pinecone/core-2020-05-10-deduplication huggingface dataset:
The Complete DNA Sequence of Myxoma Virus

AbstractMyxomatosis in European rabbits is a severely debilitating disease characterized by profound systemic cellular immunosuppression and a high rate of mortality. The causative agent, myxoma virus, is a member of the poxvirus family and prototype of the Leporipoxvirus genus. As a major step toward defining the genetic strategies by which the virus circumvents host antiviral responses, the genomic DNA sequence of myxoma virus, strain Lausanne, was determined. A total of 171 open reading frames were assigned to cover the 161.8-kb genome, including two copies each of the 12 genes that map within the 11.5-kb terminal inverted repeats. Database searches revealed a central core of approximately 120 kb that encodes more than 100 genes that exhibit close relationships to the conserved genes of members of other poxvirus genera. Open reading frames with predicted signal sequences, localization motifs, or homology to known proteins with immunomodulatory or host-range functions were examined more extensively for predicted features such as hydrophobic regions, nucleic acid binding domains, ankyrin repeats, serpin signatures, lectin domains. and structural cysteine spacings. As a result, several novel, potentially immunomodulatory proteins have been identified, including a family with multiple ankyrin-repeat domains, an OX-2 like member of the neural cell adhesion molecule family, a third myxoma serpin, a putative chemokine receptor fragment, two natural killer receptor-like species, and a variety of species with domains closely related to diverse host immune regulatory proteins. Coupled with the genomic sequencing of the related leporipoxvirus Shope fibroma virus, this work affirms the existence of a conserved complement of poxvirus-specific core genes and expands the growing repertoire of virus genes that confer the unique capacity of each poxvirus family member to counter the immune responses of the infected host
Evolution of Poliovirus Type I during 5.5 Years of Prolonged Enteral Replication in an Immunodeficient Patient

AbstractPoliovirus type 1 was isolated from an immunodeficient patient 4 days after onset of paresis (IS1) and after 5.5 years of prolonged enteral virus replication (IS2). Antigenic characterization revealed that IS1 was Sabin 1-like, whereas IS2 reacted like poliovirus 1 Mahoney. Complete genomic sequencing demonstrated the phylogenetic relationship (94.9% identity) of IS1 and IS2, which differed from the most closely related Sabin 1 by 5.4 and 8.3%, respectively. Both isolates had revertant-like mutations at nucleotides 480 and 6203. Deduced amino acid sequences indicated significant changes between IS1 and IS2 at the neutralizing antigenic site 1. Prolonged enteral replication, evolution, and shedding of poliovirus by immunodeficient patients should be considered in the poliovirus eradication strategy
The Hypervariable Region 1 Protein of Hepatitis C Virus Broadly Reactive with Sera of Patients with Chronic Hepatitis C Has a Similar Amino Acid Sequence with the Consensus Sequence

AbstractHypervariable region 1 (HVR1) proteins of hepatitis C virus (HCV) have been reported to react broadly with sera of patients with HCV infection. However, the variability of the broad reactivity of individual HVR1 proteins has not been elucidated. We assessed the reactivity of 25 different HVR1 proteins (genotype 1b) with sera of 81 patients with HCV infection (genotype 1b) by Western blot. HVR1 proteins reacted with 2–60 sera. The number of sera reactive with each HVR1 protein significantly correlated with the number of amino acid residues identical to the consensus sequence defined by Puntoriero et al. (G. Puntoriero, A. Lahm, S. Zucchelli, B. B. Ercole, R. Tafi, M. Penzzanera, M. U. Mondelli, R. Cortese, A. Tramontano, G. Galfre', and A. Nicosia. 1998. EMBO J. 17, 3521–3533.) (r = 0.561, P < 0.005). The most widely reactive HVR1 protein, 12-22, had a sequence similar to the consensus sequence. The peptide with C-terminal 13-amino-acids sequence of HVR1 protein 12-22 (NH2-CSFTSLFTPGPSQK) was injected into rabbits as an immunogen. The rabbit immune sera reacted with 9 of 25 HVR1 proteins of genotype 1b including HVR1 protein 12-22 and with 3 of 12 proteins of genotype 2a. These results indicate that the HVR1 protein broadly reactive with patients' sera has a sequence similar to the consensus sequence, can induce broadly reactive sera, and could be one of the candidate immunogens in a prophylactic vaccine against HCV
Recombinant Hepatitis E Capsid Protein Self-Assembles into a Dual-Domain T = 1 Particle Presenting Native Virus Epitopes

AbstractThe three-dimensional structure of a self-assembled, recombinant hepatitis E virus particle has been solved to 22-Å resolution by cryo-electron microscopy and three-dimensional image reconstruction. The single subunit of 50 kDa is derived from a truncated version of the open reading frame-2 gene of the virus expressed in a baculovirus system. This is the first structure of a T = 1 particle with protruding dimers at the icosahedral two-fold axes solved by cryo-electron microscopy. The protein shell of these hollow particles extends from a radius of 50 Å outward to a radius of 135 Å. In the reconstruction, the capsid is dominated by dimers that define the 30 morphological units. The outer domain of the homodimer forms a protrusion, which corresponds to the spike-like density seen in the cryo-electron micrograph. This particle retains native virus epitopes, suggesting its potential value as a vaccine
Small Amino Acid Changes in the V3 Loop of Human Immunodeficiency Virus Type 2 Determines the Coreceptor Usage for CXCR4 and CCR5

AbstractHIV-2 GH-1 is a molecular clone derived from an AIDS patient from Ghana. In contrast to the prototypic molecular clone ROD, GH-1 exhibits a narrow range of target cell specificity. By an infectious assay using HeLa-CD4 cells stably transfected with an HIV-1 LTR-β-galactosidase reporter gene and transiently expressing various cloned chemokine receptors, we have examined the coreceptor usage of GH-1. In contrast to ROD, which uses principally CXCR4, GH-1 was found to use mainly if not exclusively CCR5 but not CXCR4. The distinct coreceptor usage of these two molecular clones allowed us to further map the region of gp120 that is important for the coreceptor specificity. By constructing a series of chimeric viruses between GH-1 and ROD, we have demonstrated that the C-terminal half of the V3 loop region of gp120 determines the differential coreceptor usage between GH-1 and ROD, and only a few amino acid differences in this region appear to be able to shift the specificity between CCR5 and CXCR4. Notably, the shift in the coreceptor usage from CCR5 to CXCR4 is associated with an increase in the net positive charge in the V3 region
Bovine Leukemia Virus Gag Particle Assembly in Insect Cells: Formation of Chimeric Particles by Domain-Switched Leukemia/Lentivirus Gag Polyprotein

AbstractA key stage in the life cycle of C-type retroviruses is the assembly of Gag precursor protein at the plasma membrane of infected cells. Here we report the assembly of bovine leukemia virus (BLV) gag gene product into virus-like particles (VLPs) using the baculovirus expression system. Expression of BLV Pr44Gag resulted in the assembly and release of VLPs, thereby confirming the ability of retroviral Gag polyprotein to assemble and bud from insect cells. Efficient particle formation required a myristoylation signal at the N-terminus of BLV Pr44Gag. Recombinant baculoviruses expressing matrix (MA) or capsid–nucleocapsid (CA–NC) proteins of BLV were generated but neither of these domains was capable of assembling into particulate structures. To assess the compatibility of Gag domains between leukemia and lentivirus groups three different recombinant chimeras each expressing MA of one virus (e.g., simian immunodeficiency or BLV) and CA–NC of another (e.g., BLV or human T-cell leukemia virus type-I) were constructed. Each of the chimeric proteins assembled efficiently and budded as VLPs, suggesting that the MA and CA domains of these two evolutionary divergent retrovirus groups can be functionally exchanged without perturbation of Gag VLP formation. The lenti-leukemia chimeric Gag approach has potential for studying protein–protein interactions in other retroviruses
Nuclear F-Actin Is Required for AcMNPV Nucleocapsid Morphogenesis

AbstractDuring nucleocapsid assembly, filamentous actin (F-actin) colocalizes with the major capsid protein of Autographa californica M nucleopolyhedrovirus (AcMNPV) within nuclei of infected lepidopteran host cells. Cytochalasin D (CD) disrupts actin filaments and prevents assembly of progeny AcMNPV, suggesting that nuclear F-actin is essential for nucleocapsid morphogenesis. Direct proof for this hypothesis was provided by the demonstration that two AcMNPV recombinants engineered to express either wild-type- or CD-resistant actin at equivalent rates were differentially sensitive to CD. The AcMNPV requirement for nuclear F-actin is unique among intracellular pathogens and may constitute a significant host range factor
Integrin αVβ5 Is Not Involved in Adeno-Associated Virus Type 2 (AAV2) Infection

AbstractαVβ5 integrin was recently proposed as a coreceptor for adeno-associated virus type 2 (AAV2) infection (Summerford et al., 1999, Nat. Med. 5, 78–82), based mainly on the direct binding of AAV2 to denatured β5 by virus overlay assay. In studies using purified natural or recombinant human integrin αVβ5 we were unable to demonstrate AAV2 binding, either by virus overlay or by liquid binding assay. Furthermore, neither purified integrin αVβ5, nor RGD peptides, nor functional blocking monoclonal antibody blocked rAAV2 transduction. These data strongly suggest that integrin αVβ5 is not involved in AAV2 infection
Enhanced HIV-1 Replication by Chemokines Constitutively Expressed in Secondary Lymphoid Tissues

AbstractPersistent infection of human immunodeficiency virus (HIV) takes place in the secondary lymphoid tissues even during clinically latent stages. The CC chemokines secondary lymphoid tissue chemokine (SLC) and EBI1-ligand chemokine (ELC) are constitutively expressed in the secondary lymphoid tissues. They share CCR7 expressed on lymphocytes and mature dendritic cells and play key roles in the trafficking of these types of cells into the secondary lymphoid tissues. Here we report that growth of both X4 and R5 strains of HIV-1 in activated peripheral blood T cells was enhanced by SLC. The enhancing effect of SLC was abrogated by pretreatment of cells with pertussis toxin, indicating the involvement of signaling via a receptor coupled with a Gαi class of G-protein. Furthermore, SLC was found to enhance the promoter activity of HIV-1 LTR. These results suggest that signaling via CCR7 has a strong positive effect on HIV growth. Thus, SLC and ELC may contribute to persistent infection of HIV in the secondary lymphoid tissues by promoting viral replication in activated T cells
Four Consecutive Arginine Residues at Positions 836–839 of EBV gp110 Determine Intracellular Localization of gp110

AbstractEpstein–Barr virus (EBV) glycoprotein 110 (gp110) has sequence homology with herpes simplex virus-1 (HSV-1) gB; however the role of gp110 in EBVs' life cycle differs from that of gB. Unlike HSV-1 gB, which is essential for HSV-1 infection but dispensable for virus production, gp110 is required for assembly and egress of EBV. EBV gp110 is found mainly in the endoplasmic reticulum (ER)/nuclear membrane, whereas little or no gp110 is detected in the plasma membrane or a mature viral particle. Conversely, HSV-1 gB is abundant in the envelope of mature virions and in the plasma membrane as well as in the ER/nuclear membrane of HSV-1-infected cells. Interestingly, there are four consecutive arginine residues (at positions 836–839 of gp110) in the C-terminal domain previously shown to be important for gp110's intracellular localization. To determine whether these arginines function as an ER/nuclear localization signal, point mutants were constructed differentially substituting the four arginines. The glycosylation pattern and intracellular localization of the mutants were investigated by assessing sensitivity to endoglycosidase H (endo H) digestion and performing indirect immunofluorescence assays. Substitution of part of the four arginines changed the glycosylation profile and targeting of gp110. In addition, mutations preserving the net charge of the four arginines as well as those causing net charge shift resulted in the changed intracellular localization and altered glycosylation pattern. These results suggest that not only the net charge but also the conformation of the four arginines are important for gp110's processing and subcellular localization
Relationship between Productive HIV-1 Infection of Macrophages and CCR5 Utilization

AbstractHIV-1 isolates exhibit specificity for infection of immortalized T-cell lines and macrophages. The distinct cellular tropisms have been attributed to expression of coreceptors CXCR4 or CCR5, respectively. However, it is unclear whether or not other tissue-specific determinants regulate entry. The current study uses a panel of viruses to analyze the relationship between CCR5 utilization and macrophage infection. Only chimeric viruses with the entire V3 loop from macrophage-tropic isolates, ADA or SF162, were able to infect macrophages. In contrast, chimeric viruses with smaller portions of the ADA V3 loop or the V3 loop of SF2, sufficient to allow CCR5 use, were insufficient for macrophage infection. PCR analysis showed that the defect in macrophage infection of the latter viruses was due to a defect in entry. Moreover, strains capable of infecting macrophages showed relative resistance to neutralization by anti-CCR5 antibody, 2D7, compared to strains which utilize CCR5 but are incapable of macrophage infection
Properties of the Adenovirus Type 40 E1B Promoter That Contribute to Its Low Transcriptional Activity

AbstractThe adenovirus type 5 (Ad5) E1B promoter contains two elements essential for maximal activity, a TATA box and a GC box. The enteric adenovirus type 40 (Ad40) E1B promoter has a TATA box sequence identical to that of Ad5 and a GC box that fits the Sp1 binding site consensus. Nevertheless, Ad40 E1B RNA synthesis is severely impaired in HeLa cells, attributable in part at least to the weak transactivating activity of Ad40 E1A. However, the responsiveness of Ad40 early promoters to E1A transactivation has not been directly demonstrated. Using a transient expression assay with a chloramphenicol acetyl transferase (CAT) reporter gene, the Ad40 E1B promoter was very poorly transactivated by E1A of both Ad40 and Ad5 and showed only a limited response to the promiscuous varicella zoster virus transactivator p140. Construction of Ad5 recombinant viruses expressing the CAT gene under the control of the Ad5 or Ad40 E1B promoter allowed detection and measurement of expression from the Ad40 E1B promoter in a well-defined background and showed that overall activity is some 100-fold lower than for the Ad5 E1B promoter. Deletion analysis revealed that sequences upstream of the Sp1 binding site down-modulated Ad40 E1B promoter responsiveness, and two protein binding sites, identified by DNase footprinting and gel retardation assay, may be implicated in this effect. Gel shift analysis also showed that the Ad40 Sp1 binding site had a reduced affinity for Sp1 protein, relative to the Ad5 site, and that the context as well as the core sequence had an influence on Sp1 recognition
Characterization of Intertypic Recombinants of the Epstein–Barr Virus from the Body-Cavity-Based Lymphomas Cell Lines BC-1 and BC-2

AbstractEpstein–Barr Virus (EBV) can infect and transform human B-lymphocytes and has been associated with numerous human malignancies. Two distinct types of EBV have been described, EBV-1 and EBV-2. Whereas type 1 is known to be most widespread throughout the healthy adult population, type 2 EBV has been shown to be significantly present in certain T-cell immunocompromised patients. Some evidence also suggests that such immune impairment promotes coinfection with multiple strains of EBV and fosters the development of intertypic recombinant viruses. In this work, we have analyzed two established body-cavity-based lymphoma or primary effusion lymphoma cell lines, BC-1 and BC-2, for the presence of intertypic EBV recombinants. Using PCR primers to amplify across several markers in the genome, we have typed the BC-1 and BC-2 EBV at these loci. Immunoblot analysis of the EBNA1 protein expressed by these cell lines also suggests a change in EBV typing at this locus in these genomes. Additionally, we have analyzed the expression patterns of the latent EBNA proteins from these viruses and performed Southern blot analysis of the BamHI- and EcoRI-digested genomes to detect variations occurring from type I and II genomes. On the basis of these data, we suggest that the genomes of EBV in BC-1 and BC-2 are intertypic recombinants of type 1 and type 2 EBV genomes. This work corroborates other reports that intertypic EBV recombinants occur in the immunocompromised population. It is likely that intertypic recombination is a mechanism by which novel variants of EBV emerge having selective advantages over a strictly type 1 or type 2 strain
Localization of Rubella Virus Core Particles in Vero Cells

AbstractRubella virus (RV) infection induces a variety of morphological changes in the host cell including the modification of lysosomes to produce “replication complexes” and the alteration of mitochondrial morphology and distribution. The morphogenesis of RV was further characterized with particular emphasis on the localization of RV core particles. Thin-section electron microscopy (TSEM) studies indicated that RV core-like particles, measuring approximately 33 nm in diameter, were found associated with RV replication complexes. Immunogold-labeling electron microscopy (EM) using monoclonal antibodies to RV capsid proteins confirmed that these particles were viral cores. RV core particles were also detected in association with mitochondria as observed by TSEM and immunogold-labeling EM using monoclonal antibodies to capsid or polyclonal antibodies to RV virions. The results of this study indicate that the localization of RV core particles in relation to replication complexes is similar to that found for the alphaviruses. However, the association of RV core particles with mitochondria appears unique within the family Togaviridae
Mapping of Protein Domains of Hepatitis A Virus 3AB Essential for Interaction with 3CD and Viral RNA

AbstractThe small hydrophobic protein 3AB of the picornaviruses, encompassing the replication primer 3B, has been suggested to anchor the viral replication complex to membranes. For hepatitis A virus (HAV) 3AB, we have previously demonstrated its ability to form stable homodimers, to bind to membranes, and to interact specifically with RNA, implicating its multiple involvement in viral replication. In the present report, we show that HAV 3AB additionally interacts with HAV protein 3CD, a feature also described for the corresponding polypeptide of poliovirus. By assessing the interactions of three deletion mutants, distinct domains of HAV 3AB were mapped. The hydrophobic domain and the 3B moiety were found to be essential for the 3AB interaction with 3CD. Both electrostatic and hydrophobic forces are involved in this interaction. The cluster of charged amino acid residues at the C terminus of 3A seems to determine the specificity of 3AB interaction with RNA structures formed at either terminus of the HAV genome. Furthermore, our data implicate that 3A can interact with HAV RNA. Compared with poliovirus 3AB, which by itself is a nonspecific RNA-binding protein, HAV 3AB specifically recognizes HAV RNA structures that might be of relevance for initiation of viral RNA replication
The Nucleotide Sequence and Genome Organization of Sclerophthora macrospora Virus B

AbstractSclerophthora macrospora Virus B (SmV B) found in S. macrospora, the pathogenic fungus responsible for downy mildew in gramineous plants, is a small icosahedral, monopartite virus containing a positive-strand ssRNA genome. In the present study, the complete nucleotide sequence of the SmV B genome was determined. The viral genome consists of 5533 nucleotides and has two large open reading frames (ORFs). ORF1 encodes a putative polyprotein containing the motifs of chymotrypsin-related serine protease and RNA-directed RNA polymerase. ORF2 encodes a capsid protein. The deduced amino acid sequence shows some similarity to those of certain positive-strand RNA viruses, but the genome organization is characteristic and distinct from those of other known fungal RNA viruses. These results suggest that SmV B should be classified into a new group of mycoviruses
Influenza Virus Neuraminidase Alters Allogeneic T Cell Proliferation

AbstractInfluenza virus elicits good cellular and humoral immune responses. Unlike the cytotoxic T lymphocyte response to many other antigens, the cytotoxic T lymphocyte response to influenza virus is CD4+ T cell independent, suggesting that viral infection of antigen-presenting cells may alter their capacity to stimulate T cell responses. To clarify the role of influenza virus in these functional alterations, we compared T cell responses to uninfected and A/PR/8/34-infected dendritic cells (DC). DC were prepared from the bone marrow of C57BL/6 (H2b) mice and used to stimulate in vivo and in vitro alloreactive T cell responses. In both cases, influenza virus infection increased the capacity of DC to stimulate T cell proliferation. This enhancement was blocked by antibodies specific for neuraminidase (NA), but not hemagglutinin. Infection was not required to observe enhanced T cell proliferation, showing that NA from exogeneous virus particles can facilitate this effect. These results are the first to show that influenza virus alters the capacity of DC to stimulate T cell proliferation through mechanisms mediated by viral NA
Synthesis in Escherichia coli of Avian Reovirus Core Protein ςA and Its dsRNA-Binding Activity

AbstractThe genome segment S2 of avian reovirus (ARV) S1133 was cloned and sequenced. The entire S2 nucleotide sequence is 1325 bp long with one long open reading frame that encodes a protein of 415 amino acids, corresponding to ςA, a major core protein of ARV. S2 possesses a pentanucleotide, TCATC, at the 3′-terminus of its plus strand, common to other known genome segments of ARV and to 10 genome segments of mammalian reovirus. Amino acid sequence analysis revealed that ςA contains a carboxy-terminal region (one-fourth of the protein) that is formed from α-helices and β-turns, and the remainder (three-fourths of the protein) is formed predominantly from β-strands and β-turns. Analysis of binding activity to poly(rI)–poly(rC)–agarose suggested that ARV protein A present in total virus-infected chicken embryo fibroblasts (CEF) had dsRNA-binding activity. To further characterize the binding activity, protein ςA was subsequently expressed in Escherichia coli BL21(DE3) cells as a fusion protein and isolated by metal chelate affinity chromatography. The expressed protein eςA was further purified through a Superdex 75 HR 10/30 column after digestion of the purified fusion peptide with enterokinase. The expressed protein eςA has the same molecular weight as virion protein ςA purified from ARV-infected CEF and is indistinguishable from virion protein ςA by immunoblot analysis. The eςA binds cooperatively α 32P-labeled dsRNA probe produced by run-off transcription of clone pGEM-3Zf(+)S4. The binding reaction is blocked by homologous ARV dsRNA or heterologous infectious bursal disease virus dsRNA and poly(rI)–poly(rC), but not by salmon sperm DNA. The results indicate that the expressed protein eςA has dsRNA-binding activity similar to that of ςA obtained from infected cells, and its binding is sequence-independent