pinecone/core-2020-05-10-deduplication huggingface dataset:
Induction of V3-Specific Cytotoxic T Lymphocyte Responses by HIVgagParticles Carrying Multiple Immunodominant V3 Epitopes of gp120

AbstractEfforts to develop a vaccine to prevent infection of human immunodeficiency virus (HIV) have focused on the induction of neutralizing antibodies. In our previous study, we reported that chimericgag–envvirus-like particles (VLPs) induce neutralizing antibodies which block HIV infection. In addition to the neutralizing antibodies, the cytotoxic T-lymphocyte (CTL) response is considered to be another major immune defense mechanism required for recovery from many different viral infections. In the present study, we have constructed chimeric fusion proteins using HIV-2gagprecursor protein with (1) four neutralizing epitopes from HIV-1 gp160; (2) three tandem copies of consensus V3 domain, which have been derived from 245 different isolates of HIV-1 and carries both the principal neutralizing determinant (PND) and CTL epitopes; and (3) V3 domains from HIV-1IIIB, HIV-1MN, HIV-1RF, and HIV-1SF2. These chimeric fusion proteins were expressed in a large quantity within insect cells, and released as VLPs into the cell culture medium. The purifiedgag–envVLPs from all three constructs appear to be spherical particles similar to immature HIV but slightly larger than thegagVLPs. Immunoprecipitation analysis showed that the chimeric proteins were recognized not only by HIV-1 positive patient sera, but also by monoclonal and polyclonal antisera raised against V3 peptides of HIV-1IIIB, HIV-1MN, HIV-1RF, and the gp120 antiserum against HIV-1SF2. Balb/C mice immunized with these chimeric VLPs successfully induced CTL activity against V3 peptide-stimulated target cells. In addition, a high degree of cross-reactivity was observed among the four different strains of HIV-1 V3 domain, indicating that the tandem multiple consensus V3 peptide sequence carried by HIV-2gagcan be used as a potential HIV vaccine against various HIVs
Reduction of Respiratory Syncytial Virus Titer in the Lungs of Mice after Intranasal Immunization with a Chimeric Peptide Consisting of a Single CTL Epitope Linked to a Fusion Peptide

AbstractIn the work described here, the effect of intranasal immunization of BALB/c mice with synthetic chimeric peptides consisting of a cytotoxic T-cell epitope (amino acids 81–95) from the M2 protein of respiratory syncytial virus (RSV) and a fusion peptide (amino acids 113–131) from the F1 protein of measles virus on response to challenge with RSV has been assessed. Three intranasal immunizations with the chimeric peptides without adjuvant induce peptide- and RSV-specific cytotoxic T-cell responses (CTL) at 1 or 3 weeks after the third immunization. The CTL responses significantly declined at 6 weeks after immunization. Furthermore, viral load in the lungs following challenge with RSV was significantly reduced in mice immunized with the F/M2:81-95 chimeric peptide compared to control animals at 1 or 3 weeks after immunization and no reduction of RSV titers was detectable 6 weeks after immunization. The CTL activity induced by F/M2:81-95 was therefore short-lived (less than 6 weeks) but was significantly correlated with the reduction in viral load in the lungs
Definition of an Epitope on NS3 Recognized by Human CD4+Cytotoxic T Lymphocyte Clones Cross-Reactive for Dengue Virus Types 2, 3, and 4

AbstractThe role of dengue virus-specific serotype-cross-reactive T lymphocytes in recovery from and pathogenesis of dengue virus infections is not known. In the present paper, we have defined a dengue serotype-cross-reactive epitope recognized by two CD4+CD8−cytotoxic T lymphocyte (CTL) clones, JK36 and JK46. These T cell clones were established from the peripheral blood T lymphocytes of a dengue-3-immune donor, using a limiting dilution method. JK36 and JK46 were cross-reactive for dengue virus types 2, 3, and 4, but not for type 1, and recognized the NS3 protein. The smallest synthetic peptide recognized by JK36 was an 8-amino acid peptide that contains amino acids (aa) 226 to 233 (VVAAEMEE) of NS3. The smallest peptide recognized by JK46 was an 11-amino acid peptide that contains aa 224 to 234 (TRVVAAEMEEA). HLA-DR15 was the restriction allele for recognition of these peptides by both JK36 and JK46. This is the first epitope to be defined that is recognized by human CD4+CTL cross-reactive for dengue virus types 2, 3, and 4
Modulation of Mucosal and Systemic Immunity by Enteric Administration of Nonreplicating Herpes Simplex Virus Expressing Cytokines

AbstractIn this report the ability of enteric immunization with recombinant replication deficient (ICP4−/−) HSV expressing IFNγ to generate protection and modulate mucosal and systemic immunity was evaluated. ICP4−/−HSV, ICP4−/−HSV expressing IL4, live replicating, and uv HSV were used as controls. Following enteric administration of live HSV, a Th1cytokine response was induced in the spleen, while both Th1and notable Th2cytokine production were detected at mucosal sites. Modulation of mucosal and systemic immune response was achieved when nonreplicating recombinant HSV viruses expressing cytokines were used. Compared to the control replication defective viruses, decreased frequency of Th2cytokine producing cells in Peyer's patches was observed following enteric administration of nonreplicating HSV expressing IFNγ. When IFNγ expressing virus was given enterically, modulation was observed at the systemic level, measured by ELISPOT for cytokine producing cells, ELISA from thein vitrorestimulated splenic cell cultures, and by the increase of the IgG2a/IgG1 ratio in the serum. This report provides evidence that replication defective viruses expressing cytokine genes in contrast to uv HSV, are immunogenic when administered enterically and can generate significant immunomodulatory effects at the mucosal and systemic levels
Polyhedron-like Inclusion Body Formation by a Mutant Nucleopolyhedrovirus Expressing the Granulin Gene from a Granulovirus

AbstractThe polyhedrin gene inBombyx morinucleopolyhedrovirus (BmNPV) was replaced with the granulin gene ofTrichoplusia nigranulovirus (TnGV). The substitution was verified by Southern hybridization, and expression of granulin by the mutant virus, BmGran, was demonstrated by sodium dodecyl sulfate–polyacrylamide gel electrophoresis and by amino acid sequencing of the predominant protein of BmGran inclusion bodies (IBs). Light and electron microscopy examination of BmGran-infectedB. moriand BmN cells revealed large, cuboidal, polyhedron-like IBs in the nucleus and cytoplasm, but granules were not seen. IBs contained small, parallel, electron-dense streaks, which defined the geometric pattern of crystallization. Geometric patterns of nuclear IBs were frequently disrupted by occlusion of polyhedron envelope fragments, resulting in IB instability and fracturing. Virions were not embedded in most of the polyhedron-like IBs, but accumulated with polyhedron envelope fragments. Some virions were coated with matrix protein and were partially wrapped by polyhedron envelope. These results suggested that (1) the amino acid sequence of granulin is insufficient for determining IB morphology in TnGV-infected cells, and TnGV may have genes, not present in BmNPV, that control granule formation, and (2) interactions among the virion, the IB envelope, and the matrix protein may be important in virion occlusion and IB morphology and stability
The Rhesus Macaque CCR3 Chemokine Receptor Is a Cell Entry Cofactor for HIV-2, but Not for HIV-1

AbstractThe eotaxin receptor (CCR3) is a CD4-associated coreceptor for human immunodeficiency virus type 1 (HIV-1) and type 2 (HIV-2). By comparison with other chemokine receptors, such as CCR5 and CXCR4, the primary sequences of human CCR3 and its rhesus macaque homolog were markedly different in their extracellular domains. Human CD4+cells expressing CCR3 from either human or macaque origin could be infected by HIV-2, with apparently similar efficiency, but only cells expressing human CCR3 could be infected by HIV-1. It suggests that HIV-1 and HIV-2 envelope proteins interact differently with the CCR3 coreceptor. HIV-1 could infect cells expressing chimeric human/macaque CCR3 bearing either the first and second, or the third and fourth extracellular domains of human CCR3. As previously observed for CCR5, there seems to be a certain functional redundancy between domains supporting the coreceptor activity of CCR3. In spite of their close genetic relationship to HIV-2, two macaque simian immunodeficiency virus strains were apparently unable to use the CCR3 coreceptor from either human or simian origin
Complex Evolutionary History of Primate LentiviralvprGenes

AbstractVpx and Vpr are homologous proteins encoded by the human and simian immunodeficiency viruses. Vpr is encoded by each of the five primate lentiviral groups, whereas Vpx is restricted to members of the HIV-2 group. A recent report has proposed that thevpxgene was probably acquired from an ancestral member of the SIVagm group by nonhomologous recombination. Here, we suggest that this transfer event was more likely to have occurred via homologous recombination within the 3′ region of another gene,vif.Furthermore, phylogenetic analysis strongly suggests that there have been at least two other horizontal transfer events involving these genes: the first between ancestral members of the HIV-1 and HIV-2 groups, and the second between viruses isolated from the vervet and tantalus subspecies of African green monkey (Cercopithecus aethiopsssp)
Effect of Changes in the Glycosylation of the Human Immunodeficiency Virus Type 1 Envelope on the Immunoreactivity and Sensitivity to Thrombin of Its Third Variable Domain

AbstractThe influence of HIV Env glycosylation on the conformation of the third variable domain (V3) of Env was studied by both deglycosylation of mature Env and the use of Env produced by recombinant systems in which α-glucosidase activity was inhibited by either deoxynojirimycin (DNM) or mutation. Selective deglycosylation affected anti-V3 antibody binding. The immunoreactivity and sensitivity to thrombin cleavage of V3 presented on Env produced in baby hamster kidney cells were changed by DNM treatment. In contrast, Env expressed in α-glucosidase I-deficient Chinese hamster ovary cells or in their parental cells treated by DNM fully retained these V3 properties. These results are discussed in relation to the inconsistent data obtained on V3 property changes resulting from Env glycosylation changes
Inhibition of HIV-1 Replication by a Monoclonal Antibody Directed toward the Complementarity Determining Region 3-Like Domain of CD4 in CD45 Expressing and CD45-Deficient Cells

AbstractMonoclonal antibodies directed toward the complementarity determining region (CDR)3-like loop of the aminoterminal domain of CD4 have been shown to inhibit the replication of human immunodeficiency virus (HIV) in CD4 positive T cells. The mechanism of action of these antibodies is not yet elucidated, although several observations suggest that they inhibit viral transcription by signal transduction through the CD4 molecule, potentially implicating the activation of a protein tyrosine kinase (PTK) cascade. Since CD45 is the major protein tyrosine phosphatase associated to the plasma membrane in T cells, and has been shown to regulate the activity of several PTK, we postulated that CD45 may be necessary for the inhibitory action of the CDR3-like specific anti-CD4 antibodies. Therefore we tested the effect of one such anti-CD4 monoclonal antibody, 13B8.2, in repressing HIV replication in CD45 positive cell lines and CD45 deficient variants. Our data show that cells respond to 13B8.2 postinfection treatment regardless of CD45 expression, indicating that neither CD45 nor PTK regulated by CD45 are implicated in the mechanism of action of this antibody
Phosphate Depletion Enhances the Stability of the Amphotropic Murine Leukemia Virus Receptor mRNA

AbstractThrough its specific receptor, the amphotropic murine leukemia virus (MLV) infects cells from many mammals, including humans. We have previously demonstrated that levels of human amphotropic MLV receptor (pit2) mRNA varied considerably in different human cell lines. Removal of phosphate from the culture medium led to increases in the amount ofpit2mRNA and the quantity of a 71-kDa protein specifically recognized by antibodies against Pit2. To determine if the increases inpit2mRNA and protein levels were due to a transcriptional effect, thepit2promoter region was cloned. This region was characterized and found to contain a functional TATA-less promoter that under our experimental conditions does not respond to phosphate depletion. Instead,pit2mRNA was found to be more stable in response to Pi depletion. These results suggest that the increase inpit2mRNA levels observed in response to Pi depletion occurs at a posttranscriptional level and is due to enhanced mRNA stability
Identification of Db- and Kb-Restricted Subdominant Cytotoxic T-Cell Responses in Lymphocytic Choriomeningitis Virus-Infected Mice

AbstractAntiviral cytotoxic T-cells are critical for control of lymphoctytic choriomeningitis virus (LCMV) infection in mice. In H-2bmice, the antiviral response is directed against three Db-restricted epitopes in the viral nucleoprotein (NP396-404) and glycoprotein (GP276-286 and GP33-41). Our present data revealed a clear hierarchy among these three epitopes, in which NP396-404 is immunodominant, followed by GP33-41 and GP276-286, respectively. In order to identify additional CTL epitopes in the LCMV nucleoprotein and glycoprotein, we used the motifs for Db- and Kb-binding peptides, combined with MHC class I-binding assays. Out of 23 Dbmotif-fitting peptides, we identified 4 Dbbinders, one of which (GP92-101) turned out to be a new CTL epitope. Among 28 Kbmotif-fitting peptides, 12 bound Kb, and one of these (NP205-212) was a CTL epitope. Both newly identified CTL peptides were recognized by LCMV-immune splenocytes after secondaryin vitrostimulation. Both peptides bound their MHC class I molecules with intermediate affinity (470 and 170 nM for GP92-101 and NP205-212, respectively). Responses against these peptides were weaker than the responses against the three major epitopes. None of the high affinity binders were new epitopes, suggesting that high affinity binders are either immunodominant epiitopes or no epitopes at all. Thus, analysis of 51 Kband Dbmotif-fitting peptides yielded 2 new, subdominant epitopes. Immunization of C57BL/6 mice with these peptides, or with vaccinia virus recombinants expressing these epitopes as minigenes, protected against chronic LCMV infection, demonstrating that immunization with subdominant epitopes can confer protection against chronic viral infection
Chlorella Virus NY-2A Encodes at Least 12 DNA Endonuclease/Methyltransferase Genes

AbstractThe 380-kb chlorella virus NY-2A genome is highly methylated; 45% of the cytosines are 5-methylcytosine (5mC) and 37% of the adenines are N6-methyladenine (6mA). Based on the sensitivity/resistance of NY-2A DNA to 80 methylation-sensitive DNA restriction endonucleases, the virus is predicted to encode at least 10 DNA methyltransferases: 7 6mA-specific methyltransferases, M.CviQI (GTmAC), M.CvQII (RmAR), M.CviQIII (TCGmA), M.CviQIV (GmATC), M.CviQV (TGCmA), M.CviQVI (GmANTC), and M.CviQVII (CmATG); and 3 5mC-specific methyltransferases, M.CviQVIII [RGmC(T/C/G)], M.CviQIX (mCC), and M.CviQX (mCGR). Five of the 6mA methyltransferase genes,M.CviQI, M.CviQIII, M.CviQV, M.CviQVI,andM.CviQVII,were cloned and sequenced. In addition, 2 site-specific endonuclease activities, R.CviQI (G/TAC) and NY2A-nickase (R/AG), were detected in cell-free extracts from NY-2A virus-infected chlorella. Therefore, the NY-2A genome contains at least 12 DNA methyltransferase and endonuclease genes which, altogether, compose about 3–4% of the virus genome
Evidence for Transovarial Transmission of Tomato Yellow Leaf Curl Virus by Its Vector, the WhiteflyBemisia tabaci

AbstractThe whiteflyBemisia tabaciis the only vector of the tomato yellow leaf curl geminivirus (TYLCV). The insect transmits the virus in a persistent-circulative manner. TYLCV DNA was detected by polymerase chain reaction and by Southern blot hybridization in progeny (eggs, first and second instars, adults) of single viruliferous whiteflies that developed on eggplant or on cotton (two TYLCV nonhost plants). Furthermore, TYLCV DNA was present in the progeny of insects that had acquired the virus through the egg. The adult progeny of the viruliferous insects and their own progeny were able to infect tomato test plants, producing typical disease symptoms. Ovaries and maturing eggs of viruliferous insects contained viral DNA, as did eggs laid by viruliferous insects maintained on an artificial diet. Eggs laid by nonviruliferous whiteflies on cotton plants previously caged with viruliferous insects did not acquire viral DNA from the plant. Hence, TYLCV can be transmitted through the egg for at least two generations. In the absence of an available plant host, the whitefly may serve as a reservoir of the virus between growing seasons
Effects of Mutations in the C-terminal Region of NIa Protease oncis-Cleavage between NIa and NIb

AbstractMutational analyses were carried out to investigate whether the nuclear inclusion protein a (NIa) C-terminal amino acids of turnip mosaic potyvirus play any roles in thecis-cleavage between NIa and NIb. The processing rate of the NIa–NIb junction sequence was decreased significantly by either V240D or Q243A mutation while little affected by F226D, V228E, K230E, I232D, or L235D mutation. The mutation of W212S, G213S, or I217D abolishing the cleavage at the NIb–CP or 6K1–cylindrical inclusion protein junction sequence decreased the processing rate to half the level of that of the wild type. Deletion of the C-terminal one (K230), two (S229 and K230), three (S229 to L231), or six amino acids (S229 to D234) as well as the insertion of five glycines between S229 and K230 or between S220 and Q221 did not affect significantly the cleavage while the deletion of 20 amino acids (Q218 to S237) decreased the processing rate to 73% of that of the wild type. These results rule out the possibility that the C-terminal region plays a role as a spacer in right placement of the NIa–NIb junction sequence and demonstrate that the C-terminal 20 amino acids from Q218 to S237 are not crucial for thecis-cleavage of the NIa–NIb junction sequence
Nucleotide Sequence and Infectivity of a Full-Length cDNA Clone of Panicum Mosaic Virus

AbstractThe sequence of an infectious cDNA clone of panicum mosaic virus (PMV) showed that the single-stranded RNA genome is 4326 nucleotides (nt) and a single highly abundant subgenomic (sg) RNA of 1475 nt was synthesized during PMV infection of pearl millet plants and protoplasts. Computer comparisons revealed strong similarities between the predicted amino acid sequences of the p48 and p112 open reading frames (ORFs) and replicase proteins of members of the Tombusviridae. The sgRNA has the potential to encode five proteins. Three small ORFs, p8, p8-FS, and/or p6.6 have similarity to ORFs of carmo-, necro-, and machlomoviruses thought to be involved in virus spread in plants. The sgRNA also has the potential to encode a 26-kDa capsid protein and a 15-kDa nested gene (p15) of unknown function. PMV transcripts also supported replication and movement of SPMV, the satellite virus. Genome organization, physicochemical properties, and biological features indicate that PMV is a member of the Tombusviridae family. However, PMV differs sufficiently from previously described members to warrant its placement in a new genus provisionally designatedPanicovirus
An SP1-Binding Site and TATA Element Are Sufficient to Support Full Transactivation by Proximally Bound NS1 Protein of Minute Virus of Mice

AbstractThe minute virus of mice (MVM) P38 Sp1-binding site and TATA box, inserted in an otherwise heterologous plasmid background, could be transactivated to high levels by the MVM NS1 protein targeted proximally to these sequences, demonstrating that these core promoter regulatory elements are sufficient to support essentially wild-type levels of NS1-transactivated expression and suggesting that NS1 may act directly or indirectly with Sp1 and or elements of the general transcription machinery. Accordingly, we show that bacterially generated NS1 can interact strongly, independent of nucleic acid bridging, and most likely directly with Sp1in vitroand can associate, in a nucleic acid-independent manner, with endogenous Sp1 as it exists in a complex transcriptionally active murine nuclear extract. NS1 achieves the same fold activation of an isolated TATA element over its low basal level and can also be demonstrated to interact efficiently and specifically with the general transcription factors TBP and TFIIA (α, β)in vitro
Identification of Single Amino Acids in the Human Papillomavirus 11 E2 Protein Critical for the Transactivation or Replication Functions

AbstractThe papillomavirus E2 protein is required for viral transcriptional regulation and replication. The E2 protein has a modular structure with two highly conserved domains, a sequence-specific DNA-binding and dimerization domain and a conserved N-terminus which is important for transcriptional transactivation, replication, and interaction with the E1 protein to determine which specific amino acids or regions in the N-terminus were important for the replication or transactivation functions. Single amino acid substitutions were created at highly conserved, highly charged amino acids in the HPV 11 E2 N-terminus. Each amino acid was mutated to a nonpolar alanine residue or a similarly charged amino acid. The mutated E2 proteins were analyzed for their abilities to support transcriptional transactivation and transient DNA replication and to enhance binding of E1 to the origin of replication. Single amino acid substitutions were identified which were defective for either the replication or transactivation functions, which demonstrated that the replication and transactivation functions within the N-terminus are separable. In several cases different amino acid substitutions at the same site had variable effects on transcription or replication, highlighting the importance of hydrophobic interactions or side chain structure at each site. The replication function appeared to correlate with the ability of E2 to enhance binding of E1 to the origin of replication though these studies also suggest that other functions performed by the E2 protein may be important for replication
In VivoInduction of Specific Cytotoxic T Lymphocytes in Mice and Rhesus Macaques Immunized with DNA Vector Encoding an HIV Epitope Fused with Hepatitis B Surface Antigen

AbstractDNA immunization offers a novel means to induce humoral and cellular immunity in inbred or in outbred animals. Here we have tested the efficiency of genetic immunization with hepatitis B virus (HBV) envelope-based vectors. In naive primates, injection of a plasmid DNA encoding HBV envelope proteins induced an HBV-specific cytotoxic response and appearance of potentially protective anti-HBs antibodies. Moreover, intramuscular and intradermal injections of a DNA expression vector encoding an epitope of the human immunodeficiency virus envelope fused to the surface protein of the hepatitis B virus (HBsAg) induced strong humoral and cytotoxic responses to antigenic determinants of both viruses in mice and nonhuman primates alike. In addition, in protein-primed Rhesus monkeys B-cell memory was successfully boosted by DNA injection of hybrid vectors and animals subsequently developed a multispecific cellular response. This suggests that DNA-based immunization could be used to boost efficiently and broaden the immune response in individuals immunized with conventional vaccines, regardless of their genetic variability. These results also indicate that it might be possible to rationally design HBsAg-based expression vectors to induce multispecific immune responses for vaccination against hepatitis B and other pathogens