pinecone/core-2020-05-10-deduplication huggingface dataset:
Identification of Genes Involved in Replication and Movement of Peanut Clump Virus

AbstractThe genome of peanut clump pecluvirus (PCV) consists of two messenger RNA components which contain, respectively, three and five open reading frames (ORFs). Inoculation of transcripts from full-length cDNA clones derived from the PCV RNAs showed that RNA-1 is able to replicate in the absence of RNA-2 in protoplasts, but both RNAs are necessary for plant infection. To investigate the role of different gene products in viral RNA replication and movement, transcripts from mutant cDNA clones were inoculated to protoplasts and toChenopodium quinoaorNicotiana benthamianaplants, and progeny RNA was detected by Northern blot analysis. The protein P15, encoded by the third ORF of RNA-1, is essential for efficient replication of the viral genome. The three proteins, P51, P14, and P17, of the triple gene block contained in RNA-2 are involved in localized movement of the viral genome, whereas the coat protein (P23) is also required for vascular movement. Insertion of the β-glucuronidase reporter gene (GUS) in place of the P23 or P39 genes (the first and the second genes of RNA-2) allows visualization of the virus infection in inoculated leaves. Although the presence of the GUS gene resulted in a lower accumulation of progeny RNA and, despite instability of the constructin planta,histochemical detection of PCV multiplication was more sensitive than Northern blot detection
The Early Baculovirus he65 Promoter: On the Mechanism of Transcriptional Activation by IE1

AbstractWe have initiated studies on the mechanism of early transcriptional activation of the early he65 promoter during infection withAutographa californicamulticapsid nuclear polyhedrosis virus. This analysis is based on a comparison of the sequences required for he65 promoter activation with those sequences that support specific protein binding. The he65 promoter is located immediately downstream of the homologous region (hr) 4a. The sequences ofhr4a are characterized by two imperfect palindromes of 24 bp. The results of transient expression assays indicate promoter activation in the presence of both the proximal palindrome and the known viraltrans-regulator IE1. The results of mobility shift assays and DNaseI footprinting analyses reveal differences in specific protein binding at and close to the proximal palindrome depending on whether the nuclear protein extracts are prepared from uninfected or infected cells. The analysis of the protein binding complex at the proximal inverted repeat with extracts from infected cells suggests the involvement of both IE1 and IE0 as oligomers. The minimal protein binding sequences include the left half-site of the 24 bp repeat with 9 additional bp of the flanking sequences. The right half-site of the repeat also directs binding although with lower affinity as confirmed by phenanthroline-copper footprinting assays. Both half-sites of the repeat are thus essential for he65 promoter activation, suggesting that IE1 acts via cooperative binding. We conclude that the proximal inverted repeat is able to interact with both IE1 and IE0 although IE1 is sufficient for activation at least in transient expression assays
Complement Can Neutralize HIV-1 Plasma Virus by a C5-Independent Mechanism

AbstractA previous study showed a portion of HIV-1 plasma virus was lysed by the addition of exogenous human AB+seronegative complement. The current study was performed to determine whether infectious plasma virus was inactivated by complement. Incubation of plasma virus with AB+-seronegative serum resulted in substantial decreases in infectious titers, demonstrating that infectious plasma virus is susceptible to complement-mediated inactivation. Although complement also induced some lysis of plasma virus samples, virus was neutralized to a significantly higher degree, suggesting neutralization did not occur solely by lysis. Additionally, C5-deficient complement substantially neutralized virus, indicating coating of virus by early complement components was an important mechanism of neutralization. A portion of some freshly isolated plasma virus samples bound to complement receptor 2 in the absence of exogenous complement, indicating that early complement components bound virusin vivo. Furthermore, plasma virus samples that had less C3 deposited on their surfacein vivohad higher infectious titers than samples with a larger fraction with surface C3. These findings suggest that complement can neutralize HIV-1 plasma virusin vivoby coating with complement proteins. This is the first study to provide evidence that coating by complement leads to functional inactivation of a virusin vivo
The DF-1 Chicken Fibroblast Cell Line: Transformation Induced by Diverse Oncogenes and Cell Death Resulting from Infection by Avian Leukosis Viruses

AbstractDF-1 is a continuous cell line of chicken embryo fibroblasts. The cells are free of endogenous sequences related to avian sarcoma and leukosis viruses and have normal fibroblastic morphology. DF-1 cells support the replication of avian retroviruses; diverse oncogenes induce foci of oncogenic transformation on monolayers of DF-1, and avian leukosis viruses of envelope subgroups B, D, and C induce cell death and form plaques. The new cell line will greatly facilitate studies on oncogenic transformation and cell killing by avian viruses
The EV-O-Derived Cell Line DF-1 Supports the Efficient Replication of Avian Leukosis-Sarcoma Viruses and Vectors

AbstractThe lack of a well-behaved permanent, adherent, nontransformed chicken cell line has made some experiments with avian leukosis–sarcoma viruses (ASLV) and vectors considerably more difficult. The EV-O-derived line, DF-1, supports the efficient replication of subgroups (A), (B), and (C) ASLV, as well as amphotrophic murine leukemia virus and an ASLV-derived vector that has itsenvgene derived from theenvgene from an amphotrophic murine leukemia virus. The cell line responds appropriately to the expression of a transforming oncogene (v-myc) to a growth suppressor gene [p21(waf1)] and can be sorted (using FACS) if infected by an ASLV vector that expresses GFP
Population Diversity in Grapevine Yellow Speckle Viroid-1 and the Relationship to Disease Expression

AbstractVitis viniferacultivars Zinfandel-1A and Mission were found to harbor different grapevine yellow speckle viroid-1 (GYSVd-1) variants and characterized to define the relationship to yellow speckle (YS) and vein-banding (VB) diseases. Products from the left terminal (T1), pathogenic (P), and a portion of the central (C) domains of Zinfandel-1A and Mission displayed distinct single-stranded conformation polymorphism (SSCP) patterns, presumably reflecting nucleotide changes in the P domain. The two selections were shown to contain homogeneous populations of type 1 and type 2 GYSVd-1 variants described in Australia. Symptoms of YS were induced only in vines containing the type 2 variant by treatment at a constant temperature of 32°C in continuous light. SSCP of Pagadebit selections from Italy revealed the nonsymptomatic variant was essentially identical to Zinfandel-1A, whereas symptomatic selections were unlike any other previously described. Nucleotide sequence confirmed that nonsymptomatic selections from Italy contained the GYSVd-1 type 1 variant. A total of 43 changes were spread throughout the T1, C, V, and T2 domains from symptomatic selections. This study establishes the Australian type 1 variant as the non-symptom-inducing form of GYSVd-1 and type 2 as the symptom-inducing variant. The distinct symptom-inducing variant from Italy is proposed as a new type 3 variant of GYSVd-1
transE1 Component Requirements for Maximal Replication of E1-Defective Recombinant Adenovirus

AbstractStrategies that enable E1-defective recombinant adenoviruses to selectively undergo replication in neoplastic tissue may be useful for future investigations or therapies of malignancies. A growing body of evidence suggests that some molecular alterations commonly associated with malignancies, such as p53 mutations, can modify the specific E1 requirements for replication of human serotype adenoviruses. In the studies reported here, a panel of human non-small cell lung cancer cell lines with previously defined p53 status were characterized for basal interleukin-6 (IL-6) andbcl-2content because previous studies have indicated both proteins can functionally substitute for the replication requirements provided by native E1 viral proteins. Cell lines were infected with E1-defective adenovirus 5 and simultaneously transfected with different combinations of E1 plasmids, or abcl-2expression plasmid, and adenovirus present in the cells was quantified 6 days later. These assays demonstrated that E1A with both 19- and 55-kDa E1B-encoding plasmids were required for maximal adenoviral replication, independent of the varying p53/IL-6/basalbcl-2phenotypes of the host cell lines. E1A was required for maximal replication enablement, independent of the basal IL-6 content of these cell lines, and exogenous IL-6 also did not obviate the E1A requirement. Interestingly, thebcl-2expression plasmid did not consistently substitute for the 19-kDa expression plasmid in the context of this replication complementation assay. These results suggest that (1) basal levels of IL-6 greater than that present in these cell lines are necessary for functional replacement of the E1A replication function and (2)bcl-2does not predictably substitute for the 19-kDa E1B replication function in the context oftranscomplementation
A Human Papillomavirus Related to Human Papillomavirus MM7/LVX82 Produces Distinct Histological Abnormalities in Human Foreskin Implants Grown as Athymic Mouse Xenografts

AbstractStudies of human papillomaviruses (HPVs) 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 HPV 11 and to develop neutralizing assays for vaccine development. Recently, HPV 40 has been produced in this system, and HPV 16 has been produced using mice with severe combined immune deficiency. To identify and characterize additional genital HPV types for similar studies, condylomata acuminata lesions containing a high copy number of HPV and detectable L1 major capsid protein were used to prepare infectious virus stocks. Human foreskin fragments were infected with the virus preparations and implanted under the renal capsules of athymic mice. After 5 months of growth, implant tissue was removed and processed for studies to detect HPV infection. Evidence of HPV infection was noted in some of the implants, but in contrast to HPV 11-infected epithelium, the implants derived from the new virus preparations contained a lesser degree of acanthosis, less developed koilocytosis, and a reduced number of preserved nuclei in the hyperkeratotic material within the cyst lining. The L1 consensus region was amplified by polymerase chain reaction from implant DNA and sequenced. Alignment of the amplified sequences with those in the HPV sequence database showed that the 452-bp amplimer was closely related but not identical to HPV LVX82 and HPV MM7 (also called Pap 291). The entire 7.9-kb genome was amplified by polymerase chain reaction and cloned. The presence of virions of the new isolate (named HPV IU) in the implants was verified by immunohistochemical detection of L1 major capsid protein and by demonstration of virion particles by electron microscopy. A second extract was made from one of the new implants and used to successfully propagate HPV IU. These experiments demonstrate that experimental infection of human epithelium with the new isolate, HPV IU, is associated with histological abnormalities that differ in potentially important ways from the changes observed in experimental HPV 11 infection
Analysis of Intracellular Trafficking and Interactions of Cytoplasmic HIV-1 Rev Mutants in Living Cells

AbstractThe HIV-1 Rev protein is an essential nuclear regulatory viral protein. Rev mutants that are able to block wild-type (WT) Rev activityin transhave been reported and used in antiviral approaches. Not only nuclear but also cytoplasmic Rev mutants were described and suspected to be transdominant by retaining WT Rev in the cytoplasm. To investigate their potential for cytoplasmic retention, we studied the localization, trafficking, and interactions of cytoplasmic Rev mutants containing mutations in the N-terminal multifunctional domain. Using a novel dual-color autofluorescent protein-tagging system, we found that coexpression of the nucleolar blue-tagged WT Rev protein together with green-labeled cytoplasmic Rev mutants did not result in the retention of WT Rev in the cytoplasm but, on the contrary, in colocalization of the mutants to the nucleolus. A combination of mutations abolished the interaction with WT Rev, defining two domains important for Rev protein interaction. The identified domains were also essential for specific Rev responsive element (RRE) RNA binding and nuclear retention. Inactivation of the nuclear export signal shifted the steady-state distribution of the mutants from the cytoplasm to the nucleus, indicating their capability for nucleo-cytoplasmic shuttling. The cytoplasmic mutants were not transdominant compared to the nuclear mutant RevM10BL. These results emphasize that efficient oligomerization with WT Rev combined with RRE-specific RNA binding are prerequisites for effective transdominance
Virion Incorporation of Human Immunodeficiency Virus Type-1 Vif Is Determined by Intracellular Expression Level and May Not Be Necessary for Function

AbstractThe viral infectivity factor (Vif) of human immunodeficiency virus type-1 (HIV-1) functions at a late stage of the viral life cycle to confer infectivity on progeny virions. Although Vif is present in HIV-1 particles, both the relevance of incorporation for function and the mechanism that underlies incorporation remain unresolved. Using matched T cell systems that express high or low levels of Vif, we demonstrate that the extent of Vif incorporation into virions varies in relation to cellular expression levels. Because viral infectivity is not affected by these variations, we suggest that the packaging of Vif is neither specific nor necessary for function
Molecular Mechanism of Tumorigenesis in Mice Transgenic for the Human T Cell Leukemia VirusTaxGene

AbstractThe infection by human T lymphotropic virus type I is associated with adult T cell leukemia and several inflammatory degenerative disorders, including tropical spastic paraparesis. To investigate the role of the Tax protein in the development of diseases linked to human T lymphotropic virus type I infection, we generated two lines of transgenic mice carrying the tax gene under the control of the viral promoter. The expression of the transgene was low in these mice and was restricted to the central nervous system and testis. Mice from both lines developed various types of tumors, including fibrosarcomas and adenocarcinomas. Tax was expressed at a high level in fibrosarcomas and in cell lines derived from these tumors. In tumor-derived cells, the expression of Tax led to an increased degradation of IκBα and IκBβ and caused stable nuclear translocation of nuclear factor-κB. This translocation was essential for cell proliferation, as shown by expressing a nondegradable form of IκBβ in these cells. Therefore, Tax-induced cell transformation in mice correlates with the degradation of IκBα and IκBβ and with the constitutive activation of NF-κB
A Point Mutation in the Human Cytomegalovirus DNA Polymerase Gene Selectedin Vitroby Cidofovir Confers a Slow Replication Phenotype in Cell Culture

AbstractIn cell culture, cidofovir (CDV) was used to select a human cytomegalovirus (HCMV) strain with decreased drug susceptibility. The genotypic characterization of this virus revealed a single base substitution resulting in a K513N amino acid alteration in the viral DNA polymerase (UL54). Performed in parallel, the selection of HCMV for replication in the presence of ganciclovir (GCV) selected an M460V substitution in the phosphotransferase (UL97), as well as a K513N/V812L double substitution in DNA polymerase. Neither of the two DNA polymerase mutations has been previously identified in HCMV drug-resistant strains. To precisely elucidate their role in drug resistance, corresponding recombinant mutant viruses were generated by recombination of nine overlapping viral DNA fragments. The K513N recombinant virus showed 13- and 6.5-fold decreased susceptibility to CDV and GCVin vitro, respectively, compared with the wild-type recombinant virus. Mutation V812L was associated with a moderate (2–3-fold) decrease in susceptibility to CDV, GCV, foscarnet, and adefovir. A multiplicative interaction of the K513N and V812L mutations with regard to the profile and level of drug resistance was demonstrated in recombinant virus expressing both mutations.In vitroreplication kinetic experiments revealed that the K513N mutation significantly decreased HCMV replication capacity. Consistent with this finding, the K513N mutant DNA polymerase exhibited reduced specific activity in comparison with the wild-type enzyme and was severely impaired in its 3′-5′ exonuclease function. Unexpectedly, the K513N mutant enzyme showed no decrease in susceptibility to CDV-diphosphate or GCV-triphosphate. However, the K513N mutation decreased the susceptibility to CDV and GCV of theoriLyt plasmid replication in the transient transfection/infection assay, suggesting that the DNA replication of the K513N mutant virus is less sensitive to the corresponding inhibitors
Chronology of Genetic Changes in thevpu, env,andnefGenes of Chimeric Simian–Human Immunodeficiency Virus (Strain HXB2) during Acquisition of Virulence for Pig-Tailed Macaques

AbstractRecently, we developed a highly pathogenic variant of simian–human immunodeficiency virus, SHIV-4 (containing thetat, rev, vpu,andenvof the HXB2 strain of HIV-1 in a genetic background of SIVmac239), through a series of four bone marrow-bone marrow passages—first in rhesus monkeys and then in pig-tailed macaques [Joaget al. (1996) J. Virol.70, 3189–3197]. Inoculation of pig-tailed macaques with this pathogenic virus (SHIVKU-1) causes subtotal elimination of CD4+T cells and fatal opportunistic infections, usually within 6 months. Genetic characterization of SHIVKU-1showed that it has a functionalvpugene (the first codon is ATG vs ACG for thevpuof SHIV-4) and several amino acid substitutions in Env andnef[Stephenset al.(1997)Virology231, 313–321]. Two pig-tailed macaques, PPc and PQc, were the first to develop a severe loss of CD4+T cells and the acquired immune deficiency syndrome and were euthanized at 26 and 105 weeks, respectively. In this report, we analyzed the changes that occurred in thevpu, nef,andenv(gp120) genes of the virus used to inoculate macaques PPc and PQc and established the chronology of changes that occurred in these viral genes as these two animals lost their CD4+T cells and progressed to develop acquired immune deficiency syndrome. Compared with SHIV-4, the virus used to inoculate macaques PPc and PQc had 0, 3, and 0 consensus amino acid changes in the Vpu, gp120, and Nef, respectively. An analysis of the viral sequences amplified from peripheral blood mononuclear cells samples taken at various times after inoculation of PPc revealed that thevpuhad not reverted to an open reading frame (closedvpu,ACG) at 4 weeks after inoculation, but by 16 weeksvpuhad reverted to an open reading frame (openvpu,ATG). Macaque PQc, which had a longer course of disease, had a closedvpuat 4 and 16 weeks, but by 28 weeks, both closed and openvpuwere detected. From 39 to 105 weeks, only an openvpuwas detected. In both macaques, the reversion to an openvpucorrelated well with the second phase (major) of CD4+T cell loss. An analysis of thenefandenvsequences isolated from the same times after inoculation revealed an association between the reversion ofvputo an open reading frame and the accumulation of increased numbers of consensus changes in these two viral proteins. These data suggest that the concomitant reversion ofvputo an open reading frame along with increased substitutions in Nef and gp120 were important genetic changes in the viral genome that were responsible for the increased and highly efficient rate of replication of the virus in CD4+T cells and macrophages, which in turn led to elimination of the CD4+T cells and profound loss of immunocompetence in the infected animals
Role of CD46 in Measles Virus Infection in CD46 Transgenic Mice

AbstractThe susceptibility of CD46 (human membrane cofactor protein) transgenic mice to measles virus (MV) infection was investigated. Cell cultures (lung and kidney) established from transgenic and control mice showed that although both could be infected only those from the CD46+ mice gave fusion. A complete round of replication with the release of infectious virus was detected exclusively in the transgenic cell cultures whose permissiveness to MV was markedly less than that of Vero cells. The ability of MV to replicatein vivoin mice was studied using both vaccine and laboratory-adapted wild-type strains of virus. After intraperitoneal and intranasal inoculations of transgenic mice, virus replication could not be detected. In contrast intracerebral inoculation induced infection in both transgenic and nontransgenic mice. Our results fromin vitroinfection studies support the hypothesis that CD46 is a major host cell factor involved in the MV-induced fusion process and MV entry. The studies further indicate that MV tropism is not governed solely by the expression of the CD46 gene and that the high efficiency of the replicative cycles characteristic of fully permissive host cells requires additional factors, which are lacking in both transgenic and nontransgenic mice
The Attachment Protein of Hendra Virus Has High Structural Similarity but Limited Primary Sequence Homology Compared with Viruses in the GenusParamyxovirus

AbstractThe complete nucleotide sequence of the attachment protein gene of Hendra virus, a new member of the subfamilyParamyxovirinae, has been determined from cDNA clones derived from viral genomic RNA. The deduced mRNA is 2565 nucleotides long with one open reading frame encoding a protein of 604 amino acids, which is similar in size to the attachment protein of the members of the subfamily. However, the mRNA transcript is >600 nucleotides longer than others in the subfamily due to the presence of long untranslated regions at both the 5′ and 3′ ends. The protein is designated G because it lacks both hemagglutination and neuraminidase activities. It contains a hydrophobic transmembrane domain close to the N terminus, eight potential N-linked glycosylation sites, and 18 cysteine residues. Although the HeV G protein had low sequence homology withParamyxovirinaemembers, the predicted folding pattern of its extracellular globular head was very similar to that of members of the genusParamyxovirus,with the location of seven potential pairs of sulfide bonds absolutely conserved. On the other hand, among the seven residues known to be critical for neuraminidase activity, only one was conserved in the Hendra virus G protein compared with at least six in HN proteins of paramyxoviruses and rubulaviruses and four in H proteins of morbilliviruses. The biological significance of this finding is discussed