Biomass Formation and Modification

Research Overview | Research Publications | Intellectual Property

As part of its goal to reduce biomass recalcitrance, the BioEnergy Science Center (BESC) conducts molecular-level investigations of cell wall assembly and polysaccharide and lignin synthesis to gain an in-depth mechanistic understanding of 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 cellulosic biomass to fermentable sugars. Researchers are moving promising plants with improved traits from greenhouses into field trials where their real-world usefulness can be evaluated. Successfully reducing recalcitrance will greatly facilitate the efficiency and economic viability of advanced biofuels.

BESC plans to choose from among the thousands of natural and modified feedstocks that it has identified to a set of reduced-recalcitrance lines for integrated study across the Center. This crosscutting set of activities will include more detailed characterization and conversion tests. BESC will further select a subset of candidates for in-depth characterization and introduction into limited field trials and bench-scale conversion tests. To achieve these goals Biomass Formation and Modification will be divided into two main activities and goals:

  • Systems Analysis and Elite Populus and Switchgrass Line Selection. To identify and characterize the preeminent reduced-recalcitrance Populus 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.

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]


Biomass Formation and Modification Research Results

Publications

  Publication Date Citation
DOI
  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, 2014
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.
10.3389/fpls.2014.00732
  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, 2014
10.1074/jbc.M114.612747
  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
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, 2014
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.
10.1105/tpc.114.123885
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  10/07/2014 Payyavula, R.S., Tschaplinski, T.J., Jawdy, S.S., Sykes, R.W., Tuskan, G.A., Kalluri, U.C., Metabolic profiling reveals altered sugar and secondary metabolism in response to UGPase overexpression in Populus, BMC Plant Biology, 14:265 2014
10.1186/s12870-014-0265-8
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  10/01/2014 Chung, D., Pattathil, S., Biswal, A.K., Hahn, M.G., Mohnen, D., Westpheling, J., Deletion of a Gene Cluster Encoding Pectin Degrading Enzymes in Caldicellulosiruptor bescii Reveals an Important Role for Pectin in Plant Biomass Recalcitrance, Biotechnology for Biofuels, 7:147 2014
10.1186/s13068-014-0147-1
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  09/14/2014 Urbanowicz, B.R., Pena, M.J., Moniz, H.A., Moremen, K.W., York, W.S., Two Arabidopsis Proteins Synthesize Acetylated Xylan in Vitro, The Plant Journal, 80:2 (197-206) 2014
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  09/02/2014 Socha, A.M., Parthasarathi, J., Shi, R., Pattathil, S., Whyte, D., Bergerson, M., Venkatachalam, S., Hahn, M.G., Simmons, B.A., Singh, S., Efficient biomass pretreatment using ionic liquids derived from lignin and hemicellulose, 111:35 (3587-95) 2014.
10. 1073/pnas.1405685111/-/DCSupplemental.
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  08/30/2014 Serba, D.D., Daverdin, G., Bouton, J.H., Devos, K.M., Brummer, C.E., Saha, M.C., Quantitative trait loci (QTL) underlying biomass yield and plant height in switchgrass, Bioenergy Research, 2014
10.1007/s12155-014-9523-8
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  08/28/2014 Hao, Z., Avci, U., Tan, L., Zhu, X., Glushka, J., Pattathil, S., Eberhard, S., Scholes, T., Rothstein, Lukowitz, W., Orlando, R., Hahn, M.G., Mohnen, D., Loss of Arabidopsis GAUT12/IRX8 causes anther indehiscence and leads to reduced G lignin associated with altered matrix polysaccharide deposition, Frontiers in Plant Science, 5: 357, 2014.
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  08/24/2014 Evans, L.M., Slavov, G.T., Rodgers-Melnick, E., Martin, J., Ranjan, P., Muchero, W., Brunner, A.M., Schackwitz, W., Gunter, L., Chen, J.G., Tuskan, G.A., DiFazio, S.P., Population genomics of the model tree Populus trichocarpa identifies signatures of selection and adaptive trait associations, Nature Genetics, 46 (1089-1096) 2014
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  08/21/2014 Poovaiah, C.R., Mazarei, M., Decker, S.R., Turner, G.B., Sykes, R.W., Davis, M.F., Stewart, Jr. C.N., Transgenic switchgrass (Panicum virgatum L.) biomass is increased by overexpression of switchgrass sucrose synthase (PvSUS1), Biotechnology Journal, 2014
10.1002/biot.201400499
  08/14/2014 Chauhan, A., Smartt, A., Wang, J., Utturkar, S., Frank, A., Meng, B., Liu, J., Williams, D., Xu, T., Eldridge, M., Arreaza, A., Rogers, A., Gonzalez, H., Layton, A., Baxter, H., Mazarei, M., DeBruyn, J., Stewart Jr, C.N., Brown, S., Hauser, L., Sayler, G., Integrated metagenomics and metatranscriptomics analyses of root associated soil from transgenic switchgrass, Genome Announcements, 4, 2014.
10.1128/genomeA.00777-14
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  08/05/2014 Zhao, Q., Zeng, Y., Yin, Y., Pu, Y., Jackson, L.A., Engle, N.L., Martin, M.Z., Tschaplinski, T.J., Ding, S-Y., Ragauskas, A.J. and Dixon, R.A., Pinoresinol reductase 1 impacts lignin distribution during secondary cell wall biosynthesis in Arabidopsis. Phytochemistry, 2014
10.1016/j.phytochem.2014.07.008
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  08/01/2014 Kyrpides, et al., Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains, PLOS One, 12:8 2014.
10.1371/journal.pbio. 1001920
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  07/30/2014 Daverdin, G., Bahri, B.A., Wu, X., Serba, D.S., Tobias, C., Saha, M.C., Devos, K.M., Comparative relationships and chromosome evolution in switchgrass (Panicum virgatum) and its genomic model, foxtail millet (setaria italica), Bioenergy Research, 2014
10.1007/s12155-014-9508-7
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  07/26/2014 Nageswara-Rao, M., Hanson, M., Agarwal, S., Stewart Jr. C.N., Kwit, C., Genetic diversity analysis of switchgrass (Panicum virgatum L.) populations using microsatellites and chloroplast sequences, Agroforest Systems, 88 (823-834) 2014
10.1007/s10457-014-9728-z
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  07/22/2014 Poovaiah, C.R., Nageswara-Rao, M., Soneji, J.R., Baxter, H.L., Stewart Jr. C.N., "Altered lignin biosynthesis using biotechnology to improve lignocellulosic biofuel feedstocks", Plant Biotechnology Journal, 12:9, 1163-73, 2014.
10.1111/pbi.12225
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  07/07/2014 Bahulikar, R.A., Torres-Jerez, I., Worley, E., Craven, K., Udvardi, M.K., Diversity of nitrogen-fixing bacteria associated with switchgrass in the native tall-grass prairie of northern Oklahoma, Applied and Environmental Microbiology, 80(18), 5636-43, 2014.
10.1128/AEM.02091-14
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  06/19/2014 Myburg, et al., The genome of Eucalyptus grandis, Nature, 510, 356-364, 2014.
10.1038/nature13308
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  05/01/2014 Zhao, Q., Dixon, R.A., Altering the cell wall and its impact on plant disease: from forage to bioenergy, Annual Review of Phytopathology, 52:69-91, 2014.
10.1146/annurev-phyto-082712-102237
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  04/21/2014 Baxter, H.L., Mazarei, M., Labbe, N., Kline, L.M., Cheng, Q., Windham, M.T., Mann, D.G.J., Fu, C., Ziebell, A., Sykes, R.W., Rodriguez Jr, M., Davis, M.F., Mielenz, J.R., Dixon, R.A., Wang, Z.W., Stewart Jr, C.N., Two-year field analysis of reduced recalcitrance transgenic switchgrass, Plant Biotechnology Journal, 1-11, 2014.
10.1111/pbi.12195
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  03/18/2014 Reyes-Hernandez, B.J., Srivastava, A.C., Ugartechea-Chirino, Y., Shishkova, S., Ramos-Parra, P.A., Lira-Ruan, V., Diaz de la Garza, R.I., Dong, G., Moon, J.C., Blancaflor, E.B. Dubrovsky, J. G., The root indeterminacy-to-determinacy developmental switch is operated through a folate-dependent pathway in Arabidopsis thaliana, New Phytologist, 202:4 (1223-1236) 2014
10.1111/nph.12757
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  03/14/2014 Kwit, C., Nageswara-Rao, M., Stewart Jr., C.N., Switchgrass (Panicum virgatum L.) as a bioenergy crop: advantages, concerns, and future prospects, Compendium of Bioenergy Plants: Switchgrass, 14, 403-420, 2014.
  03/07/2014 Yin, H., Chen, C.J., Yang, J., Weston, D.J., Chen, J.G., Muchero, W., Ye, N., Tschaplinski, T.J., Wullschleger, S.D., Cheng, Z.M., Tuskan, G.A., Yang, X., Functional genomics of drought tolerance in bioenergy crops, Critical Reviews in Plant Sciences, Volume 33, Issue 2-3, 2014.
10.1080/07352689.2014.870417
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  03/03/2014 Hao, Z., Mohnen, D., A review of xylan and lignin biosynthesis: foundation for studying Arabidopsis irregular xylem mutants with pleiotropic phenotypes, Critical Reviews in Biochemistry and Molecular Biology, 49:3 (212-214) 2014
10.3109/10409238.2014.889651
  03/01/2014 Escamilla-Trevino, L.L., Shen, H., Hernandez, T., Yin, Y., Xu, Y., Dixon, R.A., Early lignin pathway enzymes and routes to chlorogenic acid in switchgrass (Panicum virgatum L.), Plant Molecular Biology, 84:4-4 (565-576) 2013
10.1007/s11103-013-0152-y
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  01/01/2014 Zhou, C., Han, L., Fu, C., Wen, J., Cheng, X., Nakashima, J., Ma., J., Tang, Y., Tadege, M., Mysore, K.S., Xia, G., Wang, Z.Y., The Trans-acting short interfering RNA3 pathway and NO APICAL MERISTEM anttagonistically regulate leaf margin development and lateral organ separation, as revealed by analysis of an argonaute7/lobed leaflet1 mutant in medicago truncatula, The Plant Cell, 25:12 (4845-4862) 2014.
10.1105/tpc.113.117788
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  12/01/2013 Muchero, W., Labbe, J., Ranjan, P., DiFazio, S., Tuskan, G.A., Genome resequencing in Populus: revealing large-scale genome variation and implications on specialized-trait genomics, Challenges and Opportunities for the World's Forests in the 21st Century Forestry Sciences, Volume 81, pp 587-595, 2013.
10.1007/978-94-007-7076-8_25
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  11/30/2013 Shen, H., Mazarei, M., Hisano, H., Escamilla-Trevino, L., Fu, C., Pu, Y., Rudis, M.R., Tang, Y., Xiao, X., Jackson, L., Li, G., Hernandez, T., Chen, F., Ragauskas, A.J., Stewart Jr., C.N., Wang, Z-Y., Dixon, R.A., A genomics approach to deciphering lignin biosynthesis in switchgrass, 25:11 (4342-61) 2013.
10.1105/tpc.113.118828
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  11/28/2013 Xie, F., Stewart Jr., C.N., Taki, F.A., He, Q., Liu, H., Zhang, B., High-throughput deep sequencing shows that microRNAs play important roles in switchgrass responses to drought and salinity stress, Plant Biotechnology Journal, 12:3 (354-366) 2013.
10.1111/pbi.12142
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  11/26/2013 Liu, W., Yuan, J.S., Stewart J., C.N., Advanced genetic tools for plant biotechnology, Nature Reviews, 14:11 (781-793) 2013.
10.1038/nrg3583
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  11/01/2013 Baxter, H.L., Stewart Jr., C.N., Effects of altered lignin biosynthesis on phenylpropanoid metabolism and plant stress, Biofuels, 4:6, 635-667, 2013.
10.4155/bfs.13.56
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  11/01/2013 King, Z.R., Bray, A.L., LaFayette, P.R., Parrott, W.A., Biolistic transformation of elite genotypes of switchgrass (Panicum virgatum L.), Plant Cell Reports, 33:2 (313-322) 2014.
10.1007/s00299-013-1531-1
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  10/01/2013 Zhao, N., Yao, J., Chaiprasongsuk, M., Li, G., Guan, J., Tschaplinski, T.J., Guo, H., Chen, F., Molecular and biochemical characterization of the jasmonic acid methyltransferase gene from black cottonwood (Populus trichocarpa), Phytochemistry, 94 (74-81), 2014.
10.1016/j.phytochem.2013.06.014
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  09/10/2013 Rodgers-Melnick, E., Culp, M., DiFazio, S.P., Predicting whole genome protein interaction networks from primary sequence data in model and non-model organisms using ENTS, BMC Genomics, 14:608, 2013.
10.1186/1471-2164-14-608
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  07/31/2013 Tobimatsu, Y., Chen, F., Nakashima, J., Escamilla-Trevino, L.L., Jackson, L., Dixon, R.A., Ralph, J., Coexistence but Independent Biosynthesis of Catechyl and Guaiacyl/Syringyl Lignin Polymers in Seed Coats, Plant Cell, 25:7:2587-600, 2013.
10.1105/tpc.113.113142
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  07/01/2013 Abraham, P., Adams, R.M., Tuskan, G.A., Hettich, R.L., Moving away from the reference genome: evaluating a peptide sequencing tagging approach for single amino acid polymorphism identifications in the genus Populus, 12(8):3642-51, 2013.
10.1021/pr400192r
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  06/28/2013 Zhao, Q., Tobimatsu, Y., Zhou, R., Pattathil, S., Gallego-Giraldo, L., Fu, Chuxiang, Jackson, L.A., Hahn, M.G., Kim, H., Chen, F., Ralph, J., Dixon, R.A., Loss of function of cinnamyl alcohol dehydrogenase 1 leads to unconventional lignin and a temperature-sensitive growth defect in Medicago truncatula, PNAS, 110, 2013.
10.1073/pnas.1312234110
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  06/01/2013 Gilna, P., Cellulosic biofuels, Science Omege Review Europe, Issue 2, 2013.
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  05/08/2013 Atmodjo, M.A., Hao, Z., Mohnen, D., Evolving views of pectin biosynthesis, Annual Review of Plant Biology, 64:, 747-779, 2013.
10.1146/annurev-arplant-042811-105534
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  05/01/2013 Nageswara-Rao, M., Soneji, J.R., Kwit, C., Stewart Jr., C.N., Advances in biotechnology and genomics of switchgrass, Biotechnology for Biofuels, 6:77, 2013.
10.1186/1754-6834-6-77
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  05/01/2013 Kataeva, I., Foston, M.B., Yang, S., Pattathil, S., Biswal, A.K., Poole, F.L., Basen, M., Rhaesa, A.M., Thomas, T.P., Azadi, P., Olman, V., Safford, T.D., Mohler, K.E., Lewis, D.L., Doeppke, C., Zeng, Y., Tschaplinski, T.J., York, W., Davis, M., Mohnen, D., Xu, Y., Ragauskas, A.J., Ding, S.Y., Kelly, R.M., Hahn, M.G., Adams, W.W.M., Carbohydrate and lignin are simultaneously solubilized from unpretreated switchgrass by microbial action at high temperature, Energy and Environmental Science, 6, 2186-2195, 2013
10.1039/C3EE40932E
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  04/15/2013 Zhu, Q., Bennetzen, J.L., Smith, S.M., Isolation and diversity analysis of resistance gene homologues from switchgrass, G3: Genes, Genomes, Genetics, 3(6):1031-42, 2013.
10.1534/g3.112.005447
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  04/09/2013 Saha, P., Ray, T., Tang, Y., Dutta, I., Evangelous, N.R., Kieliszewski, M.J., Chen, Y., Cannon, M.C., Self-rescue of an EXTENSIN mutant reveals alternative gene expression programs and candidate proteins for new cell wall assembly in Arabidopsis, The Plant Journal, 75(1):104-16, 2013.
10.111/tpj.12204
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  04/01/2013 Shen, H., Pooviah, C.R., Ziebell, A., Tschaplinski, T.J., Pattathil, S., Gjersing, E., Engle, N.L., Katahira, R., Pu, Y., Sykes, R., Chen, F., Ragauskas, A.J., Mielenz, J.R., Hahn, M.G., Davis, M., Stewart, Jr., N., Dixon, R.A., Enhanced characteristics of genetically modified switchgrass (Panicum virgatum L.) for high biofuel production, Biotechnology for Biofuels, 5:71, 2013.
10.1186/1754-6834-6-71
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  03/24/2013 Serba, D., Wu, L., Daverdin, G., Bahri, B.A., Wang, X., Kilian, A., Bouton, J.H., Brummer, E.C., Saha, M.C., Devos, K.M., Linkage maps of lowland and upland tetraploid switchgrass ecotypes, Bioenergy Research, 6 (3), 953-965, 2013.
10.1007/s12155-013-9315-6
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  01/29/2013 Muchero, W., Sewell, M.M., Ranjan P., Gunter, L.E., Tschaplinski, T.J., Yin, T., Tuskan, G.A., Genome anchored QTLs for biomass productivity in hybrid populus grown under contrasting environments, PLOS ONE, 8(1): e54468, 2013.
10.1371/journal.pone.0014021
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  01/17/2013 Hardin, C.F., Fu, C., Hisano, H., Xiao, X., Shen, H., Stewart Jr. C.N., Parrott, W., Dixon, R.A., Wang, Z-Y., Standardization of switchgrass sample collection for cell wall and biomass trait analysis, Bioenergy Research, 6 (2), 755-762, 2013.
10.1007/s12155-012-9292-1
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  01/05/2013 Zhang, J.Y., Lee, Y.C., Torres-Jerez, I., Wang, M., Yin, Y., Chou, W.C., He, J., Shen, H., Srivastava, A.C., Pennacchio, C., Lindquist, E., Grimwod, J., Schmutz, J., Xu, Y., Sharma, M., Sharma, R., Bartley, L.E., Ronald, P.C., Saha, M.C., Dixon, R.A., Tang, Y., Udvardi, M.K., Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L.), The Plant Journal, 74(1):160-73, 2012.
10.1111/tpj.12104
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  01/01/2013 Tan, L., Eberhard, S., Pattathil, S., Warder, C., Glushka, J., Yuan, C., Hao, Z., Zhu, X., Avci, U., Miller, J.S., Baldwin, D., Pham, C., Orlando, R., Darvill, A., Hahn, M.G., Kieliszewski, M.J., Mohnen, D., An Arabidopsis cell wall proteoglycan consists of pectin and arabinoxylan covalently linked to an arabinogalactan protein, The Plant Cell, 25:1, 270-287, 2012.
10.1105/tpc.112.107334
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  01/01/2013 Ramanna, H., Ding, X.S., Nelson, R.S., Rationale for developing new virus vectors to analyze gene function in grasses through virus-induced gene silencing, Methods in Molecular Biology, 975, 15-32, 2013.
10.1007/978-1-62703-278-0_2.
  12/20/2012 Porth, I., Klapste, J., Skyba, O., Lai, B.S.K., Geraldes, A., Muchero, W., Tuskan, G.A., Douglas, C.J., El-Kassaby, Y.A., Mansfield, S.D., Populus trichocarpa cell wall chemistry and ultrastructure trait variation, genetic control and genetic correleations, New Phytologist, 197: 777–790, 2012.
10.1111/nph.12014
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  12/01/2012 Xu, B., Sathitsuksanoh, N., Tang, Y., Udvardi, M.K., Zhang, J.Y., Shen, Z., Balota, M., Harich, K., Zhang, P.Y.H., Zhao, B., Overexpression of AtLOV1 in Switchgrass alters plant architecture, lignin content, and flowering time, PLOSONE, 7(12), e47399, 2012.
10.1371/journal.pone.0047399
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  11/06/2012 de Souza, A.P., Leite, D.C.C., Pattathil, S., Hahn, M.G., Buckeridge, M.S., Composition and structure of sugarcane cell wall polysaccharides: implications for second-generation bioethanol production, BioEnergy Research, Volume 6, Issue 2, pp 564-579, 2012.
10.1007/s12155-012-9268-1
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  11/04/2012 Ye, C-Y., Li, T., Yin, H., Weston, D.J., Tuskan, G.A., Tschaplinski, T.J., Yang, X., Evolutionary analyses of non-family genes in plants, The Plant Journal, 73(5): 788-97, 2013.
10.1111/tpj.12073
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  10/29/2012 Czamecki, O., Glaber, C., Chen, J.G., Mayer, K.F.X., Grimm, Evidence for a contribution of ALA synthesis to plastid-to-nucleus signaling, Frontiers in Plant Science, 3:236, 2012.
10.3389/fpls.2012.00236
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  10/25/2012 Wullschleger, S.D., Weston, D.J., DiFazio, S.P., Tuskan, G.A., Revisiting the sequencing of the first tree genome: Populus trichocarpa, Tree Physiology, 33(4):357-64, 2012.
10.1093/treephys/tps081
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  10/16/2012 Abraham, P., Giannone, R.J., Adams, R.M., Kalluri, U., Tuskan, G.A., Hettich, R.L., Putting the pieces together: high-performance LC-MS/MS provides network-, pathway-, and protein-level perspectives in Populus, Molecular and Cellular Proteomics, 12(1):106-19, 2013.
10.1074/mcp.M112.022996 mcp.M112.022996
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  10/14/2012 Uppalapati, S.R., Serba, D.D., Ishiga, Y., Szabo, L.J., Mittal, S., Bhandari, H.S., Bouton, J.H., Mysore, K.S., Saha, M.C., Characterization of the Rust Fungus, Puccinia emaculata, and Evaluation of Genetic Variability for Rust Resistance in Switchgrass Populations, Bioenergy Research, 6 (2) 458-468, 2012.
10.1007/s12155-012-9263-6
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  09/07/2012 Chen, F., Tobimatsu, Y., Jackson, L., Ralph, J., Dixon, R.A., Novel seed coat lignins in the Cactaceae: structure, districution and implications for the evolution of lignin diversity, The Plant Journal, 2012.
10.1111/tpj.12012
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  08/16/2012 Nageswara-Rao, M., Stewart Jr., C.N., Kwit, C., Genetic diversity and structure of natural and agronomic switchgrass (Panicum virgatum L.) populations, Genetic Resources and Crop Evolution, 60: 1057-1068, 2012.
10.1007/s10722-012-9903-x
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  08/14/2012 Urbanowicz, B.R., Pena, J.J., Ratnaparkhe, S., Avci, U., Backe, J., Steet, H.F., Foston, M., Li, Hongjia, O'Neill, M.A., Ragauskas, A.J., Darvill, A.G., Wyman, C., Gilbert, H.J., York, W.S., 4-O-methylation of glucuronic acid in Arabidopsis glucuronoxylan is catalyzed by a domain of unknown function family 579 protein, PNAS, 109:35, 14253-14258, 2012.
10.1073/pnas.1208097109
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  08/14/2012 Zhou, C., Han, L., Fu, C., Chai, M., Zheng, W., Li, G., Tang, Y., Wang, Z., Identification and characterization of petiolule-like pulvinus mutants with abolished nyctinastic leaf movement in the model legume Medicago truncatula, New Phytologist, 2012
10.1111/j.1469-8137.2012.04268.x
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  08/01/2012 Kulkarni, A.R., Pattathil, S., Hahn, M.G., York, W.S., O'Neill, M.A., Comparison of Arabinoxylan Structure in Bioenergy and Model Grasses, Industrial Biotechnology, 8(4):222-229, 2012.
10.1089/ind.2012.0014
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  08/01/2012 Mazumder, K., Pena, M.J., O'Neill, M.A., York, W.S., Structural Characterization of the Heteroxylans from Poplar and Switchgrass, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 908;215-228, 2012.
10.1007/978-1-61779-956-3_19
  08/01/2012 Slavov, G.T., DiFazio, S.P., Martin, J., Schackwitz, W., Muchero, W., Rodgers-Melnick, E., Lipphardt, M.F., Pennacchio, C.P., Hellsten, U., Pennacchio, L.A., Gunter, L.W., Ranjan, P., Vining, K., Pomraning, K.R., Wilhelm, L.J., Pellegrini, M., Mockler, T.C., Freitag, M., Geraldes, Ar., El-Kassaby, Y.A., Mansfield, S.D., Crong, Q.C.B., Douglas, C.J., Strauss, S.H., Rokhsar, D., Tuskan, G.A., Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa , New Phytologist, 196(3):713–725, 2012.
10.1111/j.1469-8137.2012.04258
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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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  03/28/2012 Tuskan, G., DiFazio, S., Faivre-Rampant, R., Gaudet, M., Harfouche, A., Jorge, V., Labbe, J.L., Ranjan, P., Sabatti, M., Slavov, G., Street, N., Tschplinski, T.J., Yin, T.M., The obscure events contributing to the evolution of an incipient sex chromosome in Populus: a retrospective working hypothesis, Tree Genetics and Genomes, 8(3):559-571, 2012.
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  03/08/2012 Iduri, B.R., Ellis, D.R., Slavov, G.T., Yin, T., Zhang, X., Muchero, W., Tuskan, G.A., DiFazio, S.P., Identification of quantitative trait loci and candidate genes for cadmium tolerance in Populus, Tree Physiology, 00, 1-13, 2012.
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  02/28/2012 Wang, Z.-Y. and E. C. Brummer (2012). "Is genetic engineering ever going to take off in forage, turf and bioenergy crop breeding?" Annals of Botany, 110(6):1317-1325, 2012.
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  01/06/2012 Martinez, V., Ingwers, M., Smith, J., Glushka, J., Yang, T., Bar-Peled, M., Biosynthesis of UDP-4-keto-6-deoxyglucose and UDP-rhamnose in Pathogenic Fungi Magnaporthe grisea and Botryotinia fuckeliana, The Journal of Biological Chemistry, 287: 879-892, 2012.
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  01/01/2012 Kwit, C., Stewart, C. N. (2012). Gene flow matters in switchgrass (Panicum virgatum L.), a potential widespread biofuel feedstock, Ecological Applications 22(1):3-7.
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  12/22/2011 Wisniewski-Dye´ F, Borziak K, Khalsa-Moyers G, Alexandre G, Sukharnikov LO, et al. (2011) "Azospirillum Genomes Reveal Transition of Bacteria from Aquatic to Terrestrial Environments." PLoS Genet 7(12): e1002430.
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  11/21/2011 Atmodjo, M.A., Sakuragi, Y., Zhu, X., Burrell, A.J., Mohanty, S.S., Atwood III, J.A., Orlando, R., Scheller, H.V., Mohnen, D., Galacturonosyltransferase (GAUT)1 and GAUT7 are the core of a plant cell wall pectin biosynthetic homogalacturonan–galacturonosyltransferase complex, PNAS, 108(50):20225-30, 2011.
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  11/01/2011 Broach, B., Gu, X., Bar-Peled, M., Biosynthesis of UDP-glucuronic acid and UDP-galacturonic acid in Bacillus cereus subsp. Cytotoxis NVH 391-98, The FEBS Journal, 279; 1, 2012.
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  10/14/2011 Escamilla-Trevino, L.. (2011) "Potential of Plants from the Genus Agave as Bioenergy Crops." Bioenergy Research. (published online doi:10.1007/s12155-011-9159-x)
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  10/11/2011 Shen, H., He, X., Poovaiah, C.R., Wuddineh, W.A., Ma, J., Mann, D.G.J., Abercrombie, L.A., Wang, H., Jackson, L., Tang, Y., Stewart, C.N. Jr., Chen, F. and Dixon, R.A, Functional characterization of the switchgrass (Panicum virgatum) R2R3-MYB transcription factor PvMYB4 for improvement of lignocellulosic feedstocks, New Phytologist, 2012 Jan;193(1):121-36.
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  10/05/2011 Rodgers-Melnick, E., Mane, S.P., Dharmawardhana, P., Slavov, G.T., Crasta, O.R., Strauss, S.H., Brunner, A.M., DiFazio, S.P. (2011) "Contrasting Patterns of Evolution Following Whole Genome versus Tandem Duplication Events in Populus," Genome Research, 22:95-105.
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  09/28/2011 Mann, G.J., LaFayette, P.R., Abercrombie, L.L., King, Z.R., Mazarei, M., Halter, M.C., Poovaiah, C.R., Baxter, H., Shen, H., Dixon, R.A., Parrott, W.A., Stewart Jr., C.N. (2012) "Gateway-compatible vectors for high-throughput gene functional analysis in switchgrass (Panicum virgatum L.)." Plant Biotechnology Journal 10(2):226–236.
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  09/12/2011 Ye, Xia., Busov, V., Zhao, N., Meilan, R., McDonnell, L.M., Coleman, H.D., Mansfield, S.D., Chen, F., Li, Y., Cheng, Z.M., Transgenic Populus Trees for Forest Products, Bioenergy, and Functional Genomics, Critical Reviews in Plant Science, 30:415-434, 2011.
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  09/11/2011 Gallego-Giraldo, L., Escamilla-Trevino, L., Jackson, L.A., Dixon, R.A. "Salicylic acid mediates the reduced growth of lignin down-regulated plant." PNAS. (Published online before print November 28, 2011, doi: 10.1073/pnas.1117873108)
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  09/05/2011 Stewart Jr., C. N., Liu, G.S., Bioenergy plants in the United States and China, Plant Science, 181:6, pp 621-622, 2011.
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  09/01/2011 Yuan, J.A., Qu, Y., Li, S., Stewart Jr., C.N., US-China collaborative biofuel research: towards a global solution for petroleum replacement, Biofuels, 2:5, 487-789, 2011.
10.4155/BFS.11.130
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  09/01/2011 Yuan, J.S., Wang, X., Stewart Jr., C.N., Biomass feedstock: diversity as a solution, Biofuels, 2:5, 491-493, 2011.
10.4155/BFS.11.135
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  09/01/2011 Pu, Y., Kosa, M., Kalluri, U.C., Tuskan, G.A., Ragauskas, A.J., Challenges of the utilization of wood polymers: how can they be overcome?, Applied Microbiology and Biotechnology, 91(6): 1525-1536, 2011.
10.1007/s00253-011-3350-z
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  08/18/2011 Ye, X., Yuan, S., Guo, H., Chen, F., Tuskan, G.A., Cheng, Z.M. (2012) "Evolution and divergence in the coding and promoter regions of the Populus gene family encoding exyloglucan endotransglycosylase/ hydrolases." Tree Genetics and Genomes 8:177–194.
10.1007/s11295-011-0431-1
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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.
10.1016/j.biotechadv.2011.08.006
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  08/12/2011 Zhang, Y., Zalapa, J.E., Jakubowski, A.R., Price, D.L., Acharya, A., Wei, Y., Brummer, E.C., Kaeppler, S.M., Casler, M.D, Natural Hybrids and Gene Flow between Upland and Lowland Switchgrass, Crop Science, 51, 2011.
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  08/12/2011 Ghimire, S.R., Craven, K.D.,The Ectomycorrhizal Fungus Sebacina vermifera, Enhances Biomass Production of Switchgrass (Panicum virgatum L.) Under Drought Conditions, Applied Microbiology and Biotechnology, 77(19):7063-7067, 2011
10.1128/AEM.05225-11
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  08/11/2011 Ge, Y., Fu, C., Bhandari, H., Bouton, J., Brummer, E.C., Wang, Z.Y., Pollen Viability and Longevity of Switchgrass (Panicum virgatum L.), Crop Science, volume 51, 2011.
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  07/23/2011 Zhang, Y., Zalapa, J.E., Jakubowski, A.R., Price, D.L., Acharya, A., Wei, Y., Brummer, E.C., Kaeppler, S.M., Casler, M.D., Post-glacial evolution of Panicum virgatum: centers of diversity and gene pools revealed by SSR markers and cpDNA sequences, Genetica, 139:933-948, 2011.
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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. 2011. In book "Biofuel Production-Recent Developments and Prospects", ( ed. Marco Aurélio dos Santos Bernardes), InTech, Chapter 15, p. 375-414.
ISBN: 978-953-307-478-8
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  06/17/2011 Mohnen, D., Tierney, Mary L., Plants Get Hyp to O-Glycosylation, Science, 332:1393-1394, 2011.
10.1126/science.1208641
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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.
10.1105/tpc.111.085464
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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.
10.1074/jbc.M110.217315 jbc.M110.217315
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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.
10.1016/j.plantsci.2010.12.010
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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.
10.1007/s12155-010-9080-8
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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.
10.1016/j.plantsci.2011.01.021
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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, chapter 1, pp 1-28, 2011.
10.1201/b10819-2
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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, Chapter 4, p. 99-111, 2011.
10.1007/978-3-540-85546-0_4
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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.
10.1186/1471-2105-12-79
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  03/02/2011 Yang, Xiaohan, Tschaplinski, Timothy J., Hurst, Gregory B., Jawdy, Sara, Abraham, Paul E., Lankford, Patricia K., Adams, Rachel M., Shah, Manesh B., Hettich, Robert L., Lindquist, Erika, Kalluri, Udaya C., Gunter, Lee E., Pennacchio, Christa, Tuskan, Gerald A., Discovery and annotation of small proteins using genomics, proteomics, and computational approaches, Genome Research, 21(4):634-641, 2011.
10.1101/gr.109280.110
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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, 62:127-55, 2011.
10.1146/annurev-arplant-042110-103918
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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, chapter 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.
10.1104/pp.110.168278
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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.
10.1016/J.plantsci.2011.01.020
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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, 2011 286: 15483-15495.
10.1074/jbc.M110.215962
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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.
10.1104/pp.110.168278
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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, pp 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.
ISBN: 978-0-8138-2195-5
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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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  12/22/2010 Yin, Y., Mohnen, D., Gelineo-Albersheim, I., Xu, Y. and Hahn, M. G., Glycosyltransferases of the GT8 Family, in Annual Plant Reviews: Plant Polysaccharides, Biosynthesis and Bioengineering, Volume 41 (ed P. Ulvskov), Wiley-Blackwell, Oxford, UK, 2010.
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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, pp 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, 2010, 11:600.
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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, Volume 107, Issue 51, pp 22338-22343, 2010.
10.1073/pnas.1016436107
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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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  09/30/2010 In Kole, C., and A. Albert (eds). Vol. 3: Advanced Genomics. Science Publishers, Enfield, New Hampshire (accepted)
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  09/16/2010 Gu, X. G., Lee, S. G., Bar-Peled, M., Biosynthesis of UDP-xylose and UDP-arabinose in Sinorhizobium meliloti 1021: first characterization of a bacterial UDP-xylose synthase, and UDP-xylose 4-epimerase, Microbiology, Volume 157, pp 260-269, 2011.
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  08/31/2010 Yang, Xiaohan, Ye, Chu-Yu, Cheng, Zong-Ming, Tschaplinski, Timothy J., Wullschleger, Stan D., Yin, Weilun, Xia, Xinli, Tuskan, Gerald A., Genomic aspects of research involving polyploid plants, Plant Cell Tissue and Organ Culture, 2011, 104:387-397.
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  08/01/2010 Kausch, A.P., J. Hague, M. Oliver, L . S . Watrud, C. Mallory-Smith, V. Meier, A. Snow, and C. N. Stewart, Jr. 2010. Gene flow in genetically engineered perennial grasses: lessons for modification of dedicated bioenergy crops. Pp. 285-298, In: Widholm, J. and T. Nagata (Eds) Biotechnology in Agriculture and Forestry; P.N Maschia, J. Scheffran, and J. Widholm (Eds), 66. Plant Biotechnology for Sustainable Production of Energy and Co-products. Springer Verlag, Heidelberg
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  08/01/2010 Kausch A.P., J. Hague, M. Oliver, Y. Li, H. Daniell, P.Mascia, C.N. Stewart, Jr. 2010. Genetic modification in dedicated bioenergy crops and strategies for gene confinement. Pp. 299-315. In: Widholm, J. and T. Nagata (Eds) Biotechnology in Agriculture and Forestry; P.N Maschia, J. Scheffran, and J. Widholm (Eds), 66. Plant Biotechnology for Sustainable Production of Energy and Co-products. Springer Verlag, Heidelberg.
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  07/01/2010 Mazumder, K., York, W.S., Structural analysis of arabinoxylans isolated from ball-milled switchgrass biomass, Carbohydrate Research, Volume 345, Issue 15, pp 2183-2193, 2010.
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  07/01/2010 Zhao, Q. A., Wang, H. Z., Yin, Y. B., Xu, Y., Chen, F., Dixon, R. A., Syringyl lignin biosynthesis is directly regulated by a secondary cell wall master switch, PNAS, Volume 107, Issue 32, pp 14496-14501, 2010.
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  06/17/2010 Yang T, Echols M, Martin A, Bar-Peled M. (2010) Identification and characterization of a strict and a promiscuous N-acetylglucosamine-1-P uridylyltransferase in Arabidopsis. Biochem J. 430(2):275-84.
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  06/11/2010 Kalluri U.C and Keller M, “Bioenergy Research: A new paradigm in multidisciplinary research”, Journal of the Royal Society Interface. 7 (51):1391‐1401, 2010.
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  06/07/2010 Gu X, Glushka J, Lee SG, Bar-Peled M. (2010) Biosynthesis of a new UDP-sugar, UDP-2-acetamido-2-deoxyxylose, in the human pathogen Bacillus cereus subspecies cytotoxis NVH 391-98. J Biol Chem. 285(32):24825-33.
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Intellectual Property

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