pinecone/core-2020-05-10-deduplication huggingface dataset:
The RNA Encompassing the Internal Ribosome Entry Site in the Poliovirus 5′ Nontranslated Region Enhances the Encapsidation of Genomic RNA

AbstractPoliovirus replicons were constructed which contain the internal ribosome entry site (IRES) of encephalomyocarditis virus (EMCV) substituted for the poliovirus IRES. To monitor gene expression and encapsidation, the gene encoding firefly luciferase was substituted for the P1 gene. Replicons can be encapsidated following serial passage in the presence of a recombinant vaccinia virus, VV-P1, which expresses the poliovirus P1 protein following infection. Encapsidation of the wild-type replicon (PV-Luc) was accomplished at either 33 or 37°C; the lower temperature actually resulted in greater amounts of encapsidated replicon. In contrast, the replicon with the EMCV IRES element (EMCV-Luc) was not efficiently encapsidated at 37°C and, following serial passage with VV-P1 at 37°C, was not amplified. EMCV-Luc was efficiently encapsidated, however, following serial passage with VV-P1 at 33°C. Using the encapsidated EMCV-Luc obtained at 33°C, we found that cells infected with EMCV-Luc at 33 or 37°C produced similar amounts of luciferase. Encapsidated EMCV-Luc and PV-Luc had similar thermal stability at 33 and 37°C. A single-round encapsidation analysis revealed that less EMCV-Luc was encapsidated at 37 than at 33°C; less EMCV-Luc was encapsidated at 33°C compared to PV-Luc at either 37 or 33°C. The results of our studies suggest that in addition to influencing translation/replication, the IRES region of poliovirus can function to enhance encapsidation
Sequence Parameters That Determine Specificity of Binding of the Replication-Associated Protein to Its Cognate Site in Two Strains of Tomato Leaf Curl Virus–New Delhi

AbstractThe DNA binding sites for the replication-associated protein (Rep) of two strains of tomato leaf curl virus from New Delhi (ToLCV-Nde) were identified using electrophoretic mobility shift assays (EMSAs). The Rep proteins of the two strains were found to exhibit sequence specificity in recognition of their cognate repeat motifs (iterons) in the origin, despite the fact that they share 91% sequence identity. Using a series of synthetic oligonucleotides as probes in EMSAs, the interaction of Rep protein with its binding site was found to be dependent on number, size, and sequence of the two iterons. Mutations in the sequence of the repeat motifs or alteration in the arrangement of the motifs compromised the ability of Rep protein to bind the DNA sequence and reduced accumulation of viral DNA in protoplasts, suggesting that binding of Rep protein to its cognate iterons is an essential step in virus replication. In addition, a difference in sequence of two base pairs in the binding site of two ToLCV-Nde strains was found to affect DNA binding by the corresponding Rep protein and replication of the virus DNA in protoplasts
Papillomavirus Virus-like Particles for the Delivery of Multiple Cytotoxic T Cell Epitopes

AbstractChimeric papillomavirus (PV) virus-like particles (VLPs) based on the bovine papillomavirus type 1 (BPV-1) L1 protein were constructed by replacing the 23-carboxyl-terminal amino acids of the BPV1 major protein L1 with an artificial “polytope” minigene, containing known CTL epitopes of human PV16 E7 protein, HIV IIIB gp120 P18, Nef, and reverse transcriptase (RT) proteins, and an HPV16 E7 linear B epitope. The CTL epitopes were restricted by three different MHC class I alleles (H-2b, H-2d, HLA-A*0201). The chimeric L1 protein assembled into VLPs when expressed in SF-9 cells by recombinant baculovirus. After immunization of mice with polytope VLPs in the absence of adjuvant, serum antibodies were detected which reacted with both polytope VLPs and wild-type BPV1L1 VLPs, in addition to the HPV16E7 linear B cell epitope. CTL precursors specific for the HPV16 E7, HIV P18, and RT CTL epitopes were also detected in the spleen of immunized mice. Polytope VLPs can thus deliver multiple B and T epitopes as immunogens to the MHC class I and class II pathways, extending the utility of VLPs as self-adjuvanting immunogen delivery systems
Human Monoclonal Antibody 98-6 Reacts with the Fusogenic Form of gp41

AbstractA mixture of two peptides from gp41 (N36 and C34) forms an α-helical structure that is thought to represent the fusogenic form of gp41. A human anti-gp41 monoclonal antibody (mAb 98-6), generated from the cells of an infected individual, reacted poorly with C34, but binding was strongly enhanced when N36 was added, indicating that the mAb reacts with a conformational epitope present in the fusogenic structure formed by the interaction of peptides N36 and C34. The epitope recognized by mAb 98-6 was found in lysates of virions on oligomeric forms of gp41 (dimers, trimers, and tetramers). On infected cells, the epitope was present as oligomers of gp41, as monomers of gp41, and as part of the envelope polyprotein gp160, obtained after biotinylation of intact cells, which were then lysed and immunoprecipitated with various mAbs. In lysates of infected cells, the epitope was present as part of both monomeric gp41 and gp160. These studies demonstrate that infected humans can respond to the fusogenic form of gp41 and that the anti-gp41 mAb studied here recognizes a conformational epitope formed by the interaction of two regions of gp41, which forms an α-helical bundle. This epitope is found on several forms of gp41 as it occurs in virions, on the surface of infected cells, and in infected cells
Cloning of an Infectious Milk-Borne Mouse Mammary Tumor Virus (MMTV) DNA from a Mammary Tumor That Developed in an Endogenous MMTV-Free Wild Mouse

AbstractMolecular characterization of infectious mouse mammary tumor viruses (MMTVs) has been hampered due to the problem of cloning a full-length exogenous virus into a plasmid. The present report describes our strategy for obtaining a full-length clone of an exogenous MMTV from a mouse mammary tumor that arose spontaneously in a wild Chinese mouse free of endogenous MMTV and shows that the cloned virus (JYG-MMTV) is expressed in rat RBA cells. Four-week-old C58/J × CBA/CaJ female mice, free of both endogenous and exogenous MMTVs, were injected with virus-secreting RBA cells. The progeny of these mice were bred, and their offspring were tested for the presence of MMTV. These third-generation mice were found to actively produce MMTV that was shed in their milk and transmitted to their offspring. The virus was detected not only in the mammary glands of these young mice, but also in their spleens and bone marrow. These results suggest that our plasmid-cloned exogeneous JYG-MMTV is infectious. This virus can now be used effectively in manipulating the various genes of JYG-MMTV and other MMTV strains to understand their structure/function relationships
Corf, the Rev/Rex Homologue of HTDV/HERV-K, Encodes an Arginine-Rich Nuclear Localization Signal That Exerts a trans-Dominant Phenotype When Mutated

AbstractRegulation of nucleo-cytoplasmic export of viral transcripts by a viral protein (Rev/Rex) is a characteristic feature in the replication cycle of complex retroviruses. We recently reported that the endogenous retrovirus family HTDV/HERV-K encodes a protein, Corf, that is a cellular Counterpart of Rev/Rex function and thus a new component of nucleo-cytoplasmic pathways. In HTDV/HERV—K-expressing cells, Corf is localized within the nucleoli. Here we describe the nuclear localization signal (NLS) of the Corf protein. Mutations in the NLS lead to cytoplasmic accumulation of the mutated protein and abrogate Corf function in a trans-dominant way
The Master Rep Concept in Nanovirus Replication: Identification of Missing Genome Components and Potential for Natural Genetic Reassortment

AbstractFaba bean necrotic yellows virus (FBYNV), Milk vetch dwarf virus (MDV), and Subterranean clover stunt virus (SCSV) are nanoviruses that infect leguminous plants. From MDV- and SCSV-infected tissue we identified viral DNAs that encode a replication initiator protein (Rep), essential for replication of the multiple circular single-stranded DNAs of these viruses. These previously undescribed Rep proteins of MDV and SCSV are strikingly similar in sequence and functionally equivalent to the master Rep protein of FBYNV. Moreover, we demonstrated that the master Rep proteins of the three viruses are able to trigger replication of heterologous nanovirus DNAs. Such cross-species replication may reflect a considerable potential for genetic reassortment among nanoviruses in nature and be of significance for their evolution
Nuclear Localization of Turnip Crinkle Virus Movement Protein p8

AbstractTurnip crinkle virus (TCV) is a single-stranded positive-sense RNA virus of the Carmovirus genus. Two of its five open reading frames (ORFs), encoding proteins of 8 and 9 kDa, are required for cell-to-cell movement of the virus. These movement proteins (MPs) were fused to green fluorescent protein (GFP) to determine their cellular localization. In protoplasts, p9-GFP, like GFP itself, is found throughout the cytoplasm, as well as in cell nuclei. In contrast, p8-GFP was confined to the cell nucleus. Similar localization patterns were observed when specific small peptide epitopes were fused to p8 and p9 proteins instead of GFP. The cytoplasmic localization of p9-GFP and nuclear localization of p8-GFP were also detected in leaves after particle bombardment of DNA encoding these fusion proteins or after overexpression of p8-GFP in transgenic Arabidopsis seedlings. The expression of the GFP fusion proteins by recombinant TCV viruses in infected protoplasts or on inoculated Arabidopsis leaves produced similar patterns. Unlike TMV-MP and other MPs studied to date, no obvious punctuate expression in the cell wall or association with the cytoskeleton was detected. The sequence analysis of p8 revealed two unique nuclear localization signals (NLSs), which were not conserved within p8 homologues of other viruses in the genus Carmovirus. Mutation in either of these NLSs did not disrupt the nuclear localization of p8-GFP. However, when both NLSs were mutated, p8-GFP expression was no longer restricted to cell nuclei. The NLSs are not required for cell-to-cell movement; TCV recombinant viruses mutated in one or both NLSs could still facilitate cell-to-cell movement of the virus. The nuclear localization of p8 suggests a novel function for this protein in the cell nucleus
Chemokines and Viruses: The Dearest Enemies

AbstractThe relation between viruses and the chemokine system is characterized by a complex blend of enmity and attraction. Chemokines are key regulators of innate and adaptive immune responses against invading microorganisms, including viruses. They act not only as immune system “traffic officers,” controlling leukocyte migration under both physiological and pathological conditions, but also as fine orchestrators that modulate the induction, amplification, and cytokine-secretion pattern of antiviral responses. However, viruses have succeeded in turning the chemokine system into an ally. During the course of a long parallel evolution, viruses have captured from their hosts the genetic information for encoding chemokines and chemokine receptors and have reprogrammed it for evading the control of the immune system. Moreover, selected viral agents, most notably primate immunodeficiency retroviruses, have adopted chemokine receptors as essential gateways for entry into their target cells. The endogenous secretion of chemokines is thus emerging as an important in vivo mechanism of viral control, which is potentially inducible by effective vaccines. The deepening knowledge of the interactions between viruses and chemokines may lead to novel therapeutic and preventive strategies for the control of viral and inflammatory diseases
Evaluation of Immune Responses Induced by HIV-1 gp120 in Rhesus Macaques: Effect of Vaccination on Challenge with Pathogenic Strains of Homologous and Heterologous Simian Human Immunodeficiency Viruses

AbstractThe simian human immunodeficiency virus (SHIV) macaque model of AIDS has provided a very useful system for evaluation of envelope-based candidate vaccines against HIV-1. Eight rhesus macaques were immunized with monomeric recombinant gp120 of HIV-1LAI (rgp120) and used to evaluate whether this vaccine conferred protection against challenge with pathogenic SHIVs (SHIVKU-2 and SHIV89.6P). The vaccinated macaques developed high titers of antibodies against rgp120 that reacted efficiently with the envelope proteins of homologous SHIV (SHIVKU-2) and poorly with the SHIV89.6P envelope, a heterologous strain of SHIV. This vaccine also induced neutralizing antibodies but only against SHIVKU-2. Vaccine-induced antibodies were of high avidity and predominantly against linear epitopes on the protein. Vaccinated macaques developed gp120-specific T-helper cells but no consistent cytotoxic T lymphocytes. However, cellular immune responses were short-lived in all eight vaccinates. At week 22 postimmunization, four vaccinates were challenged with SHIVKU-2 and the other four with SHIV89.6P. Four unvaccinated control macaques were also infected: two with SHIVKU-2 and two with SHIV89.6P. Vaccinated macaques generally showed anamnestic antibody and T-helper cell responses. However, T-helper responses were again short-lived. Upon challenge, the level of productive virus replication was indistinguishable between vaccine and control groups, suggesting that rgp120 did not confer protection against virus replication when animals were challenged with homologous or heterologous SHIV viruses
Production of Functionally Deficient Dendritic Cells from HTLV-I-Infected Monocytes: Implications for the Dendritic Cell Defect in Adult T Cell Leukemia

AbstractAdult T cell leukemia (ATL) is induced by an infection with human T lymphotropic virus type I (HTLV-I) and is accompanied by immunodeficiency. Monocyte-derived immature dendritic cells (DCs) donated by 11 ATL patients were suppressed in the ability to take up fluorescein isothiocyanate (FITC)–dextran and were down-regulated in the expression of CD1a and CD86 antigens (Ags). Monocytes from the patients showed impaired expression of CD14 and HLA-DR Ags. These results suggest intrinsic abnormalities of monocytes and a defect of DC maturation in ATL patients. Therefore, we examined the influence of HTLV-I infection of monocytes on their differentiation to DCs. Monocytes obtained from healthy donors were susceptible to HTLV-I infection in vitro. HTLV-I-infected monocytes were down-regulated in the expression of CD14 Ags, and immature DCs obtained from them expressed CD1a poorly and were impaired in the ability to take up FITC–dextran. Mature DCs differentiated from these cells could not stimulate autologous CD4+ T cell or CD8+ T cell proliferation, even after being secondarily pulsed with HTLV-I at an immature DC stage. These results suggest that HTLV-I-infected monocytes cannot properly differentiate to DCs and that this might be one of the important mechanisms producing dysfunctional DCs in ATL patients
Complete Genomic Sequence of the Amsacta moorei Entomopoxvirus: Analysis and Comparison with Other Poxviruses

AbstractThe genome of the genus B entomopoxvirus from Amsacta moorei (AmEPV) was sequenced and found to contain 232,392 bases with 279 unique open reading frames (ORFs) of greater than 60 amino acids. The central core of the viral chromosome is flanked by 9.4-kb inverted terminal repeats (ITRs), each of which contains 13 ORFs, raising the total number of ORFs within the viral chromosome to 292. ORFs with no known homology to other poxvirus genes were shown to constitute 33.6% of the viral genome. Approximately 28.6% of the AmEPV genome encodes homologs of the mammalian poxvirus colinear core genes, which are found dispersed throughout the AmEPV chromosome. There is also no significant gene order conservation between AmEPV and the orthopteran genus B poxvirus of Melanoplus sanguinipes (MsEPV). Novel AmEPV genes include those encoding a putative ABC transporter and a Kunitz-motif protease inhibitor. The most unusual feature of the AmEPV genome relates to the viral encoded poly(A) polymerase. In all other poxviruses this heterodimeric enzyme consists of a single large and a single small subunit. However, AmEPV appears to encode one large and two distinct small poly(A) polymerase subunits. AmEPV is one of the few entomopoxviruses which can be grown and manipulated in cell culture. The complete genomic sequence of AmEPV paves the way for an understanding and comparison of the molecular properties and pathogenesis between the entomopoxviruses of insects and the more intensively studied vertebrate poxviruses
Identification of a Novel p53 Mutation in JCV-Induced Mouse Medulloblastoma

AbstractMedulloblastoma, a malignant invasive tumor of the cerebellum, is one of the most common neoplasms of the nervous system in children. Utilization of the human neurotropic virus JC virus (JCV) early gene T-antigen allowed the development of a transgenic animal that models human medulloblastoma. Here we describe the characterization of two distinct populations of cells derived from the JCV-induced mouse medulloblastoma. Results from immunohistochemical and biochemical studies revealed the expression of T-antigen in some but not all tumor cells. In T-antigen-producing cells, T-antigen was found in association with wild-type p53 and pRb, two tumor suppressors that control cell growth and differentiation. In cells that lack expression of T-antigen, a novel mutant p53 with a deletion between residues 35 and 123 was detected. Morphological differences were observed between the two populations of cells, though there was no significant difference in their growth rates. However, subcutaneous transplantation of the T-antigen-positive, but not T-antigen-negative, cells resulted in the development of massive tumors in experimental animals. In light of earlier reports on the association of JCV with human medulloblastoma, the mouse cell lines described in this study may provide a valuable tool for deciphering the pathways involved in the formation and progression of medulloblastoma
Purified JC Virus T and T′ Proteins Differentially Interact with the Retinoblastoma Family of Tumor Suppressor Proteins

AbstractThe amino termini of polyomavirus T antigens contain LXCXE and J domains, which are necessary for binding and inactivating the retinoblastoma family of tumor suppressors. Both of these motifs are found in the JC virus (JCV) early proteins T135′, T136′, and T165′, leading to the suggestion that these recently discovered proteins complement the cell-cycle-deregulating function of the JCV large T antigen (TAg). To investigate this hypothesis, the three JCV T′ proteins were produced in a baculovirus expression system and purified by immunoaffinity chromatography. To facilitate purification, hybridomas that secrete antibodies recognizing amino-terminal epitopes of JCV early proteins were produced. Potential interactions between the early viral proteins and the cellular proteins pRB, p107, and p130 were investigated by incubating purified JCV TAg and T′ proteins with extracts of MOLT-4 cells, a human T cell line. The four viral proteins preferentially bound hypophosphorylated species of the cellular proteins and exhibited the highest binding affinity to p107 and the lowest affinity to pRB. TAg and T165′ bound more pRB and less p107 than did T135′ and T136′; T165′ also bound less p130 than the other three early proteins. Results of these in vitro interactions were compared to those obtained in vivo using POJ cells, a transformed human glial cell line that expresses JCV early proteins, relatively high levels of pRB and p107, and low levels of p130. Most of the pRB in POJ cells is hyperphosphorylated, and only a fraction of the hypophosphorylated form(s) of pRB is bound by the viral proteins. In contrast, only hypophosphorylated p130 is detected in the transformed cells, and most of this protein was found in complex with the viral proteins. Finally, nearly all of the p107 in POJ cells is bound by the JCV proteins
The Autographa californica Nucleopolyhedrovirus IE-1 Protein Complex Has Two Modes of Specific DNA Binding

AbstractMissing contact footprinting with formic acid as a modifying reagent was used to examine specific IE-1 binding contacts to double-stranded oligonucleotides that contained either a consensus hr repeat sequence or a sequence from the pe38 promoter, which is down regulated by IE-1. The hr repeat sequences contain two consensus IE-1 binding motifs (IBMs) flanking a central EcoRI site that are oriented in opposite directions with respect to each other. IE-1 was found to contact regions including both IBMs. The bases footprinted in the top strand included the left IBM (IBM-A), whereas bases in the bottom strand were footprinted in a region that included IBM-B and part of IBM-A. When substitution mutations were introduced into either IBM, bases on both strands of the remaining IBM were strongly footprinted. As with the hr IBM-mutant constructs, bases footprinted in the pe38 promoter construct included both strands of the single IBM
Virus-Specific Adaptations for the Production of a Pseudorecombinant Virus Formed by Two Distinct Bipartite Geminiviruses from Central America

AbstractMost whitefly-transmitted geminiviruses possess bipartite genomes comprising DNAs A and B. The production of viable pseudorecombinants by reassortment of infectious cloned components is generally limited to isolates/strains of a particular virus. Following exchange of cloned genomic components of Sida golden mosaic virus from Costa Rica (SiGMV/Co) and Sida golden mosaic virus from Honduras (SiGMV/Hoyv), the pseudorecombinant viruses were infectious in various plant species. Three DNA B components (B1, B2, B3), different in a few nucleotides, were isolated from Sida rhombifolia naturally infected with SiGMV/Hoyv. Only SiGMV/Hoyv DNA B2 was able to form a viable pseudorecombinant with SiGMV/Co DNA A. In protoplasts, as well as in inoculated leaves, SiGMV/Co DNA A trans-replicated the heterogenomic SiGMV/Hoyv DNA B1 component, indicating that impaired movement is involved in the deficiency of SiGMV/Hoyv DNA B1 to form a pseudorecombinant virus with SiGMV/Co DNA A. Even after extensive mutation analysis of SiGMV/Hoyv DNA B1 and B2, we were unable to pinpoint differences in SiGMV/Hoyv DNA B2 that allowed the formation of a pseudorecombinant virus with SiGMV/Co DNA A. We observed a gradual increase of infectivity from noninfectious SiGMV/Co DNA A/SiGMV/Hoyv DNA B1 and B3 pseudorecombinant virus to pseudorecombinant viruses showing normal systemic spread of both genomic components associated with symptomatic plants
A Protective Role of Interleukin-15 in a Mouse Model for Systemic Infection with Herpes Simplex Virus

AbstractTo define the role of cytokine binding to the IL-2/IL-15Rβ chain in protective immunity against systemic infection with herpes simplex virus type 2 (HSV-2), IL-2/IL-15 receptor(R)β knock-out mice were inoculated intraperitoneally with HSV-2 strain 186. IL-2/IL-15Rβ-deficient mice were susceptible to systemic HSV-2 infection compared with their heterozygous littermates. The emergence of natural killer (NK) cells was impaired in IL-2/IL-15Rβ knock-out mice, but CD4+ T cell receptor (TCR) αβ+ T cells were normally detected in the peritoneal cavity after infection with HSV-2. However, the generation of HSV-2-specific CD4+ T helper (Th) 1 cells producing interferon-γ was impaired in IL-2/IL-15Rβ knock-out mice following HSV-2 infection. The serum IL-15 level in control mice was increased in the early stage after HSV-2 infection but was not detectable in IL-2/IL-15Rβ knock-out mice. In vivo administration of recombinant IL-15 protected normal mice from HSV-2-induced lethality, accompanied by increases in numbers of NK cells and HSV-2-specific Th1 cells. Taken together, these results suggest that IL-15, using the IL-2/IL15Rβ chain, plays an important role in mounting protective immunity during the course of systemic HSV-2 infection