pinecone/core-2020-05-10-deduplication huggingface dataset:
Sequence Analysis of Normal and Rearranged NSP5 Genes from Human Rotavirus Strains Isolated in Nature: Implications for the Occurrence of the Rearrangement at the Step of Plus Strand Synthesis

AbstractWe determined the nucleotide sequences of normal and rearranged NSP5 genes from the human rotavirus strains (Mc323 and Mc345, respectively) which had previously been isolated from Thai infants with diarrhea in the same epidemic season. While the two strains shared G serotype 9 specificity and subgroup I specificity and they showed a high level of overall genomic relatedness to each other, they exhibited different RNA profiles; a long pattern for Mc323 and a super-short pattern for Mc345. Their NSP5 sequences were more closely related to those of porcine rotaviruses than to those of human rotaviruses. Mc345 NSP5 gene was shown to have concatemerization in a head-to-tail orientation resulting in its length being 1182 bp, as compared with the Mc323 NSP5 sequence which was 664 bp in length. Sequence analysis suggested that the rearrangement found in the strain Mc345 occurred at the step of plus strand synthesis
Role of Cotranslational Disulfide Bond Formation in the Folding of the Hemagglutinin-Neuraminidase Protein of Newcastle Disease Virus

AbstractThe role of cotranslational disulfide bond formation in the folding pathway of the hemagglutinin-neuraminidase (HN) glycoprotein of Newcastle disease virus was explored. Electrophoresis of pulse-labeled HN protein in the presence or absence of reducing agent showed that, characteristic of many glycoproteins, the nascent HN protein contains intramolecular disulfide bonds. As reported by Braakmanet al.(EMBO J.11, 1717–1722, 1992), incubation of cells in dithiothreitol (DTT) blocked the formation of these bonds. Removal of DTT after a pulse-label allowed for the subsequent formation of intramolecular disulfide bonds and folding of the molecule as assayed by the appearance of conformationally sensitive antigenic sites and by the formation of disulfide-linked dimers. However, thet1/2for the formation of a conformationally sensitive antigenic site after synthesis in the presence of DTT was over twice that of the control. Furthermore, the order of appearance of the antigenic sites was different from the control, suggesting that inhibition of cotranslational disulfide bond formation altered the folding pathway of the protein. Similar results were obtained in a cell-free system containing membranes. The HN protein forced to form intramolecular disulfide bonds posttranslationally had no detectable neuraminidase or cell attachment activity, suggesting that the protein had an abnormal conformation
Monoclonal Antibodies to HPV-6 L1 Virus-like Particles Identify Conformational and Linear Neutralizing Epitopes on HPV-11 in Addition to Type-Specific Epitopes on HPV-6

AbstractA set of 13 monoclonal antibodies (MAbs) was generated against HPV-6 L1 virus-like particles (VLPs), screened for reactivity to HPV-6 and HPV-11 L1 VLPs by ELISA, and tested for neutralization of HPV-11 infection. Both cross-reactive and type-specific epitopes were detected such that 4 of 13 MAbs reacted to surface conformational sites on HPV-6 L1 VLPs and the remaining 9 MAbs were cross-reactive to both HPV-6 and HPV-11 L1 VLPs. Four of the 9 cross-reactive MAbs were able to neutralize HPV-11 infectivity, and 3 of 4 of these neutralizing MAbs (N-MAbs) identified shared surface conformational sites. One N-MAb therefore recognized a surface linear epitope as judged by positive binding to L1 in a Western blot assay. The neutralization status of these cross-reactive MAbs with regard to HPV-6 could not be assayed. These results demonstrated that the closely related HPV types 6 and 11 contain both type-specific and shared neutralizing epitopes
Effects of the Estrous Cycle on Local Humoral Immune Responses and Protection of Intranasally Immunized Female Mice against Herpes Simplex Virus Type 2 Infection in the Genital Tract

AbstractThis study demonstrates that the levels of gB-specific IgG and IgA in vaginal washes of mice immunized intranasally (i.n.) with a recombinant adenovirus vector expressing herpes simplex virus (HSV) glycoprotein B (AdgB8) vary inversely with each other and are dependent on the stage of the estrous cycle. Anti-gB IgA titers in vaginal washes were significantly higher during estrus than diestrus or proestrus, whereas specific IgG titers were significantly higher during diestrus than estrus. This was further demonstrated in hormone-treated mice, where progesterone administration induced a diestrus-like state that resulted in elevated specific IgG-to-IgA ratios. Interestingly, unimmunized mice were only susceptible to intravaginal (ivag) infection with HSV-2 during diestrus. Mice immunized i.n. with AdgB8 and given progesterone were protected from a lethal intravaginal HSV-2 challenge, despite the fact that virus replication was present for 4 days postchallenge. Further, high numbers of gB-specific IgA and IgG antibody-secreting cells were present in both the genital tracts and the draining iliac lymph nodes of i.n.-immunized, but not unimmunized, mice 6 days following ivag HSV-2 challenge. These results demonstrate that the levels of specific antibodies in the female genital tract are dependent on the stage of the estrous cycle. Furthermore, i.n. AdgB8 immunization provided a significant level of protection and specific IgA and IgG antibody-secreting cells in the genital tissues during resolution of an ivag infection with HSV-2
Reciprocal Effects of Splicing and Polyadenylation on Human Immunodeficiency Virus Type 1 Pre-mRNA Processing

AbstractInsertion of a functional splicing cassette into a construct containing the HIV-1 poly(A) site followed by the adenovirus L3 poly(A) site results in both specific stimulation of 3′ end processing at the HIV-1 site and an increase in the steady-state levels of RNA processed at both sites. To further evaluate this influence of splicing on processing of the HIV-1 poly(A) site, defined mutations which alter or abolish splicing of the intron were made and analyzed for their effects on polyadenylation and steady-state levels of RNA. The data show that a point mutation at the 3′ splice site caused activation of a cryptic splice acceptor that is as efficient as the wild-type acceptor. Substitution of this mutant intron for the wild-type intron resulted in stimulation of the HIV-1 poly(A) site to levels equivalent to those caused by the wild-type intron. This mutant did not, however, have as great an effect on steady-state RNA levels as the wild-type intron. A second construct containing a mutated branch point and polypyrimidine tract resulted in abolishment of splicing and a decrease in both poly(A) site use and steady-state levels of RNA. These data demonstrate that the enhanced use of the HIV-1 poly(A) site is a direct result of the splicing reaction, and not merely due to the sequences that were inserted. The effect that poly(A) site strength has on splicing was also addressed. Using activation of the cryptic splice acceptor to indicate changes in splicing efficiency resulting from alterations in poly(A) site strength, it was determined that poly(A) site strength does have an effect on the efficiency of the splicing reaction
Role of Mason-Pfizer Monkey Virus (MPMV) Constitutive Transport Element (CTE) in the Propagation of MPMV Vectors by Genetic Complementation Using Homologous/HeterologousenvGenes

AbstractTo study Mason-Pfizer monkey virus (MPMV) replication over a single round, virus particles were generated that contain a replication-defective vector encoding a dominant selectable marker, thehygromycin B phosphotransferase (hygr)gene. Genetic complementation with a homologous MPMV envelope glycoprotein (Env-gp) or pseudotyping by several heterologous Env-gps from a variety of viruses resulted in infectious MPMV particles containing the replication-defective RNA. Recently, it has been shown that human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus (SIV) Rev and Rev-responsive element (RRE) functions can be substitutedin vitroby acis-acting sequence, the constitutive transport element (CTE), from simian type D retroviruses like MPMV and simian retrovirus type 1 (SRV-1). To determine whether CTE of MPMV is necessary for MPMV nucleic acid propagation, an MPMV vector that lacked the terminally located CTE was generated. Propagation of this vector was completely abrogated in the absence of CTE, showing the importance of CTE in MPMV replication. Insertion of CTE back into the MPMV genome in the sense orientation rescued replication to wild-type levels. Slot-blot analysis of nuclear versus cytoplasmic RNA fractions revealed that most of the messages were sequestered in the nucleus of cells transfected with the CTE(−) vectors and very little was transported to the cytoplasm. To test whether HIV-1 or SIV RREs could complement CTE function, the HIV-1 or SIV RREs were inserted in the CTE(−) vectors.transcomplementation of CTE(−)RRE(+) vectors with Env- and Rev- expression plasmids rescued propagation of the CTE(−) vectors. Computer analysis predicted an RNA secondary structure in MPMV CTE analogous to the HIV-1 and SIV RREs that could form three stable stem loops, the first of which contains a site similar to the Rev-binding domain in the HIV-1 RRE. The presence of a higher-order CTE structure was analyzed by mutational analysis. We conclude that CTE is important in the replication of MPMV and affects the nucleocytoplasmic transport and/or stability of viral messages similar to the Rev/RRE regulatory system of HIV-1 and SIV
P2 Protein Encoded by Genome Segment S2 of Rice Dwarf Phytoreovirus Is Essential for Virus Infection

AbstractLoss of infectivity to insect vector cell monolayers of rice dwarf phytoreovirus (RDV) after CCl4treatment was associated with the removal of one of the viral proteins from the virus particles. This protein, encoded by genome segment S2 and thus named P2 protein, was located at the outer capsid of the virus particle. When RDV was treated with CCl4for various times, the reduction in the amount of P2 protein and the loss of viral infectivity to vector cell monolayers were proportional to treatment time. RDV purified using CCl4treatment, thus lacking P2 protein, lost the ability to infect vector insects through feeding and consequently failed to be transmitted to plants. These results suggest that P2 protein is essential for RDV infection of the insect cells and may be related to transmission of the virus by the vector insect
CD44 Is Not Required for Poliovirus Replication in Cultured Cells and Does Not Limit Replication in Monocytes

AbstractAlthough poliovirus receptor is required to mediate poliovirus infection, its role in mediating the tissue specificity of poliovirus replication in natural infections remains unclear due to the presence of this receptor in nonsusceptible cells. It has been hypothesized that CD44 has a role in determining the susceptibility of cells to poliovirus. To test this hypothesis, we determined whether HepG2, a cultured cell line that lacks cell surface CD44, can support poliovirus replication. We found that PV(1) Mahoney, PV(2)W2, and PV(3)Leon strains of poliovirus can replicate in HepG2 cells. Jurkat cells, which also lack CD44, support PV replication. These results suggest that CD44 is not required for poliovirus replication in cultured cells. To examine this question further, expression of CD44 in primary human monocytes was examined. Greater than 90% of monocytes express the poliovirus receptor but only 6% of these cells are susceptible to poliovirus infection, making this a good system to study blocks to poliovirus replication. 97% of primary human monocytes reacted with a monoclonal antibody against CD44 that has been shown to block poliovirus binding and replication. This finding suggests that CD44 is present on more cells that poliovirus infects, making CD44 unlikely to be the factor limiting poliovirus replication in human tissues
Cloning and Expression of a Single-Chain Antibody Fragment Specific for Foot-and-Mouth Disease Virus

AbstractThe gene for a single-chain antibody (VHK) to a conformational epitope on the type A12foot-and-mouth disease virus (FMDV) particle was assembled and expressed inEscherichia coli.The VHK, purified from periplasmic extracts immunoprecipitated virus as efficiently as its parental monoclonal antibody (MAb) and exhibited the same binding specificity when tested against a panel of natural and genetically engineered virus particles. The VHK neutralized type A12virus in the presence of goat anti-mouse IgG; however, in the absence of the second antibody, only weak neutralizing activity was detected. Preliminary analysis of the mechanism of viral neutralization indicated that both the MAb and the VHK neutralize by the same mechanism. Small amounts of the VHK allowed infection of cells via Fc receptor-mediated adsorption in the presence of the second antibody. These data represent the first report of a single-chain neutralizing antibody for a picornavirus and provide insights into the mechanisms of viral neutralization and virus uptake
Molecular Characterization of the Segment 2 Gene of Epizootic Hemorrhagic Disease Virus Serotype 2: Gene Sequence and Genetic Diversity

AbstractThe complete nucleotide sequence of the gene encoding the major outer capsid protein VP2 from the Alberta isolate of epizootic hemorrhagic disease virus serotype 2 (EHDV-2) was determined. Complementary DNA (cDNA) corresponding to segment 2 was 3002 nucleotides in length with a single open reading frame that encoded a VP2 of 982 amino acids. Although the VP2 from EHDV-2 was only 34% homologous to the cognate protein from EHDV-1, their predicted hydropathic profiles were similar, suggesting that conservation of structure is important biologically to these capsid proteins. Sequence analysis of six North American EHDV-2 field isolates showed a high degree of comparative genetic identity (>97%). Phylogenetic profiles constructed suggest that regionalization of the viruses within the North American continent has contributed to the genetic diversity
Mutagenesis of Conserved Residues of the Adenovirus Protease

AbstractBased on the alignment of 12 adenovirus protease sequences, we have identified eleven conserved residues for mutagenesis. Eight of these, E5, D26, N44, E71, D77, D102, N144, and N170, are potential candidates for the third residue of the active site triad. N44, E71, N144, and N170 proved to be essential for enzyme activity. Glutamic acid 71 was proposed for the active site. Mutation of the three conserved cysteines suggested that C122 is the active nucleophile, C104 is the target for activation by peptide pVIc, and C126 is dispensable. Rescue of enzyme activity of the C104G mutant by pVIc suggested that disulfide bond formation between the peptide and the protease may not be absolutely essential for stimulation of enzyme activity
Efficient Translation of Distal Cistrons of a Polycistronic mRNA of a Plant Pararetrovirus Requires a Compatible Interaction between the mRNA 3′ End and the ProteinaceousTrans-Activator

AbstractCaulimoviruses, a type of plant pararetrovirus, employ a highly unusual mechanism to express the multiple cistrons of their pregenomic RNA. It involves translation of a polycistronic mRNA utilizingcis-acting viral RNA sequences and atrans-acting virus-encoded protein (P6). In addition to its role in polycistronic translation, the translationaltrans-activator protein P6 also activates its own expression from a monocistronic subgenomic RNA. UsingNicotiana edwardsoniicell suspension protoplasts, we analyzed the ability of P6 proteins from three different caulimoviruses to activate viral RNA-based reporter constructs.Cis-acting elements present in figwort mosaic caulimovirus (FMV) are functional not only in the presence of the cognate P6 activator protein, but also in the presence of the heterologous activators from cauliflower mosaic caulimovirus (CaMV) and peanut chlorotic streak caulimovirus (PClSV). However, when 3′cis-acting elements essential for efficient polycistronic expression of FMV are replaced by their counterparts from PClSV, reporter gene expression is only observed in the presence of PClSV P6. Derepression of monocistronic reporter constructs tailed with FMV or CaMV 3′ proximal sequences is less efficient in the presence of PClSV P6 than with either FMV or CaMV P6, but more efficient when the constructs contain a cognate PClSV 3′cis-element. Efficient expression of polycistronic and monocistronic caulimovirus mRNAs in plant cells thus requires compatible interactions between P6, a translationaltrans-activator, and its cognatecis-element at the 3′ end of the mRNA
The N-Terminal Part of Bacteriophage P2 Capsid Protein Is Essential for Postassembly Maturation of P2 and P4 Capsids

AbstractDuring capsid assembly of bacteriophage P2 and its satellite phage P4, gpN undergoes proteolytic cleavage with the removal of the first 31 amino acids. The truncated protein gpN* is unable to support formation of viable phages in complementation tests. A c-myc antigenic epitope (EQKLISEEDL) exchanged for eleven amino acids in the amino terminal part of gpN results in both proteolytic processing of gpN::c-myc as well as assembly of P2 and P4 procapsid-like structures, but gpN::c-myc failed, like N*, to support the production of infectious P2 and P4 particles
Murine Leukemia Virus Infects Early Bone Marrow Progenitors in Immunocompetent Mice

AbstractChronic murine leukemia viruses (MuLVs) are retroviruses which induce leukemias/lymphomas after long latency periods. The induction of leukemia by MuLVs is complex, requiring multiple steps beginning with infection of an appropriate target cell. A number of investigators have proposed a bone marrow–thymus axis in the development of retrovirus induced T-cell lymphoma in which cells are initially infected in the bone marrow. These bone marrow cells or their progeny migrate to the thymus during the disease process. In our system using adult, immunocompetent BALB.K mice infected with E-55(+) MuLV, a similar pattern is seen; integrated virus is initially detectable in the bone marrow and spleen and only later in the thymus. In order to better understand the leukemic process, we analyzed the bone marrow from adult, immunocompetent BALB.K mice infected with the E-55(+) MuLV in bone marrow colony assays. The results from these assays demonstrate that either a pluripotent progenitor cell or an early progenitor cell is a target in the bone marrow for the virus
Genetic Characterization of Two Phenotypically Distinct North American Ovine Lentiviruses and Their Possible Origin from Caprine Arthritis-Encephalitis Virus

AbstractOvine and caprine lentiviruses are closely related genetically and antigenically although the diseases that these viruses cause in their respective host animals can vary greatly. In sheep, syndromes consist primarily of interstitial pneumonia with rare occurrences of arthritis and encephalitis, whereas in goats, the disease expresses mainly as arthritis in adult animals with rare cases of encephalitis in newborns. Experimentally, viruses from either sheep or goats can infect animals of the reciprocal species and many field strains of ovine lentivirus have biological properties similar to those of caprine viruses. However, a molecular correlation for the phenotypic differences between ovine and caprine lentivirus strains is unknown. To investigate this, we examined genetic characteristics of two phenotypically distinct North American ovine lentiviruses. Nucleotide sequence analysis of the envelope regions from virus strains 85/34 and 84/28 showed that despite significant biological differences, these viruses are closely related to each other and are genotypically more homologous to caprine arthritis-encephalitis virus (CAEV) than to visna virus of sheep. Furthermore, analysis of the nucleotide substitutions in theirenvregions indicated that when differences between the two ovine viruses and CAEV were found, the changes often resulted in nucleotides homologous with visna virus. These results suggest that the two field strains of ovine lentivirus may have originated from a cross-species infection of sheep by a CAEV-like virus and, evolution of their genomes toward that of ovine lentivirus may be reflective of adaptation of these viruses to the new ovine host
Carboxylate Interactions Involved in the Disassembly of Tobacco Mosaic Tobamovirus

AbstractStructural studies of tobacco mosaic tobamovirus (TMV) have identified two coat protein (CP) intersubunit carboxyl–carboxylate interactions and one CP carboxylate–RNA phosphate interaction whose electrostatic repulsion is believed to drive virion disassembly. In this study, the involvement of each interaction in the disassembly process was examined. Site-directed mutagenesis was used to replace selected negatively charged CP residues, E or D, with neutral residues, Q or N, respectively. Purified mutant CPs were assayed for their ability to inhibit wild-type TMV disassembly bothin vitroandin vivo.Results indicate that the lateral carboxylate interaction made by residue E106 is much more complex than previously thought, involving three residues, E95, E97, and D109, from an adjacent subunit. Mutations at all three residues are required to inhibit disassembly significantly. Different mutant coat proteins inhibited disassembly of the wild-type virus to varying degrees. Mutant E50Q, which modified the axial intersubunit interaction, had the greatest ability to inhibit disassembly followed by mutants E95Q/E97Q/D109N and D116N, which modified the lateral and CP–RNA interactions, respectively. Within each set of interacting carboxylate groups, mutations in the face opposite the disassembling surface of the TMV virion conferred the greatest ability to inhibit disassembly. This observation is consistent with the polar nature of TMV disassembly and confirms that repulsive intersubunit interactions derived from the 5′ terminal subunits provide the key controlling mechanisms for virion disassembly
Apoptosis Correlates with Immune Activation in Intestinal Lymphoid Tissue from Macaques Acutely Infected by a Highly Enteropathic Simian Immunodeficiency Virus, SIVsmmPBj14

AbstractThe PBj14 isolate of simian immunodeficiency virus, SIVsmmPBj14, induces an acutely lethal disease in experimentally inoculated pigtailed macaques, that is characterized by severe enteropathy and extensive immune activation, particularly within gut-associated lymphoid tissue (GALT). Experiments were conducted to determine whether virally induced immune activation might promote the induction of apoptosis in GALT during acute SIVsmmPBj14infection.In situlabeling studies revealed a significant increase in the number of apoptotic cells within GALT from macaques with acute SIVsmmPBj14infection, compared to (i) other tissues from the same animals, (ii) GALT from virus-negative animals, or (iii) GALT from macaques that were sacrificed soon after infection with SIVmac239, which does not cause acutely lethal enteropathy. These findings were confirmed by biochemical assays of DNA fragmentation, using DNA laddering and ELISA techniques. Immunostaining experiments revealed a strong positive correlation between the extent of apoptosis and the degree of immune activation, as assessed either by the number of cells which contained nuclear (activated) RelA, or by the number of cells immunoreactive for CD25, a T-cell activation marker. Additional analyses of SIV antigen expression revealed that the majority of the apoptotic cells were not productively infected by SIV (i.e., that they were bystander cells). Taken together, these findings support the hypothesis that SIVsmmPBj14efficiently induces immune activation and that this results in extensive apoptosis within gut-associated lymphoid tissue during acute viral infection