pinecone/core-2020-05-10-deduplication huggingface dataset:
Molecular and Phylogenetic Analyses of 16 Novel Simian T Cell Leukemia Virus Type 1 from Africa: Close Relationship of STLV-1 from Allenopithecus nigroviridis to HTLV-1 Subtype B Strains

AbstractA serological survey searching for antibodies reacting with human T-cell leukemia virus type 1 (HTLV-1) antigens was performed on a series of 263 sera/plasma obtained from 34 monkey species or subspecies, originating from different parts of Africa. Among them, 34 samples exhibited a typical HTLV-1 Western blot pattern. Polymerase chain reaction was performed with three primer sets specific either to HTLV-1/STLV-1 or HTLV-2 and encompassing gag, pol, and tax sequences, on genomic DNA from peripheral blood mononuclear cells of 31 animals. The presence of HTLV-1/simian T-cell leukemia virus type 1 (STLV-1) related viruses was determined in the 21 HTLV-1 seropositive animals tested but not in the 10 HTLV-1 seronegative individuals. Proviral DNA sequences from the complete LTR (750 bp) and a portion of the env gene (522 bp) were determined for 16 new STLV-1 strains; some of them originating from species for which no STLV-1 molecular data were available as Allenopithecus nigroviridis and Cercopithecus nictitans. Comparative and phylogenetic analyses revealed that these 16 new sequences belong to five different molecular groups. The A. nigroviridis STLV-1 strains exhibited a very strong nucleotide similarity with HTLV-1 of the subtype B. Furthermore, four novel STLV-1, found in Cercocebus torquatus, C. m. mona, C. nictitans, and Chlorocebus aethipos, were identical to each other and to a previously described Papio anubis STLV-1 strain (PAN 503) originating from the same primate center in Cameroon. Our data extend the range of the African primates who could be permissive and/or harbor naturally STLV-1 and provide new evidences of cross-transmission of African STLV-1 between different monkey species living in the same environment and also of STLV-1 transmissions from some monkeys to humans in Central Africa
Attenuated and Wild-Type HIV-1 Infections and Long Terminal Repeat-Mediated Gene Expression from Plasmids Delivered by Gene Gun to Human Skin ex Vivo and Macaques in Vivo

AbstractGene expression from HIV-based gene therapy vectors or live-attenuated HIV-1 vaccines requires RNA transcription supported by the HIV-1 promoter, the long terminal repeat (LTR). Delivery of live-attenuated HIV-1 vaccines as plasmid DNA would overcome problems associated with production of attenuated HIV-1 strains. We investigated the expression of reporter plasmids and proviral HIV-1 constructs driven by either the HIV-1 LTR or LTRs with deletions in the U3 enhancer regions. LTR-driven plasmids were inoculated by gene gun into both human epidermis ex vivo and macaques in vivo. The HIV-1 LTR drove reporter gene expression in human and macaque skin, although with 15- to 20-fold less efficiency compared to the immediate-early cytomegalovirus promoter. A deleted LTR derived from a naturally attenuated HIV-1 strain infecting a member of the well-characterized Sydney Blood Bank Cohort of long-term nonprogressors was 5-fold less efficient in expression of the reporter gene compared to wild-type LTR. Delivery of proviral wild-type HIV-1 DNA constructs to human skin resulted in recovery of HIV-1 from cells emigrating from the epidermis, providing an ex vivo model of the infectivity of proviral HIV-1 DNA. However, delivery of proviral HIV-1 DNA containing deletions in either the LTR, Nef, or the secondary viral transcription activator,Vpr, significantly reduced HIV-1 replication in this model. The early coexpression of Tat from a second plasmid did not restore replication. Thus, although attenuated lentiviral vaccines might be deliverable as proviral DNA constructs in primate subjects, significant improvements are needed to enhance the efficiency of this method
Preferential Utilization of the Perforin/Granzyme Pathway for Lysis of Epstein–Barr Virus-Transformed Lymphoblastoid Cells by Virus-Specific CD4+ T Cells

AbstractIn this report, we show that Epstein–Barr virus (EBV)-infected lymphoblastoid cell lines (LCL) express Fas and tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) receptor 2 and that LCL are lysed following engagement of these receptors by agonist Fas and TRAIL receptor-specific monoclonal antibodies (MAb). We also show that EBV-specific CD4+ T cells mediate bystander lysis of susceptible targets through both the Fas/Fas ligand (FasL) and the TRAIL pathways, but find that the dominant mechanism of lysis following cognate, HLA class II-restricted recognition of LCL is the perforin/granzyme pathway. Killing of LCL by EBV-specific CD4+ T cells was strongly inhibited by concanamycin A, an agent that elevates granule pH, resulting in accelerated destabilization and degradation of perforin. In contrast, blocking anti-FasL MAb showed only limited inhibition of LCL killing. Blocking anti-TRAIL MAb had no effect on lysis of LCL by EBV-specific CD4+ T cells. We further show that culture of EBV-specific CD4+ T cells in the presence of interleukin 4 markedly abrogates effector cytotoxic function against LCL through direct depletion of intracellular perforin, with no evidence of a Th1 to Th2 shift in patterns of cytokine expression
The Interferon-Inducible 204 Gene Is Transcriptionally Activated by Mouse Cytomegalovirus and Is Required for Its Replication

AbstractInfection of cells with viable or UV-inactivated murine cytomegalovirus (MCMV) increased the IFN-inducible 204 gene at both the mRNA and the protein levels. The activity of a reporter gene driven by the mouse Ifi204 promoter induced following virus infection showed that this increase was due to transcriptional activation. Moreover, FACS analysis of infected mouse embryo fibroblasts (MEF) stably transfected with a p204-dominant-negative mutant (p204dmMEF) revealed that they do not accumulate at the G1/S border in the same way as infected MEF transfected with the empty vector (neoMEF). MCMV DNA synthesis is significantly delayed (144 h in p204dmMEF vs 72 h in neoMEF), due to retarded expression of viral genes, namely, IE1 and DNA polymerase, as shown by Western blot comparison of p204dmMEF and neoMEF extracts. These results demonstrate that MCMV may exploit the Ifi204 gene to regulate the cell cycle and enhance its DNA synthesis
Quantitative Analysis of Herpesvirus Sequences from Normal Tissue and Fibropapillomas of Marine Turtles with Real-Time PCR

AbstractQuantitative real-time PCR has been used to measure fibropapilloma-associated turtle herpesvirus (FPTHV) pol DNA loads in fibropapillomas, fibromas, and uninvolved tissues of green, loggerhead, and olive ridley turtles from Hawaii, Florida, Costa Rica, Australia, Mexico, and the West Indies. The viral DNA loads from tumors obtained from terminal animals were relatively homogenous (range 2–20 copies/cell), whereas DNA copy numbers from biopsied tumors and skin of otherwise healthy turtles displayed a wide variation (range 0.001–170 copies/cell) and may reflect the stage of tumor development. FPTHV DNA loads in tumors were 2.5–4.5 logs higher than in uninvolved skin from the same animal regardless of geographic location, further implying a role for FPTHV in the etiology of fibropapillomatosis. Although FPTHV pol sequences amplified from tumors are highly related to each other, single signature amino acid substitutions distinguish the Australia/Hawaii, Mexico/Costa Rica, and Florida/Caribbean groups
Nuclear Factor 1 Family Members Mediate Repression of the BK Virus Late Promoter

AbstractBK virus (BKV) is a member of the polyoma virus family that is ubiquitous in humans. Its 5-kb DNA genome consists of a bidirectional promoter region situated between two temporally regulated coding regions. We mapped the transcription initiation site of the major late promoter (MLP) of the archetype strain BKV(WW) to nt 185. We found that it lies within the sequence TGGN6GCCA, a binding site for members of the nuclear factor 1 (NF1) family of transcription factors. Competition electrophoretic mobility shift and immunoshift assays confirmed that NF1 factors present in nuclear extracts of HeLa and CV-1 cells bind to the BKV-MLP. Because BKV(WW) grew poorly in tissue culture and failed to express detectable levels of RNA in vitro, SV40-BKV chimeric viruses were constructed to investigate the transcriptional function of this NF-1 binding site. These sequence-specific factors repressed transcription in a cell-free system when template copy number was low. This repression could be relieved by the addition in trans of oligonucleotides containing wild-type, but not mutated, NF1-binding site sequences. SV40-BKV chimeric viruses defective in this NF1-binding site overproduced late RNA at early, but not late, times after transfection of CV-1 cells. Finally, transient expression in 293 cells of cDNAs encoding the family members NF1-A4, NF1-C2, and NF1-X2 specifically repressed transcription from the BKV late promoter approximately 3-, 10-, and 10-fold, respectively, in a DNA binding-dependent manner. We conclude that some members of the NF1 family of transcription factors can act as sequence-specific cellular repressors of the BKV-MLP. We propose that titration of these and other cellular repressors by viral genome amplification may be responsible in part for the replication-dependent component of the early-to-late switch in BKV gene expression
Frequency of Direct Repeat Deletion in a Human Immunodeficiency Virus Type 1 Vector during Reverse Transcription in Human Cells

AbstractRetroviral genetic rearrangements can result from reverse transcriptase template switching. Most published data suggest that errors such as base misincorporation occur at similar frequencies for HIV-1 and for simple retroviruses such as spleen necrosis virus (SNV) and murine leukemia virus (MuLV). However, previous reports have suggested that template switch-mediated recombination is much more frequent for HIV-1 than for simple retroviruses. In this report, direct repeat deletion vectors similar to those previously used for measuring template switching events for SNV and MuLV were developed for HIV-1. Forward mutation rates and the frequency of template switching during a single cycle of HIV-1 replication were determined. The frequency of HIV-1-mediated repeat deletion was measured for three separate internal repeats in lacZ and was compared to rates observed with identical repeats for MuLV. The results indicated that the error rate and the frequency of repeat deletion of HIV-1 were similar to those of MuLV
Molecular Characterization of the Polymerase Gene and Genomic Termini of Nipah Virus

AbstractIn 1998, Nipah virus (NV) emerged in peninsular Malaysia, causing fatal encephalitis in humans and a respiratory disease in swine. NV is most closely related to Hendra virus (HV), a paramyxovirus that was identified in Australia in 1994, and it has been proposed that HV and NV represent a new genus within the family Paramyxoviridae. This report describes the analysis of the sequences of the polymerase gene (L) and genomic termini of NV as well as a comparison of the full-length, genomic sequences of HV and NV. The L gene of NV is predicted to be 2244 amino acids in size and contains the six domains found within the L proteins of all nonsegmented, negative-stranded (NNS) RNA viruses. However, the GDNQ motif found in most NNS RNA viruses was replaced by GDNE in both NV and HV. The 3′ and 5′ termini of the NV genome are nearly identical to the genomic termini of HV and share sequence homology with the genomic termini of other members of the subfamily Paramyxovirinae. At 18,246 nucleotides, the genome of NV is 12 nucleotides longer than the genome of HV and they have the largest genomes within the family Paramyxoviridae. The comparison of the structures of the genomes of HV and NV is now complete and this information will help to establish the taxonomic position of these novel viruses within the family Paramyxoviridae
Phosphorylation of Marburg Virus VP30 at Serines 40 and 42 Is Critical for Its Interaction with NP Inclusions

AbstractThe Marburg virus (MBGV) nucleocapsid complex is composed of four viral proteins (NP, L, VP35, and VP30) and the negative-strand nonsegmented genomic RNA. NP, L, and VP35 are functionally conserved among the order Mononegavirales, whereas VP30, a phosphoprotein, represents a filovirus-specific nucleocapsid protein. In the present paper, we have characterized the localization and function of VP30 phosphorylation. The main phosphorylation sites are represented by seven serine residues in the region of amino acid 40 to 51 of VP30. Additionally, trace amounts of phosphothreonine were detected. Substitution of serine residues 40 and 42 by alanine abolished the interaction of VP30 with NP-induced inclusion bodies, which contain nucleocapsid-like structures formed by NP. Substitution of the other phosphoserine residues had little effect on this interaction. Replacement of the introduced alanine residues 40 and 42 by aspartate restored the interaction between VP30 and the NP inclusions pointing to the importance of negative charges at these particular positions
The Complete DNA Sequence of the Ectocarpus siliculosus Virus EsV-1 Genome

AbstractThe Ectocarpus siliculosus Virus-1, EsV-1, is the type-species of a genus of Phycodnaviridae, the phaeoviruses, infecting marine filamentous brown algae. The EsV-1 genome of 335,593 bp contains tandem and dispersed repetitive elements in addition to a large number of open reading frames of which 231 are currently counted as genes. Many genes can be assigned to functional groups involved in DNA synthesis, DNA integration, transposition, and polysaccharide metabolism. Furthermore, EsV-1 contains components of a surprisingly complex signal transduction system with six different hybrid histidine protein kinases and four putative serine/threonine protein kinases. Several other genes encode polypeptides with protein–protein interaction domains. However, 50% of the predicted genes have no counterparts in data banks. Only 28 of the 231 identified genes have significant sequence similarities to genes of the Chlorella virus PBCV-1, another phycodnavirus. To our knowledge, the EsV-1 genome is the largest viral DNA sequenced to date
Impaired Microglial Activation in the Brain of IL-18-Gene-Disrupted Mice after Neurovirulent Influenza A Virus Infection

AbstractKnockout of the inerleukin-18 (IL-18) gene predisposed mice to impaired clearance of neurovirulent influenza A virus-infected neurons from the brain. In wild-type mice, IL-18 molecule-producing microglia/macrophages emerged in virally attacked regions as early as day 3 after infection. Microglial transformation into macrophages culminated at day 7 to 9, with upregulated expression of Iba1, a novel calcium-binding protein that controls phagocytic functions of microglia/macrophages. In IL-18−/− mice, microglial transformation was interrupted with reduced Iba1 expression. Interferon-γ (IFN-γ)-immunopositive neurons appeared in and around virally invaded regions in wild-type mice, peaking in number at day 7, whereas such cells were barely detected in IL-18−/− mice. Stereotaxic microinjection of recombinant IFN-γ triggered microglial transformation in IL-18−/− mice and upregulated Iba1 expression, leading to effective eradication of virally infected neurons. Collectively, these results suggest that IL-18 plays a key role in activating microglial functions directed against the influenza virus infection by inducing neuronal IFN-γ in the brain parenchyma
A Novel Inducible Expression System to Study Transdominant Mutants of HIV-1 Vpr

AbstractIn this study, an episomal system for ecdysone-inducible gene expression was developed. Human embryonic kidney 293 cells (293VE) expressing a heterodimer of modified ecdysone and retinoid X receptors and the Epstein–Barr nuclear antigen-1 were screened. Plasmids containing the EBV replication origin, oriP, and the ecdysone-response element could replicate and persist in 293VE cells to inducibly express luciferase or Vpr. The induction level, tested with luciferase reporter plasmid, varied among cell lines from 254- to 2056-fold. In one highly inducible cell line, HIV-1 Vpr was expressed well and caused G2 cell cycle arrest in the presence of the inducer, while in the absence of the inducer, no Vpr protein or cell cycle arrest could be detected. Using different selection markers, HIV-1 Vpr was coexpressed with Vpr mutants defective in phosphorylation at Ser79 and G2 cell cycle arrest activity. These Vpr mutants were transdominant to wild-type Vpr for G2 cell cycle arrest activity, but did not alter wild-type Vpr phosphorylation. It is likely that the transdominant mutants and wild-type Vpr compete for a downstream target(s) of G2 cell cycle arrest
Mutations at Amino Acid Positions 63, 189, and 396 of Human Immunodeficiency Virus Type 1 Reverse Transcriptase (RT) Partially Restore the DNA Polymerase Activity of a TRP229TYR Mutant RT

AbstractTrp229 is part of the nonnucleoside reverse transcriptase inhibitor (NNRTI)-binding pocket of HIV-1 reverse transcriptase (RT). It is also an important constituent of the so-called “primer grip.” Using a recombinant virus assay, we tried to obtain recombinant virus containing a Trp229Phe or a Trp229Tyr mutation in its RT. Previous studies already established the very low DNA polymerase activities of both the Trp229Phe and the Trp229Tyr mutant RT enzymes. We were able to obtain a Trp229Tyr but not a Trp229Phe mutant virus. However, in addition to the Trp229Tyr mutation this mutant virus also contained an Ile63Met, a Val189Ile, and a Glu396Gly mutation in its RT. When we evaluated the quadruple mutant virus for sensitivity/resistance against a variety of NNRTIs, no significant difference with the sensitivity/resistance profile of the single Trp229Tyr mutant RT enzyme could be observed. We found that the three additional mutations partly restored the low RNA- and DNA-dependent DNA polymerase activities of the Trp229Tyr mutant enzyme. Kinetic analysis revealed that both template/primer binding and dNTP incorporation are affected by the Trp229Tyr mutation. Our findings demonstrate that a mutation at position 229 is unlikely to occur under NNRTI drug pressure due to the poor catalytic activity of the singly mutated RT and the favorable drug sensitivity profile of the mutated enzyme/viruses in both the absence and the presence of the compensatory mutations. Therefore, amino acid position 229 may be regarded as an excellent amino acid target within the NNRTI pocket for rational drug design
Mutations in the NS3 Gene and 3′-NCR of Japanese Encephalitis Virus Isolated from an Unconventional Ecosystem and Implications for Natural Attenuation of the Virus

AbstractThe T1P1 strain of Japanese encephalitis (JE) virus was recently isolated from paddy-free Liu-Chiu Islet in which natural JE antibody has been prevalent. In mouse neuroblastoma-derived Neuro-2a cells, T1P1 appeared significantly lower in virus productivity than another local isolate, CH1392. It implied that this new isolate possesses a characteristic viral replication pattern other than that of CH1392. T1P1 has also shown lower neurovirulence, which was reflected by a significantly higher LD50 (2.44 × 106 PFU) than CH1392 (2.87 × 102 PFU). In comparison of the full-length RNA sequences between T1P1 and CH1392, a total of 7 nucleotides, including 1 in preM/M and 2 each in NS3, NS5, and the 3′-end noncoding region (NCR), appeared different. Of them, only the changes in NS3 (position 325, T for CH1392, A for T1P1; and position 364, G for CH1392 and A for T1P1) resulted in substitutions of deduced amino acids. There were two additional nucleotide changes appearing in the 3′-NCR. The amino acids 109 Phe and 122 Glu in NS3 of CH1392 were substituted by Ile and Lys, respectively, in T1P1. The unique growth properties and low virulence of T1P1 presented in this report were likely related to abnormal enzymatic activity due to mutations of the NS3 gene (especially position 364) and possibly to the mutations in the 3′-NCR. The natural attenuation of T1P1 that has been circulating in paddy-free Liu-Chiu Islet may account for the absence of clinical JE cases in past years
A 10-kDa Structural Protein of Porcine Reproductive and Respiratory Syndrome Virus Encoded by ORF2b

AbstractThe major structural proteins of porcine reproductive and respiratory syndrome virus (PRRSV) are derived from ORFs 5, 6, and 7. Western blots of sucrose gradient-purified virions and PRRSV-infected MARC-145 cells, probed with immune pig serum, showed the presence of an additional 10-kDa protein. Nucleotide sequence analysis of North American PRRSV isolate SDSU-23983 revealed a small ORF within ORF2, named ORF2b, which, when translated, produced a 73-amino-acid nonglycosylated protein. Recombinant 2b protein expressed by a baculovirus clone, AcVR2, comigrated with the 10-kDa virus-associated protein. The loss of 10-kDa protein immunoreactivity after absorption of immune sera with lysates from AcVR2-infected insect cells demonstrated that the 2b and 10-kDa proteins are immunologically similar. Immunoblots were also used for the detection of anti-2b activity in serum samples from experimentally infected adult pigs. Antibodies against PRRSV were apparent by 14 days postinfection, followed by anti-2b activity and serum neutralizing activity. The putative ORF2b start codon is only 6 nucleotides downstream of the adenine of the ORF2a start codon. The expression of ORF2a and 2b as enhanced green fluorescent fusion proteins showed that both proteins were translated; however, the ORF2b was preferentially expressed. These results suggest that the 2b protein is virion associated and the principal product of ORF2
Hepatitis B Virus X Protein Interferes with Cell Viability through Interaction with the p127-kDa UV-Damaged DNA-Binding Protein

AbstractThe hepatitis B virus X protein (HBx) is essential for establishing natural viral infection and has been implicated in the development of liver cancer associated with chronic infection. The basis for HBx function in either process is not understood. In cell culture, HBx exhibits pleiotropic activities affecting transcription, DNA repair, cell growth, and apoptotic cell death. Numerous cellular proteins including the p127-kDa subunit of UV-damaged DNA-binding activity have been reported to interact with HBx but the functional significance of these interactions remains unclear. Here we show that the binding of HBx to p127 interferes with cell viability. Mutational analysis reveals that HBx contacts p127 via a region to which no function has been assigned previously. An HBx variant bearing a single-charge reversal substitution within this region loses p127 binding and concomitant cytotoxicity. This mutant regains activity when directly fused to p127. These studies confirm that p127 is an important cellular target of HBx, and they indicate that HBx does not exert its effect by sequestering p127, and thereby preventing its normal function, but instead by conferring to p127 a deleterious activity