Faculty Publications

• O’Neal L, Mukherjee T, Alexandre G. (2018) “Analyzing Chemotaxis and Related Behaviors of Azospirillum Brasilense.” Curr Protoc Microbiol. 48:3E.3.1-3E.3.11.
• Liu W, Sun Y, Shen R, Dang X, Liu X, Sui F, Li Y, Zhang Z, Alexandre G, Elmerich C, Xie Z. (2018) “A Chemotaxis-Like Pathway of Azorhizobium caulinodans Controls Flagella-Driven Motility, Which Regulates Biofilm Formation, Exopolysaccharide Biosynthesis, and Competitive Nodulation.” Mol Plant Microbe Interact. 31(7):737-749.
• Alexandre G. (2017) “Azospirillum brasilense, a Beneficial Soil Bacterium: Isolation and Cultivation.” Curr Protoc Microbiol. 47:3E.1.1-3E.1.10.
• Gullett J, O’Neal L, Mukherjee T, Alexandre G. (2017) “Azospirillum brasilense: Laboratory Maintenance and Genetic Manipulation.” Curr Protoc Microbiol. 47:3E.2.1-3E.2.17.
• Ryu MH, Fomicheva A, O’Neal L, Alexandre G, Gomelsky M. (2017) “Using Light-Activated Enzymes for Modulating Intracellular c-di-GMP Levels in Bacteria.” Methods Mol Biol. 1657:169-186.
• O’Neal L, Ryu MH, Gomelsky M, Alexandre G. (2017) “Optogenetic Manipulation of Cyclic Di-GMP (c-di-GMP) Levels Reveals the Role of c-di-GMP in Regulating Aerotaxis Receptor Activity in Azospirillum brasilense.” J Bacteriol. 199(18).
• Avasthi P, Soragni A, Bembenek JN. (2018) “Journal clubs in the time of preprints.” Elife. 7. pii: e38532.
• Melesse M, Bembenek JN, Zhulin IB. (2018) “Conservation of the separase regulatory domain.” Biol Direct. 13(1):7.
• Bembenek JN, Meshik X, Tsarouhas V. (2017) “Meeting report – Cellular dynamics: membrane-cytoskeleton interface.” J Cell Sci. 130(17):2775-2779.
• Melesse M, Sloan DE, Benthal JT, Caylor Q, Gosine K, Bai X, Bembenek JN. (2018) “Genetic Identification of Separase Regulators in Caenorhabditis elegans.” G3 (Bethesda). 8(2):695-705.
• Bai X, Bembenek JN. (2017) “Protease dead separase inhibits chromosome segregation and RAB-11 vesicle trafficking.” Cell Cycle. 16(20):1902-1917.
• Bai X, Bembenek JN. (2018) “Orchestrating early embryonic divisions.” Mol Reprod Dev. 85(2):86.
• Bakshi A, Binder BM (2018) “Plant Ethylene Sensing & Signaling. IN: Gas Sensing in Cells. Metallobiology series.” The Royal Society of Chemistry (S. Aono, ed.) ISBN 978-1-78262-895-8
• Binder BM, Kim HJ, Mathews DE, Hutchison CE, Kieber JJ, Schaller GE (2018) A role for two-component signaling elements in the growth recovery response to ethylene of Arabidopsis. Plant Direct 2:1-9.
• Lacey RF, Allen CJ, Bakshi, A, Binder BM (2018) “Ethylene Causes Transcriptomic Changes in Synechocystis During Phototaxis.” Plant Direct 2: 1-16.
• Harkey AF, Watkins JR, Olex AL, DiNapoli KT, Lewis DR, Fetrow JS, Binder BM, Muday GK. (2018) “Identification of transcriptional and receptor networks that control root responses to ethylene.” Plant Physiology 176: 2095-2118.
• Bakshi A, Piya S, Fernandez JC, Chervin C, Hewezi T, Binder BM (2018) “Ethylene receptors signal via a non-canonical pathway to regulate abscisic acid responses.” Plant Physiology 176: 910-929.
• Henry ML, Charton M, Alignan M, Maury P, Luniov A, Pelletier, Pontalier P-Y, Binder BM, Vaca-Garcia C, Chervin C. (2017) “Ethylene stimulates growth and affects fatty acid content of Synechocystis sp. PCC 6803”, Algal Research 26: 234-239.
• Shelaev IV, Mamedov MD, Gostev FE, Aybush AV, Li M, Nguyen J, Bruce BD, Nadtochenko VA. (2018) “Comparisons of Electron Transfer Reactions in a Cyanobacterial Tetrameric and Trimeric Photosystem I Complexes.” Photochem Photobiol. 94(3):564-569.
• Kapoor K, Cashman DJ, Nientimp L, Bruce BD, Baudry J. J (2018) “Binding Mechanisms of Electron Transport Proteins with Cyanobacterial Photosystem I: An Integrated Computational and Experimental Model.” Phys Chem B. 122(3):1026-1036.
• Brunkard JO, Burch-Smith TM. (2018) “Ties that bind: the integration of plastid signalling pathways in plant cell metabolism.” Essays Biochem. 62(1):95-107.
• Hewezi T, Pantalone V, Bennett M, Neal Stewart C Jr, Burch-Smith TM. (2018) “Phytopathogen-induced changes to plant methylomes.” Plant Cell Rep. 37(1):17-23.
• Fernandez EJ. (2018) “Allosteric pathways in nuclear receptors – Potential targets for drug design.” Pharmacol Ther. 183:152-159.
• Xie M, Muchero W, Bryan AC, Yee K, Guo HB, Zhang J, Tschaplinski TJ, Singan VR, Lindquist E, Payyavula RS, Barros-Rios J, Dixon R, Engle N, Sykes RW, Davis M, Jawdy SS, Gunter LE, Thompson O, DiFazio SP, Evans LM, Winkeler K, Collins C, Schmutz J, Guo H, Kalluri U, Rodriguez M, Feng K, Chen JG, Tuskan GA. (2018) “A 5-Enolpyruvylshikimate 3-Phosphate Synthase Functions as a Transcriptional Repressor in Populus.” Plant Cell. 30(7):1645-1660.
• Guo HB, Ma Y, Tuskan GA, Yang X, Guo H. (2018) “Classification of Complete Proteomes of Different Organisms and Protein Sets Based on Their Protein Distributions in Terms of Some Key Attributes of Proteins.” Int J Genomics. v2018 ID 9784161.
• Xiong W, Fu J, Köllner TG, Chen X, Jia Q, Guo H, Qian P, Guo H, Wu G, Chen F. (2018) “Biochemical characterization of microbial type terpene synthases in two closely related species of hornworts, Anthoceros punctatus and Anthoceros agrestis.” 149:116-122.
• Yue Y, Ma Y, Qian P, Guo H. (2018) “Catalytic Mechanism of the Ubiquitin-Like NEDD8 Transfer in RING E3-E2∼NEDD8-Target Complex from QM/MM Free Energy Simulations.” Chem Inf Model. 58(2):422-429.
• Yang X, Hu R, Yin H, Jenkins J, Shu S, Tang H, Liu D, Weighill DA, Cheol Yim W, Ha J, Heyduk K, Goodstein DM, Guo HB, Moseley RC, Fitzek E, Jawdy S, Zhang Z, Xie M, Hartwell J, Grimwood J, Abraham PE, Mewalal R, Beltrán JD, Boxall SF, Dever LV, Palla KJ, Albion R, Garcia T, Mayer JA, Don Lim S, Man Wai C, Peluso P, Van Buren R, De Paoli HC, Borland AM, Guo H, Chen JG, Muchero W, Yin Y, Jacobson DA, Tschaplinski TJ, Hettich RL, Ming R, Winter K, Leebens-Mack JH, Smith JAC, Cushman JC, Schmutz J, Tuskan GA. (2017) “The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism.” Nat Commun. 8(1):1899.
• Temimi AHKA, Reddy YV, White PB, Guo H, Qian P, Mecinović J. “Lysine Possesses the Optimal Chain Length for Histone Lysine Methyltransferase Catalysis.” Sci Rep. 7(1):16148.
• Nambiar D, Berhane TK, Shew R, Schwarz B, Duff MR Jr, Howell EE. (2018) “In vivo Titration of Folate Pathway Enzymes.” Appl Environ Microbiol. pii: AEM.01139-18.
• Duff MR Jr, Borreguero JM, Cuneo MJ, Ramanathan A, He J, Kamath G, Chennubhotla SC, Meilleur F, Howell EE, Herwig KW, Myles DAA, Agarwal PK. (2018) “Modulating Enzyme Activity by Altering Protein Dynamics with Solvent.” Biochemistry. 57(29):4263-4275.
• Bhojane PP, Duff MR Jr, Bafna K, Agarwal P, Stanley C, Howell EE. (2017) “Small Angle Neutron Scattering Studies of R67 Dihydrofolate Reductase, a Tetrameric Protein with Intrinsically Disordered N-Termini.” Biochemistry. 56(44):5886-5899.
• Gabel SA, Duff MR, Pedersen LC, DeRose EF, Krahn JM, Howell EE, London RE. (2017) “A Structural Basis for Biguanide Activity.” Biochemistry. 56(36):4786-4798.
• Halalipour A, Duff MR Jr, Howell EE, Reyes-De-Corcuera JI. (2017) “Effects of high hydrostatic pressure or hydrophobic modification on thermal stability of xanthine oxidase.” Enzyme Microb Technol. 103:18-24.
• Dockendorff TC, Labrador M. (2018) “The Fragile X Protein and Genome Function.” Mol Neurobiol. pp1-11
• Lindsay RJ, Pham B, Shen T, McCord RP. (2018) “Characterizing the 3D structure and dynamics of chromosomes and proteins in a common contact matrix framework.” Nucleic Acids Res. gky604
• McCord RP, Balajee A. (2018) “3D Genome Organization Influences the Chromosome Translocation Pattern.” Adv Exp Med Biol. 1044:113-133.
• Balajee AS, Sanders JT, Golloshi R, Shuryak I, McCord RP, Dainiak N. (2018) “Investigation of Spatial Organization of Chromosome Territories in Chromosome Exchange Aberrations After Ionizing Radiation Exposure.” Health Phys. 115(1):77-89.
• Golloshi R, Sanders JT, McCord RP. (2018) “Iteratively improving Hi-C experiments one step at a time.” Methods. 142:47-58.
• McCord RP. (2017) “Chromosome biology: How to build a cohesive genome in 3D.” Nature. 551(7678):38-40.
• Golloshi R, Sanders JT, McCord RP. (2017) “Genome organization during the cell cycle: unity in division.” Wiley Interdiscip Rev Syst Biol Med. 9(5).
• Chen X, Chen H, Yuan JS, Köllner TG, Chen Y, Guo Y, Zhuang X, Chen X, Zhang YJ, Fu J, Nebenführ A, Guo Z, Chen F. (2018) “The rice terpene synthase gene OsTPS19 functions as an (S)-limonene synthase in planta, and its overexpression leads to enhanced resistance to the blast fungus Magnaporthe oryzae.” Plant Biotechnol J. 16:1778-1787.
• Nebenführ A, Dixit R. (2018) “Kinesins and Myosins: Molecular Motors that Coordinate Cellular Functions in Plants.” Annu Rev Plant Biol. 69:329-361.
• Ryan JM, Nebenführ A. (2018) “Update on Myosin Motors: Molecular Mechanisms and Physiological Functions.” Plant Physiol. 176(1):119-127.
• Aufrecht JA, Ryan JM, Hasim S, Allison DP, Nebenführ A, Doktycz MJ, Retterer ST. (2017) “Imaging the Root Hair Morphology of Arabidopsis Seedlings in a Two-layer Microfluidic Platform.” J Vis Exp. (126).
• Lee G, Kim J, Kim Y, Yoo S, Park JH. (2018) “Identifying and monitoring neurons that undergo metamorphosis-regulated cell death (metamorphoptosis) by a neuron-specific caspase sensor (Casor) in Drosophila melanogaster.” Apoptosis. 23(1):41-53.
• Yaw AM, Woodruff RW, Prosser RA, Glass JD. (2018) “Paternal Cocaine Disrupts Offspring Circadian Clock Function in a Sex-Dependent Manner in Mice.” Neuroscience. 379:257-268.
• Krizo JA, Moreland LE, Rastogi A, Mou X, Prosser RA, Mintz EM. (2018) “Regulation of Locomotor activity in fed, fasted, and food-restricted mice lacking tissue-type plasminogen activator.” BMC Physiol. 18(1):2.
• Lindsay JH, Prosser RA. (2018) “The Mammalian Circadian Clock Exhibits Chronic Ethanol Tolerance and Withdrawal-Induced Glutamate Hypersensitivity, Accompanied by Changes in Glutamate and TrkB Receptor Proteins.” Alcohol Clin Exp Res. 42(2):315-328. d
• Kryvoruchko IS, Routray P, Sinharoy S, Torres-Jerez I, Tejada-Jiménez M, Finney LA, Nakashima J, Pislariu CI, Benedito VA, González-Guerrero M, Roberts DM, Udvardi MK. (2018) “An Iron-Activated Citrate Transporter, MtMATE67, Is Required for Symbiotic Nitrogen Fixation.” Plant Physiol. 176(3):2315-2329.
• Kumar P, Serpersu EH, Cuneo MJ. (2018) “A low-barrier hydrogen bond mediates antibiotic resistance in a noncanonical catalytic triad.” Sci Adv. 4(4):eaas8667
• Johnson QR, Lindsay RJ, Shen T. J (2018) “CAMERRA: An analysis tool for the computation of conformational dynamics by evaluating residue-residue associations.” Comput Chem. 39(20):1568-1578.
• Lindsay RJ, Siess J, Lohry DP, McGee TS, Ritchie JS, Johnson QR, Shen T. J. (2018) “Characterizing protein conformations by correlation analysis of coarse-grained contact matrices.” Chem Phys. 148(2):025101.
• Lindsay RJ, Siess J, Lohry DP, McGee TS, Ritchie JS, Johnson QR, Shen T. J (2018) “Characterizing protein conformations by correlation analysis of coarse-grained contact matrices.” Chem Phys. 148(2):025101.
• Chirico G, Gansen A, Leuba SH, Olins AL, Olins DE, Smith JC, Tóth K. (2018) “Jörg Langowski: his scientific legacy and the future it promises.” BMC Biophys. 11:5.
• Pi M, Kapoor K, Ye R, Hwang DJ, Miller DD, Smith JC, Baudry J, Quarles LD. (2018) “Computationally identified novel agonists for GPRC6A.” PLoS One. 13(4):e0195980.
• Amaro RE, Baudry J, Chodera J, Demir Ö, McCammon JA, Miao Y, Smith JC. (2018) “Ensemble Docking in Drug Discovery.” Biophys J. 114(10):2271-2278.
• Smith JC, Tan P, Petridis L, Hong L. (2018) “Dynamic Neutron Scattering by Biological Systems.” Annu Rev Biophys. 47:335-354.
• Pi M, Kapoor K, Ye R, Smith JC, Baudry J, Quarles LD. (2018) “GPCR6A Is a Molecular Target for the Natural Products Gallate and EGCG in Green Tea.” Mol Nutr Food Res. 62(8):e1700770.
• Xiao Z, Baudry J, Cao L, Huang J, Chen H, Yates CR, Li W, Dong B, Waters CM, Smith JC, Quarles LD. (2018) “Polycystin-1 interacts with TAZ to stimulate osteoblastogenesis and inhibit adipogenesis.” J Clin Invest. 128(1):157-174.
• Smith MD, Cheng X, Petridis L, Mostofian B, Smith JC. (2017) “Organosolv-Water Cosolvent Phase Separation on Cellulose and its Influence on the Physical Deconstruction of Cellulose: A Molecular Dynamics Analysis.” Sci Rep. 7(1):14494.
• Velazquez HA, Riccardi D, Xiao Z, Quarles LD, Yates CR, Baudry J, Smith JC. (2018) “Ensemble docking to difficult targets in early-stage drug discovery: Methodology and application to fibroblast growth factor 23.” Chem Biol Drug Des. 91(2):491-504.
• O’Neill H, Pingali SV, Petridis L, He J, Mamontov E, Hong L, Urban V, Evans B, Langan P, Smith JC, Davison BH (2017) “Dynamics of water bound to crystalline cellulose.” Sci Rep. 7(1):11840.
• Zhou J, Smith MD, Cooper SJ, Cheng X, Smith JC, Parks JM. (2017) “Modeling of the Passive Permeation of Mercury and Methylmercury Complexes Through a Bacterial Cytoplasmic Membrane.” Environ Sci Technol. 51(18):10595-10604.
• Bondar AN, Smith JC. (2017) “Protonation-state-Coupled Conformational Dynamics in Reaction Mechanisms of Channel and Pump Rhodopsins.” Photochem Photobiol. 93(6):1336-1344.
• Enganti R, Cho SK, Toperzer JD, Urquidi-Camacho RA, Cakir OS, Ray AP, Abraham PE, Hettich RL, von Arnim AG. (2018) “Phosphorylation of Ribosomal Protein RPS6 Integrates Light Signals and Circadian Clock Signals.” Front Plant Sci. 8:2210.