Publications

Publications by SCSB Faculty

Last Updated October 2019

2019

  • IgE binding to linear epitopes of Ara h 2 in peanut allergic preschool children undergoing oral Immunotherapy. Dreskin SC, Germinaro M, Reinhold D, Chen X, Vickery BP, Kulis M, Burks AW, Negi SS, Braun W, Chambliss JM, Eglite S, McNulty CMG. Pediatr Allergy Immunol. 2019 Aug 22. doi: 10.1111/pai.13117.
  • Antibody-Mediated Protective Mechanisms Induced by a Trivalent Parainfluenza Virus-Vectored Ebolavirus Vaccine. Kimble JB, Malherbe DC, Meyer M, Gunn BM, Karim MM, Ilinykh PA, Iampietro M, Mohamed KS, Negi S, Gilchuk P, Huang K, Wolf YI, Braun W, Crowe JE, Alter G, Bukreyev A. J Virol. 2019 Feb 5;93(4). pii: e01845-18. doi: 10.1128/JVI.01845-18.
  • Are the intrinsically disordered linkers involved in SSB binding to accessory proteins? Shinn MK, Kozlov AG, Nguyen B, Bujalowski WM, Lohman TM. Nucleic Acids Res. 2019 Sep 19;47(16):8581-8594. doi: 10.1093/nar/gkz606.
  • Matrix metalloproteinases cleave membrane-bound PD-L1 on CD90+ (myo-)fibroblasts in Crohn's disease and regulate Th1/Th17 cell responses. Aguirre JE, Beswick EJ, Grim C, Uribe G, Tafoya M, Chacon Palma G, Samedi V, McKee R, Villeger R, Fofanov Y, Cong Y, Yochum G, Koltun W, Powell D, Pinchuk IV. Int Immunol. 2019 Oct 21. pii: dxz060. doi: 10.1093/intimm/dxz060.
  • Janibacter species with evidence of genomic polymorphism isolated from resected heart valve in a patient with aortic stenosis. Malania L, Bai Y, Khanipov K, Tsereteli M, Metreveli M, Tsereteli D, Sidamonidze K, Imnadze P, Fofanov Y, Kosoy M. Infect Dis Rep. 2019 Sep 18;11(2):8132. doi: 10.4081/idr.2019.8132.
  • Viral RNA-dependent RNA polymerase mutants display an altered mutation spectrum resulting in attenuation in both mosquito and vertebrate hosts. Warmbrod KL, Patterson EI, Kautz TF, Stanton A, Rockx-Brouwer D, Kalveram BK, Khanipov K, Thangamani S, Fofanov Y, Forrester NL. PLoS Pathog. 2019 Apr 4;15(4):e1007610. doi: 10.1371/journal.ppat.1007610.
  • 16S rRNA gene profiling and genome reconstruction reveal community metabolic interactions and prebiotic potential of medicinal herbs used in neurodegenerative disease and as nootropics. Peterson CT, Sharma V, Iablokov SN, Albayrak L, Khanipov K, Uchitel S, Chopra D, Mills PJ, Fofanov Y, Rodionov DA, Peterson SN. PLoS One. 2019 Mar 19;14(3):e0213869. doi: 10.1371/journal.pone.0213869.
  • Global Transcriptomic Profiling of Pulmonary Gene Expression in an Experimental Murine Model of Rickettsia conorii Infection. Narra HP, Sahni A, Khanipov K, Fofanov Y, Sahni SK. Genes (Basel). 2019 Mar 8;10(3). pii: E204. doi: 10.3390/genes10030204.
  • Interleukin-33 Promotes REG3γ Expression in Intestinal Epithelial Cells and Regulates Gut Microbiota. Xiao Y, Huang X, Zhao Y, Chen F, Sun M, Yang W, Chen L, Yao S, Peniche A, Dann SM, Sun J, Golovko G, Fofanov Y, Miao Y, Liu Z, Chen D, Cong Y. Cell Mol Gastroenterol Hepatol. 2019;8(1):21-36. doi: 10.1016/j.jcmgh.2019.02.006.
  • Enhancer Associated Long Non-coding RNA Transcription and Gene Regulation in Experimental Models of Rickettsial Infection. Chowdhury IH, Narra HP, Sahni A, Khanipov K, Fofanov Y, Sahni SK. Front Immunol. 2019 Jan 9;9:3014. doi: 10.3389/fimmu.2018.03014.
  • Mobility of Histidine Side Chains Analyzed with 15N NMR Relaxation and Cross-Correlation Data: Insight into Zinc-Finger-DNA Interactions. Kemme CA, Luu RH, Chen C, Pletka CC, Pettitt BM, Iwahara J. J Phys Chem B. 2019 May 2;123(17):3706-3710. doi: 10.1021/acs.jpcb.9b03132.
  • NMR Methods for Characterizing the Basic Side Chains of Proteins: Electrostatic Interactions, Hydrogen Bonds, and Conformational Dynamics. Nguyen D, Chen C, Pettitt BM, Iwahara J. Methods Enzymol. 2019;615:285-332. doi: 10.1016/bs.mie.2018.08.017.
  • Structure and Function of the Branched Receptor-Binding Complex of Bacteriophage CBA120. Plattner M, Shneider MM, Arbatsky NP, Shashkov AS, Chizhov AO, Nazarov S, Prokhorov NS, Taylor NMI, Buth SA, Gambino M, Gencay YE, Brøndsted L, Kutter EM, Knirel YA, Leiman PG. J Mol Biol. 2019 Sep 6;431(19):3718-3739. doi: 10.1016/j.jmb.2019.07.022.
  • Structure and transformation of bacteriophage A511 baseplate and tail upon infection of Listeria cells. Guerrero-Ferreira RC, Hupfeld M, Nazarov S, Taylor NM, Shneider MM, Obbineni JM, Loessner MJ, Ishikawa T, Klumpp J, Leiman PG. EMBO J. 2019 Feb 1;38(3). pii: e99455. doi: 10.15252/embj.201899455.
  • Nucleolin Mediates the Binding of Cancer Cells to L-selectin under Conditions of Lymphodynamic Shear Stress. Goldson TM, Turner KL, Huang Y, Carlson GE, Caggiano EG, Oberhauser AF, Fennewald SM, Burdick MM, Resto VA. Am J Physiol Cell Physiol. 2019 Oct 23. doi: 10.1152/ajpcell.00035.2019.
  • Mechanical unfolding of spectrin reveals a super-exponential dependence of unfolding rate on force. Renn JP, Bhattacharyya S, Bai H, He C, Li H, Oberhauser AF, Marko JF, Makarov DE, Matouschek A. Sci Rep. 2019 Jul 31;9(1):11101. doi: 10.1038/s41598-019-46525-w.
  • Effect of N-(2-aminoethyl) ethanolamine on hypertrophic scarring changes in vitro: Finding novel anti-fibrotic therapies. Chen Z, Gu J, El Ayadi A, Oberhauser AF, Zhou J, Sousse LE, Finnerty CC, Herndon DN, Boor PJ. Toxicol Appl Pharmacol. 2019 Jan 1;362:9-19. doi: 10.1016/j.taap.2018.09.026.
  • Allosteric Discrimination at the NADH/ADP Regulatory Site of Glutamate Dehydrogenase. Nassar OM, Wong KY, Lynch GC, Smith TJ, Pettitt BM. Protein Sci. 2019 Oct 14. doi: 10.1002/pro.3748.
  • Free Energy Calculations Based on Coupling Proximal Distribution Functions and Thermodynamic Cycles. Ou SC, Pettitt BM. J Chem Theory Comput. 2019 Apr 9;15(4):2649-2658. doi: 10.1021/acs.jctc.8b01157. Epub 2019 Mar 6. Erratum in: J Chem Theory Comput. 2019 Oct 8;15(10):5759.
  • Price of disorder in the lac repressor hinge helix. Seckfort D, Pettitt BM. Biopolymers, 2019 110(1), e23239. doi: 10.1002/bip.23239.
  • Structural basis of chemokine interactions with heparan sulfate, chondroitin sulfate, and dermatan sulfate. Sepuru KM, Rajarathnam K. J Biol Chem. 2019 Oct 25;294(43):15650-15661. doi: 10.1074/jbc.RA119.009879.
  • How do chemokines navigate neutrophils to the target site: Dissecting the structural mechanisms and signaling pathways. Rajarathnam K, Schnoor M, Richardson RM, Rajagopal S. Cell Signal. 2019 Feb;54:69-80. doi: 10.1016/j.cellsig.2018.11.004.
  • Whole-Genome Sequence of Rickettsia parkeri Strain Atlantic Rainforest, Isolated from a Colombian Tick. Londoño AF, Mendell NL, Valbuena GA, Routh AL, Wood TG, Widen SG, Rodas JD, Walker DH, Bouyer DH. Microbiol Resour Announc. 2019 Sep 26;8(39). pii: e00684-19. doi: 10.1128/MRA.00684-19.
  • DPAC: A Tool for Differential Poly(A)-Cluster Usage from Poly(A)-Targeted RNAseq Data. Routh A. G3 (Bethesda). 2019 Jun 5;9(6):1825-1830. doi: 10.1534/g3.119.400273.
  • Mosquito cells persistently infected with dengue virus produce viral particles with host-dependent replication. Reyes-Ruiz JM, Osuna-Ramos JF, Bautista-Carbajal P, Jaworski E, Soto-Acosta R, Cervantes-Salazar M, Angel-Ambrocio AH, Castillo-Munguía JP, Chávez-Munguía B, De Nova-Ocampo M, Routh A, Del Ángel RM, Salas-Benito JS. Virology. 2019 May;531:1-18. doi: 10.1016/j.virol.2019.02.018.
  • Nudt21 regulates the alternative polyadenylation of Pak1 and is predictive in the prognosis of glioblastoma patients. Chu Y, Elrod N, Wang C, Li L, Chen T, Routh A, Xia Z, Li W, Wagner EJ, Ji P. Oncogene. 2019 May;38(21):4154-4168. doi: 10.1038/s41388-019-0714-9.
  • Development of Poly(A)-ClickSeq as a tool enabling simultaneous genome-wide poly(A)-site identification and differential expression analysis. Elrod ND, Jaworski EA, Ji P, Wagner EJ, Routh A. Methods. 2019 Feb 15;155:20-29. doi: 10.1016/j.ymeth.2019.01.002.
  • Editorial overview: Synapses: bridging the gap between their structure and function. Rudenko G, Takahashi H. Curr Opin Struct Biol. 2019 Feb;54:iii-vii. doi: 10.1016/j.sbi.2019.05.020.
  • Neurexins - versatile molecular platforms in the synaptic cleft. Rudenko G. Curr Opin Struct Biol. 2019 Feb;54:112-121. doi: 10.1016/j.sbi.2019.01.009.
  • Repurposing an HIV Drug for Zika Virus Therapy. Xie X, Shi PY. Mol Ther. 2019 Oct 14. pii: S1525-0016(19)30458-7. doi: 10.1016/j.ymthe.2019.10.004.
  • Molecular basis of dengue virus serotype 2 morphological switch from 29°C to 37°C. Lim XN, Shan C, Marzinek JK, Dong H, Ng TS, Ooi JSG, Fibriansah G, Wang J, Verma CS, Bond PJ, Shi PY, Lok SM. PLoS Pathog. 2019 Sep 19;15(9):e1007996. doi: 10.1371/journal.ppat.1007996.
  • Genetic stability of live-attenuated Zika vaccine candidates. Muruato AE, Shan C, Fontes-Garfias CR, Liu Y, Cao Z, Gao Q, Weaver SC, Shi PY. Antiviral Res. 2019 Nov;171:104596. doi: 10.1016/j.antiviral.2019.104596.
  • Inter- and intra-lineage genetic diversity of wild-type Zika viruses reveals both common and distinctive nucleotide variants and clusters of genomic diversity. Collins ND, Widen SG, Li L, Swetnam DM, Shi PY, Tesh RB, Sarathy VV. Emerg Microbes Infect. 2019;8(1):1126-1138. doi: 10.1080/22221751.2019.1645572.
  • Axl Promotes Zika Virus Entry and Modulates the Antiviral State of Human Sertoli Cells. Strange DP, Jiyarom B, Pourhabibi Zarandi N, Xie X, Baker C, Sadri-Ardekani H, Shi PY, Verma S. MBio. 2019 Jul 16;10(4). pii: e01372-19. doi: 10.1128/mBio.01372-19.
  • Genetic and biochemical characterizations of Zika virus NS2A protein. Zhang X, Xie X, Zou J, Xia H, Shan C, Chen X, Shi PY. Emerg Microbes Infect. 2019;8(1):585-602. doi: 10.1080/22221751.2019.1598291.
  • Anti-Zika virus RNAi in neural progenitor cells. Xie X, Shi PY. Cell Res. 2019 Apr;29(4):261-262. doi: 10.1038/s41422-019-0158-3.
  • Strategies for Zika drug discovery. Zou J, Shi PY. Curr Opin Virol. 2019 Apr;35:19-26. doi: 10.1016/j.coviro.2019.01.005.
  • Dissecting the Antenna in Human Glutamate Dehydrogenase: Understanding Its Role in Subunit Communication and Allosteric Regulation. Hoffpauir ZA, Sherman E, Smith TJ. Biochemistry. 2019 Oct 15;58(41):4195-4206. doi: 10.1021/acs.biochem.9b00722.
  • Bile Salts Alter the Mouse Norovirus Capsid Conformation: Possible Implications for Cell Attachment and Immune Evasion. Sherman MB, Williams AN, Smith HQ, Nelson C, Wilen CB, Fremont DH, Virgin HW, Smith TJ. J Virol. 2019 Sep 12;93(19). pii: e00970-19. doi: 10.1128/JVI.00970-19.
  • The Dynamic Capsid Structures of the Noroviruses. Smith HQ, Smith TJ. Viruses. 2019 Mar 8;11(3). pii: E235. doi: 10.3390/v11030235. 
  • Glutamate dehydrogenase: Structure of a hyperinsulinism mutant, corrections to the atomic model, and insights into a regulatory site. Nassar OM, Li C, Stanley CA, Pettitt BM, Smith TJ. Proteins. 2019 Jan;87(1):41-50. doi: 10.1002/prot.25620.
  • Coordinated alterations in RNA splicing and epigenetic regulation drive leukaemogenesis. Yoshimi A, Lin KT, Wiseman DH, Rahman MA, Pastore A, Wang B, Lee SC, Micol JB, Zhang XJ, de Botton S, Penard-Lacronique V, Stein EM, Cho H, Miles RE, Inoue D, Albrecht TR, Somervaille TCP, Batta K, Amaral F, Simeoni F, Wilks DP, Cargo C, Intlekofer AM, Levine RL, Dvinge H, Bradley RK, Wagner EJ, Krainer AR, Abdel-Wahab O. Nature. 2019 Oct 2. doi: 10.1038/s41586-019-1618-0.
  • The Integrator complex cleaves nascent mRNAs to attenuate transcription. Tatomer DC, Elrod ND, Liang D, Xiao MS, Jiang JZ, Jonathan M, Huang KL, Wagner EJ, Cherry S, Wilusz JE. Genes Dev. 2019 Sep 17. doi: 10.1101/gad.330167.119.
  • Cleavage factor 25 deregulation contributes to pulmonary fibrosis through alternative polyadenylation. Weng T, Ko J, Masamha CP, Xia Z, Xiang Y, Chen NY, Molina JG, Collum S, Mertens TC, Luo F, Philip K, Davies J, Huang J, Wilson C, Thandavarayan RA, Bruckner BA, Jyothula SS, Volcik KA, Li L, Han L, Li W, Assassi S, Karmouty-Quintana H, Wagner EJ, Blackburn MR. J Clin Invest. 2019 Feb 28;129(5):1984-1999. doi: 10.1172/JCI122106.
  • Biochemical and Next Generation Sequencing Approaches to Study RNA Regulation. Wagner EJ, Goldstrohm AC. Methods. 2019 Feb 15;155:1-2. doi: 10.1016/j.ymeth.2019.02.012.
  • Composition of the Survival Motor Neuron (SMN) Complex in Drosophila melanogaster. Matera AG, Raimer AC, Schmidt CA, Kelly JA, Droby GN, Baillat D, Ten Have S, Lamond AI, Wagner EJ, Gray KM. G3 (Bethesda). 2019 Feb 7;9(2):491-503. doi: 10.1534/g3.118.200874.
  • Small molecule nicotinamide N-methyltransferase inhibitor activates senescent muscle stem cells and improves regenerative capacity of aged skeletal muscle. Neelakantan H, Brightwell CR, Graber TG, Maroto R, Wang HL, McHardy SF, Papaconstantinou J, Fry CS, Watowich SJ. Biochem Pharmacol. 2019 May;163:481-492. doi: 10.1016/j.bcp.2019.02.008.
  • Chikungunya Virus: Role of Vectors in Emergence from Enzootic Cycles. Weaver SC, Chen R, Diallo M. Annu Rev Entomol. 2019 Oct 8. doi: 10.1146/annurev-ento-011019-025207.
  • Vector Competence: What Has Zika Virus Taught Us? Azar SR, Weaver SC. Viruses. 2019 Sep 17;11(9). pii: E867. doi: 10.3390/v11090867.
  • Electron Microscopy in Discovery of Novel and Emerging Viruses from the Collection of the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA). Popov VL, Tesh RB, Weaver SC, Vasilakis N. Viruses. 2019 May 25;11(5). pii: E477. doi: 10.3390/v11050477.
  • Immunogenicity and Efficacy of a Measles Virus-Vectored Chikungunya Vaccine in Nonhuman Primates. Rossi SL, Comer JE, Wang E, Azar SR, Lawrence WS, Plante JA, Ramsauer K, Schrauf S, Weaver SC. J Infect Dis. 2019 Jul 31;220(5):735-742. doi: 10.1093/infdis/jiz202.
  • An adjuvanted adenovirus 5-based vaccine elicits neutralizing antibodies and protects mice against chikungunya virus-induced footpad swelling. Dora EG, Rossi SL, Weaver SC, Tucker SN, Mateo R. Vaccine. 2019 May 27;37(24):3146-3150. doi: 10.1016/j.vaccine.2019.04.069.
  • Naturally infected Aedes aegypti collected during a Zika virus outbreak have viral titres consistent with transmission. Azar SR, Diaz-Gonzalez EE, Danis-Lonzano R, Fernandez-Salas I, Weaver SC. Emerg Microbes Infect. 2019;8(1):242-244. doi: 10.1080/22221751.2018.1561157.
  • Guild-level responses of bats to habitat conversion in a lowland Amazonian rainforest: species composition and biodiversity. Willig MR, Presley SJ, Plante JL, Bloch CP, Solari S, Pacheco V, Weaver SC. J Mammal. 2019 Feb 28;100(1):223-238. doi: 10.1093/jmammal/gyz023. Erratum in: J Mammal. 2019 Jul 27;100(4):e1.
  • Chikungunya as a paradigm for emerging viral diseases: Evaluating disease impact and hurdles to vaccine development. Rezza G, Weaver SC. PLoS Negl Trop Dis. 2019 Jan 17;13(1):e0006919. doi: 10.1371/journal.pntd.0006919.
  • Structural insights into the recognition of nucleoside reverse transcriptase inhibitors by HIV-1 reverse transcriptase: First crystal structures with reverse transcriptase and the active triphosphate forms of lamivudine and emtricitabine. Bertoletti N, Chan AH, Schinazi RF, Yin YW, Anderson KS. Protein Sci. 2019 Sep;28(9):1664-1675. doi: 10.1002/pro.3681.