mechanical properties", "microstructure", "polyol", "polyurethane foam", "reactivity", "thermal insulation" ], "topic": [ "Chemistry" ], "journal_name": "Green Chemistry", "volume": "23", "publisher_information": "Royal Society of Chemistry", "country_publication_code": "US", "creator": [ { "name": "Hima [Univ. of Queensland,Brisbane,QLD (Australia)] (ORCID:0000000177812224) Haridevan", "primaryContact": true }, { "name": "David A. C. [Univ. of Queensland,Brisbane,QLD (Australia)] (ORCID:0000000171282410) Evans", "primaryContact": false }, { "name": "Arthur J. [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:000000023536554X) Ragauskas", "primaryContact": false }, { "name": "Darren J. [Univ. of Queensland,Brisbane,QLD (Australia)] (ORCID:0000000285376765) Martin", "primaryContact": false }, { "name": "Pratheep K. [Univ. of Queensland,Brisbane,QLD (Australia)] (ORCID:0000000272840813) Annamalai", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/1844864", "active": false }, { "brc": "CBI", "title": "Structural Reorganization of Noncellulosic Polymers Observed In Situ during Dilute Acid Pretreatment by Small-Angle Neutron Scattering", "description": "Production of second-generation bioethanol from lignocellulosic biomass requires pretreatment to open the plant cell wall structure and improve enzyme access. Many different thermochemical pretreatments have been extensively developed and employed, but the exact nature of plant cell wall recalcitrance and the most efficient and economical approach to alter plant cell wall structure via pretreatment still remain elusive. In order to understand the role of noncellulosic switchgrass polymers on the overall efficiency of pretreatment, the structural evolution of the noncellulosic polymers of the plant cell wall were investigated during dilute acid pretreatment (DAP) by employing in-situ small-angle neutron scattering (in-situ SANS). In this study, we observed real-time structural changes not possible to observe by any other technique. To deconvolute the structural evolution of lignin and hemicellulose polymers during DAP, native switchgrass (NATV), and isolated holocellulose (HOLO) and cellulose (CELL) fractions from NATV were studied. Our results show that aggregate particles first appear around 80 \u00b0C for NATV and HOLO samples. Further, due to the low temperature and pretreatment severity condition, these particles are likely derived from hemicellulose. The formations of much larger aggregate particles, only observed in the NATV sample, were attributed to lignin. For the HOLO sample, as the temperature and pretreatment severity condition increased, hemicellulose-derived aggregate particle sizes increased, suggesting this process was the nucleation and early stage formation of pseudolignin particles. Consistent with our interpretation of structural evolutions in NATV and HOLO samples, no formation of aggregate particles was observed in CELL samples for the entire duration of the pretreatment. These results suggest that not only lignin but also hemicellulose can form aggregate particles within plant cell walls during pretreatment.", "abstract": "Production of second-generation bioethanol from lignocellulosic biomass requires pretreatment to open the plant cell wall structure and improve enzyme access. Many different thermochemical pretreatments have been extensively developed and employed, but the exact nature of plant cell wall recalcitrance and the most efficient and economical approach to alter plant cell wall structure via pretreatment still remain elusive. In order to understand the role of noncellulosic switchgrass polymers on the overall efficiency of pretreatment, the structural evolution of the noncellulosic polymers of the plant cell wall were investigated during dilute acid pretreatment (DAP) by employing in-situ small-angle neutron scattering (in-situ SANS). In this study, we observed real-time structural changes not possible to observe by any other technique. To deconvolute the structural evolution of lignin and hemicellulose polymers during DAP, native switchgrass (NATV), and isolated holocellulose (HOLO) and cellulose (CELL) fractions from NATV were studied. Our results show that aggregate particles first appear around 80 \u00b0C for NATV and HOLO samples. Further, due to the low temperature and pretreatment severity condition, these particles are likely derived from hemicellulose. The formations of much larger aggregate particles, only observed in the NATV sample, were attributed to lignin. For the HOLO sample, as the temperature and pretreatment severity condition increased, hemicellulose-derived aggregate particle sizes increased, suggesting this process was the nucleation and early stage formation of pseudolignin particles. Consistent with our interpretation of structural evolutions in NATV and HOLO samples, no formation of aggregate particles was observed in CELL samples for the entire duration of the pretreatment. These results suggest that not only lignin but also hemicellulose can form aggregate particles within plant cell walls during pretreatment.", "date": "2021-12-15", "issue": "1", "identifier": "https://www.osti.gov/biblio/1845810", "bibliographicCitation": "https://doi.org/10.1021/acssuschemeng.1c06276", "keywords": [ "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "Dilute acid pretreatment", "Hemicellulose aggregation", "Lignin aggregation", "Small-angle neutron scattering", "Switchgrass" ], "topic": [ "Chemistry" ], "journal_name": "ACS Sustainable Chemistry & Engineering", "volume": "10", "publisher_information": "American Chemical Society (ACS)", "country_publication_code": "US", "creator": [ { "name": "Zhi [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000180625737) Yang", "primaryContact": true }, { "name": "Marcus B. [Washington Univ.,St. Louis,MO (United States)] Foston", "primaryContact": false }, { "name": "Hugh [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000329665527) O\u2019Neill", "primaryContact": false }, { "name": "Volker S. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000279623408) Urban", "primaryContact": false }, { "name": "Arthur J. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:000000023536554X) Ragauskas", "primaryContact": false }, { "name": "Barbara R. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000225742567) Evans", "primaryContact": false }, { "name": "Brian H. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000274083609) Davison", "primaryContact": false }, { "name": "Sai Venkatesh [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000179614176) Pingali", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1845810", "active": false }, { "brc": "CBI", "title": "Functional Analysis of H\n +\n -Pumping Membrane-Bound Pyrophosphatase, ADP-Glucose Synthase, and Pyruvate Phosphate Dikinase as Pyrophosphate Sources in Clostridium thermocellum", "description": "\n Increased understanding of the central metabolism of\n
\n Increased understanding of the central metabolism of\n
\n Terrestrial plant biomass is the primary renewable carbon feedstock for enabling transition to a sustainable bioeconomy. Consolidated bioprocessing (CBP) by the cellulolytic thermophile\n
\n The total amount of biomass solubilized in the\n
\n The significant relative increase in RG-I in poplar solid residues following CBP indicates that\n
\n Terrestrial plant biomass is the primary renewable carbon feedstock for enabling transition to a sustainable bioeconomy. Consolidated bioprocessing (CBP) by the cellulolytic thermophile\n
\n The total amount of biomass solubilized in the\n
\n The significant relative increase in RG-I in poplar solid residues following CBP indicates that\n
\n The lives of microbes unfold at the micron scale, and their molecular machineries operate at the nanoscale. Their study at these resolutions is key toward achieving a better understanding of their ecology. We focus on cellulose degradation of the canonical\n
\n The lives of microbes unfold at the micron scale, and their molecular machineries operate at the nanoscale. Their study at these resolutions is key toward achieving a better understanding of their ecology. We focus on cellulose degradation of the canonical\n
Effect of ZSM-5 pore modification and gallium ions proximity inside the zeolite channels on ethanol conversion to liquid hydrocarbon yields.
", "abstract": "Effect of ZSM-5 pore modification and gallium ions proximity inside the zeolite channels on ethanol conversion to liquid hydrocarbon yields.
", "date": "2022-07-31", "issue": "15", "identifier": "https://www.osti.gov/biblio/1874385", "bibliographicCitation": "https://doi.org/10.1039/D2CY00288D", "topic": [ "Unknown" ], "journal_name": "Catalysis Science and Technology", "volume": "12", "publisher_information": "Royal Society of Chemistry (RSC)", "country_publication_code": "GB", "creator": [ { "name": "Bhogeswararao [Center for Environmental Research Technology,Bourns College of Engineering,University of California Riverside,Riverside,California,92507,USA] (ORCID:0000000223200975) Seemala", "primaryContact": true }, { "name": "Charles E. [Center for Environmental Research Technology,Bourns College of Engineering,University of California Riverside,Riverside,California,92507,USA,Department of Chemical and Environmental Engineering,Bourns College of Engineering,University of California Riverside,Riverside,California,92507,USA] (ORCID:0000000279852841) Wyman", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/1874385", "active": false }, { "brc": "CBI", "title": "Enzymatic Synthesis of Xylan Microparticles with Tunable Morphologies", "description": "Not Available", "abstract": "Not Available", "date": "2022-04-04", "issue": "4", "identifier": "https://www.osti.gov/biblio/1875989", "bibliographicCitation": "https://doi.org/10.1021/acsmaterialsau.2c00006", "keywords": [ "09 BIOMASS FUELS", "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "59 BASIC BIOLOGICAL SCIENCES", "biomaterials", "hemicellulose", "plant cell wall", "polysaccharide biosynthesis", "xylan", "xylan synthase" ], "topic": [ "Biomass & Feedstock", "Chemistry", "Microbiology" ], "journal_name": "ACS Materials Au", "volume": "2", "publisher_information": "American Chemical Society", "country_publication_code": "US", "creator": [ { "name": "Peter J. [Complex Carbohydrate Research Center,University of Georgia,315 Riverbend Road,Athens,Georgia 30602,United States,Bioscience Center,National Renewable Energy Laboratory,16253 Denver West Parkway,Golden,Colorado 80401,United States] Smith", "primaryContact": true }, { "name": "Thomas M. [Complex Carbohydrate Research Center,University of Georgia,315 Riverbend Road,Athens,Georgia 30602,United States,Department of Biochemistry and Molecular Biology,University of Georgia,315 Riverbend Road,Athens,Georgia 30602,United States] Curry", "primaryContact": false }, { "name": "Jeong-Yeh [Complex Carbohydrate Research Center,University of Georgia,315 Riverbend Road,Athens,Georgia 30602,United States,Department of Biochemistry and Molecular Biology,University of Georgia,315 Riverbend Road,Athens,Georgia 30602,United States] Yang", "primaryContact": false }, { "name": "William J. [Complex Carbohydrate Research Center,University of Georgia,315 Riverbend Road,Athens,Georgia 30602,United States] Barnes", "primaryContact": false }, { "name": "Samantha J. [Bioscience Center,National Renewable Energy Laboratory,16253 Denver West Parkway,Golden,Colorado 80401,United States] Ziegler", "primaryContact": false }, { "name": "Ashutosh [Bioscience Center,National Renewable Energy Laboratory,16253 Denver West Parkway,Golden,Colorado 80401,United States] (ORCID:0000000204340745) Mittal", "primaryContact": false }, { "name": "Kelley W. [Complex Carbohydrate Research Center,University of Georgia,315 Riverbend Road,Athens,Georgia 30602,United States,Department of Biochemistry and Molecular Biology,University of Georgia,315 Riverbend Road,Athens,Georgia 30602,United States] Moremen", "primaryContact": false }, { "name": "William S. [Complex Carbohydrate Research Center,University of Georgia,315 Riverbend Road,Athens,Georgia 30602,United States] York", "primaryContact": false }, { "name": "Yannick J. [Bioscience Center,National Renewable Energy Laboratory,16253 Denver West Parkway,Golden,Colorado 80401,United States] (ORCID:0000000176248000) Bomble", "primaryContact": false }, { "name": "Maria J. [Complex Carbohydrate Research Center,University of Georgia,315 Riverbend Road,Athens,Georgia 30602,United States] Pe\u00f1a", "primaryContact": false }, { "name": "Breeanna R. [Complex Carbohydrate Research Center,University of Georgia,315 Riverbend Road,Athens,Georgia 30602,United States,Department of Biochemistry and Molecular Biology,University of Georgia,315 Riverbend Road,Athens,Georgia 30602,United States] (ORCID:0000000152474513) Urbanowicz", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Institutes of Health (NIH)" } }, { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Basic Energy Sciences (BES)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1875989", "active": false, "has_related_ids": [ "NREL/JA-2700-82684" ] }, { "brc": "CBI", "title": "An Intein-Mediated Split\u2013nCas9 System for Base Editing in Plants", "description": "Not Available", "abstract": "Not Available", "date": "2022-06-28", "issue": "7", "identifier": "https://www.osti.gov/biblio/1876223", "bibliographicCitation": "https://doi.org/10.1021/acssynbio.1c00507", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "CRISPR/Cas9", "base editing", "biosensor", "eYGFPuv", "split-SpnCas9", "transient gene expression" ], "topic": [ "Microbiology" ], "journal_name": "ACS Synthetic Biology", "volume": "11", "publisher_information": "American Chemical Society", "country_publication_code": "US", "creator": [ { "name": "Guoliang [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States,The Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States] (ORCID:0000000265628769) Yuan", "primaryContact": true }, { "name": "Haiwei [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States] Lu", "primaryContact": false }, { "name": "Kuntal [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States] De", "primaryContact": false }, { "name": "Md Mahmudul [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States,The Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States,Department of Genetics and Plant Breeding,Patuakhali Science and Technology University,Dumki,Patuakhali 8602,Bangladesh] Hassan", "primaryContact": false }, { "name": "Yang [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States] Liu", "primaryContact": false }, { "name": "Yi [Department of Plant Science and Landscape Architecture,University of Connecticut,Storrs,Connecticut 06269,United States] Li", "primaryContact": false }, { "name": "Wellington [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States,The Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States] Muchero", "primaryContact": false }, { "name": "Paul E. [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States] Abraham", "primaryContact": false }, { "name": "Gerald A. [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States,The Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States] Tuskan", "primaryContact": false }, { "name": "Xiaohan [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States,The Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,Tennessee 37831,United States] (ORCID:0000000152074210) Yang", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1876223", "active": false }, { "brc": "CBI", "title": "Metaproteomics reveals enzymatic strategies deployed by anaerobic microbiomes to maintain lignocellulose deconstruction at high solids", "description": "Economically viable production of cellulosic biofuels requires operation at high solids loadings\u2014on the order of 15 wt%. To this end we characterize Nature\u2019s ability to deconstruct and utilize mid-season switchgrass at increasing solid loadings using an anaerobic methanogenic microbiome. This community exhibits undiminished fractional carbohydrate solubilization at loadings ranging from 30 g/L to 150 g/L. Metaproteomic interrogation reveals marked increases in the abundance of specific carbohydrate-active enzyme classes. Significant enrichment of auxiliary activity family 6 enzymes at higher solids suggests a role for Fenton chemistry. Stress-response proteins accompanying these reactions are similarly upregulated at higher solids, as are \u03b2-glucosidases, xylosidases, carbohydrate-debranching, and pectin-acting enzymes\u2014all of which indicate that\u00a0removal of deconstruction inhibitors is important for observed undiminished solubilization. Our work provides insights into the mechanisms by which natural microbiomes effectively deconstruct and utilize lignocellulose at high solids loadings, informing the future development of defined cultures for efficient bioconversion.", "abstract": "Economically viable production of cellulosic biofuels requires operation at high solids loadings\u2014on the order of 15 wt%. To this end we characterize Nature\u2019s ability to deconstruct and utilize mid-season switchgrass at increasing solid loadings using an anaerobic methanogenic microbiome. This community exhibits undiminished fractional carbohydrate solubilization at loadings ranging from 30 g/L to 150 g/L. Metaproteomic interrogation reveals marked increases in the abundance of specific carbohydrate-active enzyme classes. Significant enrichment of auxiliary activity family 6 enzymes at higher solids suggests a role for Fenton chemistry. Stress-response proteins accompanying these reactions are similarly upregulated at higher solids, as are \u03b2-glucosidases, xylosidases, carbohydrate-debranching, and pectin-acting enzymes\u2014all of which indicate that\u00a0removal of deconstruction inhibitors is important for observed undiminished solubilization. Our work provides insights into the mechanisms by which natural microbiomes effectively deconstruct and utilize lignocellulose at high solids loadings, informing the future development of defined cultures for efficient bioconversion.", "date": "2022-07-04", "issue": "1", "identifier": "https://www.osti.gov/biblio/1876270", "bibliographicCitation": "https://doi.org/10.1038/s41467-022-31433-x", "keywords": [ "09 BIOMASS FUELS", "CAZymes", "Fenton chemistry", "high solids", "lignocellulose", "microbiomes" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Nature Communications", "volume": "13", "publisher_information": "Nature Publishing Group", "country_publication_code": "US", "creator": [ { "name": "Payal [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); University of Tennessee,Knoxville,TN (United States)] Chirania", "primaryContact": true }, { "name": "Evert K. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Dartmouth College,Hanover,NH (United States)] (ORCID:000000020565392X) Holwerda", "primaryContact": false }, { "name": "Richard J. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000185510138) Giannone", "primaryContact": false }, { "name": "Xiaoyu [Dartmouth College,Hanover,NH (United States)] Liang", "primaryContact": false }, { "name": "Suresh [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Poudel", "primaryContact": false }, { "name": "Joseph C. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Ellis", "primaryContact": false }, { "name": "Yannick J. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); National Renewable Energy Lab. (NREL),Golden,CO (United States)] Bomble", "primaryContact": false }, { "name": "Robert L. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:000000017708786X) Hettich", "primaryContact": false }, { "name": "Lee R. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Dartmouth College,Hanover,NH (United States)] Lynd", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Transportation Office. Bioenergy Technologies Office" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1876270", "active": false, "has_related_ids": [ "NREL/JA-2700-83070" ] }, { "brc": "CBI", "title": "Root system architecture in cereals: progress, challenges and perspective", "description": "We report roots are essential multifunctional plant organs involved in water and nutrient uptake, metabolite storage, anchorage, mechanical support, and interaction with the soil environment. Understanding of this \u2018hidden half\u2019 provides potential for manipulation of root system architecture (RSA) traits to optimize resource use efficiency and grain yield in cereal crops. Unfortunately, root traits are highly neglected in breeding due to the challenges of phenotyping, but could have large rewards if the variability in RSA traits can be fully exploited. Until now, a plethora of genes have been characterized in detail for their potential role in improving RSA. The use of forward genetics approaches to find sequence variations in genes underpinning desirable RSA would be highly beneficial. Advances in computer vision applications have allowed image-based approaches for high-throughput phenotyping of RSA traits that can be used by any laboratory worldwide to make progress in understanding root function and dissection of the genetics. At the same time, the frontiers of root measurement include non-invasive methods like X-ray computer tomography and magnetic resonance imaging that facilitate new types of temporal studies. Root physiology and ecology are further supported by spatiotemporal root simulation modeling. The discovery of component traits providing improved resilience and yield advantage in target environments is a key necessity for mainstreaming root-based cereal breeding. The integrated use of pan-genome resources, now available in most cereals, coupled with new in-field phenotyping platforms has the potential for precise selection of superior genotypes with improved RSA.", "abstract": "We report roots are essential multifunctional plant organs involved in water and nutrient uptake, metabolite storage, anchorage, mechanical support, and interaction with the soil environment. Understanding of this \u2018hidden half\u2019 provides potential for manipulation of root system architecture (RSA) traits to optimize resource use efficiency and grain yield in cereal crops. Unfortunately, root traits are highly neglected in breeding due to the challenges of phenotyping, but could have large rewards if the variability in RSA traits can be fully exploited. Until now, a plethora of genes have been characterized in detail for their potential role in improving RSA. The use of forward genetics approaches to find sequence variations in genes underpinning desirable RSA would be highly beneficial. Advances in computer vision applications have allowed image-based approaches for high-throughput phenotyping of RSA traits that can be used by any laboratory worldwide to make progress in understanding root function and dissection of the genetics. At the same time, the frontiers of root measurement include non-invasive methods like X-ray computer tomography and magnetic resonance imaging that facilitate new types of temporal studies. Root physiology and ecology are further supported by spatiotemporal root simulation modeling. The discovery of component traits providing improved resilience and yield advantage in target environments is a key necessity for mainstreaming root-based cereal breeding. The integrated use of pan-genome resources, now available in most cereals, coupled with new in-field phenotyping platforms has the potential for precise selection of superior genotypes with improved RSA.", "date": "2022-01-11", "issue": "1", "identifier": "https://www.osti.gov/biblio/1876296", "bibliographicCitation": "https://doi.org/10.1111/tpj.15669", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "phenotyping", "root genomics", "root phenomics", "root system architecture" ], "topic": [ "Microbiology" ], "journal_name": "The Plant Journal", "volume": "110", "publisher_information": "Society for Experimental Biology", "country_publication_code": "US", "creator": [ { "name": "Saman [Quaid\u2010i\u2010Azam University Islamabad (Pakistan)] Maqbool", "primaryContact": true }, { "name": "Muhammad Adeel [Chinese Academy of Agricultural Sciences,Beijing (China)] Hassan", "primaryContact": false }, { "name": "Xianchun [Chinese Academy of Agricultural Sciences,Beijing (China)] Xia", "primaryContact": false }, { "name": "Larry M. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000219959479) York", "primaryContact": false }, { "name": "Awais [Quaid\u2010i\u2010Azam University Islamabad (Pakistan); Chinese Academy of Agricultural Sciences,Beijing (China); International Wheat and Maize Improvement Center (CIMMYT),Beijing (China)] (ORCID:000000032528708X) Rasheed", "primaryContact": false }, { "name": "Zhonghu [Chinese Academy of Agricultural Sciences,Beijing (China); International Wheat and Maize Improvement Center (CIMMYT),Beijing (China)] He", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "Indigenous Fellowship Program of Higher Education Commission (HEC)" } }, { "fundingOrganization": { "organizationName": "National Natural Science Foundation of China" } }, { "fundingOrganization": { "organizationName": "Pakistan Science Foundation" } }, { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1876296", "active": false }, { "brc": "CBI", "title": "Evaluating the performance of random forest and iterative random forest based methods when applied to gene expression data", "description": "Gene-to-gene networks, such as Gene Regulatory Networks (GRN) and Predictive Expression Networks (PEN) capture relationships between genes and are beneficial for use in downstream biological analyses. There exists multiple network inference tools to produce these gene-to-gene networks from matrices of gene expression data. Random Forest-Leave One Out Prediction (RF-LOOP) is a method that has been shown to be efficient at producing these gene-to-gene networks, frequently known as GEne Network Inference with Ensemble of trees (GENIE3). Random Forest can be replaced in this process by iterative Random Forest (iRF), which performs variable selection and boosting. Here we validate that iterative Random Forest-Leave One Out Prediction (iRF-LOOP) produces higher quality networks than GENIE3 (RF-LOOP). We use both synthetic and empirical networks from the Dialogue for Reverse Engineering Assessment and Methods (DREAM) Challenges by Sage Bionetworks, as well as two additional empirical networks created from Arabidopsis thaliana and Populus trichocarpa expression data.", "abstract": "Gene-to-gene networks, such as Gene Regulatory Networks (GRN) and Predictive Expression Networks (PEN) capture relationships between genes and are beneficial for use in downstream biological analyses. There exists multiple network inference tools to produce these gene-to-gene networks from matrices of gene expression data. Random Forest-Leave One Out Prediction (RF-LOOP) is a method that has been shown to be efficient at producing these gene-to-gene networks, frequently known as GEne Network Inference with Ensemble of trees (GENIE3). Random Forest can be replaced in this process by iterative Random Forest (iRF), which performs variable selection and boosting. Here we validate that iterative Random Forest-Leave One Out Prediction (iRF-LOOP) produces higher quality networks than GENIE3 (RF-LOOP). We use both synthetic and empirical networks from the Dialogue for Reverse Engineering Assessment and Methods (DREAM) Challenges by Sage Bionetworks, as well as two additional empirical networks created from Arabidopsis thaliana and Populus trichocarpa expression data.", "date": "2022-06-21", "issue": "na", "identifier": "https://www.osti.gov/biblio/1876307", "bibliographicCitation": "https://doi.org/10.1016/j.csbj.2022.06.037", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "gene expression networks", "iterative random forest", "network biology", "random forest" ], "topic": [ "Microbiology" ], "journal_name": "Computational and Structural Biotechnology Journal", "volume": "20", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Angelica [University of Tennessee,Knoxville,TN (United States)] (ORCID:0000000343086302) Walker", "primaryContact": true }, { "name": "Ashley [University of Tennessee,Knoxville,TN (United States)] Cliff", "primaryContact": false }, { "name": "Jonathon C. [University of Tennessee,Knoxville,TN (United States)] Romero", "primaryContact": false }, { "name": "Manesh [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Shah", "primaryContact": false }, { "name": "Piet C. [University of Tennessee,Knoxville,TN (United States)] Jones", "primaryContact": false }, { "name": "Joao Gabriel Felipe Machado [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000310230363) Gazolla", "primaryContact": false }, { "name": "Daniel A. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000298228251) Jacobson", "primaryContact": false }, { "name": "David [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Kainer", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1876307", "active": false }, { "brc": "CBI", "title": "Precision genome editing in plants using gene targeting and prime editing: existing and emerging strategies", "description": "Precise modification of plant genomes, such as seamless insertion, deletion, or replacement of DNA sequences at a predefined site, is a challenging task. Gene targeting (GT) and prime editing are currently the best approaches for this purpose. However, these techniques are inefficient in plants, which limits their applications for crop breeding programs. Recently, substantial developments have been made to improve the efficiency of these techniques in plants. Several strategies, such as RNA donor templating, chemically modified donor DNA template, and tandem-repeat homology-directed repair, are aimed at improving GT. Additionally, improved prime editing gRNA design, use of engineered reverse transcriptase enzymes, and splitting prime editing components have improved the efficacy of prime editing in plants. These emerging strategies and existing technologies are reviewed along with various perspectives on their future improvement and the development of robust precision genome editing technologies for plants.", "abstract": "Precise modification of plant genomes, such as seamless insertion, deletion, or replacement of DNA sequences at a predefined site, is a challenging task. Gene targeting (GT) and prime editing are currently the best approaches for this purpose. However, these techniques are inefficient in plants, which limits their applications for crop breeding programs. Recently, substantial developments have been made to improve the efficiency of these techniques in plants. Several strategies, such as RNA donor templating, chemically modified donor DNA template, and tandem-repeat homology-directed repair, are aimed at improving GT. Additionally, improved prime editing gRNA design, use of engineered reverse transcriptase enzymes, and splitting prime editing components have improved the efficacy of prime editing in plants. These emerging strategies and existing technologies are reviewed along with various perspectives on their future improvement and the development of robust precision genome editing technologies for plants.", "date": "2022-06-28", "issue": "10", "identifier": "https://www.osti.gov/biblio/1876324", "bibliographicCitation": "https://doi.org/10.1002/biot.202100673", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "CRISPR/Cas", "gene targeting", "plants", "precision genome editing", "prime editing" ], "topic": [ "Microbiology" ], "journal_name": "Biotechnology Journal", "volume": "17", "publisher_information": "Wiley", "country_publication_code": "US", "creator": [ { "name": "Md Mahmudul [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Patuakhali Science and Technology University (Bangladesh)] (ORCID:0000000333998121) Hassan", "primaryContact": true }, { "name": "Guoliang [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Yuan", "primaryContact": false }, { "name": "Yang [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000160454969) Liu", "primaryContact": false }, { "name": "Mobashwer [Univ. of Queensland,Nambour,QLD (Australia)] Alam", "primaryContact": false }, { "name": "Carrie A. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Eckert", "primaryContact": false }, { "name": "Gerald A. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000301061289) Tuskan", "primaryContact": false }, { "name": "John F. [Univ. of Melbourne,Parkville,VIC (Australia)] Golz", "primaryContact": false }, { "name": "Xiaohan [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000152074210) Yang", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Laboratory Directed Research and Development (LDRD) Program" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1876324", "active": false }, { "brc": "CBI", "title": "n-Butanol or isobutanol as a value-added fuel additive to inhibit microbial degradation of stored gasoline", "description": "Biofouling of gasoline can occur during fuel storage caused by bacteria and fungi that form a biofilm at a fuel/water interface and that produce organic acids and sulfides. Fuel additives are applied to gasoline to prevent biofouling but are relatively expensive, are not always effective against biofilms, and do not contribute to the combustibility of gasoline. Bio-isobutanol is an approved, certified advanced biofuel and is added up to 16% (v/v) in gasoline blends \u201ciBut16\u201d; n-butanol blends are currently under review. Microorganisms are inhibited by n-butanol or isobutanol when the aqueous concentration reaches >2-3% (w/v). We determined that n-butanol partitions into the aqueous phase of a model gasoline/water system reaching concentrations of 42 g/L and up to 48 g/L from gasoline blends at 10% and 24% (v/v), respectively. Likewise, isobutanol blended in gasoline at 10% and 24% (v/v) partitioned into an aqueous phase at 45 g/L and 53 g/L, respectively. Several bacterial and fungal strains that originate from fuel storage tanks, or are known to be solvent tolerant, were evaluated for their potential growth in a range of n- and isobutanol concentrations. Growth rates for all strains tested were reduced by 40\u2013100% relative to untreated controls in n- and isobutanol concentrations of 1.5 and 2.0% (v/v). No observable growth occurred for any of the microorganisms in solvent concentrations at 3.0% (v/v). T amphiphilic and chaotropic properties of n- or isobutanol help them inhibit microbial growth and could serve as effective biocides during fuel storage as well as being valuable fuel additives.", "abstract": "Biofouling of gasoline can occur during fuel storage caused by bacteria and fungi that form a biofilm at a fuel/water interface and that produce organic acids and sulfides. Fuel additives are applied to gasoline to prevent biofouling but are relatively expensive, are not always effective against biofilms, and do not contribute to the combustibility of gasoline. Bio-isobutanol is an approved, certified advanced biofuel and is added up to 16% (v/v) in gasoline blends \u201ciBut16\u201d; n-butanol blends are currently under review. Microorganisms are inhibited by n-butanol or isobutanol when the aqueous concentration reaches >2-3% (w/v). We determined that n-butanol partitions into the aqueous phase of a model gasoline/water system reaching concentrations of 42 g/L and up to 48 g/L from gasoline blends at 10% and 24% (v/v), respectively. Likewise, isobutanol blended in gasoline at 10% and 24% (v/v) partitioned into an aqueous phase at 45 g/L and 53 g/L, respectively. Several bacterial and fungal strains that originate from fuel storage tanks, or are known to be solvent tolerant, were evaluated for their potential growth in a range of n- and isobutanol concentrations. Growth rates for all strains tested were reduced by 40\u2013100% relative to untreated controls in n- and isobutanol concentrations of 1.5 and 2.0% (v/v). No observable growth occurred for any of the microorganisms in solvent concentrations at 3.0% (v/v). T amphiphilic and chaotropic properties of n- or isobutanol help them inhibit microbial growth and could serve as effective biocides during fuel storage as well as being valuable fuel additives.", "date": "2022-07-06", "identifier": "https://www.osti.gov/biblio/1876350", "bibliographicCitation": "https://doi.org/10.1016/j.jfueco.2022.100072", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "Biofouling", "Fuel storage", "Inhibition", "Isobutanol", "Preservative", "n-Butanol" ], "topic": [ "Microbiology" ], "journal_name": "Fuel Communications", "volume": "12", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "James G. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000280525688) Elkins", "primaryContact": true }, { "name": "Miguel [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:000000015890051X) Rodriguez", "primaryContact": false }, { "name": "Olivia N. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000330946158) Cannon", "primaryContact": false }, { "name": "Raynella M. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Connatser", "primaryContact": false }, { "name": "Gbekeloluwa B. [Morgan State Univ.,Baltimore,MD (United States)] Oguntimein", "primaryContact": false }, { "name": "Michael D. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Kass", "primaryContact": false }, { "name": "Brian H. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000344605098) West", "primaryContact": false }, { "name": "Brian H. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000274083609) Davison", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1876350", "active": false }, { "brc": "CBI", "title": "Multi-pass flow-through reductive catalytic fractionation", "description": "Reductive catalytic fractionation (RCF) is a promising lignin-first biorefining strategy that selectively extracts and depolymerizes lignin from whole biomass. Flow-through (FT)-RCF enables physical separation of the biomass and catalyst, but this process configuration typically operates at high solvent-to-biomass ratios. Here, we demonstrate multi-pass FT-RCF, wherein the lignin-enriched solvent obtained after an initial FT-RCF step is recycled and used in subsequent FT-RCF without intermediate lignin recovery. Multi-pass FT-RCF reduces the solvent-to-biomass ratio from 48 to 1.9 L/kg, which is a lower solvent loading than is accessible in batch reactors, without negative impacts on delignification and monomer yield with up to 12 wt % lignin in the solvent. Overall, this work demonstrates that solvent demand in RCF processes, which is a key cost and energy driver to enable this process at scale, can be reduced by recycling lignin oil between RCF reactions.", "abstract": "Reductive catalytic fractionation (RCF) is a promising lignin-first biorefining strategy that selectively extracts and depolymerizes lignin from whole biomass. Flow-through (FT)-RCF enables physical separation of the biomass and catalyst, but this process configuration typically operates at high solvent-to-biomass ratios. Here, we demonstrate multi-pass FT-RCF, wherein the lignin-enriched solvent obtained after an initial FT-RCF step is recycled and used in subsequent FT-RCF without intermediate lignin recovery. Multi-pass FT-RCF reduces the solvent-to-biomass ratio from 48 to 1.9 L/kg, which is a lower solvent loading than is accessible in batch reactors, without negative impacts on delignification and monomer yield with up to 12 wt % lignin in the solvent. Overall, this work demonstrates that solvent demand in RCF processes, which is a key cost and energy driver to enable this process at scale, can be reduced by recycling lignin oil between RCF reactions.", "date": "2022-07-13", "issue": "8", "identifier": "https://www.osti.gov/biblio/1877363", "bibliographicCitation": "https://doi.org/10.1016/j.joule.2022.06.016", "keywords": [ "09 BIOMASS FUELS", "flow-through", "lignin valorization", "lignocellulosic biomass", "multi-pass", "reductive catalytic fractionation", "solvent reduction" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Joule", "volume": "6", "publisher_information": "Elsevier - Cell Press", "country_publication_code": "US", "creator": [ { "name": "Jun Hee [National Renewable Energy Lab. (NREL),Golden,CO (United States)] Jang", "primaryContact": true }, { "name": "David G. [National Renewable Energy Lab. (NREL),Golden,CO (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000342964855) Brandner", "primaryContact": false }, { "name": "Reagan J. [National Renewable Energy Lab. (NREL),Golden,CO (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Dreiling", "primaryContact": false }, { "name": "Arik J. [National Renewable Energy Lab. (NREL),Golden,CO (United States)] Ringsby", "primaryContact": false }, { "name": "Jeremy R. [National Renewable Energy Lab. (NREL),Golden,CO (United States)] Bussard", "primaryContact": false }, { "name": "Lisa M. [National Renewable Energy Lab. (NREL),Golden,CO (United States)] Stanley", "primaryContact": false }, { "name": "Renee M. [National Renewable Energy Lab. (NREL),Golden,CO (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Happs", "primaryContact": false }, { "name": "Anjaneya S. [ExxonMobil Research and Engineering,Clinton,NJ (United States)] Kovvali", "primaryContact": false }, { "name": "Joshua I. [ExxonMobil Chemical Company,Baytown,TX (United States)] Cutler", "primaryContact": false }, { "name": "Tom [Katholieke Univ. Leuven,Heverlee (Belgium)] Renders", "primaryContact": false }, { "name": "James R. [ExxonMobil Research and Engineering,Clinton,NJ (United States)] Bielenberg", "primaryContact": false }, { "name": "Yuriy [Massachusetts Inst. of Technology (MIT),Cambridge,MA (United States)] Roman-Leshkov", "primaryContact": false }, { "name": "Gregg T. [National Renewable Energy Lab. (NREL),Golden,CO (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:000000023480212X) Beckham", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Bioenergy Technologies Office" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1877363", "active": false, "has_related_ids": [ "NREL/JA-2A00-81807" ] }, { "brc": "CBI", "title": "Plant carbohydrate storage: intra- and inter-specific trade-offs reveal a major life history trait", "description": "Trade-offs among carbon sinks constrain how trees physiologically, ecologically, and evolutionarily respond to their environments. These trade-offs typically fall along a productive growth to conservative, bet-hedging continuum. How nonstructural carbohydrates (NSCs) stored in living tree cells (known as carbon stores) fit in this trade-off framework is not well understood. Here, we examined relationships between growth and storage using both within species genetic variation from a common garden, and across species phenotypic variation from a global database. We demonstrate that storage is actively accumulated, as part of a conservative, bet-hedging life history strategy. Storage accumulates at the expense of growth both within and across species. Within the species Populus trichocarpa, genetic trade-offs show that for each additional unit of wood area growth (in cm2 yr\u20131) that genotypes invest in, they lose 1.2 to 1.7 units (mg g\u20131 NSC) of storage. Across species, for each additional unit of area growth (in cm2 yr\u20131), trees, on average, reduce their storage by 9.5% in stems and 10.4% in roots. Our findings impact our understanding of basic plant biology, fit storage into a widely used growth-survival trade-off spectrum describing life history strategy, and challenges the assumptions of passive storage made in ecosystem models today.", "abstract": "Trade-offs among carbon sinks constrain how trees physiologically, ecologically, and evolutionarily respond to their environments. These trade-offs typically fall along a productive growth to conservative, bet-hedging continuum. How nonstructural carbohydrates (NSCs) stored in living tree cells (known as carbon stores) fit in this trade-off framework is not well understood. Here, we examined relationships between growth and storage using both within species genetic variation from a common garden, and across species phenotypic variation from a global database. We demonstrate that storage is actively accumulated, as part of a conservative, bet-hedging life history strategy. Storage accumulates at the expense of growth both within and across species. Within the species Populus trichocarpa, genetic trade-offs show that for each additional unit of wood area growth (in cm2 yr\u20131) that genotypes invest in, they lose 1.2 to 1.7 units (mg g\u20131 NSC) of storage. Across species, for each additional unit of area growth (in cm2 yr\u20131), trees, on average, reduce their storage by 9.5% in stems and 10.4% in roots. Our findings impact our understanding of basic plant biology, fit storage into a widely used growth-survival trade-off spectrum describing life history strategy, and challenges the assumptions of passive storage made in ecosystem models today.", "date": "2022-05-05", "issue": "6", "identifier": "https://www.osti.gov/biblio/1877466", "bibliographicCitation": "https://doi.org/10.1111/nph.18213", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "allocation tradeoffs", "carbon allocation", "common garden", "growth", "heritability", "nonstructural carbohydrates", "plasticity", "storage" ], "topic": [ "Microbiology" ], "journal_name": "New Phytologist", "volume": "235", "publisher_information": "Wiley", "country_publication_code": "US", "creator": [ { "name": "Meghan [Harvard Univ.,Cambridge,MA (United States); Massachusetts Inst. of Technology (MIT),Cambridge,MA (United States)] (ORCID:0000000309056265) Blumstein", "primaryContact": true }, { "name": "Anna [Univ. of Montana,Missoula,MT (United States)] (ORCID:0000000340906758) Sala", "primaryContact": false }, { "name": "David J. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000247949913) Weston", "primaryContact": false }, { "name": "Noel Michelle [Harvard Univ.,Cambridge,MA (United States)] (ORCID:0000000333255395) Holbrook", "primaryContact": false }, { "name": "Robin [Harvard Univ.,Cambridge,MA (United States); The Arnold Arboretum,Boston,MA (United States)] (ORCID:0000000262834145) Hopkins", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Science Foundation Graduate Research Fellowship" } }, { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Workforce Development for Teachers and Scientists (WDTS)" } } ], "dataset_url": "https://www.osti.gov/biblio/1877466", "active": false }, { "brc": "CBI", "title": "Ethanol Conversion to C4+ Olefins over Bimetallic Copper- And Lanthanum-Containing Beta Zeolite Catalysts", "description": "We report ethanol conversion to C4+ olefins remains a critical yet nonselective process for producing renewable middle distillates. Here, Cu\u2013La/Beta catalysts composed of copper and lanthanum incorporated onto a dealuminated Beta support are reported for ethanol conversion to C4+ olefins (73% selectivity, ~98% ethanol conversion, 623 K,<4% C1\u2013C3 hydrocarbons) which particularly favors C5+ olefin formation (43% selectivity) as a distinction from the benchmarking Cu\u2013Y/Beta catalyst. Monometallic Cu/Beta or La/Beta samples are insufficient to catalyze the C4+ olefin formation and primarily form dehydration products (e.g., ethylene and diethyl ether), indicating the necessity of both Cu and La species for butene and C5+ olefin formation. Increasing the bulk La loading at a fixed Cu content yields higher C5+ olefins until the La/Cu molar ratio reaches 3.6. These findings indicate Cu\u2013La/Beta as an effective ethanol conversion catalyst that facilitates multiple C\u2013C bond formation events required for synthesizing C5+ olefins (i.e., hexenes and octenes).", "abstract": "We report ethanol conversion to C4+ olefins remains a critical yet nonselective process for producing renewable middle distillates. Here, Cu\u2013La/Beta catalysts composed of copper and lanthanum incorporated onto a dealuminated Beta support are reported for ethanol conversion to C4+ olefins (73% selectivity, ~98% ethanol conversion, 623 K,<4% C1\u2013C3 hydrocarbons) which particularly favors C5+ olefin formation (43% selectivity) as a distinction from the benchmarking Cu\u2013Y/Beta catalyst. Monometallic Cu/Beta or La/Beta samples are insufficient to catalyze the C4+ olefin formation and primarily form dehydration products (e.g., ethylene and diethyl ether), indicating the necessity of both Cu and La species for butene and C5+ olefin formation. Increasing the bulk La loading at a fixed Cu content yields higher C5+ olefins until the La/Cu molar ratio reaches 3.6. These findings indicate Cu\u2013La/Beta as an effective ethanol conversion catalyst that facilitates multiple C\u2013C bond formation events required for synthesizing C5+ olefins (i.e., hexenes and octenes).", "date": "2022-04-21", "issue": "18", "identifier": "https://www.osti.gov/biblio/1883667", "bibliographicCitation": "https://doi.org/10.1021/acssuschemeng.1c07442", "keywords": [ "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "beta zeolite", "catalysis", "copper", "ethanol", "lanthanum", "olefins" ], "topic": [ "Chemistry" ], "journal_name": "ACS Sustainable Chemistry & Engineering", "volume": "10", "publisher_information": "American Chemical Society (ACS)", "country_publication_code": "US", "creator": [ { "name": "Michael J. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Cordon", "primaryContact": true }, { "name": "Junyan [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); University of Maryland,College Park,MD (United States)] Zhang", "primaryContact": false }, { "name": "Nohor River [University of Alabama,Tuscaloosa,AL (United States)] Samad", "primaryContact": false }, { "name": "James W. [University of Alabama,Tuscaloosa,AL (United States)] Harris", "primaryContact": false }, { "name": "Kinga A. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Unocic", "primaryContact": false }, { "name": "Meijun [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000221648629) Li", "primaryContact": false }, { "name": "Dongxia [University of Maryland,College Park,MD (United States)] (ORCID:0000000187122219) Liu", "primaryContact": false }, { "name": "Zhenglong [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000188118625) Li", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Transportation Office. Bioenergy Technologies Office" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1883667", "active": false }, { "brc": "CBI", "title": "PARA: A New Platform for the Rapid Assembly of gRNA Arrays for Multiplexed CRISPR Technologies", "description": "Multiplexed CRISPR technologies have great potential for pathway engineering and genome editing. However, their applications are constrained by complex, laborious and time-consuming cloning steps. In this research, we developed a novel method, PARA, which allows for the one-step assembly of multiple guide RNAs (gRNAs) into a CRISPR vector with up to 18 gRNAs. Here, we demonstrate that PARA is capable of the efficient assembly of transfer RNA/Csy4/ribozyme-based gRNA arrays. To aid in this process and to streamline vector construction, we developed a user-friendly PARAweb tool for designing PCR primers and component DNA parts and simulating assembled gRNA arrays and vector sequences.", "abstract": "Multiplexed CRISPR technologies have great potential for pathway engineering and genome editing. However, their applications are constrained by complex, laborious and time-consuming cloning steps. In this research, we developed a novel method, PARA, which allows for the one-step assembly of multiple guide RNAs (gRNAs) into a CRISPR vector with up to 18 gRNAs. Here, we demonstrate that PARA is capable of the efficient assembly of transfer RNA/Csy4/ribozyme-based gRNA arrays. To aid in this process and to streamline vector construction, we developed a user-friendly PARAweb tool for designing PCR primers and component DNA parts and simulating assembled gRNA arrays and vector sequences.", "date": "2022-08-08", "issue": "16", "identifier": "https://www.osti.gov/biblio/1883861", "bibliographicCitation": "https://doi.org/10.3390/cells11162467", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "Golden Gate\r\nassembly", "PARA", "assembly method", "gRNA array", "genome editing", "multiplexed CRISPR", "web tool" ], "topic": [ "Microbiology" ], "journal_name": "Cells", "volume": "11", "publisher_information": "MDPI", "country_publication_code": "US", "creator": [ { "name": "Guoliang [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000265628769) Yuan", "primaryContact": true }, { "name": "Stanton [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Martin", "primaryContact": false }, { "name": "Md Mahmudul [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Patuakhali Science and Technology University,Dumki (Bangladesh)] (ORCID:0000000333998121) Hassan", "primaryContact": false }, { "name": "Gerald A. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000301061289) Tuskan", "primaryContact": false }, { "name": "Xiaohan [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000152074210) Yang", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1883861", "active": false }, { "brc": "CBI", "title": "In silico evaluation of a targeted metaproteomics strategy for broad screening of cellulolytic enzyme capacities in anaerobic microbiome bioreactors", "description": "Microbial-driven solubilization of lignocellulosic material is a natural mechanism that is exploited in anaerobic digesters (ADs) to produce biogas and other valuable bioproducts. Glycoside hydrolases (GHs) are the main enzymes that bacterial and archaeal populations use to break down complex polysaccharides in these reactors. Methodologies for rapidly screening the physical presence and types of GHs can provide information about their functional activities as well as the taxonomical diversity within AD systems but are largely unavailable. Targeted proteomic methods could potentially be used to provide snapshots of the GHs expressed by microbial consortia in ADs, giving valuable insights into the functional lignocellulolytic degradation diversity of a community. Such observations would be essential to evaluate the hydrolytic performance of a reactor or potential issues with it.", "abstract": "Microbial-driven solubilization of lignocellulosic material is a natural mechanism that is exploited in anaerobic digesters (ADs) to produce biogas and other valuable bioproducts. Glycoside hydrolases (GHs) are the main enzymes that bacterial and archaeal populations use to break down complex polysaccharides in these reactors. Methodologies for rapidly screening the physical presence and types of GHs can provide information about their functional activities as well as the taxonomical diversity within AD systems but are largely unavailable. Targeted proteomic methods could potentially be used to provide snapshots of the GHs expressed by microbial consortia in ADs, giving valuable insights into the functional lignocellulolytic degradation diversity of a community. Such observations would be essential to evaluate the hydrolytic performance of a reactor or potential issues with it.", "date": "2022-03-17", "issue": "1", "identifier": "https://www.osti.gov/biblio/1883948", "bibliographicCitation": "https://doi.org/10.1186/s13068-022-02125-x", "keywords": [ "09 BIOMASS FUELS", "Anaerobic digester", "Biogas", "Glycoside hydrolases", "Lignocellulose", "Microbial community", "Microbiome", "Peptides", "Targeted metaproteomics" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Biotechnology for Biofuels and Bioproducts", "volume": "15", "publisher_information": "BioMed Central", "country_publication_code": "US", "creator": [ { "name": "Manuel I. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Villalobos Solis", "primaryContact": true }, { "name": "Payal [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Univ. of Tennessee,Knoxville,TN (United States)] Chirania", "primaryContact": false }, { "name": "Robert L. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:000000017708786X) Hettich", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1883948", "active": false }, { "brc": "CBI", "title": "Catalyst choice impacts aromatic monomer yields and selectivity in hydrogen-free reductive catalytic fractionation", "description": "Pd/C and Pt/C show high activity for hydrogen-free reductive catalytic fractionation compared to Ru/C and Ni/C.
", "abstract": "Pd/C and Pt/C show high activity for hydrogen-free reductive catalytic fractionation compared to Ru/C and Ni/C.
", "date": "2022-11-21", "issue": "12", "identifier": "https://www.osti.gov/biblio/1885069", "bibliographicCitation": "https://doi.org/10.1039/D2RE00275B", "keywords": [ "09 BIOMASS FUELS", "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "lignin", "reductive catalytic fractionation" ], "topic": [ "Biomass & Feedstock", "Chemistry" ], "journal_name": "Reaction Chemistry & Engineering", "volume": "7", "publisher_information": "Royal Society of Chemistry (RSC)", "country_publication_code": "GB", "creator": [ { "name": "Jacob K. [Department of Chemical and Biological Engineering,University of Colorado Boulder,Boulder 80303,CO,USA,Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,15013 Denver W Pkwy,Golden,CO 80401,USA] (ORCID:0000000158832043) Kenny", "primaryContact": true }, { "name": "David G. [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,15013 Denver W Pkwy,Golden,CO 80401,USA] (ORCID:0000000342964855) Brandner", "primaryContact": false }, { "name": "Sasha R. [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,15013 Denver W Pkwy,Golden,CO 80401,USA] Neefe", "primaryContact": false }, { "name": "William E. [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,15013 Denver W Pkwy,Golden,CO 80401,USA] Michener", "primaryContact": false }, { "name": "Yuriy [Department of Chemical Engineering,Massachusetts Institute of Technology,25 Ames Street,Cambridge,MA 02139,USA] (ORCID:0000000200254233) Rom\u00e1n-Leshkov", "primaryContact": false }, { "name": "Gregg T. [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,15013 Denver W Pkwy,Golden,CO 80401,USA] (ORCID:000000023480212X) Beckham", "primaryContact": false }, { "name": "J. Will [Department of Chemical and Biological Engineering,University of Colorado Boulder,Boulder 80303,CO,USA] (ORCID:0000000324042443) Medlin", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "GAANN graduate fellowship" } }, { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Transportation Office. Bioenergy Technologies Office" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1885069", "active": false, "has_related_ids": [ "NREL/JA-2800-81796" ] }, { "brc": "CBI", "title": "Climatic clustering and longitudinal analysis with impacts on food, bioenergy, and pandemics", "description": "Predicted growth in world population will put unparalleled stress on the need for sustainable energy and global food production, as well as increase the likelihood of future pandemics. In this work, we identify high-resolution environmental zones in the context of a changing climate and predict longitudinal processes relevant to these challenges. We do this using exhaustive vector comparison methods that measure the climatic similarity between all locations on earth at high geospatial resolution relative to global-scale analyses. The results are captured as networks, in which edges between geolocations are defined if their historical climate similarities exceed a threshold. We apply Markov clustering and our novel Correlation of Correlations method to the resulting climatic networks, which provides unprecedented agglomerative and longitudinal views of climatic relationships across the globe. The methods performed here resulted in the fastest (9.37x1018 operations/sec) and one of the largest (168.7x1021 operations) scientific computations ever performed, with more than 100 quadrillion edges considered for a single climatic network. Our climatic analysis reveals areas of the world experiencing rapid environmental changes, which can have important implications for global carbon fluxes and zoonotic spillover events. Correlation and network analyses of this kind are widely applicable across computational and predictive biology domains, including systems biology, ecology, carbon cycles, biogeochemistry, and zoonosis research.", "abstract": "Predicted growth in world population will put unparalleled stress on the need for sustainable energy and global food production, as well as increase the likelihood of future pandemics. In this work, we identify high-resolution environmental zones in the context of a changing climate and predict longitudinal processes relevant to these challenges. We do this using exhaustive vector comparison methods that measure the climatic similarity between all locations on earth at high geospatial resolution relative to global-scale analyses. The results are captured as networks, in which edges between geolocations are defined if their historical climate similarities exceed a threshold. We apply Markov clustering and our novel Correlation of Correlations method to the resulting climatic networks, which provides unprecedented agglomerative and longitudinal views of climatic relationships across the globe. The methods performed here resulted in the fastest (9.37x1018 operations/sec) and one of the largest (168.7x1021 operations) scientific computations ever performed, with more than 100 quadrillion edges considered for a single climatic network. Our climatic analysis reveals areas of the world experiencing rapid environmental changes, which can have important implications for global carbon fluxes and zoonotic spillover events. Correlation and network analyses of this kind are widely applicable across computational and predictive biology domains, including systems biology, ecology, carbon cycles, biogeochemistry, and zoonosis research.", "date": "2022-09-14", "issue": "3", "identifier": "https://www.osti.gov/biblio/1891420", "bibliographicCitation": "https://doi.org/10.1094/pbiomes-02-22-0007-r", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "Phytobiomes Journal", "volume": "6", "publisher_information": "American Phytopathological Society (APS)", "country_publication_code": "US", "creator": [ { "name": "John [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000280927433) Lagergren", "primaryContact": true }, { "name": "Mikaela [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000306207830) Cashman McDevitt", "primaryContact": false }, { "name": "Veronica G. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States); Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:0000000243334145) Melesse Vergara", "primaryContact": false }, { "name": "Paul R. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Eller", "primaryContact": false }, { "name": "Joao Gabriel Felipe [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000310230363) Machado Gazolla", "primaryContact": false }, { "name": "Hari B. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Chhetri", "primaryContact": false }, { "name": "Jared [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Streich", "primaryContact": false }, { "name": "Sharlee [Univ. of Missouri,St. Louis,MO (United States)] Climer", "primaryContact": false }, { "name": "Peter E. [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000247595158) Thornton", "primaryContact": false }, { "name": "Wayne [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:000000034771998X) Joubert", "primaryContact": false }, { "name": "Daniel [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000298228251) Jacobson", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Institute on Aging (NIA)" } }, { "fundingOrganization": { "organizationName": "National Institutes of Health (NIH)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1891420", "active": false }, { "brc": "CBI", "title": "The Promises, Challenges, and Opportunities of Omics for Studying the Plant Holobiont", "description": "Microorganisms are critical drivers of biological processes that contribute significantly to plant sustainability and productivity. In recent years, emerging research on plant holobiont theory and microbial invasion ecology has radically transformed how we study plant\u2013microbe interactions. Over the last few years, we have witnessed an accelerating pace of advancements and breadth of questions answered using omic technologies. Herein, we discuss how current state-of-the-art genomics, transcriptomics, proteomics, and metabolomics techniques reliably transcend the task of studying plant\u2013microbe interactions while acknowledging existing limitations impeding our understanding of plant holobionts.
", "abstract": "Microorganisms are critical drivers of biological processes that contribute significantly to plant sustainability and productivity. In recent years, emerging research on plant holobiont theory and microbial invasion ecology has radically transformed how we study plant\u2013microbe interactions. Over the last few years, we have witnessed an accelerating pace of advancements and breadth of questions answered using omic technologies. Herein, we discuss how current state-of-the-art genomics, transcriptomics, proteomics, and metabolomics techniques reliably transcend the task of studying plant\u2013microbe interactions while acknowledging existing limitations impeding our understanding of plant holobionts.
", "date": "2022-10-11", "issue": "10", "identifier": "https://www.osti.gov/biblio/1892093", "bibliographicCitation": "https://doi.org/10.3390/microorganisms10102013", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "genomics", "metabolomics", "plant holobiont", "plant\u2013microbe interaction", "proteomics", "transcriptomics" ], "topic": [ "Microbiology" ], "journal_name": "Microorganisms", "volume": "10", "publisher_information": "MDPI AG", "country_publication_code": "Switzerland", "creator": [ { "name": "Dana L. Carper", "primaryContact": true }, { "name": "Manasa R. (ORCID:0000000273310478) Appidi", "primaryContact": false }, { "name": "Sameer Mudbhari", "primaryContact": false }, { "name": "Him K. (ORCID:000000019686357X) Shrestha", "primaryContact": false }, { "name": "Robert L. Hettich", "primaryContact": false }, { "name": "Paul E. (ORCID:0000000326859123) Abraham", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1892093", "active": false }, { "brc": "CBI", "title": "Energy-resolved mass spectrometry as a tool for identification of lignin depolymerization products", "description": "Lignin is the largest source of bio-based aromatic compounds in nature, and its valorization is essential to the sustainability of lignocellulosic biorefining. Characterizing lignin-derived compounds remains challenging due to the heterogeneity of this biopolymer. Tandem mass spectrometry is a promising tool for lignin structural analytics, as fragmentation patterns of model compounds can be extrapolated to identify characteristic moieties in complex samples. This work extends previous resonance excitation type collision-induced dissociation (CID) methods that identified lignin oligomers containing \u03b2-\u039f-4, \u03b2-5, and \u03b2-\u03b2 bonds, to also identify characteristics of 5-5, \u03b2-1, and 4-\u039f-5 dimers, enabled by quadrupole time-of-flight (QTOF) CID with energy-resolved mass spectrometry (ERMS). Overall, beam type ERMS offers in-depth structural information and could ultimately contribute to tools for high-throughput lignin dimer identification.", "abstract": "Lignin is the largest source of bio-based aromatic compounds in nature, and its valorization is essential to the sustainability of lignocellulosic biorefining. Characterizing lignin-derived compounds remains challenging due to the heterogeneity of this biopolymer. Tandem mass spectrometry is a promising tool for lignin structural analytics, as fragmentation patterns of model compounds can be extrapolated to identify characteristic moieties in complex samples. This work extends previous resonance excitation type collision-induced dissociation (CID) methods that identified lignin oligomers containing \u03b2-\u039f-4, \u03b2-5, and \u03b2-\u03b2 bonds, to also identify characteristics of 5-5, \u03b2-1, and 4-\u039f-5 dimers, enabled by quadrupole time-of-flight (QTOF) CID with energy-resolved mass spectrometry (ERMS). Overall, beam type ERMS offers in-depth structural information and could ultimately contribute to tools for high-throughput lignin dimer identification.", "date": "2022-10-04", "issue": "1", "identifier": "https://www.osti.gov/biblio/1892301", "bibliographicCitation": "https://doi.org/10.1002/cssc.202201441", "keywords": [ "09 BIOMASS FUELS", "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "collisionally activated dissociation", "energy-resolved mass sproctrometry", "lignin-derived compound characterization" ], "topic": [ "Biomass & Feedstock", "Chemistry" ], "journal_name": "ChemSusChem", "volume": "16", "publisher_information": "ChemPubSoc Europe", "country_publication_code": "US", "creator": [ { "name": "Xueming [National Renewable Energy Lab. (NREL),Golden,CO (United States)] Dong", "primaryContact": true }, { "name": "Heather [National Renewable Energy Lab. (NREL),Golden,CO (United States)] Mayes", "primaryContact": false }, { "name": "Kris [RIC Group,Kortrijk (Belgium)] Morreel", "primaryContact": false }, { "name": "Rui [National Renewable Energy Lab. (NREL),Golden,CO (United States)] Katahira", "primaryContact": false }, { "name": "Yanding [University of Wisconsin,Madison,WI (United States)] Li", "primaryContact": false }, { "name": "John [University of Wisconsin,Madison,WI (United States)] Ralph", "primaryContact": false }, { "name": "Brenna [National Renewable Energy Lab. (NREL),Golden,CO (United States)] Black", "primaryContact": false }, { "name": "Gregg [National Renewable Energy Lab. (NREL),Golden,CO (United States)] (ORCID:000000023480212X) Beckham", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Transportation Office. Bioenergy Technologies Office" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1892301", "active": false, "has_related_ids": [ "NREL/JA-2800-81927" ] }, { "brc": "CBI", "title": "Techno-economic analysis and life cycle assessment of a biorefinery utilizing reductive catalytic fractionation", "description": "Analysis of a promising lignin-first biorefining technique, reductive catalytic fractionation, provides useful metrics for cost and sustainability to guide researchers toward critical areas for improvement.
", "abstract": "Analysis of a promising lignin-first biorefining technique, reductive catalytic fractionation, provides useful metrics for cost and sustainability to guide researchers toward critical areas for improvement.
", "date": "2021-08-10", "issue": "8", "identifier": "https://www.osti.gov/biblio/1892343", "bibliographicCitation": "https://doi.org/10.1039/D1EE01642C", "keywords": [ "09 BIOMASS FUELS", "biochemicals", "biofuels", "biomass fractionation", "lignin valorization" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Energy & Environmental Science", "volume": "14", "publisher_information": "Royal Society of Chemistry (RSC)", "country_publication_code": "GB", "creator": [ { "name": "Andrew W. [Catalytic Carbon Transformation and Scale-Up Center,National Renewable Energy Laboratory,Golden,CO,80401,USA,Center for Bioenergy Innovation,Oak Ridge,TN 37830,USA] (ORCID:0000000262360031) Bartling", "primaryContact": true }, { "name": "Michael L. [Department of Chemical Engineering,Massachusetts Institute of Technology,Cambridge,MA,02139,USA] (ORCID:0000000263417183) Stone", "primaryContact": false }, { "name": "Rebecca J. [Center for Bioenergy Innovation,Oak Ridge,TN 37830,USA,Strategic Energy Analysis Center,National Renewable Energy Laboratory,Golden,CO,80401,USA] (ORCID:0000000215585887) Hanes", "primaryContact": false }, { "name": "Arpit [Strategic Energy Analysis Center,National Renewable Energy Laboratory,Golden,CO,80401,USA] (ORCID:0000000237801800) Bhatt", "primaryContact": false }, { "name": "Yimin [Strategic Energy Analysis Center,National Renewable Energy Laboratory,Golden,CO,80401,USA] Zhang", "primaryContact": false }, { "name": "Mary J. [Catalytic Carbon Transformation and Scale-Up Center,National Renewable Energy Laboratory,Golden,CO,80401,USA,Center for Bioenergy Innovation,Oak Ridge,TN 37830,USA] Biddy", "primaryContact": false }, { "name": "Ryan [Catalytic Carbon Transformation and Scale-Up Center,National Renewable Energy Laboratory,Golden,CO,80401,USA] Davis", "primaryContact": false }, { "name": "Jacob S. [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,Golden,CO 80401,USA] (ORCID:0000000317305575) Kruger", "primaryContact": false }, { "name": "Nicholas E. [Catalytic Carbon Transformation and Scale-Up Center,National Renewable Energy Laboratory,Golden,CO,80401,USA] (ORCID:0000000246802733) Thornburg", "primaryContact": false }, { "name": "Jeremy S. [Laboratory of Sustainable and Catalytic Processing,Institute of Chemical Sciences and Engineering \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL),CH-1015 Lausanne,Switzerland] (ORCID:0000000209670583) Luterbacher", "primaryContact": false }, { "name": "Roberto [Department of Chemical Engineering,Imperial College London,South Kensington Campus,London SW7 2AZ,UK] (ORCID:0000000271754972) Rinaldi", "primaryContact": false }, { "name": "Joseph S. M. [Department of Organic Chemistry,Stockholm University,SE-106 91 Stockholm,Sweden] (ORCID:0000000187355397) Samec", "primaryContact": false }, { "name": "Bert F. [Center for Sustainable Catalysis and Engineering,KU Leuven,Celestijnenlaan 200F,3001 Leuven,Belgium] (ORCID:0000000196571710) Sels", "primaryContact": false }, { "name": "Yuriy [Department of Chemical Engineering,Massachusetts Institute of Technology,Cambridge,MA,02139,USA] (ORCID:0000000200254233) Rom\u00e1n-Leshkov", "primaryContact": false }, { "name": "Gregg T. [Catalytic Carbon Transformation and Scale-Up Center,National Renewable Energy Laboratory,Golden,CO,80401,USA,Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,Golden,CO 80401,USA] (ORCID:000000023480212X) Beckham", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Bioenergy Technologies Office (EE-3B)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/1892343", "active": false, "has_related_ids": [ "NREL/JA--2A00-80250" ] }, { "brc": "CBI", "title": "Biological and Molecular Components for Genetically Engineering Biosensors in Plants", "description": "Not Available", "abstract": "Not Available", "date": "2021-12-31", "issue": "C", "identifier": "https://www.osti.gov/biblio/1897555", "bibliographicCitation": "https://doi.org/10.34133/2022/9863496", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "BioDesign Research", "volume": "2022", "publisher_information": "Elsevier", "country_publication_code": "India", "creator": [ { "name": "Yang (ORCID:0000000160454969) Liu", "primaryContact": true }, { "name": "Guoliang (ORCID:0000000265628769) Yuan", "primaryContact": false }, { "name": "Md Mahmudul Hassan", "primaryContact": false }, { "name": "Paul E. (ORCID:0000000326859123) Abraham", "primaryContact": false }, { "name": "Julie C. Mitchell", "primaryContact": false }, { "name": "Daniel Jacobson", "primaryContact": false }, { "name": "Gerald A. Tuskan", "primaryContact": false }, { "name": "Arjun Khakhar", "primaryContact": false }, { "name": "June Medford", "primaryContact": false }, { "name": "Cheng Zhao", "primaryContact": false }, { "name": "Chang-Jun Liu", "primaryContact": false }, { "name": "Carrie A. Eckert", "primaryContact": false }, { "name": "Mitchel J. Doktycz", "primaryContact": false }, { "name": "Timothy J. Tschaplinski", "primaryContact": false }, { "name": "Xiaohan (ORCID:0000000152074210) Yang", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Basic Energy Sciences (BES)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1897555", "active": false }, { "brc": "CBI", "title": "Molecular simulation of lignin-related aromatic compound permeation through gram-negative bacterial outer membranes", "description": "Lignin, an abundant aromatic heteropolymer in secondary plant cell walls, is the single largest source of renewable aromatics in the biosphere. Leveraging this resource for renewable bioproducts through targeted microbial action depends on lignin fragment uptake by microbial hosts and subsequent enzymatic action to obtain the desired product. Recent computational work has emphasized that bacterial inner membranes are permeable to many aromatic compounds expected from lignin depolymerization processes. In this study, we expand on these findings through simulations for 42 lignin-related compounds across a gram-negative bacterial outer membrane model. Unbiased simulation trajectories indicate that spontaneous crossing for the full outer membrane is relatively rare at molecular simulation timescales, primarily due to preferential membrane partitioning and slow diffusion within the lipopolysaccharide layer within the outer membrane. Membrane partitioning and permeability coefficients were determined through replica exchange umbrella sampling simulations to overcome sampling limitations. We find that the glycosylated lipopolysaccharides found in the outer membrane increase the permeation barrier to many lignin-related compounds, particularly the most hydrophobic compounds. However, the effect is relatively modest; at industrially relevant concentrations, uncharged lignin-related compounds will readily diffuse across the outer membrane without the need for specific porins. Together, our results provide insight into the permeability of the bacterial outer membrane for assessing lignin fragment uptake and the future production of renewable bioproducts.", "abstract": "Lignin, an abundant aromatic heteropolymer in secondary plant cell walls, is the single largest source of renewable aromatics in the biosphere. Leveraging this resource for renewable bioproducts through targeted microbial action depends on lignin fragment uptake by microbial hosts and subsequent enzymatic action to obtain the desired product. Recent computational work has emphasized that bacterial inner membranes are permeable to many aromatic compounds expected from lignin depolymerization processes. In this study, we expand on these findings through simulations for 42 lignin-related compounds across a gram-negative bacterial outer membrane model. Unbiased simulation trajectories indicate that spontaneous crossing for the full outer membrane is relatively rare at molecular simulation timescales, primarily due to preferential membrane partitioning and slow diffusion within the lipopolysaccharide layer within the outer membrane. Membrane partitioning and permeability coefficients were determined through replica exchange umbrella sampling simulations to overcome sampling limitations. We find that the glycosylated lipopolysaccharides found in the outer membrane increase the permeation barrier to many lignin-related compounds, particularly the most hydrophobic compounds. However, the effect is relatively modest; at industrially relevant concentrations, uncharged lignin-related compounds will readily diffuse across the outer membrane without the need for specific porins. Together, our results provide insight into the permeability of the bacterial outer membrane for assessing lignin fragment uptake and the future production of renewable bioproducts.", "date": "2022-10-20", "issue": "12", "identifier": "https://www.osti.gov/biblio/1900011", "bibliographicCitation": "https://doi.org/10.1016/j.jbc.2022.102627", "keywords": [ "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "aromatic compounds", "bioproducts", "gram-negative bacterial outer membrane model", "lignin", "lignin fragment uptake", "permeability" ], "topic": [ "Chemistry" ], "journal_name": "Journal of Biological Chemistry", "volume": "298", "publisher_information": "American Society for Biochemistry and Molecular Biology", "country_publication_code": "US", "creator": [ { "name": "Josh V. [National Renewable Energy Laboratory (NREL),Golden,CO (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); Michigan State University,East Lansing,MI (United States)] (ORCID:0000000331396469) Vermaas", "primaryContact": true }, { "name": "Michael F. [National Renewable Energy Laboratory (NREL),Golden,CO (United States)] (ORCID:0000000151639398) Crowley", "primaryContact": false }, { "name": "Gregg T. [National Renewable Energy Laboratory (NREL),Golden,CO (United States)] (ORCID:000000023480212X) Beckham", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "Michigan State University" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Transportation Office. Bioenergy Technologies Office" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC)" } } ], "dataset_url": "https://www.osti.gov/biblio/1900011", "active": false, "has_related_ids": [ "NREL/JA-2A00-84373" ] }, { "brc": "CBI", "title": "Lignin biosynthesis: old roads revisited and new roads explored", "description": "Lignin is a major component of secondarily thickened plant cell walls and is considered to be the second most abundant biopolymer on the planet. At one point believed to be the product of a highly controlled polymerization procedure involving just three potential monomeric components (monolignols), it is becoming increasingly clear that the composition of lignin is quite flexible. Furthermore, the biosynthetic pathways to the major monolignols also appear to exhibit flexibility, particularly as regards the early reactions leading to the formation of caffeic acid from coumaric acid. The operation of parallel pathways to caffeic acid occurring at the level of shikimate esters or free acids may help provide robustness to the pathway under different physiological conditions. Several features of the pathway also appear to link monolignol biosynthesis to both generation and detoxification of hydrogen peroxide, one of the oxidants responsible for creating monolignol radicals for polymerization in the apoplast. Monolignol transport to the apoplast is not well understood. It may involve passive diffusion, although this may be targeted to sites of lignin initiation/polymerization by ordered complexes of both biosynthetic enzymes on the cytosolic side of the plasma membrane and structural anchoring of proteins for monolignol oxidation and polymerization on the apoplastic side. We present several hypothetical models to illustrate these ideas and stimulate further research. These are based primarily on studies in model systems, which may or may not reflect the major lignification process in forest trees.", "abstract": "Lignin is a major component of secondarily thickened plant cell walls and is considered to be the second most abundant biopolymer on the planet. At one point believed to be the product of a highly controlled polymerization procedure involving just three potential monomeric components (monolignols), it is becoming increasingly clear that the composition of lignin is quite flexible. Furthermore, the biosynthetic pathways to the major monolignols also appear to exhibit flexibility, particularly as regards the early reactions leading to the formation of caffeic acid from coumaric acid. The operation of parallel pathways to caffeic acid occurring at the level of shikimate esters or free acids may help provide robustness to the pathway under different physiological conditions. Several features of the pathway also appear to link monolignol biosynthesis to both generation and detoxification of hydrogen peroxide, one of the oxidants responsible for creating monolignol radicals for polymerization in the apoplast. Monolignol transport to the apoplast is not well understood. It may involve passive diffusion, although this may be targeted to sites of lignin initiation/polymerization by ordered complexes of both biosynthetic enzymes on the cytosolic side of the plasma membrane and structural anchoring of proteins for monolignol oxidation and polymerization on the apoplastic side. We present several hypothetical models to illustrate these ideas and stimulate further research. These are based primarily on studies in model systems, which may or may not reflect the major lignification process in forest trees.", "date": "2019-12-03", "issue": "12", "identifier": "https://www.osti.gov/biblio/1903900", "bibliographicCitation": "https://doi.org/10.1098/rsob.190215", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "biochemistry & molecular biology", "lignin", "membrane transport", "metabolic channelling", "oxidative polymerization", "reactive oxygen species", "secondary cell wall" ], "topic": [ "Microbiology" ], "journal_name": "Open Biology", "volume": "9", "publisher_information": "The Royal Society", "country_publication_code": "US", "creator": [ { "name": "Richard A. [Texas A & M Univ.,College Station,TX (United States); Univ. of North Texas,Denton,TX (United States); OSTI] (ORCID:0000000183939408) Dixon", "primaryContact": true }, { "name": "Jaime [Univ. of North Texas,Denton,TX (United States)] Barros", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1903900", "active": false }, { "brc": "CBI", "title": "Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2", "description": "The association of the receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein with human angiotensin-converting enzyme 2 (hACE2) represents the first required step for cellular entry. SARS-CoV-2 has continued to evolve with the emergence of several novel variants, and amino acid changes in the RBD have been implicated with increased fitness and potential for immune evasion. Reliably predicting the effect of amino acid changes on the ability of the RBD to interact more strongly with the hACE2 can help assess the implications for public health and the potential for spillover and adaptation into other animals. Here, we introduce a two-step framework that first relies on 48 independent 4-ns molecular dynamics (MD) trajectories of RBD-hACE2 variants to collect binding energy terms decomposed into Coulombic, covalent, van der Waals, lipophilic, generalized Born solvation, hydrogen bonding, \u03c0-\u03c0 packing, and self-contact correction terms. The second step implements a neural network to classify and quantitatively predict binding affinity changes using the decomposed energy terms as descriptors. The computational base achieves a validation accuracy of 82.8% for classifying single\u2013amino acid substitution variants of the RBD as worsening or improving binding affinity for hACE2 and a correlation coefficient of 0.73 between predicted and experimentally calculated changes in binding affinities. Both metrics are calculated using a fivefold cross-validation test. Our method thus sets up a framework for screening binding affinity changes caused by unknown single\u2013 and multiple\u2013amino acid changes offering a valuable tool to predict host adaptation of SARS-CoV-2 variants toward tighter hACE2 binding.", "abstract": "The association of the receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein with human angiotensin-converting enzyme 2 (hACE2) represents the first required step for cellular entry. SARS-CoV-2 has continued to evolve with the emergence of several novel variants, and amino acid changes in the RBD have been implicated with increased fitness and potential for immune evasion. Reliably predicting the effect of amino acid changes on the ability of the RBD to interact more strongly with the hACE2 can help assess the implications for public health and the potential for spillover and adaptation into other animals. Here, we introduce a two-step framework that first relies on 48 independent 4-ns molecular dynamics (MD) trajectories of RBD-hACE2 variants to collect binding energy terms decomposed into Coulombic, covalent, van der Waals, lipophilic, generalized Born solvation, hydrogen bonding, \u03c0-\u03c0 packing, and self-contact correction terms. The second step implements a neural network to classify and quantitatively predict binding affinity changes using the decomposed energy terms as descriptors. The computational base achieves a validation accuracy of 82.8% for classifying single\u2013amino acid substitution variants of the RBD as worsening or improving binding affinity for hACE2 and a correlation coefficient of 0.73 between predicted and experimentally calculated changes in binding affinities. Both metrics are calculated using a fivefold cross-validation test. Our method thus sets up a framework for screening binding affinity changes caused by unknown single\u2013 and multiple\u2013amino acid changes offering a valuable tool to predict host adaptation of SARS-CoV-2 variants toward tighter hACE2 binding.", "date": "2021-09-28", "issue": "42", "identifier": "https://www.osti.gov/biblio/1903902", "bibliographicCitation": "https://doi.org/10.1073/pnas.2106480118", "keywords": [ "60 APPLIED LIFE SCIENCES", "MM-GBSA", "SARS-CoV-2", "binding affinity", "human ACE2", "neural network" ], "topic": [ "Plant Biology" ], "journal_name": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "118", "publisher_information": "National Academy of Sciences", "country_publication_code": "US", "creator": [ { "name": "Chen [Pennsylvania State University,University Park,PA (United States); OSTI] (ORCID:0000000283167898) Chen", "primaryContact": true }, { "name": "Veda Sheersh [Pennsylvania State University,University Park,PA (United States)] (ORCID:0000000300843975) Boorla", "primaryContact": false }, { "name": "Deepro [Pennsylvania State University,University Park,PA (United States)] (ORCID:0000000348770920) Banerjee", "primaryContact": false }, { "name": "Ratul [Pennsylvania State University,University Park,PA (United States)] (ORCID:0000000345226911) Chowdhury", "primaryContact": false }, { "name": "Victoria S. [Pennsylvania State University,University Park,PA (United States)] (ORCID:0000000233208639) Cavener", "primaryContact": false }, { "name": "Ruth H. [Pennsylvania State University,University Park,PA (United States)] (ORCID:0000000231027447) Nissly", "primaryContact": false }, { "name": "Abhinay [Pennsylvania State University,University Park,PA (United States)] Gontu", "primaryContact": false }, { "name": "Nina R. [Pennsylvania State University,University Park,PA (United States)] (ORCID:0000000309013775) Boyle", "primaryContact": false }, { "name": "Kurt [Pennsylvania State University,University Park,PA (United States)] (ORCID:0000000256903300) Vandegrift", "primaryContact": false }, { "name": "Meera Surendran [Pennsylvania State University,University Park,PA (United States)] (ORCID:0000000346868414) Nair", "primaryContact": false }, { "name": "Suresh V. [Pennsylvania State University,University Park,PA (United States)] Kuchipudi", "primaryContact": false }, { "name": "Costas D. [Pennsylvania State University,University Park,PA (United States)] (ORCID:0000000215081398) Maranas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "Penn State Huck Institutes of Life Sciences" } }, { "fundingOrganization": { "organizationName": "US Department of Agriculture (USDA)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1903902", "active": false }, { "brc": "CBI", "title": "SNPeffect: identifying functional roles of SNPs using metabolic networks", "description": "Genetic sources of phenotypic variation have been a focus of plant studies aimed at improving agricultural yield and understanding adaptive processes. Genome-wide association studies identify the genetic background behind a trait by examining associations between phenotypes and single-nucleotide polymorphisms (SNPs). Although such studies are common, biological interpretation of the results remains a challenge; especially due to the confounding nature of population structure and the systematic biases thus introduced. Here, we propose a complementary analysis (SNPeffect) that offers putative genotype-to-phenotype mechanistic interpretations by integrating biochemical knowledge encoded in metabolic models. SNPeffect is used to explain differential growth rate and metabolite accumulation in A. thaliana and P. trichocarpa accessions as the outcome of SNPs in enzyme-coding genes. To this end, we also constructed a genome-scale metabolic model for Populus trichocarpa, the first for a perennial woody tree. As expected, our results indicate that growth is a complex polygenic trait governed by carbon and energy partitioning. The predicted set of functional SNPs in both species are associated with experimentally characterized growth-determining genes and also suggest putative ones. Functional SNPs were found in pathways such as amino acid metabolism, nucleotide biosynthesis, and cellulose and lignin biosynthesis, in line with breeding strategies that target pathways governing carbon and energy partition.", "abstract": "Genetic sources of phenotypic variation have been a focus of plant studies aimed at improving agricultural yield and understanding adaptive processes. Genome-wide association studies identify the genetic background behind a trait by examining associations between phenotypes and single-nucleotide polymorphisms (SNPs). Although such studies are common, biological interpretation of the results remains a challenge; especially due to the confounding nature of population structure and the systematic biases thus introduced. Here, we propose a complementary analysis (SNPeffect) that offers putative genotype-to-phenotype mechanistic interpretations by integrating biochemical knowledge encoded in metabolic models. SNPeffect is used to explain differential growth rate and metabolite accumulation in A. thaliana and P. trichocarpa accessions as the outcome of SNPs in enzyme-coding genes. To this end, we also constructed a genome-scale metabolic model for Populus trichocarpa, the first for a perennial woody tree. As expected, our results indicate that growth is a complex polygenic trait governed by carbon and energy partitioning. The predicted set of functional SNPs in both species are associated with experimentally characterized growth-determining genes and also suggest putative ones. Functional SNPs were found in pathways such as amino acid metabolism, nucleotide biosynthesis, and cellulose and lignin biosynthesis, in line with breeding strategies that target pathways governing carbon and energy partition.", "date": "2020-03-12", "issue": "2", "identifier": "https://www.osti.gov/biblio/1903903", "bibliographicCitation": "https://doi.org/10.1111/tpj.14746", "keywords": [ "54 ENVIRONMENTAL SCIENCES", "Arabidopsis", "SNPs", "complementary GWAS", "flux balance analysis", "metabolic networks", "plant metabolic modeling", "poplar" ], "topic": [ "Environmental Science & Sustainability" ], "journal_name": "The Plant Journal", "volume": "103", "publisher_information": "Society for Experimental Biology", "country_publication_code": "US", "creator": [ { "name": "Debolina [Pennsylvania State University,University Park,PA (United States); OSTI] (ORCID:0000000249765536) Sarkar", "primaryContact": true }, { "name": "Costas D. [Pennsylvania State University,University Park,PA (United States)] (ORCID:0000000215081398) Maranas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1903903", "active": false }, { "brc": "CBI", "title": "Plant Biosystems Design Research Roadmap 1.0", "description": "Not Available", "abstract": "Not Available", "date": "2019-12-31", "issue": "C", "identifier": "https://www.osti.gov/biblio/1909245", "bibliographicCitation": "https://doi.org/10.34133/2020/8051764", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "BioDesign Research", "volume": "2020", "publisher_information": "Elsevier", "country_publication_code": "India", "creator": [ { "name": "Xiaohan (ORCID:0000000152074210) Yang", "primaryContact": true }, { "name": "June I. Medford", "primaryContact": false }, { "name": "Kasey Markel", "primaryContact": false }, { "name": "Patrick M. (ORCID:0000000221193345) Shih", "primaryContact": false }, { "name": "Henrique C. De Paoli", "primaryContact": false }, { "name": "Cong T. Trinh", "primaryContact": false }, { "name": "Alistair J. McCormick", "primaryContact": false }, { "name": "Raphael Ployet", "primaryContact": false }, { "name": "Steven G. Hussey", "primaryContact": false }, { "name": "Alexander A. Myburg", "primaryContact": false }, { "name": "Poul Erik Jensen", "primaryContact": false }, { "name": "Md Mahmudul Hassan", "primaryContact": false }, { "name": "Jin Zhang", "primaryContact": false }, { "name": "Wellington Muchero", "primaryContact": false }, { "name": "Udaya C. (ORCID:0000000259638370) Kalluri", "primaryContact": false }, { "name": "Hengfu Yin", "primaryContact": false }, { "name": "Renying Zhuo", "primaryContact": false }, { "name": "Paul E. (ORCID:0000000326859123) Abraham", "primaryContact": false }, { "name": "Jin-Gui (ORCID:0000000217524201) Chen", "primaryContact": false }, { "name": "David J. Weston", "primaryContact": false }, { "name": "Yinong Yang", "primaryContact": false }, { "name": "Degao Liu", "primaryContact": false }, { "name": "Yi Li", "primaryContact": false }, { "name": "Jessy (ORCID:0000000303682054) Labbe", "primaryContact": false }, { "name": "Bing Yang", "primaryContact": false }, { "name": "Jun Hyung Lee", "primaryContact": false }, { "name": "Robert W. Cottingham", "primaryContact": false }, { "name": "Stanton Martin", "primaryContact": false }, { "name": "Mengzhu Lu", "primaryContact": false }, { "name": "Timothy J. Tschaplinski", "primaryContact": false }, { "name": "Guoliang (ORCID:0000000265628769) Yuan", "primaryContact": false }, { "name": "Haiwei (ORCID:0000000330636555) Lu", "primaryContact": false }, { "name": "Priya Ranjan", "primaryContact": false }, { "name": "Julie C. Mitchell", "primaryContact": false }, { "name": "Stan D. (ORCID:0000000298690446) Wullschleger", "primaryContact": false }, { "name": "Gerald A. Tuskan", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "Chinese Academy of Forestry" } }, { "fundingOrganization": { "organizationName": "Leverhulme Trust" } }, { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "UK Biotechnology and Biological Sciences Research Council" } }, { "fundingOrganization": { "organizationName": "USDA" } }, { "fundingOrganization": { "organizationName": "USDOE Laboratory Directed Research and Development (LDRD) Program" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division" } } ], "dataset_url": "https://www.osti.gov/biblio/1909245", "active": false }, { "brc": "CBI", "title": "Simple and Rapid Site-Specific Integration of Multiple Heterologous DNAs into the Escherichia coli Chromosome", "description": "\n More rapid genetic tools can help accelerate strain engineering, even in advanced hosts like\n
\n More rapid genetic tools can help accelerate strain engineering, even in advanced hosts like\n
Genome-scale metabolic network models and constraint-based modeling techniques have become important tools for analyzing cellular metabolism. Thermodynamically infeasible cycles (TICs) causing unbounded metabolic flux ranges are often encountered. TICs satisfy the mass balance and directionality constraints but violate the second law of thermodynamics. Current practices involve implementing additional constraints to ensure not only optimal but also loopless flux distributions. However, the mixed integer linear programming problems required to solve become computationally intractable for genome-scale metabolic models.
\nWe aimed to identify the fewest needed constraints sufficient for optimality under the loopless requirement. We found that loopless constraints are required only for the reactions that share elementary flux modes representing TICs with reactions that are part of the objective function. We put forth the concept of localized loopless constraints (LLCs) to enforce this minimal required set of loopless constraints. By combining with a novel procedure for minimal null-space calculation, the computational time for loopless flux variability analysis (ll-FVA) is reduced by a factor of 10\u2013150 compared to the original loopless constraints and by 4\u201320 times compared to the current fastest method Fast-SNP with the percent improvement increasing with model size. Importantly, LLCs offer a scalable strategy for loopless flux calculations for multi-compartment/multi-organism models of large sizes, for example, shortening the CPU time for ll-FVA from 35\u2009h to less than 2\u2009h for a model with more than104 reactions.
\nMatlab functions are available in the Supplementary Material or at https://github.com/maranasgroup/lll-FVA
\nSupplementary data are available at Bioinformatics online.
\nGenome-scale metabolic network models and constraint-based modeling techniques have become important tools for analyzing cellular metabolism. Thermodynamically infeasible cycles (TICs) causing unbounded metabolic flux ranges are often encountered. TICs satisfy the mass balance and directionality constraints but violate the second law of thermodynamics. Current practices involve implementing additional constraints to ensure not only optimal but also loopless flux distributions. However, the mixed integer linear programming problems required to solve become computationally intractable for genome-scale metabolic models.
\nWe aimed to identify the fewest needed constraints sufficient for optimality under the loopless requirement. We found that loopless constraints are required only for the reactions that share elementary flux modes representing TICs with reactions that are part of the objective function. We put forth the concept of localized loopless constraints (LLCs) to enforce this minimal required set of loopless constraints. By combining with a novel procedure for minimal null-space calculation, the computational time for loopless flux variability analysis (ll-FVA) is reduced by a factor of 10\u2013150 compared to the original loopless constraints and by 4\u201320 times compared to the current fastest method Fast-SNP with the percent improvement increasing with model size. Importantly, LLCs offer a scalable strategy for loopless flux calculations for multi-compartment/multi-organism models of large sizes, for example, shortening the CPU time for ll-FVA from 35\u2009h to less than 2\u2009h for a model with more than104 reactions.
\nMatlab functions are available in the Supplementary Material or at https://github.com/maranasgroup/lll-FVA
\nSupplementary data are available at Bioinformatics online.
\n\n Improving the ethanol yield of\n
\n Improving the ethanol yield of\n
The discovery and valorization of the unique homogeneous linear catechyl lignin (C-lignin) are systematically summarized.
", "abstract": "The discovery and valorization of the unique homogeneous linear catechyl lignin (C-lignin) are systematically summarized.
", "date": "2023-04-23", "issue": "19", "identifier": "https://www.osti.gov/biblio/1971280", "bibliographicCitation": "https://doi.org/10.1039/D3RA01546G", "keywords": [ "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY" ], "topic": [ "Chemistry" ], "journal_name": "RSC Advances", "volume": "13", "publisher_information": "Royal Society of Chemistry (RSC)", "country_publication_code": "GB", "creator": [ { "name": "Yibing [School of Ecology and Environment,Inner Mongolia Key Laboratory of Environmental Pollution Control & Wastes Reuse,Inner Mongolia University,Hohhot 010021,China] Li", "primaryContact": true }, { "name": "Xianzhi [Department of Chemical & Biomolecular Engineering,University of Tennessee,Knoxville,TN 37996,USA] (ORCID:0000000343033403) Meng", "primaryContact": false }, { "name": "Rongqian [School of Ecology and Environment,Inner Mongolia Key Laboratory of Environmental Pollution Control & Wastes Reuse,Inner Mongolia University,Hohhot 010021,China] Meng", "primaryContact": false }, { "name": "Ting [Inner Mongolia Autonomous Region Agriculture and Animal Husbandry Technology Extension Center,Hohhot 010010,China] Cai", "primaryContact": false }, { "name": "Yunqiao [Center for Bioenergy Innovation (CBI),Joint Institute of Biological Science,Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA] (ORCID:0000000325541447) Pu", "primaryContact": false }, { "name": "Zhi-Min [School of Ecology and Environment,Inner Mongolia Key Laboratory of Environmental Pollution Control & Wastes Reuse,Inner Mongolia University,Hohhot 010021,China,Department of Chemical & Biomolecular Engineering,University of Tennessee,Knoxville,TN 37996,USA] Zhao", "primaryContact": false }, { "name": "Arthur J. [Department of Chemical & Biomolecular Engineering,University of Tennessee,Knoxville,TN 37996,USA,Center for Bioenergy Innovation (CBI),Joint Institute of Biological Science,Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA,Center for Renewable Carbon,Department of Forestry,Wildlife,and Fisheries,University of Tennessee Institute of Agriculture,Knoxville,TN 37996,USA] (ORCID:000000023536554X) Ragauskas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Natural Science Foundation of China (NSFC)" } }, { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1971280", "active": false }, { "brc": "CBI", "title": "Expanding the application of anti-CRISPR proteins in plants for tunable genome editing", "description": "Anti-CRISPR proteins are very efficient for inhibiting CRISPR/Cas9-based genome editing tools in both herbaceous and woody plant species.
", "abstract": "Anti-CRISPR proteins are very efficient for inhibiting CRISPR/Cas9-based genome editing tools in both herbaceous and woody plant species.
", "date": "2023-02-08", "issue": "1", "identifier": "https://www.osti.gov/biblio/1972250", "bibliographicCitation": "https://doi.org/10.1093/plphys/kiad076", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "Plant Physiology (Bethesda)", "volume": "192", "publisher_information": "Oxford University Press", "country_publication_code": "US", "creator": [ { "name": "Yang (ORCID:0000000160454969) Liu", "primaryContact": true }, { "name": "Guoliang (ORCID:0000000265628769) Yuan", "primaryContact": false }, { "name": "Brennan (ORCID:0000000248960030) Hyden", "primaryContact": false }, { "name": "Gerald A. Tuskan", "primaryContact": false }, { "name": "Paul E. (ORCID:0000000326859123) Abraham", "primaryContact": false }, { "name": "Xiaohan (ORCID:0000000152074210) Yang", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1972250", "active": false }, { "brc": "CBI", "title": "Lectin Receptor-like Kinase Signaling during Engineered Ectomycorrhiza Colonization", "description": "Mutualistic association can improve a plant\u2019s health and productivity. G-type lectin receptor-like kinase (PtLecRLK1) is a susceptibility factor in Populus trichocarpa that permits root colonization by a beneficial fungus, Laccaria bicolor. Engineering PtLecRLK1 also permits L. bicolor root colonization in non-host plants similar to Populus trichocarpa. The intracellular signaling reprogramed by PtLecRLK1 upon recognition of L. bicolor to allow for the development and maintenance of symbiosis is yet to be determined. In this study, phosphoproteomics was utilized to identify phosphorylation-based relevant signaling pathways associated with PtLecRLK1 recognition of L. bicolor in transgenic switchgrass roots. Our finding shows that PtLecRLK1 in transgenic plants modifies the chitin-triggered plant defense and MAPK signaling along with a significant adjustment in phytohormone signaling, ROS balance, endocytosis, cytoskeleton movement, and proteasomal degradation in order to facilitate the establishment and maintenance of L. bicolor colonization. Moreover, protein\u2013protein interaction data implicate a cGMP-dependent protein kinase as a potential substrate of PtLecRLK1.", "abstract": "Mutualistic association can improve a plant\u2019s health and productivity. G-type lectin receptor-like kinase (PtLecRLK1) is a susceptibility factor in Populus trichocarpa that permits root colonization by a beneficial fungus, Laccaria bicolor. Engineering PtLecRLK1 also permits L. bicolor root colonization in non-host plants similar to Populus trichocarpa. The intracellular signaling reprogramed by PtLecRLK1 upon recognition of L. bicolor to allow for the development and maintenance of symbiosis is yet to be determined. In this study, phosphoproteomics was utilized to identify phosphorylation-based relevant signaling pathways associated with PtLecRLK1 recognition of L. bicolor in transgenic switchgrass roots. Our finding shows that PtLecRLK1 in transgenic plants modifies the chitin-triggered plant defense and MAPK signaling along with a significant adjustment in phytohormone signaling, ROS balance, endocytosis, cytoskeleton movement, and proteasomal degradation in order to facilitate the establishment and maintenance of L. bicolor colonization. Moreover, protein\u2013protein interaction data implicate a cGMP-dependent protein kinase as a potential substrate of PtLecRLK1.", "date": "2023-04-03", "issue": "7", "identifier": "https://www.osti.gov/biblio/1973326", "bibliographicCitation": "https://doi.org/10.3390/cells12071082", "keywords": [ "ectomycorrhiza colonization", "59 BASIC BIOLOGICAL SCIENCES", "lectin receptor-like kinase", "phosphoproteomics", "plant\u2013microbe interaction", "symbiosis" ], "topic": [ "Microbiology" ], "journal_name": "Cells", "volume": "12", "publisher_information": "MDPI", "country_publication_code": "US", "creator": [ { "name": "Him K. [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:000000019686357X) Shrestha", "primaryContact": true }, { "name": "Tao [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000293820731) Yao", "primaryContact": false }, { "name": "Zhenzhen [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] Qiao", "primaryContact": false }, { "name": "Wellington [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000202009856) Muchero", "primaryContact": false }, { "name": "Robert (Bob) L. [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:000000017708786X) Hettich", "primaryContact": false }, { "name": "Jin-Gui (Jay) [Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000217524201) Chen", "primaryContact": false }, { "name": "Paul E. [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Lab. (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000326859123) Abraham", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1973326", "active": false }, { "brc": "CBI", "title": "In vivo evolution of lactic acid hyper-tolerant Clostridium thermocellum", "description": "Lactic acid (LA) has several applications in the food, cosmetics and pharmaceutical industries, as well as in the production of biodegradable plastic polymers, namely polylactides. Industrial production of LA is essentially based on microbial fermentation. Recent reports have shown the potential of the cellulolytic bacterium Clostridium thermocellum for direct LA production from inexpensive lignocellulosic biomass. However, C. thermocellum is highly sensitive to acids and does not grow at pH < 6.0. Improvement of LA tolerance of this microorganism is pivotal for its application in cost-efficient production of LA. In the present study, the LA tolerance of C. thermocellum strains LL345 (wild-type fermentation profile) and LL1111 (high LA yield) was increased by adaptive laboratory evolution. At large inoculum size (10 %), the maximum tolerated LA concentration of strain LL1111 was more than doubled, from 15 g/L to 35 g/L, while subcultures evolved from LL345 showed 50\u201385 % faster growth in medium containing 45 g/L LA. Gene mutations (pyruvate phosphate dikinase, histidine protein kinase/phosphorylase) possibly affecting carbohydrate and/or phosphate metabolism have been detected in most LA-adapted populations. Although improvement of LA tolerance may sometimes also enable higher LA production in microorganisms, C. thermocellum LA-adapted cultures showed a yield of LA, and generally of other organic acids, similar to or lower than parental strains. Based on its improved LA tolerance and LA titer similar to its parent strain (LL1111), mixed adapted culture LL1630 showed the highest performing phenotype and could serve as a framework for improving LA production by further metabolic engineering.", "abstract": "Lactic acid (LA) has several applications in the food, cosmetics and pharmaceutical industries, as well as in the production of biodegradable plastic polymers, namely polylactides. Industrial production of LA is essentially based on microbial fermentation. Recent reports have shown the potential of the cellulolytic bacterium Clostridium thermocellum for direct LA production from inexpensive lignocellulosic biomass. However, C. thermocellum is highly sensitive to acids and does not grow at pH < 6.0. Improvement of LA tolerance of this microorganism is pivotal for its application in cost-efficient production of LA. In the present study, the LA tolerance of C. thermocellum strains LL345 (wild-type fermentation profile) and LL1111 (high LA yield) was increased by adaptive laboratory evolution. At large inoculum size (10 %), the maximum tolerated LA concentration of strain LL1111 was more than doubled, from 15 g/L to 35 g/L, while subcultures evolved from LL345 showed 50\u201385 % faster growth in medium containing 45 g/L LA. Gene mutations (pyruvate phosphate dikinase, histidine protein kinase/phosphorylase) possibly affecting carbohydrate and/or phosphate metabolism have been detected in most LA-adapted populations. Although improvement of LA tolerance may sometimes also enable higher LA production in microorganisms, C. thermocellum LA-adapted cultures showed a yield of LA, and generally of other organic acids, similar to or lower than parental strains. Based on its improved LA tolerance and LA titer similar to its parent strain (LL1111), mixed adapted culture LL1630 showed the highest performing phenotype and could serve as a framework for improving LA production by further metabolic engineering.", "date": "2021-12-12", "issue": "C", "identifier": "https://www.osti.gov/biblio/1981720", "bibliographicCitation": "https://doi.org/10.1016/j.nbt.2021.12.003", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "Biochemistry & Molecular Biology", "Biotechnology & Applied Microbiology" ], "topic": [ "Microbiology" ], "journal_name": "New Biotechnology", "volume": "67", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Roberto [University of Torino (Italy); Dartmouth College,Hanover,NH (United States)] (ORCID:0000000176748187) Mazzoli", "primaryContact": true }, { "name": "Daniel G. [Dartmouth College,Hanover,NH (United States)] Olson", "primaryContact": false }, { "name": "Angela Maria [University of Torino (Italy)] Concu", "primaryContact": false }, { "name": "Evert K. [Dartmouth College,Hanover,NH (United States)] Holwerda", "primaryContact": false }, { "name": "Lee R. [Dartmouth College,Hanover,NH (United States)] Lynd", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1981720", "active": false }, { "brc": "CBI", "title": "Stereoinversion via Alcohol Dehydrogenases Enables Complete Catabolism of \u03b2-1-Type Lignin-Derived Aromatic Isomers", "description": "Sphingobium sp. strain SYK-6 is an efficient aromatic catabolic bacterium that can consume all four stereoisomers of 1,2-diguaiacylpropane-1,3-diol (DGPD), which is a ring-opened \u03b2-1-type dimer. Recently, LdpA-mediated catabolism of erythro-DGPD was reported in SYK-6, but the catabolic pathway for threo-DGPD was as yet unknown. Here, in this study, we elucidated the catabolism of threo-DGPD, which proceeds through conversion to erythro-DGPD. When threo-DGPD was incubated with SYK-6, the C\u03b1 hydroxy groups of threo-DGPD (DGPD I and II) were initially oxidized to produce the C\u03b1 carbonyl form (DGPD-keto I and II). This initial oxidation step is catalyzed by C\u03b1-dehydrogenases, which belong to the short-chain dehydrogenase/reductase (SDR) family and are involved in the catabolism of \u03b2-O-4-type dimers. Analysis of seven candidate genes revealed that NAD+-dependent LigD and LigL are mainly involved in the conversion of DGPD I and II, respectively. Next, we found that DGPD-keto I and II were reduced to erythro-DGPD (DGPD III and IV) in the presence of NADPH. Genes involved in this reduction were sought from C\u03b1-dehydrogenase and ldpA-neighboring SDR genes. The gene products of SLG_12690 (ldpC) and SLG_12640 (ldpB) catalyzed the NADPH-dependent conversion of DGPD-keto I to DGPD III and DGPD-keto II to DGPD IV, respectively. Mutational analysis further indicated that ldpC and ldpB are predominantly involved in the reduction of DGPD-keto. Together, these results demonstrate that SYK-6 harbors a comprehensive catabolic enzyme system to utilize all four \u03b2-1-type stereoisomers through successive oxidation and reduction reactions of the C\u03b1 hydroxy group of threo-DGPD with a net stereoinversion using multiple dehydrogenases.", "abstract": "Sphingobium sp. strain SYK-6 is an efficient aromatic catabolic bacterium that can consume all four stereoisomers of 1,2-diguaiacylpropane-1,3-diol (DGPD), which is a ring-opened \u03b2-1-type dimer. Recently, LdpA-mediated catabolism of erythro-DGPD was reported in SYK-6, but the catabolic pathway for threo-DGPD was as yet unknown. Here, in this study, we elucidated the catabolism of threo-DGPD, which proceeds through conversion to erythro-DGPD. When threo-DGPD was incubated with SYK-6, the C\u03b1 hydroxy groups of threo-DGPD (DGPD I and II) were initially oxidized to produce the C\u03b1 carbonyl form (DGPD-keto I and II). This initial oxidation step is catalyzed by C\u03b1-dehydrogenases, which belong to the short-chain dehydrogenase/reductase (SDR) family and are involved in the catabolism of \u03b2-O-4-type dimers. Analysis of seven candidate genes revealed that NAD+-dependent LigD and LigL are mainly involved in the conversion of DGPD I and II, respectively. Next, we found that DGPD-keto I and II were reduced to erythro-DGPD (DGPD III and IV) in the presence of NADPH. Genes involved in this reduction were sought from C\u03b1-dehydrogenase and ldpA-neighboring SDR genes. The gene products of SLG_12690 (ldpC) and SLG_12640 (ldpB) catalyzed the NADPH-dependent conversion of DGPD-keto I to DGPD III and DGPD-keto II to DGPD IV, respectively. Mutational analysis further indicated that ldpC and ldpB are predominantly involved in the reduction of DGPD-keto. Together, these results demonstrate that SYK-6 harbors a comprehensive catabolic enzyme system to utilize all four \u03b2-1-type stereoisomers through successive oxidation and reduction reactions of the C\u03b1 hydroxy group of threo-DGPD with a net stereoinversion using multiple dehydrogenases.", "date": "2023-05-14", "issue": "6", "identifier": "https://www.osti.gov/biblio/1984226", "bibliographicCitation": "https://doi.org/10.1128/aem.00171-23", "keywords": [ "09 BIOMASS FUELS", "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "Sphingobium", "alcohol dehydrogenase", "aromatic compounds", "catabolism", "lignin", "stereoinversion", "stereospecificity" ], "topic": [ "Biomass & Feedstock", "Chemistry" ], "journal_name": "Applied and Environmental Microbiology", "volume": "89", "publisher_information": "American Society for Microbiology", "country_publication_code": "US", "creator": [ { "name": "Ryo [Nagaoka University of Technology (Japan)] (ORCID:0000000314786625) Kato", "primaryContact": true }, { "name": "Kodai [Nagaoka University of Technology (Japan)] Maekawa", "primaryContact": false }, { "name": "Shota [Nagaoka University of Technology (Japan)] Kobayashi", "primaryContact": false }, { "name": "Shojiro [Forestry and Forest Products Research Institute (Japan)] Hishiyama", "primaryContact": false }, { "name": "Rui [National Renewable Energy Laboratory (NREL),Golden,CO (United States). Renewable Resources and Enabling Science Center] (ORCID:0000000236803601) Katahira", "primaryContact": false }, { "name": "Miki [Nagaoka University of Technology (Japan)] Nambo", "primaryContact": false }, { "name": "Yudai [Nagaoka University of Technology (Japan)] (ORCID:0000000228751637) Higuchi", "primaryContact": false }, { "name": "Eugene [National Renewable Energy Laboratory (NREL),Golden,CO (United States). Renewable Resources and Enabling Science Center] (ORCID:0000000287932331) Kuatsjah", "primaryContact": false }, { "name": "Gregg T. [National Renewable Energy Laboratory (NREL),Golden,CO (United States). Renewable Resources and Enabling Science Center] (ORCID:000000023480212X) Beckham", "primaryContact": false }, { "name": "Naofumi [Nagaoka University of Technology (Japan)] (ORCID:0000000287921675) Kamimura", "primaryContact": false }, { "name": "Eiji [Nagaoka University of Technology (Japan)] (ORCID:0000000191947483) Masai", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Office of Sustainable Transportation. Bioenergy Technologies Office (BETO)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1984226", "active": false, "has_related_ids": [ "NREL/JA--2A00-86481" ] }, { "brc": "CBI", "title": "Carbon capture from corn stover ethanol production\n via\n mature consolidated bioprocessing enables large negative biorefinery GHG emissions and fossil fuel-competitive economics", "description": "Potential to capture 70% of feedstock carbon while >50% of feedstock lower heating value is converted to biofuel and coproducts.
", "abstract": "Potential to capture 70% of feedstock carbon while >50% of feedstock lower heating value is converted to biofuel and coproducts.
", "date": "2023-08-07", "issue": "16", "identifier": "https://www.osti.gov/biblio/1984722", "bibliographicCitation": "https://doi.org/10.1039/D3SE00353A", "topic": [ "Unknown" ], "journal_name": "Sustainable Energy & Fuels", "volume": "7", "publisher_information": "Royal Society of Chemistry (RSC)", "country_publication_code": "GB", "creator": [ { "name": "Matthew R. [Thayer School of Engineering,Dartmouth College,14 Engineering Drive,Hanover,NH 03755,USA,The Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA] (ORCID:0000000265070291) Kubis", "primaryContact": true }, { "name": "Lee R. [Thayer School of Engineering,Dartmouth College,14 Engineering Drive,Hanover,NH 03755,USA,The Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA] (ORCID:000000025642668X) Lynd", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/1984722", "active": false }, { "brc": "CBI", "title": "Split selectable marker systems utilizing inteins facilitate gene stacking in plants", "description": "The ability to stack multiple genes in plants is of great importance in the development of crops with desirable traits but can be challenging due to limited selectable marker options. Here we establish split selectable marker systems using protein splicing elements called \u201cinteins\u201d for Agrobacterium-mediated co-transformation in plants. First, we show that such a split selectable marker system can be used effectively in plants to reconstitute a visible marker, RUBY, from two non-functional fragments through tobacco leaf infiltration. Next, to determine the general applicability of our split selectable marker systems, we demonstrate the utility of these systems in the model plants Arabidopsis and poplar by successfully stacking two reporters eYGFPuv and RUBY, using split Kanamycin or Hygromycin resistance markers. In conclusion, this method enables robust plant co-transformation, providing a valuable tool for the simultaneous insertion of multiple genes into both herbaceous and woody plants efficiently.", "abstract": "The ability to stack multiple genes in plants is of great importance in the development of crops with desirable traits but can be challenging due to limited selectable marker options. Here we establish split selectable marker systems using protein splicing elements called \u201cinteins\u201d for Agrobacterium-mediated co-transformation in plants. First, we show that such a split selectable marker system can be used effectively in plants to reconstitute a visible marker, RUBY, from two non-functional fragments through tobacco leaf infiltration. Next, to determine the general applicability of our split selectable marker systems, we demonstrate the utility of these systems in the model plants Arabidopsis and poplar by successfully stacking two reporters eYGFPuv and RUBY, using split Kanamycin or Hygromycin resistance markers. In conclusion, this method enables robust plant co-transformation, providing a valuable tool for the simultaneous insertion of multiple genes into both herbaceous and woody plants efficiently.", "date": "2023-05-25", "issue": "1", "identifier": "https://www.osti.gov/biblio/1986241", "bibliographicCitation": "https://doi.org/10.1038/s42003-023-04950-8", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "gene expression", "genetic vectors", "molecular engineering in plants" ], "topic": [ "Microbiology" ], "journal_name": "Communications Biology", "volume": "6", "publisher_information": "Springer Nature", "country_publication_code": "US", "creator": [ { "name": "Guoliang [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); Pacific Northwest National Laboratory (PNNL),Richland,WA (United States)] Yuan", "primaryContact": true }, { "name": "Haiwei [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); Central Community College,Hastings,NE (United States)] (ORCID:0000000330636555) Lu", "primaryContact": false }, { "name": "Kuntal [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] De", "primaryContact": false }, { "name": "Md Mahmudul [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); Patuakhali Science and Technology University (Bangladesh)] (ORCID:0000000333998121) Hassan", "primaryContact": false }, { "name": "Yang [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Liu", "primaryContact": false }, { "name": "Md. Torikul [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Islam", "primaryContact": false }, { "name": "Wellington [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Muchero", "primaryContact": false }, { "name": "Gerald A. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000301061289) Tuskan", "primaryContact": false }, { "name": "Xiaohan [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000152074210) Yang", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1986241", "active": false }, { "brc": "CBI", "title": "Imaging beyond the surface region: Probing hidden materials via atomic force microscopy", "description": "Probing material properties at surfaces down to the single-particle scale of atoms and molecules has been achieved, but high-resolution subsurface imaging remains a nanometrology challenge due to electromagnetic and acoustic dispersion and diffraction. The atomically sharp probe used in scanning probe microscopy (SPM) has broken these limits at surfaces. Subsurface imaging is possible under certain physical, chemical, electrical, and thermal gradients present in the material. Of all the SPM techniques, atomic force microscopy has entertained unique opportunities for nondestructive and label-free measurements. Here, we explore the physics of the subsurface imaging problem and the emerging solutions that offer exceptional potential for visualization. We discuss materials science, electronics, biology, polymer and composite sciences, and emerging quantum sensing and quantum bio-imaging applications. The perspectives and prospects of subsurface techniques are presented to stimulate further work toward enabling noninvasive high spatial and spectral resolution investigation of materials including meta- and quantum materials.", "abstract": "Probing material properties at surfaces down to the single-particle scale of atoms and molecules has been achieved, but high-resolution subsurface imaging remains a nanometrology challenge due to electromagnetic and acoustic dispersion and diffraction. The atomically sharp probe used in scanning probe microscopy (SPM) has broken these limits at surfaces. Subsurface imaging is possible under certain physical, chemical, electrical, and thermal gradients present in the material. Of all the SPM techniques, atomic force microscopy has entertained unique opportunities for nondestructive and label-free measurements. Here, we explore the physics of the subsurface imaging problem and the emerging solutions that offer exceptional potential for visualization. We discuss materials science, electronics, biology, polymer and composite sciences, and emerging quantum sensing and quantum bio-imaging applications. The perspectives and prospects of subsurface techniques are presented to stimulate further work toward enabling noninvasive high spatial and spectral resolution investigation of materials including meta- and quantum materials.", "date": "2023-06-27", "issue": "26", "identifier": "https://www.osti.gov/biblio/1987799", "bibliographicCitation": "https://doi.org/10.1126/sciadv.adg8292", "keywords": [ "74 ATOMIC AND MOLECULAR PHYSICS" ], "topic": [ "Unknown" ], "journal_name": "Science Advances", "volume": "9", "publisher_information": "AAAS", "country_publication_code": "US", "creator": [ { "name": "Amir [Ulster University (United Kingdom)] (ORCID:0000000264332261) Farokh Payam", "primaryContact": true }, { "name": "Ali [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000247364157) Passian", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1987799", "active": false }, { "brc": "CBI", "title": "Engineering and characterization of carbohydrate\u2010binding modules for imaging cellulose fibrils biosynthesis in plant protoplasts", "description": "\n Carbohydrate binding modules (CBMs) are noncatalytic domains that assist tethered catalytic domains in substrate targeting. CBMs have therefore been used to visualize distinct polysaccharides present in the cell wall of plant cells and tissues. However, most previous studies provide a qualitative analysis of CBM\u2010polysaccharide interactions, with limited characterization of engineered tandem CBM designs for recognizing polysaccharides like cellulose and limited application of CBM\u2010based probes to visualize cellulose fibrils synthesis in model plant protoplasts with regenerating cell walls. Here, we examine the dynamic interactions of engineered type\u2010A CBMs from families 3a and 64 with crystalline cellulose\u2010I and phosphoric acid swollen cellulose. We generated tandem CBM designs to determine various characteristic properties including binding reversibility toward cellulose\u2010I using equilibrium binding assays. To compute the adsorption (\n
\n Carbohydrate binding modules (CBMs) are noncatalytic domains that assist tethered catalytic domains in substrate targeting. CBMs have therefore been used to visualize distinct polysaccharides present in the cell wall of plant cells and tissues. However, most previous studies provide a qualitative analysis of CBM\u2010polysaccharide interactions, with limited characterization of engineered tandem CBM designs for recognizing polysaccharides like cellulose and limited application of CBM\u2010based probes to visualize cellulose fibrils synthesis in model plant protoplasts with regenerating cell walls. Here, we examine the dynamic interactions of engineered type\u2010A CBMs from families 3a and 64 with crystalline cellulose\u2010I and phosphoric acid swollen cellulose. We generated tandem CBM designs to determine various characteristic properties including binding reversibility toward cellulose\u2010I using equilibrium binding assays. To compute the adsorption (\n
Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64\u00a0495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.
", "abstract": "Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64\u00a0495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.
", "date": "2023-07-31", "issue": "16", "identifier": "https://www.osti.gov/biblio/1993322", "bibliographicCitation": "https://doi.org/10.1093/nar/gkad616", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "Nucleic Acids Research", "volume": "51", "publisher_information": "Oxford University Press", "country_publication_code": "GB", "creator": [ { "name": "Avinash (ORCID:0000000173367012) Sreedasyam", "primaryContact": true }, { "name": "Christopher (ORCID:0000000201095174) Plott", "primaryContact": false }, { "name": "Md Shakhawat Hossain", "primaryContact": false }, { "name": "John T. Lovell", "primaryContact": false }, { "name": "Jane (ORCID:0000000283568325) Grimwood", "primaryContact": false }, { "name": "Jerry W. Jenkins", "primaryContact": false }, { "name": "Christopher Daum", "primaryContact": false }, { "name": "Kerrie Barry", "primaryContact": false }, { "name": "Joseph Carlson", "primaryContact": false }, { "name": "Shengqiang (ORCID:0000000243368994) Shu", "primaryContact": false }, { "name": "Jeremy Phillips", "primaryContact": false }, { "name": "Mojgan Amirebrahimi", "primaryContact": false }, { "name": "Matthew Zane", "primaryContact": false }, { "name": "Mei Wang", "primaryContact": false }, { "name": "David Goodstein", "primaryContact": false }, { "name": "Fabian B. (ORCID:0000000277115282) Haas", "primaryContact": false }, { "name": "Manuel Hiss", "primaryContact": false }, { "name": "Pierre-Fran\u00e7ois (ORCID:0000000176073618) Perroud", "primaryContact": false }, { "name": "Sara S. Jawdy", "primaryContact": false }, { "name": "Yongil Yang", "primaryContact": false }, { "name": "Rongbin (ORCID:0000000159216891) Hu", "primaryContact": false }, { "name": "Jenifer Johnson", "primaryContact": false }, { "name": "Janette (ORCID:0000000189523286) Kropat", "primaryContact": false }, { "name": "Sean D. (ORCID:0000000297736051) Gallaher", "primaryContact": false }, { "name": "Anna Lipzen", "primaryContact": false }, { "name": "Eugene V. Shakirov", "primaryContact": false }, { "name": "Xiaoyu (ORCID:0000000238317551) Weng", "primaryContact": false }, { "name": "Ivone Torres-Jerez", "primaryContact": false }, { "name": "Brock Weers", "primaryContact": false }, { "name": "Daniel Conde", "primaryContact": false }, { "name": "Marilia R. Pappas", "primaryContact": false }, { "name": "Lifeng Liu", "primaryContact": false }, { "name": "Andrew Muchlinski", "primaryContact": false }, { "name": "Hui (ORCID:0000000345887074) Jiang", "primaryContact": false }, { "name": "Christine Shyu", "primaryContact": false }, { "name": "Pu Huang", "primaryContact": false }, { "name": "Jose Sebastian", "primaryContact": false }, { "name": "Carol Laiben", "primaryContact": false }, { "name": "Alyssa Medlin", "primaryContact": false }, { "name": "Sankalpi Carey", "primaryContact": false }, { "name": "Alyssa A. Carrell", "primaryContact": false }, { "name": "Jin-Gui (ORCID:0000000217524201) Chen", "primaryContact": false }, { "name": "Mariano Perales", "primaryContact": false }, { "name": "Kankshita Swaminathan", "primaryContact": false }, { "name": "Isabel Allona", "primaryContact": false }, { "name": "Dario Grattapaglia", "primaryContact": false }, { "name": "Elizabeth A. Cooper", "primaryContact": false }, { "name": "Dorothea (ORCID:0000000326366345) Tholl", "primaryContact": false }, { "name": "John P. (ORCID:0000000317862689) Vogel", "primaryContact": false }, { "name": "David J. Weston", "primaryContact": false }, { "name": "Xiaohan (ORCID:0000000152074210) Yang", "primaryContact": false }, { "name": "Thomas P. Brutnell", "primaryContact": false }, { "name": "Elizabeth A. Kellogg", "primaryContact": false }, { "name": "Ivan (ORCID:0000000166801722) Baxter", "primaryContact": false }, { "name": "Michael Udvardi", "primaryContact": false }, { "name": "Yuhong (ORCID:000000032967778X) Tang", "primaryContact": false }, { "name": "Todd C. Mockler", "primaryContact": false }, { "name": "Thomas E. Juenger", "primaryContact": false }, { "name": "John (ORCID:0000000325022671) Mullet", "primaryContact": false }, { "name": "Stefan A. (ORCID:000000020225873X) Rensing", "primaryContact": false }, { "name": "Gerald A. Tuskan", "primaryContact": false }, { "name": "Sabeeha S. (ORCID:000000022594509X) Merchant", "primaryContact": false }, { "name": "Gary (ORCID:0000000159142247) Stacey", "primaryContact": false }, { "name": "Jeremy (ORCID:0000000180629172) Schmutz", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1993322", "active": false }, { "brc": "CBI", "title": "Diel dynamics of multi-omics in elkhorn fern provide new insights into weak CAM photosynthesis", "description": "Crassulacean acid metabolism (CAM) has high water-use efficiency (WUE) and is widely recognized to have evolved from C3 photosynthesis. Different plant lineages have convergently evolved CAM, but the molecular mechanism that underlies C3-to-CAM evolution remains to be clarified. Platycerium bifurcatum (elkhorn fern) provides an opportunity to study the molecular changes underlying the transition from C3 to CAM photosynthesis because both modes of photosynthesis occur in this species, with sporotrophophyll leaves (SLs) and cover leaves (CLs) performing C3 and weak CAM photosynthesis, respectively. Here, we report that the physiological and biochemical attributes of CAM in weak CAM-performing CLs differed from those in strong CAM species. We investigated the diel dynamics of the metabolome, proteome, and transcriptome in these dimorphic leaves within the same genetic background and under identical environmental conditions. We found that multi-omic diel dynamics in P. bifurcatum exhibit both tissue and diel effects. Our analysis revealed temporal rewiring of biochemistry relevant to the energy-producing pathway (TCA cycle), CAM pathway, and stomatal movement in CLs compared with SLs. We also confirmed that PHOSPHOENOLPYRUVATE CARBOXYLASE KINASE (PPCK) exhibits convergence in gene expression among highly divergent CAM lineages. Gene regulatory network analysis identified candidate transcription factors regulating the CAM pathway and stomatal movement. Taken together, our results provide new insights into weak CAM photosynthesis and new avenues for CAM bioengineering.", "abstract": "Crassulacean acid metabolism (CAM) has high water-use efficiency (WUE) and is widely recognized to have evolved from C3 photosynthesis. Different plant lineages have convergently evolved CAM, but the molecular mechanism that underlies C3-to-CAM evolution remains to be clarified. Platycerium bifurcatum (elkhorn fern) provides an opportunity to study the molecular changes underlying the transition from C3 to CAM photosynthesis because both modes of photosynthesis occur in this species, with sporotrophophyll leaves (SLs) and cover leaves (CLs) performing C3 and weak CAM photosynthesis, respectively. Here, we report that the physiological and biochemical attributes of CAM in weak CAM-performing CLs differed from those in strong CAM species. We investigated the diel dynamics of the metabolome, proteome, and transcriptome in these dimorphic leaves within the same genetic background and under identical environmental conditions. We found that multi-omic diel dynamics in P. bifurcatum exhibit both tissue and diel effects. Our analysis revealed temporal rewiring of biochemistry relevant to the energy-producing pathway (TCA cycle), CAM pathway, and stomatal movement in CLs compared with SLs. We also confirmed that PHOSPHOENOLPYRUVATE CARBOXYLASE KINASE (PPCK) exhibits convergence in gene expression among highly divergent CAM lineages. Gene regulatory network analysis identified candidate transcription factors regulating the CAM pathway and stomatal movement. Taken together, our results provide new insights into weak CAM photosynthesis and new avenues for CAM bioengineering.", "date": "2023-03-22", "issue": "5", "identifier": "https://www.osti.gov/biblio/1993667", "bibliographicCitation": "https://doi.org/10.1016/j.xplc.2023.100594", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "PPCK", "Platycerium bifurcatum", "convergent evolution", "crassulacean acid metabolism", "multi-omics", "transcription factor" ], "topic": [ "Microbiology" ], "journal_name": "Plant Communications", "volume": "4", "publisher_information": "Cell Press", "country_publication_code": "US", "creator": [ { "name": "Cheng [Chinese Academy of Agricultural Sciences,Shenzhen (China)] Li", "primaryContact": true }, { "name": "Wenjie [Guangdong Academy of Agricultural Sciences (China)] Huang", "primaryContact": false }, { "name": "Xiaoxu [Chinese Academy of Agricultural Sciences,Shenzhen (China)] Han", "primaryContact": false }, { "name": "Guohua [Chinese Academy of Science,Shenzhen (China)] Zhao", "primaryContact": false }, { "name": "Wenyang [Guangdong Academy of Agricultural Sciences (China)] Zhang", "primaryContact": false }, { "name": "Weijun [Chinese Academy of Agricultural Sciences,Shenzhen (China)] He", "primaryContact": false }, { "name": "Bao [Chinese Academy of Agricultural Sciences,Shenzhen (China)] Nie", "primaryContact": false }, { "name": "Xufeng [Guangdong Academy of Agricultural Sciences (China)] Chen", "primaryContact": false }, { "name": "Taijie [Guangdong Provincial Key Laboratory of High Technology for Plant Protection (China)] Zhang", "primaryContact": false }, { "name": "Wenhui [Chinese Academy of Agricultural Sciences,Shenzhen (China)] Bai", "primaryContact": false }, { "name": "Xiaopeng [Chinese Academy of Agricultural Sciences,Shenzhen (China)] Zhang", "primaryContact": false }, { "name": "Jingjing [Chinese Academy of Agricultural Sciences,Shenzhen (China)] He", "primaryContact": false }, { "name": "Cheng [Chinese Academy of Agricultural Sciences,Shenzhen (China)] Zhao", "primaryContact": false }, { "name": "Alisdair R. [Max Planck Institute of Molecular Plant Physiology (Germany)] Fernie", "primaryContact": false }, { "name": "Timothy J. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000295406622) Tschaplinski", "primaryContact": false }, { "name": "Xiaohan [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000152074210) Yang", "primaryContact": false }, { "name": "Shijuan [Guangdong Academy of Agricultural Sciences (China)] Yan", "primaryContact": false }, { "name": "Li [Chinese Academy of Agricultural Sciences,Shenzhen (China)] (ORCID:0000000320687535) Wang", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Key Research and Development Program of China" } }, { "fundingOrganization": { "organizationName": "National Natural Science Foundation of China" } }, { "fundingOrganization": { "organizationName": "Shenzhen Science and Technology Program" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1993667", "active": false }, { "brc": "CBI", "title": "Double DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factors", "description": "Many eukaryotic transcription factors (TF) form homodimer or heterodimer complexes to regulate gene expression. Dimerization of BASIC LEUCINE ZIPPER (bZIP) TFs are critical for their functions, but the molecular mechanism underlying the DNA binding and functional specificity of homo- versus heterodimers remains elusive. To address this gap, we present the double DNA Affinity Purification-sequencing (dDAP-seq) technique that maps heterodimer binding sites on endogenous genomic DNA. Using dDAP-seq we profile twenty pairs of C/S1 bZIP heterodimers and S1 homodimers in Arabidopsis and show that heterodimerization significantly expands the DNA binding preferences of these TFs. Analysis of dDAP-seq binding sites reveals the function of bZIP9 in abscisic acid response and the role of bZIP53 heterodimer-specific binding in seed maturation. The C/S1 heterodimers show distinct preferences for the ACGT elements recognized by plant bZIPs and motifs resembling the yeast GCN4 cis-elements. This study demonstrates the potential of dDAP-seq in deciphering the DNA binding specificities of interacting TFs that are key for combinatorial gene regulation.", "abstract": "Many eukaryotic transcription factors (TF) form homodimer or heterodimer complexes to regulate gene expression. Dimerization of BASIC LEUCINE ZIPPER (bZIP) TFs are critical for their functions, but the molecular mechanism underlying the DNA binding and functional specificity of homo- versus heterodimers remains elusive. To address this gap, we present the double DNA Affinity Purification-sequencing (dDAP-seq) technique that maps heterodimer binding sites on endogenous genomic DNA. Using dDAP-seq we profile twenty pairs of C/S1 bZIP heterodimers and S1 homodimers in Arabidopsis and show that heterodimerization significantly expands the DNA binding preferences of these TFs. Analysis of dDAP-seq binding sites reveals the function of bZIP9 in abscisic acid response and the role of bZIP53 heterodimer-specific binding in seed maturation. The C/S1 heterodimers show distinct preferences for the ACGT elements recognized by plant bZIPs and motifs resembling the yeast GCN4 cis-elements. This study demonstrates the potential of dDAP-seq in deciphering the DNA binding specificities of interacting TFs that are key for combinatorial gene regulation.", "date": "2023-05-04", "issue": "1", "identifier": "https://www.osti.gov/biblio/1994639", "bibliographicCitation": "https://doi.org/10.1038/s41467-023-38096-2", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "plant molecular biology", "plant signalling", "transcriptional regulatory elements" ], "topic": [ "Microbiology" ], "journal_name": "Nature Communications", "volume": "14", "publisher_information": "Nature Publishing Group", "country_publication_code": "US", "creator": [ { "name": "Miaomiao [New York Univ. (NYU),NY (United States)] (ORCID:0000000321326168) Li", "primaryContact": true }, { "name": "Tao [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000293820731) Yao", "primaryContact": false }, { "name": "Wanru [New York Univ. (NYU),NY (United States)] (ORCID:0000000345273822) Lin", "primaryContact": false }, { "name": "Will E. [New York Univ. (NYU),NY (United States)] Hinckley", "primaryContact": false }, { "name": "Mary [Rutgers Univ.,Piscataway,NJ (United States)] (ORCID:0000000174139409) Galli", "primaryContact": false }, { "name": "Wellington [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000202009856) Muchero", "primaryContact": false }, { "name": "Andrea [Rutgers Univ.,Piscataway,NJ (United States)] (ORCID:0000000219012971) Gallavotti", "primaryContact": false }, { "name": "Jin-Gui [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000217524201) Chen", "primaryContact": false }, { "name": "Shao-shan Carol [New York Univ. (NYU),NY (United States)] (ORCID:0000000178110398) Huang", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Institutes of Health (NIH)" } }, { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/1994639", "active": false }, { "brc": "CBI", "title": "The good, the bad, and the future: Systematic review identifies best use of biomass to meet air quality and climate policies in California", "description": "California has large and diverse biomass resources and provides a pertinent example of how biomass use is changing and needs to change, in the face of climate mitigation policies. As in other areas of the world, California needs to optimize its use of biomass and waste to meet environmental and socioeconomic objectives. We used a systematic review to assess biomass use pathways in California and the associated impacts on climate and air quality. Biomass uses included the production of renewable fuels, electricity, biochar, compost, and other marketable products. For those biomass use pathways recently developed, information is available on the effects\u2014usually beneficial\u2014on greenhouse gas (GHG) emissions, and there is some, but less, published information on the effects on criteria pollutants. Our review identifies 34 biomass use pathways with beneficial impacts on either GHG or pollutant emissions, or both\u2014the \u201cgood.\u201d These included combustion of forest biomass for power and conversion of livestock\u2010associated biomass to biogas by anaerobic digestion. The review identified 13 biomass use pathways with adverse impacts on GHG emissions, criteria pollutant emissions, or both\u2014the \u201cbad.\u201d Wildfires are an example of one out of eight pathways which were found to be bad for both climate and air quality, while only two biomass use pathways reduced GHG emissions relative to an identified counterfactual but had adverse air quality impacts. Issues of high interest for the \u201cfuture\u201d included land management to reduce fire risk, future policies for the dairy industries, and full life\u2010cycle analysis of biomass production and use.
", "abstract": "California has large and diverse biomass resources and provides a pertinent example of how biomass use is changing and needs to change, in the face of climate mitigation policies. As in other areas of the world, California needs to optimize its use of biomass and waste to meet environmental and socioeconomic objectives. We used a systematic review to assess biomass use pathways in California and the associated impacts on climate and air quality. Biomass uses included the production of renewable fuels, electricity, biochar, compost, and other marketable products. For those biomass use pathways recently developed, information is available on the effects\u2014usually beneficial\u2014on greenhouse gas (GHG) emissions, and there is some, but less, published information on the effects on criteria pollutants. Our review identifies 34 biomass use pathways with beneficial impacts on either GHG or pollutant emissions, or both\u2014the \u201cgood.\u201d These included combustion of forest biomass for power and conversion of livestock\u2010associated biomass to biogas by anaerobic digestion. The review identified 13 biomass use pathways with adverse impacts on GHG emissions, criteria pollutant emissions, or both\u2014the \u201cbad.\u201d Wildfires are an example of one out of eight pathways which were found to be bad for both climate and air quality, while only two biomass use pathways reduced GHG emissions relative to an identified counterfactual but had adverse air quality impacts. Issues of high interest for the \u201cfuture\u201d included land management to reduce fire risk, future policies for the dairy industries, and full life\u2010cycle analysis of biomass production and use.
", "date": "2023-09-22", "issue": "11", "identifier": "https://www.osti.gov/biblio/2004594", "bibliographicCitation": "https://doi.org/10.1111/gcbb.13101", "keywords": [ "Agriculture", "Biotechnology & Applied Microbiology", "Energy & Fuels" ], "topic": [ "Unknown" ], "journal_name": "Global Change Biology. Bioenergy", "volume": "15", "publisher_information": "Wiley-Blackwell", "country_publication_code": "GB", "creator": [ { "name": "Peter [Department of Plant Sciences University of California Davis Davis California USA] (ORCID:0000000244651927) Freer\u2010Smith", "primaryContact": true }, { "name": "Jack H. [Department of Plant Sciences University of California Davis Davis California USA] (ORCID:0009000738166531) Bailey\u2010Bale", "primaryContact": false }, { "name": "Caspar L. [Department of Plant Sciences University of California Davis Davis California USA] (ORCID:0000000160527339) Donnison", "primaryContact": false }, { "name": "Gail [Department of Plant Sciences University of California Davis Davis California USA] (ORCID:0000000184706390) Taylor", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/2004594", "active": false }, { "brc": "CBI", "title": "Quantum biological insights into CRISPR-Cas9 sgRNA efficiency from explainable-AI driven feature engineering", "description": "CRISPR-Cas9 tools have transformed genetic manipulation capabilities in the laboratory. Empirical rules-of-thumb have been developed for only a narrow range of model organisms, and mechanistic underpinnings for sgRNA efficiency remain poorly understood. This work establishes a novel feature set and new public resource, produced with quantum chemical tensors, for interpreting and predicting sgRNA efficiency. Feature engineering for sgRNA efficiency is performed using an explainable-artificial intelligence model: iterative Random Forest (iRF). By encoding quantitative attributes of position-specific sequences for Escherichia coli sgRNAs, we identify important traits for sgRNA design in bacterial species. Additionally, we show that expanding positional encoding to quantum descriptors of base-pair, dimer, trimer, and tetramer sequences captures intricate interactions in local and neighboring nucleotides of the target DNA. These features highlight variation in CRISPR-Cas9 sgRNA dynamics between E. coli and H. sapiens genomes. These novel encodings of sgRNAs enhance our understanding of the elaborate quantum biological processes involved in CRISPR-Cas9 machinery.
", "abstract": "CRISPR-Cas9 tools have transformed genetic manipulation capabilities in the laboratory. Empirical rules-of-thumb have been developed for only a narrow range of model organisms, and mechanistic underpinnings for sgRNA efficiency remain poorly understood. This work establishes a novel feature set and new public resource, produced with quantum chemical tensors, for interpreting and predicting sgRNA efficiency. Feature engineering for sgRNA efficiency is performed using an explainable-artificial intelligence model: iterative Random Forest (iRF). By encoding quantitative attributes of position-specific sequences for Escherichia coli sgRNAs, we identify important traits for sgRNA design in bacterial species. Additionally, we show that expanding positional encoding to quantum descriptors of base-pair, dimer, trimer, and tetramer sequences captures intricate interactions in local and neighboring nucleotides of the target DNA. These features highlight variation in CRISPR-Cas9 sgRNA dynamics between E. coli and H. sapiens genomes. These novel encodings of sgRNAs enhance our understanding of the elaborate quantum biological processes involved in CRISPR-Cas9 machinery.
", "date": "2023-09-19", "issue": "19", "identifier": "https://www.osti.gov/biblio/2004638", "bibliographicCitation": "https://doi.org/10.1093/nar/gkad736", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "Nucleic Acids Research", "volume": "51", "publisher_information": "Oxford University Press", "country_publication_code": "GB", "creator": [ { "name": "Jaclyn M. (ORCID:000000027438193X) Noshay", "primaryContact": true }, { "name": "Tyler Walker", "primaryContact": false }, { "name": "William G. Alexander", "primaryContact": false }, { "name": "Dawn M. Klingeman", "primaryContact": false }, { "name": "Jonathon Romero", "primaryContact": false }, { "name": "Angelica M. Walker", "primaryContact": false }, { "name": "Erica Prates", "primaryContact": false }, { "name": "Carrie Eckert", "primaryContact": false }, { "name": "Stephan Irle", "primaryContact": false }, { "name": "David (ORCID:0000000172714676) Kainer", "primaryContact": false }, { "name": "Daniel A. (ORCID:0000000298228251) Jacobson", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Laboratory Directed Research and Development (LDRD) Program" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2004638", "active": false }, { "brc": "CBI", "title": "Root phenotypes for improved nitrogen capture", "description": "Suboptimal nitrogen availability is a primary constraint for crop production in low-input agroecosystems, while nitrogen fertilization is a primary contributor to the energy, economic, and environmental costs of crop production in high-input agroecosystems. In this article we consider avenues to develop crops with improved nitrogen capture and reduced requirement for nitrogen fertilizer.
\nIntraspecific variation for an array of root phenotypes has been associated with improved nitrogen capture in cereal crops, including architectural phenotypes that colocalize root foraging with nitrogen availability in the soil; anatomical phenotypes that reduce the metabolic costs of soil exploration, improve penetration of hard soil, and exploit the rhizosphere; subcellular phenotypes that reduce the nitrogen requirement of plant tissue; molecular phenotypes exhibiting optimized nitrate uptake kinetics; and rhizosphere phenotypes that optimize associations with the rhizosphere microbiome. For each of these topics we provide examples of root phenotypes which merit attention as potential selection targets for crop improvement. Several cross-cutting issues are addressed including the importance of soil hydrology and impedance, phenotypic plasticity, integrated phenotypes, in silico modeling, and breeding strategies using high throughput phenotyping for co-optimization of multiple phenes.
\nSubstantial phenotypic variation exists in crop germplasm for an array of root phenotypes that improve nitrogen capture. Although this topic merits greater research attention than it currently receives, we have adequate understanding and tools to develop crops with improved nitrogen capture. Root phenotypes are underutilized yet attractive breeding targets for the development of the nitrogen efficient crops urgently needed in global agriculture.
\nSuboptimal nitrogen availability is a primary constraint for crop production in low-input agroecosystems, while nitrogen fertilization is a primary contributor to the energy, economic, and environmental costs of crop production in high-input agroecosystems. In this article we consider avenues to develop crops with improved nitrogen capture and reduced requirement for nitrogen fertilizer.
\nIntraspecific variation for an array of root phenotypes has been associated with improved nitrogen capture in cereal crops, including architectural phenotypes that colocalize root foraging with nitrogen availability in the soil; anatomical phenotypes that reduce the metabolic costs of soil exploration, improve penetration of hard soil, and exploit the rhizosphere; subcellular phenotypes that reduce the nitrogen requirement of plant tissue; molecular phenotypes exhibiting optimized nitrate uptake kinetics; and rhizosphere phenotypes that optimize associations with the rhizosphere microbiome. For each of these topics we provide examples of root phenotypes which merit attention as potential selection targets for crop improvement. Several cross-cutting issues are addressed including the importance of soil hydrology and impedance, phenotypic plasticity, integrated phenotypes, in silico modeling, and breeding strategies using high throughput phenotyping for co-optimization of multiple phenes.
\nSubstantial phenotypic variation exists in crop germplasm for an array of root phenotypes that improve nitrogen capture. Although this topic merits greater research attention than it currently receives, we have adequate understanding and tools to develop crops with improved nitrogen capture. Root phenotypes are underutilized yet attractive breeding targets for the development of the nitrogen efficient crops urgently needed in global agriculture.
\nLignocellulosic biomass represents a carbon neutral cheap and versatile source of carbon which can be converted to biofuels. A pretreatment step is frequently used to make the lignocellulosic carbon bioavailable for microbial metabolism. Dilute acid pretreatment at high temperature and pressure is commonly utilized to efficiently solubilize the pentose fraction by hydrolyzing the hemicellulose fibers and the process results in formation of furans\u2014furfural and 5-hydroxymethyl furfural\u2014and other inhibitors which are detrimental to metabolism. The presence of inhibitors in the medium reduce productivity of microbial biocatalysts and result in increased production costs. Furfural is the key furan inhibitor which acts synergistically along with other inhibitors present in the hydrolysate. In this review, the mode of furfural toxicity on microbial metabolism and metabolic strategies to increase tolerance is discussed. Shared cellular targets between furfural and acetic acid are compared followed by discussing further strategies to engineer tolerance. Finally, the possibility to use furfural as a model inhibitor of dilute acid pretreated lignocellulosic hydrolysate is discussed. The furfural tolerant strains will harbor an efficient lignocellulosic carbon to pyruvate conversion mechanism in presence of stressors in the medium. The pyruvate can be channeled to any metabolite of interest by appropriate modulation of downstream pathway of interest. The aim of this review is to emphasize the use of hydrolysate as a carbon source for bioproduction of biofuels and other compounds of industrial importance.
", "abstract": "Lignocellulosic biomass represents a carbon neutral cheap and versatile source of carbon which can be converted to biofuels. A pretreatment step is frequently used to make the lignocellulosic carbon bioavailable for microbial metabolism. Dilute acid pretreatment at high temperature and pressure is commonly utilized to efficiently solubilize the pentose fraction by hydrolyzing the hemicellulose fibers and the process results in formation of furans\u2014furfural and 5-hydroxymethyl furfural\u2014and other inhibitors which are detrimental to metabolism. The presence of inhibitors in the medium reduce productivity of microbial biocatalysts and result in increased production costs. Furfural is the key furan inhibitor which acts synergistically along with other inhibitors present in the hydrolysate. In this review, the mode of furfural toxicity on microbial metabolism and metabolic strategies to increase tolerance is discussed. Shared cellular targets between furfural and acetic acid are compared followed by discussing further strategies to engineer tolerance. Finally, the possibility to use furfural as a model inhibitor of dilute acid pretreated lignocellulosic hydrolysate is discussed. The furfural tolerant strains will harbor an efficient lignocellulosic carbon to pyruvate conversion mechanism in presence of stressors in the medium. The pyruvate can be channeled to any metabolite of interest by appropriate modulation of downstream pathway of interest. The aim of this review is to emphasize the use of hydrolysate as a carbon source for bioproduction of biofuels and other compounds of industrial importance.
", "date": "2023-10-27", "issue": "1", "identifier": "https://www.osti.gov/biblio/2203972", "bibliographicCitation": "https://doi.org/10.1186/s12934-023-02223-x", "keywords": [ "5-hydroxymethyl furfural", "59 BASIC BIOLOGICAL SCIENCES", "Acid pretreatment", "Biotechnology & Applied Microbiology", "Ethanol", "Fermentation", "Furfural", "Hemicellulose", "Hydrolysate", "Inhibitor", "Stress", "Xylose" ], "topic": [ "Microbiology" ], "journal_name": "Microbial Cell Factories", "volume": "22", "publisher_information": "Springer Science + Business Media", "country_publication_code": "GB", "creator": [ { "name": "S. Bilal Jilani", "primaryContact": true }, { "name": "Daniel G. Olson", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2203972", "active": false }, { "brc": "CBI", "title": "A multi-organ maize metabolic model connects temperature stress with energy production and reducing power generation", "description": "Not Available", "abstract": "Not Available", "date": "2023-11-30", "issue": "12", "identifier": "https://www.osti.gov/biblio/2205528", "bibliographicCitation": "https://doi.org/10.1016/j.isci.2023.108400", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "Environmental science", "Microbial metabolism", "Science & Technology" ], "topic": [ "Microbiology" ], "journal_name": "iScience", "volume": "26", "publisher_information": "Elsevier", "country_publication_code": "Netherlands", "creator": [ { "name": "Niaz Bahar Chowdhury", "primaryContact": true }, { "name": "Margaret Simons-Senftle", "primaryContact": false }, { "name": "Berengere Decouard", "primaryContact": false }, { "name": "Isabelle Quillere", "primaryContact": false }, { "name": "Martine Rigault", "primaryContact": false }, { "name": "Karuna Anna Sajeevan", "primaryContact": false }, { "name": "Bibek Acharya", "primaryContact": false }, { "name": "Ratul Chowdhury", "primaryContact": false }, { "name": "Bertrand Hirel", "primaryContact": false }, { "name": "Alia Dellagi", "primaryContact": false }, { "name": "Costas Maranas", "primaryContact": false }, { "name": "Rajib Saha", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "French National Agency for Research (ANR)" } }, { "fundingOrganization": { "organizationName": "French National Research Institute for Agriculture, Food and the Environment (INRAE)" } }, { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "Nebraska Collaboration Initiative Grant" } }, { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2205528", "active": false }, { "brc": "CBI", "title": "Autoxidation Catalysis for Carbon\u2013Carbon Bond Cleavage in Lignin", "description": "Not Available", "abstract": "Not Available", "date": "2023-11-21", "issue": "12", "identifier": "https://www.osti.gov/biblio/2217572", "bibliographicCitation": "https://doi.org/10.1021/acscentsci.3c00813", "keywords": [ "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "Aromatic compounds", "Biopolymers", "Monomers", "Oligomers", "Organic polymers", "aromatic compounds", "biopolymers", "monomers", "oligomers", "organic polymers" ], "topic": [ "Chemistry" ], "journal_name": "ACS Central Science", "volume": "9", "publisher_information": "American Chemical Society", "country_publication_code": "US", "creator": [ { "name": "Nina X. [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,Golden,Colorado 80401,United States] Gu", "primaryContact": true }, { "name": "Chad T. [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,Golden,Colorado 80401,United States] Palumbo", "primaryContact": false }, { "name": "Alissa C. [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,Golden,Colorado 80401,United States] (ORCID:0000000315862554) Bleem", "primaryContact": false }, { "name": "Kevin P. [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,Golden,Colorado 80401,United States] Sullivan", "primaryContact": false }, { "name": "Stefan J. [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,Golden,Colorado 80401,United States] Haugen", "primaryContact": false }, { "name": "Sean P. [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,Golden,Colorado 80401,United States] (ORCID:0000000337929553) Woodworth", "primaryContact": false }, { "name": "Kelsey J. [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,Golden,Colorado 80401,United States] Ramirez", "primaryContact": false }, { "name": "Jacob K. [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,Golden,Colorado 80401,United States,Department of Chemical and Biological Engineering,University of Colorado Boulder,Boulder,Colorado 80309,United States] Kenny", "primaryContact": false }, { "name": "Lisa D. [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,Golden,Colorado 80401,United States] Stanley", "primaryContact": false }, { "name": "Rui [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,Golden,Colorado 80401,United States] (ORCID:0000000236803601) Katahira", "primaryContact": false }, { "name": "Shannon S. [Department of Chemistry,University of Wisconsin-Madison,Madison,Wisconsin 53706,United States] (ORCID:0000000290007665) Stahl", "primaryContact": false }, { "name": "Gregg T. [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,Golden,Colorado 80401,United States] (ORCID:000000023480212X) Beckham", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Office of Sustainable Transportation. Bioenergy Technologies Office (BETO)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Basic Energy Sciences (BES)" } } ], "dataset_url": "https://www.osti.gov/biblio/2217572", "active": false, "has_related_ids": [ "NREL/JA--2A00-87217" ] }, { "brc": "CBI", "title": "Characterization and molecular simulation of lignin in Cyrene pretreatment of switchgrass", "description": "Biomass-derived solvents have been proposed as a novel pathway in biorefining for the realization of biofuels and bioproducts derived from lignocellulosic biomass. Cyrene derived from cellulose has recently been shown to have a high potential as a green organic solvent for pretreating poplar biomass. However, due to its high dynamic viscosity nature, high Cyrene concentration could cause negative effects on the sugar release of the pretreated biomass as well as driving up the operational cost of the lignin recovery. In this study, we combine experimental and computational approaches to examine the impact of Cyrene pretreatment with reduced Cyrene concentration under mild conditions on switchgrass lignin. Our experimental studies indicated correlation between pretreatment condition and recovery and structure modification of lignin. Switchgrass lignin extracted by Cyrene pretreatment possessed high preservation of \u03b2-O-4 ether inter-unit linkage, which could provide versatility in the integration of downstream lignin valorization into the modern biorefinery industries. Molecular modeling examining the solvation of switchgrass lignin polymer and the disaggregation of low-molecular weight lignin aggregates under pretreatment conditions indicated that a preferential interaction exists between Cyrene and lignin, which likely drives lignin release, and that the disruption of inter-lignin contacts can be modulated as a non-monotonic function of Cyrene : water ratio. Further, while Cyrene\u2013lignin interactions permit the solubilization of lignin, simulations with proxy reactive-species reveal that changes to the diffusion of these reactive proxies and their localization near linkage sites under Cyrene conditions may inhibit chemical processes. In conclusion, the results indicated that loss of pretreatment efficacy caused by low Cyrene concentration could be compensated by prolonged pretreatment time and high catalyst dosage.", "abstract": "Biomass-derived solvents have been proposed as a novel pathway in biorefining for the realization of biofuels and bioproducts derived from lignocellulosic biomass. Cyrene derived from cellulose has recently been shown to have a high potential as a green organic solvent for pretreating poplar biomass. However, due to its high dynamic viscosity nature, high Cyrene concentration could cause negative effects on the sugar release of the pretreated biomass as well as driving up the operational cost of the lignin recovery. In this study, we combine experimental and computational approaches to examine the impact of Cyrene pretreatment with reduced Cyrene concentration under mild conditions on switchgrass lignin. Our experimental studies indicated correlation between pretreatment condition and recovery and structure modification of lignin. Switchgrass lignin extracted by Cyrene pretreatment possessed high preservation of \u03b2-O-4 ether inter-unit linkage, which could provide versatility in the integration of downstream lignin valorization into the modern biorefinery industries. Molecular modeling examining the solvation of switchgrass lignin polymer and the disaggregation of low-molecular weight lignin aggregates under pretreatment conditions indicated that a preferential interaction exists between Cyrene and lignin, which likely drives lignin release, and that the disruption of inter-lignin contacts can be modulated as a non-monotonic function of Cyrene : water ratio. Further, while Cyrene\u2013lignin interactions permit the solubilization of lignin, simulations with proxy reactive-species reveal that changes to the diffusion of these reactive proxies and their localization near linkage sites under Cyrene conditions may inhibit chemical processes. In conclusion, the results indicated that loss of pretreatment efficacy caused by low Cyrene concentration could be compensated by prolonged pretreatment time and high catalyst dosage.", "date": "2023-10-03", "issue": "6", "identifier": "https://www.osti.gov/biblio/2267627", "bibliographicCitation": "https://doi.org/10.1039/d3gc02239k", "keywords": [ "09 BIOMASS FUELS" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Green Chemistry", "volume": "26", "publisher_information": "Royal Society of Chemistry", "country_publication_code": "US", "creator": [ { "name": "Yun-Yan [University of Tennessee,Knoxville,TN (United States)] (ORCID:0000000180950484) Wang", "primaryContact": true }, { "name": "Yunxuan [University of Tennessee,Knoxville,TN (United States)] Wang", "primaryContact": false }, { "name": "Luna [University of Tennessee,Knoxville,TN (United States)] Liang", "primaryContact": false }, { "name": "Micholas Dean [University of Tennessee,Knoxville,TN (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000207777539) Smith", "primaryContact": false }, { "name": "Xianzhi [University of Tennessee,Knoxville,TN (United States)] (ORCID:0000000343033403) Meng", "primaryContact": false }, { "name": "Yunqiao [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000325541447) Pu", "primaryContact": false }, { "name": "Mitra [University of Tennessee,Knoxville,TN (United States)] Mazarei", "primaryContact": false }, { "name": "Rupesh [University of Tennessee,Knoxville,TN (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000310292281) Agarwal", "primaryContact": false }, { "name": "Shalini Jayaraman [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000184749403) Rukmani", "primaryContact": false }, { "name": "Brian H. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000274083609) Davison", "primaryContact": false }, { "name": "Arthur J. [University of Tennessee,Knoxville,TN (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:000000023536554X) Ragauskas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR)" } } ], "dataset_url": "https://www.osti.gov/biblio/2267627", "active": false }, { "brc": "CBI", "title": "Construction of lactic acid overproducing Clostridium thermocellum through enhancement of lactate dehydrogenase expression", "description": "Not Available", "abstract": "Not Available", "date": "2020-10-31", "issue": "C", "identifier": "https://www.osti.gov/biblio/2280029", "bibliographicCitation": "https://doi.org/10.1016/j.enzmictec.2020.109645", "topic": [ "Unknown" ], "journal_name": "Enzyme and Microbial Technology", "volume": "141", "publisher_information": "Elsevier", "country_publication_code": "GB", "creator": [ { "name": "R. (ORCID:0000000176748187) Mazzoli", "primaryContact": true }, { "name": "D. G. Olson", "primaryContact": false }, { "name": "L. R. Lynd", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/2280029", "active": false }, { "brc": "CBI", "title": "Systemic stomatal responses in plants: Coordinating development, stress, and pathogen defense under a changing climate", "description": "To successfully survive, develop, grow and reproduce, multicellular organisms must coordinate their molecular, physiological, developmental and metabolic responses among their different cells and tissues. This process is mediated by cell-to-cell, vascular and/or volatile communication, and involves electric, chemical and/or hydraulic signals. Within this context, stomata serve a dual role by coordinating their responses to the environment with their neighbouring cells at the epidermis, but also with other stomata present on other parts of the plant. As stomata represent one of the most important conduits between the plant and its above-ground environment, as well as directly affect photosynthesis, respiration and the hydraulic status of the plant by controlling its gas and vapour exchange with the atmosphere, coordinating the overall response of stomata within and between different leaves and tissues plays a cardinal role in plant growth, development and reproduction. Here, we discuss different examples of local and systemic stomatal coordination, the different signalling pathways that mediate them, and the importance of systemic stomatal coordination to our food supply, ecosystems and weather patterns, under our changing climate. Importantly, we further discuss the potential biotechnological implications of regulating systemic stomatal responses for enhancing agricultural productivity in a warmer and CO2-rich environment.", "abstract": "To successfully survive, develop, grow and reproduce, multicellular organisms must coordinate their molecular, physiological, developmental and metabolic responses among their different cells and tissues. This process is mediated by cell-to-cell, vascular and/or volatile communication, and involves electric, chemical and/or hydraulic signals. Within this context, stomata serve a dual role by coordinating their responses to the environment with their neighbouring cells at the epidermis, but also with other stomata present on other parts of the plant. As stomata represent one of the most important conduits between the plant and its above-ground environment, as well as directly affect photosynthesis, respiration and the hydraulic status of the plant by controlling its gas and vapour exchange with the atmosphere, coordinating the overall response of stomata within and between different leaves and tissues plays a cardinal role in plant growth, development and reproduction. Here, we discuss different examples of local and systemic stomatal coordination, the different signalling pathways that mediate them, and the importance of systemic stomatal coordination to our food supply, ecosystems and weather patterns, under our changing climate. Importantly, we further discuss the potential biotechnological implications of regulating systemic stomatal responses for enhancing agricultural productivity in a warmer and CO2-rich environment.", "date": "2023-12-31", "issue": "4", "identifier": "https://www.osti.gov/biblio/2281105", "bibliographicCitation": "https://doi.org/10.1111/pce.14797", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "abiotic stress", "climate change", "development", "global warming", "hormone", "reactive oxygen species (ROS)", "stomata", "stress combination", "systemic signalling", "transpiration" ], "topic": [ "Microbiology" ], "journal_name": "Plant, Cell and Environment", "volume": "47", "publisher_information": "Wiley", "country_publication_code": "US", "creator": [ { "name": "Mar\u00eda \u00c1ngeles [Univ. of Missouri,Columbia,MO (United States)] Pel\u00e1ez\u2010Vico", "primaryContact": true }, { "name": "Sara I. [Universitat Jaume I,Castell\u00f3 (Spain)] Zandalinas", "primaryContact": false }, { "name": "Amith R. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Devireddy", "primaryContact": false }, { "name": "Ranjita [Univ. of Missouri,Columbia,MO (United States)] Sinha", "primaryContact": false }, { "name": "Ron [Univ. of Missouri,Columbia,MO (United States)] (ORCID:0000000331927450) Mittler", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/2281105", "active": false }, { "brc": "CBI", "title": "Catalytic carbon\u2013carbon bond cleavage in lignin via manganese\u2013zirconium-mediated autoxidation", "description": "\n Efforts to produce aromatic monomers through catalytic lignin depolymerization have historically focused on aryl\u2013ether bond cleavage. A large fraction of aromatic monomers in lignin, however, are linked by various carbon\u2013carbon (C\u2013C) bonds that are more challenging to cleave and limit the yields of aromatic monomers from lignin depolymerization. Here, we report a catalytic autoxidation method to cleave C\u2013C bonds in lignin-derived dimers and oligomers from pine and poplar. The method uses manganese and zirconium salts as catalysts in acetic acid and produces aromatic carboxylic acids as primary products. The mixtures of the oxygenated monomers are efficiently converted to\n
\n Efforts to produce aromatic monomers through catalytic lignin depolymerization have historically focused on aryl\u2013ether bond cleavage. A large fraction of aromatic monomers in lignin, however, are linked by various carbon\u2013carbon (C\u2013C) bonds that are more challenging to cleave and limit the yields of aromatic monomers from lignin depolymerization. Here, we report a catalytic autoxidation method to cleave C\u2013C bonds in lignin-derived dimers and oligomers from pine and poplar. The method uses manganese and zirconium salts as catalysts in acetic acid and produces aromatic carboxylic acids as primary products. The mixtures of the oxygenated monomers are efficiently converted to\n
Counter-current chromatography is an effective unit operation for simultaneous aromatic monomer\u2013monomer and monomer\u2013oligomer separations from oil derived from reductive catalytic fractionation of lignocellulosic biomass.
", "abstract": "Counter-current chromatography is an effective unit operation for simultaneous aromatic monomer\u2013monomer and monomer\u2013oligomer separations from oil derived from reductive catalytic fractionation of lignocellulosic biomass.
", "date": "2024-05-19", "issue": "10", "identifier": "https://www.osti.gov/biblio/2339907", "bibliographicCitation": "https://doi.org/10.1039/D4GC00765D", "keywords": [ "09 BIOMASS FUELS", "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "BIOMASS FUELS", "INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "CCC solvent", "aryl-ether bond cleavage", "lignin oil separations", "lignin-first biorefining", "reductive catalytic fractionation" ], "topic": [ "Biomass & Feedstock", "Chemistry" ], "journal_name": "Green Chemistry", "volume": "26", "publisher_information": "Royal Society of Chemistry (RSC)", "country_publication_code": "GB", "creator": [ { "name": "Hoon [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,Golden,CO 80401,USA] (ORCID:0000000227913788) Choi", "primaryContact": true }, { "name": "Manar [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,Golden,CO 80401,USA] (ORCID:0000000299135647) Alherech", "primaryContact": false }, { "name": "Jun Hee [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,Golden,CO 80401,USA] (ORCID:0000000218790544) Jang", "primaryContact": false }, { "name": "Sean P. [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,Golden,CO 80401,USA] (ORCID:0000000337929553) Woodworth", "primaryContact": false }, { "name": "Kelsey J. [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,Golden,CO 80401,USA] (ORCID:000000025114742X) Ramirez", "primaryContact": false }, { "name": "Eric M. [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,Golden,CO 80401,USA] (ORCID:0000000246200919) Karp", "primaryContact": false }, { "name": "Gregg T. [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,Golden,CO 80401,USA] (ORCID:000000023480212X) Beckham", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Office of Sustainable Transportation. Bioenergy Technologies Office (BETO)" } } ], "dataset_url": "https://www.osti.gov/biblio/2339907", "active": false, "has_related_ids": [ "NREL/JA--2A00-89312" ] }, { "brc": "CBI", "title": "A century of studying plant secondary metabolism\u2014From \u201cwhat?\u201d to \u201cwhere, how, and why?\u201d", "description": "Over the past century, early advances in understanding the identity of the chemicals that collectively form a living plant have led scientists to deeper investigations exploring where these molecules localize, how they are made, and why they are synthesized in the first place. Many small molecules are specific to the plant kingdom and have been termed plant secondary metabolites, despite the fact that they can play primary and essential roles in plant structure, development, and response to the environment. The past 100 yr have witnessed elucidation of the structure, function, localization, and biosynthesis of selected plant secondary metabolites. Nevertheless, many mysteries remain about the vast diversity of chemicals produced by plants and their roles in plant biology. From early work characterizing unpurified plant extracts, to modern integration of \u2018omics technology to discover genes in metabolite biosynthesis and perception, research in plant (bio)chemistry has produced knowledge with substantial benefits for society, including human medicine and agricultural biotechnology. Here, we review the history of this work and offer suggestions for future areas of exploration. We also highlight some of the recently developed technologies that are leading to ongoing research advances.
", "abstract": "Over the past century, early advances in understanding the identity of the chemicals that collectively form a living plant have led scientists to deeper investigations exploring where these molecules localize, how they are made, and why they are synthesized in the first place. Many small molecules are specific to the plant kingdom and have been termed plant secondary metabolites, despite the fact that they can play primary and essential roles in plant structure, development, and response to the environment. The past 100 yr have witnessed elucidation of the structure, function, localization, and biosynthesis of selected plant secondary metabolites. Nevertheless, many mysteries remain about the vast diversity of chemicals produced by plants and their roles in plant biology. From early work characterizing unpurified plant extracts, to modern integration of \u2018omics technology to discover genes in metabolite biosynthesis and perception, research in plant (bio)chemistry has produced knowledge with substantial benefits for society, including human medicine and agricultural biotechnology. Here, we review the history of this work and offer suggestions for future areas of exploration. We also highlight some of the recently developed technologies that are leading to ongoing research advances.
", "date": "2024-01-01", "issue": "1", "identifier": "https://www.osti.gov/biblio/2341917", "bibliographicCitation": "https://doi.org/10.1093/plphys/kiad596", "keywords": [ "54 ENVIRONMENTAL SCIENCES", "Biological Sciences", "Botany", "Forestry", "Plant Development", "Plant Evolution", "Plant Physiology", "Plant Reproduction and Propagation", "Plant Sciences", "Science and Mathematics" ], "topic": [ "Environmental Science & Sustainability" ], "journal_name": "Plant Physiology (Bethesda)", "volume": "195", "publisher_information": "Oxford University Press", "country_publication_code": "US", "creator": [ { "name": "Richard A. (ORCID:0000000183939408) Dixon", "primaryContact": true }, { "name": "Alexandra Jazz (ORCID:0000000278405636) Dickinson", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Institutes of Health (NIH)" } }, { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2341917", "active": false }, { "brc": "CBI", "title": "Spatially distributed cytokinins: Metabolism, signaling, and transport", "description": "Not Available", "abstract": "Not Available", "date": "2024-06-30", "issue": "7", "identifier": "https://www.osti.gov/biblio/2345102", "bibliographicCitation": "https://doi.org/10.1016/j.xplc.2024.100936", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "biosynthesis", "cytokinin", "environmental changes", "signaling transduction", "transporter" ], "topic": [ "Microbiology" ], "journal_name": "Plant Communications", "volume": "5", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Jiangzhe Zhao", "primaryContact": true }, { "name": "Jingqi Wang", "primaryContact": false }, { "name": "Jie Liu", "primaryContact": false }, { "name": "Penghong Zhang", "primaryContact": false }, { "name": "Guzel Kudoyarova", "primaryContact": false }, { "name": "Chang-Jun Liu", "primaryContact": false }, { "name": "Kewei (ORCID:0000000208441121) Zhang", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Natural Science Foundation of China (NSFC)" } }, { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division (CSGB)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } }, { "fundingOrganization": { "organizationName": "Zhejiang Provincial Natural Science Foundation of China" } } ], "dataset_url": "https://www.osti.gov/biblio/2345102", "active": false, "has_related_ids": [ "BNL--225910-2024-JAAM" ] }, { "brc": "CBI", "title": "The plant cell wall\u2014dynamic, strong, and adaptable\u2014is a natural shapeshifter", "description": "Mythology is replete with good and evil shapeshifters, who, by definition, display great adaptability and assume many different forms\u2014with several even turning themselves into trees. Cell walls certainly fit this definition as they can undergo subtle or dramatic changes in structure, assume many shapes, and perform many functions. In this review, we cover the evolution of knowledge of the structures, biosynthesis, and functions of the 5 major cell wall polymer types that range from deceptively simple to fiendishly complex. Along the way, we recognize some of the colorful historical figures who shaped cell wall research over the past 100 years. The shapeshifter analogy emerges more clearly as we examine the evolving proposals for how cell walls are constructed to allow growth while remaining strong, the complex signaling involved in maintaining cell wall integrity and defense against disease, and the ways cell walls adapt as they progress from birth, through growth to maturation, and in the end, often function long after cell death. We predict the next century of progress will include deciphering cell type\u2013specific wall polymers; regulation at all levels of polymer production, crosslinks, and architecture; and how walls respond to developmental and environmental signals to drive plant success in diverse environments.", "abstract": "Mythology is replete with good and evil shapeshifters, who, by definition, display great adaptability and assume many different forms\u2014with several even turning themselves into trees. Cell walls certainly fit this definition as they can undergo subtle or dramatic changes in structure, assume many shapes, and perform many functions. In this review, we cover the evolution of knowledge of the structures, biosynthesis, and functions of the 5 major cell wall polymer types that range from deceptively simple to fiendishly complex. Along the way, we recognize some of the colorful historical figures who shaped cell wall research over the past 100 years. The shapeshifter analogy emerges more clearly as we examine the evolving proposals for how cell walls are constructed to allow growth while remaining strong, the complex signaling involved in maintaining cell wall integrity and defense against disease, and the ways cell walls adapt as they progress from birth, through growth to maturation, and in the end, often function long after cell death. We predict the next century of progress will include deciphering cell type\u2013specific wall polymers; regulation at all levels of polymer production, crosslinks, and architecture; and how walls respond to developmental and environmental signals to drive plant success in diverse environments.", "date": "2024-01-31", "issue": "5", "identifier": "https://www.osti.gov/biblio/2345108", "bibliographicCitation": "https://doi.org/10.1093/plcell/koad325", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "Biochemistry & Molecular Biology", "Cell Biology", "Plant Sciences" ], "topic": [ "Microbiology" ], "journal_name": "The Plant Cell", "volume": "36", "publisher_information": "American Society of Plant Biologists (ASPB)", "country_publication_code": "US", "creator": [ { "name": "Deborah [University of California,Davis,CA (United States)] (ORCID:0000000159111985) Delmer", "primaryContact": true }, { "name": "Richard A. [University of North Texas,Denton,TX (United States)] (ORCID:0000000183939408) Dixon", "primaryContact": false }, { "name": "Kenneth [Michigan State University,East Lansing,MI (United States)] (ORCID:0000000232276664) Keegstra", "primaryContact": false }, { "name": "Debra [University of Georgia,Athens,GA (United States)] (ORCID:000000015249635X) Mohnen", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division (CSGB)" } } ], "dataset_url": "https://www.osti.gov/biblio/2345108", "active": false }, { "brc": "CBI", "title": "Deuterated water as a substrate-agnostic isotope tracer for investigating reversibility and thermodynamics of reactions in central carbon metabolism", "description": "Stable isotope tracers are a powerful tool for the quantitative analysis of microbial metabolism, enabling pathway elucidation, metabolic flux quantification, and assessment of reaction and pathway thermodynamics. 13C and 2H metabolic flux analysis commonly relies on isotopically labeled carbon substrates, such as glucose. However, the use of 2H-labeled nutrient substrates faces limitations due to their high cost and limited availability in comparison to 13C-tracers. Furthermore, isotope tracer studies in industrially relevant bacteria that metabolize complex substrates such as cellulose, hemicellulose, or lignocellulosic biomass, are challenging given the difficulty in obtaining these as isotopically labeled substrates. In this study, we examine the potential of deuterated water (2H2O) as an affordable, substrate-neutral isotope tracer for studying central carbon metabolism. We apply 2H2O labeling to investigate the reversibility of glycolytic reactions across three industrially relevant bacterial species -C. thermocellum, Z. mobilis, and E. coli-harboring distinct glycolytic pathways with unique thermodynamics. We demonstrate that 2H2O labeling recapitulates previous reversibility and thermodynamic findings obtained with established 13C and 2H labeled nutrient substrates. Furthermore, we exemplify the utility of this 2H2O labeling approach by applying it to high-substrate C. thermocellum fermentations -a setting in which the use of conventional tracers is impractical-thereby identifying the glycolytic enzyme phosphofructokinase as a major bottleneck during high-substrate fermentations and unveiling critical insights that will steer future engineering efforts to enhance ethanol production in this cellulolytic organism. This study demonstrates the utility of deuterated water as a substrate-agnostic isotope tracer for examining flux and reversibility of central carbon metabolic reactions, which yields biological insights comparable to those obtained using costly 2H-labeled nutrient substrates.", "abstract": "Stable isotope tracers are a powerful tool for the quantitative analysis of microbial metabolism, enabling pathway elucidation, metabolic flux quantification, and assessment of reaction and pathway thermodynamics. 13C and 2H metabolic flux analysis commonly relies on isotopically labeled carbon substrates, such as glucose. However, the use of 2H-labeled nutrient substrates faces limitations due to their high cost and limited availability in comparison to 13C-tracers. Furthermore, isotope tracer studies in industrially relevant bacteria that metabolize complex substrates such as cellulose, hemicellulose, or lignocellulosic biomass, are challenging given the difficulty in obtaining these as isotopically labeled substrates. In this study, we examine the potential of deuterated water (2H2O) as an affordable, substrate-neutral isotope tracer for studying central carbon metabolism. We apply 2H2O labeling to investigate the reversibility of glycolytic reactions across three industrially relevant bacterial species -C. thermocellum, Z. mobilis, and E. coli-harboring distinct glycolytic pathways with unique thermodynamics. We demonstrate that 2H2O labeling recapitulates previous reversibility and thermodynamic findings obtained with established 13C and 2H labeled nutrient substrates. Furthermore, we exemplify the utility of this 2H2O labeling approach by applying it to high-substrate C. thermocellum fermentations -a setting in which the use of conventional tracers is impractical-thereby identifying the glycolytic enzyme phosphofructokinase as a major bottleneck during high-substrate fermentations and unveiling critical insights that will steer future engineering efforts to enhance ethanol production in this cellulolytic organism. This study demonstrates the utility of deuterated water as a substrate-agnostic isotope tracer for examining flux and reversibility of central carbon metabolic reactions, which yields biological insights comparable to those obtained using costly 2H-labeled nutrient substrates.", "date": "2023-10-31", "identifier": "https://www.osti.gov/biblio/2369586", "bibliographicCitation": "https://doi.org/10.1016/j.ymben.2023.10.006", "keywords": [ "09 BIOMASS FUELS", "59 BASIC BIOLOGICAL SCIENCES", "Acetivibrio thermocellus", "Biofuels", "Clostridium thermocellum", "Clostridium thermocellum", "Zymomonas mobilis", "Acetivibrio thermocellus", "Isotope tracers", "Metabolic flux analysis", "Deuterated water", "Thermodynamics\r\nBiofuels", "Metabolic bottleneck", "Deuterated water", "Isotope tracers", "Metabolic bottleneck", "Metabolic flux analysis", "Thermodynamics", "Zymomonas mobilis" ], "topic": [ "Biomass & Feedstock", "Microbiology" ], "journal_name": "Metabolic Engineering", "volume": "80", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Melanie M. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); University of Wisconsin\u2013Madison,WI (United States); University of Wisconsin-Madison] Callaghan", "primaryContact": true }, { "name": "Eashant [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); University of Wisconsin\u2013Madison,WI (United States)] Thusoo", "primaryContact": false }, { "name": "Bishal D. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); Dartmouth College,Hanover,NH (United States)] Sharma", "primaryContact": false }, { "name": "Fitsum [University of Wisconsin\u2013Madison,WI (United States)] Getahun", "primaryContact": false }, { "name": "David M. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); University of Wisconsin\u2013Madison,WI (United States)] Stevenson", "primaryContact": false }, { "name": "Costas [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); Pennsylvania State University,University Park,PA (United States)] Maranas", "primaryContact": false }, { "name": "Daniel G. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); Dartmouth College,Hanover,NH (United States)] Olson", "primaryContact": false }, { "name": "Lee R. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); Dartmouth College,Hanover,NH (United States)] Lynd", "primaryContact": false }, { "name": "Daniel [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); University of Wisconsin\u2013Madison,WI (United States)] (ORCID:0000000235683070) Amador-Noguez", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2369586", "active": false }, { "brc": "CBI", "title": "The State of the Art in Root System Architecture Image Analysis Using Artificial Intelligence: A Review", "description": "Roots are essential for acquiring water and nutrients to sustain and support plant growth and anchorage. However, they have been studied less than the aboveground traits in phenotyping and plant breeding until recent decades. In modern times, root properties such as morphology and root system architecture (RSA) have been recognized as increasingly important traits for creating more and higher quality food in the \u201cSecond Green Revolution\u201d. To address the paucity in RSA and other root research, new technologies are being investigated to fill the increasing demand to improve plants via root traits and overcome currently stagnated genetic progress in stable yields. Artificial intelligence (AI) is now a cutting-edge technology proving to be highly successful in many applications, such as crop science and genetic research to improve crop traits. A burgeoning field in crop science is the application of AI to high-resolution imagery in analyses that aim to answer questions related to crops and to better and more speedily breed desired plant traits such as RSA into new cultivars. This review is a synopsis concerning the origins, applications, challenges, and future directions of RSA research regarding image analyses using AI.", "abstract": "Roots are essential for acquiring water and nutrients to sustain and support plant growth and anchorage. However, they have been studied less than the aboveground traits in phenotyping and plant breeding until recent decades. In modern times, root properties such as morphology and root system architecture (RSA) have been recognized as increasingly important traits for creating more and higher quality food in the \u201cSecond Green Revolution\u201d. To address the paucity in RSA and other root research, new technologies are being investigated to fill the increasing demand to improve plants via root traits and overcome currently stagnated genetic progress in stable yields. Artificial intelligence (AI) is now a cutting-edge technology proving to be highly successful in many applications, such as crop science and genetic research to improve crop traits. A burgeoning field in crop science is the application of AI to high-resolution imagery in analyses that aim to answer questions related to crops and to better and more speedily breed desired plant traits such as RSA into new cultivars. This review is a synopsis concerning the origins, applications, challenges, and future directions of RSA research regarding image analyses using AI.", "date": "2024-04-17", "identifier": "https://www.osti.gov/biblio/2371104", "bibliographicCitation": "https://doi.org/10.34133/plantphenomics.0178", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "Plant Phenomics", "volume": "6", "publisher_information": "AAAS", "country_publication_code": "US", "creator": [ { "name": "Brandon J. [US Dept. of Agriculture (USDA),St. Paul,MN (United States). Agricultural Research Service (ARS). Plant Science Research; Univ. of Minnesota,St. Paul,MN (United States)] (ORCID:0009000825187541) Weihs", "primaryContact": true }, { "name": "Deborah-Jo [US Dept. of Agriculture (USDA),St. Paul,MN (United States). Agricultural Research Service (ARS). Plant Science Research; Univ. of Minnesota,St. Paul,MN (United States)] (ORCID:0000000281578458) Heuschele", "primaryContact": false }, { "name": "Zhou [Washington State Univ.,Pullman,WA (United States)] Tang", "primaryContact": false }, { "name": "Larry M. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] (ORCID:0000000219959479) York", "primaryContact": false }, { "name": "Zhiwu [Washington State Univ.,Pullman,WA (United States)] Zhang", "primaryContact": false }, { "name": "Zhanyou [US Dept. of Agriculture (USDA),St. Paul,MN (United States). Agricultural Research Service (ARS). Plant Science Research] (ORCID:000000027633036X) Xu", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDA" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2371104", "active": false }, { "brc": "CBI", "title": "Modular Engineering of Biomass Degradation Pathways", "description": "Production of fuels and chemicals from renewable lignocellulosic feedstocks is a promising alternative to petroleum-derived compounds. Due to the complexity of lignocellulosic feedstocks, microbial conversion of all potential substrates will require substantial metabolic engineering. Non-model microbes offer desirable physiological traits, but also increase the difficulty of heterologous pathway engineering and optimization. The development of modular design principles that allow metabolic pathways to be used in a variety of novel microbes with minimal strain-specific optimization will enable the rapid construction of microbes for commercial production of biofuels and bioproducts. In this review, we discuss variability of lignocellulosic feedstocks, pathways for catabolism of lignocellulose-derived compounds, challenges to heterologous engineering of catabolic pathways, and opportunities to apply modular pathway design. Implementation of these approaches will simplify the process of modifying non-model microbes to convert diverse lignocellulosic feedstocks.
", "abstract": "Production of fuels and chemicals from renewable lignocellulosic feedstocks is a promising alternative to petroleum-derived compounds. Due to the complexity of lignocellulosic feedstocks, microbial conversion of all potential substrates will require substantial metabolic engineering. Non-model microbes offer desirable physiological traits, but also increase the difficulty of heterologous pathway engineering and optimization. The development of modular design principles that allow metabolic pathways to be used in a variety of novel microbes with minimal strain-specific optimization will enable the rapid construction of microbes for commercial production of biofuels and bioproducts. In this review, we discuss variability of lignocellulosic feedstocks, pathways for catabolism of lignocellulose-derived compounds, challenges to heterologous engineering of catabolic pathways, and opportunities to apply modular pathway design. Implementation of these approaches will simplify the process of modifying non-model microbes to convert diverse lignocellulosic feedstocks.
", "date": "2019-04-22", "issue": "4", "identifier": "https://www.osti.gov/biblio/2373198", "bibliographicCitation": "https://doi.org/10.3390/pr7040230", "keywords": [ "09 BIOMASS FUELS", "biofuels", "hemicellulose", "lignin valorization", "lignocellulose", "metabolic engineering" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Processes", "volume": "7", "publisher_information": "MDPI AG", "country_publication_code": "Switzerland", "creator": [ { "name": "Julie E. Chaves", "primaryContact": true }, { "name": "Gerald N. (ORCID:0000000255067419) Presley", "primaryContact": false }, { "name": "Joshua K. (ORCID:0000000323028180) Michener", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/2373198", "active": false }, { "brc": "CBI", "title": "Solubilization of sugarcane bagasse by mono and cocultures of thermophilic anaerobes with and without cotreatment", "description": "Not Available", "abstract": "Not Available", "date": "2024-07-31", "issue": "C", "identifier": "https://www.osti.gov/biblio/2373347", "bibliographicCitation": "https://doi.org/10.1016/j.biortech.2024.130982", "keywords": [ "Agriculture", "Biotechnology & Applied Microbiology", "Energy & Fuels" ], "topic": [ "Unknown" ], "journal_name": "Bioresource Technology", "volume": "406", "publisher_information": "Elsevier", "country_publication_code": "GB", "creator": [ { "name": "Luisa P. Vaz", "primaryContact": true }, { "name": "Helen B. (ORCID:0000000204737515) Sears", "primaryContact": false }, { "name": "Everson A. Miranda", "primaryContact": false }, { "name": "Evert K. Holwerda", "primaryContact": false }, { "name": "Lee R. Lynd", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/2373347", "active": false }, { "brc": "CBI", "title": "Characterization of sugarcane bagasse solubilization and utilization by thermophilic cellulolytic and saccharolytic bacteria at increasing solid loadings", "description": "Not Available", "abstract": "Not Available", "date": "2024-07-31", "issue": "C", "identifier": "https://www.osti.gov/biblio/2373350", "bibliographicCitation": "https://doi.org/10.1016/j.biortech.2024.130973", "keywords": [ "Agriculture", "Biotechnology & Applied Microbiology", "Energy & Fuels" ], "topic": [ "Unknown" ], "journal_name": "Bioresource Technology", "volume": "406", "publisher_information": "Elsevier", "country_publication_code": "GB", "creator": [ { "name": "Isabela U. Zambello", "primaryContact": true }, { "name": "Evert K. Holwerda", "primaryContact": false }, { "name": "Lee R. Lynd", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2373350", "active": false }, { "brc": "CBI", "title": "Expression and Characterization of Monofunctional Alcohol Dehydrogenase Enzymes in Clostridium thermocellum", "description": "Not Available", "abstract": "Not Available", "date": "2024-05-31", "identifier": "https://www.osti.gov/biblio/2376283", "bibliographicCitation": "https://doi.org/10.1016/j.mec.2024.e00243", "topic": [ "Unknown" ], "journal_name": "Metabolic Engineering Communications", "publisher_information": "Elsevier", "country_publication_code": "Netherlands", "creator": [ { "name": "Daniela Prates Chiarelli", "primaryContact": true }, { "name": "Bishal Dev Sharma", "primaryContact": false }, { "name": "Shuen Hon", "primaryContact": false }, { "name": "Luana Walravens Bergamo", "primaryContact": false }, { "name": "Lee R. Lynd", "primaryContact": false }, { "name": "Daniel G. (ORCID:0000000153936302) Olson", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2376283", "active": false }, { "brc": "CBI", "title": "Current State, Challenges, and Opportunities in Genome-Scale Resource Allocation Models: A Mathematical Perspective", "description": "Stoichiometric genome-scale metabolic models (generally abbreviated GSM, GSMM, or GEM) have had many applications in exploring phenotypes and guiding metabolic engineering interventions. Nevertheless, these models and predictions thereof can become limited as they do not directly account for protein cost, enzyme kinetics, and cell surface or volume proteome limitations. Lack of such mechanistic detail could lead to overly optimistic predictions and engineered strains. Initial efforts to correct these deficiencies were by the application of precursor tools for GSMs, such as flux balance analysis with molecular crowding. In the past decade, several frameworks have been introduced to incorporate proteome-related limitations using a genome-scale stoichiometric model as the reconstruction basis, which herein are called resource allocation models (RAMs). This review provides a broad overview of representative or commonly used existing RAM frameworks. This review discusses increasingly complex models, beginning with stoichiometric models to precursor to RAM frameworks to existing RAM frameworks. RAM frameworks are broadly divided into two categories: coarse-grained and fine-grained, with different strengths and challenges. Discussion includes pinpointing their utility, data needs, highlighting framework strengths and limitations, and appropriateness to various research endeavors, largely through contrasting their mathematical frameworks. Finally, promising future applications of RAMs are discussed.
", "abstract": "Stoichiometric genome-scale metabolic models (generally abbreviated GSM, GSMM, or GEM) have had many applications in exploring phenotypes and guiding metabolic engineering interventions. Nevertheless, these models and predictions thereof can become limited as they do not directly account for protein cost, enzyme kinetics, and cell surface or volume proteome limitations. Lack of such mechanistic detail could lead to overly optimistic predictions and engineered strains. Initial efforts to correct these deficiencies were by the application of precursor tools for GSMs, such as flux balance analysis with molecular crowding. In the past decade, several frameworks have been introduced to incorporate proteome-related limitations using a genome-scale stoichiometric model as the reconstruction basis, which herein are called resource allocation models (RAMs). This review provides a broad overview of representative or commonly used existing RAM frameworks. This review discusses increasingly complex models, beginning with stoichiometric models to precursor to RAM frameworks to existing RAM frameworks. RAM frameworks are broadly divided into two categories: coarse-grained and fine-grained, with different strengths and challenges. Discussion includes pinpointing their utility, data needs, highlighting framework strengths and limitations, and appropriateness to various research endeavors, largely through contrasting their mathematical frameworks. Finally, promising future applications of RAMs are discussed.
", "date": "2024-06-27", "issue": "7", "identifier": "https://www.osti.gov/biblio/2378054", "bibliographicCitation": "https://doi.org/10.3390/metabo14070365", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "biochemistry & molecular biology", "computational biology", "genome-scale modeling", "systems biology" ], "topic": [ "Microbiology" ], "journal_name": "Metabolites", "volume": "14", "publisher_information": "MDPI AG", "country_publication_code": "Switzerland", "creator": [ { "name": "Wheaton L. Schroeder", "primaryContact": true }, { "name": "Patrick F. (ORCID:0000000255609986) Suthers", "primaryContact": false }, { "name": "Thomas C. Willis", "primaryContact": false }, { "name": "Eric J. (ORCID:0000000298795205) Mooney", "primaryContact": false }, { "name": "Costas D. Maranas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2378054", "active": false }, { "brc": "CBI", "title": "The role of AdhE on ethanol tolerance and production in Clostridium thermocellum", "description": "Not Available", "abstract": "Not Available", "date": "2024-07-31", "issue": "8", "identifier": "https://www.osti.gov/biblio/2396980", "bibliographicCitation": "https://doi.org/10.1016/j.jbc.2024.107559", "keywords": [ "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "59 BASIC BIOLOGICAL SCIENCES", "Acetivibrio thermocellus", "Hungateiclostridium", "Ruminiclostridium", "acetaldehyde dehydrogenase", "alcohol dehydrogenase", "cellulosic biofuels", "ethanol production", "ethanol tolerance" ], "topic": [ "Chemistry", "Microbiology" ], "journal_name": "Journal of Biological Chemistry", "volume": "300", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Angel (ORCID:000000021874322X) Pech-Canul", "primaryContact": true }, { "name": "Sarah K. Hammer", "primaryContact": false }, { "name": "Samantha J. Ziegler", "primaryContact": false }, { "name": "Isaiah D. (ORCID:0009000677285851) Richardson", "primaryContact": false }, { "name": "Bishal D. (ORCID:0000000283264444) Sharma", "primaryContact": false }, { "name": "Marybeth I. Maloney", "primaryContact": false }, { "name": "Yannick J. Bomble", "primaryContact": false }, { "name": "Lee R. Lynd", "primaryContact": false }, { "name": "Daniel G. Olson", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2396980", "active": false, "has_related_ids": [ "NREL/JA--2700-90909" ] }, { "brc": "CBI", "title": "Application of functional genomics for domestication of novel non-model microbes", "description": "With the expansion of domesticated microbes producing biomaterials and chemicals to support a growing circular bioeconomy, the variety of waste and sustainable substrates that can support microbial growth and production will also continue to expand. The diversity of these microbes also requires a range of compatible genetic tools to engineer improved robustness and economic viability. As we still do not fully understand the function of many genes in even highly studied model microbes, engineering improved microbial performance requires introducing genome-scale genetic modifications followed by screening or selecting mutants that enhance growth under prohibitive conditions encountered during production. These approaches include adaptive laboratory evolution, random or directed mutagenesis, transposon-mediated gene disruption, or CRISPR interference (CRISPRi). Although any of these approaches may be applicable for identifying engineering targets, here we focus on using CRISPRi to reduce the time required to engineer more robust microbes for industrial applications.
\nThe development of genome scale CRISPR-based libraries in new microbes enables discovery of genetic factors linked to desired traits for engineering more robust microbial systems.
\nWith the expansion of domesticated microbes producing biomaterials and chemicals to support a growing circular bioeconomy, the variety of waste and sustainable substrates that can support microbial growth and production will also continue to expand. The diversity of these microbes also requires a range of compatible genetic tools to engineer improved robustness and economic viability. As we still do not fully understand the function of many genes in even highly studied model microbes, engineering improved microbial performance requires introducing genome-scale genetic modifications followed by screening or selecting mutants that enhance growth under prohibitive conditions encountered during production. These approaches include adaptive laboratory evolution, random or directed mutagenesis, transposon-mediated gene disruption, or CRISPR interference (CRISPRi). Although any of these approaches may be applicable for identifying engineering targets, here we focus on using CRISPRi to reduce the time required to engineer more robust microbes for industrial applications.
\nThe development of genome scale CRISPR-based libraries in new microbes enables discovery of genetic factors linked to desired traits for engineering more robust microbial systems.
\nWe review recent advances in the utilization of lignin as a viable alternative to fossil-based feedstock in the synthesis of a wide range of vitrimeric materials targeted towards the achievement of a sustainable and circular economy.
", "abstract": "We review recent advances in the utilization of lignin as a viable alternative to fossil-based feedstock in the synthesis of a wide range of vitrimeric materials targeted towards the achievement of a sustainable and circular economy.
", "date": "2023-12-31", "identifier": "https://www.osti.gov/biblio/2403590", "bibliographicCitation": "https://doi.org/10.1039/D4MA00281D", "keywords": [ "36 MATERIALS SCIENCE", "Bio-based Vitrimers", "Covalent Adaptable Networks", "Lignin", "Lignin Modification", "Trans-esterification" ], "topic": [ "Materials Science & Bioproducts" ], "journal_name": "Materials Advances", "publisher_information": "Royal Society of Chemistry (RSC)", "country_publication_code": "GB", "creator": [ { "name": "Peter K. [Department of Chemical & Biomolecular Engineering,University of Tennessee Knoxville,Knoxville,TN 37996,USA] (ORCID:0009000917232979) Karoki", "primaryContact": true }, { "name": "Shuyang [Department of Chemical & Biomolecular Engineering,University of Tennessee Knoxville,Knoxville,TN 37996,USA] (ORCID:0000000239043046) Zhang", "primaryContact": false }, { "name": "Yunqiao [Joint Institute for Biological Sciences,Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA] (ORCID:0000000325541447) Pu", "primaryContact": false }, { "name": "Arthur J. [Department of Chemical & Biomolecular Engineering,University of Tennessee Knoxville,Knoxville,TN 37996,USA,Center for Renewable Carbon,The University of Tennessee Knoxville,Institute of Agriculture,Knoxville,TN 37996,USA,Joint Institute for Biological Sciences,Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA] (ORCID:000000023536554X) Ragauskas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2403590", "active": false }, { "brc": "CBI", "title": "Chemo-Enzymatic Synthesis of Long-Chain Oligosaccharides for Studying Xylan-Modifying Enzymes", "description": "Plant research is hampered in several aspects by a lack of pure oligosaccharide samples that closely represent structural features of cell wall glycans. An alternative to purely chemical synthesis to access these oligosaccharides is chemo-enzymatic synthesis using glycosynthases. These enzymes enable the ligation of oligosaccharide donors, when activated for example as \u03b1-glycosyl fluorides, with suitable acceptor oligosaccharides. Herein, the synthesis of xylan oligosaccharides up to dodecasaccharides is reported, with glycosynthase-mediated coupling reactions as key steps. The xylo-oligosaccharide donors were protected at the non-reducing end with a 4-O-tetrahydropyranyl (THP) group to prevent polymerization. Installation of an unnatural 3-O-methylether substituent at the reducing end xylose of the oligosaccharides ensured good water solubility. Biochemical assays demonstrated enzymatic activity for the xylan acetyltransferase XOAT1 from Arabidopsis thaliana, xylan arabinofuranosyl-transferase XAT3 enzymes from rice and switchgrass, and the xylan glucuronosyltransferase GUX3 from Arabidopsis thaliana. In case of the glucuronosyltransferase GUX3, MALDI-MS/MS analysis of the reaction product suggested that a single glucuronosyl substituent was installed primarily at the central xylose residues of the dodecasaccharide acceptor, demonstrating the value of long-chain acceptors for assaying biosynthetic glycosyltransferases.", "abstract": "Plant research is hampered in several aspects by a lack of pure oligosaccharide samples that closely represent structural features of cell wall glycans. An alternative to purely chemical synthesis to access these oligosaccharides is chemo-enzymatic synthesis using glycosynthases. These enzymes enable the ligation of oligosaccharide donors, when activated for example as \u03b1-glycosyl fluorides, with suitable acceptor oligosaccharides. Herein, the synthesis of xylan oligosaccharides up to dodecasaccharides is reported, with glycosynthase-mediated coupling reactions as key steps. The xylo-oligosaccharide donors were protected at the non-reducing end with a 4-O-tetrahydropyranyl (THP) group to prevent polymerization. Installation of an unnatural 3-O-methylether substituent at the reducing end xylose of the oligosaccharides ensured good water solubility. Biochemical assays demonstrated enzymatic activity for the xylan acetyltransferase XOAT1 from Arabidopsis thaliana, xylan arabinofuranosyl-transferase XAT3 enzymes from rice and switchgrass, and the xylan glucuronosyltransferase GUX3 from Arabidopsis thaliana. In case of the glucuronosyltransferase GUX3, MALDI-MS/MS analysis of the reaction product suggested that a single glucuronosyl substituent was installed primarily at the central xylose residues of the dodecasaccharide acceptor, demonstrating the value of long-chain acceptors for assaying biosynthetic glycosyltransferases.", "date": "2023-02-14", "issue": "26", "identifier": "https://www.osti.gov/biblio/2423980", "bibliographicCitation": "https://doi.org/10.1002/chem.202203941", "keywords": [ "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "MALDI-TOF analysis", "carbohydrates", "chemistry", "glycosynthase", "plant cell wall", "xylan biosynthesis" ], "topic": [ "Chemistry" ], "journal_name": "Chemistry - A European Journal", "volume": "29", "publisher_information": "Wiley", "country_publication_code": "US", "creator": [ { "name": "Ignacio [University of Natural Resources and Life Sciences,Vienna (Austria); Max Planck Institute of Colloids and Interfaces,Potsdam (Germany)] \u00c1lvarez\u2010Mart\u00ednez", "primaryContact": true }, { "name": "Colin [University of Natural Resources and Life Sciences,Vienna (Austria); Max Planck Institute of Colloids and Interfaces,Potsdam (Germany)] Ruprecht", "primaryContact": false }, { "name": "Deborah [Max Planck Institute of Colloids and Interfaces,Potsdam (Germany)] Senf", "primaryContact": false }, { "name": "Hsin\u2010tzu [University of Georgia,Athens,GA (United States); Joint BioEnergy Institute,Emeryville,CA (United States)] Wang", "primaryContact": false }, { "name": "Breeanna R. [University of Georgia,Athens,GA (United States)] Urbanowicz", "primaryContact": false }, { "name": "Fabian [University of Natural Resources and Life Sciences,Vienna (Austria); Max Planck Institute of Colloids and Interfaces,Potsdam (Germany)] (ORCID:0000000322066636) Pfrengle", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "Deutsche Forschungsgemeinschaft" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2423980", "active": false }, { "brc": "CBI", "title": "De novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the\n Genetic modification of plants fundamentally relies upon customized vector designs. The ever-increasing complexity of transgenic constructs has led to increased adoption of modular cloning systems for their ease of use, cost effectiveness, and rapid prototyping. GreenGate is a modular cloning system catered specifically to designing bespoke, single transcriptional unit vectors for plant transformation\u2014which is also its greatest flaw. MultiGreen seeks to address GreenGate\u2019s limitations while maintaining the syntax of the original GreenGate kit. The primary limitations MultiGreen addresses are 1) multiplexing in series, 2) multiplexing in parallel, and 3) repeated cycling of transcriptional unit assembly through binary intermediates. MultiGreen efficiently concatenates bespoke transcriptional units using an additional suite of level 1acceptor vectors which serve as an assembly point for individual transcriptional units prior to final, level 2, condensation of multiple transcriptional units. Assembly with MultiGreen level 1 vectors scales at a maximal rate of 2*\u2308\n
\n Genetic modification of plants fundamentally relies upon customized vector designs. The ever-increasing complexity of transgenic constructs has led to increased adoption of modular cloning systems for their ease of use, cost effectiveness, and rapid prototyping. GreenGate is a modular cloning system catered specifically to designing bespoke, single transcriptional unit vectors for plant transformation\u2014which is also its greatest flaw. MultiGreen seeks to address GreenGate\u2019s limitations while maintaining the syntax of the original GreenGate kit. The primary limitations MultiGreen addresses are 1) multiplexing in series, 2) multiplexing in parallel, and 3) repeated cycling of transcriptional unit assembly through binary intermediates. MultiGreen efficiently concatenates bespoke transcriptional units using an additional suite of level 1acceptor vectors which serve as an assembly point for individual transcriptional units prior to final, level 2, condensation of multiple transcriptional units. Assembly with MultiGreen level 1 vectors scales at a maximal rate of 2*\u2308\n
Comparison of microbial strains for tolerance to and catabolism of lignin stream constituents toward evaluating microbial hosts for lignin bioconversion.
", "abstract": "Comparison of microbial strains for tolerance to and catabolism of lignin stream constituents toward evaluating microbial hosts for lignin bioconversion.
", "date": "2024-12-08", "issue": "24", "identifier": "https://www.osti.gov/biblio/2477137", "bibliographicCitation": "https://doi.org/10.1039/D4GC03876B", "keywords": [ "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "APL corn stover", "lignin valorization", "microbial catabolism" ], "topic": [ "Chemistry" ], "journal_name": "Green Chemistry", "volume": "26", "publisher_information": "Royal Society of Chemistry (RSC)", "country_publication_code": "GB", "creator": [ { "name": "Rebecca A. [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,Golden,CO 80401,USA,Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,TN,USA] (ORCID:0000000246280170) Wilkes", "primaryContact": true }, { "name": "Andrew J. [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,Golden,CO 80401,USA,Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,TN,USA] (ORCID:0000000314353643) Borchert", "primaryContact": false }, { "name": "Valentina E. [Joint BioEnergy Institute,Lawrence Berkeley National Laboratory,Emeryville,CA 94608,USA,Biomanufacturing and Biomaterials Department,Sandia National Laboratories,Livermore,CA 94550,USA] Garcia", "primaryContact": false }, { "name": "Gina M. [Joint BioEnergy Institute,Lawrence Berkeley National Laboratory,Emeryville,CA 94608,USA,Biomanufacturing and Biomaterials Department,Sandia National Laboratories,Livermore,CA 94550,USA] Geiselman", "primaryContact": false }, { "name": "Sarah [Great Lakes Bioenergy Research Center,University of Wisconsin\u2013Madison,Madison,Wisconsin,USA] Liu", "primaryContact": false }, { "name": "Adam M. [Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,TN,USA,Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,TN,37830,USA] (ORCID:0000000158235329) Guss", "primaryContact": false }, { "name": "Joshua K. [Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,TN,USA,Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,TN,37830,USA] (ORCID:0000000323028180) Michener", "primaryContact": false }, { "name": "Daniel R. [Great Lakes Bioenergy Research Center,University of Wisconsin\u2013Madison,Madison,Wisconsin,USA] Noguera", "primaryContact": false }, { "name": "Eiji [Department of Materials Science and Bioengineering,Nagaoka University of Technology,Nagaoka,Niigata 940-2188,Japan] (ORCID:0000000191947483) Masai", "primaryContact": false }, { "name": "John M. [Joint BioEnergy Institute,Lawrence Berkeley National Laboratory,Emeryville,CA 94608,USA,Biomanufacturing and Biomaterials Department,Sandia National Laboratories,Livermore,CA 94550,USA] (ORCID:0000000269852485) Gladden", "primaryContact": false }, { "name": "John [Great Lakes Bioenergy Research Center,University of Wisconsin\u2013Madison,Madison,Wisconsin,USA] (ORCID:0000000260934521) Ralph", "primaryContact": false }, { "name": "Gregg T. [Renewable Resources and Enabling Sciences Center,National Renewable Energy Laboratory,Golden,CO 80401,USA,Center for Bioenergy Innovation,Oak Ridge National Laboratory,Oak Ridge,TN,USA] (ORCID:000000023480212X) Beckham", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Office of Sustainable Transportation. Bioenergy Technologies Office (BETO)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2477137", "active": false, "has_related_ids": [ "NREL/JA--2A00-91436" ] }, { "brc": "CBI", "title": "AtDGCR14L contributes to salt-stress tolerance via regulating pre-mRNA splicing in Arabidopsis", "description": "In plants, the pre-mRNA alternative splicing has been demonstrated to be a crucial tier that regulates gene expression in response to salt stress. However, the underlying mechanisms remain elusive. Here, in this study, we studied the roles of DIGEORGE-SYNDROME CRITICAL REGION 14-like (AtDGCR14L) in regulating pre-mRNA splicing and salt stress tolerance. We discovered that Arabidopsis AtDGCR14L is required for maintaining plant salt stress tolerance and the constitutively spliced and active isoforms of important stress- and/or abscisic acid (ABA)-responsive genes. We also identified the interaction between AtDGCR14L and splicing factor U1-70k, which needs a highly conserved three amino acid (TWG) motif in DGCR14. Different from wild-type AtDGCR14L, the overexpression of TWG-substituted AtDGCR14L mutant did not change salt stress tolerance or pre-mRNA splicing of stress/ABA-responsive genes. Additionally, SWITCH3A (SWI3A) is a core subunit of the SWI/SUCROSE NONFERMENTING (SWI/SNF) chromatin-remodeling complexes. We found that SWI3A, whose splicing depends on AtDGCR14L, actively enhances salt stress tolerance. These results revealed that AtDGCR14L may play an essential role in crosstalk between plant salt-stress response and pre-mRNA splicing mechanisms. We also unveiled the potential role of SWI3A in controlling salt stress tolerance. The TWG motif in the intrinsically disordered region of AtDGCR14L is highly conserved and crucial for DGCR14 functions.", "abstract": "In plants, the pre-mRNA alternative splicing has been demonstrated to be a crucial tier that regulates gene expression in response to salt stress. However, the underlying mechanisms remain elusive. Here, in this study, we studied the roles of DIGEORGE-SYNDROME CRITICAL REGION 14-like (AtDGCR14L) in regulating pre-mRNA splicing and salt stress tolerance. We discovered that Arabidopsis AtDGCR14L is required for maintaining plant salt stress tolerance and the constitutively spliced and active isoforms of important stress- and/or abscisic acid (ABA)-responsive genes. We also identified the interaction between AtDGCR14L and splicing factor U1-70k, which needs a highly conserved three amino acid (TWG) motif in DGCR14. Different from wild-type AtDGCR14L, the overexpression of TWG-substituted AtDGCR14L mutant did not change salt stress tolerance or pre-mRNA splicing of stress/ABA-responsive genes. Additionally, SWITCH3A (SWI3A) is a core subunit of the SWI/SUCROSE NONFERMENTING (SWI/SNF) chromatin-remodeling complexes. We found that SWI3A, whose splicing depends on AtDGCR14L, actively enhances salt stress tolerance. These results revealed that AtDGCR14L may play an essential role in crosstalk between plant salt-stress response and pre-mRNA splicing mechanisms. We also unveiled the potential role of SWI3A in controlling salt stress tolerance. The TWG motif in the intrinsically disordered region of AtDGCR14L is highly conserved and crucial for DGCR14 functions.", "date": "2024-11-09", "issue": "6", "identifier": "https://www.osti.gov/biblio/2478428", "bibliographicCitation": "https://doi.org/10.1111/tpj.17136", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "Arabidopsis 43 thaliana", "DGCR14", "alternative splicing", "chromatin-remodeling complex", "functional motif", "salt stress" ], "topic": [ "Microbiology" ], "journal_name": "The Plant Journal", "volume": "120", "publisher_information": "Society for Experimental Biology", "country_publication_code": "US", "creator": [ { "name": "Meng [Brookhaven National Laboratory (BNL),Upton,NY (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:0000000302473701) Xie", "primaryContact": true }, { "name": "Dimiru [Brookhaven National Laboratory (BNL),Upton,NY (United States)] (ORCID:0000000255233704) Tadesse", "primaryContact": false }, { "name": "Jin [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); Zhejiang A&F University,Hangzhou,Zhejiang (China)] (ORCID:0000000283975078) Zhang", "primaryContact": false }, { "name": "Tao [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000293820731) Yao", "primaryContact": false }, { "name": "Li [Univ. of Oklahoma,Norman,OK (United States)] Zhang", "primaryContact": false }, { "name": "Sara S. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000281235439) Jawdy", "primaryContact": false }, { "name": "Amith [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Devireddy", "primaryContact": false }, { "name": "Kaijie [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Biosciences Division] Zheng", "primaryContact": false }, { "name": "Emily B. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Biosciences Division] Smith", "primaryContact": false }, { "name": "Jennifer [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Biosciences Division] (ORCID:0000000293627528) Morrell\u2010Falvey", "primaryContact": false }, { "name": "Chongle [Univ. of Oklahoma,Norman,OK (United States)] Pan", "primaryContact": false }, { "name": "Feng [Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:0000000232674646) Chen", "primaryContact": false }, { "name": "Gerald A. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000301061289) Tuskan", "primaryContact": false }, { "name": "Wellington [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000202009856) Muchero", "primaryContact": false }, { "name": "Jin\u2010Gui [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000217524201) Chen", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2478428", "active": false, "has_related_ids": [ "BNL--226330-2024-JAAM" ] }, { "brc": "CBI", "title": "Enzymatic Routes to Designer Hemicelluloses for Use in Biobased Materials", "description": "Various enzymes can be used to modify the structure of hemicelluloses directly in vivo or following extraction from biomass sources, such as wood and agricultural residues. Generally, these enzymes can contribute to designer hemicelluloses through four main strategies: (1) enzymatic hydrolysis such as selective removal of side groups by glycoside hydrolases (GH) and carbohydrate esterases (CE), (2) enzymatic cross-linking, for instance, the selective addition of side groups by glycosyltransferases (GT) with activated sugars, (3) enzymatic polymerization by glycosynthases (GS) with activated glycosyl donors or transglycosylation, and (4) enzymatic functionalization, particularly via oxidation by carbohydrate oxidoreductases and via amination by amine transaminases. Thus, this Perspective will first highlight enzymes that play a role in regulating the degree of polymerization and side group composition of hemicelluloses, and subsequently, it will explore enzymes that enhance cross-linking capabilities and incorporate novel chemical functionalities into saccharide structures. These enzymatic routes offer a precise way to tailor the properties of hemicelluloses for specific applications in biobased materials, contributing to the development of renewable alternatives to conventional materials derived from fossil fuels.", "abstract": "Various enzymes can be used to modify the structure of hemicelluloses directly in vivo or following extraction from biomass sources, such as wood and agricultural residues. Generally, these enzymes can contribute to designer hemicelluloses through four main strategies: (1) enzymatic hydrolysis such as selective removal of side groups by glycoside hydrolases (GH) and carbohydrate esterases (CE), (2) enzymatic cross-linking, for instance, the selective addition of side groups by glycosyltransferases (GT) with activated sugars, (3) enzymatic polymerization by glycosynthases (GS) with activated glycosyl donors or transglycosylation, and (4) enzymatic functionalization, particularly via oxidation by carbohydrate oxidoreductases and via amination by amine transaminases. Thus, this Perspective will first highlight enzymes that play a role in regulating the degree of polymerization and side group composition of hemicelluloses, and subsequently, it will explore enzymes that enhance cross-linking capabilities and incorporate novel chemical functionalities into saccharide structures. These enzymatic routes offer a precise way to tailor the properties of hemicelluloses for specific applications in biobased materials, contributing to the development of renewable alternatives to conventional materials derived from fossil fuels.", "date": "2024-10-07", "issue": "11", "identifier": "https://www.osti.gov/biblio/2478856", "bibliographicCitation": "https://doi.org/10.1021/jacsau.4c00469", "keywords": [ "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "59 BASIC BIOLOGICAL SCIENCES", "amine transaminase", "biobased material", "carbohydrate oxidoreductase", "carbohydrate-active enzyme", "carbohydrates", "cells", "chemical structure", "free radicals", "glycoside hydrolase", "glycosyl transferase", "hemicellulose", "lignocellulose", "peptides and proteins" ], "topic": [ "Chemistry", "Microbiology" ], "journal_name": "JACS Au", "volume": "4", "publisher_information": "American Chemical Society (ACS)", "country_publication_code": "US", "creator": [ { "name": "Thu V. [University of Toronto,ON (Canada)] (ORCID:0000000247536975) Vuong", "primaryContact": true }, { "name": "Mohammad [University of Georgia,Athens,GA (United States)] (ORCID:000000030042528X) Aghajohari", "primaryContact": false }, { "name": "Xuebin [University of Toronto,ON (Canada)] Feng", "primaryContact": false }, { "name": "Amanda K. [University of Georgia,Athens,GA (United States)] Woodstock", "primaryContact": false }, { "name": "Deepti M. [University of Georgia,Athens,GA (United States)] Nambiar", "primaryContact": false }, { "name": "Zeina C. [University of Georgia,Athens,GA (United States)] (ORCID:0000000152133559) Sleiman", "primaryContact": false }, { "name": "Breeanna R. [University of Georgia,Athens,GA (United States)] (ORCID:0000000152474513) Urbanowicz", "primaryContact": false }, { "name": "Emma R. [University of Toronto,ON (Canada); Aalto University,Espoo (Finland)] (ORCID:0000000268379817) Master", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "NIGMS" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2478856", "active": false }, { "brc": "CBI", "title": "Lignin Deoxygenation for the Production of Sustainable Aviation Fuel Blendstocks", "description": "Lignin is an abundant source of renewable aromatics that has long been targeted for valorization. Traditionally, the inherent heterogeneity and reactivity of lignin has relegated it to direct combustion, but its higher energy density compared with polysaccharides makes it an ideal candidate for biofuel production. This Review critically assesses lignin's potential as a substrate for sustainable aviation fuel blendstocks. Lignin can generate the necessary cyclic compounds for a fully renewable, sustainable aviation fuel when integrated with current paraffinic blends and can meet the current demand 2.5 times over. Using an energy-centric analysis, we show that lignin conversion technologies have the near-term potential to match the enthalpic yields of existing commercial sustainable aviation fuel production processes. Key factors influencing the viability of technologies for converting lignin to sustainable aviation fuel include lignin structure, delignification extent, depolymerization performance, and the development of stable and tunable deoxygenation catalysts.", "abstract": "Lignin is an abundant source of renewable aromatics that has long been targeted for valorization. Traditionally, the inherent heterogeneity and reactivity of lignin has relegated it to direct combustion, but its higher energy density compared with polysaccharides makes it an ideal candidate for biofuel production. This Review critically assesses lignin's potential as a substrate for sustainable aviation fuel blendstocks. Lignin can generate the necessary cyclic compounds for a fully renewable, sustainable aviation fuel when integrated with current paraffinic blends and can meet the current demand 2.5 times over. Using an energy-centric analysis, we show that lignin conversion technologies have the near-term potential to match the enthalpic yields of existing commercial sustainable aviation fuel production processes. Key factors influencing the viability of technologies for converting lignin to sustainable aviation fuel include lignin structure, delignification extent, depolymerization performance, and the development of stable and tunable deoxygenation catalysts.", "date": "2024-11-25", "issue": "12", "identifier": "https://www.osti.gov/biblio/2481287", "bibliographicCitation": "https://doi.org/10.1038/s41563-024-02024-6", "keywords": [ "09 BIOMASS FUELS", "BIOMASS FUELS", "biofuel production", "deoxygenation catalyst", "lignin valorization", "sustainable aviation fuel (SAF)" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Nature Materials", "volume": "23", "country_publication_code": "US", "creator": [ { "name": "Matthew [Massachusetts Institute of Technology] Webber", "primaryContact": true }, { "name": "Jamison [Massachusetts Institute of Technology] Watson", "primaryContact": false }, { "name": "Jie [Massachusetts Institute of Technology] Zhu", "primaryContact": false }, { "name": "Jun Hee [National Renewable Energy Lab.,Golden,CO (United States)] Jang", "primaryContact": false }, { "name": "Mustafa [National Renewable Energy Lab.,Golden,CO (United States)] Caglayan", "primaryContact": false }, { "name": "Joshua [Pacific Northwest National Laboratory; Washington State University] Heyne", "primaryContact": false }, { "name": "Gregg [National Renewable Energy Lab.,Golden,CO (United States)] (ORCID:000000023480212X) Beckham", "primaryContact": false }, { "name": "Yuriy [Massachusetts Institute of Technology] Roman-Leshkov", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Transportation Office. Bioenergy Technologies Office" } } ], "dataset_url": "https://www.osti.gov/biblio/2481287", "active": false, "has_related_ids": [ "NREL/JA-2A00-89317" ] }, { "brc": "CBI", "title": "Tree drought physiology: critical research questions and strategies for mitigating climate change effects on forests", "description": "Droughts of increasing severity and frequency are a primary cause of forest mortality associated with climate change. Yet, fundamental knowledge gaps regarding the complex physiology of trees limit the development of more effective management strategies to mitigate drought effects on forests. Here, in this work, we highlight some of the basic research needed to better understand tree drought physiology and how new technologies and interdisciplinary approaches can be used to address them. Our discussion focuses on how trees change wood development to mitigate water stress, hormonal responses to drought, genetic variation underlying adaptive drought phenotypes, how trees \u2018remember\u2019 prior stress exposure, and how symbiotic soil microbes affect drought response. Next, we identify opportunities for using research findings to enhance or develop new strategies for managing drought effects on forests, ranging from matching genotypes to environments, to enhancing seedling resilience through nursery treatments, to landscape-scale monitoring and predictions. We conclude with a discussion of the need for co-producing research with land managers and extending research to forests in critical ecological regions beyond the temperate zone.", "abstract": "Droughts of increasing severity and frequency are a primary cause of forest mortality associated with climate change. Yet, fundamental knowledge gaps regarding the complex physiology of trees limit the development of more effective management strategies to mitigate drought effects on forests. Here, in this work, we highlight some of the basic research needed to better understand tree drought physiology and how new technologies and interdisciplinary approaches can be used to address them. Our discussion focuses on how trees change wood development to mitigate water stress, hormonal responses to drought, genetic variation underlying adaptive drought phenotypes, how trees \u2018remember\u2019 prior stress exposure, and how symbiotic soil microbes affect drought response. Next, we identify opportunities for using research findings to enhance or develop new strategies for managing drought effects on forests, ranging from matching genotypes to environments, to enhancing seedling resilience through nursery treatments, to landscape-scale monitoring and predictions. We conclude with a discussion of the need for co-producing research with land managers and extending research to forests in critical ecological regions beyond the temperate zone.", "date": "2024-12-16", "issue": "5", "identifier": "https://www.osti.gov/biblio/2483400", "bibliographicCitation": "https://doi.org/10.1111/nph.20326", "keywords": [ "54 ENVIRONMENTAL SCIENCES", "climate change", "drought", "forest management", "forests", "physiology" ], "topic": [ "Environmental Science & Sustainability" ], "journal_name": "New Phytologist", "volume": "245", "publisher_information": "Wiley", "country_publication_code": "US", "creator": [ { "name": "Andrew T. [USDA Forest Service,Burlington,VT (United States); USDA Forest Service,Placerville,CA (United States)] (ORCID:0000000266865774) Groover", "primaryContact": true }, { "name": "N. Michele [Harvard Univ.,Cambridge,MA (United States)] (ORCID:0000000333255395) Holbrook", "primaryContact": false }, { "name": "Andrea [Gottingen Univ. (Germany)] (ORCID:0000000186976394) Polle", "primaryContact": false }, { "name": "Anna [Univ. of Montana,Missoula,MT (United States)] (ORCID:0000000340906758) Sala", "primaryContact": false }, { "name": "Belinda [Western Sydney University,Penrith,NSW (Australia)] (ORCID:0000000157289827) Medlyn", "primaryContact": false }, { "name": "Craig [Yale Univ.,New Haven,CT (United States)] (ORCID:0000000209242570) Brodersen", "primaryContact": false }, { "name": "Jarmila [Univ. of California,Santa Cruz,CA (United States)] (ORCID:0000000318801888) Pittermann", "primaryContact": false }, { "name": "Jessica [Smith College,Northampton,MA (United States)] (ORCID:0000000326193851) Gersony", "primaryContact": false }, { "name": "Katarzyna [Univ. of Wroclaw (Poland)] (ORCID:0000000179716113) Soko\u0142owska", "primaryContact": false }, { "name": "Laura [Univ. of California,Davis,CA (United States)] (ORCID:0000000161212224) Bogar", "primaryContact": false }, { "name": "Nate G. [Pacific Northwest National Laboratory (PNNL),Richland,WA (United States); Washington State Univ.,Pullman,WA (United States)] (ORCID:0000000221782254) McDowell", "primaryContact": false }, { "name": "Rachel [Connecticut College,New London,CT (United States)] Spicer", "primaryContact": false }, { "name": "Rakefet [Volcani Institute (Israel). Agricultural Research Organization] (ORCID:0000000159238636) David\u2010Schwartz", "primaryContact": false }, { "name": "Stephen [Univ. of Vermont,Burlington,VT (United States)] (ORCID:0000000188879213) Keller", "primaryContact": false }, { "name": "Timothy J. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000295406622) Tschaplinski", "primaryContact": false }, { "name": "Yakir [Harvard Univ.,Cambridge,MA (United States); Volcani Institute (Israel). Agricultural Research Organization] (ORCID:0000000158618362) Preisler", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2483400", "active": false, "has_related_ids": [ "PNNL-SA--207588" ] }, { "brc": "CBI", "title": "Understanding the Origin of Negative Temperature Dependence and Activity of N-Coordinated Cobalt Sites During Ethylene Dimerization", "description": "The on-demand production of short-chain linear alpha olefins (LAOs; C4-C8) via C2H4 dimerization and oligomerization is industrially attractive, prompting extensive research on designing active, selective, and stable catalysts for industrial use. Cobalt supported on ammoniated carbon (Co(NH3)x/C) catalysts have shown remarkable activity and selectivity in this process. However, critical aspects such as the active phase, active site structure, the role of the catalyst support, cobalt loading effects, and the inverse correlation of the reaction rate with temperature remain inadequately understood. This study systematically explores these factors using a combination of steady-state differential catalytic tests, in situ molecular characterization including diffuse reflectance UV-Vis (DR-UV-Vis), Infrared, and Raman spectroscopies, and ex situ X-ray diffraction (XRD) and high annular aberration-corrected dark field transmission electron microscopy (HAADF-STEM). Various supports (SiO2, Al2O3, NH4-ZSM-5, g-C3N4, and C) and cobalt loadings (1.0-3.0 Co nm-2) were studied to determine the optimal catalyst composition and identify the active phase and sites. Carbon-supported catalysts uniquely produce C4-8 LAOs during C2H4 dimerization, with site-time-yield remaining constant (~10-3 s-1) for 1.0-4.0 Co nm-2 at prolonged reaction times (24-48?h time-on-stream). At higher loadings of 6.0 Co nm-2, the formation of crystalline CoO and Co3O4 phases reduces catalytic activity and LAO selectivity. Our findings show that active catalysts lack crystalline cobalt oxides and instead feature dispersed Co2+ sites, tetra-coordinated to a mix of N/NH3 and O/H2O ligands, which catalyze C2H4 dimerization via the Cossee-Arlman mechanism, exhibiting 1st order dependence on C2H4 concentration. The observed inverse rate-temperature correlation is attributed to compensation effects (i.e., presence of Cremer-Constable relationship) linked to changes in adsorption enthalpic and entropic factors.", "abstract": "The on-demand production of short-chain linear alpha olefins (LAOs; C4-C8) via C2H4 dimerization and oligomerization is industrially attractive, prompting extensive research on designing active, selective, and stable catalysts for industrial use. Cobalt supported on ammoniated carbon (Co(NH3)x/C) catalysts have shown remarkable activity and selectivity in this process. However, critical aspects such as the active phase, active site structure, the role of the catalyst support, cobalt loading effects, and the inverse correlation of the reaction rate with temperature remain inadequately understood. This study systematically explores these factors using a combination of steady-state differential catalytic tests, in situ molecular characterization including diffuse reflectance UV-Vis (DR-UV-Vis), Infrared, and Raman spectroscopies, and ex situ X-ray diffraction (XRD) and high annular aberration-corrected dark field transmission electron microscopy (HAADF-STEM). Various supports (SiO2, Al2O3, NH4-ZSM-5, g-C3N4, and C) and cobalt loadings (1.0-3.0 Co nm-2) were studied to determine the optimal catalyst composition and identify the active phase and sites. Carbon-supported catalysts uniquely produce C4-8 LAOs during C2H4 dimerization, with site-time-yield remaining constant (~10-3 s-1) for 1.0-4.0 Co nm-2 at prolonged reaction times (24-48?h time-on-stream). At higher loadings of 6.0 Co nm-2, the formation of crystalline CoO and Co3O4 phases reduces catalytic activity and LAO selectivity. Our findings show that active catalysts lack crystalline cobalt oxides and instead feature dispersed Co2+ sites, tetra-coordinated to a mix of N/NH3 and O/H2O ligands, which catalyze C2H4 dimerization via the Cossee-Arlman mechanism, exhibiting 1st order dependence on C2H4 concentration. The observed inverse rate-temperature correlation is attributed to compensation effects (i.e., presence of Cremer-Constable relationship) linked to changes in adsorption enthalpic and entropic factors.", "date": "2024-12-15", "identifier": "https://www.osti.gov/biblio/2496247", "bibliographicCitation": "https://doi.org/10.1016/j.apcatb.2024.124952", "keywords": [ "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "ammines", "compensation", "constable-cremer", "molecular complexes", "olefin valorization" ], "topic": [ "Chemistry" ], "journal_name": "Applied Catalysis B: Environment and Energy", "volume": "365", "country_publication_code": "US", "creator": [ { "name": "Daniyal [National Renewable Energy Lab.,Golden,CO (United States)] Kiani", "primaryContact": true }, { "name": "Faysal [University of Wisconsin-Madison] Ibrahim", "primaryContact": false }, { "name": "Steven [National Renewable Energy Lab.,Golden,CO (United States)] Hayden", "primaryContact": false }, { "name": "Ive [University of Wisconsin-Madison] Hermans", "primaryContact": false }, { "name": "Gregg [National Renewable Energy Lab.,Golden,CO (United States)] (ORCID:000000023480212X) Beckham", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE National Renewable Energy Laboratory (NREL), Laboratory Directed Research and Development (LDRD) Program" } } ], "dataset_url": "https://www.osti.gov/biblio/2496247", "active": false, "has_related_ids": [ "NREL/JA-2A00-91408" ] }, { "brc": "CBI", "title": "Poplar transformation with variable explant sources to maximize transformation efficiency", "description": "For decades, Agrobacterium tumefaciens-mediated plant transformation has played an integral role in advancing fundamental and applied plant biology. The recent omnipresent emergence of synthetic biology, which relies on plant transformation to manipulate plant DNA and gene expression for novel product biosynthesis, has further propelled basic as well as applied interests in plant transformation technologies. The strong demand for a faster design-build-test-learn cycle, the essence of synthetic biology, is, however, still ill-matched with the long-standing issues of high tissue culture recalcitrance and low transformation efficiency of a wide range of plant species especially food, fiber and energy crops. To maximize the utility of plant material and improve the transformation productivity per unit plant form, we studied the regeneration and transformation efficiency of different types of explants, including leaf, stem, petiole, and root from Populus, a woody perennial bioenergy crop. Our results show that root explants, in addition to the above-ground tissues, have considerable regeneration capacity and amenability to A. tumefaciens and, the resulting transformants have largely comparable morphology, reporter gene expression, and transcriptome profile, independent of the explant source tissue. Transcriptome analyses mapped to regeneration stages and transformation efficiencies further revealed the expression of the auxin and cytokinin signaling and various developmental pathway genes in leaf and root explants undergoing early organogenesis. We further report high-potential candidate genes that may potentially be associated with higher regeneration and transformation efficiency. Overall, our study shows that explants from above- and belowground organs of a Populus plant are suitable for genetic transformation and tissue culture regeneration, and together with the underlying transcriptome data open new routes to maximize plant explant utilization, stable transformation productivity, and plant transformation efficiency.", "abstract": "For decades, Agrobacterium tumefaciens-mediated plant transformation has played an integral role in advancing fundamental and applied plant biology. The recent omnipresent emergence of synthetic biology, which relies on plant transformation to manipulate plant DNA and gene expression for novel product biosynthesis, has further propelled basic as well as applied interests in plant transformation technologies. The strong demand for a faster design-build-test-learn cycle, the essence of synthetic biology, is, however, still ill-matched with the long-standing issues of high tissue culture recalcitrance and low transformation efficiency of a wide range of plant species especially food, fiber and energy crops. To maximize the utility of plant material and improve the transformation productivity per unit plant form, we studied the regeneration and transformation efficiency of different types of explants, including leaf, stem, petiole, and root from Populus, a woody perennial bioenergy crop. Our results show that root explants, in addition to the above-ground tissues, have considerable regeneration capacity and amenability to A. tumefaciens and, the resulting transformants have largely comparable morphology, reporter gene expression, and transcriptome profile, independent of the explant source tissue. Transcriptome analyses mapped to regeneration stages and transformation efficiencies further revealed the expression of the auxin and cytokinin signaling and various developmental pathway genes in leaf and root explants undergoing early organogenesis. We further report high-potential candidate genes that may potentially be associated with higher regeneration and transformation efficiency. Overall, our study shows that explants from above- and belowground organs of a Populus plant are suitable for genetic transformation and tissue culture regeneration, and together with the underlying transcriptome data open new routes to maximize plant explant utilization, stable transformation productivity, and plant transformation efficiency.", "date": "2025-01-07", "issue": "1", "identifier": "https://www.osti.gov/biblio/2497853", "bibliographicCitation": "https://doi.org/10.1038/s41598-024-81235-y", "keywords": [ "60 APPLIED LIFE SCIENCES", "Agrobacterium tumefaciens", "Bioenergy", "Leaf", "Molecular factors", "Root", "Transformation" ], "topic": [ "Plant Biology" ], "journal_name": "Scientific Reports", "volume": "15", "publisher_information": "Nature Publishing Group", "country_publication_code": "US", "creator": [ { "name": "Haiwei [Univ. of Nebraska,Kearney,NE (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Lu", "primaryContact": true }, { "name": "Sara [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Jawdy", "primaryContact": false }, { "name": "Jin-Gui [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Chen", "primaryContact": false }, { "name": "Xiaohan [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Yang", "primaryContact": false }, { "name": "Udaya C. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000259638370) Kalluri", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Laboratory Directed Research and Development (LDRD) Program" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2497853", "active": false }, { "brc": "CBI", "title": "Phenotyping Alfalfa (Medicago sativa L.) Root Structure Architecture via Integrating Confident Machine Learning with ResNet-18", "description": "Not Available", "abstract": "Not Available", "date": "2023-12-31", "issue": "C", "identifier": "https://www.osti.gov/biblio/2499570", "bibliographicCitation": "https://doi.org/10.34133/plantphenomics.0251", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "Plant Phenomics", "volume": "6", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Brandon J. Weihs", "primaryContact": true }, { "name": "Zhou Tang", "primaryContact": false }, { "name": "Zezhong Tian", "primaryContact": false }, { "name": "Deborah Jo Heuschele", "primaryContact": false }, { "name": "Aftab Siddique", "primaryContact": false }, { "name": "Thomas H. Terrill", "primaryContact": false }, { "name": "Zhou Zhang", "primaryContact": false }, { "name": "Larry M. (ORCID:0000000219959479) York", "primaryContact": false }, { "name": "Zhiwu Zhang", "primaryContact": false }, { "name": "Zhanyou (ORCID:000000027633036X) Xu", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2499570", "active": false }, { "brc": "CBI", "title": "Advances in the Application of Single-Cell Transcriptomics in Plant Systems and Synthetic Biology", "description": "Not Available", "abstract": "Not Available", "date": "2023-12-31", "issue": "C", "identifier": "https://www.osti.gov/biblio/2500945", "bibliographicCitation": "https://doi.org/10.34133/bdr.0029", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "cell-type", "plant", "scRNA-seq", "synthetic biology", "systems biology" ], "topic": [ "Microbiology" ], "journal_name": "BioDesign Research", "volume": "6", "publisher_information": "Elsevier", "country_publication_code": "India", "creator": [ { "name": "Md Torikul Islam", "primaryContact": true }, { "name": "Yang Liu", "primaryContact": false }, { "name": "Md Mahmudul Hassan", "primaryContact": false }, { "name": "Paul E. Abraham", "primaryContact": false }, { "name": "Jean Merlet", "primaryContact": false }, { "name": "Alice Townsend", "primaryContact": false }, { "name": "Daniel Jacobson", "primaryContact": false }, { "name": "C. Robin Buell", "primaryContact": false }, { "name": "Gerald A. Tuskan", "primaryContact": false }, { "name": "Xiaohan Yang", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2500945", "active": false }, { "brc": "CBI", "title": "Major facilitator family transporters specifically enhance caffeyl alcohol uptake during C\u2010lignin biosynthesis", "description": "The mode of transport of lignin monomers to the sites of polymerization in the apoplast remains controversial. C-Lignin is a recently discovered form of lignin found in some seed coats that is composed exclusively of units derived from caffeyl alcohol. RNA-seq and proteome analyses identified a number of transporters co-expressed with C-lignin deposition in the seed coat of Cleome hassleriana. Cloning and influx/efflux analysis assays in yeast identified two low-affinity transporters, ChPLT3 and ChSUC1, that were active with caffeyl alcohol but not with the classical monolignols p-coumaryl, coniferyl, and sinapyl alcohols, consistent with molecular modeling and docking studies. Expression of ChPLT3 in Arabidopsis seedlings enhanced root growth in the presence of caffeyl alcohol, and expression of ChPLT3 and ChSUC1 correlated with lignin C-unit content in hairy roots of Medicago truncatula. We present a model, consistent with phylogenetic and evolutionary considerations, whereby passive caffeyl alcohol transport may be supplemented by hitchhiking on secondary active transporters to ensure the synthesis of C-lignin, and inhibition of synthesis of G-lignin, in the apoplast.", "abstract": "The mode of transport of lignin monomers to the sites of polymerization in the apoplast remains controversial. C-Lignin is a recently discovered form of lignin found in some seed coats that is composed exclusively of units derived from caffeyl alcohol. RNA-seq and proteome analyses identified a number of transporters co-expressed with C-lignin deposition in the seed coat of Cleome hassleriana. Cloning and influx/efflux analysis assays in yeast identified two low-affinity transporters, ChPLT3 and ChSUC1, that were active with caffeyl alcohol but not with the classical monolignols p-coumaryl, coniferyl, and sinapyl alcohols, consistent with molecular modeling and docking studies. Expression of ChPLT3 in Arabidopsis seedlings enhanced root growth in the presence of caffeyl alcohol, and expression of ChPLT3 and ChSUC1 correlated with lignin C-unit content in hairy roots of Medicago truncatula. We present a model, consistent with phylogenetic and evolutionary considerations, whereby passive caffeyl alcohol transport may be supplemented by hitchhiking on secondary active transporters to ensure the synthesis of C-lignin, and inhibition of synthesis of G-lignin, in the apoplast.", "date": "2024-12-06", "identifier": "https://www.osti.gov/biblio/2502147", "bibliographicCitation": "https://doi.org/10.1111/nph.20325", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "C-lignin", "Cleome hassleriana", "active transport", "caffeyl alcohol", "monolignol", "passive diffusion" ], "topic": [ "Microbiology" ], "journal_name": "New Phytologist", "volume": "Early View", "publisher_information": "Wiley", "country_publication_code": "US", "creator": [ { "name": "Chunliu [Univ. of North Texas,Denton,TX (United States). BioDiscovery Institute; Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] (ORCID:0000000323076270) Zhuo", "primaryContact": true }, { "name": "Xiaoqiang [Univ. of North Texas,Denton,TX (United States). BioDiscovery Institute] (ORCID:0000000191351663) Wang", "primaryContact": false }, { "name": "Him K. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:000000019686357X) Shrestha", "primaryContact": false }, { "name": "Paul E. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000326859123) Abraham", "primaryContact": false }, { "name": "Robert L. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:000000017708786X) Hettich", "primaryContact": false }, { "name": "Fang [Univ. of North Texas,Denton,TX (United States). BioDiscovery Institute; Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] (ORCID:0000000177929967) Chen", "primaryContact": false }, { "name": "Jaime [Univ. of North Texas,Denton,TX (United States). BioDiscovery Institute; Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] (ORCID:000000029545312X) Barros", "primaryContact": false }, { "name": "Richard A. [Univ. of North Texas,Denton,TX (United States). BioDiscovery Institute; Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] (ORCID:0000000183939408) Dixon", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2502147", "active": false }, { "brc": "CBI", "title": "Soil application of high-lignin fermentation byproduct to increase the sustainability of liquid biofuel production from crop residues", "description": "When digestates from anaerobic digestion of crop residues are added to soil, a considerable body of information indicates that soil organic carbon (SOC) levels are comparable to those when crop residues are left in the field. This occurs although the amount of digestate added to soil is diminished by digestion and implies that digestion increases the proportion of carbon inputs stabilized as SOC. Here we examine the likelihood and implications of these features being manifested for soil application of high lignin-fermentation byproduct (HLFB) from liquid biofuel production. We show that steady-state SOC levels are much less sensitive to crop residue removal with HLFB return than without it, and provide an example supporting the feasibility of foregoing process energy and coproduct revenue when HLFB is returned to the soil. Informed by this review and analysis, we expect with moderate confidence that long-term SOC levels for soils amended with HLFB from some liquid cellulosic biofuel processes will not be substantially lower than those occurring when crop residues are left in the field. We have high confidence that the economically optimum rate of fertilizer nitrogen (N) application and N2O emissions will be lower at most sites for HLFB return to the soil than if crop residues were left in the field. We estimate that the per hectare N demand for processing crop residues to liquid biofuels is about a third of the per hectare demand for crop production, giving rise to an opportunity to use N twice and thereby realize cost savings and environmental benefits. These observations support but do not prove the hypothesis that a \u2018win-win\u2019 is possible wherein large amounts of liquid biofuel feedstock can be obtained from crop residues while improving the economics and sustainability of food and feed production. A research agenda aimed at exploring and testing this hypothesis is offered.", "abstract": "When digestates from anaerobic digestion of crop residues are added to soil, a considerable body of information indicates that soil organic carbon (SOC) levels are comparable to those when crop residues are left in the field. This occurs although the amount of digestate added to soil is diminished by digestion and implies that digestion increases the proportion of carbon inputs stabilized as SOC. Here we examine the likelihood and implications of these features being manifested for soil application of high lignin-fermentation byproduct (HLFB) from liquid biofuel production. We show that steady-state SOC levels are much less sensitive to crop residue removal with HLFB return than without it, and provide an example supporting the feasibility of foregoing process energy and coproduct revenue when HLFB is returned to the soil. Informed by this review and analysis, we expect with moderate confidence that long-term SOC levels for soils amended with HLFB from some liquid cellulosic biofuel processes will not be substantially lower than those occurring when crop residues are left in the field. We have high confidence that the economically optimum rate of fertilizer nitrogen (N) application and N2O emissions will be lower at most sites for HLFB return to the soil than if crop residues were left in the field. We estimate that the per hectare N demand for processing crop residues to liquid biofuels is about a third of the per hectare demand for crop production, giving rise to an opportunity to use N twice and thereby realize cost savings and environmental benefits. These observations support but do not prove the hypothesis that a \u2018win-win\u2019 is possible wherein large amounts of liquid biofuel feedstock can be obtained from crop residues while improving the economics and sustainability of food and feed production. A research agenda aimed at exploring and testing this hypothesis is offered.", "date": "2024-08-01", "issue": "8", "identifier": "https://www.osti.gov/biblio/2502162", "bibliographicCitation": "https://doi.org/10.1088/1748-9326/ad601a", "keywords": [ "09 BIOMASS FUELS", "biofuels", "crop residues", "soil organic carbon" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Environmental Research Letters", "volume": "19", "publisher_information": "IOP Publishing", "country_publication_code": "US", "creator": [ { "name": "Lee [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI); Dartmouth College,Hanover,NH (United States)] (ORCID:000000025642668X) Lynd", "primaryContact": true }, { "name": "Armen R. [Pennsylvania State Univ.,University Park,PA (United States)] (ORCID:0000000276823527) Kemanian", "primaryContact": false }, { "name": "Jo [Univ. of Aberdeen (United Kingdom)] Smith", "primaryContact": false }, { "name": "Tom L. [Pennsylvania State Univ.,University Park,PA (United States)] (ORCID:0000000208334844) Richard", "primaryContact": false }, { "name": "Anela [Dartmouth College,Hanover,NH (United States); Stanford Univ.,CA (United States)] Arifi", "primaryContact": false }, { "name": "Stefano [Biogas Refinery Development SRI,Cittadella (Italy)] Bozzetto", "primaryContact": false }, { "name": "Claudio [Biogas Refinery Development SRI,Cittadella (Italy)] Fabbri", "primaryContact": false }, { "name": "John [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000344518947) Field", "primaryContact": false }, { "name": "Caitlin Hicks [Dartmouth College,Hanover,NH (United States)] Pries", "primaryContact": false }, { "name": "Matt [Dartmouth College,Hanover,NH (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI); LanzaTech,Inc.,Skokie,IL (United States)] Kubis", "primaryContact": false }, { "name": "Pete [Univ. of Aberdeen (United Kingdom)] Smith", "primaryContact": false }, { "name": "Michelle [Dartmouth College,Hanover,NH (United States)] Wang", "primaryContact": false }, { "name": "Madeline [Dartmouth College,Hanover,NH (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] Hoey", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "US Dept. of Agriculture (USDA)" } }, { "fundingOrganization": { "organizationName": "USDOE Laboratory Directed Research and Development (LDRD) Program" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2502162", "active": false }, { "brc": "CBI", "title": "Plant Promoters and Terminators for High-Precision Bioengineering", "description": "Not Available", "abstract": "Not Available", "date": "2022-12-31", "issue": "C", "identifier": "https://www.osti.gov/biblio/2507387", "bibliographicCitation": "https://doi.org/10.34133/bdr.0013", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "BioDesign Research", "volume": "5", "publisher_information": "Elsevier", "country_publication_code": "India", "creator": [ { "name": "Emily G. Brooks", "primaryContact": true }, { "name": "Estefania Elorriaga", "primaryContact": false }, { "name": "Yang Liu", "primaryContact": false }, { "name": "James R. Duduit", "primaryContact": false }, { "name": "Guoliang Yuan", "primaryContact": false }, { "name": "Chung-Jui Tsai", "primaryContact": false }, { "name": "Gerald A. Tuskan", "primaryContact": false }, { "name": "Thomas G. Ranney", "primaryContact": false }, { "name": "Xiaohan Yang", "primaryContact": false }, { "name": "Wusheng (ORCID:0000000192564310) Liu", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDA" } }, { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2507387", "active": false }, { "brc": "CBI", "title": "Virulence and Genetic Diversity of Puccinia spp., Causal Agents of Rust on Switchgrass (Panicum virgatum L.) in the USA", "description": "Switchgrass (Panicum virgatum L.) is an important cellulosic biofuel grass native to North America. Rust, caused by Puccinia spp. is the most predominant disease of switchgrass and has the potential to impact biomass conversion. In this study, virulence patterns were determined on a set of 38 switchgrass genotypes for 14 single-spore rust isolates from 14 field samples collected in seven states. Single nucleotide polymorphism (SNP) variation was also assessed in 720 sequenced cloned amplicons representing 654 base pairs of the elongation factor 1-\u03b1 gene from the field samples. Five major haplotypes were identified differing by 11 out of the 39 SNP positions identified. STRUCTURE, Principal Coordinate Analysis, and phylogenetic analyses divided the rust population into two genetic clusters. Virginia and Georgia had the highest and lowest rust genetic diversity, respectively. Only nine accessions showed a differential disease response between the 14 isolates, allowing the identification of eight races, differing by 1\u20133 virulence factors. Overall, the results suggested clonal reproduction of the pathogen and a North\u2013South differentiation via local adaptation. However, similar haplotypes and races were also recovered from several states, suggesting migration events, and highlighting the need to further investigate the switchgrass rust population structure and evolution in the USA.
", "abstract": "Switchgrass (Panicum virgatum L.) is an important cellulosic biofuel grass native to North America. Rust, caused by Puccinia spp. is the most predominant disease of switchgrass and has the potential to impact biomass conversion. In this study, virulence patterns were determined on a set of 38 switchgrass genotypes for 14 single-spore rust isolates from 14 field samples collected in seven states. Single nucleotide polymorphism (SNP) variation was also assessed in 720 sequenced cloned amplicons representing 654 base pairs of the elongation factor 1-\u03b1 gene from the field samples. Five major haplotypes were identified differing by 11 out of the 39 SNP positions identified. STRUCTURE, Principal Coordinate Analysis, and phylogenetic analyses divided the rust population into two genetic clusters. Virginia and Georgia had the highest and lowest rust genetic diversity, respectively. Only nine accessions showed a differential disease response between the 14 isolates, allowing the identification of eight races, differing by 1\u20133 virulence factors. Overall, the results suggested clonal reproduction of the pathogen and a North\u2013South differentiation via local adaptation. However, similar haplotypes and races were also recovered from several states, suggesting migration events, and highlighting the need to further investigate the switchgrass rust population structure and evolution in the USA.
", "date": "2025-02-13", "issue": "2", "identifier": "https://www.osti.gov/biblio/2519268", "bibliographicCitation": "https://doi.org/10.3390/pathogens14020194", "topic": [ "Unknown" ], "journal_name": "Pathogens", "volume": "14", "publisher_information": "MDPI AG", "country_publication_code": "Switzerland", "creator": [ { "name": "Bochra A. (ORCID:0000000159055880) Bahri", "primaryContact": true }, { "name": "Peng Tian", "primaryContact": false }, { "name": "Samikshya (ORCID:0000000223688616) Rijal", "primaryContact": false }, { "name": "Katrien M. Devos", "primaryContact": false }, { "name": "Jeffrey L. Bennetzen", "primaryContact": false }, { "name": "Shavannor M. Smith", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/2519268", "active": false }, { "brc": "CBI", "title": "Metabolic Modification of Sphingobium lignivorans SYK-6 for Lignin Valorization Through the Discovery of an Unusual Transcriptional Repressor of Lignin-Derived Dimer Catabolism", "description": "Sphingobium lignivorans SYK-6 catabolizes guaiacylglycerol-..beta..-guaiacyl ether (GGE, a ..beta..-O-4-type dimer) and 1,2-diguaiacylpropane-1,3-diol (DGPD, a ..beta..-1-type dimer) derived from lignin. Recently, SLG_35860 containing TetR- and MarR-type transcriptional regulator motifs was suggested to be involved in the regulation of GGE and DGPD catabolism. Here we investigated the role of SLG_35860 in the transcriptional regulation of GGE and DGPD catabolism genes. SLG_35860 designated ligS repressed 11 genes involved in GGE and DGPD catabolism. LigS binds directly to specific sequences in the promoter region of each gene. The MarR domain was shown to be involved in these bindings; however, GGE, DGPD, and their metabolites did not function as effectors of LigS. We discovered unidentified compound(s) in the black liquor of oxygen-soda anthraquinone pulping of Japanese cedar that SYK-6 cannot metabolize and that acted as effector(s). Therefore, LigS constantly represses the transcription of the GGE and DGPD catabolism genes to low levels. Based on these findings, we examined the productivity of a polymer building block, 2-pyrone-4,6-dicarboxylic acid (PDC), from GGE, DGPD, and a GGE metabolite using an engineered ligS mutant. The rates of PDC production from each compound by this strain were 1.5-6.0 times higher than those of a PDC-producing strain carrying ligS.", "abstract": "Sphingobium lignivorans SYK-6 catabolizes guaiacylglycerol-..beta..-guaiacyl ether (GGE, a ..beta..-O-4-type dimer) and 1,2-diguaiacylpropane-1,3-diol (DGPD, a ..beta..-1-type dimer) derived from lignin. Recently, SLG_35860 containing TetR- and MarR-type transcriptional regulator motifs was suggested to be involved in the regulation of GGE and DGPD catabolism. Here we investigated the role of SLG_35860 in the transcriptional regulation of GGE and DGPD catabolism genes. SLG_35860 designated ligS repressed 11 genes involved in GGE and DGPD catabolism. LigS binds directly to specific sequences in the promoter region of each gene. The MarR domain was shown to be involved in these bindings; however, GGE, DGPD, and their metabolites did not function as effectors of LigS. We discovered unidentified compound(s) in the black liquor of oxygen-soda anthraquinone pulping of Japanese cedar that SYK-6 cannot metabolize and that acted as effector(s). Therefore, LigS constantly represses the transcription of the GGE and DGPD catabolism genes to low levels. Based on these findings, we examined the productivity of a polymer building block, 2-pyrone-4,6-dicarboxylic acid (PDC), from GGE, DGPD, and a GGE metabolite using an engineered ligS mutant. The rates of PDC production from each compound by this strain were 1.5-6.0 times higher than those of a PDC-producing strain carrying ligS.", "date": "2025-01-02", "issue": "5", "identifier": "https://www.osti.gov/biblio/2526220", "bibliographicCitation": "https://doi.org/10.1039/D4GC05328A", "keywords": [ "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "Japanese cedar", "Sphingobium lignivorans SYK-6", "lignin" ], "topic": [ "Chemistry" ], "journal_name": "Green Chemistry", "volume": "27", "country_publication_code": "US", "creator": [ { "name": "Ryo [Nagaoka University of Technology] Kato", "primaryContact": true }, { "name": "Eugene [National Renewable Energy Lab.,Golden,CO (United States)] Kuatsjah", "primaryContact": false }, { "name": "Masaya [Nagaoka University of Technology] Fujita", "primaryContact": false }, { "name": "Alissa [National Renewable Energy Lab.,Golden,CO (United States)] Bleem", "primaryContact": false }, { "name": "Shojiro [Forestry & Forest Products Research Institute] Hishiyama", "primaryContact": false }, { "name": "Rui [National Renewable Energy Lab.,Golden,CO (United States)] Katahira", "primaryContact": false }, { "name": "Toshiya [High Energy Accelerator Research Organization] Senda", "primaryContact": false }, { "name": "Gregg [National Renewable Energy Lab.,Golden,CO (United States)] (ORCID:000000023480212X) Beckham", "primaryContact": false }, { "name": "Naofumi [Nagaoka University of Technology] Kamimura", "primaryContact": false }, { "name": "Eiji [Nagaoka University of Technology] Masai", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2526220", "active": false, "has_related_ids": [ "NREL/JA-2800-93551" ] }, { "brc": "CBI", "title": "Alpha ketoacid decarboxylases: Diversity, structures, reaction mechanisms, and applications for biomanufacturing of platform chemicals and fuels", "description": "In living cells, alpha-ketoacid decarboxylases (KDCs, EC 4.1.1.-) are a class of enzymes that convert alpha-ketoacids into aldehydes through decarboxylation. These aldehydes serve as either drop-in chemicals or precursors for the biosynthesis of alcohols, carboxylic acids, esters, and alkanes. These compounds play crucial roles in cellular metabolism and fitness and the bioeconomy, facilitating the sustainable and renewable biomanufacturing of platform chemicals and fuels. This review explores the diversity and classification of KDCs, detailing their structures, mechanisms, and functions. We highlight recent advancements in repurposing KDCs to enhance their efficiency and robustness for biomanufacturing. Additionally, we present modular KDC-dependent metabolic pathways for the microbial biosynthesis of aldehydes, alcohols, carboxylic acids, esters, and alkanes. Lastly, we discuss recent developments in the modular cell engineering technology that can potentially be applied to harness the diversity of KDC-dependent pathways for biomanufacturing platform chemicals and fuels.", "abstract": "In living cells, alpha-ketoacid decarboxylases (KDCs, EC 4.1.1.-) are a class of enzymes that convert alpha-ketoacids into aldehydes through decarboxylation. These aldehydes serve as either drop-in chemicals or precursors for the biosynthesis of alcohols, carboxylic acids, esters, and alkanes. These compounds play crucial roles in cellular metabolism and fitness and the bioeconomy, facilitating the sustainable and renewable biomanufacturing of platform chemicals and fuels. This review explores the diversity and classification of KDCs, detailing their structures, mechanisms, and functions. We highlight recent advancements in repurposing KDCs to enhance their efficiency and robustness for biomanufacturing. Additionally, we present modular KDC-dependent metabolic pathways for the microbial biosynthesis of aldehydes, alcohols, carboxylic acids, esters, and alkanes. Lastly, we discuss recent developments in the modular cell engineering technology that can potentially be applied to harness the diversity of KDC-dependent pathways for biomanufacturing platform chemicals and fuels.", "date": "2025-02-12", "identifier": "https://www.osti.gov/biblio/2530898", "bibliographicCitation": "https://doi.org/10.1016/j.biotechadv.2025.108531", "keywords": [ "09 BIOMASS FUELS", "Alcohols", "Aldehydes", "Alpha-ketoacid decarboxylase", "Aromatic pathway", "Biomanufacturing", "C1 substrates", "CO2", "Carboxylic acids", "Consolidated bioprocessing", "Esters", "Lignocellulosic biomass", "Methane", "Modular cell engineering", "Modular cells", "One\u2011carbon recursive elongation pathway", "Organic wastes" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Biotechnology Advances", "volume": "81", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Khanh [University of Tennessee,Knoxville,TN (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Ha", "primaryContact": true }, { "name": "Seunghyun [University of Tennessee,Knoxville,TN (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Ryu", "primaryContact": false }, { "name": "Cong T. [University of Tennessee,Knoxville,TN (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Trinh", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2530898", "active": false }, { "brc": "CBI", "title": "Function and Evolution of the Plant MES Family of Methylesterases", "description": "Land plant evolution has been marked by numerous genetic innovations, including novel catalytic reactions. Plants produce various carboxyl methyl esters using carboxylic acids as substrates, both of which are involved in diverse biological processes. The biosynthesis of methyl esters is catalyzed by SABATH methyltransferases, and understanding of this family has broadened in recent years. Meanwhile, the enzymes catalyzing demethylation\u2014known as methylesterases (MESs)\u2014have received less attention. Here, we present a comprehensive review of the plant MES family, focusing on known biochemical and biological functions, and evolution in the plant kingdom. Thirty-two MES genes have been biochemically characterized, with substrates including methyl esters of plant hormones and several other specialized metabolites. One characterized member demonstrates non-esterase activity, indicating functional diversity in this family. MES genes regulate biological processes, including biotic and abiotic defense, as well as germination and root development. While MES genes are absent in green algae, they are ubiquitous among the land plants analyzed. Extant MES genes belong to three groups of deep origin, implying ancient gene duplication and functional divergence. Two of these groups have yet to have any characterized members. Much remains to be uncovered about the enzymatic functions, biological roles, and evolution of the MES family.", "abstract": "Land plant evolution has been marked by numerous genetic innovations, including novel catalytic reactions. Plants produce various carboxyl methyl esters using carboxylic acids as substrates, both of which are involved in diverse biological processes. The biosynthesis of methyl esters is catalyzed by SABATH methyltransferases, and understanding of this family has broadened in recent years. Meanwhile, the enzymes catalyzing demethylation\u2014known as methylesterases (MESs)\u2014have received less attention. Here, we present a comprehensive review of the plant MES family, focusing on known biochemical and biological functions, and evolution in the plant kingdom. Thirty-two MES genes have been biochemically characterized, with substrates including methyl esters of plant hormones and several other specialized metabolites. One characterized member demonstrates non-esterase activity, indicating functional diversity in this family. MES genes regulate biological processes, including biotic and abiotic defense, as well as germination and root development. While MES genes are absent in green algae, they are ubiquitous among the land plants analyzed. Extant MES genes belong to three groups of deep origin, implying ancient gene duplication and functional divergence. Two of these groups have yet to have any characterized members. Much remains to be uncovered about the enzymatic functions, biological roles, and evolution of the MES family.", "date": "2024-11-28", "issue": "23", "identifier": "https://www.osti.gov/biblio/2538231", "bibliographicCitation": "https://doi.org/10.3390/plants13233364", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "defense", "demethylation", "methyl esters", "\u03b1/\u03b2 hydrolase" ], "topic": [ "Microbiology" ], "journal_name": "Plants", "volume": "13", "publisher_information": "MDPI", "country_publication_code": "US", "creator": [ { "name": "Timothy A. [Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:0009000983259723) Chaffin", "primaryContact": true }, { "name": "Weijiao [Univ. of Tennessee,Knoxville,TN (United States)] Wang", "primaryContact": false }, { "name": "Jin-Gui [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000217524201) Chen", "primaryContact": false }, { "name": "Feng [Univ. of Tennessee,Knoxville,TN (United States)] Chen", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2538231", "active": false }, { "brc": "CBI", "title": "A Novel Gene Stacking Method in Plant Transformation Utilizing Split Selectable Markers", "description": "Gene stacking, the process of introducing multiple genes into a single plant to enhance desired traits, is essential for plant genetic improvement through both conventional breeding and genetic transformation. In general, transformation-based gene stacking can be achieved through either co-transformation to simultaneously introduce multiple genes or sequential multi-round transformation. While co-transformation is generally faster and more efficient than sequential multi-round transformation, it often requires two selectable marker genes, which confer resistance to antibiotics, for selecting transgenic events. However, in most cases, there is only one best selectable marker gene for a specific plant species or genotype. Also, it is harder to optimize the concentrations of two antibiotics for co-transformation than using one antibiotic for selecting transgenic events. To overcome this challenge, we recently developed an innovative split selectable marker system for plant co-transformation, allowing the use of one selectable marker gene to select transgenic events. This method involves constructing two binary vectors, each carrying a subset of genes of interest and a partial fragment of the selectable marker gene, which is connected to a partial intein fragment. Following Agrobacterium-mediated co-transformation, plants harboring both binary vectors are selected using a single antibiotic, such as kanamycin. This split-marker system can be used to co-transform multiple genes into both herbaceous and woody plants, accelerating genetic improvement of polygenic traits or integrative improvement of multiple traits to simultaneously increase crop yield and quality.", "abstract": "Gene stacking, the process of introducing multiple genes into a single plant to enhance desired traits, is essential for plant genetic improvement through both conventional breeding and genetic transformation. In general, transformation-based gene stacking can be achieved through either co-transformation to simultaneously introduce multiple genes or sequential multi-round transformation. While co-transformation is generally faster and more efficient than sequential multi-round transformation, it often requires two selectable marker genes, which confer resistance to antibiotics, for selecting transgenic events. However, in most cases, there is only one best selectable marker gene for a specific plant species or genotype. Also, it is harder to optimize the concentrations of two antibiotics for co-transformation than using one antibiotic for selecting transgenic events. To overcome this challenge, we recently developed an innovative split selectable marker system for plant co-transformation, allowing the use of one selectable marker gene to select transgenic events. This method involves constructing two binary vectors, each carrying a subset of genes of interest and a partial fragment of the selectable marker gene, which is connected to a partial intein fragment. Following Agrobacterium-mediated co-transformation, plants harboring both binary vectors are selected using a single antibiotic, such as kanamycin. This split-marker system can be used to co-transform multiple genes into both herbaceous and woody plants, accelerating genetic improvement of polygenic traits or integrative improvement of multiple traits to simultaneously increase crop yield and quality.", "date": "2025-02-19", "issue": "4", "identifier": "https://www.osti.gov/biblio/2538318", "bibliographicCitation": "https://doi.org/10.21769/bioprotoc.5214", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "Arabidopsis", "Intein", "Plant transformation", "Poplar", "Protein splicing", "Selectable marker" ], "topic": [ "Microbiology" ], "journal_name": "Bio-Protocol", "volume": "15", "publisher_information": "Bio-protocol LLC", "country_publication_code": "US", "creator": [ { "name": "Guoliang [Pacific Northwest National Laboratory (PNNL),Richland,WA (United States)] Yuan", "primaryContact": true }, { "name": "Torikul [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000175092411) Islam", "primaryContact": false }, { "name": "Gerald [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000301061289) Tuskan", "primaryContact": false }, { "name": "Xiaohan [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000152074210) Yang", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2538318", "active": false }, { "brc": "CBI", "title": "Suppression of Chorismate Mutase 1 in Hybrid Poplar to Investigate Potential Redundancy in the Supply of Lignin Precursors", "description": "Chorismate is an important branchpoint metabolite in the biosynthesis of lignin and a wide array of metabolites in plants. Chorismate mutase (CM), the enzyme responsible for transforming chorismate into prephenate, is a key regulator of metabolic flux towards the synthesis of aromatic amino acids and onwards to lignin. We examined three CM genes in hybrid poplar (Populus alba \u00d7 grandidentata; P39, abbreviated as Pa\u00d7g) and used RNA interference (RNAi) to suppress the expression of Pa\u00d7gCM1, the most highly expressed isoform found in xylem tissue. Although this strategy was successful in disrupting Pa\u00d7gCM1 transcripts, there was also an unanticipated increase in lignin content, a shift towards guaiacyl lignin units, and more xylem vessels with smaller lumen areas, at least in the most severely affected transgenic line. This was accompanied by compensatory expression of the other two CM isoforms, Pa\u00d7gCM2 and Pa\u00d7gCM3, as well as widespread changes in gene expression and metabolism. This study investigates potential redundancy within the CM gene family in the developing xylem of poplar and highlights the pivotal role of chorismate in plant metabolism, development, and physiology.", "abstract": "Chorismate is an important branchpoint metabolite in the biosynthesis of lignin and a wide array of metabolites in plants. Chorismate mutase (CM), the enzyme responsible for transforming chorismate into prephenate, is a key regulator of metabolic flux towards the synthesis of aromatic amino acids and onwards to lignin. We examined three CM genes in hybrid poplar (Populus alba \u00d7 grandidentata; P39, abbreviated as Pa\u00d7g) and used RNA interference (RNAi) to suppress the expression of Pa\u00d7gCM1, the most highly expressed isoform found in xylem tissue. Although this strategy was successful in disrupting Pa\u00d7gCM1 transcripts, there was also an unanticipated increase in lignin content, a shift towards guaiacyl lignin units, and more xylem vessels with smaller lumen areas, at least in the most severely affected transgenic line. This was accompanied by compensatory expression of the other two CM isoforms, Pa\u00d7gCM2 and Pa\u00d7gCM3, as well as widespread changes in gene expression and metabolism. This study investigates potential redundancy within the CM gene family in the developing xylem of poplar and highlights the pivotal role of chorismate in plant metabolism, development, and physiology.", "date": "2025-03-11", "issue": "3", "identifier": "https://www.osti.gov/biblio/2539836", "bibliographicCitation": "https://doi.org/10.1002/pld3.70053", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "RNAi", "aromatic amino acids", "lignin biosynthesis", "salicylic acid", "shikimate pathway" ], "topic": [ "Microbiology" ], "journal_name": "Plant Direct", "volume": "9", "publisher_information": "Wiley", "country_publication_code": "US", "creator": [ { "name": "Yaseen [University of British Columbia,Vancouver,BC (Canada); University of Ottawa,ON (Canada)] (ORCID:0000000241066159) Mottiar", "primaryContact": true }, { "name": "Timothy J. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000295406622) Tschaplinski", "primaryContact": false }, { "name": "John [University of Wisconsin,Madison,WI (United States); Great Lakes Bioenergy Research Center (GLBRC),Madison,WI (United States)] (ORCID:0000000260934521) Ralph", "primaryContact": false }, { "name": "Shawn D. [University of British Columbia,Vancouver,BC (Canada); Great Lakes Bioenergy Research Center (GLBRC),Madison,WI (United States)] (ORCID:000000020175554X) Mansfield", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2539836", "active": false }, { "brc": "CBI", "title": "Accessing monomers from lignin through carbon\u2013carbon bond cleavage", "description": "Lignin, the heterogeneous aromatic macromolecule found in the cell walls of vascular plants, is an abundant feedstock for the production of biochemicals and biofuels. Here, many valorization schemes rely on lignin depolymerization, with decades of research focused on accessing monomers through C\u2013O bond cleavage, given the abundance of \u03b2\u2013O\u20134 bonds in lignin and the large number of available C\u2013O bond cleavage strategies. Monomer yields are, however, invariably lower than desired, owing to the presence of recalcitrant C\u2013C bonds whose selective cleavage remains a major challenge in catalysis. In this Review, we highlight lignin C\u2013C cleavage reactions, including those of linkages arising from biosynthesis (\u03b2\u20131, \u03b2\u20135, \u03b2\u2013\u03b2 and 5\u20135) and industrial processing (5\u2013CH2\u20135 and \u03b1\u20135). We examine multiple approaches to C\u2013C cleavage, including homogeneous and heterogeneous catalysis, photocatalysis and biocatalysis, to identify promising strategies for further research and provide guidelines for definitive measurements of lignin C\u2013C bond cleavage.", "abstract": "Lignin, the heterogeneous aromatic macromolecule found in the cell walls of vascular plants, is an abundant feedstock for the production of biochemicals and biofuels. Here, many valorization schemes rely on lignin depolymerization, with decades of research focused on accessing monomers through C\u2013O bond cleavage, given the abundance of \u03b2\u2013O\u20134 bonds in lignin and the large number of available C\u2013O bond cleavage strategies. Monomer yields are, however, invariably lower than desired, owing to the presence of recalcitrant C\u2013C bonds whose selective cleavage remains a major challenge in catalysis. In this Review, we highlight lignin C\u2013C cleavage reactions, including those of linkages arising from biosynthesis (\u03b2\u20131, \u03b2\u20135, \u03b2\u2013\u03b2 and 5\u20135) and industrial processing (5\u2013CH2\u20135 and \u03b1\u20135). We examine multiple approaches to C\u2013C cleavage, including homogeneous and heterogeneous catalysis, photocatalysis and biocatalysis, to identify promising strategies for further research and provide guidelines for definitive measurements of lignin C\u2013C bond cleavage.", "date": "2024-10-03", "issue": "11", "identifier": "https://www.osti.gov/biblio/2540082", "bibliographicCitation": "https://doi.org/10.1038/s41570-024-00652-9", "keywords": [ "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "Biocatalysis", "C-C bond cleavage", "Catalysis", "Energy", "Green chemistry", "INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "catalysis", "lignin depolymerization", "lignin valorization" ], "topic": [ "Chemistry" ], "journal_name": "Nature Reviews Chemistry", "volume": "8", "publisher_information": "Springer Nature", "country_publication_code": "US", "creator": [ { "name": "Chad T. [National Renewable Energy Laboratory,Golden,CO (United States)] (ORCID:0000000164364602) Palumbo", "primaryContact": true }, { "name": "Erik T. [National Renewable Energy Laboratory,Golden,CO (United States)] (ORCID:0000000321386259) Ouellette", "primaryContact": false }, { "name": "Jie [Massachusetts Institute of Technology,Cambridge,MA (United States)] (ORCID:0000000291529326) Zhu", "primaryContact": false }, { "name": "Yuriy [Massachusetts Institute of Technology,Cambridge,MA (United States)] (ORCID:0000000200254233) Rom\u00e1n-Leshkov", "primaryContact": false }, { "name": "Shannon S. [University of Wisconsin,Madison,WI (United States)] (ORCID:0000000290007665) Stahl", "primaryContact": false }, { "name": "Gregg T. [National Renewable Energy Laboratory,Golden,CO (United States); Center for Bioenergy Innovation,Oak Ridge,TN (United States)] (ORCID:000000023480212X) Beckham", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Office of Sustainable Transportation. Bioenergy Technologies Office (BETO)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Transportation Office. Bioenergy Technologies Office" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Basic Energy Sciences (BES)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division (CSGB)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2540082", "active": false, "has_related_ids": [ "NREL/JA-2A00-89469" ] }, { "brc": "CBI", "title": "RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species", "description": "We introduce RWRtoolkit, a multiplex generation, exploration, and statistical package built for R and command-line users. RWRtoolkit enables the efficient exploration of large and highly complex biological networks generated from custom experimental data and/or from publicly available datasets, and is species agnostic. A range of functions can be used to find topological distances between biological entities, determine relationships within sets of interest, search for topological context around sets of interest, and statistically evaluate the strength of relationships within and between sets. The command-line interface is designed for parallelization on high-performance cluster systems, which enables high-throughput analysis such as permutation testing. Several tools in the package have also been made available for use in reproducible workflows via the KBase web application.
", "abstract": "We introduce RWRtoolkit, a multiplex generation, exploration, and statistical package built for R and command-line users. RWRtoolkit enables the efficient exploration of large and highly complex biological networks generated from custom experimental data and/or from publicly available datasets, and is species agnostic. A range of functions can be used to find topological distances between biological entities, determine relationships within sets of interest, search for topological context around sets of interest, and statistically evaluate the strength of relationships within and between sets. The command-line interface is designed for parallelization on high-performance cluster systems, which enables high-throughput analysis such as permutation testing. Several tools in the package have also been made available for use in reproducible workflows via the KBase web application.
", "date": "2025-04-23", "identifier": "https://www.osti.gov/biblio/2562699", "bibliographicCitation": "https://doi.org/10.1093/gigascience/giaf028", "topic": [ "Unknown" ], "journal_name": "GigaScience", "volume": "14", "publisher_information": "Oxford University Press", "country_publication_code": "GB", "creator": [ { "name": "David (ORCID:0000000172714676) Kainer", "primaryContact": true }, { "name": "Matthew (ORCID:0000000277506822) Lane", "primaryContact": false }, { "name": "Kyle A. (ORCID:0000000246215598) Sullivan", "primaryContact": false }, { "name": "J. Izaak (ORCID:0000000261145401) Miller", "primaryContact": false }, { "name": "Mikaela (ORCID:0000000306207830) Cashman", "primaryContact": false }, { "name": "Mallory (ORCID:0000000233091813) Morgan", "primaryContact": false }, { "name": "Ashley (ORCID:0000000178095546) Cliff", "primaryContact": false }, { "name": "Jonathon (ORCID:0000000152491946) Romero", "primaryContact": false }, { "name": "Angelica (ORCID:0000000343086302) Walker", "primaryContact": false }, { "name": "D. (ORCID:0000000197427585) Dakota\u00a0Blair", "primaryContact": false }, { "name": "Hari (ORCID:0000000168208789) Chhetri", "primaryContact": false }, { "name": "Yongqin (ORCID:0000000223361680) Wang", "primaryContact": false }, { "name": "Mirko (ORCID:0000000229083183) Pavicic", "primaryContact": false }, { "name": "Anna (ORCID:0000000273765923) Furches", "primaryContact": false }, { "name": "Jaclyn (ORCID:000000027438193X) Noshay", "primaryContact": false }, { "name": "Meghan (ORCID:0000000179694823) Drake", "primaryContact": false }, { "name": "A. J. (ORCID:0000000319829065) Ireland", "primaryContact": false }, { "name": "Ali (ORCID:0000000317101142) Missaoui", "primaryContact": false }, { "name": "Yun (ORCID:0000000285564723) Kang", "primaryContact": false }, { "name": "John C. (ORCID:0000000249301627) Sedbrook", "primaryContact": false }, { "name": "Paramvir (ORCID:0000000158102497) Dehal", "primaryContact": false }, { "name": "Shane (ORCID:000000028440738X) Canon", "primaryContact": false }, { "name": "Daniel (ORCID:0000000298228251) Jacobson", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "U.S. Department of Energy Office of Science" } }, { "fundingOrganization": { "organizationName": "US Department of Energy" } }, { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22), Scientific User Facilities Division (SC-22.3 )" } } ], "dataset_url": "https://www.osti.gov/biblio/2562699", "active": false }, { "brc": "CBI", "title": "Solid-state NMR at natural isotopic abundance for bioenergy applications", "description": "Not Available", "abstract": "Not Available", "date": "2025-04-27", "issue": "1", "identifier": "https://www.osti.gov/biblio/2563006", "bibliographicCitation": "https://doi.org/10.1186/s13068-025-02648-z", "keywords": [ "BIOMASS FUELS", "bioenergy", "biomass", "carbon management", "cellulose", "lignin", "lignocellulose", "magic angle spinning", "natural abundance", "renewable energy", "solid-state nuclear magnetic resonance" ], "topic": [ "Unknown" ], "journal_name": "Biotechnology for Biofuels and Bioproducts", "volume": "18", "publisher_information": "Springer Science + Business Media", "country_publication_code": "GB", "creator": [ { "name": "Bennett Addison", "primaryContact": true }, { "name": "Malitha C. Dickwella Widange", "primaryContact": false }, { "name": "Yunqiao Pu", "primaryContact": false }, { "name": "Arthur J. Ragauskas", "primaryContact": false }, { "name": "Anne E. Harman-Ware", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2563006", "active": false, "has_related_ids": [ "NREL/JA-2800-93171" ] }, { "brc": "CBI", "title": "Crash\u2013and\u2013dash: a new era in tree genome editing", "description": "In less than a decade since the first demonstrations of CRISPR genome editing of agronomic genes in several tree species (Zhou et al., 2015; Jia et al., 2016; Ren et al., 2016), this disruptive technology has been deployed for a growing number of traits in both basic and applied research. The precision and efficiency of CRISPR editing allow for the recovery of null mutants in the first generation (Zhou et al., 2015; Elorriaga et al., 2018; Muhr et al., 2018), which is a significant benefit for perennial trees with long generation times. The stability of editing outcomes over multiple years or clonal propagation cycles (Bewg et al., 2022; Chen et al., 2023; Goralogia et al., 2024) is another key advantage since most woody perennials are vegetatively propagated in commercial operations. However, in many countries, gene-edited trees with stably integrated T-DNA face the same regulatory hurdles as traditional transgenics, slowing field trial characterization and the integration of transgenesis with conventional breeding (Boerjan & Strauss, 2024). In an article recently published in New Phytologist, Hoengenaert et al. (2025; doi: 10.1111/nph.20415) demonstrate transgene-free editing in poplar (Populus tremula \u00d7 alba) that shows promise for wide adoption. The CRISPR-edited, transgene-free canker-resistant citrus (Citrus sinensis) trees (Su et al., 2023) have recently been approved by USDA-APHIS and are exempt from regulation by the US Environmental Protection Agency (EPA) for commercial production. The work by Hoengenaert et al. (2025) suggests a similar path could be followed for purpose-grown plantations for bioenergy, bioproducts, and biomaterials.", "abstract": "In less than a decade since the first demonstrations of CRISPR genome editing of agronomic genes in several tree species (Zhou et al., 2015; Jia et al., 2016; Ren et al., 2016), this disruptive technology has been deployed for a growing number of traits in both basic and applied research. The precision and efficiency of CRISPR editing allow for the recovery of null mutants in the first generation (Zhou et al., 2015; Elorriaga et al., 2018; Muhr et al., 2018), which is a significant benefit for perennial trees with long generation times. The stability of editing outcomes over multiple years or clonal propagation cycles (Bewg et al., 2022; Chen et al., 2023; Goralogia et al., 2024) is another key advantage since most woody perennials are vegetatively propagated in commercial operations. However, in many countries, gene-edited trees with stably integrated T-DNA face the same regulatory hurdles as traditional transgenics, slowing field trial characterization and the integration of transgenesis with conventional breeding (Boerjan & Strauss, 2024). In an article recently published in New Phytologist, Hoengenaert et al. (2025; doi: 10.1111/nph.20415) demonstrate transgene-free editing in poplar (Populus tremula \u00d7 alba) that shows promise for wide adoption. The CRISPR-edited, transgene-free canker-resistant citrus (Citrus sinensis) trees (Su et al., 2023) have recently been approved by USDA-APHIS and are exempt from regulation by the US Environmental Protection Agency (EPA) for commercial production. The work by Hoengenaert et al. (2025) suggests a similar path could be followed for purpose-grown plantations for bioenergy, bioproducts, and biomaterials.", "date": "2025-03-31", "issue": "1", "identifier": "https://www.osti.gov/biblio/2566735", "bibliographicCitation": "https://doi.org/10.1111/nph.70118", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "CRISPR", "Populus", "base editing", "perennial", "transgene-free editing" ], "topic": [ "Microbiology" ], "journal_name": "New Phytologist", "volume": "247", "publisher_information": "Wiley", "country_publication_code": "US", "creator": [ { "name": "Chung\u2010Jui [University of Georgia,Athens,GA (United States)] (ORCID:0000000292827704) Tsai", "primaryContact": true } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2566735", "active": false }, { "brc": "CBI", "title": "Variation in Biomass Yield and Cell Wall Composition in Switchgrass Natural Variants Under Two Nitrogen Regimes", "description": "Switchgrass (Panicum virgatum) is a promising lignocellulosic biofuel crop for which biomass and processing quality are important. Inherent plant variability across genotypes and environments challenges uniformity and product quality. In this study, the impact of nitrogen (N) application on switchgrass yield and quality was examined under field conditions using a highly diverse switchgrass panel over a 4-year period at Knoxville, TN. Overall, biomass production was correlated between low (0 kg of added N/ha) and moderate (135 kg of added N/ha) nitrogen treatments, suggesting that the N impact is largely uniform across the genotypes. Nonetheless, high biomass genotypes were identified with high nitrogen-use efficiency ; biomass was congruent or even higher (up to 9-fold) in the low N treatment. Genotypes were also identified with up to 94% nitrogen-remobilization efficiency. Furthermore, nitrogen application appeared to impact lignin content in whole tillers but was neutral to lignin monomer syringyl-to-guaiacyl (S/G) ratio. The same panel grown under natural conditions in Watkinsville, GA, produced significantly more biomass than the Tennessee panel in the first 3 years, but biomass was similar across both sites and treatments in year 4. Top performing genotypes overlapped between sites by 20-37%. There were low correlations in lignin content in whole tillers across the two field sites, but moderate correlations were observed for S/G ratios. The high yielding genotypes from the low N plot identified in this study can be used in breeding programs and management strategies in switchgrass to evade adverse environmental and economic effects.", "abstract": "Switchgrass (Panicum virgatum) is a promising lignocellulosic biofuel crop for which biomass and processing quality are important. Inherent plant variability across genotypes and environments challenges uniformity and product quality. In this study, the impact of nitrogen (N) application on switchgrass yield and quality was examined under field conditions using a highly diverse switchgrass panel over a 4-year period at Knoxville, TN. Overall, biomass production was correlated between low (0 kg of added N/ha) and moderate (135 kg of added N/ha) nitrogen treatments, suggesting that the N impact is largely uniform across the genotypes. Nonetheless, high biomass genotypes were identified with high nitrogen-use efficiency ; biomass was congruent or even higher (up to 9-fold) in the low N treatment. Genotypes were also identified with up to 94% nitrogen-remobilization efficiency. Furthermore, nitrogen application appeared to impact lignin content in whole tillers but was neutral to lignin monomer syringyl-to-guaiacyl (S/G) ratio. The same panel grown under natural conditions in Watkinsville, GA, produced significantly more biomass than the Tennessee panel in the first 3 years, but biomass was similar across both sites and treatments in year 4. Top performing genotypes overlapped between sites by 20-37%. There were low correlations in lignin content in whole tillers across the two field sites, but moderate correlations were observed for S/G ratios. The high yielding genotypes from the low N plot identified in this study can be used in breeding programs and management strategies in switchgrass to evade adverse environmental and economic effects.", "date": "2025-04-28", "issue": "1", "identifier": "https://www.osti.gov/biblio/2566770", "bibliographicCitation": "https://doi.org/10.1007/s12155-025-10838-8", "keywords": [ "09 BIOMASS FUELS", "BIOMASS FUELS", "cell wall composition", "lignocellulosic biomass", "nitrogen use efficiency", "pyrolysis-molecular beam mass spectrometry", "switchgrass" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "BioEnergy Research", "volume": "18", "country_publication_code": "US", "creator": [ { "name": "Mitra [Oak Ridge National Laboratory; University of Tennessee at Knoxville] Mazarei", "primaryContact": true }, { "name": "Anne [National Renewable Energy Lab.,Golden,CO (United States)] (ORCID:0000000279279424) Harman-Ware", "primaryContact": false }, { "name": "Thomas [Oak Ridge National Laboratory; University of Georgia] Pendergast IV", "primaryContact": false }, { "name": "Vivek [Oak Ridge National Laboratory; University of Tennessee at Knoxville] Shrestha", "primaryContact": false }, { "name": "Yaping [Oak Ridge National Laboratory; University of Tennessee at Knoxville] Xu", "primaryContact": false }, { "name": "Cristiano [Oak Ridge National Laboratory; University of Tennessee at Knoxville] Piasecki", "primaryContact": false }, { "name": "Reginald [Oak Ridge National Laboratory; University of Tennessee at Knoxville] Milwood", "primaryContact": false }, { "name": "Katrien [Oak Ridge National Laboratory; University of Georgia] Devos", "primaryContact": false }, { "name": "C. Neal [Oak Ridge National Laboratory; University of Tennessee at Knoxville] Stewart Jr.", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2566770", "active": false, "has_related_ids": [ "NREL/JA-2800-91809" ] }, { "brc": "CBI", "title": "Structural Characterization and Dynamics of AdhE Ultrastructures from Clostridium thermocellum Show a Containment Strategy for Toxic Intermediates", "description": "Clostridium thermocellum, a cellulolytic thermophilic anaerobe, is considered by many to be a prime candidate for the realization of consolidated bioprocessing (CBP) and is known as an industry standard for biofuel production. C. thermocellum is among the best biomass degraders identified to date in nature and produces ethanol as one of its main products. Many studies have helped increase ethanol titers in this microbe; however, ethanol production using C. thermocellum is still not economically viable. Therefore, a better understanding of its ethanol synthesis pathway is required. The main pathway for ethanol production in C. thermocellum involves the bifunctional aldehyde-alcohol dehydrogenase (AdhE). To better understand the function of the C. thermocellum AdhE, we used cryo-electron microscopy (cryo-EM) to obtain a 3.28 A structure of the AdhE complex. This high-resolution structure, in combination with molecular dynamics simulations, provides insight into the substrate channeling of the toxic intermediate acetaldehyde, indicates the potential role of C. thermocellum AdhE to regulate activity and cofactor pools, and establishes a basis for future engineering studies. The containment strategy found in this enzyme offers a template that could be replicated in other systems where toxic intermediates need to be sequestered to increase the production of valuable biochemicals.", "abstract": "Clostridium thermocellum, a cellulolytic thermophilic anaerobe, is considered by many to be a prime candidate for the realization of consolidated bioprocessing (CBP) and is known as an industry standard for biofuel production. C. thermocellum is among the best biomass degraders identified to date in nature and produces ethanol as one of its main products. Many studies have helped increase ethanol titers in this microbe; however, ethanol production using C. thermocellum is still not economically viable. Therefore, a better understanding of its ethanol synthesis pathway is required. The main pathway for ethanol production in C. thermocellum involves the bifunctional aldehyde-alcohol dehydrogenase (AdhE). To better understand the function of the C. thermocellum AdhE, we used cryo-electron microscopy (cryo-EM) to obtain a 3.28 A structure of the AdhE complex. This high-resolution structure, in combination with molecular dynamics simulations, provides insight into the substrate channeling of the toxic intermediate acetaldehyde, indicates the potential role of C. thermocellum AdhE to regulate activity and cofactor pools, and establishes a basis for future engineering studies. The containment strategy found in this enzyme offers a template that could be replicated in other systems where toxic intermediates need to be sequestered to increase the production of valuable biochemicals.", "date": "2024-05-23", "identifier": "https://www.osti.gov/biblio/2568050", "bibliographicCitation": "https://doi.org/10.7554/eLife.96966.3", "keywords": [ "09 BIOMASS FUELS", "BIOMASS FUELS", "Cryo-EM", "biofuel", "consolidated bio-processing", "ethanol", "molecular dynamics" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "eLife", "volume": "13", "country_publication_code": "US", "creator": [ { "name": "Samantha [National Renewable Energy Lab.,Golden,CO (United States)] Ziegler", "primaryContact": true }, { "name": "Brandon [National Renewable Energy Lab.,Golden,CO (United States)] Knott", "primaryContact": false }, { "name": "Josephine [National Renewable Energy Lab.,Golden,CO (United States)] Gruber", "primaryContact": false }, { "name": "Neal [National Renewable Energy Lab.,Golden,CO (United States)] Hengge", "primaryContact": false }, { "name": "Qi [National Renewable Energy Lab.,Golden,CO (United States)] Xu", "primaryContact": false }, { "name": "Daniel [Dartmouth College] Olson", "primaryContact": false }, { "name": "Eduardo [University of Colorado Anschutz Medical Campus] Romero", "primaryContact": false }, { "name": "Lydia [SLAC National Accelerator Laboratory] Joubert", "primaryContact": false }, { "name": "Yannick [National Renewable Energy Lab.,Golden,CO (United States)] Bomble", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2568050", "active": false, "has_related_ids": [ "NREL/JA-2700-87838" ] }, { "brc": "CBI", "title": "Elucidating the drought-responsive changes in Poplar cuticular waxes: A GWAS analysis of genes involved in fatty acid biosynthesis", "description": "Drought and episodic drought events are major impending impacts of climate change, limiting the productivity of plants and especially trees due to their inherent high transpiration rates. One common mechanism used by plants to cope with drought stress is to change the composition of their leaf cuticular waxes. Cuticular waxes are essential for controlling non-stomatal water loss and are typically composed of a homologous series of very-long-chain fatty acid-derived compounds, as well as flavonoids, tocopherols, triterpenoids, and phytosterols. In this study, we compared the cuticular waxes of 339 natural accessions of Populus trichocarpa (black cottonwood) grown under control and drought conditions in a common garden. A Genome-Wide Association Study (GWAS) was then used to identify candidate genes associated with cuticular wax biosynthesis and/or its regulation. Although no major differences were observed in total wax load when subject to drought conditions, the amounts of the individual wax constituents were indeed responsive to drought. Specifically, changes in alkenes, alcohols, esters, and aldehydes were evident, and suggest that they contribute to the drought response/tolerance in poplar. GWAS uncovered several genes linked to fatty acid biosynthesis, including CER1, CER3, CER4, FATB, FAB1, FAR3, FAR4, KCS, and a homolog of SOH1, as well as other candidate genes that may be involved in coordinating the drought responses in poplar trees. Our findings provide new evidence that genotype-specific shifts in wax composition, rather than total wax accumulation, contribute to drought adaptation in poplar. Additionally, we show that genetic variation in key wax biosynthetic genes drives cuticular wax plasticity in P. trichocarpa under drought, identifying putative molecular targets for improving stress resilience in trees. This study expands our understanding of the adaptative mechanisms of the cuticle and their potential for enhancing drought tolerance in poplar species.", "abstract": "Drought and episodic drought events are major impending impacts of climate change, limiting the productivity of plants and especially trees due to their inherent high transpiration rates. One common mechanism used by plants to cope with drought stress is to change the composition of their leaf cuticular waxes. Cuticular waxes are essential for controlling non-stomatal water loss and are typically composed of a homologous series of very-long-chain fatty acid-derived compounds, as well as flavonoids, tocopherols, triterpenoids, and phytosterols. In this study, we compared the cuticular waxes of 339 natural accessions of Populus trichocarpa (black cottonwood) grown under control and drought conditions in a common garden. A Genome-Wide Association Study (GWAS) was then used to identify candidate genes associated with cuticular wax biosynthesis and/or its regulation. Although no major differences were observed in total wax load when subject to drought conditions, the amounts of the individual wax constituents were indeed responsive to drought. Specifically, changes in alkenes, alcohols, esters, and aldehydes were evident, and suggest that they contribute to the drought response/tolerance in poplar. GWAS uncovered several genes linked to fatty acid biosynthesis, including CER1, CER3, CER4, FATB, FAB1, FAR3, FAR4, KCS, and a homolog of SOH1, as well as other candidate genes that may be involved in coordinating the drought responses in poplar trees. Our findings provide new evidence that genotype-specific shifts in wax composition, rather than total wax accumulation, contribute to drought adaptation in poplar. Additionally, we show that genetic variation in key wax biosynthetic genes drives cuticular wax plasticity in P. trichocarpa under drought, identifying putative molecular targets for improving stress resilience in trees. This study expands our understanding of the adaptative mechanisms of the cuticle and their potential for enhancing drought tolerance in poplar species.", "date": "2025-05-13", "issue": "13", "identifier": "https://www.osti.gov/biblio/2569829", "bibliographicCitation": "https://doi.org/10.1093/treephys/tpaf060", "keywords": [ "Alkanes", "Alkenes", "Drought stress", "Leaf Waxes", "Populus trichocarpa" ], "topic": [ "Unknown" ], "journal_name": "Tree Physiology (Online)", "volume": "45", "publisher_information": "Oxford University Press", "country_publication_code": "US", "creator": [ { "name": "Melike [University of British Columbia,Vancouver,BC (Canada)] Karaca-Bulut", "primaryContact": true }, { "name": "Eliana [University of Toronto Scarborough,Toronto,ON (Canada)] Gonzales-Vigil", "primaryContact": false }, { "name": "Wellington [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Muchero", "primaryContact": false }, { "name": "Shawn D. [University of British Columbia,Vancouver,BC (Canada)] Mansfield", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2569829", "active": false }, { "brc": "CBI", "title": "A framework for challenges and solutions in biodesign research", "description": "The bioeconomy represents an advanced economic paradigm that builds upon previous agricultural, industrial, and digital economic models. It seeks to tackle critical global challenges such as resource scarcity, escalating healthcare demands, and environmental degradation. At the heart of the bioeconomy is biomanufacturing, which uses natural or engineered enzymes or cell factories built from \u200bbiological components like promoters, terminators, regulatory sequences, reporters, and functional genes into various chassis hosts (including animal, microbial, plant, and de novo systems) to create products such as food, energy, medicine, materials, chemicals, and engineered tissue/organs. An enabler of biomanufacturing is biodesign \u2013 also known as biosystems design and closely related to synthetic biology or engineering biology. This interdisciplinary field aims to understand and predictably modify existing life forms or create entirely new biological entities/systems using rational engineering strategies and automated design tools. Through these capabilities, biodesign supports the discovery, optimization, and creation of efficient platforms for biomanufacturing.", "abstract": "The bioeconomy represents an advanced economic paradigm that builds upon previous agricultural, industrial, and digital economic models. It seeks to tackle critical global challenges such as resource scarcity, escalating healthcare demands, and environmental degradation. At the heart of the bioeconomy is biomanufacturing, which uses natural or engineered enzymes or cell factories built from \u200bbiological components like promoters, terminators, regulatory sequences, reporters, and functional genes into various chassis hosts (including animal, microbial, plant, and de novo systems) to create products such as food, energy, medicine, materials, chemicals, and engineered tissue/organs. An enabler of biomanufacturing is biodesign \u2013 also known as biosystems design and closely related to synthetic biology or engineering biology. This interdisciplinary field aims to understand and predictably modify existing life forms or create entirely new biological entities/systems using rational engineering strategies and automated design tools. Through these capabilities, biodesign supports the discovery, optimization, and creation of efficient platforms for biomanufacturing.", "date": "2025-06-03", "issue": "3", "identifier": "https://www.osti.gov/biblio/2573188", "bibliographicCitation": "https://doi.org/10.1016/j.bidere.2025.100029", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "BioDesign Research", "volume": "7", "publisher_information": "AAAS", "country_publication_code": "US", "creator": [ { "name": "Xiaohan [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000152074210) Yang", "primaryContact": true }, { "name": "Zhihua [Washington State University,Pullman,WA (United States)] Jiang", "primaryContact": false }, { "name": "Shihui [Hubei University,Wuhan (China)] Yang", "primaryContact": false }, { "name": "Zong-Ming [Nanjing Agricultural University (China)] Cheng", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDA" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2573188", "active": false }, { "brc": "CBI", "title": "\u03b3-Aminobutyric acid modulates terpene biosynthesis through the ATG8a-mediated pathway", "description": "Terpenes play crucial roles in plant growth, development, and stress responses. The biosynthesis of terpenes is influenced by abiotic stress factors, such as drought, temperature, or light. Here, however, the molecular network underlying how terpenes are regulated in response to environmental stimuli remains largely unknown. Here, we identified the autophagy protein SgATG8a as a key mediator of GABA-regulated terpene production and drought tolerance in Sindora glabra. SgATG8a, evolutionarily related to the animal GABA receptor-associated protein (GABARAP) subfamily, localizes in both the nucleus and cytoplasm. Exogenous GABA treatment not only increased the expression level of terpene synthase genes (SgTPSs) but also led to enhanced accumulation of six main terpene components in Sindora glabra. In addition, GABA alleviated the photosynthesis damage and enhanced leaf biomass under drought conditions. Consistently, overexpression of SgATG8a in Arabidopsis increased terpene synthase gene (SgTPS) expression, leading to the enhanced production of four major terpenes and improved the tolerance of transgenic plants to drought stress by regulating reactive oxygen species (ROS) scavenging systems. Moreover, the transcription factors SgWRKY13 and SgERF4 were identified as interacting partners of SgATG8a, activating SgTPS3 expression. Lectin receptor-like kinase (LecRK1) is involved in the GABA-mediated pathway by interacting with the SgWRKY13/SgERF4-SgATG8a proteins, and the LecRK1-SgWRKY13/SgERF4 phosphorylation module fine-tunes the transcription of the downstream SgTPS3 gene. Taken together, these findings reveal a novel role for GABA in regulating terpene biosynthesis and drought tolerance, providing insights into the molecular mechanism underlying GABA-mediated terpene production.", "abstract": "Terpenes play crucial roles in plant growth, development, and stress responses. The biosynthesis of terpenes is influenced by abiotic stress factors, such as drought, temperature, or light. Here, however, the molecular network underlying how terpenes are regulated in response to environmental stimuli remains largely unknown. Here, we identified the autophagy protein SgATG8a as a key mediator of GABA-regulated terpene production and drought tolerance in Sindora glabra. SgATG8a, evolutionarily related to the animal GABA receptor-associated protein (GABARAP) subfamily, localizes in both the nucleus and cytoplasm. Exogenous GABA treatment not only increased the expression level of terpene synthase genes (SgTPSs) but also led to enhanced accumulation of six main terpene components in Sindora glabra. In addition, GABA alleviated the photosynthesis damage and enhanced leaf biomass under drought conditions. Consistently, overexpression of SgATG8a in Arabidopsis increased terpene synthase gene (SgTPS) expression, leading to the enhanced production of four major terpenes and improved the tolerance of transgenic plants to drought stress by regulating reactive oxygen species (ROS) scavenging systems. Moreover, the transcription factors SgWRKY13 and SgERF4 were identified as interacting partners of SgATG8a, activating SgTPS3 expression. Lectin receptor-like kinase (LecRK1) is involved in the GABA-mediated pathway by interacting with the SgWRKY13/SgERF4-SgATG8a proteins, and the LecRK1-SgWRKY13/SgERF4 phosphorylation module fine-tunes the transcription of the downstream SgTPS3 gene. Taken together, these findings reveal a novel role for GABA in regulating terpene biosynthesis and drought tolerance, providing insights into the molecular mechanism underlying GABA-mediated terpene production.", "date": "2025-05-26", "issue": "4", "identifier": "https://www.osti.gov/biblio/2573555", "bibliographicCitation": "https://doi.org/10.1111/tpj.70232", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "GABA", "Sesquiterpene biosynthesis", "Sindora glabra", "autophagy protein", "terpene synthase" ], "topic": [ "Microbiology" ], "journal_name": "The Plant Journal", "volume": "122", "publisher_information": "Society for Experimental Biology", "country_publication_code": "US", "creator": [ { "name": "Niu [Chinese Academy of Forestry,Guangzhou (China)] (ORCID:0000000238412815) Yu", "primaryContact": true }, { "name": "Jinchang [Chinese Academy of Forestry,Guangzhou (China)] Yang", "primaryContact": false }, { "name": "Shengqing [Chinese Academy of Forestry,Beijing (China)] Shi", "primaryContact": false }, { "name": "Tao [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000293820731) Yao", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Natural Science Foundation of China" } }, { "fundingOrganization": { "organizationName": "Natural Science Foundation of Guangdong Province" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2573555", "active": false }, { "brc": "CBI", "title": "Through the lens of bioenergy crops: advances, bottlenecks, and promises of plant engineering", "description": "Advances in engineering of bioenergy crops were driven over the past years by adapting technological breakthroughs and accelerating conventional applications but also exposed intriguing challenges. New tools revealed rich interconnectivity in the exponentially growing and dynamic 'big' omics data' of metabolomes, transcriptomes, and genomes at previously inaccessible magnitude (global, cross-species, meta-) and resolution (single cell). Insights enabled fresh hypotheses and stimulated disciplines such as functional genomics with discovery of broad regulatory networks and their determinants, that is, DNA parts, including promoters, regulatory elements, and transcription factors. Their rational design, assembly into increasingly complex blueprints, and installation into diverse chassis is an existing frontier that may benefit from emerging technologies to address bottlenecks. Interweaving nature-inspired to fully synthetic parts has already allowed building of fine-tuned regulatory circuits, or new-to-nature metabolic routes insulated from the biological context of the chassis species. Similarly, developments and the evolving need for unifying principles in plant transformation and species-agnostic technologies highlight future opportunities for engineering the next generation of bioenergy plants.", "abstract": "Advances in engineering of bioenergy crops were driven over the past years by adapting technological breakthroughs and accelerating conventional applications but also exposed intriguing challenges. New tools revealed rich interconnectivity in the exponentially growing and dynamic 'big' omics data' of metabolomes, transcriptomes, and genomes at previously inaccessible magnitude (global, cross-species, meta-) and resolution (single cell). Insights enabled fresh hypotheses and stimulated disciplines such as functional genomics with discovery of broad regulatory networks and their determinants, that is, DNA parts, including promoters, regulatory elements, and transcription factors. Their rational design, assembly into increasingly complex blueprints, and installation into diverse chassis is an existing frontier that may benefit from emerging technologies to address bottlenecks. Interweaving nature-inspired to fully synthetic parts has already allowed building of fine-tuned regulatory circuits, or new-to-nature metabolic routes insulated from the biological context of the chassis species. Similarly, developments and the evolving need for unifying principles in plant transformation and species-agnostic technologies highlight future opportunities for engineering the next generation of bioenergy plants.", "date": "2025-07-16", "issue": "2", "identifier": "https://www.osti.gov/biblio/2574029", "bibliographicCitation": "https://doi.org/10.1111/tpj.70294", "keywords": [ "60 APPLIED LIFE SCIENCES", "ATAC-seq (transposase accessible chromatin sequencing)", "DAP-seq (DNA-affinity purification and sequencing)", "bioenergy crops", "cis-regulatory elements", "modified/synthetic promoters", "multi-part constructs" ], "topic": [ "Plant Biology" ], "journal_name": "The Plant Journal", "volume": "123", "publisher_information": "Society for Experimental Biology", "country_publication_code": "US", "creator": [ { "name": "Angel [Michigan State University,East Lansing,MI (United States)] Indibi", "primaryContact": true }, { "name": "Pengfei [Michigan State University,East Lansing,MI (United States)] Cao", "primaryContact": false }, { "name": "Federica [Michigan State University,East Lansing,MI (United States)] Brandizzi", "primaryContact": false }, { "name": "Jenny [Joint BioEnergy Institute,Emeryville,CA (United States); Lawrence Berkeley National Laboratory (LBNL),Berkeley,CA (United States); University of Adelaide (Australia)] Mortimer", "primaryContact": false }, { "name": "Kankshita [HudsonAlpha Institute for Biotechnology,Huntsville,AL (United States); Center for Advanced Bioenergy and Bioproducts Innovation,Urbana,IL (United States)] Swaminatha", "primaryContact": false }, { "name": "Chung-Jui [University of Georgia,Athens,GA (United States)] Tsai", "primaryContact": false }, { "name": "Bjoern [Michigan State University,East Lansing,MI (United States)] Hamberger", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Institutes of Health (NIH)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2574029", "active": false }, { "brc": "CBI", "title": "A distinct class of ferredoxin:NADP+ oxidoreductase enzymes driving thermophilic ethanol production", "description": "Biofuel production from lignocellulosic biomass offers a transformative solution to reduce global fossil fuel dependency. Certain thermophilic anaerobes, including Clostridium thermocellum, show promise for renewable ethanol production due to their ability to break down plant material at high temperatures. However, achieving commercially viable ethanol yields has proven challenging despite extensive engineering efforts. Here, we characterized 27 ferredoxin:NADP+ oxidoreductase (Fnor) enzymes for their enzyme activity, nicotinamide cofactor specificity, thermotolerance, and functional expression in C. thermocellum. We identified a subset of 10 of these enzymes as a novel class of Fnor enzymes suited for metabolic pathways aimed at high-titer ethanol production. When expressed in engineered C. thermocellum, these enzymes increased ethanol production up to 2.2-fold. These findings establish a novel ethanol pathway and provide insights into physiological roles and biotechnological applications of this new class of Fnor enzymes.", "abstract": "Biofuel production from lignocellulosic biomass offers a transformative solution to reduce global fossil fuel dependency. Certain thermophilic anaerobes, including Clostridium thermocellum, show promise for renewable ethanol production due to their ability to break down plant material at high temperatures. However, achieving commercially viable ethanol yields has proven challenging despite extensive engineering efforts. Here, we characterized 27 ferredoxin:NADP+ oxidoreductase (Fnor) enzymes for their enzyme activity, nicotinamide cofactor specificity, thermotolerance, and functional expression in C. thermocellum. We identified a subset of 10 of these enzymes as a novel class of Fnor enzymes suited for metabolic pathways aimed at high-titer ethanol production. When expressed in engineered C. thermocellum, these enzymes increased ethanol production up to 2.2-fold. These findings establish a novel ethanol pathway and provide insights into physiological roles and biotechnological applications of this new class of Fnor enzymes.", "date": "2025-05-20", "issue": "7", "identifier": "https://www.osti.gov/biblio/2574685", "bibliographicCitation": "https://doi.org/10.1016/j.jbc.2025.110263", "keywords": [ "09 BIOMASS FUELS", "FNOR", "FNR", "biofuel", "enzyme", "ferredoxin", "metabolic engineering", "reductase" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Journal of Biological Chemistry", "volume": "301", "publisher_information": "American Society for Biochemistry and Molecular Biology", "country_publication_code": "US", "creator": [ { "name": "Shu [Dartmouth College,Hanover,NH (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] (ORCID:0000000263125957) Huang", "primaryContact": true }, { "name": "Syed Muhammad [National Renewable Energy Laboratory (NREL),Golden,CO (United States)] (ORCID:000000022416016X) Saad Imran", "primaryContact": false }, { "name": "Anthony A. [Dartmouth College,Hanover,NH (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] Lanahan", "primaryContact": false }, { "name": "Sarah K. [Dartmouth College,Hanover,NH (United States)] Hammer", "primaryContact": false }, { "name": "Carolyn E. [National Renewable Energy Laboratory (NREL),Golden,CO (United States)] (ORCID:0000000315954483) Lubner", "primaryContact": false }, { "name": "Lee R. [Dartmouth College,Hanover,NH (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] Lynd", "primaryContact": false }, { "name": "Daniel G. [Dartmouth College,Hanover,NH (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] (ORCID:0000000153936302) Olson", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF)" } } ], "dataset_url": "https://www.osti.gov/biblio/2574685", "active": false, "has_related_ids": [ "NREL/JA--2700-93966" ] }, { "brc": "CBI", "title": "Drop-in sustainable aviation fuels enabled by feedstock-agnostic lignin deoxygenation", "description": "Current sustainable aviation fuels (SAFs) require blending with petroleum-derived fuels due to incomplete hydrocarbon distributions, most notably a lack of aromatics. Lignin, the most abundant renewable source of aromatics, is a promising feedstock for addressing this limitation. Here, we demonstrate a sequential reductive catalytic fractionation and continuous hydrodeoxygenation process that converts multiple woody feedstocks into aromatic hydrocarbons at up to 93% of the theoretical carbon yield. Blending these products with commercial SAFs produces drop-in compatible fuels with elastomer swell performances equivalent to conventional aviation fuels. The process is adaptable across multiple biomass sources, yielding aromatic hydrocarbons with consistent enthalpic efficiencies and fuel properties. These findings establish a scalable route to 100% drop-in SAFs, leveraging lignin-derived aromatics within the existing biofuels infrastructure.", "abstract": "Current sustainable aviation fuels (SAFs) require blending with petroleum-derived fuels due to incomplete hydrocarbon distributions, most notably a lack of aromatics. Lignin, the most abundant renewable source of aromatics, is a promising feedstock for addressing this limitation. Here, we demonstrate a sequential reductive catalytic fractionation and continuous hydrodeoxygenation process that converts multiple woody feedstocks into aromatic hydrocarbons at up to 93% of the theoretical carbon yield. Blending these products with commercial SAFs produces drop-in compatible fuels with elastomer swell performances equivalent to conventional aviation fuels. The process is adaptable across multiple biomass sources, yielding aromatic hydrocarbons with consistent enthalpic efficiencies and fuel properties. These findings establish a scalable route to 100% drop-in SAFs, leveraging lignin-derived aromatics within the existing biofuels infrastructure.", "date": "2025-07-06", "issue": "7", "identifier": "https://www.osti.gov/biblio/2574735", "bibliographicCitation": "https://doi.org/10.1016/j.xcrp.2025.102687", "keywords": [ "09 BIOMASS FUELS", "biofuels", "biorefining", "feedstock agnostic", "hydrodeoxygenation", "lignin valorization", "reductive catalytic fractionation lignocellulose", "sustainable aviation fuels" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Cell Reports Physical Science", "volume": "6", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Matthew S. [Massachusetts Inst. of Technology (MIT),Cambridge,MA (United States)] Webber", "primaryContact": true }, { "name": "Zhibin [Washington State Univ.,Pullman,WA (United States)] Yang", "primaryContact": false }, { "name": "David C. [Washington State Univ.,Pullman,WA (United States)] Bell", "primaryContact": false }, { "name": "David G. [National Renewable Energy Laboratory (NREL),Golden,CO (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] (ORCID:0000000342964855) Brandner", "primaryContact": false }, { "name": "Jeremy R. [National Renewable Energy Laboratory (NREL),Golden,CO (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] Bussard", "primaryContact": false }, { "name": "Jamison [Massachusetts Inst. of Technology (MIT),Cambridge,MA (United States)] Watson", "primaryContact": false }, { "name": "Michael L. [National Renewable Energy Laboratory (NREL),Golden,CO (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] (ORCID:0000000263417183) Stone", "primaryContact": false }, { "name": "Xianyuan [Massachusetts Inst. of Technology (MIT),Cambridge,MA (United States)] Wu", "primaryContact": false }, { "name": "Quinn S. [National Renewable Energy Laboratory (NREL),Golden,CO (United States)] Neuendorf", "primaryContact": false }, { "name": "Logan C. [National Renewable Energy Laboratory (NREL),Golden,CO (United States)] Myers", "primaryContact": false }, { "name": "Joshua S. [Washington State Univ.,Pullman,WA (United States); Pacific Northwest National Laboratory (PNNL),Richland,WA (United States)] Heyne", "primaryContact": false }, { "name": "Gregg T. [National Renewable Energy Laboratory (NREL),Golden,CO (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] (ORCID:000000023480212X) Beckham", "primaryContact": false }, { "name": "Yuriy [Massachusetts Inst. of Technology (MIT),Cambridge,MA (United States)] (ORCID:0000000200254233) Rom\u00e1n-Leshkov", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Office of Sustainable Transportation. Bioenergy Technologies Office (BETO)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2574735", "active": false, "has_related_ids": [ "NREL/JA--2A00-93478" ] }, { "brc": "CBI", "title": "Enhancing anaerobic digestion of lignocellulosic biomass by mechanical cotreatment", "description": "Abstract Background\nThe aim of this study was to increase the accessibility and accelerate the breakdown of lignocellulosic biomass to methane in an anaerobic fermentation system by mechanicalcotreatment: milling during fermentation, as an alternative to conventionalpretreatment prior to biological deconstruction. Effluent from a mesophilic anaerobic digester running with unpretreated senescent switchgrass as the predominant carbon source was collected and subjected to ball milling for 0.5, 2, 5 and 10 min. Following this, a batch fermentation test was conducted with this material in triplicate for an additional 18 days with unmilled effluent as the \u2018status quo\u2019 control.
\nResults\nThe results indicate 0.5 \u2013 10 min of cotreatment increased sugar solubilization by 5\u2013 13% when compared to the unmilled control, with greater solubilization correlated with increased milling duration. Biogas concentrations ranged from 44% to 55.5% methane with the balance carbon dioxide. The total biogas production was statistically higher than the unmilled control for all treatments with 2 or more minutes of milling (\u03b1\u2009=\u20090.1). Cotreatment also decreased mean particle size. Energy consumption measurements of a lab-scale mill indicate that longer durations of milling offer diminishing benefits with respect to additional methane production.
\nConclusions\nCotreatment in anaerobic digestion systems, as demonstrated in this study, provides an alternative approach to conventional pretreatments to increase biogas production from lignocellulosic grassy material.
", "abstract": "Abstract Background\nThe aim of this study was to increase the accessibility and accelerate the breakdown of lignocellulosic biomass to methane in an anaerobic fermentation system by mechanicalcotreatment: milling during fermentation, as an alternative to conventionalpretreatment prior to biological deconstruction. Effluent from a mesophilic anaerobic digester running with unpretreated senescent switchgrass as the predominant carbon source was collected and subjected to ball milling for 0.5, 2, 5 and 10 min. Following this, a batch fermentation test was conducted with this material in triplicate for an additional 18 days with unmilled effluent as the \u2018status quo\u2019 control.
\nResults\nThe results indicate 0.5 \u2013 10 min of cotreatment increased sugar solubilization by 5\u2013 13% when compared to the unmilled control, with greater solubilization correlated with increased milling duration. Biogas concentrations ranged from 44% to 55.5% methane with the balance carbon dioxide. The total biogas production was statistically higher than the unmilled control for all treatments with 2 or more minutes of milling (\u03b1\u2009=\u20090.1). Cotreatment also decreased mean particle size. Energy consumption measurements of a lab-scale mill indicate that longer durations of milling offer diminishing benefits with respect to additional methane production.
\nConclusions\nCotreatment in anaerobic digestion systems, as demonstrated in this study, provides an alternative approach to conventional pretreatments to increase biogas production from lignocellulosic grassy material.
", "date": "2024-06-02", "issue": "1", "identifier": "https://www.osti.gov/biblio/2582853", "bibliographicCitation": "https://doi.org/10.1186/s13068-024-02521-5", "keywords": [ "Biotechnology & Applied Microbiology", "Energy & Fuels" ], "topic": [ "Unknown" ], "journal_name": "Biotechnology for Biofuels and Bioproducts", "volume": "17", "publisher_information": "BioMed Central", "country_publication_code": "US", "creator": [ { "name": "Anahita Bharadwaj", "primaryContact": true }, { "name": "Evert Holwerda", "primaryContact": false }, { "name": "John Regan", "primaryContact": false }, { "name": "Lee Lynd", "primaryContact": false }, { "name": "Tom Richard", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/2582853", "active": false }, { "brc": "CBI", "title": "Complete biosynthesis of salicylic acid from phenylalanine in plants", "description": "Salicylic acid (SA) is a pivotal phytohormone for plant responses to biotic and abiotic stresses. Plants have evolved two pathways to produce SA: the isochorismate synthase and phenylalanine ammonia lyase (PAL) pathways. Whereas the isochorismate synthase pathway has been fully identified, the PAL pathway remains incomplete. Here we report the full characterization of the PAL pathway for SA biosynthesis via functional analysis of rice (Oryza sativa) SA-DEFICIENT GENE 1 (OSD1) to OSD4. The cinnamoyl-coenzyme A (CoA) ligase OSD1 catalyses the conversion of trans-cinnamic acid to cinnamoyl-CoA, which is subsequently transformed to benzoyl-CoA via the \u03b2-oxidative pathway in peroxisomes. The resulting benzoyl-CoA is further converted to benzyl benzoate by the peroxisomal benzoyltransferase OSD2. Benzyl benzoate is subsequently hydroxylated to benzyl salicylate by the endoplasmic reticulum membrane-resident cytochrome P450 OSD3, which is ultimately hydrolysed to salicylic acid by the cytoplasmic carboxylesterase OSD4. Evolutionary analyses reveal that the PAL pathway was first assembled before the divergence of gymnosperms and has been conserved in most seed plants. Activation of the PAL pathway in rice significantly enhances salicylic acid levels and plant immunity. Completion of the PAL pathway provides critical insights into the primary salicylic acid biosynthetic pathway across plant species and offers a precise target for modulating crop immunity.", "abstract": "Salicylic acid (SA) is a pivotal phytohormone for plant responses to biotic and abiotic stresses. Plants have evolved two pathways to produce SA: the isochorismate synthase and phenylalanine ammonia lyase (PAL) pathways. Whereas the isochorismate synthase pathway has been fully identified, the PAL pathway remains incomplete. Here we report the full characterization of the PAL pathway for SA biosynthesis via functional analysis of rice (Oryza sativa) SA-DEFICIENT GENE 1 (OSD1) to OSD4. The cinnamoyl-coenzyme A (CoA) ligase OSD1 catalyses the conversion of trans-cinnamic acid to cinnamoyl-CoA, which is subsequently transformed to benzoyl-CoA via the \u03b2-oxidative pathway in peroxisomes. The resulting benzoyl-CoA is further converted to benzyl benzoate by the peroxisomal benzoyltransferase OSD2. Benzyl benzoate is subsequently hydroxylated to benzyl salicylate by the endoplasmic reticulum membrane-resident cytochrome P450 OSD3, which is ultimately hydrolysed to salicylic acid by the cytoplasmic carboxylesterase OSD4. Evolutionary analyses reveal that the PAL pathway was first assembled before the divergence of gymnosperms and has been conserved in most seed plants. Activation of the PAL pathway in rice significantly enhances salicylic acid levels and plant immunity. Completion of the PAL pathway provides critical insights into the primary salicylic acid biosynthetic pathway across plant species and offers a precise target for modulating crop immunity.", "date": "2025-07-22", "issue": "8079", "identifier": "https://www.osti.gov/biblio/2583882", "bibliographicCitation": "https://doi.org/10.1038/s41586-025-09175-9", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES" ], "topic": [ "Microbiology" ], "journal_name": "Nature (London)", "volume": "645", "publisher_information": "Nature Publishing Group", "country_publication_code": "US", "creator": [ { "name": "Bao [Zhejiang Normal University,Jinhua (China)] (ORCID:0009000989391020) Zhu", "primaryContact": true }, { "name": "Yanjun [Zhejiang Normal University,Jinhua (China)] (ORCID:000000027475103X) Zhang", "primaryContact": false }, { "name": "Rong [Zhejiang Normal University,Jinhua (China)] Gao", "primaryContact": false }, { "name": "Zhihua [Zhejiang Normal University,Jinhua (China)] (ORCID:0000000228957256) Wu", "primaryContact": false }, { "name": "Wei [Zhejiang Normal University,Jinhua (China)] (ORCID:0000000181785433) Zhang", "primaryContact": false }, { "name": "Chao [Zhejiang Normal University,Jinhua (China)] Zhang", "primaryContact": false }, { "name": "Penghong [Zhejiang Normal University,Jinhua (China)] Zhang", "primaryContact": false }, { "name": "Can [Zhejiang Normal University,Jinhua (China)] Ye", "primaryContact": false }, { "name": "Linbo [Zhejiang Normal University,Jinhua (China)] Yao", "primaryContact": false }, { "name": "Ying [Zhejiang Normal University,Jinhua (China)] Jin", "primaryContact": false }, { "name": "Hui [Zhejiang Normal University,Jinhua (China)] Mao", "primaryContact": false }, { "name": "Peiyao [Zhejiang Normal University,Jinhua (China)] Tou", "primaryContact": false }, { "name": "Peng [Zhejiang Normal University,Jinhua (China)] Huang", "primaryContact": false }, { "name": "Jiangzhe [Zhejiang Normal University,Jinhua (China)] Zhao", "primaryContact": false }, { "name": "Qiao [Chinese Academy of Sciences (CAS),Shenzhen (China)] (ORCID:0000000209584300) Zhao", "primaryContact": false }, { "name": "Chang-Jun [Brookhaven National Laboratory (BNL),Upton,NY (United States)] (ORCID:0000000161898756) Liu", "primaryContact": false }, { "name": "Kewei [Zhejiang Normal University,Jinhua (China)] (ORCID:0000000208441121) Zhang", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division (CSGB)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2583882", "active": false, "has_related_ids": [ "BNL--228539-2025-JAAM" ] }, { "brc": "CBI", "title": "Stomatal Parameters in a Changing Environment", "description": "Here, we recommend that stomatal slope parameters (g1) be inferred by inversion so that variations in g1 may be attributed to variations physiological and environmental conditions. Understanding g1 will advance predictions of plant gas exchange and performance under global climate.", "abstract": "Here, we recommend that stomatal slope parameters (g1) be inferred by inversion so that variations in g1 may be attributed to variations physiological and environmental conditions. Understanding g1 will advance predictions of plant gas exchange and performance under global climate.", "date": "2024-12-11", "issue": "5", "identifier": "https://www.osti.gov/biblio/2584450", "bibliographicCitation": "https://doi.org/10.1111/pce.15293", "keywords": [ "Stomatal conductance modeling", "marginal carbon profit of water", "photosynthesis", "stomatal optimization", "transpiration", "water-use efficiency" ], "topic": [ "Unknown" ], "journal_name": "Plant, Cell and Environment", "volume": "48", "publisher_information": "Wiley", "country_publication_code": "US", "creator": [ { "name": "Aaron [University of Minnesota,Twin Cities,Minneapolis,MN (United States)] (ORCID:0000000331012701) Potkay", "primaryContact": true }, { "name": "Brandon [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000316304271) Sloan", "primaryContact": false }, { "name": "Xue [University of Minnesota,Twin Cities,Minneapolis,MN (United States)] (ORCID:0000000313813118) Feng", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Science Foundation Faculty Early Career Development (CAREER)" } }, { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/2584450", "active": false }, { "brc": "CBI", "title": "Scale sensitivity of ethanol production via consolidated bioprocessing with consideration of feedstock cost", "description": "We examine feedstock cost and minimum selling price for ethanol production from corn stover as a function of scale, stover yield, participation rate, and price incentives for two conversion technologies: a conventional base case featuring thermochemical pretreatment with added cellulase, and an advanced case featuring consolidated bioprocessing with cotreatment (C-CBP). Delivered feedstock cost ranged from $\\$85$ Mg\u22121 at small (10 million gallons year\u22121 or ~38 million L year\u22121) scale with high yield and participation rates to $\\$124$ Mg\u22121 at large scale (60 million gallons year\u22121 or 227 million L year\u22121) and low yield and participation rates. The minimum ethanol selling price (MESP) was approximately twofold lower for the advanced case compared with the base case. The payback period was several times lower for the advanced case compared with the base case, with increasing disparity at smaller scales, and was highly sensitive to ethanol price supports. For both C-CBP and the conventional processing paradigm, MESP decreased with increasing scale, indicating that the cost penalty due to higher feedstock transport distances was more than outweighed by lower capital costs. However, the cost penalty for operation at small scale, expressed in $ gallon\u22121 ethanol, is lower for C-CBP than for the conventional paradigm by roughly twofold. Particularly for initial applications of C-CBP, we speculate that this cost penalty will likely be modest compared with the anticipated benefits of small-scale operation such as increased opportunity to use existing infrastructure, easier plant siting and supply chain establishment, and lower total investment required.", "abstract": "We examine feedstock cost and minimum selling price for ethanol production from corn stover as a function of scale, stover yield, participation rate, and price incentives for two conversion technologies: a conventional base case featuring thermochemical pretreatment with added cellulase, and an advanced case featuring consolidated bioprocessing with cotreatment (C-CBP). Delivered feedstock cost ranged from $\\$85$ Mg\u22121 at small (10 million gallons year\u22121 or ~38 million L year\u22121) scale with high yield and participation rates to $\\$124$ Mg\u22121 at large scale (60 million gallons year\u22121 or 227 million L year\u22121) and low yield and participation rates. The minimum ethanol selling price (MESP) was approximately twofold lower for the advanced case compared with the base case. The payback period was several times lower for the advanced case compared with the base case, with increasing disparity at smaller scales, and was highly sensitive to ethanol price supports. For both C-CBP and the conventional processing paradigm, MESP decreased with increasing scale, indicating that the cost penalty due to higher feedstock transport distances was more than outweighed by lower capital costs. However, the cost penalty for operation at small scale, expressed in $ gallon\u22121 ethanol, is lower for C-CBP than for the conventional paradigm by roughly twofold. Particularly for initial applications of C-CBP, we speculate that this cost penalty will likely be modest compared with the anticipated benefits of small-scale operation such as increased opportunity to use existing infrastructure, easier plant siting and supply chain establishment, and lower total investment required.", "date": "2024-10-23", "issue": "1", "identifier": "https://www.osti.gov/biblio/2584451", "bibliographicCitation": "https://doi.org/10.1002/bbb.2691", "keywords": [ "biorefinery scale", "cellulosic ethanol", "consolidated bioprocessing", "delivered feedstock cost" ], "topic": [ "Unknown" ], "journal_name": "Biofuels, Bioproducts & Biorefining", "volume": "19", "publisher_information": "Wiley", "country_publication_code": "US", "creator": [ { "name": "Madeline [Dartmouth College,Hanover,NH (United States)] (ORCID:0009000879264928) Hoey", "primaryContact": true }, { "name": "Robin [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000202171124) Clark", "primaryContact": false }, { "name": "Erin [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000215018647) Webb", "primaryContact": false }, { "name": "Lee [Dartmouth College,Hanover,NH (United States)] Lynd", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2584451", "active": false }, { "brc": "CBI", "title": "Leveraging hyperspectral phenotyping for accurate, non-destructive prediction of metabolite profiles in poplar under drought stress", "description": "Accurately predicting drought tolerance in woody perennial bioenergy crops is critical for sustainable biomass production under fluctuating precipitation. Hyperspectral imaging (HSI) in the visible-near-infrared (VNIR) and shortwave-infrared (SWIR) ranges offers a promising approach for predicting plant biochemical traits, yet its application in metabolite profiling remains underexplored. We integrated VNIR+SWIR HSI with untargeted metabolomics to investigate drought-induced metabolic shifts in Populus leaves from eight Populus genotypes. Metabolite profiling identified 127 compounds, with 73 showing significant drought responses spanning amino acids (AA), carbohydrates (CHO), phenolic glycosides (PG), organic acids (OA), fatty acids and alcohols (FA), terpenes (T), phenolic metabolites (P), and unclassified metabolites. Spectral analysis revealed consistently higher reflectance across VNIR and SWIR wavelengths in drought-stressed plants, corresponding with increased accumulation of AA and reduced CHO and PG levels. Least absolute shrinkage and selection operator (LASSO) regression modeling identified robust spectral predictors of metabolite concentrations, associating VNIR wavelengths (500\u2013700\u202fnm) predominantly with AA and P, whereas SWIR wavelengths (1680\u20131700\u202fnm) reliably predicted CHO, OA, and T. Several stable spectral-metabolite associations persisted across the two watering regimes (drought vs. well-watered), highlighting their potential as spectral biomarkers for non-destructive stress monitoring. Minimal genotype-specific variation suggests that observed spectral and metabolic responses were driven primarily by environmental factors, likely reflecting limited genetic diversity among the commercial Populus genotypes examined. This work establishes VNIR+SWIR hyperspectral imaging as a powerful, non-destructive phenotyping tool for precision monitoring and targeted improvement of drought resilience in bioenergy crops.", "abstract": "Accurately predicting drought tolerance in woody perennial bioenergy crops is critical for sustainable biomass production under fluctuating precipitation. Hyperspectral imaging (HSI) in the visible-near-infrared (VNIR) and shortwave-infrared (SWIR) ranges offers a promising approach for predicting plant biochemical traits, yet its application in metabolite profiling remains underexplored. We integrated VNIR+SWIR HSI with untargeted metabolomics to investigate drought-induced metabolic shifts in Populus leaves from eight Populus genotypes. Metabolite profiling identified 127 compounds, with 73 showing significant drought responses spanning amino acids (AA), carbohydrates (CHO), phenolic glycosides (PG), organic acids (OA), fatty acids and alcohols (FA), terpenes (T), phenolic metabolites (P), and unclassified metabolites. Spectral analysis revealed consistently higher reflectance across VNIR and SWIR wavelengths in drought-stressed plants, corresponding with increased accumulation of AA and reduced CHO and PG levels. Least absolute shrinkage and selection operator (LASSO) regression modeling identified robust spectral predictors of metabolite concentrations, associating VNIR wavelengths (500\u2013700\u202fnm) predominantly with AA and P, whereas SWIR wavelengths (1680\u20131700\u202fnm) reliably predicted CHO, OA, and T. Several stable spectral-metabolite associations persisted across the two watering regimes (drought vs. well-watered), highlighting their potential as spectral biomarkers for non-destructive stress monitoring. Minimal genotype-specific variation suggests that observed spectral and metabolic responses were driven primarily by environmental factors, likely reflecting limited genetic diversity among the commercial Populus genotypes examined. This work establishes VNIR+SWIR hyperspectral imaging as a powerful, non-destructive phenotyping tool for precision monitoring and targeted improvement of drought resilience in bioenergy crops.", "date": "2025-08-13", "identifier": "https://www.osti.gov/biblio/2584490", "bibliographicCitation": "https://doi.org/10.1016/j.envexpbot.2025.106218", "keywords": [ "Biochemical trait prediction", "Drought stress", "Hyperspectral imaging", "LASSO regression", "Non-destructive phenotyping", "Populus", "SWIR", "Stress biomarkers", "Untargeted metabolomics", "VNIR" ], "topic": [ "Unknown" ], "journal_name": "Environmental and Experimental Botany", "volume": "237", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Mengjun [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000263232664) Shu", "primaryContact": true }, { "name": "Antoine L. [University of Tuscia,Viterbo (Italy)] (ORCID:0000000339980694) Harfouche", "primaryContact": false }, { "name": "Martin [Photon Systems Instruments (PSI),Prumyslova (Czech Republic)] Trt\u00edlek", "primaryContact": false }, { "name": "Kl\u00e1ra [Photon Systems Instruments (PSI),Prumyslova (Czech Republic)] Panzarov\u00e1", "primaryContact": false }, { "name": "Omar F. [Franco Alasia Vivai,Savigliano (Italy)] Alasia", "primaryContact": false }, { "name": "John H. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000280927433) Lagergren", "primaryContact": false }, { "name": "Audrey [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Labb\u00e9", "primaryContact": false }, { "name": "Nancy L. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000302907987) Engle", "primaryContact": false }, { "name": "Miranda M. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000248391309) Clark", "primaryContact": false }, { "name": "Jin-Gui [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000217524201) Chen", "primaryContact": false }, { "name": "Gerald A. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000301061289) Tuskan", "primaryContact": false }, { "name": "Timothy J. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000295406622) Tschaplinski", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2584490", "active": false }, { "brc": "CBI", "title": "Borate-assisted alkaline extraction of hemicellulose from switchgrass with enhanced structural stability and purity", "description": "Valorization of non-cellulosic polysaccharides is crucial for enhancing the economic competitiveness of biorefinery processes. In this study, a mixture of boric acid and sodium hydroxide was employed to efficiently extract hemicellulose from holocellulose switchgrass. Borate-assisted alkaline extraction resulted in a higher xylan content (59.5 %) compared to conventional alkaline extraction. Here, the hemicellulose fractions derived from the borate-alkaline treatment exhibited a higher molecular weight (Mw = 51.2 kDa) and a relatively lower degree of polydispersity (1.28), indicating improved structural stability. The presence of borate had a protective effect against chain scission, preserving glucuronic acid residues and increasing galactose content. Additionally, borate improved hemicellulose purity, with up to 74.1 % of the extracted hemicellulose being suitable for further enzymatic applications. Extended extraction time further enhanced hemicellulose recovery, reaching 97.9 % under NaOH/boric acid conditions while maintaining structural integrity, as confirmed by SEM, FTIR and 2D HSQC NMR analyses. These findings provide insights into the role of borate in optimizing hemicellulose extraction and improving its potential for bioconversion processes.", "abstract": "Valorization of non-cellulosic polysaccharides is crucial for enhancing the economic competitiveness of biorefinery processes. In this study, a mixture of boric acid and sodium hydroxide was employed to efficiently extract hemicellulose from holocellulose switchgrass. Borate-assisted alkaline extraction resulted in a higher xylan content (59.5 %) compared to conventional alkaline extraction. Here, the hemicellulose fractions derived from the borate-alkaline treatment exhibited a higher molecular weight (Mw = 51.2 kDa) and a relatively lower degree of polydispersity (1.28), indicating improved structural stability. The presence of borate had a protective effect against chain scission, preserving glucuronic acid residues and increasing galactose content. Additionally, borate improved hemicellulose purity, with up to 74.1 % of the extracted hemicellulose being suitable for further enzymatic applications. Extended extraction time further enhanced hemicellulose recovery, reaching 97.9 % under NaOH/boric acid conditions while maintaining structural integrity, as confirmed by SEM, FTIR and 2D HSQC NMR analyses. These findings provide insights into the role of borate in optimizing hemicellulose extraction and improving its potential for bioconversion processes.", "date": "2025-07-18", "issue": "2", "identifier": "https://www.osti.gov/biblio/2586823", "bibliographicCitation": "https://doi.org/10.1016/j.ijbiomac.2025.146180", "keywords": [ "Borate alkaline", "Glucuronic acids", "Hemicellulose extraction", "PAA delignification", "Switchgrass solid residue" ], "topic": [ "Unknown" ], "journal_name": "International Journal of Biological Macromolecules", "volume": "321", "publisher_information": "Elsevier BV", "country_publication_code": "US", "creator": [ { "name": "Jinhua [Chinese Academy of Sciences (CAS),Tianjin (China)] Ding", "primaryContact": true }, { "name": "Shu [Donghua University,Shanghai (China)] Yang", "primaryContact": false }, { "name": "Xianzhi [University of Tennessee,Knoxville,TN (United States)] Meng", "primaryContact": false }, { "name": "Chang Geun [State University of New York (SUNY),Syracuse,NY (United States). College of Environmental Science and Forestry] Yoo", "primaryContact": false }, { "name": "Luna [University of Tennessee,Knoxville,TN (United States)] Liang", "primaryContact": false }, { "name": "Naijia [University of Tennessee,Knoxville,TN (United States)] Hao", "primaryContact": false }, { "name": "Yunqiao [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000325541447) Pu", "primaryContact": false }, { "name": "Chongwen [Donghua University,Shanghai (China)] Yu", "primaryContact": false }, { "name": "Arthur J. [University of Tennessee,Knoxville,TN (United States)] Ragauskas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2586823", "active": false }, { "brc": "CBI", "title": "Multigene engineering in plants: Technologies, applications, and future prospects", "description": "The emerging bioeconomy presents a promising solution to both economic and environmental challenges. Within the bioeconomy, plants serve as a renewable, sustainable, and cost-effective source of foods, fuels, chemicals, and materials. However, traditional breeding and single-gene engineering approaches fall short in addressing complex traits (e.g., drought tolerance, disease resistance, yield, nutrient use efficiency) which are controlled by multiple genes. The complexity of plant biology often necessitates the use of multigene engineering (MGE), which involves simultaneous ectopic expression, up/down-regulation, or editing of multiple genes, to enhance plant traits relevant to the bioeconomy. These genes may be associated with distinct traits or function as components of specific metabolic and regulatory pathways. This review summarizes current technologies for MGE within the synthetic biology-driven Design-Build-Test-Learn (DBTL) framework, detailing its four key stages: Design \u2013 gene construct development; Build \u2013 DNA assembly and plant transformation; Test \u2013 the molecular, biochemical, and physiological characterization of engineered plants; and Learn \u2013 computational modeling to refine, multiplex and iterate the process. Despite good progress in the applications of MGE in biofortification, metabolic engineering, and stress resilience, challenges remain in construct stability, coordinated gene expression, and regulatory predictability. We identified optimization paths and future directions to accelerate MGE deployment in sustainable agriculture, with possible societal benefits including reduced production costs, increased yield, and improved food and nutritional security.", "abstract": "The emerging bioeconomy presents a promising solution to both economic and environmental challenges. Within the bioeconomy, plants serve as a renewable, sustainable, and cost-effective source of foods, fuels, chemicals, and materials. However, traditional breeding and single-gene engineering approaches fall short in addressing complex traits (e.g., drought tolerance, disease resistance, yield, nutrient use efficiency) which are controlled by multiple genes. The complexity of plant biology often necessitates the use of multigene engineering (MGE), which involves simultaneous ectopic expression, up/down-regulation, or editing of multiple genes, to enhance plant traits relevant to the bioeconomy. These genes may be associated with distinct traits or function as components of specific metabolic and regulatory pathways. This review summarizes current technologies for MGE within the synthetic biology-driven Design-Build-Test-Learn (DBTL) framework, detailing its four key stages: Design \u2013 gene construct development; Build \u2013 DNA assembly and plant transformation; Test \u2013 the molecular, biochemical, and physiological characterization of engineered plants; and Learn \u2013 computational modeling to refine, multiplex and iterate the process. Despite good progress in the applications of MGE in biofortification, metabolic engineering, and stress resilience, challenges remain in construct stability, coordinated gene expression, and regulatory predictability. We identified optimization paths and future directions to accelerate MGE deployment in sustainable agriculture, with possible societal benefits including reduced production costs, increased yield, and improved food and nutritional security.", "date": "2025-08-26", "identifier": "https://www.osti.gov/biblio/2586915", "bibliographicCitation": "https://doi.org/10.1016/j.biotechadv.2025.108697", "keywords": [ "AI-aided plant engineering", "Crop biofactories", "DBTL cycle", "Gene stacking", "Metabolic pathway engineering", "Synthetic biology" ], "topic": [ "Unknown" ], "journal_name": "Biotechnology Advances", "volume": "85", "publisher_information": "Elsevier BV", "country_publication_code": "US", "creator": [ { "name": "Ruchika [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000341031973) Rajput", "primaryContact": true }, { "name": "Brandon A. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] (ORCID:0000000264758000) Boone", "primaryContact": false }, { "name": "Rushil [University of Maryland,College Park,MD (United States)] Mandlik", "primaryContact": false }, { "name": "Md Torikul [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Islam", "primaryContact": false }, { "name": "Yiping [University of Maryland,College Park,MD (United States); University of Maryland,Rockville,MD (United States)] Qi", "primaryContact": false }, { "name": "Jack [North Carolina State University,Raleigh,NC (United States)] Wang", "primaryContact": false }, { "name": "Rodolphe [North Carolina State University,Raleigh,NC (United States)] Barrangou", "primaryContact": false }, { "name": "Rosangela [North Carolina State University,Raleigh,NC (United States)] Sozzani", "primaryContact": false }, { "name": "Carrie A. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000342012926) Eckert", "primaryContact": false }, { "name": "Gerald A. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000301061289) Tuskan", "primaryContact": false }, { "name": "Jin-Gui [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000217524201) Chen", "primaryContact": false }, { "name": "Xiaohan [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000152074210) Yang", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "Foundation for Food & Agriculture Research (FFAR)" } }, { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "USDA" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2586915", "active": false }, { "brc": "CBI", "title": "Cleavage of C-O and C-C Bonds in Lignin-Derived Compounds to Produce Aromatics Using Molybdenum-Containing MFI Zeolites", "description": "Lignin, the most abundant source of renewable arenes, is a viable feedstock for the production of aromatic compounds. However, the prevalence of resilient C-C bonded oligomeric fragments in lignin-derived streams can compromise monomer yields during reductive catalytic fractionation (RCF). To address this issue, we developed a bifunctional molybdenum-containing MFI (Mo/H-MFI) zeolite catalyst capable of cleaving both C-O and C-C bonds in lignin-derived molecules to produce aromatic monomers. Using propylguaiacol as a model compound, we demonstrated the importance of proximity between metallic molybdenum carbide sites and the Bronsted acid sites in the zeolite in achieving high carbon yields (~80%) of benzene, toluene, propylbenzene, and phenol while maintaining catalyst stability (>98% stable conversion for 20 h). A reaction network involving both C-O and C-C bond cleavage pathways was proposed based on kinetic studies using key intermediates as feeds. Finally, we successfully depolymerized partially deoxygenated lignin oil obtained from the RCF of poplar using a continuous, two-pass catalytic process. This work highlights the potential of the bifunctional Mo/H-MFI catalyst in upgrading complex lignin feedstocks and provides a methodological approach for converting lignin-derived compounds into platform aromatic chemicals.", "abstract": "Lignin, the most abundant source of renewable arenes, is a viable feedstock for the production of aromatic compounds. However, the prevalence of resilient C-C bonded oligomeric fragments in lignin-derived streams can compromise monomer yields during reductive catalytic fractionation (RCF). To address this issue, we developed a bifunctional molybdenum-containing MFI (Mo/H-MFI) zeolite catalyst capable of cleaving both C-O and C-C bonds in lignin-derived molecules to produce aromatic monomers. Using propylguaiacol as a model compound, we demonstrated the importance of proximity between metallic molybdenum carbide sites and the Bronsted acid sites in the zeolite in achieving high carbon yields (~80%) of benzene, toluene, propylbenzene, and phenol while maintaining catalyst stability (>98% stable conversion for 20 h). A reaction network involving both C-O and C-C bond cleavage pathways was proposed based on kinetic studies using key intermediates as feeds. Finally, we successfully depolymerized partially deoxygenated lignin oil obtained from the RCF of poplar using a continuous, two-pass catalytic process. This work highlights the potential of the bifunctional Mo/H-MFI catalyst in upgrading complex lignin feedstocks and provides a methodological approach for converting lignin-derived compounds into platform aromatic chemicals.", "date": "2025-08-10", "issue": "17", "identifier": "https://www.osti.gov/biblio/2587290", "bibliographicCitation": "https://doi.org/10.1021/acscatal.5c02259", "keywords": [ "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "C-C bond cleavage", "hydrodeoxygenation", "lignin", "molybdenum-containing MFI zeolite", "platform aromatics" ], "topic": [ "Chemistry" ], "journal_name": "ACS Catalysis", "volume": "15", "country_publication_code": "US", "creator": [ { "name": "Jie [Massachusetts Institute of Technology] Zhu", "primaryContact": true }, { "name": "Matthew [Massachusetts Institute of Technology] Webber", "primaryContact": false }, { "name": "Jamison [Massachusetts Institute of Technology] Watson", "primaryContact": false }, { "name": "Gregg [National Renewable Energy Lab.,Golden,CO (United States)] (ORCID:000000023480212X) Beckham", "primaryContact": false }, { "name": "Yuriy [Massachusetts Institute of Technology] Roman-Leshkov", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Transportation Office. Bioenergy Technologies Office" } } ], "dataset_url": "https://www.osti.gov/biblio/2587290", "active": false, "has_related_ids": [ "NREL/JA-2A00-91434" ] }, { "brc": "CBI", "title": "Elucidation of a bacterial pathway for catabolism of the \u03b2\u2013\u03b2-linked dilignol pinoresinol", "description": "Monolignol-derived dimers containing \u03b2\u2013\u03b2 linkages are synthesized by vascular plants and can be released during lignin depolymerization. In this work, we isolated a bacterium, Novosphingobium rhizosphaerae LY, that grows with the \u03b2\u2013\u03b2 lignan (+)-pinoresinol as a sole growth substrate. Sequence analysis suggested that this strain encodes a broad range of pathways for assimilation of aromatic monomers as well as one enzyme implicated in pinoresinol catabolism but lacks other known pathways for aromatic dimer catabolism. We constructed a genome-wide barcoded transposon library and identified genes required for pinoresinol catabolism. Using feeding studies, compound isolation, targeted synthesis, and analysis of purified enzymes, we elucidated the biochemical intermediates and reaction pathway involved in pinoresinol catabolism. We demonstrated that the first enzymatic reaction is the reductive cleavage of a furan ring in (\u00b1)-pinoresinol with retention of configuration to yield lariciresinol. We additionally confirmed that the final pathway enzyme, PinU, is related to lignostilbene dioxygenases and oxidatively cleaves a diguaiacylbutadiene intermediate to yield vanillin and coniferaldehyde. Finally, based on the enzyme characterization, we demonstrated that the strain can grow with a second \u03b2\u2013\u03b2 lignan, (\u2013)-syringaresinol, as a sole growth substrate. In combination, these results demonstrate a new biocatalytic route for transforming a widely occurring group of plant phenylpropanoid natural products.", "abstract": "Monolignol-derived dimers containing \u03b2\u2013\u03b2 linkages are synthesized by vascular plants and can be released during lignin depolymerization. In this work, we isolated a bacterium, Novosphingobium rhizosphaerae LY, that grows with the \u03b2\u2013\u03b2 lignan (+)-pinoresinol as a sole growth substrate. Sequence analysis suggested that this strain encodes a broad range of pathways for assimilation of aromatic monomers as well as one enzyme implicated in pinoresinol catabolism but lacks other known pathways for aromatic dimer catabolism. We constructed a genome-wide barcoded transposon library and identified genes required for pinoresinol catabolism. Using feeding studies, compound isolation, targeted synthesis, and analysis of purified enzymes, we elucidated the biochemical intermediates and reaction pathway involved in pinoresinol catabolism. We demonstrated that the first enzymatic reaction is the reductive cleavage of a furan ring in (\u00b1)-pinoresinol with retention of configuration to yield lariciresinol. We additionally confirmed that the final pathway enzyme, PinU, is related to lignostilbene dioxygenases and oxidatively cleaves a diguaiacylbutadiene intermediate to yield vanillin and coniferaldehyde. Finally, based on the enzyme characterization, we demonstrated that the strain can grow with a second \u03b2\u2013\u03b2 lignan, (\u2013)-syringaresinol, as a sole growth substrate. In combination, these results demonstrate a new biocatalytic route for transforming a widely occurring group of plant phenylpropanoid natural products.", "date": "2025-09-23", "issue": "11", "identifier": "https://www.osti.gov/biblio/2589405", "bibliographicCitation": "https://doi.org/10.1128/mbio.02010-25", "keywords": [ "Novosphingobium", "lignin", "pinoresinol" ], "topic": [ "Unknown" ], "journal_name": "mBio (Online)", "volume": "16", "publisher_information": "American Society for Microbiology (ASM)", "country_publication_code": "US", "creator": [ { "name": "Marco N. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000292907296) Allemann", "primaryContact": true }, { "name": "Fachuang [University of Wisconsin,Madison,WI (United States)] (ORCID:0000000282309129) Lu", "primaryContact": false }, { "name": "Gerald N. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); Oregon State University,Corvallis,OR (United States)] (ORCID:0000000255067419) Presley", "primaryContact": false }, { "name": "Hannah R. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0009000831173541) Valentino", "primaryContact": false }, { "name": "Diana L. [Washington State University,Pullman,WA (United States)] Bedgar", "primaryContact": false }, { "name": "Michael A. [Washington State University,Pullman,WA (United States)] (ORCID:0009000686382151) Costa", "primaryContact": false }, { "name": "Syed G. A. [Washington State University,Pullman,WA (United States)] (ORCID:000000029907416X) Moinuddin", "primaryContact": false }, { "name": "Christopher C. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000223763057) Azubuike", "primaryContact": false }, { "name": "Delyana P. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000279197883) Vasileva", "primaryContact": false }, { "name": "Dawn Marie [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000243072560) Klingeman", "primaryContact": false }, { "name": "Leah H. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0009000692820832) Hochanadel", "primaryContact": false }, { "name": "Alexander R. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000154924864) Fisch", "primaryContact": false }, { "name": "Brian C. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000197541687) Sanders", "primaryContact": false }, { "name": "Lindsay D. [University of British Columbia,Vancouver,BC (Canada)] (ORCID:0000000267748158) Eltis", "primaryContact": false }, { "name": "Richard J. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000185510138) Giannone", "primaryContact": false }, { "name": "Laurence B. [Washington State University,Pullman,WA (United States)] (ORCID:0000000232486485) Davin", "primaryContact": false }, { "name": "Norman G. [Washington State University,Pullman,WA (United States)] (ORCID:000000015742032X) Lewis", "primaryContact": false }, { "name": "John [University of Wisconsin,Madison,WI (United States)] (ORCID:0000000260934521) Ralph", "primaryContact": false }, { "name": "James G. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000280525688) Elkins", "primaryContact": false }, { "name": "Joshua K. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000323028180) Michener", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/2589405", "active": false }, { "brc": "CBI", "title": "Engineering 2\u2010Pyrone\u20104,6\u2010Dicarboxylic Acid Production Reveals Metabolic Plasticity of Poplar", "description": "Woody biomass is a promising source of fermentable sugars for biofuels and bio-based chemicals, but its industrial use is limited by the costly biorefinery process. A viable strategy to reduce costs involves enhancing both biomass processability and the generation of high-value co-products. Here, we report the implementation of a synthetic metabolic pathway in Populus tremula \u00d7 P. alba to produce 2-pyrone-4,6-dicarboxylic acid (PDC), a key building block for biodegradable plastics and high-performance materials. This artificial pathway\u2014comprising microbial genes AroG, QsuB, PmdA, PmdB, and PmdC\u2014enabled de novo PDC production in the stems of transgenic poplar. Pathway expression also induced substantial metabolic reprogramming and altered cell wall composition. These include the hyperaccumulation of simple phenolics like protocatechuic acid (PCA) and vanillic acid (VA), alongside reduced levels of p-hydroxybenzoic acid. A large portion of VA was ester-linked to cell wall lignin, while PCA was incorporated into the lignin backbone, forming novel benzodioxane units; concurrently, lignin in transgenic plants exhibited a drastic reduction in guaiacyl- and syringyl-units, with a notable increase in p-hydroxyphenyl-units. Hemicellulose content, particularly xylan, was also significantly increased. Moreover, expression of the PDC-pathway led to the formation of novel VA-derived suberin aromatics, enhancing suberization in bark and roots and improving salt stress tolerance. These changes led to improved saccharification efficiency, with up to 25% more glucose and 2.5 times xylose released from woody biomass. These results demonstrate the metabolic flexibility of poplar and highlight its potential for engineering cost-effective, stress-resilient bioenergy crops with enhanced biorefinery traits.", "abstract": "Woody biomass is a promising source of fermentable sugars for biofuels and bio-based chemicals, but its industrial use is limited by the costly biorefinery process. A viable strategy to reduce costs involves enhancing both biomass processability and the generation of high-value co-products. Here, we report the implementation of a synthetic metabolic pathway in Populus tremula \u00d7 P. alba to produce 2-pyrone-4,6-dicarboxylic acid (PDC), a key building block for biodegradable plastics and high-performance materials. This artificial pathway\u2014comprising microbial genes AroG, QsuB, PmdA, PmdB, and PmdC\u2014enabled de novo PDC production in the stems of transgenic poplar. Pathway expression also induced substantial metabolic reprogramming and altered cell wall composition. These include the hyperaccumulation of simple phenolics like protocatechuic acid (PCA) and vanillic acid (VA), alongside reduced levels of p-hydroxybenzoic acid. A large portion of VA was ester-linked to cell wall lignin, while PCA was incorporated into the lignin backbone, forming novel benzodioxane units; concurrently, lignin in transgenic plants exhibited a drastic reduction in guaiacyl- and syringyl-units, with a notable increase in p-hydroxyphenyl-units. Hemicellulose content, particularly xylan, was also significantly increased. Moreover, expression of the PDC-pathway led to the formation of novel VA-derived suberin aromatics, enhancing suberization in bark and roots and improving salt stress tolerance. These changes led to improved saccharification efficiency, with up to 25% more glucose and 2.5 times xylose released from woody biomass. These results demonstrate the metabolic flexibility of poplar and highlight its potential for engineering cost-effective, stress-resilient bioenergy crops with enhanced biorefinery traits.", "date": "2025-10-22", "issue": "3", "identifier": "https://www.osti.gov/biblio/3001648", "bibliographicCitation": "https://doi.org/10.1111/pbi.70414", "keywords": [ "2-pyrone-4", "59 BASIC BIOLOGICAL SCIENCES", "6-dicarboxylic acid", "lignin", "poplar", "protocatechuic acid", "saccharification", "suberin", "vanillic acid", "wall-bound phenolics" ], "topic": [ "Microbiology" ], "journal_name": "Plant Biotechnology Journal", "volume": "24", "publisher_information": "Wiley", "country_publication_code": "US", "creator": [ { "name": "Nidhi [Brookhaven National Laboratory (BNL),Upton,NY (United States); Joint BioEnergy Institute (JBEI),Emeryville,CA (United States)] (ORCID:0000000311485579) Dwivedi", "primaryContact": true }, { "name": "Pingping [Kyoto Univ. (Japan)] (ORCID:0000000247316331) Ji", "primaryContact": false }, { "name": "Yang [Joint BioEnergy Institute (JBEI),Emeryville,CA (United States); Lawrence Berkeley National Laboratory (LBNL),Berkeley,CA (United States)] Tian", "primaryContact": false }, { "name": "Dasmeet [Brookhaven National Laboratory (BNL),Upton,NY (United States)] Kaur", "primaryContact": false }, { "name": "Vijaya Kumar Reddy [Brookhaven National Laboratory (BNL),Upton,NY (United States)] Vulavala", "primaryContact": false }, { "name": "Yuki [Kyoto Univ. (Japan)] (ORCID:0000000275787392) Tobimatsu", "primaryContact": false }, { "name": "Aymerick [Joint BioEnergy Institute (JBEI),Emeryville,CA (United States); Lawrence Berkeley National Laboratory (LBNL),Berkeley,CA (United States)] (ORCID:0000000213876111) Eudes", "primaryContact": false }, { "name": "Chang\u2010Jun [Brookhaven National Laboratory (BNL),Upton,NY (United States); Joint BioEnergy Institute (JBEI),Emeryville,CA (United States)] (ORCID:0000000161898756) Liu", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "Japan Society for the Promotion of Science (JSPS)" } }, { "fundingOrganization": { "organizationName": "US Department of Energy" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division (CSGB)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23), Biological Systems Science Division (SC-23.2 )" } } ], "dataset_url": "https://www.osti.gov/biblio/3001648", "active": false, "has_related_ids": [ "BNL--229124-2025-JAAM" ] }, { "brc": "CBI", "title": "Drought adaptation index (DAI) based on BLUP as a selection approach for drought-resilient switchgrass germplasm", "description": "This study introduces a Drought Adaptation Index (DAI), derived from Best Linear Unbiased Prediction (BLUP), as a method to assess drought resilience in switchgrass (Panicum virgatum L.). A panel of 404 genotypes was evaluated under drought-stressed (CV) and well-watered (UC) conditions over four consecutive years (2019\u20132022). BLUP-estimated biomass yields were used to calculate the DAI, which enabled classification of genotypes into four adaptation groups: very well-adapted, well-adapted, adapted, and unadapted. The DAI was compared with conventional drought tolerance indices, including the Stress Susceptibility Index (SSI), Stress Tolerance Index (STI), Geometric Mean Productivity (GMP), and Yield Stability Index (YSI). Correlation analyses demonstrated strong agreement between DAI and these indices, supporting its validity and consistency. Biplot analyses using the Genotype plus Genotype-by-Environment Interaction (GGE) and Additive Main Effects and Multiplicative Interaction (AMMI) models revealed significant genotype-by-environment interactions (GEI) and identified J222.A, J463.A, and J295.A. A as high-performing genotypes, with J222.A exhibiting greater yield stability across treatments and years. Additionally, DAI isoline curves provided a graphical representation of differential genotype performance under drought and control conditions. These visualizations aided in distinguishing genotypes with stable and superior biomass yield across contrasting environments. Overall, the BLUP-based DAI is a robust and practical selection tool that improves the accuracy of identifying drought-resilient, high-yielding switchgrass genotypes. Its integration into breeding programs offers a comprehensive framework for improving biomass productivity and stress adaptation under variable climatic conditions. The application of DAI supports the development of climate-resilient cultivars and contributes to sustainable bioenergy and forage production systems.", "abstract": "This study introduces a Drought Adaptation Index (DAI), derived from Best Linear Unbiased Prediction (BLUP), as a method to assess drought resilience in switchgrass (Panicum virgatum L.). A panel of 404 genotypes was evaluated under drought-stressed (CV) and well-watered (UC) conditions over four consecutive years (2019\u20132022). BLUP-estimated biomass yields were used to calculate the DAI, which enabled classification of genotypes into four adaptation groups: very well-adapted, well-adapted, adapted, and unadapted. The DAI was compared with conventional drought tolerance indices, including the Stress Susceptibility Index (SSI), Stress Tolerance Index (STI), Geometric Mean Productivity (GMP), and Yield Stability Index (YSI). Correlation analyses demonstrated strong agreement between DAI and these indices, supporting its validity and consistency. Biplot analyses using the Genotype plus Genotype-by-Environment Interaction (GGE) and Additive Main Effects and Multiplicative Interaction (AMMI) models revealed significant genotype-by-environment interactions (GEI) and identified J222.A, J463.A, and J295.A. A as high-performing genotypes, with J222.A exhibiting greater yield stability across treatments and years. Additionally, DAI isoline curves provided a graphical representation of differential genotype performance under drought and control conditions. These visualizations aided in distinguishing genotypes with stable and superior biomass yield across contrasting environments. Overall, the BLUP-based DAI is a robust and practical selection tool that improves the accuracy of identifying drought-resilient, high-yielding switchgrass genotypes. Its integration into breeding programs offers a comprehensive framework for improving biomass productivity and stress adaptation under variable climatic conditions. The application of DAI supports the development of climate-resilient cultivars and contributes to sustainable bioenergy and forage production systems.", "date": "2025-08-24", "identifier": "https://www.osti.gov/biblio/3002096", "bibliographicCitation": "https://doi.org/10.3389/fgene.2025.1626083", "keywords": [ "BLUP", "bioenergy", "biomass", "drought adaptation", "drought adaptation index", "stress tolerance indices", "switchgrass", "yield stability" ], "topic": [ "Unknown" ], "journal_name": "Frontiers in Genetics", "volume": "16", "publisher_information": "Frontiers Media S.A.", "country_publication_code": "US", "creator": [ { "name": "Shiva Om [Univ. of Georgia,Athens,GA (United States)] Makaju", "primaryContact": true }, { "name": "Hari Bahadur [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000168208789) Chhetri", "primaryContact": false }, { "name": "Chanaka Roshan [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000295613955) Abeyratne", "primaryContact": false }, { "name": "Mirko [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000229083183) Pavicic", "primaryContact": false }, { "name": "Hari [Agriculture and Agri-Food Canada (AAFC),Lethbridge,AB (Canada). Lethbridge Research and Development Centre (RDC)] Poudel", "primaryContact": false }, { "name": "Jazib Ali [Univ. of Georgia,Athens,GA (United States)] Irfan", "primaryContact": false }, { "name": "Anita [Univ. of Georgia,Athens,GA (United States)] Giabardo", "primaryContact": false }, { "name": "Katrien M. [Univ. of Georgia,Athens,GA (United States)] Devos", "primaryContact": false }, { "name": "Daniel [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000298228251) Jacobson", "primaryContact": false }, { "name": "Ali Mekki [Univ. of Georgia,Athens,GA (United States)] Missaoui", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3002096", "active": false }, { "brc": "CBI", "title": "Transcription factor binding divergence drives transcriptional and phenotypic variation in maize", "description": "Regulatory elements are essential components of plant genomes that have shaped the domestication and improvement of modern crops. However, their identity, function and diversity remain poorly characterized, limiting our ability to harness their full power for agricultural advances using induced or natural variation. Here, in this study, we mapped transcription factor (TF) binding for 200 TFs from 30 families in two distinct maize inbred lines historically used in maize breeding. TF binding comparison revealed widespread differences between inbreds, driven largely by structural variation, that correlated with gene expression changes and explained complex quantitative trait loci such as Vgt1, an important determinant of flowering time, and DICE, an herbivore resistance enhancer. CRISPR\u2013Cas9 editing of TF binding regions validated the function and structure of regulatory regions at various loci controlling plant architecture and biotic resistance. Our maize TF binding catalogue identifies functional regulatory regions and enables collective and comparative analysis, highlighting its value for agricultural improvement.", "abstract": "Regulatory elements are essential components of plant genomes that have shaped the domestication and improvement of modern crops. However, their identity, function and diversity remain poorly characterized, limiting our ability to harness their full power for agricultural advances using induced or natural variation. Here, in this study, we mapped transcription factor (TF) binding for 200 TFs from 30 families in two distinct maize inbred lines historically used in maize breeding. TF binding comparison revealed widespread differences between inbreds, driven largely by structural variation, that correlated with gene expression changes and explained complex quantitative trait loci such as Vgt1, an important determinant of flowering time, and DICE, an herbivore resistance enhancer. CRISPR\u2013Cas9 editing of TF binding regions validated the function and structure of regulatory regions at various loci controlling plant architecture and biotic resistance. Our maize TF binding catalogue identifies functional regulatory regions and enables collective and comparative analysis, highlighting its value for agricultural improvement.", "date": "2025-06-11", "issue": "6", "identifier": "https://www.osti.gov/biblio/3002496", "bibliographicCitation": "https://doi.org/10.1038/s41477-025-02007-8", "topic": [ "Unknown" ], "journal_name": "Nature Plants (Online)", "volume": "11", "publisher_information": "Nature Publishing Group", "country_publication_code": "US", "creator": [ { "name": "Mary [Rutgers Univ.,Piscataway,NJ (United States)] (ORCID:0000000174139409) Galli", "primaryContact": true }, { "name": "Zongliang [Rutgers Univ.,Piscataway,NJ (United States)] (ORCID:0000000314693699) Chen", "primaryContact": false }, { "name": "Tara [New York Univ. (NYU),NY (United States)] Ghandour", "primaryContact": false }, { "name": "Amina [Rutgers Univ.,Piscataway,NJ (United States)] (ORCID:0009000324267025) Chaudhry", "primaryContact": false }, { "name": "Jason [Rutgers Univ.,Piscataway,NJ (United States)] (ORCID:0000000250307292) Gregory", "primaryContact": false }, { "name": "Fan [Rutgers Univ.,Piscataway,NJ (United States)] Feng", "primaryContact": false }, { "name": "Miaomiao [New York Univ. (NYU),NY (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000321326168) Li", "primaryContact": false }, { "name": "Nathaniel [Univ. of Wisconsin,Madison,WI (United States)] Schleif", "primaryContact": false }, { "name": "Xuan [Univ. of Georgia,Athens,GA (United States)] (ORCID:000000026635371X) Zhang", "primaryContact": false }, { "name": "Yinxin [Univ. of Georgia,Athens,GA (United States)] Dong", "primaryContact": false }, { "name": "Gaoyuan [Iowa State Univ.,Ames,IA (United States)] (ORCID:0000000316339159) Song", "primaryContact": false }, { "name": "Justin W. [Iowa State Univ.,Ames,IA (United States)] (ORCID:0000000175532237) Walley", "primaryContact": false }, { "name": "George [Univ. of California,Berkeley,CA (United States)] (ORCID:0000000255763959) Chuck", "primaryContact": false }, { "name": "Clinton [Brigham Young Univ.,Provo,UT (United States)] (ORCID:000000017879235X) Whipple", "primaryContact": false }, { "name": "Heidi F. [Univ. of Wisconsin,Madison,WI (United States)] Kaeppler", "primaryContact": false }, { "name": "Shao-shan Carol [New York Univ. (NYU),NY (United States)] (ORCID:0000000178110398) Huang", "primaryContact": false }, { "name": "Andrea [Rutgers Univ.,Piscataway,NJ (United States); Rutgers Univ.,New Brunswick,NJ (United States)] (ORCID:0000000219012971) Gallavotti", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Institutes of Health (NIH)" } }, { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3002496", "active": false }, { "brc": "CBI", "title": "Which Plant Traits Increase Soil Carbon Sequestration? Empirical Evidence From a Long\u2010Term Poplar Genetic Diversity Trial", "description": "Plants play a key role in mediating soil response to global change, and breeding or engineering crops to increase soil organic carbon (SOC) storage is a potential route to land-based carbon dioxide removal in agricultural systems. However, due to limited observational datasets plus shifting paradigms of SOC stabilization, it is unclear which plant traits are most important for enhancing different types of soil organic matter. Existing long-term common gardens of genetically diverse plant populations may provide an opportunity to evaluate biological controls on SOC, separate from environmental or management variability. Here we report on soil and root chemical data collected for 24 genotypes within a 13-year-old common garden in northwestern Oregon planted with a large natural variant population of Populus trichocarpa. Fractionating surface soil (0\u201315 cm) revealed substantial variation in stocks of mineral-associated organic matter (MAOM; 18\u201367 t C/ha) and particulate organic matter (POM; 2\u201322 t C/ha). Tree genotype explained 24% and 26% of the MAOM and POM stock variability, respectively, after controlling for background variability. We found minimal association between SOC concentration and either aboveground tree productivity or root biomass recalcitrance (C/N ratios and lignin content). In contrast, root elemental content appeared influential for MAOM-C concentration, which showed a strong positive association with root aluminum (Al) and a strong negative association with root boron (B) and magnesium (Mg). Furthermore, root concentrations of these elements were highly heritable (57%\u201378%) and not simply a reflection of background variation in soil elemental concentrations. We estimate that surface SOC stocks under these 24 genotypes have diverged at rates of up to 1.2\u20134.3 t C/ha/year. These results suggest that long-term genetic diversity trials have value for elucidating biological controls on soil organic matter dynamics, and that traits associated with root elemental content may be a useful target for enhancing biosequestration.", "abstract": "Plants play a key role in mediating soil response to global change, and breeding or engineering crops to increase soil organic carbon (SOC) storage is a potential route to land-based carbon dioxide removal in agricultural systems. However, due to limited observational datasets plus shifting paradigms of SOC stabilization, it is unclear which plant traits are most important for enhancing different types of soil organic matter. Existing long-term common gardens of genetically diverse plant populations may provide an opportunity to evaluate biological controls on SOC, separate from environmental or management variability. Here we report on soil and root chemical data collected for 24 genotypes within a 13-year-old common garden in northwestern Oregon planted with a large natural variant population of Populus trichocarpa. Fractionating surface soil (0\u201315 cm) revealed substantial variation in stocks of mineral-associated organic matter (MAOM; 18\u201367 t C/ha) and particulate organic matter (POM; 2\u201322 t C/ha). Tree genotype explained 24% and 26% of the MAOM and POM stock variability, respectively, after controlling for background variability. We found minimal association between SOC concentration and either aboveground tree productivity or root biomass recalcitrance (C/N ratios and lignin content). In contrast, root elemental content appeared influential for MAOM-C concentration, which showed a strong positive association with root aluminum (Al) and a strong negative association with root boron (B) and magnesium (Mg). Furthermore, root concentrations of these elements were highly heritable (57%\u201378%) and not simply a reflection of background variation in soil elemental concentrations. We estimate that surface SOC stocks under these 24 genotypes have diverged at rates of up to 1.2\u20134.3 t C/ha/year. These results suggest that long-term genetic diversity trials have value for elucidating biological controls on soil organic matter dynamics, and that traits associated with root elemental content may be a useful target for enhancing biosequestration.", "date": "2025-08-31", "issue": "9", "identifier": "https://www.osti.gov/biblio/3002702", "bibliographicCitation": "https://doi.org/10.1111/gcb.70450", "keywords": [ "biomass recalcitrance", "carbon farming", "heritability", "mineral-associated organic matter", "plant traits", "soil carbon" ], "topic": [ "Unknown" ], "journal_name": "Global Change Biology", "volume": "31", "publisher_information": "Wiley", "country_publication_code": "US", "creator": [ { "name": "John L. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000344518947) Field", "primaryContact": true }, { "name": "Brandon P. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000316304271) Sloan", "primaryContact": false }, { "name": "Matthew E. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000288907920) Craig", "primaryContact": false }, { "name": "Parker [North Carolina State University,Raleigh,NC (United States)] (ORCID:0000000292692993) Calloway", "primaryContact": false }, { "name": "Sarah L. [Tennessee Valley Authority (TVA),Knoxville,TN (United States)] (ORCID:0000000230118523) Ottinger", "primaryContact": false }, { "name": "Thomas [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0009000904155329) Mead", "primaryContact": false }, { "name": "Rose Z. [Univ. of Maine,Orono,ME (United States); Wintergreen Earth Science,Kennebunk,ME (United States)] (ORCID:0000000233933064) Abramoff", "primaryContact": false }, { "name": "Mirko Pavicic [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000229083183) Venegas", "primaryContact": false }, { "name": "Hari B. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000168208789) Chhetri", "primaryContact": false }, { "name": "Kathy [Poplar Innovations,Inc.,Castle Rock,WA (United States)] Haiby", "primaryContact": false }, { "name": "Udaya C. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000259638370) Kalluri", "primaryContact": false }, { "name": "Wellington [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000202009856) Muchero", "primaryContact": false }, { "name": "Christopher Warren [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000187592448) Schadt", "primaryContact": false }, { "name": "Melanie A. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000163689210) Mayes", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Laboratory Directed Research and Development (LDRD) Program" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3002702", "active": false }, { "brc": "CBI", "title": "Effects of chemical composition and physicochemical properties of poplar biomass on the performance of 3D printed poplar-reinforced PLA materials", "description": "Lignocellulosic biomass has been well-acknowledged as a filler for making 3D printed composites. The technical performances of composites were influenced by the characteristics of the components. The correlations between poplar biomass properties and the mechanical and thermal performances of the 3D printed poplar-plastic composites were investigated. The characteristics of poplar were modified by different pretreatment methods, including using hot water, dilute acid, and organic solvent (organosolv), and each treated poplar biomass was applied as a filler in a polylactic acid (PLA) polymer matrix to produce eco-friendly materials. These solvent pretreatments increased the hydrophobicity and surface area of poplar. Organosolv treated poplar showed the highest cellulose content and significantly increased Young's modulus of its biocomposites. Principal component analysis revealed that the specific surface area and water contact angle of biomass contributed to the thermal stability of biocomposites. Additionally, the degree of polymerization of cellulose and xylan content within the biomass correlated with the biocomposites' break stress. Notably, the crystallinity of biocomposites impacted the modulus of these materials. The reported relationships between biomass characteristics and 3D printed composite behaviors provide guidance for optimizing biomass processing in biocomposite applications.", "abstract": "Lignocellulosic biomass has been well-acknowledged as a filler for making 3D printed composites. The technical performances of composites were influenced by the characteristics of the components. The correlations between poplar biomass properties and the mechanical and thermal performances of the 3D printed poplar-plastic composites were investigated. The characteristics of poplar were modified by different pretreatment methods, including using hot water, dilute acid, and organic solvent (organosolv), and each treated poplar biomass was applied as a filler in a polylactic acid (PLA) polymer matrix to produce eco-friendly materials. These solvent pretreatments increased the hydrophobicity and surface area of poplar. Organosolv treated poplar showed the highest cellulose content and significantly increased Young's modulus of its biocomposites. Principal component analysis revealed that the specific surface area and water contact angle of biomass contributed to the thermal stability of biocomposites. Additionally, the degree of polymerization of cellulose and xylan content within the biomass correlated with the biocomposites' break stress. Notably, the crystallinity of biocomposites impacted the modulus of these materials. The reported relationships between biomass characteristics and 3D printed composite behaviors provide guidance for optimizing biomass processing in biocomposite applications.", "date": "2025-09-02", "issue": "10", "identifier": "https://www.osti.gov/biblio/3002910", "bibliographicCitation": "https://doi.org/10.1039/D5SU00327J", "topic": [ "Unknown" ], "journal_name": "RSC Sustainability", "volume": "3", "publisher_information": "Royal Society of Chemistry", "country_publication_code": "US", "creator": [ { "name": "Anqi [State Univ. of New York (SUNY),Syracuse,NY (United States); Howard Univ.,Washington,DC (United States)] (ORCID:0009000641299266) Ji", "primaryContact": true }, { "name": "Samarthya [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000294951880) Bhagia", "primaryContact": false }, { "name": "Nara [State Univ. of New York (SUNY),Syracuse,NY (United States)] (ORCID:0000000194217531) Han", "primaryContact": false }, { "name": "Kwang Ho [Univ. of British Columbia,Vancouver,BC (Canada)] (ORCID:0000000339431927) Kim", "primaryContact": false }, { "name": "Gyu [State Univ. of New York (SUNY),Syracuse,NY (United States)] (ORCID:0000000301691096) Leem", "primaryContact": false }, { "name": "Nidia C. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000282520194) Gallego", "primaryContact": false }, { "name": "Shuyang [Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:0000000239043046) Zhang", "primaryContact": false }, { "name": "Kai [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000314453206) Li", "primaryContact": false }, { "name": "Soydan [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000238254589) Ozcan", "primaryContact": false }, { "name": "Arthur J. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:000000023536554X) Ragauskas", "primaryContact": false }, { "name": "Chang Geun [State Univ. of New York (SUNY),Syracuse,NY (United States)] (ORCID:0000000261792414) Yoo", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "USDOE Laboratory Directed Research and Development (LDRD) Program" } } ], "dataset_url": "https://www.osti.gov/biblio/3002910", "active": false }, { "brc": "CBI", "title": "Structure-guided utilization of lignocellulose for catalysis, energy, and biomaterials", "description": "As a complex composite of cellulose, hemicellulose, and lignin, plant lignocellulose has long served as a major resource for biomass conversion, materials engineering, and bio-based product development. High-resolution structural insights enabled by solid-state nuclear magnetic resonance (ssNMR) now allow the mapping of polymer interfaces, identification of functional group accessibility, and tracking of molecular organization during processing, all of which are critical factors for optimizing catalytic strategies. These insights could drive transformative progress in lignocellulose-based applications, including selective depolymerization, improved pretreatment design, and efficient upcycling of lignin into resins, plastics, and biomedical materials. In industry-relevant contexts, such as biofuel generation and renewable material manufacturing, understanding the hydration dynamics, cross-linking patterns, and structural heterogeneity is also essential. The ability to visualize these features in native biomass presents a unique opportunity to develop new strategies for sustainability and performance. As the structural toolbox continues to expand, it is becoming a central enabler for innovations in renewable energy, green chemistry, and advanced bioproducts.", "abstract": "As a complex composite of cellulose, hemicellulose, and lignin, plant lignocellulose has long served as a major resource for biomass conversion, materials engineering, and bio-based product development. High-resolution structural insights enabled by solid-state nuclear magnetic resonance (ssNMR) now allow the mapping of polymer interfaces, identification of functional group accessibility, and tracking of molecular organization during processing, all of which are critical factors for optimizing catalytic strategies. These insights could drive transformative progress in lignocellulose-based applications, including selective depolymerization, improved pretreatment design, and efficient upcycling of lignin into resins, plastics, and biomedical materials. In industry-relevant contexts, such as biofuel generation and renewable material manufacturing, understanding the hydration dynamics, cross-linking patterns, and structural heterogeneity is also essential. The ability to visualize these features in native biomass presents a unique opportunity to develop new strategies for sustainability and performance. As the structural toolbox continues to expand, it is becoming a central enabler for innovations in renewable energy, green chemistry, and advanced bioproducts.", "date": "2025-10-19", "issue": "11", "identifier": "https://www.osti.gov/biblio/3003738", "bibliographicCitation": "https://doi.org/10.1016/j.xcrp.2025.102911", "keywords": [ "bioproduct", "catalysis", "cell wall", "lignin", "lignocellulose", "plant biomass", "polysaccharide", "solid-state NMR" ], "topic": [ "Unknown" ], "journal_name": "Cell Reports Physical Science", "volume": "6", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Debkumar [Michigan State Univ.,East Lansing,MI (United States)] (ORCID:0009000687930770) Debnath", "primaryContact": true }, { "name": "Priya [Michigan State Univ.,East Lansing,MI (United States)] (ORCID:0009000455004348) Sahu", "primaryContact": false }, { "name": "Mojgan [Michigan State Univ.,East Lansing,MI (United States)] (ORCID:0000000313066108) Nejad", "primaryContact": false }, { "name": "Yunqiao [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Joint Institute for Biological Sciences (JIBS)] (ORCID:0000000325541447) Pu", "primaryContact": false }, { "name": "Jean-Philippe [Iowa State Univ.,Ames,IA (United States)] Tessonnier", "primaryContact": false }, { "name": "Arthur [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Joint Institute for Biological Sciences (JIBS); Univ. of Tennessee,Knoxville,TN (United States)] Ragauskas", "primaryContact": false }, { "name": "Long [Ames Lab.,and Iowa State Univ.,Ames,IA (United States)] Qi", "primaryContact": false }, { "name": "Tuo [Michigan State Univ.,East Lansing,MI (United States)] (ORCID:000000021801924X) Wang", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "USDOE" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division (CSGB)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/3003738", "active": false }, { "brc": "CBI", "title": "Rheology of lignin and lignin-based solutions, dispersions, gels, polymer blends, and melts", "description": "Lignin is an abundant resource that finds application in energy and sustainable materials development. In addition to the utilization of lignin in three-dimensional (3D) printing and hydrogel production, recent studies have reported the use of lignin as a liquid fuel additive. The characterization of the rheological properties of lignin and its derivatives is a dynamic and evolving field, underpinned by advances in experimental, analytical, and modeling techniques. Here, this review provides a comprehensive overview of the recent progress in the study of lignin rheology, highlighting the interplay between structure, modification, and flow behavior in lignin-based solutions, dispersions, gels, polymer blends, and melts. A specific highlight of this review is how lignin concentration affects the rheological properties of lignin-based solutions and dispersions. Furthermore, the effect of lignin type on the properties of 3D-printed lignin-based composites is discussed. For polymer systems, this review discussed lignin-in-polymer solutions separately from lignin-filled polymer systems. Finally, challenges and perspectives on lignin rheology are presented.", "abstract": "Lignin is an abundant resource that finds application in energy and sustainable materials development. In addition to the utilization of lignin in three-dimensional (3D) printing and hydrogel production, recent studies have reported the use of lignin as a liquid fuel additive. The characterization of the rheological properties of lignin and its derivatives is a dynamic and evolving field, underpinned by advances in experimental, analytical, and modeling techniques. Here, this review provides a comprehensive overview of the recent progress in the study of lignin rheology, highlighting the interplay between structure, modification, and flow behavior in lignin-based solutions, dispersions, gels, polymer blends, and melts. A specific highlight of this review is how lignin concentration affects the rheological properties of lignin-based solutions and dispersions. Furthermore, the effect of lignin type on the properties of 3D-printed lignin-based composites is discussed. For polymer systems, this review discussed lignin-in-polymer solutions separately from lignin-filled polymer systems. Finally, challenges and perspectives on lignin rheology are presented.", "date": "2025-11-04", "identifier": "https://www.osti.gov/biblio/3005416", "bibliographicCitation": "https://doi.org/10.1016/j.biortech.2025.133584", "keywords": [ "Dispersions", "Gels", "Lignin", "Melts", "Rheology", "Solutions" ], "topic": [ "Unknown" ], "journal_name": "Bioresource Technology", "volume": "441", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Christian O. [Univ. of Tennessee,Knoxville,TN (United States)] Kemefa", "primaryContact": true }, { "name": "Peter K. [Univ. of Tennessee,Knoxville,TN (United States)] Karoki", "primaryContact": false }, { "name": "Xianzhi [Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:0000000343033403) Meng", "primaryContact": false }, { "name": "Yunqiao [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Pu", "primaryContact": false }, { "name": "Charles M. [Univ. of California,Riverside,CA (United States)] (ORCID:0000000250470815) Cai", "primaryContact": false }, { "name": "Ria D. [Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:0000000160782233) Corder", "primaryContact": false }, { "name": "Arthur J. [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:000000023536554X) Ragauskas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3005416", "active": false }, { "brc": "CBI", "title": "Plant synthetic biology innovations for biofuels and bioproducts", "description": "Plant-based biosynthesis of fuels, chemicals, and materials promotes environmental sustainability, which includes decreases in greenhouse gas emissions, water pollution, and loss of biodiversity. Advances in plant synthetic biology (synbio) should improve precision and efficacy of genetic engineering for sustainability. Applicable synbio innovations include genome editing, gene circuit design, synthetic promoter development, gene stacking technologies, and the design of environmental sensors. Moreover, recent advancements in developing spatially resolved and single-cell omics contribute to the discovery and characterization of cell-type-specific mechanisms and spatiotemporal gene regulations in distinct plant tissues for the expression of cell- and tissue-specific genes, resulting in improved bioproduction. In conclusion, this review highlights recent plant synbio progress and new single-cell molecular profiling towards sustainable biofuel and biomaterial production.", "abstract": "Plant-based biosynthesis of fuels, chemicals, and materials promotes environmental sustainability, which includes decreases in greenhouse gas emissions, water pollution, and loss of biodiversity. Advances in plant synthetic biology (synbio) should improve precision and efficacy of genetic engineering for sustainability. Applicable synbio innovations include genome editing, gene circuit design, synthetic promoter development, gene stacking technologies, and the design of environmental sensors. Moreover, recent advancements in developing spatially resolved and single-cell omics contribute to the discovery and characterization of cell-type-specific mechanisms and spatiotemporal gene regulations in distinct plant tissues for the expression of cell- and tissue-specific genes, resulting in improved bioproduction. In conclusion, this review highlights recent plant synbio progress and new single-cell molecular profiling towards sustainable biofuel and biomaterial production.", "date": "2022-10-11", "issue": "12", "identifier": "https://www.osti.gov/biblio/3007193", "bibliographicCitation": "https://doi.org/10.1016/j.tibtech.2022.09.007", "topic": [ "Unknown" ], "journal_name": "Trends in Biotechnology", "volume": "40", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Yongil [Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:0000000269255410) Yang", "primaryContact": true }, { "name": "Timothy Alexander [Univ. of Tennessee,Knoxville,TN (United States)] Chaffin", "primaryContact": false }, { "name": "Amir H. [Pacific Northwest National Laboratory (PNNL),Richland,WA (United States)] (ORCID:0000000205451236) Ahkami", "primaryContact": false }, { "name": "Eduardo [Univ. of California,Davis,CA (United States)] (ORCID:0000000264496469) Blumwald", "primaryContact": false }, { "name": "Charles Neal [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000330269193) Stewart", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/3007193", "active": false, "has_related_ids": [ "PNNL-SA--174610" ] }, { "brc": "CBI", "title": "Land conversion to energy crops for sustainable aviation fuel production reduces greenhouse gas emissions in the United States", "description": "Energy crops will be critical for scaling up production of Sustainable Aviation Fuel in the United States and reducing greenhouse gas emissions. Here we examine the economic incentives for the extent and type of land conversion needed to scale up fuel production from a mix of cellulosic feedstocks and quantify its greenhouse gas intensity. We show that even with the availability of marginal non-cropland, there will be incentives for converting cropland to produce energy crops as the price of sustainable aviation fuel increases. But contrary to expectations, we find that scaling up fuel production by converting more cropland and more non-cropland from existing uses to energy crops lowers its net greenhouse gas intensity, due to high soil carbon sequestration rate of energy crops, even after considering land use change emissions. The potential savings in emissions are larger than the foregone soil carbon accumulation benefits from keeping that land in current uses.", "abstract": "Energy crops will be critical for scaling up production of Sustainable Aviation Fuel in the United States and reducing greenhouse gas emissions. Here we examine the economic incentives for the extent and type of land conversion needed to scale up fuel production from a mix of cellulosic feedstocks and quantify its greenhouse gas intensity. We show that even with the availability of marginal non-cropland, there will be incentives for converting cropland to produce energy crops as the price of sustainable aviation fuel increases. But contrary to expectations, we find that scaling up fuel production by converting more cropland and more non-cropland from existing uses to energy crops lowers its net greenhouse gas intensity, due to high soil carbon sequestration rate of energy crops, even after considering land use change emissions. The potential savings in emissions are larger than the foregone soil carbon accumulation benefits from keeping that land in current uses.", "date": "2025-11-24", "issue": "1", "identifier": "https://www.osti.gov/biblio/3009412", "bibliographicCitation": "https://doi.org/10.1038/s43247-025-02913-x", "topic": [ "Unknown" ], "journal_name": "Communications Earth & Environment", "volume": "6", "publisher_information": "Springer Nature", "country_publication_code": "US", "creator": [ { "name": "Weiwei [Nanjing Univ. of Information Science and Technology (China)] Wang", "primaryContact": true }, { "name": "Elena [Center for Advanced Bioenergy and Bioproducts Innovation (CABBI),Urbana,IL (United States); Univ. of Illinois at Urbana-Champaign,IL (United States)] (ORCID:0000000220494613) Blanc-Betes", "primaryContact": false }, { "name": "Madhu [Center for Advanced Bioenergy and Bioproducts Innovation (CABBI),Urbana,IL (United States); Univ. of Illinois at Urbana-Champaign,IL (United States)] (ORCID:0000000349944451) Khanna", "primaryContact": false }, { "name": "Chongya [Center for Advanced Bioenergy and Bioproducts Innovation (CABBI),Urbana,IL (United States); Univ. of Illinois at Urbana-Champaign,IL (United States)] Jiang", "primaryContact": false }, { "name": "Kaiyu [Center for Advanced Bioenergy and Bioproducts Innovation (CABBI),Urbana,IL (United States); Univ. of Illinois at Urbana-Champaign,IL (United States)] (ORCID:0000000234996382) Guan", "primaryContact": false }, { "name": "Jeremy S. [Center for Advanced Bioenergy and Bioproducts Innovation (CABBI),Urbana,IL (United States); Univ. of Illinois at Urbana-Champaign,IL (United States)] (ORCID:0000000324892579) Guest", "primaryContact": false }, { "name": "John L. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000344518947) Field", "primaryContact": false }, { "name": "Evan H. [Center for Advanced Bioenergy and Bioproducts Innovation (CABBI),Urbana,IL (United States); Univ. of Illinois at Urbana-Champaign,IL (United States)] DeLucia", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3009412", "active": false }, { "brc": "CBI", "title": "Building an expanded bio-based economy through synthetic biology", "description": "The field of synthetic biology is essential to the continued development of a bio-based economy, creating mechanisms to supply carbon needed in the economy by both converting existing end-of-life wastes as well as by creating novel, purpose-grown and sustainable feedstocks. Here, we first discuss the near- and long-term resources available for use as feedstocks for bioconversion as well as the output molecules needed for building the foundation of an expanded bio-based economy. We then outline the organisms and phenotypic traits that are needed for the performance-advantaged chassis organisms of the future. Furthermore, we detail the advances, challenges, and opportunities in both microbial and plant synthetic biology relevant to expanding the bio-based economy. Finally, we explore technologies that have and will further enable advances in synthetic biology and the greater bio-based economy.", "abstract": "The field of synthetic biology is essential to the continued development of a bio-based economy, creating mechanisms to supply carbon needed in the economy by both converting existing end-of-life wastes as well as by creating novel, purpose-grown and sustainable feedstocks. Here, we first discuss the near- and long-term resources available for use as feedstocks for bioconversion as well as the output molecules needed for building the foundation of an expanded bio-based economy. We then outline the organisms and phenotypic traits that are needed for the performance-advantaged chassis organisms of the future. Furthermore, we detail the advances, challenges, and opportunities in both microbial and plant synthetic biology relevant to expanding the bio-based economy. Finally, we explore technologies that have and will further enable advances in synthetic biology and the greater bio-based economy.", "date": "2025-12-05", "identifier": "https://www.osti.gov/biblio/3009460", "bibliographicCitation": "https://doi.org/10.1016/j.biotechadv.2025.108775", "keywords": [ "09 BIOMASS FUELS", "97 MATHEMATICS AND COMPUTING", "Bio-based economy", "Feedstocks", "Genetic engineering", "Lignocellulosic biomass", "Machine learning", "Performance-advantaged", "Synthetic biology" ], "topic": [ "Biomass & Feedstock", "Computational Biology & Modeling" ], "journal_name": "Biotechnology Advances", "volume": "87", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Andrea M. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000155278980) Garza Elizondo", "primaryContact": true }, { "name": "Ilenne [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000204832141) del Valle Kessra", "primaryContact": false }, { "name": "Erica Teixeira [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000265815054) Prates", "primaryContact": false }, { "name": "Evan [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); National Renewable Energy Laboratory (NREL),Golden,CO (United States)] Komp", "primaryContact": false }, { "name": "Elise Kammerdiener [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000233617475) Phillips", "primaryContact": false }, { "name": "Nandhini [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000195062375) Ashok", "primaryContact": false }, { "name": "Daniel A. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000298228251) Jacobson", "primaryContact": false }, { "name": "Erin G. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000215018647) Webb", "primaryContact": false }, { "name": "Yannick J. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); National Renewable Energy Laboratory (NREL),Golden,CO (United States)] Bomble", "primaryContact": false }, { "name": "William G. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000342126392) Alexander", "primaryContact": false }, { "name": "Joanna [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Tannous", "primaryContact": false }, { "name": "Chung-Jui [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); Univ. of Georgia,Athens,GA (United States)] Tsai", "primaryContact": false }, { "name": "Wayne A. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); Univ. of Georgia,Athens,GA (United States)] Parrott", "primaryContact": false }, { "name": "Xiaohan [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000152074210) Yang", "primaryContact": false }, { "name": "Breeanna R. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); Univ. of Georgia,Athens,GA (United States)] Urbanowicz", "primaryContact": false }, { "name": "Laura E. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); Washington State Univ.,Pullman,WA (United States)] Bartley", "primaryContact": false }, { "name": "Costas D. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); Pennsylvania State Univ.,University Park,PA (United States)] Maranas", "primaryContact": false }, { "name": "Gerald A. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000301061289) Tuskan", "primaryContact": false }, { "name": "Adam M. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000158235329) Guss", "primaryContact": false }, { "name": "Carrie A. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000342012926) Eckert", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Energy Efficiency Office. Advanced Materials & Manufacturing Technologies Office (AMMTO)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Office of Sustainable Transportation. Bioenergy Technologies Office (BETO)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3009460", "active": false, "has_related_ids": [ "NLR/JA--2800-99378" ] }, { "brc": "CBI", "title": "Structure-performance relationships in lignin-based transesterification vitrimers: The role of lignin structural features", "description": "Lignin has been hailed as an ideal renewable alternative for petrochemical-based prepolymers in material synthesis for a sustainable and circular economy, due to its abundant aromatic network and high carbon content. However, the properties and performance of lignin-derived macromolecules are strongly influenced by the lignin itself. While numerous studies have explored the impact of lignin content on the thermomechanical performance of lignin-based vitrimers, literature on how the inherent structural features of lignin affect these properties is scanty. In this study, hardwood organosolv lignin was fractionated in ethyl acetate, ethanol, and acetone to obtain lignin fractions with varying structural characteristics. These fractions were then modified through carboxylation and crosslinked with epoxidized soybean oil (ESO) at a hydroxyl to epoxy group ratio of 1:1 to produce lignin-based transesterification vitrimers (LVs). The thermal properties (i.e. glass transition temperature and thermal stability), tensile strength, storage modulus, and stress relaxation behavior of the LVs were studied and carefully related to the structural features of lignin. The results revealed a positive relationship between strong hydroxyl content in modified lignin and the tensile strength (5.10\u20139.71 MPa), storage modulus (1099.4 \u2013 1372.8 MPa), crosslinking density, and stress relaxation of the LVs. Additionally, both the storage modulus and tensile strength exhibited a positive relationship with the ratio of rigid linkages in modified lignin, while lignin molecular weight was found to significantly impact the thermal properties of LVs (i.e Tg and thermal stability). This study not only highlights the valorization of lignin in vitrimer synthesis but also provide insights for designing lignin-based materials with tailored properties for specific applications.", "abstract": "Lignin has been hailed as an ideal renewable alternative for petrochemical-based prepolymers in material synthesis for a sustainable and circular economy, due to its abundant aromatic network and high carbon content. However, the properties and performance of lignin-derived macromolecules are strongly influenced by the lignin itself. While numerous studies have explored the impact of lignin content on the thermomechanical performance of lignin-based vitrimers, literature on how the inherent structural features of lignin affect these properties is scanty. In this study, hardwood organosolv lignin was fractionated in ethyl acetate, ethanol, and acetone to obtain lignin fractions with varying structural characteristics. These fractions were then modified through carboxylation and crosslinked with epoxidized soybean oil (ESO) at a hydroxyl to epoxy group ratio of 1:1 to produce lignin-based transesterification vitrimers (LVs). The thermal properties (i.e. glass transition temperature and thermal stability), tensile strength, storage modulus, and stress relaxation behavior of the LVs were studied and carefully related to the structural features of lignin. The results revealed a positive relationship between strong hydroxyl content in modified lignin and the tensile strength (5.10\u20139.71 MPa), storage modulus (1099.4 \u2013 1372.8 MPa), crosslinking density, and stress relaxation of the LVs. Additionally, both the storage modulus and tensile strength exhibited a positive relationship with the ratio of rigid linkages in modified lignin, while lignin molecular weight was found to significantly impact the thermal properties of LVs (i.e Tg and thermal stability). This study not only highlights the valorization of lignin in vitrimer synthesis but also provide insights for designing lignin-based materials with tailored properties for specific applications.", "date": "2025-10-23", "identifier": "https://www.osti.gov/biblio/3011553", "bibliographicCitation": "https://doi.org/10.1016/j.indcrop.2025.122108", "keywords": [ "Bio-based polymer", "Lignin modification", "Lignin-based vitrimers", "Stress relaxation", "Transesterification" ], "topic": [ "Unknown" ], "journal_name": "Industrial Crops and Products", "volume": "237", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Peter K. [Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:0009000917232979) Karoki", "primaryContact": true }, { "name": "Christian O. [Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:0009000054420367) Kemefa", "primaryContact": false }, { "name": "Rohit [Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:0000000214454404) Kousika", "primaryContact": false }, { "name": "Yunqiao [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000325541447) Pu", "primaryContact": false }, { "name": "Charles M. [Univ. of California,Riverside,CA (United States)] (ORCID:0000000250470815) Cai", "primaryContact": false }, { "name": "Arthur J. [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:000000023536554X) Ragauskas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Advanced Research Projects Agency - Energy (ARPA-E)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3011553", "active": false }, { "brc": "CBI", "title": "Tunable structure and reinforcement of polyvinyl alcohol (PVA) hydrogels using fungal chitin particles", "description": "Polysaccharides, including chitin, are one of the most abundant biopolymers in nature and are increasingly recognized as a sustainable alternative to petroleum-derived plastics and synthetic fillers in polymer composites. Traditionally sourced from crustacean shells, chitin offers mechanical strength and biocompatibility with limitations also in processability and functionality. Fungal-derived chitin material represents a promising alternative, with advantages including scalable fermentation on low-cost substrates, absence of shellfish allergens, and tunable molecular architectures that vary by species, developmental stage, and growth environment. Here, in this study, we systematically examined chitinous materials obtained from taxonomically and functionally distinct fungi, Laccaria bicolor, Trichoderma reesei and Rhizopus oryzae, to assess their structural, chemical, and morphological properties as reinforcement agents in polymer composites. Mild alkaline pretreatment was employed to obtain mycelium chitin particles, thereby improving accessibility to chitin and co-occurring \u03b2-D-glucans while maintaining microparticle integrity. Comprehensive FTIR and solid-state NMR analyses revealed species-specific differences in chemical composition and microstructure, with R. oryzae exhibiting a unique spectral signature. These fungal-derived chitin were then incorporated into poly(vinyl alcohol) (PVA) hydrogels, where they acted as reinforcing fillers without the need for additional chemical crosslinkers. Comparative evaluation of hydrogel properties demonstrated that fungal chitin significantly enhanced mechanical performance, with all mycelium fillers mitigating the water weakening in PVA hydrogels. R. oryzae-derived composites tripled the hydrogel tensile strength while the submicron fibrous morphology in L. bicolor contributes to over 45 % tensile improvement in dry PVA composites. Our findings highlight the potential of fungal biomass as a tunable, sustainable platform for producing chitin-based reinforcing agents.", "abstract": "Polysaccharides, including chitin, are one of the most abundant biopolymers in nature and are increasingly recognized as a sustainable alternative to petroleum-derived plastics and synthetic fillers in polymer composites. Traditionally sourced from crustacean shells, chitin offers mechanical strength and biocompatibility with limitations also in processability and functionality. Fungal-derived chitin material represents a promising alternative, with advantages including scalable fermentation on low-cost substrates, absence of shellfish allergens, and tunable molecular architectures that vary by species, developmental stage, and growth environment. Here, in this study, we systematically examined chitinous materials obtained from taxonomically and functionally distinct fungi, Laccaria bicolor, Trichoderma reesei and Rhizopus oryzae, to assess their structural, chemical, and morphological properties as reinforcement agents in polymer composites. Mild alkaline pretreatment was employed to obtain mycelium chitin particles, thereby improving accessibility to chitin and co-occurring \u03b2-D-glucans while maintaining microparticle integrity. Comprehensive FTIR and solid-state NMR analyses revealed species-specific differences in chemical composition and microstructure, with R. oryzae exhibiting a unique spectral signature. These fungal-derived chitin were then incorporated into poly(vinyl alcohol) (PVA) hydrogels, where they acted as reinforcing fillers without the need for additional chemical crosslinkers. Comparative evaluation of hydrogel properties demonstrated that fungal chitin significantly enhanced mechanical performance, with all mycelium fillers mitigating the water weakening in PVA hydrogels. R. oryzae-derived composites tripled the hydrogel tensile strength while the submicron fibrous morphology in L. bicolor contributes to over 45 % tensile improvement in dry PVA composites. Our findings highlight the potential of fungal biomass as a tunable, sustainable platform for producing chitin-based reinforcing agents.", "date": "2025-12-28", "issue": "2", "identifier": "https://www.osti.gov/biblio/3012502", "bibliographicCitation": "https://doi.org/10.1016/j.ijbiomac.2025.149960", "keywords": [ "Chitin", "Fungal mycelium", "Hydrogel reinforcement" ], "topic": [ "Unknown" ], "journal_name": "International Journal of Biological Macromolecules", "volume": "339", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Yue [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Nanophase Materials Sciences (CNMS)] (ORCID:0000000327297580) Yuan", "primaryContact": true }, { "name": "Tom\u00e1s A. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000232071466) Rush", "primaryContact": false }, { "name": "Yunqiao [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000325541447) Pu", "primaryContact": false }, { "name": "Kehao [Univ. of Tennessee,Knoxville,TN (United States)] Ren", "primaryContact": false }, { "name": "Lu [Univ. of Tennessee,Knoxville,TN (United States)] Wang", "primaryContact": false }, { "name": "L. P. Tharika [Univ. of Tennessee,Knoxville,TN (United States)] Nirmani", "primaryContact": false }, { "name": "Toby L. [Univ. of Tennessee,Knoxville,TN (United States)] Nelson", "primaryContact": false }, { "name": "John C. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Nanophase Materials Sciences (CNMS)] Lasseter", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Laboratory Directed Research and Development (LDRD) Program" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3012502", "active": false }, { "brc": "CBI", "title": "Ectopic expression of pectate lyase PtxtPL1-27 in aspen affects leaf cuticle development", "description": "Cuticle - a hydrophobic barrier of cutin and waxes covering the outer cell wall surface of plants - enables survival in terrestrial habitats. However, it is not understood how the hydrophobic cuticle precursors travel through the homogalacturonan-rich hydrophilic cell wall. To elucidate the role of homogalacturonan in cuticle development, we disrupted its integrity by overexpressing a pectate lyase, PtxtPL1-27, in aspen. PtxtPL1-27 had pleiotropic effects on shoot development, including the reduction of cuticle thickness and changes in cutin and wax composition, but the expression of cutin biosynthetic genes was little affected. Despite a reduction in homogalacturonan content in the leaves, labeling with the homogalacturonan-specific antibody JIM5 in the outer epidermal cell wall layer increased and displayed an altered pattern. Moreover, the ultrastructure of cell walls was changed concomitant with lipid accumulation. We propose that the disruption of homogalacturonan integrity affected the cutinsome-dependent transport and polymerization of cutin monomers in the cell wall.", "abstract": "Cuticle - a hydrophobic barrier of cutin and waxes covering the outer cell wall surface of plants - enables survival in terrestrial habitats. However, it is not understood how the hydrophobic cuticle precursors travel through the homogalacturonan-rich hydrophilic cell wall. To elucidate the role of homogalacturonan in cuticle development, we disrupted its integrity by overexpressing a pectate lyase, PtxtPL1-27, in aspen. PtxtPL1-27 had pleiotropic effects on shoot development, including the reduction of cuticle thickness and changes in cutin and wax composition, but the expression of cutin biosynthetic genes was little affected. Despite a reduction in homogalacturonan content in the leaves, labeling with the homogalacturonan-specific antibody JIM5 in the outer epidermal cell wall layer increased and displayed an altered pattern. Moreover, the ultrastructure of cell walls was changed concomitant with lipid accumulation. We propose that the disruption of homogalacturonan integrity affected the cutinsome-dependent transport and polymerization of cutin monomers in the cell wall.", "date": "2025-11-30", "issue": "12", "identifier": "https://www.osti.gov/biblio/3012711", "bibliographicCitation": "https://doi.org/10.1016/j.isci.2025.113963", "keywords": [ "Plant Biology", "Plant anatomy", "Plant development", "Plant physiology" ], "topic": [ "Unknown" ], "journal_name": "iScience", "volume": "28", "country_publication_code": "US", "creator": [ { "name": "Ajaya K Biswal", "primaryContact": true }, { "name": "Alicja Banasiak", "primaryContact": false }, { "name": "Josefina-Patricia Fern\u00e1ndez-Moreno", "primaryContact": false }, { "name": "Madhusree Mitra", "primaryContact": false }, { "name": "Jesper Harholt", "primaryContact": false }, { "name": "Marta Derba-Maceluch", "primaryContact": false }, { "name": "Mateusz Majda", "primaryContact": false }, { "name": "Sunita Kushwah", "primaryContact": false }, { "name": "Vikash Kumar", "primaryContact": false }, { "name": "Ilka Abreu", "primaryContact": false }, { "name": "Pramod Sivan", "primaryContact": false }, { "name": "Sivakumar Pattathil", "primaryContact": false }, { "name": "Peter Immerzeel", "primaryContact": false }, { "name": "Andr\u00e1s Gorzs\u00e1s", "primaryContact": false }, { "name": "Thomas Moritz", "primaryContact": false }, { "name": "Michael G Hahn", "primaryContact": false }, { "name": "Henrik Vibe Scheller", "primaryContact": false }, { "name": "Asaph Aharoni", "primaryContact": false }, { "name": "Ewa J Mellerowicz", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "US Department of Energy" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)" } } ], "dataset_url": "https://www.osti.gov/biblio/3012711", "active": false }, { "brc": "CBI", "title": "From lignin to market: a technical and economic perspective of reductive depolymerization approaches", "description": "Lignin has grown into one of the main candidates to replace fossil-based resources as it is the largest renewable source of aromatic building blocks. The complex structure of polymeric lignin, however, requires depolymerization to simpler building blocks for the chemical industry. One of the most promising depolymerization approaches is reductive depolymerization of which two process configurations are currently studied in pilot scale installations for upscaling to industrial scale: (i) reductive catalytic fractionation (RCF), and (ii) reductive catalytic depolymerization (RCD). Both technical and techno-economic aspects will be covered within this review, discussing the advantages and challenges of both approaches regarding processing, production costs, product output, and applications. In this regard, RCF benefits from its decreased energy and solvent consumption linked with being a one-step process and delivers a product with a high monomer content (\u223c25\u201345 wt%). RCD, on the other hand, has the advantage of continuous processing and reduced catalyst fouling and delivers a product that mainly consists of oligomers (<10 wt% monomers). The complete overview of both processes presented here addresses their potential, and can guide future researchers, policy makers and companies to make thoughtful decisions on lignin valorization.", "abstract": "Lignin has grown into one of the main candidates to replace fossil-based resources as it is the largest renewable source of aromatic building blocks. The complex structure of polymeric lignin, however, requires depolymerization to simpler building blocks for the chemical industry. One of the most promising depolymerization approaches is reductive depolymerization of which two process configurations are currently studied in pilot scale installations for upscaling to industrial scale: (i) reductive catalytic fractionation (RCF), and (ii) reductive catalytic depolymerization (RCD). Both technical and techno-economic aspects will be covered within this review, discussing the advantages and challenges of both approaches regarding processing, production costs, product output, and applications. In this regard, RCF benefits from its decreased energy and solvent consumption linked with being a one-step process and delivers a product with a high monomer content (\u223c25\u201345 wt%). RCD, on the other hand, has the advantage of continuous processing and reduced catalyst fouling and delivers a product that mainly consists of oligomers (<10 wt% monomers). The complete overview of both processes presented here addresses their potential, and can guide future researchers, policy makers and companies to make thoughtful decisions on lignin valorization.", "date": "2025-10-06", "issue": "42", "identifier": "https://www.osti.gov/biblio/3013272", "bibliographicCitation": "https://doi.org/10.1039/D5GC02316E", "keywords": [ "09 BIOMASS FUELS", "biomass", "continuous depolymerization", "lignin", "reductive catalytic fractionation", "techno-economic assessment" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Green Chemistry", "volume": "27", "publisher_information": "Royal Society of Chemistry", "country_publication_code": "US", "creator": [ { "name": "Brent [Flemish Institute for Technological Research (VITO N.V.),Mol (Belgium)] (ORCID:0000000152429202) Daelemans", "primaryContact": true }, { "name": "Balaji [Flemish Institute for Technological Research (VITO N.V.),Mol (Belgium)] (ORCID:0000000191221674) Sridharan", "primaryContact": false }, { "name": "Paul [Flemish Institute for Technological Research (VITO N.V.),Mol (Belgium)] (ORCID:0000000281524433) Jusner", "primaryContact": false }, { "name": "Agneev [Flemish Institute for Technological Research (VITO N.V.),Mol (Belgium)] (ORCID:0000000280589059) Mukherjee", "primaryContact": false }, { "name": "Jiazhao [University of Groningen (Netherlands)] (ORCID:0000000263142781) Chen", "primaryContact": false }, { "name": "Jacob K. [National Renewable Energy Laboratory (NREL),Golden,CO (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] (ORCID:0000000158832043) Kenny", "primaryContact": false }, { "name": "Miet [Flemish Institute for Technological Research (VITO N.V.),Mol (Belgium); Hasselt University,Diepenbeek (Belgium)] (ORCID:0000000309225735) Van Dael", "primaryContact": false }, { "name": "Karolien [Flemish Institute for Technological Research (VITO N.V.),Mol (Belgium)] (ORCID:0000000311736497) Vanbroekhoven", "primaryContact": false }, { "name": "Peter J. [University of Groningen (Netherlands)] (ORCID:0000000222542500) Deuss", "primaryContact": false }, { "name": "Michael L. [National Renewable Energy Laboratory (NREL),Golden,CO (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] (ORCID:0000000263417183) Stone", "primaryContact": false }, { "name": "Elias [Flemish Institute for Technological Research (VITO N.V.),Mol (Belgium); Notre Dame University-Louaize,Zouk Mosbeh (Lebanon)] (ORCID:0000000315613259) Feghali", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Office of Sustainable Transportation. Bioenergy Technologies Office (BETO)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3013272", "active": false, "has_related_ids": [ "NREL/JA--2800-94330" ] }, { "brc": "CBI", "title": "Thermophilic Chassis-Enabled High-Throughput Selection of a Thermostable Fluorogenic Reporter", "description": "Thermostable proteins show increased shelf life and performance at elevated temperatures and under harsh conditions, resulting in lower costs for various industrial and biotechnological applications. However, due to a limited understanding of the relationship between stability and function, protein stabilization remains primarily a trial-and-error approach. Therefore, building a combinatorial library of mutations predicted to improve stability, followed by experimental testing, represents a markedly improved methodology. However, the lack of high-throughput approaches to screen even a moderately sized library presents a major bottleneck in the field. Here, in this study, we use a thermophile, Parageobacillus thermoglucosidasius (Ptherm) to rapidly screen combinatorial libraries consisting of rationally designed thermostabilizing mutations (\u223c103\u2013104) of a mesophilic fluorescent reporter, Y-FAST. On a Petri dish, microbial growth at an elevated temperature and exposure to fluorogen yielded several colonies of Ptherm that showed distinct fluorescence at 55 and 68 \u00b0C in our two sequentially generated libraries using Rosetta and ProteinMPNN, respectively. The Y-FAST variants isolated from fluorescent colonies were brighter than Y-FAST and showed higher resistance to thermal and chemical denaturation. AlphaFold-predicted structures and MD simulations revealed stability-enhancing salt bridges and hydrogen bond networks in the isolated FAST variants. The moderately thermostable FAST (tsFAST) and hyperstable FAST (hsFAST) were then demonstrated as translation reporters for protein expression and folding at elevated temperatures, such as 55 and 68 \u00b0C. Our approach of combinatorial library generation and high-throughput screening in a thermophilic chassis could, in principle, be extended to other proteins fused to these translation reporters. Furthermore, the hsFAST protein is small\u2500half the size of the green fluorescent protein\u2500and does not require oxygen for maturation, making it ideal for engineering extremophilic anaerobes for biosensing and bioconversion.", "abstract": "Thermostable proteins show increased shelf life and performance at elevated temperatures and under harsh conditions, resulting in lower costs for various industrial and biotechnological applications. However, due to a limited understanding of the relationship between stability and function, protein stabilization remains primarily a trial-and-error approach. Therefore, building a combinatorial library of mutations predicted to improve stability, followed by experimental testing, represents a markedly improved methodology. However, the lack of high-throughput approaches to screen even a moderately sized library presents a major bottleneck in the field. Here, in this study, we use a thermophile, Parageobacillus thermoglucosidasius (Ptherm) to rapidly screen combinatorial libraries consisting of rationally designed thermostabilizing mutations (\u223c103\u2013104) of a mesophilic fluorescent reporter, Y-FAST. On a Petri dish, microbial growth at an elevated temperature and exposure to fluorogen yielded several colonies of Ptherm that showed distinct fluorescence at 55 and 68 \u00b0C in our two sequentially generated libraries using Rosetta and ProteinMPNN, respectively. The Y-FAST variants isolated from fluorescent colonies were brighter than Y-FAST and showed higher resistance to thermal and chemical denaturation. AlphaFold-predicted structures and MD simulations revealed stability-enhancing salt bridges and hydrogen bond networks in the isolated FAST variants. The moderately thermostable FAST (tsFAST) and hyperstable FAST (hsFAST) were then demonstrated as translation reporters for protein expression and folding at elevated temperatures, such as 55 and 68 \u00b0C. Our approach of combinatorial library generation and high-throughput screening in a thermophilic chassis could, in principle, be extended to other proteins fused to these translation reporters. Furthermore, the hsFAST protein is small\u2500half the size of the green fluorescent protein\u2500and does not require oxygen for maturation, making it ideal for engineering extremophilic anaerobes for biosensing and bioconversion.", "date": "2025-10-07", "issue": "10", "identifier": "https://www.osti.gov/biblio/3015155", "bibliographicCitation": "https://doi.org/10.1021/acssynbio.5c00573", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "ProteinMPNN", "ROSETTA", "Y-FAST", "high throughput screening", "protein engineering", "thermophile", "thermostability", "translational reporter" ], "topic": [ "Microbiology" ], "journal_name": "ACS Synthetic Biology", "volume": "14", "publisher_information": "American Chemical Society (ACS)", "country_publication_code": "US", "creator": [ { "name": "Sang-Min [Los Alamos National Laboratory (LANL),Los Alamos,NM (United States); BOTTLE Consortium,Golden,CO (United States); USDOE Agile BioFoundry,Emeryville,CA (United States)] (ORCID:0000000257945510) Shin", "primaryContact": true }, { "name": "Ellin-Kristina Hillert [Los Alamos National Laboratory (LANL),Los Alamos,NM (United States); USDOE Agile BioFoundry,Emeryville,CA (United States)] (ORCID:0000000156196450) Triola", "primaryContact": false }, { "name": "Rommel Santiago [Los Alamos National Laboratory (LANL),Los Alamos,NM (United States); BOTTLE Consortium,Golden,CO (United States)] (ORCID:0000000150858740) Granja-Travez", "primaryContact": false }, { "name": "Cesar Augusto [Los Alamos National Laboratory (LANL),Los Alamos,NM (United States)] (ORCID:0000000346843364) Lopez Bautista", "primaryContact": false }, { "name": "Neely M. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Wood", "primaryContact": false }, { "name": "Lauren A. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Riley", "primaryContact": false }, { "name": "Adam M. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); BOTTLE Consortium,Golden,CO (United States); USDOE Agile BioFoundry,Emeryville,CA (United States)] Guss", "primaryContact": false }, { "name": "Taraka T. [Los Alamos National Laboratory (LANL),Los Alamos,NM (United States); BOTTLE Consortium,Golden,CO (United States); USDOE Agile BioFoundry,Emeryville,CA (United States)] (ORCID:0000000190361210) Dale", "primaryContact": false }, { "name": "Ramesh Kumar [Los Alamos National Laboratory (LANL),Los Alamos,NM (United States); BOTTLE Consortium,Golden,CO (United States); USDOE Agile BioFoundry,Emeryville,CA (United States)] (ORCID:0000000159043441) Jha", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Laboratory Directed Research and Development (LDRD) Program" } }, { "fundingOrganization": { "organizationName": "USDOE National Nuclear Security Administration (NNSA)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Energy Efficiency Office. Advanced Materials & Manufacturing Technologies Office (AMMTO)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Office of Sustainable Transportation. Bioenergy Technologies Office (BETO)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3015155", "active": false, "has_related_ids": [ "LA-UR--25-25037" ] }, { "brc": "CBI", "title": "Cu\u2010Catalyzed Aerobic Oxidative C\u2500C Cleavage in Lignin\u2010Derived Oligomers and Biological Funneling of the Monomeric Products", "description": "Existing methods for lignin deconstruction to aromatic monomers primarily cleave carbon\u2013oxygen bonds within the polymer, resulting in sub-optimal monomer yields and formation of oligomers that retain intact carbon\u2013carbon bonds. Here, we demonstrate that copper-catalyzed aerobic oxidation under aqueous alkaline conditions promotes oxidative cleavage of carbon\u2013carbon bonds in lignin oligomers derived from reductive catalytic fractionation (RCF) of pine and poplar biomass. Fundamental insights are gained from reactions of model compounds that resemble subunits present in RCF oligomers. Optimal results are achieved in a flow reactor that provides precise control over O2 delivery, temperature, and reaction residence time. The Cu-catalyzed aerobic oxidation conditions access aromatic monomers in 19 and 34 wt% monomer yields, respectively, from pine- and poplar-derived RCF oligomers. Overall, the sequence consisting of biomass RCF into monomers and oligomers followed by oxidative deconstruction of the RCF oligomers generates substantially higher yields of aromatic monomers from lignin. Engineered strains of Pseudomonas putida support biological funneling of the oligomer-derived oxygenated aromatic compounds into cis,cis-muconic acid from pine or 2-pyrone-4,6-dicarboxylic acid from poplar.", "abstract": "Existing methods for lignin deconstruction to aromatic monomers primarily cleave carbon\u2013oxygen bonds within the polymer, resulting in sub-optimal monomer yields and formation of oligomers that retain intact carbon\u2013carbon bonds. Here, we demonstrate that copper-catalyzed aerobic oxidation under aqueous alkaline conditions promotes oxidative cleavage of carbon\u2013carbon bonds in lignin oligomers derived from reductive catalytic fractionation (RCF) of pine and poplar biomass. Fundamental insights are gained from reactions of model compounds that resemble subunits present in RCF oligomers. Optimal results are achieved in a flow reactor that provides precise control over O2 delivery, temperature, and reaction residence time. The Cu-catalyzed aerobic oxidation conditions access aromatic monomers in 19 and 34 wt% monomer yields, respectively, from pine- and poplar-derived RCF oligomers. Overall, the sequence consisting of biomass RCF into monomers and oligomers followed by oxidative deconstruction of the RCF oligomers generates substantially higher yields of aromatic monomers from lignin. Engineered strains of Pseudomonas putida support biological funneling of the oligomer-derived oxygenated aromatic compounds into cis,cis-muconic acid from pine or 2-pyrone-4,6-dicarboxylic acid from poplar.", "date": "2025-11-16", "issue": "2", "identifier": "https://www.osti.gov/biblio/3018721", "bibliographicCitation": "https://doi.org/10.1002/anie.202515588", "keywords": [ "09 BIOMASS FUELS", "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "Aerobic oxidation", "C-C bond cleavage", "Catalysis", "C\u2013C bond cleavage", "C\u2500C bond cleavage", "Lignin monomers", "Lignin oligomer", "aerobic oxidation", "catalysis", "lignin monomers", "lignin oligomer" ], "topic": [ "Biomass & Feedstock", "Chemistry" ], "journal_name": "Angewandte Chemie (International Edition)", "volume": "65", "publisher_information": "Wiley", "country_publication_code": "US", "creator": [ { "name": "Surajudeen [University of Wisconsin\u2010Madison,WI (United States)] Omolabake", "primaryContact": true }, { "name": "Dillon T. [University of Wisconsin\u2010Madison,WI (United States)] Hofsommer", "primaryContact": false }, { "name": "Kathryn M. [National Renewable Energy Laboratory (NREL),Golden,CO (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Mains", "primaryContact": false }, { "name": "Chad T. [National Renewable Energy Laboratory (NREL),Golden,CO (United States)] Palumbo", "primaryContact": false }, { "name": "Davide [National Renewable Energy Laboratory (NREL),Golden,CO (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Rigo", "primaryContact": false }, { "name": "Allison Z. [National Renewable Energy Laboratory (NREL),Golden,CO (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000171472863) Werner", "primaryContact": false }, { "name": "Gregg T. [National Renewable Energy Laboratory (NREL),Golden,CO (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:000000023480212X) Beckham", "primaryContact": false }, { "name": "Shannon S. [University of Wisconsin\u2010Madison,WI (United States)] (ORCID:0000000290007665) Stahl", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Office of Sustainable Transportation. Bioenergy Technologies Office (BETO)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3018721", "active": false, "has_related_ids": [ "NLR/JA--2A00-96429" ] }, { "brc": "CBI", "title": "An overview of switchgrass phenotypes variability across diverse populations and their implications for conversion to fuels", "description": "There have been substantial changes to the human lifestyle over the past two centuries, which are reflected in the amount of fuel we consume to power our day-to-day needs. The way we use these resources has indeed manifested in an overdependence on non-renewable energy sources, such as coal and petroleum, for generating electricity and powering our transportation needs. There is a pressing need to explore alternative ways of fueling our current lifestyle without impacting the environment. Biofuels have long been touted as a sustainable solution for use as drop-in fuels in aviation and maritime applications. Still, they have yet to establish themselves as a competitive commercial alternative, necessitating further research and development. Lignocellulosic biomass is an underutilized resource that is widely accessible for the commercial processing of renewable biofuels. Bioenergy crops, such as switchgrass (Panicum virgatum L.), which can be cultivated on marginal lands with minimal competition for agricultural land, are an ideal and promising candidate for bulk-scale biofuel synthesis. Over the past 30 years, significant progress has been made in breeding and genetically modifying these grasses to enhance their drought resilience and subsequent yields. However, discrepancies in biomass composition can lead to irregular feedstocks for downstream operations, which in turn affect overall production targets for biofuels. Here, this review examines the variability in switchgrass (P. virgatum L.) biomass phenotypes across diverse populations and plant components, and their implications for biofuel conversion. The study highlights significant variations in biomass yield, composition, and cell wall chemistry both between switchgrass genotypes and within individual cultivars. Key findings include differences in cellulose, hemicellulose, and lignin content between leaves and stems, which affect biomass digestibility and ethanol yield. The review also discusses the impact of lignin chemistry, particularly the syringyl/guaicyl (S/G) ratio, on the efficiency of biomass saccharification. Furthermore, it explores how these variations respond differently to various pretreatment techniques, affecting overall biofuel production. We conclude that understanding and quantifying this variability is crucial for optimizing switchgrass as a feedstock for commercial biofuel production, thereby potentially addressing the pressing need for sustainable energy sources in sectors such as aviation.", "abstract": "There have been substantial changes to the human lifestyle over the past two centuries, which are reflected in the amount of fuel we consume to power our day-to-day needs. The way we use these resources has indeed manifested in an overdependence on non-renewable energy sources, such as coal and petroleum, for generating electricity and powering our transportation needs. There is a pressing need to explore alternative ways of fueling our current lifestyle without impacting the environment. Biofuels have long been touted as a sustainable solution for use as drop-in fuels in aviation and maritime applications. Still, they have yet to establish themselves as a competitive commercial alternative, necessitating further research and development. Lignocellulosic biomass is an underutilized resource that is widely accessible for the commercial processing of renewable biofuels. Bioenergy crops, such as switchgrass (Panicum virgatum L.), which can be cultivated on marginal lands with minimal competition for agricultural land, are an ideal and promising candidate for bulk-scale biofuel synthesis. Over the past 30 years, significant progress has been made in breeding and genetically modifying these grasses to enhance their drought resilience and subsequent yields. However, discrepancies in biomass composition can lead to irregular feedstocks for downstream operations, which in turn affect overall production targets for biofuels. Here, this review examines the variability in switchgrass (P. virgatum L.) biomass phenotypes across diverse populations and plant components, and their implications for biofuel conversion. The study highlights significant variations in biomass yield, composition, and cell wall chemistry both between switchgrass genotypes and within individual cultivars. Key findings include differences in cellulose, hemicellulose, and lignin content between leaves and stems, which affect biomass digestibility and ethanol yield. The review also discusses the impact of lignin chemistry, particularly the syringyl/guaicyl (S/G) ratio, on the efficiency of biomass saccharification. Furthermore, it explores how these variations respond differently to various pretreatment techniques, affecting overall biofuel production. We conclude that understanding and quantifying this variability is crucial for optimizing switchgrass as a feedstock for commercial biofuel production, thereby potentially addressing the pressing need for sustainable energy sources in sectors such as aviation.", "date": "2025-12-17", "issue": "2", "identifier": "https://www.osti.gov/biblio/3020177", "bibliographicCitation": "https://doi.org/10.1002/bbb.70104", "topic": [ "Unknown" ], "journal_name": "Biofuels, Bioproducts & Biorefining", "volume": "20", "publisher_information": "Wiley", "country_publication_code": "US", "creator": [ { "name": "Rohit [Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:0000000214454404) Kousika", "primaryContact": true }, { "name": "Yunqiao [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Pu", "primaryContact": false }, { "name": "Arthur J. [Univ. of Tennessee,Knoxville,TN (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:000000023536554X) Ragauskas", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3020177", "active": false }, { "brc": "CBI", "title": "Climate change drives convergent evolution of root traits on Sky Island climate relicts", "description": "Roots are essential to the strategies plants use to survive in variable environments, yet we know little of how they vary within species. Experimental conditions demonstrate that intraspecific plant root traits respond strongly to variation in the environment; however, it is unclear when these responses can be characterized as evolution in response to selective pressures of climate change over many generations. Sky Islands are model, natural climate relict ecosystems to examine climate-change driven evolution. Utilizing a common garden with replicate genotypes of Populus angustifolia (Narrowleaf cottonwood) from six Sky Island (SI) populations and nine adjacent Mountain Chain (MC) populations across three genetic provenances, we hypothesized that SI root traits have diverged due to historical isolation in warmer, drier climates. When grown in common conditions, populations originating on SI\u2019s showed convergent evolution across three distinct genetic provenances, which was characterized by 44.16% decreased total root length, 42.64% decreased average root volume, 43.31% decreased root surface area, and significantly less root trait variation, relative to adjacent mountain chains. Convergent evolution of root traits from trees originating on SI\u2019s is correlated with changes in mean annual precipitation and potential evapotranspiration in the field over the past ~ 125 years. These results demonstrate a consistent pattern in root trait evolution at the landscape scale and the role of climate on the evolution of root traits in a genetic and geographic context relevant to climate change.", "abstract": "Roots are essential to the strategies plants use to survive in variable environments, yet we know little of how they vary within species. Experimental conditions demonstrate that intraspecific plant root traits respond strongly to variation in the environment; however, it is unclear when these responses can be characterized as evolution in response to selective pressures of climate change over many generations. Sky Islands are model, natural climate relict ecosystems to examine climate-change driven evolution. Utilizing a common garden with replicate genotypes of Populus angustifolia (Narrowleaf cottonwood) from six Sky Island (SI) populations and nine adjacent Mountain Chain (MC) populations across three genetic provenances, we hypothesized that SI root traits have diverged due to historical isolation in warmer, drier climates. When grown in common conditions, populations originating on SI\u2019s showed convergent evolution across three distinct genetic provenances, which was characterized by 44.16% decreased total root length, 42.64% decreased average root volume, 43.31% decreased root surface area, and significantly less root trait variation, relative to adjacent mountain chains. Convergent evolution of root traits from trees originating on SI\u2019s is correlated with changes in mean annual precipitation and potential evapotranspiration in the field over the past ~ 125 years. These results demonstrate a consistent pattern in root trait evolution at the landscape scale and the role of climate on the evolution of root traits in a genetic and geographic context relevant to climate change.", "date": "2026-02-06", "issue": "1", "identifier": "https://www.osti.gov/biblio/3020882", "bibliographicCitation": "https://doi.org/10.1038/s41598-025-31134-7", "keywords": [ "Convergent evolution", "Local adaptation", "Populus", "Root functional traits", "Sky Islands" ], "topic": [ "Unknown" ], "journal_name": "Scientific Reports", "volume": "16", "publisher_information": "Nature Publishing Group", "country_publication_code": "US", "creator": [ { "name": "Lorren E. [Univ. of Tennessee,Knoxville,TN (United States)] (ORCID:0000000292896232) Politano", "primaryContact": true }, { "name": "Larry M. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000219959479) York", "primaryContact": false }, { "name": "Joseph K. [Univ. of Tennessee,Knoxville,TN (United States)] Bailey", "primaryContact": false }, { "name": "Jennifer A. [Univ. of Tennessee,Knoxville,TN (United States)] Schweitzer", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3020882", "active": false }, { "brc": "CBI", "title": "Biochemical parallels between catabolic pathways for lignin-associated aromatic dimers", "description": "Lignin is one of the most common biopolymers on Earth. In nature, lignin is primarily deconstructed by fungi into mixtures of aromatic compounds that are then assimilated by bacteria and fungi. Industrially, lignin is primarily generated as a byproduct of pulp and paper production and burned for process heat. However, if the appropriate assimilatory pathways were identified, deconstructed lignin could be funneled into value-added products using engineered bacteria. Foundational work has described pathways for assimilation of diverse monomeric aromatic compounds such as protocatechuate, ferulate, and syringate, as well as select dimers including those with \u03b2-O-4 and 5-5 interunit linkages. Recent advances have elucidated additional pathways for dimer assimilation, including pathways for new substrates as well as parallel pathways for previously characterized substrates. Comparing these dimer assimilation pathways can illuminate the underlying biochemical logic of assimilation for lignin-associated aromatic dimers and provide opportunities for metabolic engineering to enhance lignin valorization.", "abstract": "Lignin is one of the most common biopolymers on Earth. In nature, lignin is primarily deconstructed by fungi into mixtures of aromatic compounds that are then assimilated by bacteria and fungi. Industrially, lignin is primarily generated as a byproduct of pulp and paper production and burned for process heat. However, if the appropriate assimilatory pathways were identified, deconstructed lignin could be funneled into value-added products using engineered bacteria. Foundational work has described pathways for assimilation of diverse monomeric aromatic compounds such as protocatechuate, ferulate, and syringate, as well as select dimers including those with \u03b2-O-4 and 5-5 interunit linkages. Recent advances have elucidated additional pathways for dimer assimilation, including pathways for new substrates as well as parallel pathways for previously characterized substrates. Comparing these dimer assimilation pathways can illuminate the underlying biochemical logic of assimilation for lignin-associated aromatic dimers and provide opportunities for metabolic engineering to enhance lignin valorization.", "date": "2026-02-17", "issue": "3", "identifier": "https://www.osti.gov/biblio/3020917", "bibliographicCitation": "https://doi.org/10.1128/aem.00276-25", "keywords": [ "Sphingomonas", "lignin" ], "topic": [ "Unknown" ], "journal_name": "Applied and Environmental Microbiology", "volume": "92", "publisher_information": "American Society for Microbiology", "country_publication_code": "US", "creator": [ { "name": "Joshua K. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000323028180) Michener", "primaryContact": true } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3020917", "active": false }, { "brc": "CBI", "title": "1H NMR Quantification of Aromatic Monomers from Reductive Catalytic Fractionation", "description": "Reductive catalytic fractionation (RCF) can produce high yields of aromatic monomers from lignin in native biomass. Quantification of these aromatic monomers is a well-known but demanding task, in part due to the lack of commercially available standards. Here, we demonstrate 1H NMR spectroscopy as a complementary method to rapidly quantify aromatic monomer concentrations in RCF oils. The method exhibited good agreement with measurements from ultrahigh pressure liquid chromatography (UHPLC) for 96 RCF oils with varying monomer selectivity, with average absolute deviations of individual monomer yields between 0.5 and 1.1 wt % (relative 11\u201317%) and R2 values above 0.9 compared to conventional UHPLC quantification. Quantification of S-type monomers, including for 4-ethylsyringol and 4-propenylsyringol, was generally reliable. The validity of G-type monomer quantifications depended on reaction selectivity due to overlap between peaks of 4-ethylguaiacol and 4-(3-hydroxypropyl)-guaiacol. The method could be applied on crude RCF oils without needing to perform the liquid\u2013liquid extraction typically done for RCF reactions, thereby providing a convenient way to quantify lignin extraction and aromatic monomer yield. Overall, 1H NMR spectroscopy can serve as a rapid primary quantification or secondary validation method for RCF monomer yield and selectivity measurements.", "abstract": "Reductive catalytic fractionation (RCF) can produce high yields of aromatic monomers from lignin in native biomass. Quantification of these aromatic monomers is a well-known but demanding task, in part due to the lack of commercially available standards. Here, we demonstrate 1H NMR spectroscopy as a complementary method to rapidly quantify aromatic monomer concentrations in RCF oils. The method exhibited good agreement with measurements from ultrahigh pressure liquid chromatography (UHPLC) for 96 RCF oils with varying monomer selectivity, with average absolute deviations of individual monomer yields between 0.5 and 1.1 wt % (relative 11\u201317%) and R2 values above 0.9 compared to conventional UHPLC quantification. Quantification of S-type monomers, including for 4-ethylsyringol and 4-propenylsyringol, was generally reliable. The validity of G-type monomer quantifications depended on reaction selectivity due to overlap between peaks of 4-ethylguaiacol and 4-(3-hydroxypropyl)-guaiacol. The method could be applied on crude RCF oils without needing to perform the liquid\u2013liquid extraction typically done for RCF reactions, thereby providing a convenient way to quantify lignin extraction and aromatic monomer yield. Overall, 1H NMR spectroscopy can serve as a rapid primary quantification or secondary validation method for RCF monomer yield and selectivity measurements.", "date": "2026-02-15", "issue": "8", "identifier": "https://www.osti.gov/biblio/3021378", "bibliographicCitation": "https://doi.org/10.1021/acssuschemeng.5c10351", "keywords": [ "1H NMR spectroscopy", "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "42 ENGINEERING", "Proton nuclear magnetic resonance", "RCF oils", "aromatic compounds", "biopolymers", "lignin monomers", "lignin-first biorefining", "lipids", "model compound", "monomers", "nuclear magnetic resonance spectroscopy", "quantification", "reductive catalytic fractionation", "reductive catalytic fractionation (RCF)" ], "topic": [ "Chemistry", "Process Engineering" ], "journal_name": "ACS Sustainable Chemistry & Engineering", "volume": "14", "publisher_information": "American Chemical Society (ACS)", "country_publication_code": "US", "creator": [ { "name": "Jacob K. [National Laboratory of the Rockies,Golden,CO (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000158832043) Kenny", "primaryContact": true }, { "name": "Sierra [National Laboratory of the Rockies,Golden,CO (United States)] Schlussel", "primaryContact": false }, { "name": "Alexander F. [National Laboratory of the Rockies,Golden,CO (United States)] Benson", "primaryContact": false }, { "name": "Sean P. [National Laboratory of the Rockies,Golden,CO (United States)] (ORCID:0000000337929553) Woodworth", "primaryContact": false }, { "name": "Hannah M. [National Laboratory of the Rockies,Golden,CO (United States)] (ORCID:0000000265597800) Alt", "primaryContact": false }, { "name": "Yuriy [Massachusetts Institute of Technology,Cambridge,MA (United States)] Rom\u00e1n-Leshkov", "primaryContact": false }, { "name": "Gregg T. [National Laboratory of the Rockies,Golden,CO (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:000000023480212X) Beckham", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Office of Sustainable Transportation. Bioenergy Technologies Office (BETO)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3021378", "active": false, "has_related_ids": [ "NLR/JA--2A00-97357" ] }, { "brc": "CBI", "title": "Genetic and metabolic drivers of membrane remodeling in Clostridium thermocellum under alcohol stress", "description": "Clostridium thermocellum is a leading candidate for consolidated bioprocessing of lignocellulosic biomass into biofuels due to its native cellulolytic capabilities. Beyond ethanol, C. thermocellum is being developed as a platform for producing higher-chain alcohols such as isobutanol and n-butanol. However, its physiological adaptations to alcohol stress remain poorly understood. Here, we investigate how C. thermocellum remodels its membrane lipid composition in response to exogenous ethanol, n-butanol, isobutanol, and butyrate. Exposure to linear alcohols such as n-butanol or to organic acids like butyrate increased the proportion of straight-chain fatty acids in the membrane at the expense of branched-chain species, whereas exposure to the branched alcohol isobutanol produced the opposite effect. Isotope tracer experiments demonstrated that C. thermocellum directly incorporates the carbon backbones of exogenous alcohols and acids into fatty acids, providing a mechanistic basis for these contrasting shifts. We show that the bifunctional aldehyde/alcohol dehydrogenase AdhE is essential for the assimilation of exogenous alcohols into fatty acids, acting through its oxidative activity by first oxidizing alcohols to aldehydes and then converting them to acyl-CoA intermediates. Deletion of the pyruvate:ferredoxin oxidoreductase isozyme pfor4 abolished branched-chain fatty acid synthesis, but supplementation with isobutanol restored production, indicating that Pfor4 substitutes for the canonical branched-chain \u03b1-keto acid dehydrogenase complex. These findings reveal two distinct routes for branched-chain fatty acid production in C. thermocellum: a Pfor4-dependent pathway from \u03b1-keto acid intermediates derived from amino acid synthesis, and an AdhE-dependent salvage pathway that assimilates exogenous branched-chain alcohols.", "abstract": "Clostridium thermocellum is a leading candidate for consolidated bioprocessing of lignocellulosic biomass into biofuels due to its native cellulolytic capabilities. Beyond ethanol, C. thermocellum is being developed as a platform for producing higher-chain alcohols such as isobutanol and n-butanol. However, its physiological adaptations to alcohol stress remain poorly understood. Here, we investigate how C. thermocellum remodels its membrane lipid composition in response to exogenous ethanol, n-butanol, isobutanol, and butyrate. Exposure to linear alcohols such as n-butanol or to organic acids like butyrate increased the proportion of straight-chain fatty acids in the membrane at the expense of branched-chain species, whereas exposure to the branched alcohol isobutanol produced the opposite effect. Isotope tracer experiments demonstrated that C. thermocellum directly incorporates the carbon backbones of exogenous alcohols and acids into fatty acids, providing a mechanistic basis for these contrasting shifts. We show that the bifunctional aldehyde/alcohol dehydrogenase AdhE is essential for the assimilation of exogenous alcohols into fatty acids, acting through its oxidative activity by first oxidizing alcohols to aldehydes and then converting them to acyl-CoA intermediates. Deletion of the pyruvate:ferredoxin oxidoreductase isozyme pfor4 abolished branched-chain fatty acid synthesis, but supplementation with isobutanol restored production, indicating that Pfor4 substitutes for the canonical branched-chain \u03b1-keto acid dehydrogenase complex. These findings reveal two distinct routes for branched-chain fatty acid production in C. thermocellum: a Pfor4-dependent pathway from \u03b1-keto acid intermediates derived from amino acid synthesis, and an AdhE-dependent salvage pathway that assimilates exogenous branched-chain alcohols.", "date": "2026-03-04", "issue": "3", "identifier": "https://www.osti.gov/biblio/3024137", "bibliographicCitation": "https://doi.org/10.1128/msystems.01345-25", "keywords": [ "Acetivibrio thermocellus", "CBI", "branched-chain fatty acid synthesis", "lipid membrane remodeling", "mass spectrometry", "membrane remodeling", "Clostridium thermocellum" ], "topic": [ "Unknown" ], "journal_name": "mSystems", "volume": "11", "publisher_information": "American Society for Microbiology", "country_publication_code": "US", "creator": [ { "name": "Eashant [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI); Univ. of Wisconsin,Madison,WI (United States)] (ORCID:0009000100884235) Thusoo", "primaryContact": true }, { "name": "Tyler [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI); Univ. of Wisconsin,Madison,WI (United States)] Jacobson", "primaryContact": false }, { "name": "Bishal D. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI); Dartmouth College,Hanover,NH (United States)] (ORCID:0000000283264444) Sharma", "primaryContact": false }, { "name": "Isabella M. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI); Univ. of Wisconsin,Madison,WI (United States)] Col\u00f3n", "primaryContact": false }, { "name": "Lee R. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI); Dartmouth College,Hanover,NH (United States)] Lynd", "primaryContact": false }, { "name": "Daniel G. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI); Dartmouth College,Hanover,NH (United States)] (ORCID:0000000153936302) Olson", "primaryContact": false }, { "name": "Daniel [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI); Univ. of Wisconsin,Madison,WI (United States); Great Lakes Bioenergy Research Center (GLBRC),Madison,WI (United States)] (ORCID:0000000235683070) Amador-Noguez", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3024137", "active": false }, { "brc": "CBI", "title": "Construct design for precise DNA insertion in plants", "description": "Precise insertion of DNA sequences at targeted locations in plant genomes is pivotal for synthetic biology, genetics, and crop improvement. Construct design plays a critical role in achieving precise insertions, yet practical guidance remains limited. This review provides an in-depth overview of construct design principles and targeted DNA insertion (knock-in) strategies in plants. We assess the strengths, limitations, and construct requirements of current knock-in methods for specific applications, including short, large, and multifragment insertions. Additionally, we explore the potential of adopting advanced nonplant technologies to enhance knock-in efficiency and precision in plants. This review provides a valuable resource for facilitating the effective application of knock-in technologies to genetically improve crops with minimal off-target effects.", "abstract": "Precise insertion of DNA sequences at targeted locations in plant genomes is pivotal for synthetic biology, genetics, and crop improvement. Construct design plays a critical role in achieving precise insertions, yet practical guidance remains limited. This review provides an in-depth overview of construct design principles and targeted DNA insertion (knock-in) strategies in plants. We assess the strengths, limitations, and construct requirements of current knock-in methods for specific applications, including short, large, and multifragment insertions. Additionally, we explore the potential of adopting advanced nonplant technologies to enhance knock-in efficiency and precision in plants. This review provides a valuable resource for facilitating the effective application of knock-in technologies to genetically improve crops with minimal off-target effects.", "date": "2026-03-16", "identifier": "https://www.osti.gov/biblio/3024784", "bibliographicCitation": "https://doi.org/10.1016/j.tplants.2026.01.005", "keywords": [ "DNA construct", "genome editing", "high-precision engineering", "knock-in", "plant biotechnology", "synthetic biology" ], "topic": [ "Unknown" ], "journal_name": "Trends in Plant Science", "publisher_information": "Cell Press", "country_publication_code": "US", "creator": [ { "name": "Adnan [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000297920211) Muzaffar", "primaryContact": true }, { "name": "Md Torikul [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000175092411) Islam", "primaryContact": false }, { "name": "Adam M. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000158235329) Guss", "primaryContact": false }, { "name": "Gerald A. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000301061289) Tuskan", "primaryContact": false }, { "name": "Jin-Gui [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000217524201) Chen", "primaryContact": false }, { "name": "Xiaohan [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000152074210) Yang", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3024784", "active": false }, { "brc": "CBI", "title": "Selection and multi-environment yield stability analysis in a switchgrass (Panicum virgatum L.) half-sib panel", "date": "2026-05-31", "identifier": "https://www.osti.gov/biblio/3025251", "bibliographicCitation": "https://doi.org/10.1016/j.biombioe.2025.108885", "topic": [ "Unknown" ], "journal_name": "Biomass and Bioenergy", "volume": "209", "publisher_information": "Elsevier BV", "country_publication_code": "US", "creator": [ { "name": "Jazib Ali (ORCID:0000000229121979) Irfan", "primaryContact": true }, { "name": "Shiva Om (ORCID:0000000212288174) Makaju", "primaryContact": false }, { "name": "Mitra (ORCID:0000000261167758) Mazarei", "primaryContact": false }, { "name": "Charles Neal Stewart", "primaryContact": false }, { "name": "Ali Mekki (ORCID:0000000317101142) Missaoui", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "Biological and Environmental Research" } }, { "fundingOrganization": { "organizationName": "Center for Bioenergy Innovation" } }, { "fundingOrganization": { "organizationName": "Oak Ridge National Laboratory" } }, { "fundingOrganization": { "organizationName": "Office of Science" } }, { "fundingOrganization": { "organizationName": "U.S. Department of Energy" } } ], "dataset_url": "https://www.osti.gov/biblio/3025251", "active": false }, { "brc": "CBI", "title": "Rhythmic Mechanisms Governing CAM Photosynthesis in Kalanchoe fedtschenkoi: High-Resolution Temporal Transcriptomics", "description": "Crassulacean acid metabolism (CAM) is a specialized photosynthetic pathway that enhances water-use efficiency by temporally separating nocturnal CO2 uptake from daytime decarboxylation and carbon fixation. To uncover the regulatory mechanisms coordinating these temporal dynamics, we generated high-resolution, 48 h time-course transcriptomes for the CAM model Kalanchoe fedtschenkoi under both 12 h/12 h light/dark (LD) cycles and continuous light (LL). A rhythmicity analysis revealed that diel light cues are the dominant driver of transcript oscillations: 16,810 genes (54.3% of annotated genes) exhibited rhythmic expression only under LD, whereas just 399 genes (1.3%) remained rhythmic under LL. A smaller set of 3009 genes (9.7%) oscillated in both conditions, indicating that the intrinsic circadian clock sustains rhythmicity for a limited subset of the transcriptome. A gene co-expression network analysis revealed extensive integration between circadian clock components, core CAM pathway enzymes, and stomatal regulators, defining regulatory modules that coordinate metabolic and physiological timing. Notably, key hub genes associated with post-translational and post-transcriptional regulation, including the E3 ubiquitin ligase HUB2 and several pentatricopeptide repeat (PPR) proteins, act as central nodes in CAM-associated networks. This discovery implicates epigenetic and organellar regulation as previously unrecognized critical tiers of control in CAM. Together, our results support a regulatory model in which CAM rhythmicity is governed by both external light/dark cues and the endogenous circadian clock through multi-level control spanning transcriptional and protein-level regulation. To support community exploration, we also provide an interactive eFP (electronic Fluorescent Pictograph) browser for visualizing time-resolved gene expression profiles.", "abstract": "Crassulacean acid metabolism (CAM) is a specialized photosynthetic pathway that enhances water-use efficiency by temporally separating nocturnal CO2 uptake from daytime decarboxylation and carbon fixation. To uncover the regulatory mechanisms coordinating these temporal dynamics, we generated high-resolution, 48 h time-course transcriptomes for the CAM model Kalanchoe fedtschenkoi under both 12 h/12 h light/dark (LD) cycles and continuous light (LL). A rhythmicity analysis revealed that diel light cues are the dominant driver of transcript oscillations: 16,810 genes (54.3% of annotated genes) exhibited rhythmic expression only under LD, whereas just 399 genes (1.3%) remained rhythmic under LL. A smaller set of 3009 genes (9.7%) oscillated in both conditions, indicating that the intrinsic circadian clock sustains rhythmicity for a limited subset of the transcriptome. A gene co-expression network analysis revealed extensive integration between circadian clock components, core CAM pathway enzymes, and stomatal regulators, defining regulatory modules that coordinate metabolic and physiological timing. Notably, key hub genes associated with post-translational and post-transcriptional regulation, including the E3 ubiquitin ligase HUB2 and several pentatricopeptide repeat (PPR) proteins, act as central nodes in CAM-associated networks. This discovery implicates epigenetic and organellar regulation as previously unrecognized critical tiers of control in CAM. Together, our results support a regulatory model in which CAM rhythmicity is governed by both external light/dark cues and the endogenous circadian clock through multi-level control spanning transcriptional and protein-level regulation. To support community exploration, we also provide an interactive eFP (electronic Fluorescent Pictograph) browser for visualizing time-resolved gene expression profiles.", "date": "2026-01-28", "issue": "3", "identifier": "https://www.osti.gov/biblio/3027633", "bibliographicCitation": "https://doi.org/10.3390/ijms27031342", "keywords": [ "09 BIOMASS FUELS", "CBI", "Feedstock Development", "circadian clock", "crassulacean acid metabolism", "drought stress", "gene expression", "photosynthesis", "stomatal movement", "water-use efficiency" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "International Journal of Molecular Sciences (Online)", "volume": "27", "publisher_information": "MDPI", "country_publication_code": "US", "creator": [ { "name": "Rongbin [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000159216891) Hu", "primaryContact": true }, { "name": "Sara [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000281235439) Jawdy", "primaryContact": false }, { "name": "Avinash [HudsonAlpha Institute for Biotechnology,Huntsville,AL (United States)] (ORCID:0000000173367012) Sreedasyam", "primaryContact": false }, { "name": "Anna [USDOE Joint Genome Institute (JGI),Berkeley,CA (United States); Lawrence Berkeley National Laboratory (LBNL),Berkeley,CA (United States)] (ORCID:0000000322939329) Lipzen", "primaryContact": false }, { "name": "Mei [USDOE Joint Genome Institute (JGI),Berkeley,CA (United States); Lawrence Berkeley National Laboratory (LBNL),Berkeley,CA (United States)] Wang", "primaryContact": false }, { "name": "Vivian [USDOE Joint Genome Institute (JGI),Berkeley,CA (United States); Lawrence Berkeley National Laboratory (LBNL),Berkeley,CA (United States)] (ORCID:0000000189416931) Ng", "primaryContact": false }, { "name": "Christopher [USDOE Joint Genome Institute (JGI),Berkeley,CA (United States); Lawrence Berkeley National Laboratory (LBNL),Berkeley,CA (United States)] (ORCID:0000000338955892) Daum", "primaryContact": false }, { "name": "Keykhosrow [USDOE Joint Genome Institute (JGI),Berkeley,CA (United States); Lawrence Berkeley National Laboratory (LBNL),Berkeley,CA (United States)] Keymanesh", "primaryContact": false }, { "name": "Degao [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); Texas Tech University,Lubbock,TX (United States)] Liu", "primaryContact": false }, { "name": "Alex [Texas Tech University,Lubbock,TX (United States)] Hu", "primaryContact": false }, { "name": "Asher [University of Toronto,ON (Canada)] (ORCID:0000000293150520) Pasha", "primaryContact": false }, { "name": "Nicholas J. [University of Toronto,ON (Canada)] (ORCID:0000000155517232) Provart", "primaryContact": false }, { "name": "Anne M. [Newcastle University,Newcastle upon Tyne (United Kingdom)] Borland", "primaryContact": false }, { "name": "Timothy J. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000295406622) Tschaplinski", "primaryContact": false }, { "name": "Gerald A. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000301061289) Tuskan", "primaryContact": false }, { "name": "Jeremy [HudsonAlpha Institute for Biotechnology,Huntsville,AL (United States); USDOE Joint Genome Institute (JGI),Berkeley,CA (United States); Lawrence Berkeley National Laboratory (LBNL),Berkeley,CA (United States)] (ORCID:0000000180629172) Schmutz", "primaryContact": false }, { "name": "Xiaohan [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000152074210) Yang", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3027633", "active": false }, { "brc": "CBI", "title": "Techno-economic analysis of sugarcane bagasse and straw conversion into cellulosic ethanol via consolidated bioprocessing", "description": "Cellulosic biofuels offer a sustainable alternative to fossil fuels and a means to mitigate climate change. Consolidated bioprocessing (CBP) featuring engineered thermophilic bacteria, combined with mechanical disruption during fermentation (cotreatment), has potential to lower production costs compared to featuring thermochemical pretreatment and added cellulase. A techno-economic analysis was conducted (230 million L ethanol/year) from sugarcane bagasse and straw at stand-alone facilities generating electricity from residues. Three scenarios were evaluated: Conventional, featuring hydrothermal pretreatment, fungal cellulase, and yeast fermentation (current commercial standard); Mid-term CBP, relying on bagasse solubilization without pretreatment or cotreatment; and Mature CBP, incorporating cotreatment but no pretreatment. Results for these scenarios in this order were: fixed capital investment (CapEx) $\\$$589M, $\\$$658M, and $\\$$472M; net annual revenue (EBITDA) $\\$$56M, $\\$$96M, and $\\$$94M; and minimum ethanol selling price 0.73, 0.61, and 0.48 US$\\$$/L. Payback periods were 10.5, 6.9, and 5.1 years, while all scenarios showed <5 years at European prices for scales >100M L/year. Sensitivity and risk analysis highlighted ethanol price as the most critical variable. It is notable that Mid-term CBP had shorter payback times and better overall economic feasibility compared to Conventional. Our results underscore opportunities for research-driven innovation on low-cost cellulosic ethanol technologies in Brazil and elsewhere.", "abstract": "Cellulosic biofuels offer a sustainable alternative to fossil fuels and a means to mitigate climate change. Consolidated bioprocessing (CBP) featuring engineered thermophilic bacteria, combined with mechanical disruption during fermentation (cotreatment), has potential to lower production costs compared to featuring thermochemical pretreatment and added cellulase. A techno-economic analysis was conducted (230 million L ethanol/year) from sugarcane bagasse and straw at stand-alone facilities generating electricity from residues. Three scenarios were evaluated: Conventional, featuring hydrothermal pretreatment, fungal cellulase, and yeast fermentation (current commercial standard); Mid-term CBP, relying on bagasse solubilization without pretreatment or cotreatment; and Mature CBP, incorporating cotreatment but no pretreatment. Results for these scenarios in this order were: fixed capital investment (CapEx) $\\$$589M, $\\$$658M, and $\\$$472M; net annual revenue (EBITDA) $\\$$56M, $\\$$96M, and $\\$$94M; and minimum ethanol selling price 0.73, 0.61, and 0.48 US$\\$$/L. Payback periods were 10.5, 6.9, and 5.1 years, while all scenarios showed <5 years at European prices for scales >100M L/year. Sensitivity and risk analysis highlighted ethanol price as the most critical variable. It is notable that Mid-term CBP had shorter payback times and better overall economic feasibility compared to Conventional. Our results underscore opportunities for research-driven innovation on low-cost cellulosic ethanol technologies in Brazil and elsewhere.", "date": "2025-12-19", "identifier": "https://www.osti.gov/biblio/3027659", "bibliographicCitation": "https://doi.org/10.1016/j.renene.2025.125094", "keywords": [ "Consolidated bioprocessing", "Ethanol", "Lignocellulose", "Process simulation", "Thermophilic bacteria" ], "topic": [ "Unknown" ], "journal_name": "Renewable Energy", "volume": "259", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Isabela U. [Univ. of Campinas (UNICAMP),Sao Paulo (Brazil)] (ORCID:0000000342336568) Zambello", "primaryContact": true }, { "name": "Luisa P. [Univ. of Campinas (UNICAMP),Sao Paulo (Brazil)] Vaz", "primaryContact": false }, { "name": "Tassia L. [Brazilian Center for Research in Energy and Materials (CNPEM),Campinas (Brazil). Brazilian Biorenewables National Laboratory (LNBR)] (ORCID:0000000191087751) Junqueira", "primaryContact": false }, { "name": "Matthew R. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] (ORCID:0000000265070291) Kubis", "primaryContact": false }, { "name": "Lee R. [Univ. of Campinas (UNICAMP),Sao Paulo (Brazil); Dartmouth College,Hanover,NH (United States); Terragia,Hanover,NH (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] Lynd", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science (BSS)" } } ], "dataset_url": "https://www.osti.gov/biblio/3027659", "active": false }, { "brc": "CBI", "title": "Higher Wood Density Lowers Feedstock Cost and Has Minimal Impact on Biomass Conversion to Biofuels", "description": "Poplar and other woody feedstocks have the potential to provide up to 200 million tons of biomass per year that can be converted to liquid fuels. Most forestry strategies that aim to increase biomass productivity per hectare rely on short rotation plantations of fast-growing varieties. The improvement of the wood density as a key trait itself has largely been overlooked. We evaluated natural variation in wood density across a population of genetically diverse Populus trichocarpa trees grown in a common garden. Wood density varies greatly within this population but is heritable; higher wood density was not systematically associated with reduced growth, challenging assumptions of a trade-off between wood density and biomass accumulation. Furthermore, denser wood led to significant improvements throughout the supply chain including lowering biomass production and transportation costs. Higher density did not correlate with changes in biomass composition. Density did not impact bioconversion in the two feedstock-to-fuel pipelines tested (pretreatment by ionic liquids and fermentation to bisabolene or soaking in aqueous ammonia and fermentation to ethanol) on a representative subset of poplars. These findings highlight wood density as a promising breeding target for accelerating the development of high-yielding, conversion-efficient bioenergy crops and as an avenue for increasing landuse efficiency and reducing biomass transportation cost.", "abstract": "Poplar and other woody feedstocks have the potential to provide up to 200 million tons of biomass per year that can be converted to liquid fuels. Most forestry strategies that aim to increase biomass productivity per hectare rely on short rotation plantations of fast-growing varieties. The improvement of the wood density as a key trait itself has largely been overlooked. We evaluated natural variation in wood density across a population of genetically diverse Populus trichocarpa trees grown in a common garden. Wood density varies greatly within this population but is heritable; higher wood density was not systematically associated with reduced growth, challenging assumptions of a trade-off between wood density and biomass accumulation. Furthermore, denser wood led to significant improvements throughout the supply chain including lowering biomass production and transportation costs. Higher density did not correlate with changes in biomass composition. Density did not impact bioconversion in the two feedstock-to-fuel pipelines tested (pretreatment by ionic liquids and fermentation to bisabolene or soaking in aqueous ammonia and fermentation to ethanol) on a representative subset of poplars. These findings highlight wood density as a promising breeding target for accelerating the development of high-yielding, conversion-efficient bioenergy crops and as an avenue for increasing landuse efficiency and reducing biomass transportation cost.", "date": "2026-03-23", "issue": "13", "identifier": "https://www.osti.gov/biblio/3028781", "bibliographicCitation": "https://doi.org/10.1021/acssuschemeng.5c10590", "keywords": [ "09 BIOMASS FUELS", "ammonia pretreatment", "biofuels", "biomass", "biomass pretreatment", "biomass productivity", "carbohydrates", "feedstock costs", "genetics", "ionic liquids", "poplar", "pretreatment", "wood", "wood density" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "ACS Sustainable Chemistry & Engineering", "volume": "14", "publisher_information": "American Chemical Society (ACS)", "country_publication_code": "US", "creator": [ { "name": "Raphael AP [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); University of Tennessee,Knoxville,TN (United States)] (ORCID:0000000348095988) Ployet", "primaryContact": true }, { "name": "Chanaka Roshan. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Abeyratne", "primaryContact": false }, { "name": "Robin J. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000202171124) Clark", "primaryContact": false }, { "name": "Hari B. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Chhetri", "primaryContact": false }, { "name": "Doug [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Hyatt", "primaryContact": false }, { "name": "Jr.,Miguel [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Rodriguez", "primaryContact": false }, { "name": "Sara [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Jawdy", "primaryContact": false }, { "name": "Dan [University of Wisconsin-Madison,WI (United States)] Xie", "primaryContact": false }, { "name": "Kallysa [University of Wisconsin-Madison,WI (United States)] Taylor", "primaryContact": false }, { "name": "Morgan [University of Wisconsin-Madison,WI (United States)] Davies", "primaryContact": false }, { "name": "Venkataramana R. [Joint BioEnergy Institute,Emeryville,CA (United States); Lawrence Berkeley National Laboratory (LBNL),Berkeley,CA (United States)] Pidatala", "primaryContact": false }, { "name": "Anne E. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); National Laboratory of the Rockies,Golden,CO (United States)] (ORCID:0000000279279424) Harman-Ware", "primaryContact": false }, { "name": "Renee M. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); National Laboratory of the Rockies,Golden,CO (United States)] (ORCID:0000000171390083) Happs", "primaryContact": false }, { "name": "Alberto [Joint BioEnergy Institute,Emeryville,CA (United States); Sandia National Lab. (SNL-CA),Livermore,CA (United States)] (ORCID:0000000240450108) Rodriguez", "primaryContact": false }, { "name": "Trey K. [University of Wisconsin-Madison,WI (United States)] Sato", "primaryContact": false }, { "name": "Erin G. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000215018647) Webb", "primaryContact": false }, { "name": "Stephen P. [West Virginia University,Morgantown,WV (United States)] DiFazio", "primaryContact": false }, { "name": "Jin-Gui [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Chen", "primaryContact": false }, { "name": "Gerald A. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Tuskan", "primaryContact": false }, { "name": "Wellington [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Muchero", "primaryContact": false }, { "name": "Brian H. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000274083609) Davison", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "Biological and Environmental Research" } }, { "fundingOrganization": { "organizationName": "USDOE National Nuclear Security Administration (NNSA)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3028781", "active": false, "has_related_ids": [ "NLR/JA-2700-97219" ] }, { "brc": "CBI", "title": "F\u2010Box Protein\u2010Mediated Proteolytic Regulation of Phenylpropanoid Metabolism in Response to Biotic and Abiotic Stresses", "description": "Protein ubiquitination is a central regulatory mechanism governing plant growth, development and environmental adaptation. Ubiquitylomic studies have revealed that many enzymes in phenylpropanoid biosynthetic pathways are subject to ubiquitination. Increasing evidence indicates that specific F-box proteins target key enzymes in these pathways, including PAL, CCR, CAD, COMT and peroxidases in the lignin biosynthetic branch, and CHS in the flavonoid biosynthetic branch, thereby promoting their ubiquitination and selective degradation. These F-box proteins act in response to diverse developmental and environmental cues, including cellular carbon status, light quality and intensity, and biotic stresses (e.g., pathogen and insect attack). By regulating the stability and activity of both enzymes and regulatory proteins involved in phenylpropanoid biosynthesis, F-box proteins modulate the accumulation of simple phenolics and lignin polymers, ultimately contributing to plant resilience. This review summarizes recent advances in the characterization of F-box proteins involved in phenylpropanoid metabolism and their regulatory roles in response to biotic and abiotic stresses and identifies key knowledge gaps that limit mechanistic understanding of F-box protein-mediated proteolytic regulation of phenylpropanoid metabolism. In conclusion, insights into ubiquitin-mediated proteolytic control of phenylpropanoid metabolism offer promising avenues for enhancing bioactive phenolic production, advancing biofuel feedstock engineering and improving crop stress tolerance.", "abstract": "Protein ubiquitination is a central regulatory mechanism governing plant growth, development and environmental adaptation. Ubiquitylomic studies have revealed that many enzymes in phenylpropanoid biosynthetic pathways are subject to ubiquitination. Increasing evidence indicates that specific F-box proteins target key enzymes in these pathways, including PAL, CCR, CAD, COMT and peroxidases in the lignin biosynthetic branch, and CHS in the flavonoid biosynthetic branch, thereby promoting their ubiquitination and selective degradation. These F-box proteins act in response to diverse developmental and environmental cues, including cellular carbon status, light quality and intensity, and biotic stresses (e.g., pathogen and insect attack). By regulating the stability and activity of both enzymes and regulatory proteins involved in phenylpropanoid biosynthesis, F-box proteins modulate the accumulation of simple phenolics and lignin polymers, ultimately contributing to plant resilience. This review summarizes recent advances in the characterization of F-box proteins involved in phenylpropanoid metabolism and their regulatory roles in response to biotic and abiotic stresses and identifies key knowledge gaps that limit mechanistic understanding of F-box protein-mediated proteolytic regulation of phenylpropanoid metabolism. In conclusion, insights into ubiquitin-mediated proteolytic control of phenylpropanoid metabolism offer promising avenues for enhancing bioactive phenolic production, advancing biofuel feedstock engineering and improving crop stress tolerance.", "date": "2026-02-14", "issue": "6", "identifier": "https://www.osti.gov/biblio/3030184", "bibliographicCitation": "https://doi.org/10.1111/pce.70445", "keywords": [ "(A)biotic stress", "59 BASIC BIOLOGICAL SCIENCES", "F-box proteins", "Flavonoids", "Lignin", "Phenylpropanoids", "Phytopathogen", "Sugar signaling", "Ubiquitination" ], "topic": [ "Microbiology" ], "journal_name": "Plant, Cell and Environment", "volume": "49", "publisher_information": "Wiley", "country_publication_code": "US", "creator": [ { "name": "Guoqian [Brookhaven National Laboratory (BNL),Upton,NY (United States)] (ORCID:0000000210454562) Yang", "primaryContact": true }, { "name": "Chang\u2010Jun [Brookhaven National Laboratory (BNL),Upton,NY (United States)] (ORCID:0000000161898756) Liu", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division (CSGB)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3030184", "active": false, "has_related_ids": [ "BNL-229524-2026-JAAM" ] }, { "brc": "CBI", "title": "Depth-dependent links between microbial taxa and nitrous oxide emissions in a long-term cotton cropping system employing soil health practices", "description": "Long-term management practices can shape soil microbial communities in ways that influence nitrogen (N) dynamics and nitrous oxide (N2O) emissions. We leverage a 41-year continuous cotton cropping experiment with contrasting tillage, cover cropping, and N fertilization regimes to investigate how these long-term strategies influence soil microbial communities and their associations with N2O fluxes during the cotton growing season. Using 16S rRNA gene metabarcoding, we assessed microbial composition in surface and subsurface soils and evaluated its relationship with temporal N2O emissions. Among the management practices, N fertilization \u2013 a known driver of N2O emissions \u2013 had the strongest effect on microbial community composition and was linked to a greater number of taxa correlated to N2O emissions, particularly in surface soils. Soil pH emerged as a key variable influencing microbial structure across depth and was negatively associated with both N2O emissions and microbial composition in the surface layers of fertilized soils. In total, 57 archaeal/bacterial taxa were correlated with N2O fluxes, but only seven were shared across depths, suggesting distinct microbial contributors in surface and subsurface soils. Several of these taxa have been previously reported to be associated with N and C cycling processes such as nitrate respiration or carbon turnover, indicating functional context to their correlation with N2O fluxes. Temporal shifts in the abundance of key taxa aligned with seasonal peaks in N2O emissions, notably in early and late August, and were most pronounced under conventional tillage, hairy vetch cover cropping, and N fertilization. While 16S-based associations cannot confirm functional gene presence or activity, these findings demonstrate that long-term fertilization and associated soil acidification are dominant drivers of microbial shifts linked to N2O emissions and highlight the importance of accounting for depth-specific and seasonal microbial dynamics when evaluating management impacts on greenhouse gas emissions.", "abstract": "Long-term management practices can shape soil microbial communities in ways that influence nitrogen (N) dynamics and nitrous oxide (N2O) emissions. We leverage a 41-year continuous cotton cropping experiment with contrasting tillage, cover cropping, and N fertilization regimes to investigate how these long-term strategies influence soil microbial communities and their associations with N2O fluxes during the cotton growing season. Using 16S rRNA gene metabarcoding, we assessed microbial composition in surface and subsurface soils and evaluated its relationship with temporal N2O emissions. Among the management practices, N fertilization \u2013 a known driver of N2O emissions \u2013 had the strongest effect on microbial community composition and was linked to a greater number of taxa correlated to N2O emissions, particularly in surface soils. Soil pH emerged as a key variable influencing microbial structure across depth and was negatively associated with both N2O emissions and microbial composition in the surface layers of fertilized soils. In total, 57 archaeal/bacterial taxa were correlated with N2O fluxes, but only seven were shared across depths, suggesting distinct microbial contributors in surface and subsurface soils. Several of these taxa have been previously reported to be associated with N and C cycling processes such as nitrate respiration or carbon turnover, indicating functional context to their correlation with N2O fluxes. Temporal shifts in the abundance of key taxa aligned with seasonal peaks in N2O emissions, notably in early and late August, and were most pronounced under conventional tillage, hairy vetch cover cropping, and N fertilization. While 16S-based associations cannot confirm functional gene presence or activity, these findings demonstrate that long-term fertilization and associated soil acidification are dominant drivers of microbial shifts linked to N2O emissions and highlight the importance of accounting for depth-specific and seasonal microbial dynamics when evaluating management impacts on greenhouse gas emissions.", "date": "2025-12-02", "identifier": "https://www.osti.gov/biblio/3030350", "bibliographicCitation": "https://doi.org/10.1016/j.geoderma.2025.117620", "keywords": [ "16S rRNA gene sequencing", "Depth-specific microbial responses", "Greenhouse gas", "Long-term fertilization", "Metabarcoding", "Soil health practices", "Soil microbial communities" ], "topic": [ "Unknown" ], "journal_name": "Geoderma", "volume": "464", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Facundo [University of Tennessee,Knoxville,TN (United States)] Lussich", "primaryContact": true }, { "name": "Jashanjeet Kaur [University of Tennessee,Knoxville,TN (United States)] (ORCID:000000023527033X) Dhaliwal", "primaryContact": false }, { "name": "Shawn P. [University of Memphis,TN (United States)] Brown", "primaryContact": false }, { "name": "Melissa A. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:000000018329366X) Cregger", "primaryContact": false }, { "name": "Debasish [University of Tennessee,Knoxville,TN (United States)] (ORCID:000000019425675X) Saha", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDA" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3030350", "active": false }, { "brc": "CBI", "title": "Unraveling plant phenotype to genotype associations with daily hyperspectral traits in Populus trichocarpa", "description": "Hyperspectral remote sensing is a powerful, high-throughput phenotyping tool that quantifies physiologically and structurally relevant wavelengths across diverse genotypes and over varying temporal scales. In this study, we combined tower-based continuous hyperspectral sensing with genome-wide association studies to analyze 1423 wavebands (400-900 nm) and derivative vegetation indices across 505 genotypes and the genetic architecture of hyperspectral phenotypes over time in Populus trichocarpa Torr. & Gray grown under field conditions. Wavelengths related to chlorophyll and carotenoid absorption spectra exhibited the strongest genetic variation resulting in 98 significant SNP associations. Notably, we found substantial overlap in genetic association between the blue and red spectral regions, indicative of carotenoids and chlorophyll, respectively, and identified more than 10 candidate genes associated with chloroplast function, underpinning photosynthetic activity. Furthermore, fluctuations in associations for vegetative indices, such as the chlorophyll:carotenoid index (CCI), across the growing season reveal a temporally dynamic genetic architecture of physiological traits associated with fall senescence of this temperate tree species. Finally, we also observed correlations (spearman rho = 0.3, p < 1x10\u22128) between individual wavebands or vegetative indices and growth rate, assessed as the relative change of tree height over the growing season. The growth rate prediction was substantially improved by a regularization multivariate model (spearman rho>0.5, p < 1x10\u221216), reinforcing the value of hyperspectral measurements for predicting traits linked to tree productivity. These findings highlight the potential of high-throughput, rapid, hyperspectral genome wide association studies GWAS to uncover physiologically meaningful genetic variation and offer promising insights for future acceleration for plant breeding.", "abstract": "Hyperspectral remote sensing is a powerful, high-throughput phenotyping tool that quantifies physiologically and structurally relevant wavelengths across diverse genotypes and over varying temporal scales. In this study, we combined tower-based continuous hyperspectral sensing with genome-wide association studies to analyze 1423 wavebands (400-900 nm) and derivative vegetation indices across 505 genotypes and the genetic architecture of hyperspectral phenotypes over time in Populus trichocarpa Torr. & Gray grown under field conditions. Wavelengths related to chlorophyll and carotenoid absorption spectra exhibited the strongest genetic variation resulting in 98 significant SNP associations. Notably, we found substantial overlap in genetic association between the blue and red spectral regions, indicative of carotenoids and chlorophyll, respectively, and identified more than 10 candidate genes associated with chloroplast function, underpinning photosynthetic activity. Furthermore, fluctuations in associations for vegetative indices, such as the chlorophyll:carotenoid index (CCI), across the growing season reveal a temporally dynamic genetic architecture of physiological traits associated with fall senescence of this temperate tree species. Finally, we also observed correlations (spearman rho = 0.3, p < 1x10\u22128) between individual wavebands or vegetative indices and growth rate, assessed as the relative change of tree height over the growing season. The growth rate prediction was substantially improved by a regularization multivariate model (spearman rho>0.5, p < 1x10\u221216), reinforcing the value of hyperspectral measurements for predicting traits linked to tree productivity. These findings highlight the potential of high-throughput, rapid, hyperspectral genome wide association studies GWAS to uncover physiologically meaningful genetic variation and offer promising insights for future acceleration for plant breeding.", "date": "2026-03-26", "issue": "2", "identifier": "https://www.osti.gov/biblio/3030360", "bibliographicCitation": "https://doi.org/10.1016/j.plaphe.2026.100174", "keywords": [ "09 BIOMASS FUELS", "Carotenoids", "Chlorophyll", "Chloroplasts", "Feedstock Development", "CBI", "Field-based", "Genetic basis of hyperspectral traits", "Heritability", "Hyperspectral GWAS", "Hyperspectral remote sensing", "Poplar", "Populus Trichocarpa", "Vegetation indices", "hyperspectral" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Plant Phenomics", "volume": "8", "publisher_information": "AAAS", "country_publication_code": "US", "creator": [ { "name": "Marie C. [Univ. of California,Davis,CA (United States)] (ORCID:0009000341998970) Klein", "primaryContact": true }, { "name": "Christopher YS. [Univ. of California,Davis,CA (United States); Univ. of New Brunswick,Fredericton NB (Canada)] Wong", "primaryContact": false }, { "name": "J. Grey [Univ. of California,Davis,CA (United States)] Monroe", "primaryContact": false }, { "name": "Jack [Univ. of California,Davis,CA (United States)] Bailey-Bale", "primaryContact": false }, { "name": "Thomas N. [Univ. of California,Davis,CA (United States)] Buckley", "primaryContact": false }, { "name": "Jin-Gui [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] (ORCID:0000000217524201) Chen", "primaryContact": false }, { "name": "Mengjun [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] (ORCID:0000000263232664) Shu", "primaryContact": false }, { "name": "Timothy J. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] (ORCID:0000000295406622) Tschaplinski", "primaryContact": false }, { "name": "Gerald A. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States). Center for Bioenergy Innovation (CBI)] (ORCID:0000000301061289) Tuskan", "primaryContact": false }, { "name": "Troy S. [Univ. of California,Davis,CA (United States); Univ. of Montana,Missoula,MT (United States)] (ORCID:0000000290330024) Magney", "primaryContact": false }, { "name": "Gail [Univ. of California,Davis,CA (United States); Univ. College London (United Kingdom)] (ORCID:0000000184706390) Taylor", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3030360", "active": false }, { "brc": "CBI", "title": "Woody Plant Transformation: Current Status, Challenges, and Future Perspectives", "description": "Woody plants, comprising forest and fruit tree species, provide essential ecological and economic benefits to society. Their genetic improvement is challenging due to long generation intervals and high heterozygosity. Genetic transformation, which combines targeted DNA delivery with plant regeneration from transformed cells, offers a powerful alternative to accelerating their domestication and improvement. Agrobacterium tumefaciens, Rhizobium rhizogenes, and particle bombardment have been widely used for DNA delivery into a wide variety of explants, including leaves, stems, hypocotyls, roots, and embryos, with regeneration occurring via direct organogenesis, callus-mediated organogenesis, somatic embryogenesis, or hairy root formation. Despite successes, conventional approaches are hampered by low efficiency, genotype dependency, and a reliance on challenging tissue culture. This review provides a critical analysis of the current landscape in woody plant transformation, moving beyond a simple summary of techniques to evaluate the co-evolution of established platforms with disruptive technologies. Key advances among these include the use of developmental regulators to engineer regeneration, the rise in in planta systems to bypass tissue culture, and the imperative for DNA-free genome editing to meet regulatory and public expectations. By examining species-specific breakthroughs in key genera, including Populus, Malus, Citrus, and Pinus, this review highlights a paradigm shift from empirical optimization towards rational, predictable engineering of woody plants for a sustainable future.", "abstract": "Woody plants, comprising forest and fruit tree species, provide essential ecological and economic benefits to society. Their genetic improvement is challenging due to long generation intervals and high heterozygosity. Genetic transformation, which combines targeted DNA delivery with plant regeneration from transformed cells, offers a powerful alternative to accelerating their domestication and improvement. Agrobacterium tumefaciens, Rhizobium rhizogenes, and particle bombardment have been widely used for DNA delivery into a wide variety of explants, including leaves, stems, hypocotyls, roots, and embryos, with regeneration occurring via direct organogenesis, callus-mediated organogenesis, somatic embryogenesis, or hairy root formation. Despite successes, conventional approaches are hampered by low efficiency, genotype dependency, and a reliance on challenging tissue culture. This review provides a critical analysis of the current landscape in woody plant transformation, moving beyond a simple summary of techniques to evaluate the co-evolution of established platforms with disruptive technologies. Key advances among these include the use of developmental regulators to engineer regeneration, the rise in in planta systems to bypass tissue culture, and the imperative for DNA-free genome editing to meet regulatory and public expectations. By examining species-specific breakthroughs in key genera, including Populus, Malus, Citrus, and Pinus, this review highlights a paradigm shift from empirical optimization towards rational, predictable engineering of woody plants for a sustainable future.", "date": "2025-11-07", "issue": "22", "identifier": "https://www.osti.gov/biblio/3030399", "bibliographicCitation": "https://doi.org/10.3390/plants14223420", "keywords": [ "Agrobacterium tumefaciens", "Rhizobium rhizogenes", "developmental regulators", "hairy root", "in planta transformation" ], "topic": [ "Unknown" ], "journal_name": "Plants", "volume": "14", "publisher_information": "MDPI", "country_publication_code": "US", "creator": [ { "name": "Bal Krishna [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:000000027166837X) Maharjan", "primaryContact": true }, { "name": "Md Torikul [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000175092411) Islam", "primaryContact": false }, { "name": "Adnan [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000297920211) Muzaffar", "primaryContact": false }, { "name": "Timothy J. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000295406622) Tschaplinski", "primaryContact": false }, { "name": "Gerald A. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000301061289) Tuskan", "primaryContact": false }, { "name": "Jin-Gui [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000217524201) Chen", "primaryContact": false }, { "name": "Xiaohan [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000152074210) Yang", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3030399", "active": false }, { "brc": "CBI", "title": "A haplotype-resolved, chromosome-scale genome assembly for the southern live oak, Quercus virginiana", "description": "Hybridization is a major force driving diversification, migration, and adaptation in Quercus species. While population genetics and phylogenetics have traditionally been used for studying these processes, advances in sequencing technology now enable us to incorporate comparative and pan-genomic approaches as well. Here, we present a highly contiguous, chromosome-scale and haplotype-resolved genome assembly for the southern live oak, Quercus virginiana, the first reference genome for section Virentes, as part of the American Campus Tree Genomes program. Originating from a clone of Auburn University's historic \u201cToomer's Oak,\u201d this assembly contributes to the pool of genomic resources for investigating recombination, haplotype variation, and structural genomic changes influencing hybridization potential in this clade and across Quercus. It also provides insights into the architecture of the putative centromeric regions within the genus. Alongside other oak references, the Q. virginiana genome will support research into the evolution and adaptation of the Quercus genus.", "abstract": "Hybridization is a major force driving diversification, migration, and adaptation in Quercus species. While population genetics and phylogenetics have traditionally been used for studying these processes, advances in sequencing technology now enable us to incorporate comparative and pan-genomic approaches as well. Here, we present a highly contiguous, chromosome-scale and haplotype-resolved genome assembly for the southern live oak, Quercus virginiana, the first reference genome for section Virentes, as part of the American Campus Tree Genomes program. Originating from a clone of Auburn University's historic \u201cToomer's Oak,\u201d this assembly contributes to the pool of genomic resources for investigating recombination, haplotype variation, and structural genomic changes influencing hybridization potential in this clade and across Quercus. It also provides insights into the architecture of the putative centromeric regions within the genus. Alongside other oak references, the Q. virginiana genome will support research into the evolution and adaptation of the Quercus genus.", "date": "2026-02-01", "issue": "4", "identifier": "https://www.osti.gov/biblio/3030808", "bibliographicCitation": "https://doi.org/10.1093/g3journal/jkag023", "keywords": [ "Quercus virginiana", "genome assembly", "live oak", "syngameon" ], "topic": [ "Unknown" ], "journal_name": "G3", "volume": "16", "publisher_information": "Genetics Society of America", "country_publication_code": "US", "creator": [ { "name": "Laramie [Auburn Univ.,AL (United States); HudsonAlpha Institute for Biotechnology,Huntsville,AL (United States)] (ORCID:0000000333413509) Ak\u00f6zbek", "primaryContact": true }, { "name": "Zachary [Auburn Univ.,AL (United States); HudsonAlpha Institute for Biotechnology,Huntsville,AL (United States)] Meharg", "primaryContact": false }, { "name": "Jillian [Auburn Univ.,AL (United States)] Abendroth-McGhee", "primaryContact": false }, { "name": "Tosin [Auburn Univ.,AL (United States)] Akinsipe", "primaryContact": false }, { "name": "Rijan [Univ. of Alabama,Huntsville,AL (United States)] Dhakal", "primaryContact": false }, { "name": "Nicholas [Auburn Univ.,AL (United States)] Gladstone", "primaryContact": false }, { "name": "Zahida [Alabama Department of Agriculture and Industries (AGI),Montgomery,AL (United States)] Pervaiz", "primaryContact": false }, { "name": "Sejal [Auburn Univ.,AL (United States)] Patel", "primaryContact": false }, { "name": "Giovani [Auburn Univ.,AL (United States)] Rossi", "primaryContact": false }, { "name": "Claudia Ann [Savannah River National Laboratory (SRNL),Aiken,SC (United States)] Rutland", "primaryContact": false }, { "name": "Caroline [HudsonAlpha Institute for Biotechnology,Huntsville,AL (United States); Univ. of Alabama,Huntsville,AL (United States)] Bendickson", "primaryContact": false }, { "name": "Adam [Univ. of New Mexico,Albuquerque,NM (United States)] Kranz", "primaryContact": false }, { "name": "Ellen O. [Univ. of New Mexico,Albuquerque,NM (United States)] Martinson", "primaryContact": false }, { "name": "Scott P. [Rice Univ.,Houston,TX (United States)] Egan", "primaryContact": false }, { "name": "F. Alex [Praxis AI LLC,Clemson,SC (United States)] Feltus", "primaryContact": false }, { "name": "David J. [Praxis AI LLC,Clemson,SC (United States)] Clarke", "primaryContact": false }, { "name": "John T. [HudsonAlpha Institute for Biotechnology,Huntsville,AL (United States)] (ORCID:0000000289381166) Lovell", "primaryContact": false }, { "name": "Jenell [HudsonAlpha Institute for Biotechnology,Huntsville,AL (United States)] Webber", "primaryContact": false }, { "name": "Lori Beth [HudsonAlpha Institute for Biotechnology,Huntsville,AL (United States)] Boston", "primaryContact": false }, { "name": "Haley [HudsonAlpha Institute for Biotechnology,Huntsville,AL (United States)] Hale", "primaryContact": false }, { "name": "Hannah [HudsonAlpha Institute for Biotechnology,Huntsville,AL (United States)] McCoy", "primaryContact": false }, { "name": "Jane [HudsonAlpha Institute for Biotechnology,Huntsville,AL (United States); USDOE Joint Genome Institute (JGI),Berkeley,CA (United States); Lawrence Berkeley National Laboratory (LBNL),Berkeley,CA (United States)] (ORCID:0000000283568325) Grimwood", "primaryContact": false }, { "name": "Sarah B. [HudsonAlpha Institute for Biotechnology,Huntsville,AL (United States)] Carey", "primaryContact": false }, { "name": "Leslie [Univ. of Alabama,Huntsville,AL (United States)] Goertzen", "primaryContact": false }, { "name": "Alex [HudsonAlpha Institute for Biotechnology,Huntsville,AL (United States)] (ORCID:0000000220350871) Harkess", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "National Science Foundation (NSF)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science (BSS)" } } ], "dataset_url": "https://www.osti.gov/biblio/3030808", "active": false }, { "brc": "CBI", "title": "Nonenergy Biomass Carbon Removal and Storage (BiCRS): Assessing Durability of Nongaseous Carbon Products Across Terrestrial Storage Fates", "description": "Biomass Carbon Removal and Storage, or BiCRS, pathways use plants or algae that remove carbon dioxide from the atmosphere through photosynthesis and store it underground or in long-lived products. While some BiCRS approaches generate an energy product, all BiCRS approaches generate a carbon product. A new subset of BiCRS approaches focus on the storage of these raw or converted carbon products for generation of carbon credits. However, the durability of these approaches is highly variable as carbon products vary widely in their \u201cform\u201d and the conditions of their \u201cfate.\u201d We organize our thinking about carbon products and their durability around these two primary axes. The durability of carbon product \u201cforms\u201d is mediated by chemical recalcitrance and ranges substantially across agricultural residues, municipal solid waste, woody biomass, and nongaseous products of thermochemical conversion (e.g., biochars and bio-oils). Meanwhile, terrestrial storage \u201cfates\u201d vary in the mechanism employed to stall decay, including surface storage, dry storage, shallow anoxic storage, and deep or geologic anoxic storage (or injection). Each mechanism has different implications for suitability with different feedstock forms as well as long-term risks. We present a framework for assessing durability of solid or liquid raw and conversion carbon products under terrestrial storage fates, highlighting knowns, unknowns, and research priorities moving forward.", "abstract": "Biomass Carbon Removal and Storage, or BiCRS, pathways use plants or algae that remove carbon dioxide from the atmosphere through photosynthesis and store it underground or in long-lived products. While some BiCRS approaches generate an energy product, all BiCRS approaches generate a carbon product. A new subset of BiCRS approaches focus on the storage of these raw or converted carbon products for generation of carbon credits. However, the durability of these approaches is highly variable as carbon products vary widely in their \u201cform\u201d and the conditions of their \u201cfate.\u201d We organize our thinking about carbon products and their durability around these two primary axes. The durability of carbon product \u201cforms\u201d is mediated by chemical recalcitrance and ranges substantially across agricultural residues, municipal solid waste, woody biomass, and nongaseous products of thermochemical conversion (e.g., biochars and bio-oils). Meanwhile, terrestrial storage \u201cfates\u201d vary in the mechanism employed to stall decay, including surface storage, dry storage, shallow anoxic storage, and deep or geologic anoxic storage (or injection). Each mechanism has different implications for suitability with different feedstock forms as well as long-term risks. We present a framework for assessing durability of solid or liquid raw and conversion carbon products under terrestrial storage fates, highlighting knowns, unknowns, and research priorities moving forward.", "date": "2026-04-09", "issue": "8", "identifier": "https://www.osti.gov/biblio/3363067", "bibliographicCitation": "https://doi.org/10.1021/acs.chemrev.5c00618", "keywords": [ "09 BIOMASS FUELS", "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "biomass", "carbon removal", "carbon storage", "durability" ], "topic": [ "Biomass & Feedstock", "Chemistry" ], "journal_name": "Chemical Reviews", "volume": "126", "publisher_information": "American Chemical Society", "country_publication_code": "US", "creator": [ { "name": "Sin\u00e9ad M. [Carbon Containment Lab (CC Lab),New Haven,CT (United States)] (ORCID:0000000326899395) Crotty", "primaryContact": true }, { "name": "Peter W. [Univ. of Arizona,Tucson,AZ (United States)] Reiners", "primaryContact": false }, { "name": "Leah K. [Carbon Containment Lab (CC Lab),New Haven,CT (United States)] (ORCID:0000000274938101) Clayton", "primaryContact": false }, { "name": "Edward [Charm Industrial,San Francisco,CA (United States)] Young", "primaryContact": false }, { "name": "Andrew [Carba,Inc.,Eden Prairie,MN (United States)] Jones", "primaryContact": false }, { "name": "Melissa A. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Cregger", "primaryContact": false }, { "name": "Anne K. [National Laboratory of the Rockies (NLR),Golden,CO (United States)] (ORCID:0000000292042050) Starace", "primaryContact": false }, { "name": "Anne E. [National Laboratory of the Rockies (NLR),Golden,CO (United States)] (ORCID:0000000279279424) Harman-Ware", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "Hydrocarbons and Geothermal Energy Office (HGEO)" } }, { "fundingOrganization": { "organizationName": "Office of Technology Commercialization (OTC)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3363067", "active": false, "has_related_ids": [ "NLR/JA-2700-95725" ] }, { "brc": "CBI", "title": "Turbo\u2010charging crop improvement: harnessing multiplex editing for polygenic trait engineering and beyond", "description": "Multiplex CRISPR editing has emerged as a transformative platform for plant genome engineering, enabling the simultaneous targeting of multiple genes, regulatory elements, or chromosomal regions. This approach is effective for dissecting gene family functions, addressing genetic redundancy, engineering polygenic traits, and accelerating trait stacking and de novo domestication. Its applications now extend beyond standard gene knockouts to include epigenetic and transcriptional regulation, chromosomal engineering, and transgene\u2010free editing. These capabilities are advancing crop improvement not only in annual species but also in more complex systems such as polyploids, undomesticated wild relatives, and species with long generation times. At the same time, multiplex editing presents technical challenges, including complex construct design and the need for robust, scalable mutation detection. We discuss current toolkits and recent innovations in vector architecture, such as promoter and scaffold engineering, that streamline workflows and enhance editing efficiency. High\u2010throughput sequencing technologies, including long\u2010read platforms, are improving the resolution of complex editing outcomes such as structural rearrangements\u2014often missed by standard genotyping\u2014when targeting repetitive or tandemly spaced loci. To fully realize the potential of multiplex genome engineering, there is growing demand for user\u2010friendly, synthetic biology\u2010compatible, and scalable computational workflows for gRNA design, construct assembly, and mutation analysis. Experimentally validated inducible or tissue\u2010specific promoters are also highly desirable for achieving spatiotemporal control. As these tools continue to evolve, multiplex CRISPR editing is poised to become a foundational technology of next\u2010generation crop improvement to address challenges in agriculture, sustainability, and climate resilience.", "abstract": "Multiplex CRISPR editing has emerged as a transformative platform for plant genome engineering, enabling the simultaneous targeting of multiple genes, regulatory elements, or chromosomal regions. This approach is effective for dissecting gene family functions, addressing genetic redundancy, engineering polygenic traits, and accelerating trait stacking and de novo domestication. Its applications now extend beyond standard gene knockouts to include epigenetic and transcriptional regulation, chromosomal engineering, and transgene\u2010free editing. These capabilities are advancing crop improvement not only in annual species but also in more complex systems such as polyploids, undomesticated wild relatives, and species with long generation times. At the same time, multiplex editing presents technical challenges, including complex construct design and the need for robust, scalable mutation detection. We discuss current toolkits and recent innovations in vector architecture, such as promoter and scaffold engineering, that streamline workflows and enhance editing efficiency. High\u2010throughput sequencing technologies, including long\u2010read platforms, are improving the resolution of complex editing outcomes such as structural rearrangements\u2014often missed by standard genotyping\u2014when targeting repetitive or tandemly spaced loci. To fully realize the potential of multiplex genome engineering, there is growing demand for user\u2010friendly, synthetic biology\u2010compatible, and scalable computational workflows for gRNA design, construct assembly, and mutation analysis. Experimentally validated inducible or tissue\u2010specific promoters are also highly desirable for achieving spatiotemporal control. As these tools continue to evolve, multiplex CRISPR editing is poised to become a foundational technology of next\u2010generation crop improvement to address challenges in agriculture, sustainability, and climate resilience.", "date": "2025-10-14", "issue": "1", "identifier": "https://www.osti.gov/biblio/3364122", "bibliographicCitation": "https://doi.org/10.1111/tpj.70527", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "CRISPR-Cas", "chromosomal engineering", "combinatorial mutagenesis", "de novo domestication", "multiplex genome editing", "polygenic trait stacking", "synthetic biology" ], "topic": [ "Microbiology" ], "journal_name": "The Plant Journal", "volume": "124", "publisher_information": "Society for Experimental Biology", "country_publication_code": "US", "creator": [ { "name": "Kangquan [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); Univ. of Georgia,Athens,GA (United States)] (ORCID:0000000246276585) Yin", "primaryContact": true }, { "name": "Chung\u2010Jui [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); Univ. of Georgia,Athens,GA (United States)] (ORCID:0000000292827704) Tsai", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3364122", "active": false }, { "brc": "CBI", "title": "Valorization of consolidated bioprocessing residues for bioplastics", "description": "This study demonstrates an organic solvent-free processing strategy to valorize consolidated bioprocessing (CBP) residues, from switchgrass and poplar biomass, into functional poly(butylene succinate) (PBS)-based biocomposites using high-shear homogenization (HSH). HSH transformed the switchgrass and poplar CBP residues (CBP-R) into fine, uniformly distributed particles and microfibers. The composites of PBS with homogenized switchgrass residues (H-CBP-R-SG) or homogenized poplar residues (H-CBP-R-P) at a 70/30 weight ratio exhibited improved processability and mechanical integrity, with the Young's modulus for the PBS/H-CBP-R-SG and PBS/H-CBP-R-P nearly doubling to 0.66 \u00b1 0.07 GPa and 0.65 \u00b1 0.04 GPa, respectively, compared to neat PBS (0.36 \u00b1 0.02 GPa). Dynamic Mechanical Analysis (DMA) reveals a significant suppression of the tan \u03b4 peak magnitude, indicating that HSH-mediated physical activation facilitates stress transfer in composites typical of covalent chemical grafting systems. While the transition to a stiffness-dominated profile reduces ductility, the resulting composites exhibit the dimensional stability and resistance to thermal warping required for high-fidelity FDM 3D printing and injection molding. Beyond material performance, comprehensive techno-economic analysis (TEA) and life cycle assessment (LCA) confirmed that diverting CBP residues into composite products can improve the economic viability of the biorefinery without substantially increasing biorefinery global warming potential (GWP). At a 30 wt% blend ratio, incorporating residuals into PBS yielded a minimum selling price for the composite of $\\$4.07$ per kg compared to the conventional bioplastic price of $\\$5.00$ per kg. This approach aligns with circular bioeconomy principles by converting waste streams into value-added products. Furthermore, this innovative strategy addresses key challenges in bioplastic development, including cost, compatibility, and performance, while simultaneously advancing waste minimization strategies for sustainable manufacturing systems.", "abstract": "This study demonstrates an organic solvent-free processing strategy to valorize consolidated bioprocessing (CBP) residues, from switchgrass and poplar biomass, into functional poly(butylene succinate) (PBS)-based biocomposites using high-shear homogenization (HSH). HSH transformed the switchgrass and poplar CBP residues (CBP-R) into fine, uniformly distributed particles and microfibers. The composites of PBS with homogenized switchgrass residues (H-CBP-R-SG) or homogenized poplar residues (H-CBP-R-P) at a 70/30 weight ratio exhibited improved processability and mechanical integrity, with the Young's modulus for the PBS/H-CBP-R-SG and PBS/H-CBP-R-P nearly doubling to 0.66 \u00b1 0.07 GPa and 0.65 \u00b1 0.04 GPa, respectively, compared to neat PBS (0.36 \u00b1 0.02 GPa). Dynamic Mechanical Analysis (DMA) reveals a significant suppression of the tan \u03b4 peak magnitude, indicating that HSH-mediated physical activation facilitates stress transfer in composites typical of covalent chemical grafting systems. While the transition to a stiffness-dominated profile reduces ductility, the resulting composites exhibit the dimensional stability and resistance to thermal warping required for high-fidelity FDM 3D printing and injection molding. Beyond material performance, comprehensive techno-economic analysis (TEA) and life cycle assessment (LCA) confirmed that diverting CBP residues into composite products can improve the economic viability of the biorefinery without substantially increasing biorefinery global warming potential (GWP). At a 30 wt% blend ratio, incorporating residuals into PBS yielded a minimum selling price for the composite of $\\$4.07$ per kg compared to the conventional bioplastic price of $\\$5.00$ per kg. This approach aligns with circular bioeconomy principles by converting waste streams into value-added products. Furthermore, this innovative strategy addresses key challenges in bioplastic development, including cost, compatibility, and performance, while simultaneously advancing waste minimization strategies for sustainable manufacturing systems.", "date": "2026-05-20", "identifier": "https://www.osti.gov/biblio/3364558", "bibliographicCitation": "https://doi.org/10.1039/D6GC00489J", "topic": [ "Unknown" ], "journal_name": "Green Chemistry", "publisher_information": "Royal Society of Chemistry (RSC)", "country_publication_code": "US", "creator": [ { "name": "Nataraja S. [University of Georgia,Athens,GA (United States)] (ORCID:0000000178498900) Yadavalli", "primaryContact": true }, { "name": "Mohammad [University of Georgia,Athens,GA (United States)] (ORCID:000000030042528X) Aghajohari", "primaryContact": false }, { "name": "Neal N. [National Laboratory of the Rockies,Golden,CO (United States)] Hengge", "primaryContact": false }, { "name": "Daniel C. [University of Georgia,Athens,GA (United States)] Josey", "primaryContact": false }, { "name": "Jacob [National Laboratory of the Rockies,Golden,CO (United States)] Dempsey", "primaryContact": false }, { "name": "Jacob K. [National Laboratory of the Rockies,Golden,CO (United States)] Kenny", "primaryContact": false }, { "name": "Bruno C. [National Laboratory of the Rockies,Golden,CO (United States)] (ORCID:000000033438253X) Klein", "primaryContact": false }, { "name": "Rebecca J. [National Laboratory of the Rockies,Golden,CO (United States)] (ORCID:0000000215585887) Hanes", "primaryContact": false }, { "name": "Evert K. [Dartmouth College,Hanover,NH (United States)] Holwerda", "primaryContact": false }, { "name": "Yannick J. [National Laboratory of the Rockies,Golden,CO (United States)] Bomble", "primaryContact": false }, { "name": "Kush G. [University of Georgia,Athens,GA (United States)] (ORCID:0009000622734250) Patel", "primaryContact": false }, { "name": "Jason J. [University of Georgia,Athens,GA (United States)] (ORCID:0000000192722403) Locklin", "primaryContact": false }, { "name": "Sergiy [University of Georgia,Athens,GA (United States)] (ORCID:0000000277479668) Minko", "primaryContact": false }, { "name": "Breeanna R. [University of Georgia,Athens,GA (United States)] (ORCID:0000000152474513) Urbanowicz", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3364558", "active": false }, { "brc": "CBI", "title": "Harnessing citizen science to contextualize adaptation mechanism discovery", "description": "Species occupying broad geographic regions have evolved multiple mechanisms to regulate phenological characteristics, enabling adaptations to diverse native habitats. By developing computer vision AI to process citizen science observations across native habitats over North America, we uncovered a consistent latitudinal trend of earlier flowering at higher latitudes in warm-season perennial grasses. To explore the underlying mechanisms of adaptation, we conducted common garden experiments with one species (switchgrass) and discovered the opposite latitudinal flowering-time trend. Integration of differential plasticity of GI-Hd1-FTL1 haplotypes of flowering time regulatory genes, haplotype range, and local environmental profiles found that observations from native habitats capture only part of the genotype-environment-phenotype spectrum established in common garden experiments, therefore reconciling the discrepancy. Two mechanisms emerged as key forces shaping current haplotype ranges and influencing future shifts. Our study highlights the power of combining citizen science observations with designed experiments to uncover mechanisms of adaptation across spatiotemporal scales.", "abstract": "Species occupying broad geographic regions have evolved multiple mechanisms to regulate phenological characteristics, enabling adaptations to diverse native habitats. By developing computer vision AI to process citizen science observations across native habitats over North America, we uncovered a consistent latitudinal trend of earlier flowering at higher latitudes in warm-season perennial grasses. To explore the underlying mechanisms of adaptation, we conducted common garden experiments with one species (switchgrass) and discovered the opposite latitudinal flowering-time trend. Integration of differential plasticity of GI-Hd1-FTL1 haplotypes of flowering time regulatory genes, haplotype range, and local environmental profiles found that observations from native habitats capture only part of the genotype-environment-phenotype spectrum established in common garden experiments, therefore reconciling the discrepancy. Two mechanisms emerged as key forces shaping current haplotype ranges and influencing future shifts. Our study highlights the power of combining citizen science observations with designed experiments to uncover mechanisms of adaptation across spatiotemporal scales.", "date": "2026-04-30", "identifier": "https://www.osti.gov/biblio/3364589", "bibliographicCitation": "https://doi.org/10.1016/j.cell.2026.04.039", "keywords": [ "FTL1", "GI", "Hd1", "adaptation", "citizen science", "common garden experiment", "flowering time", "haplotype range", "phenotypic plasticity", "switchgrass" ], "topic": [ "Unknown" ], "journal_name": "Cell", "publisher_information": "Elsevier BV", "country_publication_code": "US", "creator": [ { "name": "Laura E. [USDA-ARS Wheat Health,Pullman,WA (United States); USDA-ARS Corn Insects and Crop Research Unit,Ames,IA (United States)] Tibbs-Cortes", "primaryContact": true }, { "name": "Linqian [Washington State University,Pullman,WA (United States)] Han", "primaryContact": false }, { "name": "Jeremy B. [Washington State University,Pullman,WA (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Jewell", "primaryContact": false }, { "name": "Puranjit [University of Delaware,Newark,DE (United States)] Singh", "primaryContact": false }, { "name": "Haiyan [Washington State University,Pullman,WA (United States)] Huang", "primaryContact": false }, { "name": "Ryan [USDA-ARS Wheat Health,Pullman,WA (United States)] Benke", "primaryContact": false }, { "name": "Tony [HudsonAlpha Institute for Biotechnology,Huntsville,AL (United States)] Trieu", "primaryContact": false }, { "name": "Zhou [Washington State University,Pullman,WA (United States)] Tang", "primaryContact": false }, { "name": "Soyeon [University of Georgia,Athens,GA (United States); Stanford University,CA (United States)] Choi", "primaryContact": false }, { "name": "Jianxin [University of Georgia,Athens,GA (United States)] Zhao", "primaryContact": false }, { "name": "Eudald Illa [University of Georgia,Athens,GA (United States)] Berenguer", "primaryContact": false }, { "name": "Thomas H. [University of Georgia,Athens,GA (United States)] Pendergast", "primaryContact": false }, { "name": "Bing [University of Georgia,Athens,GA (United States)] Liu", "primaryContact": false }, { "name": "Tina [Washington State University,Pullman,WA (United States)] Le", "primaryContact": false }, { "name": "Kankshita [HudsonAlpha Institute for Biotechnology,Huntsville,AL (United States)] Swaminathan", "primaryContact": false }, { "name": "Xiaoyu [University of Texas,Austin,TX (United States)] Weng", "primaryContact": false }, { "name": "Carson [USDA-ARS Corn Insects and Crop Research Unit,Ames,IA (United States)] Andorf", "primaryContact": false }, { "name": "Michelle A. [USDA-ARS Corn Insects and Crop Research Unit,Ames,IA (United States)] Graham", "primaryContact": false }, { "name": "Karen [Washington State University,Pullman,WA (United States); South Dakota State University,Brookings,SD (United States)] Sanguinet", "primaryContact": false }, { "name": "Zhiwu [Washington State University,Pullman,WA (United States)] Zhang", "primaryContact": false }, { "name": "Laura E. [Washington State University,Pullman,WA (United States); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Bartley", "primaryContact": false }, { "name": "Yin [University of Delaware,Newark,DE (United States)] Bao", "primaryContact": false }, { "name": "Wayne [University of Georgia,Athens,GA (United States)] Parrott", "primaryContact": false }, { "name": "Katrien M. [University of Georgia,Athens,GA (United States)] Devos", "primaryContact": false }, { "name": "Thomas [University of Texas,Austin,TX (United States)] Juenger", "primaryContact": false }, { "name": "Jianming [Iowa State University,Ames,IA (United States)] Yu", "primaryContact": false }, { "name": "Xianran [USDA-ARS Wheat Health,Pullman,WA (United States); Washington State University,Pullman,WA (United States)] Li", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDA-ARS" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3364589", "active": false }, { "brc": "CBI", "title": "Multi-site Milling Strategy Reveals Significant Variation in Biomass Composition of Switchgrass (Panicum virgatum) Grown at Ten Locations", "description": "Cell wall composition influences biomass use as a forage and as a feedstock for biofuel and chemical conversion. To examine the influence of environment on composition of switchgrass (Panicum virgatum L.), we utilized a multi-environment experiment consisting of clones of switchgrass genotypes grown at up to ten locations in the continental US. We tested the influence of different milling treatments on biomass composition trait predictions via near-infrared reflectance spectroscopy (NIRS). We found that most compositional trait predictions (29/34) were significantly different (P < 0.05) when a single lot of biomass was subjected to disparate milling treatments, i.e., knife milling vs. knife milling with an additional cyclone milling. Further, depending on the plant material tested, three to eight compositional trait predictions vary (P < 0.05) when identical biomass was knife milled at different sites followed by cyclone milling at a single site, including for traits such as Klason lignin, nitrogen, and carbon. In some cases, variation due to milling site exceeded environmentally induced compositional variation of a single switchgrass genotype grown at different sites. From these observations, we recommend a protocol with two sequential millings that decouples growth environment from a particular mill. Utilizing this approach, we found that 46/46 biomass composition traits from the warm season herbaceous forage and switchgrass bioethanol NIRS equations vary significantly (P < 0.001) in clones of a switchgrass genotype (WBC) grown at ten sites, with the growth site representing the largest average source of variation (41%). This multi-site milling approach can be used to examine environmental and gene-by-environment influences on composition with the goal of optimizing cell wall composition in different environments for biomass utilization.", "abstract": "Cell wall composition influences biomass use as a forage and as a feedstock for biofuel and chemical conversion. To examine the influence of environment on composition of switchgrass (Panicum virgatum L.), we utilized a multi-environment experiment consisting of clones of switchgrass genotypes grown at up to ten locations in the continental US. We tested the influence of different milling treatments on biomass composition trait predictions via near-infrared reflectance spectroscopy (NIRS). We found that most compositional trait predictions (29/34) were significantly different (P < 0.05) when a single lot of biomass was subjected to disparate milling treatments, i.e., knife milling vs. knife milling with an additional cyclone milling. Further, depending on the plant material tested, three to eight compositional trait predictions vary (P < 0.05) when identical biomass was knife milled at different sites followed by cyclone milling at a single site, including for traits such as Klason lignin, nitrogen, and carbon. In some cases, variation due to milling site exceeded environmentally induced compositional variation of a single switchgrass genotype grown at different sites. From these observations, we recommend a protocol with two sequential millings that decouples growth environment from a particular mill. Utilizing this approach, we found that 46/46 biomass composition traits from the warm season herbaceous forage and switchgrass bioethanol NIRS equations vary significantly (P < 0.001) in clones of a switchgrass genotype (WBC) grown at ten sites, with the growth site representing the largest average source of variation (41%). This multi-site milling approach can be used to examine environmental and gene-by-environment influences on composition with the goal of optimizing cell wall composition in different environments for biomass utilization.", "date": "2025-11-20", "issue": "1", "identifier": "https://www.osti.gov/biblio/3364779", "bibliographicCitation": "https://doi.org/10.1007/s12155-025-10897-x", "keywords": [ "09 BIOMASS FUELS", "60 APPLIED LIFE SCIENCES", "Bioenergy", "Composition", "Milling", "Multi-environment trial", "NIRS", "Near-infrared spectroscopy", "Switchgrass" ], "topic": [ "Biomass & Feedstock", "Plant Biology" ], "journal_name": "BioEnergy Research", "volume": "18", "publisher_information": "Springer Science and Business Media LLC", "country_publication_code": "US", "creator": [ { "name": "David J. [University of Oklahoma,Norman,OK (United States); Washington State University,Pullman,WA (United States)] (ORCID:0000000194430527) Thomas", "primaryContact": true }, { "name": "Jason [The University of Texas,Austin,TX (United States)] (ORCID:0000000318358409) Bonnette", "primaryContact": false }, { "name": "Steven D. [United States Department of Agriculture,Lincoln,NE (United States)] (ORCID:0009000939709862) Masterson", "primaryContact": false }, { "name": "Robert B. [United States Department of Agriculture,Lincoln,NE (United States)] (ORCID:0000000345252335) Mitchell", "primaryContact": false }, { "name": "Thomas E. [The University of Texas,Austin,TX (United States)] (ORCID:0000000195509288) Juenger", "primaryContact": false }, { "name": "Laura E. [Washington State University,Pullman,WA (United States)] (ORCID:0000000186107551) Bartley", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3364779", "active": false }, { "brc": "CBI", "title": "Biomass carbon removal can help sustainable aviation fuels achieve on-time arrival", "description": "Biofuels, including sustainable aviation and marine fuels, and biomass carbon removal and storage (BiCRS) are often viewed as potentially competing pathways for advancing climate and energy goals. Their comparative economic, environmental, and temporal advantages remain debated. Rather than identifying a \u201cbest-use\u201d for biomass, we show that the relative economic advantages of BiCRS versus biofuels exist along a continuum shaped by energy- and decarbonization-focused market conditions. These pathways need not be adversarial: BiCRS can enable, rather than displace, future biofuel deployment. While the lignocellulosic biofuel sector continues to face barriers associated with underdeveloped supply chains and technologies that have not yet been commercialized at scale, emerging BiCRS approaches are comparatively feedstock-flexible, rapidly deployable, and responsive to carbon removal markets. Early BiCRS deployment can help establish reliable biomass supply chains, reducing investment risk for future lignocellulosic biorefineries. By easing initial supply chain constraints, BiCRS can serve as a practical stepping stone toward meeting both near-term carbon removal needs and long-term sustainable fuel objectives under uncertain future market and policy conditions.", "abstract": "Biofuels, including sustainable aviation and marine fuels, and biomass carbon removal and storage (BiCRS) are often viewed as potentially competing pathways for advancing climate and energy goals. Their comparative economic, environmental, and temporal advantages remain debated. Rather than identifying a \u201cbest-use\u201d for biomass, we show that the relative economic advantages of BiCRS versus biofuels exist along a continuum shaped by energy- and decarbonization-focused market conditions. These pathways need not be adversarial: BiCRS can enable, rather than displace, future biofuel deployment. While the lignocellulosic biofuel sector continues to face barriers associated with underdeveloped supply chains and technologies that have not yet been commercialized at scale, emerging BiCRS approaches are comparatively feedstock-flexible, rapidly deployable, and responsive to carbon removal markets. Early BiCRS deployment can help establish reliable biomass supply chains, reducing investment risk for future lignocellulosic biorefineries. By easing initial supply chain constraints, BiCRS can serve as a practical stepping stone toward meeting both near-term carbon removal needs and long-term sustainable fuel objectives under uncertain future market and policy conditions.", "date": "2026-05-21", "issue": "6", "identifier": "https://www.osti.gov/biblio/3367069", "bibliographicCitation": "https://doi.org/10.1016/j.isci.2026.115956", "keywords": [ "bioenvironmental engineering", "biomass", "bioresources", "environmental science" ], "topic": [ "Unknown" ], "journal_name": "iScience", "volume": "29", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Matthew [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] (ORCID:0000000281537154) Langholtz", "primaryContact": true }, { "name": "Charlotte [Carbon180,Washington,DC (United States)] Levy", "primaryContact": false }, { "name": "John [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Field", "primaryContact": false }, { "name": "Daniel L. [University of California,Berkeley,CA (United States)] Sanchez", "primaryContact": false }, { "name": "Pete [Loamist Co.,Berkeley,CA (United States)] Christensen", "primaryContact": false }, { "name": "Lawrence [Clemson University,SC (United States)] Murdoch", "primaryContact": false }, { "name": "Daniel de la Torre [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Ugarte", "primaryContact": false }, { "name": "Oluwafemi [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Oyedeji", "primaryContact": false }, { "name": "Ryan [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Jacobson", "primaryContact": false }, { "name": "Ning [University of Maryland,College Park,MD (United States)] Zeng", "primaryContact": false }, { "name": "Emily A. [University of Illinois Urbana-Champaign,IL (United States)] Heaton", "primaryContact": false }, { "name": "Charles [Massachusetts Institute of Technology,Cambridge,MA (United States)] Forsberg", "primaryContact": false }, { "name": "William Joe [North Carolina State University,Raleigh,NC (United States)] (ORCID:0000000180369120) Sagues", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/3367069", "active": false }, { "brc": "CBI", "title": "Telomere-to-telomere assemblies of chromosome 10 reveal complex adaptive variation of 3-ketoacyl-CoA-synthases in Populus trichocarpa likely driven by Helitrons", "description": "The model woody plant Populus trichocarpa displays an atypical alkene-diverse wax cuticle likely driven by copy number variation (CNV) of 3-ketoacyl-CoA synthases (KCS), which has been difficult to confirm with short-read assemblies. Long-read sequencing enables the development of telomere-to-telomere resources to detect cryptic variation, including CNVs, which are currently missed. Integrating this information can improve genomic prediction for breeding and provide insights into the evolutionary basis of important traits. Our analysis of 78 long-read haplotypes from chromosome 10 identified more than twice as many KCS genes as previously reported, and numerous intragenic non-synonymous substitutions. Random Forest predictive models highlighted the importance of Potri.010G079500 in producing very long chain alkenes; however, its absence did not predict previously reported alkene-deficient phenotypes. Instead, alkene levels are best predicted by the combinations of KCS copies. Additionally, amino acid substitutions clustered around ligand and donor binding pockets, suggesting they contribute to differing wax cuticle composition. Finally, each KCS gene and copy was linked to a Helitron transposon. A phylogenetic analysis suggests Helitrons are the evolutionary mechanism for generating KCS tandem arrays. Long-read generated telomere-to-telomere assemblies of P. trichocarpa chromosome 10 revealed large-effect loci critical to genetic studies that are unattainable from short-reads. This new resource produced novel insights into genome structure and function, and a novel mechanism for generating tandem gene duplication. Our results highlight that, given current challenges in annotation and assembly, detailed and focused long-read sequences are key to interpreting complex genomic regions that contain tandem copy number variants.", "abstract": "The model woody plant Populus trichocarpa displays an atypical alkene-diverse wax cuticle likely driven by copy number variation (CNV) of 3-ketoacyl-CoA synthases (KCS), which has been difficult to confirm with short-read assemblies. Long-read sequencing enables the development of telomere-to-telomere resources to detect cryptic variation, including CNVs, which are currently missed. Integrating this information can improve genomic prediction for breeding and provide insights into the evolutionary basis of important traits. Our analysis of 78 long-read haplotypes from chromosome 10 identified more than twice as many KCS genes as previously reported, and numerous intragenic non-synonymous substitutions. Random Forest predictive models highlighted the importance of Potri.010G079500 in producing very long chain alkenes; however, its absence did not predict previously reported alkene-deficient phenotypes. Instead, alkene levels are best predicted by the combinations of KCS copies. Additionally, amino acid substitutions clustered around ligand and donor binding pockets, suggesting they contribute to differing wax cuticle composition. Finally, each KCS gene and copy was linked to a Helitron transposon. A phylogenetic analysis suggests Helitrons are the evolutionary mechanism for generating KCS tandem arrays. Long-read generated telomere-to-telomere assemblies of P. trichocarpa chromosome 10 revealed large-effect loci critical to genetic studies that are unattainable from short-reads. This new resource produced novel insights into genome structure and function, and a novel mechanism for generating tandem gene duplication. Our results highlight that, given current challenges in annotation and assembly, detailed and focused long-read sequences are key to interpreting complex genomic regions that contain tandem copy number variants.", "date": "2026-06-07", "issue": "1", "identifier": "https://www.osti.gov/biblio/3367327", "bibliographicCitation": "https://doi.org/10.48130/forres-0026-0019", "keywords": [ "09 BIOMASS FUELS", "Copy number variation", "Helitrons", "KCS genes", "Long-read sequencing", "Populus trichocarpa", "Wax biosynthesis" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Forestry Research", "volume": "6", "publisher_information": "Maximum Academic Press", "country_publication_code": "US", "creator": [ { "name": "David [Univ. of Queensland,Brisbane,QLD (Australia); Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Kainer", "primaryContact": true }, { "name": "Stanton [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Martin", "primaryContact": false }, { "name": "Daniel [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Hopp", "primaryContact": false }, { "name": "Sophie [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Mosher", "primaryContact": false }, { "name": "Timothy J. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Tschaplinski", "primaryContact": false }, { "name": "P. Doug [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Hyatt", "primaryContact": false }, { "name": "Madhavi Z. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Martin", "primaryContact": false }, { "name": "Jared M. [Oregon State Univ.,Corvallis,OR (United States)] LeBoldus", "primaryContact": false }, { "name": "Kelsey L. [Oregon State Univ.,Corvallis,OR (United States)] S\u00f8ndreli", "primaryContact": false }, { "name": "Posy E. [Oregon State Univ.,Corvallis,OR (United States)] Busby", "primaryContact": false }, { "name": "Mengjun [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Shu", "primaryContact": false }, { "name": "Kerrie [USDOE Joint Genome Institute (JGI),Berkeley,CA (United States)] Barry", "primaryContact": false }, { "name": "Jeremy [USDOE Joint Genome Institute (JGI),Berkeley,CA (United States)] Schmutz", "primaryContact": false }, { "name": "Anna [Univ. of Tennessee,Knoxville,TN (United States)] Furches", "primaryContact": false }, { "name": "Nan [Southeast Univ.,Nanjing (China)] Zhao", "primaryContact": false }, { "name": "Daniel A. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Jacobson", "primaryContact": false }, { "name": "Jin-Gui [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Chen", "primaryContact": false }, { "name": "Mirko [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Pavicic", "primaryContact": false }, { "name": "Priya [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Ranjan", "primaryContact": false }, { "name": "Wellington [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Muchero", "primaryContact": false }, { "name": "Gerald A. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States)] Tuskan", "primaryContact": false }, { "name": "Michael R. [Oak Ridge National Laboratory (ORNL),Oak Ridge,TN (United States); Univ. of New Mexico,Albuquerque,NM (United States)] Garvin", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "Joint Genome Institute (JGI)" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3367327", "active": false }, { "brc": "CBI", "title": "Advancing specialized biofoundries via automated adaptive laboratory evolution", "description": "Adaptive laboratory evolution (ALE) is a powerful strategy for improving microbial phenotypes by harnessing natural selection under defined environmental conditions. Through applying selection regimes, beneficial mutations accumulate, enabling the generation of strains with enhanced properties. However, conventional ALE is labor-intensive and difficult to scale, limiting reproducibility and broader discovery of evolutionary principles. Recent advances in robotics, automation, and computational infrastructure are transforming ALE into a scalable, data-rich experimental paradigm. Automated platforms enable standardized and complex protocols, real-time monitoring, and highly parallel evolution campaigns, improving consistency while generating longitudinal datasets that reveal convergent adaptive mechanisms. Here, we discuss the role of specialized biofoundries in advancing automated ALE and enabling large-scale evolutionary engineering. We review major automated ALE formats and outline key design principles for effective ALE biofoundries, highlighting how automated ALE can support autonomous experimentation and AI-guided strain engineering.", "abstract": "Adaptive laboratory evolution (ALE) is a powerful strategy for improving microbial phenotypes by harnessing natural selection under defined environmental conditions. Through applying selection regimes, beneficial mutations accumulate, enabling the generation of strains with enhanced properties. However, conventional ALE is labor-intensive and difficult to scale, limiting reproducibility and broader discovery of evolutionary principles. Recent advances in robotics, automation, and computational infrastructure are transforming ALE into a scalable, data-rich experimental paradigm. Automated platforms enable standardized and complex protocols, real-time monitoring, and highly parallel evolution campaigns, improving consistency while generating longitudinal datasets that reveal convergent adaptive mechanisms. Here, we discuss the role of specialized biofoundries in advancing automated ALE and enabling large-scale evolutionary engineering. We review major automated ALE formats and outline key design principles for effective ALE biofoundries, highlighting how automated ALE can support autonomous experimentation and AI-guided strain engineering.", "date": "2026-04-16", "identifier": "https://www.osti.gov/biblio/3367793", "bibliographicCitation": "https://doi.org/10.1016/j.copbio.2026.103496", "keywords": [ "59 BASIC BIOLOGICAL SCIENCES", "Adaptive Laboratory Evolution", "CBI", "Conversion" ], "topic": [ "Microbiology" ], "journal_name": "Current Opinion in Biotechnology", "volume": "99", "publisher_information": "Elsevier", "country_publication_code": "US", "creator": [ { "name": "Adam M. [Univ. of California,San Diego,CA (United States); Joint BioEnergy Institute (JBEI),Emeryville,CA (United States); Technical Univ. of Denmark,Lyngby (Denmark)] (ORCID:0000000286304800) Feist", "primaryContact": true }, { "name": "Sunghwa [Univ. of California,San Diego,CA (United States); Joint BioEnergy Institute (JBEI),Emeryville,CA (United States)] Woo", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3367793", "active": false }, { "brc": "CBI", "title": "Lignin to Adipic Acid in a High-Yield Chemical and Biological Redox Process", "description": "Viable manufacturing pathways to produce bio-based chemicals from renewable feedstocks, such as lignin derived from plant biomass, are needed to decarbonize the chemicals manufacturing sector. Converting the recalcitrant lignin polymer to valuable bioproducts remains a longstanding challenge in biorefining, with the highest reported single-product yield from lignin currently around 20 wt% (refs. 1,2,3,4). Most existing lignin depolymerization strategies target aryl-ether bond cleavage, which can produce aromatic monomers in yields of only about 30 wt%, and still as complex mixtures with C-C-linked dimers and oligomers5,6. The recalcitrance of these C-C linkages between aromatic moieties fundamentally limits single-product yields from lignin, prompting the development of strategies to efficiently cleave these C-C bonds3,7,8,9. Here we show how reductive processing of lignin from poplar accesses a hydrocarbon mixture of alkyl-aromatic monomers and oligomers that is privileged for oxidative conversion to monomeric aromatic carboxylic acids, comprising mostly benzoic acid and phthalic acid isomers in up to 73 wt% monomer yields, using a Co/Mn/Br catalyst. The soil bacterium Pseudomonas putida KT2440 was engineered to convert this mixture of aromatic carboxylic acids to muconolactone, a precursor to bio-based nylons, enabling final adipic acid yields up to 26 wt% (gram adipic acid per gram lignin) with a maximum theoretical yield of 57 wt%. This pairing of reductive and oxidative steps with lignin resembles processes in petrochemical refining and shows how lignin may be converted into a single, valuable bioproduct in high yields.", "abstract": "Viable manufacturing pathways to produce bio-based chemicals from renewable feedstocks, such as lignin derived from plant biomass, are needed to decarbonize the chemicals manufacturing sector. Converting the recalcitrant lignin polymer to valuable bioproducts remains a longstanding challenge in biorefining, with the highest reported single-product yield from lignin currently around 20 wt% (refs. 1,2,3,4). Most existing lignin depolymerization strategies target aryl-ether bond cleavage, which can produce aromatic monomers in yields of only about 30 wt%, and still as complex mixtures with C-C-linked dimers and oligomers5,6. The recalcitrance of these C-C linkages between aromatic moieties fundamentally limits single-product yields from lignin, prompting the development of strategies to efficiently cleave these C-C bonds3,7,8,9. Here we show how reductive processing of lignin from poplar accesses a hydrocarbon mixture of alkyl-aromatic monomers and oligomers that is privileged for oxidative conversion to monomeric aromatic carboxylic acids, comprising mostly benzoic acid and phthalic acid isomers in up to 73 wt% monomer yields, using a Co/Mn/Br catalyst. The soil bacterium Pseudomonas putida KT2440 was engineered to convert this mixture of aromatic carboxylic acids to muconolactone, a precursor to bio-based nylons, enabling final adipic acid yields up to 26 wt% (gram adipic acid per gram lignin) with a maximum theoretical yield of 57 wt%. This pairing of reductive and oxidative steps with lignin resembles processes in petrochemical refining and shows how lignin may be converted into a single, valuable bioproduct in high yields.", "date": "2026-06-09", "identifier": "https://www.osti.gov/biblio/3376125", "bibliographicCitation": "https://doi.org/10.1038/s41586-026-10580-x", "keywords": [ "37 INORGANIC", "ORGANIC", "PHYSICAL", "AND ANALYTICAL CHEMISTRY", "aromatic carboxylic acid", "biological redox", "muconolactone", "nylon" ], "topic": [ "Chemistry" ], "journal_name": "Nature", "volume": "654", "country_publication_code": "US", "creator": [ { "name": "Kathryn [National Laboratory of the Rockies,Golden,CO (United States)] Mains", "primaryContact": true }, { "name": "Chad [National Laboratory of the Rockies,Golden,CO (United States)] Palumbo", "primaryContact": false }, { "name": "Davide [National Laboratory of the Rockies,Golden,CO (United States)] Rigo", "primaryContact": false }, { "name": "Matthew [National Laboratory of the Rockies,Golden,CO (United States)] Webber", "primaryContact": false }, { "name": "Gloria [National Laboratory of the Rockies,Golden,CO (United States)] Rosetto", "primaryContact": false }, { "name": "Austin [Oak Ridge National Laboratory] Carroll", "primaryContact": false }, { "name": "Nicolette [National Laboratory of the Rockies,Golden,CO (United States)] Meyer", "primaryContact": false }, { "name": "Alexander [National Laboratory of the Rockies,Golden,CO (United States)] Benson", "primaryContact": false }, { "name": "Brett [National Laboratory of the Rockies,Golden,CO (United States)] Boyle", "primaryContact": false }, { "name": "Stefan [National Laboratory of the Rockies,Golden,CO (United States)] Haugen", "primaryContact": false }, { "name": "Morgan [National Laboratory of the Rockies,Golden,CO (United States)] (ORCID:0000000273504862) Ingraham", "primaryContact": false }, { "name": "William [Oak Ridge National Laboratory] Alexander", "primaryContact": false }, { "name": "Miriam [Oak Ridge National Laboratory] Silberman", "primaryContact": false }, { "name": "Logan [National Laboratory of the Rockies,Golden,CO (United States)] Myers", "primaryContact": false }, { "name": "Kelsey [National Laboratory of the Rockies,Golden,CO (United States)] Ramirez", "primaryContact": false }, { "name": "Kevin [National Laboratory of the Rockies,Golden,CO (United States)] Sullivan", "primaryContact": false }, { "name": "Adam [Oak Ridge National Laboratory] Guss", "primaryContact": false }, { "name": "Davinia [National Laboratory of the Rockies,Golden,CO (United States)] (ORCID:000000030799061X) Salvachua", "primaryContact": false }, { "name": "Yuriy [Massachusetts Institute of Technology] Roman-Leshkov", "primaryContact": false }, { "name": "Shannon [University of Wisconsin-Madison] Stahl", "primaryContact": false }, { "name": "Allison [National Laboratory of the Rockies,Golden,CO (United States)] (ORCID:0000000171472863) Werner", "primaryContact": false }, { "name": "Gregg [National Laboratory of the Rockies,Golden,CO (United States)] (ORCID:000000023480212X) Beckham", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE Office of Energy Efficiency and Renewable Energy (EERE), Transportation Office. Bioenergy Technologies Office" } }, { "fundingOrganization": { "organizationName": "USDOE Office of Science (SC), Biological and Environmental Research (BER)" } } ], "dataset_url": "https://www.osti.gov/biblio/3376125", "active": false, "has_related_ids": [ "NLR/JA-2A00-96426" ] }, { "brc": "CBI", "title": "Transformative Impacts of Laser-Induced Breakdown Spectroscopy on Environmental and Biological Research at Oak Ridge National Laboratory", "description": "This manuscript will present an advancement of transformative research that has been conducted at Oak Ridge National Laboratory (ORNL) over a 25-year period (2000\u20132025) on a variety of environmental and biological matrices. These investigations derived a fundamental understanding of how elemental detection and analysis of these matrices led to the knowledge and discovery of natural processes in plants and the environment. Each project led to the initiation of a new research area which unearthed awesome and novel breakthroughs. Highlights are listed below: 1. The preliminary research at ORNL centered on the detection of aerosols utilizing Laser-induced Breakdown Spectroscopy (LIBS) technology. The Clean Air Act Amendment (CAAA) of 1990 highlighted the importance of identifying hazardous air pollutants (HAPs) due to their impact on environmental and human health, thereby underscoring the need to detect various toxic elements. Research in aerosol chemistry aimed to identify these harmful elements released by factories during periods of increased emissions in their manufacturing processes. LIBS emerged as the most effective method for real-time, in situ measurements of metal species in both gaseous and aerosol phases. 2. An understanding of the presence of total carbon in soils gives perspective on how to develop carbon sequestration strategies. The recognition that carbon sinks can evolve back to carbon sources to emit back to the atmosphere was an important consideration. Also, the concentration of carbon in soil indicates the health of land areas for growing crops successfully. 3. The direct detection of most of the elements in a wood sample in a single emission spectrum, without sample preparation, encouraged the research to use the LIBS technique for preservative treated wood coupled with use of multivariate statistical methodology. Additionally, it encouraged the researchers to try to differentiate natural woods from different parts of the country, and it was successfully demonstrated that LIBS coupled with MVA analysis could differentiate wood of different species from each other and of similar species grown in different environments based on their elemental spectra. This was a breakthrough since it revealed a systematic approach to connect elemental scarcity and abundance to either drought or typical rainfall conditions for the hardwood trees grown in specific areas. 4. Furthermore, the research progressed to reveal physiological and developmental processes contributing to biomass production such that the variation in leaf elemental composition increases our understanding of terrestrial nutrient cycles, as well as tracking the transfer of toxic elements from soils to living organisms. 5. Recently another breakthrough viz., ionomics initiated the correlation of elements to specific genes, uncovering the function that the element performed in the plant. More recently, this has been extended from plants to fungi as well as fungi growing in symbiotic relations with plants.", "abstract": "This manuscript will present an advancement of transformative research that has been conducted at Oak Ridge National Laboratory (ORNL) over a 25-year period (2000\u20132025) on a variety of environmental and biological matrices. These investigations derived a fundamental understanding of how elemental detection and analysis of these matrices led to the knowledge and discovery of natural processes in plants and the environment. Each project led to the initiation of a new research area which unearthed awesome and novel breakthroughs. Highlights are listed below: 1. The preliminary research at ORNL centered on the detection of aerosols utilizing Laser-induced Breakdown Spectroscopy (LIBS) technology. The Clean Air Act Amendment (CAAA) of 1990 highlighted the importance of identifying hazardous air pollutants (HAPs) due to their impact on environmental and human health, thereby underscoring the need to detect various toxic elements. Research in aerosol chemistry aimed to identify these harmful elements released by factories during periods of increased emissions in their manufacturing processes. LIBS emerged as the most effective method for real-time, in situ measurements of metal species in both gaseous and aerosol phases. 2. An understanding of the presence of total carbon in soils gives perspective on how to develop carbon sequestration strategies. The recognition that carbon sinks can evolve back to carbon sources to emit back to the atmosphere was an important consideration. Also, the concentration of carbon in soil indicates the health of land areas for growing crops successfully. 3. The direct detection of most of the elements in a wood sample in a single emission spectrum, without sample preparation, encouraged the research to use the LIBS technique for preservative treated wood coupled with use of multivariate statistical methodology. Additionally, it encouraged the researchers to try to differentiate natural woods from different parts of the country, and it was successfully demonstrated that LIBS coupled with MVA analysis could differentiate wood of different species from each other and of similar species grown in different environments based on their elemental spectra. This was a breakthrough since it revealed a systematic approach to connect elemental scarcity and abundance to either drought or typical rainfall conditions for the hardwood trees grown in specific areas. 4. Furthermore, the research progressed to reveal physiological and developmental processes contributing to biomass production such that the variation in leaf elemental composition increases our understanding of terrestrial nutrient cycles, as well as tracking the transfer of toxic elements from soils to living organisms. 5. Recently another breakthrough viz., ionomics initiated the correlation of elements to specific genes, uncovering the function that the element performed in the plant. More recently, this has been extended from plants to fungi as well as fungi growing in symbiotic relations with plants.", "date": "2026-06-25", "issue": "7", "identifier": "https://www.osti.gov/biblio/3377187", "bibliographicCitation": "https://doi.org/10.3390/chemosensors14070146", "keywords": [ "09 BIOMASS FUELS", "CBI", "Feedstock DEvelopment LIBS", "biological samples", "elemental characterization", "environmental" ], "topic": [ "Biomass & Feedstock" ], "journal_name": "Chemosensors", "volume": "14", "publisher_information": "MDPI AG", "country_publication_code": "US", "creator": [ { "name": "Madhavi [Biosciences Division,Oak Ridge National Laboratory,Oak Ridge,TN 37831,USA] (ORCID:0000000266772180) Martin", "primaryContact": true } ], "funding": [ { "fundingOrganization": { "organizationName": "US Department of Energy" } } ], "dataset_url": "https://www.osti.gov/biblio/3377187", "active": false }, { "brc": "CBI", "title": "Coupling of high-resolution mass spectrometer and photosynthesis system for comprehensive leaf volatile metabolite profiling", "description": "Background: Leaf-level biogenic volatile organic compounds (BVOCs) emissions represent a major source of organic gases in the atmosphere, influencing both climate and air quality. These emissions are strongly driven by environmental perturbations, which affect individual plant- to ecosystem-level processes. Uncovering all the BVOCs and understanding how their emissions respond to altered environmental conditions provide critical insights into vegetation-driven changes in atmospheric chemistry. We developed a tandem instrumentation setup that integrates a proton transfer reaction time-of-flight mass spectrometer (PTR-ToF-MS) with parts-per-trillion detection limits and a photosynthetic infrared gas exchange system for the untargeted survey of all the BVOCs. This novel system enables simultaneous, real-time monitoring of BVOC emissions and photosynthetic parameters at the leaf level, offering new opportunities to disentangle the physiological and environmental drivers of VOC release. Furthermore, we established the VOC Analysis and Processing Optimization Resource (VAPOR), an open-access software tool designed for rapid data post-processing and the analysis of the variability of hundreds of BVOCs. We assessed the performance of the tandem system under varying background conditions, using standard gas mixtures and a range of environmental factors. \nResults: Blank emissions were substantially lower for major BVOCs (e.g., isoprene) compared to those observed in plant emissions. Despite this, the observation of background-level VOCs highlights the importance of routinely acquiring and accounting for blank measurements in analyses using the coupled instrumentation. Introduction of known VOC concentrations to the system demonstrated a linear response across different compounds with varying molecular compositions, indicating minimal gas loss regardless of chemical moieties within the coupled instrumentation. We applied the optimized system to investigate the physiological mechanisms driving BVOC emissions across different genotypes of poplar and pennycress. The high mass resolution capabilities of the PTR-ToF-MS, coupled with comprehensive VAPOR-driven data analysis, enabled the identification of several important BVOCs, including methanol and methanethiol; these BVOCs displayed substantial variation across pennycress genotypes and showed concentrations ~100\u2013350% higher than the blank. Moreover, isoprene emissions varied significantly among poplar genotypes grown in different potting media. \nConclusions: Tandem instrumentation offers a powerful tool for profiling volatile molecular markers and elucidating their genetic and environmental underpinnings. This approach enhances our ability to predict BVOC emissions in response to genotype by environmental interactions and contributes to a deeper understanding of vegetation responses to environmental changes.", "abstract": "Background: Leaf-level biogenic volatile organic compounds (BVOCs) emissions represent a major source of organic gases in the atmosphere, influencing both climate and air quality. These emissions are strongly driven by environmental perturbations, which affect individual plant- to ecosystem-level processes. Uncovering all the BVOCs and understanding how their emissions respond to altered environmental conditions provide critical insights into vegetation-driven changes in atmospheric chemistry. We developed a tandem instrumentation setup that integrates a proton transfer reaction time-of-flight mass spectrometer (PTR-ToF-MS) with parts-per-trillion detection limits and a photosynthetic infrared gas exchange system for the untargeted survey of all the BVOCs. This novel system enables simultaneous, real-time monitoring of BVOC emissions and photosynthetic parameters at the leaf level, offering new opportunities to disentangle the physiological and environmental drivers of VOC release. Furthermore, we established the VOC Analysis and Processing Optimization Resource (VAPOR), an open-access software tool designed for rapid data post-processing and the analysis of the variability of hundreds of BVOCs. We assessed the performance of the tandem system under varying background conditions, using standard gas mixtures and a range of environmental factors. \nResults: Blank emissions were substantially lower for major BVOCs (e.g., isoprene) compared to those observed in plant emissions. Despite this, the observation of background-level VOCs highlights the importance of routinely acquiring and accounting for blank measurements in analyses using the coupled instrumentation. Introduction of known VOC concentrations to the system demonstrated a linear response across different compounds with varying molecular compositions, indicating minimal gas loss regardless of chemical moieties within the coupled instrumentation. We applied the optimized system to investigate the physiological mechanisms driving BVOC emissions across different genotypes of poplar and pennycress. The high mass resolution capabilities of the PTR-ToF-MS, coupled with comprehensive VAPOR-driven data analysis, enabled the identification of several important BVOCs, including methanol and methanethiol; these BVOCs displayed substantial variation across pennycress genotypes and showed concentrations ~100\u2013350% higher than the blank. Moreover, isoprene emissions varied significantly among poplar genotypes grown in different potting media. \nConclusions: Tandem instrumentation offers a powerful tool for profiling volatile molecular markers and elucidating their genetic and environmental underpinnings. This approach enhances our ability to predict BVOC emissions in response to genotype by environmental interactions and contributes to a deeper understanding of vegetation responses to environmental changes.", "date": "2026-04-30", "issue": "1", "identifier": "https://www.osti.gov/biblio/3384934", "bibliographicCitation": "https://doi.org/10.1186/s13007-026-01531-8", "topic": [ "Unknown" ], "journal_name": "Plant Methods", "volume": "22", "country_publication_code": "US", "creator": [ { "name": "Kelsey [ORNL] (ORCID:0000000183276413) Carter", "primaryContact": true }, { "name": "Christian [ORNL] (ORCID:0000000283287777) Salvador", "primaryContact": false }, { "name": "Savana [ORNL] Colegate", "primaryContact": false }, { "name": "Alyssa [ORNL] (ORCID:0000000311424709) Carrell", "primaryContact": false }, { "name": "Jun [ORNL] (ORCID:0000000271377169) Lee", "primaryContact": false }, { "name": "Robert [ORNL] (ORCID:0000000260581025) Smith", "primaryContact": false }, { "name": "Marshall [ORNL] (ORCID:0000000237132117) McDonnell", "primaryContact": false }, { "name": "Sara [ORNL] (ORCID:0000000281235439) Jawdy", "primaryContact": false }, { "name": "Mac [ORNL] (ORCID:0000000218742614) McLennan", "primaryContact": false }, { "name": "Tyler [ORNL] Hackworth", "primaryContact": false }, { "name": "Lianhong [ORNL] (ORCID:0000000157568738) Gu", "primaryContact": false }, { "name": "Melanie A [ORNL] (ORCID:0000000163689210) Mayes", "primaryContact": false }, { "name": "Udaya C [ORNL] (ORCID:0000000259638370) Kalluri", "primaryContact": false }, { "name": "Thomas [Michigan State University] Sharkey", "primaryContact": false }, { "name": "David [ORNL] (ORCID:0000000247949913) Weston", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/3384934", "active": false }, { "brc": "CBI", "title": "Improved nylon polymerization using amide diads", "description": "Nylons, a major class of synthetic polyamides, are widely used due to their excellent mechanical strength, thermal stability, and chemical resistance. Conventional nylon production relies on the polymerization of lactams or stoichiometric nylon salts. However, applying these approaches to unconventional precursors such as bio-derived glutaric acid produces polymers with low molecular weight and limited applications. To address these challenges, we demonstrated that chemically-synthesized nylon diads enable the production of higher-molecular-weight polyamides compared with traditional salts. We then identified a biosynthetic approach using amide synthetases to convert unprotected bifunctional substrates into nylon-relevant diads. Using a cofactor regeneration system, enzymatic diad synthesis was scaled to produce sufficient material for laboratory-scale characterization and solid-state polymerization. Amide synthetases demonstrated broad substrate scope, catalyzing the regioselective assembly of diverse nylon-relevant diacids, diamines, and \u03c9-amino acids. This strategy offers a novel route to synthesize challenging nylon monomers and advances production of bioderived nylons.", "abstract": "Nylons, a major class of synthetic polyamides, are widely used due to their excellent mechanical strength, thermal stability, and chemical resistance. Conventional nylon production relies on the polymerization of lactams or stoichiometric nylon salts. However, applying these approaches to unconventional precursors such as bio-derived glutaric acid produces polymers with low molecular weight and limited applications. To address these challenges, we demonstrated that chemically-synthesized nylon diads enable the production of higher-molecular-weight polyamides compared with traditional salts. We then identified a biosynthetic approach using amide synthetases to convert unprotected bifunctional substrates into nylon-relevant diads. Using a cofactor regeneration system, enzymatic diad synthesis was scaled to produce sufficient material for laboratory-scale characterization and solid-state polymerization. Amide synthetases demonstrated broad substrate scope, catalyzing the regioselective assembly of diverse nylon-relevant diacids, diamines, and \u03c9-amino acids. This strategy offers a novel route to synthesize challenging nylon monomers and advances production of bioderived nylons.", "date": "2023-05-31", "identifier": "https://www.osti.gov/biblio/3385030", "bibliographicCitation": "https://doi.org/10.1039/d6gc00885b", "topic": [ "Unknown" ], "journal_name": "Green Chemistry", "volume": "28", "country_publication_code": "US", "creator": [ { "name": "Liangyu [ORNL] (ORCID:0009000212029938) Qian", "primaryContact": true }, { "name": "Isaiah [ORNL] (ORCID:0000000273339182) Dishner", "primaryContact": false }, { "name": "Dana Lynn [ORNL] (ORCID:0000000247588054) Carper", "primaryContact": false }, { "name": "Vilmos [ORNL] (ORCID:0000000301865797) Kertesz", "primaryContact": false }, { "name": "Nicholas [ORNL] Zolnierczuk", "primaryContact": false }, { "name": "Nikki [ORNL] (ORCID:0000000333010849) Thiele", "primaryContact": false }, { "name": "John F [ORNL] (ORCID:0000000298664010) Cahill", "primaryContact": false }, { "name": "Jeff [ORNL] (ORCID:0000000290978680) Foster", "primaryContact": false }, { "name": "Josh [ORNL] (ORCID:0000000323028180) Michener", "primaryContact": false } ], "funding": [ { "fundingOrganization": { "organizationName": "USDOE" } } ], "dataset_url": "https://www.osti.gov/biblio/3385030", "active": false } ] }