pinecone/core-2020-05-10-deduplication huggingface dataset:
High Diversity of HIV-1 Subtype F Strains in Central Africa

AbstractIn this paper, we studied the variability of HIV-1 subtype F strains in Africa. For 11 viruses, mainly of Central African origin, different parts of the genome were genetically characterized. For all strains the V3–V5 region of the envelope gene was sequenced, and for 7 strains, the entire envelope gene was studied. For 10 strains, the p24 region of the gag gene was also sequenced. For each region studied, three subgroups in the F subtype were identified, F1, F2, and F3. These three subgroups were supported by high bootstrap values and the intra- and inter-subgroup F distances were comparable to those obtained for the known subtypes A, B, C, D, E, G, and H. In subgroup F1, some African strains clustered with previously described strains from Brazil and Romania, suggesting an African origin of the HIV-1 epidemic in these countries. A more detailed analysis of the gag and the envelope sequences allowed the identification of four recombinant viruses. Our data show a high diversity among subtype F strains, suggesting the presence of new subtypes in the regions studied. If biological differences exist among subtypes, it is important that these subtypes be well defined. The data from our study show that there is a need to clearly identify the different subgroups within the F subtype
Activation of Ste20 by Nef from Human Immunodeficiency Virus Induces Cytoskeletal Rearrangements and Downstream Effector Functions in Saccharomyces cerevisiae

AbstractThe negative factor (Nef) from human and simian immunodeficiency viruses is important for the pathogenesis of acquired immune deficiency syndrome. Among other targets, it activates the Nef-associated kinase, which is related to the p21-activated kinase. In this study, we demonstrate that Nef activates Ste20, the homolog of p21-activated kinase in Saccharomyces cerevisiae. Nef binds to the adaptor proteins Bem1 and Ste20 via its proline-rich (PXXP) and diarginine (RR) motifs, respectively. These interactions induce the mitogen-activated protein kinase and increase the rates of budding, sizes of cells, and patterns of mating projections. These effects of Nef depend on the small GTPase Cdc42 and guanine nucleotide exchange factor Cdc24. Thus, studies in S. cerevisiae identified specific interactions between Nef and cellular proteins and their associated signaling cascade
Response to IL-6 of HPV-18 Cervical Carcinoma Cell Lines

AbstractThe human papillomavirus type 18 (HPV-18) upstream regulatory region (URR) controls cell type-specific expression of the viral oncoproteins E6 and E7. The HPV-18 URR is active in the cervical carcinoma cell line HeLa but inactive in the hepatoma cell line HepG2. C/EBPß (NF-IL-6) was shown to participate as an important regulator in HPV transcription dependent on the cell type. The finding that C/EPBß is critical for HPV-18 URR activity and that C/EPBß is induced by IL-6 offers the opportunity of manipulating HPV activity by specific cytokine treatment. In this report, we show that treatment with IL-6 results in activation of HPV-18 URR activity in HepG2 cells. In contrast, the HPV-18 URR is not inducible by IL-6 in three cervical carcinoma cell lines. In all three cell lines we found decreased expression of the IL-6 receptor compared to the IL-6-responsive HepG2 cells, whereas the level of expression of the signal transduction component gp130 is present in all cells. These results suggest that cervical carcinoma cells may circumvent the IL-6-induced cellular defense mechanism through downregulation of the IL-6-receptor
The Polysulfonated Compound Suramin Blocks Adsorption and Lateral Difusion of Herpes Simplex Virus Type-1 in Vero Cells

AbstractSeveral polysulfonate compounds have been shown to have the potential to inhibit the replication of herpesviruses by blocking binding and penetration of the host cell. We analyzed the actions of the polysulfonate compound suramin on the replication of herpes simplex virus type 1 (HSV-1) and compared them with the actions of heparin. We used the expression of a reporter gene (β-galactosidase) recombined into the latency-associated transcript region of the 17syn+strain of HSV-1 to quickly evaluate productive cycle activity and have shown that it can be directly correlated with virus replication under the conditions used. We find that suramin, like heparin, blocks the binding of HSV-1 to the cell membrane. Also, suramin efficiently blocks the cell-to-cell spread of the virus; this effect has not been previously reported. Our control experiments demonstrate that heparin also has some effect on intercellular spread of HSV-1 but to a significantly lesser degree than does suramin. We suggest that suramin and related polysulfonate compounds have potential for developing of antiherpes treatments
Tetracycline-Mediated Regulation of Gene Expression within the Human Cytomegalovirus Genome

AbstractTo evaluate the utility of tetracycline gene regulation in the study of human cytomegalovirus gene functions, expression of luciferase under the control of tetracycline-regulatable promoters was studied following transient plasmid transfections and from within recombinant human cytomegalovirus genomes. The tetracycline-regulatable promoter PhCMV*-1 contains sequences from the human cytomegalovirus ie1/ie2 promoter and seven upstream tet operator sites which bind the activator protein tTA only in the absence of tetracycline (Gossen and Bujard (1992). Proc. Natl. Acad. Sci. USA 89, 5547–5551). Two modifications of PhCMV*-1 were also studied: P1129, in which the tet operator sites were reduced from seven to one; and P1125, in which human cytomegalovirus sequences were replaced by adenovirus major late promoter and terminal deoxynucleotidyltransferase initiator sequences. In transient assays, PhCMV*-1 and P1125 exhibited modest differential regulation but were strongly activated by viral infection. P1129 exhibited less viral activation and narrower regulation. In the viral genome, PhCMV*-1 exhibited regulation up to 7-fold during late times of infection, whereas P1125 displayed nearly 100-fold regulation. Regulation of P1125 was fully reversed within 12 to 24 h of adding or removing tetracycline. These results suggest that P1125 may provide sufficient conditional expression to effectively regulate human cytomegalovirus late genes
Potyvirus Helper Component-Proteinase Self-Interaction in the Yeast Two-Hybrid System and Delineation of the Interaction Domain Involved

AbstractUsing the yeast two-hybrid system, a screen was performed for possible interactions between the proteins encoded by the 5′ region of potyviral genomes [P1, helper component-proteinase (HC-Pro), and P3]. A positive self-interaction involving HC-Pro was detected with lettuce mosaic virus (LMV) and potato virus Y (PVY). The possibility of heterologous interaction between the HC-Pro of LMV and of PVY was also demonstrated. No interaction involving either the P1 or the P3 proteins was detected. A series of ordered deletions from either the N- or C-terminal end of the LMV HC-Pro was used to map the domain involved in interaction to the 72 N-terminal amino acids of the protein, a region known to be dispensable for virus viability but necessary for aphid transmission. A similar but less detailed analysis mapped the interacting domain to the N-terminal half of the PVY HC-Pro
Both RNA Rearrangement and Point Mutation Contribute to Repair of Defective Chimeric Viral Genomes to Form Functional Hybrid Viruses in Plants

AbstractThe putative movement protein gene (p27) plus 5′ and 3′ flanking sequences of cucumber leaf spot aureusvirus (CLSV) was inserted into an infectious cucumber necrosis tombusvirus (CNV) cDNA clone containing a deletion in the cell-to-cell movement protein gene. Approximately 5% of plants inoculated with synthetic transcripts of two such defective chimeric CNV/CLSV cDNA clones developed systemic symptoms 7–19 days postinoculation. Reverse transcription-polymerase chain reaction and sequence analysis of virus obtained from systemically infected leaves indicated that both point mutation and RNA rearrangement (deletion) contributed to the formation of movement competent CNV/CLSV hybrid viruses. The hybrid viruses were found to accumulate to high levels in infected plants, to form stable virions, and to be mechanically transmissible. In addition, a hybrid virus that lacked 50 amino acids at the carboxyl-terminal region of CLSV p27 was still capable of facilitating CNV movement. These data provide experimental evidence for the role of CLSV p27 in viral cell-to-cell movement and demonstrate that p27 can enable efficient movement of the CNV genome. Moreover, the data show that RNA rearrangements known to occur during CNV RNA replication can contribute to rapid evolution of the CNV genome
Nuclear Localization of Human Immunodeficiency Virus Type 1 Integrase Expressed as a Fusion Protein with Green Fluorescent Protein

AbstractLentiviruses in general and the human immunodeficiency virus type 1 (HIV-1) in particular have the ability to integrate their genome stably into the chromosome of nondividing cells. Integration of HIV cDNA is mediated by the viral integrase (IN). Apart from its catalytic activity, this enzyme seems to play an important role in the transport of the HIV preintegration complex into the nucleus of nondividing cells. We studied the karyophilic properties of IN by constructing an N-terminal fusion protein of HIV-1 integrase and green fluorescent protein (GFP-IN). Transient expression of GFP-IN in various mammalian cell lines was demonstrated by fluorescence microscopy, flow cytometry, and Western blotting. Although wild-type GFP was localized throughout the cell, GFP-IN was localized predominantly in the nucleus. Nuclear localization of GFP-IN was also obtained after transient transfection of the cells arrested in the G1/S phase of the cell cycle. These results provide compelling evidence for the karyophilic properties of the HIV-1 integrase
Sequence Comparison of JSRV with Endogenous Proviruses: Envelope Genotypes and a Novel ORF with Similarity to a G-Protein-Coupled Receptor

AbstractOvine pulmonary carcinoma, a contagious lung cancer of sheep, is caused by the oncogenic jaagsiekte sheep retrovirus (JSRV) that is closely related to a family of endogenous sheep retroviral sequences (ESRVs). By using exogenous virus-specific U3 oligonucleotide primers, the entire JSRV proviral genome or its 3′ part was amplified from tumor DNA. Analysis of these proviral sequences revealed a novel open reading frame (ORF) within the pol coding region, designated ORF X, which was well conserved in ESRV and JSRV sequences. Deduced amino acids of ORF X showed similarity to a portion of the mammalian adenosine receptor subtype 3, a member of the G-protein-coupled receptor family. Comparison of deduced env amino acids of six JSRV strains from three continents identified 15 residues that defined two distinct genotypes of JSRVs. Sequence analysis identified two highly variable regions between JSRV and ESRV in the transmembrane domain of env (TM) and the 3′ unique sequence (U3) of the long terminal repeat, from which JSRV-specific DNA probes were derived. By using these DNA probes in Southern hybridization, for the first time we successfully identified JSRV proviral sequences in tumor genomic DNA in the presence of multiple ESRV loci, validating the use of exogenous virus-specific DNA probes in the analysis of oncogenic proviral integration sites and identification of integrated exogenous proviral sequences
Mutagenesis of Amino Acids at Two Tomato Ringspot Nepovirus Cleavage Sites: Effect on Proteolytic Processingin cisandin transby the 3C-like Protease

AbstractTomato ringspot nepovirus (ToRSV) encodes two polyproteins that are processed by a 3C-like protease at specific cleavage sites. Analysis of ToRSV cleavage sites identified previously and in this study revealed that cleavage occurs at conserved Q/(G or S) dipeptides. In addition, a Cys or Val is found in the −2 position. Amino acid substitutions were introduced in the −6 to +1 positions of two ToRSV cleavage sites: the cleavage site between the protease and putative RNA-dependent RNA polymerase, which is processedin cis, and the cleavage site at the N-terminus of the movement protein, which is cleavedin trans. The effect of the mutations on proteolytic processing at these sites was tested usingin vitrotranslation systems. Substitution of conserved amino acids at the −2, −1, and +1 positions resulted in a significant reduction in proteolytic processing at both cleavage sites. The effects of individual substitutions were stronger on the cleavage site processedin transthan on the one processedin cis. The cleavage site specificity of the ToRSV protease is discussed in comparison to that of related proteases
Broadly Cross-Reactive, High-Affinity Antibody to Hypervariable Region 1 of the Hepatitis C Virus in Rabbits

AbstractThe HCV hypervariable region 1 (HVR1) of the main E2 envelope protein is critically important in HCV neutralization but its extreme variability makes immune therapy and vaccine development particularly difficult. To explore the hypothesis that HVR1 carries a common epitope susceptible of eliciting cross-reactive neutralizing and inhibitory antibodies, rabbits were immunized with a series of synthetic HVR1 peptides. The anti-HVR1 produced were purified and characterized. Several lines of evidence supported the working hypothesis: (1) although injected only once, a boosting effect from poorly homologous peptides was observed; (2) purified rabbit IgG reacted with high affinity with immunizing peptides and cross-reacted with 16 of 17 unrelated HVR1 peptides; (3) antibodies appeared of restricted diversity irrespective of the linear HVR1 peptide sequences; (4) anti-HVR1 peptides effectively captured HCV in 22 of 33 plasmas from random infected patients; (5) anti-HVR1 IgG blocked the binding of antibody-captured HCV to MOLT-4 cells. These findings suggest that with an appropriate HVR1 peptide immunization scheme, high titer, broadly cross-reactive, blocking antibodies to HCV can be produced. Antibodies to the putative ubiquitous HVR1 epitope may have important clinical uses
Effects of Egg-Adaptation on the Receptor-Binding Properties of Human Influenza A and B Viruses

AbstractPropagation of human influenza viruses in embryonated chicken eggs (CE) results in the selection of variants with amino acid substitutions near the receptor-binding site of the hemagglutinin (HA) molecule. To evaluate the mechanisms by which these substitutions enable human virus growth in CE, we studied the binding of 10 human influenza A (H1N1, H3N2) and B strains, isolated and propagated solely in MDCK cells, and of their egg-adapted counterparts to preparations of cellular membranes, gangliosides, sialylglycoproteins, and sialyloligosaccharides. All egg-adapted variants differed from nonadapted strains by increased binding to the plasma membranes of chorio-allantoic (CAM) cells of CE and by the ability to bind to CAM gangliosides. In addition, there was no decrease in affinity for inhibitors within allantoic fluid. These findings indicate that growth of human influenza viruses in CE is restricted because of their inefficient binding to receptors on CAM cells and that gangliosides can play an important role in virus binding and/or penetration. The effects of the egg-adaptation substitutions on the receptor-binding properties of the viruses include (i) enhancement of virus binding to the terminal Sia(α2–3)Gal determinant (substitutions in HA positions 190, 225 of H1N1 strains and in position 186 of H3N2 strains); (ii) a decrease of steric interference with more distant parts of the Sia(α2–3Gal)-containing receptors (a loss of glycosylation sites in positions 163 of H1 HA and 187 of type B HA); and (iii) enhanced ionic interactions with the negatively charged molecules due to charged substitutions at the tip of the HA [187, 189, 190 (H1), and 145, 156 (H3)]. Concomitantly with enhanced binding to Sia(α2–3)Gal-terminated receptors, all egg-adapted variants decreased their affinity for equine macroglobulin, a glycoprotein bearing terminal 6′-sialyl(N-acetyllactosamine)-moieties
Expression of the HPV E7 Oncoprotein Mimics but Does Not Evoke a p53-Dependent Cellular DNA Damage Response Pathway

AbstractAcute expression of the human papillomavirus E7 oncoprotein in preimmortal human fibroblasts induces changes in the abundances of multiple cellular regulatory proteins. These alterations include a destabilization of the retinoblastoma tumor suppressor protein pRB, stabilization of the tumor suppressor protein p53, and increases in the level of the cyclin-dependent kinase inhibitor p21cip1. Since the HPV E7 oncoproteins can interfere with several cell cycle checkpoints and similar alterations in the levels of pRB, p53, and p21cip1 are also observed in a p53-dependent response to DNA damage, we investigated whether E7 expression triggers this signal transduction pathway. The results demonstrate that E7-mediated destabilization of pRB does not require p53 activity and is independent of the ability of E7 to induce apoptosis. Moreover, E7-mediated increases in p21cip1 levels are largely p53-independent and involve stabilization of the p21cip1 protein. In contrast the decreases in pRB expression in response to DNA damage involve transcriptional downregulation of RB gene expression
Neuronal Expression of NOS-1 Is Required for Host Recovery from Viral Encephalitis

AbstractThe role of nitric oxide synthase (NOS) in host defense and clearance of vesicular stomatitis virus (VSV) from the central nervous system (CNS) was examined. NOS-1, NOS-2, and NOS-3 knockout mice were infected with VSV and were treated with either IL-12 or medium. IL-12 treatment resulted in substantially decreased VSV titers in wildtype and NOS-3 knockout mice, but had a marginal effect in the NOS-1 and NOS-2 knockout mice. NOS-1 expression in neurons was associated with survival from VSV infection. The data indicate that the enzyme activity is local, since NOS-2 expression in microglia and inflammatory macrophages and NOS-3 expression in astrocytes, endothelial cells, and ependymal cells did not compensate
A 189-bp Repeat Region within the Human Cytomegalovirus Replication Origin Contains a Sequence Dispensable but Irreplaceable with Other Sequences

AbstractThe human cytomegalovirus (HCMV) replication origin exhibits a strain-dependent difference in the number of copies of a 189-bp region: the AD169 and Towne strains contain one and three copies of the region, respectively. A nearly complete deletion of the 189-bp repeat region of the Towne strain does not eliminate the origin's ability to initiate DNA synthesis. Here we report that the replication ability of the HCMV replication origin in infected cells disappeared after replacements of an internal sequence (152 bp) of the 189-bp repeat region with λ DNA of identical and different lengths as well as after introduction of multiple nucleotide substitutions within the 152-bp internal sequence of the 189-bp repeat. In contrast, a variation in the copy number of 189-bp region (either one or two copies) or an inversion of the 152-bp internal sequence of the 189-bp repeat maintained replication abilities similar to those of the wild-type origin of the Towne strain. These results indicate that the 189-bp repeat region within the HCMV replication origin is not just a dispensable spacer sequence but instead contains an irreplaceable sequence that may play a supporting role in HCMV DNA replication
The Dileucine-Based Sorting Motif in HIV-1 Nef Is Not Required for Down-Regulation of Class I MHC

AbstractA dileucine-based protein sorting motif has recently been identified within the C-terminal, solvent-exposed loop of HIV-1 Nef and has been shown to be required for Nef-mediated down-regulation of CD4 and for optimal viral infectivity. Here, we report that mutation of the dileucine motif has no effect on Nef-mediated down-regulation of class I MHC heavy chain. Instead, deletion of an acidic domain just N-terminal of the polyproline helix of the SH3-binding domain significantly impairs this function. These data indicate that down-regulation of class I MHC and CD4 are mechanistically distinct processes. The data also suggest that protein interactions mediated by the acidic domain, rather than by the dileucine motif, may contribute to this function of Nef
Platelets from Thrombocytopenic Ponies Acutely Infected with Equine Infectious Anemia Virus Are Activated in Vivo and Hypofunctional

AbstractThrombocytopenia is a consistent finding and one of the earliest hematological abnormalities in horses acutely infected with equine infectious anemia virus (EIAV), a lentivirus closely related to human immunodeficiency virus. Multifactorial mechanisms, including immune-mediated platelet destruction and impaired platelet production, are implicated in the pathogenesis of EIAV-associated thrombocytopenia. This study was undertaken to investigate whether regenerative thrombopoiesis and platelet destruction occurred in ponies acutely infected with EIAV. Circulating large, immature platelets were increased in ponies acutely infected with EIAV late in the infection when platelet count was at a nadir. Morphometric analysis of bone marrow from acutely infected ponies revealed significant increased in megakaryocyte area and megakaryocyte nuclear area. A trend toward increased numbers of megakaryocytes was also observed. Platelets from acutely infected ponies had increased surface-bound fibrinogen and ultrastructural changes consistent with in vivo platelet activation. Platelets also had hypofunctional aggregation responses to three agonists in vitro. We conclude that thrombocytopenia in ponies acutely infected with EIAV is regenerative and suggest that bone marrow platelet production is not severely compromised in these ponies. Our findings reveal that in vivo platelet activation occurs in ponies acutely infected with EIAV, and as a result platelets are hypofunctional in vitro. Activation of platelets in vivo may cause platelet degranulation or formation of platelet aggregates, which would result in removal of these damages platelets from circulation. This may represent a form of nonimmune-mediated platelet destruction in ponies acutely infected with EIAV
Interferon Action in Triply Deficient Mice Reveals the Existence of Alternative Antiviral Pathways

AbstractAntiviral proteins encoded by the interferon (IFN)-stimulated genes provide a front-line defense against viral infections. In particular, PKR, RNase L, and Mx are considered to be the principal proteins through which IFNs mount an antiviral state. To determine whether alternative antiviral pathways exist, RNase L−/− mice and PKR−/− mice were crossed onto an Mx1−/− background to generate a strain of triply deficient (TD) mice. After infections with encephalomyocarditis virus, the TD mice died 3–4 days earlier than infected, wild-type mice. However, there was an IFN dose-dependent increase in survival times after encephalomyocarditis virus infections for both the TD and wild-type mice. Mice that were deficient for PKR or RNase L showed intermediate survival times between those of the TD and wild-type mice. Surprisingly, cultured embryonic fibroblasts lacking RNase L, PKR, or both proteins were still able to mount a substantial residual antiviral response against encephalomyocarditis virus or vesicular stomatitis virus after IFN-α treatments. These results confirm the antiviral functions of RNase L and PKR in vivo but also provide unequivocal evidence for the existence of novel, innate immune pathways against viruses