pinecone/core-2020-05-10-deduplication huggingface dataset:
Sequences of European Wheat Mosaic Virus and Oat Golden Stripe Virus and Genome Analysis of the Genus Furovirus

AbstractThe complete nucleotide sequences of both RNAs of oat golden stripe virus (OGSV) and a wheat-infecting furovirus isolate from France, previously thought to be soil-borne wheat mosaic virus (SBWMV), have been determined. Both viruses had a similar genomic organisation to SBWMV and Chinese wheat mosaic virus, the two other furoviruses previously sequenced but had <70% nucleotides identical to them. The French isolate has been named European wheat mosaic virus (EWMV). Phylogenetic analyses supported the recognition of these isolates as distinct viruses in the genus Furovirus. Analysis of the coat protein readthrough domain on RNA2 of all furoviruses strongly predicts two mutually compatible conserved transmembrane domains that may be significant for fungus transmission. The second of these regions is eliminated by a deletion in the isolate of OGSV studied. Leaky opal (UGA) stop codons occur on both RNAs of all four furoviruses characterised and, in common with most other leaky opal codons identified in plant viruses, they are followed by a CGG codon
Human Cytomegalovirus US3 Gene Expression Is Regulated by a Complex Network of Positive and Negative Regulators

AbstractOne immediate early gene of human cytomegalovirus, the US3 gene, causes retention of major histocompatibility locus class I heavy chain proteins in the endoplasmic reticulum and is postulated to have a role in viral pathogenicity. Expression of the US3 gene is regulated by a number of cis-acting elements. In addition, numerous viral proteins are involved in regulating US3 gene expression. US3 transcription was activated modestly by a virion protein, ppUL82. The immediate early proteins encoded by UL122–123 (IE1 and IE2) further activate US3 expression, with the activation enhanced by expression of pTRS1. Other proteins, the immediate early protein encoded by UL37ex1/UL38 and the early protein, pUL84, inhibited IE1 and IE2 activation of US3 expression. US3 transcription is regulated both positively and negatively by a complex network of viral proteins, the interaction of which contributes to precise regulation of US3 gene expression. The ability of pUL37ex1/UL38 to repress expression of the immediate early US3 gene while activating early gene expression suggests that pUL37ex1/UL38 may function to switch viral gene expression from immediate early to early genes
Induction of Apoptosis by Cadmium and the Adeno-Associated Virus Rep Proteins

AbstractThe parvoviruses exert antiproliferative effects on transformed cells in culture. The development of cell lines that inducibly express the parvovirus nonstructural proteins have implicated these proteins in the limitation of cell growth. To study the host cell interactions of the nonstructural proteins we have developed a human 293 cell line that expresses the adeno-associated virus (AAV) rep gene upon induction with heavy metal salts. When induced with both Zn2+ and Cd2+, Rep protein expression correlates with a cell cycle block in S phase (Yang, Q., Chen, F., and Trempe, J. P. (1994). J. Virology 68,7169–7177). However when induced with Cd2+ alone, the Rep proteins are expressed and the cells are killed. Production of a nucleosomal DNA repeat pattern and degradation of poly-ADP ribose polymerase (PARP) suggest that killing occurs by apoptosis. These results demonstrate that AAV Rep protein expression in chemically stressed cells is cytotoxic due to induction of apoptotic pathways
Vaccinia Virus Serpin-1 Deletion Mutant Exhibits a Host Range Defect Characterized by Low Levels of Intermediate and Late mRNAs

AbstractOrthopoxviruses encode three serpin homologs—SPI-1, SPI-2 and SPI-3—of which SPI-2 has been well characterized as an inhibitor of ICE-like proteases. A rabbitpox virus SPI-1 deletion mutant exhibited a host range restriction in human lung A549 and pig kidney 15 cell lines that was attributed to apoptosis. Here we report that replication of a vaccinia virus SPI-1 deletion mutant (ΔSPI-1) was restricted in primary human keratinocytes as well as A549 cells. Although chromatin condensation was detected in some A549 cells, other morphological or biochemical signs of apoptosis including DNA fragmentation, cleavage of poly(ADP-ribose)polymerase or nuclear mitotic apparatus protein, or caspase 3 activation were not found. Moreover, ΔSPI-1 protected A549 cells from apoptosis induced by tumor necrosis factor, whereas the corresponding ΔSPI-2 mutant did not. Further studies indicated undiminished amounts of vaccinia virus early mRNA and replicated DNA in the absence of the SPI-1 product. However, there were reduced amounts of viral intermediate and late mRNAs, viral late proteins, cleaved core proteins, and virus particles. These data suggested that apoptosis is not the determining factor in the host range restriction of ΔSPI-1 and that the SPI-1 gene product is needed to allow efficient expression of intermediate and late genes in A549 cells
The Interferon-Inducible 204 Gene, a Member of the Ifi 200 Family, Is Not Involved in the Antiviral State Induction by IFN-α, but Is Required by the Mouse Cytomegalovirus for Its Replication

AbstractTo examine whether Ifi 200 genes are involved in antiviral state induction by IFNs we expressed mutant forms capable of inactivating the endogenous p204 and analyzed replication of both RNA and DNA viruses following IFN-α treatment. Inactivation of p204 does not impair replication of vesicular stomatitis virus, encephalomyocarditis virus, ectromelia virus, and herpes simplex virus 1 and does not alter an IFN-α induced antiviral state. By contrast, in cells lacking functional p204, mouse cytomegalovirus (MCMV) replication is strongly inhibited and is not further modulated by IFN-α. These results suggest that p204, a member of the Ifi 200 gene family, is not involved in the IFN-α-induced antiviral activity against some RNA or DNA viruses, but is required by MCMV for its replication
A 23-bp Sequence Element from Human Neurotropic JC Virus Is Responsive to NF-κB Subunits

AbstractThe regulatory region of the human neurotropic JC virus (JCV) is composed of several cis-acting motifs that confer cell type specificity to viral gene transcription and enable the viral promoters to respond to extracellular stimuli. For example, the bidirectional 98-bp tandem repeat sequences, positioned between the JCV early and late genes, were shown to be responsible for basal and activated levels of viral gene transcription in central nervous system (CNS) cells. Additionally, the NF-κB site located approximately 75 bp from the repeats on the early side of the viral genome was also found to influence both levels of viral transcription. Recently, we isolated a novel JCV variant, JCVPhila-1, from a clinical specimen that contains a 23-bp sequence element (23-bpse) within its promoter–enhancer region. Here we demonstrate that this element is responsive to an extracellular stimulatory factor, such as phorbol 12-myristate 13-acetate (PMA), and can augment the basal levels of the viral early and to a lesser degree late promoter activities in cells derived from the CNS. The 23-bpse, by associating with nuclear proteins present in uninduced cells, forms a 40-kDa DNA–protein complex. Although no direct correlation between transcriptional enhancement of the JCV promoter by PMA treatment and the level of the 40-kDa DNA–protein complex was observed, results from site-directed mutagenesis indicated that formation of this complex is critical for the transcriptional activation of the viral promoter by PMA. These observations suggested that transcriptional enhancement of the JCV promoter activity upon PMA treatment may be an indirect event and mediated by an intermediary factor(s). In this respect, we demonstrated that overexpression of the inducible NF-κB subunits, p50 and p65, enhanced transcriptional activity of the JCV promoter through the 23-bp region with no evidence for their direct association with the 23-bpse DNA. Of importance, the p50/p65-induced JCV promoter activity requires the nucleotide sequences within the 23-bpse that are critical for the assembly of the 40-kDa DNA–protein complex. Thus, it is likely that the NF-κB subunits, by recruiting the cellular factors such as those associated with the 40-kDa DNA–protein complex, influence the basal level of the viral gene transcription. The implications of these findings with respect to regulation of viral and cellular genomes by extracellular stimuli and NF-κB pathway are discussed
Development of a Novel Mouse Model for Dengue Virus Infection

AbstractIn the present study, we established an animal model for dengue virus infection using severe combined immunodeficient mice transplanted with a human hepatocarcinoma cell line (HepG2). At 7–8 weeks after transplantation, the HepG2-grafted mice were infected intraperitoneally with dengue virus type 2 (DEN-2). A higher titer of the virus was detected in the liver and serum but not in the brain in the early stage of postinfection. When the mice showed paralysis, the highest titer of virus was detected in the serum and brain. DEN-2 antigens were also found in HepG2 cells of the liver in the early stage and some neurons of the brain in the late stage. Upon clinical examination, thrombocytopenia, prolonged partial thromboplastin time, and increased hematocrit, blood urea nitrogen, and tumor necrosis factor α were seen in the paralyzed mice. Moreover, mild hemorrhage in the liver and tarry stool in the small intestine were observed in some mice. Our results show some similarities to human DEN infection and this mouse model might be valuable for studying some aspects of pathogenesis of this disease
Characterization of Wild Lambdoid Bacteriophages: Detection of a Wide Distribution of Phage Immunity Groups and Identification of a Nus-Dependent, Nonlambdoid Phage Group

AbstractTemperate phages were isolated from fresh human fecal samples. Lambdoid phages were screened for growth on Nus+ but not Nus− bacteria. Approximately 100 independent lysogens of Nus-dependent phages were constructed and tested for immunity to superinfection by the same Nus-dependent phages. This identified 20 different phage immunity groups, 18 of which belonged to the lambdoid phage family. The DNA from the majority of these phages hybridized with a λ DNA probe, and ∼50% were recognized by anti-λ antibodies. Furthermore most were inducible by UV light. Eleven phage recombinants with different immunity were obtained when a phage from each group was coinfected with λ or its derivative λBLK20. We also identified another immunity group with 48 members. None of these hybridized with either λ or φ80 DNA probes nor were they recognized by anti-λ serum. Most were not induced by UV light treatment, and no recombinants were obtained when crossed with either λ or λBLK20. Consequently, this group of Nus-dependent phages represent a new nonlambdoid phage family
Hepatitis C Virus: An Infectious Molecular Clone of a Second Major Genotype (2a) and Lack of Viability of Intertypic 1a and 2a Chimeras

AbstractOf the six major genotypes of hepatitis C virus (HCV), infectious cDNA clones of only genotype 1 have been reported. Here, we report the construction of an infectious cDNA clone representing a second major HCV genotype, genotype 2. This infectious clone (pJ6CF) encodes the consensus polyprotein of strain HC-J6CH, genotype 2a. Its encoded polyprotein differs from those of the infectious clones of genotypes 1a and 1b by approximately 30%. Intertypic chimeric cDNA clones constructed from infectious clones of genotypes 1a and 2a of HCV were not infectious. RNA transcripts of four chimeras containing the 2a structural genes (C, E1, and E2) in the backbone of an infectious genotype 1a clone (pCV-H77C) were not viable in a chimpanzee regardless of whether p7 was from the 1a or 2a clone. However, the chimpanzee was subsequently infected with RNA transcripts of each of the two infectious parent clones, indicating that the inability of the chimeras to replicate was intrinsic to the clones and not the result of preexisting protective immune responses
The Signal for Clathrin-Mediated Endocytosis of the Paramyxovirus SV5 HN Protein Resides at the Transmembrane Domain–Ectodomain Boundary Region

AbstractThe hemagglutinin-neuraminidase (HN) glycoprotein of the paramyxovirus SV5 is internalized from the cell surface via clathrin-coated pits. However, the cytoplasmic domain of SV5 HN does not contain a previously characterized internalization motif. A cell-surface-expressed chimeric protein (APK), consisting of the cytoplasmic tail, transmembrane (TM) domain, and 12 residues of the ectodomain of HN joined to the cytoplasmic protein pyruvate kinase is internalized, indicating that the N-terminal region of HN contains an internalization signal. Although SV5 HN is internalized at a rate similar to that of influenza virus hemagglutinin (HA) mutant Y543, which contains a degenerate tyrosine-based signal in its cytoplasmic tail, the elimination of the majority of the HN cytoplasmic tail, or substitution of the HN TM domain with leucine residues, did not affect the rate of HN internalization. The HN protein of the closely related virus, Newcastle disease virus (NDV), is not internalized from the cell surface. Working under the usual convention that the TM domain consists of the hydrophobic residues bounded by two charged residues, analysis of internalization of mutant and chimeric NDV HN molecules indicates that the first seven SV5 HN ectodomain residues are critical for internalization of HN. A glutamic acid residue (E37) that abuts this presumptive HN TM domain/ectodomain boundary is important for SV5 HN internalization
Treatment of HSV-1 Infection with Immunoglobulin or Acyclovir: Comparison of Their Effects on Viral Spread, Latency, and Reactivation

AbstractWe compared immunoglobulin (IgG) and acyclovir (ACV) therapies on the establishment, maintenance, and reactivation from latency of HSV-1(McKrae) in a mouse ocular infection model. Mice were given one intraperitoneal (IP) dose of human IgG 24 h after infection (Day 1 p.i.) or ACV in the drinking water from Days 1 to 7 p.i. Both treatments allowed similar percentages of mice to survive the infection and decreased ocular virus shedding as compared with untreated controls. At most time points, there were no differences between IgG- and ACV-treated animals with respect to tissue virus titers or in the rates of virus reactivation during explant cocultivation. However, after ultraviolet exposure, HSV reactivated in 30% of ACV-treated mice compared with 90% of IgG-treated mice (P = 0.02). Also by quantitative PCR, we found more latent HSV-1 DNA copies in IgG-treated mice compared with those given ACV (P = 0.02). IgG treatment protects mice from HSV-1 infection essentially as well as ACV does. Nonetheless, it permits higher levels of latent infection and subsequent in vivo reactivation. These studies have implications for the mechanism by which IgG functions to attenuate HSV infections and for its potential value as a therapeutic agent in humans
Selection of Receptor-Binding Variants of Human Influenza A and B Viruses in Baby Hamster Kidney Cells

AbstractCultivation of human influenza viruses in the allantoic cavity of embryonated chicken eggs leads to a selection of receptor-binding variants with amino acid substitutions on the globular head of the hemagglutinin (HA) molecule. Such selection can be avoided by growing the human viruses in Madin Darby canine kidney (MDCK) cells. In the present study, we tested whether baby hamster kidney (BHK) cells select receptor-binding mutants of human influenza viruses. After isolating H1N1, H3N2, and type B influenza viruses from clinical samples in MDCK cells, we passaged them in either BHK cells or chicken eggs. The BHK-grown viruses differed from their MDCK-grown counterparts by virtue of mutations in the HA: 225D → G (H1N1 virus), 128T → A and 226I → V (H3N2), and 187N → D (type B) (H3 numbering). Variants with different substitutions were selected by passaging of the same MDCK-grown parents in eggs: 141L → H, 208R → H, and 225D → G (H1N1), 194L → I (H3N2), and 137G → R (B). Compared with their MDCK-grown counterparts, both BHK- and egg-grown viruses possessed a higher affinity for the cellular membranes of BHK cells and of the chorioallantoic cells of chicken embryos and for a 3′-sialylgalactose-containing synthetic sialylglycopolymer. By contrast, changes in the affinity of mutants for a 6′-sialyl-(N-acetyllactosamine)-containing sialylglycopolymer varied from negative to positive. Fluorescence-activated cell-sorting analysis with linkage-specific lectins showed that the density of the 6′-sialyl-(N-acetyllactosamine)-containing receptors is substantially lower on the surface of BHK cells than on MDCK cells, providing an explanation for the growth restriction of human viruses in the former cells. Our data demonstrate that cultures of BHK cells, like eggs, can select receptor-binding variants of human influenza viruses
Hepatitis C Virus RNA Polymerase and NS5A Complex with a SNARE-like Protein

AbstractHepatitis C virus (HCV) NS5A is a phosphoprotein that possesses a cryptic trans-activation activity. To investigate its potential role in viral replication, we searched for the cellular proteins interacting with NS5A protein by yeast two-hybrid screening of a human hepatocyte cDNA library. We identified a newly discovered soluble N-ethylmaleimide-sensitive factor attachment protein receptor-like protein termed human vesicle-associated membrane protein-associated protein of 33 kDa (hVAP-33). In vitro binding assay and in vivo coimmunoprecipitation studies confirmed the interaction between hVAP-33 and NS5A. Interestingly, hVAP-33 was also shown to interact with NS5B, the viral RNA-dependent RNA polymerase. NS5A and NS5B bind to different domains of hVAP-33: NS5A binds to the C-terminus, whereas NS5B binds to the N-terminus of hVAP-33. Immunofluorescent staining showed a significant colocalization of hVAP-33 with both NS5A and NS5B proteins. hVAP-33 contains a coiled-coil domain followed by a membrane-spanning domain at its C-terminus. Cell fractionation analysis revealed that hVAP-33 is predominantly associated with the ER, the Golgi complex, and the prelysosomal membrane, consistent with its potential role in intracellular membrane trafficking. These interactions provide a mechanism for membrane association of the HCV RNA replication complex and further suggest that NS5A is a part of the viral RNA replication complex
Sequence Analysis of the Xestia c-nigrum Granulovirus Genome

AbstractThe nucleotide sequence of the Xestia c-nigrum granulovirus (XcGV) genome was determined and found to comprise 178,733 bases with a G+C content of 40.7%. It contained 181 putative genes of 150 nucleotides or greater that showed minimal overlap. Eighty-four of these putative genes, which collectively accounted for 43% of the genome, are homologs of genes previously identified in the Autographa californica multinucleocapsid nucleopolyhedrovirus (AcMNPV) genome. These homologs showed on average 33% amino acid sequence identity to those from AcMNPV. Several genes reported to have major roles in AcMNPV biology including ie-2, gp64, and egt were not found in the XcGV genome. However, open reading frames with homology to DNA ligase, two DNA helicases (one similar to a yeast mitochondrial helicase and the other to a putative AcMNPV helicase), and four enhancins (virus enhancing factors) were found. In addition, several ORFs are repeated; there are 7 genes related to AcMNPV orf2, 4 genes related to AcMNPV orf145/150, and a number of repeated genes unique to XcGV. Eight major repeated sequences (XcGV hrs) that are similar to sequences found in the Trichoplusia ni GV genome (TnGV) were found
Apoptosis Is Induced by Hantaviruses in Cultured Cells

AbstractHantaviruses replicate in primary and cultured animal cells with little or no cytopathic effect. We report here that the cultured Vero E6 cells infected by the Hantaan or by the Prospect Hill viruses exhibited characteristic features of apoptosis, including condensation and segmentation of nuclei and internucleosomal cleavage of nuclear DNA. Apoptosis was not seen in the cells adsorbed by UV-inactivated virus, indicating that the viral replication is required for the induction of apoptosis. Furthermore, level of the proto-oncogenic Bcl-2 protein was significantly reduced, whereas its mRNA level remained unchanged in Hantaan virus-infected cells, suggesting possible involvement and posttranscriptional regulation of this antiapoptotic protein in the process
Analysis of the SH3-Binding Region of HIV-1 Nef: Partial Functional Defects Introduced by Mutations in the Polyproline Helix and the Hydrophobic Pocket

AbstractAn SH3-binding domain within the Nef protein of primate lentiviruses has been reported to be important to viral replication and infectivity and dispensable for CD4 downregulation, but its precise role remains unclear. This study investigates the effects of mutations in both the polyproline helix and in the hydrophobic pocket that constitute the SH3-binding domain of Nef. The data demonstrate that the well-studied mutation of the central prolines is only partially disruptive to viral infectivity and replication. The central prolines also make a subtle contribution to the efficiency of CD4 downregulation, detectable only using low levels of Nef expression. Mutation of a conserved arginine in the polyproline helix abrogated more completely Nef-mediated enhancement of viral infectivity; this mutation also adversely affected CD4 downregulation at low levels of Nef expression. Only the R77A mutation substantially impaired downregulation of class I MHC. However, mutation of the central prolines and of R77 yielded proteins that were expressed less efficiently than wild-type Nef. The R77A mutant was expressed most poorly, compatible with its defective phenotypes in all assays. Mutations of the hydrophobic pocket were minimally detrimental to both the virologic and the receptor modulatory functions of Nef. Taken together, this analysis suggests that mutations in the SH3-binding domain do not abrogate fully any Nef-associated phenotype in the absence of detrimental effects on protein expression. We suggest that mutations in this domain can introduce incomplete effects caused by subtle impairments to protein expression; these effects may appear selective under certain experimental conditions due to different sensitivities of the assays to the level of Nef expression