pinecone/core-2020-05-10-deduplication huggingface dataset:
Type I IFN Modulates the Immune Response Induced by DNA Vaccination to Pseudorabies Virus Glycoprotein C

AbstractDNA vaccines have the capacity to induce strong Th1-biased immune responses that are of major importance to providing protection against intracellular pathogens. In the present study we have focused on the role played by type I IFN in immune responses induced after DNA vaccination. Mice lacking the IFNAR1 chain of the type I IFN receptor (IFNAR K/O mice) were immunized with a plasmid encoding glycoprotein C of pseudorabies virus (PRV-gC). After DNA vaccination, wild-type (WT) mice showed features characteristic of Th1 immune responses, such as high IgG2a:IgG1 anti-PRV Ab ratio and antigen-specific IFN-γ production by spleen cells. In contrast, IFNAR K/O mice showed a significantly lower IgG2a:IgG1 Ab ratio and IFN-γ production. In addition, the percentage of CD8+ and B lymph-node cells expressing CD69 after PRV-gC DNA vaccination was lower in IFNAR K/O than in WT mice. These results support a major role played by type I IFN in shaping Th1 immune responses after DNA vaccination. Codelivery of plasmids encoding IL-12 and IL-18 along with the plasmid encoding PRV-gC restored Th1 responses in IFNAR K/O mice
Protection from Immunodeficiency Virus Challenges in Rhesus Macaques by Multicomponent DNA Immunization

AbstractMulticomponent DNA vaccines were used to elicit immune responses, which can impact viral challenge in three separate rhesus macaque models. Eight rhesus macaques were immunized with DNA vaccines for HIV env/rev and SIV gag/pol and were challenged intravenously with 10 animal infective doses (AID50) of cell-free SHIV IIIB. Three of eight immunized rhesus macaques were protected, exhibiting no detectable virus. Animals protected from nonpathogenic SHIVIIIB challenge were rested for extended periods of time and were rechallenged first with pathogenic SIVmac239 and subsequently with pathogenic SHIV89.6P viruses. Following the pathogenic challenges, all three vaccinated animals were negative for viral coculture and antigenemia and were negative by PCR. In contrast, the control animals exhibited antigenemia by 2 weeks postchallenge and exhibited greater than 10 logs of virus/106 cells in limiting dilution coculture. The control animals exhibited CD4 cell loss and developed SIV-related wasting with high viral burden and subsequently failed to thrive. Vaccinated animals remained virus-negative and were protected from the viral load, CD4 loss, disease, and death. We observed strong Th1-type cellular immune responses in the protected macaques throughout the study, suggesting their important roles in protection. These studies support the finding that multicomponent DNA vaccines can directly impact viral replication and disease in a highly pathogenic challenge system, thus potentially broadening our strategies against HIV
Amino Acid Substitution(s) in the Stem-Anchor Region of Langat Virus Envelope Protein Attenuates Mouse Neurovirulence

AbstractThe identification of variants that are unable to bind membrane receptor preparations (MRPs) has previously been shown to select attenuated yellow fever and Japanese encephalitis viruses. In this study, this methodology has been extended to the tick-borne serocomplex of flaviviruses. Langat (LGT) virus strain TP21 was bound to mouse or human brain MRPs and viruses that escaped binding were isolated and characterized. In addition, variant viruses escaping neutralization by the monoclonal antibody (MAb) 9F9 were also isolated. All of the variant viruses were attenuated for mouse neurovirulence (≥13-fold). Sequence analysis of the prM/E region of the variant viruses identified mutations within the stem-anchor region of the E protein in variants isolated following incubation with mouse or human brain MRPs at a pH ≥ 7.0. The MAb 9F9 variants and MRP variants isolated at pH 5.0, which should induce a conformational shift in the viral E protein, had nearly identical mutations in the prM/M protein immediately N-terminal to the prM/E cleavage site. MAb 9F9 neutralized none of the variant viruses and hemagglutination inhibition assays suggest that the variant virus surface proteins have slightly different conformations compared to the parental virus. These data support previous work indicating that the stem-anchor region of the E protein is important to the surface architecture of the tick-borne flaviviruses. In addition, this study demonstrates that the M protein is at least partially solvent accessible on the virion surface and that the M protein plays a role in maintaining the conformation of the M/E surface complex
Deletion and Substitution Analysis Defines Regions and Residues within the Phosphoprotein of Bovine Respiratory Syncytial Virus That Affect Transcription, RNA Replication, and Interaction with the Nucleoprotein

AbstractThe phosphoprotein (P) of bovine respiratory syncytial virus (BRSV) is a multifunctional protein that plays a central role in transcription and replication of the viral genomic RNA. To investigate the domains and specific residues involved in different activities of the P protein, we generated a total of 22 deletion and 17 point mutants of the P protein. These mutants were characterized using an intracellular BRSV-CAT minigenome replication system for the ability to (1) direct minigenome transcription, (2) direct minigenome replication, and (3) form complexes with nucleocapsid protein (N) and large polymerase protein (L). These studies revealed that all the regions of P protein except amino acids 41–80 are essential for minigenome transcription and replication. Interestingly, amino acids 41–60 appeared to contain sequences that negatively regulate transcription and replication. Analysis of the N- or C-terminal ends indicated that deletion of up to 3 amino acids from the N- or C-terminus completely ablated the replication, while leaving substantial residual transcription. Single amino acid substitutions within the N-terminal 4 or C-terminal 13 amino acids showed that substitution at position 2, 4, 234, 236, 238, 240, or 241 was highly inhibitory to both transcription and replication, whereas substitution at position 3 was highly inhibitory to replication while leaving substantial residual transcription. Substitution of serine residues at the C-terminus indicated that loss of phosphorylation sites did not appear to have any effect on transcription and replication. Coimmunoprecipitation of P–N and P–L complexes with P-specific antiserum revealed that substitution mutations at the N- or C-terminus did not affect binding to N and L proteins, except that substitution mutation at C-terminus position 234, 236, 238, 240, or 241 affected binding to N protein by 10-fold
Mutations in the Measles Virus C Protein That Up Regulate Viral RNA Synthesis

AbstractThe measles virus RNA-dependent RNA polymerase consists of two virus-encoded subunits, the phosphoprotein (P) and the large (L) protein. The P mRNA also codes for a C protein in the +1 reading frame relative to P. The activities of the measles P and C proteins from the vaccine strain, EdB, a wild-type CM strain, and an SSPE P4 strain were investigated using a CAT reporter minigenome assay. CAT is synthesized following replication and transcription of a DI-CAT minigenome supported by individual P, L, and N plasmids expressed in a mammalian expression system. As measured by CAT activity, CMP1 and P4P1 stimulate transcription and replication four- to six- and six- to eightfold, respectively, better than EdP. There are 10 and 16 amino acid changes in the P protein and three and four changes in C in CMP1 and P4P1, respectively, relative to EdP. By constructing chimeric P genes we showed that mutations throughout P4P1 were required for enhanced polymerase activity, while only mutations in the 5′-terminal portion, encompassing the C ORF, of the CMP1 gene mediated stimulation. Abrogation of C expression from the Ed and CM P genes resulted in an increase in RNA synthesis of twofold for CMP1S and four- to fivefold for EdPS. With the addition of C protein expressed from a separate plasmid that contains only the C ORF, EdC reduces viral RNA synthesis more strongly than CMC. These data suggest that EdC and CMC proteins give a differential inhibition that accounts for most of the differences in RNA synthesis by EdP and CMP1
Analysis of the First Complete DNA Sequence of an Invertebrate Iridovirus: Coding Strategy of the Genome of Chilo Iridescent Virus

AbstractChilo iridescent virus (CIV), the type species of the genus Iridovirus, a member of the Iridoviridae family, is highly pathogenic for a variety of insect larvae. The virions contain a single linear ds DNA molecule that is circularly permuted and terminally redundant. The coding capacity and strategy of the CIV genome was elucidated by the analysis of the complete DNA nucleotide sequence of the viral genome (212,482 bp) using cycle sequencing by primer walking technology. Both DNA strands were sequenced independently and the average redundancy for each nucleotide was found to be 1.85. The base composition of the viral genomic DNA sequence was found to be 71.37% A+T and 28.63% G+C. The CIV genome contains 468 open reading frames (ORFs). The size of the individual viral gene products ranges between 40 and 2432 amino acids. The analysis of the coding capacity of the CIV genome revealed that 50% (234 ORFs) of all identified ORFs were nonoverlapping. The comparison of the deduced amino acid sequences to entries in protein data banks led to the identification of several genes with significant homologies, such as the two major subunits of the DNA-dependent RNA polymerase, DNA polymerase, protein kinase, thymidine and thymidylate kinase, thymidylate synthase, ribonucleoside-diphosphate reductase, major capsid protein, and others. The highest homologies were detected between putative viral gene products of CIV and lymphocystis disease virus of fish (LCDV). Although many CIV putative gene products showed significant homologies to the corresponding viral proteins of LCDV, no colinearity was detected when the coding strategies of the CIV and LCDV-1 were compared to each other. An intriguing result was the detection of a viral peptide of 53 amino acid residues (ORF 160L) showing high homology (identity/similarity: 60.0%/30.0%) to sillucin, an antibiotic peptide encoded by Rhizomucor pusillus. Iridovirus homologs of cellular genes possess particular implications for the molecular evolution of large DNA viruses
T Cell Apoptosis Causes Peripheral T Cell Depletion in Mice Transgenic for the HIV-1 vpr Gene

AbstractVpr, an accessory protein of HIV, is known to affect viral replication as well as cell growth, differentiation, and apoptosis in vitro. To investigate its pathogenicity in vivo, we have produced mice transgenic for the HIV-1 vpr gene with the CD4 enhancer/promoter. Interestingly, apoptotic death of T lymphocytes was enhanced in those mice, causing marked reduction of T cells in lymphatic organs and peripheral blood. Involvement of Bcl-x, Bax, and Caspase-1, but not of the Fas–Fas ligand system, was suggested in the apoptotic processes. These observations suggest that Vpr is involved in the pathogenesis of T cell depletion in HIV-infected people
12-O-Tetradecanoylphorbol-13-acetate Induces Epstein–Barr Virus Reactivation via NF-κB and AP-1 as Regulated by Protein Kinase C and Mitogen-Activated Protein Kinase

AbstractSignaling pathway components mediating Epstein–Barr virus (EBV) reactivation by 12-O-tetradecanoylphorbol-13-acetate (TPA) were characterized in terms of induction and modification of specific transacting factors. The consequences of protein kinase C (PKC) activation by TPA in inhibiting inducible nitric oxide synthase (iNOS) mRNA expression were analyzed in the EBV-infected gastric epithelial cell line GT38. Spontaneous expression of the EBV BZLF1 gene product ZEBRA became undetectable upon long-term culturing of GT38 cells, while iNOS mRNA expression increased. In such cells the PKC inhibitors 1-(5-isoquinolinesulphonyl)-2,5-dimethylpiperazine (H7) and staurosporine inhibited TPA-induced expression of BZLF1 and BRLF1 and reversed TPA-mediated inhibition of iNOS gene expression. The mitogen-activated protein kinase inhibitor PD98059 inhibited TPA-induced BZLF1 expression. Electrophoretic mobility shift assays demonstrated that transcription factors NF-κB and AP-1 were also activated by TPA in a time-dependent manner. The TPA-induced NF-κB activation was inhibited by prior treatment of the cells with the NF-κB inhibitor pyrrolidine dithiocarbamate (PDTC). TPA-induced BZLF1 expression was also inhibited by the treatment with PDTC. Northern blot analyses characterized changes in levels of the c-jun and junB expressions of the AP-1 family. These results show that TPA induces EBV reactivation via NF-κB and AP-1 and that PKC is an important mediator in regulating gene expression leading to EBV reactivation after TPA treatment of GT38 cells
The NS2 Protein Generated by the Parvovirus Minute Virus of Mice Is Degraded by the Proteasome in a Manner Independent of Ubiquitin Chain Elongation or Activation

AbstractThe NS2 protein generated by the parvovirus minute virus of mice is very labile, having a half-life during infection of approximately 90 min. The degradation of NS2 is blocked by proteasome inhibitors but is likely ubiquitin independent: NS2 does not form detectable higher molecular weight ubiquitin-containing conjugates, and NS2 degradation requires neither ubiquitin chain elongation nor intracellular ubiquitin activation. We have also identified a region in the carboxyl half of NS2 that is required for its proteasome-mediated degradation
Altered Biology of Adeno-associated Virus Type 2 and Human Papillomavirus during Dual Infection of Natural Host Tissue

AbstractAdeno-associated virus (AAV), a common genital virus, may have a “protective” role against human papillomavirus (HPV)-associated cervical cancer. Epidemiological studies indicate a negative correlation between AAV infection and the incidence of cervical cancer. In contrast, HPV is positively associated with cervical cancer. To investigate interactions between these two viruses we used the organotypic “raft” culture system. The raft culture system is capable of supporting the complete HPV life cycle. Raft tissues that were actively replicating HPV were superinfected with AAV type 2 (AAV-2). We observed a multiplicity of infection (m.o.i.)-dependent enhancement and inhibition of HPV DNA replication, concomitant with AAV-2 replication. The data suggest that at low m.o.i. of AAV-2 infection, HPV DNA replication was slightly increased compared to controls and AAV-2 replicated poorly. At high AAV-2 m.o.i., HPV DNA replication was reduced and AAV-2 replicated to high levels. AAV-2 replication was increased in the presence of HPV compared to primary human keratinocyte, squamous cell carcinoma, and HaCat raft cultures infected with AAV-2 alone. These data suggest that HPV may provide types of “enhancer/helper” functions for AAV-2 replication and progeny formation. Infection with AAV-2 had significant effects on epithelial morphology. During infection with low m.o.i. of AAV-2 the epithelium stratified to a greater extent than in controls. With high m.o.i. of AAV-2 infections, tissue cytopathic effects were observed, indicating an additional factor responsible for the effect of AAV-2 on HPV replication and infection. Our results demonstrate a complex interaction between AAV-2, HPV, and skin during dual infection
Self-Priming of Retroviral Minus-Strand Strong-Stop DNAs

AbstractAfter minus-strand strong-stop DNA (−sssDNA) is synthesized, the RNA template is degraded by the RNase H activity of the reverse transcriptase (RT), generating a single-stranded DNA. The 3′ end of −sssDNA from HIV-1 can form a hairpin; this hairpin will self-prime in vitro. We previously used a model substrate, −R ssDNA, which corresponds to the 3′ end of the −sssDNA of HIV-1, to show that the self-priming of this model substrate could be prevented by annealing a 17-nt-long DNA oligonucleotide to the 3′ end of −R ssDNA in the presence of HIV-1 nucleocapsid (NC) protein. Similar model substrates were prepared for HIV-2 and HTLV-1; the R regions of these two viruses are longer and form more complex structures than the R region of the HIV-1 genome. However, the size of the R region and the complexity of the secondary structures they can form do not affect self-priming or its prevention. The efficiency of the self-priming is related to the relative stabilities of the conformations of −R ssDNA that can and cannot induce self-priming. For the three viruses (HIV-1, HIV-2, and HTLV-1), the size of the DNA oligonucleotide needed to block self-priming in the presence of NC is similar to the expected size of the piece of RNA left after degradation of the RNA template during reverse transcription. We also found that when the 3′ end of −R ssDNA is annealed to a complementary DNA oligonucleotide, it is a good substrate for efficient nonspecific strand transfer to other single-stranded DNA molecules
Characterization of Pseudotype VSV Possessing HCV Envelope Proteins

AbstractThe genome of hepatitis C virus (HCV) encodes two envelope glycoproteins (E1 and E2), which are thought to be responsible for receptor binding and membrane fusion resulting in virus penetration. To investigate cell surface determinants important for HCV infection, we used a recombinant vesicular stomatitis virus (VSV) in which the glycoprotein gene was replaced with a reporter gene encoding green fluorescent protein (GFP) and produced HCV-VSV pseudotypes possessing chimeric HCV E1 or E2 glycoproteins, either individually or together. The infectivity of the pseudotypes was determined by quantifying the number of cells expressing the GFP reporter gene. Pseudotypes that contained both of the chimeric E1 and E2 proteins exhibited 10–20 times higher infectivity on HepG2 cells than the viruses possessing either of the glycoproteins individually. These results indicated that both E1 and E2 envelope proteins are required for maximal infection by HCV. The infectivity of the pseudotype virus was not neutralized by anti-VSV polyclonal antibodies. Bovine lactoferrin specifically inhibited the infection of the pseudotype virus. Treatment of HepG2 cells with Pronase, heparinase, and heparitinase but not with phospholipase C and sodium periodate reduced the infectivity. Therefore, cell surface proteins and some glycosaminoglycans play an important role in binding or entry of HCV into susceptible cells. The pseudotype VSV possessing the chimeric HCV glycoproteins might offer an efficient tool for future research on cellular receptors for HCV and for the development of prophylactics and therapeutics for hepatitis C
Inhibition of Cellular Functions of HIV-1 Nef by Artificial SH3 Domains

AbstractSH3 domains regulate many normal and pathological cellular processes by guiding specific protein interactions. Studies on binding of HIV-1 Nef to the SH3 domain of the Hck tyrosine kinase have indicated an important role for the SH3 RT-loop region in ligand binding. Here we have tested the potential of artificial Hck-derived SH3 domains carrying tailored RT-loops providing high affinity for Nef as intracellular inhibitors of Nef. These artificial SH3 domains efficiently associated with Nef in cells and thereby potently inhibited SH3-dependent Nef functions, such as association with p21-activated kinase-2 and induction of the transcription factor NFAT. On the other hand, biochemical and functional data indicated that the Nef-targeted SH3 domains were not prone to compete with normal SH3-mediated processes. Thus, RT-loop-modified SH3 domains represent a novel approach for selectively interfering with cellular signaling events, which could be exploited in research as well as in therapeutic applications
Influence of the Small Leader Exons 2 and 3 on Human Immunodeficiency Virus Type 1 Gene Expression

AbstractThe human immunodeficiency virus type 1 (HIV-1) uses an elaborate alternative splicing pattern for the generation of both the 1.8-kb as well as the 4-kb classes of mRNA. An additional diversity of transcripts in both classes is created by the optional inclusion of the small exons 2 and 3 in the leader sequence. To analyze a possible influence of these leader exons on HIV-1 gene expression, several series of expression vectors with different leaders were constructed, expressing either Rev and Env or a heterologous coding sequence, i.e., the chloramphenicol acetyl transferase (CAT) ORF. Transfection experiments of HeLa-T4+ cells revealed for all series of constructs that mRNA as well as protein expression was stimulated by the presence of exon 2 and reduced by exon 3. The function of the leader exons 2 and 3 is neither dependent on the regulatory proteins Tat or Rev nor on viral coding sequences. Neither transcription rates nor stability of polyadenylated RNAs were found to be responsible for the different levels of steady-state mRNA. When either exon 2 or 3 was inserted into a heterologous intron, processing of the primary transcripts generated identical mRNA species while maintaining the differences in exon 2/3-dependent mRNA steady-state levels. These results may be explained by exon-specific nuclear RNA degradation rates, as also indicated by results from an in vitro degradation assay using a HeLa nuclear extract
The AG Recombinant IbNG and Novel Strains of Group M HIV-1 Are Common in Cameroon

AbstractThe genetic diversity of group M HIV-1 is highest in west central Africa. Blood samples from four locations in Cameroon were collected to determine the molecular epidemiology of HIV-1. The C2-V5 region of envelope was sequenced from 39 of the 40 samples collected, and 7 samples were sequenced across the genome. All strains belonged to group M of HIV-1. The circulating recombinant form CRF02 AG (IbNG) was the most common strain (22/39, 56%). Two of these were confirmed by full genome analysis. Four samples (4/39, 10%) clustered with the sub-subtype F2 and one of these was confirmed by full genome sequencing. Recombinant forms, each different but containing subtype A, accounted for the next most common form (7/39, 18%). Among these recombinants, those combining subtypes A and G were the most common (4/7, 57%). Also found were 3 subtype A, 2 subtype G, and 1 subtype B strain. Many recombination break points were shared between IbNG and the other AG recombinants, though none of these other AG recombinants included IbNG as a parent. This suggests that there was an ancestral AG recombinant that gave rise to CRF02 AG (IbNG), the successful circulating recombinant form, and to others that were less successful and are now rare