Publications

Selected Publications by SCSB Faculty

Last Updated April 2021

2021

  • Read CM, Plante K, Rafael G, Rossi SL, Braun W, Weaver SC, Schein CH. Designing multivalent immunogens for alphavirus vaccine optimization. Virology. 2021 Feb 5:S0042-6822(20)30236-1. doi: 10.1016/j.virol.2020.11.010.
  • Dreskin SC, Koppelman SJ, Andorf S, Nadeau KC, Kalra A, Braun W, Negi SS, Chen X, Schein CH. The importance of the 2S albumins for allergenicity and cross-reactivity of peanuts, tree nuts, and sesame seeds. J Allergy Clin Immunol. 2021 Apr;147(4):1154-1163. doi: 10.1016/j.jaci.2020.11.004.
  • Grim C, Noble R, Uribe G, Khanipov K, Johnson P, Koltun WA, Watts T, Fofanov Y, Yochum GS, Powell DW, Beswick EJ, Pinchuk IV. Impairment of tissue resident mesenchymal stem cells in chronic ulcerative colitis and Crohn's disease. J Crohns Colitis. 2021 Jan 28:jjab001. doi: 10.1093/ecco-jcc/jjab001.
  • Yu B, Pletka CC, Iwahara J. Quantifying and visualizing weak interactions between anions and proteins. Proc Natl Acad Sci U S A. 2021 Jan 12;118(2):e2015879118. doi: 10.1073/pnas.2015879118.
  • Iwahara J, Kolomeisky AB. Discrete-state stochastic kinetic models for target DNA search by proteins: Theory and experimental applications. Biophys Chem. 2021 Feb;269:106521. doi: 10.1016/j.bpc.2020.106521.
  • Singh MK, Kenney LJ. Super-resolution imaging of bacterial pathogens and visualization of their secreted effectors. FEMS Microbiol Rev. 2021 Mar 16;45(2):fuaa050. doi: 10.1093/femsre/fuaa050.
  • Dunne M, Prokhorov NS, Loessner MJ, Leiman PG. Reprogramming bacteriophage host range: design principles and strategies for engineering receptor binding proteins. Curr Opin Biotechnol. 2021 Mar 18;68:272-281. doi: 10.1016/j.copbio.2021.02.006.
  • Drobysheva AV, Panafidina SA, Kolesnik MV, Klimuk EI, Minakhin L, Yakunina MV, Borukhov S, Nilsson E, Holmfeldt K, Yutin N, Makarova KS, Koonin EV, Severinov KV, Leiman PG, Sokolova ML. Structure and function of virion RNA polymerase of a crAss-like phage. Nature. 2021 Jan;589(7841):306-309. doi: 10.1038/s41586-020-2921-5.
  • Sepuru KM, Rajarathnam K. Structural basis of a chemokine heterodimer binding to glycosaminoglycans. Biochem J. 2021 Mar 12;478(5):1009-1021. doi: 10.1042/BCJ20200927.
  • Sawant KV, Sepuru KM, Lowry E, Penaranda B, Frevert CW, Garofalo RP, Rajarathnam K. Neutrophil recruitment by chemokines Cxcl1/KC and Cxcl2/MIP2: Role of Cxcr2 activation and glycosaminoglycan interactions. J Leukoc Biol. 2021 Apr;109(4):777-791. doi: 10.1002/JLB.3A0820-207R.
  • Gallardo CM, Wang S, Montiel-Garcia DJ, Little SJ, Smith DM, Routh AL, Torbett BE. MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host evolution. Nucleic Acids Res. 2021 Apr 13:gkab231. doi: 10.1093/nar/gkab231.
  • Johnson BA, Xie X, Bailey AL, Kalveram B, Lokugamage KG, Muruato A, Zou J, Zhang X, Juelich T, Smith JK, Zhang L, Bopp N, Schindewolf C, Vu M, Vanderheiden A, Winkler ES, Swetnam D, Plante JA, Aguilar P, Plante KS, Popov V, Lee B, Weaver SC, Suthar MS, Routh AL, Ren P, Ku Z, An Z, Debbink K, Diamond MS, Shi PY, Freiberg AN, Menachery VD. Loss of furin cleavage site attenuates SARS-CoV-2 pathogenesis. Nature. 2021 Mar;591(7849):293-299. doi: 10.1038/s41586-021-03237-4.
  • Gribble J, Stevens LJ, Agostini ML, Anderson-Daniels J, Chappell JD, Lu X, Pruijssers AJ, Routh AL, Denison MR. The coronavirus proofreading exoribonuclease mediates extensive viral recombination. PLoS Pathog. 2021 Jan 19;17(1):e1009226. doi: 10.1371/journal.ppat.1009226.
  • Kozlova EV, Hegde S, Roundy CM, Golovko G, Saldaña MA, Hart CE, Anderson ER, Hornett EA, Khanipov K, Popov VL, Pimenova M, Zhou Y, Fovanov Y, Weaver SC, Routh AL, Heinz E, Hughes GL. Microbial interactions in the mosquito gut determine Serratia colonization and blood-feeding propensity. ISME J. 2021 Jan;15(1):93-108. doi: 10.1038/s41396-020-00763-3.
  • Fan S, Gangwar SP, Machius M, Rudenko G. Interplay between hevin, SPARC, and MDGAs: modulators of neurexin-neuroligin transsynaptic bridges. Structure. 2021 Jan 29:S0969-2126(21)00003-4. doi: 10.1016/j.str.2021.01.003.
  • Zou J, Xie X, Fontes-Garfias CR, Swanson KA, Kanevsky I, Tompkins K, Cutler M, Cooper D, Dormitzer PR, Shi PY. The effect of SARS-CoV-2 D614G mutation on BNT162b2 vaccine-elicited neutralization. NPJ Vaccines. 2021 Mar 25;6(1):44. doi: 10.1038/s41541-021-00313-8.
  • Suryadevara N, Shrihari S, Gilchuk P, VanBlargan LA, Binshtein E, Zost SJ, Nargi RS, Sutton RE, Winkler ES, Chen EC, Fouch ME, Davidson E, Doranz BJ, Chen RE, Shi PY, Carnahan RH, Thackray LB, Diamond MS, Crowe JE Jr. Neutralizing and protective human monoclonal antibodies recognizing the N-terminal domain of the SARS-CoV-2 spike protein. Cell. 2021 Mar 16:S0092-8674(21)00357-3. doi: 10.1016/j.cell.2021.03.029.
  • Liu Y, Liu J, Xia H, Zhang X, Fontes-Garfias CR, Swanson KA, Cai H, Sarkar R, Chen W, Cutler M, Cooper D, Weaver SC, Muik A, Sahin U, Jansen KU, Xie X, Dormitzer PR, Shi PY. Neutralizing Activity of BNT162b2-Elicited Serum. N Engl J Med. 2021 Mar 8. doi: 10.1056/NEJMc2102017.
  • Chen RE, Zhang X, Case JB, Winkler ES, Liu Y, VanBlargan LA, Liu J, Errico JM, Xie X, Suryadevara N, Gilchuk P, Zost SJ, Tahan S, Droit L, Turner JS, Kim W, Schmitz AJ, Thapa M, Wang D, Boon ACM, Presti RM, O'Halloran JA, Kim AHJ, Deepak P, Pinto D, Fremont DH, Crowe JE Jr, Corti D, Virgin HW, Ellebedy AH, Shi PY, Diamond MS. Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Nat Med. 2021 Mar 4. doi: 10.1038/s41591-021-01294-w.
  • Xu P, Gao J, Shan C, Dunn TJ, Xie X, Xia H, Zou J, Thames BH, Sajja A, Yu Y, Freiberg AN, Vasilakis N, Shi PY, Weaver SC, Wu P. Inhibition of innate immune response ameliorates Zika virus-induced neurogenesis deficit in human neural stem cells. PLoS Negl Trop Dis. 2021 Mar 3;15(3):e0009183. doi: 10.1371/journal.pntd.0009183.
  • Bailey AL, Dmytrenko O, Greenberg L, Bredemeyer AL, Ma P, Liu J, Penna V, Winkler ES, Sviben S, Brooks E, Nair AP, Heck KA, Rali AS, Simpson L, Saririan M, Hobohm D, Stump WT, Fitzpatrick JA, Xie X, Zhang X, Shi PY, Hinson JT, Gi WT, Schmidt C, Leuschner F, Lin CY, Diamond MS, Greenberg MJ, Lavine KJ. SARS-CoV-2 Infects Human Engineered Heart Tissues and Models COVID-19 Myocarditis. JACC Basic Transl Sci. 2021 Feb 26. doi: 10.1016/j.jacbts.2021.01.002.
  • Zhang X, Liu Y, Liu J, Bailey AL, Plante KS, Plante JA, Zou J, Xia H, Bopp NE, Aguilar PV, Ren P, Menachery VD, Diamond MS, Weaver SC, Xie X, Shi PY. A trans-complementation system for SARS-CoV-2 recapitulates authentic viral replication without virulence. Cell. 2021 Feb 23:S0092-8674(21)00233-6. doi: 10.1016/j.cell.2021.02.044.
  • Adam A, Fontes-Garfias CR, Sarathy VV, Liu Y, Luo H, Davis E, Li W, Muruato AE, Wang B, Ahatov R, Mahmoud Y, Shan C, Osman SR, Widen SG, Barrett ADT, Shi PY, Wang T. A genetically stable Zika virus vaccine candidate protects mice against virus infection and vertical transmission. NPJ Vaccines. 2021 Feb 17;6(1):27. doi: 10.1038/s41541-021-00288-6.
  • Liu Y, Liu J, Xia H, Zhang X, Fontes-Garfias CR, Swanson KA, Cai H, Sarkar R, Chen W, Cutler M, Cooper D, Weaver SC, Muik A, Sahin U, Jansen KU, Xie X, Dormitzer PR, Shi PY. Neutralizing Activity of BNT162b2-Elicited Serum - Preliminary Report. N Engl J Med. 2021 Feb 17. doi: 10.1056/NEJMc2102017.
  • Diamond M, Chen R, Xie X, Case J, Zhang X, VanBlargan L, Liu Y, Liu J, Errico J, Winkler E, Suryadevara N, Tahan S, Turner J, Kim W, Schmitz A, Thapa M, Wang D, Boon A, Pinto D, Presti R, O'Halloran J, Kim A, Deepak P, Fremont D, Corti D, Virgin H, Crowe J, Droit L, Ellebedy A, Shi PY, Gilchuk P. SARS-CoV-2 variants show resistance to neutralization by many monoclonal and serum-derived polyclonal antibodies. Res Sq [Preprint]. 2021 Feb 10:rs.3.rs-228079. doi: 10.21203/rs.3.rs-228079/v1. Update in: Nat Med. 2021 Mar 4.
  • Xie X, Liu Y, Liu J, Zhang X, Zou J, Fontes-Garfias CR, Xia H, Swanson KA, Cutler M, Cooper D, Menachery VD, Weaver SC, Dormitzer PR, Shi PY. Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K and N501Y variants by BNT162b2 vaccine-elicited sera. Nat Med. 2021 Feb 8. doi: 10.1038/s41591-021-01270-4.
  • Xie X, Lokugamage KG, Zhang X, Vu MN, Muruato AE, Menachery VD, Shi PY. Engineering SARS-CoV-2 using a reverse genetic system. Nat Protoc. 2021 Mar;16(3):1761-1784. doi: 10.1038/s41596-021-00491-8.
  • Kotaki T, Xie X, Shi PY, Kameoka M. A PCR amplicon-based SARS-CoV-2 replicon for antiviral evaluation. Sci Rep. 2021 Jan 26;11(1):2229. doi: 10.1038/s41598-021-82055-0.
  • Williams AN, Sherman MB, Smith HQ, Taube S, Pettitt BM, Wobus CE, Smith TJ. A norovirus uses bile salts to escape antibody recognition while enhancing receptor binding. J Virol. 2021 Apr 7:JVI.00176-21. doi: 10.1128/JVI.00176-21.
  • Enwerem III, Elrod ND, Chang CT, Lin A, Ji P, Bohn JA, Levdansky Y, Wagner EJ, Valkov E, Goldstrohm AC. Human Pumilio proteins directly bind the CCR4-NOT deadenylase complex to regulate the transcriptome. RNA. 2021 Apr;27(4):445-464. doi: 10.1261/rna.078436.120.
  • Sampson CM, Dimet AL, Neelakantan H, Ogunseye KO, Stevenson HL, Hommel JD, Watowich SJ. Combined nicotinamide N-methyltransferase inhibition and reduced-calorie diet normalizes body composition and enhances metabolic benefits in obese mice. Sci Rep. 2021 Mar 11;11(1):5637. doi: 10.1038/s41598-021-85051-6.
  • Adam A, Luo H, Osman SR, Wang B, Roundy CM, Auguste AJ, Plante KS, Peng BH, Thangamani S, Frolova EI, Frolov I, Weaver SC, Wang T. Optimized production and immunogenicity of an insect virus-based chikungunya virus candidate vaccine in cell culture and animal models. Emerg Microbes Infect. 2021 Dec;10(1):305-316. doi: 10.1080/22221751.2021.1886598.
  • McDougal AN, Elhassani D, DeMaet MA, Shores S, Plante KS, Plante JA, Pyles R, Weaver SC, Williams-Bouyer N, Tyler BJ, Davis HR, Patel J. Outbreak of coronavirus disease 2019 (COVID-19) among operating room staff of a tertiary referral center: An epidemiologic and environmental investigation. Infect Control Hosp Epidemiol. 2021 Mar 19:1-7. doi: 10.1017/ice.2021.116.
  • Plante KS, Dwivedi V, Plante JA, Fernandez D, Mirchandani D, Bopp N, Aguilar PV, Park JG, Tamayo PP, Delgado J, Shivanna V, Torrelles JB, Martinez-Sobrido L, Matos R, Weaver SC, Sastry KJ, Newman RA. Antiviral activity of oleandrin and a defined extract of Nerium oleander against SARS-CoV-2. Biomed Pharmacother. 2021 Mar 3;138:111457. doi: 10.1016/j.biopha.2021.111457.
  • Plante JA, Mitchell BM, Plante KS, Debbink K, Weaver SC, Menachery VD. The variant gambit: COVID-19's next move. Cell Host Microbe. 2021 Mar 1:S1931-3128(21)00099-8. doi: 10.1016/j.chom.2021.02.020.
  • Campos RK, Mirchandani D, Rafael G, Saada N, McMahon R, Weaver SC. SARS-CoV-2 decontamination of skin with disinfectants active during and after application. J Hosp Infect. 2021 Feb 10:S0195-6701(21)00050-5. doi: 10.1016/j.jhin.2021.02.004.
  • Liu J, Liu Y, Shan C, Nunes BTD, Yun R, Haller SL, Rafael GH, Azar SR, Andersen CR, Plante K, Vasilakis N, Shi PY, Weaver SC. Role of mutational reversions and fitness restoration in Zika virus spread to the Americas. Nat Commun. 2021 Jan 26;12(1):595. doi: 10.1038/s41467-020-20747-3.
  • Weaver SC, Forrester NL, Liu J, Vasilakis N. Population bottlenecks and founder effects: implications for mosquito-borne arboviral emergence. Nat Rev Microbiol. 2021 Mar;19(3):184-195. doi: 10.1038/s41579-020-00482-8.
  • Aljak ER, Eldigail M, Mahmoud I, Elhassan RM, Elduma A, Ibrahim AA, Ali Y, Weaver SC, Ahmed A. The first laboratory-confirmed imported infections of SARS-CoV-2 in Sudan. Trans R Soc Trop Med Hyg. 2021 Jan 7;115(1):103-109. doi: 10.1093/trstmh/traa151.
  • Mugabe VA, Borja LS, Cardoso CW, Weaver SC, Reis MG, Kitron U, Ribeiro GS. Changes in the dynamics of dengue incidence in South and Central America are possibly due to cross-population immunity after Zika virus epidemics. Trop Med Int Health. 2021 Mar;26(3):272-280. doi: 10.1111/tmi.13526.
  • Herrmann GK, Russell WK, Garg NJ, Yin YW. Poly(ADP-Ribose) polymerase 1 regulates mitochondrial DNA repair in a metabolism-dependent manner. J Biol Chem. 2021 Jan 19;296:100309. doi: 10.1016/j.jbc.2021.100309.