pinecone/core-2020-05-10-deduplication huggingface dataset:
Mutation Rate of GB Virus C/Hepatitis G Virus over the Entire Genome and in Subgenomic Regions

AbstractA patient on maintenance hemodialysis was infected with a recently discovered putative non-A to -E hepatitis virus designated GB virus C (GBV-C) or hepatitis G virus (HGV) by transfusion. The viral isolate was recovered from the patient soon after she turned positive for GBV-C/HGV RNA in serum (GSI85) and 8.4 years thereafter (GSI93), and the entire nucleotide sequences were determined. They both had a genomic length of 9391 nucleotides with a defective C gene made of only 42 nucleotides. Between GSI85 and GSI93, 31 (0.33%) nucleotides were different, which changed 5 (0.18%) of the encoded 2842 amino acids. Thus, GBV-C/HGV was estimated to have a mutation rate of 3.9 × 10−4base substitutions per site per year. Nucleotide conversions were distributed over subgenomic regions, except in the 5′ untranslated region of 552 nucleotides and a defective short C gene, which were conserved in sequence. The change in the putative envelope genes (E1 and E2) was no different from that in the entire genome with only 6 (0.35%) nucleotide substitutions among the 1730, just 1 of which induced an amino acid conversion. Taken along with the comparison of the two isolates with the reported five GBV-C or HGV isolates, these results indicate that GBV-C/HGV would not have hypervariable regions and would use a strategy for viral persistence that is different from immune escape
Kinetics of Cytokine Expression and Regulation of Host Protection Following Infection with Molecularly Cloned Venezuelan Equine Encephalitis Virus

AbstractIn the mouse model, the arbovirus Venezuelan equine encephalitis virus (VEE) replicates in lymphoid tissues prior to either inducing protective immunity (attenuated VEE mutant) or progressing to lethal encephalitis (virulent parent VEE). To investigate the mechanism of the protective response, cytokine gene expression was examined during the course of the primaryin vivoimmune response to molecularly cloned, virulent VEE and a single-site attenuated VEE mutant, using a quantitative reverse transcriptase-polymerase chain reaction assay. VEE-induced cytokine gene expression was 100-fold elevated over that of untreated controls for IFN-γ and IL-6 and 10-fold increased for IL-12, IL-10, and TNF-α. There was no qualitative difference in cytokine gene induction comparing mice infected with the attenuated and the virulent VEE; however, there were significant differences in the cytokine gene expression kinetics. In mice infected with the attenuated VEE, elevated cytokine gene expression was delayed 24 hr when compared to mice infected with the virulent parent VEE clone at the same dose. Further, IFN-γ protein secretion by cells from the draining lymph node mimicked the pattern of IFN-γ gene induction by cells harvested from the same site. IFN-γ gene expression was elevated at an earlier time point in mice given virulent V3000 24 hr after attenuated V3032 injection compared to mice infected with virulent V3000 alone. The combined V3000/V3032 infection resulted in host protection. Treatment of mice with IL-12 prior to infection with virulent VEE failed to reduce the severity of infection, while anti-IL-12 antibody did not prevent the early protective effect of attenuated virus. In contrast, administration of anti-IFN-α/β antibody prior to VEE infection worsened virulent VEE disease. These results indicate that the attenuated VEE strain elicits a similar but delayed cytokine response compared to the virulent strain, suggesting that the kinetics of cytokine expression and the particular cytokine produced may influence the development of a host protective response. Furthermore, IFN-α/β, but not IL-12, seems to be a major factor in the induction of early protection against VEE infection and disease
Modulation of Stress Protein (hsp27 and hsp70) Expression in CD4+ Lymphocytic Cells Following Acute Infection with Human Immunodeficiency Virus Type-1

AbstractThis study was designed to assess the impact of acute human immunodeficiency virus (HIV-1) infection on host intracellular expression of the heat shock family of stress proteins (hsps). Experimental conditions were established wherein CD4+ lymphocytic cell lines undergo a synchronous HIV-1 infection cycle. During the early phase of infection, HIV-1 mRNA expression was restricted to singly and multiply spliced subspecies, with no genomic viral RNA present until 30 hr following infection. In contrast, hsp27 and hsp70 mRNA transcription appeared as early as 3–8 hr following viral infection. No corresponding induction was observed in mock-infected cells. Notably, hsp27 and hsp70 mRNA transcripts were down-regulated by 24 hr, concomitant to the first appearance of full-length genomic HIV-1 mRNA. Hsp27 and hsp70 mRNA transcripts reemerged at end stages of the viral replicative cycle, coincident to virion release and CD4 cell death. Similarly, a transient induction ofde novohsp27 protein expression occurred between 12 and 24 hr. The generated hsp27 stress response was viral dose-related, suppressed by heat-inactivation of virus, and abrogated by neutralizing antibodies to HIV-1. Acute infection did not alter levels of hsp60, hsp70, and hsp90 protein synthesis. However, two-dimensional Western blot analysis did show the appearance of novel hsp70 homologues between 6 and 24 hr following infection. CEM.NKR, Jurkat, H9, and MT-2 cells showed similar patterns of viral-associated modulation of host hsp27 and hsp70 protein and RNA expression. Thus, host hsp27 and hsp70 stress pathways are selectively implicated in the HIV-1 viral life cycle
Unique Sequence and Lesional Tropism of a New Variant of Neuropathogenic Friend Murine Leukemia Virus

AbstractFrC6 murine leukemia virus (MuLV) is a replication-competent, neuropathogenic variant derived from Friend MuLV (F-MuLV) complex. The A8 virus (a molecular clone of the FrC6 virus) induced marked spongiform degeneration in the brain similar to the FrC6 virus, but only mild lesions were found in the spinal cord. In contrast, PVC211 virus, which is also a neuropathogenic F-MuLV variant, caused marked spongiform degeneration in the spinal cord. Virus recovery from the spinal cord of A8 virus-infected rat was the same as that of PVC211-infected rat, indicating that there is no direct correlation between the titer of virus and the intensity of lesions. Furthermore, rats infected with the A8 virus at 3 weeks of age did not undergo spongiform degeneration, although recovery of high titer of virus occurred in the central nervous system (CNS). Studies using chimeric viruses between the A8 virus and nonneuropathogenic F-MuLV clone 57 also indicated that the sequences responsible for virus titers in the CNS and neuropathogenicity are different. The chimeric virus studies proved that the env gene and the LTR and/or 5′ leader sequence of A8 are critical for the induction of neuropathogenicity. These sequences in A8 and PVC211 were compared, focusing in on the sites that account for neurovirulence and viral lesional tropism
Population Dynamics Studies of Wild-Type and Drug-Resistant Mutant HIV in Mixed Infections

AbstractWe have studied the population dynamics in response to selective drug pressure of mixtures of wild-type and mutant HIV viruses exposed to either an inhibitor of the viral protease or a nonnucleoside allosteric inhibitor of the viral reverse transcriptase. In order to quantitate mutant virus present in a mixed population, we developed a selective plaque assay, which appears to be generally applicable to population dynamics studies where the viruses in question differ in the sensitivity to a given drug by at least 10-fold. In this assay system, the titer of virus in a mixture is measured in the absence and presence of a concentration of a specific inhibitor known to suppress virus replication by 99%. Virus detected in the presence of inhibitor corresponds to mutant virus, whereas detection in the absence of drug results in quantitation of the total virion population. Wild-type virus is then estimated by difference. Utilizing this system we studied the fate of mixtures of wild-type and the protease-resistant mutant variant I84V in the presence and absence of the cyclic urea HIV protease inhibitor, DMP 450. We also examined the dynamics of mixtures of wild-type and the resistant mutant variant, L100I, in the presence and absence of the drug DMP 266. In both systems we demonstrated that in the absence of drug, mutant virus is at a selective disadvantage for growth compared to wild-type, whereas in the presence of a specific inhibitor, mutant virus exhibits the selective growth advantage over wild-type virus. Better understanding of HIV population dynamics may allow the development of superior inhibitors and the careful application of combination therapy in the clinical setting
Turnip Yellow Mosaic Virus RNA-Dependent RNA Polymerase: Initiation of Minus Strand Synthesisin Vitro

AbstractAn RNA-dependent RNA polymerase (RdRp) activity was detergent-solubilized from the chloroplast membranes of Chinese cabbage leaves infected with turnip yellow mosaic virus (TYMV). The template-dependent, micrococcal nuclease-treated activity synthesized full-length minus strands from TYMV RNA and 3′-fragments as short as a 28-nucleotide-long RNA comprising the amino acid acceptor stem of the 3′-tRNA-like structure (TLS). Minus strands were shown to arise byde novoinitiation with the insertion of GTP opposite the penultimate (C) residue of the 3′-terminal -CCA. The TYMV RdRp activity was template specific in that poly(A) RNA was not copied, and alfalfa mosaic virus (AlMV) RNA, which does not contain a 3′-TLS, was a very poor template. However, other viral RNAs with a 3′-TLS andin vitrotranscripts of tRNAs were copied to varying degrees. Fully modified tRNAs were either inactive or poorly active templates, and AlMV 3′-RNA, even when provided with a 3′-terminal -ACCA, was not copied detectably. A potential role of the acceptor stem pseudoknot as a promoter element was assessed with mutations that drastically altered the structure and sequence of the pseudoknot, revealing only a twofold effect in decreasing template activity. The data show that RNAs with both a tRNA-like conformation and a -CCA 3′-terminus are potential templates for TYMV RdRp and suggest that promoter elements are not limited to the acceptor stem pseudoknot
Tick-Borne Encephalitis Virus Transmission between Ticks Cofeeding on Specific Immune Natural Rodent Hosts

AbstractTo determine whether the portion of a vertebrate host population having specific immunity to tick-borne encephalitis (TBE) virus can participate in the TBE virus transmission cycle, natural hosts immunized against TBE virus were challenged with infected and uninfected ticks. Yellow-necked field mice (Apodemus flavicollis) and bank voles (Clethrionomys glareolus) were either immunized with TBE virus by subcutaneous inoculation of the virus, or they were exposed to virus-infectedIxodes ricinusticks. One month later, when serum neutralizing antibody was detectable, the animals were infested with infected (donor) adult female ticks and uninfected (recipient) nymphal ticks; recipients were allowed to feed either in close contact (chamber 1) or physically separated (chamber 2) from the infected donor ticks. Following challenge with infected (and uninfected) ticks, viremia developed in all the control, nonimmune animals, whereas viremia was undetectable in all those animals naturally immunized by previous exposure to infected ticks. Despite the presence of neutralizing antibodies in all the immunized animals, 89% (24/27) immune animals supported virus transmission between infected and uninfected cofeeding ticks. Most transmission was localized, occurring within chamber 1; disseminated transmission from chamber 1 to chamber 2 was reduced. Immunization by tick bite was more effective than immunization by syringe inoculation in blocking cofeeding virus transmission. Nevertheless 75% (9/12) animals with “natural” immunity still supported transmission. The results demonstrate that natural hosts having neutralizing antibodies to TBE virus (and no detectable viremia) can still support virus transmission between infected and uninfected ticks feeding closely together on the same animal. These observations have important epidemiological implications relating to the survival of TBE virus in Nature
Transduction of the Human Immunodeficiency Virus Type 1 Promoter into Human Chromosomal DNA by Adeno-Associated Virus: Effects on Promoter Activity

AbstractTranscription of the human immunodeficiency virus type 1 (HIV-1) genome takes place after integration of the provirus into human chromosomal DNA. HIV transcription is known to be modulated by viral and cellular factors but the influence of flanking chromosomal sequences on proviral gene expression has not been well defined. To investigate the activity of the integrated HIV promoter, we exploited the ability of recombinant adeno-associated virus (AAV-2) to transfer and stably integrate genes into the human genome at random or site-specifically. Chimeric AAV vectors were constructed containing an HIV-CAT reporter cassette; some vectors also contained the neomycin resistance gene to facilitate the isolation of positive clones. HeLa cells were infected with recombinant AAV, in some instances together with wild-type virus as a source of AAV rep function. We isolated 25 clones of G418-resistant cells which carried the integrated HIV-CAT cassette, generally occupying unique sites that did not correspond to the AAV-specific region of chromosome 19. The HIV promoter was transcriptionally active in most of the clones. Basal promoter activity varied substantially among the clones, and its responsivity to the HIV transactivator Tat was also variable. The integrated HIV promoter was transactivated to comparable degrees by the one-exon form and two-exon form of Tat. These findings provide evidence that the transcriptional activity of the HIV promoter can be greatly influenced by the site of proviral insertion
Varicella-Zoster Virus Glycoproteins E and I Expressed in Insect Cells Form a Heterodimer That Requires the N-Terminal Domain of Glycoprotein I

AbstractVaricella-zoster virus (VZV) glycoproteins E and I (gE and gI), which are major components of the virion envelope, form a noncovalently linked complex. To understand their properties and functions, we expressed and purified soluble forms of gE and gI in the baculovirus system. Extracellular domains of gE and gI were cloned into baculoviruses, using either native or insect-derived signal peptides. Each recombinant virus yielded soluble protein in culture medium although a higher level of secretion was achieved with insect-derived signal peptides in recombinant gE baculoviruses. A soluble gE–gI complex was formed by co-infecting insect cells with recombinant gE and gI baculoviruses and detected by immunoprecipitation followed by Western blotting analyses. By gel filtration and cross-linking studies, we showed that the VZV gE–gI complex expressed in insect cells is a heterodimer. Interestingly, two recombinant gI proteins in which signal peptides were replaced with insect-derived signal peptides did not associate with gE. Amino-terminal sequencing and site-specific mutational studies showed that the replacement of only the signal peptides did not prevent complex formation but alterations in the processed amino-terminus of gI abrogated its ability to complex with gE. These findings indicate that the mature amino-terminus of gI is required for gE–gI complex formation by the external domains of VZV gE and gI
Adaptation of Egg-Grown and Transfectant Influenza Viruses for Growth in Mammalian Cells: Selection of Hemagglutinin Mutants with Elevated pH of Membrane Fusion

AbstractA series of eight transfectant influenza viruses was generated by reverse genetics for studies of the palmitylated cysteine residues in the cytoplasmic tail of the hemagglutinin glycoprotein (HA). Following amplification of these viruses in MDCK cells we found that all had developed an elevated pH of membrane fusion—an unexpected result since previous mutant HA expression studies had shown that substitutions of the cysteine residues had no effect on fusion properties. Sequence analyses revealed that each of the viruses had at least one additional mutation in the ectodomain of HA which was responsible for the increase in fusion pH. Similarly, when we passaged egg-grown wild-type X-31 virus in three different lines of MDCK cells or in MDBK cells, high pH fusion mutants were selected within a few passages in every case. The locations of the substitutions in the HA structure are in or near the “fusion peptide” or at subunit interfaces throughout the length of the trimer—reminiscent of the changes selected in earlier studies on amantadine resistance. The observation that passage of certain viruses in mammalian cells can result in the selection of mutants with elevated fusion pH has potential implications both for reverse genetic experiments and, perhaps more importantly, for the choice of substrates for propagation of vaccine viruses
The Signal Sequence of Lymphocytic Choriomeningitis Virus Contains an Immunodominant Cytotoxic T Cell Epitope That Is Restricted by both H-2Dband H-2KbMolecules

AbstractInfection of H-2bmice with lymphocytic choriomeningitis virus (LCMV) generates three well-characterized H-2Db-restricted immunodominant epitopes delineated in the NP, GP1, and GP2 proteins. Here we report that the H-2Db-restricted GP1 epitope GP33-41/43 (KAVYNFATC/GI) located in the signal sequence of LCMV is also the immunodominant epitope recognized by CTL at the surface of the same infected cells in the context of H-2Kbrestriction. The GP1 epitope bound to H-2Dband H-2Kbmolecules with comparable affinities. The respective binding processes involved different sets of peptide anchoring residues and required dramatically different conformations of the peptide backbone as well as rearrangement of residue side chains. The 10-mer peptide GP34-43 (AVYNFATCGI) was the optimal H-2Kb-binding sequence and the 8-mer peptide GP34-41 (AVYNFATC) the minimal sequence for optimal H-2Kb-restricted CTL recognition. Comparison of lytic activities of primary splenic anti-LCMV CTL from C57BL/6 (Db+/Kb+), B10A.[5R] (Db−/Kb+), and B10A.[2R] (Db+/Kb−) mice against LCMV-infected or peptide-coated target cells expressing either one or the two MHC alleles revealed that the H-2Kb-restricted component of the anti-GP1 CTL response was mounted independently of but as efficiently as its H-2Dbcounterpart. Analysis of the immune response against a GP1 variant that escapes CTL recognition showed that the GP1 epitope: (i) was likely the only immunodominant LCMV epitope in the context of H-2Kb, and (ii) could efficiently evade H-2Dband H-2Kb-restricted CTL mediated lysis
Masking of Retroviral Envelope Functions by Oligomerizing Polypeptide Adaptors

AbstractWe have constructed chimeric retroviral envelopes displaying N-terminal polypeptides that are known to form homotrimeric associations. The amphotropic receptor (RAM-1) binding domain from the trimeric surface (SU) glycoprotein of 4070A murine leukemia virus (MLV)-inhibited ecotropic receptor (Rec-1) mediated infection by the SU glycoprotein of Moloney MLV when grafted to its N-terminus. The block to Rec-1-mediated infection was reversed when the RAM-1 binding domain was cleaved from the vector particles using an engineered factor Xa protease-sensitive cleavage signal between the envelope glycoprotein and its N-terminal extension. Trimeric leucine zipper peptides and the trimeric C-terminal domain of CD40 ligand were shown to inhibit RAM-1-mediated infection of NIH3T3 cells by the 4070A envelope when fused to its N-terminus, whereas monomeric helical peptides and the monomeric epidermal growth factor domain did not. The block to RAM-1-mediated infection was reversed when the trimeric polypeptides were cleaved from the vector particles by addition of factor Xa protease. Envelope binding assays using cleaved and uncleaved chimeric 4070A envelopes revealed that binding to RAM-1 receptors on mammalian cells was hindered by trimeric, but not by monomeric, N-terminal polypeptides. These results have important implications for the design of protease-activatable vectors for targeted gene delivery
The Elevation of Cellular Phosphatidic Acid Levels Caused by Polyomavirus Transformation Can Be Disassociated from the Activation of Phospholipase D

AbstractMiddle T (mT), the oncogene of murine polyomavirus, causes transformation of rat fibroblasts by activating a number of signal transducing pathways usually used by polypeptide growth factors and their receptors. Here, we report data regarding the activation of signal transducing pathways involving phospholipase D (PL-D). The hydrolysis of phospholipids by PL-D produces phosphatidic acid (PA), a compound with multiple biological effects. The PA content of cells expressing wild-type mT, introduced via a number of different methods, is approximately 50% higher than their untransformed counterparts. This increase in cellular PA content is associated with an approximately 65% increase in PL-D activity in cells expressing wild-type mT. We have also examined the effects of a number of site-directed mutants of mT, on both cellular PA levels and on PL-D activity. Mutants that do not produce mT (Py808A) or that produce a truncated, nonmembrane bound mT (Py1387T) have PA levels similar to that of control cells. Cells expressing the 322YF mutant of mT (which abolishes interaction of mT with phospholipase C γ1) show increases in both PA levels and PL-D activity that are similar to those seen with wild-type mT. Expression of mutants that abolish the interaction of mT with either shc or with phosphatidylinositol 3-kinase (250YS and 315YF, respectively) cause an increase in PL-D activity comparable to that seen with wild-type mT. However, the PA content of cells expressing these mutants is not elevated. These results suggest that mT causes activation of cellular PL-D, but this activation alone is not sufficient to cause an increase in cellular PA content. Therefore, wild-type mT must affect another, as yet unknown, step in PA metabolism
Expression, Assembly, and Proteolytic Processing of Helminthosporium victoriae 190S Totivirus Capsid Protein in Insect Cells

AbstractThe dsRNA genome (5.2 kbp) of Helminthosporium victoriae 190S totivirus (Hv190SV) consists of two large overlapping open reading frames (ORFs). The 5′ proximal ORF codes for the capsid protein (CP) and the 3′ ORF codes for an RNA-dependent RNA polymerase. Although the capsid of Hv190SV is encoded by a single gene, it is composed of two major closely related polypeptides, either p88 and p83 or p88 and p78. Whereas p88 and p83 are phosphoproteins, p78 is nonphosphorylated. Expression of the CP ORF in insect cells generated both p78 and p88 which assembled into virus-like particles. The finding that p78, p83, and p88 share a common N-terminal amino acid sequence is consistent with the determination that N-terminal, but not C-terminal, CP deletions were incompetent for assembly. Evidence was obtained that p78 is derived from p88 via proteolytic cleavage at the C-terminus. Proteolytic processing may play a regulatory role in the virus life cycle since it leads to dephosphorylation of CP and a subsequent decrease in virion transcriptional activity