pinecone/core-2020-05-10-deduplication huggingface dataset:
Gene Regulation Mediated by Interaction between HTLV-1 Promoter Elements and Transcription Factors Tax and CREB

AbstractIn this work we examine the role of three genetic control components in the regulation of HTLV-1 transcription: cyclic AMP-responsive element (CRE)-binding protein (CREB), the HTLV-1 trans-activator Tax, and the three Tax-responsive elements (TREs). We demonstrate that the in vivo efficiency of the HTLV-1 promoter basal expression in cell culture depends on the spacing between the three TRE elements, located at the HTLV-1 LTR (long terminal repeat), whereas the level of transcription activation mediated by Tax is affected by the number of TREs. In the presence of only one TRE, the enhancement of expression by Tax is affected by the distance between the single TRE and the transcription start site. Following CREB binding to the LTR, additional DNase I hypersensitive sites are generated in the region between the two distal TREs (I and II), while in the presence of Tax, such sites are generated also in the region between TREs II and III. Neither cooperative binding of CREB to the TREs nor preferential binding of CREB to a particular TRE was observed. Tax binding to the CREB/TRE complex does not change the DNase I protection pattern. Taken together, these results suggest that the basal CREB-mediated transcription is determined by the number and the position of the viral TREs relative to each other. Tax protein stabilizes the protein/DNA complex and suppresses the spacing limitations, probably by bridging between the CREB/TRE complexes and the basal initiation transcription complex
Human Immunodeficiency Virus Type 1 Genetic Evolution in Patients with Prolonged Suppression of Plasma Viremia

AbstractTreatment of human immunodeficiency virus type 1 (HIV-1)-infected patients with combination drug regimens results in a reduction of plasma viral load to levels below the limit of detection. To investigate the genomic fluctuations in HIV-1 populations from long-term responders to antiviral therapies we analyzed the viral sequence evolution of env and pol genes from sequential peripheral blood mononuclear cell (PBMC) DNA samples of three infected patients. Analyses of sequences covering the V3 and flanking env regions obtained from blood samples at the beginning of the therapy and at 14 or 24 months from baseline revealed that HIV-1 quasispecies continue to evolve in the three patients following combination antiretroviral therapy. Minor drug-resistant mutant subpopulations were also searched for and found in one patient. Interestingly, no minor resistant subpopulations were found in the other two patients despite the fact that they showed evidence of ongoing viral replication. Finally, the genetic analysis of the env gene shows a reduction in PBMC env viral population diversity after long-term response to the therapy in all the patients analyzed
Protective Effects of Type I and Type II Interferons toward Rous Sarcoma Virus-Induced Tumors in Chickens

AbstractGrowth of tumors induced by Rous sarcoma virus (RSV) is controlled by alleles at the major histocompatibility complex locus in chickens, indicating that immunological host defense mechanisms play a major role. We show here that the resistance phenotype of CB regressor chickens can be partially reverted by treating the animals with a monoclonal antibody that neutralizes the major serotype of chicken type I interferon, ChIFN-α. Injection of recombinant ChIFN-α into susceptible CC progressor chickens resulted in a dose-dependent inhibition of RSV-induced tumor development. This treatment was not effective, however, in CC chickens challenged with a DNA construct expressing the v-src oncogene, suggesting that the beneficial effect of type I interferon in this system resulted from its intrinsic antiviral activity and probably not from indirect immunmodulatory effects. By contrast, recombinant chicken interferon-γ strongly inhibited tumor growth when given to CC chickens that were challenged with the v-src oncogene, indicating that the two cytokines target different steps of tumor development
Generation of Transmissible Hepatitis C Virions from a Molecular Clone in Chimpanzees

AbstractMultiple alignments of hepatitis C virus (HCV) polyproteins from six different genotypes identified a total of 22 nonconsensus mutations in a clone derived from the Hutchinson (H77) isolate. These mutations, collectively, may have contributed to the failure in generating a “functionally correct” or “infectious” clone in earlier attempts. A consensus clone was constructed after systematic repair of these mutations, which yielded infectious virions in a chimpanzee after direct intrahepatic inoculation ofin vitrotranscribed RNAs. This RNA-infected chimpanzee has developed hepatitis and remained HCV positive for more than 11 months. To further verify this RNA-derived infectivity, a second naive chimpanzee was injected intravenously with serum collected from the first chimpanzee. Infectivity analysis of the second chimpanzee demonstrated that the HCV infection was successfully transmitted, which validated unequivocally the infectivity of our repaired molecular clone. Amino acid sequence comparisons revealed that our repaired infectious clone had 4 mismatches with the isogenic clone reported by Kolykhalovet al.(1997,Science277, 570–574) and 8 mismatches with that reported by Yanagiet al.(1997,Proc. Natl. Acad. Sci. USA94, 8738–8743). At the RNA level, more mismatches (43 and 67, respectively) were identified; most of them were synonymous substitutions. Further comparisons with 16 isolates from different genotypes demonstrated that our repaired clone shares greater consensus than the reported isogenic clones. This approach of generating infectious HCV RNA validates the importance of amino acid sequence consensus in relation to the biology of HCV
Characterization of a Neutralization-Escape Variant of SHIVKU-1, a Virus That Causes Acquired Immune Deficiency Syndrome in Pig-Tailed Macaques

AbstractA chimeric simian-human immunodeficiency virus (SHIV-4) containing thetat, rev, vpu,andenvgenes of HIV type 1 (HIV-1) in a genetic background of SIVmac239 was used to develop an animal model in which a primate lentivirus expressing the HIV-1 envelope glycoprotein caused acquired immune deficiency syndrome (AIDS) in macaques. An SHIV-infected pig-tailed macaque that died from AIDS at 24 weeks postinoculation experienced two waves of viremia: one extending from weeks 2–8 and the second extending from week 18 until death. Virus (SHIVKU-1) isolated during the first wave was neutralized by antibodies appearing at the end of the first viremic phase, but the virus (SHIVKU-1b) isolated during the second viremic phase was not neutralized by these antibodies. Inoculation of SHIVKU-1binto 4 pig-tailed macaques resulted in severe CD4+T cell loss by 2 weeks postinoculation, and all 4 macaques died from AIDS at 23–34 weeks postinoculation. Because this virus had a neutralization-resistant phenotype, we sequenced theenvgene and compared these sequences with those of theenvgene of SHIVKU-1and parental SHIV-4. With reference to SHIV-4, SHIVKU-1bhad 18 and 6 consensus amino acid substitutions in the gp120 and gp41 regions of Env, respectively. These compared with 10 and 3 amino acid substitutions in the gp120 and gp41 regions of SHIVKU-1. Our data suggested that SHIVKU-1and SHIVKU-1bprobably evolved from a common ancestor but that SHIVKU-1bdid not evolve from SHIVKU-1. A chimeric virus, SHIVKU-1bMC17, constructed with the consensusenvfrom the SHIVKU-1bon a background of SHIV-4, confirmed that amino acid substitutions in Env were responsible for the neutralization-resistant phenotype. These results are consistent with the hypothesis that neutralizing antibodies induced by SHIVKU-1in pig-tailed macaque resulted in the selection of a neutralization-resistant virus that was responsible for the second wave of viremia
Effects of Double-Site Mutations of Vesicular Stomatitis Virus Glycoprotein G on Membrane Fusion Activity

AbstractSite-directed mutagenesis of specific amino acids within a conserved amino-terminal region (H2) and a conserved carboxyl-terminal region (H10/A4) of the fusion protein G of vesicular stomatitis virus have previously identified these two segments as an internal fusion peptide and a region influencing low-pH induced conformational change, respectively. Here, we combined a number of the substitution mutants in the H2 and H10/A4 regions to produce a series of double-site mutants and determined the effect of these mutations on membrane fusion activity at acid pH and on pH-dependent conformational change. The results show that most of the double-site mutants have decreased cell–cell fusion activity and that the effects appeared to be additive in terms of inhibition of fusion, except for one mutant, which appeared to be a revertant. The double-site mutants also had pH optima for fusion that were lower than those observed with wild-type G but same as the pH optima for the parent fusion peptide (H2) mutants. The results suggest that although the H2 and H10/A4 sites may affect membrane fusion independently, a possible interaction between these two sites cannot be ruled out
The Host-Cell Architectural Protein HMG I(Y) Modulates Binding of Herpes Simplex Virus Type 1 ICP4 to Its Cognate Promoter

AbstractThe productive infection cycle of herpes simplex virus is controlled in part by the action of ICP4, an immediate-early gene product that acts as both an activator and repressor of transcription. ICP4 is autoregulatory, and IE-3, the gene that encodes it, contains a high-affinity binding site for the protein at its cap site. Previously, we had demonstrated that this site could be occupied by proteins found in nuclear extracts from uninfected cells. A HeLa cell cDNA expression library was screened with a DNA probe containing the IE-3 gene cap site, and clones expressing the architectural chromatin proteins HMG I and HMG Y were identified by this technique. HMG I is shown to augment binding of ICP4 to its cognate site inin vitroassays and to enhance the activity of this protein in short-term transient expression assays
The γ2 Late Glycoprotein K Promoter of Equine Herpesvirus 1 Is Differentially Regulated by the IE and EICP0 Proteins

AbstractThe equine herpesvirus 1 immediate-early (IE) phosphoprotein is essential for the activation of transcription from viral early and late promoters and trans-represses its own promoter. Transient-transfection assays showed that the IE protein trans-represses the γ2 late gK promoter. Gel shift and DNase I footprinting assays demonstrated that the IE protein binds to the gK promoter sequences from −42 to −26 and from −13 to +12 that overlap the transcription initiation site (+1). These results indicated that the IE protein binds to the transcription initiation site of the gK promoter sequences, thereby repressing transcription. On the other hand, the EICP0 protein trans-activates the γ2 late gK promoter [Bowles, D. E., Holden, V. R., Zhao, Y., and O'Callaghan, D. J. (1997). The ICP0 protein of equine herpesvirus 1 is an early protein that independently transactivates expression of all classes of viral promoters. J. Virol. 71, 4904–4914]. Overall, the EICP0 protein is able to release the gK promoter from the repressive effects of the IE protein. It has not been previously demonstrated that the major immediate-early transcriptional regulator of a herpesvirus represses expression of a late gene during infection
Infectious Laryngotracheitis Virus, an Alpha Herpesvirus That Does Not Interact with Cell Surface Heparan Sulfate

AbstractAmong the alpha herpesviruses studied to date, the initial stage of wild-type virus attachment involves an interaction between virally encoded structural envelope glycoproteins (predominantly glycoprotein C) and cell surface heparan sulfate proteoglycans. An analysis of the infectious laryngotracheitis virus (ILTV) glycoprotein C and glycoprotein B sequences suggested that these proteins lacked consensus heparin-binding domains. This indicated that ILTV might attach to its host cell in a heparan-independent manner, distinct from other alpha herpesviruses. The infectivity of two ILTV strains, a tissue-culture-adapted vaccine strain and a virulent field challenge strain, were found to be insensitive to the presence of exogenous heparin or chondroitin. Furthermore, infectivity was retained in chicken embryonic liver cells treated with heparinase. However, 4°C attachment studies and penetration studies in the presence of citrate buffer clearly demonstrated that ILTV attaches stably to and effectively penetrates chicken embryonic liver cells. Consequently, ILTV represents an alpha herpesvirus whose initial attachment step does not involve interactions with heparan or chondroitin sulfate containing proteoglycans
Role of Nitric Oxide in Pathogenesis of Herpes Simplex Virus Encephalitis in Rats

AbstractThe role of nitric oxide (NO) in the pathogenesis of viral encephalitis was investigated by using an experimental model of herpes simplex virus type 1 (HSV-1) encephalitis in Lewis rats. The expression of inducible NO synthase (iNOS) mRNA determined by Northern blotting was observed first in the olfactory bulb and the brain stem on day 5 after intranasal inoculation of HSV-1, and thereafter iNOS mRNA was detected in other brain regions, i.e., cerebrum and cerebellum. In various parts of the brain, excessive NO production was identified by electron spin resonance spectroscopy. The temporal and spatial patterns of iNOS expression coincided with those of viral propagation, as demonstrated by polymerase chain reaction for HSV-1 gene expression as well as by the plaque-forming assay. Immunohistochemical study determined that iNOS was localized mainly in monocyte-derived macrophages. Treatment of virus-infected animals with the NOS inhibitor Nω-monomethyl-l-arginine (l-NMMA), but not Nω-monomethyl-d-arginine, significantly ameliorated not only clinical symptoms such as paralysis and seizures but also mortality. Virus yield from brain tissue was not affected by l-NMMA treatment. It is of interest that increased expression of the antioxidant enzyme heme oxygenase-1 was observed in the HSV-1-infected brain; this increased expression was strongly inhibited by l-NMMA treatment. These data suggest that the high level of NO produced by iNOS is a pathogenic factor in HSV-1-induced encephalitis in rats
Reovirus Type 3 Clone 9 Increases Interleukin-1α Level in the Brain of Neonatal, but Not Adult, Mice

AbstractReovirus Type 3 clone 9 (T3C9)-induced lethal encephalitis is age dependent. We examined the effects of T3C9 inoculated into neonatal and adult mice by intracerebral, intramuscular, or peroral routes and the effect of lipopolysaccharide (LPS) on IL-1α levels in the blood and the brain. In parallel, we measured mice survival to T3C9 challenge, primary replication, and growth in and spread to the brain. The results show that T3C9 infection increased IL-1α only in the brain of neonatal mice, whereas LPS enhanced IL-1α in the brain and in the blood in both neonatal and adult mice. In neonatal mice, a T3C9-induced IL-1α increase coincided with viral replication-induced nervous tissue injury and preceded death. Anti-IL-1α antibody partially protected neonatal mice against T3C9 peroral challenge, further suggesting that this cytokine is involved in the mechanisms leading to lethal encephalitis. In adult mice, T3C9 was not lethal and did not modify IL-1α levels although it slowly replicated in nervous tissues when inoculated directly into the brain. Together, these results suggest that differences in nervous tissue response to T3C9 replication between newborn and adult mice could account in part for the age-dependent susceptibility to T3C9-induced lethal encephalitis
Antigenic Heterogeneity of the Hepatitis C Virus NS4 Protein as Modeled with Synthetic Peptides

AbstractThe effect of sequence heterogeneity on the immunologic properties of two strong antigenic regions of the hepatitis C virus (HCV) NS4 protein was studied by using a set of 443 overlapping 20-mer synthetic peptides. One antigenic region comprising the cleavage site between NS4a and NS4b (region 5-1-1) was modeled with peptides derived from 73 different known sequences, representing HCV genotypes 1–6. The other antigenic region, designated region 59 and located at the C-terminus of the NS4b protein, was modeled with peptides from 7 known sequences representing genotypes 1–3. All peptides were tested for antigenic reactivity by enzyme immunoassay with a panel of anti-HCV-positive serum specimens representing genotypes 1–5. The data demonstrated that immunoreactive peptides fell into two groups. One group, represented by N-terminal peptides, demonstrated genotype-independent immunoreactivity; the other group, from the central part of region 5-1-1, showed strict genotype specificity. Nineteen peptides from the genotype-independent group strongly immunoreacted with a wide range of serum samples containing antibodies to all 5 HCV genotypes. Twenty-five peptides from the genotype-specific group were found to strongly react with serum containing antibodies only to the genotype from which the peptides were derived. Similar to the N-terminal part of region 5-1-1, peptides derived from region 59 did not show genotype-specific immunoreactivity. Some peptides derived from the central part of region 59 showed very strong and broad antigenic reactivity. Thus, after examining two antigenic regions of the NS4 protein, we identified short sequences that can be used for the efficient detection of either genotype-independent or genotype-specific HCV antibodies
Resistance to Herpetic Stromal Keratitis in Immunized B-Cell-Deficient Mice

AbstractThis study evaluates the role of antibody as an indicator of immunity to ocular challenge with herpes simplex virus (HSV). Two genotypes of mice, BALB/c or BALB/c with μ-chain knockout (μK/O; which lack functional B cells), were immunized systemically either with nonvirulent infectious virus or with a eukaryotic expression plasmid encoding glycoprotein B (gB). Whereas naive μK/O mice were 10- to 100-fold more susceptible to HSV infection than BALB/c mice, following immunization both groups showed similar levels of resistance to ocular challenge. Thus both HSV-immunized groups cleared virus within 3 days and showed no signs of ocular lesions. gB DNA-immunized mice cleared virus less rapidly (5 days), and the incidence of lesions was 10 and 25% in BALB/c and μK/O mice, respectively. Since μK/O mice failed to produce detectable anti-HSV antibody, the mechanism of rapid viral removal was assumed to have a T cell basis. However, T cells would likely not mediate any protection directly since such cells were absent in infected corneas during clearance. A likely mechanism of immunity could involve innate defenses, perhaps enhanced by the action of cytokines released from antigen-reactive CD4+ cells in vascularized tissue adjacent to the cornea. Thus an abrupt inflammatory response consisting principally of neutrophils occurred in the corneal stroma in immune mice, and this subsided when virus disappeared. These data reveal that even though the deficiency in generating antibody renders mice more susceptible to HSV infection, once primed, resistance to disease expression is mediated solely by the cellular components and their products
Interferon-Induced Guanylate Binding Protein-1 (GBP-1) Mediates an Antiviral Effect against Vesicular Stomatitis Virus and Encephalomyocarditis Virus

AbstractA cDNA encoding the human guanylate binding protein-1 (hGBP-1) was expressed in HeLa cells using a constitutive expression vector. Stably transfected clones expressing hGBP-1 exhibited resistance to the cytopathic effect mediated by both vesicular stomatitis virus (VSV) and encephalomyocarditis virus (EMCV) and produced less viral progeny than control cells following infection with these viruses. To study the role hGBP-1 plays in the IFN-mediated antiviral effect, cells were stably transfected with a construct expressing antisense RNA for hGBP-1. VSV infection of IFN-α-treated antisense RNA-expressing cells produced an amount of virus comparable to that produced in the parental cell line, while EMCV infection of the IFN-α-treated transfected cells and VSV and EMCV infection of the IFN-γ-treated transfected cells produced far more virus than was produced in the parental cell line. These results demonstrate that GBP-1 mediates an antiviral effect against VSV and EMCV and plays a role in the IFN-mediated antiviral response against these viruses
Identification of a Human Immunodeficiency Virus Type 1 That Stably Uses tRNALys1,2Rather Than tRNALys,3for Initiation of Reverse Transcription

AbstractHIV-1 virions contain approximately equal amounts of tRNALys,3and tRNALys1,2, yet tRNALys,3has been found to be exclusively used for initiation of reverse transcription. Since previous studies have shown that even if the primer binding site (PBS) was mutated to be complementary to tRNALys1,2, the virus did not stably use tRNALys1,2to initiate reverse transcription, the virus must have evolved a mechanism for the exclusive use of tRNALys,3to initiate reverse transcription. To investigate how HIV-1 discriminates tRNALys1,2from tRNALys,3for initiation of reverse transcription, two proviral genomes that contain nucleotide changes in U5 and a PBS to be complementary to regions of tRNALys1,2were constructed. One genome contains 5 [HXB2(L12-AC)] nucleotides while another contains 15 [HXB2(L12-ACgg)] nucleotides in U5 complementary to the anticodon region of tRNALys1,2. Viruses derived from the transfection of the proviral genomes were infectious in SupT1 cells. Analysis of the endogenous reverse transcription reactions from viruses derived from HXB2 (L12-AC) and HXB2 (L12-ACgg) obtained from transfection revealed that both exclusively used tRNALys1,2to initiate reverse transcription. Following extensivein vitroculture, though, sequence analysis of proviral genomes revealed that while the virus derived from HXB2(L12-AC) stably maintained a PBS complementary to tRNALys1,2, the virus derived from HXB2 (L12-ACgg) had reverted back to contain a PBS complementary to tRNALys,3. RNA modeling of the U5-PBS of the genome from HXB2(L12-AC) supports the conclusion that the fine specificity for discrimination between tRNALys,3and tRNALys1,2for use as a primer for HIV-1 reverse transcription resides in the structure of the U5–PBS region of the viral genome
Bean Yellow Dwarf Virus RepA, but Not Rep, Binds to Maize Retinoblastoma Protein, and the Virus Tolerates Mutations in the Consensus Binding Motif

AbstractIt has previously been reported that complementary-sense gene products of wheat dwarf virus (WDV), a geminivirus of the genus Mastrevirus that infects monocotyledonous plants, bind to human and maize retinoblastoma (Rb) protein. Rb proteins control cell-cycle progression by sequestering transcription factors required for entry into S-phase, suggesting that the virus modifies the cellular environment to produce conditions suitable for viral DNA replication. Using a yeast two-hybrid assay, we have investigated whether the complementary-sense gene products of bean yellow dwarf virus, a mastrevirus that is adapted to dicotyledonous plants, also bind maize Rb protein. We demonstrate that whereas RepA binds to Rb protein, Rep does not, suggesting that RepA alone regulates host gene expression and progression of cells to S-phase. RepA mutants containing L → I, C → S, C → G, and E → Q mutations within the consensus Rb protein binding motif LXCXE retained the ability to bind to Rb, but with reduced efficiency. Most notably, the E → Q mutation reduced binding by approximately 95%. Nonetheless, all LXCXE mutants were able to replicate in tobacco protoplasts and to systemically infect Nicotiana benthamiana and bean, in which they produced wild-type symptoms