pinecone/core-2020-05-10-deduplication huggingface dataset:
Polypyrimidine-Tract-Binding Protein Affects Transcription but Not Translation of Mouse Hepatitis Virus RNA

AbstractPolypyrimidine-tract-binding protein (PTB) has been shown to bind specifically to the 5′ ends of mouse hepatitis virus (MHV) RNA and its complementary strand. To further characterize the function of PTB in MHV replication, we generated dominant-negative mutant cell lines that express a full-length PTB or a truncated form of PTB, which includes only the N-terminal half of the protein, retaining its protein-dimerization domain. The truncated form of PTB was localized in the cytoplasm, whereas the full-length PTB was present mainly in the nucleus. The truncated form can interact with the full-length PTB in vitro. We observed that both the full-length and the truncated PTB, when overexpressed, functioned in a dominant-negative manner in MHV replication. However, the truncated form exhibited more severe effects on syncytia formation, virus production, and synthesis of viral RNA and viral proteins. To clarify the precise function of PTB in MHV replication, we dissociated the processes of viral transcription from translation by transfecting different types of MHV defective-interfering (DI) RNA that contain various reporter genes into these stable cell lines. Transcription of the DI RNA during MHV infection was greatly inhibited in these cell lines, indicating that PTB modulates MHV transcription. In contrast, translation of the DI RNA was not affected by PTB depletion in in vitro translation in rabbit reticulocyte lysate or by PTB overexpression in in vivo translation experiments in MHV-infected cells. Given that PTB interacts with the viral N protein, which is one of the components of the MHV replication complex, PTB may exert its function on viral replication/transcription by association with viral RNA as well as other viral and cellular factors in the replication complex
Signaling Pathways Triggered by HIV-1 Tat in Human Monocytes to Induce TNF-α

AbstractIn this study we investigated the signaling pathways triggered by Tat in human monocyte to induce TNF-α. In monocytes, the calcium, the PKA, and the PKC pathways are highly implicated in the expression of cytokine genes. Thus, these three major signaling pathways were investigated. Our data show that (i) PKC and calcium pathways are required for TNF-α production, whereas the PKA pathway seems to be not involved; (ii) downstream from PKC, activation of NFκB is essential while ERK1/2 MAP kinases, even though activated by Tat, are not directly involved in the pathway signaling leading to TNF-α production
Recombinant Chimeric Western and Eastern Equine Encephalitis Viruses as Potential Vaccine Candidates

AbstractChimeric cDNA clones, pMWE1000 and pMWE2000, differing by five nucleotides at their 5′ termini, were constructed of the 5′ two-thirds of the western equine encephalitis (WEE) virus genome (encoding nonstructural proteins) and the 3′ one-third of the eastern equine encephalitis (EEE) virus genome (encoding structural proteins). The WEE virus sequences were derived from full-length cDNA clones, pWE1000 and pWE2000, which were isogenic except for five nucleotide differences at their 5′ termini and were responsible for significant differences in mouse virulence. Each cDNA clone was placed downstream from a T7 promoter to allow in vitro transcription of full-length RNA. Transfection of BHK-21 cells with the chimeric RNA by electroporation gave rise to high-titer infectious virus. The in vitro characteristics of each chimera virus were determined by electrophoretic analysis of its structural proteins, plaque morphology, neutralization characteristics, replication kinetics, and rate of viral RNA synthesis. With the exception of plaque morphology, the in vitro characteristics of MWE1000 and MWE2000 were indistinguishable from the parental EEE virus. Subcutaneous inoculation of 5-week-old C57BL/6 mice with varying doses of MWE1000 or MWE2000 virus demonstrated that both chimeric viruses were significantly attenuated compared to the parental WEE virus (Cba 87) and EEE virus (PE-6). Animals infected with 105 PFU or more of either MWE1000 or MWE2000 were completely protected from lethal challenge with the virulent EEE virus, FL91-4679, but were not protected from virulent WEE virus Cba 87 challenge. Construction of viable virus chimeras often results in attenuated viruses that may hold promise as genetically engineered alphavirus vaccine candidates (R. J. Kuhn, D. E. Griffin, K. E. Owen, H. G. M. Niesters, and J. H. Strauss, 1996, J. Virol. 70, 7900–7909)
Mycophenolic Acid Inhibits Dengue Virus Infection by Preventing Replication of Viral RNA

AbstractDengue fever is a mosquito-borne viral disease of global importance with no available antiviral therapy. We assessed the ability of mycophenolic acid (MPA), a drug currently used as an immunosuppressive agent, to inhibit dengue virus (DV) antigen expression, RNA replication, and virus production. Pharmacological concentrations of MPA effectively blocked DV infection, decreasing the percentage of infected cells by 99% and the levels of secreted virus by up to a millionfold. Results were reproduced with four hepatoma cell lines and different flaviviruses, including a recent West Nile virus isolate. Experiments were performed to define the stage in the viral lifecycle at which MPA abrogates infection. Early steps in viral infection, such as viral entry and nucleocapsid uncoating, were not the primary targets of MPA action since its inhibitory effect was retained when naked DV RNA was transfected directly into cells. Biosynthetic labeling experiments showed that MPA did not block the initial phase of viral translation but did interfere with viral protein synthesis in the amplification phase. Quantitative RT-PCR demonstrated that MPA prevented the accumulation of viral positive- and negative-strand RNA as the infection proceeded. We conclude that MPA inhibits flavivirus infection by preventing synthesis and accumulation of viral RNA
Diversity and Evolution of the Envelope Gene of Dengue Virus Type 1

AbstractThe genetic diversity and phylogenetic relationships of a collection of strains of dengue virus type 1 (DV-1), isolated from different parts of the world, were investigated. Phylogenetic trees derived from the complete sequence of the E gene of 44 strains suggested the existence of five genetic types defined by a maximum nucleotide divergence within each group of 6%. The 22 strains from America were classified into a single genetic type that included strains associated either with classical dengue or hemorrhagic dengue episodes. Using a maximum likelihood procedure based on a single rate with dated tips model and substitution rates calculated at the third codon position, evolution of the five DV-1 genotypes was shown to conform to a molecular clock. The average rate of evolution was estimated to be approximately 16.2 × 10−4 substitutions/third codon position site/year. Using this estimate, divergence among the DV-1 genotypes was calculated to have occurred approximately 100 years ago. Very low average value of the ratio of nonsynonymous-to-synonymous nucleotide substitutions, relative to the respective sites (0.046), indicated that the evolution of the E gene of the DV-1 is subject mostly to purifying selection
Inducible System in Human Hepatoma Cell Lines for Hepatitis C Virus Production

AbstractWe cloned the complete complementary DNA of an isolate of the hepatitis C virus, HCV-S1, into a tetracycline-inducible expression vector and stably transfected it into two human hepatoma cell lines, Huh7 and HepG2. Twenty-six Huh7 and two HepG2-positive clones were obtained after preliminary screening. Two Huh7 (SH-7 and -9) and one HepG2 (G-19) clones were chosen for further characterisation. Expression of HCV proteins in these cells accumulated from 6 h to 4 days posttreatment. Full-length viral plus-strand RNA was detected by Northern analyses. Using RT-PCR and ribonuclease protection assay, we also detected the synthesis of minus-strand HCV RNA. Plus- and minus-strand viral RNA was still detected after treatment with actinomycin D. Indirect immunofluorescence staining with anti-E2, NS4B, and NS5A revealed that these proteins were mostly localised to the endoplasmic reticulum (ER). Culture media from tet-induced SH-9 cells was separated on sucrose density gradients and analysed for the presence of HCV RNA. Viral RNA levels peaked at two separate ranges, one with a buoyant density of 1.08 g/ml and another from 1.17 to 1.39 g/ml. Electron microscopy demonstrated the presence of subviral-like particles (approximately 20–25 nm in diameter) in the cytoplasm of SH-9 and G-19 cells, which were positively labelled by anti-HCV core antibodies. Anti-E2 antibodies strongly labelled cytoplasmic vesicular structures and some viral-like particles. Complete viral particles of about 50 nm which reacted with anti-E2 antibodies were observed in the culture media of tet-induced SH-9 cells following negative staining. Supernatant from tet-treated SH-9 cells was found to infect naı&#x0308;ve Huh7 and stable Huh7-human CD81 cells
Mapping of the Bovine Immunodeficiency Virus Packaging Signal and RRE and Incorporation into a Minimal Gene Transfer Vector

AbstractGene transfer systems based on lentiviruses have emerged as promising gene delivery vehicles for human gene therapy due to their ability to efficiently transduce nondividing target cells. Both primate and nonprimate lentiviruses have been used for construction of lentiviral vectors. An early generation of gene transfer system based on bovine immunodeficiency virus (BIV) has been developed (R. D. Berkowitz, H. Ilves, W. Y. Lin, K. Eckert, A. Coward, S. Tamaki, G. Veres, and I. Plavec, 2001, J. Virol. 75, 3371–3382). In this study, we mapped the BIV Rev response element (RRE) to 312 bp of the Env coding region. Furthermore, we compared transduction efficiencies of vectors containing different portions of the BIV Gag coding region and found that the first 104 bp of gag contains a functional part of the BIV packaging signal. These findings enabled the generation of a minimal BIV-based lentiviral vector. The minimal transfer vector construct consists of a self-inactivating long terminal repeats (LTR), minimal packaging sequence, putative central polypurine tract, minimal RRE, an internal promoter driving the gene of interest, and a woodchuck hepatitis posttranscriptional regulatory element. In addition, we constructed a BIV packaging construct containing gag/pol, minimal Rev/RRE, and the accessory gene vpy. The regulatory gene tat and the accessory genes vif and vpw have been inactivated or truncated. The current system has significantly reduced regions of homologies between the transfer vector and the packaging constructs. The vectors generated from this system achieved a titer of greater than 1 × 106 transducing units per milliliter and are fully functional as indicated by their ability to efficiently transduce both dividing and nondividing cells. These modifications should provide improved safety features for the BIV-based gene transfer system
Adaptation of a CXCR4-Using Human Immunodeficiency Type 1 NDK Virus in Intestinal Cells Is Associated with CD4-Independent Replication

AbstractInfection of epithelial colon carcinoma cell line HT29 with human immunodeficiency virus type 1 (HIV-1) NDK, a subtype D virus highly cytopathic for CD4-positive lymphocytes, results in the selection of HIV-1 variants, 1000 times more infectious for CD4− intestinal cells than the parental virus. Here, we demonstrate that the envelope gene of intestinal cell-adapted virus conferred to recombinant clone HIV-1 iNDK the ability to utilize CXCR4 without CD4 while retaining its tropism for CD4 lymphocytes. Among the major genetic changes required for infection of intestinal cells and CD4 independence, two potential N-glycosylation sites appeared as a result of the extension of five amino acids in the V1/V2 region and three amino acid changes (296KYT → 296NNI) were identified in the V3 loop of HIV-1 iNDK gp120. Our studies suggest that CD4-independent use of CXCR4 can be mediated by different adaptive changes related to the microenvironment of CD4− cell
Neuroprotective Effects of IGF-I against TNFα-Induced Neuronal Damage in HIV-Associated Dementia

AbstractHuman immunodeficiency virus type 1 (HIV-1) infection often results in disorders of the central nervous system, including HIV-associated dementia (HAD). It is suspected that tumor necrosis factor-α (TNFα) released by activated and/or infected macrophages/microglia plays a role in the process of neuronal damage seen in AIDS patients. In light of earlier studies showing that the activation of the insulin-like growth factor I receptor (IGF-IR) exerts a strong neuroprotective effect, we investigated the ability of IGF-I to protect neuronal cells from HIV-infected macrophages. Our results demonstrate that the conditioned medium from HIV-1-infected macrophages, HIV/CM, causes loss of neuronal processes in differentiated PC12 and P19 neurons and that these neurodegenerative effects are associated with the presence of TNFα. Furthermore, we demonstrate that IGF-I rescues differentiated neurons from both HIV/CM and TNFα-induced damage and that IGF-I-mediated neuroprotection is strongly enhanced by overexpression of the wt IGF-IR cDNA and attenuated by the antisense IGF-IR cDNA. Finally, IGF-I-mediated antiapoptotic pathways are continuously functional in differentiated neurons exposed to HIV/CM and are likely supported by TNFα-mediated phosphorylation of IκB. All together these results suggest that the balance between TNFα and IGF-IR signaling pathways may control the extent of neuronal injury in this HIV-related experimental setting
The Sequential Introduction of HIV-1 Subtype B and CRF01AE in Singapore by Sexual Transmission: Accelerated V3 Region Evolution in a Subpopulation of Asian CRF01 Viruses

AbstractThe rapid spread of the human immunodeficiency virus type 1 (HIV-1) circulating recombinant form (CRF) 01AE throughout Asia demonstrates the dynamic nature of emerging epidemics. To further characterize the dissemination of these strains regionally, we sequenced 58 strains from Singapore and found that subtype B and CRF01 were introduced separately, by homosexual and heterosexual transmission, respectively. Protein similarity scores of the Singapore CRF01, as well as all Asian strains, demonstrated a complex distribution of scores in the V3 loop—some strains had very similar V3 loop sequences, while others were highly divergent. Furthermore, we found a strong correlation between the loss of a V3 glycosylation site and the divergent strains. This suggests that loss of this glycosylation site may make the V3 loop more susceptible to immune surveillance. The identification of a rapidly evolving population of CRF01AE variants should be considered when designing new candidate vaccines and when evaluating breakthrough strains from current vaccine trials
Time Course of Gag Protein Assembly in HIV-1-Infected Cells: A Study by Immunoelectron Microscopy

AbstractRecent biochemical studies have identified high molecular complexes of the HIV Gag precursor in the cytosol of infected cells. Using immunoelectron microscopy we studied the time course of the synthesis and assembly of a HIV Gag precursor protein (pr55gag) in Sf9 cells infected with recombinant baculovirus expressing the HIV gag gene. We also immunolabeled for pr55gag human T4 cells acutely or chronically infected with HIV-1. In Sf9 cells, the time course study showed that the first Gag protein appeared in the cytoplasm at 28–30 h p.i. and that budding started 6–8 h later. Colloidal gold particles, used to visualize the Gag protein, were first scattered randomly throughout the cytoplasm, but soon clusters representing 100 to 1000 copies of pr55gag were also observed. By contrast, in cells with budding or released virus-like particles the cytoplasm was virtually free of gold particles while the released virus-like particles were heavily labeled. Statistical analysis showed that between 80 and 90% of the gold particles in the cytoplasm were seen as singles, as doublets, or in small groups of up to five particles probably representing small oligomers. Clusters of gold particles were also observed in acutely infected lymphocytes as well as in multinuclear cells of chronically infected cultures of T4 cells. In a few cases small aggregates of gold particles were found in the nuclei of T4 lymphocytes. These observations suggest that the Gag polyprotein forms small oligomers in the cytoplasm of expressing cells but that assembly into multimeric complexes takes place predominantly at the plasma membrane. Large accumulations of Gag protein in the cytoplasm may represent misfolded molecules destined for degradation
High Genetic Divergence and Recombination in Arenaviruses from the Americas

AbstractThe rodent-borne Arenaviruses are divided into two major antigenic groups: the Old World and New World complexes. Of the 15 known New World arenaviruses, four (Junin, Machupo, Sabia, and Guanarito) have been associated with hemorrhagic fever in humans. It has been difficult to assess the pathogenic or epidemic potential of the remaining viruses and the threat of emerging disease. We obtained full-length small (S) segment sequence data, encoding the nucleoprotein (NP) and glycoprotein precursor (GPC), from all American arenaviruses to predict their evolutionary and functional relationships. Phylogenetic analysis of NP or GPC amino acid sequences from all New World arenaviruses revealed three lineages and that Tamiami and Whitewater Arroyo viruses were probably derived from a single recombinant progenitor. The results imply that arenaviruses have been evolving independently for a very long time, leading to very diverse groupings that do not correlate with geography, rodent host, or human epidemic potential
Ribonucleotide Reductase of Shrimp White Spot Syndrome Virus (WSSV): Expression and Enzymatic Activity in a Baculovirus/Insect Cell System and WSSV-Infected Shrimp

AbstractInfection of shrimp cells with white spot syndrome virus (WSSV) results in an increase in ribonucleotide reductase (RR) expression at the RNA level. In this article we further express and characterize the induction of a novel ribonucleotide reductase after WSSV infection of shrimp cells. A baculovirus/insect system was used to express the two recombinant protein subunits RR1 and RR2, and a DNA polymerase coupled RR activity assay showed a marked increase in ribonucleotide reductase activity when cell extracts containing recombinant RR1 and RR2 were combined. The same assay revealed that RR activity increased as infection advanced in the gills of experimentally infected shrimp. An increase in RR expression was also detected at the protein level in WSSV-infected shrimp cells. An immunocytochemistry assay by confocal laser scanning microscopy showed that in hemocytes collected from WSSV-infected shrimp, both of the subunit proteins (RR1 and RR2) were concentrated mainly around the nucleus, but only RR1 was detected inside it. All of these results suggest that WSSV RR is functionally involved during WSSV infection
Type 3 Reovirus Neuroinvasion after Intramuscular Inoculation: Viral Genetic Determinants of Lethality and Spinal Cord Infection

AbstractTo better understand the mechanisms by which neurotropic viruses invade peripheral nerve pathways and produce CNS disease, we defined the type 3 (T3) reovirus genes that are determinants of the capacity of reovirus T3 strain Dearing (T3D) and T3 clone 9 (C9) to infect the spinal cord and kill mice after hindlimb injection. T3D and C9 viruses are both highly virulent (LD50 < 101 PFU) after intracranial injection of neonatal mice. However, C9 is significantly more lethal than T3D after either intramuscular injection (LD50 < 101 vs LD50 104 PFU) or peroral injection (LD50 103.4 vs LD50 > 108.3 PFU). Using reassortant viruses containing different combinations of genes derived from T3D and C9, we found that the S1 gene, encoding the cell attachment protein sigma 1 and the nonstructural protein sigma 1s, and the L3 gene, encoding the core shell protein lambda 1 were the primary determinants of lethality after intramuscular injection. The L3 gene and the L2 gene encoding spike protein, lambda 2, determined differences in spinal cord titer after intramuscular injection. A C9 × T3D mono-reassortant containing all T3D genes except for the C9-derived L3 was lethal after peroral injection. These studies indicate that the S1, L2, and L3 genes all play a potential role in neuroinvasiveness and provide the first identification of a role in pathogenesis for the L3 gene
Type 3 Reovirus Neuroinvasion after Intramuscular Inoculation: Direct Invasion of Nerve Terminals and Age-Dependent Pathogenesis

AbstractNeonatal but not adult mice are vulnerable to reovirus invasion of the central nervous system after peripheral inoculation. After hindlimb injection, type 3 reovirus travels via the sciatic nerve to replicate in spinal cord motor neurons before spread to the brain and development of lethal encephalitis. Here we provide ultrastructural evidence for direct reovirus invasion of unmyelinated neonatal motor nerve terminals within 2 h and replication in spinal cord motor neurons within 14 h after hindlimb injection of 1-day-old mice. In adult mice, resistance to reovirus lethality after intracranial (IC) injection correlates with the restriction of virus growth in cortical neurons. We found that neuroinvasion also is age dependent after intramuscular injection. Virus lethality and CNS infection decreased sharply during the first postnatal week, while lethality after IC injection continued for 2 additional weeks. Mice inoculated at 7 days of age with high virus doses suffered paralysis of the injected limb, but significant brain infection was not lethal. These results suggest that reovirus invasion of the neonatal CNS is restricted by several progressive age-dependent mechanisms
T Helper Cell-Independent Antibody Responses to the Transgene Product of an E1-Deleted Adenoviral Vaccine Require NK1.1 T Cells

AbstractMice lacking CD4+ T cells due to a knock-out mutation respond to vaccination with a replication-defective adenoviral recombinant expressing the glycoprotein of rabies virus with a long-lasting virus-neutralizing antibody response. The vaccine-induced B cells secrete antibodies that are mainly of IgG isotypes. The response can be enhanced upon booster immunization, indicating the induction of B cell memory in the absence of CD4+ T cells. The antibody response is independent of CD8+ T cells but requires the presence of CD3+ cells carrying the NK1.1 markers
Hepatitis C Virus NS2 Protein Inhibits Gene Expression from Different Cellular and Viral Promoters in Hepatic and Nonhepatic Cell Lines

AbstractThe mechanisms leading to viral persistence and hepatocarcinogenesis in hepatitis C virus (HCV) infection are not fully understood. Recently, evidence has been accumulated that HCV viral proteins might interfere with gene expression of host cells. Here, we demonstrate that the amino-terminal portion of HCV NS2 protein inhibits the expression of reporter genes driven by different promoters or enhancer elements and also inhibits hepatitis B virus (HBV) gene expression and HBV DNA replication. The inhibitory effect of HCV NS2 on liver and non-liver-specific promoters and enhancer elements might be relevant for the pathogenesis of chronic HCV infection