pinecone/core-2020-05-10-deduplication huggingface dataset:
Avian Influenza A Viruses Differ from Human Viruses by Recognition of Sialyloligosaccharides and Gangliosides and by a Higher Conservation of the HA Receptor-Binding Site

AbstractAvian influenza virus strains representing most hemagglutinin (HA) subtypes were compared with human influenza A (H1N1, H3N2) and B virus isolates, including those with no history of passaging in embryonated hen's eggs, for their ability to bind freeN-acetylneuraminic acid (Neu5Ac) and sialyloligosaccharides in a competitive binding assay and to attach to gangliosides in a solid-phase adsorption assay. The avian viruses, irrespective of their HA subtype, showed a higher affinity for sialyl-3-lactose and the other Neu5Ac2-3Gal-terminated oligosaccharides and a lower affinity for sialyl-6-lactose than for free Neu5Ac, indicative of specific interactions between the HA and the 3-linked Gal and poor accommodation of 6-linked Gal in the avian receptor-binding site (RBS). Human H1 and H3 strains, by contrast, were unable to bind to 3-linked Gal, interacting instead with the asialic portion of sialyl-6-(N-acetyllactosamine). Different parts of this moiety were recognized by H3 and H1 subtype viruses (Gal and GlcNAc, respectively). Comparison of the HA amino acid sequences revealed that residues in positions 138, 190, 194, 225, 226, and 228 are conserved in the avian RBS, while the human HAs harbor substitutions at these positions. A characteristic feature of avian viruses was their binding to Neu5Ac2-3Gal-containing gangliosides. This property of avian precursor viruses was preserved in early human H3 isolates, but was gradually lost with further circulation of the H3 HA in humans. Consequently, later human H3 isolates, as well as H1 and type B human strains, were unable to bind to short Neu5Ac2-3Gal-terminated gangliosides, an incompatibility that correlated with higher glycosylation of the HA globular head of human viruses. Our results suggest that the RBS is highly conserved among HA subtypes of avian influenza virus, while that of human viruses displays distinctive genotypic and phenotypic variability
Measles Virus Recognizes Its Receptor, CD46, via Two Distinct Binding Domains within SCR1-2

AbstractMeasles virus (MV) enters cells by attachment of the viral hemagglutinin to the major cell surface receptor CD46 (membrane cofactor protein). CD46 is a transmembrane glycoprotein whose ectodomain is largely composed of four conserved modules called short consensus repeats (SCRs). We have previously shown that MV interacts with SCR1 and SCR2 of CD46. (M. Manchesteret al.(1995)Proc. Natl. Acad. Sci. USA92, 2303–2307) Here we report mapping the MV interaction with SCR1 and SCR2 of CD46 using a combination of peptide inhibition and mutagenesis studies. By testing a series of overlapping peptides corresponding to the 126 amino acid SCR1-2 region for inhibition of MV infection, two domains were identified that interacted with MV. One domain was found within SCR1 (amino acids 37–56) and another within SCR2 (amino acids 85–104). These results were confirmed by constructing chimeras with complementary regions from structurally similar, but non-MV-binding, SCRs of decay accelerating factor (DAF; CD55). These results indicate that MV contacts at least two distinct sites within SCR1-2
Transcriptional Induction of Multiple Cytokines by Human Respiratory Syncytial Virus Requires Activation of NF-κB and Is Inhibited by Sodium Salicylate and Aspirin

AbstractInfection of the lung epithelial cell line A549 by respiratory syncytial virus (RSV) resulted in the elevated synthesis of multiple cellular cytokines, including a number of interleukins (ILs). Detailed studies of IL-11 induction revealed that it required infection by viable virus and involved a net increase in the steady state level of IL-11 mRNA. Nuclear run-on assays showed a direct effect of RSV on IL-11 gene transcription. Mutational analysis of the IL-11 promoter fused to a reporter luciferase gene demonstrated the requirement of a region 720 nucleotides upstream of the mRNA start site in the transcriptional induction of IL-11 by RSV. Two nearly identical 10-nucleotide-long sequences GGGGTCTCCC and GGGTCTCCCC in this region resembled the NF-κB consensus motif. Mutation of either sequence greatly reduced RSV-mediated induction of IL-11 promoter activity. NF-κB sites in IL-1α, IL-6, and IL-8 promoters were also required for RSV-mediated induction of transcription of these promoters. Immunological studies and use of reporter gene constructs provided direct evidence for the activation and nuclear translocation of NF-κB by RSV. Sodium salicylate and aspirin, inhibitors of NF-κB activation, abolished transcriptional induction of all these cytokines by RSV. Together, these studies demonstrated an essential role of NF-κB in RSV-mediated transcription of multiple cytokines genes and suggested a possible use of salicylates in managing airway inflammation and viral pathogenesis during RSV infection
RNA Synthesis by the Brome Mosaic Virus RNA-Dependent RNA Polymerase: Transition from Initiation to Elongation

AbstractThe initiation and elongation phases of (−)-strand RNA synthesisin vitroby the brome mosaic virus RNA-dependent RNA polymerase (RdRp) are differentially sensitive to inhibitors. In an attempt to characterize further the transition RdRp makes from initiation to elongation, we determined the conditions needed to pause the ternary complex and complete only one round of RNA synthesis. During the transition we were able to discern step-wise increases in the affinity of RdRp for RNA by measuring sensitivity to heparin and competition for RdRp by an alternative template. Three distinct stability levels of RdRp–template interactions were found. The first stable RdRp–RNA complex was observed when RdRp bound to the RNA template. A further increase occurred when RdRp synthesized the first phosphodiester bond. A final increase occurred upon formation of between 3 and 13 phosphodiester bonds. After this last transition, RdRp appeared to be tightly committed to the template RNA. These results are analogous to the mechanism of action of DNA-dependent RNA polymerases and are relevant to protein–RNA interaction and template switching by an RdRp
Cell Proliferation Is Not Required for Productive HIV-1 Infection of Macrophages

AbstractLentiviruses, including HIV-1, are considered a rare example of retroviruses which do not require cell proliferation for their replication. However, this notion was questioned in several publications where productive HIV-1 infection was found to be restricted to a small fraction of macrophages with proliferative capacity. Since the mode of HIV-1 replication in macrophages is of great clinical relevance, we performed a single-cell analysis of HIV-1 replication and [3H]thymidine incorporation. Our results indicate that while 17% macrophages were detected as HIV-1 DNA-positive 12 hr after infection, only 2% of those cells had incorporated tritium, about the same percentage as in the uninfected cell population. Forty-eight hours after infection, 38% macrophages were HIV-1 DNA-positive and 47% of those had incorporated tritium, while the percentage of tritium-positive uninfected cells did not change (1%). These results demonstrate directly that HIV-1 DNA does not colocalize with [3H]thymidine and support the notion that cell proliferation is not required for HIV-1 infection of macrophages
Ultrastructure of HIV-1 Genomic RNA

AbstractThe HIV-1 RNA genome is a dimer which consists of two identical strands of RNA linked near their 5′ ends by a dimer linkage structure (DLS). We have structurally characterized full-length HIV-1 genomic RNA isolated from HIV-1 virions by electron microscopy. As in other retroviruses, the HIV-1 RNA genome contains a central dimer linkage structure and additional loop structures within each monomer subunit. In contrast to the DLS of other retroviruses, the DLS region of HIV-1 contains a loop of 323 ± 44 nucleotides. The free 5′ ends of the two RNA strands were not visualized, suggesting that the 5′ end regions are involved in interstrand complementary base pairing. Computer modeling identified a single stable structure that was consistent with the electron microscopy data. In this model, the two RNA strands are linked at their 5′ ends by two contact points derived from “kissing–loop” interactions between r-u5 and SL1 stem–loops and their counterparts on the second strand. These interactions may contribute to the formation of stable HIV-1 RNA dimersin vivo
Activity of Human Immunodeficiency Virus Type 1 Promoter/TAR Regions andtat1 Genes Derived from Individuals with Different Rates of Disease Progression

AbstractDifferent rates of disease progression may be associated with different human immunodeficiency virus type 1 (HIV-1) promoter and/or transactivator activities. We therefore analyzed the sequences and activities of the first exon of Tat,tat1, and the promoter/trans-acting responsive (TAR) regions amplified directly from peripheral blood mononuclear cells obtained from five long-term nonprogressors and eight progressing HIV-1-infected individuals. The majority oftat1 alleles and promoter/TAR regions from all patients were intact and showed comparable activities in transient reporter assays. A substantial number of point mutations and some length variations were observed in the promoter/TAR region. In a single nonprogressor, the Sp1 binding site 3 was consistently altered and the transcriptional activity in the presence of Tat was diminished. Some LTR clones from a rapid progressor contained a fourth Sp1 binding site, which was associated with an elevated basal promoter activity. These data suggest that defects in the promoter/TAR region ortat1 are rare and that different promoter/transactivator activities are not commonly associated with different progression rates
Growth of Lion and Puma Lentiviruses in Domestic Cat Cells and Comparisons with FIV

AbstractFeline immunodeficiency virus (FIV-Fca) is a lentivirus that causes gradual immunological deterioration in domestic cats. Lentiviruses related to FIV have been detected in several nondomestic feline species; the biologic significance of these viruses remains to be defined. To examine thein vitrocell tropism of these nondomestic cat lentiviruses, prototypical puma and lion lentiviruses (FIV-Pco and FIV-Ple) were cultured in a variety of feline cell cultures. A domestic cat T lymphoma cell line, 3201, best supported the replication of both FIV-Pco and FIV-Ple. Moreover, FIV-Ple was lytic for these cells. RT-PCR amplification of a conservedpolgene region demonstrated species-specific primer homology. Sequence and phylogenetic analyses of this amplification product confirmed the identity of the replicating viruses and classified two previously uncharacterized viruses within predictable lion and puma clades. Sequence analysis of a conservedpolregion demonstrated homology with previously characterized FIV-Ple and FIV-Pco. Western blot analysis using domestic cat anti-FIV-Fca sera showed that both FIV-Pco and FIV-Ple were antigenically related, to differing degrees, to three serotypes of FIV-Fca. These studies demonstrate that though nondomestic cat lentiviruses differ significantly from FIV-Fca and that a viral-specific protocol may be necessary for sensitive viral detection, these viruses can replicate in cells of domestic cats, suggesting the potential for cross-species transmission
Bovine Immunodeficiency VirustatGene: Cloning of Two Distinct cDNAs and Identification, Characterization, and Immunolocalization of thetatGene Products

AbstractcDNAs encoding the bovine immunodeficiency virus (BIV) transactivator gene (tat) were cloned from virally infected cells and characterized. BIV expresses two distincttatmRNAs composed of three exons that are derived by alternative splicing. The BIV tat mRNA splice variants encode Tat proteins of 103 (Tat103) and 108 (Tat108) amino acids. The Tat103 coding region is specified only by exon 2, while that of Tat108 is specified by a truncated exon 2 and the first 30 nt of exon 3. Thus, the first 98 amino acids of each Tat are identical, and have amino terminal, cysteine-rich, conserved core, basic, and carboxyl-terminal domains similar to Tats encoded by primate lentiviruses. BIV-infected bovine cells express a 14-kDa phosphorylated Tat protein identical in size to recombinant Tat expressed in bacteria. BIV Tat was shown to localize exclusively in the nucleoli of virally infected and Tat-expressing cells. Reporter gene assays indicated that Tat103 and Tat108 can strongly transactivate the BIV long terminal repeat (LTR) in virally permissive canine Cf2Th and nonpermissive HeLa and mouse NIH 3T3 cells, but not in permissive lapine EREp cells. However, an intact BIVtatgene is required for viral replication in both Cf2Th and EREp cells. Strong LTR activation by BIV Tat requires a TAR (transactivation responsive) element delimited by viral nt +1 to +31 and the Tat basic domain. BIV Tat strongly cross-transactivates the HIV-1 LTR in a TAR-dependent manner in Cf2Th, but not in EREp, HeLa, or NIH 3T3 cells. In contrast, strong, TAR-dependent cross-transactivation of the BIV LTR by HIV-1 Tat could not be demonstrated in any of these cell types. In Cf2Th cells Tat108 effects a moderately stronger transactivation of the BIV LTR than Tat103, indicative of a functional difference in BIV Tat proteins encoded by the mRNA splice variants. The present studies demonstrate that BIV Tat parallels the primate lentiviral Tats in structure and biochemistry but is not interchangeable with the latter
Comparative Analyses of LTRs of the ERV-H Family of Primate-Specific Retrovirus-like Elements Isolated from Marmoset, African Green Monkey, and Man

AbstractWe have isolated 8 different long terminal repeat (LTR) sequences of the ERV-H family of endogenous retrovirus-like elements from human chromosome 18, 9 from African green monkey, and 28 from marmoset. Human ERV-H LTRs have been divided into three types designated Type I, Type Ia, and Type II. Comparative analyses of the 45 isolated LTRs and 60 human ERV-H LTRs enabled a further subdivision into 13 subtypes. Type I elements were widely distributed in all three species. Their average evolutionary age (40 MYr), estimated by a consensus sequence approach, suggests that they first expanded in the genomes at the time New- and Old World monkeys diverged. The occurence of some very old Type I sequences indicate that ERV-H elements may have integrated even before prosimians and primates diverged. Type Ia and -II elements were found in both monkey species. Promoter active Type I and Type Ia LTRs were found while Type II LTRs were inactive. Promoter active Type I LTRs generally contained a functional GC/GT box immediately 3′ to the TATA box, providing strong binding of Sp1 family proteins, while the highly promoter active Type Ia element H6 contained synergistically acting Sp1 binding sites located in the U3 enhancer region
Chimeric Papillomavirus-like Particles

AbstractWe have constructed chimeric papillomavirus-like particles (CVLPs) by replacing the 34-carboxy-terminal amino acids of the HPV 16 L1 protein with various parts of the HPV 16 E7 protein. Chimeric proteins were expressed by recombinant baculoviruses and analyzed by electron microscopy for their ability to assemble into virus capsids. We were able to produce CVLPs in high efficiencies with inserts of up to 60 amino acids. CVLPs are able to induce a neutralizing antibody response, assayed by inhibition of hemagglutination of mouse erythrocytes. CVLPs are interacting with the putative receptor for papillomaviruses as they were shown to hemagglutinate mouse red blood cells and bind to and penetrate cellsin vitro.As CVLPs follow a similar intracellular pathway as observed earlier for BPV VLPs, we speculate that CVLPs can be used to deliver peptides into mammalian cellsin vitroandin vivo,possibly reaching the pathway for MHC class I presentation
Coxsackievirus-Induced Chronic Inflammatory Myopathy: Virus Variants Distinguish between Acute Cytopathic Effects and Pathogenesis of Chronic Disease

AbstractInfection with the Tucson strain of coxsackievirus B1 (CVB1T) causes the development of chronic inflammatory myopathy (CIM) and hind limb weakness in susceptible strains of mice. In this study, a panel of six plaque-purified viruses exhibiting either small or large plaque phenotypes was derived from parental CVB1Tand parental CVB1Tthat had been passaged through monkey kidney cells. All six variants caused similar acute histopathology in muscle, but three of four passaged viruses (AMP1, AMP2, and AMP3) did not induce CIM while the fourth (MP3) caused some hind limb weakness but without associated muscle inflammation. In contrast, both viruses (MP1 and MP2) isolated directly from the parental CVB1Tstock were myopathic. Large plaque MP2 caused higher mortality and more rapid inhibition of host cell biosynthesis, but both MP1 and MP2 induced CIM that was comparable to that induced by parental CVB1T. Plaque size was a stable characteristic of the variants but did not correlate with their ability to induce CIM. Five of the six variants showed equivalent levels of replication in muscle, monkey kidney cells, and G8 myoblasts while one, AMP3, was selectively impaired for replication. Receptor binding and virus-induced inhibition of host cell transcription and translation were not linked to myopathogenicity. Thus, most of the passaged variants are robust infectious viruses, suggesting that viral induction of CIM does not depend solely on cytopathogenicity during the acute infection
The Murine Cytomegalovirus (MCMV) Homolog of the HCMV Phosphotransferase (UL97(pk)) Gene

AbstractThe murine cytomegalovirus (MCMV) M97 gene is homologous with both eukaryotic protein kinases and the phosphotransferases of herpesviruses. The gene conserves the domain structure of protein kinases and of the human cytomegalovirus UL97 (phosphotransferase) gene. An M97 transcript of 2.5 kb is present predominantly at late times, and much smaller quantities of the transcript are detected at early times postinfection. Comparison of the DNA sequences of the complete M97 genes from 12 ganciclovir-sensitive and aciclovir-sensitive strains of MCMV showed that the sensitive isolates strongly conserve the sequence of the catalytic domains, but have only moderate conservation of the sequence of the amino-terminal (regulatory) region. MCMV provides a useful model for studying thein vivofunction of the phosphotransferase genes of the betatherpesviruses and has potential for use in studies of antiviral resistance
Biologic Properties of Hepatitis B Viral Genomes with Mutations in the Precore Promoter and Precore Open Reading Frame

AbstractIt is now well recognized that mutations in the hepatitis B virus (HBV) genome occur during the natural course of chronic viral infection. Regions of the viral genome that are frequently affected by such mutations, rearrangements, and/or deletions generally involve the precore promoter, precore, and core as well as the preS gene regions. However, little is known regarding the biologic consequences of these mutations on the functional properties of the variant viral strains with respect to effects on viral replication. In this study, we investigated the functional significance of precore promoter and precore gene mutations that reduce or abolish the synthesis of hepatitis B e antigen (HBeAg). We found that precore promoter mutations diminished the expression of HBeAg but did not affect the synthesis of pregenomic RNA. However, these precore mutations were associated with a modest increase in HBV replication. In contrast, a naturally occurring mutant that carries a termination codon in position 28 of the precore open reading frame demonstrated increased encapsidation of pregenomic mRNA into nucleocapsid particles. Consequently, this variant viral strain demonstrated a substantial increase in the level of viral replication compared to “wild-type” HBV and other precore promoter mutant viral strains. These studies suggest that substitutions in the precore promoter and precore gene not only alter the synthesis of HBeAg but also affect the level of viral replication
Mutational Analyses Support a Model for the HRV2 2A Proteinase

AbstractThe proteinase 2A of human rhinovirus 2 is a cysteine proteinase which contains a tightly bound Zn ion thought to be required for structural integrity. A three-dimensional model for human rhinovirus type 2 proteinase 2A (HRV2 2A) was established using sequence alignments with small trypsin-like Ser-proteinases and, for certain regions, elastase. The model was tested by expressing selected proteinase 2A mutants in bacteria and examining the effect on both intramolecular (“cis”) and intermolecular (“trans”) activities. The HRV2 proteinase 2A is proposed to have a two domain structure, with the catalytic site and substrate binding region on one face of the molecule and a Zn-binding motif on the opposite face. Residues Gly 123, Gly 124, Thr 121, and Cys 101 are proposed to be involved in the architecture of the substrate binding pocket and to provide the correct environment for the catalytic triad of His 18, Asp 35, and Cys 106. Residues Tyr 85 and Tyr 86 are thought to participate in substrate recognition. The presence of an extensive C-terminal helix, in which Asp 132, Arg 134, Phe 130, and Phe 136 play important roles, explains why mutations in this region are generally detrimental to proteinase activity. The proposed Zn-binding motif comprises Cys 52, Cys 54, Cys 112, and His 114. Exchange of these residues inactivates the enzyme. Furthermore, as measured by atom emission spectroscopy, Zn was absent from purified preparations of proteinase 2A in which His 114 had been replaced by Asn. The absence of disulphide bridges was confirmed by subjecting highly purified HRV2 proteinase 2A to one- and two-step alkylation procedures
Roles ofN-Glycans with α2,6 as well as α2,3 Linked Sialic Acid in Infection by Polyoma Virus

AbstractSpecific glycosylation inhibitors were used to show that N-glycans, and not O-glycans or glycolipids, constitute the major class of receptors on 3T3 cells for polyoma virus. Sialic acid (SA)-specific lectins were used in attempts to confirm the expected SA linkage on N-linked glycans. A lectin specific for α2,6 linked SA, a non-receptor type, was slightly more effective in blocking infection than a lectin specific for α2,3 linked SA which corresponds to the known receptor specificity. Possible explanations are suggested for this unexpected result
Cloning and Sequencing of the Cellular–Viral Junctions from the Human Adenovirus Type 5 Transformed 293 Cell Line

AbstractThe human–viral junctions of integrated adenovirus type 5 (Ad5) DNA in 293 cells have been cloned and sequenced. The Ad5 sequences extend from nucleotides (nt) 1 to 4344 and are located in the pregnancy-specific β-1-glycoprotein 4 (PSG 4) gene. This maps the insertion of Ad5 DNA to human chromosome 19 (19q13.2). The Ad5 sequences are represented as a single collinear insertion of viral DNA with no rearrangements. There were 19 bp of PSG4 DNA deleted at the site of insertion and an extra 3 nt (GTC) at the left viral/cellular junction. A short patch of homology between viral DNA and PSG4 DNA (6 nt with 1 mismatch) was present at the right junction