pinecone/core-2020-05-10-deduplication huggingface dataset:
Human Cytomegalovirus Inhibits Cellular DNA Synthesis and Arrests Productively Infected Cells in Late G1

AbstractHuman embryonic lung fibroblasts (LU) can be productively infected with human cytomegalovirus (HCMV). During the course of productive infection, the virus elicits a number of responses that resemble certain aspects of G1 cell cycle progression. The virus activates cyclin E/Cdk2 kinase in both subconfluent, serum-arrested, and density-arrested cultures. Activation of cyclin E-dependent kinase is due, in part, to induction of cyclin E and, in part, to inhibition of the cyclin kinase inhibitors, Cip1 and Kip1. However, G1 progression is incomplete in HCMV-infected cells. Neither cyclin A nor cyclin D is induced, and cellular DNA synthesis does not occur if one takes care to avoid addition of fresh serum to serum-starved cultures. The data indicate that the virus induces a state of late G1 arrest, in which cyclin E/Cdk2 activates nucleotide metabolism and other biosynthetic processes that are necessary for viral replication. Failure to activate host cell DNA synthesis ensures that the virus will have uncompeted access to such precursors
Viral Isolates Derived from Simian Varicella Epizootics Are Genetically Related but Are Distinct from Other Primate Herpesviruses

AbstractEpizootics of a natural varicella-like disease occur in populations of nonhuman primates. Several primate herpesviruses have been isolated from these epizootics, but the relatedness of these isolates to each other is not well-defined. In this study, we demonstrated that the restriction endonuclease (REn) profiles of four epidemiologically distinct isolates were similar, although not identical, indicating that simian varicella epizootics are caused by various strains of simian varicella virus (SVV). The genetic variation among the isolates did not map to a specific region of the SVV genome and REn differences were detected within the SVV DNA long component and the inverted repeat region. Southern blot hybridization demonstrated that SVV is more closely related to varicella-zoster virus than to other primate herpesviruses. The study indicates that the current herpesvirus classification scheme should be changed to include SVV as a single taxonomic group within theVaricellovirusgenus of alphaherpesviruses. In addition, REn profiles of SVV isolates, derived from primary and secondary episodes of simian varicella in the same monkey, were identical, providing evidence for SVV reactivation in a latently infected monkey
Induction of Pleckstrin by the Epstein–Barr Virus Nuclear Antigen 3 Family

AbstractThe Epstein–Barr virus (EBV) encoded nuclear antigens, EBNA-3, -4, and -6 (EBNA 3 family) are expressed in latently infected human B-cells and are involved in the transformation of lymphocytes by EBV. Human Burkitt's lymphoma (BL) dG75 cells which stably expressed either the complete EBNA 3 gene family or the vector alone were generated and changes in gene activity in these transfectants were assayed using the differential display of mRNA technique. For the first time, the human gene pleckstrin, which is thought to be involved in signalling and differentiation of hemopoietic cells, was found to be upregulated in the presence of the EBNA 3 protein family, but not in cells expressing the individual EBNA-3, -4, or -6 gene. Pleckstrin was increased up to sevenfold in different cell clones and the bulk culture of EBNA 3 gene family expressing cells as demonstrated by Northern blot, RT-PCR, and immunoblot. In contrast to EBV-negative BL cells, pleckstrin RNA and protein were highly expressed in EBV growth transformed lymphoblastoid cell lines which are thought to play an important role in EBV persistencein vivo.These data suggest that induction of pleckstrin might be important for the EBV-controlled activation of cells and offers a unique biological system for analyzing pleckstrin function
Genetic Variation in Neuraminidase Genes of Influenza A (H3N2) Viruses

AbstractNucleotide sequences of the neuraminidase (NA) genes of 33 influenza A (H3N2) epidemic strains isolated between 1968 and 1995 were analyzed to determine their evolutionary relationships. Phylogenetic analysis using the DNA maximum-likelihood method indicates that the NA genes of recent H3N2 field strains, like their hemagglutinin genes (HA), have evolved as two distinct lineages represented by the vaccine strains, A/Beijing/353/89 and A/Beijing/32/92 (or A/Shanghai/24/90). Furthermore, genetic reassortment of NA genes between the two lineages occurred during their circulation. Genetic reassortants, which bear an A/Beijing/32/92-like HA and an A/Beijing/353/89-like NA, have circulated worldwide and are representative of current influenza A (H3N2) epidemic strains. The mutation rate of the NA gene was found to be 2.28 × 10−3per nucleotide site per year with 42% of the mutations resulting in amino acid substitutions. Thirty-five percent of the amino acid substitutions was located in sites previously suggested to be reactive to antibody. Amino acid residues involved in NA enzyme activity have been conserved. Seven potential glycosylation sites identified in the NA of A/Hong Kong/8/68 virus were conserved by the majority of isolates, with more recently circulating viruses having an additional glycosylation site. Comparison of the rate of amino acid substitutions in the NA stalk to that of entire NA revealed high variability in this region. These findings demonstrate the importance of closely monitoring both the HA and the NA genes of influenza viruses to aid vaccine strain selection
Interaction of Mouse Adenovirus Type 1 Early Region 1A Protein with Cellular Proteins pRb and p107

AbstractWe demonstrated functional associations between mouse adenovirus type 1 (MAV-1) early region 1A (E1A) protein and both the mouse retinoblastoma protein (pRb) and the mouse pRb-related protein, p107. Interactions between MAV-1 E1A and mouse pRb or mouse p107 proteins were examined in infected cell lysates using a mouse embryonic fibroblast cell line infected with wild-type and mutant MAV-1 viruses. Using a polyclonal antibody to MAV-1 E1A, exogenously added mouse pRb or mouse p107 was coimmunoprecipitated from wild-type-, dlE105 (CR1Δ)-, and dlE106 (CR3Δ)-infected cell lysates. No coimmunoprecipitation was seen with cell lysates from dlE102 (CR2Δ) or pmE109, a mutant virus that produces no detectable E1A protein due to an ATG to TTG point mutation in the initiator methionine. Introduction of mouse pRb into SAOS-2 cells resulted in a flat and enlarged cell phenotype, whereas cotransfection of mouse pRb and MAV-1 E1A resulted in a significant reduction of flat cells, presumably due to E1A binding pRb. CR1Δ and CR2Δ E1A proteins were less effective at reducing the number of flat, enlarged cells induced by pRb expression than were the CR3Δ or wild-type E1A proteins. The reduced ability of these mutants to inactivate pRb relative to wild-type E1A correlated with their reduced ability to bind pRb in thein vitrocoimmunoprecipitation experiments. As a measure of p107/MAV-1 E1A complex formation in MAV-1-infected cells, we used mobility shift assays to examine cell extracts for the presence of p107-containing E2F protein–DNA complexes. Mock-, dlE102-, and pmE109-infected cell extracts formed a p107-containing complex, whereas wild-type-infected cell extracts did not. Thus the formation of a p107–E2F complex in wild-type- or these mutant-infected extracts inversely correlated with the presence of E1A–p107 complexes identified in thein vitrocoimmunoprecipitation experiments. This is consistent with E1A–p107 complexes forming in wild-type MAV-1-infected cells
Cholesterol-Depleted Cells That Are Relatively Permissive for Semliki Forest Virus Infection

AbstractSemliki Forest virus (SFV), an enveloped alphavirus, infects cells by endocytosis followed by low pH-triggered fusion of the virus and endocytic vesicle membranes. Progeny virus is released by budding from the cell plasma membrane.In vitro,SFV fusion with artificial liposomes is triggered by low pH and is dependent on the presence of cholesterol and sphingolipid in the target liposome membrane. In tissue culture, both SFV fusion and virus exit are strongly cholesterol-dependent when assayed in cholesterol-depleted insect cells. We here describe the preparation of insect cells that while not containing detectable amounts of cholesterol, have adapted to sterol-depleted conditions, resulting in a more permissive phenotype for SFV infection. Although still less efficient at supporting SFV infection than control cholesterol-containing cells, the adapted cells show a 45-fold increase in primary infection by SFV, increased release of progeny virus, and enhanced virus growth kinetics compared to nonadapted cholesterol-depleted cells. The adapted cells are also about 85-fold more permissive for low pH-induced fusion of SFV with the plasma membrane, suggesting that adaptation correlates with a change in the cell membrane
Activation of the HTLV-I Long Terminal Repeat by the Hepatitis B Virus X Protein

AbstractThe human T-cell leukemia virus type I (HTLV-I) Tax protein and the hepatitis B virus (HBV) X protein have each been shown to activate transcription of their respective viral promoters as well as a subset of cellular gene promoters. Here we show that the HTLV-I long terminal repeat (LTR) is responsive to HBV X transactivation. Maximum levels of X-mediated transactivation of the LTR were 8-fold. An X-responsive-region (XRR) of the LTR is located between nucleotides −355 and −276 and contains an AP-2 binding site, a previously recognized X-responsive element. We demonstrated that Tax and X synergize to activate transcription from the HTLV-I LTR, although the AP-2 binding site was not required for this synergy. These results raise the possibility that the HBV X protein may affect the level of HTLV-I gene expression in co-infected individuals
Differential Regulation of the HIV-1 LTR by Specific NF-κB Subunits in HSV-1-Infected Cells

AbstractPrevious studies have shown that expression of HIV-1 provirus was enhanced in cells co-infected with the herpes virus and that HSV-1-mediated induction of the HIV-1 provirus expression involved both NF-κB-dependent and NF-κB-independent mechanisms. Nuclear NF-κB complexes could be detected approximately 8 hr after HSV-1 infection. Using NF-κB-specific antibodies in a mobility shift assay, we have found that HSV-1 increases binding of p50, p65, and c-relto the HIV-1 NF-κB probe in both Jurkat T cells and NIH/3T3 cells. HSV-1 infection also increases transiently the levels of p50 mRNA but an increase in the level of p65 mRNA was not detected. Furthermore, HSV-1 infection induces a rapid degradation of the IκBα protein. Transfection of HIV-1 LTR CAT into cell lines which overexpressed individual NF-κB proteins showed the highest constitutive expression of CAT activity in cells overexpressing p65. Infection with HSV-1 further enhanced the expression of HIV-1 LTR CAT in cell lines producing p52, p100, and c-rel.In contrast, HSV-1 did not significantly enhance the expression of HIV-1 LTR CAT in cell lines overexpressing p105 and IκBγ. In the transient expression assay the p65/c-rel heterodimer was the most effective inducer of the HIV-1 LTR expression. Thus it appears that p65 plays a limited role in the NF-κB-dependent activation of the HIV-1 LTR following HSV-1 infection and that the stimulation is mediated by the p50/p65 and p65/c-rel heterodimers. Thus the magnitude of HIV-1 provirus induction depends on the relative levels of NF-κB subunits present in the infected cells
Mml1,a New Common Integration Site in Murine Leukemia Virus-Induced Promonocytic Leukemias Maps to Mouse Chromosome 10

AbstractMuLV-induced myeloid leukemias (MML) having promonocytic characteristics are produced with high incidence in some strains of adult mice that are undergoing chronic peritoneal inflammation. Previously we showed that many leukemias have rearrangements of the c-myblocus due to insertional mutagenesis, however, we also identified a number of leukemias that had proviral integrations in the absence of c-mybrearrangement. In the present study, a new locus,Mml1,was found to be a target of insertional mutagenesis in 10 of the promonocytic leukemias that lacked c-mybalterations. Chromosomal mapping studies, performed using progeny from interspecies backcross mice generated by mating (BALB/cAn ×M. spretus)F1females to BALB/cAN males, determined thatMml1is located on the proximal end of mouse chromosome 10. Interestingly, there were no recombinants between c-mybandMml1in 101 backcross progeny andMml1was mapped approximately 20–25 kb upsteam ofc-myb.Interestingly, c-mybmRNA and Myb protein are expressed at levels similar to the levels observed in myeloid progenitor cells, but are not overexpressed. It is anticipated that future experiments will determine whetherMml1integration prevents down regulation of c-mybexpression or activates another gene on chromosome 10
Structure–Function Analysis of theAutographa californicaMultinucleocapsid Nuclear Polyhedrosis Virus Homologous Region Palindromes

AbstractHomologous regions (hrs), which are present at eight dispersed locations on theAutographa californicamultinucleocapsid nuclear polyhedrosis virus genome, are composed of repeated imperfect palindromes within directly repeated sequences.Hrsact as transcriptional enhancers of RNA polymerase II-mediated transcription and as origins of DNA replication when incorporated into plasmids and tested in transient replication assays. To characterize the physical structure of these elements and to determine the role that mismatched nucleotides may play inhrfunction, oligonucleotides containing a consensus mismatched “imperfect” palindrome and a closely related “perfect” palindrome were synthesized. These sequences were cloned into individual plasmids and tested for their ability to form cruciform structures using nuclease P1 assays and two-dimensional (2-D) gel analyses of topoisomers. The perfect palindrome formed a cruciform structure and the energy requirement for its formation was predicted to occur under physiological conditions. In contrast, the construct containing an imperfect palindrome did not form a cruciform under these conditions. Bothhrconstructs were found to bind IE-1 in electrophoresis mobility shift assays and act as enhancers when cis-linked to the baculovirus 39K early gene promoter. However, a single oligonucleotide containing the palindrome sequence did not bind IE-1 when annealed under conditions conducive to hairpin formation
Requirement of Caprine Arthritis Encephalitis VirusvifGene forin VivoReplication

AbstractReplication ofvif-caprine arthritis encephalitis virus (CAEV) is highly attenuated in primary goat synovial membrane cells and blood-derived macrophages compared to the wild-type (wt) virus. We investigated the requirement for CAEV Vif forin vivoreplication and pathogenicity in goats by intra-articular injection of either infectious proviral DNA or viral supernatants. Wild-type CAEV DNA or virus inoculation induced persistent infection resulting in severe inflammatory arthritic lesions in the joints. We were unable to detect any sign of virus replication invif-CAEV DNA inoculated goats, whilevif-CAEV virus inoculation resulted in the seroconversion of the goats. However, virus isolation and RT-PCR analyses on blood-derived macrophage cultures remained negative throughout the experiment as well as in joint or lymphoid tissues taken at necropsy. No pathologic lesions could be observed in joint tissue sections examined at necropsy. Goats inoculated with thevif-virus demonstrated no protection against a pathogenic virus challenge. These results demonstrate that CAEV Vif is absolutely required for efficientin vivovirus replication and pathogenicity and provide additional evidence that live attenuated lentiviruses have to establish a persistent infection to induce efficient protective immunity
Common Modular Structure of Lentivirus LTRs

AbstractRetroviruses are expressed under the control of viral control regions designated long terminal repeats (LTRs), which contain all signals for transcriptional initiation as well as transcriptional termination. However, retroviral LTRs from different species within a common genus, such as Lentivirus, do not show significant overall sequence homology. We compiled a model of the functional organization of 20 Lentivirus LTRs which we show to recognize all known Lentivirus LTRs. To this end we combined our previously published methods for identification of transcription elements with secondary structure element analysis in a novel modular approach. We deduced descriptions for three new Lentivirus-specific sequence elements present in most of the Lentivirus LTRs but absent in LTRs of other retrovirus families (B, C, D-type, BLV-HTLV, Spuma). Four of the 10 elements defined in our study were primate-specific. We were able to deduce a phylogeny based on our model which agrees in general with the phylogeny derived from the polymerase genes of these viruses. Our model indicated that more than 100 LTRs from the databases are of Lentivirus origin and can be clearly separated from all other LTR types (B, C, D, BLV-HTLV, Spuma). This selectivity appears to be a unique feature of our modular approach
Comparative Properties of Feline Immunodeficiency Virus (FIV) and Human Immunodeficiency Virus Type 1 (HIV-1) Proteinases Prepared by Total Chemical Synthesis

AbstractThe aspartyl proteinase (PR) encoded by the feline immunodeficiency virus (FIV) was prepared by total chemical synthesis. The 116-amino-acid polypeptide chain was assembled in a stepwise fashion using a Boc chemistry solid-phase peptide synthesis approach and subsequently folded into the biologically active dimeric proteinase. The synthetic enzyme showed proteolytic activity against a variety of different peptide substrates corresponding to putative cleavage sites of the Gag and Gag–Pol polyproteins of FIV. A comparative study with the proteinase of human immunodeficiency virus type 1 (HIV-1) showed that the FIV and HIV-1 enzymes have related but distinct substrate specificities. In particular, HIV-1 PR and FIV PR each show a strong preference for their own MA/CA substrates, despite identical amino acid residues at four of seven positions from P3–P4′ of the substrate including an identical MA/CA cleavage site (between Tyr ∼ Pro residues). FIV PR also showed a requirement for a longer peptide substrate than HIV-1 PR. Defining the similarities and the differences in the properties of these two retroviral enzymes will have a significant impact on structure-based drug design
Expression of CD26 Does Not Correlate with the Replication of Macrophage-Tropic Strains of HIV-1 in T-Cell Lines

AbstractStrains of human immunodeficiency virus type 1 (HIV-1) differ significantly in both genetic content and biological properties. One of the earliest discovered differences between HIV-1 strains was divergence in the relative ability of different strains to replicate in either T-cell lines or monocytes/macrophages. This observation has led to the suggestion that molecules present on the surface of HIV-susceptible cells other than CD4 may interact with gp120 in facilitating the entry of HIV-1 into host cell populations. Several reports have suggested that CD26, a cell surface protease expressed on many cells of the immune system including some CD4+T-cells and macrophage, may be an accessory molecule for HIV-1 entry. Recently, it has also been reported that the expression of high levels of CD26 correlates with the entry and replication of macrophage-tropic strains of HIV-1 in a T-cell line. In this report, we demonstrate that replication of macrophage-tropic strains of HIV-1 in T-cell lines is independent of CD26 expression. From this observation, we conclude that CD26 plays no role in the entry of HIV-1 into these cells
High Sp1/Sp3 Ratios in Epithelial Cells during Epithelial Differentiation and Cellular Transformation Correlate with the Activation of the HPV-16 Promoter

AbstractGene expression of human papillomavirus type 16 (HPV-16) and other HPV types is epithelial specific. Specificity is brought about by synergism between several different transcription factors that seem to occur ubiquitously but differ qualitatively and quantitatively between cells in which HPV genomes are transcriptionally active or inactive. Here, we report on the contribution to this combinatorial mechanism by the activator Sp1 and the related antagonist Sp3, both of which can bind a single site at the E6 promoter of all genital HPVs. In the Sp-factor-free background of Drosophila cells, Sp1 activates HPV-16 transcription, while Sp3 fails to do so and even inhibits the activation by Sp1. The same differential activation occurs in the case of promoters of the epithelial-specific cellular genes encoding keratin 18 and E-cadherin. All cell types that we examined contain similar amounts of Sp3 factor. In contrast, Sp1 levels, determined by supershifts and Western blots, are higher in several human epithelial cell lines that support HPV transcription than in human fibroblasts, liver, and muscle cells. This suggests that cell-type differential transcription is regulated by Sp1 and Sp3. In primary keratinocytes, Sp3 levels exceed those of Sp1. This ratio became inverted after differentiating these cells in high calcium, or methyl cellulose containing medium. The simultaneous transcriptional stimulation of the HPV promoter points to a role of the Sp1–Sp3 antagonism during a differentiation of stratified epitheliain vivo,as these culture techniques mimick this processin vitro.Transformationin vivoorin vitroseems to override these cell-type-specific controls and leads to a general increase of Sp1 activity
HIV-1 Nef Association with Cellular Serine Kinase Correlates with Enhanced Virion Infectivity and Efficient Proviral DNA Synthesis

AbstractWe previously reported on the association of Nef with a cellular serine kinase (E. T. Sawaiet al., Proc. Natl. Acad. Sci. USA91, 1539–1543, 1994). In the present study, we further define the Nef sequence requirements for this kinase association and investigate the effect of this kinase association on functions of HIV-1 Nef. We observe that, in addition to the membrane targeting signal and the conserved arg–arg residues within the core region, mutations in the proline-rich domain of Nef also affect its ability to associate with the serine kinase activity. The region encompassing the arg–arg residues of Nef is shown to be important for Nef-mediated cell-surface CD4 down-modulation as well as enhancement of viral growth properties. This is similar to what has previously been observed for the membrane targeting site at the N-terminus of Nef. In contrast, the proline-rich region of Nef is found to be involved in mediating efficient proviral DNA synthesis and the enhanced virion-infectivity function, but is not necessary for CD4 down-modulation by Nef. Thus, it appears that serine kinase association of Nef is necessary for efficient proviral DNA synthesis and for promotion of virion infectivity of Nef+viruses, but is dispensable for down-regulation of the CD4 receptor by Nef. These findings define three functional domains of Nef that are required for its interaction with the serine kinase activity and suggest that the cellular interaction events via the myristoylation and arg–arg regions of Nef lie upstream of the interaction event via the proline-rich domain