pinecone/core-2020-05-10-deduplication huggingface dataset:
The ORF I and II Proteins ofCommelinaYellow Mottle Virus Are Virion-Associated

AbstractAntibodies were prepared against bacterially expressedCommelinayellow mottle badnavirus (CoYMV) proteins. Antiserum against purified virions and antiserum against the C-terminus of the putative coat protein-encoding region of ORF III detected the same virus-specific proteins, indicating that the CoYMV coat protein is encoded in ORF III. In addition to the two major forms of the coat protein (37 and 39 kDa), several high molecular weight virus-specific proteins were detected when virions were isolated without chloroform treatment. These proteins are possible ORF III polyprotein processing intermediates and might be associated with “immature” virions which are eliminated by chloroform treatment. As predicted by the genomic sequence, a 20-kDa virus-specific protein was detected by an antiserum raised against the C-terminus of the putative ORF I protein. Results of filtration experiments suggest that the ORF I protein is equally associated with virions and with plant component(s). The association between the ORF I protein and the virions was further confirmed using immunosorbent electron microscopy and immunogold labeling. The ORF I protein was not detected in virus preparations treated with chloroform, and colocalized with virions containing immature coat protein on sucrose–cesium sulfate density gradients, suggesting that it is associated with immature virions. An antiserum raised against the putative ORF II gene product detected a 15-kDa virus-specific protein whose association with the virions was unaffected by chloroform treatment. The ORF II protein was found to be sensitive to some protease(s) that copurified with the virions, and protease inhibitors preventing this degradation have been identified
Detection of Borna Disease Virus Antigen and RNA in Human Autopsy Brain Samples from Neuropsychiatric Patients

AbstractBorna disease virus (BDV) causes a central nervous system disease in several vertebrate species which is characterized by behavioral disturbances. Seroepidemiological data indicate an association of BDV infection with certain human mental disorders. Sclerosis of the hippocampus and astrocytosis constitute histopathological hallmarks of BDV infection in animals. Therefore, we searched for human brain autopsy cases with such histopathological features. Five of 600 cases examined were identified as having hippocampus sclerosis and astrocytosis. Using immunocytochemistry, RT-PCR, andin situhybridization, we detected both BDV antigen and RNA in autopsy brain samples from 4 of these 5 patients, who presented with a clinical history of mental disorders involving memory loss and depression. This is the first demonstration that BDV can infect human brain tissue, possibly contributing to the pathophysiology of specific human neuropsychiatric disorders
A Single Codon Change in a Conserved Motif of a Bromovirus Movement Protein Gene Confers Compatibility with a New Host

AbstractBrome mosaic virus (BMV) and cowpea chlorotic mottle virus (CCMV) are closely related bromoviruses with tripartite RNA genomes, but distinct host ranges: BMV systemically infects the monocot barley, while CCMV systemically infects the dicot cowpea. We have previously shown that in approximately 10% of inoculated cowpea plants, a CCMV hybrid [CCMV(B3a)] with the 3a cell-to-cell movement protein gene replaced by that of cowpea-nonadapted BMV directs systemic infections, which are caused by secondary mutation(s) of the hybrid virus. Here, to further analyze the role of RNA3 in adaptation to a new host, RNA3 cDNA clones were constructed from total RNA recovered from the uninoculated upper leaves of systemically infected cowpea plants inoculated with CCMV(B3a). Sequence and mutational analysis of two such RNA3 clones revealed that a single codon change (A776 → C) in a conserved motif of the 3a movement protein gene conferred compatibility for systemic infection of a new host, cowpea, suggesting that this site in the 3a gene is directly or indirectly involved in crucial host interactions associated with host-range specificity. The adaptive hybrid viruses carrying this mutation induced exacerbated symptoms, while wt CCMV appeared nearly symptomless, showing that the bromovirus 3a movement protein gene can significantly contribute to regulating symptom development. However, introducing this cowpea-adaptive mutation into the BMV genome had little effect on the ability of BMV to systemically infect barley
The Acidic Domain of the Human Cytomegalovirus UL37 Immediate Early Glycoprotein Is Dispensable for Its Transactivating Activity and Localization but Is Not for Its Synergism

AbstractThe product of the human cytomegalovirus (HCMV) immediate early (IE) UL37 gene, gpUL37, is predicted to be a type I membrane-bound glycoprotein. Typically for HCMV IE proteins, gpUL37 transactivates nuclear gene expression and acts synergistically with other IE proteins. We have initiated mutational analysis of the gpUL37 domains to determine which are required for its transactivating activity. The acidic domain, a feature notably required for the activity of many nuclear transcription factors, was deleted from gpUL37. Similar to wild-type gpUL37, the mutant retained a dose responsive transactivating activity in transiently transfected HeLa cells. Transactivating activity of the mutant was also observed in permissive human diploid fibroblasts when it was cotransfected with IE1. However, the gpUL37 acidic domain mutant is defective for synergism with another HCMV IE protein, pUS3. We found that wild-type gpUL37 and its acidic domain mutant (Δaa53-140) are nonnuclear proteins and are indistinguishable in localization. Confocal microscopy of human cell types coexpressing both HCMV IE regulatory proteins, IE1 and gpUL37, showed gpUL37 does not colocalize with the IE1 nuclear protein. Taken together, our results establish that gpUL37 is a nonnuclear protein that requires its acidic domain for synergism with pUS3 but not for its transactivating activity or its localization
Analysis of 76 kb of the Chlorella Virus PBCV-1 330-kb Genome: Map Positions 182 to 258

AbstractAnalysis of 76 kb of newly sequenced DNA, located between map positions 182 and 258 kb in the 330-kb chlorella virus PBCV-1 genome, revealed 175 open reading frames (ORFs) of 65 codons or longer. One hundred and five of these 175 ORFs were considered major ORFs. Twenty-one of the 105 major ORFs resembled proteins in databases including ribonucleotide reductase small subunit, RNase III, thioredoxin, glutaredoxin, protein disulfide isomerase, deoxynucleoside kinase, frog virus 3 ATPase,Acetobactercellulose synthase, a bacteriophage encoded endonuclease, and two C-5 cytosine DNA methyltransferases. One of the ORFs was the PBCV-1 major capsid protein. The 105 major ORFs were evenly distributed along the genome. One set of ORFs was separated by 543 nucleotides whereas 75 of the ORFs were separated by fewer than 100 nucleotides. Nineteen of the 175 ORFs resembled other PBCV-1 ORFs, suggesting that they represent either gene duplications or gene families
HIV Envelope Glycoprotein-Induced Cell Killing by Apoptosis Is Enhanced with Increased Expression of CD26 in CD4+T Cells

AbstractThe membrane-expressed HIV-1 envelope glycoprotein complex, gp120 and gp41, has been shown to be responsible for the initiation of cell killing by apoptosis in CD4+T cells. By using two experimental approaches we demonstrate here that CD26, also known as dipeptidyl peptidase IV (DPP IV), appears to be implicated in this function of the gp120/gp41 complex to initiate apoptosis. In the first experimental model, we used persistently HIV-1-infected H9/IIIB cells expressing the membrane-associated gp120/gp41 complex as effector cells to induce apoptosis in Jurkat CD4+T cells: parental or transfected in order to express high levels of recombinant CD26, either wild-type or mutated at its Ser-630 which inactivates the DPP IV activity of CD26. Parental Jurkat cells and transfected control cell clones express low but reproducibly detectable levels of endogenous CD26. In coculturing experiments using H9/IIIB and Jurkat cells, the occurrence of apoptosis was found to be retarded by at least 24 hr in Jurkat cells expressing low levels of endogenous CD26, compared to cell clones expressing high levels of either wild-type or mutated catalytically inactive transfected CD26. In the second experimental model, the different Jurkat cell lines were infected with vaccinia recombinant viruses expressing HIV-1envgene, either wild-type to generate a functional gp120/gp41 complex or mutated to generate an uncleavable membrane-expressed precursor of the envelope glycoprotein gp160. At 18 hr postinfection with such vaccinia recombinant viruses, apoptosis was observed only in Jurkat cells with enhanced levels of CD26 and expressing the gp120/gp41 complex. Apoptosis was not detected in the different Jurkat cell lines expressing the uncleavable precursor gp160. In both of the experimental models used, no significant differences were observed between the transfected cells expressing either the wild-type or the mutated form of CD26, thus suggesting that the DPP IV activity of CD26 is not essential for its function as a cofactor of CD4 in the mechanism of initiation of apoptosis by the HIV envelope gp120/gp41 complex. Taken together, these results indicate that CD26 in CD4+T cells may determine the rate of initiation of apoptosis by the mature HIV-1 envelope glycoproteins, i.e., CD26 is being involved as a cofactor of CD4 in the mechanism of triggering apoptosis by the gp120/gp41 complex. As signaling through CD26 could lead to T cell activation, we propose that this latter might be modified following the binding of the gp120/gp41 complex to CD4 and thus leading to apoptosis
Activation of Type III Nitric Oxide Synthase in Astrocytes Following a Neurotropic Viral Infection

AbstractType III nitric oxide synthase (type III NOS), also known as endothelial cell nitric oxide synthase (eNOS or ecNOS or NOS-3), is a constitutively expressed, calcium- and calmodulin-dependent, isoform of NOS. Its expression has been localized to endothelial cells and a subset of neurons in the brain. We report here that resident astrocytes of the central nervous system (CNS) of mice express type III NOS. Following an experimental neurotropic viral infection, the expression of type III NOS on reactive astrocytes increases substantially, predominately in virally infected regions of the brain. This upregulation of type III NOS expression is also evident following cytokine treatmentin vitro.The intraperitoneal (i.p.) administration of IL-12, a potent activator of IFN-γ and TNF-α production, results in a substantial increase in type III NOS immunoreactivity in astrocytes. Cytokine-mediated activation of type III NOS is observedin vitrofollowing exposure of a C6 glioma cells, which constitutively express type III NOS, to IL-12, IFN-γ, and TNF-α treatment. We conclude that astrocytes of the murine CNS express type III NOS, which may be positively regulated by a number of cytokines following viral infection. Type III NOS expression by astrocytes represents a novel source of nitric oxide in the brain. It may be important in regulating perfusion and maintaining the blood–brain barrier. Given the intimate association of astrocytes with endothelial cells and neurons, increased activity of type III NOS following viral infection may be beneficial in inhibition of viral infection in neighboring cells
The Immunogenic and Pathogenic Potential of Short Poly(C) Tract Mengo Viruses

AbstractWe have shown previously that genetically engineered Mengo viruses with artificial deletions in their 5′ noncoding polyribocytidylic acid (poly(C)) tracts are highly attenuated for the natural murine host and also for other animals such as baboons, macaques, and domestic pigs. The present report further characterizes select short poly(C) tract Mengo viruses in the natural murine host. A positive correlation was found between the length of the poly(C) tract and murine virulence, as measured by virus brain titers and brain lesion scores after infection. Histological examination of brain tissue collected from infected animals clearly showed that the short poly(C) tract viruses did not induce the devastating pathological effects characteristic of animals inoculated with wild-type virus. Instead, the short-tract Mengo viruses proved excellent immunological agents. A dose of only 100 plaque-forming units of vMC24(poly(C) tract: C13UC10), injected subcutaneously, protected 80% of recipient animals against a normally lethal dose of encephalomyocarditis virus. The protection was long-lived, and animals similarly immunized with vMC0virus (poly(C) tract: C0) still had protective neutralizing antibody titers up to 16 months after inoculation. In addition, the short-tract viruses proved genetically stable, in that the vMC24virus did not yield detectable pathogenic revertants even after multiple, forced passages in 4-week-old mice. These studies suggest that Mengo viruses containing deletions in their poly(C) tracts are biologically safe and potent immunogens and imply that they may have uses as cardiovirus vaccines
High Viral Load and CD4 Lymphopenia in Rhesus and Cynomolgus Macaques Infected by a Chimeric Primate Lentivirus Constructed Using theenv, rev, tat,andvpuGenes from HIV-1 Lai

AbstractChimeric primate lentiviruses composed of SIV and HIV genes may allow the analysis of the role of these discrete HIV genes in viral pathogenesis in macaque monkeys. We have constructed a chimeric virus in which theenv, rev, tat,andvpugenes of HIV-1 Lai replace theenv, rev,andtatgenes of the SIVmac239 genome. This virus, SHIVsbg, replicates efficiently in rhesus (Indian and Chinese subspecies) and cynomolgus monkeys with viral loads in PBMC and lymph nodes of up to one infected cell per 30 cells during the acute phase of the infection. Sera from all monkeys recognize specific HIV-1 glycoproteins. The onset of lymphadenopathy in all animals was concurrent with a depletion of CD4 lymphocytes in peripheral blood. The virulence of this SHIV for rhesus and cynomolgus monkeys therefore closely parallels that of HIV-1 for human in the acute phase of the infection. Changes in theenvandvpugenes of a molecular clone of HIV-1 can now be analyzed after passage in nonhuman primate species as the SHIVsbg replicates efficiently. The SHIVsbg-macaque model is an important step in the development of a readily available animal model for HIV-1 vaccine studies
Clonal Expansion of Human T-Cell Leukemia Virus Type II in Patients with High Proviral Load

AbstractIn previous studies we demonstrated that individuals infected by human T-cell leukemia virus type II (HTLV-II) presented a high degree of variation in proviral load and that the cellular tropism of this virus was expanded in some patients to B-lymphocytes. To understand whether the observed high proviral load could be associated with the clonal expansion of the infected cells, we have studied the mode of integration of HTLV-II in six infected individuals with proviral load higher than 1% of total peripheral blood mononuclear cells (PBMCs). An inverse polymerase chain reaction (PCR) analysis, which allowed the amplification of the region flanking the 5′ end of the provirus, was developed for HTLV-II. A single band, corresponding to a monoclonal expansion, was found in four of six patients analyzed, while in the other two patients an oligoclonal type of integration was observed. The results for inverse PCR analysis were confirmed by sequencing the PCR products and showing that the 5′ LTR flanking sequences of proviral DNA obtained from the different subjects presented no homology, thus suggesting that no specific site or sequence is required for the integration process of HTLV-II. The results indicate that the HTLV-II high proviral load observed in PBMCs from infected patients is associated with a clonal expansion of HTLV-II-infected cells. This study also suggests that the very high genetic stability of HTLV-II could be explained by viral amplification via clonal expansion rather than by reverse transcription
AZT-Related Mutation Lys70Arg in Reverse Transcriptase of Human Immunodeficiency Virus Type 1 Confers Decrease in Susceptibility to ddATP inin VitroRT Inhibition Assay

AbstractThe genetic basis for didanosine (ddI) resistance in human immunodefeciency virus (HIV-1) has previously been shown to be commonly associated with a Leu to Val change at codon 74 in the HIV-1 RT gene. In this study sequential viral isolates were analyzed from five patients with prior zidovudine (AZT) use who received 6 to 16 months of ddI therapy. Following ddI therapy, viral isolates exhibited an increased AZT susceptibility and decreased ddI susceptibility. Sequence and nested PCR analysis of the HIV-1 RT gene revealed that two viral isolates contained the Leu to Val change at codon 74, and three other isolates with reduced susceptibility to ddI each contained changes at codons 65, 70, and 72. Site-directed mutagenesis was employed to insert specific mutations in RT gene of proviral clone pNL4-3. Analysis of virion-associated reverse transcriptase activity indicated that the Lys70Arg mutation resulted in an enzyme with 2- to 4-fold decreased susceptibility to ddATP. Statistical analysis of the inhibitory concentration for RT activity between pNL4-3 and mutant Lys70Arg viruses obtained in three independent RT inhibition assays was significant (P= 0.05) by studentttest paired analysis. Drug susceptibility assays on the virus with Lys70Arg mutation showed a marginal decrease in susceptibility to ddI (1.5- to 2-fold) and about 4- to 6-fold decrease in susceptibilty to AZT. Mutations Lys65Glu and Arg72Ser resulted in an impaired RT with greatly diminished functional RT activity. The AZT-associated Lys70Arg mutation results in an RT enzyme with decreased susceptibility to ddATP
Nucleotide Sequence, Temporal Expression, and Transcriptional Mapping of the p34 Late Gene of the Hz-1 Insect Virus

AbstractA late gene of the Hz-1 insect virus (Hz-1V) encoding a predicted polypeptide of 34 kilodaltons (kDa) was isolated from a cDNA library and mapped to theHindIII-T region (50.3 to 52.4 map units) of the viral genome. The p34 gene was characterized by DNA sequence, Northern blot, and primer extension analyses. The 765-bp open reading frame (ORF) is transcribed in the clockwise direction as a 1.2-kb RNA. Primer extension analysis detected two late transcription initiation sites at −16 and −17 nt relative to the start of the p34 ORF. Transcription initiation was observed between 4 and 18 hr postinfection (hr p.i.) with maximum expression at 12 hr p.i. No nucleotide sequence homology was detected between the regulatory region of the p34 gene and the baculovirus conserved late promoter motif NTAAG. This observation was substantiated by results obtained from an investigation of Hz-1V late gene expression using a transient expression assay system which suggested that Hz-1V late gene promoters do not resemble the baculovirus late promoter motif. This is the first molecular analysis of Hz-1V late gene expression and offers a basis by which to compare Hz-1V to other insect viruses
Termini of All mRNA Species of Marburg Virus: Sequence and Secondary Structure

AbstractThe 3′ and 5′ ends of Marburg virus (MBG)-specific mRNA species have been determined using reverse transcription-PCR, rapid amplification of cDNA ends, or the reverse ligation-mediated PCR procedure after removal of cap structures with tobacco acid pyrophosphatase. The polyadenylation sites of all MBG-specific mRNAs were strictly conserved and corresponded to the predicted transcriptional stop signals of genomic RNA. Determination of the 5′ ends of the mRNA species showed that mRNA synthesis started precisely at the first nucleotide of a highly conserved transcriptional start site. The 5′ ends of the mRNA species can build a stable secondary structure with the conserved nucleotides always located in the stem region of a hairpin. Nucleotide substitutions in the conserved 5′ regions are accompanied by compensatory mutations of the complementary nucleotide thus leading to a conservation of the secondary structures. Compensatory mutations were also found when 5′ ends of mRNA of MBG strain Musoke were compared with MBG strain Popp or the closely related Ebola virus, indicating that the secondary structures will be conserved even if the sequence is altered
Deletion of CD4+T Cells by Mouse Mammary Tumor Virus (FM) Superantigen with Broad Specificity of T Cell Receptor β-Chain Variable Region

AbstractWe previously identified a superantigen from the exogenous mouse mammary tumor virus carried by FM mice [MMTV (FM)], which can preferentially activate Vβ8.2+CD4+T cells by subcutaneous injection. In the present study we investigated the effect of neonatal infection with the virus on the T cell receptor (TCR) β-chain variable region (Vβ) repertoire, T cell immune response, and development of experimental allergic encephalomyelitis (EAE). The infection, surprisingly, resulted in deletion of a large portion of CD4+T cells including Vβ2+, 6+, 8.1+, 8.3+, and 14+CD4+T cells in addition to Vβ8.2+CD4+T cells. Nevertheless, the infection marginally affected T cell immune response to various antigens such as ovalbumin (OVA) and alloantigen except the abrogated response to anti-Vβ8.2 antibody-mediated receptor cross-linking. Moreover, the infection exerted a protective effect on the development of EAE in (PL/J × SJL)F1 mice. Thus, MMTV (FM) superantigen has the ability to delete a large portion of CD4+T cells with broad TCR Vβ specificity, including Vβ8.2+CD4+T cells, and may have potential as a therapeutic agent against autoimmune diseases
Herpes Simplex 1716—an ICP 34.5 Mutant—Is Severely Replication Restricted in Human Skin Xenograftsin Vivo

AbstractHSV-1716 is a replication-restricted, neuroattenuated ICP 34.5 gene mutant of herpes simplex virus type 1 (HSV-1). Because of the attenuated phenotype of ICP 34.5 mutants in rodent models of HSV disease, they have been promoted as potential vaccine strains and gene therapy vectors and have been used by us and others as therapeutic agents for the treatment of experimental malignant tumors. However, all data on the phenotype of HSV-1716 and other ICP 34.5 mutants are from animal model systems, while humans are the natural hosts of HSV-1. To achieve an initial characterization of the phenotype of 1716 in human tissue, we have studied its replication in mature human skin xenografts on SCID mice. We find that replication of 1716 is severely restricted in such human skin grafts relative to both parental wild-type HSV-1 strain 17+and the HSV-1716 revertant virus 1716R, in which the 759-bp ICP 34.5 gene deletions have been repaired. Moreover, the replication of both 1716 and 17+is significantly better in the human skin grafts than it is in mouse skin. The implications of these findings are discussed
Identification, Molecular Cloning, and Transcription Analysis of theChoristoneura fumiferanaNuclear Polyhedrosis VirusSpindle-like ProteinGene

AbstractTheChoristoneura fumiferananuclear polyhedrosis virusspindle-like protein(slp) gene has been identified and localized immediately downstream and in the same orientation as the CfMNPV DNA polymerase gene. Theslpgene is 1101 bp long, predicted to code for a 366 amino acid (42.1 kDa) polypeptide. Transcriptional analysis revealed that the CfMNPVslpgene is expressed at late times postinfection, beginning at 24 hr postinfection and is most abundantly expressed after 36 hr. Transcription initiates within a single baculovirus consensus late start site sequence (GTAAG) at position −18 relative to the translation start codon. Based on amino acid comparisons, the CfMNPV gene is closely related to other similar baculovirus genes and distantly but recognizably related to the fusolin proteins of two entomopoxviruses. The conservation of amino acid sequence, glycosylation signals and specific domains throughout the protein suggest that this gene product may play an important role in insect DNA virus replication