pinecone/core-2020-05-10-deduplication huggingface dataset:
Self-Cleaving Circular RNA Associated with Rice Yellow Mottle Virus Is the Smallest Viroid-like RNA

AbstractWe report the sequence, structural features, and self-cleaving activity of the small circular RNA (sc-RNA) associated with rice yellow mottle sobemovirus (RYMV). At 220 nucleotides, the RYMV sc-RNA represents the smallest naturally occurring viroid-like RNA currently documented in the literature. It is similar to other circular satellite RNAs (sat-RNAs) and viroids in being G-C-rich with a high level of self-complementarity. The predicted native structure is essentially a rod with one branched terminus. A region of the RYMV sc-RNA, constituting 24% of the sequence, exhibits 89% identity to the sat-RNA associated with the Australasian isolates of lucerne transient streak sobemovirus. This region is also structurally similar in all three RNAs in that it forms the left terminus of each rod. Dimeric runoff transcripts of cloned RYMV sc-RNA undergo efficient autocatalyticin vitrocleavage in the (+) but not the (−) polarity. Analysis of the (+) sequence indicates the presence of a hammerhead ribozyme resembling that of carnation small retroviroid-like RNA and the genomic satellite transcript of newt. Inefficient cleavage of (+) monomeric transcripts, and a short stem III in the hammerhead, are features consistent with adouble-hammerhead mode of self-cleavage. The presence of sat-RNA and retroviroid-like structures within a single RNA suggests a possible role for the RYMV sc-RNA as an evolutionary intermediate between these subviral RNAs
UL13 Protein Kinase of Herpes Simplex Virus 1 Complexes with Glycoprotein E and Mediates the Phosphorylation of the Viral Fc Receptor: Glycoproteins E and I

AbstractHerpes simplex virus 1 encodes a Fc receptor consisting of glycoproteins E (gE) and I (gI) and two protein kinases specified by UL13 and US3, respectively. We report the following: (i) Antibody to UL13 formed immune complexes containing gE and gI in addition to UL13 protein. Immune complexes formed by monoclonal antibody to gE, but not those formed by monoclonal antibody to gI, also contained the UL13 protein. This association may reflect direct interaction between gE and UL13 inasmuch as IgG in preimmune rabbit serum and an antiserum made against another viral protein which does not react with the UL13 protein directly also bound gE and UL13. (ii) In cells infected with the wild-type virus, gE formed two sharp bands and a diffuse, slower migrating band. The slower sharp band was undetectable, and the diffuse slower migrating forms of gE were diminished in lysates of cells infected with a mutant virus lacking the UL13 gene (ΔUL13). (iii) Both gE and gI were labeled with32Pi in cells infected with wild-type or the ΔUL13 virus, but the labeling was significantly stronger in cells infected with the wild-type virus than in those infected with the ΔUL13 virus. (iv) In anin vitroprotein kinase assay, UL13 immunoprecipitated from cells infected with wild-type virus labeled gE in the presence of [γ-32P]ATP. This activity was absent in precipitates from cells infected with ΔUL13 virus. The labeled gE comigrated with the slower, sharp band of gE. (v) gI present in the UL13 immune complex was also phosphorylated in thein vitrokinase assay. (vi) The cytoplasmic domain of gE contains recognition sequences for phosphorylation by casein kinase II (CKII). Exogenous CKII phosphorylated gE in immune complexes from lysates of cells infected with the ΔUL13 mutant or in immune complexes from lysates of cells infected with wild-type virus that had been heated to inactivate all endogenous kinase activity including that of UL13. In both instances, CKII phosphorylated gE in both the slow and fast migrating sharp bands. We conclude that UL13 physically associates with gE and mediates the phosphorylation of gE and gI. UL13 may also be a determinant in posttranslational processing of gE
Interferon Treatment Inhibits the Replication of Simian Immunodeficiency Virus at an Early Stage: Evidence for a Block between Attachment and Reverse Transcription

AbstractInterferon (IFN) dramatically reduces both SIV and HIV-1 replicationin vitro. However, we previously found that whereas IFN treatment of SIV-infected cells results in a decrease in the level of viral RNA, IFN treatment of HIV-1-infected cells has no effect on viral RNA expression but rather leads to a decrease in viral protein stability and a deregulation of polyprotein processing (M. B. Agy, R. L. Acker, C. H. Sherbert, and M.G. Katze,Virology214, 379–386, 1995). To more closely define the stage of SIV replication adversely affected by IFN, we used several approaches, including PCR amplification, to examine the effects of IFN on viral DNA synthesis and integration in MT4 and 174 × CEM cells synchronously infected with SIV. Unexpectedly, we found that IFN blocked the synthesis of viral DNA in SIV-infected cells but appeared to have no effect on HIV-1 DNA synthesis. Using a p27 ELISA, we demonstrated that IFN had no effect on the attachment of SIV to MT4 cells. Thus, our results indicate that IFN blocks an early stage of SIV replication, at a step between attachment and reverse transcription. To our knowledge this is the first report to examine the effects of IFN on discrete stages of the SIV life cycle
The Intracellular Expression Pattern of the Human Papillomavirus Type 11 E1∧E4 Protein Correlates with Its Ability to Self Associate

AbstractThe function of the human papillomavirus type 11 (HPV 11) E1∧E4 spliced protein is not known. E1∧E4 protein in HPV-infected tissue is detected in the cytoplasm of differentiated epithelial cells and as immunoreactive bands corresponding to potential monomers, dimers and trimers in immunoblots. The yeast two-hybrid system was employed to test for self association of the HPV 11 E1∧E4 protein. To confirm the results of the yeast two-hybrid experiments, coimmunofluorescence studies of a green fluorescent fusion protein (GFP-E1∧E4) and a T7 epitope-tagged E1∧E4 protein were performed in C33a keratinocytes. E1∧E4 protein was shown to self associate in the yeast two-hybrid system, and this result was confirmed by colocalization of GFP-E1∧E4 and T7-E1∧E4 proteins in keratinocytes. Analysis of E1∧E4 mutants established that the C-terminus was required for self association and that sequences in the N-terminus influenced the intracellular localization of E1∧E4 protein. The intracellular expression patterns of GFP-E1∧E4 and GFP-E1∧E4 mutants were correlated with E1∧E4 binding in the yeast two-hybrid system. Those E1∧E4 mutants that did not self associate in the yeast two-hybrid system were detected as diffuse cellular fluorescence when expressed as GFP fusions. In contrast, GFP-E1∧E4 was detected as a perinuclear aggregate. All E1∧E4 mutants capable of associating with E1∧E4 in the yeast two-hybrid system were detected as aggregates when expressed as GFP fusion proteins in keratinocytes
Infectivity Enhancement by HIV-1 Nef Is Dependent on the Pathway of Virus Entry: Implications for HIV-Based Gene Transfer Systems

AbstractRetroviruses have been extensively used in the development of gene transfer systems. Recently, there has been a great deal of interest in the use of lentiviruses for gene transfer because they infect nondividing cells. Human immunodeficiency virus (HIV) has been the lentivirus most often used for this purpose, but its genomic complexity and limited tropism present some challenges to the establishment of efficient gene transfer systems. In this paper we present data showing intrinsic differences between the infectivity of wild-type HIV and HIV particles pseudotyped with heterologous envelope glycoproteins. Interestingly, HIV pseudotypes with envelope glycoproteins from the amphotropic murine leukemia virus or the vesicular stomatitis virus (VSV) are 3 and 40 times more infectious than wild-type HIV, respectively. In addition, we show that the reliance on Nef expression for maximal infectivity of HIV particles is dependent on the path of virus entry. The dependence on Nef for higher infectivity is greater for amphotropic pseudotypes and wild-type HIV than for VSV-G pseudotypes. We conclude that VSV-G pseudotypes of HIV vectors are an excellent choice for gene transfer purposes and Nef-mediated viral infectivity enhancement is affected by virus entry pathway
A Single Conserved Amino Acid in the Coat Protein Gene of Pea Seed-Borne Mosaic Potyvirus Modulates the Ability of the Virus to Move Systemically inChenopodium quinoa

AbstractTwo isolates of pea seed-borne mosaic potyvirus, DPD1 and NY, which both infect pea (Pisum sativum) systemically, differ in their ability to move long distance inChenopodium quinoa.DPD1 spreads to uninoculated leaves, whereas NY is restricted to the inoculated leaves. The NY isolate was found to move from cell to cell infecting all parts of the inoculated leaves, including the petiole. The coat protein (CP) coding region was identified as the determinant of long-distance movement. Virus chimeras containing the CP coding sequence of NY were restricted to inoculated leaves, whereas chimeras containing the CP coding sequence of DPD1 infectedC. quinoasystemically. Mutational analysis of the CP demonstrated that changing the serine at position 47 of the NY CP to proline was sufficient to permit systemic spread of the NY(S47P) mutant. The reverse mutant, DPD1(P47S), in which the proline at position 47 of the CP was changed to serine, was restricted to inoculated leaves. The movement characteristics and CP sequences of 10 additional PSbMV isolates were determined. All isolates caused systemic infection in pea. InC. quinoa6 of the isolates that were restricted to inoculated leaves had a serine at position 47. Two isolates that infectedC. quinoasystemically had a proline at position 47. Two isolates, S6 and NEP-1, infectedC. quinoasystemically, but had a serine at position 47 of the CP. This shows that although a proline/serine difference at position 47 of the CP determined systemic spread of the isolates DPD1 and NY, this amino acid alone does not govern the spread of PSbMV inC. quinoa
Human T-Cell Leukemia Virus Type 1 Tax Protein Induces the Expression of Lymphocyte Chemoattractant SDF-1/PBSF

AbstractWe investigated the mechanism of lymphocyte infiltration into tissues infected with human T-cell leukemia virus type 1 (HTLV-1). The cytokine SDF-1/PBSF is a highly efficient chemoattractant for lymphocytes. Reverse transcription–PCR analysis showed that among various human T-cell lines, those infected with HTLV-1 selectively expressed theSDF-1gene. Expression of the viral protein Tax in a human T-cell line induced the expression of theSDF-1gene, indicating that the constitutive expression ofSDF-1in virus-infected cell lines is at least in part mediated by Tax. HTLV-1-infected T-cell lines also expressed CXCR-4, a receptor for SDF-1. Moreover, chemotaxis assay showed that a HTLV-1-infected cell line migrated toward synthetic SDF-1. Thus, HTLV-1-infected cells are themselves responders for SDF-1. Our results suggest that SDF-1 induced by Tax may alter the distribution of HTLV-1-infected cellsin vivo;hence it may contribute to their infiltration into affected tissues in HTLV-1-associated inflammatory diseases
Murine Cytomegalovirus Infection Inhibits IFNγ-Induced MHC Class II Expression on Macrophages: The Role of Type I Interferon

AbstractMacrophage (Mφ) activation, as measured by cell surface expression of MHC class II, was examined during infection of immunocompetent and immunocompromised mice with murine cytomegalovirus (MCMV). Intraperitoneal infection of CB17 SCID mice with 106PFU of MCMV elicited a large population of Mφ which expressed low levels of MHC class II. This was surprising since infection of SCID mice with lower doses (e.g., 104PFU) of MCMV elicits Mφ expressing high levels of MHC class II (M. T. Heise and H. W. Virgin,J. Virol.(1995) 69, 904–909).In vivoadministration of recombinant mouse IFNγ resulted in high levels of MHC class II expression on Mφ from control but not MCMV-infected SCID mice, suggesting that MCMV infection generates a state in which IFNγ is not effective at activating Mφ. The effect of MCMV infection was MHC class II specific, since MHC class I and ICAM-1 levels were increased on Mφ expressing low levels of MHC class II. Interference with IFNγ action was not due to productive or abortive infection of Mφ. This suggested that MCMV infection induces a soluble factor that alters Mφ responsiveness to IFNγ. Infection of SCID mice with 106PFU of MCMV induced higher levels of serum IFNαβ (one candidate for inhibition of IFNγ induction of MHC class II expression) than infection with 104PFU. We therefore evaluated the role of MCMV-induced IFNαβ on IFNγ responses of bone marrow-derived (BMMφ) or thioglycollate-elicited Mφin vitro.Infection of normal Mφ with MCMV at a low m.o.i. (0.1 to 0.2) impaired IFNγ-mediated induction of Mφ MHC class II expression, but not MHC class I expression. Inhibition of IFNγ responses was not observed in Mφ from mice with a null mutation in the IFNαβ receptor (IFNαβR−/−). To test thein vivorelevance of virus-induced IFNαβ to IFNγ-mediated responses, the kinetics of MHC class II induction during MCMV infection of IFNαβR−/− mice was evaluated. MCMV-infected IFNαβR−/− mice mounted an earlier Mφ MHC class II response than normal mice. We conclude that MCMV infection specifically impairs IFNγ-mediated MHC class II expression on Mφ and that induction of IFNαβ is one mechanism by which this inhibition occurs
Evidence for a Continued Requirement for CD40/CD40 Ligand (CD154) Interactions in the Progression of LP-BM5 Retrovirus-Induced Murine AIDS

AbstractIn genetically susceptible C57BL/6 mice the LP-BM5 isolate of murine retroviruses causes profound splenomegaly, lymphadenopathy, hypergammaglobulinemia, and an immunodeficiency syndrome bearing many similarities to the pathologies seen in AIDS. Because of these similarities, which also include terminal B cell lymphoma formation, this syndrome has been called murine AIDS or MAIDS. Prompted by previous reports showing that the onset of MAIDS is dependent on the presence of both CD4+T and B cells, we have previously shown that anti-gp39/CD40 ligand mAb (anti-CD40L mAb) treatment of LP-BM5-infected mice is effective in inhibiting the induction of MAIDS when a short course of anti-CD40L mAb treatment was started on the same day as LP-BM5 administration. The success of anti-CD40L mAb therapy, as indicated by a much reduced degree of splenomegaly, hypergammaglobulinemia, and mitogen and allogeneic CTL unresponsiveness, demonstrated that CD40L/CD40 interactions were critical to the establishment of MAIDS. Here we extend these findings through the use of delayed anti-CD40L mAb treatment of mice, beginning 3–4 weeks after LP-BM5 infection, by showing that interruption of CD40L/CD40 interactions also interferes with the progression of MAIDS. About 60% of LP-BM5-preinfected mice were affected by delayed anti-CD40L mAb treatment, with substantially reduced spleen weights and serum hypergammaglobulinemia and normal or greatly restored proliferative responses to Con A stimulation and CTL responses to allogeneic stimulation. The other LP-BM5-infected mice that did not respond to anti-CD40L therapy were found to have made antibodies to the anti-CD40L mAb. Thus, in a majority of mice anti-CD40L mAb therapy was very effective in interfering with MAIDS pathogenesis well after the establishment of the virus infection and MAIDS symptomatology, indicating that CD40L/CD40 interactions are crucial to the maintenance and progression of the disease, as well as its initiation
Temporal Expression of the AcMNPVlef-4Gene and Subcellular Localization of the Protein

AbstractAutographa californicanucleopolyhedrovirus (AcMNPV)lef-4gene [ORF 90; Ayreset al.(1994)Virology202, 586–605] is involved in both late and very late gene expression [Passarelli and Miller (1993)Virology197, 704–714]. The transcriptional properties of this gene have been analyzed. It is transcribed as a single 1.6-kb mRNA and transcripts were first detected 3 h postinfection (pi). The extremities of the transcript have been mapped by primer extension and 3′ RACE–PCR to positions −56 from the translation start codon and +96 downstream of the stop codon. A rabbit polyclonal antiserum has been raised against an internal polypeptide of LEF-4. A 55-kDa protein was observed by Western blot analysis from 5 h pi. LEF-4 localizes preferentially in the nucleus of infected cells and is associated with the virogenic stroma
Conservation of the Architecture of the Golgi Apparatus Related to a Differential Organization of Microtubules in Polykaryocytes Induced bysyn−Mutants of Herpes Simplex Virus 1

AbstractInfection of Vero and HEp-2 but not of 143TK−cells with herpes simplex virus 1 results in fragmentation and dispersal of the Golgi apparatus. Concurrently, in all three infected cell lines the microtubular network is disrupted, suggesting that the disruption of microtubules is essential but not sufficient to induce the fragmentation of the Golgi apparatus. We now report the following: (i) In polykaryocytes formed in Vero cells infected with HSV-1syn−mutant viruses, intact Golgi stacks were readily detected by electron microscopy. These aggregated in the center of large polykaryocytes. (ii) The distribution of viral glycoprotein D, examined in both fixed and nonfixed cells, appeared to match the distribution of the Golgi stacks, suggesting that the aggregated Golgi stacks funnel viral glycoproteins and viral particles to a limited region of the plasma membrane of the polykaryocytes rather than directing exocytic flow in a more dispersed fashion as seen insyn+virus-infected cells exhibiting fragmented and dispersed Golgi. (iii) In most polykaryocytes, the microtubules formed parallel bundles extending along the axis of recruitment of new cells. (iv) Fragmentation of the microtubules at the periphery of the cell near the plasma membrane was observed in untreated or cycloheximide-treated cells 2 h after infection withsyn−virus HSV-1(MP) orsyn+HSV-1(mP) but not in mock-infected cells. These observations suggest that peripheral depolymerization is initiated at the time of infection and that a factor which determines thesyn−orsyn+phenotype is whether the microtubular network regenerates concomitant with cell fusion or reorganizes to form a collapsed network surrounding nuclei ofsyn+infected cells
Functional Significance of Three Basic N-Terminal Amino Acids of Alfalfa Mosaic Virus Coat Protein

AbstractInfection of tobacco protoplasts with mutant alfalfa mosaic virus (AMV) RNAs indicated that three basic amino acids in the N-terminus of AMV coat protein are important for the biological activity of the coat protein in the beginning of infection. Substitution of alanines for lysines at position 14 or 17 in the coat protein resulted in a 5- or 10-fold reduction in the activity of the protein, respectively. However, substitution of alanine for arginine at position 18 entirely abolished activity. Arginine 18 was also required for the coat protein to bind to the 3′ noncoding region of the virus RNAin vitro, whereas lysine 14 or 17 was not required. Thus, these results indicate that arginine 18 is essential for the activity of the coat protein in early infection and that binding of the coat protein to AMV RNA correlates with activity
Distinct Regions of EBV DNase Are Required for Nuclease and DNA Binding Activities

AbstractEpstein-Barr virus (EBV) DNase possesses both endonuclease and exonuclease activities and accepts both double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) as substrates. To map regions of EBV DNase responsible for nuclease and DNA binding activities, a series of mutant DNase polypeptides was expressed using a bacterial system for the nuclease assay and in anin vitrotranscription/translation system to assay binding activity to dsDNA or ssDNA cellulose. The results indicated that the C-terminus of EBV DNase, residues 450–460, is essential for nuclease activity but dispensable for DNA binding. However, deletion of residues 441–470 resulted in the loss of both nuclease and DNA binding activities. Substitution of Phe452 and Val458 led to inactive enzymes. In the N-terminus, deletion of residues 23–28 and residues 7–61 resulted in the loss of nuclease activity but the DNA binding activities of the deleted enzymes were intermediate and low, respectively. Mutation of Leu23 to Gly showed drastically reduced nuclease activity but its DNA binding ability was not affected. Based on the amino acid sequence alignment of various herpesvirus DNases, we chose four highly conserved and two less well conserved regions as controls for mutagenesis studies. These six internal deletion (ID) mutants were prepared using a recombinant PCR method. Each of the polypeptides was expressed in a bacterial system for the nuclease assay and using anin vitrotranscription/translation system for the DNA binding assay. DNA binding and nuclease activities of all six internal deletion mutants were abolished, except that mutant ID2, with deletion of residues 138–152, retained an intermediate ability to bind DNA. These data indicate that since mutations at distinct regions within EBV DNase resulted in the loss of nuclease and/or DNA binding activities, it is suggested that these distinct regions are required for maintenance of an intact and highly ordered structure(s) for both activities
The Genomic Sequence of Defective Interfering Semliki Forest Virus (SFV) Determines Its Ability to Be Replicated in Mouse Brain and to Protect against a Lethal SFV Infectionin Vivo

AbstractWe have recently cloned and sequenced two genomes of defective interfering (DI) Semliki Forest virus (SFV), DI-6 (2146 nt), and DI-19 (1244 nt). These are similar in that both contain two large central deletions (encompassing the 5′ part of the nsP1 gene and the 3′ part of the nsP2 gene and all of the structural genes), and all the sequence of the latter is represented in the genome of SFV DI-6. RNA was transcribed from both and transfected into SFV-infected BHK-21 cells. RT–PCR analysis of tissue culture fluid harvested 18 h after transfection suggested that SFV DI virions had been rescued from the cloned genomes. Unlike the genomes of noncloned DI SFV, these genomes bred true for at least 7 serial passages. Cloned DI-6 and DI-19 viruses interfered to a similar extent with the multiplication of SFV in cultured cells, but only DI-19 protected mice from a lethal intranasal dose of SFV. Further investigation by RT–PCR analysis showed that DI-19 but not DI-6 genomes were replicated in mouse brain after direct intracerebral injection of DI virus together with an excess of infectious helper SFV. Thus the replication and hence antiviral activity of two closely related DI SFV genomes appears to be exquisitely sequence specific and cell specific. These findings mark a significant step on the way to using DI genomes as antivirals and also may explain why so few animal-protecting DI viruses have been identified