Recent publications from the Plant Physiology Program at the University of Kentucky

Research is central to the training provided by the Plant Physiology Ph.D. Program at the University of Kentucky. Our success in this regard is manifest as a strong and consistent record of publications co-authored by our students. This page provides references to recent papers co-authored by current students or recent graduates of the Plant Physiology Ph.D. Program.

Papers published in 2011

• Joshi CP, Thammannagowda S, Fujino T, Gou JQ, Avci U, Haigler CH, McDonnell LM, Mansfield SD, Mengesha B, Carpita NC, Harris D, Debolt S, Peter GF. (2011) Perturbation of wood cellulose synthesis causes pleiotropic effects in transgenic aspen. Mol Plant. 4:331-345.
• Mendu V, Stork J, Harris D, Debolt S. (2011) Cellulose synthesis in two secondary cell wall processes in a single cell type. Plant Signal Behav. 6:1638-1643. 
• Nair M, Debolt S. Analysing cellulose biosynthesis with confocal microscopy. (2011) Methods Mol Biol. 715:141-152.
• Niehaus TD, Okada S, Devarenne TP, Watt DS, Sviripa V, Chappell J (2011). Identification of unique mechanisms for triterpene biosynthesis in Botryococcus braunii. Proc Natl Acad Sci U S A. 108(30):12260-12265.
• Pattanaik S, Werkman JR, Yuan L. Bimolecular fluorescence complementation as a tool to study interactions of regulatory proteins in plant protoplasts. (2011) Methods Mol Biol. 754:185-193.
• Suttipanta N, Pattanaik S, Kulshrestha M, Patra B, Singh SK, Yuan L. (2011) The transcription factor CrWRKY1 positively regulates the terpenoid indole alkaloid biosynthesis in Catharanthus roseus. Plant Physiol. 157:2081-2093.
• Werkman JR, Pattanaik S, Yuan L. Directed evolution through DNA shuffling for  the improvement and understanding of genes and promoters. (2011) Methods Mol Biol. 754:325-342.
• Zheng Y, Perry SE. Chromatin immunoprecipitation to verify or to identify in vivo protein-DNA interactions. (2011) Methods Mol Biol.;754:277-291.

Papers published in 2010

• Bell SA, Hunt AG. (2010) The Arabidopsis ortholog of the 77 kDa subunit of the cleavage stimulatory factor (AtCstF-77) involved in mRNA polyadenylation is an RNA-binding protein. FEBS Lett. 584:1449-1454.
• Harris D, Bulone V, Ding SY, DeBolt S. (2010) Tools for cellulose analysis in plant cell walls. Plant Physiol. 153:420-426.
• Harris D, DeBolt S. (2010) Synthesis, regulation and utilization of lignocellulosic biomass. Plant Biotechnol J. 8:244-262.
• Jia X, Mendu V, Tang G. (2010) An array platform for identification of stress-responsive microRNAs in plants. Methods Mol Biol. 639:253-269.
• Pattanaik S, Werkman JR, Kong Q, Yuan L. (2010) Site-directed mutagenesis and saturation mutagenesis for the functional study of transcription factors involved in plant secondary metabolite biosynthesis. Methods Mol Biol. 643:47-57.
• Pattanaik S, Kong Q, Zaitlin D, ß, Xie CH, Patra B, Yuan L. (2010) Isolation and functional characterization of a floral tissue-specific R2R3 MYB regulator from tobacco. Planta. 231:1061-1076.
• Stork J, Harris D, Griffiths J, Williams B, Beisson F, Li-Beisson Y, Mendu V,  Haughn G, Debolt S. (2010) CELLULOSE SYNTHASE9 serves a nonredundant role in secondary cell wall synthesis in Arabidopsis epidermal testa cells. Plant Physiol. 153:580-589.

Papers published in 2009

• Fan ZM, Wagschal K, Lee C., Kong Q, Shen KA, Maiti IB, Yuan L. (2009) The Construction and Characterization of Two Xylan-degrading Chimeric Enzymes. Biotechnology and Bioengineering 102: 684-692.
• Fan ZM, Werkman JR, Yuan L. (2009) Engineering of a Multifunctional Hemicellulase. Biotechnology Letters 31: 751-757.
• Galli F, Archbol, DD, Pomper KW. (2009) Pawpaw fruit chilling injury and antioxidant protection. Journal of the American Society for Horticultural Science 134: 466-471.
• Jia X, Wang W-X, Ren L, Chen Q-L, Mendu V, Willcut B, Dinkins R, Tang X, Tang G. (2009) Differential and dynamic regulation of miR398 and its targets in response to ABA and salt stress in Populus tremula and Arabidopsis thaliana. Plant Molecular Biology 71: 51-59.
• Kurepa J, Wang S, Li Y, Zaitlin D, Pierce AJ, Smalle J. (2009). Loss of 26S proteasome function leads to increased cell size and decreased cell number in Arabidopsis shoot organs. Plant Physiology 150, 178-189.
• Meeks LR, Addepalli B, Hunt AG. (2009) Characterization of genes encoding poly(A) polymerases in plants: evidence for duplication and functional specialization. PLoS One 4, e8082.
• Nakaminami K, Hill K, Perry SE, Sentoku N, Long JA, Karlson DT. (2009) Arabidopsis cold shock domain proteins: relationships to floral and silique development. Journal of Experimental Botany 60:1047-1062.
• Sigal Escalada V, Archbold DD. (2009) Effects of aminoethoxyvinylglycine plus 1-methylcyclopropene on 'Royal Gala' apple volatile production after cold storage. HortScience 44:1390-1394.
• Sigal Escalada V, Archbold DD. (2009) Preharvest aminoethoxyvinylglycine plus postharvest heat treatments influence apple fruit ripening after cold storage. HortScience 44: 1637-1640.
• Zheng Y, Ren N, Wang H, Stromberg AJ, Perry SE. (2009) Global identification of targets of the Arabidopsis MADS domain protein AGAMOUS-Like15. Plant Cell 21:2563-2577.

Papers published in 2008

• Chakrabarti M, Bowen SW, Coleman NP, Meekins KM, Dewey RE, Siminszky B. (2008) CYP82E4-mediated nicotine to nornicotine conversion in tobacco is regulated by a senescence-specific signaling pathway. Plant Mol. Biol. 66: 415-427.
• Dinkins RD, Majee SM, Nayak NR, Martin D, Xu Q, Belcastro MP, Houtz RL, Beach CM, Downie AB. (2008) Changing transcriptional initiation sites and alternative 5'- and 3'-splice site selection of the first intron deploys Arabidopsis protein isoaspartyl methyltransferase 2 variants to different subcellular compartments. Plant J. 55:1-13.
• Galli F, Archbold DD, Pomper KW. (2008) Loss of Ripening Capacity of Pawpaw Fruit with Extended Cold Storage. J Agric Food Chem. 56: 10683–10688.
• Harris D, DeBolt S. (2008) Relative crystallinity of plant biomass: studies on assembly, adaptation and acclimation. PLoS ONE 3: e2897.
• Hill K, Wang H, Perry SE. (2008) A transcriptional repression motif in the MADS factor AGL15 is involved in recruitment of histone deacetylase complex components. Plant J. 53:172-85.
• Hunt AG, Xu R, Addepalli B, Rao S, Forbes KP, Meeks LR, Xing D, Mo M, Zhao H, Bandyopadhyay A, Dampanaboina L, Marion A, Von Lanken C, Li QQ. (2008) Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling. BMC Genomics 9:220.
• Lee S, Chappell J. (2008) Biochemical and genomic characterization of terpene synthases in Magnolia grandiflora. Plant Physiol. 147:1017-33. Rao S, Taha M, Hildebrand D. 2008. Characteristics of High α-Linolenic acid Accumulation in Seed Oils. Lipids 43: 749-755.
• Thakare D, Tang W, Hill K, Perry SE. (2008) The MADS-domain transcriptional regulator AGAMOUS-LIKE15 promotes somatic embryo development in Arabidopsis and soybean. Plant Physiol. 146:1663-72.

Papers published in 2007

• Chakrabarti M, Meekins KM, Gavilano LB, Siminszky B. (2007) Inactivation of the cytochrome P450 gene CYP82E2 by degenerative mutations was a key event in the evolution of the alkaloid profile of modern tobacco. New Phytol. 175: 565-74.
• Kroumova AB, Shepherd RW, Wagner GJ. (2007) Impacts of T-Phylloplanin gene knockdown and of Helianthus and Datura phylloplanins on Peronospora tabacina spore germination and disease potential. Plant Physiol. 144: 1843-1851.
• Myung K, Hamilton-Kemp TR, Archbold DD. (2007) Interaction with and effects on the profile of proteins of Botrytis cinerea by C6 aldehydes. J Agric Food Chem. 55: 2182-2188.
• Nosarzewski M, Archbold DD. (2007) Tissue-specific expression of SORBITOL DEHYDROGENASE in apple fruit during early development. J Exp Bot. 58: 1863-1872.
• Suttipanta N, Pattanaik S, Gunjan S, Xie CH, Littleton J, Yuan L. (2007) Promoter analysis of the Catharanthus roseus geraniol 10-hydroxylase gene involved in terpenoid indole alkaloid biosynthesis. Biochim Biophys Acta. 1769: 139-148.
• Tang X, Gal J, Zhuang X, Wang W, Zhu H, Tang G. (2007) A simple array platform for microRNA analysis and its application in mouse tissues. RNA. 2007 13: 1803-1822.

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