pinecone/core-2020-05-10-deduplication huggingface dataset:
Alteration of Intrahepatic Cytokine Expression and AP-1 Activation in Transgenic Mice Expressing Hepatitis C Virus Core Protein

AbstractHepatitis C virus (HCV) infection often leads to the development of hepatocellular carcinoma (HCC), but its molecular mechanism has not been clearly elucidated. Previously, transgenic mice constitutively expressing HCV core protein have been shown to develop HCC, suggesting a pivotal role of the core protein in hepatocarcinogenesis. Here, we analyzed the expression of cytokines associated with a variety of cellular processes, including cell proliferation, in the mouse model for HCV-associated HCC to define the molecular events prior to oncogenesis. The expression of tumor necrosis factor-α and interleukin-1β was increased at both protein and mRNA levels. In addition, the activities of c-Jun N-terminal kinase and activator protein-1 (AP-1), downstream effectors, were enhanced, while IκB kinase or nuclear factor-κB activities were not enhanced. Thus, the altered in vivo expression of cytokines with AP-1 activation in consequence to the core protein expression may contribute to hepatocarcinogenesis in persistent HCV infection
Differential Cellular Distribution of HIV-1 Drug Resistance in Vivo: Evidence for Infection of CD8+ T Cells during HAART

AbstractThis study presents a detailed analysis of HIV-1 populations isolated from total PBMC, plasma, CD4+ T cells, CD8+ T cells, and monocytes/macrophages in 13 patients receiving HAART. Sequence analysis of the reverse transcriptase and protease genes indicated that viral strains isolated from different blood leukocytes were genetically distinct in each subject. Notably, HIV variants isolated from CD8+ T cells were distantly related to strains derived from other blood cell types, providing evidence for the strain-specific infection of CD8+ T cells in vivo. Compartmentalization of drug resistance mutations in specific blood cell types was observed in approximately 50% of patients. The prevalence of resistance mutations was higher in either CD4+ T cells or monocytes/macrophages in these subjects. However, CD8+ T cells showed markedly lower levels of viral drug resistance in these patients, indicating a lack of viral replication in this compartment. This study is the first to demonstrate the differential distribution of HIV drug resistance in different blood cell types during HAART and provides new insights into the infection of CD8+ T cells in vivo
High Levels of Plasma Dengue Viral Load during Defervescence in Patients with Dengue Hemorrhagic Fever: Implications for Pathogenesis

AbstractStudies of the pathogenesis of dengue hemorrhagic fever (DHF), a potentially life-threatening disease, have revealed the importance of initial high levels of virus replication. However, the possible involvement of virus during the transition from fever to defervescence, a critical stage in determining the severity of disease, has not been appreciated. Using quantitative reverse transcription-polymerase chain reaction, we examined the levels of plasma dengue viral load during both fever and defervescence periods in patients from a DEN-3 outbreak in southern Taiwan in 1998. Higher levels of plasma dengue viral RNA were found in DHF patients than in DF patients. During defervescence, while the level of plasma dengue viral RNA was undetectable in most DF patients, it remains high in all DHF patients. Using a modified immunoprecipitation assay, we demonstrated for the first time that the plasma dengue viruses persisting during defervescence were in the immune complexes for most DHF patients. These findings suggest that continued active viral replication or delay in the clearance of viremia contributes to the pathogenesis of DHF. Moreover, high levels of plasma dengue viral RNA during defervescence may serve as a disease marker for DHF
Association of Primate T-Cell Lymphotropic Virus Infection of Pig-Tailed Macaques with High Mortality

AbstractNatural infection of humans with human T-cell lymphotropic virus type I (HTLV-I) and of old world nonhuman primates with the simian counterpart, STLV-I, is associated with development of neoplastic disease in a small percentage of individuals after long latent periods. HTLV-I is also the etiologic agent of a more rapidly progressive neurologic disease, HTLV-I-associated myelopathy/tropical spastic paraparesis (HAM/TSP). Macaques have been used experimentally in studies to evaluate HTLV-I candidate vaccines for efficacy, but no evidence of disease was observed. Here we report experimental infection of pig-tailed macaques with STLV-I(sm) and HTLV-I(ACH), both of which were associated with a disease syndrome characterized by rapid onset, hypothermia, lethargy, and death within hours to days. Other pathologic sequelae included diarrhea, rash, bladder dysfunction, weight loss, and, in one animal, arthropathy. Both retroviruses were detected in the central nervous systems of some animals, either by culture or by direct antigen capture for p19 Gag in cerebrospinal fluid. Although virus was recovered throughout infection from peripheral blood mononuclear cells (PBMC), all infected macaques maintained low antiviral antibody titers and stable proviral burdens, which generally ranged between 10 and 100 copies per 106 PBMC. However, of 13 macaques infected with HTLV-I(ACH) or STLV-I(sm), seven animals (54%) died between 35 weeks and 412 years after infection. This unexpected high mortality within a relatively short time suggests that infection of pig-tailed macaques might be a useful model for studying immune responses to and pathologic events resulting from HTLV-I infection
Rotavirus-Specific B Cells Induced by Recent Infection in Adults and Children Predominantly Express the Intestinal Homing Receptor α4β7

AbstractIn vivo replication of rotaviruses is generally limited to enterocytes. Because of this restriction, most blood circulating rotavirus-specific B cells are hypothesized to originate in Peyer's patches and should express the intestinal homing receptor α4β7. To test this hypothesis in humans, we used a flow cytometry assay that identifies antigen-activated (IgD−) B cells (CD19+) that express surface rotavirus-specific immunoglobulin. With this assay we could detect rotavirus-specific B cells in both children and adults with an acute rotavirus (RV) infection. Staining with an anti-α4β7 monoclonal antibody, we could determine that B cells that express rotavirus-specific surface immunoglobulin predominantly express α4β7. The response of rotavirus-specific antibody-secreting cells in the peripheral blood of children and adults with acute rotavirus infection was also studied by ELISPOT. The antibody-secreting cells of children were mainly of the IgM isotype, while the antibody-secreting cells of adults were predominantly of the IgA and IgG isotype. α4β7+ and α4β7− subsets of peripheral blood mononuclear cells were purified using paramagnetic beads and then tested in the ELISPOT assay. Rotavirus-specific antibody-secreting cells were predominantly present in the α4β7+ subpopulation. The flow cytometry assay we have described will permit future studies to characterize the phenotype of virus-specific B cells and could be useful in the study of the immunogenicity and protective efficacy of RV vaccines and the identification of markers of protective immunity
Down-Regulation of Spontaneous Epstein–Barr Virus Reactivation in the P3HR-1 Cell Line by l-Arginine

AbstractWe tested the hypothesis that inhibition of Epstein–Barr virus (EBV) reactivation is controlled in part by nitric oxide (NO) generated from l-arginine (Arg). The spontaneous reactivation of EBV in the Burkitt's lymphoma (BL) cell line P3HR-1 was inhibited when the cells were cultured in L-Arg-supplemented medium. The expression of EBV early antigen (EA), immediate-early BZLF1 mRNA and the protein ZEBRA, and production of infectious virus were reduced by L-Arg supplementation in a dose-dependent manner. We demonstrated that inducible NO synthase (iNOS) mRNA was constitutively expressed in P3HR-1 cells, as quantitated by the reverse transcription-polymerase chain reaction. L-Arg supplementation enhanced iNOS and NOx expression in the cells. A specific NOS inhibitor, NG-monomethyl-l-Arg enhanced the expression of ZEBRA and early BMRF1 protein EA-D in the cells. L-Arg supplementation also inhibited the spontaneous EBV reactivation in another BL cell line EB1 and a B lymphoblastoid cell line OB. These results indicated that L-Arg induces iNOS and generates NO, which inhibits EBV reactivation in EBV-positive cells
Herpesvirus Papio 2 Encodes a Virion Host Shutoff Function

AbstractInfection of baboons with herpesvirus papio 2 (HVP-2) produces a disease that is similar to human infection with herpes simplex viruses (HSV). Molecular characterization of HVP-2 has demonstrated that the virion contains a factor which rapidly shuts off host cell protein synthesis after infection. Reduction of host cell protein synthesis occurs in parallel with the degradation of mRNA species. A homolog of the HSV virion host shutoff (vhs) gene was identified by Southern and DNA sequence analysis. The sequence of the HVP-2 vhs gene homolog had greater than 70% identity with the vhs genes of HSV 1 and 2. Disruption of the HVP-2 vhs open reading frame diminished the ability of the virus to shut off protein synthesis and degrade cellular mRNA, indicating that this gene was responsible for the vhs activity. The HVP-2 model system provides the opportunity to study the biological role of vhs in the context of a natural primate host. Further development of this system will provide a platform for proof-of-concept studies that will test the efficacy of vaccines that utilize vhs-deficient viruses
Mechanism of DI RNA Formation in Tombusviruses: Dissecting the Requirement for Primer Extension by the Tombusvirus RNA-Dependent RNA Polymerase in Vitro

AbstractTombusviruses, which are positive-strand RNA viruses of plants, frequently generate defective interfering (DI) RNAs that consist of three to four noncontiguous segments of the parental RNA. Replicase jumping was postulated to cause multiple deletions leading to the de novo formation of DI RNAs in planta. This model was tested using a partially purified RNA-dependent RNA polymerase (RdRp) preparation from tombusvirus-infected plants in vitro. The tombusvirus RdRp was capable of primer extension without the need for sequence complementarity between the primer and the acceptor template in vitro, although the most efficient primer extension was obtained with primers forming a 5-bp duplex with the acceptor region. Primers forming 14- to 20-bp duplexes with the acceptor region were used less efficiently by the tombusvirus RdRp in vitro. In addition, primers with 3′ noncomplementary nucleotides were also extended by the tombusvirus RdRp, albeit with a reduced efficiency. The preference of the tombusvirus RdRp for short base-paired primers in vitro is consistent with the lack of extended sequence similarities at the junction sites in the de novo generated tombusvirus-associated DI RNAs. The in vitro experiments also revealed that the acceptor region plays a significant role in primer extension. Comparison of tombusvirus-derived, heterologous and artificial acceptor regions revealed that the conserved regions present in DI RNAs are the best acceptor regions when they are available in the minus-strand orientation. These data suggest that recombination/deletion events may be more frequent at some regions, rather than occurring randomly throughout the parental genome. In addition, these findings support a model that predicts a higher frequency of replicase jumping, i.e., recombination/deletion events, during plus-strand synthesis than during minus-strand synthesis
Host-Dependent Recombination of a Tomato bushy stunt virus Coat Protein Mutant Yields Truncated Capsid Subunits That Form Virus-like Complexes Which Benefit Systemic Spread

AbstractThis study examined the contribution of the Tomato bushy stunt virus (TBSV) coat protein (CP) and its corresponding RNA to systemic infection of plants. Compared to results obtained with a mutant lacking the 5′-half of the CP gene, the presence of those CP-RNA sequences in another mutant benefited TBSV infection on Nicotiana benthamiana even though wild-type CP expression was eliminated by introduction of a small out-of-frame deletion. RT-PCR of viral RNA associated with rapid infections established by this CP frameshift deletion mutant revealed that in planta recombination had provided the progeny with the ability to express a truncated CP (tCP) with a block of N-proximal 30 residues deleted from the 66 amino acid RNA-binding domain. Subsequent biochemical characterizations revealed the presence of large ribonucleoprotein complexes that were shown to contain viral RNA as well as the ∼38-kDa tCP. Electron microscopic examination of purified complexes showed particle-like structures that were nonuniform in size and shape compared to wild-type TBSV particles. Inoculation of pepper with the tCP-containing ribonucleoprotein complexes resulted in a rapid systemic infection similar to that caused by wild-type TBSV. In contrast, infections established in pepper by the original CP frameshift deletion mutant transcripts were restricted to inoculated leaves and did not yield recombinants capable of systemically infecting this host. In summary, TBSV possesses the flexibility to form alternative virion-like structures even if a substantial portion of the RNA-binding domain is deleted from the CP; mutants producing the tCP-containing particle-like structures are more effective for virus spread than those devoid of CP expression; and recombination events to produce the alternative tCP–RNA complexes are host-dependent
Evidence against Ebola Virus sGP Binding to Human Neutrophils by a Specific Receptor

AbstractThe issue of whether Ebola secretory glycoprotein (sGP) binds to human neutrophils via the IgG Fc receptor IIIb (FcγRIIIb, CD16b) or other receptors has been controversial. To clarify this, FACS analysis, an sGP absorption assay, and direct binding of 125I-sGP to neutrophils were performed. Results from FACS analysis demonstrated that limited washing conditions leads to the nonspecific formation of immune complexes on the neutrophil surface and this, but not a specific interaction between sGP and CD16b, is responsible for the previous observations. An sGP absorption assay also demonstrated that sGP is not specifically bound but is nonspecifically proteolysed by proteases released from neutrophils. Finally, there was no difference in 125I-sGP binding to neutrophils compared to other control cell types. Taken together, these results demonstrate that neutrophils do not express a specific receptor for Ebola virus sGP. It is unlikely that sGP plays a role in the Ebola virus pathogenesis through interfering with the innate immunity by targeting neutrophils
Epstein–Barr Virus Encoded Interleukin-10 Inhibits HLA-Class I, ICAM-1, and B7 Expression on Human Monocytes: Implications for Immune Evasion by EBV

AbstractMonocytes and macrophages play a central role in viral infections, as a target for viruses and in activation of both innate and adaptive immune responses. Epstein–Barr virus (EBV) has evolved elaborate strategies to dampen the immune system and to persist within the host. There is evidence that the product of the BCRF-1 open reading frame of EBV, viral interleukin-10 (vIL-10), inhibits the capacity of monocytes/macrophages to induce T cell activation, but the full mechanism of this effect is unknown. To determine whether this effect might involve modulation of the expression of accessory molecules known to be important in T cell activation, we analyzed by flow cytometry the influence of vIL-10 on the basal as well as on IFN-γ-induced up-regulation of HLA molecules, ICAM-1, and two members of the B7 family B7.1 (CD80) and B7.2 (CD86) at the surface of human monocytes. Viral IL-10 in a concentration-dependent manner inhibited both basal- and IFN-γ-induced HLA-class II, ICAM-1 (basal levels of ICAM-2 and ICAM-3 is unaffected), CD80, and CD86 up-regulation when added simultaneously with IFN-γ. In contrast, complete inhibition of HLA-class I expression on monocytes/macrophages occurred only when vIL-10 was present 2 h prior to the addition of IFN-γ, implying that vIL-10 affects an early step in the IFN-γ signaling pathway. As both monocytes and macrophages can be infected by EBV, we propose that vIL-10-mediated impairment of monocyte/macrophage antigen-presenting function could help the virus-infected cells to avoid detection by the host's T cells on one hand and contribute to its immunosuppressive properties on the other
Reappearance and Global Spread of Variants of Influenza B/Victoria/2/87 Lineage Viruses in the 2000–2001 and 2001–2002 Seasons

AbstractTwo antigenically and genetically distinct lineages of influenza B viruses, represented by the reference strains B/Victoria/2/1987 and B/Yamagata/16/1988, have cocirculated in humans since at least 1983. Between 1992 and 2000, Victoria lineage viruses were detected only in eastern Asia. From March to September of 2001 and during the 2001–2002 influenza season, Victoria lineage viruses were detected for the first time in a decade in several countries including Canada, USA, Italy, Netherlands, Norway, Philippines, India, and Oman. Phylogenetic analysis of the hemagglutinin (HA) gene of these viruses revealed that the viruses fell into two distinct clades: one group, represented by the reference strain B/Hong Kong/330/2001, contained viruses sharing three signature amino acids, Arg116, Asn121, and Glu164, while the other group of viruses, represented by B/Oman/16296/2001, shared Thr121 compared to the previous reference strain, B/Shandong/7/97. A number of the viruses in the latter group have been found to be reassortants having a Victoria lineage HA and a Yamagata lineage NA. In the current 2001–2002 season, Victoria-like viruses have now been associated with outbreaks in Asia, Europe, and North America. The reemergence of these Victoria lineage viruses worldwide, the fact that the majority of the B/Victoria-like isolates have poor cross-reactivity to B/Sichuan/379/99-like viruses in current vaccines, and the lack of exposure of young children in many areas of the world to these viruses has resulted in a World Health Organization Northern Hemisphere recommendation for the inclusion of a B/Victoria-like strain in vaccines for the 2002–2003 influenza season
Intragenic Complementation and Oligomerization of the L Subunit of the Sendai Virus RNA Polymerase

AbstractThe RNA-dependent RNA polymerase of Sendai virus consists of two subunits, the L and P proteins, where L is thought to be responsible for all the catalytic activities necessary for viral RNA synthesis. Sequence alignment of the L proteins of a variety of negative-stranded RNA viruses revealed six regions of good conservation, designated domains I–VI, which are thought to correspond to functional domains of the protein. Analysis of a number of site-directed mutants within the six domains of L allowed us to conclude that the activities of the polymerase are not simply compartmentalized and that each domain contributes to multiple steps in viral RNA synthesis. Nevertheless these domains can function in trans since we demonstrate here that intragenic complementation between pairs of coexpressed inactive L mutants can restore viral RNA synthesis on an added template. Although intragenic complementation is typically very inefficient, complementation to restore leader RNA synthesis was surprisingly very efficient for some pairs and complementation of mRNA synthesis and genome replication was less, but still significant. Complementation occurred with L mutants in five of the six domains, the exception being a domain III mutant, and required the cotranslation of the two L mutants. C-terminal truncations deleting up to half of L were capable of restoring transcription of an inactive domain I L mutant at amino acid 379. Oligomerization of L in the polymerase complex was demonstrated directly by the co-immunoprecipitation of differentially epitope-tagged full-length and truncated L proteins. These data are consistent with L protein being an oligomer with multiple independent domains each of which exhibits several functions
Mapping Interaction Sites of the A20R Protein Component of the Vaccinia Virus DNA Replication Complex

AbstractThe vaccinia virus A20R protein is required for DNA replication, is associated with the processive form of the viral DNA polymerase, and directly interacts with the viral proteins encoded by the D4R, D5R, and H5R open reading frames as determined by a genome-wide yeast two-hybrid analysis. The purpose of the present study was to further analyze the latter protein–protein interactions. Association of an epitope-tagged A20R protein with an epitope-tagged D4R or H5R protein, expressed in vaccinia virus-infected cells, was demonstrated by binding the complex to one mAb followed by Western blotting with another. Interaction between the A20R and D5R proteins, which was weakest in the yeast two-hybrid analysis, could not be demonstrated by this method. A panel of N- and C-terminal truncated forms of the A20R protein was tested for interaction with the D4R, H5R, and D5R proteins using the yeast two-hybrid system. These studies revealed that nonoverlapping regions of A20R comprising amino acids 1 to 25, 26 to 76, and 201 to 251 were required for binding of D4R, H5R, and D5R, respectively. By contrast, no interaction of A20R with D4R could be detected after deletion of only 25 codons from either end of the latter open reading frame. A fusion protein containing either full-length A20R or only the N-terminal 25 amino acids of A20R was sufficient to capture the D4R protein, whereas the fusion protein containing A20R amino acids 26 to 426 was not, confirming the results of the yeast two-hybrid analysis. The distinct protein binding domains of the A20R protein may contribute to the assembly or stability of the multiprotein DNA replication complex
Equivalent Immunogenicity of the Highly Attenuated Poxvirus-Based ALVAC-SIV and NYVAC-SIV Vaccine Candidates in SIVmac251-Infected Macaques

AbstractTherapeutic immunization of HIV-1-infected individuals may induce and/or enhance HIV-1-specific immune responses and decrease the dependency on antiretroviral drug treatment. However, repeated immunizations with live-recombinant vectors may induce vector-specific immune responses that interfere with the elicitation of vigorous immune responses to the desired antigen. Therefore, the use of mixed-modality vaccinations may be necessary to induce sustained virus-specific immune responses in HIV-1-infected individuals treated with antiretroviral therapy (ART). Thus, the relative immunogenicity of various vaccine modalities needs to be assessed. Here we compared the immunogenicity of two vaccine candidates, the canarypox-based ALVAC-SIV-gag-pol-env (ALVAC-SIV-gpe) and the vaccinia-based NYVAC-SIV-gag-pol-env (NYVAC-SIV-gpe), in rhesus macaques infected with SIVmac251 and treated with ART by 2 weeks postinfection. Both ALVAC-SIV-gpe and NYVAC-SIV-gpe vaccine candidates induced and/or enhanced a virus-specific CD8+ T cell response to a similar extent, as demonstrated by tetramer staining of Gag-specific CD8+ T cells. Similarly, both vaccines elicited comparable lymphoproliferative responses (LPRs) to the SIV p27 Gag and gp120 Env proteins. Thus, both these vaccine modalities alone or in combination may be suitable candidate vaccines for immune therapy of HIV-1-infected individuals