pinecone/core-2020-05-10-deduplication huggingface dataset:
NF-κB Protects HIV-1-Infected Myeloid Cells from Apoptosis

AbstractHIV-1 infection of primary monocytic cells and myeloid cell lines results in sustained NF-κB activation. Recently, NF-κB induction has been shown to play a role in protecting cells from programmed cell death. In the present study, we sought to investigate whether constitutive NF-κB activity in chronically HIV-1-infected promonocytic U937 (U9-IIIB) and myeloblastic PLB-985 (PLB-IIIB) cells affects apoptotic signaling. TNFα and cycloheximide caused infected cells to undergo apoptosis more rapidly than parental U937 and PLB-985 cells. Inhibition of TNFα-induced NF-κB activation using the antioxidantN-acetylcysteine (NAC) resulted in increased apoptosis in both U937 and U9-IIIB cells, while preactivation of NF-κB with the non-apoptotic inducer IL-1β caused a relative decrease in apoptosis. Inhibition of constitutive NF-κB activity in U9-IIIB and PLB-IIIB cells also induced apoptosis, suggesting that NF-κB protects cells from a persistent apoptotic signal. TNFα plus NAC treatment resulted in a marked decrease in Bcl-2 protein levels in HIV-1-infected cells, coupled with an increase in Bax protein compared to uninfected cells, suggesting that the difference in susceptibility to TNFα-induced apoptosis may relate to the differences in relative levels of Bcl-2 and Bax. The protective role of NF-κB in blocking TNFα- and HIV-1-induced apoptosis was supported by studies in Jurkat T cells engineered to express IκBα repressor mutants (TD-IκB) under the control of a tetracycline-responsive promoter. Cells underwent apoptosis in response to TNFα only when NF-κB activation was inhibited by TD-IκB expression. As was observed for the U9-IIIB cells, TNFα treatment also induced a marked decrease in Bcl-2 protein levels in TD-IκB expressing cells. These experiments demonstrate that apoptotic signaling is perturbed in HIV-1-infected U9-IIIB cells and indicate that NF-κB activation may play an additional protective role against HIV-1-induced apoptosis in myeloid cells
The Early HPV16 Proteins Can Regulate mRNA Levels of Cell Cycle Genes in Human Cervical Carcinoma Cells by p53-Independent Mechanisms

AbstractCervical carcinoma-associated human papillomavirus type 16 (HPV16) encodes E6 and E7 oncoproteins which inactivate p53 and Rb, respectively, but these interactions are not sufficient to account for the oncogenic potential of the virus. Several viral promoters were shown to be regulated by E6 and E7. To identify genes as cellular targets of the HPV16 early proteins, we transfected a new HPV-negative and p53-mutated cervical carcinoma-derived cell line with either the HPV16 full-length genome or the HPV16 E6 gene. HPV16 clones but not 16E6 clones showed a decreased doubling time that was not related to the viral DNA and mRNA patterns. In exponentially growing cells as well as in cells synchronized by serum starvation, expression of the E6 gene was associated with upregulation of the c-fosand c-junproto-oncogenes and with downregulation of the c-Ha-rasgene. Furthermore, a viral gene other than E6 may be involved in downregulation of p53 because a reduced mRNA level at the G1/S transition was observed only in HPV16-cells. The present study on natural host cells indicates p53-independent transcriptional modulations of cell cycle regulatory genes related to HPV16 E6 and E7 expression
Effects of Vpu Expression onXenopusOocyte Membrane Conductance

AbstractThe HIV-1-specificvpugene encodes an integral membrane phosphoprotein which affects three aspects of the HIV-1 infectious cycle: it enhances virion release from infected cells; it causes degradation of the CD4 protein in the endoplasmic reticulum; and it delays syncytia formation in HIV-1-infected CD4+T-cells. Although little is known about how Vpu mediates these effects, it has been proposed to function as a nonspecific cation channel. In this report, voltage clamp measurements ofXenopusoocytes show that Vpu expression is not associated with increased transmembrane currents. Instead, Vpu expression diminishes membrane conductance. Injection of 4.6 ng of Vpu mRNA into these cells reduces endogenous potassium conductance by 50%. Only Vpu mutants which retain the ability to degrade CD4 can diminish K+conductance. Inhibition by Vpu is not unique to K+channels as it is also observed on several coexpressed membrane proteins but not on a coexpressed cytoplasmic protein. These results indicate that the CD4 degradative capability of Vpu and the Vpu-mediated modulation of membrane protein expression are mechanistically coupled and that Vpu may contribute to HIV pathogenesis by altering plasma membrane protein expression at the cell surface
Anti-HIV Effects of HIV Vectors

AbstractWe have recently developed an HIV-1 packaging cell line, Ψ422, as an improved tool for anti-HIV gene therapy. After stable transfection with an HIV-1 or HIV-2 vector, Ψ422 has been shown to synthesize virions able to transduce CD4+T cells and macrophages. We now report that HIV vectors per se, in the absence of antiviral genes, inhibit HIV infection of transduced cells. This antiviral effect was shown to be due, at least in part, to a TAR and RRE decoy effect. These data highlight further advantages of HIV-derived gene delivery systems for HIV therapy, in addition to CD4 cell targeting and the ability to transduce nondividing cells
Mutational Analysis of Stem-Loops in the RNA Packaging Signal of the Moloney Murine Leukemia Virus

AbstractThe retroviral RNA genome is targeted for incorporation into the nascent virion particle by the ψ region, a specific block of RNA sequences near the 5′ end. A number of deletions and linker insertion mutations were introduced into the ψ region of cloned DNA of the Moloney murine leukemia virus, and the mutants were introduced into cells in culture and tested for their ability to direct the assembly of virions and the packaging of viral RNA. Only a small portion of the ψ region was important for packaging, containing the so-called stem-loops C and D. Additional mutants were used to demonstrate that the base pairing of stem D, and the sequence of loop D, were essential for normal packaging of the RNA. Two mutants with alterations near the 5′ splice donor were also replication-defective, probably due to effects on gene expression. The results allow a high-resolution definition of the RNA structures required during virus replication in culture
Transcripts of a Chimeric cDNA Clone of Hepatitis C Virus Genotype 1b Are Infectiousin Vivo

AbstractWe constructed a chimeric cDNA clone of hepatitis C virus (HCV) that is infectious. The chimeric genome encodes the polyprotein of a genotype 1b strain (HC-J4) of HCV and replicates via 5′ and 3′ untranslated regions of a genotype 1a strain. The infectivity of three full-length cDNA clones was tested by direct injection of RNA transcripts into the liver of a chimpanzee. The chimpanzee became infected with HCV and the viral titer increased over time from 102genome equivalents (GE)/ml at week 1 postinoculation (p.i.) to 104–105GE/ml during weeks 3–11 p.i. Antibodies to HCV were detected from week 18 p.i. However, the chimpanzee did not develop hepatitis. Sequence analysis of PCR products amplified from the serum of the chimpanzee demonstrated that only one of the three clones was infectious. Sequence comparisons with the cloning source, an acute-phase infectious plasma pool derived from an experimentally infected chimpanzee, showed that this infectious clone had three amino acids that differed from the consensus sequence of HC-J4, whereas the two noninfectious clones had seven and nine amino acid differences, respectively. Together, genotype 1b, represented by the infectious molecular clone described herein, and genotype 1a, represented by the two cDNA clones previously shown to be infectious for chimpanzees, account for the majority of HCV infections in the United States, Europe, and Japan
Molecular andin VitroAnalysis of Eight Dengue Type 2 Viruses Isolated from Patients Exhibiting Different Disease Severities

AbstractPotential genetic determinants of dengue virulence were studied by sequencing the entire genomes of eight dengue 2 virus strains isolated from patients exhibiting different disease severities during an epidemic season in northeastern Thailand in 1993. The isolates came from one dengue shock syndrome (ThNH-7/93), three dengue hemorrhagic fever, and four dengue fever patients. Phylogenetic analysis showed that the isolates belonged to the Southeast Asian genotype. The 3′ noncoding regions showed distinctive secondary structures, with one specific structure for the isolate ThNH-7/93. Analysis of the predicted polyprotein showed several amino acid (aa) changes scattered mostly in the nonstructural region. Of 30 positions with aa changes, 7 were unique to the isolate ThNH-7/93 and 3 of those led to radical alterations in aa character. Several aa changes coincided with previous studies relating genome sequence and virulence. Minimal changes in computer-predicted protein secondary structures were observed. Infective particles in the inoculum for all isolates were approximately equal as measured by focus formation on BHK-21 cells, but this did not correlate with the number of plaques formed on LLC-MK2 cells. Isolates from patients that experienced secondary infections were shown to have significantly larger plaques than the isolates from primary infection patients
An Insect Picorna-like Virus, Plautia stali Intestine Virus, Has Genes of Capsid Proteins in the 3′ Part of the Genome

AbstractThe complete genome of an insect picorna-like virus, Plautia stali intestine virus (PSIV), was cloned and sequenced. The genome had 8797 nucleotides including two consecutive long open reading frames. The deduced amino acid sequence of the first open reading frame (nucleotides 571 to 6003) contained conserved sequence motifs for picornavirus RNA helicase, cysteine protease, and RNA-dependent RNA polymerase. The order of the three motifs in the genome was the same as those of mammalian picornaviruses. The coding regions of four capsid proteins (33, 30, 26, and 4.5 kDa) were mapped by determining their N-terminal sequences. Unlike mammalian picornaviruses, the genes for these proteins were in the 3′ region of the PSIV genome.In vitrotranslation assay suggested that the capsid protein precursor of PSIV would be translated by internal initiation. The deduced amino acid sequence of the capsid proteins showed homology to those of the proteins encoded in the 3′ part of the genomes of widely distributed insect picorna-like viruses, cricket paralysis virus, and Drosophila C virus. Some insect picorna-like viruses would have the same unique coding strategy as PSIV
Characterization of Age- and Dose-Related Outcomes of Duck Hepatitis B Virus Infection

AbstractExperimental inoculation of naive ducks with duck hepatitis B virus (DHBV) can lead to one of three outcomes, namely, persistent viremia, transient infection with or without viremia, or no evidence of infection. The ability of individual ducks to resolve DHBV infection was found to be linked to the age of the duck at the time of inoculation and the dose of inoculated virus. (1) In recently hatched ducks inoculated intravenously (i.v.) with 4 × 104DHBV DNA genomes, a switch from persistent viremia to transient antibody appearance was seen at an age of inoculation between 7 and 14 days. A 25-fold increase in the dose of virus (1 × 106DHBV genomes) delayed this switch by 7 days. (2) When 4-month-old ducks were inoculated i.v. with different doses of virus, only those receiving the highest dose (2 × 1011DHBV genomes) showed viremia and extensive viral replication and histological changes in the liver; 2/3 ducks in this group had a transient infection, while the third duck had viral replication and histological changes in the liver that were still present at day 120 postinoculation (p.i.). In all ducks receiving lower doses (1 × 103, 1 × 106, 1 × 109DHBV genomes) antibodies to viral surface and core antigens developed without detectable viral replication in the liver on days 6, 9, or 12 p.i. (3) When 10- to 16-month-old ducks were inoculated i.v. with 2 × 1011DHBV genomes, all showed extensive viral replication in hepatocytes and mild to moderate histological changes in the liver on days 4 or 6 p.i. In 4/5 ducks viremia was not detected, anti-surface antibodies were first detected on day 8 p.i., and viral DNA and antigen were cleared from the liver by days 35–47 p.i. The remaining duck became viremic with persistence of virus in the liver until at least day 46 p.i. The findings of the study are consistent with a model for noncytopathic viruses (R. M. Zinkernagel (1996)Science271, 173–178)
The First Strand Transfer during HIV-1 Reverse Transcription Can Occur either Intramolecularly or Intermolecularly

AbstractReverse transcription is a complicated process that involves at least two cDNA transfer reactions to produce a full-length copy DNA of the retroviral RNA genome. Because one retrovirus particle contains two identical genomic RNA molecules, the transfers can occur in an intramolecular or intermolecular manner. The mechanism of the first transfer step (minus-strand strong-stop cDNA transfer) has been studied previously in detail in transduction experiments with spleen necrosis virus vectors containing genetic markers. Different results have been reported with respect to the type of strand transfer mechanism. In this study, we analyzed the first strand transfer for human immunodeficiency virus type 1 (HIV-1). Two genetically marked genomes were copackaged into virions and reverse transcription was initiated within these particles upon permeabilization by NP-40 and addition of dNTPs. To test whether intrastrand or interstrand transfer had occurred, the cDNA products of this endogenous reverse transcription reaction were extracted from the virions and analyzed for the presence of restriction enzyme recognition sites provided by the genetic markers. The results of this analysis demonstrated that the first DNA transfer reaction occurs in a random manner, with approximately the same contribution of intrastrand and interstrand transfers. The ability to perform intermolecular strand transfer was lost upon extraction of the dimeric RNA template from the virion particle
Cellular Factors in the Transcription and Replication of Viral RNA Genomes: A Parallel to DNA-Dependent RNA Transcription

AbstractViral RNA replication and transcription involves not only viral RNA-dependent RNA polymerases, but also cellular proteins, the majority of which are subverted from the RNA-processing or translation machineries of host cells. These factors interact with viral RNA or polymerases to form transcription or replication ribonucleoprotein complexes and may provide template specificity for RNA-dependent RNA synthesis, suggesting a close parallel to the mechanism of DNA-dependent RNA synthesis. The types of cellular proteins involved and their modes of action are reviewed
Intersubunit Interactions Allowing a Carboxylate Mutant Coat Protein to Inhibit Tobamovirus Disassembly

AbstractTobacco mosaic tobamovirus (TMV) coat protein (CP) mutant E50Q lacks a repulsive intersubunit carboxylate group and can effectively inhibit the disassembly of wild-type TMV (Culveret al.,1995,Virology206,724). To investigate the ability of this mutant CP to block disassembly, a series of second-site amino acid substitutions were added to the E50Q CP. These second-site mutations were designed to disrupt specific intersubunit stabilizing interactions involving hydrophobic or polar residues, salt bridges, and CP–RNA contacts. Results showed substitutions disrupting intersubunit interactions that face the disassembling surface of the virion dramatically reduced the ability of CP E50Q to inhibit TMV disassembly. Substitutions that disrupted the CP inner loop, RNA binding capabilities, or intersubunit interactions that faced away from the disassembling surface did not dramatically interfere with CP E50Q's ability to inhibit disassembly. Taken together, these findings suggest that intersubunit interactions made by 5′ terminal E50Q subunits, not associated with RNA, provide the stabilizing forces that prevent virion disassembly. The role of these stabilizing interactions in TMV disassembly and their potential use for creating disassembly inhibiting CPs are discussed
Expression of the Rice Yellow Mottle Virus P1 Proteinin Vitroandin Vivoand Its Involvement in Virus Spread

AbstractRice yellow mottle sobemovirus (RYMV) is responsible for the yellow mottle disease on rice in Africa. The expression and function of the protein P1 (17.8 kDa) encoded by the first open reading frame (ORF) of RYMV was investigated. Using an antibody raised against purified P1, two proteins with apparent molecular masses of 18 and 19 kDa were identified inin vitrotranslation reactions of transcripts of the full-length cDNA of RYMV. Likewise, gene products with similar molecular mass were detected in inoculated and systemically infected rice leaves and in infected rice protoplasts. A mutant from which ORF1 nucleotides 88 to 547 were deleted and a frameshift mutant that resulted in truncation of 83 amino acids from the C terminus of P1 were incapable of replicating in protoplasts. In contrast, a mutant that does not express P1 due to a mutation at the initiation codon replicated efficiently in protoplasts but at a reduced level (about 0.5- to 2-fold less) compared to replication of wild-type RNA. None of these mutants caused systemic infection in rice plants. Transgenic rice plants that express P1 complemented the initiation codon mutant, but not the deletion mutants, and produced systemic infection. These experiments demonstrate that P1 of RYMV is dispensible for virus replication, although nucleotide deletions or additions in ORF1 are apparently lethal for virus replication. Furthermore, P1 of RYMV is required for the infection of plants and is important for virus spread
Human Cells Arrest in S Phase in Response to Adenovirus 12 E1A

AbstractIt has previously been shown that following viral infection, Ad5 E1A induces cell cycle progression of quiescent rodent cells, leading to DNA synthesis and mitosis. Here we have examined the effect of Ad12 E1A on the cell cycle characteristics of human cells. Human tumor (A549, KB, and HeLa) cells were infected with Ad12dl620, a mutant virus which has a lesion in the E1B gene and essentially expresses only E1A. These infected cells progressed from being largely in G1into S phase, where they arrested. Even up to 96 h postinfection (p.i.) the cells remained blocked in S phase. DNA synthesis did, however, proceed in Ad12dl620-infected cells, giving rise to multiple copies of cellular DNA. Similar results were obtained when primary human skin fibroblasts were infected, although the polyploidy was less marked. The expression of cyclins A, B1, and E in the tumor cells increased appreciably in response to E1A. In contrast, there was a dramatic reduction in the levels of cyclin D1 and D3. Increases in cyclin D1 expression could be detected at very late times p.i. In those cell lines expressing low levels of cdc2 and cdk2 an appreciable increase in expression was seen soon after Ad12 E1A could be detected. The elevated levels of cyclins A, B1, and E were associated with increased protein kinase activity directed against histone H1. An increase in cyclin D1-associated kinase activity against Rb1 was also observed at late times. This deregulation of the cell cycle was not solely dependent on E1A inactivation of Rb, since similar effects were seen in Ad12dl620-infected retinoblastoma (Y-79) cells, implicating p107 and p130 in E1A-mediated changes in cell cycle progression. We propose that the E1A-induced levels of cyclins A, B1, and E by Ad12 E1A in human cells may lead to an uncoupling of S phase from cell cycle progression
Role for the Vaccinia Virus A36R Outer Envelope Protein in the Formation of Virus-Tipped Actin-Containing Microvilli and Cell-to-Cell Virus Spread

AbstractA small-plaque-forming vaccinia virus mutant with a deletion in the A36R gene encoding an outer envelope protein (Parkinson and Smith,Virology,204, 376–390, 1994) was shown to assemble wrapped forms of intra- and extracellular virus particles and to mediate acid-induced polykaryon formation. The intracellular virions, however, did not acquire actin tails and those on the cell surface were not associated with specialized microvilli. This phenotype is similar to that of the A34R (E. J. Wolffe, E. Katz, A. Weisberg, and B. Moss,J. Virol.71, 3904–3915, 1997) and A33R (R. Roper, E. J. Wolffe, A. Weisberg, and B. Moss,J. Virol.,in press) deletion mutants. Taken together, these data support a model in which the envelope proteins encoded by the A33R, A34R, and A36R genes are all required for nucleation of actin tails, which facilitate dissemination rather than egress of virus particles
Cytotoxic T Cells and Neutralizing Antibodies Induced in Rhesus Monkeys by Virus-like Particle HIV Vaccines in the Absence of Protection from SHIV Infection

AbstractHIV Pr55gaghas in the absence of other viral components the capacity to self assemble in budding noninfectious virus-like particles (VLP). The immunological spectrum of the HIV-1IIIBgag-derived VLP was expanded either by stable anchoring of chimeric modified gp120 on the surface of the VLP (type 1) or by replacing sequences of the Pr55gagprecursor by the V3 loop and a linear portion of the CD4 binding domain (type 2). This noninfectious antigen delivery system was evaluated for immunogenicity and efficacy in rhesus macaques without adjuvants. Intramuscular immunization with both types of VLP induced high titers ofgag-specific antibodies ranging from 1/8000 to 1/510,000 for type 1 VLP and from 1/4000 to 1/16,000 for type 2 VLP. Only animals immunized with type 1 VLP developed substantial endpoint titers ofenv-specific antibodies (1/2000–1/32,000) with a neutralizing capacity at serum dilutions of 1/32–1/128.Gag- andenv-specific cytotoxic T lymphocyte (CTL) activity was induced by both types of VLP at similar levels. Four weeks after the last immunization animals were challenged intravenously with 20 MID50of the cell free homologous envelope simian/HIV-1IIIBchimeric challenge stock. Despite HIV-1-specific neutralizing and CTL responses, all vaccinated animals became infected
The DNA Sequence of the RK Strain of Human Herpesvirus 7

AbstractThe complete DNA sequence of human herpesvirus-7 (HHV-7) strain RK was determined following direct cloning of virion DNA fragments into a sequencing vector. The sequence was compared with the previously published complete sequences of HHV-7 strain JI and human herpesvirus-6 (HHV-6) strain U1102. Despite a very close relationship between the two HHV-7 strains, differences are apparent in regions containing tandem reiterations, particularly in the “telomeric” reiterations located near the termini of the large direct repeat at the genome ends, and in a total of 179 additional positions distributed throughout the genome (i.e., about one nucleotide difference per kbp). This extent of divergence implies that the two strains arose from an ancestral virus several thousands of years ago. Differences that affect coding potential do not cluster in particular protein-coding regions, indicating that specific HHV-7 genes have not been measurably subject to unusual evolutionary pressures since divergence. Reassessments of genetic content indicated that the HHV-7 genome contains 84 different genes, whereas the HHV-6 genome contains 85. All HHV-7 genes but 1 have direct HHV-6 counterparts, and all but 2 HHV-6 genes have HHV-7 homologues. Sequence comparisons between HHV-7 and HHV-6 provided evidence that the protein-coding regions of 11 genes are expressed by splicing