Publications | Department of Biological Sciences

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Research Publications for the Past 10 Years

  1. Chen, X., Ma, Q., Rao, X., Tang, Y., Zhang, C., Wang, Y., Li, G., Mao, X., Dixon, R.A. and Xu, Y. (2015). Genome-Scale Identification of Cell-Wall Related Genes in Switchgrass through Comparative Genomics and Computational Analyses of Transcriptomic Data. BioEnergy Research, in press.
  2. Baxter, H., Alexander, L., Mazarei, M., Haynes, E., Turner, G., Sykes, R., Decker, S., Davis, M., Dixon, R.A., Wang, Z-Y. and Stewart, N. (2015). Hybridization of downregulated-COMT transgenic switchgrass lines with field selected switchgrass for improved biomass traits. Euphytica, in review.
  3. Nar, M., Rizvi, H.R., Dixon, R.A., Chen, F., Kovalcik, A. and D'Souza, N. (2015). Carbon fibers from electronspun poly-(caffeyl alcohol) and Kraft lignin. Carbon, in review.
  4. Muchero, W., Bryan, A.C., Chen, J-G., Guo, H-B., Tschaplinski, T., Singan, V.R., Lindquist, E., Payyavula, R.S., Barros-Rios, J., Dixon, R.A., Engle, N., Yee, K., Sykes, R.W., Jawdy, S., Gunter, L.E., Thompson, O., DiFazio, S.P., Evans, L.M., Winkler, K., Collins, C., Schmutz, J., Guo, H., Kalluri, U., Rodriguez, M., Feng, K., Xie, M. and Tuskan, G.A. (2015). A 5-enolpyruvylshikimate-3-phosphate synthase-like gene is a transcriptional regulator of phenylpropanoid and flavonoid pathways. Nature Biotechnology, in review.
  5. Jiang, W., Yin, Q., Wu, R., Zheng, G., Liu, J., Dixon, R.A. and Pang, Y. (2015). Role of a chalcone isomerase-like protein in flavonoid biosynthesis in Arabidopsis thaliana. Journal of Experimental Botany, in press.
  6. Jun, J.H., Liu, C., Xiao, X. and Dixon, R.A. (2015). The transcriptional repressor Mt MYB2 regulates both spatial and temporal patterns of proanthocyandin and anthocyanin pigmentation in Medicago truncatula. Plant Cell, in press.
  7. Gallego-Giraldo, L., Shadle, G., Shen, H., Barros-Rios, J., Corrales, S.F., Wang, H. and Dixon, R.A. (2015). Combining enhanced biomass density with reduced lignin level for improved forage quality. Plant Biotechnology Journal, in press. doi: 10.1111/pbi.12439.
  8. Faraji, M., Fonseca, L.L., Escamilla-Trevino, L., Dixon, R.A., and Voit, E.O. (2015). Computational inference of the structure and regulation of the lignin pathway in Panicum virgatum. Biotechnology for Biofuels, in press.
  9. Srivastava, A.C., Chen, F., Ray, T., Pattathil, S., Peña, M.J., Backe, J., Urbanowicz, B., Avci, U., Li, H., Miller, J.S., Huhman, D.V., Bedair, M., Wyman, C.E., Sumner, L.W., York, W.S., Hahn, M.G., Dixon, R.A., Blancaflor, E.B., Tang, Y. (2014). Repression of folylpolyglutamate synthetase alters lignin composition and improves cell wall digestibility in Arabidopsis. Molecular Plant, in review.
  10. Blount, J.W., Redan, B.W., Feruzzi, M.G., Reuhs, B.L., Cooper, B.R., Harwood, J.S., Shulaev, V., Pasinetti, G. and Dixon, R.A. (2015). Synthesis and quantitative analysis of plasma-targeted metabolites of catechin and epicatechin. Journal of Food and Agricultural Chemistry, 63(8): 2233-40.
  11. Casler, M.D., Vermerris, W. and Dixon, R.A. (2015). Scale, form, and amount of replication for BioEnergy Research experiments. BioEnergy Research 8, 1-16.
  12. Baxter, H.L., Poovaiah, C.R., Yee , K.L., 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. and Stewart Jr., C.N. (2015). Field evaluation of transgenic switchgrass plants overexpressing PvMYB4 for reduced biomass recalcitrance. Bioenergy Research, in press.
  13. Tadege, M., Chen, F., Murray, J., Wen, J., Ratet, P., Udvardi, M.K., Dixon, R.A. and Mysore, K.S. (2014). Control of vegetative to reproductive phase transition improves biomass yield and reduces lignin content in Medicago truncatula. BioEnergy Research, 8, 857-867.
  14. 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. (2014). Pinoresinol reductase 1 impacts lignin distribution during secondary cell wall biosynthesis in Arabidopsis. Phytochemistry, 112: 170-8.
  15. Rao, X., Krom, N., Tang, Y., Widiez, T., Havkin-Frenkel, D., Belanger, F.C., Dixon, R.A. and Fang Chen, F. (2014). A deep transcriptomic analysis of pod development in the vanilla orchid (Vanilla planifolia). BMC Genomics 15, 964 doi: 10.1186/1471-2164-15-964.
  16. Liu, C., Jun, J and Dixon, R.A. (2014). MYB5 and MYB14 play pivotal roles in seed coat polymer biosynthesis in Medicago truncatula. Plant Physiology 165, 1424-1439.
  17. Pan, H., Zhou, R., Louie, G.V., Mühlemann, J.K., Bomati, E.K., Bowman, M.E., Dudareva, N., Dixon, R.A., Noel, J.P. and Wang, X. (2014). Structural studies of cinnamoyl-CoA reductase and cinnamyl-alcohol dehydrogenase, key enzymes of monolignol biosynthesis. Plant Cell, 26(9): 3709-27.
  18. Blumberg, J.B., Ding, E.L., Dixon, R.A., Pasinetti, G.M. and Villarreal, F. (2014). The science of cocoa flavanols: bioavailability, emerging evidence and proposed mechanisms. Advances in Nutrition 5, 547-549.
  19. Ragauskas, A.J., Beckham, G.T., Biddy, M.J., Chandra, R., Chen, F., Davis, M.F., Davison, B.H., Dixon, R.A., Gilna, P., Keller, M., Langan, P., Naskar, A.K., Saddler, J.N., Tschaplinski, T.J., Tuskan, G.A., Wyman, C.E. (2014). Lignin valorization: improving lignin processing in the biorefinery. Science, 344, 1246843 (2014). DOI: 10.1126/science.1246843.
  20. Baxter, H., Mazarei, M., Labbe, N., Kline, L., Cheng, Q., Windham, M., Mann, D., Fu, C., Ziebell, A., Sykes, R., Rodriguez, M., Davis, M., Mielenz, J., Dixon, R.A., Wang, Z-Y., Stewart, N. (2014). Two-year field analysis of reduced recalcitrance transgenic switchgrass. Plant Biotechnology Journal, in press.
  21. Gallego-Giraldo, L., Bhattarai, K., Pislariu, C.I., Nakahisma, J., Jikamura, Y., Kamiya, Y., Udvardi, M.K., Monteros, M.J. and Dixon, R.A. (2014). Lignin modification leads to increased nodule numbers in alfalfa (Medicago sativa L.) Plant Physiology 164, 1139-1150.
  22. Zhao, Q. and Dixon, R.A. (2014). Altering the cell wall and its impact on plant disease: from forage to bioenergy. Annual Review of Phytopathology, in press.
  23. Dixon, R.A., Reddy, M.S.S. and Gallego-Giraldo, L. (2013). Monolignol biosynthesis and its genetic manipulation: the good, the bad and the ugly. Recent Advances in Polyphenol Research, in press.
  24. Escamilla-Treviño, L.L., Shen, H., Hernandez, T., Yin, Y., Xu, Y. and Dixon, R.A. (2013). Early lignin pathway enzymes and routes to chlorogenic acid in switchgrass (Panicum virgatum L.). Plant Molecular Biology 84, 565-576.
  25. Shen, H., Hisano, H., Hardin, F., Mazarei, M., Fu, C., Escamilla-Treviño, L.L., Xiao, X., Rudis, M.R., Tang, Y., Jackson, L.A., Li, G., Hernandez, T., Nandakumar, R., D., Chen, F., Stewart Jr C.N., Wang, Z.-Y. and Dixon, R.A. (2013). A genomic approach to deciphering the monolignol pathway in switchgrass (Panicum virgatum L.). Plant Cell 25, 4342-4361.
  26. Zhao, Q., Nakashima, J., Chen, F., Yin, Y., Fu, C., Yun, J., Shao, H., Wang, X., Wang, Z-Y. and Dixon, R.A. (2013). LACCASE is necessary and non-redundant with PEROXIDASE for lignin polymerization during vascular development in Arabidopsis thaliana. Plant Cell 25, 3976-87.
  27. Zhao, Q., Tobamitsu, Y., Zhou, R., Pattathil, S., Gallego-Giraldo, L., Fu, C., Shadle, G.L., Jackson, L.A., Hahn, M.G., Kim, H., Ralph, J., Chen, F. and Dixon, R.A. (2013). Loss of function of cinnamyl alcohol dehydrogenase 1 leads to unconventional lignin and temperature-sensitive growth reduction in Medicago truncatula. Proceedings of the National Academy of Sciences USA, 110,13660-13665.
  28. Tobimatsu, Y., Chen, F., Jin Nakashima, J., Jackson, L.A., Dixon, R.A. and Ralph, J. (2013). Coexistence but independent biosynthesis of catechyl and guaiacyl/syringyl lignin polymers in seed coats. Plant Cell, 25,2587-2600.
  29. Xu, H., Zhang, F., Liu, B., Huhman, D.V., Sumner, L.W., Dixon, R.A. and Wang, G. (2013). Characterization of the formation of branched short-chain fatty acid:CoAs for bitter acid biosynthesis in hop glandular trichomes. Molecular Plant 6, 1301-1317.
  30. Shen, H., Poovaiah, 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., C.N. and Dixon, R.A. (2013). Enhanced characteristics of genetically modified switchgrass (Panicum virgatum L.) for high biofuel production. Biotechnology for Biofuels, 6: 71 doi:10.1186/1754-6834-6-71.
  31. Pang, Y., Cheng, X., Huhman, D., Ma, J., Peel, J.G., Yonekura-Sakakibara, K., Saito, K., Shen, G., Sumner, L.W., Tang, Y., Wen, J, Yun, J, and Dixon, R.A. (2013). Medicago glucosyltransferase UGT72L1: potential roles in proanthocyanidin biosynthesis. Planta 238, 139-154.
  32. Hardin, C.F., Chunxiang Fu, C., Hisano, H., Xaio, X., Shen, H., Stewart Jr., C.N., Parrott, W., Dixon, R.A. and Wang, Z.Y. (2013). Standardization of switchgrass sample collection for cell wall and biomass trait analysis. BioEnergy Research, 6,755-762.
  33. Pang, Y., I. Abeysinghe, S.B., He, J., He, X-Z., Huhman, D.V., Mewan, K.M., Sumner, L.W., Yun J. and Dixon, R.A. (2013) Functional characterization of proanthocyanidin pathway enzymes from tea (Camellia sinensis) and their application for metabolic engineering. Plant Physiology 161, 1103-1116.
  34. Dixon, R.A. (2013). News and Views. Microbiology: Break down the walls. Nature 493, 36-37, 2013.
  35. 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., Grimwood, J., Schmutz, J., Xu, Y., Sharma, M., Sharma, R., Bartley, L.E., Ronald, P.C., Saha, M.C., Dixon, R.A., Tang, Y., and Udvardi, M.K. (2013). Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L.). Plant Journal, 74, 160-173.
  36. Dixon, R.A., Liu, C. and Jun, J.H. (2013). Metabolic engineering of anthocyanins and condensed tannins in plants. Current Opinion in Biotechnology. 24, 329-335.
  37. Chen, F., Tobimatsu, Y., Jackson, L. Ralph, J. and Dixon, R.A. (2013). Novel seed coat lignins in the Cactaceae: structure, distribution and implications for the evolution of lignin diversity. Plant Journal 73, 201-211.
  38. Tschaplinski, T.J., Standaert, R.F., Engle, N.L., Martin, M.Z., Sangha, A.K., Parks, J.M., Smith, J.C., Samuel, R., Pu, Y., Ragauskas, A.J., Hamilton, C.Y., Fu, C., Wang, Z-Y., Davison, B.H., and Dixon, R.A. (2012). Down-regulation of the caffeic acid O-methyltransferase gene in switchgrass reveals a novel monolignol analog. Biotechnology for Biofuels 5, 71 doi: 10.1186/1754-6834-5-71.
  39. Lee, Y., Escamilla-Treviño, L., Dixon, R.A. and Voit, E.O. (2012). Functional analysis of metabolic channeling and regulation in lignin biosynthesis: a computational approach. PLOS Computational Biology 8 (11), e1002769 doi:10.1371/journal.pcbi.1002769.
  40. Pattathil, S., Saffold, T., Gallego-Giraldo, L., O'Neill, M., York, W.S., Dixon, R.A. and Hahn, M.G. (2012). Changes in cell wall carbohydrate extractability are correlated with reduced recalcitrance of HCT down-regulated alfalfa biomass. Industrial Biotechnology 8, 217-221.
  41. Shen, G., Huhman, D., Lei, Z., Snyder, J., Sumner, L.W. and Dixon, R.A. (2012). Characterization of an isoflavonoid-specific prenyltransferase from Lupinus albus. Plant Physiology 159, 70-80.
  42. Wang, J., Ferruzzi, M.G., Ho, L., Blount, J., Janle, E., Arrieta-Cruz, I., Sharma, V., Cooper, B., Lobo, J., Simon, J.E., Zhang, C., Cheng, A., Qian, X., Pavlides, C., Dixon, R.A. and Pasinetti, G.M. (2012). Brain-targeted proanthocyanidin metabolites for Alzheimer's disease treatment. Journal of Neuroscience 32, 5144-5150.
  43. Chen, F., Tobimatsu, Y., Havkin-Frenkel, D., Dixon, R.A. and Ralph, J. (2012). A polymer of caffeyl alcohol in plant seeds. Proceedings of the National Academy of Sciences USA.109, 1772-1777 (cover article).
  44. Verdier, J., Zhao, J., Torres-Jerez, I., Ge, S., Liu, C., He, X., Mysore, K.S., Dixon, R.A. and Udvardi, M.K. (2012). The MtPAR MYB transcription factor acts as an on-switch for proanthocyanidin biosynthesis in Medicago truncatula. Proceedings of the National Academy of Sciences USA. 109, 1766-1771.
  45. Gallego-Giraldo, L., Escamilla-Trevino, L., Jackson, L.A. and Dixon, R.A. (2011). Salicylic acid mediates the reduced growth of lignin down-regulated plants. Proceedings of the National Academy of Sciences USA 108, 20814-20819.
  46. Wang, H. and Dixon, R.A. (2012). On-off switches for secondary cell wall biosynthesis. Molecular Plant 5, 297-303.
  47. 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. (2012). Functional characterization of the switchgrass (Panicum virgatum) R2R3-MYB transcription factor PvMYB4 for improvement of lignocellulosic feedstocks. New Phytologist 193, 121-136.
  48. Blount, J.W., Ferruzzi, M., Raftery, D., Pasinetti, G.M., and Dixon, R.A. (2011). Enzymatic synthesis of substituted epicatechins for bioactivity studies in neurological disorders. Biochemical and Biophysical Research Communications 417, 457-461.
  49. Mann, D.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. and Stewart, Jr. C.N. (2011). Gateway-compatible vectors for high-throughput gene functional analysis in switchgrass and other monocot species. Plant Biotechnology Journal 10, 226-236.
  50. Nevin D. Young, Frédéric Debellé, Giles Oldroyd, Rene Geurts, Steven B. Cannon, Klaus F. X. Mayer, Jérôme Gouzy, Yves Van de Peer, Heiko Schoof, Michael K. Udvardi, Douglas R. Cook, Blake C. Meyers, Manuel Spannagl, Foo Cheung, Stephane De Mita, Sebastian Proost, Vivek Krishnakumar, Heidrun Gundlach, Shiguo Zhou, Joann Mudge, Arvind K. Bharti, Vagner A. Benedito, Jeremy D. Murray, Marina A. Naoumkina, Benjamin Rosen, Kevin A. Silverstein, Haibao Tang, Stephane Rombauts, Patrick X. Zhao, Peng Zhou, Valérie Barbe, Philippe Bardou, Michael Bechner, Arnaud Bellec, Anne Berger, Hélène Bergès, Shelby Bidwell, Ton Bisseling, Nathalie Choisne, Arnaud Couloux, Roxanne Denny, Shweta Deshpande, Jeffrey J. Doyle, Anne-Marie Dudez, Andrew D. Farmer, Stéphanie Fouteau, Carolien Franken, Chrystel Gibelin, John Gish, Alvaro J. González, Pamela J. Green, Asis Hallab, Marijke Hartog, Axin Hua, Sean Humphray, Dong-Hoon Jeong, Yi Jing, Anika Jöcker, Steve M. Kenton, Dong-Jin Kim, Kathrin Klee, Hongshing Lai, Chunting Lang, Shaoping Lin, Simone L Macmil, Ghislaine Magdelenat, Lucy Matthews, Jamison McCorrison, Erin L. Monaghan, Jeong-Hwan Mun, Fares Z. Najar, Christine Nicholson, Céline Noirot, Charles R. Paule, Julie Poulain, Florent Prion, Baifang Qin, Chunmei Qu, Ernest F. Retzel, Clare Riddle, Erika Sallet, Sylvie Samain, Nicolas Samson, Olivier Saurat, Claude Scarpelli, Thomas Schiex, Béatrice Segurens, Majesta Seigfried, Andrew Severin, D. Janine Sherrier, Ruihua Shi, Sarah Sims, Senjuti Sinharoy, Lieven Sterck, Iryna Vasylenko, Agnès Viollet, Keqin Wang, Bing-Bing Wang, Xiaohong Wang, Jens Warfsmann, Jean Weissenbach, Doug D. White, Jim D. White, Graham B. Wiley, Patrick Wincker, Yanbo Xing, Limei Yang, Ziyun Yao, Fu Ying, Jixian Zhai, Liping Zhou, Antoine Zuber, Jean Dénarié, Richard A. Dixon, Gregory D. May, David C. Schwartz, Jane Rogers, Francis Quétier, Christopher D. Town, and Bruce A. Roe. (2011). The Medicago genome provides insight into evolution of rhizobial symbiosis. Nature 480, 520-524.
  51. Wang, H., Zhao, Q., Chen, F. and Dixon, R.A. (2011). NAC domain function and transcriptional control of a secondary cell wall master switch. Plant Journal 68, 1104-1114.
  52. Xu, B., Escamilla-Treviño, L.L., Noppadon, S., Shen, Z., Shen, H., Zhang, Y-H. P., Dixon, R.A. and Zhao, B. (2011). Silencing of 4-coumarate: Coenzyme A ligase in switchgrass leads to reduced lignin content and improved fermentable sugar yields for biofuel production. New Phytologist 92, 611-625.
  53. Zhao, J., Huhman, D.V., Shadle, G., Sumner, L.W., Tang, Y. and Dixon. R.A. (2011). MATE2 mediates vacuolar sequestration of flavonoid glycosides and glycoside malonates in Medicago truncatula. Plant Cell 23, 1536-1555.
  54. Lee, Y., Chen, F., Dixon, R.A. and Voit, E.G. (2011) Constraint-based analysis of transgenic alfalfa (Medicago sativa L.) suggests new postulates for monolignol biosynthesis. PloS Computational Biology, published 19 May, 10.1371/journal.pcbi.1002047.
  55. Fu, C., Xiao, X., Xi, Y., Ge, Y., Chen, F., Bouton, J., Dixon, R.A., and Wang Z-Y. (2011). Downregulation of cinnamyl alcohol dehydrogenase (CAD) leads to improved saccharification efficiency in switchgrass. BioEnergy Research 4, 153-164.
  56. Fu, C., Mielenz, J.R., Xiao, X., Ge, Y., Hamilton, C.Y., Chen, F., Bouton, J., Foston, M., Dixon, R.A. and Wang, Z-Y. (2011) Genetic manipulation of lignin biosynthesis in switchgrass significantly reduces recalcitrance and improves biomass ethanol production. Proceedings of the National Academy of Sciences USA 108, 3803-3808.
  57. Dien, B.S., Miller, D.J., Hector, R.E., Dixon, R.A., Chen, F., McCaslin, M., Reisen, P., Sarath, G. and Cotta. M.A. (2011) Enhancing alfalfa conversion efficiencies for production of sugars and ethanol by altering lignin composition. Bioresource Technology 102, 6479-6486.
  58. Zhao, Q, and Dixon, R.A. (2011). Transcriptional networks for lignin biosynthesis: more complex than we thought? Trends in Plant Science 16, 227-233.
  59. Dixon, R.A. (2011). Chris Lamb: A visionary leader in plant science. Annual Review of Phytopathology 49, 31-45.
  60. He, X.-Z., Blount, J.W., Ge, S., Tang, Y. and Dixon, R.A. (2011). A genomic approach to isoflavone biosynthesis in kudzu (Pueraria lobata). Planta, 233, 843-855.
  61. Gallego-Giraldo, L., Jikumaru, Y., Kamiya, Y., Tang, Y. and Dixon, R.A. (2011). Selective lignin down-regulation leads to constitutive defense response expression in alfalfa (Medicago sativa L.). New Phytologist 190: 627-639.
  62. Naoumkina, M.A., and Dixon, R.A. (2011) Characterization of the mannan synthase promoter from guar (Cyamopsis tetragonoloba). Plant Cell Reports 30, 997-1106.
  63. Dixon, R.A. (2011). Vanillin biosynthesis- not as simple as it seems? In Handbook of Vanilla Science and Technology, First Edition, edited D. Havkin-Frenkel and F. C. Belanger, Blackwell Publishing Ltd. pps 292-298.
  64. Lei, Z., Chen, F., Watson, B., Nagaraj, S., Elmer, A., Dixon, R.A. and Sumner, L.W. (2010). Comparative proteomics of yeast-elicited Medicago truncatula cell suspensions reveal induction of isoflavonoid biosynthesis and cell wall modifications. Journal of Proteome Research 9, 6220-6231.
  65. Wang, H., Avci, U., Nakashima, J., Hahn, M.G., Chen, F. and Dixon, R.A. (2010). Mutation of WRKY transcription factors initiates pith secondary wall formation and increases stem biomass in dicotyledonous plants. Proceedings of the National Academy of Sciences USA 107, 22338-22343. (Featured as an Editor's Choice article in Science).
  66. Ziebell, A., Gracom, K., Katahira, R., Chen, F., Pu, Y., Ragauskas, A., Dixon, R.A. and Davis, M. (2010). Increase in 4-coumaryl alcohol (H) units during lignification in alfalfa (Medicago sativa) alters extractability and molecular weight of lignin. Journal of Biological Chemistry 285, 38961-38968.
  67. Dixon, R.A. and Pasinetti, G.M. (2010). Flavonoids and isoflavonoids: from plant biology to agriculture and neuroscience. Plant Physiology 154, 453-457.
  68. Zhao, J., Pang, Y. and Dixon, R.A. (2010) The mysteries of proanthocyanidin transport and polymerization. Plant Physiology 153, 437-443.
  69. Naoumkina, M.A., Zhao, Q., Gallego-Giraldo, L., Dai, X. Zhao, P.X. and Dixon, R.A. (2010). Genome-wide analysis of phenylpropanoid defence pathways. Molecular Plant Pathology 11: 829-846. (cover article).
  70. Zhao, J. and Dixon, R.A. (2010). The "ins" and "outs" of flavonoid transport. Trends in Plant Science 15: 72-80.
  71. Zhou, R., Nakashima, J., Jackson, L., Shadle, G., Temple, S., Chen, F. and Dixon, R.A. (2010). Distinct cinnamoyl CoA reductases involved in parallel routes to lignin in Medicago truncatula. Proceedings of the National Academy of Sciences USA 107: 17803-17808.
  72. Zhao, Q., Wang, H., Yin, Y., Xu, Y., Chen, F. and Dixon, R.A. (2010). Syringyl lignin biosynthesis is directly regulated by a secondary cell wall master switch. Proceedings of the National Academy of Sciences USA 107: 14496-14501.
  73. Zhao, Q., Gallego-Giraldo, L., Wang, H., Zeng, Y., Ding, S-Y., Chen, F. and Dixon, R.A. (2010) A NAC transcription factor orchestrates multiple features of cell wall development in Medicago truncatula. Plant Journal 63: 100-114.
  74. Naoumkina, M.A., Modolo, L.V., Huhman, D.V., Urbanczyk-Wochniak, E., Tang, Y., Sumner, L.W. and Dixon, R.A. (2010) Genomic and co-expression analyses predict multiple genes involved in triterpene saponin biosynthesis in Medicago truncatula. Plant Cell 22: 850-866.
  75. Zeng, Y., Saar, B.G., Friedrich, M.G., Chen, F., Liu, Y-S., Dixon, R.A., Himmel, M.E., Xie, X.S., and Ding, S-Y. (2010) Imaging lignin-down-regulated alfalfa using Coherent Anti-Stoke Raman Scattering Microscopy. BioEnergy Research 3: 272-277.
  76. Sharma, V., Zhang, C., Pasinetti, G.M. and Dixon, R.A. (2010) Fractionation of grape seed proanthocyanidins for bioactivity assessment. In The Biological Activity of Phytochemicals, ed Gang, D.R. Recent Advances in Phytochemistry (Springer, New York) 41: 33-46.
  77. Dai, X., Wang, G., Yang, D.S., Tang, Y., Broun, P., Marks, M.D., Sumner, L.W., Dixon, R.A. and Zhao, P.Z. (2010) TrichOME: A comparative omics database for plant trichomes. Plant Physiology 152: 44-54.
  78. Escamilla-Treviño, L.L., Shen, H., Uppalapati, S.R., Ray, T., Tang, Y., Hernandez, T., Yin, Y., Xu, Y. and Dixon, R.A. (2010). Switchgrass (Panicum virgatum L.) possesses a divergent family of cinnamoyl CoA reductases with distinct biochemical properties. New Phytologist 185: 143-155.
  79. Shen, H., Yin Y, Chen, F. Xu, Y. and Dixon, R.A. (2009) A bioinformatic analysis of NAC genes for plant cell wall development in relation to lignocellulosic bioenergy production. BioEnergy Research 2: 217-312.
  80. Chory, J., Dean, C., and Dixon, R.A. (2009) Obituary. Chris Lamb. American Society of Plant Biologists Newsletter. 36: 32-34.
  81. Dixon, R.A. (2009) DOE Bioenergy Center Special Issue. The Bioenergy Sciences Center (BESC). Editorial. BioEnergy Research 2: 175-176.
  82. Modolo, L.V., Reichert, A.I., and Dixon, R.A. (2009) Introduction to the different classes of biosynthetic enzymes. In Plant-Derived Natural Products, Synthesis, Function and Application. eds. Osbourn, A and Lanzotti, V., Springer, pp 143-163.
  83. Reichert, A.I., He, X-Z. and Dixon, R.A. (2009). Phenylalanine ammonia-lyase from tobacco (Nicotiana tabacum)-characterization of the four tobacco PAL genes and active heterotetrameric enzymes. Biochemical Journal 424: 233-242.
  84. Modolo, L.V., Li, L., Dixon, R.A., and Wang, X. (2009) Crystal structures of glycosyltransferase UGT78G1 reveal the molecular basis for glycosylation and deglycosylation of (iso)flavonoids. Journal of Molecular Biology 392: 1292-1302.
  85. Zhao, J. and Dixon, R.A. (2009). MATE transporters facilitate vacuolar uptake of epicatechin 3'-O-glucoside for proanthocyanidin biosynthesis. Plant Cell 21: 2323-2340.
  86. Pang, Y., Wenger, J.P., Saathoff, K., Peel, G.J., Wen, J., Huhman, D., Allen, S.N.,Tang, Y., Cheng, X., Tadege, M., Ratet, P., Mysore, K.S., Sumner, L.W., Marks, M.D. and Dixon, R.A. (2009). A WD40 repeat protein from Medicago truncatula is necessary for tissue-specific anthocyanin and proanthocyanidin biosynthesis, but not for trichome development. Plant Physiology 151: 1114-1129.
  87. Marks, M.D., Tian, L., Soto-Fuentes, W., He, J, Gang, D.R., Weiblen, G.D. and Dixon, R.A. (2009) Identification of candidate genes affecting Δ9-tetrahydrocannabinol biosynthesis in Cannabis sativa. Journal of Experimental Botany 60: 3715-3726.
  88. Wang, G. and Dixon, R.A. (2009). Heterodimeric geranyl(geranyl)diphosphate synthase from hop (Humulus lupulus) and the evolution of monoterpene biosynthesis. Proceedings of the National Academy of Sciences USA 106: 9914-9919.
  89. Marks, M.D., Wenger, J., Gilding, E., Jilk, R. and Dixon, R.A. (2009) Transcriptome analysis of Arabidopsis wild-type and gl3-sst sim trichomes identifies five additional genes required for trichome development. Molecular Plant 2: 803-822.
  90. Modolo, L.V., Escamilla-Trevino, L.L., Dixon, R.A. and Wang, X. (2009). Single amino acid mutations of Medicago glycosyltransferase UGT85H2 enhance activity and impart reversibility. FEBS Letters 583: 2131-2135.
  91. Peel, G.J., Modolo, L.V., Pang, Y. and Dixon, R.A. (2009) The LAP1 MYB transcription factor orchestrates anthocyanidin biosynthesis and glycosylation in Medicago. Plant Journal 59: 136-149. (cover article).
  92. Farag, M.A., Deavours, B.E., De-Fatima, A., Naoumkina, M., Dixon, R.A. and Sumner, L.W. (2009) Integrated metabolite and transcript profiling identify a biosynthetic mechanism for hispidol in Medicago truncatula cell cultures. Plant Physiology 151: 1096-1113.
  93. Besser, K., Harper, A., Welsby, N., Schauvinhold, I., Slocombe, S., Li, Y., Dixon, R.A. and Broun, P. (2009). Divergent regulation of terpenoid metabolism in the trichomes of wild and cultivated tomato species. Plant Physiology 149: 499-514.
  94. Uppalapati, S.R., Marek, S.M., Lee, H-K., Nakashima, J., Tang, Y., Sledge, M.K., Dixon, R.A. and Mysore, K.S. (2009) Global gene expression profiling during Medicago truncatula-phymatotrichopsis omnivore interaction reveals a role for jasmonic acid, ethylene, and the flavonoid pathway in disease development. Molecular Plant-Microbe Interactions 22: 7-17. (cover article).
  95. Tian, L., Peel, G.J., Lei, Z., Aziz, N., Dai, X., He, J.,Watson, B., Zhao, P.X., Sumner, L.W. and Dixon, R.A. (2009). Transcript and proteomic analysis of developing white lupin (Lupinus albus L.) roots. BMC Plant Biology 9: 1 (online).
  96. Naoumkina, M. and Dixon, R.A. (2008) Subcellular localization of flavonoid natural products- a signaling function? Plant Signaling and Behavior 3: 573-575.
  97. Ralph, J., Brunow, G., Harris, P., Dixon, R.A. and Boerjan, W. (2008). Lignification: are lignins biosynthesized via simple combinatorial chemistry or via proteinaceous control and template replication? Recent Advances in Polyphenols Research 1: 36-66.
  98. Modolo, L.V., Pang, Y., Tian, L. and Dixon, R.A. (2008). Gene discovery and metabolic engineering in the phenylpropanoid pathway. Recent Advances in Polyphenols Research 1: 113-138.
  99. Tian, L., Pang, Y. and Dixon, R.A. (2008). Biosynthesis and genetic engineering of proanthocyanidins and (iso)flavonoids. Phytochemistry Reviews 7: 445-465.
  100. Slocombe, S.P., Schauvinhold, I., McQuinn, R.P., Besser, K., Welsby, N.A., Harper, A., Aziz, N., Li, Y., Larson, T.R., Giovannoni, J., Dixon, R.A. and Broun, P. (2008) Transcriptomic and reverse genetic analyses of branched chain fatty acid and acyl sugar production in Solanum pennellii and Nicotiana benthamiana. Plant Physiology 148: 1830-1846.
  101. Wang, G., Tian, L., Aziz, N., Broun, P., Dai, X., He, J., King, A., Zhao, P.X, and Dixon, R.A. (2008) Terpene biosynthesis in glandular trichomes of hop (Humulus lupulus L.). Plant Physiology 148: 1254-1266.
  102. Naoumkina, M., He, X-Z. and Dixon, R.A. (2008). Elicitor-induced transcription factors for metabolic reprogramming of secondary metabolism in Medicago truncatula. BMC Plant Biology 8: 132.
  103. Pang, Y., Peel, G.J., Sharma, S.B., Tang, Y. and Dixon, R.A. (2008). A transcript profiling approach reveals an epicatechin-specific glucosyltransferase expressed in the seed coat of Medicago truncatula. Proceedings of the National Academy of Sciences USA 105: 14210-14215.
  104. Nakashima, J., Chen, F., Jackson, L., Shadle, G., and Dixon, R.A. (2008). Multi-site genetic modification of monolignol biosynthesis in alfalfa (Medicago sativa L.) - effects on lignin composition in specific cell types. New Phytologist 179: 738-750.
  105. Jackson, L.A., Shadle, G.L., Zhou, R., Nakashima, J., Chen, F., and Dixon, R.A. (2008). Improving saccharification efficiency of alfalfa stems through modification of the terminal stages of monolignol biosynthesis. Bioenergy Research 1: 180-192.
  106. Naoumkina, M., Vaghchhipawala, S., Tang, Y., Ben, Y., Powell, R.J. and Dixon, R.A. (2008) Metabolic and genetic perturbations accompany the modification of galactomannan in seeds of Medicago truncatula expressing mannan synthase from guar (Cyamopsis tetragonoloba L.) Plant Biotechnology Journal 6: 619-631.
  107. Marks, M.D., Gilding, E., Betancur, L., Chen, F., Bauer, S., Wenger, J.P., Sommerville, C., Dixon, R.A., and Haigler, C.H. (2008) A new method for isolating large quantities of Arabidopsis trichomes for transcriptome, cell wall and other types of analyses. Plant Journal 56: 483-492. (cover article).
  108. He, X.-Z., Li, W.-S., Blount, J.W. and Dixon, R.A. (2008). Regioselective synthesis of plant flavonoid glycosides in E.coli. Applied Microbiology and Biotechnology 80: 253-260.
  109. Farag, M.A., Huhman, D.V., Dixon, R.A. and Sumner, L.W. (2008). Metabolomics reveals novel pathways and differential mechanistic and elicitor-specific responses in phenylpropanoid and isoflavonoid biosynthesis in Medicago truncatula cell cultures. Plant Physiology 146: 387-402.
  110. Dixon, R.A. (2007) Tom Mabry: Over 45 Years of Phytochemistry, Texas-Style. Natural Product Communications 2 (10).
  111. Dixon, R.A., Bouton, J.H., Narasimhamoorthy, B., Saha, M., Wang, Z.-Y., and May, G.D. (2007). Beyond structural genomics for plant science. Advances in Agronomy 95: 77-161.
  112. Naoumkina, M., Torres-Jerez, I., Allen, S., He, J., Zhao, P. Dixon, R.A. and May, G.D. (2007) Analysis of cDNA libraries from developing seeds of guar (Cyamopsis tetragonoloba (L.) Taub). BMC Plant Biology 7: 62 (online).
  113. Naoumkina, M., Farag, M.A., Sumner, L.W., Tang, Y., Liu, C.-J. and Dixon, R.A. (2007) Different mechanisms for phytoalexin induction by pathogen- and wound signals in Medicago truncatula. Proceedings of the National Academy of Sciences USA 104: 17909-17915.
  114. Peel, G.J. and Dixon, R.A. (2007) Detection and quantification of engineered proanthocyanidins in transgenic plants. Natural Product Communications 2: 1009-1014.
  115. Pang, Y., Peel, G.J., Wright, E., Wang, Z-Y, and Dixon, R.A. (2007). Early steps in proanthocyanidin biosynthesis in the model legume Medicago truncatula. Plant Physiology 145: 601-615.
  116. Shrestha, R., Kim, S-C. Dyer, J.M., Dixon, R.A. and Chapman, K.D. (2006). Plant fatty acid (ethanol) amide hydrolases. Biochimica et Biophysica Acta- Molecular and Cellular Biology of Lipids 1761: 324-334.
  117. Tian, L., DellaPenna, D. and Dixon, R.A. (2007) The pds2 mutation is a lesion in the Arabidopsis homogentisate solanesyltransferase gene involved in plastoquinone biosynthesis. Planta 226: 1067-1073.
  118. Chen, F., and Dixon, R.A. (2007) Lignin modification improves fermentable sugar yields for biofuel production. Nature Biotechnology 25: 759-761.
  119. Li, L., Modolo, L.V., Escamilla-Trevino, L.L., Achnine, L., Dixon, R.A. and Wang, X. (2007) Crystal structure of Medicago truncatula UGT85H2 - insights into the structural basis of a multifunctional (iso)flavonoid glycosyltransferase. Journal of Molecular Biology 370: 951-963.
  120. Shao, H., Dixon, R.A. and Wang, X. (2007) Crystal structure of vestitone reductase from alfalfa (Medicago sativa L.). Journal of Molecular Biology 369, 265-276.
  121. Shadle, G., Chen, F., Reddy, M.S.S., Jackson, L., Nakashima, J., and Dixon, R.A. (2007). Down-regulation of hydroxycinnamoyl CoA: shikimate hydroxy cinnamoyl transferase in transgenic alfalfa impacts lignification, development and forage quality. Phytochemistry 68: 1521-1529.
  122. Modolo, L., Blount, J.W., Achnine, L., Naoumkina, M., Wang, X. and Dixon, R.A. (2007) A functional genomics approach to (iso)flavonoid glycosylation in the model legume Medicago truncatula. Plant Molecular Biology 64: 499-518.
  123. Marais, J.P.J., Deavours, B.E., Dixon, R.A. and Ferreira, D. (2006). The stereochemistry of flavonoids. In The Science of Flavonoids, ed E. Grotewold, Springer, pp. 1-46.
  124. Dixon, R.A., Gang, D.R., Charlton, A.J., Fiehn, O., Kuiper, H.A., Reynolds, T.L., Tjeerdema, R.S., Jeffrey, E.H., Germans, J.B., Ridley, W.P. and Seiber, J.N. (2006). Applications of metabolomics to agriculture. Journal of Agricultural and Food Chemistry 54: 8984-8994.
  125. Dixon, R.A., Achnine, L., Deavours, B.E. and Naoumkina, M. (2006). Metabolomics and gene identification in plant natural product pathways. In: Biotechnology in Agriculture and Forestry, "Plant Metabolomics", edited by K. Saito, R. A. Dixon and L. Willmitzer, Springer, pp 243-259.
  126. Tian, L., Blount, J.W. and Dixon, R.A. (2006). Phenylpropanoid glycosyltransferases from osage orange (Maclura pomifera) fruit. FEBS Letters 580: 6915-6920.
  127. He, X., Wang, X. and Dixon, R.A. (2006) Mutational analysis of the Medicago glycosyltransferase UGT71G1 reveals residues that control regio-selectivity for (iso)flavonoid glycosylation. Journal of Biological Chemistry 281: 34441-34447.
  128. Chen, F., Reddy, M.S.S., Temple, S., Jackson, L., Shadle, G. and Dixon, R.A. (2006). Multi-site genetic modulation of monolignol biosynthesis suggests new routes for the formation of syringyl lignin and wall-bound ferulic acid in alfalfa (Medicago sativa L.). Plant Journal 48: 113-124.
  129. Deavours, B.E., Liu, C.-J., Naoumkina, M.A., Tang, Y., Farag, M.A., Sumner, L.W., Noel, J.P. and Dixon, R.A. (2006). Functional analysis of members of the isoflavone and isoflavanone O-methyltransferase enzyme families from the model legume Medicago truncatula. Plant Molecular Biology 62: 715-733.
  130. Liu, C.-J., Deavours, B.E., Richard, S.B., Ferrer, J.-L., Blount, J.W., Huhman, D., Dixon, R.A. and Noel, J.P. (2006). Structural basis for dual functionality of isoflavonoid O-methyltransferases in the evolution of plant defense responses. Plant Cell 18: 3656-3669.
  131. Wang, X., He, X., Lin, J., Shao, H. and Dixon, R.A. (2006). Crystal structure of isoflavone reductase from alfalfa (Medicago sativa L.). Journal of Molecular Biology 358: 1341-1352.
  132. Ralph, J., Akiyama, T., Kim, H., Lu, F., Schatz, P.F., Marita, J.M., Ralph, S.A., Reddy, M.S.S., Chen, F. and Dixon, R.A. (2006). Effects of coumarate 3-hydroxylase down-regulation on lignin structure. Journal of Biological Chemistry 281: 8843-8853.
  133. Crane, C., Dixon, R.A. and Wang, Z.-TY. (2006). Medicago truncatula transformation using root explants. In "Agrobacterium Protocols" (Ed. K. Wang), Humana Press, pp. 137-142.
  134. Wright, E., Dixon, R.A. and Wang, Z.-Y. (2006). Medicago truncatula transformation using cotyledon explants. In Agrobacterium Protocols (Ed. K. Wang), Humana Press, pp. 129-135.
  135. Tian, L. and Dixon, R.A. (2006). An artificial bifunctional enzyme for engineering of isoflavone metabolism in non-legume plants. Planta 224: 496-507.
  136. Crane, C., Wright, E., Dixon, R.A. and Wang, Z.-Y. (2006) Transgenic Medicago truncatula plants obtained from Agrobacterium tumefaciens-transformed roots and Agrobacterium rhizogenes-transformed hairy roots. Planta 223: 1344-1354.
  137. Xie, D.-Y., Sharma, S.B., Wright, E., Wang, Z.-Y. and Dixon, R.A. (2006). Metabolic engineering of proanthocyanidins through co-expression of anthocyanidin reductase and the PAP1 MYB transcription factor. Plant Journal 45: 895-907.
  138. Dixon, R.A. (2005). Plant biotechnology kicks off into the 21st century (Editorial). Trends in Plant Science 10: 560-561.
  139. Dixon, R.A. (2005). A two-for-one in tomato nutritional enhancement. Nature Biotechnology 23: 825-826.
  140. Kutchan, T and Dixon, R.A. (2005) Secondary metabolism: nature's chemical reservoir under deconvolution. Current Opinion in Plant Biology 8: 227-229.
  141. Dixon, R.A. (2005). Engineering plant natural product pathways. Current Opinion in Plant Biology 8: 329-336.
  142. Xie, D.-Y. and Dixon, R.A. (2005). Proanthocyanidin biosynthesis- still more questions than answers? Phytochemistry 66: 2126-2143.
  143. Dixon, R.A., Xie, D.-Y., and Sharma, S.B. (2005). Tansley Review. Proanthocyanidins- a final frontier in flavonoid research. New Phytologist 165: 9-28.
  144. Lei, Z., Elmer, A.M., Watson, B.S., Dixon, R.A., Mendes, P.J. and Sumner, L.W. (2005). A 2-DE proteomics reference map and systematic identification of 1367 proteins from a cell suspension culture of the model legume Medicago truncatula. Molecular and Cellular Proteomics 4: 1812-1825.
  145. Reddy, M.S.S., Chen, F., Shadle, G., Jackson, L., Aljoe, H. and Dixon, R.A. (2005). Targeted down-regulation of cytochrome P450 enzymes for forage quality improvement in alfalfa (Medicago sativa L.). Proceedings of the National Academy of Sciences USA, 102: 16573-16578.
  146. Shao, H., He, X., Achnine, L., Blount, J.W., Dixon, R.A. and Wang, X. (2005). Crystal structures of a multifunctional triterpene/flavonoid uridine diphosphate glycosyltransferase from the model legume Medicago truncatula. Plant Cell 17: 3141-3154.
  147. Bomati, E.K., Austin, M.B., Bowmann, M.E., Dixon, R.A. and Noel, J.P. (2005). Structural elucidation of chalcone reductase and implications for deoxychalcone biosynthesis. Journal of Biological Chemistry 280: 30496-30503.
  148. Sharma, S.B. and Dixon, R.A. (2005). Metabolic engineering of proanthocyanidins by ectopic expression of transcription factors in Arabidopsis thaliana. Plant Journal 44: 62-75.
  149. Deavours, B.E. and Dixon, R.A. (2005). Metabolic engineering of isoflavonoid biosynthesis in alfalfa (Medicago sativa L.). Plant Physiology 138: 2245-2259.
  150. Achnine, L., Huhman, D.V., Sumner, L.W., Blount, J.W. and Dixon, R.A. (2005). Genomics-based selection and functional characterization of triterpene glycosyltransferases from the model legume Medicago truncatula. Plant Journal 41: 875-887.
  151. Ferrer, J.L., Zubieta, C., Dixon, R.A. and Noel, J.P. (2005). Crystal structures of alfalfa caffeoyl CoA 3-O-methyltransferase. Plant Physiology 137: 1009-1017.
  152. Suzuki, H., Reddy, M.S.S., Naoumkina, M., Aziz, N., May, G.D., Huhman, D.V., Sumner, L.W., Blount, J.W., Mendes, P. and Dixon, R.A. (2005). Methyl jasmonate and yeast elicitor induce differential genetic and metabolic reprogramming in cell suspension cultures of the model legume Medicago truncatula. Planta 220: 698-707.
  153. Broeckling, C.D., Huhman, D.V., Farag, M. Smith, J.T., May, G.D., Mendes, P., Dixon, R.A. and Sumner, L.W. (2005). Metabolic profiling of Medicago truncatula cell cultures reveals effects of biotic and abiotic elicitors on metabolism. Journal of Experimental Botany 56: 323-336.
  154. Aziz, N., Paiva, N.L., May, G.D. and Dixon, R.A. (2005). Profiling the transcriptome of alfalfa glandular trichomes. Planta 221: 28-38.

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