Our Research Efforts

Research is central to the training provided by the Plant Physiology/Plant Biology 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/Plant Biology Ph.D. Program.

Papers published in 2018

• Patra B, Pattanaik S, Schluttenhofer C, Yuan L. (2018) A network of jasmonate-responsive bHLH factors modulate monoterpenoid indole alkaloid biosynthesis in Catharanthus roseus. New Phytol. 217(4):1566-1581.

Papers published in 2017

• Brabham C, Stork J, Barrett M, DeBolt S. (2017) Grass cell walls have a role in the inherent tolerance of grasses to the cellulose biosynthesis inhibitor isoxaben. Pest Manag Sci. 2017 Oct 31. doi: 10.1002/ps.4779.
• Paul P, Singh SK, Patra B, Sui X, Pattanaik S, Yuan L. (2017) A differentially regulated AP2/ERF transcription factor gene cluster acts downstream of a MAP kinase cascade to modulate terpenoid indole alkaloid biosynthesis in Catharanthus roseus. New Phytol. 213(3):1107-1123
• Pook VG, Nair M, Ryu K, Arpin JC, Schiefelbein J, Schrick K, DeBolt S. (2017) Positioning of the SCRAMBLED receptor requires UDP-Glc:sterol glucosyltransferase 80B1 in Arabidopsis roots. Sci Rep. 7(1):5714.
• Roy S, Nuckles E, Archbold DD. (2017) Effects of Phenolic Compounds on Growth of Colletotrichum spp. In Vitro. Curr Microbiol. 2017 Dec 15. doi: 10.1007/s00284-017-1415-7.
• Schluttenhofer C, Yuan L. (2017) Challenges towards Revitalizing Hemp: A Multifaceted Crop. Trends Plant Sci. 22(11):917-929.
• Shen EM, Singh SK, Ghosh JS, Patra B, Paul P, Yuan L, Pattanaik S. (2017) The miRNAome of Catharanthus roseus: identification, expression analysis, and potential roles of microRNAs in regulation of terpenoid indole alkaloid biosynthesis. Sci Rep. 22;7:43027.

Papers published in 2016

• Bell SA, Shen C, Brown A, Hunt AG. (2016) Experimental Genome-Wide Determination of RNA Polyadenylation in Chlamydomonas reinhardtii. PLoS One. 11(1):e0146107.
• Hatanaka T, Serson W, Li R, Armstrong P, Yu K, Pfeiffer T, Li XL, Hildebrand D. (2016) A Vernonia Diacylglycerol Acyltransferase Can Increase Renewable Oil Production. J Agric Food Chem. 64(38):7188-94.
• Jiang Z, Kempinski C, Bush CJ, Nybo SE, Chappell J. (2016) Engineering Triterpene and Methylated Triterpene Production in Plants Provides Biochemical and Physiological Insights into Terpene Metabolism. Plant Physiol. 170(2):702-16.
• Jiang Z, Kempinski C, Chappell J. (2016) Extraction and Analysis of Terpenes/Terpenoids. Curr Protoc Plant Biol. 2016;1:345-358.
• Kumar S, Kempinski C, Zhuang X, Norris A, Mafu S, Zi J, Bell SA, Nybo SE, Kinison SE, Jiang Z, Goklany S, Linscott KB, Chen X, Jia Q, Brown SD, Bowman JL, Babbitt PC, Peters RJ, Chen F, Chappell J. (2016) Molecular Diversity of Terpene Synthases in the Liverwort Marchantia polymorpha. Plant Cell. 28(10):2632-2650.
• Linscott KB, Niehaus TD, Zhuang X, Bell SA, Chappell J. (2016) Mapping a kingdom-specific functional domain of squalene synthase. Biochim Biophys Acta. 1861(9 Pt A):1049-57.
• Rising KA, Crenshaw CM, Koo HJ, Subramanian T, Chehade KA, Starks C, Allen KD, Andres DA, Spielmann HP, Noel JP, Chappell J. (2016) Formation of a Novel Macrocyclic Alkaloid from the Unnatural Farnesyl Diphosphate Analogue Anilinogeranyl Diphosphate by 5-Epi-Aristolochene Synthase. ACS Chem Biol. 10(7):1729-36.
• Rojas X, Guo J, Leff JW, McNear DH Jr, Fierer N, McCulley RL. (2016) Infection with a Shoot-Specific Fungal Endophyte (Epichloë) Alters Tall Fescue Soil Microbial Communities. Microb Ecol. 72(1):197-206.
• Shull TE, Kurepa J, Smalle JA. (2016) Cytokinin signaling promotes differential stability of type-B ARRs. Plant Signal Behav. 11(4):e1169354
• Tateno M, Brabham C, DeBolt S. (2016) J Exp Bot. 67(2):533-42.

Papers published in 2015

• Afitlhile M, Duffield-Duncan K, Fry M, Workman S, Hum-Musser S, Hildebrand D. (2015) The toc132toc120 heterozygote mutant of Arabidopsis thaliana accumulates reduced levels of hexadecatrienoic acid. Plant Physiol Biochem. 96:426-35.
• Chen C, Unrine JM, Judy JD, Lewis RW, Guo J, McNear DH Jr, Tsyusko OV. (2015) Toxicogenomic Responses of the Model Legume Medicago truncatula to Aged Biosolids Containing a Mixture of Nanomaterials (TiO(2), Ag, and ZnO) from a Pilot Wastewater Treatment Plant. Environ Sci Technol. 49(14):8759-68.
• Griffiths JS, Šola K, Kushwaha R, Lam P, Tateno M, Young R, Voiniciuc C, Dean G, Mansfield SD, DeBolt S, Haughn GW. (2015) Unidirectional movement of cellulose synthase complexes in Arabidopsis seed coat epidermal cells deposit cellulose involved in mucilage extrusion, adherence, and ray formation. Plant Physiol. 168(2):502-20.
• Guo J, McCulley RL, McNear DH Jr. (2015) Tall fescue cultivar and fungal endophyte combinations influence plant growth and root exudate composition. Front Plant Sci. 6:183.
• Kempinski C, Jiang Z, Bell S, Chappell J. Metabolic engineering of higher plants and algae for isoprenoid production. Adv Biochem Eng Biotechnol 148:161-99.
• Ma L, Hunt AG. (2015) A 3' RACE protocol to confirm polyadenylation sites. Methods Mol Biol. 1255:135-44.
• Pati PK, Ma L, Hunt AG. Genome-wide determination of poly(A) site choice in plants. (2015) Methods Mol Biol. 1255:159-74.
• Schluttenhofer C, Yuan L. (2015) Regulation of specialized metabolism by WRKY transcription factors. Plant Physiol. 167(2):295-306.
• Zhuang X, Chappell J. (2015) Building terpene production platforms in yeast. Biotechnol Bioeng. 112(9):1854-64.

Papers published in 2014

• Bell SA, Chappell J. (2014) Now playing: farnesol in the biofilm. Chem Biol. 21(11):1421-2.
• Bell SA, Niehaus TD, Nybo SE, Chappell J. (2014) Structure-function mapping of key determinants for hydrocarbon biosynthesis by squalene and squalene synthase-like enzymes from the green alga Botryococcus braunii race B. Biochemistry. 53(48):7570-81.
• Brabham C, Lei L, Gu Y, Stork J, Barrett M, DeBolt S. (2014) Indaziflam herbicidal action: a potent cellulose biosynthesis inhibitor. Plant Physiol 166(3):1177-85.
• Fernandez DE, Wang CT, Zheng Y, Adamczyk BJ, Singhal R, Hall PK, Perry SE. (2014) The MADS-Domain Factors AGAMOUS-LIKE15 and AGAMOUS-LIKE18, along with SHORT VEGETATIVE PHASE and AGAMOUS-LIKE24, Are Necessary to Block Floral Gene Expression during the Vegetative Phase. Plant Physiol. 165(4):1591-1603.
• Kurepa J, Li Y, Perry SE, Smalle JA. (2014) Ectopic expression of the phosphomimic mutant version of Arabidopsis response regulator 1 promotes a constitutive cytokinin response phenotype. BMC Plant Biol. 14:28.
• Kurepa J, Li Y, Smalle JA. (2014) Cytokinin signaling stabilizes the response activator ARR1. Plant J. 78(1):157-68.
• Ma L, Pati PK, Liu M, Li QQ, Hunt AG. (2014) High throughput characterizations of poly(A) site choice in plants. Methods. 67(1):74-83.
• Petti C, Kushwaha R, Tateno M, Harman-Ware AE, Crocker M, Awika J, Debolt S. (2014) Mutagenesis breeding for increased 3-deoxyanthocyanidin accumulation in leaves of Sorghum bicolor (L.) Moench: a source of natural food pigment. J Agric Food Chem. 62(6):1227-32.
• Petti C, Nair M, DeBolt S. (2014) The involvement of J-protein AtDjC17 in root development in Arabidopsis. Front Plant Sci 5:532.
• Radkov AD, Moe LA. (2014) Bacterial synthesis of D-amino acids. Appl Microbiol Biotechnol. 98(12):5363-74.
• Schluttenhofer C, Pattanaik S, Patra B, Yuan L. (2014) Analyses of Catharanthus roseus and Arabidopsis thaliana WRKY transcription factors reveal involvement in jasmonate signaling. BMC Genomics. 15:502.  
• Wu X, Gaffney B, Hunt AG, Li QQ. (2014) Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. BMC Genomics. 15:615.
• Xia Y, Lei L, Brabham C, Stork J, Strickland J, Ladak A, Gu Y, Wallace I, DeBolt S. (2014) Acetobixan, an inhibitor of cellulose synthesis identified by microbial bioprospecting. PLoS One. 9(4):e95245.
• Yang S, Tang F, Zhu H. (2014) Alternative splicing in plant immunity. Int J Mol Sci. 15(6):10424-45.

Papers published in 2013

• Banerjee J, Magnani R, Nair M, M Dirk L, Debolt S, Maiti IB, Houtz RL. (2013) Calmodulin-mediated signal transduction pathways in Arabidopsis are fine-tuned by methylation. Plant Cell 25(11):4493-511.
• Brabham C, Debolt S. (2013) Chemical genetics to examine cellulose biosynthesis. Front Plant Sci. 3:309.
• Cai B, Jack AM, Lewis RS, Dewey RE, Bush LP. (2013) (R)-nicotine biosynthesis, metabolism and translocation in tobacco as determined by nicotine demethylase mutants. Phytochemistry 95:188-96.
• Kurepa J, Li Y, Smalle JA. (2013) Proteasome-dependent proteolysis has a critical role in fine-tuning the feedback inhibition of cytokinin signaling. Plant Signal Behav. 8(3):e23474.
• Kurepa J, Li Y, Smalle JA. (2013) Reversion of the Arabidopsis rpn12a-1 exon-trap mutation by an intragenic suppressor that weakens the chimeric 5' splice site. Version 2. F1000Res. 2:60.
• Li Y, Kurepa J, Smalle J. (2013) AXR1 promotes the Arabidopsis cytokinin response by facilitating ARR5 proteolysis. Plant J. 74(1):13-24.
• Patra B, Schluttenhofer C, Wu Y, Pattanaik S, Yuan L. (2013) Transcriptional regulation of secondary metabolite biosynthesis in plants. Biochim Biophys Acta 1829(11):1236-47.
• Petti C, Harman-Ware AE, Tateno M, Kushwaha R, Shearer A, Downie AB, Crocker M, Debolt S. (2013) Sorghum mutant RG displays antithetic leaf shoot lignin accumulation resulting in improved stem saccharification properties. Biotechnol Biofuels 6(1):146.
• Petti C, Shearer A, Tateno M, Ruwaya M, Nokes S, Brutnell T, Debolt S. (2013) Comparative feedstock analysis in Setaria viridis L. as a model for C4 bioenergy grasses and Panicoid crop species. Front Plant Sci. 4:181.
• Radkov AD, Moe LA. (2013) Amino acid racemization in Pseudomonas putida KT2440. J Bacteriol. 195(22):5016-24.
• Tang F, Yang S, Gao M, Zhu H. (2013) Alternative splicing is required for RCT1-mediated disease resistance in Medicago truncatula. Plant Mol Biol. 82(4-5):367-74.
• Yang S, Tang F, Caixeta ET, Zhu H. (2013) Epigenetic regulation of a powdery mildew resistance gene in Medicago truncatula. Mol Plant. 6(6):2000-3.

Papers published in 2012

• Cai B, Bush LP. (2012) Variable nornicotine entantiomeric composition caused by nicotine demethylase CYP82E4 in tobacco leaf.  J Agric Food Chem., in press. (published on-line November 2012).  JIF 2.906 1/57
• Cai B, Siminszky B, Chappell J, Dewey RE, Bush LP. (2012) Enantioselective demethylation of nicotine as a mechanism for variable nornicotine composition in tobacco leaf.  J. Biol. Chem., in press (published online Oct. 25, 2012). 4.651 62/290
• Harris DM, Corbin K, Wang T, Gutierrez R, Bertolo AL, Petti C, Smilgies DM, Estevez JM, Bonetta D, Urbanowicz BR, Ehrhardt DW, Somerville CR, Rose JK, Hong M, Debolt S. (2012) Cellulose microfibril crystallinity is reduced by mutating C-terminal transmembrane region residues CESA1A903V and CESA3T942I of cellulose synthase. Proc Natl Acad Sci U S A. 109: 4098-103
• Jamboonsri,W, Phillips TD, Geneve RL, Cahill JP, Hildebrand DF. (2012) Extending the range of an ancient crop; a new ω3 source. Genetic Resources and Crop Evolution 59: 171-178.
• Kong Q, Pattanaik S, Feller A, Werkman JR, Chai C, Wang Y, Grotewold E, Yuan L. Regulatory switch enforced by basic helix-loop-helix and ACT-domain mediated dimerizations of the maize transcription factor R. (2012) Proc Natl Acad Sci U S A. 109: E2091-7.
• Li R, Yu K, Wu Y, Tateno M, Hatanaka T, Hildebrand DF. (2012) Vernonia DGATs can complement the disrupted oil and protein metabolism in epoxygenase-expressing soybean seeds. Metab Eng. 14:29-38.
• Niehaus TD, Kinison S, Okada S, Yeo YS, Bell SA, Cui P, Devarenne TP, Chappell J. (2012) Functional identification of triterpene methyltransferases from Botryococcus braunii race B. J Biol Chem. 287: 8163-73.
• Thomas PE, Wu X, Liu M, Gaffney B, Ji G, Li QQ, Hunt AG. (2012) Genome-wide control of poly(A) site choice by CPSF30 in Arabidopsis. Plant Cell 24, 4376-4388.
• Wang D, Yang S, Tang F, Zhu H. Symbiosis specificity in the legume: rhizobial mutualism. (2012) Cell Microbiol. 14: 334-42.

Papers published in 2011

• Bai Y, Pattanaik S, Patra B, Werkman JR, Xie CH, Yuan L. (2011). Flavonoid-related basic helix-loop-helix regulators, NtAn1a and NtAn1b, of tobacco have originated from two ancestors and are functionally active. Planta 234: 363-375.
• 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, 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.
• 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.
• 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.

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