pinecone/core-2020-05-10-deduplication huggingface dataset:
An Inducible Packaging Cell System for Safe, Efficient Lentiviral Vector Production in the Absence of HIV-1 Accessory Proteins

AbstractLentiviral vectors based on human immunodeficiency virus type 1 (HIV-1) possess the ability to deliver exogenous genes to both dividing and nondividing cells and to subsequently establish a stable provirus in these target cells, which can allow long-term expression of the transferred gene. Herein we describe a stable packaging cell line that is devoid of HIV-1 tat, vif, vpr, vpu, and nef. In order to avoid any risk of cytotoxicity associated with constitutive expression of HIV-1 protease or the VSV-G envelope protein, transcription of the packaging and envelope constructs was tightly controlled by employing the ecdysone-inducible system. Using this cell line, we have been able to consistently generate concentrated pseudotyped vector virus stocks with titers in the range of 108 IU/ml, which can efficiently transduce actively dividing and growth-arrested cells in vitro. This novel packaging cell line for lentiviral vectors facilitates the production of high-titer virus stocks in the absence of replication-competent virus and provides us with an important tool for use in future gene transfer studies
Regression of Canine Oral Papillomas Is Associated with Infiltration of CD4+ and CD8+ Lymphocytes

AbstractCanine oral papillomavirus (COPV) infection is used in vaccine development against mucosal papillomaviruses. The predictable, spontaneous regression of the papillomas makes this an attractive system for analysis of cellular immunity. Immunohistochemical analysis of the timing and phenotype of immune cell infiltration revealed a marked influx of leukocytes during wart regression, including abundant CD4+ and CD8+ cells, with CD4+ cells being most numerous. Comparison of these findings, and those of immunohistochemistry using TCRαβ-, TCRγδ-, CD1a-, CD1c-, CD11a-, CD11b-, CD11c-, CD18-, CD21-, and CD49d-specific monoclonal antibodies, with previously published work in the human, ox, and rabbit models revealed important differences between these systems. Unlike bovine papillomavirus lesions, those of COPV do not have a significant gamma/delta T-cell infiltrate. Furthermore, COPV lesions had numerous CD4+ cells, unlike cottontail rabbit papillomavirus lesions. The lymphocyte infiltrate in the dog resembled that in human papillomavirus lesions, indicating that COPV is an appropriate model for human papillomavirus immunity
A New Strategy in Design of (+)RNA Virus Infectious Clones Enabling Their Stable Propagation in E. coli

AbstractInfectious clone methodology is a valuable tool of modern experimental virology. However, its use is often constrained by the instability of infectious clone constructs during propagation in E. coli. To circumvent this problem, we have devised a strategy that could be suitable for design of (+)RNA virus molecular clones in general. An infectious clone is assembled as “infectious DNA,” and expression of problem regions present in the viral cDNA is prevented during propagation in E. coli by insertion of short introns. To demonstrate the feasibility of this approach, a highly unstable Japanese encephalitis flavivirus infectious clone has been successfully converted into a remarkably stable infectious DNA construct with the specific infectivity of 106 pfu/μg in cell culture. The proposed strategy may be useful in the design of self-amplifying gene therapy vectors and development of new immunization methodologies, and could facilitate creation of molecular repositories of existing viral vaccines
Modified HPV16 E7 Genes as DNA Vaccine against E7-Containing Oncogenic Cells

AbstractTherapeutic vaccines against tumors associated with human papillomaviruses (HPV) should elicit cellular immune responses against early HPV antigens, primarily the oncoproteins E7 and E6. Because of safety concerns, the direct use of an unmodified oncogene is impossible in human DNA vaccination. Therefore, we introduced three point mutations into the pRb-binding site of HPV16 E7 oncogene to eliminate its transformation potential. The resultant gene was denoted E7GGG. The rates of expression and the cellular localization of E7 and E7GGG proteins were comparable. In immunization-challenge experiments, the efficacy of plasmids containing the E7, E7GGG, or fusion genes of HPV16 E7, viz. L1ΔCE71–60 (M. Muller et al., 1997, Virology 234, 93–111), and Sig/E7/LAMP-1 (T. C. Wu et al., 1995, Proc. Natl. Acad. Sci. USA 92, 11671–11675), was compared. While tumors developed in all animals immunized with the wild-type E7 gene, a significant proportion of mice remained tumor-free after vaccination with the E7GGG gene. The fusion gene L1ΔCE71–60 induced negligible protection, but Sig/E7/LAMP-1 conferred the highest protection. Intradermal immunization by gene gun proved superior to i.m. inoculation. In “therapeutic” experiments, a 1-day delay between inoculation of oncogenic cells and the start of DNA immunization resulted in partial therapeutic effect, but a 3-day delay produced a substantially lower immunization effect. A combination of Sig/E7/LAMP-1 and E7GGG genes did not enhance the immune response. These results demonstrate a significant enhancement of HPV16 E7 immunogenicity after mutagenesis of the pRb-binding site, but the mutated E7 gene did not excel the Sig/E7/LAMP-1 fusion gene
An Infectious Clone of the West Nile Flavivirus

AbstractWest Nile (WN) virus is the most widespread among flaviviruses, but until recently it was not known on the American continent. We describe here design of a subgenomic replicon, as well as a full-length infectious clone of the lineage II WN strain, which appeared surprisingly stable compared to other flavivirus infectious clones. This infectious clone was used to investigate effects of 5′- and 3′-nonrelated sequences on virus replication and infectivity of synthetic RNA. While a long nonrelated sequence at the 3′-end delayed but did not prevent establishment of the productive infectious cycle, a much shorter extra sequence at the 5′-end completely abrogated virus replication. Replacement of the conserved 5′-adenosine residue substantially delayed, but did not prevent, establishment of virus infection. In all cases, the recovered virus had restored its authentic 5′- and 3′-end genome sequences. However, the presence of extensive nonrelated sequences at both 5′- and 3′-ends could not be repaired
Membrane-Associated Respiratory Syncytial Virus F Protein Expressed from a Human Rhinovirus Type 14 Vector Is Immunogenic

AbstractHuman rhinovirus (HRV) replicons have the potential to serve as respiratory vaccine vectors for mucosal immunization in humans. However, since many vaccine immunogens of interest are glycosylated, an important concern is whether HRV replicons are capable of expressing glycosylated proteins. The human respiratory syncytial virus (RSV) fusion (F) protein was chosen as a model glycoprotein and the HRV replicon ΔP1FVP3 was generated by inserting the F protein-coding sequence in frame and in lieu of the 5′ proximal 1489 nucleotides of the capsid-coding segment in the HRV-14 genome. When transfected into H1-HeLa cells, ΔP1FVP3 replicated and led to the expression of the F protein. Inhibition with guanidine demonstrated that F-protein expression was dependent on ΔP1FVP3 replication and did not result from translation of input RNA. Although most of the F protein remained as an immature, glycosylated precursor (F0), a readily detectable fraction of the protein was processed into the mature glycosylated subunit F1, an event known to occur within the Golgi apparatus. Packaged ΔP1FVP3 replicons were generated in transfected HeLa cells by coexpression of homologous HRV capsid proteins using the vaccinia virus/T7 RNA polymerase hybrid system. Packaged replicon RNAs were capable of infecting fresh cells, leading to accumulation of the F protein as in RNA-transfected cells. Mice immunized with HeLa cell lysates containing F protein expressed from ΔP1FVP3 produced neutralizing antibodies against RSV. These results indicate that an HRV-14 replicon can express a foreign glycosylated protein, providing further support for the potential of HRV replicons as a vaccine delivery system
Marek's Disease Virus Down-Regulates Surface Expression of MHC (B Complex) Class I (BF) Glycoproteins during Active but not Latent Infection of Chicken Cells

AbstractInfection of chicken cells with three Marek's disease virus (MDV) serotypes interferes with expression of the major histocompatibility complex (MHC or B complex) class I (BF) glycoproteins. BF surface expression is blocked after infection of OU2 cells with MDV serotypes 1, 2, and 3. MDV-induced T-cell tumors suffer a nearly complete loss of cell surface BF upon virus reactivation with 5-bromo-2′-deoxyuridine (BUdR). The recombinant virus (RB1BUS2gfpΔ) transforming the MDCC-UA04 cell line expresses green fluorescent protein (GFP) during the immediate early phase of viral gene expression. Of the UA04 cells induced to express the immediate early GFP, approximately 60% have reduced levels of BF expression. All of the reactivated UA04 and MSB1 tumor cells expressing the major early viral protein pp38 display reduced levels of BF. Thus, BF down-regulation begins in the immediate early phase and is complete by the early phase of viral gene expression. The intracellular pool of BF is not appreciably affected, indicating that the likely mechanism is a block in BF transport and not the result of transcriptional or translational regulation
Porcine HveC, a Member of the Highly Conserved HveC/Nectin 1 Family, Is a Functional Alphaherpesvirus Receptor

AbstractHuman herpesvirus entry mediator C (HveC) is an alphaherpesvirus receptor which binds to virion glycoprotein D (gD). We identified porcine HveC and studied its interaction with pseudorabies virus (PrV) and herpes simplex virus type 1 (HSV-1) gD. Porcine and human HveC have 96% amino acid identity and HveC from African green monkey, mouse, hamster, and cow are similarly conserved. Porcine HveC mediates entry of HSV-1, HSV-2, PrV, and bovine herpesvirus type 1. Truncated soluble forms of HSV-1 and PrV gD bind competitively to porcine HveC. Biosensor analysis shows that PrV gD binds with a 10-fold higher affinity than HSV-1 gD. Monoclonal antibodies against human HveC recognize the porcine homologue and can block gD binding and entry of HSV-1 and PrV. Porcine HveC is functionally indistinguishable from human HveC. Our results are consistent with the suggestion that HveC is a pan-alphaherpesvirus receptor that interacts with a conserved structural domain of gD
H9N2 Influenza A Viruses from Poultry in Asia Have Human Virus-like Receptor Specificity

AbstractH9N2 influenza A viruses are currently widespread in chickens, quail, and other poultry in Asia and have caused a few cases of influenza in humans. In this study, we found that H9N2 viruses from Hong Kong live bird markets have receptor specificity similar to that of human H3N2 viruses. In addition, the neuraminidase of poultry H9N2 viruses has mutations in its hemadsorbing site, a characteristic resembling that of human H2N2 and H3N2 viruses but differing from that of other avian viruses. Peculiar features of surface glycoproteins of H9N2 viruses from Hong Kong suggest an enhanced propensity for introduction into humans and emphasize the importance of poultry in the zoonotic transmission of influenza viruses
Disruption of Differentiated Functions during Viral Infection in Vivo V. Mapping of a Locus Involved in Susceptibility of Mice to Growth Hormone Deficiency Due to Persistent Lymphocytic Choriomeningitis Virus Infection

AbstractLymphocytic choriomeningitis virus (LCMV) Armstrong strain selectively and persistently infects the majority of growth hormone (GH) producing cells in the anterior lobe of pituitary glands of C3H/St mice but negligibly infects GH producing cells of BALB/WEHI mice (Oldstone et al., Virology 142, 175–182, 1985; Oldstone et al., Science 218, 1125–1127, 1982). Although infected GH cells remain free of structural damage, disrupted initiation of GH transcription (Klavinskis and Oldstone, J. Gen. Virol. 68, 1867–1873, 1989; Valsamakis et al., Virology 156, 214–220, 1987) occurs with a resultant decrease in the synthesis of GH, leading to a failure of growth and development (Oldstone et al., Science 218, 1125–1127, 1982). Microsatellite mapping of DNA obtained from 101 individual C3H/St × BALB/WEHI F1 × F1 mice shows that the growth failure correlates with host genes linked (P value 0.0008) on chromosome 17 just outside of the H-2D MHC site between D17 Mit24 and D17 Mit51, a distance of 2.5 cM. The genetic mapping done here excludes alpha-dystroglycan (α-DG), a known receptor for LCMV (Cao et al., Science 282, 2079–2081, 1998) in pathogenesis of GH disease, as α-DG is encoded in the mouse by a gene residing on chromosome 9 (Yotsumoto et al., Hum. Mol. Genet. 5, 1259–1267, 1996)
A Critical Role for Inducible Nitric Oxide Synthase in Host Survival Following Coxsackievirus B4 Infection

AbstractCoxsackieviral infections have been linked etiologically to multiple diseases. The serotype CB4 is associated with acute pancreatitis and autoimmune type 1 diabetes. To delineate the mechanisms of host survival after an acute infection with CB4 (strain E2), we have investigated the role of nitric oxide (NO), generated by the inducible form of nitric oxide synthase (NOS2), in viral clearance and pancreatic β-cell maintenance. Mice deficient in NOS2 (NOS2−/− mice) and their wild-type (wt) counterparts were injected with CB4, after which both groups developed severe pancreatitis, hepatitis, and hypoglycemia within 3 days. Within 4 to 7 days postinfection (p.i.), most of the NOS2−/− mice died and at a strikingly higher mortality rate than wt mice. Histological examination of pancreata from both infected NOS2−/− and infected wt mice revealed early and complete destruction of the pancreatic acinar tissue, but intact, insulin-stained islets. When examined up to 8 weeks p.i., neither surviving NOS2−/− mice nor surviving wt mice developed hyperglycemia. However, the clearance of infectious CB4 was different between the mice. The spleens of NOS2−/− survivors were cleared of infectious virus with kinetics similar to that of wt mice, but the livers, pancreata, kidneys, and hearts of the NOS2−/− groups cleared virus more slowly than those of the wt group. This delayed clearance was particularly prominent in the livers of infected NOS2−/− mice, which also showed prolonged histopathological features of viral hepatitis. Taken together, this outcome suggests that NOS2 (and NO) is not required for the prevention of pancreatic β-cell depletion after CB4 infection. Instead the critical actions of NOS2 apparently occur early in the host immune response, allowing mice to survive and clear virus. Moreover, the data support the existence of an organ-specific dependency on NO for a rapid clearance of CB4
Potent Broad Cross-Neutralizing Sera Inhibit Attachment of Primary HIV-1 Isolates (Groups M and O) to Peripheral Blood Mononuclear Cells

AbstractGp160-directed antibody-mediated neutralization is thought to function by at least two different mechanisms that impair virus entry into the host cell: inhibition of virus attachment and inhibition of virus–cell membrane fusion. Previously, the neutralization spectra of sera derived from human immunodeficiency virus type 1 (HIV-1) infected patients were determined using 17 primary isolates belonging to HIV-1 group M (env clades A–H) and group O. The sera could be categorized as potent broad cross-neutralizing, limited cross-neutralizing, and nonneutralizing sera. The aim of this study was to examine whether the neutralizing capacity of polyclonal human sera correlates with their capacity to inhibit the attachment of infectious virions to the surface of peripheral blood mononuclear cells. A 100% correlation was found between the broad cross-neutralizing capacity and the ability to inhibit binding of primary isolates belonging to different genetic clades and groups to peripheral blood mononuclear cells. These results may indicate that broad cross-neutralizing antibodies are directed against those conserved regions on gp120 that interact with the cell receptor(s) and that those antibodies can therefore interfere with the binding of virus to the host cell
Allpahuayo Virus: A Newly Recognized Arenavirus (Arenaviridae) from Arboreal Rice Rats (Oecomys Bicolor and Oecomys Paricola) in Northeastern Peru

AbstractAllpahuayo virus was initially isolated from arboreal rice rats (Oecomys bicolor and Oecomys paricola) collected during 1997 at the Allpahuayo Biological Station in northeastern Peru. Serological and genetic studies identified the virus as a new member of the Tacaribe complex of the genus Arenavirus. The small (S) segment of the Allpahuayo virus prototype strain CLHP-2098 (Accession No. AY012686) was sequenced, as well as that of sympatric isolate CLHP-2472 (Accession No. AY012687), from the same rodent species. The S segment was 3382 bases in length and phylogenetic analysis indicated that Allpahuayo is a sister virus to Pichinde in clade A. Two ambisense, nonoverlapping reading frames were identified, which result in two predicted gene products, a glycoprotein precursor (GPC) and a nucleocapsid protein (NP). A predicted stable single hairpin secondary structure was identified in the intergenic region between GPC and NP. Details of the genetic organization of Allpahuayo virus are discussed
In Vitro Dissection of the Membrane and RNP Binding Activities of Influenza Virus M1 Protein

AbstractSpontaneous proteolysis of influenza virus M1 protein during crystallisation has defined an N-terminal domain of amino acids 1–164. Full-length M1, the N-terminal domain, and the C-terminal part of M1 (residues 165–252) were produced in Escherichia coli. In vitro tests showed that only full-length M1 and its N-terminal domain bind to negatively charged liposomes and that only full-length M1 and its C-terminal part bind to RNP. However, only full-length M1 had transcription inhibition activity. Several independent experimental approaches indicate that in vitro transcription inhibition occurs through polymerisation/aggregation of M1 onto RNP, or of M1 onto M1 already bound to RNP, rather than by binding to a specific active site on the nucleoprotein or the polymerase. The structure/function of influenza virus M1 will be compared with that of the Ebola virus matrix protein, VP40
Rinderpest Virus C and V Proteins Interact with the Major (L) Component of the Viral Polymerase

AbstractRinderpest virus, like other Morbilliviruses, expresses three proteins from the single P gene. In addition to the P protein, which interacts both with the viral polymerase (L) and the nucleocapsid (N) protein, the virus expresses a C and a V protein from the same gene. The functions of these two proteins in the viral life cycle are not clear. Although both C and V proteins are dispensable, in that viable viruses can be made that express neither, each seems to play a role in optimum viral replication. We have used the yeast-two hybrid system, binding to coexpressed fusions of C and V to glutathione-S-transferase, and studies of the native size of these proteins to investigate interactions of the rinderpest virus C and V proteins with other virus-encoded proteins. The V protein was found to interact with both the N and L proteins, while the C protein was found to bind to the L protein, and to self-associate in high-molecular-weight aggregates
In Vitro Translational Analysis of Genomic, Defective, and Satellite RNAs of Cryphonectria hypovirus 3-GH2

AbstractCryphonectria hypovirus 3-GH2 (CHV3-GH2) is a member of the fungal virus family Hypoviridae that differs from previously characterized members in having a single large open reading frame with the potential to encode a protein of 326 kDa from its 9.8-kb genome. The N-terminal portion of the ORF contains sequence motifs that are somewhat similar to papain-like proteinases identified in other hypoviruses. Translation of the ORF is predicted to release autocatalytically a 32.5-kDa protein. A defective RNA, predicted to encode a 91.6-kDa protein representing most of the N-terminal proteinase fused to the entire putative helicase domain, and two satellite RNAs, predicted to encode very small proteins, also are associated with CHV3-GH2 infected fungal cultures. We performed in vitro translation experiments to examine expression of these RNAs. Translation of three RT–PCR clones representing different lengths of the amino-terminal portion of the ORF of the genomic RNA resulted in autocatalytic release of the predicted 32.5-kDa protein. Site-directed mutagenesis was used to map the processing site between Gly297 and Thr298. In vitro translation of multiple independent cDNA clones of CHV3-GH2-defective RNA 2 resulted in protein products of ∼92 kDa, predicted to be the full-length translation product, 32 kDa, predicted to represent the N-terminal proteinase, and 60 kDa, predicted to represent the C-terminal two-thirds of the full-length product. In vitro translation of cDNA clones representing satellite RNA 4 resulted in products of slightly less than 10 kDa, consistent with the predicted 9.4 kDa product
Coreceptor Choice and T Cell Depletion by R5, X4, and R5X4 HIV-1 Variants in CCR5-Deficient (CCR5Δ32) and Normal Human Lymphoid Tissue

AbstractCoreceptor utilization by HIV-1 is an important determinant of pathogenesis. However, coreceptor selectivity is defined in vitro, while in vivo critical pathogenic events occur in lymphoid tissues. Using pharmacological inhibitors, we recently provided evidence that coreceptor selectivity by the R5X4 dual-tropic isolate 89.6 was more restricted in ex vivo infected lymphoid tissue than in vitro [S. Glushakova, Y. Yi, J. C. Grivel, A. Singh, D. Schols, E. De Clercq, R. G. Collman, and L. Margolis (1999). J. Clin. Invest. 104, R7–R11]. Here we extend those observations using CCR5-deficient (CCR5Δ32) lymphoid tissue as well as additional primary isolates. We definitively show that neither CCR5 nor secondary coreceptors used in vitro mediate 89.6 infection in lymphoid tissue. We also demonstrate that restricted coreceptor use in lymphoid tissue ex vivo compared with in vitro utilization occurs with other dual-tropic primary isolates and is not unique to 89.6. For all strains tested that are dual tropic in vitro, severe CD4 T cell depletion in lymphoid tissue correlated with preferential CXCR4 use in this ex vivo system
Generation of Replication-Defective Helper-Free Vectors Based on Simian Immunodeficiency Virus

AbstractA systematic study on generating simian immunodeficiency virus (SIV)-based vectors was carried out. The goal was to generate helper-free, replication-defective SIVmac-based vectors at high titers. The general approach was to cotransfect into human 293T cells a plasmid carrying the vector construct along with two helper plasmids that together expressed the SIVmac virion proteins. Initial vectors carried the bacterial β-galactosidase gene (β-gal). These vectors had a technical difficulty: “pseudotransduction” of β-gal protein produced during the 293T cell transfections. As a result, infection of cultures with these vector stocks also resulted in passive transfer into, and X-gal staining of, cells that had not actually been infected by the vector. A second generation of vectors expressing the enhanced jellyfish green fluorescence protein (EGFP) was not subject to this artifact. A systematic study of the SIVmac-based EGFP vectors was carried out. Helper-free vector stocks were obtained when helper plasmids lacking the SIVmac packaging signals were used. By employing envelope helper plasmids derived from different SIVmac isolates, it was possible to generate SIVmac-based vectors pseudotyped with envelope proteins of different cell tropism. Optimization of vector and helper plasmid structures, transfection conditions, and infection procedures ultimately yielded vector titers in excess of 106/ml