pinecone/core-2020-05-10-deduplication huggingface dataset:
Coamplification and Dispersion of Adjacent Human Endogenous Retroviral HERV-H and HERV-E Elements; Presence of Spliced Hybrid Transcripts in Normal Leukocytes

AbstractIn an RT–PCR study of HERV-H spliced subgenomic transcripts, we found transcripts with HERV-H leader and protease-encoding sequences spliced to HERV-E integrase-encoding sequences in lymphocytes from healthy blood donors. In other cell types, including two T-cell leukemia cell lines, these transcripts were absent. The PCR fragments of the hybrid transcripts contained two open reading frames (ORFs). One was a hybrid HERV-H protease/HERV-E integrase ORF and the other was the HERV-E envelope surface glycoprotein ORF. Alternative splice products were also identified. The genomic DNA origin of the hybrid transcripts was shown to be a HERV-H element with a large 3′-end deletion, adjacent to a HERV-E element lacking the 5′-LTR. This hybrid structure was shown to be amplified and dispersed to six different human chromosomes. Thus, a relatively large part of full-length HERV-E elements (15–20%) is potentially under the transcriptional control of HERV-H LTRs. The HERV-H/HERV-E junction was present in multiple copies also in the chimpanzee and gorilla, but not in the orangutan or old world monkeys
Determinants of Rotavirus Host Range Restriction—A Heterologous Bovine NSP1 Gene Does Not Affect Replication Kinetics in the Pig

AbstractThe genetic basis of rotavirus host range restriction (host species specificity) is unknown but the NSP1 (fifth) gene has been implicated in some studies. We studied the replication kineticsin vivoof a NSP1 gene monoreassortant, E11, to assess the influence of a heterologous NSP1 gene on the ability to replicate in pigs. The monoreassortant possessed 10 genes from the porcine parent rotavirus SW20/21, which replicated productively in pigs, and the NSP1 gene from the bovine rotavirus UK which produced an abortive infection in pigs. Groups of up to four pigs were inoculated orally with 105to 106TCID50of the monoreassortant, the porcine parent rotavirus, or the bovine parent rotavirus or were sham inoculated. The monoreassortant replicated productively in pigs with replication kinetics almost identical to the porcine parent rotavirus. During a 9-day observation period after inoculation, the number of days with virus in the faeces, the onset and duration of virus excretion, and peak titres in faeces were similar for the monoreassortant and the parent porcine rotavirus. The genetic composition of the viruses excreted in the faeces was confirmed as that of the inocula by PAGE. Thus possession of a heterologous NSP1 gene from a bovine rotavirus which failed to replicate in pigs did not produce an abortive infection or affect the replication kineticsin vivo.The genetic basis of host range restriction between porcine and bovine rotaviruses remains to be established
The Induction of Apoptosis by SV40 T Antigen Correlates with c-junOverexpression

AbstractSimian virus (SV40) T antigen shares many characteristics with adenovirus E1A which is known to induce apoptosis. To verify the potential of SV40 T antigen-mediated apoptosis, we stably expressed T antigen in immortalized human epithelial cells (Z172 and HaCaT). We found that SV40 T antigen could directly cause apoptosis in 22–27% of these cells under normal growth condition as measured by chromatin condensation and nucleosomal fragmentation. The apoptosis of HaCaT cells which contain mutant p53 suggests the p53-independent nature of T antigen-mediated apoptosis. T antigen-induced apoptosis was associated with increased expression of c-Jun protein. Moreover, the overexpression of c-junalone in these cells also induced apoptosis, indicating that c-junmight play an important role in T antigen-induced apoptosis
Subcellular Localization of Human Immunodeficiency Virus Type 1 RNAs, Rev, and the Splicing Factor SC-35

AbstractThe HIV-1 protein Rev regulates the cytoplasmic levels of incompletely spliced HIV-1 mRNAs. The plasmid pSVc21, which contains a HIV-1 provirus, was introduced into COS cells by transient transfection. Simultaneous detection of HIV-1 RNAs and Rev proteins produced in transfected cells was then performed in order to determine the relative distribution of these two components. HIV-1 RNAs and the Rev protein localized to the same areas of the nucleoplasm, implying that these locations represent sites where Rev interacts with its target RNAs. Using a monoclonal antibody targeted to the splicing factor SC-35 it was demonstrated that the sites where HIV-1 mRNAs and Rev were detected often contained weak anti-SC-35 staining, whereas little RNA and Rev were found in strongly labeled SC-35-containing speckles. The same distribution of HIV-1 RNAs relative to SC-35 was also seen in transfected HeLa cells and in primary human lymphocytes infected with HIV-1 primary isolates. In addition, transiently expressed intron-containing β-globin RNAs were shown to distribute to weak anti-SC-35 staining in a manner similar to that of HIV-1 RNAs. The findings suggest that Rev and HIV-1 RNAs interact at putative sites of mRNA transcription and splicing
De NovoReverse Transcription of HTLV-1 Following Cell-to-Cell Transmission of Infection

AbstractAnalogous to transmission of human T-cell leukemia virus type 1 (HTLV-1)in vivo,anin vitrocell-to-cell infection model was established by coculturing MT-2 cells as virus donors and HUT78 cells as recipients. At a donor:recipient ratio of 1:2, cell fusion occurred and a new round of HTLV-1 genome replication was initiated in the cocultured cells. Newly synthesized unintegrated viral DNA was detected by Southern blot within 4–8 h and then increased between 8 and 48 h following cell mixing. The most dominant species of unintegrated viral DNA was 3.7 kb in size which hybridized to a full-length HTLV-1 DNA probe but not to aKpnI viral DNA fragment that is absent from a defective proviral genome that has been previously identified in MT-2 cells. Northern blot analysis showed large amounts of viral RNA in the virus donor cells and in the cocultured cells, with a 3.4-kb species being the most abundant. This 3.4-kb RNA gave a pattern identical to that of the 3.7-kb unintegrated viral DNA in hybridization studies using the two probes. It seems likely that the unspliced RNA transcript from the defective proviral genome in MT-2 cells was effectively reverse transcribed upon initiation of cell-to-cell viral transmission to susceptible HUT78 cells. Despite activede novoreverse transcription, however, viral RNA levels remained unchanged following cell-to-cell transmission of HTLV-1 infection and no viral antigen production could be attributed to the newly initiated round of viral genome replication. As an abortive infection model this simple cell-to-cell infection system warrants more detailed study as it has the potential to provide reliable information regarding the early events in HTLV-1 transmission and infection
Establishment of MAIDS-Defective Virus-Infected B Cell Lines and Their Characterization

AbstractMice inoculated with the murine AIDS (MAIDS)-defective virus develop severe B and T cell dysfunctions. The primary event in the development of this disease is the infection and polyclonal expansion of the target cells of this defective virus, which have been reported to belong to the B cell lineage. To further study the central role that these cells play in the development of MAIDS, we attempted to establish MAIDS-defective virus-infected B cell linesin vitro.We succeeded in establishing two cell lines, SD1 and CSTB5, from the enlarged organs of C57BL/6 mice inoculated with helper-free stocks of the MAIDS-defective virus. Both cell lines are not transplantable in syngeneic C57BL/6 mice or in nude or CD8−/−mice and are apparently not malignant. They both belong to the B lineage, as their immunoglobulin (Ig) genes, but not the T cell receptor (TcR) β locus, are rearranged, suggesting that they are relatively mature B cells. However, analysis of cell surface marker expression by FACS revealed a surface phenotype similar to that of pre-B cells (MHC I+, MHC II+, B7.2+, sIgM−, sIgG−, κ−, B220−, CD5−, Thy1.2−, TcR−, CD3−, CD4−, CD8−, Mac-1−, 33D1−). Additionally, the CSTB5 cells express CD40 and the SD1 cells express CD43. Both cell lines contain the MAIDS-defective provirus and express the expected 4.2-kb viral RNA and the corresponding Pr60gagprotein. The CSTB5 cells are nonproducer, while the SD1 cell line produces what appears to be an endogenous MuLV. The phenotype of these cell lines is very similar to what is known about the target B cells of this virusin vivo.These new established cell lines are likely to be useful in elucidating the mechanism(s) by which the MAIDS-defective virus causes its target B cells to proliferate and induce T cell anergy in infected animals
Detection of Subgenomic cDNAs and Mapping of Feline Foamy Virus mRNAs Reveals Complex Patterns of Transcription

AbstractFeline foamy virus (FeFV) belongs to the group of spumaretroviruses that contain in addition togag, pol,andenvaccessory genes collectively calledbelgenes. Primate FVs have been shown to utilize internal promoters in addition to the 5′ LTR promoters. In contrast to other known retroviruses, the FVpolgenes are expressed via spliced transcripts. Northern blot analysis and reverse transcription-coupled polymerase chain reactions (RT-PCR) were used to amplify, clone, and characterize cDNAs generated from subgenomic viral transcripts. Sequencing of the splice site junctions of the different FeFV mRNAs showed that singly and multiply spliced subgenomic transcripts were expressed in virus-infected cells. The relative amount of the splicedpol-specific transcripts was quantitated and FeFVpolmRNA found to be expressed at about one-half of that of the genomic mRNA. The major FeFV internal start site of transcription was identified at RNA position 7925. Comparison of the FeFV transcriptional patterns to those of the human foamy virus revealed that the FeFVbel 1mRNA was expressedexclusivelyfrom the internal promoter in contrast to primate foamy viruses that use both the LTR and the internal promoter for Bel 1 expression. Unexpectedly, anenv-bel 2mRNA was identified in FeFV-infected cells. In addition, cDNAs from FeFV-infected cells were directly amplified by PCR without RT reactions and found to correspond to genomic and to a subset of different subgenomic FeFV mRNAs
The Bis-Azo Compound FP-21399 Inhibits HIV-1 Replication by Preventing Viral Entry

AbstractThe bis-azo compound FP-21399 inhibits HIV-1 infection. We now show that FP-21399 acts on the HIV-1 envelope glycoprotein to prevent viral replication. This compound targets the entry step of the HIV-1 replication cycle as demonstrated by time-of-addition and single cycle viral entry assays. The entry of SIVmac239, which uses the same coreceptors (CD4/CCR5) as HIV-1, was not inhibited by FP-21399, indicating that the antiviral effect of FP-21399 is specific for the HIV-1 envelope glycoprotein and is not dependent upon the cellular receptors CD4 and CCR5. FP-21399 inhibits neither the activity of HIV-1 reverse transcriptase nor the expression of HIV-1 early mRNA. Finally, this compound inhibits gp120 shedding of the T-tropic virus. Our results suggest that the anti-HIV activity of FP-21399 is due to its interaction with HIV-1 gp120/41 complex during viral entry
Mapping of ORF121, a Factor That Activates Baculovirus Early Gene Expression

AbstractThe protein product of the39kgene ofAutographa californicanuclear polyhedrosis virus is thought to be important for viral replication because of its association with the virogenic stroma and its role in activation of late gene expression. Transient expression assays showed that addition of a DNA fragment encoding a 58-amino-acid polypeptide increased expression of a39kreporter plasmid. This stimulation was dependent on cotransfection of a plasmid encoding IE1. Cotransfection of this gene,orf121,also stimulatedie1expression, and the activation ofie1was even more dramatic in the presence of IE1. These data suggested that ORF121 stimulated39kexpression by upregulation of IE1 expression. Activation of39kby ORF121 and the viral transcription factor IE2 was additive, while activation by ORF121 and the apoptotic suppressor P35 was synergistic. Cotransfection of p39cat and pIE1 with plasmids encoding ORF121, IE2, and P35 stimulated 39cat expression more than 100-fold compared to cells transfected with only p39cat and pIE1. These data suggest that IE2 and ORF121 work by similar mechanisms and indirectly activate p39cat by increasing IE1 expression, while P35 increases 39cat expression by a different mechanism
The Movement Protein and Coat Protein of Alfalfa Mosaic Virus Accumulate in Structurally Modified Plasmodesmata

AbstractIn systemically infected tissues ofNicotiana benthamiana, alfalfa mosaic virus (AMV) coat protein (CP) and movement protein (MP) are detected in plasmodesmata in a layer of three to four cells at the progressing front of infection. Besides the presence of these viral proteins, the plasmodesmata are structurally modified in that the desmotubule is absent and the diameter has increased drastically (almost twofold) when compared to plasmodesmata in uninfected cells or cells in which AMV infection had been fully established. Previously reported observations on virion-containing tubule formation at the surface of AMV-infected protoplasts suggest that AMV employs a tubule-guided mechanism for intercellular movement. Although CP and MP localization to plasmodesmata is consistent with such a mechanism, no tubules were found in plasmodesmata of AMV-infected tissues. The significance of these observations is discussed
Postreassortment Changes in Influenza A Virus Hemagglutinin Restoring HA–NA Functional Match

AbstractAn important function of influenza virus neuraminidase (NA) is the removal of sialic acid residues from virion components in order to prevent the aggregation of virus particles. In previous communications we have reported that reassortant viruses containing the NA gene of A/USSR/90/77 (H1N1) virus and HA genes of H3, H4, H10, or H13 subtypes had a tendency to virion aggregation at 4°C and that the virion clusters irreversibly dissociated after the treatment with bacterial neuraminidase. It was concluded that in such reassortants the removal of sialic acid residues is inefficient. Nonaggregating variants of the reassortants were selected in the course of serial passages in embryonated chicken eggs. In the present paper a reassortant virus, R2, having the HA gene of A/Duck/Ukraine/1/63 (H3N8) virus and the other genes of A/USSR/90/77 (H1N1) virus, as well as its non-aggregating passage variants and both parent viruses, have been studied in order to reveal the presence of unremoved sialic acid residues in the virions. An assay of sialic acid content by high-performance liquid chromatography with fluorescent detection has revealed the presence of sialic acid in the purified virus preparations of A/USSR/90/77 (H1N1) virus and the R2 reassortant and its nonaggregating variants, whereas only trace amounts of sialic acid have been detected in the A/Duck/Ukraine/1/63 (H3N8) parent virus. The data obtained with the use of the labeled “indicator” virus suggest that the unremoved sialic acid residues are present at the virion surface. The nonaggregating variants have been shown to possess a lower affinity toward high-molecular-weight sialic acid-containing substrates compared to the initial reassortant R2. Sequencing of HA genes has revealed amino acid changes in the nonaggregating variants compared to the initial reassortant. One substitution, N248D in HA1, is the same in two independently selected nonaggregating variants. The presented data suggest that the complete removal of sialic acid residues by viral NA from the virion components is not obligatory for the absence of virus particle aggregation: the latter may be achieved (in the reassortants and, presumably, in the wild-type virus) through a balance between the degree of HA affinity toward the sialic acid-containing receptors and the extent of the removal of sialic acid residues by NA
Production of HIV-1 by Human B Cells Infectedin Vitro:Characterization of an EBV Genome-Negative B Cell Line Chronically Synthetizing a Low Level of HIV-1 after Infection

AbstractHuman immunodeficiency virus type 1 (HIV-1) has tropism for helper T lymphocytes and cells of the monocyte/macrophage lineages. HIV-1 can also infect other cell types, including B cells. We show here that 10% of fresh circulating B cells from HIV-1-seronegative donors (i) express the CD4 receptor and CCR5 and CXCR4, two recently described coreceptors for HIV-1 and (ii) are permissive to HIV-1 withde novoproviral DNA integration followingex vivoinfection by either SI (syncytium-inducing) or NSI (non-syncytium-inducing) isolates. To get further information on the interaction between HIV and B cells, the susceptibility of several EBV-positive or -negative B cell lines to infection by SI and NSI isolates was checked. Following infection of an EBV−CD4+CXCR4+CCR5−B cell line (DG75) by an SI HIV-1 isolate, we obtained a cell line which chronically produced low-level infectious HIV-1 for 2 years (HIV-DG75). Immunocytochemical data, combined within situPCR data, established that HIV-DG75 cells consist of at least three populations: uninfected cells, infected virus-producing cells, and infected but nonproducing cells. Moreover, HIV-DG75 cells which express p24 antigen do not go into apoptosis, contrary to T lymphocytes. We infer from these results that B cells could constitute a reservoir of infectious virus in infected patients
Roles in Cell-to-Cell Fusion of Two Conserved Hydrophobic Regions in the Murine Coronavirus Spike Protein

AbstractThe spike (S) protein of coronavirus, mouse hepatitis virus (MHV), mediates attachment and fusion during viral entry and cell-to-cell fusion later in infection. By analogy with other viral proteins that induce cell fusion the MHV S protein would be expected to have a hydrophobic stretch of amino acids that serves as a fusion peptide. Sequence analysis suggests that the S protein falls within the group of fusion proteins having internal rather than N-terminal fusion peptides. Based on the features of known viral fusion peptides, we identified two regions (PEP1 and PEP2) of MHV-A59 S2 as possible fusion peptides. Site-directed mutagenesis and anin vitrocell-to-cell fusion assay were used to evaluate the roles of PEP1 and PEP2, as well as a third previously identified putative fusion domain (PEP3) in membrane fusion. Substitution of bulky hydrophobic residues with charged residues within PEP1 affects the fusion activity of the S protein without affecting processing and surface expression. Similar substitutions within PEP2 result in a fusion-negative phenotype; however, these mutant S proteins also exhibit defects in protein processing and surface expression which likely explain the loss of the ability to induce fusion. Thus PEP1 remains a candidate fusion peptide, while PEP2 may play a significant role in the overall structure or oligomerization of the S protein. PEP3 is an unlikely putative fusion peptide since it is not conserved among coronaviruses and nonconservative amino acid substitutions in PEP3 have minimal effects on cell-to-cell fusion
Cardiovirulent Coxsackieviruses and the Decay-Accelerating Factor (CD55) Receptor

AbstractGroup B coxsackieviruses are etiologically linked with many human diseases including acute myocarditis and associated chronic dilated cardiomyopathy. Well-established CVB3 cardiovirulent strains (CVB3c(s)) with known phenotypic differences have been used to study the pathogenesis of virus-induced heart disease. The receptor-binding characteristics ofcardiovirulentCVB3 are not known, but may represent one mechanism accounting for differences in disease virulence. In this study, interactions between CVB3c(s)and the decay-accelerating factor (DAF or CD55) cell surface receptor were examined. Anti-DAF monoclonal antibodies (MAbs) blocked virus binding and infection of susceptible HeLa cells. Virus binding was significantly reduced by treatment of these cells with phosphatidylinositol phospholipase C enzyme, which rendered them DAF-deficient. CVB3c(s)exhibited a differential propensity for the DAF receptor, as several cardiovirulent strains interacted more strongly than others. However, virus binding and infection was always most effectively blocked by MAbs directed against the SCR 2 and 3 domains of DAF, suggesting that binding occurs at a similar site(s) on the molecule for all strains. Virus binding and internalization were associated with DAF down-regulation at the cell surface, as monitored by flow cytometry analysis. Cardiovirulent CVB3 did not interact with molecules functionally and/or structurally related to DAF, including CD35, CD46, Factor H, or C4-binding protein. Adenovirus type 2 (Ad2) does not use the DAF receptor. However, competitive binding assays between Ad2 and CVB1-6, CVB3c(s), anti-DAF MAbs, or DAF-reduced cells indicated that DAF is associated with Ad2 receptors on the HeLa cell membrane. In summary, this study indicates that DAF is an attachment receptor for cardiovirulent CVB3 and that DAF interaction may be important in the pathogenesis of CVB-mediated heart disease
Improved Envelope Function Selected by Long-Term Cultivation of a Translation-Impaired HIV-1 Mutant

AbstractThe untranslated leader region of the human immunodeficiency virus (HIV) RNA genome contains multiple regulatory elements that fold into stable hairpin structures. Because extensive secondary structure can block the scanning of ribosomes, an alternative mechanism for HIV translation seems feasible. To study the mechanism of HIV-1 mRNA translation, a start codon was introduced in the leader region that will usurp scanning ribosomes. This upstream AUG mutation (uAUG) inhibited HIV gene expression, indicating that HIV-1 mRNA translation occurs via the regular scanning mechanism. Revertant viruses with increased replication capacity were obtained upon prolonged culturing of the mutant virus. To our surprise, the introduced start codon had not been inactivated in these phenotypic revertants. Instead, these revertants contain additional mutations in the envelope (Env) protein that stimulated HIV-1 replication. These second-site Env mutations did not specifi- cally overcome the gene expression defect of the uAUG mutant, as the replication capacity of other HIV-1 mutants with an unrelated defect could also be improved. The uAUG construct appears to be a unique tool in forced HIV-1 adaptation studies because the deleterious uAUG mutation is stably maintained in the progeny, yielding phenotypic revertants with second-site mutations elsewhere in the viral genome