@article{sosnowski_rojo-wissar_peng_parade_sharkey_hoyo_murphy_hernandez_johnson_2024, title={Maternal childhood adversity and infant epigenetic aging: Moderation by restless sleep during pregnancy}, volume={66}, ISSN={["1098-2302"]}, DOI={10.1002/dev.22464}, abstractNote={Abstract}, number={2}, journal={DEVELOPMENTAL PSYCHOBIOLOGY}, author={Sosnowski, David W. and Rojo-Wissar, Darlynn M. and Peng, Gang and Parade, Stephanie H. and Sharkey, Katherine and Hoyo, Cathrine and Murphy, Susan K. and Hernandez, Raquel G. and Johnson, Sara B.}, year={2024}, month={Feb} }
 @article{azevedo_cardoso_caldas_vieira werneck_cohen_yamamoto_silva meira_meneses_erthal_sa_et al._2020, title={The impact of Zika virus infection on human semen: a case study}, volume={15}, ISSN={["1746-0808"]}, DOI={10.2217/fvl-2019-0159}, abstractNote={ The outbreak of Zika virus (ZIKV) in Brazil and in many countries was marked by the occurrences of fetal malformations and neurological effects upon infection of pregnant women. Like other members of the Flaviviridae family, ZIKV in semen is infectious and sexually transmitted. Viral persistence in the male genital tract is unresolved and still needs further understanding. A regular semen donor was followed from the acute phase of ZIKV infection, up to 8 months after ZIKV in his body fluids became undetected. Immunofluorescence assay was performed in semen samples before and after the infection. A significant decrease in sperm concentration and in the percentage of progressive motility of sperm was observed. The methodology adopted for clearance of sexually transmitted viruses decreased virus load, but the complete clearance of ZIKV from semen was not achieved. }, number={1}, journal={FUTURE VIROLOGY}, author={Azevedo, Renata Campos and Cardoso, Maria Cecilia A. and Caldas, Lucio Ayres and Vieira Werneck, Caio Luis and Cohen, Cristiane Napoleao and Yamamoto, Kristie Aimi and Silva Meira, Guilherme Louzada and Meneses, Marcelo Damiao and Erthal, Maria Cecilia and Sa, Paulo Gallo and et al.}, year={2020}, month={Jan}, pages={5–12} }
 @article{hernandez_glaros_rizzo_ferreira_2019, title={Purification and Proteomic Analysis of Alphavirus Particles from Sindbis Virus Grown in Mammalian and Insect Cells}, volume={9}, ISSN={["2331-8325"]}, DOI={10.21769/BioProtoc.3239}, abstractNote={Current mass spectrometry (MS) methods and new instrumentation now allow for more accurate identification of proteins in low abundance than previous protein fractionation and identification methods. It was of interest if this method could serve to define the virus proteome of a membrane-containing virus. To evaluate the efficacy of mass spec to determine the proteome of medically important viruses, Sindbis virus (SINV), the prototypical alphavirus was chosen for evaluation. This model system was chosen specifically because the alphaviruses contain members which are human pathogens, this virus is well defined biochemically and structurally, and grows to high titers in both vertebrate and non-vertebrate host cells. The SINV proteome was investigated using this method to determine if host proteins are specifically packaged into infectious virions. It was also of interest if the SINV proteome, when grown in multiple host cells representing vertebrate and mosquito hosts, incorporated specific host proteins from all hosts. Observation of recurrent or distinctive proteins in the virus proteome aided in the determination of proteins incorporated into the virion as opposed to those bound to the particle exterior. Mass spectrometry analysis identified the total protein content of purified virions within limits of detection. The most significant finding was that in addition to the host proteins, SINV non-structural protein 2 (nsP2) was detected within virions grown in all host cells examined. This analysis identified host factors not previously associated with alphavirus entry, replication, or egress, identifying at least one host factor integrally involved in alphavirus replication. Key to the success of this analysis is the method of virus purification which must deliver measurably infectious virus free of high levels of contaminants. For SINV and other members of the alphavirus family, this is accomplished by isopycnic centrifugation through potassium tartrate, followed by a high salt wash.}, number={10}, journal={BIO-PROTOCOL}, author={Hernandez, Raquel and Glaros, Trevor and Rizzo, Gabrielle and Ferreira, Davis F.}, year={2019}, month={May} }
 @article{schuchman_kilianski_piper_vancini_ribeiro_sprague_nasar_boyd_hernandez_glaros_2018, title={Comparative Characterization of the Sindbis Virus Proteome from Mammalian and Invertebrate Hosts Identifies nsP2 as a Component of the Virion and Sorting Nexin 5 as a Significant Host Factor for Alphavirus Replication}, volume={92}, ISSN={["1098-5514"]}, DOI={10.1128/jvi.00694-18}, abstractNote={ABSTRACT}, number={14}, journal={JOURNAL OF VIROLOGY}, author={Schuchman, Ryan and Kilianski, Andy and Piper, Amanda and Vancini, Ricardo and Ribeiro, Jose M. C. and Sprague, Thomas R. and Nasar, Farooq and Boyd, Gabrielle and Hernandez, Raquel and Glaros, Trevor}, year={2018}, month={Jul} }
 @article{schuchman_vancini_piper_breuer_ribeiro_ferreira_magliocca_emmerich_hernandez_brown_2018, title={Role of the vacuolar ATPase in the Alphavirus replication cycle}, volume={4}, ISSN={2405-8440}, url={http://dx.doi.org/10.1016/J.HELIYON.2018.E00701}, DOI={10.1016/J.HELIYON.2018.E00701}, abstractNote={We have shown that Alphaviruses can enter cells by direct penetration at the plasma membrane (R. Vancini, G. Wang, D. Ferreira, R. Hernandez, and D. Brown, J Virol, 87:4352-4359, 2013). Direct penetration removes the requirement for receptor-mediated endocytosis exposure to low pH and membrane fusion in the process of RNA entry. Endosomal pH as well as the pH of the cell cytoplasm is maintained by the activity of the vacuolar ATPase (V-ATPase). Bafilomycin is a specific inhibitor of V-ATPase. To characterize the roll of the V-ATPase in viral replication we generated a Bafilomycin A1(BAF) resistant mutant of Sindbis virus (BRSV). BRSV produced mature virus and virus RNA in greater amounts than parent virus in BAF-treated cells. Sequence analysis revealed mutations in the E2 glycoprotein, T15I/Y18H, were responsible for the phenotype. These results show that a functional V-ATPase is required for efficient virus RNA synthesis and virus maturation in Alphavirus infection.}, number={7}, journal={Heliyon}, publisher={Elsevier BV}, author={Schuchman, Ryan M. and Vancini, Ricardo and Piper, Amanda and Breuer, Denitra and Ribeiro, Mariana and Ferreira, Davis and Magliocca, Joseph and Emmerich, Veronica and Hernandez, Raquel and Brown, Dennis T.}, year={2018}, month={Jul}, pages={e00701} }
 @article{magliocca_vancini_hernandez_brown_2016, title={Single-Site Glycoprotein Mutants Inhibit a Late Event in Sindbis Virus Assembly}, volume={90}, ISSN={["1098-5514"]}, DOI={10.1128/jvi.00948-16}, abstractNote={ABSTRACT}, number={18}, journal={JOURNAL OF VIROLOGY}, author={Magliocca, Joseph and Vancini, Ricardo and Hernandez, Raquel and Brown, Dennis T.}, year={2016}, month={Sep}, pages={8372–8380} }
 @article{schuchman_vancini_piper_breuer_ribeiro_farreira_magliocca_emmerich_hernandez_brown_2016, title={The role of the vacuolar ATPase in alphavirus replication.}, volume={27}, journal={Molecular Biology of the Cell}, author={Schuchman, R. and Vancini, R. and Piper, A. and Breuer, D. and Ribeiro, M. and Farreira, D. and Magliocca, J. and Emmerich, V. and Hernandez, R. and Brown, D.}, year={2016} }
 @misc{vancini_hernandez_brown_2015, title={Alphavirus Entry into Host Cells}, volume={129}, journal={Molecular basis of viral infection}, author={Vancini, R. and Hernandez, R. and Brown, D.}, year={2015}, pages={33–62} }
 @article{briggs_smith_piper_huitt_spears_quiles_ribeiro_thomas_brown_hernandez_2014, title={Live Attenuated Tetravalent Dengue Virus Host Range Vaccine Is Immunogenic in African Green Monkeys following a Single Vaccination}, volume={88}, ISSN={["1098-5514"]}, DOI={10.1128/jvi.00541-14}, abstractNote={ABSTRACT}, number={12}, journal={JOURNAL OF VIROLOGY}, author={Briggs, Caitlin M. and Smith, Katherine M. and Piper, Amanda and Huitt, Emerson and Spears, Carla J. and Quiles, Michelle and Ribeiro, Mariana and Thomas, Malcolm E. and Brown, Dennis T. and Hernandez, Raquel}, year={2014}, month={Jun}, pages={6729–6742} }
 @article{piper_ribeiro_smith_briggs_huitt_nanda_spears_quiles_cullen_thomas_et al._2013, title={Chikungunya Virus Host Range E2 Transmembrane Deletion Mutants Induce Protective Immunity against Challenge in C57BL/6J Mice}, volume={87}, ISSN={["1098-5514"]}, DOI={10.1128/jvi.03357-12}, abstractNote={ABSTRACT}, number={12}, journal={JOURNAL OF VIROLOGY}, author={Piper, Amanda and Ribeiro, Mariana and Smith, Katherine M. and Briggs, Caitlin M. and Huitt, Emerson and Nanda, Kavita and Spears, Carla J. and Quiles, Michelle and Cullen, John and Thomas, Malcolm E. and et al.}, year={2013}, month={Jun}, pages={6748–6757} }
 @article{vancini_kramer_ribeiro_hernandez_brown_2013, title={Flavivirus infection from mosquitoes in vitro reveals cell entry at the plasma membrane}, volume={435}, ISSN={["0042-6822"]}, DOI={10.1016/j.virol.2012.10.013}, abstractNote={Dengue and West Nile viruses are enveloped RNA viruses that belong to genus Flavivirus (family Flaviviridae) and are considered important mosquito-borne viral pathogenic agents worldwide. A potential target for intervention strategies is the virus cell entry mechanism. Previous studies of flavivirus entry have focused on the effects of biochemical and molecular inhibitors on viral entry leading to controversial conclusions suggesting that the process is dependent upon endocytosis and low pH mediated membrane fusion. In this study we analyzed the early events in the infection process by means of electron microscopy and immuno-gold labeling of viral particles during cell entry, and used as a new approach for infecting cells with viruses obtained directly from mosquitoes. The results show that Dengue and West Nile viruses may infect cells by a mechanism that involves direct penetration of the host cell plasma membrane as proposed for alphaviruses.}, number={2}, journal={VIROLOGY}, author={Vancini, Ricardo and Kramer, Laura D. and Ribeiro, Mariana and Hernandez, Raquel and Brown, Dennis}, year={2013}, month={Jan}, pages={406–414} }
 @article{he_piper_meilleur_hernandez_heller_brown_2012, title={Conformational Changes in Sindbis Virus Induced by Decreased pH Are Revealed by Small-Angle Neutron Scattering}, volume={86}, ISSN={["0022-538X"]}, url={http://europepmc.org/abstract/med/22156534}, DOI={10.1128/jvi.06569-11}, abstractNote={ABSTRACT}, number={4}, journal={JOURNAL OF VIROLOGY}, author={He, Lilin and Piper, Amanda and Meilleur, Flora and Hernandez, Raquel and Heller, William T. and Brown, Dennis T.}, year={2012}, month={Feb}, pages={1982–1987} }
 @article{brown_hernandez_2012, title={Infection of cells by alphaviruses}, volume={726}, journal={Viral molecular machines}, author={Brown, D. T. and Hernandez, R.}, year={2012}, pages={181–199} }
 @article{smith_nanda_mccarl_spears_piper_ribeiro_quiles_briggs_thomas_thomas_et al._2012, title={Testing of Novel Dengue Virus 2 Vaccines in African Green Monkeys: Safety, Immunogenicity, and Efficacy}, volume={87}, ISSN={["1476-1645"]}, DOI={10.4269/ajtmh.2012.12-0004}, abstractNote={The immunogenicity and safety of three novel host-range vaccines containing deletions in the transmembrane domain of dengue virus serotype 2 (DV2) E glycoprotein were evaluated in African green monkeys. The shorter transmembrane domains are capable of functionally spanning an insect but not a mammalian cell membrane, resulting in production of viral mutants that have reduced infectivity in mammalian hosts but efficient growth in insect cells. Groups of four monkeys received one dose each of test vaccine candidate with no booster immunization. After immunization, levels of viremia produced by each vaccine were determined by infectious center assay. Vaccine recipient immune response to wild-type DV2 challenge was measured on Day 57 by enzyme-linked immunosorbent assay and plaque reduction neutralization test. Two vaccines, DV2ΔGVII and DV2G460P, generated neutralizing antibody in the range of 700–900 50% plaque reduction neutralization test units. All three vaccine strains decreased the length of viremia by at least two days. No safety concerns were identified.}, number={4}, journal={AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE}, author={Smith, Katherine M. and Nanda, Kavita and McCarl, Victoria and Spears, Carla J. and Piper, Amanda and Ribeiro, Mariana and Quiles, Michelle and Briggs, Caitlin M. and Thomas, Gwynneth S. and Thomas, Malcolm E. and et al.}, year={2012}, month={Oct}, pages={743–753} }
 @article{hunt_hernandez_brown_2011, title={Role of the Vacuolar-ATPase in Sindbis Virus Infection}, volume={85}, ISSN={["1098-5514"]}, DOI={10.1128/jvi.01864-10}, abstractNote={ABSTRACT}, number={3}, journal={JOURNAL OF VIROLOGY}, author={Hunt, Sabrina R. and Hernandez, Raquel and Brown, Dennis T.}, year={2011}, month={Feb}, pages={1257–1266} }
 @article{smith_nanda_spears_ribeiro_vancini_piper_thomas_thomas_brown_hernandez_2011, title={Structural mutants of dengue virus 2 transmembrane domains exhibit host-range phenotype}, volume={8}, ISSN={["1743-422X"]}, DOI={10.1186/1743-422x-8-289}, abstractNote={There are over 700 known arboviruses and at least 80 immunologically distinct types that cause disease in humans. Arboviruses are transmitted among vertebrates by biting insects, chiefly mosquitoes and ticks. These viruses are widely distributed throughout the world, depending on the presence of appropriate hosts (birds, horses, domestic animals, humans) and vectors. Mosquito-borne arboviruses present some of the most important examples of emerging and resurgent diseases of global significance. A strategy has been developed by which host-range mutants of Dengue virus can be constructed by generating deletions in the transmembrane domain (TMD) of the E glycoprotein. The host-range mutants produced and selected favored growth in the insect hosts. Mouse trials were conducted to determine if these mutants could initiate an immune response in an in vivo system. The DV2 E protein TMD defined as amino acids 452SWTMKILIGVIITWIG467 was found to contain specific residues which were required for the production of this host-range phenotype. Deletion mutants were found to be stable in vitro for 4 sequential passages in both host cell lines. The host-range mutants elicited neutralizing antibody above that seen for wild-type virus in mice and warrant further testing in primates as potential vaccine candidates. Novel host-range mutants of DV2 were created that have preferential growth in insect cells and impaired infectivity in mammalian cells. This method for creating live, attenuated viral mutants that generate safe and effective immunity may be applied to many other insect-borne viral diseases for which no current effective therapies exist.}, journal={VIROLOGY JOURNAL}, author={Smith, Katherine M. and Nanda, Kavita and Spears, Carla J. and Ribeiro, Mariana and Vancini, Ricardo and Piper, Amanda and Thomas, Gwynneth S. and Thomas, Malcolm E. and Brown, Dennis T. and Hernandez, Raquel}, year={2011}, month={Jun} }
 @article{hernandez_brown_2010, title={Growth and Maintenance of Baby Hamster Kidney (BHK) Cells}, volume={17}, ISSN={1934-8525}, url={http://dx.doi.org/10.1002/9780471729259.MCA04HS17}, DOI={10.1002/9780471729259.MCA04HS17}, abstractNote={Abstract}, number={1}, journal={Current Protocols in Microbiology}, publisher={Wiley}, author={Hernandez, Raquel and Brown, Dennis T.}, year={2010}, month={May}, pages={A.4H.1-A.4H.7} }
 @article{hernandez_brown_2010, title={Growth and Maintenance of Chick Embryo Fibroblasts (CEF)}, volume={17}, ISSN={1934-8525}, url={http://dx.doi.org/10.1002/9780471729259.MCA04IS17}, DOI={10.1002/9780471729259.MCA04IS17}, abstractNote={Abstract}, number={1}, journal={Current Protocols in Microbiology}, publisher={Wiley}, author={Hernandez, Raquel and Brown, Dennis T.}, year={2010}, month={May}, pages={A.4I.1-A.4I.8} }
 @article{hernandez_brown_2010, title={Growth and Maintenance of Mosquito Cell Lines}, volume={17}, ISSN={1934-8525}, url={http://dx.doi.org/10.1002/9780471729259.MCA04JS17}, DOI={10.1002/9780471729259.MCA04JS17}, abstractNote={Abstract}, number={1}, journal={Current Protocols in Microbiology}, publisher={Wiley}, author={Hernandez, Raquel and Brown, Dennis T.}, year={2010}, month={May}, pages={A.4J.1-A.4J.8} }
 @article{mudiganti_hernandez_brown_2010, title={Insect response to alphavirus infection-Establishment of alphavirus persistence in insect cells involves inhibition of viral polyprotein cleavage}, volume={150}, ISSN={["1872-7492"]}, DOI={10.1016/j.virusres.2010.02.016}, abstractNote={Alphavirus persistence in the insect vector is an essential element in the vector–host transmission cycle of the virus and provides a model to study the biochemical and molecular basis for virus–vector coexistence. The prototype alphavirus Sindbis (SV) establishes persistent infections in invertebrate cell cultures which are characterized by low levels of virus production. We hypothesized that antiviral factors may be involved in decreasing the virus levels as virus persistence is established in invertebrate cells. Transcription profiles in Drosophila S2 cells at 5 days post-infection with SV identified families of gene products that code for factors that can explain previous observations seen in insect cells infected with alphaviruses. Genomic array analysis identified up-regulation of gene products involved in intracellular membrane vesicle formation, cell growth rate changes and immune-related functions in S2 cells infected with SV. Transcripts coding for factors involved in different aspects of the Notch signaling pathway had increased in expression. Increased expression of ankyrin, plap, syx13, unc-13, csp, rab1 and rab8 may aid in formation of virus containing vesicles and in intracellular transport of viral structural proteins. Possible functions of these gene products and relevant hypotheses are discussed. We confirmed the up-regulation of a wide-spectrum protease inhibitor, Thiol-ester containing Protein (TEP) II. We report inhibition of the viral polyprotein cleavage at 5 days post-infection (dpi) and after superinfection of SV-infected cells at 5 dpi. We propose that inefficient cleavage of the polyprotein may, at least in part, lead to reduced levels of virus seen as persistence is established.}, number={1-2}, journal={VIRUS RESEARCH}, author={Mudiganti, Usharani and Hernandez, Raquel and Brown, Dennis T.}, year={2010}, month={Jun}, pages={73–84} }
 @article{he_piper_meilleur_myles_hernandez_brown_heller_2010, title={The Structure of Sindbis Virus Produced from Vertebrate and Invertebrate Hosts as Determined by Small-Angle Neutron Scattering}, volume={84}, ISSN={["1098-5514"]}, url={http://europepmc.org/abstract/med/20219936}, DOI={10.1128/jvi.00044-10}, abstractNote={ABSTRACT}, number={10}, journal={JOURNAL OF VIROLOGY}, author={He, Lilin and Piper, Amanda and Meilleur, Flora and Myles, Dean A. A. and Hernandez, Raquel and Brown, Dennis T. and Heller, William T.}, year={2010}, month={May}, pages={5270–5276} }
 @article{nanda_vancini_ribeiro_brown_hernandez_2009, title={A high capacity Alphavirus heterologous gene delivery system}, volume={390}, ISSN={["0042-6822"]}, DOI={10.1016/j.virol.2009.05.026}, abstractNote={A novel replication competent Sindbis virus based gene delivery vector has been developed for the introduction of genetic cargo into cell lines in vitro and potentially, animal models in vivo. This delivery system expands the previous uses of Sindbis virus as a gene delivery system in that no replicons are required and the resulting cargo containing virus particles are infectious. The heterologous vector is based on a morphological mutant in C, Ser180/Gly183 which produces larger than the normal size T=4 virus particles of 70 nm in size. This mutant produced particles up to 205 nm in size equal to a triangulation number of 36. It was postulated that because the Ser180/Gly183 mutant was capable of assembling such large particles, that increasing the size of the RNA genome incorporated into this mutant capsid protein would favor the assembly of larger than T=4 wild type sized virions. The first generation prototype larger vehicle, described here, carries a approximately 18 kb cDNA insert, however it is conceivable that RNA as large as 32 kb could be transcribed and packaged. The large variant produces a high virus titer of approximately 10(9) pfu/ml from either mammalian or insect cells in culture. Multiple passages of the virus show no loss of the inserted genetic material.}, number={2}, journal={VIROLOGY}, author={Nanda, Kavita and Vancini, Ricardo and Ribeiro, Mariana and Brown, Dennis T. and Hernandez, Raquel}, year={2009}, month={Aug}, pages={368–373} }
 @article{hafer_whittlesey_brown_hernandez_2009, title={Differential Incorporation of Cholesterol by Sindbis Virus Grown in Mammalian or Insect Cells}, volume={83}, ISSN={["1098-5514"]}, DOI={10.1128/JVI.00755-09}, abstractNote={ABSTRACT}, number={18}, journal={JOURNAL OF VIROLOGY}, author={Hafer, Amanda and Whittlesey, Rebecca and Brown, Dennis T. and Hernandez, Raquel}, year={2009}, month={Sep}, pages={9113–9121} }
 @article{kononchik_nelson_hernandez_brown_2009, title={Helical virus particles formed from morphological subunits of a membrane containing icosahedral virus}, volume={385}, ISSN={["0042-6822"]}, DOI={10.1016/j.virol.2008.12.015}, abstractNote={The classic publication by Caspar and Klug in 1962 [Physical principles in the construction of regular viruses. Cold Spring Harbor Symp. Quant. Biol. 27:1–24.] has formed the basis of much research on virus assembly. Caspar and Klug predicted that a single virus morphological unit could form a two dimensional lattice composed of 6-fold arrays (primitive plane), a family of icosahedra of increasing triangulation numbers (T) and helical arrays of varying length. We have shown that icosahedral viruses of varying T numbers can be produced using Sindbis virus [Ferreira, D. F. et al. 2003. Morphological variants of Sindbis virus produced by a mutation in the capsid protein. Virology 307:54–66]. Other studies have shown that Sindbis glycoproteins can also form a 2-dimensional lattice confirming Caspar and Klug's prediction of the primitive plane as a biologically relevant structure [VonBonsdorff, C. H., and S. C. Harrison. 1978. Sindbis virus glycoproteins form a regular icosahedral surface lattice. J. Virol. 28:578]. In this study we have used mutations in the glycoproteins of membrane containing Sindbis virus to create helical-virus-like particles from the morphological subunits of a virus of icosahedral geometry. The resulting virus particles were examined for subunit organization and were determined to be constructed of only 6-fold rotational arrays of the virus glycoproteins. A model of the tubular virus particles created from the 6-fold rotational arrays of Sindbis virus confirmed the observed structure. These experiments show that a common morphological unit (the Sindbis E1–E2 heterodimer) can produce three different morphological entities of varying dimensions in a membrane-containing virus system.}, number={2}, journal={VIROLOGY}, author={Kononchik, Joseph R., Jr. and Nelson, Steevenson and Hernandez, Raquel and Brown, Dennis I.}, year={2009}, month={Mar}, pages={285–293} }
 @misc{hernandez_paredes_2009, title={Sindbis virus as a model for studies of conformational changes in a metastable virus and the role of conformational changes in in vitro antibody neutralisation}, volume={19}, ISSN={["1099-1654"]}, DOI={10.1002/rmv.619}, abstractNote={Abstract}, number={5}, journal={REVIEWS IN MEDICAL VIROLOGY}, author={Hernandez, Raquel and Paredes, Angel}, year={2009}, month={Sep}, pages={257–272} }
 @article{smith_nanda_slominski_hernandez_brown_thomas_2008, title={Construction and characterization of mutant Dengue2 virus vaccine candidates displaying a host-range phenotype}, journal={Vaccine}, author={Smith, K. M. and Nanda, K. and Slominski, C. J. and Hernandez, R. and Brown, D. T. and Thomas, M. E.}, year={2008} }
 @article{hernandez_paredes_brown_2008, title={Sindbis virus conformational changes induced by a neutralizing anti-E1 monoclonal antibody}, volume={82}, ISSN={["0022-538X"]}, DOI={10.1128/JVI.02673-07}, abstractNote={ABSTRACT}, number={12}, journal={JOURNAL OF VIROLOGY}, author={Hernandez, Raquel and Paredes, Angel and Brown, Dennis T.}, year={2008}, month={Jun}, pages={5750–5760} }
 @article{wang_hernandez_keith_brown_2007, title={Infection of cells by Sindbis virus at low temperature}, volume={362}, DOI={10.1016/j.virol.2006.12.036}, abstractNote={Sindbis virus, which belongs to the family Togaviridae genus Alphavirus infects a variety of vertebrate and invertebrate cells. The initial steps of Sindbis virus infection involve attachment, penetration and uncoating. Two different pathways of infection have been proposed for Alphaviruses. One proposed mechanism involves receptor mediated virion endocytosis followed by membrane fusion triggered by endosome acidification. This virus–host membrane fusion model, well established by influenza virus, has been applied to other unrelated membrane-containing viruses including Alphaviruses. The other mechanism proposes direct penetration of the cell plasma membrane by the virus glycoproteins in the absence of membrane fusion. This alternate model is supported by both ultrastructural [Paredes, A.M., Ferreira, D., Horton, M., Saad, A., Tsuruta, H., Johnston, R., Klimstra, W., Ryman, K., Hernandez, R., Chiu, W., Brown, D.T., 2004. Conformational changes in Sindbis virions resulting from exposure to low pH and interactions with cells suggest that cell penetration may occur at the cell surface in the absence of membrane fusion. Virology 324(2), 373–386] and biochemical [Koschinski, A., Wengler, G., Wengler, G., and Repp, H., 2005. Rare earth ions block the ion pores generated by the class II fusion proteins of alphaviruses and allow analysis of the biological functions of these pores. J. Gen. Virol. 86(Pt. 12), 3311–3320] studies. We have examined the ability of Sindbis virus to infect Baby Hamster Kidney (BHK) cells at temperatures which block endocytosis. We have found that under these conditions Sindbis virus infects cells in a temperature- and time-dependent fashion.}, number={2}, journal={Virology}, author={Wang, G. B. and Hernandez, R. and keith and Brown, D. T.}, year={2007}, pages={461–467} }
 @article{whitehurst_soderblom_west_hernandez_goshe_brown_2007, title={Location and role of free cysteinyl residues in the Sindbis virus E1 and E2 glycoproteins}, volume={81}, ISSN={["0022-538X"]}, DOI={10.1128/JVI.02859-06}, abstractNote={ABSTRACT}, number={12}, journal={JOURNAL OF VIROLOGY}, author={Whitehurst, Christopher B. and Soderblom, Erik J. and West, Michelle L. and Hernandez, Raquel and Goshe, Michael B. and Brown, Dennis T.}, year={2007}, month={Jun}, pages={6231–6240} }
 @article{heldt_hernandez_mudiganti_gurgel_brown_carbonell_2006, title={A  colorimetric assay for viral agents that produce cytopathic effects}, volume={135}, DOI={10.1016/j.j.viromet.2006.01.022}, number={1}, journal={Journal of Virological Methods}, author={Heldt, C. L. and Hernandez, R. and Mudiganti, U. and Gurgel, P. V. and Brown, D. T. and Carbonell, R. G.}, year={2006}, pages={56–65} }
 @article{heldt_hernandez_mudiganti_gurgel_brown_carbonell_2006, title={A colorimetric assay for viral agents that produce cytopathic effects}, volume={135}, ISSN={0166-0934}, url={http://dx.doi.org/10.1016/j.jviromet.2006.01.022}, DOI={10.1016/j.jviromet.2006.01.022}, abstractNote={Many animal viruses produce cytopathic effects in their host cells during a productive infection. While some virus infections can be assayed by the production of plaques, many viruses, while producing cytotoxicity, do not easily form plaques, or do not form plaques at all. Additionally, viruses within families such as the parvoviruses may have different preferred forms of titration making comparative virology difficult even among related groups. Porcine parvovirus (PPV), canine parvovirus (CPV), and minute virus of mice (MVM) are usually titrated using different infectivity assays. A direct comparison of infectious virus titer between these parvoviruses was sought, and a tetrazolium salt assay, MTT has been applied to measure cytopathic effect produced by viral infection for different members of the parvovirus family. Infectious PPV measured using the MTT and the TCID50 assays exhibited excellent correlation and titers for CPV and MVM were consistently duplicated using the MTT assay. The MTT assay was also applied to an unrelated virus, Sindbis, which is routinely titrated by plaque assay. MTT titration of Sindbis virus mutants was found to be valuable for preliminary screening. This assay can be adapted, by correlation to an accepted titration method, to any viral system which produces measurable cytopathic effect.}, number={1}, journal={Journal of Virological Methods}, publisher={Elsevier BV}, author={Heldt, Caryn L. and Hernandez, Raquel and Mudiganti, Usharani and Gurgel, Patrick V. and Brown, Dennis T. and Carbonell, Ruben G.}, year={2006}, month={Jul}, pages={56–65} }
 @article{west_hernandez_ferreira_brown_2006, title={Mutations in the endodomain of Sindbis virus glycoprotein E2 define sequences critical for virus assembly}, volume={80}, ISSN={["1098-5514"]}, DOI={10.1128/jvi.80.9.4458-4468.2006}, abstractNote={ABSTRACT}, number={9}, journal={JOURNAL OF VIROLOGY}, author={West, J and Hernandez, R and Ferreira, D and Brown, DT}, year={2006}, month={May}, pages={4458–4468} }
 @article{mudiganti_hernandez_ferreira_brown_2006, title={Sindbis virus infection of two model insect cell systems - A comparative study}, volume={122}, DOI={10.1016/j.virusres.2006.06.007}, abstractNote={Sindbis, the prototype of the Alphaviruses causes mosquito-borne diseases in mammals and replicates in a wide variety of vertebrate and invertebrate cell cultures. This characteristic can be exploited to use the vast array of Drosophila genetic information available for investigations of the interaction of Sindbis virus with an alternate invertebrate host. For this purpose, a comparative study of Sindbis virus infection of Schnieder-2 Drosophila (S2) cells to cells of the mosquito Aedes albopictus (clone U4.4) was undertaken. After infection, vertebrate cells die within 24–48 h, while invertebrate cell cultures survive an acute phase of infection and become persistently infected. In this study, infection of a model Drosophila system, S2 cells, was compared to U4.4 cells. Virus production, the time course of the establishment of persistence and changes in growth properties of the S2 cells upon infection, were studied in comparison to those of the U4.4 cells. S2 cells survived acute Sindbis infection without any significant cytopathology and continued to produce low levels of virus characteristic of persistently infected cells. S2 cells produced 10 PFU/cell on day 1 post-infection, which falls to 2 PFU/cell on day 2. This result is in contrast to U4.4 cells, which produce peak virus titer on day 2 post-infection and establish persistence by day 5. Onset of the persistent phase of infection of either U4.4 or S2 cells did not result in any change in morphology or growth characteristics. This study establishes S2 cells as an additional invertebrate model system to study the interactions of an invertebrate host with Sindbis virus.}, number={1-2}, journal={Virus Research}, author={Mudiganti, U. and Hernandez, R. and Ferreira, D. and Brown, D. T.}, year={2006}, pages={28–34} }
 @article{whitehurst_willis_sinodis_hernandez_brown_2006, title={Single and multiple deletions in the transmembrane domain of the Sindbis virus E2 glycoprotein identify a region critical for normal virus growth}, volume={347}, ISSN={["0042-6822"]}, DOI={10.1016/j.virol.2005.11.029}, abstractNote={Sindbis virus is composed of two nested T = 4 icosahedral protein shells containing 240 copies each of three structural proteins: E1, E2, and Capsid in a 1:1:1 stoichiometric ratio. E2 is a 423 amino acid glycoprotein with a membrane spanning domain 26 amino acids in length and a 33 amino acid cytoplasmic endodomain. The interaction of the endodomain with the nucleocapsid is an essential step in virus maturation and directs the formation of the outer protein shell as envelopment occurs. A previous study had determined that deletions in the transmembrane domain could affect virus assembly and infectivity (Hernandez et al., 2003. J. Virol. 77 (23), 12710-12719). Unexpectedly, a single deletion mutant (from 26 to 25 amino acids) resulted in a 1000-fold decrease in infectious virus production while another deletion of eight amino acids had no affect on infectious virus production. To further investigate the importance of these mutants, other single deletion mutants and another eight amino acid deletion mutant were constructed. We found that deletions located closer to the cytoplasmic (inner leaflet) of the membrane bilayer had a more detrimental effect on virus assembly and infectivity than those located closer to the luminal (outer leaflet) of the membrane bilayer. We also found that selective pressure can restore single amino acid deletions in the transmembrane domain but not necessarily to the wild type sequence. The partial restoration of an eight amino acid deletion (from 18 to 22 amino acids) also partially restored infectious virus production. The amount of infectious virus produced by this revertant was equivalent to that produced for the four amino acid deletion produced by site directed mutagenesis. These results suggest that the position of the deletion and the length of the C terminal region of the E2 transmembrane domain is vital for normal virus production. Deletion mutants resulting in decreased infectivity produce particles that appear to be processed and transported correctly suggesting a role involved in virus entry.}, number={1}, journal={VIROLOGY}, author={Whitehurst, CB and Willis, JH and Sinodis, CN and Hernandez, R and Brown, DT}, year={2006}, month={Mar}, pages={199–207} }
 @article{nelson_hernandez_ferreira_brown_2005, title={In vivo processing and isolation of furin protease-sensitive alphavirus glycoproteins: a new technique for producing mutations in virus assembly}, volume={332}, ISSN={["0042-6822"]}, DOI={10.1016/j.virol.2004.12.013}, abstractNote={Sindbis virus particles are composed of three structural proteins (Capsid/E2/E1). In the mature virion the E1 glycoprotein is organized in a highly constrained, energy-rich conformation. It is hypothesized that this energy is utilized to drive events that deliver the viral genome to the cytoplasm of a host cell. The extraction of the E1 glycoprotein from virus membranes with detergent results in disulfide-bridge rearrangement and the collapse of the protein to a number of low-energy, non-native configurations. In a new approach to the production of membrane-free membrane glycoproteins, furin protease recognition motifs were installed at various positions in the E1 glycoprotein ectodomain. Proteins containing the furin-sensitive sites undergo normal folding and assembly in the endoplasmic reticulum and only experience the consequence of the mutation during transport to the cell surface. Processing by furin in the Golgi results in the release of the protein from the membrane. Processing of the proteins also impacts the envelopment of the nucleocapsid in the modified plasma membrane. This technique provides a unique method for studying the mechanism of virus assembly and protein structure without altering crucial early events in protein assembly, folding, and maturation.}, number={2}, journal={VIROLOGY}, author={Nelson, S and Hernandez, R and Ferreira, D and Brown, DT}, year={2005}, month={Feb}, pages={629–639} }
 @article{hernandez_ferreira_sinodis_litton_brown_2005, title={Single amino acid insertions at the junction of the Sindbis virus e2 transmembrane domain and endodomain disrupt virus envelopment and alter infectivity}, volume={79}, DOI={10.1128/JVI.79.7682-7697.2005}, number={12}, journal={Journal of Virology}, author={Hernandez, R. and Ferreira, D. and Sinodis, C. and Litton, K. and Brown, D. T.}, year={2005}, pages={7682–7697} }
 @article{paredes_ferreira_horton_saad_tsuruta_johnston_klimstra_ryman_hernandez_chiu_et al._2004, title={Conformational changes in Sindbis virions resulting from exposure to low pH and interactions with cells suggest that cell penetration may occur at the cell surface in the absence of membrane fusion}, volume={324}, DOI={10.1016/j.virus.2004.03.046}, number={2}, journal={Virology}, author={Paredes, A. M. and Ferreira, D. and Horton, M. and Saad, A. and Tsuruta, H. and Johnston, R. and Klimstra, W. and Ryman, K. and Hernandez, R. and Chiu, W. and et al.}, year={2004}, pages={373–386} }
 @article{paredes_ferreira_horton_saad_tsuruta_johnston_klimstra_ryman_hernandez_chiu_et al._2004, title={Conformational changes in Sindbis virions resulting from exposure to low pH and interactions with cells suggest that cell penetration may occur at the cell surface in the absence of membrane fusion}, volume={324}, ISSN={0042-6822}, url={http://dx.doi.org/10.1016/j.virol.2004.03.046}, DOI={10.1016/j.virol.2004.03.046}, abstractNote={Alphaviruses have the ability to induce cell–cell fusion after exposure to acid pH. This observation has served as an article of proof that these membrane-containing viruses infect cells by fusion of the virus membrane with a host cell membrane upon exposure to acid pH after incorporation into a cell endosome. We have investigated the requirements for the induction of virus-mediated, low pH-induced cell–cell fusion and cell–virus fusion. We have correlated the pH requirements for this process to structural changes they produce in the virus by electron cryo-microscopy. We found that exposure to acid pH was required to establish conditions for membrane fusion but that membrane fusion did not occur until return to neutral pH. Electron cryo-microscopy revealed dramatic changes in the structure of the virion as it was moved to acid pH and then returned to neutral pH. None of these treatments resulted in the disassembly of the virus protein icosahedral shell that is a requisite for the process of virus membrane–cell membrane fusion. The appearance of a prominent protruding structure upon exposure to acid pH and its disappearance upon return to neutral pH suggested that the production of a "pore"-like structure at the fivefold axis may facilitate cell penetration as has been proposed for polio (J. Virol. 74 (2000) 1342) and human rhino virus (Mol. Cell 10 (2002) 317). This transient structural change also provided an explanation for how membrane fusion occurs after return to neutral pH. Examination of virus–cell complexes at neutral pH supported the contention that infection occurs at the cell surface at neutral pH by the production of a virus structure that breaches the plasma membrane bilayer. These data suggest an alternative route of infection for Sindbis virus that occurs by a process that does not involve membrane fusion and does not require disassembly of the virus protein shell.}, number={2}, journal={Virology}, publisher={Elsevier BV}, author={Paredes, Angel M and Ferreira, Davis and Horton, Michelle and Saad, Ali and Tsuruta, Hiro and Johnston, Robert and Klimstra, William and Ryman, Kate and Hernandez, Raquel and Chiu, Wah and et al.}, year={2004}, month={Jul}, pages={373–386} }
 @article{hernandez_rusa_rusa_lopez_mijangos_tonelli_2004, title={Controlling PVA hydrogels with gamma-cyclodextrin}, volume={37}, ISSN={["0024-9297"]}, DOI={10.1021/ma048375i}, abstractNote={We report on the preparation and characterization of poly(vinyl alcohol) (PVA) hydrogels formed during freeze−thaw (F−T) cycles of their aqueous solutions containing γ-cyclodextrin (γ-CD). Crystalline inclusion compound (IC) formation was observed between PVA and γ-CD in these gels at low concentrations of γ-CD (γ-CD:PVA molar ratios < 1:25). Confirmation of the existence of the channel structure for γ-CD was achieved by characterizing the dried PVA/γ-CD hydrogels with solid-state DSC, TGA, WAXD, and 13C NMR. Some aspects regarding the mechanism and structure of PVA gels obtained via F−T cycles in the presence/absence of γ-CD are presented based on UV−vis, swelling, solution 1H NMR, and rheological observations. It was observed that the swelling and rheological responses of the aqueous PVA gels formed during F−T cycles in the presence of γ-CD can be controlled by adjustment of the PVA:γ-CD molar ratio employed during their gelation.}, number={25}, journal={MACROMOLECULES}, author={Hernandez, R and Rusa, M and Rusa, CC and Lopez, D and Mijangos, C and Tonelli, AE}, year={2004}, month={Dec}, pages={9620–9625} }
 @article{hernandez_nelson_salm_brown_alpert_2004, title={Rapid preparative purification of West Nile and Sindbis virus PCR products utilizing a microbore anion-exchange column}, volume={120}, DOI={10.1016/j.viromet.2004.04.013}, number={2}, journal={Journal of Virological Methods}, author={Hernandez, R. and Nelson, S. and Salm, J. R. and Brown, D. T. and Alpert, A. J.}, year={2004}, pages={141–149} }
 @article{hernandez_nelson_salm_brown_alpert_2004, title={Rapid preparative purification of West Nile and Sindbis virus PCR products utilizing a microbore anion-exchange column}, volume={120}, ISSN={0166-0934}, url={http://dx.doi.org/10.1016/j.jviromet.2004.04.013}, DOI={10.1016/j.jviromet.2004.04.013}, abstractNote={Analysis and purification of specific PCR products from PCR reactions can be problematic due to several issues relating to amplification and low product yield. The use of HPLC as a preparative tool in PCR product analysis is common but has not replaced traditional electrophoretic techniques for purifying DNA to be used in subsequent experiments. Gel purification of PCR products can result in a net loss greater than 50% of the starting DNA amount. Thus, this method of recovery can become the limiting factor in the overall cloning protocol. This paper describes a simple and relatively inexpensive micro-preparative HPLC method to purify and analyze nM quantities of DNA. A microbore polyethyleneimine-based anion-exchange column fractionates PCR mixtures in less than 40 min with a recovery of the purified specific product as high as 80%, thus eliminating the need for gel purification. Using this method, nested PCR products from Sindbis virus differing by 18 bp in some cases and a 277 bp fragment from West Nile virus were resolved and quantified. This method differs from existing methodologies because separation is based on size and charge as well as the overall G + C content of the PCR product.}, number={2}, journal={Journal of Virological Methods}, publisher={Elsevier BV}, author={Hernandez, Raquel and Nelson, Steevenson and Salm, Jeffery R and Brown, Dennis T and Alpert, Andrew J}, year={2004}, month={Sep}, pages={141–149} }
 @article{hernandez_sinodis_horton_ferreira_yang_brown_2003, title={Deletions in the transmembrane domain of a Sindbis virus glycoprotein alter virus infectivity, stability, and host range}, volume={77}, ISSN={["0022-538X"]}, DOI={10.1128/JVI.77.23.12710-12719.2003}, abstractNote={ABSTRACT}, number={23}, journal={JOURNAL OF VIROLOGY}, author={Hernandez, R and Sinodis, C and Horton, M and Ferreira, D and Yang, CN and Brown, DT}, year={2003}, month={Dec}, pages={12710–12719} }
 @article{ferreira_hernandez_horton_brown_2003, title={Morphological variants of Sindbis virus produced by a mutation in the capsid protein}, volume={307}, ISSN={["0042-6822"]}, DOI={10.1016/S0042-6822(02)00034-X}, abstractNote={Sindbis virus is a complex aggregate of RNA, protein and lipid. The virus is organized as two nested T = 4 icosahedral protein shells between which is sandwiched a lipid bilayer. The virus RNA resides within the inner protein shell. The inner protein shell is attached to the outer protein shell through contacts to proteins in the outer shell, which penetrate the lipid bilayer. The data presented in the following manuscript show that mutations in the capsid protein can result in the assembly of the virus structural proteins into icosahedra of different triangulation numbers. The triangulation numbers calculated, for these morphological variants, follow the sequence T = 4, 9, 16, 25 and 36. All fall into the class P = 1 of icosadeltahedra as was predicted by Caspar and Klug (1962). The data support their hypothesis that families of icosahedra would be developed by altering the distance between the points of insertion of the five-fold axis. This capsid protein defect also results in the incorporation of much of the capsid protein, into large cytoplasmic aggregates of protein and RNA. These observations support models suggesting that the geometry of a pre-formed nucleocapsid organizes the assembly of the virus membrane proteins into a structure of identical configuration and argues against models suggesting that assembly of the membrane glycoproteins directs the assembly of the nucleocapsid.}, number={1}, journal={VIROLOGY}, author={Ferreira, D and Hernandez, R and Horton, M and Brown, DT}, year={2003}, month={Mar}, pages={54–66} }
 @article{hernandez_luo_brown_2001, title={Exposure to low pH is not required for penetration of mosquito cells by Sindbis virus}, volume={75}, ISSN={["0022-538X"]}, DOI={10.1128/jvi.75.4.2010-2013.2001}, abstractNote={ABSTRACT}, number={4}, journal={JOURNAL OF VIROLOGY}, author={Hernandez, R and Luo, TC and Brown, DT}, year={2001}, month={Feb}, pages={2010–2013} }
 @article{pletnev_zhang_mukhopadhyay_fisher_hernandez_brown_baker_rossmann_kuhn_2001, title={Locations of carbohydrate sites on alphavirus glycoproteins show that E1 forms an icosahedral scaffold}, volume={105}, ISSN={["0092-8674"]}, DOI={10.1016/S0092-8674(01)00302-6}, abstractNote={There are 80 spikes on the surface of Sindbis virus arranged as an icosahedral surface lattice. Each spike consists of three copies of each of the glycoproteins E1 and E2. There are two glycosylation sites on E1 and two on E2. These four sites have been located by removal of the glycosylation recognition motifs using site-specific mutagenesis, followed by cryoelectron microscopy. The positions of these sites have demonstrated that E2 forms the protruding spikes and that E1 must be long and narrow, lying flat on the viral surface, forming an icosahedral scaffold analogous to the arrangement of the E glycoprotein in flaviviruses. This arrangement of E1 leads to both dimeric and trimeric intermolecular contacts, consistent with the observed structural changes that occur on fusion with host cell membranes, suggesting a similar fusion mechanism for alpha- and flaviviruses.}, number={1}, journal={CELL}, author={Pletnev, SV and Zhang, W and Mukhopadhyay, S and Fisher, BR and Hernandez, R and Brown, DT and Baker, TS and Rossmann, MG and Kuhn, RJ}, year={2001}, month={Apr}, pages={127–136} }
 @article{hernandez_lee_nelson_brown_2000, title={A single deletion in the membrane-proximal region of the Sindbis virus glycoprotein E2 endodomain blocks virus assembly}, volume={74}, ISSN={["1098-5514"]}, DOI={10.1128/JVI.74.9.4220-4228.2000}, abstractNote={ABSTRACT}, number={9}, journal={JOURNAL OF VIROLOGY}, author={Hernandez, R and Lee, H and Nelson, C and Brown, DT}, year={2000}, month={May}, pages={4220–4228} }