pinecone/core-2020-05-10-deduplication huggingface dataset:
The DNA Sequence of the Simian Varicella Virus Genome

AbstractIn nonhuman primates, simian varicella virus (SVV) causes a natural disease which is clinically similar to human varicella-zoster virus (VZV) infections. The SVV and VZV genomes are similar in size and structure and share extensive DNA homology. This report presents the complete DNA sequence of the SVV genome. SVV DNA is 124,138 bp in size, 746 bp shorter than VZV DNA, and 40.4% G + C. The viral genome includes a 104,104-bp unique long component bracketed by 8-bp inverted repeat sequences and a short component composed of a 4904-bp unique short region bracketed by 7557-bp inverted repeat sequences. A total of 69 distinct SVV open reading frames (ORFs) were identified, including three that are duplicated within the inverted repeats of the short component. Each of the SVV ORFs shares extensive homology to a corresponding VZV gene. The only major difference between SVV and VZV DNA occurs at the leftward terminus. SVV lacks a VZV ORF 2 homolog. In addition, SVV encodes an 882-bp ORF A that is absent in VZV, but has homology to the SVV and VZV ORF 4. The results of this study confirm the relatedness of SVV and VZV and provide further support for simian varicella as a model to investigate VZV pathogenesis and latency
COUP-TFII Is Up-regulated in Adenovirus Type 12 Tumorigenic Cells and Is a Repressor of MHC Class I Transcription

AbstractDown-regulation of the MHC class I enhancer in tumorigenic Ad12 cells is associated with strong binding of COUP-TF and negligible binding of activator NF-κB. By comparison, in nontumorigenic Ad5 cells, class I expression is high due to negligible binding of COUP-TF and strong binding of NF-κB. Here, we show that COUP-TFII, but not COUP-TFI, is expressed in Ad12-transformed cells. The dramatically stronger DNA binding of COUP-TFII to the class I enhancer in Ad12- compared to Ad5-transformed cells correlates with higher COUP-TFII promoter activity and higher levels of COUP-TFII mRNA and protein. Significantly, NF-κB p50/p52 double-knockout cells enabled us to demonstrate directly that COUP-TFII can completely repress both nonactivated and NF-κB-activated MHC class I transcription
Generation and Genetic Characterization of Avian Reovirus Temperature-Sensitive Mutants

AbstractThere currently is little known about the genetic and biological functions of avian reovirus (ARV), an atypical member of the family Reoviridae and the prototype of all nonenveloped viruses that induce syncytia formation. In this study, we created ARV temperature-sensitive (ts) mutants by chemical mutagenesis of ARV strain 138. We developed a novel efficiency of lysis (EOL) screening technique and used it and the classical efficiency of plating (EOP) assay to identify 17 ARV ts mutants. Pairwise mixed infections of these mutants and evaluation of recombinant progeny ts status led to their organization into seven recombination groups. This indicates that these new groups of mutants represent the majority of the ARV genome. To phenotypically characterize the ts mutants, progeny double-stranded RNA (dsRNA) produced at permissive and nonpermissive temperature was measured. Some mutants were capable of dsRNA synthesis at the restrictive temperature (RNA+), which indicates the effects of their ts lesions occur after RNA replication. Most mutants were RNA−, which suggests their mutations affect stages in viral replication that precede progeny genome synthesis
Responses of Coxsackievirus B4-Specific T-Cell Lines to 2C Protein—Characterization of Epitopes with Special Reference to the GAD65 Homology Region

AbstractCoxsackie B viruses (CBV) have been indicated as environmental triggers initiating autoimmune destruction of insulin-producing pancreatic β-cells, and molecular mimicry might be the mechanism. A prime candidate for inducing cross-reactive immune responses is a homology sequence, PEVKEK, found both in CBV4 2C protein and in GAD65. To characterize the CBV4-specific T-cell epitopes, overlapping peptides covering the 2C protein were synthesized and CBV4-specific T-cell lines were established from healthy and diabetic subjects. The T-cell epitopes were dependent on the HLA-DR genotype of the T-cell donor, but no difference between diabetic and healthy subjects could be detected. Peptide p4, which included the PEVKEK sequence, contained an HLA-DR1-restricted T-cell epitope. Three randomly selected CBV4-specific T-cell lines, which responded to peptide p4, failed to recognize GAD65 protein or GAD65 peptides containing the PEVKEK sequence. We conclude that the CBV4 2C protein is strongly immunogenic for T-cells and PEVKEK is included in a T-cell epitope. However, presentation of this epitope in the context of neutral HLA-DR1 allele does not support its role in pathogenesis of type 1 diabetes
Human Herpesvirus 8 Envelope-Associated Glycoprotein B Interacts with Heparan Sulfate-like Moieties

AbstractCell-surface heparan sulfate (HS) serves as an initial attachment receptor for several herpesviruses. The γ2-human herpesvirus-8 (HHV-8) or Kaposi's sarcoma associated herpesvirus DNA and transcripts have been detected in B cells, endothelial cells, macrophages, and epithelial cells. HHV-8 infects a variety of human and animal cell lines leading to latent or abortive infection. Our studies showed that this broad cellular tropism may be in part due to HHV-8's interaction with the ubiquitous host cell-surface HS-like molecules. HHV-8 binding to the target cells and the infection were inhibited by soluble heparan, a glycosaminoglycan (GAG) closely related to HS. Since HHV-8 gB possess a putative heparan-binding domain (HBD) in the extracellular domain, the interaction of gB with HS-like moieties was examined. Unlike gB of γ1-Epstein–Barr virus and γ2-murine herpesvirus 68, HHV-8 gB was expressed on the surface of the infected cell membranes and virion envelopes. Envelope-associated gB was made up of 75 and 54 kDa polypeptides forming disulfide-linked heterodimers and multimers. Rabbit anti-gB antibodies neutralized HHV-8 infection. Virion envelope-associated gB specifically bound to heparan-agarose, which was eluted by high concentration of soluble heparan, but not by chondroitin sulfates. In vitro transcribed and translated products of gB gene specifically bound to heparan-agarose beads, which was blocked by HS and heparan, but not by other GAGs such as chondroitin sulfates (A, B, and C), N-acetyl heparan, and de-N-sulfated heparan. Biotinylated gB peptide corresponding to the putative HBD also bound to heparan. These results suggest that gB plays an important role in the infectious process of HHV-8 and virus interaction with cell-surface HS-like moieties could be in part mediated by the envelope-associated gB
Nuclear Localization of the ORF2 Protein Encoded by Porcine Circovirus Type 2

AbstractInfectious porcine circovirus type 2 (PCV2) was generated following transfection of a porcine retina cell line (VIDO R1) with cloned circovirus DNA. Expression of open reading frame 2 (ORF2) was detected at 24 h postinfection and onwards increasingly throughout the infection by Western blot analysis using ORF2 specific polyclonal antibody. Moreover, the ORF2 protein was also detected in purified PCV2 virus, indicating that ORF2 is a structural component of PCV2 viral capsid. Nuclear localization of PCV2 ORF2 was demonstrated by immunofluorescence assay in PCV2-infected cells. An analysis of the subcellular localization of a series of truncation mutants of ORF2 fused with the green fluorescent protein indicated that the nuclear localization signal of ORF2 was conferred by the N-terminal 41 amino acids. This domain was further analyzed through site-directed mutagenesis, suggesting that the presence of basic amino acid residues at positions 12 to 18 and 34 to 41 are important for the strict nuclear targeting of PCV2 ORF2
Role of c-myc Regulation in Zta-Mediated Induction of the Cyclin-Dependent Kinase Inhibitors p21 and p27 and Cell Growth Arrest

AbstractLatency-associated Epstein–Barr virus (EBV) gene expression induces cell proliferation. Unlike the latency associated genes, lytic gene expression in EBV, as well as other herpesviruses, elicits cell cycle arrest. Previous studies have shown that the EBV immediate early lytic transactivator, Zta, induces a G0/G1 cell cycle arrest through induction of the cyclin-dependent kinase inhibitors, p21 and p27. Here we show that while EBV latency is intimately linked to activation of the protooncogene, c-myc, Zta represses c-myc expression. We also show that inhibition of c-myc expression is required for Zta-mediated growth arrest and for maximal induction of p21 and p27. Nevertheless, induction of p21 and p27 is also influenced by a c-myc-independent mechanism. A detailed genetic analysis of Zta's basic/DNA binding region identified two distinct subregions that contribute to full induction of p21 and p27. One subdomain influences p21 and p27 expression through the c-myc-dependent mechanism and the other subdomain influences p21 and p27 induction through the c-myc-independent pathway. Together, these studies further our understanding of the complex nature of Zta-induced growth arrest
The Use of Recombinant Baculoviruses for Sustained Expression of Human Cytomegalovirus Immediate Early Proteins in Fibroblasts

AbstractThe isolation of viruses with mutations in essential genes requires that they be propagated in cells expressing the wild-type proteins. This has been a particularly challenging problem for studying mutations in the human cytomegalovirus (HCMV) immediate early (IE) gene, IE2 86. In the past, we tried a number of approaches to derive human fibroblasts expressing wild-type IE2 86, but were unable to maintain expression of a fully functional protein. To overcome this obstacle, we developed a strategy whereby recombinant baculoviruses were used as vectors for the expression of HCMV IE proteins in primary human fibroblasts (FFs). The IE2 86 and IE1 72 cDNAs, as well as the genomic fragment of the UL122-123 region under the control of a chicken actin promoter, were introduced into the baculovirus genome by site-specific transposition in Escherichia coli. Recombinant “bacmid” DNAs were then transfected into Sf9 cells to generate recombinant baculoviruses. FFs infected at high m.o.i. with these baculoviruses expressed high levels of the HCMV protein for at least 1 week, as determined by immunofluorescence assays and Western blots. Moreover, the IE2 86 protein was found to be fully functional with respect to its ability to activate the HCMV UL112-113 early promoter. Recombinant baculoviruses expressing IE1 72 were also able to efficiently complement HCMV ie1 mutants. These data demonstrate the potential of using recombinant baculoviruses as vectors for the expression of toxic viral genes in human cells and for subsequent isolation of mutant HCMV lacking these essential genes
Mutations in the N-Terminus of VP5 Alter Its Interaction with the Scaffold Proteins of Herpes Simplex Virus Type 1

AbstractDuring the assembly process of herpes simplex virus type 1 capsids, there is an essential interaction between the C-terminal tail of the scaffold proteins (22a and 21) and the major capsid protein (VP5). Recent studies of spontaneous revertant viruses that overcome a blocked maturation cleavage site of the scaffold proteins have shown that the N-terminus of VP5 is important for this interaction. One of the revertant viruses, PR7, encodes a second-site mutation at residue 69 of VP5 which unlike wild-type VP5 fails to interact with 22a and thus gives white colonies in the yeast two-hybrid assay. In the present study a small DNA fragment, encoding residues 1 to 85 of wild-type and PR7 VP5, was mutagenized using error-prone PCR. Mutagenized DNA was used in the yeast two-hybrid assay to identify mutations in wild-type VP5 that resulted in loss of 22a binding (white colonies), or in PR7 VP5 that resulted in a gain of function (blue colonies). For the loss of function experiments, using KOS VP5, a row of eight thymidine nucleotides (codons 37–40) resulted in many frameshift mutations, which led us to terminate the study without reaching a statistically significant result. For the PR7 experiment, 30 clones were identified that had single amino acid substitutions, and these mutations were localized to amino acids 27–45 and 63–84 of VP5. The most frequent mutation was a reversion back to wild-type. The next most frequent were E28K and N63S, and these gave the highest β-galactosidase enzyme activities (indicative of PR7VP5-22a interaction), 30 and 20% of wild-type, respectively. When E28K and N63S were transferred into the wild-type VP5 background, that is, in the absence of the PR7 mutation, they gave rise to different phenotypes. The E28K mutation lost its ability to interact with the scaffold proteins as judged by this assay. Therefore, it may be acting as a compensatory mutation whose phenotype is only expressed in the presence of the original PR7 mutation. However, the N63S mutation in the wild-type VP5 background increased the interaction, as judged by the β-galactosidase activity, by a factor of 9 relative to when the PR7 mutation was present. Even more surprising, in the absence of the PR7 mutation the enzyme activity was still greater, by a factor of 2, than that observed for wild-type VP5. This study provides further evidence that the N-terminus of VP5 is in intimate association with the C-terminus of the scaffold proteins
Binding of PKA-RIIα to the Adenovirus E1A12S Oncoprotein Correlates with its Nuclear Translocation and an Increase in PKA-dependent Promoter Activity

AbstractThe adenovirus type 12 (Ad12) E1A12S oncoprotein utilizes the cAMP/protein kinase A (PKA) signal transduction pathway to activate expression of the viral E2 gene, the products of which are essential for viral replication. A central unsolved question is, however, whether E1A12S interacts directly with PKA in the process of promoter activation. We show here that E1A12S binds to the regulatory subunits (R) of PKA in vitro and in vivo. Interaction depends on the N-terminus and the conserved region 1 (CR1) of E1A12S. Both domains are also essential for the activation of viral E2 gene expression. Infection of cells with Ad12 leads to the cellular redistribution of RIIα from the cytoplasm into the nucleus. Furthermore, RIIα is also located in the nucleus of cells transformed by E1 of Ad12 and transient expression of E1A12S leads to the redistribution of RIIα into the nucleus in a N-terminus- and CR1-dependent manner. Cotransfection of E1A12S with RIIα results in strong activation of the E2 promoter. Based on these results we conclude that E1A12S functions as a viral A-kinase anchoring protein redistributing RIIα from the cytoplasm into the nucleus where it is involved in E1A12S-mediated activation of the E2 promoter
HIV Envelope Proteins Differentially Utilize CXCR4 and CCR5 Coreceptors for Induction of Apoptosis

AbstractThe involvement of CXCR4 and CCR5 coreceptors in apoptosis induced by the HIV envelope (Env) proteins has not been well defined. We found that simian human immunodeficiency virus (SHIV) virus-like particles (VLPs) containing HIV Env proteins preferentially induce apoptosis of cells corresponding to their coreceptor usage in a CD4+ T cell line. We also demonstrated that induction of apoptosis by SHIV VLPs is correlated with coreceptor usage in a non-T cell line. We examined the effects of SHIV VLPs containing Env proteins derived from either a T-cell-tropic HIV (BH10) strain or a dual-tropic HIV (89.6) strain on induction of apoptosis in recombinant CD4+ human osteosarcoma (HOS) cells expressing either CXCR4 (HOS-CD4.CXCR4) or CCR5 coreceptors (HOS-CD4.CCR5). HOS-CD4.CXCR4 or HOS-CD4.CCR5 cells were activated with concanavalin A and cocultured with VLPs. By TUNEL (TdT-mediated dUTP-X nick end labeling) fluorescence staining and flow cytometry assays, SHIV BH10 VLPs were found to preferentially induce apoptosis in HOS-CD4.CXCR4 cells but not in HOS-CD4 or HOS-CD4.CCR5 cells. On the other hand, SHIV 89.6 VLPs induced an elevated level of apoptosis in both HOS-CD4.CXCR4 and HOS-CD4.CCR5 cells in a dose-dependent fashion. These data demonstrate that T-cell-tropic BH10 Env preferentially utilizes CXCR4, but not CCR5, for induction of apoptosis, whereas dual-tropic 89.6 Env induces apoptosis in both CXCR4- and CCR5-containing cell lines
White Spot Syndrome Virus Envelope Protein VP28 Is Involved in the Systemic Infection of Shrimp

AbstractWhite spot syndrome virus (WSSV) is a large DNA virus infecting shrimp and other crustaceans. The virus particles contain at least five major virion proteins, of which three (VP26, VP24, and VP15) are present in the rod-shaped nucleocapsid and two (VP28 and VP19) reside in the envelope. The mode of entry and systemic infection of WSSV in the black tiger shrimp, Penaeus monodon, and the role of these proteins in these processes are not known. A specific polyclonal antibody was generated against the major envelope protein VP28 using a baculovirus expression vector system. The VP28 antiserum was able to neutralize WSSV infection of P. monodon in a concentration-dependent manner upon intramuscular injection. This result suggests that VP28 is located on the surface of the virus particle and is likely to play a key role in the initial steps of the systemic WSSV infection in shrimp
Vector Specificity of Barley Yellow Dwarf Virus (BYDV) Transmission: Identification of Potential Cellular Receptors Binding BYDV-MAV in the Aphid, Sitobion avenae

AbstractTwo proteins (SaM35 and SaM50) isolated from head tissues of the aphid vector, Sitobion avenae, were identified as potential receptors for barley yellow dwarf virus MAV isolate (Luteoviridae) based on MAV virus overlay assays and immunoblots of urea SDS 2-D gels. An anti-idiotypic antibody (MAV4 anti-ID) that mimics an epitope on MAV virions and competes with MAV in antibody binding assays also bound to SaM50 and SaM35 and to six additional proteins including a GroEL homolog. No MAV-binding proteins were detected from the nonvector aphid, Rhopalosiphum maidis, although MAV4 anti-ID did react with four proteins from R. maidis. It is hypothesized that SaM35 and SaM50 may be MAV receptors involved in MAV transmission based on their high affinity for MAV and their unique association with the vector, S. avenae. The additional aphid proteins binding the MAV4 anti-ID may represent less specific virus-binding proteins facilitating transmission through different aphid tissues
VZV gB Endocytosis and Golgi Localization Are Mediated by YXXφ Motifs in Its Cytoplasmic Domain

AbstractThe cytoplasmic domains of many membrane proteins contain sorting signals that mediate their endocytosis from the plasma membrane. VZV gB contains three consensus internalization motifs within its cytoplasmic domain: YMTL (aa 818–821), YSRV (aa 857–860), and LL (aa 841–842). To determine whether VZV gB is internalized from the plasma membrane, and whether these motifs are required for its endocytosis, we compared the internalization of native gB to that of gB containing mutations in each of the predicted internalization motifs. VZV gB present on the surface of transfected cells associated with clathrin and was efficiently internalized to the Golgi apparatus within 60 min at 37°C. VZV gB containing the mutation Y857 failed to be internalized, while gB-Y818A was internalized but did not accumulate in the Golgi. These data indicate that the internalization of VZV gB, and its subsequent localization to the Golgi, is mediated by two tyrosine-based sequence motifs in its cytoplasmic domain
Beet Necrotic Yellow Vein Virus Particles Localize to Mitochondria during Infection

AbstractFluorescent beet necrotic yellow vein virus (BNYVV) particles were produced by replacing part of the readthrough domain of the minor coat protein P75 with the green fluorescent protein (GFP). The recombinant virus was functional in plants and P75–GFP was incorporated at one end of the rod-shaped virions. Laser scanning confocal microscopy and transmission electron microscopy showed that virus-like particles, almost certainly authentic BNYVV virions, localized to the cytoplasmic surface of mitochondria at early times postinfection but relocated at later times to semiordered clusters in the cytoplasm. This is the first report of specific targeting of plant virus particles to the mitochondria in vivo
Mouse Hepatitis Virus Replicase Protein Complexes Are Translocated to Sites of M Protein Accumulation in the ERGIC at Late Times of Infection

AbstractThe coronavirus mouse hepatitis virus (MHV) directs the synthesis of viral RNA on discrete membranous complexes that are distributed throughout the cell cytoplasm. These putative replication complexes are composed of intimately associated but biochemically distinct membrane populations, each of which contains proteins processed from the replicase (gene 1) polyprotein. Specifically, one membrane population contains the gene 1 proteins p65 and p1a-22, while the other contains the gene 1 proteins p28 and helicase, as well as the structural nucleocapsid (N) protein and newly synthesized viral RNA. In this study, immunofluorescence confocal microscopy was used to define the relationship of the membrane populations comprising the putative replication complexes at different times of infection in MHV-A59-infected delayed brain tumor cells. At 5.5 h postinfection (p.i.) the membranes containing N and helicase colocalized with the membranes containing p1a-22/p65 at foci distinct from sites of M accumulation. By 8 to 12 h p.i., however, the membranes containing helicase and N had a predominantly perinuclear distribution and colocalized with M. In contrast, the p1a-22/p65-containing membranes retained a peripheral, punctate distribution at all times of infection and did not colocalize with M. By late times of infection, helicase, N, and M each also colocalized with ERGIC p53, a specific marker for the endoplasmic reticulum–Golgi–intermediate compartment. These data demonstrated that the putative replication complexes separated into component membranes that relocalized during the course of infection. These results suggest that the membrane populations within the MHV replication complex serve distinct functions both in RNA synthesis and in delivery of replication products to sites of virus assembly
Differential Effects of Parainfluenza Virus Type 3 on Human Monocytes and Dendritic Cells

AbstractTo understand the lack of protective immunity observed after infection with parainfluenza virus type 3 (PIV3), we tested the effect of the virus on human monocytes and monocyte-derived immature dendritic cells (DCs). Expression of viral antigens on the cell surfaces correlated with replication of the virus, which was marginal in monocytes but extremely efficient in DCs. The virus increased monocyte survival at least in part through the production of granulocyte–macrophage colony-stimulating factor but, in contrast, accelerated DC apoptosis. In addition, PIV3 infection failed to activate monocytes but induced maturation of DCs with increased expression of CD54, HLA-DR, CD86, and CD83 and production of bioactive IL-12. However, PIV3-infected DCs demonstrated low stimulatory properties in DC–T cell cocultures, a finding that could not be attributed to the production of infectious virus or IL-10. These results demonstrate for the first time that PIV3 dramatically modifies the survival and/or the function of antigen-presenting cells and might therefore prevent the development of efficient antiviral immune responses