pinecone/core-2020-05-10-deduplication huggingface dataset:
A Novel Vpr Peptide Interactor Fused to Integrase (IN) Restores Integration Activity to IN-Defective HIV-1 Virions

AbstractA novel approach to complement human immunodeficiency virus type I (HIV-1) integrase (IN)-defective virions has been identified. The approach involves fusion of a 23-amino-acid stretch to the N-terminus of wild-type IN and coexpression of this chimera with the IN-defective proviral template in virus producing cells. The 23-amino-acid peptide represents a Vpr “interactor,” referred to as the the WxxF or WF domain, which apparently leads to docking of the domain along with the fusion partner onto HIV-1 Vpr, thus permitting virion incorporation of the chimeric protein when expressed,in trans,with other viral products. Transfection of the WF-IN expression plasmid along with HIV-1 viral clones that produce Vpr, but bear an IN mutation, results in the release of a proportion of viral particles that are competent for integration. The extent of complementation was assessed using the MAGI cell assay, where integration of viral DNA results in the eventual appearance of easily visible multinucleated blue syncytia. The efficiency of dWF-IN (double copy of WF domain) complementation is not improved markedly by incorporation of a HIV-1 protease cleavage site (PR) between the dWF domain and IN (dWF-PR-IN), unlike that observed with Vpr fusions to IN. Furthermore, the ability of Vpr-PR-IN and dWF-PR-IN to complement IN-defective proviral clones, both of which bear an intervening protease cleavage site, appear comparable. Western blotting analyses using virions isolated through sucrose cushions demonstrate clearly the incorporation of the dWF-IN fusion protein into Vpr containing HIV-1 particles but not in Vpr-deficient virions. Additional Western blotting analyses indicate that all Vpr-IN and dWF-IN chimeras, with or without a PR site, are packaged into virions. The efficiency of virion incorporation of Vpr-IN and dWF-IN chimeras appears approximately comparable by Western blotting analysis. The ability of dWF-IN to complement IN-defective proviruses with efficiency similar to that of Vpr-PR-IN and dWF-PR-IN indicates that dWF-IN retains the full complement of functions necessary for integration of proviral DNA and is likely due to the benign nature of this small domain at the amino-terminus of IN
Mapping Sequences Active in Homologous RNA Recombination in Brome Mosaic Virus: Prediction of Recombination Hot Spots

AbstractThe mechanism of homologous recombination has been studied previously in brome mosaic virus (BMV), a tricomponent, positive-stranded RNA virus of plants, by using artificial sequences (reviewed by J. J. BujarskiP. D. Nagy (1996).Semin. Virol.7, 363–372). Here we extend these studies over BMV-derived sequences to obtain clues on prediction of homologous recombination hot spots. First, mismatch mutations, which reduced the AU content, were introduced into the common 60-nt recombination hot-spot sequence, either in the RNA2 or in both RNA2RNA3 components. This decreased the frequency of targeted homologous RNA2/RNA3 recombinationchanged the distribution of junction sites. Second, several short BMV RNA1- or RNA2-derived sequences were introduced into the RNA3 component,homologous recombination activity of these sequences was compared with that observed for previously characterized artificial sequences. Third, sequences at homologous recombinant junctions were compared among a large number of targetednontargeted recombinants. All these studies revealed several factors important for homologous recombination including the length of sequence identity, the extent of sequence identity, the AU content of the common sequences, the relative position of the AU-rich segmentvsa GC-rich segment,the presence of GC-rich sequences. Based on this novel model, we suggest that recombination hot spots can be predicted by means of RNA sequence analysis. In addition, we show that recombination can occur between positivenegative strands of BMV RNAs. This provides further clues toward the mechanism of recombination processes in BMV
Identification of Additional Genes That Influence Baculovirus Late Gene Expression

AbstractWe were unable to confirm transient late gene expression using constructs of 18 genes that had been reported to supportAutographa californicamultinucleocapsid nucleopolyhedrovirus (AcMNPV) late gene expression when transfected intoSpodoptera frugiperdacells [Lu, A., and Miller, L. K. (1995).J. Virol.69, 975–982]. Three genes (orf66, orf68,andorf41) were included, all or in part, in the constructs used in that study, but they had not been independently tested. Therefore we investigated these and neighboringorfs for their influence on late gene expression. We found thatorf41was required for late gene expression and that sequences withinorf45appeared to be required for the expression oforf41. Althoughorf66andorf68did not appear to affect late gene expression,orf69stimulated expression.orf69was found to have high homology to recent entries in GenBank from a variety of organisms. In addition, it was found thatorf121, which was shown to be involved in early gene expression, and the viral homolog ofpcnadid not influence late gene expression
A 43-Nucleotide RNACis-Acting Element Governs the Site-Specific Formation of the 3′ End of a Poxvirus Late mRNA

AbstractThe 3′ ends of late mRNAs of theatigene, encoding the major component of the A-type inclusions, are generated by endoribonucleolytic cleavage at a specific site in the primary transcript [Antczaket al.,(1992),Proc. Natl. Acad. Sci. USA89, 12033–12037]. In this study, sequence analysis of cDNAs of the 3′ ends ofatimRNAs showed these mRNAs are 3′ polyadenylated at the RNA cleavage site. This suggests thatatimRNA 3′ end formation involves cleavage of a late transcript, with subsequent 3′ polyadenylation of the 5′ cleavage product. The RNAcis-acting element, the AX element, directing orientation-dependent formation of these mRNA 3′ ends, was mapped to a 345-bpAluI–XbaI fragment. Deletion analyses of this fragment showed that the boundaries of the AX element are within −5 and +38 of the RNA cleavage site. Scanning mutagenesis showed that the AX element contains at least two subelements: subelement I, 5′-UUUAU↓CCGAUAAUUC-3′, containing the cleavage site (↓), separated from the downstream subelement II, 5′-AAUUUCGGAUUUGAAUGC-3′, by a 10-nucleotide region, whose composition may be altered without effect on RNA 3′ end formation. These features, which differ from those of other elements controlling RNA processing, suggest that the AX element is a component of a novel mechanism of RNA 3′ end formation
Hepatitis A Virus Translation Is Rate-Limiting for Virus Replication in MRC-5 Cells

AbstractTranslation of hepatitis A virus (HAV) RNA is controlled by an internal ribosome entry site (IRES) located within the 5′ untranslated region (UTR). In some cell types, the characteristically slow growth of HAV may be due to inefficient viral translation. We investigated whether this is true in MRC-5 cells, which are used for vaccine production. We measured the impact of two clusters of mutations in the 5′ UTR on virus translation and replication: the AG group was selected during passage in African green monkey kidney cells, and the MR group was selected during subsequent passage in MRC-5 cells. The efficiency of cap-independent translation was assessed by inserting cDNA encoding an HAV IRES upstream of the chloramphenicol acetyl transferase gene and transcription was drivenin vivoby a hybrid T7/vaccinia virus system. A luciferase gene was inserted upstream of the IRES to serve as an internal control. Each HAV UTR was also inserted into an infectious cDNA clone; the average rate of viral RNA accumulation was determined for each mutant virus. In MRC-5 cells, the rate of virus replication was highly correlated with the efficiency of cap-independent translation (P= 0.006). The MR but not the AG mutations significantly increased both translation and viral RNA accumulation. Reversion of just one MR mutation (687 G to A) eliminated all of the replication-stimulating and translation-enhancing effects of the MR mutations. In the control BS-C-1 cells, there was no discernible correlation between the rate of virus replication and the efficiency of cap-independent translation (P= 0.136): the AG and MR groups combined had a small impact on translation, but no detectable impact on virus replication. We conclude that in MRC-5 cells viral translation is rate-limiting for HAV replication
Characterization of Conformation-Dependent Anti-gp120 Murine Monoclonal Antibodies Produced by Immunization with Monomeric and Oligomeric Human Immunodeficiency Virus Type 1 Envelope Proteins

AbstractTwenty-five conformation-dependent monoclonal antibodies (MAbs) produced by immunization of mice with oligomeric forms of the human immunodeficiency virus type 1 (HIV-1) envelope (env) glycoprotein were used to map exposed, immunogenic regions on oligomeric env. Based on MAb cross-competition, reactivity with diverse env proteins, and reactivity with a panel of gp120 mutants, seven distinct epitope clusters were identified. These include the classic CD4 binding site, V1/V2, and V3. in addition, several novel epitope clusters, including one mapping to the N- and C-termini of gp120, were identified. The locations of the seven epitope clusters on the gp120 core structure are proposed
A Particulate Viral Protein Vaccine Reduces Viral Load and Delays Progression to Disease in Immunized Ponies Challenged with Equine Infectious Anemia Virus

AbstractImmunization regimens that induce a broadly reactive cytolytic T lymphocyte (CTL) response specific for lentiviral antigens have emerged as the leading candidates in efficacy trials conducted in both animal modelshumans. To date, lentivirus vaccination strategies have overlooked one such immunization strategy, namely the use of particulate antigens. To evaluate the efficacy of targeting antigen into the phagocytic pathway to elicit a cell-mediated immune response to lentiviral antigens, we initiated the first study of a particulate-based vaccination protocol using a large animal model system. Gradient-purified equine infectious anemia virus (EIAV) was covalently coupled to glutaraldehyde-activated iron oxide beads.In vitrostudies demonstrated the effectiveness of the inactivated whole virus particulate to prime antigen presenting cells for the activationexpansion of virus-specific CD8+CTL. Thein vivoeffectiveness of the particulate antigen was evaluated by experimental immunization of ponies. Ponies receiving the viral particulate vaccinechallenged with infectious EIAV had a delayed progression to diseasea reduced viral load compared with infected ponies that had not been vaccinated. Interestingly,in vitrovirus-specific CTL activity was detected in only one of four immunized animals at the day of challenge. The beneficial effects of the particulate vaccine regimen were not clearly associated with anyin vitromeasurable parameters of the virus-specific cellular or humoral immune responses elicited by the vaccine at the day of challenge. However, within 3 weeks after virus challenge, anamnestic humoral responses characterized by a rapid emergence of neutralizing activity in the seruma predominance of conformationally dependent epitopes recognized by virus-specific antibodies were observed in the vaccinates. Taken together, further studies are clearly warranted in large animal model systems using a particulate-based vaccine regimen considering the beneficial effects of this regimen in our studythe protective effects of particulate antigen delivery in the murine model
The Influenza Virus M2Ion Channel Protein: Probing the Structure of the Transmembrane Domain in Intact Cells by Using Engineered Disulfide Cross-Linking

AbstractThe influenza A virus M2integral membrane protein is an ion channel that permits protons to enter virus particles during uncoating of virions in endosomes, and it also modulates the pH of thetrans-Golgi network in virus-infected cells. M2protein is a homo-oligomer of 97 residues with a single transmembrane (TM) domain whose residues encompass the pore region of the channel and the biologically active form of the channel is a homotetramer. To understand the structural arrangement of the TM domains, each residue of the TM domain was changed in turn to cysteine, and oxidative disulfide cross-linking used to identify residues in close proximity. Oxidative treatment of M2protein in membranes using iodine resulted in maximum cross-linking at TM domain residues 27, 34, and 41. Oxidation of M2protein in membranes using the catalyst Cu(II)(1,10-phenanthroline)3resulted in cross-linking of many TM domain residues when the reaction was allowed to proceed at 37°C, suggesting that rotational movements of the TM domains in the membrane can occur. However, analysis of the kinetics of disulfide-linked dimer formation showed that TM domain residues 27, 30, 34, 37, and 41 formed most rapidly. Furthermore, when oxidation was performed at 4°C, maximum cross-linking occurred at TM domain residues 27, 30, 34, 37, and 41. These positions correspond to theaanddpositions of a heptad repeat. Thus these biochemical data are consistent with the TM domain region of the M2tetramer forming a four-helix bundle. Analysis of the disulfide bonds that formed when oxidation of M2protein in membranes was performed at pH 5.2 showed greatly reduced cross-linking at TM domain residues 40, 42, and 43 than that found at pH 7.4. This pH-dependent change in cross-linking of residues toward the cytoplasmic side of the TM domain parallels with the activation of the M2ion channel at low pH
Cellular Expression of Bovine Herpesvirus 1 gD Inhibits Cell-to-Cell Spread of Two Closely Related Viruses without Blocking Their Primary Infection

AbstractAlphaherpesviral glycoprotein D (gD) is a critical component of the cell membrane penetration system. Cells that express gD of herpes simplex virus type 1 (HSV1), pseudorabies virus (PRV), or bovine herpesvirus type 1.1 (BHV1.1) resist infection by the homologous virus due to interference with viral entry at the level of penetration. BHV1.1 gD interferes with the distantly related viruses HSV1 and PRV despite only a 30–40% sequence similarity and the complete absence of antigenic cross-reactivity among the three gDs. The six cysteines that form three intrachain disulfide bonds in HSV1 are also present in PRV and BHV1.1 gD, suggesting structural similarities among the gD homologs. Functional similarities were postulated to be responsible for cross-interference. To test this hypothesis, we constructed a BHV1.1 gD-expressing cell line (MDBKgD) and assessed its resistance to the homologous BHV1.1 and two closely related viruses, BHV1.2 and BHV5. The gDs of these viruses share 98.3% and 86% amino acid identity with BHV1.1 gD and bound monoclonal antibodies directed against all five neutralizing epitopes mapped on BHV1.1 gD. MDBKgDcells were resistant to BHV1.1 but fully susceptible to BHV1.2 and BHV5 infection as measured by plaque numbers and single cycle growth kinetics. However, all three viruses, but not vesicular stomatitis virus, made smaller plaques on MDBKgDcells than on control cells. These data suggest that gD-mediated interference is expressed both at the level of initial infection and at the level of cell-to-cell spread and that these two levels can be distinguished by using closely related viruses
Flexibility of the Major Antigenic Loop of Foot-and-Mouth Disease Virus Bound to a Fab Fragment of a Neutralising Antibody: Structure and Neutralisation

AbstractThe interaction of foot-and-mouth disease virus (FMDV) serotype C (clone C-S8c1) with a strongly neutralising monoclonal antibody (MAb) 4C4 has been studied by combining data from cryoelectron microscopy and x-ray crystallography. The MAb 4C4 binds to the exposed flexible GH-loop of viral protein 1 (VP1), which appears to retain its flexibility, allowing movement of the bound Fab. This is in striking contrast to MAb SD6, which binds to the same GH-loop of VP1 but exhibits no movement of the bound Fab when observed under identical conditions. However, MAbs 4C4 and SD6 have very similar neutralisation characteristics. The known atomic structure of FMDV C-S8c1 and that of the 4C4 Fab cocrystallised with a synthetic peptide corresponding to the GH-loop of VP1 were fitted to the cryoelectron microscope density map. The best fit of the 4C4 Fab is compatible only with monovalent binding of the MAb in agreement with the neutralisation data on 4C4 MAbs, Fab2s, and Fabs. The position of the bound GH-loop is related to other known positions of this loop by a hinge rotation about the base of the loop. The 4C4 Fab appears to interact almost exclusively with the G-H loop of VP1, making no other contacts with the viral capsid
Influenza Virus Inhibits Cleavage of the HSP70 Pre-mRNAs at the Polyadenylation Site

AbstractInfluenza virus infection is known to shut off the expression of host genes. To study the mechanism, we examined the effects of influenza A/Udorn/72 virus infection on the heat induction of a major heat shock protein, HSP70, in Madin–Darby canine kidney cells. The induction of HSP70 protein synthesis was progressively suppressed with postinfection time when heat shock was applied. Northern hybridization analysis revealed the appearance of longer, heterogeneous HSP70 transcripts in the range of 2.7 to 30 kb with a concomitant decrease in the amount of the mature 2.7-kb mRNAs in the nucleus of the infected cells. Such longer β-actin transcripts were also observed but with much less intensity. The longer HSP70 transcripts contained the downstream sequence of the polyadenylation site, as demonstrated by RNase protection with an antisense RNA probe containing the sequence through the polyadenylation sites. This clearly proved that influenza virus infection inhibits the polyadenylation-site cleavage of the pre-mRNAs by the host cleavage and polyadenylation machinery. One temperature-sensitive mutant virus carrying a temperature-sensitive mutation on the NS1gene failed to inhibit the cleavage at the nonpermissive temperature, indicating that the NS1protein is involved in the inhibition of the pre-mRNA cleavage. This is the first report of the down-regulation of cellular mRNA maturation at the point of polyadenylation-site cleavage by virus infection and identifies a new mechanism by which the influenza virus shuts off host gene expression
A New Picornavirus Isolated from Bank Voles (Clethrionomys glareolus)

AbstractA previously unknown picornavirus was isolated from bank voles (Clethrionomys glareolus). Electron microscopy images and sequence data of the prototype isolate, named Ljungan virus, showed that it is a picornavirus. The amino acid sequences of predicted Ljungan virus capsid proteins VP2 and VP3 were closely related to the human pathogen echovirus 22 (approximately 70% similarity). A partial 5′ noncoding region sequence of Ljungan virus showed the highest degree of relatedness to cardioviruses. Two additional isolates were serologically and molecularly related to the prototype
RANTES, IFN-γ, CCR1, and CCR5 mRNA Expression in Peripheral Blood, Lymph Node, and Bronchoalveolar Lavage Mononuclear Cells during Primary Simian Immunodeficiency Virus Infection of Macaques

AbstractPrimary infection of macaques with pathogenic isolates of simian immunodeficiency virus (SIV) (as a model of HIV infection in humans) represents a unique opportunity to study early lentivirus/host interactions. We sought to determine whether there is a temporal relationship linking SIV replication and dissemination and the expression of the chemokine RANTES (regulated upon activation normal T cell expressed and secreted) and the SIV/HIV coreceptor CCR5 in different tissues during acute SIV infection of macaques. Four cynomolgus macaques were inoculated intravenously with a pathogenic primary isolate of SIVmac251. RT-PCR was used to monitor the expression of RANTES and CCR5 mRNA in fresh isolated mononuclear cells from blood, lymph node, and bronchoalveolar lavages. These expressions were compared to those of IFN-γ as an indicator of the development of the immune response and to another receptor for RANTES, CCR1, which is not described as a coreceptor for SIV/HIV-1 entry. An enhancement of CCR1/CCR5 mRNA expression was noticed during primary SIVmac251 infection of macaques, mainly in tissue. In the three different compartments investigated, IFN-γ and RANTES overexpression was noticed by the time of systemic viral replication containment. Our results put CCR5 and RANTES mRNA expression back in the context of inflammatory and immune responses to SIV primary infection
A Novel Epitope for the Specific Detection of Exogenous Prion Proteins in Transgenic Mice and Transfected Murine Cell Lines

AbstractPrion diseases are closely linked to the conversion of host-encoded cellular prion protein (PrPC) into its pathological isoform (PrPSc). PrP conversion experiments in scrapie infected tissue culture cells, transgenic mice, and cell-free systems usually require unique epitopes and corresponding monoclonal antibodies (MAbs) for the immunological discrimination of exogenously introduced and endogenous PrP compounds (e.g., MAb 3F4, which is directed to an epitope on hamster and human but not on murine PrP). In the current work, we characterize a novel MAb designated L42 that reacts to PrP of a variety of species, including cattle, sheep, goat, dog, human, cat, mink, rabbit, and guinea pig, but does not bind to mouse, hamster, and rat PrP. Therefore, MAb L42 may allow futurein vitroconversion and transgenic studies on PrPs of the former species. The MAb L42 epitope on PrPCincludes a tyrosine residue at position 144, whereas mouse, rat, and hamster PrPs incorporate tryptophane at this site. To verify this observation, we generated PrP expression vectors coding for authentic or mutated murine PrPCs (i.e., codon 144 encoding tyrosine instead of tryptophan). After transfection into neuroblastoma cells, MAb L42 did not react with immunoblotted wild-type murine PrPC, whereas L42 epitope-tagged murine PrPCwas strongly recognized. Immunoblot and fluorescence-activated cell sorting data revealed that tagged PrPCwas correctly posttranslationally processed and translocated to the cell surface
Rubella Virus-Induced Apoptosis Varies among Cell Lines and Is Modulated by Bcl-XLand Caspase Inhibitors

AbstractRubella virus (RV) causes multisystem birth defects in the fetuses of infected women. To investigate the cellular basis of this pathology, we examined the cytopathic effect of RV in three permissive cell lines: Vero 76, RK13, and BHK21. Electron microscopy and the TUNEL assay showed that the cytopathic effect resulted from RV-induced programmed cell death (apoptosis) in all three cell lines, but the extent of apoptosis varied among these cells. At 48 h postinfection, the RK13 cell line showed the greatest number of apoptotic cells, the Vero 76 cell line was ∼3-fold less, and BHK21 had very few. An increased multiplicity of infection and longer time postinfection were required for the BHK21 cell line to reach the level of apoptotic cells in Vero 76 at 48 h. Purified RV induced apoptosis in a dose-dependent fashion, but not UV-inactivated RV or virus-depleted culture supernatant. Specific inhibitors of the apoptosis-specific proteases caspases reduced RV-induced apoptosis and led to higher levels of RV components in infected cells. To address the role of regulatory proteins in RV-induced apoptosis, the antiapoptotic gene Bcl-2 or Bcl-XLwas transfected into RK13 cells. Although a high level of Bcl-2 family proteins was expressed, no protection was observed from apoptosis induced by RV, Sindbis virus, or staurosporine in RK13 cells. In BHK21 cells, however, increased expression of Bcl-XLprotected cells from apoptosis. The observed variability in apoptotic response to RV of these cell lines demonstrates that programmed cell death is dependent on the unique properties of each cell and may be indicative of how selective organ damage occurs in a congenital rubella syndrome fetus