pinecone/core-2020-05-10-deduplication huggingface dataset:
Temperature Sensitivity of Two Different Steps in the Viral Life Cycle of Feline Immunodeficiency Virus

AbstractFeline immunodeficiency virus (FIV) multiplication is totally blocked by incubation of infected cells at 41°. This inhibition does not take place with a thermoresistant strain of FIV, designated m41, indicating the role played by the viral genome in temperature sensitivity. We have investigated the steps in the life cycle of wild-type FIV that are thermosensitive and found that they depend on the host cells infected. In CrFK cells, FIV replication was inhibited after the penetration step at 41°. Synthesis of viral RNA and DNA was barely detectable and no viral antigen appeared in the extracellular medium. Nevertheless, viral multiplication resumed on incubation at 37°, suggesting a state of latency at the elevated temperature. In peripheral blood mononuclear cells (PBMCs), the FIV cycle was inhibited at 41° after the synthesis of viral DNA. Several viral mRNAs failed to appear as fully spliced products and no viral antigen was found in the extracellular medium. As in CrFK cells, viral multiplication occurred in PBMCs after a shift to the permissive temperature. These results suggest that at least two steps in the viral life cycle are sensitive to 41° and that two different viral functions of the thermoresistant mutant m41 are modified to overcome temperature sensitivity
Barley Yellow Dwarf Virus RNA Requires a Cap-Independent Translation Sequence because It Lacks a 5′ Cap

AbstractA 3′ translation enhancer (3′TE) sequence that facilitates cap-independent translation is located near the 3′ end of barley yellow dwarf luteovirus RNA. Here, we show that the 3′TE is required for translation of the viral genome and thus for viral replication. Antisense inhibition showed that the 3′TE has significant secondary structure and is required for translation of virion RNA from infected plants and uncapped genomic transcripts but not for translation of capped transcripts. Direct end-labeling of RNAs verified the absence of a 5′ modification on virion RNA. Thus barley yellow dwarf virus differs from related viruses by having neither a genome-linked protein nor a 5′ cap
Influenza A Virus Lacking the NS1 Gene Replicates in Interferon-Deficient Systems

AbstractThe NS1 protein is the only nonstructural protein encoded by influenza A virus. It has been proposed that the NS1 performs several regulatory functions during the viral replication cycle, including the regulation of synthesis, transport, splicing, and translation of mRNAs. Through the use of reverse genetics, a viable transfectant influenza A virus (delNS1) which lacks the NS1 gene has been generated. Our results indicate that the NS1 of influenza A virus is an auxiliary (virulence) factor which plays a crucial role in inhibiting interferon-mediated antiviral responses of the host
Characterization of Early Region 1 and pIX of Bovine Adenovirus-3

AbstractThe mRNAs from early region 1 (E1) and pIX of bovine adenovirus type 3 (BAV-3) have been studied by Northern blot, S1 nuclease, and cDNA analysis and transcriptional maps for the regions were constructed. The transcriptional map for the E1 region of BAV-3 is different from those of mouse and human adenoviruses for which transcriptional maps for the regions have been constructed. The E1A region of BAV-3 is located between 0.8 and 10.5 map units and several different transcripts are produced from the region using alternative splice donor sites. The transcripts from the E1A region overlap with those of E1B and pIX. In BAV-3, the E1B region maps between 4.2 and 10.5 map units and encodes two major mRNA species. The mRNAs of E1B region differ from each other in that the smaller mRNA coding for the 157R protein has a large intron removed from a region corresponding to the coding region of E1B 420R protein. As in HAVs, the E1B 420R protein of BAV-3 could be translated only by internal initiation from the larger bicistronic mRNA as there are no transcripts produced exclusively for the production of 420R protein. The transcriptional unit of pIX is transcribed from an independent promoter and encodes a structural component of the adenovirus capsid. To identify and characterize the proteins produced from the region, antibodies were raised in rabbits that recognized specific proteins in Western blot and immunoprecipitation assays
Coexpression of the Adenovirus 12 E1B 55 kDa Oncoprotein and Cellular Tumor Suppressor p53 Is Sufficient to Induce Metaphase Fragility of the HumanRNU2Locus

AbstractAdenovirus 12 (Ad12), but not adenovirus 2 or 5, induces metaphase chromosome fragility at four specific loci in humans:RNU1, RNU2, PSU1,andRN5S.As each of these sites corresponds to a tandemly repeated multigene family encoding a small, abundant structural RNA, we proposed that Ad12 hinders metaphase chromatin condensation, interfering either directly or indirectly with transcriptional regulation or chromatin packing of these small RNA genes. We and others subsequently found that Ad12-induced fragility of theRNU2locus requires U2 promoter elements, viral early functions, and p53. We now show thatRNU2fragility can be induced by transfection with an expression vector encoding Ad12 E1B 55 kDa alone but not by an E1 vector encoding all E1 products (3 E1A proteins, as well as the E1B 19 kDa and 55 kDa proteins). Although Ad12 E1B 55 kDa efficiently induced fragility in transfected cells, Ad2 E1B 55 kDa did not. By swapping domains between the Ad12 and Ad2 E1B, we found that the aminoterminus of Ad12 E1B is required for induction of fragility and that the ability of the hybrid E1B proteins to induce fragility appears to correlate with nuclear localization. Furthermore, in Saos-2 cells lacking p53 function,RNU2fragility could be induced by cotransfection with vectors encoding Ad12 E1B 55 kDa and either wild-type p53 or the R273H mutant with impaired DNA binding activity. We conclude that a functional (and probably physical) interaction between Ad12 E1B 55 kDa and p53 within the nucleus is sufficient to induce metaphase fragility of theRNU2locus
Nucleocapsid Protein Zinc-Finger Mutants of Simian Immunodeficiency Virus Strain Mne Produce Virions That Are Replication Defectivein Vitroandin Vivo

AbstractAll retroviruses (except the spumaretroviruses) contain a nucleocapsid (NC) protein that encodes one or two copies of the Zn2+-finger sequence -Cys-X2-Cys-X4-His-X4-Cys-. This region has been shown to be essential for recognition and packaging of the genomic RNA during virion particle assembly. Additionally, this region has been shown to be involved in early infection events in a wide spectrum of retroviruses, including mammalian type C [e.g., murine leukemia virus (MuLV)], human immunodeficiency virus type 1 (HIV-1),Rous sarcomavirus, and other retroviruses. Mutations in the two Zn2+-fingers of the NC protein of simian immunodeficiency virus strain Mne [SIV(Mne)] have been generated. The resulting virions contained the normal complement of processed viral proteins with densities indistinguishable from wild-type SIV(Mne). All of the mutants had electron micrograph morphologies similar to those of immature particles observed in wild-type preparations. RNA packaging was less affected by mutations in the NC protein of SIV(Mne) than has been observed for similar mutants in the MuLV and HIV-1 systems. Nevertheless,in vitroreplication of SIV(Mne) NC mutants was impaired to levels comparable to those observed for MuLV and HIV-1 NC mutants; replication defective NC mutants are typically 105- to 106-fold less infectious than similar levels of wild-type virus. One mutant, ΔCys33–Cys36, was also found to be noninfectiousin vivowhen mutant virus was administered intravenously to a pig-tailed macaque. NC mutations can therefore be used to generate replication defective virions for candidate vaccines in the SIV macaque model for primate lentiviral diseases
The Bovine Newbury Agent-2 Is Genetically More Closely Related to Human SRSVs Than to Animal Caliciviruses

AbstractThe hypothesis that the enteric bovine calici-like virus Newbury agent (NA-2) belongs to the familyCaliciviridaewas examined by genome sequence analysis. Use of solid-phase immune electron microscopy allowed samples with good levels of virus to be identified and amplification of the genome was achieved by reverse transcription–polymerase chain reaction. Examination of a 216-amino-acid sequence in the RNA-dependent RNA polymerase gene and a 116-amino-acid sequence in the capsid gene showed that NA-2 had the closest deduced amino acid identity (77 to 80% for the polymerase region and 67 to 73% for the capsid region) to the morphologically indistinguishable human SRSVs (small round structured viruses) of genogroup 1, which are classified as members of theCaliciviridae.It had a weak relationship (<34.5% deduced amino acid identity) in both the polymerase and the capsid regions to animal caliciviruses, all of which have classical morphology. This is the first genomic data from a nonhuman virus with SRSV morphology. It confirms the hypothesis that the bovine enteric calici-like virus NA-2 is a member of the familyCaliciviridaeand endorses the observation to date that viruses with SRSV morphology are genomically distinct
Neutralizing and Protective Antibodies Directed against Vaccinia Virus Envelope Antigens

AbstractThe infection mechanism of vaccinia virus is largely unknown. Neither the attachment protein of extracellular enveloped virus (EEV), the biologically relevant infectious form of the virus, nor its cellular receptor has been identified. Surprisingly, all former attempts using antibodies to block EEV infection of cellsin vitrohad failed. Here, we report the production of an anti-envelope hyperimmune serum with EEV neutralizing activity and show that a polyclonal antiserum against the extraviral domain of protein B5R also inhibited EEV infection.In vivo,mice vaccinated with B5R protein were protected against a lethal vaccinia virus challenge. This protectivity is likely to be mediated by neutralizing antibodies. Protein A33R, but not A34R and A36R, also proved to be protective in active and passive vaccination experiments. However, in contrast to B5R, A33R protectivity did not correlate with antibody titers. Because anti-A33R antibodies did not neutralize EEVin vitro,the protectivity mediated by A33R protein probably involves a mechanism different from simple antibody binding. Taken together, our results suggest that antibodies to a specific protective epitope or epitopes on protein B5R are able to prevent EEV infection. The protein encoded by the B5R gene is therefore likely to play a crucial role in the initial steps of vaccinia virus infection—binding to a host cell and entry into its cytoplasm
De NovoInitiation of RNA Synthesis by a Recombinant Flaviridae RNA-dependent RNA Polymerase

AbstractRecombinant RNA-dependent RNA polymerases have been reported to synthesize RNAs by extending from the 3′ hydroxyl of a template or an oligonucleotide primer.De novoinitiation has not been reported. Establishment of such an assay would facilitate the analysis of the initiation requirements and allow the testing of antiviral compounds specifically targeting initiation. Using chemically synthesized RNAs and DNAs, we demonstrate that the recombinant RNA-dependent RNA polymerase (NS5B) of bovine viral diarrhea virus initiatesde novoRNA synthesis. Nucleotides required for efficient initiation of RNA synthesis and for stable interaction with NS5B were identified
A Novel Parvovirus Isolated from Manchurian Chipmunks

AbstractA novel parvovirus was identified in Manchurian chipmunks inhabiting Korea. Hepatitis B surface antigen (HBsAg) was detected in sera from 4 animals among 62 apparently healthy chipmunks. Electron microscopic examination of the HBsAg-positive sera revealed virus-like spherical particles 20–22 nm in diameter. Extraction of nucleic acid under annealing conditions from the serum samples containing virus-like particles yielded a single species of DNA molecule with the electrophoretic mobility of 5.6-kb double-stranded DNA. Four overlapping clones that encompassed almost the full-length viral genome, except both ends, were obtained. By sequencing these clones, we determined the sequence of 5097 nucleotides of the viral DNA. Two open reading frames were identified, with the left side open reading frame encoding a putative nonstructural protein and the right side open reading frame encoding a putative capsid protein. The nucleotide and amino acid sequences showed significant homology to parvovirus B19 and simian parvovirus, but showed little homology to other mammalian autonomous parvoviruses or adeno-associated viruses. These observations indicate that the virus isolated from Manchurian chipmunks is a novel parvovirus and may be a potentially useful animal model of human B19 infection as a new member of the Erythrovirus genus of theParvoviridae
Rice Tungro Bacilliform Virus Open Reading Frame 3 Encodes a Single 37-kDa Coat Protein

AbstractRice tungro bacilliform virus (RTBV) is a plant pararetrovirus and a member of the Caulimoviridae family and closely related to viruses in theBadnavirusgenus. The coat protein of RTBV is part of the large polyprotein encoded by open reading frame 3 (ORF3). ORF3 of an RTBV isolate from Malaysia was sequenced (accession no. AF076470) and compared with published sequences for the region that encodes the coat protein or proteins. Molecular mass of virion proteins was determined by mass spectrometry (matrix-assisted laser desorption/ionization–TOF) performed on purified virus particles from three RTBV isolates from Malaysia. The N- and C-terminal amino acid sequences of the coat protein were deduced from the mass spectral analysis, leading to the conclusion that purified virions contain a single coat protein of 37 kDa. The location of the coat protein domain in ORF3 was reinforced as a result of immunodetection reactions using antibodies raised against six different segments of ORF3 using Western immunoblots after SDS–PAGE and isoelectrofocusing of proteins purified from RTBV particles. These studies demonstrate that RTBV coat protein is released from the polyprotein as a single coat protein of 37 kDa
Controlled Conformational Transitions in the MVM Virion Expose the VP1 N-Terminus and Viral Genome without Particle Disassembly

AbstractAntisera were raised against peptides corresponding to the N-termini of capsid proteins VP1 and VP2 from the parvovirus minute virus of mice. Epitopes in the 142-amino-acid VP1-specific region were not accessible in the great majority of newly released viral particles, and sera directed against them failed to neutralize virus directly or deplete stocks of infectious virions. However, brief exposure to temperatures of 45°C or more induced a conformational transition in a population of full virions, but not in empty viral particles, in which VP1-specific sequences became externally accessible. In contrast, the VP2 N-terminus was antibody-accessible in all full, but not empty, particles without prior treatment. An electrophoretic mobility shift assay, in which particles were heat-treated and/or preincubated with antibodies prior to electrophoresis, confirmed this pattern of epitope accessibility, showing that the heat-induced conformational transition produces a retarded form of virion that can be supershifted by incubation with VP1-specific sera. The proportion of virions undergoing transition increased with temperature, but at all temperatures up to 70°C viral particles retained structure-specific antigenic determinants and remained essentially intact, without shedding individual polypeptide species or subunits. However, despite the apparent integrity of its protective coat, the genome became accessible to externally applied enzymes in an increasing proportion of virions through this temperature range, suggesting that the conformational transitions that expose VP1 likely also allow access to the genome. Heating particles to 80°C or above finally induced disassembly to polypeptide monomers
Heterosubtypic Immunity to Lethal Influenza A Virus Infection Is Associated with Virus-Specific CD8+Cytotoxic T Lymphocyte Responses Induced in Mucosa-Associated Tissues

AbstractHeterosubtypic immunity, defined as cross-reactive immune responses to influenza virus of a different serotype than the virus initially encountered, was investigated in association with virus-specific cytotoxic T lymphocyte (CTL) responses induced in systemic and mucosa-associated lymph nodes after immunization via different routes. Mice immunized by the pulmonary route with live nonpathogenic influenza virus, strain Udorn (H3N2), survived challenge with mouse-adapted pathogenic influenza virus, strain PR/8/34 (H1N1). These mice developed strong heterosubtypic CTL responses in spleen, cervical lymph nodes (CLN), and mediastinal lymph nodes (MLN). Alternately, only 20% of mice immunized intravenously, intraperitoneally, or intranasally survived the challenge; all of these developed CTL responses in spleen and CLN, but not in MLN. Direct correlation between short-term and long-term memory heterosubtypic CTL responses induced in MLN and host recovery after lethal infection indicates that these CTL responses may play an important role in heterosubtypic immunity. Furthermore, induction and maintenance of memory CTL in regional mucosa-associated lymphoid tissues are highly dependent on mucosal immunization. The results implicate the mechanism of heterosubtypic immunity and should be an important consideration in the development of protective mucosal vaccines against variant strains of influenza and HIV
Selection of the R17Y Substitution in SIVmac239 Nef Coincided with a Dramatic Increase in Plasma Viremia and Rapid Progression to Death

AbstractThree rhesus macaques were infected with an SIVmac239 variant containing substitutions of 73/74PA→ED and 204D→R in Nef that disrupted the ability of Nef to downregulate CD4 surface expression. One of these animals, Mm8155, rapidly progressed to AIDS and died 21 weeks postinfection. During the final 5 weeks of infection, the levels of viral RNA and of p27 antigenemia were about 100-fold higher than usually observed in SIVmac239 infection. Postmortem examination revealed giant cell disease of the lymph nodes and the gastrointestinal tract, opportunistic infections, and a severe chronic enteritis. The majority of proviruses in spleen, kidney, and lymph nodes, and almost 100% of the viral RNA sequences, contained mutations of CGA→TAT in codon 17 ofnef,predicting a change of 17R→Y. The appearance of this substitution, which has recently been shown to confer the phenotype of the acutely pathogenic SIVpbj14, coincided with the dramatic increase in viral load and rapid progression to fatal disease. In comparison, reversions of 204R→D and changes of 72-74NED→DKD, which restored the ability of Nef to downregulate CD4, were already selected earlier in infection. Similarly to SIVpbj14, virus reisolated at late time points from Mm8155 replicated efficiently in unstimulated monkey lymphocytes. The Y17 substitution was not detected in 14 additional SIVmac239-infected macaques at the time of AIDS-related death or in the two slowly progressing animals initially infected with the same Nef variant. Although infection of macaques with SIV is commonly used as an animal model for HIV-1 infection in humans, this is only the second example for the emergence of an acutely lethal SIVmac Nef variant
Requirement for GP64 to Drive Efficient Budding ofAutographa californicaMulticapsid Nucleopolyhedrovirus

AbstractBudded virions (BV) ofAutographa californicamulticapsid nucleopolyhedrovirus (AcMNPV) contain a major envelope glycoprotein (GP64) that is present on the plasma membrane of infected cells. GP64 is acquired by virions during budding through the plasma membrane, the final step in assembly of the budded virion at the cell surface. Previous studies (S. A. Monsma, A. G. P. Oomens, and G. W. Blissard (1996).J. Virol.70, 4607–4616) showed that insertional inactivation of the AcMNPVgp64gene resulted in a virus unable to move from cell to cell and nonlethal to orally infectedTrichoplusia nilarvae. To determine whether GP64 is involved in virion budding, we measured BV production from Sf9 cells infected with a gp64null virus. Sf9 cells infected with gp64null virus vAc64−were pulse labeled, and progeny BV were isolated on equilibrium sucrose gradients and quantified. BV production from vAc64−was reduced to ∼2% of that from wild-type AcMNPV. Thus the GP64 protein is important for efficient virion budding. To determine whether the highly charged 7-amino acid cytoplasmic tail domain (CTD) of GP64 was required for virion production, we generated a series of GP64 constructs containing C-terminal truncations or substitutions. Modified forms of GP64 were analyzed in transfected cells and in recombinant viruses in which the wild-typegp64gene was replaced with a modifiedgp64.Deletion of 1–7 amino acids from the CTD did not affect GP64 trimerization, protein transport to the cell surface, or membrane fusion activity. However, deletions of 11 or 14 amino acids, which removed the CTD and portions of the predicted transmembrane (TM) domain, were trimerized but were present at lower levels on the cell surface due to shedding of these truncated proteins. Comparisons of growth curves and quantitative measurements of labeled progeny BV production from recombinant viruses expressing either wild-type or mutant GP64 proteins showed that deletion of the 7-residue CTD only moderately reduced the production of infectious virions (∼50%). However, deletions of the C terminal 11 or 14 amino acids had more substantial effects. Removal of the C terminal 11 amino acids reduced titers of infectious virus by 78–96% and labeled progeny virions were reduced by 91–92%. Removal of 14 amino acids from the C terminus resulted in an ∼98% reduction in progeny BV and a virus that was apparently incapable of efficient propagation in cell culture. Thus the GP64 CTD is not essential for production of infectious BV, but removal of the CTD results in a measurable reduction in budding efficiency. Deletion of the CTD plus small portions of the transmembrane domain resulted in shedding of GP64, reduced surface levels, and a dramatic reduction in the production of BV. Together, these data indicate that GP64 is an important and limiting factor in BV production
Analysis of the Integration Functions of φ304L: An Integrase Module among Corynephages

AbstractPlasmid p12929 was shown to integrate into the chromosome ofCorynebacterium glutamicumRM3 and BL15. The minimal integrating fragment was subsequently defined. The arms flanking the integrated plasmid (attLandattR) were identified, allowing for the determination of theattPand theattBattachment sites. TheattBsite is located at the 3′ end of an ORF presenting 62–78% identity with L19 ribosomal proteins. Integration in theattBsite does not result in the inactivation of this gene because its end is also present on theattRarm of the integrated plasmid and is reconstituted. The minimal integrating fragment is 1663 bp long and contains two ORFs. TheintORF was identified as φ304L integrase on the basis of the amino acid homologies it shared with the tyrosine recombinases of the λ integrase family. Moreover this integrase is highly homologous throughout its sequence with the integrase of φ16 corynephage, the percentage of identity reaching 89% at the NH2end. The identity also extends upstream of the initiation codon, while both phages are elsewhere nonhomologous. An integrase module was proposed to explain this extensive homology