pinecone/core-2020-05-10-deduplication huggingface dataset:
Sequence Diversity of Jeryl Lynn Strain of Mumps Virus: Quantitative Mutant Analysis for Vaccine Quality Control

AbstractThe Jeryl Lynn strain of mumps vaccine live (MVL) was developed in 1966 by Merck Co. and has been widely used in the U.S. and other countries since the early 1970s. Partial sequencing has recently shown that the vaccine contains a mixture of two substrains with substantially different nucleotide sequences. We have determined the complete genomic sequences of both substrains and identified 414 nucleotide differences (2.69%), leading to 87 amino acid substitutions (1.67%). We used this information to develop methods for quantification of the substrain components in vaccine samples based on PCR and restriction enzyme cleavage and oligonucleotide microarray hybridization and monitored their dynamics in viral populations propagated in different conditions. Passaging Jeryl Lynn strain in Vero or CEF cell cultures resulted in rapid selection of the major component JL1, while growth in embryonated chicken eggs (ECE) favored accumulation of the minor component JL2. Based on the findings presented here, it is proposed that the substrain composition of Jeryl Lynn vaccine can be monitored as a part of its quality control to ensure consistency of the vaccine
CCAAT/Enhancer Binding Proteins Are Not Required for HIV-1 Entry but Regulate Proviral Transcription by Recruiting Coactivators to the Long-Terminal Repeat in Monocytic Cells

AbstractCCAAT/enhancer binding proteins (C/EBP) have been shown to be required for HIV-1 transcription and replication in macrophages. However, whether these transcription factors influence the ability of virus to establish infection by altering cytokine or receptor expression or primarily regulate HIV-1 transcription has not been determined. By inhibiting endogenous C/EBP activity with a dominant-negative protein, we demonstrate that functional C/EBPs are not required for HIV-1 infection and that these factors influence replication by a transcriptional mechanism. C/EBPβ recruits coactivators to the HIV-1 long-terminal repeat (LTR) and physically interacts with histone acetyltransferase (HAT) complexes, suggesting that C/EBPs participate in remodeling the chromatin organization of the HIV-1 provirus. Furthermore, overexpression of a C/EBP dominant-negative inhibits displacement of nucleosomes located at the HIV-1 transcriptional start site. These results provide insight into the general mechanisms by which C/EBPs regulate macrophage-restricted HIV-1 transcription
Activation of HTLV-I Transcription in the Presence of Tax Is Independent of the Acetylation of CREB-2 (ATF-4)

AbstractWe have previously demonstrated that the bZIP transcription factor CREB-2, also called ATF-4, trans-activates, in association with the viral protein Tax, the human T-cell leukemia virus type I (HTLV-I) promoter. In this study, we have examined whether CREB-2 acetylation affects transcriptional activation mediated by Tax. We present evidence that CREB-2 is acetylated in vitro and in vivo. CREB-2 is acetylated in two regions: the basic domain of the bZIP (from amino acid residue 270 to 300) and the short basic domain (from 342 to 351) located downstream from the bZIP. We also demonstrate that CREB-2 is acetylated by p300/CBP but not by p/CAF. Moreover, replacement of lysine by arginine in the basic domains decreases the trans-activating capacity of CREB-2. However, in the presence of Tax, the HTLV-I transcription remains fully activated by these CREB-2 mutants. Although we cannot totally exclude that the mutations could also affect CREB-2 structure and activity independent of acetylation, our results suggest that activation of the viral promoter in the presence of Tax is independent of the CREB-2 acetylation
Adenovirus Type 37 Binds to Cell Surface Sialic Acid Through a Charge-Dependent Interaction

AbstractMost adenoviruses use the coxsackie-adenovirus receptor (CAR) as a major cellular receptor. We have shown recently that adenovirus types 8, 19a, and 37, which are the major causes of epidemic keratoconjunctivitis, use sialic acid rather than CAR as a major cellular receptor. The predicted isoelectric point of the receptor-interacting knob domain in the adenovirus fiber protein is unusually high (9.0–9.1) in type 8, 19a, and 37. The pKa of sialic acid is low, 2.6, implying a possible involvement of charge in fiber knob–sialic acid interactions. Here we show that (i) positively charged adenovirus knobs require sialic acid for efficient cell membrane interactions; (ii) viral and knob interactions with immobilized sialic acid or cell-surface sialic acid are sensitive to increased ionic strength; (iii) negatively charged molecules such as sulfated glycosaminoglycans inhibit the binding of virions to target cells in a nonspecific, charge-dependent manner; and that (iv) the ability of adenovirus knobs to interact with sialic acid correlates with the overall charge on the top surface of the respective knobs as predicted by homology modeling. Taken together, the results presented provide strong evidence for a charge mechanism during the interaction between the Ad37 fiber knob and sialic acid
Expression, Purification, and Characterization of the RNA 5′-Triphosphatase Activity of Dengue Virus Type 2 Nonstructural Protein 3

AbstractDengue virus type 2 (DEN2), a member of the Flaviviridae family of positive-strand RNA viruses, contains a single RNA genome having a type I cap structure at the 5′ end. The viral RNA is translated to produce a single polyprotein precursor that is processed to yield three virion proteins and at least seven nonstructural proteins (NS) in the infected host. NS3 is a multifunctional protein having a serine protease catalytic triad within the N-terminal 180 amino acid residues which requires NS2B as a cofactor for activation of protease activity. The C-terminal portion of this catalytic triad has conserved motifs present in several nucleoside triphosphatases (NTPases)/RNA helicases. In addition, subtilisin-treated West Nile (WN) virus NS3 from infected cells was reported to have 5′-RNA triphosphatase activity, suggesting its role in the synthesis of the 5′-cap structure. In this study, full-length DEN2 NS3 was expressed with an N-terminal histidine tag in Escherichia coli and purified in a soluble form. The purified protein has 5′-RNA triphosphatase activity that cleaves the γ-phosphate moiety of the 5′-triphosphorylated RNA substrate. Biochemical and mutational analyses of the NS3 protein indicate that the nucleoside triphosphatase and 5′-RNA triphosphatase activities of NS3 share a common active site
Cell-to-Cell Movement of the PVX 12K, 8K, or Coat Proteins May Depend on the Host, Leaf Developmental Stage, and the PVX 25K Protein

AbstractThe requirements for intercellular movement of Potato virus X (PVX) 12K, 8K, and coat proteins (CP) differed in two Nicotiana spp. Plasmids containing the green fluorescent protein (GFP) gene fused to PVX 12K, 8K, or CP genes were bombarded to tobacco leaves. Protein movement was observed in N. benthamiana but not N. tabacum leaves. GFP:12K and GFP:8K moved cell-to-cell in 25K-expressing transgenic N. tabacum source but not sink leaves. In N. tabacum, GFP:12K and GFP:8K intercellular movement depends on the 25K and leaf developmental stage. Leaves were bombarded using two biolistic delivery methods and the results were similar indicating that movement of GFP:12K or GFP:8K is independent of the delivery system. Mutations in 12K, 8K, and CP genes within the PVX genome inhibited viral intercellular movement in both Nicotiana spp. Thus plasmodesmata gating is not an essential function of these proteins for virus cell-to-cell movement. These proteins likely provide additional activities for virus cell-to-cell movement
Influenza A Virus with Defective M2 Ion Channel Activity as a Live Vaccine

AbstractWe propose a rational approach to the design of live virus vaccines against influenza infection by alteration of the influenza A virus M2 protein, which is responsible for ion channel activity. Previously we demonstrated that a mutant A/WSN/33 (H1N1) influenza virus with defective M2 ion channel activity did not show appreciable growth defects in cell culture, although its growth was attenuated in mice (T. Watanabe, S. Watanabe, H. Ito, H. Kida, and Y. Kawaoka, 2001, J. Virol. 75, 5656–5662). Here, we show that this M2 ion channel defective mutant virus, the M2del29-31, protected mice against challenge with lethal doses of influenza virus, indicating the potential of incorporating this M2 alteration in a live influenza vaccine as one of the attenuating mutations
The Carboxyl Segment of the Mumps Virus V Protein Associates with Stat Proteins in Vitro Via a Tryptophan-Rich Motif

AbstractViruses of the Paramyxovirinae, similar to other viruses, have evolved specific proteins that interdict IFN action as part of a general strategy to counteract host innate immunity. In many (but not all) cases, this interdiction is accompanied by a lowering of the intracellular levels of the STAT proteins. Among rubulaviruses, there is a notable variation in how they interfere with IFN action. Whereas SV41, SV5, and MuV all act by lowering Stat1, hPIV2 acts by lowering Stat2. Here, we show that the mumps and hPIV2 V proteins both form a complex with several Stat proteins in a mixed-extract assay. This suggests that the specific degradation of these Stat proteins is not determined by complex formation, but presumably at some later stage of the degradation pathway. V/Stat complex formation requires a specific carboxyl segment of V. However, a previously unrecognized trp-rich motif, rather than the Zn++-binding cys-cluster of this segment, appears to be required for V/Stat interaction. The C protein of Sendai (respiro-) virus, another P gene encoded protein, also forms a complex with Stat1, and prebinding of MuV V to Stat1 prevents the subsequent binding of SeV C. Our results suggest that rubulavirus V proteins may be related to both the C and the V proteins of respiroviruses
Adenovirus–Microbead Conjugates Possess Enhanced Infectivity: A New Strategy for Localized Gene Delivery

AbstractWe have created a novel method for coupling adenoviral vectors to solid microbeads in a way that does not adversely affect the infectivity of the attached virions. This method utilizes the extremely tight interaction between the protein streptavidin and its ligand biotin as a means of tethering viral particles to microbeads. The adenovirus–microbead conjugates that were created functioned as fully infectious entities and possessed several functional advantages over free, unmodified viral particles. The adenovirus–microbead conjugates possessed enhanced ability to transduce target cells in culture. For target cells of a highly permissive nature, this increase in infectivity was modest. However for target cells of moderate to low permissivity, the enhancement of transduction efficiency was substantial. Adenoviral vectors, previously incapable of infecting a particular colon cancer cell line, were made fully infectious on the same cell line when delivered as solid-phase conjugates. Additionally, solid-phase adenovirus–microbead conjugates showed highly limited diffusion in solution, allowing for focused delivery of viral vectors only to cells that come into contact with the conjugates. When the solid phase to which the viral particles were attached had paramagnetic properties, the location of viral infections was tightly controllable by magnetic force through the use of strategically placed magnets
Immunogold Localization of Tobravirus 2b Nematode Transmission Helper Protein Associated with Virus Particles

AbstractTransmission of the tobraviruses Tobacco rattle virus (TRV) and Pea early-browning virus (PEBV) by trichodorid vector nematodes requires the viral coat protein (CP) and the 2b protein, a nonstructural protein encoded by RNA2, the smaller of the two viral genomic RNAs. It is hypothesized that the 2b protein functions by interacting with a small, flexible domain located at the C-terminus of the CP, forming a bridge between the virus particle and the internal surface of the vector nematode feeding apparatus. Antibodies specific for the 2b protein of PEBV or TRV did not bind to virus particles that were adsorbed to electron microscope grids and were not able to trap virus particles from extracts of infected plants. However, electron microscopy of thin sections of plants infected with PEBV probed with 2b-specific antibodies which were further gold-labeled showed that the 2b protein localizes exclusively to virus particles. Similarly, immunogold localization studies showed that the 2b protein of TRV isolate PaY4 is associated only with TRV PaY4 virus particles. When a recombinant TRV encoding the PaY4 2b protein and the CP from TRV isolate PpK20 was examined, the 2b protein could not be detected by Western blotting and in IGL experiments was not associated with virus particles. These results suggest that in the absence of a specific interaction between compatible CP and 2b proteins, the 2b protein does not accumulate
Differential Effects of DNA Tumor Virus Genes on the Expression Profiles, Differentiation, and Morphogenetic Reprogramming Potential of Epithelial Cells

AbstractThe availability of cell lines that retain their differentiation programs is important for the study of differentiated cell types and the development of cell therapies. DNA tumor virus genes are often used to establish cell lines from primary culture for the analysis of cell-specific functions. To ascertain whether viral immortalizing or transforming genes differed in their effects on cellular differentiation programs, the E1A 12S (WT12S) gene of adenovirus and the large T antigen (LT) gene of SV40 were used to derive stable cell lines from primary kidney. The resultant cell types exhibited very different morphologies, growth and behavior patterns, differentiation states, and plasticities. Renal cells immortalized by LT exhibited branching tubulogenesis in response to Matrigel. This was in contrast to their behavior under normal culture conditions, wherein they were less differentiated, very nonadhesive, very rapidly growing, and transformed. These cells coexpressed adult epithelial (keratin) and embryonic mesenchymal (vimentin, osteopontin, FSP1, PAX-2, and WT1) genes. WT12S-immortalized cells grown on or in Matrigel formed cysts or tubules, consistent with their expression profiles, which consisted of both epithelial and adult kidney markers (E-cadherin, α-catenin, circumferential actin filaments (CAF), alkaline phosphatase, aminopeptidase M, BMP7, or podocalyxin), but not embryonic/mesenchymal markers (PAX-2 or WT1). The WT12S-expressing cells were well differentiated, adhesive, slow growing, and nontransformed. Thus, cells expressing WT12S maintained their original differentiation status and were less sensitive to reprogramming, while cells expressing LT were dedifferentiated, but had the potential for reprogramming by exogenous factors
Emergence of Influenza A H1N2 Reassortant Viruses in the Human Population during 2001

AbstractInfluenza A H1N2 viruses, which emerged during 2001, are genetic reassortants between H1N1 and H3N2 subtype viruses which have cocirculated in the human population since 1977. They possess a H1 hemagglutinin antigenically and genetically similar to contemporary A/New Caledonia/20/99 (H1N1)-like viruses and seven genes closely related to those of recent A/Moscow/10/99 (H3N2)-like viruses. The viruses have spread to many regions of the world and have predominated over H1N1 viruses in several countries. Since half of the amino acid changes which accumulated in the HAs of H1N1 viruses since 1995 are in residues implicated in receptor binding, functional changes in the H1 HA may have facilitated its replacement of the H3 HA and may contribute to the future epidemiologic significance of these H1N2 viruses
Nairobi Sheep Disease Virus, an Important Tick-Borne Pathogen of Sheep and Goats in Africa, Is Also Present in Asia

AbstractNairobi sheep disease (NSD) virus is the prototype of the tick-borne NSD serogroup, genus Nairovirus, family Bunyaviridae. It is highly pathogenic for sheep and goats, causes disease in humans, and is widespread throughout East Africa. Ganjam virus has caused disease in goats and humans in India. Due to their occurrence on different continents and association with different ticks, these viruses were considered distinct despite serologic cross-reactivity. Their S RNA genome segments and encoded nucleocapsid proteins were found to be 1590 nucleotides and 482 amino acids in length and differed by only 10 and 3% at nucleotide and amino acid levels, respectively. Genetic and serologic data demonstrate that Ganjam virus is an Asian variant of NSD virus. These viruses were phylogenetically more closely related to Hazara virus than Dugbe virus
Effect of Ku80 Depletion on the Preintegrative Steps of HIV-1 Replication in Human Cells

AbstractTo gain new insights regarding the role of Ku, the DNA-PK DNA-binding component, during lentiviral DNA integration, we have investigated the HIV-1 replication in Ku80-depleted human cells. CEM4fx cells underexpressing the Ku80 factor were selected after transduction by a retroviral vector expressing the Ku80 full-length antisense sequence. De novo infection experiment with NL4.3 HIV-1 strain led to the observation that the viral replication was delayed in the Ku80-depleted cells. Early events of the replicative cycle, including nuclear import of the viral DNA, were not affected. In contrast, the formation of the 2-LTR circles was impaired, thus demonstrating the implication of Ku in HIV-1 DNA circularization, for the first time in human cells. Furthermore, the detection of integrated proviruses by an Alu-LTR-nested PCR amplification method was affected in cells underexpressing Ku80. These results suggest that this factor may also be involved in the mechanisms leading to the stable establishment of HIV-1 provirus
Mutational Analysis of the Sendai Virus V Protein: Importance of the Conserved Residues for Zn Binding, Virus Pathogenesis, and Efficient RNA Editing

AbstractThe V protein of Sendai virus (SeV) is nonessential for virus replication in cell culture but indispensable for viral pathogenicity in mice. At the C terminus of the V protein, there are amino acid residues conserved among the members of the Paramyxovinae subfamily that are clustered in three regions: region I, just downstream of the RNA editing site; and regions II and III, cysteine-rich zinc-finger-like regions. In the present study, we introduced mutations into the conserved amino acids and generated nine mutant viruses. All of the viruses had impaired virus replication in mouse lungs and attenuated virulence in mice. Furthermore, the C-terminal polypeptides fused with glutathione-S-transferase with a mutation in region I, II, or III all had impaired Zn binding in a 65Zn-binding assay in solution. These results demonstrate that the conserved amino acids are important for V protein function, probably via protein conformation dependent on Zn binding. One mutant, SeV V-H318N, had inefficient RNA editing, indicating that the nucleotide that is a part of the codon encoding histidine at position 318 is conserved for the RNA editing machinery. In addition, to determine the function of the C-terminal extension of the V protein, which is not translated in recent virulent field isolates, a translational stop codon was introduced to generate the corresponding short V protein. The mutant virus showed similar virus propagation and pathogenicity, indicating that C-terminal extension of the V protein is not relevant to virus pathogenesis
Chimeric Ecotropic MLV Envelope Proteins that Carry EGF Receptor-Specific Ligands and the Pseudomonas Exotoxin A Translocation Domain to Target Gene Transfer to Human Cancer Cells

AbstractRedirecting retroviral vector transduction simply by insertion of a ligand into the envelope (Env) protein has met with several obstacles. For example, virions targeted to epidermal growth factor receptor (EGFR), after receptor binding, rapidly traffic to the lysosomes, where they are degraded. Exotoxin A of Pseudomonas aeruginosa has the ability to translocate from endosomes to the cytoplasm by means of a translocation domain (TLD). We generated a series of chimeric Env proteins of Moloney murine leukemia virus containing EGFR ligands, where TLD was inserted into different regions. These chimeric proteins were successfully produced, if the translocation domain was not located at the immediate N-terminus of Env. The ability to transduce murine cells via the ecotropic receptor varied but correlated with the amount of Env proteins incorporated into the virions. Chimeric vector particles could bind to EGFR, demonstrating the functional exposure of the peptide ligand. However, transduction of human cells expressing EGFR but not the ecotropic receptor by virions carrying the chimeric protein was not observed
The Death Effector Domains (DEDs) of the Molluscum Contagiosum Virus MC159 v-FLIP Protein Are Not Functionally Interchangeable with Each Other or with the DEDs of Caspase-8

AbstractThe molluscum contagiosum virus (MCV) MC159 protein contains two death effector domains (DEDs) that bind to the DEDs of caspase-8 and FADD and inhibit apoptosis. We constructed MC159 truncation mutants and found that the amino-terminal region before the first DED and nearly all the carboxyl terminus after the second DED were dispensable for the antiapoptotic activity of MC159. We also engineered tandem repeats of two identical MC159 DEDs, MC159 DEDs in the reverse orientation, and MC159-caspase-8 chimeras in which a DED of MC159 was replaced with the corresponding DED of caspase-8. Each of these constructs bound to caspase-8, but was unable to bind to FADD or block apoptosis. In addition, we constructed mutants containing only a single DED of MC159. These mutants bound to both FADD and caspase-8, but could not block apoptosis or the formation of death effector filaments. Thus, the DEDs of MC159 are not functionally interchangeable with each other or with those of caspase-8
Mutations in Turnip mosaic virus P3 and Cylindrical Inclusion Proteins Are Separately Required to Overcome Two Brassica napus Resistance Genes

AbstractThe Brassica napus differential line 165 is resistant to infection by Turnip mosaic virus (TuMV) isolates belonging to pathotypes 1 and 3. Nucleotide sequences of resistance-breaking mutants of pathotype 1 (UK 1), pathotype 3 (CHN 12), and wild-type isolates have been determined. When the mutations identified were introduced into an infectious clone of UK 1, a single mutation in the viral P3 protein induced a hypersensitive (necrotic) response in inoculated leaves of line 165 plants. Full systemic nonnecrotic infection was only possible when another mutation (in the cylindrical inclusion protein) was introduced. Tests on segregating populations derived from line 165 indicated that the two viral genes were pathogenicity determinants for two different resistance genes in line 165. One gene responsible for an extreme form of resistance (no symptoms seen) was epistatic to a second responsible for the hypersensitive reaction. These results help to explain the relative stability of the resistance in line 165 and to further define the genetic basis of the TuMV pathotyping system