Biomass Formation and Modification

Better Plants

Biomass Formation and Modification research seeks to understand the scientific basis of recalcitrance and generate improved biomass with reduced recalcitrance. As part of this goal, the BioEnergy Science Center (BESC) conducts molecular-level investigations of cell wall assembly and polysaccharide and lignin synthesis to gain an in-depth understanding of the mechanisms that control biomass recalcitrance. Scientists also use targeted modification of plant cell walls and selection of natural feedstock variants to reduce recalcitrance and improve biomass characteristics. Although these methods can be applied to a wide range of woody and herbaceous plants, BESC focuses on two potential bioenergy crops, poplar and switchgrass, with improved characteristics for converting lignocellulosic biomass to fermentable sugars. Researchers are moving promising plants with improved traits from greenhouses into field trials where their real-world usefulness is being evaluated. Successfully reducing recalcitrance, which translates into more easily deconstructed biomass feedstocks, will greatly facilitate the efficiency and economic viability of advanced biofuels.

BESC is choosing from among the thousands of natural and modified feedstocks that it has identified to a set of high-performing, reduced-recalcitrance lines for integrated study across the Center. This crosscutting set of activities includes more detailed characterization and conversion tests. BESC will further select a subset of candidates (i.e., TOP Lines) for in-depth characterization and introduction into limited field trials and bench-scale conversion tests. To accomplish these efforts, Biomass Formation and Modification is divided into two main activities and goals:

  • Systems Analysis and TOP Line Poplar and Switchgrass Selection. To identify and characterize the preeminent reduced-recalcitrance poplar and switchgrass lines and to initiate field tests of potential commercial lines.
  • Cell Wall Synthesis and the Mechanisms of Recalcitrance. To develop a fundamental understanding of the molecular basis of cell wall formation and recalcitrance that enables movement toward commercial, engineered bioenergy feedstocks.

Information gained from these activities will provide the scientific basis for enabling the bioenergy industry’s effective use of lignocellulosic feedstocks.

poplar feedstock field trial poplar feedstock field trial switchgrass feedstock field trial switchgrass feed stock field trial

Field Testing of Improved Feedstocks. BESC is conducting field trials of poplar and switchgrass species with enhanced biofuel-relevant characteristics. Testing includes (A) assessments of over 40 poplar constructs in South Carolina, (B) more than a thousand poplar genotypes in four common gardens in the Pacific Northwest, and genetically improved switchgrass plots in (C) Texas and (D) Tennessee. [Images courtesy BESC]

BESC Progress Snapshot: Feedstocks

2007: Where Research Was Then

  • Lignin and cellulose accessibility believed to be the primary causes of recalcitrance
  • Low transformation efficiencies for switchgrass
  • Range of natural variation and genetic control of recalcitrance within a species not established
  • Viability of low lignin transgenic perennials not confirmed in field

Where Research Is Now

  • Proved core concept that multiple genes—many outside of the lignin pathway—control plant cell wall recalcitrance, and demonstrated that these genes can be manipulated, or selected, in plants to yield perennial feedstocks with enhanced deconstruction potential
  • Used BESC transformation pipeline to target ~900 candidate recalcitrance gene constructs to date
  • Verified multiple reduced recalcitrance lines in Populus and switchgrass and more than 30 TOP Lines (i.e., high-performing lines with reduced recalcitrance and wild type or better growth) selected for deeper study
  • Data now returning from field trials of initial transgenic lines
Debra Mohnen

Debra Mohnen

Biomass Formation and Modification Lead

Dr. Debra Mohnen is the BESC Biomass Formation and Modification lead and a professor in the Department of Biochemistry and Molecular Biology and at the Complex Carbohydrate Research Center at the University of Georgia. Her research program centers on the biosynthesis function and structure of plant cell wall polysaccharides. Her emphasis is on the biosynthesis of pectin, pectin function in plants, human health, and the improvement of plant cell wall structure to enhance conversion efficiency of plant wall biomass to biofuels.


Biomass Formation and Modification Research Results

Publications

Publication Date Citation
DOI
12/22/2016 Li, M., Pu, Y., Yoo, C.G., Gjersing, E., Decker, S.R., Doeppke, C., Shollenberger, T., Tschaplinski, T.J., Engle, N.L., Sykes, R.W., Davis, M.F., Baxter, H.L., Mazarei, M., Fu, C., Dixon, R.R., Wang, Z-Y., Stewart Jr., C.N., Ragauskas, A.J., "Study of traits and recalcitrance reduction of field-grown COMT down-regulated switchgrass", Biotechnology for Biofuels, 10:12, 2016.
DOI: 10.1186/s13068-016-0695-7
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12/20/2016 Serba, D.D., Uppalapati, S.R., Krom, N., Mukherjee, S., Tang, Y., Mysore, K.S., Saha, M.C., "Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency", BMC Genomics, 17:1040, 2016.
DOI: 10.1186/s12864-016-3377-8
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10/10/2016 Rao, X., Dixon, R.A., "The differences between NAD-ME and NADP-ME subtypes of C4 photosynthesis: more than decarboxylating enzymes", Frontiers in Plant Sciences, 7:1525, 2016.
DOI: 10.3389/fpls.2016.01525
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08/25/2016 Bali, G., Khunsupat, R., Akinosho, H., Payyavula, R.S., Samuel, R., Tuskan, G.A., Kalluri, U.C., Ragauskas, A.J., "Characterization of cellulose structure of Populus plants modified in candidate cellulose biosynthesis genes", Biomass and Bioenergy, 94:146-154, 2016.
DOI: 10.1016/j.biombioe.2016.08.013
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07/19/2016 Salazar, M.M., Grandis, A., Pattathil, S, Neto, J.L., Camargo, E.L.O., Alves, A., Rodrigues, J.C., Squina, F., Cairo, J.P.F., Buckeridge, M.S., Hahn, M.G., Pereira, G.A.G., "Eucalyptus cell wall architecture: clues for lignocellulosic biomass deconstruction", BioEnergy Research, 9(3):969-979, 2016.
DOI: 10.1007/s12155-016-9770-y
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06/29/2016 Shi, J., Pattathil, S., Ramakrishnan, P., Anderson, N., Kim, J.I., Venkatachalam, Hahn, M.G., Chapple, C., Simmons, B., Singh, S., "Impact of engineered lignin composition on biomass recalcitrance and ionic liquid pretreatment efficiency", Green Chemistry, 2016
DOI: 10.1039/C6GC01193D
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06/24/2016 Pattathil, S., Ingwers, M.W., Victoriano, O.L., Kandemkavil, S., McGuire, M.A., Teskay, R.O., Aubrey, D.P., "Cell wall ultrastructure of stem wood, roots, and needles of a conifer varies in response to moisture availability", Frontiers in Plant Science, 7:882, 2016
DOI: 10.3389/fpls.2016.00882
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06/20/2016 Sun, Q., Khunsupat, R., Akato, K., Tao, J., Labbe, N., Gallego, N.C., Bozell, J.J., Rials, T.G., Tuskan, G.A., Tschaplinski, T.J., Naskar, A.F., Pu, Yunqiao; Ragauskas, A.J., "A study of poplar organosolv lignin after melt rheology treatment as carbon fiber precursors", Green Chemistry, 2016
DOI: 10.1037/c6gc000977h
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06/20/2016 Chai, M., Zhou, C., Molina, I., Fu, C., Nakashima, J., Li, G., Zhang, W., Park, J., Tang, Y., Jiang, Q., Wang, Z-Y, "A class II KNOX gene, KNOX4, controls seed physical dormancy", PNAS, 113(25):6997-7002, 2016.
DOI: 10.1073/pnas.1601256113
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06/20/2016 Tolbert, A., Ma, T., Kalluri, U., Ragauskas, A.J., "Determing lignin S/G ration in the vessel and fiber cell walls of transgenic Populus plants", Energy & Fuels, 39(7):5716-5720, 2016.
DOI: 10.1021/acs.energyfuels.6b00560
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06/20/2016 Ha, C.M., Escamilla-Trevino, L., Yarce, S., Kim, J.C., Ralph, H., Chen, F., Dixon, R.A., An essential role of caffeoyl shikimate esterase in monolignol biosynthesis in Medicago truncatula, Plant Journal, 86(5):363-375, 2016.
DOI: 10.1111/tpj.13177
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06/11/2016 Li, Z., Hwang, S., Bar-Peled, M., "Discovery of a unique extracellular polysaccharide in members of the pathogenic bacillus that can co-form with spores", The Journal of Biological Chemistry, 291:19051-19067, 2016.
DOI: 10.1074/jbc.M116.724708
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05/31/2016 Huang, Y., Wang, Y., Tan, L., Sun, L., Petrosino, J., Cui, M-Z., Hao, F., Zhang, M., "Nanospherical arabinogalactan proteins are a key component of the high-strength adhesive secreted by English Ivy," PNAS, 113(23):3193-3202, 2016.
DOI: 10.1073/pnas.1600406113
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05/31/2016 Willis, J.D., Mazarei, M., Stewart Jr., C.N., "Transgenic Plant-produced hydrolytic enzymes and the potential of insect gut-derived hydrolases for biofuels", Frontiers in Plant Science, 7(675), 2016.
DOI: 10.3389/fpls.2016.00675
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05/24/2016 Bhagia, S., Muchero, W., Kumar, R., Tuskan, G.A., Wyman, C.E., "Natural genetic variability reduces recalcitrance in poplar", Biotechnology for Biofuels, 9:106, 2016.
DOI: 10.1186/s13068-016-0521-2
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05/09/2016 Barros, J., Serrani-Yarce, J.C., Chen, F., Baxter, D., Venables, B.J., Dixon, R.A., "Role of bifunctional ammonia-lyase in grass cell wall biosynthesis", Nature Plants, 2, 2016.
DOI: 10.1038/nplants.2016.50
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04/28/2016 Wuddineh, W.A., Mazarei, M., Zhang, J., Turner, G.B., Decker, S.R., Sykes, R.W., Davis, M.F., Udvardi, M.K., Stewart, Jr., C.N., "Identification and overexpression of a Knotted1-like transcription factor in switchgrass (Panicum virgatum L.) for lignocellulosic feedstock improvement", Frontiers in Plant Science, 7(520), 2016.
DOI: 10.3389/fpls.2016.00520
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04/26/2016 Pena, M.J., Kulkarni, A.R., Backe, J., Boyd, M., O'Neill, M.A., York, W.S., "Structural diversity of xylans in the cell walls of monocots", Planta, 244(3):589-606, 2016.
DOI: 10.1007/s00425-016-2527-1
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04/26/2016 Serba, D.D., Sykes, R.W., Gjersing, E.L., Decker, S.R., Daverdin, G., Devos, K.M.; Brummer, E.C., Saha, M.C., "Cell wall composition and underlying QTL in an F1 Pseudo-testcross population of switchgrass", BioEnergy Research, 9(3):836-850, 2016.
DOI: 10.1007/s12155-016-9733-3
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04/18/2016 Baxter, H.L., Mazarei, M., Fu, C., Cheng, Q., Turner, G.B., Sykes, R.W., Windham, M.T., Davis, M.F., Dixon, R.A., Wang, Z-Y., Stewart Jr., C.N., "Time course field analysis of COMT-downregulated switchgrass: Lignification, recalcitrance, and rust susceptibility", BioEnergy Research, 9(33):1-14, 2016.
DOI: 10.1007/s12155-016-9751-1
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04/11/2016 Panday, S.K., Nookaraju, A., Fujino, T., Pattathil, S., Joshi, C.P., "Virus-induced gene silencing (VIGS)-mediated functional characterization of two genes involved in lignocellulosic secondary cell wall formation", Plant Cell Reports, 2016
DOI: 10.1007/s00299-016-2039-2
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03/21/2016 Bryan, A.C., Jawdy, S., Gunter, L., Gjersing, E., Sykes, R., Hinchee, M.A.W., Winkeler, K.A., Collins, C.M., Engle, N., Tschaplinski, T.J., Yang, X., Tuskan, G.A., Muchero, W., Chen, J-G., "Knockdown of a laccase in Populus deltoides confers altered cell wall chemistry and increased sugar release", Plant Biotechnology Journal, 1-11, 2016.
DOI: 10.1111/pbi.12560
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03/03/2016 Yang, J., Worley, E., Ma, Q., Li, J., Torres-Jerez, I., Li, G., Zhao, P.X., Xu, Y., Tang, Y., Udvardi, M., "Nitrogen remobilization and conservation, and underlying senescence-associated gene expression in the perennial switchgrass Panicum virgatum", New Phytologist, 211(1):75-89, 2016.
DOI: 10.1111/nph.13898
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02/19/2016 Rao, X., Lu, N., Li, G., Nakashima, J., Tang, Y., Dixon, R.A., "Comparative cell-specific transcriptomics revelas differentiation of C4 photosynthesis pathways in switchgrass and other C4 lineages", Journal of Experimental Botany, 67(6):1649-1662, 2016.
DOI: 10.1093/jxb/erv553
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02/16/2016 Nar, M., Rizvi, H.R., Dixon, R.A., Chen, F., Kovalcik, A., D'Souza, N., "Superior plant-based carbon fibers from electronspum poly-(caffeyl alcohol)", Carbon, 103:372-383, 2016.
DOI: 10.1016/j.carbon.2016.02.053
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01/01/2016 Vandavasi, V.G., Putnam, D.K., Zhang, Q., Petridis, L.; Heller, W.T., Nixon, B.T., Haigler, C.H., Kalluri, U., Coates, L., Langan, P., Smith, J.C., Meiler, J., O'Neill, H., "A structural study of CESA21 catalytic domain of arabidopsis cellulose synthesis complex: evidence for CESA trimers", Plant Physiology, 170(1):123-135 2015.
DOI: 10.1104/pp.15.01356
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12/31/2015 Baxter, H.L., Alexander, L.W., Mazarei, M., Haynes, E., Turner, G.B., Sykes, R.W., Decker, S.R., Davis, M.F., Dixon, R.A., Wang, Z-Y., Stewart Jr., C.N., "Hybridization of downregulated-COMT transgenic switchgrass lines with field-selected switchgrass for improved biomass traits", Euphtica, 209:341-355, 2016.
DOI: 10.1007/s10681-016-1632-3
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12/31/2015 Ziebell, A., Gjersing, E., Hinchee, M., Katahira, R., Sykes, R.W., Johnson, D.K., Davis, M.F., "Downregulation of p-Coumaroyl Quinate/Shikimate 3′-Hydroxylase (C3′H) or Cinnamate-4-hydrolylase (C4H) in Eucalyptus urophylla×Eucalyptus grandis Leads to Increased Extractability", Bioenergy Research, 8(128):1-9 2016
DOI: 10.1007/s12155-016-9713-7
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12/29/2015 Srivastava, A.C., Chen, F., Ray, T., Pattathil, S., Pena, M.J., Avci, U., Li, H., Huhman, D.V., Backe, J., Urbanowica, B., Miller, J.D., Bedair, M., Wyman, C.E., Sumner, L.W., York, W.S., Hahn, M.G., Dixon, R.A., Blancaflor, E.B., Tang, Y., Loss of function of folylpolyglutamate synthetase 1 reduces lignin content and improves cell wall digestibility in Arabidopsis, Biotechnology for Biofuels, 8(224), 2015
DOI: 10.1186/s13068-015-0403-z
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12/26/2015 Ray, P., Craven, K.D., "Sebancina vermifera: a unique root symbiont with vast agronomic potential", World Journal of Microbiology and Biotechnology, 32(16), 2015.
DOI: 10.1007/s11274-015-1970-7
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11/06/2015 Liu, W., Stewart Jr., C.N., "Plant synthetic promoters and transcription factors", Current Opinion in Biotechnology, 37:36-44, 2015.
DOI: 10.1016/j.copbio.2015.10.001
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10/26/2015 Abraham, P.E., Wang, X., Ranjan, P., Nookaew, I., Zhang, B., Tuskan, G.A., Hettich, R.L., "Integrating mRNA and protein sequencing enables the detection and quantitative profiling of natural protein sequence variants of Populus trichocarpa," Journal of Proteome Research, 14(12):5318-5326 2015.
DOI: 10.1021/acs.jproteome.5b00823
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10/19/2015 Sykes, V.R., Allen ,F.L., Mielenz, J.R., Stewart Jr., C.N., Windham, M.T., Hamilton, C.Y., Rodriguez Jr., M., Yee, K.L., "Reduction of ethanol yield from switchgrass infected with rust caused by puccinia emaculata", BioEnergy Research, 9(1):239-247 2015.
DOI: 10.1007/s12155-015-9680-4
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10/05/2015 Joyce, B.L., Zheljazkov, V.D., Sykes, R., Cantrell, C.L., Hamilton, C., Mann, D.G.J., Rodriguez, M., Mielenz, J., Astatkie, T., Stewart Jr., C.N., "Ethanol and high-value terpene co-production from lignocellulosic biomass of cymbopogon flexuosus and cymbopogon martinii", PLOS ONE, 10(10):e0139195, 2015.
DOI: 10.1371/journal.pone.0139195
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09/22/2015 Faraji, M., Fonseca, L.L., Escamilla-Trevino, L., Dixon, R.A., Voit, E.O., "Computational inference of the structure and regulation of the lignin pathway in Panicum virgatum", Biotechnology for Biofuels, 8(151), 2015.
DOI: 10.1186/s13068-015-0334-8
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09/14/2015 Chen, X., Ma, Q., Rao, X., Tang, Y., Wang, Y., Li, G., Zhang, C., Mao, X., Dixon, Richard A., Xu, Y., "Genome-scale identification of cell-wall-related genes in switchgrass through comparative genomics and computational analyses of transcriptomic data", Bioenergy Research, 9(1):172-180 2015.
DOI: 10.1007/s12155-015-9674-2
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08/30/2015 Hwang, S., Li, Z., Bar-Peled, Y., Aronov, A., Ericson, J., Bar-Peled, M., "The Biosynthesis of UDP-D-FucNAc-4N-(2)-oxoglutarate (UDP-Yelosamine) in Bacillus cereus ATCC 14579", The Journal of Biological Chemistry, 19(289):35620-35632, 2015.
DOI: 10.1074/jbc.M114.614917
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08/27/2015 Sykes, R.W., Gjersing, E.L., Foutz, K., Rottmann, W.H., Kuhn, S.A., Foster, C.E., Ziebell, A., Turner, G.B., Decker, S.R., Hinchee, M.A.W., Davis, M.F., "Down-regulation of p-coumaroyl quinate/shikimate 3′-hydroxylase (C3′H) and cinnamate 4-hydroxylase (C4H) genes in the lignin biosynthetic pathway of Eucalyptus urophylla × E. grandis leads to improved sugar release", Biotechnology for Biofuels, 8(128), 2015.
DOI: 10.1186/s13068-015-0316-x
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08/24/2015 Slater, S.C., Simmons, B.A., Rogers, T.S., Phillips, M.E., Nordahl, K., Davison, B.H., "The DOE Bioenergy Research Centers: history, operations and scientific output," Bioenergy Research, 8(3):881-896, 2015.
DOI: 10.1007/s12155-015-9660-8
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08/11/2015 Yao, J., Guo, H., Chairprasongsuk, M., Zhao, N., Chen, F., Yang, Y., Guo, H., "Substrate-assisted catalysis in the reaction catalyzed by salicylic acid binding protein 2 (SABP2), a potential mechanism of substrate discrimination for some promiscuous enzymes", Biochemistry, 54(34):5366-5375, 2015.
DOI: 10.1021/acs.biochem.5b00638
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07/20/2015 Wuddineh, W.A., Mazarei, M., Turner, G.B., Sykes, R.W., Decker, S.R., Davis, M.F., Stewart, Jr., C.N., "Identification and molecular characterization of the switchgrass AP2/ERF transcription factor superfamily, and overexpression of PvERF001 for improvement of biomass characteristics for biofuel", Frontiers in Bioengineering and Biotechnology, 3(101), 2015.
DOI: 10.3389/fbioe.2015.00101
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07/09/2015 McLean, R., Hobbs, J.K., Suits, M.D., Tuomivaara, S.T., Jones, D., Boraston, A.B., Abbott, D.W., "Functional analyses of resurrected and contemporary enzymes illuminate an evolutionary path for the emergence of exolysis in polysaccharide lyase family two", The Journal of Biological Chemistry, 290(35):21231-21243 2015.
DOI: 10.1074/jbs.M115.664847
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07/01/2015 Gallego-Giraldo, L., Shadle, G., Shen, H., Barros-Rios, J., Corrales, S. F., Wang, H., Dixon, R.A., "Combining enhanced biomass density with reduced lignin level for improved forage quality", Plant Biotechnology Journal, 14(3):895-904, 2015.
DOI: 10.1111/pbi.12439
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06/22/2015 Ray, P., Ishiga, T., Decker, S.R., Turner, G.B., Craven, K. D., "A Novel Delivery System for the Root Symbiotic Fungus, Sebacina vermifera, and Consequent Biomass Enhancement of Low Lignin COMT Switchgrass Lines", Bioenergy Research, 8(3):922-933, 2015.
DOI: 10.1007/s12155-015-9636-8
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05/14/2015 Davison, B.H., Brandt, C.C., Guss, A.M., Kaluri, U.C., Palumbo, A.V., Stouder, R.L., Webb, E.G., "The impact of biotechnological advances on the future of U.S. bioenergy", Biofuels, Bioproducts and Biorefining, 9(5):454-467, 2015.
DOI: 10.1002/bbb.1549
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05/01/2015 Liu, W., Stewart, Jr., C.N., "Plant synthetic biology", Trends in Plant Science, 20:309-317, 2015.
DOI: 10.1016/j.tplants.2015.02.004
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04/23/2015 De Souza, A.P., Kamel, C.L.A., Torres, A.F., Pattathil, S., Hahn, M.G., Trindade, L.M., Buckeridge, M.S., "How cell wall complexity influences saccharification efficiency in Miscanthus sinensis", Journal of Experimental Botany, 66(14):4351-4365, 2015.
DOI: 10.1093/jxb/erv183
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03/01/2015 Biswal, A.K., Hao, Z., Pattathil, S., Yang, X., Winkeler, K., Collins, C., Mohanty, S.S., Richardson, E.A., Gelineo-Albersheim, I., Hunt, K., Ryno, D., Sykes, R.W., Turner, G.B., Ziebell, A., Gjersing, E., Lukowitz, W., Davis, M.F., Decker, S.R., Hahn, M.G., Mohnen, D., "Downregulation of GAUT12 in Populus deltoides by RNA silencing results in reduced recalcitrance, increased growth and reduced xylan and pectin in a woody biofuel feedstock", Biotechnology for Biofuels, 8(41), 2015.
DOI: 10.1186/s13068-015-0204-4
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02/24/2015 Trumbo, J.L., Zhang, B., Stewart, Jr., C.N., "Manipulating microRNAs for improved biomass and biofuels from plant feedstocks", Plant Biotechnology Journal, 13(3):337-354, 2015.
DOI: 10.1111/pbi.12319
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02/05/2015 Casler, M.D., Vermerris, W., Dixon, R.A., "Replication concepts for bioenergy research experiments", BioEnergy Research, 8(1):1-16, 2015.
DOI: 10.1007/s12155-015-9580-7
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02/01/2015 Pattathil, S., Hahn, M.G., Dale, B.E., Chundawat, P.S., "Insights into plant cell wall structure, architecture and integrity using glycome profiling of native and AFEXtm pretreated biomass", Journal of Experimental Botany, 66(14):4279-4294, 2015.
DOI: 10.1093/jxb/erv107
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01/30/2015 Muchero, W., Guo, J., DiFazio, S.P., Chen, J-G., Ranjan, P., Slavov, G.T., Gunter, L.E., Jawdy, S., Bryan, A.C., Sykes, R., Ziebell, A., Klapste, J., Porth, I., Skyba, O., Unda, F., El-Kassaby, Y.A., Douglas, C.J., Mansfield, S.D., Martin, J., Schackwitz, W., Evans, L.M., Czarnecki, O., Tuskan, G.A., "High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus", BMC Genomics, 16(24), 2015.
DOI: 10.1186/s12864-015-1215-z
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01/20/2015 Serba, D.D., Uppalapati, S.R., Mukherjee, S., Krom, N., Tang, Y., Mysore, K.S., Saha, M.C., "Transcriptome profiling of rust resistance in switchgrass using RNA-Seq analysis", The Plant Genome, 8(2), 2015
DOI: 10.3835/plantgenome2014.10.0075
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01/07/2015 Baxter, H.L., Poovaiah, C.R., Yee, K., Mazarei, M., Rodriguez Jr., M., Thompson, O.A., Shen, H., Turner, G.B., Decker, S.R., Sykes, R.W., Chen, F., Davis, M.F., Mielenz, J.R., Davison, B.H., Dixon, R.A., Stewart Jr., C.N., "Field evaluation of transgenic switchgrass plants overexpressing PvMYB4 for reduced biomass recalcitrance", BioEnergy Research, 8(3):910-921, 2015.
DOI: 10.1007/s12155-014-9570-1
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12/29/2014 Yang, J., Worley, E., Udvardi, M., "A NAP-AA03 regulatory module promotes chlorophyll degradation via ABA biosynthesis in Arabidopsis leaves", The Plant Cell, 26(12):4862-4874, 2014.
DOI: 10.1105/tpc.114.133769
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12/16/2014 Yang, J., Worley, E., Torres-Jerez, I., Miller, R., Wang, M., Fu, C., Wang, Z-Y., Tang, Y., Udvardi, M., "PvNAC1 and PvNAC2 are associated with leaf senescence and nirtrogen use efficiency in switchgrass", Bioenergy Research, 8(2):868-880, 2014.
DOI: 10.1007/s12155-014-9566-x
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12/02/2014 Brunner, A.M., Evans, L.M., Hsu, C-Y, Sheng, X., "Vernalization and the chilling requirement to exit bud dormancy: shared or separate regulation?", Frontiers in Plant Science, 5(732), 2014.
DOI: 10.3389/fpls.2014.00732
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11/25/2014 Li, Z., Hwang, S., Ericson, J., Bowler, K., Bar-Peled, Maor, "Pen and Pal are nucleotide-sugar-dehydratases that convert UDP-GlcNAc to UDP-6-deoxy-D-GlcNAc-5,6-ene and then to UDP-4-keto-6-deoxy-L-AltNAc for CMP-pseudaminic acid synthesis in Bacillus thuringiensis", The Journal of Biological Chemistry, 290(2):691-704, 2014.
DOI: 10.1074/jbc.M114.612747
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11/11/2014 Kalluri, U.C., Yin, H., Davison, B.H., "Systems and synthetic biology approaches to alter plant cell walls and reduce biomass recalcitrance, Plant Biotechnology Journal", 12(9):1207-1216, 2014.
DOI: 10.1111/pbi.12283
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11/02/2014 Wuddineh, W.A., Mazarei, M., Poovaiah, C.R., Mann, D.G.J., Ziebell, A., Sykes, R.W., Davis, M.F., Udvardi, M.K., Stewart Jr., C.N., "Identification and overexpress of gibberellin 2-oxidase (GA2ox) in switchgrass (Panicum virgatum L.) for improved plant architecture and reduced biomass recalcitrance", Plant Biotechnology Journal, 13(5):636-647) 2014.
DOI: 10.1111/pbi.12287
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10/30/2014 Zhou, C., Han, L., Li, G., Chai, M., Fu, C., Cheng, X., Wen, J., Tang, Y., Wang, Z-Y., "STM/BP-Like KNOXI Is Uncoupled fromARP in the Regulation of Compound Leaf Development in Medicago truncatula", The Plant Cell, 26(4):1464-1479 2014.
DOI: 10.1105/tpc.114.123885
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05/11/2012 Bar-Peled, M., Urbanowicz, B.R., O'Neill, M.A., "The Synthesis and Origin of the Pectic Polysaccharide Rhamnogalacturonan II - Insights from Nucleotide Sugar Formation and Diversity", Frontiers in Plant Science, 3(92), 2012.
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04/03/2012 Mann, D.G.J., Abercrombie, L.L., Rudis, M.R., Milwood, R.J., Dunlap, J.R., Stewart, C.N., Very bright orange fluorescent plants: endoplasmic reticulum targeting of orange fluorescent proteins as visual reporters in transgenic plants, BMC Biotechnology, 12(17), 2012.
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03/28/2012 Sun, G.L., Stewart, C.N., Xiao, P., Zhang, B.H., MicroRNA Expression Analysis in the Cellulosic Biofuel Crop Switchgrass (Panicum virgatum) under Abiotic Stress, PLOS ONE 7(3):e32017, 2012.
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08/12/2011 Joyce, B.L., Stewart Jr., C.N., Designing the perfect plant feedstock for biofuel production: Using the whole buffalo to diversify fuels and products, Biotechnology Advance, 30(5):1011-1022, 2012.
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07/11/2011 Mann, D.G., King, Z.R., Liu, W., Joyce, B.L., Percifield, R.J., Hawkins, J.S., LaFayette, Peter R., Artelt, B.J., Burris, J.N., Mazarei, M., Bennetzen, J.L., Parrott, W.A., Stewart Jr., C. Neal, Switchgrass (Panicum virgatum L.) ubiquitin gene (PvUbi1 and PvUbi2) promoters for use in plant transformation, BMC Biotechnology, 11(74), 2011.
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07/05/2011 Xiaohan Yang, Ting Li, David Weston, Abhijit Karve, Jessy L. Labbe, Lee E. Gunter, Poornima Sukumar, Anne Borland, Jin-Gui Chen, Stan D. Wullschleger, Timothy J. Tschaplinski and Gerald A. Tuskan. Innovative Biological Solutions to Challenges in Sustainable Biofuels Production. In book "Biofuel Production-Recent Developments and Prospects", ( ed. Marco Aurélio dos Santos Bernardes), InTech, 15:375-414, 2011.
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06/17/2011 Mohnen, D., Tierney, Mary L., Plants Get Hyp to O-Glycosylation, Science, 332(6036):1393-1394, 2011.
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06/01/2011 Zhou, Chuanen, Han, Lu, Hou, Chunyan, Metelli, Allessandra, Qi, Liying, Tadege, Million, Mysore, Kirankumar S., Wang, Zeng-Yu, Developmental Analysis of a Medicago truncatula smooth leaf margin1 Mutant Reveals Context-Dependent Effects on Compound Leaf development, The Plant Cell, 23(6):2106-2124, 2011.
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05/20/2011 Correia, Marcia A., Mazumder, K., Bras, J.L., Firbank, S.J., Zhu, Y., Lewis, R.J., York, W.S., Fontes, C.M., Gilbert, H.J., The structure and function of an arabinoxylan-specific xylanase, Journal of Biological Chemistry, 286:22510-22520, 2011.
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05/16/2011 Lee, Y., Chen, F., Gallego-Giraldo, L., Dixon, Richard A., Voit, E.O.,Integrative analysis of transgenic alfalfa (Medicago sativa L.) suggests new metabolic control mechanisms for monolignol biosynthesis, PLoS Computational Biology, 7(5):e1002047, 2011.
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05/01/2011 Deshpande, A., Pontaroli, A.C., Chaluvadi, S.R., Lu, F., Bennetzen, J.L., Plant Genetics for Study of the Roles of Root Exudates and Microbes in the Soil, Root Genomics, 4:99-111, 2011.
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05/01/2011 Srivastava, A.C., Palanichelvam, K., Ma, J.Y., Steele, J., Blancaflor, E.B., Tang, Y.H., Collection and Analysis of Expressed Sequence Tags Derived from Laser Capture Microdissected Switchgrass (Panicum virgatum L. Alamo) Vascular Tissues, BioEnergy Research, 3(3):278-294, 2010.
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05/01/2011 Ye, Chu-Yu, Li, Ting, Tuskan, Gerald A., Tschaplinski, Timothy J., Yang, Xiaohan, Comparative analysis of GT14/GT14-like gene family in Arabidopsis, Oryza, Populus, Sorghum and Vitis, Plant Science, 181(6):688-695, 2011.
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05/01/2011 Mazarei, Mitra, Al-Ahmad, Hani, Rudis, Mary R., Joyce, Blake J., Stewart Jr., C. Neal, Switchgrass (Panicum virgatum L.) cell suspension cultures: Establishment, characterization, and application, Plant Science, 18(6): 712-715, 2011.
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05/01/2011 DiFazio S.P., G.T. Slavov, and C.S. Joshi, Populus: A premier pioneer system for plant genomics, In Joshi, C.P., and S.P. DiFazio (eds). Poplar. Science Publishers, Enfield, New Hampshire, 1:1-28, 2011.
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03/18/2011 Cai, Bin, Yang, Xiaohan, Yang, Tuskan, Gerald A., Cheng, Zong-Ming, MicroSyn: A user friendly tool for detection of microsynteny in a gene family, BMC Bioinformatics, 12(79), 2011.
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03/01/2011 Studer, Michael E., DeMartini, Jaclyn D., Davis, Mark F., Sykes, Robert W., Davison, Brian H., Keller, Martin, Tuskan, Gerald A., Wyman, Charles E., Lignin content in natural Populus variants affects sugar release, PNAS, 108(15):6300-6305, 2011.
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03/01/2011 Bar-Peled, Maor, O'Neill, Malcolm A., "Plant Nucleotide Sugar Formation, Interconversion, and Salvage by Sugar Recycling", Annual Review of Plant Biology, 62:127-155, 2011.
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03/01/2011 Fu, Chunxiang, Mielenz, Jonathan R., Xiao, Xirong, Ge, Yaxin, Hamilton, Choo Y., Rodriguez, Jr., Miguel, Chen, Fang, Foston, Marcus, Ragauskas, Arthur, Bouton, Joseph, Dixon, Richard A., Wang, Zeng-Yu, Genetic manipulation of lignin reduces recalcitrance and improves ethanol production from switchgrass, PNAS, 108(9):3803-3808, 2011.
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03/01/2011 Tsai, C.J., Ranjan, P., DiFazio, S.P., Tuskan, G.A., Johnson, V.E., Poplar Genome Microarrays, Genetics, Genomics and Breeding of Popular, 5:112-127, 2011.
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03/01/2011 Srivastava, Avinach C., Tang, Yuhong, Diaz de la Garza, Rocio I., Blancaflor, Elison B., The plastidial folylpolyglutamate synthetase and root apical meristem maintenance, Plant Signaling and Behavior, 155(3):1237-1251, 2011.
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02/17/2011 Yang, Xiaohan, Ye, Chu-Yu, Bisaria, Anjali, Tuskan, Gerald A., Kalluri, Udaya C., Identification of candidate genes in Arabidopsis and Populus cell wall biosynthesis using text-mining, co-expression network analysis and comparative genomics, Plant Science, 181(6):675-687, 2011.
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02/16/2011 Cartmell, A., McKee, Lauren S., Pena, Maria J., Larsbring, Johan, Brumer, Harry, Kaneko, Satoshi, Ichinose, Hitomi, Lewis, Richard J., Vikso-Nielson, Anders, Gilbert, Harry J., Marles-Wright, Jon, The Structure and Function of an Arabinan-specific α-1,2-Arabinofuranosidase Identified from Screening the Activities of Bacterial GH43 Glycoside Hydrolases , The Journal of Biological Chemistry, 286:15483-15495, 2011.
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01/13/2011 Srivastava, Avinash C., Ramos-Parra, Perla A., Bedair, Mohamed, Robledo-Hernández, Ana L., Tang, Yuhong, Sumner, Lloyd W., Díaz de la Garza, Rocío I., Blancaflor, Elison B., The Folylpolyglutamate Synthetase Plastidial Isoform is Required for Postembryonic Root Development in Arabidopsis, Plant Physiology, Plant Physiology 155 (3):1237-1251, 2011.
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01/07/2011 Chunxiang Fu, Xirong Xiao, Yajun Xi, Yaxin Ge, Fang Chen, Joseph Bouton, Richard A. Dixon and Zeng-Yu Wang Downregulation of Cinnamyl Alcohol Dehydrogenase (CAD) Leads to Improved Saccharification Efficiency in Switchgrass, Bioenergy Research, 4(3):153-164, 2011.
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01/01/2011 Mann, D.G.J, P.R. LaFayette, L.G Abercrombie, W.A. Parrott, C.N. Stewart, Jr. , pANIC: A versatile set of Gateway-compatible vectors for gene overexpression and RNAi-mediated down-regulation in monocots, Plant Trnasformation Technologies, Journal, 10(2):226-236, 2012.
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01/01/2011 Chen, F., Tholl, D., Bohlmann, J., Pichersky, E., The family of terpene synthases in plants: a mid-size family of genes for specialized metabolism that is highly diversified throughout the kingdom, The Plant Journal, 66:212-229, 2011.
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12/17/2010 Yao, Jianzhuang, Xu, Qin, Chen, Feng, Guo, Hong, QM/MM Free Energy Simulations of Salicylic Acid Methyltransferase: Effects of Stabilization of TS-like Structures on Substrate Specificity, The Journal of Physical Chemistry B, 115:389-396, 2011.
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11/22/2010 Yin, T., Zhang, X., Gunter, L., Priya, R., Sykes, R., Davis, M., Wullschleger, S.D., Tuskan, G.A.,Differential Detection of Genetic Loci Underlying Stem and Root Lignin Content in Populus, PLOS ONE, 5(11):e14021, 2010.
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11/01/2010 Ghimire, S.R., Charlton, N.D., Bell, J.D., Krishnamurthy, Y.L. Craven, K.D., Biodiversity of fungal endophyte communities inhabiting switchgrass (Panicum virgatum L.) growing in the native tallgrass prairie of northern Oklahoma, Fungal Diversity, 47(1):19-27, 2010.
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10/25/2010 Tyler, Ludmila, Bragg, Jennifer N., Wu, Hiajie, Yang, Xiaohan, Guskan, Gerald A., Vogel, John P., Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon, BMC Genomics, 11(600), 2010.
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10/04/2010 Ziebell, A., Gracom, K., Katahira, R., Chen, F., Pu, Y. Q., Ragauskas, A., Dixon, R. A., Davis, M., Increase in 4-coumaryl alcohol units during lignification in alfalfa (Medicago sativa) alters the extractability and molecular weight of lignin, The Journal of Biological Chemistry, 285(50):38961-38968, 2010.
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10/01/2010 Wang, H. Z., Avci, U., Nakashima, J., Hahn, M. G., Chen, F., Dixon, R. A., Mutation of WRKY transcription factors initiates pith secondary wall formation and increases stem biomass in dicotyledonous plants, PNAS, 107(51):22338-22343, 2010.
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10/01/2010 Jiang, Yingnan, McKinnon, Tyler, Varatharajan, Janani, Glushka, John, Prestegard, James H., Sornborger, Andrew T., Schuttler, Heiza-Berd, Bar-Peled, Maor, Time-Resolved NMR: Extracting the Topology of Complex Enzyme Networks, Biophysical Journal, 99(7):2318-26, 2010.
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Intellectual Property

Inventors Title
Davison, Brian; Dixon, Richard A; Engle, Nancy; Mielenz, Jonathan; Pu, Yunqiao; Ragauskas, Art; Standaert, Robert F; Tschaplinski, Timothy J; A Novel Monolignol That Reduces Recalcitrance of Plant Cell Walls
Bar-Peled, Maor; Yang, Ting; The "In-Microbe", High-yield Production of Sugar Nucleotides and their use in Glycan Production
Backe, Jason; O'Neill, Malcolm A; Pena, Maria; Urbanowicz, Breeanna; York, William S.; Modified Expression of Genes Significantly Reduces Recalcitrance of Lignocellulosic Biomass
Pattathil, Sivakumar; York, William S.; The Use of Monoclonal Antibodies in Biomass Characterization and Quantitation
Mohnen, Debra; Higher Yielding Biomass Plants Developed Utilizing Newly Discovered Cell Wall Structures and Proteins
Craven, Kelly; Grass Fungal Endophytes and Uses Thereof
Chen, Fang; Dixon, Richard A; Wang, Huanzhong; Transcription Factors for Modification of Lignin Content in Plants
Udvardi, Michael; Regulating Nutrient Allocation in Plants
Wang, Zeng-Yu; Method for Transformation of Grasses
Mann, David; Stewart, Neal; Identification of a Novel Promoter for Tissue Culture Transformation
Chen, Fang; Dixon, Richard A; Shen, Hui; Compositions and Methods for Improved Plant Feedstock
Stewart, Neal; Engineering Male Sterility or Non-Transgenic Pollen by Pollen-Specific Expression of a Restriction Enzyme
Stewart, Neal; Genes to Increase Growth in Monocots
Adams, Michael A; Albersheim, Ivana G.; Biswal, Ajaya; Hahn, Michael; Hao, Zhangying A.; Hunt, Kimberly D.; Kataeva, Irina; Mohanty, Sushree P.; Mohnen, Debra; Pattathil, Sivakumar; Plants with Altered Pectin and Lignin Biosynthesis and with Improved Growth and Recalcitrance
DiFazio, Stephen P; Muchero, Wellington; Slavov, Gancho; Tuskan, Gerald A; A key gene A regulating plant cell-wall recalcitrance and sugar release
DiFazio, Stephen P; Muchero, Wellington; Slavov, Gancho; Tuskan, Gerald A; A key gene G regulating plant cell-wall recalcitrance and sugar release
Chen, Fang; C-Lignin-Like Polymers and Methods of Use
DiFazio, Stephen P; Gunter, Lee E; Muchero, Wellington; Ranjan, Priya; Slavov, Gancho; Allelic variants regulating cellulose, lignin biosynthesis and biomass sugar yield
Chen, Jay; Gunter, Lee E; Jawdy, Sara S; Muchero, Wellington; Tuskan, Gerald A; An Amino Acid Transporter enhancing lignin quality and sugar release
Chen, Jin-Gui; DiFazio, Stephen P; Gunter, Lee E; Jawdy, Sara S; Muchero, Wellington; Tuskan, Gerald A; An EPSP Enzyme which Regulates Phenylpropanoid, Tyrosine and Tryptophan Pathways
Chen, Jay; DiFazio, Stephen P; Gunter, Lee E; Guo, Jianjun; Jawdy, Sara S; Muchero, Wellington; Ranjan, Priya; Tuskan, Gerald A; Key gene regulating plant cell wall recalcitrance
Chen, Jay; DiFazio, Stephen P; Gunter, Lee E; Jawdy, Sara S; Muchero, Wellington; Transcription Factor which regulates flavonoid, phenylpropanoid, tyrosine, and trypotophan pathways

BioEnergy Science Center one of three DOE Bioenergy Research Centers established by the U.S. Department of Energy.