pinecone/core-2020-05-10-deduplication huggingface dataset:
The Open Reading Frame 2 Product of Cacao Swollen Shoot Badnavirus Is a Nucleic Acid-Binding Protein

AbstractThe function of the open reading frame 2 product (p2) of cacao swollen shoot virus (CSSV) and of other badnaviruses is not yet determined. Their carboxyl-termini are lysine and proline rich and also contain alanine residues, amino acids present at the C-termini of histone-like proteins. Full-length CSSV p2 (132 amino acids) or versions truncated at the C-terminus (128, 113, 103, or 101 amino acids) were expressed inEscherichia coliand partially purified. When assayed in nucleic acid-binding tests, p2 was able to interact with CSSV and other double-stranded DNAs and with CSSV and other single-stranded RNA transcripts in a sequence-nonspecific manner. Moreover, this binding activity was progressively lost as the C-terminus was gradually deleted
Gradual Shutdown of Virus Production Resulting in Latency Is the Norm during the Chronic Phase of Human Immunodeficiency Virus Replication and Differential Rates and Mechanisms of Shutdown Are Determined by Viral Sequences

AbstractMost CD4+lymphocytes in lymph nodes of both asymptomatic HIV-1-infected individuals and AIDS patients are nonproductively or latently infected. It is not clear how these cells come about because infection of resting lymphocytes results in abortive infection and infection of activated lymphocytes results in productive infection. The frequency and mechanisms underlying nonproductive or latent HIV infections of normal CD4+lymphocytes largely remain unexplored, and because HIV latency has principally been studied in latently infected cell clones of established cell lines, it is not even clear how often this type of infection occurs in cell lines. We demonstrate herein that chronic HIV replication in populations of normal phytohemagglutinin-stimulated peripheral blood CD4+-enriched lymphocytes, as well as an established T-cell line (CEM), gradually shuts down in the vast majority of cells. The nonproducing cells in these cultures still harbored HIV provirus, and HIV could be reactivated in CEM cells by treatment with phorbol ester, showing that this was latent infection. Thus, HIV's life cycle should probably be considered as consisting of two phases: an acute exponential rise in production of virus progeny which levels at some peak, followed by a gradual decline of progeny production during the chronic phase leading to viral latency. Temporal analyses of the steady-state levels of viral mRNAs in populations of chronically infected CEM cells as virus production declined revealed the two mechanisms of HIV latency which have previously been described in the OM-10.1 and U1 or ACH-2 latently infected cell clones (i.e., apparent overall shutdown of HIV transcription and “blocked early-stage latency” involving enhanced splicing of viral pre-mRNAs). However, which mechanism was employed, as well as the rate of shutdown, depended on the virus strain
Topically Applied Human Recombinant Monoclonal IgG1Antibody and Its Fab and F(ab′)2Fragments Protect Mice from Vaginal Transmission of HSV-2

AbstractA recombinant human anti-herpes simplex virus monoclonal IgG1antibody and the corresponding Fab and F(ab′)2fragments were tested for efficacy in preventing vaginal transmission of HSV-2 infection in a well-established mouse model for genital herpes. IgG1, Fab, and F(ab′)2were approximately equally protective; vaginal delivery of 1–5 ng provided approximately 50% protection, and vaginal delivery of 400 ng completely protected mice from genital herpes infection (P< 0.001). These results suggest that topical applications of human monoclonal antibodies may be useful in developing new methods for preventing sexually transmitted disease
Calnexin Associates with the Precursors of Glycoproteins B, C, and D of Herpes Simplex Virus Type 1

AbstractBy a pulse-chase approach combined with immunoprecipitation, we showed that the newly synthesized precursors of glycoprotein B (gB), glycoprotein C (gC), and glycoprotein D (gD) of herpes simplex virus type 1 (HSV-1) were associated with calnexin, a membrane-bound chaperone in the endoplasmic reticulum. Kinetics of association and dissociation was quite different among the precursors. For the precursors of gC and gD of HSV-1, the maximal association was observed immediately after the synthesis and they dissociated rapidly with half-times of 25 min for gC and 30 min for gD, respectively. In contrast, the precursor of gB showed prolonged association with calnexin. Their maximum association was observed 30 min after the synthesis, and thereafter, they dissociated slowly with a half-time of 70 min. The results suggest that, while glycoproteins that have a rapid processing rate, such as gC and gD of HSV-1, rapidly associate with calnexin and their association is quite short, those that take much time to be processed to a mature form, such as gB of HSV-1, have prolonged association kinetics with calnexin. Complete inhibition of the binding of these glycoprotein precursors to calnexin by tunicamycin or castanospermine indicates the importance of partially trimmed N-linked oligosaccharides for their association
Adhesion-Dependency of Serum-Induced p42/p44 MAP Kinase Activation Is Released by Retroviral Oncogenes

AbstractG1/S transition of the cell cycle is blocked when cells are cultured without cell adhesion, even if nutrients and serum are present. Shift experiments involving transfer from adhesion to suspension cultures have revealed that cell adhesion in the early half of G1 phase is required for induction of DNA synthesis. We found that activation of p42/p44 mitogen-activated protein (MAP) kinases, one of the earliest responses induced by serum stimulation, was also dependent on cell adhesion in rat F2408 and mouse Swiss3T3 fibroblast cell lines, suggesting that MAP kinase activation is a critical step in adhesion-dependent G1 progression. F2408 cell lines transformed by the v-src,v-K-ras,and v-mosoncogenes showed constitutively high MAP kinase activity, even in the absence of serum and cell adhesion, while both serum stimulation and cell adhesion were necessary to induce intensive activation of MAP kinase in a F2408 cell line transformed by the E6 and E7 genes of human papillomavirus type 16, as well as in untransformed F2408
African Swine Fever Virus GeneA179L,a Viral Homologue ofbcl-2, Protects Cells from Programmed Cell Death

AbstractThe African swine fever virus (ASFV) open reading frameA179L,which is similar to the human proto-oncogenebcl-2, has been cloned and expressed in vaccinia virus under control of thepE/Lsynthetic early/late promoter. TheA179Lgene product prevented cell death in HeLa and BSC-40 cells doubly infected with another recombinant vaccinia virus expressing the interferon-induced double-stranded RNA-activated protein kinase (p68 kinase), which activates a rapid cell death characteristic of apoptosis. This finding suggests that theA179Lgene has a function similar to that ofbcl-2 in preventing apoptosis and may play an important role during productive ASFV infection
Deletions in the 3′ Untranslated Region of Cowpea Chlorotic Mottle Virus Transgene Reduce Recovery of Recombinant Viruses in Transgenic Plants

AbstractThe 3′ untranslated region (UTR) adjacent to the capsid gene is frequently included with the transgene in the construction of capsid protein mediated virus resistant transgenic plants. Since ribonucleotide sequences within the 3′ UTR are involved in the initiation of viral replication, the presence of this sequence may encourage the participation of the transgene in RNA recombination. Experiments were designed to explore the involvement of the 3′ UTR of cowpea chlorotic mottle virus (CCMV) in RNA recombination events between transgenes and challenging viruses.Nicotiana benthamianawas transformed with CCMV transgenes consisting of the 3′ two-thirds of the capsid gene and fragments of the associated 3′ UTR lacking the terminal 69, 83, or 214 nucleotides. Plants were inoculated with wild-type CCMV transcripts for RNAs 1 and 2 and a movement defective RNA 3 transcript lacking the 3′ third of the capsid gene. While no recombinant virus was detected in plants expressing 3′ deletion constructs, 3% of control transformants containing an identical segment of the capsid gene with the complete 3′ UTR yielded viable recombinant virus. These results suggest that RNA recombination between transgenic RNA and viral RNA can be reduced significantly by omitting or disrupting the 3′ UTR in the transgene
The Hepatitis B Virus Large Surface Protein (LHBs) Is a Transcriptional Activator

AbstractIt has been shown that a C-terminally truncated form of the middle-sized hepatitis B virus (HBV) surface protein (MHBst) functions as a transcriptional activator. This function is dependent on the cytosolic orientation of the N-terminal PreS2 domain of MHBst, but in the case of wild-type MHBs, the PreS2 domain is cotranslationally translocated into the ER lumen. Recent reports demonstrated that the PreS2 domain of the large HBV surface protein (LHBs) initially remains on the cytosolic side of the ER membrane after translation. Therefore, the question arose as to whether the LHBs protein exhibits the same transcriptional activator function as MHBst. We show that LHBs, like MHBst, is indeed able to activate a variety of promoter elements. There is evidence for a PKC-dependent activation of AP-1 and NF-κB by LHBs. Downstream of the PKC the functionality of c-Raf-1 kinase is a prerequisite for LHBs-dependent activation of AP-1 and NF-κB since inhibition of c-Raf-1 kinase abolishes LHBs-dependent transcriptional activation of AP-1 and NF-κB
Mutation in the Influenza Virus Neuraminidase Gene Resulting in Decreased Sensitivity to the Neuraminidase Inhibitor 4-Guanidino-Neu5Ac2en Leads to Instability of the Enzyme

AbstractWe previously isolated a variant of the influenza virus NWS/G70C, with a decreased sensitivity to the neuraminidase-specific inhibitor 4-guanidino-Neu5Ac2enin vitro,which has a mutation in one of the conserved residues of the neuraminidase Glu 119 to Gly. Despite the mutation, purified neuraminidase demonstrated the same specific activity as the parent neuraminidase. In contrast, characterization of a similar mutant by another group revealed a low specific activity of the enzyme. We confirm here that the specific activity of our variant is the same as that of the parent, but report that this mutation makes the enzyme inherently unstable, at high and low temperatures, either on the virion or as purified neuraminidase. Thus, for a valid determination of specific activity the concentration of native NA needs to be determined at the time of enzyme assay. Structurally, the instability may be partially explained by the introduction of a side chain (Gly), which carries a greater entropy penalty in condensation of the structure from the unfolded to the folded state and this, together with the loss of stabilizing interaction between Glu 119 and its neighbors in the active site, is not compensated for by the water molecule occupying the position of the carboxylate group (6)
The Extracellular Domain of La Crosse Virus G1 Forms Oligomers and Undergoes pH-Dependent Conformational Changes

AbstractThe La Crosse virus G1 glycoprotein plays a critical role in virus binding to susceptible cells and in the subsequent fusion of viral and cellular membranes. A soluble form of the G1 glycoprotein (sG1) prepared in a recombinant baculovirus system mimics the cell-binding pattern of La Crosse virus and inhibits La Crosse virus infection (A. Pekoszet al., Virology214, 339–348, 1995), presumably by competing for a cellular receptor, a finding that implies that sG1 can perform some functions absent G2, the smaller of the two bunyavirus glycoproteins. We have performed experiments to determine whether sG1 is present as an oligomer and whether it undergoes the conformational changes associated with fusion (F. Gonzalez-Scarano,Virology140, 209–216, 1985). Our results indicate that both sG1 and native G1 undergo similar changes in conformation after exposure to an acidic environment, as detected by reactivity with monoclonal antibodies. Furthermore, using chemical cross-linking, both proteins were detected as oligomers (most likely dimers). Sucrose density gradient analysis of sG1 verified that it was present in monomeric and oligomeric forms. These results demonstrate that the isolated G1 glycoprotein can undergo a pH-dependent change in conformation in the absence of its transmembrane and cytoplasmic tail domains and that the extracellular portion of the glycoprotein can oligomerize
Dual Function of a Human Immunodeficiency Virus (HIV)-Specific Cytotoxic T-Lymphocyte Clone: Inhibition of HIV Replication by Noncytolytic Mechanisms and Lysis of HIV-Infected CD4+ Cells

AbstractCD8+ T cells may play a beneficial role in human immunodeficiency virus (HIV)-infected patients by two mechanisms: HIV-specific cytotoxic activity and secretion of a soluble mediator(s) that inhibits HIV replicationin vitro.Here we characterized both activities mediated by an HIV p24gag-specific cytotoxic T lymphocyte (CTL) CD8+ clone derived from an HIV-infected patient. When the CTL clone was mixed with HIV-infected autologous CD4+ T cells, viral replication was suppressed. This viral inhibition was observed in heterologous CD4+ T cells and when CD8+ and CD4+ populations were separated by a semipermeable membrane, demonstrating the involvement of a diffusible factor(s). The lysis of autologous HIV-infected T cells was also detected. However, HIV suppression was more efficient when CD4+ and CD8+ T cells shared major histocompatibility complex alleles and were in direct contact. Thus, one and the same CD8+ T cell population can mediate both lysis of HIV-infected targets and nonlytic suppression of HIV replication. These results underline the multiple roles of CD8+ T lymphocytes in the suppression of HIV-infected cells
Characterization of the Membrane Association of the Influenza Virus Matrix Protein in Living Cells

AbstractTo determine if membrane association is an intrinsic property of the influenza virus matrix protein (M1) it was expressed from cDNA in living cells in the absence of other influenza virus proteins. By using a membrane fractionation scheme the M1protein was found to associate with membranes in a time-dependent manner (0 time = 45% total; after a 3-hr chase period = 68% total M1protein). Coexpression of the integral membrane proteins HA+NA+M2did not significantly increase the association of the M1protein with cellular membranes, indicating that putative interactions of the M1protein and the cytoplasmic tails of the integral membranes cannot be detected by this assay. Biochemical treatments of the M1protein associated with membranes with alkali, high salt conditions, or Triton X-114 yielded data that challenge the normal criteria for integral membrane proteins or peripheral membrane proteins. Examination of the solubility of the M1protein in influenza virus-infected cells to Triton X-100 extraction indicated it became increasingly insoluble with time, but the M1protein could be solubilized in Triton X-100 containing 1MNaCl, suggesting an association of the M1protein with the cytoskeleton. However, when the M1protein was expressed from cDNA, it did not become insoluble to Triton X-100 extraction, suggesting an interaction of the M1protein unique to the influenza virus-infected cell
Characterization of a Promoter in the E7 Open Reading Frame of Human Papillomavirus Type 11

AbstractA human papillomavirus type 11 (HPV-11) early gene promoter, PE1E4, in the E7 open reading frame and involved in the transcription of E1E4 and E1E4, L1 mRNAs was characterized by chloramphenicol acetyl transferase (CAT) assay, gel-shift assay,in vitrotranscription, and primer extension. By CAT assay with CAT-expression plasmids containing various portions of the HPV-11 genome from nucleotide position (nt) 235 to nt 743, we identified a 112-basepair (bp) sequence (nt 632–743) that had high promoter activity and a 188-bp upstream sequence from nt 395 to nt 572 that strongly suppressed activity. The 112-bp sequence contained a 7-bp repeat (7-bp Rep) with high homology to the Sp1-binding motif (BM) in the E6 promoter of HPV-11 but lacked an identifiable TATA-box. A cellular protein other than Sp1 bound to the 7-bp Rep. Removal of a 21-bp segment (nt 632–652) containing the 7-bp Rep significantly reduced activity. Byin vitrotranscription assay and primer extension, one of the transcription start sites was mapped to near nt 719. These results suggested that a cellular protein that binds to the 7-bp Rep may act as an activator for PE1E4
Genetic Variation in Yellow Fever Virus: Duplication in the 3′ Noncoding Region of Strains from Africa

AbstractThe nucleotide sequences of three regions of the genomes of 13 yellow fever (YF) virus isolates were determined to define genetic variation and evolution of the virus. Phylogenetic trees generated from sequences of either the 5′ terminal 1320 nucleotides of the genome, 754 nucleotides from the NS4A and NS4B genes, or the 3′ terminal 511 nucleotides were very similar and contained minor differences. Overall, these results suggested that there were at least four major genotypes of YF virus, including one in Central/East Africa, one in West Africa, and two in South America. Examination of the 3′ noncoding region (3′NCR) showed that only West African strains had a 3′NCR of 511 nucleotides while strains from Central/East Africa and South America had shorter 3′NCRs (443–469 nucleotides) due to the absence of YF specific repeat sequences (RYFs). Central/East African strains have two RYFs and West African strains have three RYFs while South American strains only have one copy of the RYF. It is speculated that duplication of the RYF took place in West Africa subsequent to the presumed introduction of YF virus into South America. Thus, both tick-borne (Mandlet al., J. Virol.65, 4070–4077, 1991 and Wallneret al., Virology213, 169–178, 1995) and mosquito-borne flaviviruses have variable 3′NCRs
Expression of the GB Virus C E2 Glycoprotein Using the Semliki Forest Virus Vector System and Its Utility as a Serologic Marker

AbstractA 336-amino-acid segment of the GB virus C second envelope protein (E2) has been produced in BHK-21 cells using the Semliki Forest virus vector system. Secretion of this protein was facilitated by deletion of a hydrophobic region at the C-terminus that may represent the membrane anchoring domain. The E2 protein recovered from the culture supernatant exhibited a molecular mass of approximately 52 kDa, with the increase in size relative to the polyprotein backbone being contributed by N-linked glycosylation. A radioimmunoprecipitation assay using GBV-C E2 was developed to test for the presence of antibodies against this protein in human sera. The prevalence of antibodies to E2 was high among injection drug users and other individuals at risk for acquiring parenterally transmitted agents. There was a much higher percentage of anti-E2 seropositivity in GBV-C RT-PCR negative compared to GBV-C RT-PCR positive samples from these populations. In addition, serial samples from patients transfused with blood containing GBV-C showed seroconversion to anti-E2 positivity and loss of GBV-C viremia as measured by RT-PCR within 11 months of transfusion in five of seven individuals. Thus, this system provided a rapid means to identify GBV-C E2 as a useful antigen for the study of GBV-C exposure
Immunization with Plasmid DNA Encoding for the Measles Virus Hemagglutinin and Nucleoprotein Leads to Humoral and Cell-Mediated Immunity

AbstractWe have evaluated the DNA vaccination strategy for measles virus (MV) hemagglutinin (HA) and nucleoprotein (NP) genes. Plasmids encoding either the MV, HA, or NP proteins inoculated intramuscularly into Balb/c mice induced both humoral and CTL class I restricted responses. Antibody responses were not increased by multiple inoculations. The major antibody isotype induced by both the HA and NP was IgG2a consistent with a Th1 response. In contrast, immunization with a plasmid which directed the synthesis of a partially secreted form of HA gave mainly IgG1 antibodies. When the amount of DNA was reduced for the HA plasmid (1 or 10 μg/animal), although the antibody was not induced, a CTL response was observed
Single Amino Acid Changes in the Murine Leukemia Virus Capsid Protein Gene Define the Target ofFv1Resistance

AbstractThe mouseFv1genetic locus controls resistance to subgroups of ecotropic, MCF, and amphotropic murine leukemia viruses (MuLVs). In addition to the four previously defined alleles ofFv1(Fv1n, Fv1b, Fv1nr, Fv10), we present evidence that the novel restriction pattern characteristic of DBA/2J mice maps to theFv1locus and therefore represents a novel allele, here designatedFv1d.Previous studies had demonstrated that theFv1-mediated viral tropism is determined within the capsid protein gene, and that N- and B-tropic virus capsids differ only in two adjacent amino acids. We introduced various amino acid substitutions at these two sites in the N-tropic AKV MLV capsid gene, and typed resulting viruses for host range on cells carrying all fiveFv1alleles as well as on cells from additional wild mouse species withFv1-like differences in virus susceptibility. Results indicate that alteration of the first of the two amino acids does not alter tropism, but alteration of the second alone is sufficient to convert the N-tropic AKV MLV to a B-tropic virus. Substitution of leucine for arginine at this site produced a virus with an unusual tropism not characteristic of any of the naturally occurring or laboratory strains of MuLV
A Specific RNA Structural Motif Mediates High Affinity Binding by the HIV-1 Nucleocapsid Protein (NCp7)

AbstractCurrent research indicates that the nucleocapsid protein (NCp7) of human immunodeficiency virus type 1 (HIV-1) interacts with a variety of RNA substrates during the progression of the viral life cycle. The RNA features specifically recognized by the protein, however, have yet to be identified. SELEX was used to generate a set of RNAs whose affinities for nucleocapsid were on the order of 2 × 10−9M.Comparative analysis revealed that each RNA contains a highly conserved fourteen nucleotide sequence-block. Computer modeling and structure probing experiments indicate that the RNA ligands use the consensus sequence to fold into hairpins with an identical asymmetric bulge. The presence of the nucleocapsid protein protects the asymmetric bulge from ribonuclease attack, suggesting that it is the key element in protein recognition. A search for similar structural motifs within the HIV genome reveals several potential interaction sites for the nucleocapsid protein