pinecone/core-2020-05-10-deduplication huggingface dataset:
HIV-1 Infection Induces Differentiation of Immature Neural Cells through Autocrine Tumor Necrosis Factor and Nitric Oxide Production

AbstractImmature neural cell lines could be productively infected by HIV-1. Interestingly, this infection was associated with a differentiation to a mature neuronal phenotype, characterized by the expression of mature neurofilaments and cell adhesion molecules, intercellular cell adhesion molecule-1, and vascular cell adhesion molecule-1. Infection also induced TNF-α and IL-1β mRNA expression, as well as the synthesis of inducible nitric oxide synthase by neuroblastoma cells. Exogenous addition of TNF-α, but not of IL-1β or many other cytokines, including nerve growth factor, mimicked those effects induced by infection. Moreover, blocking endogenous TNF-α or NO production in cultures of infected cells with a neutralizing anti-TNF-α antibody or inducible nitric oxide synthase inhibitors prevented the expression of the mature cell phenotype as well as expression of intercellular cell adhesion molecule-1 and vascular cell adhesion molecule-1. Addition of NO generators and TNF-α activated NF-κB- and intercellular cell adhesion molecule-1-dependent promoter transcription, whereas inducible nitric oxide synthase inhibitors prevented the transcriptional activation of intercellular cell adhesion molecule-1 promoter that was induced by TNF-α. Those results suggest that HIV can infect immature neural cells and this infection induces their neural development via a TNF-α- and NO-mediated mechanism
Structure of the Human Adenovirus Serotype 2 Fiber Head Domain at 1.5 Å Resolution

AbstractAdenovirus binds to its receptor via the head domain of its fiber protein. We have crystallized the adenovirus serotype 2 (subgroup C) receptor binding domain and solved the structure at 1.5 Å resolution by the molecular replacement technique using the known adenovirus type 5 head structure. Included in the high-resolution model are 306 water molecules, five alternative side chain conformations, and individual anisotropic temperature factors for each atom. The overall structure of the serotype 2 head is very similar to its serotype 5 homologue, apart from differences in some of the flexible loops. All but subgroup B adenoviruses are believed to use the recently identified protein CAR (Coxsackievirus and adenovirus receptor) as receptor. By comparison of the two structures and sequence alignment of CAR binding and non-CAR binding serotype fiber heads, we discuss possible receptor binding sites and propose a receptor binding site in a crevice between two monomers on the side of the trimer. The structural basis of the extraordinary stability of the fiber head trimer is also discussed
Self-Inactivating Lentiviral Vectors with U3 and U5 Modifications

AbstractLentiviral vectors have gained much attention in recent years mainly because they integrate into nondividing host-cell genomes. For clinical applications, a safe and efficient lentiviral vector system is required. Previously, we have established a human immunodeficiency virus type 1 (HIV-1)-derived three-plasmid lentiviral vector system for viral vector production which includes a packaging vector pHP, a transducing vector pTV, and an envelope-encoding plasmid pHEF-VSVG. Cotransfection of these three plasmids into TE671 human rhabdomyosarcoma cells routinely yields 105–106 infectious units per milliliter in 24 h. Here we have extensively modified long terminal repeats (LTRs) of pTV to generate a safer lentiviral vector system. The 5′ U3 was replaced with a truncated cytomegalovirus (CMV) immediate early (IE) enhancer/TATA promoter and the 3′ U3 (except for the integration attachment site) was also deleted. These modifications resulted in a vector with 80% wild-type vector efficiency. Further deletion of 3′ U5 impaired vector function; however, this problem was solved by replacing the 3′ U5 with bovine growth hormone polyadenylation (bGHpA) sequence. The pTV vector containing all these modifications including the 5′ promoter substitution, the 3′ U3 deletion, and the substitution of 3′ U5 with bGHpA exhibited a self-inactivating (SIN) phenotype after transduction, transduced both dividing and nondividing cells at similar efficiencies, and produced vector titers twice as high as that of the wild-type construct. Thus, both safety and efficacy of the HP/TV vector have been improved by these LTR modifications. Further deletion of 5′ U5 impaired vector efficiency, suggesting that the 5′ U5 has critical roles in vector function
Additive Effect of Sp1 and Sp3 in Regulation of the ED-L1E Promoter of the EBV LMP 1 Gene in Human Epithelial Cells

AbstractThe ED-L1E promoter of the LMP 1 gene is a GC box-containing promoter. To test if Sp1/Sp3 are important for modulating ED-L1E promoter activity through the GC box, site-specific mutation and deletion constructs carrying a reporter gene were transfected into NPCTW076 and C33A cells. Results showed that deletion or mutation of the GC box abolished ED-L1E activity. Association of Sp1/Sp3 with the GC box was confirmed by electrophoretic mobility shift and supershift assays using Sp1- and Sp3-specific antibodies. Transfection of Sp1- and Sp3-expressing vectors into NPCTW076 and Sp-deficient Drosophila SL2 cells activated ED-L1E in a dose-dependent fashion and showed an additive effect. Data suggest that both factors may function as transcriptional activators and regulate the ED-L1E promoter in human epithelial cells
Differential Regulation of CC Chemokine Gene Expression in Human Immunodeficiency Virus-Infected Myeloid Cells

AbstractThe importance of chemokine expression on HIV infection has been emphasized by the discovery that infection of CD4+ T cells by M-tropic strains of HIV-1 is antagonized by the chemokines RANTES, MIP-1α, and MIP-1β, which are natural ligands of CCR5, a major coreceptor for macrophagetropic (M-tropic) isolates of HIV-1. Similarly, the CCR2b ligands MCP-1 and MCP-3 inhibit productive infection of PBMCs by both CCR5- and CXCR4-dependent strains of HIV-1, suggesting that expression of the MCP-1 chemokine may affect HIV infection via signaling through the CCR2 receptor and subsequent desensitization of the CCR5 and/or CXCR4 signaling pathway. Given the major role played by chemokine receptors in HIV-1 fusion/entry and the regulatory effects of chemokines on HIV-1 infection, we examined the pattern of chemokine gene expression in HIV-1-infected myeloid cells and in primary monocyte/macrophages. Chronic HIV-1 infection of U937 monocytic cells increased the expression of RANTES, MIP-1α, MIP-1β, and IL-8 chemokine genes, but strongly inhibited PMA/PHA- and TNFα-induced MCP-1 gene transcription. HIV-1-mediated inhibition of MCP-1 transcription and secretion was further confirmed in de novo HIV-1-infected U937 cells and correlated with a delay in HIV- and signal-induced NF-κB binding to the MCP-1 promoter. The inhibition of MCP-1 gene expression may provide a mechanism by which HIV-1 escapes the early influence of chemokine expression in monocytic cells
Individuals from North America, Australasia, and Africa Are Infected with Four Different Genotypes of Human Herpesvirus 8

AbstractTo study human herpesvirus 8 (HHV-8) transmission between individuals and in populations, we developed a system for genetic fingerprinting of HHV-8 strains based on variation in the HHV-8 K1, glycoprotein B (gB), and glycoprotein H (gH) genes. Using this system, we sequenced nearly the entire K1 gene (840 bp); two segments of the gB gene (open reading frame 8), totaling 813 bp; and a 702-bp segment of the gH gene (open reading frame 22) from blood and tissue samples obtained from 40 human immunodeficiency virus-infected and noninfected individuals, including those with Kaposi's sarcoma, primary effusion lymphoma, or Castleman's disease. The specimen collection was assembled from individuals living in diverse geographical locations, including the United States, Australia, New Zealand, Uganda, and Zambia. As reported by others, K1 was the most variable gene, with up to 16% variation at the nucleotide sequence level and up to 32% variation at the amino acid sequence level. Despite this extensive sequence variation, the K1 amino acid sequence contained 14 conserved cysteine sites, suggesting a conserved tertiary structure. gB and gH sequences were highly conserved, in most cases differing by <0.6% in pairwise comparisons. K1 was the most useful gene for strain discrimination, but the other genes enabled the discrimination of strains with identical K1 sequences. Individuals from diverse geographic locations were infected with four different HHV-8 genotypes; strains did not strictly segregate by continent of origin. The majority of HHV-8 strains from the United States and Europe were relatively closely related, whereas some strains identified from Uganda and Australia were phylogenetically distant. Genotype I strains were the most common and were found on three continents. Identical sequences were found in specimens obtained from different body sites and at different times from the same individual
Interactions of Epstein–Barr Virus Origins of Replication with Nuclear Matrix in the Latent and in the Lytic Phases of Viral Infection

AbstractEukaryotic DNA is organized into domains or loops generated by the attachment of chromatin fibers to the nuclear matrix via specific regions called scaffold or matrix attachment regions. The role of these regions in DNA replication is currently under investigation since they have been found in close association with origins of replication. Also, viral DNA sequences, containing the origins of replication, have been found attached to the nuclear matrix. To investigate the functional role of this binding we have studied, in Raji cells, the interaction between Epstein–Barr virus (EBV) origins of replication and the nuclear matrix in relation to the viral cycle of infection. We report here that both the latent (ori P) and the lytic (ori Lyt) EBV origins of replication are attached to the nuclear matrix, the first during the latent cycle of infection and the second after induction of the lytic cycle. These findings suggest that the binding of the origins of replication with the nuclear matrix modulates viral replication and expression in the two different phases of infection
Signature Amino Acid Changes in Latent Membrane Protein 1 Distinguish Epstein–Barr Virus Strains

AbstractSequence variations in the Epstein–Barr virus (EBV) latent membrane protein 1 gene have been described in numerous EBV-associated tumors with some of these variations, most notably a 30-base pair deletion in the cytoplasmic carboxyl-terminal domain, suggested as associated with an increase in tumorigenicity. In this study, EBV DNA sequence was determined from 92 tissue specimens or cell lines, including nasopharyngeal carcinoma, oral hairy leukoplakia, post-transplant lymphoma, post-transplant without pathology, mononucleosis, Burkitt's lymphoma, parotid tumor, and normal from distinct geographical regions. The amino- and carboxyl-terminal sequences and, in some cases, the full-length sequences of latent membrane protein 1 were determined. Characteristic sequence patterns distinguished strains, with the carboxyl-terminal sequence being the most informative in distinguishing among the strains. Phylogenetic relationships between strains were determined, as were signature amino acid changes that discriminate between them. A correlation between strain and disease or strain and geographic location was not detected. The sequence variation and signature sequences identified at least seven distinct strains, as well as hybrid strains that apparently result from recombination
Assembly of Nucleocapsids with Cytosolic and Membrane-Derived Matrix Proteins of Vesicular Stomatitis Virus

AbstractDuring budding of vesicular stomatitis virus (VSV), the viral matrix (M) protein binds the viral nucleocapsid to the host plasma membrane and condenses the nucleocapsid into the tightly coiled nucleocapsid–M protein (NCM) complex observed in virions. In infected cells, the viral M protein exists mostly as a soluble molecule in the cytoplasm, and a small amount is bound to the plasma membrane. Despite the high concentrations of M protein and intracellular nucleocapsids in the cytoplasm, they are not associated with each other except at the sites of budding. The experiments presented here address the question of why M protein and nucleocapsids associate with each other only at the plasma membrane but not in the cytoplasm of infected cells. An assay for exchange of soluble M protein into NCM complexes in vitro was used to show that both cytosolic and membrane-derived M proteins bound to virion NCM complexes with affinities similar to that observed for virion M protein, indicating that both cytosolic and membrane-derived M proteins are competent for virus assembly. However, neither cytosolic nor membrane-derived M protein bound to intracellular nucleocapsids with the same high affinity observed for virion NCM complexes. Cytosolic M protein was able to bind intracellular nucleocapsids, but with an affinity approximately eightfold less than that observed in virion NCM complexes. Membrane-derived M protein exhibited little or no binding activity for intracellular nucleocapsids. These data indicate that intracellular nucleocapsids, and not intracellular M proteins, need to undergo an assembly-initiating event in order to assemble into an NCM complex. Since neither membrane-derived nor cytosolic M protein could initiate high-affinity binding to intracellular nucleocapsids, the results suggest that another viral or host factor is required for assembly of the NCM complex observed in virions
Secretion of Rubella Virions and Virus-like Particles in Cultured Epithelial Cells

AbstractRubella virus (RV) is an enveloped RNA virus that causes systemic infections in humans. More importantly, first trimester in utero infection leads to a collection of devastating birth defects known as congenital rubella syndrome. Epithelial cells are the first line of defense against viruses and consequently, the polarity of virus secretion is an important factor affecting viral spread. As a first step toward understanding how RV interacts with epithelial cells, we have examined the release of RV-like particles and virions from polarized cells in culture. RV structural proteins were targeted to the Golgi complex and virus particle formation occurred on intracellular membranes in three different polarized epithelial cells. Polarized cells could be infected from the apical and basal membranes, indicating that receptors are not confined to one surface. The secretion of virus-like particles and infectious virions varied according to cell type. In two of the three polarized cell lines examined, virus was released primarily from the apical surface, but significant quantities were also secreted from the basolateral membrane. Release of virus from the apical surface may facilitate virus spread from person to person, whereas basolateral secretion could be important for establishing a systemic infection and/or crossing the placenta prior to fetal infection
Molecular Cloning and Cell-Specific Growth Characterization of Polymorphic Variants of Type D Serogroup 2 Simian Retroviruses

AbstractSimian retroviruses (SRVs), the etiological agent of a spontaneous Simian acquired immunodeficiency syndrome, endemically infects large percentages of Asian macaques housed in biomedical research colonies and severely compromises the effective use of these species as a viable research animal. We recently described the molecular cloning of a serogroup 2 SRV, D2/RHE/OR, which causes mild immunosuppression in rhesus macaques. A restriction site variant, D2/RHE/OR/V1, has also been recovered from severely ill animals endemically infected with D2/RHE/OR. We now report the complete nucleotide sequences of D2/RHE/OR and D2/RHE/OR/V1. Both infectious molecular clones retain the genetic structure typical of type D SRVs (5′ LTR-gag-prt-pol-env-3′LTR) and encode identically sized 8105-bp proviruses. D2/RHE/OR and D2/RHE/OR/V1 are 99.3% similar at the amino acid level, exhibiting only 17 residue differences, of which 10 are located in the envelope glycoproteins. The molecular clones and reciprocal chimeric viruses were used to assess the contribution of different genetic domains to virus infectivity in a T cell infection assay. These experiments indicate that D2/RHE/OR has a reduced ability to infect specific T cell lines, especially Hut-78 and MT-4 cells, and that the envelope gene is not the sole determinant of in vitro tropism
Prediction of Three-Dimensional Structure and Mapping of Conformational Epitopes of Envelope Glycoprotein of Japanese Encephalitis Virus

AbstractJapanese encephalitis virus (JEV), a mosquito-borne flavivirus, is an important human pathogen. The envelope glycoprotein (Egp), a major structural antigen, is responsible for viral haemagglutination and eliciting neutralising antibodies. The three-dimensional structure of the Egp of JEV was predicted using the knowledge-based homology modeling approach and X-ray structure data of the Egp of tick-borne encephalitis virus as a template (Rey et al., 1995). In the initial stages of optimisation, a distance-dependent dielectric constant of 4rij was used to simulate the solvent effect. The predicted structure was refined by solvating the protein in a 10-Å layer of water by explicitly considering 4867 water molecules. Four independent structure evaluation methods report this structure to be acceptable stereochemically and geometrically. The Egp of JEV has an extended structure with seven β-sheets, two α-helices, and three domains. The water-solvated structure was used to delineate conformational and sequential epitopes. These results document the importance of tertiary structure in understanding the antigenic properties of flaviviruses in general and JEV in particular. The conformational epitope prediction method could be used to identify conformational epitopes on any protein antigen with known three-dimensional structure. This is one of the largest proteins whose three-dimensional structure has been predicted using an homology modeling approach and water as a solvent
Domains of Glycoprotein H of Herpes Simplex Virus Type 1 Involved in Complex Formation with Glycoprotein L

AbstractThe complex formation between glycoproteins H (gH) and L (gL) of herpes simplex virus type 1 (HSV-1) was studied by using five recombinant baculoviruses expressing open reading frames that contain deletions in the coding region of the extracellular domain of gH. In addition, the gH-deletion mutants contained a C-terminal tag. Complex formation of gL and the gH-deletion mutants was studied by immunoprecipitations with anti-tag monoclonal antibody (MAb) A16 and with the gH-specific MAbs 37S, 46S, and 52S. All gH-deletion mutants were complexed to gL when analyzed by MAb A16. MAb 37S precipitated complexes between gL and the two gH-deletion mutants that contain the epitope of this MAb. When the gH conformation-dependent MAbs 46S and 52S were used, gL was coprecipitated together with the gH-deletion mutant lacking amino acids 31–299, but gL was not coprecipitated with the gH-deletion mutant lacking amino acids 31–473. The data from the precipitation studies do allow at least two interpretations. There is either one site for gL binding on gH (residue 300–473) or gL contacts multiple regions of gH. We were unable to demonstrate gL-dependent cell surface expression of either of the gH-deletion mutants. This suggests that the coassociation of gH with gL is necessary but not sufficient for transport of gH to the cell surface
LAT Expression during an Acute HSV Infection in the Mouse

AbstractPrevious studies using cell culture systems to evaluate LAT expression demonstrated that the LAT promoter expresses at much higher levels in neuroblastoma cell lines than fibroblast lines. The high level of LAT expression in neuronal-derived cell lines correlates with the high level of LAT accumulation observed in sensory ganglia neurons during a latent infection. We have found that using LAT promoters to express reporter genes from recombinant viruses in vivo produces high levels of LAT promoter activity in the epithelium of the mouse foot. An analysis of LAT promoter activity during an acute infection in the mouse clearly demonstrates that in contrast to studies performed with selected cell lines, the LAT promoter expresses similar levels of reporter gene product in peripheral cells and in neurons. In addition, the amount of reporter gene product is higher when the LAT promoter is located within the RL as compared to the UL region, and when expression is adjusted for copy number of the reporter construct, expression is roughly the same. These results suggest the activity of the LAT promoter varies greatly according to cell type and that high levels of expression is not limited solely to neurons, especially in the in vivo setting
Natural Variation of Equine Infectious Anemia Virus Gag Protein Cytotoxic T Lymphocyte Epitopes

AbstractTwo defined cytotoxic T lymphocyte (CTL) epitopes from equine infectious anemia virus (EIAV)-infected horses, equine leukocyte alloantigen (ELA)-A5.1-restricted epitope 18a, and ELA-A9-restricted epitope 28b-1 were evaluated for conservation among three wild-type EIAV strains. Epitope 18a variation occurred in all three wild-type EIAV strains, while epitope 28b-1 varied in one strain. Further, 12% amino acid changes occurred in the Gag proteins of a recently isolated wild-type strain, documenting a much greater Gag protein variation than previously reported. Evaluation of epitope 18a among two virus isolates from sequential disease episodes in a single horse, H513 (ELA-A5.1/A8), demonstrated that no variation that affected CTL recognition occurred. H513 PBMC had CTLm to epitope 18a before the occurrence of disease episodes caused by viruses expressing epitope 18a; however, the frequencies were low (5–15/106 PBMC). Later in infection there was an absence of disease episodes associated with an increase in CTLm frequency to EIAVWSU5-infected targets, but not epitope 18a-pulsed targets. Therefore, if CTLm to EIAV epitopes were involved in maintaining the carrier state in H513, they recognized epitopes other than 18a
Cellular Uptake and Nuclear Delivery of Recombinant Adenovirus Penton Base

AbstractAn Ad2 capsid component, the penton base, expressed as recombinant protein, was found to be capable of affecting the entire entry pathway of adenovirion in HeLa cells, i.e., cell attachment, endocytosis, vesicular escape, intracytoplasmic movement, and translocation through the nuclear pore complex. Data with pentamerization-defective mutants suggested that none of these successive steps depended upon penton base pentamer status, indicating that the peptide domains responsible for these functions were carried by the monomer. Observations performed with wild-type (WT) and an integrin-binding-site double-mutant (K288E340) suggested that the penton base could enter the cell via an alternative, RGD- and LDV-independent, pathway. Of three mutants that were found to be defective in nuclear addressing in insect cells, only one, W165H, was also altered in nuclear transport in HeLa cells. The other two, W119H and RRR547EQQ, showed a WT pattern of nuclear localization in HeLa cells, suggesting that the region including tryptophan-119 and the basic signal at position 547 did not act as a nuclear localization signal in the human cell context. The integrity of cellular structures and the cytoskeleton seemed to be required for the vectorial movement and nuclear import of WT penton base, as suggested by experiments using permeabilized HeLa cells, isolated nuclear membranes, and cytoskeleton-targeted drugs