pinecone/core-2020-05-10-deduplication huggingface dataset:
Derivation and Biological Characterization of a Molecular Clone of SHIVKU-2 That Causes AIDS, Neurological Disease, and Renal Disease in Rhesus Macaques

AbstractPreviously, we described the derivation of a pathogenic strain of simian–human immunodeficiency virus (SHIVKU-2) consisting of the tat, rev, vpu, and env genes of HIV-1 (strain HXB2) in a genetic background of SIVmac239 that causes AIDS and productive infection of the CNS in rhesus macaques (Macca mulatta) (Raghavan et al., 1997, Brain Pathol. 7, 851–861). We report here on the characterization of a molecular clone of SHIVKU-2, designated SHIVKU-2MC4, that caused CD4+ T cell loss as well as neurological and renal disease in macaques. DNA sequence analysis of selected SIV regions of SHIVKU-2MC4 revealed 10 nucleotide changes in the LTR, whereas Gag, Vif, Vpr, Vpx, and Nef had 1, 1, 1, 2, and 13 predicted amino acid substitutions, respectively, compared to SIVmac239. DNA sequence analysis of HIV-1 derived regions of SHIVKU-2MC4 revealed 2, 1, 2, and 18 predicted amino acid substitutions in the Tat, Rev, Vpu, and Env proteins, respectively, when compared to SHIV-4. Unlike the parental SHIV-4, which is not tropic for macrophages, SHIVKU-2MC4 replicated efficiently in macrophage cultures as determined by p27 assays. However, despite the numerous changes in the Env protein and newly acquired tropism for macrophages, SHIVKU-2MC4, like the parental SHIV-4, used CXCR4 exclusively as its coreceptor for entry into susceptible cells. Inoculation of SHIVKU-2MC4 into two rhesus macaques resulted in severe infection in which the numbers of circulating CD4+ T cells in the blood declined rapidly by 2 weeks postinoculation and virus producing cells in the peripheral blood mononuclear cells were identified throughout the course of infection. At the time of euthanasia (20 and 22 weeks), both macaques had lost a significant amount of weight and had no circulating CD4+ T cells. In addition, one macaque developed intension tremors and uncoordinated movements. Virological examination of tissues at necropsy revealed active virus replication in both lymphoid and nonlymphoid tissues such as the lung and brain. Histological examination revealed that the induced immunodeficiency was associated with lymphoid depletion of the lymph nodes and spleen, opportunistic infections, lentiviral encephalitis, and severe glomerulosclerosis of the kidney. This molecular clone will serve as the basis for analyzing the molecular determinants through which SHIVKU-2 causes severe CD4+ T cell loss, neurological disease, and SHIV nephropathy in rhesus macaques
Antigenic Epitopes of the Hepatitis A Virus Polyprotein

AbstractForty-two antigenic domains were identified across the hepatitis A virus (HAV) polyprotein by using a set of 237 overlapping 20-mer synthetic peptides spanning the entire HAV polyprotein and a panel of serum samples from acutely HAV-infected patients. The term “antigenic domain” is used in this study to define a protein region spanned with consecutive overlapping immunoreactive peptides. Nineteen antigenic domains were found within the structural proteins, and 22 were found within the nonstructural proteins, with 1 domain spanning the junction of VP1 and P2A proteins. Five of these domains were considered immunodominant, as judged by both the breadth and the strength of their immunoreactivity. One domain is located within the VP2 protein at position 57–90 aa. A second domain, located at position 767–842 aa, contains the C-terminal part of the VP1 protein and the entire P2A protein. A third domain, located at position 1403–1456 aa, comprises the C-terminal part of the P2C protein and the N-terminal half of the P3A protein. The fourth domain, located at position 1500–1519 aa, includes almost the entire P3B, and the last domain, located at position 1719–1764 aa, contains the C-terminal region of the P3C protein and the N-terminal region of the P3D protein. It is interesting to note that four of the five most immunoreactive domains are derived from small HAV proteins and/or encompass protein cleavage sites separating different HAV proteins. The HAV-specific immunoreactivity of each antigenically reactive peptide was confirmed by using seven HAV seroconversion panels. Collectively, these data demonstrate that HAV structural and nonstructural proteins contain antigenic epitopes that can be efficiently modeled with short synthetic peptides
The Genetic Relationship between Virulent and Temperate Streptococcus thermophilus Bacteriophages: Whole Genome Comparison of cos-Site Phages Sfi19 and Sfi21

AbstractThe virulent cos-site Streptococcus thermophilus bacteriophage Sfi19 has a 37,392-bp-long genome consisting of 44 open reading frames all encoded on the same DNA strand. The genome of the temperate cos-site S. thermophilus phage Sfi21 is 3.3 kb longer (40,740 bp, 53 orfs). Both genomes are very similarly organized and differed mainly by gene deletion and DNA rearrangement events in the lysogeny module; gene replacement, duplication, and deletion events in the DNA replication module, and numerous point mutations. The level of point mutations varied from <1% (lysis and DNA replication modules) to >15% (DNA packaging and head morphogenesis modules). A dotplot analysis showed nearly a straight line over the left 25 kb of their genomes. Over the right genome half, a more variable dotplot pattern was observed. The entire lysogeny module from Sfi21 comprising 12 genes was replaced by 7 orfs in Sfi19, six showed similarity with genes from temperate pac-site S. thermophilus phages. None of the genes implicated in the establishment of the lysogenic state (integrase, superinfection immunity, repressor) or remnants of it were conserved in Sfi19, while a Cro-like repressor was detected. Downstream of the highly conserved DNA replication module 11 and 13 orfs were found in Sfi19 and φSfi21, respectively: Two orfs from Sfi21 were replaced by a different gene and a duplication of the phage origin of replication in Sfi19; a further orf was only found in Sfi21. All other orfs from this region, which included a second putative phage repressor, were closely related between both phages. Two noncoding regions of Sfi19 showed sequence similarity to pST1, a small cryptic plasmid of S. thermophilus
Influence of the Human High-Affinity IgG Receptor FcγRI (CD64) on Residual Infectivity of Neutralized Dengue Virus

AbstractWe examined dengue virus immune complex–phagocyte interaction with respect to a single Fc receptor class using a transient expression system involving the high-affinity human macrophage receptor, FcγRI. We found that New Guinea C strain dengue 2 virus formed well-defined plaques in normal and transfected COS cells and we analyzed the structural determinants of FcγRI-mediated binding and internalization of dengue 2 virus immune complexes by expressing native or truncated forms of the receptor in COS cells, alone or with its accessory γ chain signaling unit, which bears an immunoreceptor tyrosine-based activation motif (ITAM). The residual infectivity of dengue 2 virus treated with neutralizing human antiserum was strikingly higher in FcγRI-bearing COS cells than in controls. Compatible with the IgG subclass specificity of FcγRI, this difference was abrogated quantitatively by treatment of FcγRI-transfected cells with human IgG1 but not IgG2 myeloma protein. The magnitude of receptor-mediated plaque formation after cotransfection with γ chain was also significantly higher than in controls but was less than that observed with FcγRI transfection only, a difference probably explained by reduced levels of FcγRI expression in γ chain cotransfectants. Deletion of the FcγRI cytoplasmic domain had no effect on receptor-mediated immune complex infectivity. We conclude that the FcγRI extracellular domain is sufficient for internalization of infectious dengue virus immune complexes through a mechanism that does not involve classical ITAM-dependent signaling
Equine Arteritis Virus Derived from an Infectious cDNA Clone Is Attenuated and Genetically Stable in Infected Stallions

AbstractVirus derived from an infectious cDNA clone of equine arteritis virus (EAV030H) was intranasally inoculated into two stallions, neither of which subsequently developed clinical manifestations of equine viral arteritis (EVA). Virus was isolated from nasal swabs and mononuclear cells collected from both stallions ≤14 days p.i. and from the semen of one stallion only at 7 days p.i. Similarly, viral RNA was detected by RT nested-PCR in nasal swabs and mononuclear cells for ≤14 days p.i. and at 7 days p.i. in the semen of the one stallion. Both stallions seroconverted to EAV by 10 days p.i. and maintained high neutralizing antibody titers thereafter. Sequence and restriction digestion analysis demonstrated that the recombinant virus present in nasal swabs, mononuclear cells, and semen from the two stallions was identical to the infectious clone-derived virus that was used to inoculate them. Furthermore analysis of multiple clones derived by RT nested-PCR amplification from several samples indicated that the recombinant EAV030H virus was stable during replication in horses. These studies document for the first time that a recombinant virus derived from an infectious cDNA clone of a member of the order Nidovirales is replication competent in animals, and the genetic stability of the recombinant virus during in vivo replication indicates that it will be useful for the characterization of genetic determinants of virulence and persistence of EAV. The genetic conservation of the cloned recombinant virus during in vivo infection is similar to that which occurs during natural horizontal and vertical transmission of EAV in horses and contrasts with the heterogeneous virus population (quasispecies) that occurs in the semen of carrier stallions
Oligomerization of the Influenza Virus Nucleoprotein: Identification of Positive and Negative Sequence Elements

AbstractThe RNA genome of influenza virus is encapsidated by the virus nucleoprotein (NP) to form ribonucleoprotein (RNP) structures of defined morphology. These structures result from the ability of NP to oligomerise and to bind single-strand RNA. To characterise NP oligomerization, we developed a binding assay using immobilised NP fusion proteins and in vitro translated NP. This system was used to estimate a dissociation constant for NP–NP contacts of 2 × 10 −7M. Analysis of NP deletion mutants identified three sequence elements important for oligomerization. Two regions corresponding to the middle and C-terminal thirds of the polypeptide were identified as the minimal sequences capable of promoting NP–NP contacts. However, the C-terminal 23 amino-acids of NP inhibited oligomerization, as their removal increased self-association 10-fold. Single codon changes identified amino acids important for the function of these regions. Alanine substitution of R199 decreased binding affinity threefold, whereas alteration of R416 had a more drastic effect, reducing binding >10-fold. In contrast, mutation of F479 increased self-association fivefold. Mutations altering NP oligomerization affected the ability of the polypeptides to support influenza virus gene expression in an in vivo assay. Decreased oligomerization activity correlated with decreased transcriptional function. However, mutations that increased self-association also decreased transcription competence. This indicates that NP contains both positive and negative sequence elements involved in oligomerization and is consistent with the importance of NP–NP contacts for the formation of a transcriptionally active RNP
Genetic Characterization of the Pathogenic Influenza A/Goose/Guangdong/1/96 (H5N1) Virus: Similarity of Its Hemagglutinin Gene to Those of H5N1 Viruses from the 1997 Outbreaks in Hong Kong

AbstractAnalysis of the sequences of all eight RNA segments of the influenza A/Goose/Guangdong/1/96 (H5N1) virus, isolated from a sick goose during an outbreak in Guangdong Province, China, in 1996, revealed that the hemagglutinin (HA) gene of the virus was genetically similar to those of the H5N1 viruses isolated in Hong Kong in 1997. However, the remaining genes showed greater similarity to other avian influenza viruses. Notably, the neuraminidase gene did not have the 19-amino-acid deletion in the stalk region seen in the H5N1 Hong Kong viruses and the NS gene belonged to allele B, while that of the H5N1 Hong Kong viruses belonged to allele A. These data suggest that the H5N1 viruses isolated from the Hong Kong outbreaks derived their HA genes from a virus similar to the A/Goose/Guangdong/1/96 virus or shared a progenitor with this goose pathogen
Structural Analysis of Adeno-Associated Virus Transduction Circular Intermediates

AbstractRecombinant adeno-associated virus (rAAV) has recently been demonstrated to form circular intermediates following transduction in muscle tissue and cell lines. Although restriction enzyme and Southern blot analysis has revealed a consistent monomer and multimer head-to-tail conformation, detailed structural sequence analysis has been lacking due to the high secondary structure of the ITR arrays. To gain further insight into potential mechanisms by which AAV circular genomes are formed from linear single-stranded viral DNA, we have performed chemical sequencing of ITR arrays within seven circular intermediates independently isolated from primary fibroblasts and Hela cells. Results from these studies demonstrated several types of circular intermediates with mosaic ITR elements flanked by two D sequences. The most predominant form consisted of a structure similar to that of previously generated AAV double-D plasmids, with one complete ITR flanked by two D-region elements. However, intermediately deleted ITR arrays with more than one complete ITR were also seen. Based on this structural information, we have proposed a model for formation of AAV circular intermediates by recombination/ligation between ITR ends of panhandle single-stranded AAV genomes
Nucleotide Sequence and Characterization of Human Papillomavirus Type 83, a Novel Genital Papillomavirus

AbstractStudies of human papillomaviruses (HPV) are hampered by the lack of a conventional culture system, because HPV completes its life cycle only in fully differentiated human tissue. To overcome this obstacle, the athymic mouse xenograft system has been used to study the pathogenesis of a limited number of HPV types. We recently reported the propagation of a novel HPV type in the mouse xenograft system and the cloning of its genome. Consensus primer PCR had previously identified this virus as MM7, LVX82, or PAP291. Here we report the nucleotide sequence of the 8104-bp genome of this virus, now called HPV 83. HPV 83 is most closely related to HPV 61 and HPV 72, placing it in the papillomavirus genome homology group A3. Based on limited epidemiological data, the histological appearance of infected human foreskin implants, and the structure of the predicted HPV 83 E7 protein, this virus is probably of at least intermediate cancer risk. Like other papillomaviruses, HPV 83 produces an E1char̂E4, E5 transcript, but the position of the splice acceptor differs from that of other HPVs. The presence of an E5 open reading frame in the HPV 83 genome is uncertain; the most likely candidate to be the HPV 83 E5 protein has some structural similarity to the bovine papillomavirus 1 E5 oncoprotein, and is unlike most other HPV E5 proteins. HPV 83 is a relatively prevalent genital papillomavirus that has the largest genome of any characterized HPV and several other novel structural features that merit further study
Fusogenic Activity of Hepadnavirus Peptides Corresponding to Sequences Downstream of the Putative Cleavage Site

AbstractSequence homology between the amino-terminal region of the S protein of hepatitis B Virus (HBV) and known fusion peptides from retroviruses and paramyxoviruses led us to propose that this region might be equally involved in the initial infective steps of hepadnaviruses. In fact, we showed that a synthetic peptide corresponding to the N-terminus region of the S protein of HBV had membrane-interacting properties and was able to induce liposome fusion adopting an extended (β-sheet) conformation (Rodrı́guez-Crespo et al., 1996, 1995). We describe herein studies on the interaction of peptides derived from the N-terminal region of the S protein of duck (DHBV: Met-Ser-Gly-Thr-Phe-Gly-Gly-Ile-Leu-Ala-Gly-Leu-Ile-Gly-Leu-Leu) and woodchuck hepatitis B viruses (WHV: Met-Ser-Pro-Ser-Ser-Leu-Leu-Gly-Leu-Leu-Ala-Gly-Leu-Gln-Val-Val) with liposomes. These peptides were able to induce to a different extent aggregation, lipid mixing, and leakage of internal aqueous contents from both neutral and negatively charged phospholipid vesicles in a concentration-dependent and pH-independent manner. Fluorescence depolarization of 1,6-diphenyl-1,3,5-hexatriene-labeled vesicles indicated that both peptides become inserted into the hydrophobic core of the lipid bilayer. Circular dichroism studies indicated that the DHBV peptide adopts an extended conformation in the presence of lipids, whereas the WHV peptide displays a high content of α-helical conformation. Therefore, these results extend our previous findings obtained for human hepatitis B virus to other members of the hepadnavirus family and suggest that this region of the S protein is important in the initial steps of the infective cycle
Expression of a Chitinase Gene and Lysis of the Host Cell Wall during Chlorella Virus CVK2 Infection

AbstractA chitinase gene (vChti-1) encoded by the Chlorella virus CVK2 was cloned and characterized. The vChti-1 open reading frame consisted of 2508 bp corresponding to 836 amino acid residues. The predicted amino acid sequence contained two sets of a family 18 catalytic domain that is responsible for chitinase activity. Northern blot analysis revealed that the vChti-1 gene was expressed in virus-infected Chlorella cells late in infection, when a single transcript of about 2.5 kb appeared at 120 min postinfection. This result was confirmed by Western blotting with a specific anti-vChti-1 protein antibody; a protein of about 94 kDa was detected specifically beginning at 240 min postinfection and was present until cell lysis. The protein was not incorporated into viral particles but remained in the medium after cell lysis. The vChti-1 protein produced in virus-infected cells showed chitinase activity on zymogram assays
Expression of the α6 Integrin Confers Papillomavirus Binding upon Receptor-Negative B-Cells

AbstractPapillomaviruses (PV) bind to a wide range of cell lines in a specific and saturable manner. We have recently identified a candidate receptor for papillomavirus as the α6 integrin (Evander et al., J. Virol. 71, 2449–2456, 1997). We have further investigated the role the α6 integrin plays in PV binding. Here we show that the cells expressing the α6 integrin, partnered with either the β4 integrin or the β1 integrin, are equally able to bind PV HPV6b L1 virus-like particles, indicating that the beta partner does not play a major role in virus binding. In order to provide definitive evidence that the α6 integrin is required for PV binding we undertook to genetically complement the receptor-negative B-cell line DG75 by expressing the human α6A gene. The transduction of the α6 integrin gene into DG75 cells results in the cell surface expression of the α6 protein and this expression confers upon DG75 cells the ability to bind laminin, a normal ligand for α6 integrin. Furthermore, the α6 protein is partnered with the β1 integrin in DG75 cells. Finally, we show that the DG75-α6 cells were able to bind papillomavirus VLPs and this binding was inhibited by a functionally blocking anti-α6 antibody. Together these data indicate that the α6 integrin is a primary cell receptor for papillomaviruses and is both necessary and sufficient for PV binding
Transcription Map and Expression of Bovine Herpesvirus-1 Glycoprotein D in Early Region 4 of Bovine Adenovirus-3

AbstractEarly region 4 (E4) of bovine adenovirus type 3 (BAV-3) was analyzed by Northern blotting, RT–PCR analysis, cDNA sequencing, and S1 nuclease protection assays. The transcriptional map of the E4 region of BAV-3 has marked dissimilarities from those of mouse adenovirus-1, ovine adenovirus-287, and human adenovirus-2, for which the transcriptional maps have been constructed. The E4 region of BAV-3, located between 98.6 and 89.8 MU transcribes seven distinct classes of bovine adenovirus type 3 mRNA. The seven mRNA species formed by the removal of one to three introns share both the 3′ end and a short 5′ leader (25 nucleotides). The E4 mRNAs can encode at least five unique polypeptides, namely, 143R1, 69R, 143R2, 268R, and 219R. Isolation of a replication-competent recombinant “BAV404” containing 1.9-kb insertion [glycoprotein (gD) of bovine herpesvirus 1, under the control of a SV40 early promoter and poly(A)] in the region between E4 and the right ITR suggested that this region is nonessential for BAV-3 replication. Expression of gD by BAV404 recombinant virus was confirmed by immunoprecipitation with gD-specific monoclonal antibodies. Analysis of the kinetics of protein expression indicated that gD is expressed at both early and late times postinfection. These results suggest that: (a) E4 produces seven 5′–3′ coterminal mRNAs and (b) the right terminal region of BAV-3 can be used for the expression of vaccine antigens
Global Protein Synthesis Shutdown in Autographa californica Nucleopolyhedrovirus-Infected Ld652Y Cells Is Rescued by tRNA from Uninfected Cells

AbstractGlobal protein synthesis arrest occurs in Autographa californica nucleopolyhedrovirus (AcNPV)-infected Ld652Y cells at late times postinfection (p.i.). A Lymantria dispar nucleopolyhedrovirus gene, hrf-1, precludes this protein synthesis arrest. We used in vitro translation assays to characterize the translation defect. Cell-free lysates prepared from uninfected Ld652Y cells, AcNPV-infected cells harvested at early times p.i., and cells infected with vAchrf-1, a recombinant AcNPV bearing hrf-1, all supported translation. Lysates prepared from AcNPV-infected Ld652Y cells at late times p.i. did not support translation, but activity was restored by adding small RNA species from mock-, vAchrf-1- (24 or 48 h p.i.), and AcNPV- (6 h p.i.) infected cells. Small RNA species (24 and 48 h p.i.) from AcNPV-infected cells did not rescue translation. Assays of RNA species further fractionated by ion exchange chromatography demonstrated that tRNA rescued translation. Although specific defective tRNA species were not revealed by comparative two-dimensional gel analysis, analysis of 32P-labeled tRNAs showed a reduction in de novo synthesis of small RNA isolated from AcNPV-infected cells compared with mock- and vAchrf-1-infected cells. This study suggests a mechanism of translation arrest involving defective or depleted tRNA species in AcNPV-infected Ld652Y cells
Induction of Humoral and Cellular Immune Responses against the Nucleocapsid of Bovine Viral Diarrhea Virus by an Adenovirus Vector with an Inducible Promoter

AbstractA new recombinant adenovirus was constructed that expressed the nucleocapsid (C protein or p14) of the bovine viral diarrhea virus (BVDV) under the control of a tetracycline-regulatable promoter. Mice covaccinated with this recombinant adenovirus, accompanied by another recombinant adenovirus expressing the trans-activator protein, induced a strong humoral immune response to the BVDV/C protein as detected by ELISA. Splenocytes from mice immunized with the recombinant adenovirus showed a specific proliferation response to both genotypes (type 1 and 2) of BVDV. High levels of IFN-γ were detected in the supernatant of murine mononuclear cells of mice immunized by the recombinant adenovirus when stimulated in vitro by both genotypes of BVDV. These results indicate that this recombinant adenovirus is highly immunogenic and stimulates both cellular and humoral immune responses against the nucleocapsid of BVDV