pinecone/core-2020-05-10-deduplication huggingface dataset:
Inter-retroviral Fusion Mediated by Human Immunodeficiency Virus or Murine Leukemia Virus Glycoproteins: Independence of Cellular Membranes and Membrane Vesicles

AbstractWe have recently demonstrated for the first time that inter-retroviral membrane fusion, i.e., membrane fusion between individual retroviral particle populations with incorporated HIV-1 Env and cellular receptors, respectively, can occur (Sparacio et al. 2000, Virology 271: 248–252). We have extended these analyses here and confirmed that fusion between particles can occur in the extracellular medium independent of any cellular membranes and that luciferase transduction, mediated by the fused structures, is independent of significant potential contribution by contaminating membrane vesicles. We have additionally analyzed whether membrane fusion between HIV-like particles can be mediated by amphotropic murine leukemia virus (MuLV) glycoprotein and its respective cellular receptor, PiT-2. We demonstrate that PiT-2 can be incorporated into HIV-like particles and can fuse with MuLV-Env-carrying particles. This occurs only in the situation in which the incorporated MuLV-Env protein has been activated to fusion activity by HIV protease-mediated removal of the C-terminal R-peptide and is completely inhibited when the respective particles are generated in the presence of the HIV protease inhibitor, Saquinavir
Innate Differences between Simian–Human Immunodeficiency Virus (SHIV)KU-2-Infected Rhesus and Pig-Tailed Macaques in Development of Neurological Disease

AbstractNeurological disease associated with HIV infection results from either primary replication of the virus or a combination of virus infection and replication of opportunistic pathogens in the CNS. Recent studies indicate that the primary infection is mediated mainly by viruses that utilize CCR5 as the coreceptor; it is not known whether the syndrome can be mediated by viruses that use the CXCR4 coreceptor. The macaque model of the disease using simian immunodeficiency virus (SIV) has confirmed that CCR5-using viruses such as SIVmac251 can cause primary disease in the CNS. In this report we have examined the role of simian–human immunodeficiency virus (SHIV)KU-2, a CXCR4 virus which replicates productively in rhesus macrophages, in causing CNS disease. A survey of archival brain tissues from SHIVKU-2-infected rhesus and pig-tailed macaques that succumbed to AIDS showed productive viral replication in the CNS of 10 of 14 rhesus animals. Eight of these 10 had additional infections with opportunistic pathogens. In contrast, 21 of 22 pig-tailed macaques had no evidence of productive viral infection in the brain. In an earlier study we had shown that inoculation of SHIV-infected rhesus macaques with eggs of Schistosoma mansoni, a potent inducer of IL-4, resulted in enhanced replication of the virus in tissue macrophages. In the present study, we compared the replication of the virus in macrophages from normal rhesus and pig-tailed macaques and determined further whether exogenous IL-4 could cause enhancement of virus replication in these cells. These studies showed that the virus replicated productively in rhesus macrophages, and this was enhanced significantly after recombinant macaque IL-4 was added to the medium. IL-4 also caused enhancement of virus production in macrophages isolated from virus-infected animals. In contrast, the virus replicated only minimally in pig-tailed macaque macrophages and supplemental IL-4 had negligible effects. The data thus suggested that failure of pig-tailed macaques to develop encephalitis was due to the innate resistance of macrophages from this species of macaque to support replication of SHIVKU-2. The ability of the virus to replicate in the brains of rhesus macaques was dependent on coinfection in the brain with opportunistic pathogens which presumably induced both macrophages and IL-4 in the CNS microenvironment. A supportive role for IL-4 in the CNS disease was suggested by the presence of IL-4 RNA in the encephalitic brains of rhesus macaques and reduced levels of this cytokine in the brains from pig-tailed macaques
Differential Regulation of HIV-1 Clade-Specific B, C, and E Long Terminal Repeats by NF-κB and the Tat Transactivator

AbstractThe major group of human immunodeficiency viruses (HIV-1) that comprise the current global pandemic have diversified during their worldwide spread and may be divided into at least 10 distinct subtypes or clades, A through J. Subtype B predominates in North America and Europe, subtype E predominates in Southeast Asia, and subtype C predominates in sub-Saharan Africa. Functional distinctions in long terminal repeat (LTR) architecture among HIV subtypes have been identified, thus raising the possibility that regulatory divergence among the subtypes of HIV-1 has occurred. In addition to the transcriptional specificity of the HIV-1 LTR, productive HIV-1 replication is also dependent upon the viral Tat protein. Therefore, we sought to investigate whether interactions between host signaling pathways and the NF-κB regions of different HIV-1 subtypes, together with subtype-specific interactions between Tat, TAR, and cellular proteins, modulate the efficiency of HIV-1 clade-specific gene transcription. We demonstrate that the NF-κB sites of subtypes B and E both bind NF-κB-related complexes. However, the duplicated κB sites of the C subtype do not compete for NF-κB binding. Also, clade E Tat protein possesses the highest transactivation capacity, regardless of the LTR context. Furthermore, preliminary evidence suggests that the acetylation of subtype-specific Tat proteins may correlate with their transactivation efficiency
Analysis of the Infectious Entry Pathway of Human Papillomavirus Type 33 Pseudovirions

AbstractHuman papillomavirus type 33 (HPV-33) pseudovirus infection is a slow process dependent on the initial interaction with cell-surface heparan sulfate (T. Giroglou, L. Florin, F. Schafer, R. E. Streeck, and M. Sapp, 2001a, J. Virol. 75, 1565–1570). We have now further dissected the initial steps of pseudovirus uptake using removal of cell-surface proteoglycans and selective inhibition of entry pathways. Treatment of cells with heparinase I, but not with phosphoinositol-specific phospholipase C (PIPLC), prevented binding of papillomavirus-like particles and infection with HPV-33 pseudovirions, indicating that GPI-linked proteoglycans (glypicans) are not required for productive infection. The slow entry of pseudovirions was inhibited by cytochalasin D and nocodazole in a concentration-dependent manner, suggesting actin polymerization and intact microtubuli be required. Inhibitors of the caveolae-mediated uptake did not significantly affect pseudoinfection. Interestingly, pseudoinfection was blocked by selective inhibitors of endosomal acidification up to 12 h postinfection. Together, our results suggest that binding of HPV pseudovirions to heparan sulfate proteoglycans, most likely syndecans, is followed by delayed internalization via the endosomal pathway
Regulation of HIV-1 Transcription in Activated Monocyte Macrophages

AbstractDNA-binding and functional assays examined the role played by NF-IL6 in regulation of HIV-1 transcription in human monocyte/macrophages (U937 cells), stimulated with LPS+PMA. When incubated with nuclear extracts from stimulated cells, a region (−189/−147), containing the major NF-IL6-binding sequence and the USF site, interacted selectively with USF1 and USF2. Anti-C/EBPβ reacted poorly with the complexes produced with the wild-type probe. In contrast, complex formation with NF-IL6 was clearly evident in experiments analyzing a probe containing an insertion in the USF site. In functional assays, increasing concentrations of a decoy against NF-IL6 reduced gene expression from the LTR of the wild-type HIV-1 variant, supporting a critical role for NF-IL6 in regulation of HIV-1 transcription in stimulated monocyte/macrophages. The decoy also reduced gene expression from a deletion construct lacking NF-IL6-binding sequences. The results implied that in LPS+PMA-stimulated monocyte/macrophages, the endogenous NF-IL6 could act via a site-independent pathway in upregulation of HIV-1 transcription. Analysis of a short DNA segment, containing the −189/−147 region, suggested functional interactions of NF-IL6 and USF. In activated cells exogenous NF-IL6 enhanced dramatically gene expression through a short DNA segment containing the NF-κB sites, supporting functional interactions of NF-IL6 and NF-κB
Coreceptor Switch of [MLV(SIVagm)] Pseudotype Vectors by V3-Loop Exchange

AbstractRetroviral vectors derived from murine leukemia virus (MLV) have been pseudotyped with a variant of the envelope glycoprotein (Env) of nonpathogenic simian immunodeficiency virus from African green monkeys (SIVagm) to result in [MLV(SIVagm-wt)] vector particles. The variant env gene encodes a full-length surface envelope glycoprotein (SU) and a C-terminally truncated transmembrane protein (TM). To change the coreceptor usage of this vector from CCR5 to CXCR4, which is predominant on human CD4-positive lymphocytes, the putative V3-loop of SIVagm SU was replaced by that of the T cell tropic HIV-1 variant BH10. The resulting [MLV(SIVagm-X4)] vectors were shown to specifically transduce CD4/CXCR4-positive cell lines, demonstrating the equivalent function in cell entry and choice of coreceptor usage of the V3-loops of SIVagm and HIV-1. These modified vectors were able to transduce primary human lymphocytes and were resistant to neutralization by sera from HIV-1-infected individuals. The [MLV(SIVagm-X4)] pseudotype vector generated is thus a promising candidate vector, e.g., for in vivo gene therapy of HIV-1 infection
Patterns of Polymorphism in Wheat streak mosaic virus: Sequence Space Explored by a Clade of Closely Related Viral Genotypes Rivals That between the Most Divergent Strains

AbstractNucleotide (nt) sequence polymorphism within a collection of Wheat streak mosaic virus (WSMV) isolates was examined. An ∼1267-nt region encompassing the coat protein (CP) cistron and flanking sequences was amplified by reverse transcription–polymerase chain reaction (RT-PCR) for each of 49 isolates not previously sequenced. Consensus sequences were compiled for each isolate based on sequences derived from three clones per RT-PCR product. Among 59 consensus sequences examined, only two were identical. Clades A–C contained divergent isolates from Mexico (Clade A); the Czech Republic, Hungary, and Russia (Clade B); and Iran (Clade C). Fifty-four closely related consensus sequences of isolates from the U.S. (51 sequences), Canada (1 sequence), and Turkey (2 sequences) comprised Clade D. Pair-wise nt divergence between two of the most distantly related sequences (Sidney 81 of Clade D and El Batán 3 of Clade A) was 20%, representing over half of the variable sites (34.1%) in the entire WSMV data set. Maximum pairwise nt divergence within Clade D was 3.6%, yet the proportion of all variable sites within Clade D (21.4%) was similar to that of the Sidney 81–El Batán 3 pair. Patterns of polymorphism within Clade D and the Sidney 81-El Batán 3 pair were remarkably similar with respect to synonymous, nonsynonymous, and noncoding substitutions, as were the proportions of substitutions as a function of nt position within codons. The majority of substitutions within Clade D were synonymous and randomly distributed throughout the coding region examined, whereas nonsynonymous substitutions exhibited a clumped distribution and mostly occurred within the 5′-proximal portion of the CP cistron. Because over half of the polymorphic sites within Clade D were of allele size class 1, the isolates appear to be evolving independently and in a nondeterministic manner, within the constraints of selection. These results indicate that Clade D has undergone substantial and, most likely, recent divergence with the majority of consensus sequence substitutions potentially neutral with respect to fitness. An estimate of evolution rate suggests that the present diversity within the U.S. population arose in about a century, a timeframe corresponding to the establishment of wheat monoculture in the Great Plains
Silencing of a Gene Encoding a Protein Component of the Oxygen-Evolving Complex of Photosystem II Enhances Virus Replication in Plants

AbstractIt has been suggested that, in addition to viral proteins, host proteins are involved in RNA virus replication. In this study the RNA helicase domain of the Tobacco mosaic virus (TMV) replicase proteins was used as bait in the yeast two-hybrid system to identify tobacco proteins with a putative role in TMV replication. Two host proteins were characterized. One protein (designated #3) belongs to a protein family of ATPases associated with various activities (AAA), while the second host protein (designated #13) is the 33K subunit of the oxygen-evolving complex of photosystem II. Using Tobacco rattle virus vectors, genes #3 and #13 were silenced in Nicotiana benthamiana, after which the plants were challenged by TMV infection. Silencing of gene #13 resulted in a 10-fold increase of TMV accumulation, whereas silencing of gene #3 caused a twofold reduction of TMV accumulation. Additionally, silencing of genes #3 and #13 decreased and increased, respectively, the accumulation of two other viruses. Similar to silencing of gene #13, inhibition of photosystem II by application of an herbicide increased TMV accumulation several fold. Infection of N. benthamiana with TMV resulted in a decrease of #13 mRNA levels. Silencing of gene #13 may reflect a novel strategy of TMV to suppress basal host defense mechanisms. The two-hybrid screenings did not identify tobacco proteins involved in helicase domain-induced N-mediated resistance
Diversity and Complexity of CD8+ T Cell Responses against a Single Epitope of Adenovirus E1B

AbstractThis study describes the characteristics of the immune responses against adenovirus in C57BL/6 mice. CTL responses could be induced against E1Bp of adenovirus type 5, when whole viruses were immunized. A panel of E1Bp-specific CTL clones showed a wide range of T cell avidity. Recognition of the E1Bp peptide and a panel of variant peptides containing a single alanine substitution by CTL clones revealed that the fine specificity of the CTL response was quite diverse, rather than being limited to a certain clonal preference. Moreover, the variant peptides with a substitution at the TCR contact residue had antagonistic properties to some of the CTL clones, while being agonistic to others, reflecting the extensive diversity of the T cells. These results imply that the functional diversity of T cells to even a single epitope should be considered in manipulating immunity to viruses and in developing adoptive immunotherapy for immunocompromised individuals
Differential Display RT–PCR Analysis of Enterovirus-71-Infected Rhabdomyosarcoma Cells Reveals mRNA Expression Responses of Multiple Human Genes with Known and Novel Functions

AbstractIn order to better understand cellular responses to viral infection at the transcriptional level, we employed differential display RT–PCR to analyze mRNAs from RD rhabdomyosarcoma cells following infection with a neurovirulent enterovirus 71 (EV71) strain, compared with mRNAs from uninfected cells. Of 250 expressed sequence tags (ESTs) isolated, sequenced, and identified, all were of cellular origin except 1 that was of viral origin. Of these, 156 were individual distinctive clones, comprising 45 mRNAs showing unaltered expression and 111 mRNAs exhibiting upregulation or downregulation. Of the 45 uniformly expressed mRNAs, 14 represented unknown genes. Of the 111 differentially expressed mRNAs, 63 did not match any known genes. Forty-eight of the 111 mRNAs modified by EV71 infection matched known genes, including those encoding components of cell cycle, cytoskeleton, and cell death mediators; protein degradation mediators; mitochondrial-related proteins; components of protein translation and modification; and cellular transport proteins. The altered expression profiles of representative genes were authenticated by semiquantitative RT–PCR and real-time RT–PCR. We also identified a novel alternatively spliced transcript of TRIP7 thyroid receptor interactor protein; the putative human homolog of murine mc7 mRNA predominantly expressed in the brain; and a novel mRNA similar to that encoding vacuolar protein 8 involved in protein targeting. These results underscore the applicability of the mRNA differential display technique for elucidating the expression profiles of known and even novel genes in response to cellular infection with pathogenic viruses
In Vivo Effects of the Epstein–Barr Virus Small RNA EBER-1 on Protein Synthesis and Cell Growth Regulation

AbstractRecent studies have suggested a role for the Epstein–Barr virus-encoded RNA EBER-1 in malignant transformation. EBER-1 inhibits the activity of the protein kinase PKR, an inhibitor of protein synthesis with tumour suppressor properties. In human 293 cells and murine embryonic fibroblasts, transient expression of EBER-1 promoted total protein synthesis and enhanced the expression of cotransfected reporter genes. However reporter gene expression was stimulated equally well in cells from control and PKR knockout mice. NIH 3T3 cells stably expressing EBER-1 exhibited a greatly increased frequency of colony formation in soft agar, and protein synthesis in these cells was relatively resistant to inhibition by the calcium ionophore A23187. Nevertheless clones containing a high concentration of EBER-1 were not invariably tumourigenic. We conclude that EBER-1 can enhance protein synthesis by a PKR-independent mechanism and that, although this RNA may contribute to the oncogenic potential of Epstein–Barr virus, its expression is not always sufficient for malignant transformation
Regulation of the Interferon-Inducible PKR Kinase Gene: The KCS Element Is a Constitutive Promoter Element That Functions in Concert with the Interferon-Stimulated Response Element

AbstractThe RNA-dependent protein kinase PKR plays important roles in the antiviral and antiproliferative actions of IFN. The IFN-inducible promoter of the human PKR gene contains a 15-bp DNA element designated KCS. The KCS element is located 4 bp upstream of the interferon-stimulated response element (ISRE) and is required for both basal and IFN-inducible transcription. We have examined the effect of insertion mutations between the KCS and the ISRE elements, as well as altered orientation of the KCS element relative to the ISRE element, to assess a possible functional interaction between them. Large insertions (≥93 bp) between the KCS and ISRE elements significantly reduced both basal and IFN-inducible promoter activity. The function of the KCS element was dependent on the orientation of KCS relative to the ISRE element. Multimerization of the KCS element increased both basal and IFN-inducible transcription. Electrophoretic mobility shift analyses (EMSA) identified IFN-inducible protein complex formation that required both the KCS and the ISRE DNA element sequences. The novel IFN-inducible protein complexes contained the transcription factor STAT1, as shown by supershift analyses and by their presence in extracts prepared from STAT1 wild-type but not from STAT1−/− null cells. These results, taken together, strongly suggest that the KCS and ISRE elements of the human PKR promoter represent a functional unit
Comparison of CREB- and NF-κB-Mediated Transactivation by Human T Lymphotropic Virus Type II (HTLV-II) and Type I (HTLV-I) Tax Proteins

AbstractThe function of the transactivator protein Tax from HTLV-II subtype A, subtype B, Brazilian subtype C, and African subtype D isolates was compared to that of Tax from an HTLV-I isolate. HTLV-II subtypes A, B, and C were less active in the transactivation of a NF-κB reporter compared to HTLV-I Tax in 293T but not Jurkat T cells. In both cell types there were no significant differences between the functions of HTLV-II B, C, and D and HTLV-I Tax proteins on either a full-length HTLV-I LTR or a 21-bp repeat reporter, suggesting that there is equivalent CREB-mediated transactivation between the viruses and these subtypes. In contrast, Tax of some but not all HTLV-II subtype A isolates, including the prototype Mo, had a greatly decreased ability to transactivate, and this could be directly correlated with a decrease in protein expression. Employment of cDNA clones encoding both Rex and Tax demonstrated that Rex was unable to rescue the expression or activity of the IIA Mo isolate. These studies demonstrate that with the exception of some HTLV-IIA subtypes there are no significant differences in Tax transactivation via the CREB and NF-κB pathways between the two viruses and suggest that the HTLV-II Tax may have a pathogenic potential equivalent to that of HTLV-I
Human Influenza A Viral Genes Responsible for the Restriction of Its Replication in Duck Intestine

AbstractAlthough influenza A viruses are occasionally transmitted from one animal species to another, their host range tends to be restricted. Currently circulating human influenza A viruses are thought to have originated from avian viruses, yet none of these strains replicate in duck intestine, a major site of avian virus replication. Although the hemagglutinin (HA) and neuraminidase (NA) genes are known to restrict human virus replication in ducks, the contribution of the other viral genes remains unknown. To determine the genetic basis for host range restriction of the replication of human influenza A virus in duck intestine, we first established a reverse genetics system for generating A/Memphis/8/88 (H3N2) (Mem/88) and A/mallard/New York/6750/78 (H2N2) (Mal/NY) viruses from cloned cDNAs. Using this system, we then attempted to generate reassortant viruses with various combinations of candidate genes. We were able to generate single-gene reassortants, which possessed PB2, NP, M, or NS from Mem/88, with the remainder from Mal/NY. Despite unsuccessful production of other single-gene reassortants from Mem/88, we did generate reassortant viruses comprised of both the HA and the NA, all three polymerase genes (PB2, PB1, and PA), or all polymerase genes and the NP gene from Mem/88, with the rest derived from Mal/NY. Among these reassortants, only those possessing the M or NS gene from Mem/88 and the remainder from Mal/NY replicated in duck intestine. These results indicate incompatibility between the genes of avian and human influenza A viruses and indicate that all genes other than the M and NS restrict replication of human influenza A virus in duck intestine