pinecone/core-2020-05-10-deduplication huggingface dataset:
Protective Immune Responses Induced by the Immunization of Mice with a Recombinant Bacteriophage Displaying an Epitope of the Human Respiratory Syncytial Virus

AbstractWe investigated whether a recombinant bacteriophage displaying a disease-specific protective epitope could be experimentally used as a vaccine to confer protection of immunized animals against infection. We genetically engineered a recombinant phage, fd, displaying at its surface a chimeric pIII coat protein fused to the previously identified protective epitope 173-187 from the glycoprotein G of the human respiratory syncytial virus (RSV). A selected recombinant fd phage elicited a strong immune response in mice, inducing a high level of circulating RSV-specific antibodies. Mice immunized with the recombinant phage acquired a complete resistance to RSV infection as evidenced by the lack of detectable virus particles in their lungs following intranasal challenge with live RSV. In contrast, a high level of virus particles was found in the lungs of either animals immunized with the wild-type fd phage or nonimmunized mice. To our knowledge, this is the first study to report the ability of a phage presenting an immunogenic peptide to prevent infection of immunized animals by a pathogen. This finding should facilitate the identification of pathogen-specific protective epitopes selected from random phage peptide libraries, as it is simpler and less expensive than the conventional method of synthesis and coupling of phage-specific peptide ligand sequences for immunization
Interaction of the Viral Protein Genome Linked of Turnip Mosaic Potyvirus with the Translational Eukaryotic Initiation Factor (iso) 4E ofArabidopsis thalianaUsing the Yeast Two-Hybrid System

AbstractThe yeast LexA interaction trap was used to screen a cDNA library fromArabidopsis thalianain order to identify proteins that interact with the viral protein genome linked (VPg)–proteinase of turnip mosaic potyvirus. The screen allowed the isolation of four candidate cDNA clones. Clones pHC4, pHC21, and pHC40 were partially sequenced but no homologies to known proteins were found. However, the amino acid sequence deduced from the complete nucleotide sequence of pSW56 revealed that it was the eukaryotic initiation factor (iso) 4E [eIF(iso)4E]. Deletion analysis indicated that the VPg domain was involved in the interaction with the plant protein. Interaction between the viral protein and the cellular protein was confirmed by ELISA-based binding experiments. eIF(iso)4E plays an essential role in the initiation of the translation of capped mRNAs and its association with VPg would point to a role of the viral protein in the translation of the virus
A Cucumber Necrosis Virus Variant Deficient in Fungal Transmissibility Contains an Altered Coat Protein Shell Domain

AbstractLittle is currently known regarding the specific interactions that govern transmission of plant viruses by their vectors. A cucumber necrosis virus (CNV) variant (LL5) deficient in fungal transmissibility has been isolated from mechanically passaged CNV and characterized. Although LL5 accumulates to wild-type (WT) levels, is capable of rapid systemic infection, and produces stable, highly infectious particles, it is only inefficiently transmitted byOlpidium bornovanuszoospores. The LL5 coat protein (CP) gene was amplified by RT-PCR and cloned in place of the WT CNV CP gene in an infectious CNV cDNA clone. Particles derived from this construct also failed to be efficiently transmitted. The LL5 CP gene was sequenced and found to contain two amino acid substitutions relative to WT CNV CP. One substitution (Phe to Cys) occurred in the arm region and another (Glu to Lys) in the shell domain. These amino acid changes were separately introduced into the WT CNV genome throughin vitromutagenesis and it was found that the Glu to Lys change in the LL5 CP shell domain is largely responsible for the loss of transmissibility.In vitrobinding assays were developed to determine if the defect in transmissibility was due to a defect in binding zoospores. LL5 particles were found to bind less efficiently than WT CNV. Furthermore, the nontransmissible tomato bushy stunt virus did not detectably bind zoospores. These binding studies suggest that the specificity of CNV transmission byO. bornovanusoccurs through specific recognition of a putative zoospore receptor
Signaling via the CD2 Receptor Enhances HTLV-1 Replication in T Lymphocytes

AbstractHuman T lymphotropic virus type 1 (HTLV-1) is considered the etiologic agent of adult T cell leukemia/lymphoma and several chronic progressive immune-mediated diseases. Approximately 1–4% of infected individuals develop disease, generally decades following infection. Increased proviral transcription, mediated by the viral 40-kDatrans-activating protein, Tax, has been implicated in the pathogenesis of HTLV-1-associated diseases. Since the HTLV-1 promoter contains sequences responsive to cyclic AMP and protein kinase C, we hypothesized that lymphocyte activation signals initiated through the TCR/CD3 complex or CD2 receptor promote viral replication in HTLV-1-infected lymphocytes. We demonstrate that mAbs directed against the CD2, but not the CD3 receptor increase viral p24 capsid protein 1.5- to 5.7-fold in CD2/CD3+ HTLV-1-infected cell culture supernatants. Northern blot analysis demonstrated a 2.5- to 4-fold increase in all species of viral mRNA following CD2 cross-linking of OSP2/4 cells, an immortalized HTLV-1 cell line. Consistent with transcriptional regulation, reporter gene activity increased approximately 11-fold in CD2-stimulated Jurkat T cells cotransfected with a Tax-expressing plasmid and a CAT reporter gene construct under control of the HTLV-1 promoter. These data suggest a possible physiologic mechanism, whereby CD2-mediated cell adhesion and lymphocyte activation may promote viral transcription in infected lymphocytes
Viral Determinants of Pea Early Browning Virus Seed Transmission in Pea

AbstractPea early browning virus (PEBV) is a member of the genus, Tobravirus. It is transmitted by soil-inhabiting trichodorid nematodes and through seeds from diseased plants. By introducing mutations into the PEBV genome, we have studied the viral determinants of seed transmission in pea. Neither deleting a portion of the genome containing the three nonstructural genes in RNA2 nor the interuption of any of the three genes individually prevented PEBV seed transmission. However, a comparison of two PEBV isolates indicated a minor role for RNA2 or its products. In contrast, the removal of the coding sequence of the 12K gene in RNA1 almost completely abolished viral seed transmission. The virus lacking the 12K gene caused more severe symptoms on leaves and pods, and accumulated to a higher level than the wild-type virus in both types of tissues. However, the 12K deletion mutant accumulated poorly in anthers and carpels, and could not be detected in pollen grains and ovules. These results suggest that the 12K gene is involved in the infection of the gametic cells and hence the seed transmission of PEBV in pea
Early Detection of the Lytic LMP-1 Protein in EBV-Infected B-Cells Suggests Its Presence in the Virion

AbstractThe Epstein–Barr virus (EBV)-positive B958 cell line expresses two related membrane proteins encoded by BNLF-1 open reading frames. One protein (LMP-1) has been shown to be essential for the growth transforming properties of EBV. The second protein (the lytic LMP-1) is an amino-terminally truncated form of LMP-1 whose expression is associated with induction of EBV's lytic cycle. We have investigated the expression of full-length and lytic forms of LMP-1 immediately after infection of the EBV-negative, B-lymphoma cell line BJAB. Only the lytic LMP-1 protein is present in BJAB cells early (within minutes following addition of virus) after infection with virus derived from either uninduced or tetradecanoyl phorbol acetate and sodium butyrate-induced B958 cells. Lytic LMP-1 protein levels begin to decline by 48 hr after infection, whereas levels of full-length LMP-1 increase between 24 and 48 hr after infection and then remain constant. The presence of the lytic LMP-1 protein in infected cells is independent of both protein synthesis and virus internalization. We also find the lytic LMP-1 protein in BJAB cells early after infection (within 3 hr of addition of virus) with the HH514 strain of EBV, and HH514 cells treated with tetradecanoyl phorbol acetate and sodium butyrate, express high levels of both the lytic LMP-1 and full-length LMP-1 proteins. The lytic LMP-1 protein is enriched in purified virion preparations, and immunoelectron microscopic analysis indicates that EBV virions can be specifically labeled with anti-LMP-1 antisera. Together, these results are consistent with a model in which the lytic LMP-1 protein is present in the EBV virion and is carried into the B-cell upon infection and suggest a role for this protein in early infection events and/or in EBV's lytic cycle
Intravirion Generation of the C-Terminal Core Domain of HIV-1 Nef by the HIV-1 Protease Is Insufficient to Enhance Viral Infectivity

AbstractWild-type HIV-1 is more infectious thannef-deleted HIV-1 in both limiting dilution and single-cycle infectivity assays. Moreover, Nef expression from a separate plasmid in the virus-producing cells is capable of restoring the infectivity of geneticallynef-deficient HIV-1. These observations indicate that the virion itself is altered by Nef expression to promote viral infectivity. Sucrose gradient-purified HIV-1 virions contain full-length Nef protein and its inclusion is dependent on N-terminal myristylation of Nef. As myristylation-defective mutants of Nef do not enhance infectivity, incorporation of Nef into virions may mediate the enhanced infectivity. Studies with recombinant Nef have further shown that HIV-1 protease can cleave Nef into two polypeptides, a 20-kDa C-terminal core domain and a small N-terminal domain. Our analysis of purified HIV-1 virions also showed a 20-kDa form of Nef. The generation of this 20-kDa form of Nef was inhibited by an HIV-1 protease inhibitor, and its C-terminal core domain identity was confirmed through epitope-tagging. Immunoblots of virions demonstrated that 60–80% of the incorporated Nef is cleaved by the HIV-1 protease. This finding raised the possibility that the Nef core domain, which may no longer be tethered to the membrane due to absence of an N-terminal myristyl anchor, might mediate the enhanced infectivity. Therefore, a panel of mutants surrounding the proteolytic cleavage site in Nef were analyzed for effects on cleavage and enhancement of viral infectivity. Although some Nef mutants both failed to cleave and did not enhance viral infectivity, other mutants proved discordant in these functions. Specifically, two mutants that contained point mutations in the N-terminal domain cleaved normally, hence generating wild-type Nef core domain, yet failed to enhance infectivity. Thus, although the majority of the Nef protein in HIV-1 virions is cleaved by the viral protease into a 20-kDa C-terminal core domain, generation of this core domain of Nef appears insufficient to enhance HIV-1 infectivity. These findings suggest that protease cleavage of the Nef protein in virions is irrelevant for the infectivity function of Nef
Selective Inhibition of IκBα Phosphorylation and HIV-1 LTR-Directed Gene Expression by Novel Antioxidant Compounds

AbstractOxidative stress activates the NF-κB/Rel transcription factors which are involved in the activation of numerous immunoregulatory genes and the human immunodeficiency virus type 1 (HIV-1) long terminal repeat (LTR). In the present study, we examined the effects of established and novel compounds including antioxidants, ribonucleotide reductase inhibitors, and iron chelators on NF-κB activation and HIV LTR-mediated gene expression induced by TNF-α.N-Acetylcysteine (NAC), pyrrolidinedithiocarbamate (PDTC), and Trimidox (TD) at various concentrations inhibited TNF-α-induced NF-κB binding in Jurkat cells. Pretreatment of cells with these compounds prior to stimulation prevented IκBα degradation. Phosphorylation of IκBα, a prerequisite for its signal-induced degradation, was abrogated in these cells, indicating that oxidative stress is an essential step in the NF-κB activation pathway. On the other hand, iron chelators desferrioxamine, pyridoxal isonicotinoyl hydrazone (PIH), and salicylaldehyde isonicotinoyl hydrazone (SIH) showed no inhibition of TNF-α-induced NF-κB DNA-binding activity. Synergistic induction of HIV-1 LTR-mediated gene expression by TNF-α and the HIV-1 transactivator Tat in Jurkat cells was significantly suppressed in the presence of NAC and TD, but not PDTC. The inhibition of NAC and TD on LTR-directed gene expression was diminished when NF-κB-binding sites in the LTR were deleted, indicating that these compounds affected the NF-κB component of the synergism. Iron chelators PIH and SIH also showed some inhibitory effect on LTR-mediated gene activation, presumably through an NF-κB-independent mechanism. These experiments demonstrate that TD, at concentration 50 times lower than the effective concentration of NAC, potently inhibits NF-κB activity and suppresses HIV LTR expression
A Highly Conserved DNA Replication Module fromStreptococcus thermophilusPhages Is Similar in Sequence and Topology to a Module fromLactococcus lactisPhages

AbstractA highly conserved DNA region extending over 5 kb was observed inStreptococcus thermophilusbacteriophages. Comparative sequencing of one temperate and 26 virulent phages demonstrated in the most extreme case an 18% aa difference for a predicted protein, while the majority of the phages showed fewer, if any aa changes. The relative degree of aa conservation was not homogeneous over the DNA segment investigated. Sequence analysis of the conserved segment revealed genes possibly involved in DNA transactions. Three predicted proteins (orf 233, 443, and 382 gene product (gp)) showed nucleoside triphosphate binding motifs. Orf 443 gp showed in addition a DEAH box motif, characteristically found in a subgroup of helicases, and a variant zinc finger motif known from a phage T7 helicase/primase. Tree analysis classified orf 443 gp as a distant member of the helicase superfamily. Orf 382 gp showed similarity to putative plasmid DNA primases. Downstream of orf 382 a noncoding repeat region was identified that showed similarity to a putative minus origin from a crypticS. thermophilusplasmid. Four predicted proteins showed not only high degrees of aa identity (34 to 63%) with proteins fromLactococcus lactisphages, but their genes showed a similar topological organization. We interpret this as evidence for a horizontal gene transfer event between phages of the two bacterial genera in the distant past
Geographic Distribution and Genetic Variability of Hepatitis Delta Virus Genotype I

AbstractThree genotypes of hepatitis delta virus (HDV) have been identified, each with different geographic distributions and disease associations. To better define the geographic distribution and genetic variability of HDV genotype I, and to evaluate the extent of genome variability in populations with different patterns of HDV infection, we have analyzed the sequence of HDV RNA in the sera of 72 patients from different areas. Patients were primarily residents of the United States and areas in and around Greece, including Archangelos, Rhodes. All sequences obtained belonged to HDV genotype I, confirming the wide geographic distribution of this genotype and its predominance in Europe and the United States. In contrast to previous studies, phylogenetic analysis of this large and diverse group of sequences, along with all available previously published HDV sequences, showed no well-defined subtypes within genotype I. Low sequence diversity was found for isolates from the United States, Archangelos, Turkey, and Albania, suggesting that HDV was introduced more recently and/or from fewer sources into these areas as compared to mainland Greece, Italy, and north Africa, where sequence diversity is much greater. The low sequence diversity among isolates from Archangelos is particularly interesting in light of the unusually mild pattern of HDV disease found in this community. Comparison of nucleic acid and amino acid sequences within and among genotypes indicated both highly conserved regions as well as genotype-specific sequences that could be related to functional differences. The most distinctive of the latter was that corresponding to the C-terminal 19–20 amino acids of the long form of hepatitis delta antigen, which is highly conserved within each genotype but considerably diverged among them
The Large Subunit of Herpes Simplex Virus Type 2 Ribonucleotide Reductase (ICP10) Is Associated with the Virion Tegument and Has PK Activity

AbstractThe large subunit of herpes simplex virus type 2 (HSV-2) ribonucleotide reductase (ICP10) was identified in sucrose gradient-purified HSV-2 virions by immunoprecipitation/immunoblotting with antibody specific for the protein kinase (PK) domain. Immunoblotting of individual gradient fractions indicated that ICP10 cosediments with the major capsid protein and the highest virus titers. ICP10 was not labeled by iodination of purified virions, indicating that it is not located on the virion surface. After envelope glycoproteins were removed by detergent treatment, ICP10 was associated with capsid-tegument particles and became sensitive to trypsin digestion. The capsid-tegument-associated ICP10 was phosphorylated and had PK activityin vitroand on Immobilon membranes. A mutant ICP10 protein deleted in the PK domain (p95) was also associated with purified virions (ICP10ΔPK virus) but it lacked PK activity. The data indicate that ICP10 is contained within the tegument component where it retains intrinsic PK activity
Reciprocal Regulation of the Early Promoter Region of Bacteriophage HP1 by the Cox and CI Proteins

AbstractWe have identified a transcriptional switch at the early promoter region of bacteriophage HP1. This switch controls the transcription of the early lytic operon from the PR1and PR2promoters and the transcription of the lysogenic operon from the PLpromoter. The start sites of the three promoters were mapped, and using a chloramphenicol acetyl transferase assay, we have investigated the levels of transcription from the promoters in the absence or in the presence of two phage-encoded transcription factors: HP1 Cox and HP1 CI. The HP1 Cox protein repressed the production of PLtranscripts 30-fold, while the HP1 CI protein repressed lytic transcription at least 70-fold. Binding sites for HP1 Cox and CI were identified in the early promoter region; mutations of these sites eliminated transcriptional repression. In addition, a mutant CI protein was isolated which is temperature sensitive for repression. Taken together, these data demonstrate the reciprocal regulation of a transcriptional switch in which the actions of the two phage-encoded proteins at the phage early promoters determine the choice between lytic and lysogenic growth
A Noncanonical Poly(A) Signal, UAUAAA, and Flanking Elements in Epstein–Barr Virus DNA Polymerase mRNA Function in Cleavage and Polyadenylation Assays

AbstractTwo forms of the Epstein–Barr virus DNA polymerase (pol) mRNA (3.7 and 5.1 kb) have been detected, neither of which contains a canonical poly(A) signal. The 5.1-kb pol mRNA, which contains a rare poly(A) signal, UAUAAA, studied only in transcripts of Hepadnaviridae and a plant pararetrovirus, was analyzed in cleavage and polyadenylation assays. Incubation of the pol transcript in cell extracts produced relatively low efficiency of cleavage (12 to 14%), which was improved by conversion of the poly(A) signal to AAUAAA. Deletion of the UAUAAA signal abolished cleavage and polyadenylation. An auxiliary element, UUUGUA, 3–8 nt upstream of the poly(A) signal and two downstream core elements, a GU-rich sequence 36–46 nt, and an AUUUGUGU sequence 47–53 nt downstream of the signal (8–19 nt and 20–28 nt downstream of cleavage site) facilitated processing of pol mRNA. Replacement of sequences near the cleavage/poly(A) site affected cleavage accuracy. Binding of the 64-kDa cleavage stimulatory factor to the U-rich as well as the GU-rich elements correlated with cleavage efficiency. Thus the UAUAAA hexanucleotide plus the other cis-acting elements are clearly functional in the native pol mRNA, but are relatively inefficient. Implications of the use of an anomalous poly(A) signal and its elements are discussed
Recognition of Dengue Virus NS1-NS2a Proteins by Human CD4+ Cytotoxic T Lymphocyte Clones

AbstractWe examined nine dengue virus-specific human CD4+ CD8− cytotoxic T lymphocyte (CTL) clones for protein recognition, using recombinant vaccinia viruses which contain genes coding for dengue virus proteins. These clones were established from peripheral blood mononuclear cells of a donor previously immunized with a live-attenuated experimental dengue-1 vaccine. Of nine CD4+ T cell clones, seven were dengue-1-specific and two were dengue-1–dengue-3 cross-reactive. Four dengue-1-specific clones and one dengue-1–dengue-3 cross-reactive clone recognized epitopes within the NS1 or NS2a proteins. Analysis of human leukocyte antigen (HLA) restriction revealed that three dengue-1-specific clones are HLA-DR1-restricted and one dengue-1–dengue-3 cross-reactive clone is HLA-DPw3-restricted. These results indicate that NS1 and NS2a proteins as well as C, E, and NS3 proteins reported earlier contain one or more epitopes recognized by dengue virus-specific human CD4+ T lymphocytes
A Peptide Encoding a B-Cell Epitope from the N-Terminus of the Capsid Protein L2 of Bovine Papillomavirus-4 Prevents Disease

AbstractThe first 200 N-terminus amino acids of the L2 capsid protein of BPV-4 (designated L2a) are an effective prophylactic vaccine against BPV-4 infection. Vaccination with L2a induces the production of virus neutralizing antibodies, and when L2a antibodies are removed from immune sera, the sera lose their neutralization activity. L2a encodes three dominant B-cell epitopes, defined as epitope 1 (amino acids 101–120), epitope 2 (aa 131–151), and epitope 3 (aa 151–170). To investigate whether any of these epitopes are responsible individually or in combination for protection against viral challenge, synthetic peptides, corresponding to the three epitopes (peptides 11, 14, and 16, respectively) and conjugated to keyhole limpet hemocyanin (KLH) were tested in vaccination challenge experiments. Calves vaccinated with the three peptides together showed no evidence of papillomavirus infection; those vaccinated with peptide 14 alone developed only early lesions which did not progress to proper papillomas and regressed rapidly; those vaccinated with peptide 11 or peptide 16 alone were not protected and proceeded to develop papillomas. Therefore the three B-cell epitopes are not conventionally “neutralizing” when presented individually, but in combination they form a complex neutralization domain, and, in particular, epitope 2, represented by peptide 14, encodes a domain responsible for disease prevention