pinecone/core-2020-05-10-deduplication huggingface dataset:
Interferon Treatment Inhibits Virus Replication in HIV-1- and SIV-Infected CD4+ T-Cell Lines by Distinct Mechanisms: Evidence for Decreased Stability and Aberrant Processing of HIV-1 Proteins

AbstractWe have examined the effects of interferon (IFN)-α/β on HIV-1 and SIV replication in CD4+ T-cell lines. To enable us to examine these effects on a single cycle of virus replication, cells were synchronously infected with HIV-1 LAI or SIV mac251. Cell lines included MT4 cells which were responsive to IFN and, as controls, C8166 cells which failed to respond to interferon treatment. Similar to previous reports, we found that replication of both HIV-1 and SIV was markedly inhibited in responsive MT4 cell lines treated with IFN. No such decreases were observed in HIV-1-infected, IFN-treated C8166 cells. Levels of both intracellular and extracellular viral antigens decreased in both HIV-1- and SIV-infected MT4 cells treated with IFN. Whereas steady state levels of viral-specific RNAs dramatically declined in SIV-infected cells, no such decrease was observed in IFN-treated HIV-1-infected cells. In accordance with these data, the rate of viral protein synthesis did not significantly change in HIV-1-infected, IFN-treated MT-4 cells. Western blot analysis of extracts prepared from IFN-treated HIV-1-infected cells revealed a decreased accumulation of most HIV-1-specific glycoproteins and proteins with the exception of the pr55 gag precursor. Pulse–chase experiments confirmed the enhanced stability of pr55 in IFN-treated cells, but also unexpectedly demonstrated the accelerated and quantitative processing of the p26 precursor (p24 capsid [CA] plus p2) to the final processed p24 (CA) polypeptide. These data, taken together, suggest that IFN deregulated viral protein processing and caused reduced protein stability in HIV-1-infected cells while inhibiting an earlier stage of replication in SIV-infected cells
Effector Functions of Antibody and CD8+Cells in Resolution of Rotavirus Infection and Protection against Reinfection in Mice

AbstractThe importance of antibody and CD8+cells in resolution of murine rotavirus (EDIM) infection and protection against reinfection was examined with two strains of B-cell-deficient mice. Following inoculation of one strain (JHD), rotavirus infection was resolved within days, but when later reinoculated with EDIM, these mice again shed rotavirus. Thus, effector mechanisms other than antibody resolved viral shedding in JHD mice but were insufficient to prevent reinfection. EDIM shedding in another B-cell-deficient mouse strain (μMT) diminished but was not fully resolved 93 days after the initial infection, thus demonstrating that antibody could also be important in resolution of rotavirus infection. When depleted of CD8+cells by monoclonal antibody treatment before EDIM inoculation, JHD mice were unable to resolve shedding. Even though μMT mice did not fully resolve their initial infection, depletion of CD8+cells 49 days after initial inoculation resulted in a burst of shedding. Thus, CD8+cells were involved in resolution of the initial EDIM infection in both strains of B-cell-deficient mice. Finally, when μMT mice were depleted of CD8+cells before the initial EDIM infection, gradual resolution of rotavirus shedding was still observed, suggesting a third effector mechanism was also involved in resolution of rotavirus infection in mice
Immune Effector Mechanisms Required for Protection to Rabies Virus

AbstractGenetically engineered mice with targeted mutations in genes encoding immunologically relevant molecules were used to elucidate the role of different immune effector mechanisms in protection against a rabies virus (RV) infection. In vaccinated animals challenged with a highly virulent strain of RV, antibodies were crucial in protection. In naive mice challenged with an attenuated strain of the virus that does not cause disease in adult fully immunocompetent mice but kills RAG mice that lack functionally active T and B cells, different immune effector mechanisms were shown to suffice for protection
Large Deletions in the Genome ofChlorellaVirus CVK1

AbstractLarge (30–45 kbp) deletions were induced in theChlorellavirus CVK1 genome by UV irradiation. Restriction endonuclease maps of the mutant genomes showed that these deletions occurred in a region located from 1.5 kbp to 47 kbp from the left DNA end. The nucleotide sequences determined around the deletion boundaries indicate that the deletion process took place by both homologous and nonhomologous recombinations. In one case, the recombination site was within a region of about 600 bp, consisting of 40 tandem repetitions of a 15-bp sequence element. The deleted region may contain several multigene families. Northern blot analyses with probes including the genes for translational elongation factor 3 and DNA polymerase showed no discernible aberrancy in the gene expression patterns in the mutants. However, at least two protein bands were missing from the mutant virions
GP mRNA of Ebola Virus Is Edited by the Ebola Virus Polymerase and by T7 and Vaccinia Virus Polymerases1

AbstractThe glycoprotein gene of Ebola virus contains a translational stop codon in the middle, thus preventing synthesis of full-length glycoprotein. Twenty percent of the mRNA isolated from Ebola virus-infected cells was shown to be edited, containing one additional nontemplate A in a stretch of seven consecutive A residues. Only the edited mRNA species encoded full-length glycoprotein, whereas the exact copies of the viral template coded for a smaller secreted glycoprotein. Expression of the glycoprotein by anin vitrotranscription/translation system, by the vaccinia virus/T7 polymerase system, and by recombinant vaccinia virus revealed that full-length glycoprotein was synthesized not only when the edited glycoprotein gene (8A's) was used as a template for T7 and vaccinia virus polymerases, but also when the nonedited (genomic) glycoprotein gene was used. Analysis of mRNA produced by T7 and vaccinia virus polymerase from the 7A's construct revealed that 1–5% contained alterations at the same site that was also edited by the Ebola virus polymerase. Our data indicate that the editing site in the Ebola virus glycoprotein gene is recognized not only by Ebola virus polymerase but also by DNA-dependent RNA polymerases of different origin
Genetic Determinants of Feline Leukemia Virus-Induced Multicentric Lymphomas

AbstractThree discrete forms of feline leukemia virus (FeLV)-associated lymphoma have been described clinically: (1) thymic, (2) alimentary, and (3) multicentric. The most common and best-characterized lymphomas are of T-cell origin, generally occurring in the thymus. These tumors typically contain mature T-cells, involve the activation of a distinctive set of proto-oncogenes, and contain FeLV proviruses whose long terminal repeat (LTR) sequences contain tandemly repeated enhancers. Previous studies of a small group of extrathymic, multicentric lymphomas implicated a different set of genetic determinants. The present study expands those observations by examining the lineage of origin, the involvement of proto-oncogenes, and the structure of LTR andenvgene sequences in a set of 11 natural, extrathymic lymphomas of the multicentric type. A pattern of genetic events associated with FeLV-positive multicentric lymphomas emerges from this analysis that is clearly distinct from the pattern associated with thymic lymphomas. The tumors do not contain T-cells or B-cells, as evidenced by the germ line organization of TCRβ and IgH loci. Proto-oncogenes strongly implicated in T-cell lymphomagenesis are not involved in these tumors. Rather, a distinct set of proto-oncogenes may be involved. Most striking is the repeated occurrence of an FeLV isolate whose LTR andenvgene bear unique sequence elements
Avian Sarcoma Leukemia Virus Protease Linked to the AdjacentGagPolyprotein Is Enzymatically Active

AbstractThe activity of avian sarcoma leukemia virus (ASLV) protease (PR) prior to its release from the precursor protein was determined by introducing mutations at the cleavage site between PR and the adjacent upstream nucleocapsid (NC) protein.GagDNA fragments containing these mutations were cloned into expression vectors and introduced intoEscherichia coliin which the ASLV proteins were expressed. The dipeptide NC-PR containing these mutations did not undergo autoprocessing when expressed in bacterial cells and the fused proteins were devoid of enzymatic activity. However, when the wholeGagpolyprotein containing these mutations was expressed in bacterial cells, other PR cleavage sites in the viralGagpolyprotein underwent normal cleavage, indicating that the release of free PR is not a prerequisite for correct processing of the ASLVGagprecursor
Influenza A Virus-Specific H-2dRestricted Cross-Reactive Cytotoxic T Lymphocyte Epitope(s) Detected in the Hemagglutinin HA2 Subunit of A/Udorn/72

AbstractBALB/c mice immunized with a vaccinia virus recombinant expressing the influenza A virus (A/Udorn/72; subtype H3) hemagglutinin HA2 (H3HA2) induced a strong CD8+cytotoxic T lymphocyte (CTL) response which wasH-2d-restricted. Two peptides, derived from the primary sequence of the H3HA2 and consistent with the predictive motif for Kd-restricted epitopes, were tested for their ability to be presented to the CTLs by P815 cells. Peptides corresponding to the amino acids93SYNAELLVAL102and181GYKDWILWI189of the HA2 primary sequence sensitized target cells for lysis by the HA2-specific CTLs. Secondaryin vitrostimulation with dendritic cells as a source of antigen presenting cells treated with peptide 93-102, or infected with recombinant vaccinia virus (HA2-VACC), induced type A cross-reactive CTLs from A/Udorn/72 immune spleen cells. This CD8+CTL epitope overlaps with an H3HA2 I-Ad-restricted T helper epitope 96-104 recently reported by others. The H3HA2 epitope described here is the first CTL epitope in the influenza hemagglutinin which is found in all three subtypes of influenza A virus
Mutational Analysis of the Murine Coronavirus Spike Protein: Effect on Cell-to-Cell Fusion

AbstractThe spike (S) protein of murine coronavirus strain A59 (MHV-A59) is a type I membrane protein that induces membrane fusion. In this study we have analyzed the role of two domains in the S protein on fusion. The 180-kDa mature S protein is partially cleaved into two 90-kDa subunits during transport to the plasma membrane. We have identified several amino acids that are important for cleavage of S, and we show that cleavage is not strictly required for fusion. However, the level of cleavage seems to influence the fusion kinetics. After introduction of an arginine at position P2to mimick the MHV-JHM cleavage site, full cleavage of the spike protein was obtained. Further, we analyzed the effect of mutations in the transmembrane (TM) domain of the S protein. Maturation and cell surface expression of the mutant proteins were not affected, and all proteins became acylated. The mutant in which the predicted transmembrane domain was shortened did not induce syncytia. From a group of mutants in which several conserved cysteines in the TM domain had been replaced by serines, one was unable to induce syncytia, another showed delayed syncytia formation, and the third mutant induced syncytia as did the wild-type protein. The potential role of the transmembrane domain in fusion is discussed
Coding Changes in the 3a Cell-to-Cell Movement Gene Can Extend the Host Range of Brome Mosaic Virus Systemic Infection

AbstractThe M1 and M2 strains of brome mosaic virus (BMV) both systemically infect the monocot host barley, but only the M2 strain systemically infects the dicot cowpea line TVu-612. We have shown previously that this difference in host range maps primarily to RNA3. To further characterize the role of RNA3 in host specificity, a series of RNA3 hybrids were tested, in inoculations with M1 RNA1 and RNA2, for ability to systemically infect TVu-612 cowpea. Although all hybrids were amplified well in cowpea protoplasts and all supported systemic infection in barley plants, only those with the 3a cell-to-cell movement gene of BMV-M2 supported systemic infection of cowpea. The sequences of the M1 and M2 3a proteins differ at four positions. Introducing these four coding differences individually or in various combinations into M1 RNA3 revealed that all four influenced BMV adaptation to cowpea and that these four differences were sufficient to account for the difference in ability between M1 and M2 RNA3s to support systemic infection of this legume. These coding changes were also associated with faster spread of infection in inoculated cowpea leaves, suggesting that they influence the ability to systemically infect TVu-612 cowpea through effects on the rate of cell-to-cell spread
Generation and Characterization of an Influenza Virus Neuraminidase Variant with Decreased Sensitivity to the Neuraminidase-Specific Inhibitor 4-Guanidino-Neu5Ac2en

AbstractA variant of the influenza virus NWS/G70C has been generated which has decreased sensitivityin vitroto the neuraminidase-specific inhibitor, 4-guanidino-Neu5Ac2en. The virus is 1000-fold less sensitive to the 4-guanidino-Neu5Ac2en in a plaque assay, but only 10-fold less sensitive to 4-amino-Neu5Ac2en. In an enzyme inhibition assay 250-fold more drug was needed to achieve inhibition comparable to that observed with the parent virus. In contrast to the plaque assay, the virus was fully sensitive to 4-amino-Neu5Ac2en in the enzyme inhibition assay. Kinetic analysis of 4-guanidino-Neu5Ac2en binding demonstrated that the variant no longer exhibited the slow binding characteristic seen with the parent and other influenza viruses and inhibition by Neu5Ac2en was also decreased. However, binding to 4-amino-Neu5Ac2en remained the same as the parent. Sequence analysis of this virus revealed a mutation at a previously conserved site in the enzyme active site of the neuraminidase, Glu 119 to Gly. Crystallographic analysis of the mutant neuraminidase with and without bound inhibitor confirmed this mutation and suggested that the reduced affinity for the 4-guanidino-Neu5Ac2en derives partly from the loss of a stabilizing interaction between the guanidino moiety and the carboxylate at residue 119, and partly from alterations to the solvent structure of the active site
The Nonstructural NSm Protein of Tomato Spotted Wilt Virus Induces Tubular Structures in Plant and Insect Cells

AbstractThe expression and subcellular location of the 33.6-kDa nonstructural protein NSm of tomato spotted wilt virus (TSWV) was analyzed inNicotiana rusticaplants and protoplasts as a function of time. Immunofluorescent studies in protoplasts isolated from TSWV-infectedN. rusticaleaves showed that this protein could first be detected close to the periphery of the cell, near the plasmamembrane, and later in tubular structures emerging from the cell surface.In situ,these tubules appeared specifically in the plasmodesmata, suggesting their involvement in cell-to-cell movement of the virus during systemic infection. In protoplasts transfected with an expression vector containing the NSm gene, similar tubules were formed, indicating that NSm has the ability to form these structures in the absence of other virus-specific components. To test whether plant-specific components were involved in tubule formation, the NSm gene was also expressed in a heterologous expression system, i.e., insect cells.Spodoptera frugiperdaandTrichoplusia nicells were infected with a recombinant baculovirus expressing the NSm-gene (AcNPV/NSm). The efficient formation of NSm-containing tubules emerging from the surface of both cell types indicate that no plant-specific cell structures or proteins are involved in their development
Involvement of Spicules in the Formation of Vaccinia Virus Envelopes Elucidated by a Conditional Lethal Mutant1

AbstractThe envelope of immature vaccinia virions consists of a lipoprotein bilayer upon which a precise curvature is imposed by acquisition of an external scaffold of spicules. Self-assembly of this tegument was examined employing our ts 6757 mutant, which induces accumulation of immature envelopes at the restrictive temperature. With ts 6757 the envelope bilayers were also assembled into an alternative membrane configuration in the form of flexible cylinders or tubes of uniform width, lacking the spicule coat. Such tubes became extensions of or were continuous with the spherical virion envelopes. The ∼65 kDa spicule protein, L65, product of gene D13L on theHindIII map, generally designated as a late protein, was expressed as an early function in presence of hydroxyurea, an inhibitor which entirely blocked vaccinia DNA synthesis without stopping assembly of immature envelopes. Labeling of thin sections by immunogold for electron microscopy demonstrated that L65 is present at the surface of immature virions, consistent with the position of spicules on envelopes. Transiency of the spicule scaffold was documented by (a) absence of L65 from intracellular mature virions (IMV) and (b) rapid turnover of L65 during ts 6757 virus replication at the permissive temperature but conservation of this protein at restrictive temperature, as demonstrated in pulse–chase experiments. Time-related decrease in MW of L65 to a smaller polypeptide is interpreted as evidence suggesting that the spicules attached to the envelope are assembled from a higher MW precursor
Organization of the Vaccinia Envelope and Relationship to the Structure of Intracellular Mature Virions

AbstractProtrusions covering the surface of intracellular mature virions (IMV), termed by us surface tubular elements (STE), are released in a quasi-intact form during stripping of the envelope. The concentrated, reproducibly isolable STE were shown to contain the 58-kDa 4c polypeptide and prominent protein antigens residing at the surface of IMV. The major core protein 4b, identified as a minor contaminant of STE, presumably became detached along with STE during the shearing off process. Antibodies against protein 4b became specifically bound to the surface of isolated cores, where a palisade layer of rodlets occurs. The same antibodies absorbed onto isolated STE where similar rodlets were evident. Based on the new observations we constructed a model of the organization of the IMV envelope and its relationship to the core
Role of Glucocorticoid Receptor Binding Sites in the Human Immunodeficiency Virus Type 1 Long Terminal Repeat in Steroid-Mediated Suppression of HIV Gene Expression

AbstractDexamethasone inhibited human immunodeficiency virus type 1 (HIV-1) long terminal repeat (LTR)-directed gene expression in cells of T and B lymphoblastoid lineages, but not in monocytic cells. Suppression required an intact glucocorticoid receptor (GR), as it was amplified by transfection of lymphocytes with a plasmid encoding the human GR and blocked by the receptor antagonist RU486. These results were in direct contrast to the effects of dexamethasone on a murine leukemia retrovirus promoter where, consistent with the findings of others, activation of gene expression was obtained. Potential regions of the HIV-1 LTR mediating these effects were sought, with sequence homologies predicting two new glucocorticoid response element half-sites, GRE-II (nucleotides −6 to −1) and GRE-III (+15 to +20), downstream from a previously identified GR DNA binding domain, GRE-I (−264 to −259). Mutational analyses documented the loss of inhibitory activity attendant on changes in GRE-III and the independence of steroid-mediated effects from GRE-I and GRE-II. Consistent with these findings, electrophoretic mobility shift assays revealed a difference in binding of cellular factors to GRE-III in cells of T and B lymphocyte vs. monocytic lineages. Binding sites for the cellular transcription factor leader binding protein (LBP-1) were found to overlap with GRE-III, and LBP-1 interacted with this element in the HIV LTR only in T and B lymphocytic extracts. We hypothesize that GRE-III sequence-specific effects, including modulation of LBP-GR interactions, underlie the negative regulatory effect of glucocorticoids on HIV-1 gene expression, with some specificity for cell type
Polymerase Activity ofin VitroMutated Rabies Virus L Protein

AbstractThe large (L) protein of nonsegmented negative-strand RNA viruses is the multifunctional catalytic component of the viral ribonucleoprotein (RNP) complex. To address the role of conserved rabies virus (RV) L protein sequences predicted to be involved in RNA polymerase activity, a reverse genetics approach was applied that allows intracellular reconstitution of transcriptionally active RV RNPs from plasmid-encoded proteins. Artificial RV model genomes encoding bacterial chloramphenicol acetyltransferase or firefly luciferase were used to determine the polymerase activity of a series of 23 RV L proteins mutated in the highly conserved C motif of the proposed polymerase module. All constructs with mutations of the GDN core sequence of motif C, which is proposed to be a variant of the catalytical XDD residues of RNA polymerases and reverse transcriptases, failed to express the reporter genes. In addition, the identity of the upstream residues AQ was crucial for maintenance of polymerase activity. Several conservative and nonconservative mutations introduced into the three amino acids QVL located downstream of the GDN core resulted in reduced polymerase activities and expression of luciferase in the range 0.4 to 92% compared to the parental L protein
Identification of Immunodominant Regions and Linear B Cell Epitopes of the gE Envelope Protein of Varicella-Zoster Virus

AbstractThe envelope proteins of varicella-zoster virus (VZV) are highly immunogenic and one of the most abundant is glycoprotein E (gE). However, its immunodominant regions and epitopes have not been identified. In this study, using human sera from individuals with recent varicella or zoster infections, we have localized antigenic sequences of gE using recombinant hybrid Ty-virus-like particles (VLPs) carrying overlapping fragments of the gE protein. gE(1–134)–VLPs (particles carrying amino acids 1–134 of gE) and, to a lesser extent, gE(101–161)–VLPs were found to be the most antigenic when tested by Western blotting and ELISA. Other fragments of gE (spanning residues 161–623) showed weak or no antigenicity. Pepscan analysis of human sera on overlapping synthetic peptides representing residues 1–135 of gE revealed that the most antigenic region was between residues 50 and 135. Three immunodominant sequences (residues 86–105, 116–135, and, to a lesser extent, 56–75) were detected using sera from both varicella and zoster patients. All sera from varicella, but not zoster, patients reacted strongly with an epitope in peptide 66–85. Other epitopes were recognized weakly by some varicella or zoster sera. More sera need to be tested to assess the potential disease specificity of these epitopes. The neutralizing monoclonal antibody (MAb) IF-B9 reacted with residues 71–90; however, another neutralizing MAb, SG1A, which bound to both gE(1–134)–VLPs and gE(101–161)–VLPs did not bind to any peptide. The identification of immunodominant sequences of gE will help toward the development of a subunit VZV vaccine