pinecone/core-2020-05-10-deduplication huggingface dataset:
Identification of Determinants of Interaction between CXCR4 and gp120 of a Dual-tropic HIV-1DH12Isolate

AbstractUsing a panel of chimeric viruses and their chimeric envelope glycoproteins, we have previously reported that the V1/V2 or the V3 regions of a dual-tropic primary human immunodeficiency virus type 1 (HIV-1) isolate (HIV-1DH12) could individually confer CXCR4 usage when introduced into the backbone of a macrophage-tropic (M-tropic) virus isolate (HIV-1AD8). In this study, chimeric CXCR4–CXCR2 chemokine receptors were employed to identify the determinants involved in the interaction between CXCR4 and the dual-tropic HIV-1DH12gp120. Our results indicate that (i) HIV-1DH12gp120 interacts primarily with the extracellular domains 1 (E1) and 2 (E2) of CXCR4, (ii) the V1/V2 and the V3 regions interact with different domains of CXCR4, and (iii) the V1/V2 region plays a more critical role in the interaction between CXCR4 and HIV-1DH12gp120. Combining our data and those of others suggests that the pattern of CXCR4 usage is highly dependent on HIV-1 isolates. In addition, an M-tropic virus may evolve to become dual-tropic by first acquiring the ability to interact with CXCR4 through the V1/V2 region of gp120
Role of the Leukocyte Function Antigen-1 Conformational State in the Process of Human Immunodeficiency Virus Type 1-Mediated Syncytium Formation and Virus Infection

AbstractHuman immunodeficiency virus type 1 (HIV-1)-mediated syncytium formation is recognized as being highly dependent on intercellular adhesion molecule (ICAM)-1–leukocyte function-associated molecule 1 (LFA)-1 interaction, whereas the process of infection with cell-free virions is independent of such complementary interaction. Our group has recently demonstrated that an antibody-mediated induction of the high affinity state of LFA-1 for ICAM-1 renders target T cells more prone to HIV-1-dependent syncytium formation and infection by ICAM-1-bearing virions. To further substantiate these results, we made use of mutant cell lines expressing LFA-1 in either a low (parental HPB-ALL and HAmut) or a high affinity state for ICAM-1 (HAP4) and compared syncytium formation and virus infection. Cells expressing the activated form of LFA-1 were found to be more susceptible to HIV-1-induced syncytium formation and to infection by ICAM-1-bearing HIV-1 particles. The observed increase was solely due to the LFA-1 activation state because it was abrogated by anti-LFA-1 or anti-ICAM-1 antibodies and not due to variations in surface expression of LFA-1, CD4, or the chemokine coreceptor CXCR4. However, a linear relation was seen between the level of CXCR4 surface expression and susceptibility to syncytium formation/virus infection when ICAM-1–LFA-1 interaction was either absent (i.e., infection with ICAM-1-negative virions) or abrogated (treatment with anti-LFA-1 or anti-ICAM-1 antibodies). These results emphasize the important role of the LFA-1 activation state with respect to virus-induced syncytium formation and HIV-1 infection
Activation of Bcl-2 Promoter-Directed Gene Expression by the Human Immunodeficiency Virus Type-1 Tat Protein

AbstractHuman immunodeficiency virus type 1 (HIV-1) Tat transcriptionally activates expression from a number of viral and cellular promoters. Recent studies demonstrate the ability of Tat to differentially modulate cellular responses to apoptotic signaling. The antiapoptotic effects of Tat appear to correlate with increased expression of Bcl-2, a cellular protein that enhances cellular survival. Here, endogenous expression of HIV-1 Tat in HeLa and Jurkat cells elevates levels of Bcl-2. Transient expression assays performed in HeLa cells demonstrate that Tat directly or indirectly enhances Bcl-2 promoter-directed gene expression by more than 10-fold. Analyses of Tat mutants demonstrate that two noncontiguous regions in the N- and C-termini of Tat mediate maximal transactivation of the Bcl-2 promoter. The requirement for C-terminal sequences contrasts with transactivation of the HIV-1 long terminal repeat in which the N-terminal 57 amino acids are required but downstream residues are not. Bcl-2 promoter analyses suggest that sequences required for Tat responsiveness are located upstream of P1 and between the P1 and P2 promoter units. Results from these studies reveal effects of HIV-1 Tat on Bcl-2 expression and provide a putative mechanism by which endogenously expressed Tat affects cellular survival through the up-regulation of Bcl-2
Multiple Mitochondrial Viruses in an Isolate of the Dutch Elm Disease FungusOphiostoma novo-ulmi

AbstractThe nucleotide sequences of three mitochondrial virus double-stranded (ds) RNAs, RNA-4 (2599 nucleotides), RNA-5 (2474 nucleotides), and RNA-6 (2343 nucleotides), in a diseased isolate Log1/3–8d2(Ld) of the Dutch elm disease fungusOphiostoma novo-ulmihave been determined. All these RNAs are A-U-rich (71–73% A + U residues). Using the fungal mitochondrial genetic code in which UGA codes for tryptophan, the positive-strand of each of RNAs 4, 5, and 6 contains a single open reading frame (ORF) with the potential to encode a protein of 783, 729, and 695 amino acids, respectively, all of which contain conserved motifs characteristic of RNA-dependent RNA polymerases (RdRps). Sequence comparisons showed that these RNAs are related to each other and to a previously characterized RNA, RNA-3a, from the sameO. novo-ulmiisolate, especially within the RdRp-like motifs. However, the overall RNA nucleotide and RdRp amino acid sequence identities were relatively low (43–55% and 20–32%, respectively). The 5′- and 3′-terminal sequences of these RNAs are different, but they can all be folded into potentially stable stem-loop structures. Those of RNA-4 and RNA-6 have inverted complementarity, potentially forming panhandle structures. Their molecular and biological properties indicate that RNAs 3a, 4, 5, and 6 are the genomes of four different viruses, which replicate independently in the same cell. These four viruses are also related to a mitochondrial RNA virus from another fungus,Cryphonectria parasitica, recently designated the type species of theMitovirusgenus of the Narnaviridae family, and to a virus from the fungusRhizoctonia solani. It is proposed that the fourO. novo-ulmimitochondrial viruses are assigned to theMitovirusgenus and designatedO. novo-ulmimitovirus (OnuMV) 3a-Ld, 4-Ld, 5-Ld, and 6-Ld, respectively. Northern blot analysis indicated thatO. novo-ulmiLd nucleic acid extracts contain more single-stranded (ss, positive-stranded) RNA than dsRNA for all three newly described mitoviruses.O. novo-ulmiRNA-7, previously believed to be a satellite-like RNA, is shown to be a defective RNA, derived from OnuMV4-Ld RNA by multiple internal deletions. OnuMV4-Ld is therefore the helper virus for the replication of both RNA-7 and another defective RNA, RNA-10. Sequence comparisons indicate that RNA-10 could be derived from RNA-7, as previously suggested, or derived directly from RNA-4
Infectious Virus in Transgenic Plants Inoculated with a Nonviable, P1-Proteinase Defective Mutant of a Potyvirus

AbstractA mutant (P1-616) of the tobacco vein mottling potyvirus that contains a four-codon insertion in the P1 protein coding region of the viral RNA is unable to infect the normal host plant of the virus. Processing of the P1/HC-Pro cleavage site does not occur duringin vitrotranslation of the mutant viral RNA. When plants transformed with the P1/HC-Pro/P3 coding region of tobacco vein mottling potyvirus RNA were inoculated with P1-616, some of them became infected, although there was a delay in the production of disease symptoms. Virus isolated from these plants was able to infect nontransgenic plants. Two variants of the recovered, infectious virus contained single-nucleotide alterations in the four-codon insertion in the P1-616 genome.In vitrotranslation of the variant genomic RNAs resulted in partial processing of the P1/HC-Pro cleavage site, although serological analysis of infected tissue showed complete processingin vivo. These results indicate that limited complementation of P1-616 occurs in the transgenic plants and that eventually there arises one or more variants of the mutant sequence that can effect P1/HC-Pro processing and therefore be replicated
Isolation and Molecular Characterization of a Novel Cytopathogenic Paramyxovirus from Tree Shrews

AbstractA cytopathic infectious agent was isolated from the kidneys of an apparently healthy tree shrew (Tupaia belangeri) that had been captured in the area around Bangkok. The infectivity was propagated in Tupaia fibroblast and kidney cell cultures. Paramyxovirus-like pleomorphic enveloped particles and helical nucleocapsids were observed by electron microscopy and accordingly the infectious agent was termed Tupaia paramyxovirus (TPMV). However, no serological cross-reactions were detected between TPMV and known paramyxoviruses. For the molecular characterization of TPMV an experimental strategy that allows the random-primed synthesis of relatively large cDNA molecules from viral genomic RNA was applied. Nucleotide sequence analysis of a TPMV-specific cDNA fragment (1544 bp) revealed two nonoverlapping partial open reading frames corresponding to paramyxoviral N and P transcription units. Using modified rapid amplification of cDNA ends techniques, a substantial contiguous portion of the viral genome (4065 nt) was elucidated including the complete N and P/V/C genes. The coding strategy of TPMV as well as significant amino acid sequence homologies clearly indicates an evolutionary relationship between TPMV and members of the genus Morbillivirus. Highest homologies were detected between TPMV and Hendra virus (equine morbillivirus), which recently emerged in Australia, causing outbreaks of fatal respiratory and neurological disease in horses and humans
Hepatitis C Virus Core Protein Regulates Cell Growth and Signal Transduction Pathway Transmitting Growth Stimuli

AbstractTo investigate the transforming potential of hepatitis C virus (HCV), HCV core protein was produced in BALB/3T3 A31-I-1 cells. The cells expressing HCV core gene cooperatively with the v-H-ras gene showed loss of contact inhibition, morphological alterations, and anchorage-independent and serum-independent growth. The cells producing HCV core protein showed enhanced growth against stimulus of growth factor. In addition, antisense oligodeoxynucleotides against mRNA encoding HCV core protein suppressed the growth of HCV core-producing cells. Furthermore, HCV core protein activated mitogen-activated protein kinase and serum response element, which respond to growth stimuli. From these results, we concluded that HCV core protein is involved in the acquisition of cell growth advantage
Immunogenicity, Genetic Stability, and Protective Efficacy of a Recombinant, Chimeric Yellow Fever-Japanese Encephalitis Virus (ChimeriVax-JE) as a Live, Attenuated Vaccine Candidate against Japanese Encephalitis

AbstractYellow fever (YF) 17D vaccine virus, having a 60-year history of safe and effective use, is an ideal vector to deliver heterologous genes from other medically important flaviviruses. A chimeric YF/Japanese encephalitis (JE) virus (ChimeriVax-JE virus) was constructed by insertion of the premembrane and envelope (prME) genes of an attenuated human vaccine strain (SA14–14-2) of Japanese encephalitis (JE) virus between core and nonstructural (NS) genes of a YF 17D infectious clone. The virus grew to high titers in cell cultures and was not neurovirulent for 3- to 4-week-old mice at doses ≤6 log10plaque forming units (pfu) inoculated by the intracerebral (IC) route. In contrast, commercial YF 17D vaccine was highly neurovirulent for weanling mice by the same route. Mice inoculated subcutaneously with one dose of ≥103pfu of ChimeriVax-JE virus were solidly protected against intraperitoneal challenge with a virulent JE virus. Genetic stability of the chimera was assessed by sequential passages in cell cultures or in mouse brain. All attenuating residues and the avirulent phenotype were preserved after 18 passages in cell cultures or 6 passages in mouse brains
Inclusion of the NS2-Specific Exon in Minute Virus of Mice mRNA Is Facilitated by an Intronic Splicing Enhancer That Affects Definition of the Downstream Small Intron

AbstractAlternative splicing of pre-mRNAs plays a critical role in maximizing the coding capacity of the small parvovirus genome. The small-intron region of minute virus of mice (MVM) pre-mRNAs undergoes an unusual pattern of overlapping alternative splicing, using two donors, D1 and D2, and two acceptors, A1 and A2, within a region of 120 nucleotides, that governs the steady-state ratios of the various viral mRNAs. In a previous report we demonstrated that a complex interaction between both donor and acceptor sequences, as well as the constraints of size, defines the small intron and governs its alternative splicing. We also identified a G-rich intronic splicing enhancer sequence (IES) that appeared to function as both an intron- and an exon-defining element. In this report we further examined the components that govern MVM small-intron splicing. In fully processed wild-type mRNAs, A1 is used preferentially over A2. In this report, we show that in the context of the wild-type small intron the position of the downstream acceptor A2 was preferred, and the primary sequence of A1 must be stronger for it to be utilized at wild-type efficiency. Use of A2 in generation of the minor spliced forms D2/A2 required the IES because of a weak A2 polypyrimidine tract and because of the relative strength of A1. The small size of the intron and the relative position of the IES were also shown to play a critical role in donor and acceptor site selection. Finally, we have further characterized how the IES functions as an intronic enhancer of upstream exon definition. When the small intron was expanded, upstream exon inclusion was dependent upon the position of the IES. Within the context of the small intron, alterations of the small intron that overcame the requirement for the IES for splicing to A2 also permitted wild-type levels of upstream exon inclusion in the absence of the IES, suggesting that, in its natural context, the IES facilitates upstream exon inclusion by affecting small-intron definition
Bovine Viral Diarrhea Virus Quasispecies during Persistent Infection

AbstractAnalysis of viral genome sequences from two calves persistently infected with bovine viral diarrhea virus revealed a quasispecies distribution. The sequences encoding the glycoprotein E2 were variable, translating to a number of changes in predicted amino acid sequences. The NS3 region was found to be highly conserved in both animals. The number of E2 clones showing variant amino acids increased with the age of the animal and comparison of the consensus sequences at the different time points confirmed differences in the predicted E2 sequences over time. The immune tolerance that allows the lifelong persistence of this viral infection is highly specific. It is likely that some of the variant viruses generated within these animals will differ antigenically from the persisting virus and be recognized by the immune system. Evidence of an immune response to persisting virus infection was gathered from a larger sample of cattle. Serum neutralizing antibodies were found in 4 of 21 persistently infected animals. Accumulations of viral RNA in the lymph nodes of all animals examined, particularly in the germinal center light zone, may represent antigenic variants held in the form of immune complexes on the processes of follicular dendritic cells
Self-Interaction of the Herpes Simplex Virus Type 1 Regulatory Protein ICP27

AbstractThe herpes simplex virus type 1 (HSV-1) regulatory protein ICP27 is a nuclear phosphoprotein required for viral lytic infection, which acts partly at the posttranscriptional level to affect RNA processing and export. In the present study, we show that ICP27 can interact with itselfin vivo.Immunofluorescent staining of cells expressing both an ICP27 mutant with a deletion of the major nuclear localization signal and wild-type ICP27 showed that the mutant protein was efficiently imported into the nucleus in the majority of the cotransfected cells, suggesting heterodimer formation between the wild-type and mutant proteins. Coimmunoprecipitation experiments using epitope-tagged wild-type ICP27 and a series of ICP27 mutants with deletions and insertions in important functional regions of the protein revealed that the C-terminal cysteine-histidine-rich zinc-finger-like region of ICP27 was required for the self-association. Furthermore the self-association was also shown in yeast using two-hybrid assays, and again, an intact C-terminal zinc-finger-like region was required for the interaction. This study provides biochemical evidence that ICP27 may function as a multimer in infected cells
Intracellular Transport and Maturation Pathway of Human Herpesvirus 6

AbstractA peculiar characteristic of cells infected with human herpesvirus 6 (HHV6) is the absence of viral glycoproteins on the plasma membrane, which may reflect an atypical intracellular transport of the virions and/or the viral glycoproteins, different from that of the other members of the herpesvirus family. To investigate the maturation pathway of HHV-6 in the human T lymphoid cell line HSB-2, we used lectin cytochemistry and immunogold labeling combined with several electron microscopical techniques, such as ultrathin frozen sections, postembedding, and fracture-label. Immunolabeling with anti-gp116 and anti-gp82-gp105 monoclonal antibodies revealed that the viral glycoproteins are undetectable on nuclear membranes and that at the inner nuclear membrane nucleocapsids acquire a primary envelope lacking viral glycoproteins. After de-envelopment, cytoplasmic nucleocapsids acquire a thick tegument and a secondary envelope with viral glycoproteins at the level of neo-formed annulate lamellae or at thecis-side of the Golgi complex. Cytochemical labeling using helix pomatia lectin revealed that the newly acquired secondary viral envelopes contain intermediate forms of glycocomponents, suggesting a sequential glycosylation of the virions during their transit through the Golgi area before their final release into the extracellular space. Immunogold labeling also showed that the viral glycoproteins, which are not involved in the budding process, reach and accumulate in the endosomal/lysosomal compartment. Pulse-chase analysis indicated degradation of the gp116, consistent with its endosomal localization and with the absence of viral glycoproteins on the cell surface of the infected cells
Sequence Requirements for the Nuclear Localization of the Murine Cytomegalovirus M44 Gene Product pp50

AbstractThe murine cytomegalovirus (MCMV) M44 gene product pp50 is normally present in the nuclei of virus-infected cells. During transient expression of pp50 in COS-1 cells, the phosphoprotein was readily detectable in the nuclei, indicating that it possesses a nuclear localization signal (NLS). Studies on the subcellular locations of N- and C-terminal deletion mutants of pp50 suggested that alterations in both the C terminus and the highly conserved N-terminal domains of pp50 affect nuclear localization. In particular, the C-terminal 11 amino acids of pp50, which includes a “KKQK” motif, were able to mediate the import of a β-galactosidase fusion protein into the nucleus. The pair of lysine residues in this motif constitutes an essential element of the C-terminal NLS as mutation of this motif to AAQK directly affected the nuclear localization of either pp50 or β-galactosidase fusion proteins containing the C-terminal portion of pp50. Furthermore our results indicated that the functionality of the C-terminal NLS is dependent on the structural integrity of the highly conserved N-terminal portion of the molecule, as deletion of amino acids 157–201 alone adversely affected nuclear localization. In the absence of a functional C-terminal NLS, the subcellular localization of pp50 is sensitive to potential conformational changes induced by mutations within the N-terminal half of the molecule. Under those circumstances, mutation of the YK residues at position 22–23 or deletion of amino acids 267–283 was sufficient to produce a protein that was impaired in nuclear import or retention
Production and Characterization of Human Monoclonal Antibody Fab Fragments to Vaccinia Virus from a Phage-Display Combinatorial Library

AbstractA combinatorial, phage-display library of human Fab antibody fragments was generated from IgG heavy chain (HC) and light chain (LC) genes cloned from the lymphocytes of a vaccinia virus (VACV)-immune donor. To ascertain the complexity of the library, nucleotide sequences of the variable regions of the HC and LC genes were determined. Fourteen distinct HC and 18 distinct LC (7 κ and 11 λ) that formed a combinatorial library of 22 Fabs were identified. Immune-precipitation of radiolabeled VACV revealed that at least six different VACV proteins were recognized by the antibodies. Plaque-reduction neutralization demonstrated that six of the Fabs neutralized VACV in the presence of anti-human antibody. ELISA studies indicated that 15 of the Fabs were cross-reactive with monkeypox virus
Absence of Lung Immunopathology Following Respiratory Syncytial Virus (RSV) Challenge in Mice Immunized with a Recombinant RSV G Protein Fragment

AbstractThe relative immunopathogenic potential of a recombinant fusion protein incorporating residues 130–230 of respiratory syncytial virus (RSV-A) G protein (BBG2Na), formalin-inactivated RSV-A (FI-RSV), and phosphate-buffered saline (PBS) was investigated in mice after immunization and RSV challenge. FI-RSV priming resulted in massive infiltration of B cells and activated CD4+and CD8+T lymphocytes in mediastinal lymph nodes (MLN) and lungs, where eosinophilia and elevated IFN-γ, IL-2, -4, -5, -10, and -13 mRNA transcripts were also detected. PBS-primed mice showed only elevated pulmonary IL-2 and IFN-γ mRNAs, while an activated CD8+T cell peak was detected in MLN and lungs. Cell infiltration also occurred in MLN of BBG2Na-immunized mice. However, there was no evidence of T cell, B cell, or granulocyte infiltration or activation in lungs, while transient transcription of Th1-type cytokine genes was evident. The absence of pulmonary infiltration is unlikely due to insufficient viral antigen. Thus, this recombinant fusion RSV G fragment does not prime for adverse pulmonary immunopathologic responses
Genetic Recombination of Poliovirusin Vitroandin Vivo: Temperature-Dependent Alteration of Crossover Sites

AbstractGenetic recombination that occurs with high frequency during poliovirus genome replication is a process whose molecular mechanism is poorly understood. Studies of genetic recombination in a cell-free systemin vitroand in infected tissue culture cellsin vivohave led to the unexpected observation that temperature strongly influences the loci at which cross-over between the two recombining RNA strands occurs. Specifically, cross-over between two genetically marked RNA strandsin vitroandin vivoat 34°C occurred over a wide range of the genome. In contrast, recombinationin vivoat 37 and 40°C yielded cross-over patterns that had shifted dramatically to a region encoding nonstructural proteins. Preferential selection of recombinants at 37 and 40°C was ruled out by analyses of the growth kinetics of the recombinants. During the studies of recombination in the cell-free system we found that there is a direct correlation between the ability of a poliovirus RNA molecule to replicate in the cell-free system and its capacity to complementde novovirus synthesis programmed by another viral RNA