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RECENT PUBLICATIONS BY GST STUDENTS

  • Jia Q, Li G, Köllner TG, Fu J, Chen X, Xiong W, Crandall-Stotler BJ, Bowman JL, Weston DJ, Zhang Y, Chen L, Xie Y, Li FW, Rothfels CJ, Larsson A, Graham SW, Stevenson DW, Wong GK, Gershenzon J, Chen F. (2016) Microbial-type terpene synthase genes occur widely in nonseed land plants, but not in seed plants. Proc Natl Acad Sci USA.  113:12328-12333.
  • Chen X, Köllner TG, Jia Q, Norris A, Santhanam B, Rabe P, Dickschat JS, Shaulsky G, Gershenzon J, Chen F. (2016) Terpene synthase genes in eukaryotes beyond plants and fungi: Occurrence in social amoebae. Proc Natl Acad Sci USA.113:12132-12137.
  • Smolensky D, Rathore K, Cekanova M. (2016) Molecular targets in urothelial cancer: detection, treatment, and animal models of bladder cancer. Drug Des Devel Ther. 10:3305-3322. Review.
  • Smolensky D, Rathore K, Bourn J, Cekanova M. (2016) Inhibition of the PI3K/AKT Pathway Sensitizes Oral Squamous Cell Carcinoma Cells to Anthracycline-Based Chemotherapy In Vitro. J Cell Biochem. [Epub ahead of print] .
  • Evangelista W, Weir RL, Ellingson SR, Harris JB, Kapoor K, Smith JC, Baudry J. (2016) Ensemble-based docking: From hit discovery to metabolism and toxicity predictions. Bioorg Med Chem. 24:4928-4935.
  • Hu X, Hong L, Smith MD, Neusius T, Cheng X, Smith JC (2016) The dynamics of single protein molecules is non-equilibrium and self-similar over thirteen decades in time. Nature Physics 12: 171–174.
  • Manga P, Klingeman DM, Lu TY, Mehlhorn TL, Pelletier DA, Hauser LJ, Wilson CM, Brown SD (2016) Replicates, Read Numbers, and Other Important Experimental Design Considerations for Microbial RNA-seq Identified Using Bacillus thuringiensis Datasets. Front Microbiol. 7:794
  • Qian C, Johs A, Chen H, Mann BF, Lu X, Abraham PE, Hettich RL, Gu B. (2016) Global Proteome Response to Deletion of Genes Related to Mercury Methylation and Dissimilatory Metal Reduction Reveals Changes in Respiratory Metabolism in Geobacter sulfurreducens PCA. J Proteome Res [Epub ahead of print]
  • Jia Q, Chen F. (2016) Catalytic Functions of the Isoprenyl Diphosphate Synthase Superfamily in Plants: A Growing Repertoire. Mol Plant 9:189-91.
  • Lindsay RJ, Johnson QR, Evangelista W, Nellas RB, Shen T. (2016) DMSO enhanced conformational switch of an interfacial enzyme. Biopolymers [Epub ahead of print]
  • Utturkar SM, Cude WN, Robeson MS 2nd, Yang ZK, Klingeman DM, Land ML, Allman SL, Lu TS, Brown SD, Schadt CW, Podar M, Doktycz MJ, Pelletier DA. (2016) Enrichment of root endophytic bacteria from Populus deltoides and single-cell genomics analysis. Appl Environ Microbiol [Epub ahead of print].
  • Wurch L, Giannone, RJ, Belisle BS, Swift C, Utturkar S, Hettich RL, Reysenbach AL, Podar M. (2016) Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment. Nat Commun 7:12115.
  • Upadhyay AA, Fleetwood AD, Adebali O, Finn RD, Zhulin IB. (2016) Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes. PLoS Comput Biol 12:e1004862.
  • Adebali O, Reznik AO, Ory DS, Zhulin IB. (2016) Establishing the precise evolutionary history of a gene improves prediction of disease-causing missense mutations. Genet Med [Epub ahead of print].
  • Johnson QR, Lindsay RJ, Nellas RB, Shen T. (2016) Pressure-induced con-formational switch of an interfacial protein. Proteins 84:820-7.
  • Kapoor K, McGill N, Peterson CB, Meyers HV, Blackburn MN, Baudry J. (2016) Discovery of Novel Nonactive Site Inhibitors of the Prothrombinase Enzyme Complex. J Chem Inf Model 56:535-47.
  • Smith MD, Mostofian B, Petridis L, Cheng X, Smith JC. (2016) Molecular Driving Forces behind the Tetrahydrofuran-Water Miscibility Gap. J Phys Chem B 120:740-7.
  • Missra A, Ernest B, Lohoff T, Jia Q, Satterlee J, Ke K, von Arnim AG.(2015) The Circadian Clock Modulates Global Daily Cycles of mRNA Ribosome Loading. Plant Cell 27:2582-99.
  • Bakshi A, Wilson RL, Lacey RF, Kim H, Wuppalapati SK, Binder BM. (2015) Identification of Regions in the Receiver Domain of the ETHYLENE RESPONSE1 Ethylene Receptor of Arabidopsis Important for Functional Divergence. Plant Physiol 169:219-32.
  • Chotewutmontri P, Bruce BD. (2015) Non-native, N-terminal Hsp70 mo-lecular motor recognition elements in transit peptides support plastid protein translocation. J Biol Chem 290:7602-21.
  • Smolensky D, Rathore K, Cekanova M. (2015) Phosphatidylinositol- 3-kinase inhibitor induces chemosensitivity to a novel derivative of doxorubicin, AD198 chemotherapyin human bladder cancer cells in vitro. BMC Cancer 15:927.
  • Ellingson SR, Miao Y, Baudry J, Smith JC. (2015) Multi-conformer ensemble docking to difficult protein targets. J Phys Chem B 119:1026-34.
  • Lane TS, Rempe CS, (…),Stewart CN Jr. (2016) Diversity of ABC transporter genes across the plant kingdom and their potential utility in biotechnology. BMC Biotechnol 16:47.
  • Abraham PE, Wang X, Ranjan P, Nookaew I, Zhang B, Tuskan GA, Hettich RL. (2015) Integrating mRNA and Protein Sequencing Enables the Detection and Quantitative Profiling of Natural Protein Sequence Variants of Populus trichocarpa. J Proteome Res 14:5318-26.
  • Xiong W, Abraham PE, Li Z, Pan C, Hettich RL. (2015) Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota. Proteomics 15:3424-38.
  • Johnson QR, Lindsay RJ, Petridis L, Shen T. (2015) Investigation of Carbohydrate Recognition via Computer Simulation. Molecules 20:7700-18.
  • Adebali O, Ortega DR, Zhulin IB (2015) CDvist: a webserver for identification and visualization of conserved domains in protein sequences. Bioinformatics 31: 1475-1477.
  • Berthelier V, Harris JB, Estenson KN, Baudry J (2015) Discovery of an inhibitor of Z-alpha1 antitrypsin polymerization. PLoS One 10: e0126256.
  • Hultman J,Shah MB, Verberkmoes NV, Lee LH, Mavrommatis K, Jansson JK (2015) Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes. Nature 521: 208-212.
  • Johnson QR, Lindsay RJ, Nellas RB, Fernandez EJ, Shen T (2015) Mapping allostery through computational glycine scanning and correlation analysis of residue-residue contacts. Biochemistry 54: 1534-1541.
  • Pluchino LA, Liu AK, Wang HC (2015) Reactive oxygen species-mediated breast cell carcinogenesis enhanced by multiple carcinogens and intervened by dietary ergosterol and mimosine. Free Radic Biol Med 80: 12-26.
  • Rempe CS, Burris KP, Woo HL, Goodrich B, Gosnell DK, Tschaplinski TJ, Stewart CN (2015) Computational Ranking of Yerba Mate Small Molecules Based on Their Predicted Contribution to Antibacterial Activity against Methicillin-Resistant Staphylococcus aureus. PLoS One 10: e0123925.
  • Utturkar SM, Klingeman DM, Bruno-Barcena JM, Chinn MS, Grunden AM, Kopke M, Brown SD (2015) Sequence data for Clostridium autoethanogenum using three generations of sequencing technologies. Sci Data 2: 150014.
  • Xiong W, Giannone RJ, Morowitz MJ, Banfield JF, Hettich RL (2015) Development of an enhanced metaproteomic approach for deepening the microbiome characterization of the human infant gut. J Proteome Res 14: 133-141.
  • Iyer S, Doktycz MJ (2014) Thrombin-mediated transcriptional regulation using DNA aptamers in DNA-based cell-free protein synthesis. ACS Synth Biol 3: 340-346.
  • Johnson QR, Lindsay RJ, Raval SR, Shen T, et al (2014) Effects of branched O-glycosylation on a semiflexible peptide linker. J Phys Chem B 118: 2050-2057.
  • Kelemen RK, He GF, Woo HL, Lane T, Rempe C, Ganusov VV, Berry MW (2014) Classification of T cell movement tracks all ows for prediction of cell function. Int J Comput Biol Drug Des 7: 113-129.
  • Li Z, Wang Y, Yao Q, Justice NB, Ahn TH, Xu D, Hettich RL, Banfield JF, Pan C (2014) Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community. Nat Commun 5: 4405.
  • Mostofian B, Cheng X, Smith JC (2014) Replica-exchange molecular dynamics simulations of cellulose solvated in water and in the ionic liquid 1-butyl-3-methylimidazolium chloride. J Phys Chem B 118: 11037-11049.
  • Pluchino LA, Wang HC (2014) Chronic exposure to combined carcinogens enhances breast cell carcinogenesis with mesenchymal and stem-like cell properties. PLoS One 9: e108698.
  • Zhou J, Riccardi D, Beste A, Smith JC, Parks JM (2014) Mercury methylation by HgcA: theory supports carbanion transfer to Hg(II). Inorg Chem 53: 772-777.

SELECTED PUBLICATIONS

  • Campbell AG, Campbell JH, Schwientek P, Woyke T, Sczyrba A, Allman S, Beall CJ, Griffen A, Leys E, Podar M. (2013). Multiple single-cell genomes provide insight into functions of uncultured deltaproteobacteria in the human oral cavity. PLoS One. 2013;8(3):e59361.
  • Glass DC, Krishnan M, Smith JC, Baudry J. (2013). Three entropic classes of side chain in a globular protein. J Phys Chem B. 117:3127-34.
  • McClintock CS, Hettich RL. (2013). Experimental approach to controllably vary protein oxidation while minimizing electrode adsorption for boron-doped diamond electrochemical surface mapping applications. Anal Chem. 85(1):213-9.
  • Rathore K, Wang HC. (2013). Mesenchymal and stem-like cell properties targeted in suppression of chronically-induced breast cell carcinogenesis. Cancer Lett. 2013 Jun 1;333(1):113-23.
  • Campbell JH, O’Donoghue P, Campbell AG, Schwientek P, Sczyrba A, Woyke T, Söll D, Podar M. (2013). UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. Proc Natl Acad Sci U S A. 110(14):5540-5.
  • Hong, L., Glass, D.C., Nickels, J.D., Perticaroli, S., Yi, Z., Madhusudan, T., O’Neill, H., (…), Smith, J.C. 2013. Elastic and conformational softness of a globular protein. Physical Review Letters 110: 028104.
  • Lee G, Sehgal R, Wang Z, Nair S, Kikuno K, Chen CH, Hay B, Park JH. (2013). Essential role of grimled programmed cell death for the establishment of corazonin-producing peptidergic nervous system during embryogenesis and metamorphosis in Drosophila melanogaster. Biol Open. 2(3):283-94.
  • Logan RW, Robledo RF, Recla JM, Philip VM, Bubier JA, Jay JJ, Harwood C, Wilcox T, Gatti DM, Bult CJ, Churchill GA, Chesler EJ. (2013). High-precision genetic mapping of behavioral traits in the diversity outbred mouse population. Genes Brain Behav. 2013 Feb 21.
  • Abraham P, Adams R, Giannone RJ, Kalluri U, Ranjan P, Erickson B, Shah M, Tuskan GA, Hettich RL. (2012). Defining the boundaries and characterizing the landscape of functional genome expression in vascular tissues of Populus using shotgun proteomics. J Proteome Res. 11(1):449-60.
  • Close DM, Xu T, Smartt A, Rogers A, Crossley R, Price S, Ripp S, Sayler G. (2012). The evolution of the bacterial luciferase gene cassette (lux) as a real-time bioreporter. Sensors 12(1):732-52.
  • Close DM, Xu T, Sayler GS, Ripp S. (2012). In vivo bioluminescent imaging (BLI): noninvasive visualization and interrogation of biological processes in living animals. Sensors 11:180-206.
  • Erickson AR, Cantarel BL, Lamendella R, Darzi Y, Mongodin EF, Pan C, Shah M, Halfvarson J, Tysk C, Henrissat B, Raes J, Verberkmoes NC, Fraser CM, Hettich RL, Jansson JK. (2012). Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn’s disease. PLoS One. 7(11):e49138.
  • Fletcher SJ, Kalupahana NS, Soltani-Bejnood M, Kim JH, Saxton AM, Wasserman DH, De Taeye B, Voy BH, Quignard-Boulange A, Moustaid-Moussa N. (2012). Transgenic mice overexpressing Renin exhibit glucose intolerance and diet-genotype interactions. Front Endocrinol 3:166.
  • Glass, D.C., Moritsugu, K., Cheng, X., Smith, J.C. 2012. REACH coarse-grained simulation of a cellulose fiber. Biomacromolecules 13: 2634-2644
  • Gobena D, Roig J, Galmarini C, Hulvey J, Lamour K. (2012). Genetic diversity of Phytophthora capsici isolates from pepper and pumpkin in Argentina. Mycologia. 104:102-7.
  • Lindner, B., Smith, J.C. (2012). Computer Physics Communications vol:pp-pp.
  • Rathore K, Choudhary S, Odoi A, Wang HC. (2012). Green tea catechin intervention of reactive oxygen species-mediated ERK pathway activation and chronically induced breast cell carcinogenesis. Carcinogenesis. 33(1):174-83.
  • Rathore K, Wang HC. (2012). Green tea catechin extract in intervention of chronic breast cell carcinogenesis induced by environmental carcinogens. Mol Carcinog. 51(3):280-9.
  • Sarode N, Miracle B, Peng X, Ryan O, Reynolds TB. (2012). Vacuolar protein sorting genes regulate mat formation in Saccharomyces cerevisiae by Flo11p-dependent and -independent mechanisms. PLoS One. 7(5):e38077.
  • Siuti P, Retterer ST, Choi CK, Doktycz MJ. (2012). Enzyme reactions in nanoporous, picoliter volume containers. Anal Chem. 84:1092-7.
  • Young JC, Dill BD, Pan C, Hettich RL, Banfield JF, Shah M, Fremaux C, Horvath P, Barrangou R, Verberkmoes NC. (2012). Phage-induced expression of CRISPR-associated proteins is revealed by shotgun proteomics in Streptococcus thermophiles.
  • Campbell JH, Foster CM, Vishnivetskaya T, Campbell AG, Yang ZK, Wymore A, Palumbo AV, Chesler EJ, Podar M. (2012). Host genetic and environmental effects on mouse intestinal microbiota. ISME J. 6(11):2033-44.
  • Hong, L., Cheng, X., Glass, D.C., Smith, J.C. (2012). Surface hydration amplifies single-well protein atom diffusion propagating into the macromolecular core. Physical Review Letters 108: 238102.
  • Lamour KH, Mudge J, Gobena D, Hurtado-Gonzales OP, Schmutz J, Kuo A, Miller NA, Rice BJ, Raffaele S, Cano LM, Bharti AK, Donahoo RS, Finley S, Huitema E, Hulvey J, Platt D, Salamov A, Savidor A, Sharma R, Stam R, Storey D, Thines M, Win J, Haas BJ, Dinwiddie DL, Jenkins J, Knight JR, Affourtit JP, Han CS, Chertkov O, Lindquist EA, Detter C, Grigoriev IV, Kamoun S, Kingsmore SF. (2012). Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici. Mol Plant Microbe Interact. 25(10):1350-60.
  • Miao Y, Yi Z, Cantrell C, Glass DC, Baudry J, Jain N, Smith JC. (2012). Coupled flexibility change in cytochrome P450cam substrate binding determined by neutron scattering, NMR, and molecular dynamics simulation. Biophys J. 103(10):2167-76.
  • Miao Y, Yi Z, Glass DC, Hong L, Tyagi M, Baudry J, Jain N, Smith JC. (2012). Temperature-dependent dynamical transitions of different classes of amino acid residue in a globular protein. J Am Chem Soc. 134(48):19576-9.
  • Siriwardhana N, Kalupahana NS, Fletcher S, Xin W, Claycombe KJ, Quignard-Boulange A, Zhao L, Saxton AM, Moustaid-Moussa N. (2012). n-3 and n-6 polyunsaturated fatty acids differentially regulate adipose angiotensinogen and other inflammatory adipokines in part via NF-?Bdependent mechanisms. J Nutr Biochem. 23(12):1661-7.
  • Parsons MJ, Grimm C, Paya-Cano JL, Fernandes C, Liu L, Philip VM, Chesler EJ, Nietfeld W, Lehrach H, Schalkwyk LC. (2012). Genetic variation in hippocampal microRNA expression differences in C57BL/6 J X DBA/2 J (BXD) recombinant inbred mouse strains. BMC Genomics 13:476.
  • Thaisz J, Tsaih SW, Feng M, Philip VM, Zhang Y, Yanas L, Sheehan S, Xu L, Miller DR, Paigen B, Chesler EJ, Churchill GA, Dipetrillo K. (2012). Genetic analysis of albuminuria in collaborative cross and multiple mouse intercross populations. Am J Physiol Renal Physiol. 303(7):F972-81.
  • Wallace IS, Shakesby AJ, Hwang JH, Choi WG, Martínková N, Douglas AE, Roberts DM. (2012). Acyrthosiphon pisum AQP2: a multifunctional insect aquaglyceroporin. Biochim Biophys Acta. 1818(3):627-35.
  • Wheeler KE, Erickson BK, Mueller R, Singer SW, Verberkmoes NC, Hwang M, Thelen MP, Hettich RL. (2012). Metal affinity enrichment increases the range and depth of proteome identification for extracellular microbial proteins. J Proteome Res. 11(2):861-70.
  • Close DM, Hahn RE, Patterson SS, Baek SJ, Ripp SA, Sayler GS. (2011). Comparison of human optimized bacterial luciferase, firefly luciferase, and green fluorescent protein for continuous imaging of cell culture and animal models. J Biomed Opt. 16(4):047003.
  • Edwards, A.N., Siuti, P., Bible, A.N., Alexandre, G., Retterer, S.T., Doktycz, M.J., and Morrell-Falvey, J.L. Characterization of cell surface and extracellular matrix remodeling of Azospirillum brasilense chemotaxis-like 1 signal transduction pathway mutants by atomic force microscopy. (2011). FEMS Microbiol Lett 314, 131-139.
  • Philip VM, Sokoloff G, Ackert-Bicknell CL, Striz M, Branstetter L, Beckmann MA, Spence JS, Jackson BL, Galloway LD, Barker P, Wymore AM, Hunsicker PR, Durtschi DC, Shaw GS, Shinpock S, Manly KF, Miller DR, Donohue KD, Culiat CT, Churchill GA, Lariviere WR, Palmer AA, O’Hara BF, Voy BH, Chesler EJ. (2011). Genetic analysis in the Collaborative Cross breeding population. Genome Res. 21:1223-38.
  • Siuti P, Green C, Edwards AN, Doktycz MJ, Alexandre G. (2011). The chemotaxis-like Che1 pathway has an indirect role in adhesive cell properties of Azospirillum brasilense. FEMS Microbiol Lett. 323:105-12.
  • Siuti P, Retterer ST, Doktycz MJ. (2011). Continuous protein production in nanoporous, picolitre volume containers. Lab Chip. 11:3523-9.
  • Choudhary, S., Rathore, K., Wang, H.C. (2011). Differential induction of reactive oxygen species through Erk1/2 and Nox-1 by FK228 for selective apoptosis of oncogenic H-Ras-expressing human urinary bladder cancer J82 cells. J Cancer Res Clin Oncol. 137, 471-80.
  • Collignon, B., Schulz, R., Smith, J.C., and Baudry, J. (2011). Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using highperformance super-computers. J Comput Chem.
  • Karig DK, Siuti P, Dar RD, Retterer ST, Doktycz MJ, Simpson ML. (2011). Model for biological communication in a nanofabricated cell-mimic driven by stochastic resonance. Nano Commun Netw. 2:39-49.
  • Cantarel BL, Erickson AR, VerBerkmoes NC, Erickson BK, Carey PA, Pan C, Shah M, Mongodin EF, Jansson JK, Fraser-Liggett CM, Hettich RL. (2011). Strategies for metagenomic-guided wholecommunity proteomics of complex microbial environments. PLoS One. 6(11):e27173.
  • Hong L, Smolin N, Lindner B, Sokolov AP, Smith JC. (2011). Three classes of motion in the dynamic neutron-scattering susceptibility of a globular protein. Phys Rev Lett. 107:148102.
  • Karig DK, Iyer S, Simpson ML, Doktycz MJ. (2011). Expression optimization and synthetic gene networks in cell-free systems. Nucleic Acids Res. 40:3763-74.
  • Lee, G., Wang, Z., Sehgal, R., Chen, C.H., Kikuno, K., Hay, B., Park, J.H. (2011). Drosophila caspases involved in developmentally regulated programmed cell death of peptidergic neurons during early metamorphosis. J Comp Neurol 519, 34-48.
  • Nair HK, Hain H, Quock RM, Philip VM, Chesler EJ, Belknap JK, Lariviere WR. (2011). Genomic loci and candidate genes underlying inflammatory nociception. Pain 152:599-606
  • Stanley CB, Perevozchikova T, Berthelier V. (2011). Structural formation of huntingtin exon 1 aggregates probed by small-angle neutron scattering. Biophys J. 100(10):2504-12
  • Wisniewski-Dyé F, Borziak K, Khalsa-Moyers, G, Alexandre G, Sukharnikov LO, Wuichet K, Hurst GB, McDonald WH, Robertson JS, Barbe V, Calteau A, Rouy Z, Mangenot S, Prigent-Combaret C, Normand P, Boyer M, Siguier P, Dessaux Y, Elmerich C, Condemine G, Krishnen G, Kennedy I, Paterson AH, González V, Mavingui P, Zhulin IB. (2011). Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments. PLoS Genet. 7:e1002430.

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