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Publications by SCSB Faculty

Last Update: 2016

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  • Publications

    2015

    • Protein folding. Translational tuning optimizes nascent protein folding in cells. Kim SJ, Yoon JS, Shishido H, Yang Z, Rooney LA, Barral JM, Skach WR. Science. 2015 Apr 24;348(6233):444-8. doi: 10.1126/science.aaa3974.
    • Allosteric inhibitors of Coxsackie virus A24 RNA polymerase. Schein CH, Rowold D, Choi KH. Bioorg Med Chem. 2015 Dec 15. pii: S0968-0896(15)30189-9. doi: 10.1016/j.bmc.2015.12.023.
    • Flaviviral Replication Complex: Coordination between RNA Synthesis and 51-RNA Capping. Klema VJ, Padmanabhan R, Choi KH. Viruses. 2015 Aug 13;7(8):4640-56. doi: 10.3390/v7082837.
    • Flavivirus RNA synthesis in vitro. Padmanabhan R, Takhampunya R, Teramoto T, Choi KH. Methods. 2015 Dec;91:20-34. doi: 10.1016/j.ymeth.2015.08.002.
    • Sequence specificity for uridylylation of the viral peptide linked to the genome (VPg) of enteroviruses. Schein CH, Ye M, Paul AV, Oberste MS, Chapman N, van der Heden van Noort GJ, Filippov DV, Choi KH. Virology. 2015 Oct;484:80-5. doi: 10.1016/j.virol.2015.05.016.
    • Bacterial small RNAs in the Genus Rickettsia. Schroeder CL, Narra HP, Rojas M, Sahni A, Patel J, Khanipov K, Wood TG, Fofanov Y, Sahni SK. BMC Genomics. 2015 Dec 18;16(1):1075. doi: 10.1186/s12864-015-2293-7.
    • The main challenges that remain in applying high-throughput sequencing to clinical diagnostics. Loeffelholz M, Fofanov Y. Expert Rev Mol Diagn. 2015;15(11):1405-8. doi: 10.1586/14737159.2015.1088385.
    • Survey of viral populations within Lake Michigan nearshore waters at four Chicago area beaches. Sible E, Cooper A, Malki K, Bruder K, Watkins SC, Fofanov Y, Putonti C. Data Brief. 2015 Aug 13;5:9-12. doi: 10.1016/j.dib.2015.08.001.
    • Mycoplasma CG- and GATC-specific DNA methyltransferases selectively and efficiently methylate the host genome and alter the epigenetic landscape in human cells. Chernov AV, Reyes L, Xu Z, Gonzalez B, Golovko G, Peterson S, Perucho M, Fofanov Y, Strongin AY. Epigenetics. 2015;10(4):303-18. doi: 10.1080/15592294.2015.1020000.
    • Metagenomic analysis of the airborne environment in urban spaces. Be NA, Thissen JB, Fofanov VY, Allen JE, Rojas M, Golovko G, Fofanov Y, Koshinsky H, Jaing CJ. Microb Ecol. 2015 Feb;69(2):346-55. doi: 10.1007/s00248-014-0517-z.
    • Secondary Analysis of the NCI-60 Whole Exome Sequencing Data Indicates Significant Presence of Propionibacterium acnes Genomic Material in Leukemia (RPMI-8226) and Central Nervous System (SF-295, SF-539, and SNB-19) Cell Lines. Rojas M, Golovko G, Khanipov K, Albayrak L, Chumakov S, Pettitt BM, Strongin AY, Fofanov Y. PLoS One. 2015 Jun 3;10(6):e0127799. doi: 10.1371/journal.pone.0127799.
    • Influence of Quasi-Specific Sites on Kinetics of Target DNA Search by a Sequence-Specific DNA-Binding Protein. Kemme CA, Esadze A, Iwahara J. Biochemistry. 2015 Nov 10;54(44):6684-91. doi: 10.1021/acs.biochem.5b00967.
    • Physicochemical Properties of Ion Pairs of Biological Macromolecules. Iwahara J, Esadze A, Zandarashvili L. Biomolecules. 2015 Sep 30;5(4):2435-63. doi: 10.3390/biom5042435.
    • Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate. Zandarashvili L, Nguyen D, Anderson KM, White MA, Gorenstein DG, Iwahara J. Biophys J. 2015 Sep 1;109(5):1026-37. doi: 10.1016/j.bpj.2015.07.032.
    • Balancing between affinity and speed in target DNA search by zinc-finger proteins via modulation of dynamic conformational ensemble. Zandarashvili L, Esadze A, Vuzman D, Kemme CA, Levy Y, Iwahara J. Proc Natl Acad Sci U S A. 2015 Sep 15;112(37):E5142-9. doi: 10.1073/pnas.1507726112.
    • Dynamic Equilibria of Short-Range Electrostatic Interactions at Molecular Interfaces of Protein-DNA Complexes. Chen C, Esadze A, Zandarashvili L, Nguyen D, Pettitt BM, Iwahara J. J Phys Chem Lett. 2015 Jul 16;6(14):2733-7.
    • Structural impact of complete CpG methylation within target DNA on specific complex formation of the inducible transcription factor Egr-1. Zandarashvili L, White MA, Esadze A, Iwahara J. FEBS Lett. 2015 Jul 8;589(15):1748-53. doi: 10.1016/j.febslet.2015.05.022.
    • A chemical approach for site-specific identification of NMR signals from protein side-chain NH3+ groups forming intermolecular ion pairs in protein-nucleic acid complexes. Anderson KM, Nguyen D, Esadze A, Zandrashvili L, Gorenstein DG, Iwahara J. J Biomol NMR. 2015 May;62(1):1-5. doi: 10.1007/s10858-015-9909-8.
    • Temperature dependence of internal motions of protein side-chain NH3(+) groups: insight into energy barriers for transient breakage of hydrogen bonds. Zandarashvili L, Iwahara J. Biochemistry. 2015 Jan 20;54(2):538-45. doi: 10.1021/bi5012749.
    • Long-Range Communication Network in the Type 1B Bone Morphogenetic Protein Receptor. Evangelista W, Yeh LC, Gmyrek A, Lee JC, Lee JC. Biochemistry. 2015 Dec 8;54(48):7079-88. doi: 10.1021/acs.biochem.5b00955.
    • Analysis of the TGFβ-induced program in primary airway epithelial cells shows essential role of NF-κB/RelA signaling network in type II epithelial mesenchymal transition. Tian B, Li X, Kalita M, Widen SG, Yang J, Bhavnani SK, Dang B, Kudlicki A, Sinha M, Kong F, Wood TG, Luxon BA, Brasier AR. BMC Genomics. 2015 Jul 18;16:529. doi: 10.1186/s12864-015-1707-x.
    • Structural insights into the architecture of the hyperthermophilic Fusellovirus SSV1. Stedman KM, DeYoung M, Saha M, Sherman MB, Morais MC. Virology. 2015 Jan 1;474:105-9. doi: 10.1016/j.virol.2014.10.014.
    • N-(2-Aminoethyl) Ethanolamine-Induced Morphological, Biochemical, and Biophysical Alterations in Vascular Matrix Associated With Dissecting Aortic Aneurysm. Chen Z, Xu Y, Bujalowski P, Oberhauser AF, Boor PJ. Toxicol Sci. 2015 Dec;148(2):421-32. doi: 10.1093/toxsci/kfv194.
    • Thermally-induced structural changes in an armadillo repeat protein suggest a novel thermosensor mechanism in a molecular chaperone. Bujalowski PJ, Nicholls P, Barral JM, Oberhauser AF. FEBS Lett. 2015 Jan 2;589(1):123-30. doi: 10.1016/j.febslet.2014.11.034.
    • Examining the Assumptions Underlying Continuum-Solvent Models. Harris RC, Pettitt BM. J Chem Theory Comput. 2015 Oct 13;11(10):4593-600. doi: 10.1021/acs.jctc.5b00684.
    • Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins. Nguyen BL, Pettitt BM. J Chem Theory Comput. 2015;11(4):1399-1409.
    • Computation of virial coefficients from integral equations. Zhang C, Lai CL, Pettitt BM. J Chem Phys. 2015 Jun 7;142(21):214110. doi: 10.1063/1.4921790.
    • Force field-dependent solution properties of glycine oligomers. Drake JA, Pettitt BM. J Comput Chem. 2015 Jun 30;36(17):1275-85. doi: 10.1002/jcc.23934.
    • Twist-induced defects of the P-SSP7 genome revealed by modeling the cryo-EM density. Wang Q, Myers CG, Pettitt BM. J Phys Chem B. 2015 Apr 16;119(15):4937-43. doi: 10.1021/acs.jpcb.5b00865.
    • Solubility Limits in Lennard-Jones Mixtures: Effects of Disparate Molecule Geometries. Dyer KM, Perkyns JS, Pettitt BM. J Phys Chem B. 2015 Jul 23;119(29):9450-9. doi: 10.1021/jp512992n.
    • Systematic identification of single amino acid variants in glioma stem-cell-derived chromosome 19 proteins. Lichti CF, Mostovenko E, Wadsworth PA, Lynch GC, Pettitt BM, Sulman EP, Wang Q, Lang FF, Rezeli M, Marko-Varga G, VégváriÁ, Nilsson CL. J Proteome Res. 2015 Feb 6;14(2):778-86. doi: 10.1021/pr500810g.
    • Solvation and cavity occupation in biomolecules. Lynch GC, Perkyns JS, Nguyen BL, Pettitt BM. Biochim Biophys Acta. 2015 May;1850(5):923-31. doi: 10.1016/j.bbagen.2014.09.020.
    • CXCL1/MGSA is a novel glycosaminoglycan (GAG)-binding chemokine: structural evidence for two distinct non-overlapping binding domains. Sepuru KM, Rajarathnam K. J Biol Chem. 2015 Dec 31. pii: jbc.M115.697888.
    • Solution NMR characterization of chemokine CXCL8/IL-8 monomer and dimer binding to glycosaminoglycans: structural plasticity mediates differential binding interactions. Joseph PR, Mosier PD, Desai UR, Rajarathnam K. Biochem J. 2015 Nov 15;472(1):121-33. doi: 10.1042/BJ20150059.
    • Flexible Linker Modulates Glycosaminoglycan Affinity of Decorin Binding Protein A. Morgan A, Sepuru KM, Feng W, Rajarathnam K, Wang X. Biochemistry. 2015 Aug 18;54(32):5113-9. doi: 10.1021/acs.biochem.5b00253.
    • Chemokine CXCL1-Mediated Neutrophil Trafficking in the Lung: Role of CXCR2 Activation. Sawant KV, Xu R, Cox R, Hawkins H, Sbrana E, Kolli D, Garofalo RP, Rajarathnam K. J Innate Immun. 2015;7(6):647-58. doi: 10.1159/000430914.
    • Erratum: using isothermal titration calorimetry to determine thermodynamic parameters of protein-glycosaminoglycan interactions. Dutta AK, Rösgen J, Rajarathnam K. Methods Mol Biol. 2015;1229:E1. doi: 10.1007/978-1-4939-1714-3_48.
    • Solution NMR characterization of WT CXCL8 monomer and dimer binding to CXCR1 N-terminal domain. Joseph PR, Rajarathnam K. Protein Sci. 2015 Jan;24(1):81-92. doi: 10.1002/pro.2590.
    • Characterizing protein-glycosaminoglycan interactions using solution NMR spectroscopy. Joseph PR, Poluri KM, Sepuru KM, Rajarathnam K. Methods Mol Biol. 2015;1229:325-33. doi: 10.1007/978-1-4939-1714-3_26.
    • Using isothermal titration calorimetry to determine thermodynamic parameters of protein-glycosaminoglycan interactions. Dutta AK, Rösgen J, Rajarathnam K. Methods Mol Biol. 2015;1229:315-24. doi: 10.1007/978-1-4939-1714-3_25.
    • A high-throughput drop microfluidic system for virus culture and analysis. Fischer AE, Wu SK, Proescher JB, Rotem A, Chang CB, Zhang H, Tao Y, Mehoke TS, Thielen PM, Kolawole AO, Smith TJ, Wobus CE, Weitz DA, Lin JS, Feldman AB, Wolfe JT. J Virol Methods. 2015 Mar;213:111-7. doi: 10.1016/j.jviromet.2014.12.003.
    • Norepinephrine Reduces Reactive Oxygen Species (ROS) and DNA Damage in Ovarian Surface Epithelial Cells. Patel PR, Hegde ML, Theruvathu J, Mitra SA, Boldogh I, Sowers L. J Bioanal Biomed. 2015;7(3):75-80.
    • Aryl Hydrocarbon Receptor Ligand 5F 203 Induces Oxidative Stress That Triggers DNA Damage in Human Breast Cancer Cells. McLean LS, Watkins CN, Campbell P, Zylstra D, Rowland L, Amis LH, Scott L, Babb CE, Livingston WJ, Darwanto A, Davis WL Jr, Senthil M, Sowers LC, Brantley E. Chem Res Toxicol. 2015 May 18;28(5):855-71. doi: 10.1021/tx500485v.
    • Dimeric Organization of Blood Coagulation Factor VIII bound to Lipid Nanotubes. Daniela Dalm, Jesus Galaz-Montoya, Jaimy Miller, Kirill Grushin, Alexander Villalobos, Alexey Koyfman, Michael Schmid, Svetla Stoilova-McPhie. Sci. Rep. 2015;17(5):11212. doi: 10.1038/srep11212.
    • Factor VIII organization on nanodiscs with different lipid composition. Kirill Grushin, Jaimy Miller, Daniela Dalm, Svetla Stoilova-McPhie. Thrombosis and Haemostasis, 2015; 113(4):741-9. doi: 10.1160/TH14-09-0725.
    • T(H)17 cells promote microbial killing and innate immune sensing of DNA via interleukin 26. Meller S, Di Domizio J, Voo KS, Friedrich HC, Chamilos G, Ganguly D, Conrad C, Gregorio J, Le Roy D, Roger T, Ladbury JE, Homey B, Watowich S, Modlin RL, Kontoyiannis DP, Liu YJ, Arold ST, Gilliet M. Nat Immunol. 2015 Sep;16(9):970-9. doi: 10.1038/ni.3211.
    • Editorial overview: Virus-vector interactions. Weaver SC, Simon AE. Curr Opin Virol. 2015 Dec;15:iv-vi. doi: 10.1016/j.coviro.2015.11.001.
    • Isolation and Characterization of Madariaga Virus from a Horse in Paraíba State, Brazil. Silva ML, Auguste AJ, Terzian AC, Vedovello D, Riet-Correa F, Macário VM, Mourão MP, Ullmann LS, Araújo JP Jr, Weaver SC, Nogueira ML. Transbound Emerg Dis. 2015 Nov 25. doi: 10.1111/tbed.12441.
    • Molecular Characterisation of Chikungunya Virus Infections in Trinidad and Comparison of Clinical and Laboratory Features with Dengue and Other Acute Febrile Cases. Sahadeo N, Mohammed H, Allicock OM, Auguste AJ, Widen SG, Badal K, Pulchan K, Foster JE, Weaver SC, Carrington CV. PLoS Negl Trop Dis. 2015 Nov 18;9(11):e0004199. doi: 10.1371/journal.pntd.0004199.
    • Potential of selected Senegalese Aedes spp. mosquitoes (Diptera: Culicidae) to transmit Zika virus. Diagne CT, Diallo D, Faye O, Ba Y, Faye O, Gaye A, Dia I, Faye O, Weaver SC, Sall AA, Diallo M. BMC Infect Dis. 2015 Nov 2;15:492. doi: 10.1186/s12879-015-1231-2.
    • Utilization of an Eilat Virus-Based Chimera for Serological Detection of Chikungunya Infection. Erasmus JH, Needham J, Raychaudhuri S, Diamond MS, Beasley DW, Morkowski S, Salje H, Fernandez Salas I, Kim DY, Frolov I, Nasar F, Weaver SC. PLoS Negl Trop Dis. 2015 Oct 22;9(10):e0004119. doi: 10.1371/journal.pntd.0004119.
    • Neuropathogenesis of Chikungunya infection: astrogliosis and innate immune activation. Inglis FM, Lee KM, Chiu KB, Purcell OM, Didier PJ, Russell-Lodrigue K, Weaver SC, Roy CJ, MacLean AG. J Neurovirol. 2015
    • First Report of Aedes aegypti Transmission of Chikungunya Virus in the Americas. Dí az-González EE, Kautz TF, Dorantes-Delgado A, Malo-Garcí a IR, Laguna-Aguilar M, Langsjoen RM, Chen R, Auguste DI, Sánchez-Casas RM, Danis-Lozano R, Weaver SC, Fernández-Salas I. Am J Trop Med Hyg. 2015 Dec 9;93(6):1325-9. doi: 10.4269/ajtmh.15-0450.
    • Extended Preclinical Safety, Efficacy and Stability Testing of a Live-attenuated Chikungunya Vaccine Candidate. Plante KS, Rossi SL, Bergren NA, Seymour RL, Weaver SC. PLoS Negl Trop Dis. 2015 Sep 4;9(9):e0004007. doi: 10.1371/journal.pntd.0004007.
    • Brennan B, Weber F, Kormelink R, Schnettler E, Bouloy M, Failloux AB, Weaver SC, Fazakerley JK, Fragkoudis R, Harris M, Barr JN, Palese P, García-Sastre A, Dalziel RG, Dutia BM, Lowen AC, Steel J, Randall RE, Paul Duprex W, Rice CM, Tesh RB, Murphy FA, Ebihara H, Vasconcelos PF, Nunes MR, Fooks AR, Smith GL, Goodfellow I, Pappu HR, Lamb RA, Paterson RG, Higgs S, Vanlandingham DL, Dietzgen RG, Stephen Lodmell J, Nichol ST, Daly J, Ullman DE, Plyusnin A, Plyusnina A, Efstathiou S, Hewson R, Tordo N, Cherry S, Boutell C, Hosie MJ, Murcia PR, Neil JC, Palmarini M, Patel AH, Willett BJ, Kohl A, McLauchlan J. J Gen Virol. 2015 Aug;96(8):1975-8. doi: 10.1099/jgv.0.000241.
    • Mercadeo Virus: A Novel Mosquito-Specific Flavivirus from Panama. Carrera JP, Guzman H, Beltrán D, Díaz Y, López-Vergès S, Torres-Cosme R, Popov V, Widen SG, Wood TG, Weaver SC, Cáceres-Carrera L, Vasilakis N, Tesh RB. Am J Trop Med Hyg. 2015 Nov 4;93(5):1014-9. doi: 10.4269/ajtmh.15-0117.
    • A Rodent Model of Chikungunya Virus Infection in RAG1 -/- Mice, with Features of Persistence, for Vaccine Safety Evaluation. Seymour RL, Adams AP, Leal G, Alcorn MD, Weaver SC. PLoS Negl Trop Dis. 2015 Jun 26;9(6):e0003800. doi: 10.1371/journal.pntd.0003800.
    • Eilat virus induces both homologous and heterologous interference. Nasar F, Erasmus JH, Haddow AD, Tesh RB, Weaver SC. Virology. 2015 Oct;484:51-8. doi: 10.1016/j.virol.2015.05.009.
    • Assessing the epidemiological effect of wolbachia for dengue control. Lambrechts L, Ferguson NM, Harris E, Holmes EC, McGraw EA, O'Neill SL, Ooi EE, Ritchie SA, Ryan PA, Scott TW, Simmons CP, Weaver SC. Lancet Infect Dis. 2015 Jul;15(7):862-6. doi: 10.1016/S1473-3099(15)00091-2.
    • IRES-Containing VEEV Vaccine Protects Cynomolgus Macaques from IE Venezuelan Equine Encephalitis Virus Aerosol Challenge. Rossi SL, Russell-Lodrigue KE, Killeen SZ, Wang E, Leal G, Bergren NA, Vinet-Oliphant H, Weaver SC, Roy CJ. PLoS Negl Trop Dis. 2015 May 28;9(5):e0003797. doi: 10.1371/journal.pntd.0003797.
    • Chikungunya: Evolutionary history and recent epidemic spread. Weaver SC, Forrester NL. Antiviral Res. 2015 Aug;120:32-9. doi: 10.1016/j.antiviral.2015.04.016.
    • IFIT1 Differentially Interferes with Translation and Replication of Alphavirus Genomes and Promotes Induction of Type I Interferon. Reynaud JM, Kim DY, Atasheva S, Rasalouskaya A, White JP, Diamond MS, Weaver SC, Frolova EI, Frolov I. PLoS Pathog. 2015 Apr 30;11(4):e1004863. doi: 10.1371/journal.ppat.1004863.
    • The 5' and 3' ends of alphavirus RNAs--Non-coding is not non-functional. Hyde JL, Chen R, Trobaugh DW, Diamond MS, Weaver SC, Klimstra WB, Wilusz J. Virus Res. 2015 Aug 3;206:99-107. doi: 10.1016/j.virusres.2015.01.016.
    • Demographics of natural oral infection of mosquitos by Venezuelan equine encephalitis virus. Gutiérrez S, Thébaud G, Smith DR, Kenney JL, Weaver SC. J Virol. 2015 Apr;89(7):4020-2. doi: 10.1128/JVI.03265-14.
    • Eilat virus displays a narrow mosquito vector range. Nasar F, Haddow AD, Tesh RB, Weaver SC. Parasit Vectors. 2014 Dec 17;7:595. doi: 10.1186/s13071-014-0595-2.
    • Isolation and characterization of Mayaro virus from a human in Acre, Brazil. Terzian AC, Auguste AJ, Vedovello D, Ferreira MU, da Silva-Nunes M, Sperança MA, Suzuki RB, Juncansen C, Araújo JP Jr, Weaver SC, Nogueira ML. Am J Trop Med Hyg. 2015 Feb;92(2):401-4. doi: 10.4269/ajtmh.14-0417.
    • Chikungunya virus-vector interactions. Coffey LL, Failloux AB, Weaver SC. Viruses. 2014 Nov 24;6(11):4628-63. doi: 10.3390/v6114628.
    • Impact of climate and mosquito vector abundance on sylvatic arbovirus circulation dynamics in Senegal. Althouse BM, Hanley KA, Diallo M, Sall AA, Ba Y, Faye O, Diallo D, Watts DM, Weaver SC, Cummings DA. Am J Trop Med Hyg. 2015 Jan;92(1):88-97. doi: 10.4269/ajtmh.13-0617.
    • Eilat virus host range restriction is present at multiple levels of the virus life cycle. Nasar F, Gorchakov RV, Tesh RB, Weaver SC. J Virol. 2015 Jan 15;89(2):1404-18. doi: 10.1128/JVI.01856-14.
    • A newly isolated reovirus has the simplest genomic and structural organization of any reovirus. Auguste AJ, Kaelber JT, Fokam EB, Guzman H, Carrington CV, Erasmus JH, Kamgang B, Popov VL, Jakana J, Liu X, Wood TG, Widen SG, Vasilakis N, Tesh RB, Chiu W, Weaver SC. J Virol. 2015 Jan;89(1):676-87. doi: 10.1128/JVI.02264-14.
    • Yeast Mitochondrial Transcription Factor Mtf1 Determines the Precision of Promoter-Directed Initiation of RNA Polymerase Rpo41. Yang X, Chang HR, Yin YW. PLoS One. 2015 Sep 2;10(9):e0136879. doi: 10.1371/journal.pone.0136879.
    • Transcription yield of fully 2'-modified RNA can be increased by the addition of thermostabilizing mutations to T7 RNA polymerase mutants. Meyer AJ, Garry DJ, Hall B, Byrom MM, McDonald HG, Yang X, Yin YW, Ellington AD. Nucleic Acids Res. 2015 Sep 3;43(15):7480-8. doi: 10.1093/nar/gkv734.
    • Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase γ. Sohl CD, Szymanski MR, Mislak AC, Shumate CK, Amiralaei S, Schinazi RF, Anderson KS, Yin YW. Proc Natl Acad Sci U S A. 2015 Jul 14;112(28):8596-601. doi: 10.1073/pnas.1421733112.
    • Structural basis for processivity and antiviral drug toxicity in human mitochondrial DNA replicase. Szymanski MR, Kuznetsov VB, Shumate C, Meng Q, Lee YS, Patel G, Patel S, Yin YW. EMBO J. 2015 Jul 14;34(14):1959-70. doi: 10.15252/embj.201591520.