pinecone/core-2020-05-10-deduplication huggingface dataset:
HERV-H Endogenous Retroviruses: Presence in the New World Branch but Amplification in the Old World Primate Lineage

AbstractThe evolutionary origin and age of the HERV-H family of human endogenous retrovirus-like sequences was investigated in this study. HERV-H elements exist in approximately 900 partially deleted copies and 50–100 more intact forms in humans and Old World monkeys. However, their possible presence in more divergent species is unknown. We have isolated a 1.6-kb genomic DNA segment from the New World monkey marmoset that had been PCR amplified using human HERV-H primers. DNA and protein comparisons and database searches indicate that this marmoset clone is more closely related to human HERV-H elements than to any other sequence, indicating that HERV-H-related sequences do exist in New World monkeys. In contrast to the high copy numbers of deleted elements in Old World primates, Southern blot analysis shows that such elements are present in less than 50 copies in two different species of New World monkey. To estimate evolutionary ages of the common deleted form of the element, a selected DNA segment from thepolregion was compared from multiple human HERV-H elements. This comparison suggests that many HERV-H elements of the abundant deleted subfamily integrated approximately 30–35 million years ago. Very similar percentage divergence values between 5′ and 3′ long terminal repeats of individual elements of the deleted subfamily also suggest that these elements are close in age. These results indicate that HERV-H elements first appeared in the germline prior to the New World/Old World divergence over 40 million years ago. Interestingly, they remained in low numbers in the New World branch while a subfamily underwent a major amplification in Old World primates before the time of divergence of hominoids from Old World monkeys
Phosphorylation of Ser232Directly Regulates the Transcriptional Activity of the P Protein of Human Respiratory Syncytial Virus: Phosphorylation of Ser237May Play an Accessory Role

AbstractThe phosphoprotein P of human respiratory syncytial virus (RSV) was expressed in eukaryotic cells in phosphorylated form. Site-directed mutagenesis of the recombinant protein established Ser232as the major site of phosphorylationin vivo.Phosphorylation of bacterially made P proteinin vitroby purified casein kinase II (CKII) resulted in the phosphorylation of Ser237, whereas mainly Ser232was phosphorylated by a crude cell extract. The P kinase activity in the cell extract exhibited properties characteristic of CKII. While the Ser232,237to Ala double mutant was nearly completely defective for phosphorylation and transcription, phosphorylation at Ser232, through the use of appropriate P mutant or kinase, activated P protein. Phosphorylation of Ser237restored activity only to the extent it facilitated phosphorylation of Ser232. Phosphate groups of P protein in RSV-infected cells were highly stable; inhibitors of protein serine phosphatases had no effect on the intracellular turn-over of the phosphates. Highly purified viral polymerase L was transcriptionally active but devoid of P protein kinase activity. Thus, CKII-mediated phosphorylation of Ser232appears to be the primary regulator of P protein activity while phosphorylation of Ser237may be involved in a modulatory role under certain conditions
HIV-1 Tat Directly Interacts with the Interferon-Induced, Double-Stranded RNA-Dependent Kinase, PKR

AbstractWe present evidence that the HIV-1 Tat protein and the RNA-dependent cellular protein kinase, PKR, interact with each other bothin vitroandin vivo.Using GST fusion chromatography, we demonstrate that PKR, interacts directly with the HIV-1 Tat protein. The region in Tat sufficient for binding PKR maps within amino acids 20 to 72. Inin vitroassays, the two-exon form of Tat (Tat 86) was phosphorylated by PKR, while the one exon form of Tat (Tat 72) inhibited PKR autophosphorylation and substrate phosphorylation. The ability of Tat to interact with PKR was demonstrated in both yeast and mammalian cells. Expression of PKR in yeast results in a growth suppressor phenotype which was reversed by coexpression of a one exon form of Tat. Expression of Tat 72 in HeLa cells resulted in direct interaction with PKR as detected by coimmunprecipitation with a Tat antibody. Tat and PKR also form a coimmunoprecipitable complex in cell-free extracts prepared from productively infected T lymphocytes. The interaction of Tat with PKR provides a potential mechanism by which HIV could suppress the interferon system
Tomato Bushy Stunt Virus Spread Is Regulated by Two Nested Genes That Function in Cell-to-Cell Movement and Host-Dependent Systemic Invasion

AbstractWe have investigated the importance of two small nested genes (p19 and p22) located near the 3′ end of the genome of tomato bushy stunt virus (TBSV) for infectivity in several hosts. Our results show that both genes are dispensable for replication and transcription and that the p19 gene encodes a soluble protein, whereas the p22 gene specifies a membrane-associated protein. Assays using TBSV derivatives that have the β-glucuronidase gene substituted for the capsid protein gene demonstrate that p22 is required for cell-to-cell movement in all plants tested. Mutations inactivating p19 ameliorate the severe necrotic systemic symptoms elicited by wild-type TBSV inNicotiana benthamianaandNicotiana clevelandii,but p19 does not obviously affect movement in these hosts. However, in some local lesion hosts p19 influences the lesion diameter, which suggests that it has an auxiliary host-dependent role in movement. This notion is supported by the observation that p19 is required for long-distance spread of TBSV in spinach and for systemic infection of pepper plants. Thus, movement of TBSV is regulated by two nested genes; p22 governs cell-to-cell movement and p19 has a host-specific role in systemic invasion
Analysis of Trafficking of Rev and Transdominant Rev Proteins in Living Cells Using Green Fluorescent Protein Fusions: Transdominant Rev Blocks the Export of Rev from the Nucleus to the Cytoplasm1

AbstractExpression ofgag/polandenvgenes of human immunodeficiency virus requires the viral Rev protein. Mutant Rev proteins, displaying a transdominant phenotype (TDRev), were shown to inhibit Rev function. To investigate the underlying mechanism of this inhibition, the green fluorescent protein (GFP) ofAequorea victoriawas fused to Rev and TDRev, which allowed the study of their trafficking and interactions in living human cells. Both Rev-GFP and TDRev-GFP were shown to retain appropriate nucleolar localization and function. Upon actinomycin D treatment, Rev-GFP was transported to the cytoplasm within 1.5 hr, while TDRev, although partially dissociated from the nucleolus, was retained in the nucleus. Coexpression of Rev-GFP and TDRev in the same cell demonstrated that TDRev inhibited the transport of Rev-GFP from the nucleus to the cytoplasm. This inhibition was specific for Rev, since the export of the functionally analogous Rex protein of the human T-cell leukemia virus type I was not inhibited by TDRev. These results indicate that Rev and TDRev form heteromultimers in the nucleolus and that this interaction prevents Rev's export from the nucleus to the cytoplasm. In addition to providing a model for the function of TDRev, these results also demonstrate the successful application of protein fusions to GFP to study localization and trafficking of proteins in living mammalian cells
HIV-1 Mediates Rapid Apoptosis of Lymphocytes from Human CD4 Transgenic but Not Normal Rabbits

AbstractNormal rabbit lymphocytes can be infected with HIV-1 although infection is much less efficient than in human lymphocytes. When peripheral blood mononuclear cells (PBMC) from rabbits transgenic for human CD4 (HuCD4) were exposed to HIV-1, enhanced infection and a rapid depletion of lymphocytes were observed. Cell death in the infected cultures occurred via apoptosis, but no similar effect was seen in nontransgenic rabbit PBMC cultures. Induction of apoptosis in HuCD4-expressing cells required virus replication; heat-inactivated virus or recombinant viral proteins had no effect on cell viability. Expression of the Fas antigen was increased in HIV-1-infected CD4+rabbit lymphocytes. Characterization of the infected PBMC cultures revealed that apoptosis occurs both in HuCD4+and HuCD4−cells, indicating that bystander cells are killed. These data define a requirement for HuCD4 in initiation, but not the spread, of HIV-1-induced apoptosis in rabbit PBMC and provide a model to probe mechanisms leading to lymphocyte depletion in HIV-1 infection
Differential Subcellular Localization of Hepatitis C Virus Core Gene Products

AbstractThe expression of the core gene of two different hepatitis C virus (HCV) isolates was analyzed. In the presence of its downstream E1 envelope protein sequence, two major core protein products with molecular masses of 21 kDa (P21) and 19 kDa (P19) and a minor protein product with molecular mass of 16 kDa (P16) were detected. In the absence of its downstream E1 envelope protein sequence, P21 and P19 remained the major protein products expressed from the core gene of the HCV-RH isolate, whereas P16 became the major protein product of the core gene of the HCV-1 isolate. Analysis of the amino-terminal sequences of P21 and P16 expressed inEscherichia colirevealed that P21 and P16 were co-amino terminal. Deletion-mapping analysis indicated that P16 lacked the carboxy-terminal sequence of P21. Immunofluorescence analysis of the subcellular localization of different HCV core proteins indicated that P21 and P19 displayed a reticular and punctate staining pattern typical of endoplasmic reticulum-associated proteins, while P16 was localized to the nucleus. The distinct subcellular localization of P16 raises the possibility that P16 may have a biological function very different from those of P21 and P19
Kinetic and Functional Mapping of Viral Epitopes Using Biosensor Technology

AbstractSome monoclonal antibodies (Mabs) that react with the extremity of the tobacco mosaic virus (TMV) particle containing the 5′ end of the RNA are able to block the disassembly of TMV by ribosomes while others are totally devoid of such activity. No correlation could be established between the binding kinetics and affinity of the Mabs and their inhibitory capacity. An epitope map of the Mab binding sites was constructed on the basis of kinetic two-site binding assays with the viral monomeric protein (TMVP) performed using biosensor technology (BIAcore). Mabs possessing inhibitory activity were found to bind to the part of the TMVP surface closest to the central axis in the polymerized particle. As this part of the subunit is known to interact with the viral RNA, it seems that inhibitory Mabs act by sterically preventing the interaction between virus and ribosomes. This study illustrates the advantages of the biosensor technology for locating conformational epitopes in viral proteins
Expression of Tobacco Ringspot Virus Capsid Protein and Satellite RNA in Insect Cells and Three-Dimensional Structure of Tobacco Ringspot Virus-like Particles

AbstractThe capsid protein gene of tobacco ringspot virus (TobRV), which had been modified to contain an amino-terminal methionine codon, was ligated into a baculovirus transfer vector downstream from the polyhedrin promoter. The resulting plasmid was cotransfected with linearized baculovirus DNA into insect cells. Recombinant baculovirus expressed high levels of the TobRV capsid protein that assembled to form virus-like particles that were similar in size and shape to authentic TobRV capsids. These virus-like particles did not encapsidate any RNA, including the capsid protein mRNA. The capsid protein mRNA is a truncated RNA 2, which may lack a putative encapsidation signal. To determine whether an intact packaging substrate could be encapsidated by the TobRV capsid protein, another recombinant baculovirus, concomitantly expressing both capsid protein and TobRV satellite RNA, was constructed. Surprisingly, the vast majority of the satellite RNA molecules expressed from this recombinant baculovirus were ligated in the insect cells to form circular RNA molecules. Like circular forms of satellite RNA generatedin planta,these circular satellite molecules remained unencapsidated by the TobRV capsid protein. Computer-generated three-dimensional reconstruction using electron cryomicrographs of the empty virus-like particles allowed the first structural analyses of any nepovirus capsid. This 22-Å resolution reconstruction resembled capsids of other members of the picornavirus superfamily. These data support the hypothesis that the nepovirus capsid is structurally analogous to those of the como- and picornaviruses
Activation of Astrocytes in the Spinal Cord of Mice Chronically Infected with a Neurotropic Coronavirus

AbstractMice infected with the neurotropic JHM strain of mouse hepatitis virus (MHV-JHM) develop a demyelinating encephalomyelitis several weeks after infection. Astrogliosis and infiltration of inflammatory cells are prominent findings in the brains and spinal cords of infected mice. In this report, astrocytes in infected spinal cords were analyzed for expression of three pleiotropic cytokines, TNF-α, IL-1β, and IL-6; Type 2 nitric oxide synthase (iNOS); and MHC class I and II antigen. The data show that all three cytokines and iNOS are expressed by astrocytes in chronically infected spinal cords. These activated astrocytes are localized to areas of virus infection and demyelination, although most of the astrocytes expressing these proteins are not MHV-infected. MHC class I and II antigen can be detected in these spinal cords as well, but not in cells with the typical morphology of astrocytes. TNF-α, IL-6, and iNOS are also evident in the brains of mice with MHV-induced acute encephalitis, but in marked contrast to the results obtained with the chronically infected mice, most of the cells expressing these cytokines or iNOS had the morphology of macrophages or other mononuclear cells and very few appeared to be astrocytes. Additionally, astrocytes and, most likely, oligodendrocytes are infected in the spinal cords of mice with chronic demyelination. These results are consistent with a role for both viral infection of glial cells and high localized levels of proinflammatory cytokines and nitric oxide in the demyelinating process in mice infected with MHV-JHM. They also show that analogously to the human demyelinating disease, multiple sclerosis, astrocytes are a major cellular source for these cytokines in mice with chronic, but not acute disease
Induction of Antibodies Protecting against Transmissible Gastroenteritis Coronavirus (TGEV) by Recombinant Adenovirus Expressing TGEV Spike Protein

AbstractTen recombinant adenoviruses expressing either fragments of 1135, 1587, or 3329 nt or the full-length spike gene of transmissible gastroenteritis coronavirus (TGEV) have been constructed. These recombinants produce S polypeptides with apparent molecular masses of 68, 86, 135, and 200 kDa, respectively. Expression of the recombinant antigen driven by Ad5 promoters was inhibited by the insertion of an exogenous SV-40 promoter. Most of the recombinant antigens remain intracytoplasmic in infected cells. All the recombinant-directed expression products contain functional antigenic sites C and B (Gebaueret al.,1991,Virology183, 225–238). The recombinant antigen of 135 kDa and that of 200 kDa, which represents the whole spike protein, also contain antigenic sites D and A, which have previously been shown to be the major inducers of TGEV-neutralizing antibodies. Interestingly, here we show that recombinant S protein fragments expressing only sites C and B also induced TGEV-neutralizing antibodies. The chimeric Ad5–TGEV recombinants elicited lactogenic immunity in hamsters, including the production of TGEV-neutralizing antibodies. The antisera induced in swine by the Ad5 recombinants expressing the amino-terminal 26% of the spike protein (containing sites C and B) or the full-length spike protein, when mixed with a lethal dose of virus prior to administration to susceptible piglets, delayed or completely prevented the induction of symptoms of disease, respectively
Expression, Purification, and Identification of a Novel Self-Cleavage Site of the NIa C-Terminal 27-kDa Protease of Turnip Mosaic Potyvirus C5

AbstractThe gene encoding the C-terminal protease domain (27 kDa) of the nuclear inclusion protein a of turnip mosaic potyvirus C5 was cloned and expressed as a fusion protein with glutathione S-transferase inEscherichia coliXL1-blue. Two forms of the protease (27 and 25 kDa) were purified from the fusion protein by glutathione affinity chromatography and Mono S chromatography and exhibited the specific proteolytic activity when a synthetic undecapeptide, Glu-Pro-Thr-Val-Tyr-His-Gln-Thr-Leu-Asn-Glu, or anin vitrotranslation product of the polyprotein containing the cleavage site between the nuclear inclusion protein b and the capsid protein, was used as a substrate. The purified proteases showed aKmof 1.15 ± 0.16 mMand aVmaxof 0.74 ± 0.091 μmol/mg/min with the synthetic peptide substrate. The 25-kDa protein was found to be generated by the cleavage between Ser223and Gly224near the C-terminus of the 27-kDa protease and to retain the specific proteolytic activity. The point mutation of Asp81or Cys151, two putative active site residues in the 27-kDa protease, to Asn or Ser, respectively, prevented the generation of the 25-kDa protein and diminished the proteolytic activity of the protease drastically, suggesting that the 27-kDa protease cleaves itself between Ser223and Gly224to generate the 25-kDa protein
Limited Viral Spread and Rapid Immune Response in Lymph Nodes of Macaques Inoculated with Attenuated Simian Immunodeficiency Virus

AbstractA comparative study was undertaken to characterize the very early events that distinguish attenuated and pathogenic simian immunodeficiency virus (SIV) infections. Three rhesus macaques were inoculated with the attenuated SIVmac 251 Δnef virus, and three others with a virus of intermediate phenotype, SIVmac 239 nef stop. They were compared to four macaques inoculated with the pathogenic SIVmac 251 isolate. Lymph nodes (LN) taken between 7 days and 2 months postinoculation were analyzed for SIV expression byin situhybridization. During acute infection, SIV 251 Δnef infected 1 to 1.5 log10fewer cells in LN tissue than the pathogenic SIV 251 isolate. The reduction was more marked in the blood, as SIV 251 Δnef infected 2 to 3 log10fewer PBMC than the isolate and did not yield detectable antigenemia. Morphometric measurements showed that the development of germinal centers (GC) was more rapid in the Δnef infection, which led to a more efficient trapping of viral particles, and could account for antigenemia clearance. The SIV 239 nef stop clone reverted to a nef+genotype at Week 2, but induced a lower viral burden than a directly pathogenic virus. The kinetics of GC development was rapid, indicating that SIV 239 nef stop induced an immune response similar to that seen in attenuated infection. This study provides evidence that attenuated SIV elicits a more rapid immune response than pathogenic SIV and suggests that an early immunosuppressive episode may facilitate the dissemination of pathogenic SIV
Murine Leukemia Virus-Induced Neurodegeneration of Rats: Enhancement of Neuropathogenicity Correlates with Enhanced Viral Tropism for Macrophages, Microglia, and Brain Vascular Cells

AbstractA highly neuropathogenic retrovirus, NT40, was generated by serially passaging an infectious molecular clone of Friend murine leukemia virus, FB29, through F344 Fisher rats. NT40 induced severe neurological signs such as reflex abnormalities and ataxia within 4–6 weeks following neonatal inoculation. FB29 led to only very mild neurological dysfunctions with longer incubation periods. Pathological alterations were characterized by mild (FB29) to extensive (NT40) noninflammatory spongiform degeneration, mainly of brain-stem areas. Infectious center assays revealed that viral titers in brain tissues of NT40-infected rats were 100-fold higher than those of FB29-infected animals. Employing immunohistochemistry,in situhybridization, and flow cytometry, NT40 was found to infect many endothelial cells of brain blood vessels and microglia, whereas FB29 infected only microglia and those to a lower extent. However, when isolated from adult diseased rats, microglial cells turned out in both cases to be nonproductively infected with either FB29 or NT40. Of peripheral organs, we found enhanced levels of NT40 in peritoneal macrophages but not in spleen, thymus, or serum when compared to FB29. Altogether these data suggest that an expanded cellular tropism within the CNS and elevated viral titers in macrophages and microglia correlated with enhancement of neuropathogenicity
Differentiation-Dependent Transcription of the Epidermodysplasia Verruciformis-Associated Human Papillomavirus Type 5 in Benign Lesions

AbstractHuman papillomavirus type 5 (HPV 5) induces cutaneous lesions and persists in skin carcinomas of patients with epidermodysplasia verruciformis (EV). We investigated the expression pattern of HPV 5 in biopsies from benign skin lesions of EV patients by cDNA analysis andin situhybridization. Nine different cDNAs could be generated from total RNA of one of these lesions by reverse transcription and PCR amplification with HPV 5-specific primers. We could identify two major splice donors: one was found in the E6-proximal part of the noncoding region (NCR), and the other just downstream of the first ATG codon of ORF E1. Each of the characterized transcripts was processed at one or the other donor site and the two corresponding leader exons were found in combination with both 3′-early and late exons. Two transcripts appear to be specific for EV-associated papillomaviruses: one species might encode an E1 up angle E2C fusion protein, and the other mRNA (NCR/E2) is probably encoding for the full-length E2 protein. According to the results of the cDNA analysis, riboprobes were designed forin situhybridization experiments to study the cell differentiation-dependent expression of the different exons. Only the E7/E1 and E4 probes led to strong signals almost throughout the epithelium. The signals generated by the 5′-E2 and E1 probe increased with cell differentiation and were mainly confined to the nucleus. The NCR, E6, E7, L2, and L1 probes yielded more or less strong signals in the terminally differentiated epidermal layers. The difference in the cell differentiation-dependent expression of the 5′-early region exon (probe E7/1) and L2/L1 exons may point to a differentiation-dependent processing of transcripts