pinecone/core-2020-05-10-deduplication huggingface dataset:
Multiple Sequence-Reactive Antibodies Induced by a Single Peptide Immunization with Hypervariable Region 1 of Hepatitis C Virus

AbstractHypervariable region 1 (HVR1) of hepatitis C virus (HCV) is known to contain neutralizing epitopes. We previously found that murine antibodies against HVR1-#6 captured a different isolate, HCV-#7, and cross-reacted with the HVR1 peptide of HCV-#7. We investigated the inducibility and generality of cross-reaction of animal anti-HVR1 antibody responses in this study. Anti-HVR1-#7 antibodies, which were induced in mice and a chimpanzee by immunization, were found to be cross-reactive to HVR1-#6 peptide. Antibody responses against HVR1-#6-1 and HVR1-#7 peptides were detected in 11/165 (6.7%) and 26/165 (15.8%) HCV-infected individuals, respectively. Nine HVR1 sequences from six individuals, who were strongly positive for anti-HVR1-#7 antibodies, were only 50–64.5% identical to that of HVR1-#7. All nine of these HVR1 peptides were reactive to sera from the six patients and/or to antisera against HVR1-#6 and HVR1-#7 produced in mice and chimpanzees. Cross-inhibition tests of chimpanzee antisera indicated that a given species of anti-HVR1 antibodies was reactive to multiple HVR1 sequences. Fine epitope mapping of polyclonal and monoclonal anti-HVR1 antibodies showed that conserved subregions in HVR1 sequences determined the observed immunological cross-reactivity. Our data demonstrate that cross-reacting anti-HVR1 antibodies are inducible by a single peptide immunization
Differentiation-Induced Changes in Promoter Usage for Transcripts Encoding the Human Papillomavirus Type 31 Replication Protein E1

AbstractThe life cycle of human papillomaviruses (HPVs) is tied to keratinocyte differentiation. One key event in the viral life cycle is the differentiation-dependent increase in viral replication. This increase in replication activity results in an amplification of the HPV genome from approximately 50 copies per cell in basal keratinocytes to thousands of copies of the viral genome per cell in suprabasal keratinocytes. To characterize the events associated with this differentiation-dependent increase in HPV replication, we have initiated studies of mRNAs encoding the HPV replication protein E1 during the differentiation of cell lines that stably maintain episomal HPV DNA. Differentiation induced the expression of several transcripts that hybridized to an E1-specific probe. One of these messages, a 3.7-kb transcript, did not hybridize to a probe specific for the early promoter upstream of the E6 open reading frame. RNase protection analysis confirmed an induction of unspliced messages derived from the differentiation-dependent promoter at nucleotide 742 in the middle of the E7 open reading frame. These observations demonstrate a differentiation-induced increase in E1 mRNAs derived from the viral late promoter and suggest a role for increased E1 expression during amplification of the HPV genome
Identification of MaTu-MX Agent as a New Strain of Lymphocytic Choriomeningitis Virus (LCMV) and Serological Indication of Horizontal Spread of LCMV in Human Population

AbstractIn this study we elucidated the molecular character of MaTu-MX, previously described as an unusual transmissible agent. Amino acid sequencing of peptides generated from a 58-kDa MX-related protein purified from MaTu human carcinoma cells allowed us to identify it as a nucleoprotein (NP) of lymphocytic choriomeningitis virus (LCMV). Northern blot analysis detected LCMV-specific RNAs in MaTu cells. Comparative immunoprecipitations showed cross-reactivity between NP of LCMV strain WE and MX NP. Using RT-PCR, we have cloned MX NP cDNA. According to sequence comparison, MX LCMV is as closely related to both LCMV strains WE and Armstrong as these strains are to one another. Based on this finding we propose that MX is a new strain of LCMV. We also showed that the stability of MX NP in MaTu cells is very high and that the virus is transmissible by cell-to-cell contact or by cell-free extract to human HeLa and monkey Vero cells, but not to human AGS, canine MDCK, mouse NIH 3T3, and hamster CHO cells. Finally, employing MX LCMV NP in immunoprecipitation and solid-phase radioimmunoassay, we found 37.5% prevalence of anti-LCMV antibodies in human sera, suggesting possible horizontal spread of the virus in the human population
Cellular Proteins Bind to the Poly(U) Tract of the 3′ Untranslated Region of Hepatitis C Virus RNA Genome

AbstractUV cross-linking analyses were performed in an attempt to determine cellular protein–viral RNA interactions with the 3′ untranslated region (3′ UTR) of the hepatitis C virus RNA genome. Two cellular proteins, with estimated molecular masses of 58 kDa (p58) and 35 kDa (p35), respectively, were found to specifically bind to the 3′ UTR. The p58 protein was determined to be the polypyrimidine tract-binding protein. In addition to binding to the conserved 98 nucleotides (nt) of the 3′ UTR, p58 also binds to the poly(U) tract of the 3′ UTR. The p35 protein was found to interact only with the poly(U) tract of the 3′ UTR. These conclusions are supported by the following findings: (1) p58, and not p35, binds to the 3′ end conserved 98 nt, (2) both p58 and p35 bind to a 3′ UTR RNA with a deletion of the conserved 98 nt, (3) the 98-nt deletion mutant 3′ UTR competed out both p58 and p35 binding, (4) a poly(U) homopolymer competed out both p58 and p35 binding, (5) a 3′ UTR RNA with deletion of the poly(U) tract competed out only p58 binding but not p35 binding, and (6) an RNA containing the variable region of the 3′ UTR with a deletion of both poly(U) tract and 98 nt failed to compete for binding of either p58 or p35. Interaction of these cellular proteins with the HCV 3′ UTR is probably involved in regulation of translation and/or replication of the HCV RNA genome
The Major Product of Porcine Transmissible Gastroenteritis Coronavirus Gene 3b Is an Integral Membrane Glycoprotein of 31 kDa

AbstractThe open reading frame potentially encoding a polypeptide of 27.7 kDa and located as the second of three ORFs (gene 3b) between the S and M genes in the genome of the Purdue strain of porcine transmissible gastroenteritis coronavirus (TGEV) was cloned and expressedin vitroto examine properties of the protein. Gene 3b has a postulated role in pathogenesis, but its truncated form in some laboratory-passaged strains of TGEV has led to the suggestion that it is not essential for virus replication. During synthesisin vitroin the presence of microsomes, the 27.7-kDa polypeptide became an integral membrane protein, retained its postulated hydrophobic N-terminal signal sequence, and underwent glycosylation on apparently two asparagine linkage sites to attain a final molecular mass of 31 kDa. A 20-kDa N-terminally truncated, nonglycosylated, nonanchored form of the protein was also made via an unknown mechanism. The existence of both transmembrane and soluble forms of the gene 3 product in the cell is suggested by immunofluorescence patterns showing both a punctated perinuclear and diffuse intracytoplasmic distribution. No gene 3b product was found on gradient-purified Purdue TGEV by a Western blotting procedure that would have detected as few as 4 molecules/virion, indicating the protein probably is not a structural component of the virion
Protection of Chickens against Very Virulent Infectious Bursal Disease Virus (IBDV) and Marek's Disease Virus (MDV) with a Recombinant MDV Expressing IBDV VP2

AbstractTo develop a herpes virus vaccine that can induce immunity for an extended period, a recombinant Marek's disease (MD) virus (MDV) CVI-988 strain expressing infectious bursal disease virus (IBDV) host-protective antigen VP2 at theUS2site (rMDV) was developed under the control of an SV40 early promoter. Chickens vaccinated with the rMDV showed no clinical signs and no mortality and 55% of the chickens were considered protected histopathologically after challenge with very virulent IBDV (vvIBDV), whereas all of the chickens vaccinated with the conventional IBDV vaccine showed no clinical signs and were protected. Chickens vaccinated with the CVI-988 or chickens in the challenge control showed severe clinical signs and high mortality (70–75%) and none of them were protected. Also, the rMDV conferred full protection to chickens against vvMDV just as the CVI-988 strain did, whereas 90% of the challenge control chickens died of MD. Antibody levels against IBDV and MDV following the vaccination increased continuously for at least 10 weeks. No histopathological lesions in the rMDV-vaccinated chickens and no contact transmission of the rMDV to their penmates were confirmed. These results demonstrate that an effective and safe recombinant herpesvirus-based IBD vaccine could be constructed by expressing the VP2 antigen at theUS2site of the CVI-988 vaccine strain
HIV-1 Nef Plays an Essential Role in Two Independent Processes in CD4 Down-regulation: Dissociation of the CD4–p56lckComplex and Targeting of CD4 to Lysosomes

AbstractHuman immunodeficiency virus type 1 (HIV-1) Nef down-regulates CD4 by triggering rapid endocytosis of cell surface CD4. To better understand how Nef induces CD4 down-regulation, we generated a series of Nef mutants with small in-frame deletions in the coding region. Three classes of mutants were obtained. The first class produces neither CD4 down-regulation nor dissociation of the CD4–p56lckcomplex. The second class induces CD4 down-regulation in cells lacking p56lckexpression, but not in cells with p56lck; these mutants fail to dissociate CD4 from p56lck. These results show that Nef-mediated CD4 dissociation from p56lckis important for CD4 down-regulation. The third class of mutants is able to dissociate the CD4–p56lckcomplex but fails to down-regulate surface CD4; internalized CD4 molecules are recycled back to the cell surface. This result suggests that Nef diverts the CD4 recycling pathway to a degradative pathway. We also demonstrate that Nef associates with phosphatidylinositol-3-kinase (PI3K) activity, which is known to be involved in several aspects of membrane trafficking. However, Nef mutants that cause internalized CD4 to be recycled do not associate with PI3K activity; thus Nef-associated PI3K activity might be involved in the latter process of targeting CD4 to a degradative pathway. We conclude that HIV-1 Nef plays a critical role in multiple processes in CD4 down-regulation: (i) disrupting the CD4–p56lckcomplex on the cell surface to allow CD4 internalization and (ii) diverting the internalized CD4 to a lysosomal pathway for its degradation, likely through a PI3K activity
The Genome Nucleotide Sequence of a Contemporary Wild Strain of Measles Virus and Its Comparison with the Classical Edmonston Strain Genome

AbstractThe only complete genome nucleotide sequences of measles virus (MeV) reported to date have been for the Edmonston (Ed) strain and derivatives, which were isolated decades ago, passaged extensively under laboratory conditions, and appeared to be nonpathogenic. Partial sequencing of many other strains has identified ≥15 genotypes. Most recent isolates, including those typically pathogenic, belong to genotypes distinct from the Edmonston type. Therefore, the sequence of Ed and related strains may not be representative of those of pathological measles circulating at that or any time in human populations. Taking into account these issues as well as the fact that so many studies have been based upon Ed-related strains, we have sequenced the entire genome of a recently isolated pathogenic strain, 9301B. Between this recent isolate and the classical Ed strain, there were 465 nucleotide differences (2.93%) and 114 amino acid differences (2.19%). Computation of nonsynonymous and synonymous substitutions in open reading frames as well as direct comparisons of noncoding regions of each gene and extracistronic regulatory regions clearly revealed the regions where changes have been permissible and nonpermissible. Notably, considerable nonsynonymous substitutions appeared to be permissible for the P frame to maintain a high degree of sequence conservation for the overlapping C frame. However, the cause and the effect were largely unclear for any substitution, indicating that there is a considerable gap between the two strains that cannot be filled. The sequence reported here would be useful as a reference of contemporary wild-type MeV
The Acidic Region and Conserved Putative Protein Kinase C Phosphorylation Site in Nef Are Important for SIV Replication in Rhesus Macaques

AbstractVariants of the pathogenic SIVmac239 clone with changes in Nef were analyzed to assess the functional relevance of two highly conserved regions in Nefin vitroandin vivo.Changes in a region with an acidic charge (Aci-Nef), or a potential protein kinase C phosphorylation site (PKC-Nef), impaired the ability of Nef to down-regulate CD4 and MHC class I surface expression and to alter CD3-initiated signal transduction in Jurkat T cells. The Aci-Nef, but not the PKC-Nef, associated with the previously described p65 phosphoprotein. SIV containing Aci-Nef, but not SIV containing PKC-Nef, showed reduced infectivity and replication in cell culture systems. One of two rhesus macaques infected with the PKC-Nef mutant virus showed rapid reversion and progressed to disease. In the second animal no reversions and nonprogressive infection was observed. In one of two macaques infected with the Aci-Nef variant, the mutations were stable during the first 40 weeks after infection. Thereafter, variants evolved in which up to six of the eight mutated positions in Nef were reverted and functional activityin vitrowas partially restored. These changes occurred concomitantly with increasing viral load and disease progression. The second animal infected with the Aci-Nef variant showed no reversions and remained asymptomatic. Our study suggests that the acidic region and conserved PKC phosphorylation site in Nef are important for SIV replication in rhesus macaques and for severalin vitroNef functions. An almost wild-type activity inin vitroinfectivity and replication assays seems insufficient to confer a fullnef-positive phenotypein vivo
Rotavirus-Specific Cytotoxic T Lymphocytes Recognize Overlapping Epitopes in the Amino-Terminal Region of the VP7 Glycoprotein

AbstractRotavirus-specific cytotoxic T lymphocytes (CTL) play an important role in the resolution of rotavirus infection. The outer capsid glycoprotein, VP7, elicits a class I MHC-restricted CTL response. Vaccinia virus recombinants expressing the VP7 genes from simian rotavirus SA11 (serotype G3) and from the RF strain of bovine rotavirus (serotype G6) were used to analyze the CTL activity to this antigen in BALB/c (H-2d) and C57BL/6 (H-2b) mice neonatally infected with homologous and heterologous rotaviruses. A vaccinia virus recombinant expressing the first amino-terminal 88 amino acids of VP7 was constructed and used to search for cross-reactive CTL against this region of the protein. By using synthetic Kb, Db, and Kdmotif-fitting peptides two overlapping CTL epitopes have been identified located in the first hydrophobic domain (H1) of VP7. Splenocytes obtained from rotavirus SA11-infected C57BL/6 mice induced the strongest CTL response against target cells sensitized with a peptide containing a Kb-restricted CTL epitope (amino acids 8–16). A second Kd-restricted epitope (residues 5–13) was recognized by splenocytes derived from rotavirus-infected BALB/c mice. These findings reveal the existence of CTL epitopes in the H1 signal sequence of the VP7 glycoprotein that coexist with a CTL epitope (residues 31–40) previously described within the H2 region
Limitation of Tat-Associated Transcriptional Processivity in HIV-Infected PBMC

AbstractThe ability of HIV to match levels of viral mRNA to the activation state of the host cell may play a role in its ability to persist as well as to replicate. This linkage depends on the function of the viral transcriptional regulatory protein, Tat, which increases the efficiency of RNA elongation (transcriptional processivity) in response to cellular activation. To quantify levels of Tat functionin vivo,a quantitative competitive RT-PCR assay was developed that reflects levels of TAR leader fragments (nonprocessive transcripts) and viral mRNA (processive transcripts), indicating low or high levels of Tat function, respectively. The abundance of these RNA species was measured in peripheral blood mononuclear cells (PBMC) of 22 HIV-1-positive individuals (CD4+T cell counts 63–934/mm3) and in established cell line models of HIV constitutive replication (H9IIIB) and reversible latency (U1 and ACH-2). In PBMC, the level of total viral transcripts ranged over four orders of magnitude; however, nonprocessive transcription predominated: 70% of PBMC samples had a ratio of processive to total transcripts of <0.3 and none of the samples had 100% processivity. The cell line studies revealed that, even in activated H9IIIBcells, nonprocessive transcription dominates and that latently infected cells can have different transcriptional responses to activation. This is the first study that enumerates degrees of transcriptional processivity in the circulating mononuclear cell compartment and the results suggest that limitation of Tat function may be a common phenotype throughout the course of the disease
Identification of the Canarypox Virus Thymidine Kinase Gene and Insertion of Foreign Genes

AbstractWe mapped the canarypox virus (CaPV) thymidine kinase (TK) gene within a 5.8-kbp XbaI fragment of the genome by Southern blotting using the fowlpox virus (FPV) TK gene as a probe. Nucleotide sequence analysis of the fragment revealed seven open reading frames (ORFs) showing gene organization similar to that of FPV. The TK gene contained in this region had an ORF of 179 amino acids encoding a polypeptide with a putative molecular mass of 20.0 kDa. An A/T-rich region and a transcription termination signal, TTTTTAT, were found upstream and at the end of the ORF, which is consistent with poxvirus early gene regulation. The consensus sequence of the late promoter TAAAT also overlapped with the initiation codon of the ORF. The amino acid sequence similarity between the TK genes of CaPV and FPV, avipoxviruses, was 64.2%, which was lower than the similarities between vaccinia and variola orthopoxviruses (97.2%) and between Shope fibroma and myxoma leporipoxviruses (82.6%). However, the monophyly of avian clades of CaPV and FPV was supported by phylogenetic analysis. We then inserted the genes encoding lacZ, luciferase (luci), and envelope of human T-lymphotropic virus type 1 (HTLV-1 env) into the TK gene of CaPV to evaluate its suitability as an expression vector. The recombinant viruses obtained were unstable, although the foreign genes were expressed efficiently in the mammalian cells infected with the viruses
Characterization of Early Gene Transcripts of Molluscum Contagiosum Virus

AbstractMolluscum contagiosum virus (MCV), a member of the family Poxviridae, replicates wellin vivobut cannot be propagated in cell culture. The coding capacity of the MCV genome was previously determined by DNA nucleotide sequence analysis. The objective of the present study was to establish experimental systems for the identification and characterization of early MCV gene transcripts. MCV mRNA was obtained in three ways: (1) MCV early mRNA was synthesizedin vitrousing permeabilized virions, (2) MCV mRNA was extracted from MCV-infected skin tissue, and (3) MCV mRNA was extracted from MCV-infected human embryonic fibroblasts. RNA/DNA hybridization experiments showed significant early transcriptional activity in two parts of the MCV genome. Transcripts of 11 early MCV genes located in these parts of the genome, including two subunits of the MCV DNA-dependent RNA polymerase (mc077R and mc079R), the MCV poly(A)+polymerase gene (mc076R), and the MCV MHC class I homolog (mc080R), were detected in reverse transcription-polymerase chain reaction experiments. Total RNA obtained from MCV-infected skin tissue was used to confirm these results. Three MCV early transcripts, mc002L, mc004.1L, and mc005L, produced distinct bands on rapid amplification of their 3′ ends (3′ RACE). The 5′ mapping of transcription start sites of MCV open reading frames (ORFs) mc002L, mc004.1L, mc005L, and mc148R revealed that the MCV RNA polymerase transcription start sites are consistently located between 11 and 13 nucleotides downstream of the early MCV consensus promoter signal. When cDNA from both 5′ and 3′ mapping experiments was analyzed, MCV ORFs mc004.1L and mc005L were found to be transcribed as a single bicistronic mRNA. The transcript from MCV ORF mc066L, encoding a glutathione peroxidase, was detected inin vitrosynthesized MCV mRNA as well as in total RNA from MCV-infected human embryonic fibroblasts and MCV-infected skin. This indicates that despite the lack of an early MCV consensus promoter signal immediately proximal to the start codon, this particular gene is transcribed early during MCV infection
Induction of CD95 (Fas) and Apoptosis in Respiratory Epithelial Cell Cultures Following Respiratory Syncytial Virus Infection

AbstractRespiratory syncytial virus (RSV) infection is associated with epithelial cell death and vigorous inflammation. In mouse models, and in immunosuppressed patients, CD8+T cells are necessary for RSV clearance.In vitro,RSV has been shown to induce expression of several proteins on the respiratory epithelial cell, including RSV proteins, ICAM-1, and MHC class I, that can potentially interact with CD8+T cells in initiating apoptosis of the target cell. One mechanism of T-cell-directed cell death is the interaction of FasL on the CD8+T lymphocytes and Fas expressed on the target cell. In order to determine the ability of RSV to induce Fas on the respiratory epithelium, we studied the RSV infection of a human respiratory epithelial cell line (A549)in vitro.Fas mRNA and protein levels are increased two-to-fourfold following RSV infection, and transcriptional upregulation of Fas was demonstrated using promoter/reporter gene constructs. RSV infection directly resulted in cellular apoptosis, and the frequency of apoptotic cells was further increased by cross-linking with antibodies to Fas. These data demonstrate that RSV infection induces cellular apoptosis and suggest that interactions of surface Fas with T cells may further augment this processin vivo