pinecone/core-2020-05-10-deduplication huggingface dataset:
Rapid Generation of Antibodies against the HTLV-II External Envelope Protein by Growth of Mouse Plasmacytomas in SCID Mice

AbstractRecombinant human T-cell leukemia virus type II (HTLV-II) envelope external glycoprotein, gp46-II, was expressed using a vaccinia virus vector. A recombinant gp46-II fused to an epitope of the influenza virus hemagglutinin, YPYDVPDYA, was purified by immunoaffinity chromatography. The purified glycoprotein was used to immunize Balb/c mice, and antibodies against gp46-II were detected by Western blot analysis and syncytium inhibition assays. We transformed spleen cells from the immunized mice by retroviral infection with ABL-MYC (Ψ2) and intraperitoneally transplanted the infected cells into syngeneic Balb/c and severe combined immunodeficient (SCID) mice. The plasmacytomas established ascitic tumors that produced antibodies directed against HTLV-II gp46-II. Ascites developed more rapidly in SCID mice than in normal syngeneic mice. This procedure provides a general means to generate antibodies rapidly
Infectious Proviral Clones of Chimpanzee Foamy Virus (SFVcpz) Generated by Long PCR Reveal Close Functional Relatedness to Human Foamy Virus

AbstractInfectious proviral clones of simian foamy virus isolated from chimpanzee (SFVcpz) were generated by long PCR. Two overlapping fragments representing the complete provirus were amplified from genomic DNA of infected cells. Four 8.8-kbp amplimers extending from base 1 of the provirus into theenvgene and five 4.45-kbp amplimers reaching fromenvto the end of the 3′-LTR were cloned into pCR II. Subsequently, the proviral fragments were combined in a chessboard manner to generate 20 plasmids containing full-length proviral DNA. Four plasmids produced infectious virus after transfection of susceptible cells. A distinct proviral form bearing a deletion in the transactivator gene joining both exons of a second regulatory gene present in wild-type foamy virus-infected cells started to emerge 48 hr after transfection of BHK cells with infectious SFVcpz DNA. This observation supports a novel hypothesis to explain establishment of foamy virus latency. The transactivator protein Taf of SFVcpz transcomplemented for the homologous protein Bel-1 of the unique human foamy virus isolate (HFV) and Bel-1 exhibited the reciprocal activity, suggesting that HFV could represent a variant of chimpanzee foamy virus
Phylogenetic Analysis of Open Reading Frame 5 of Field Isolates of Equine Arteritis Virus and Identification of Conserved and Nonconserved Regions in the GLEnvelope Glycoprotein

AbstractThe variation and phylogenetic relationship of open reading frame 5 (ORF5) of 3 different laboratory strains of the original prototype Bucyrus strain of equine arteritis virus (EAV), the modified live virus vaccine (ARVAC, Fort Dodge Laboratories), and 18 field isolates of EAV from North America and Europe were determined by comparison of their gene sequences. The viruses differed from the published sequence by between 3 (99.6% homology) and 94 (87.8%) nucleotides and by between 3 (98.8%) and 24 (90.6%) amino acids. The field isolates differed from each other by between 2 (99.7%) and 110 (85.7%) nucleotides and by between 1 (99.6%) and 26 (89.8%) amino acids. Comparison of the nucleotide sequences of these viruses indicates that although they are very closely related, the ORF5 of each virus is distinct. The ORF5 of EAV encodes the GLenvelope glycoprotein which expresses the neutralization determinants of the virus. Comparative analysis of the deduced amino acid sequence of the GLprotein of the viruses identified three distinct variable regions (V1[aa 61–121], V2[141–178], and V3[aa 202–222]), a putative signal sequence (S [aa 1–18]), and four conserved regions (C1[aa 19–60], C2[aa 122–140], C3[aa 179–201], and C4[aa 223–255]). Amino acid substitutions in the V1region of the GLprotein of EAV field isolates had significant effects on the predicted hydrophobicity and secondary structure of the protein, which is potentially important because this region contains a major neutralization site. Estimation of genetic distances and phylogenetic tree analysis of these viruses identified four distinct groups of EAV isolates, including two North American (NA1and NA2) and two European (E1and E2) groups. The sequence data obtained from individual European and North American isolates suggest movement of viruses between the two continents
Tissue-Specific Gene Expression from Mo-MLV Retroviral Vectors with Hybrid LTRs Containing the Murine Tyrosinase Enhancer/Promoter

AbstractTranscriptional tissue specificity was engineered directly into Moloney Murine Leukaemia Virus (Mo-MLV)-derived retroviral vectors by replacing the viral enhancer in the 3′ long terminal repeat (LTR) with two different lengths (2.5 kbp or 769 bp) of the murine tyrosinase promoter/enhancer. The hybrid tyrosinase-LTR was transferred to the proviral 5′ LTR following viral packaging and infection of target cell lines. Hybrid tyrosinase-LTR-driven IL-2 production was barely above background levels in infected nonmelanoma cell lines containing intact provirus, whereas infected melanoma cell lines expressed high levels of IL-2 and the larger tyrosinase promoter/enhancer fragment directed higher levels of transgene expression. By replacing the viral enhancer with the tyrosinase promoter/enhancer sequences, promoter interference effects which we have previously observed when the tyrosinase promoter was included as an internal promoter within a similar retroviral vector were effectively abolished. Our data show that the hybrid tyrosinase-LTR behaves as a tightly regulated melanocytic-specific regulatory element when embedded in an enhancer-deleted Mo-MLV LTR. The use of other heterologous cellular promoter/enhancer elements in similar vectors should allow the development of simpler, targeted retroviral vectors for the expression of genes in selected cell types and may eventually provide for the development of safer, more efficient vectors for use in human gene therapy
Stimulation of Human Papillomavirus Type 1a DNA Replication by a Multimerized AT-Rich Palindromic Sequence

AbstractReplication of most papillomaviruses requires the viral E1 and E2 proteins and an origin of replication containing the E1 and E2 binding sites. In the case of human papillomavirus type 1a (HPV-1a), the E1 protein alone is sufficient for DNA replication although the E2 protein significantly stimulates replication. We have further analyzed the role ofcis-acting sequences and the E1 and E2 proteins in HPV-1a replication. Previous studies have shown that a 60-bp region lacking the E2 binding sites but containing an imperfect 16-bp AT-rich palindrome corresponding to the putative E1 binding site contains the minimal origin of replication (ori). Using a transient replication assay, we demonstrate that duplication of this 60-bp region causes a severalfold increase in replication. Synthetic oligonucleotides containing a 39-bp region centered around the above palindromic sequence supported only low-level replication in the presence of either E1 alone or both E1 and E2, but replication was significantly increased in the presence of multiple copies of this sequence. Plasmids containing a 19-bp sequence which includes the AT-rich palindrome failed to replicate, but multiple copies of this region supported replication in the presence of both E1 and E2 to significant levels. The results presented indicate that the HPV-1a E1 protein is capable of recruiting all the cellular factors required for replication. Our results also suggest that multimerization of the AT-rich palindromic sequence may result in a significant increase in the recruitment of the E1 protein to the origin, thereby stimulating replication. This increased targeting of the E1 protein to the origin containing multiple copies of the putative E1 binding site may be functionally similar to the targeting of E1 to the origin by E2
Hemagglutinin–Neuraminidase of Human Parainfluenza 3: Role of the Neuraminidase in the Viral Life Cycle

AbstractThe function of neuraminidase in the life cycle and pathogenesis of human parainfluenza virus type 3 (HPF3) was studied by analyzing a variant of HPF3 that has decreased neuraminidase enzymatic activity. The variant virus is more fusogenic than the wild-type virus during an acute infection. Cloning and sequencing of the fusion (F) and hemagglutinin–neuraminidase (HN) genes from this variant revealed a single amino acid change in the HN protein and no alterations in the F protein sequence. Analysis of the growth properties of this variant revealed a delay in release of virus particles into the supernatant. Addition of exogenous neuraminidase to the culture resulted in increased release of infectious viral particles, suggesting that the viral neuraminidase is important for release of HPF3 from the infected cell surface. In addition, the behavior of the variant virus during high-multiplicity infection and in the presence of exogenous neuraminidase provided evidence that the neuraminidase of HPF3 determines the outcome of viral infection (cytopathic versus persistent) in cell culture
Sequence Analyses and Antigenic Epitope Mapping of the Putative RNA-Directed RNA Polymerase of Five U.S. Bluetongue Viruses

AbstractWe determined the complete nucleotide sequences of the cognate L1 double-stranded RNA segments of bluetongue virus (BTV) serotypes 2, 11, 13, and 17, which encode the putative RNA-directed RNA polymerase VP1. Each L1 gene contained 3944 nucleotides and was 10 bases shorter than the previously reported L1 gene of BTV 10. A single open reading frame which could encode the reported VP1 protein, 1302 amino acids in size, began with an initiation codon at nucleotides 12–14 and a termination codon at nucleotides 3918–3920. Analyses of the nucleotides of L1 genes and the deduced amino acid sequences of VP1 proteins of the five U. S. BTV serotypes indicated that the most recently isolated BTV-2 serotype from Florida was more distantly related than BTV-10, 11, 13, and 17, which were isolated primarily in the western U.S.A. The results are consistent with our hypothesis that BTVs-10, −11, −13, and −17 are derived from a single and common gene pool, and that BTV-2 belongs to a second, distinct gene pool. These genetic distinctions also reflected well with the known geographic distribution of the five U.S. BTV serotypes in North America. This putative RNA-directed RNA polymerase (149 KDa) was a basic protein, and the deduced amino acid sequences of the VP1 proteins contained seven highly conserved hydrophobic domains and many other sequence motifs which were also found in other known RNA polymerases. Four immunodominant but linear antigenic epitopes conserved among the VP1 of five U.S. BTVs were also been identified and mapped using monospecific oligoclonal antibodies
DNA Rearrangements Impairing BK Virus Productive Infection in Urinary Tract Tumors

AbstractEighty-nine tissue specimens from the urinary tract and prostate were analyzed for the presence and physical state of BK virus (BKV) DNA. Large T antigen gene sequences were amplified by PCR from prostate, kidney, ureter, and bladder with prevalences ranging from 50 to 83%. Sequence analysis of PCR products from the high variable BKV regulatory region showed that these tissues contained a new BKV strain (URO1). URO1 presents a duplication of part of the 68- and 39-bp elements of the viral enhancer, and a 68-bp deletion spanning part of the 39- and 63-bp enhancer elements. Six neoplastic specimens (11.5%), but none of the control tissues, contained viral DNA in amounts detectable by Southern blot hybridization (P< 0.05). The tumors positive by Southern blot hybridization harbored rearranged and/or integrated DNA sequences whose size was apparently incompatible with assembly into a viral particle. A full-length, macroscopically intact BKV early region was amplified from these tumors by PCR. The restriction pattern of the rearranged sequences was simple, suggesting that tumors were clonal and that DNA rearrangement occurred at an early stage of neoplastic initiation or progression
3′ Terminal Putative Stem–Loop Structure Required for the Accumulation of Cymbidium Ringspot Viral RNA

AbstractDefective interfering (DI) RNA of cymbidium ringspot tombusvirus (CymRSV) was used to identify thecis-acting nature of the last 77-nt sequence of the viral genome which is required for DI RNA accumulation. The 3′-terminalcis-essential domain of both genomic and DI RNAs can be folded into a stable stem–loop structure composed of three hairpins and two short non-base-paired regions. None of the three conserved stem–loops can be deleted without abolishing the infectivity of DI RNA. Similarly, those mutants in which base-paired stem regions were disrupted by single-, double-, or triple-base substitutions were unable to replicate. However, when the original structures were reconstructed by compensatory mutations the viability of the molecules was also restored. Limited mutation (1 or 2 nt) in the non-base-paired region did not show any significant effect on viral replication. Our results strongly suggest that the proposed structure for the 3′ terminus of the viral genome is very important for viral RNA replication. It is very likely that the function of this structure is to promote the minus-strand synthesis of CymRSV DI RNA. Evidence is provided that the proposed 3′-terminal structure is relevant not only for CymRSV DI but for genomic RNA as well
Multiple Species of Defective RNAs in Plants Infected with Citrus Tristeza Virus

AbstractAlemow (Citrus macrophylla) and sweet orange (C. sinensis) plants infected, respectively, with several Israeli and Florida isolates of the citrus tristeza virus (CTV) were found to contain multiple species of RNA molecules with features similar to defective-interfering RNAs. Northern blot hybridizations of dsRNAs extracted from serial passages of the Israeli VT isolate (CTV-VT) and from different plants infected with a single source of inoculum showed considerable variation both in the presence and in the relative abundance of the defective RNA (D-RNA) bands. The D-RNA molecules were found to be encapsidated in the CTV particles. Sequence analysis of two VT D-RNA molecules of 2.7 and 4.5 kb revealed that they were composed of two regions corresponding to 1818 and 4036 nucleotides from the 5′ and 938 and 442 nucleotides from the 3′ termini of the CTV-VT genomic RNA, respectively. A short (ca. 0.8 kb) nonencapsidated single-stranded positive-sense RNA species was also found in infected plants. This ssRNA, which copurified with dsRNAs, was shown by hybridization to encompass the 5′-terminal part of the CTV genome and might have an extensive secondary structure
Human Papillomavirus Type 11 E1 up angle E4 and L1 Proteins Colocalize in the Mouse Xenograft System at Multiple Time Points

AbstractThe most abundant viral mRNA species in HPV 11-infected tissue consists of two exons, joining a segment of open reading frame (ORF) E1 to ORF E4, potentially encoding the E1 up angle E4 protein. The L1 ORF encodes the major capsid protein of HPV. Our previous studies demonstrated colocalization of the HPV 11 E1 up angle E4 and L1 proteins within the same cells of HPV 11-infected human foreskin implants grown in athymic mice (the mouse xenograft system) and removed 12 weeks after implantation. Prior studies have demonstrated E1 up angle E4 transcripts early in infection and throughout the HPV 11-infected epithelium, while L1 transcripts are detected later, and in a subset of E1 up angle E4 mRNA-positive differentiated epithelial cells. Therefore, E1 up angle E4 protein may be produced at an earlier time point or in less differentiated cells than the L1 protein. To study these questions, athymic mice were implanted with HPV 11-infected human foreskin fragments. Mice were sacrificed at 1-week intervals beginning 2 weeks after implantation of tissue. The E1 up angle E4 and L1 proteins colocalized to the same differentiated epithelial cells or to tight clusters of cells in differentiated epithelial layers of HPV 11-infected implants. The E1 up angle E4 and L1 proteins were first detected 4 weeks after implantation. E1 up angle E4 protein was detected in the region of the cell membrane and cytoplasm, and never in the nucleus. L1 protein was only detected in the nucleus. Both proteins were detected in implants containing high viral copy numbers. No specific histologic changes were uniformly associated with detection of these proteins. The tight coupling of the E1 up angle E4 and L1 proteins at multiple time points suggests that expression of both proteins is necessary to complete the virus life cycle
The Varicella-Zoster Virus Immediate-Early 62 Promoter Contains a Negative Regulatory Element That Binds Transcriptional Factor NF-Y

AbstractThe varicella-zoster virus (VZV) immediate-early (IE) open reading frame 62 (ORF62) promoter sequence contains a CCAAT box, located between positions −117 and −113. Mutation of this motif resulted in a five-fold increase of promoter activity. In mobility shift assays, we demonstrated that NF-Y, a CCAAT box-binding protein critical for the expression of diverse eukaryotic genes, binds to this motif. Thus, the VZV IE ORF62 promoter contains a negative regulatory element that binds the ubiquitous transcriptional factor NF-Y
Cucumber Mosaic Cucumovirus Antibodies from a Synthetic Phage Display Library

AbstractAntibody fragments (scFv) that bind specifically to particles of cucumber mosaic cucumovirus (CMV) were obtained from a library which encodes a diverse array of synthetic antibody fragments, each displayed on the surface of filamentous bacteriophage. After four rounds of selection and enrichment, several clones were obtained which produced scFv that bound specifically to purified particles of CMV in ELISA.BstNI digestion of phagemid DNA resulted in the same restriction pattern for all clones. The nucleotide sequences of three of the clones showed that they belonged to the human VH1 family and that they had a complementarity determining region loop of 7 amino acids. Phage-displayed antibodies and soluble scFv secreted by these clones reacted with particles of CMV in sap from infected plants in ELISA. In immunoblotting tests, soluble scFv preparations reacted with SDS-denatured coat protein extracted from purified preparations of CMV isolates belonging to either subgroup I or II and also with protein extracted by SDS treatment of seeds harvested from naturally infected lupin plants. The results demonstrate the feasibility, and potential applicability, of recombinant antibody methods in plant pathology
Recurrence of WHV Integration in theb3nLocus in Woodchuck Hepatocellular Carcinoma

AbstractFrequent occurrence of woodchuck hepatitis virus DNA (WHV DNA) integration into or in proximity tomyconcogenes and in thewinlocus of cellular genome in woodchuck hepatocellular carcinomas (HCC) has been described by several authors. We report a further cellular locus as a recurrent target for WHV integration in woodchuck HCCs. A WHV DNA integration and its cellular flanking regions were cloned from a HCC developed in a chronically WHV-infected woodchuck. Sequence analysis showed integration of rearranged C, PreS1, and 5′ truncated X regions of the WHV genome, located in a cellular locus previously described for WHV integration in another woodchuck HCC. The two integration sites are only about 0.5 kb apart. In addition toAlu-like repeats and agag-like coding region, previously described, we found several features of MAR (matrix attachment region) chromosomal sequences in the normal cellular locus, leading us to predict that part of it might be a previously unrecognized MAR
Binding of the Influenza Virus NS1 Protein to Double-Stranded RNA Inhibits the Activation of the Protein Kinase That Phosphorylates the eIF-2 Translation Initiation Factor

AbstractThe NS1 protein of influenza A virus binds not only to poly(A) and a stem-bulge region in U6 small nuclear RNA (snRNA), but also to double-stranded (ds) RNA. Binding assays with NS1 protein mutants established that the previously identified RNA-binding domain of the NS1 protein is required for binding to ds RNA as well as for binding to poly(A) and U6 snRNA. In addition, dsRNA competed with U6 snRNA for binding to the NS1 protein, consistent with both RNAs sharing the same binding site on the protein. As a consequence of its binding to dsRNA, the NS1 protein blocks the activation of the dsRNA-activated protein kinase (PKR)in vitro.This kinase phosphorylates the α subunit of eukaryotic translation initiation factor 2 (eIF-2α), leading to a decrease in the rate of initiation of translation. Assays using purified PKR and purified eIF2 demonstrated that the NS1 protein blocks the dsRNA activation of PKR, and experiments using reticulocyte extracts showed that the NS1 protein blocks the inhibition of translation caused by dsRNA activation of PKR. The implications of these results for control mechanisms occurring in influenza virus-infected cells are discussed
Interference with Replication of Two Double-Stranded RNA Viruses by Production of N-Terminal Fragments of Capsid Polypeptides

AbstractIt is possible to interfere with the replication of a number of plant RNA viruses by systemic production of viral capsid polypeptides or RNA-dependent RNA polymerases, or by production of untranslatable portions of viral plus strands or minus strands. Interference can occur by a number of mechanisms. We have discovered that theSaccharomyces cerevisiaedouble-stranded RNA viruses ScVL1 and ScVLa, which exist as permanent persistent infections of their host cells, can be cured very efficiently by production of N-terminal fragments of their capsid polypeptides. These totiviruses produce only two polypeptides: a capsid polypeptide (Cap) and a Cap–Pol fusion polypeptide with RNA-dependent RNA polymerase activity. Three types of interference can be detected: interference due to overproduction of both Cap and Cap–Pol, interference due to overproduction of Cap (and consequent distortion of the Cap to Cap–Pol ratio), and interference due to negative complementation by N-terminal fragments of Cap. Some N-terminal fragments of Cap appear to be incorporated into viral particles, but only in the presence of a complete Cap protein. We postulate that incorporation of N-terminal fragments of Cap results in the formation of defective particles
Interaction of Bovine Leukemia Virus Transactivator Tax with bZip Proteins

AbstractThe bovine leukemia virus transactivator, BLV Tax, augments transcription from three imperfect 21-bp repeats in the viral transcriptional regulatory region. Each BLV 21-bp repeat contains a cAMP response element (CRE) in the center and unique 5′ and 3′ neighboring sequences which are crucial for the transcriptional activation by BLV Tax. Here we describe the interactions of recombinant BLV Tax with cellular bZip proteins. The recombinant BLV Tax, tagged at the carboxy terminus with a hexahistidine extension, was prepared by solubilization in 6Mguanidine hydrochloride and renaturation on the Ni2+-chelating Sepharose gel matrix. The renatured BLV TaxH6activates the BLV LTR when introduced into HeLa cells by scrape loading. Furthermore, the purified BLV TaxH6enhances binding of members of the CREB/ATF family of bZip proteins to CRE motifs by interacting with their bZip domainsin vitro.Chemical cross-linking indicates that dimerization of bZip proteins such as CREB becomes greatly facilitated in the presence of BLV Tax. These results suggest that BLV Tax interacts directly with CREB/ATF-like factors to activate viral mRNA transcription