pinecone/core-2020-05-10-deduplication huggingface dataset:
Sequence and Organization of the Mamestra configurata Nucleopolyhedrovirus Genome

AbstractThe nucleotide sequence of the genome of the nucleopolyhedrovirus (NPV) from Mamestra configurata (MacoNPV, isolate 90/2), a group II NPV, was determined and analyzed. The MacoNPV DNA genome consists of 155,060 bp and has an overall G+C content of 41.7%. Computer-assisted analysis predicted 169 open reading frames (ORFs) of 150 nucleotides or greater that showed minimal overlap. BLAST searches and comparisons with completely sequenced baculoviruses indicated that there were 66 ORFs conserved among the nine baculoviruses compared and an additional 17 ORFs were conserved among the NPVs. The gene content and gene arrangement in MacoNPV were most similar to those of SeMNPV, including two putative odv-e66 and p26 gene homologues. However, in contrast to SeMNPV, 8 ORFs with homology to baculovirus repeat ORFs (bro) and single copies of enhancin and conotoxin-like protein ORFs were found in MacoNPV. The MacoNPV genome contained four homologous regions, each with 10 to 17 repeated sequences. Each repeat was 60 to 86 nucleotides in length and contained an approximately 43-bp-long imperfect palindrome. There were 13 ORFs unique to MacoNPV, ranging from a small ORF of 196 bp to larger ORFs of up to 1047 bp, and many of these contained typical early and late baculovirus consensus promoters
Targeting Retroviral Vector Infection to Cells That Express Heregulin Receptors Using a TVA–Heregulin Bridge Protein

AbstractPreviously we have shown that it is possible to target retroviral vectors to cells using avian sarcoma and leukosis virus (ASLV) receptor–ligand and receptor–single-chain antibody bridge proteins (now designated as GATEs for guided adaptors for targeted entry). In this report we were interested in determining whether this approach can be used to deliver retroviral vectors specifically to cells that express heregulin receptors. Heregulin receptors are attractive targets for retroviral vector-based gene delivery protocols since they are often overexpressed on the surfaces of cancer cells. To explore this possibility, the TVA–herβ1 protein was generated, consisting of the extracellular domain of the TVA receptor for ASLV-A fused to the EGF-like region of heregulin β1. TVA–herβ1 bound specifically to cells that express heregulin receptors, rendering them susceptible to efficient and specific infection by subgroup A ASLV vectors. In addition, these activities of TVA–herβ1 were abrogated specifically in the presence of another bridge protein that contained the same ligand domain. These data confirm that the GATE protein TVA–herβ1 mediates targeted retroviral infection via cell surface heregulin receptors
Identification of a Minimal HIV-1 Gag Domain Sufficient for Self-Association

AbstractGag polyprotein precursors play an essential role in the assembly of the HIV particle by polymerizing into a spherical shell at the plasma membrane. In order to define the domains within Gag responsible for this homotypic interaction, we have coupled the technology of the yeast two-hybrid system with the technology of a gene-based, semirandom library. By this method, we have identified a minimal region of Gag capable of efficient self-interaction. This region consists of the N-terminal portion of the nucleocapsid protein (NC), including the first zinc finger and the previously described interaction, or I, domain. In parallel with this randomized approach, individual HIV Gag domains, and combinations of these domains, were tested for potential homotypic and heterotypic interactions in the yeast two-hybrid system. Consistent with the results from the semirandom library screen, only combinations of species containing NC were strongly interacting
Human Immunodeficiency Virus Nucleocapsid Protein Polymorphisms Modulate the Infectivity of RNA Packaging Mutants

AbstractThe nucleocapsid protein (NC) of retroviruses is involved in viral RNA packaging and initiation of reverse transcription. NC also mediates interactions between Gag and actin filaments. We found that residues at the amino terminus of NC are involved in efficient actin binding. When alanine residues were substituted for the arginine and lysine at positions 10 and 11 of NC in HIVNL4-3, these mutations decreased actin binding but had only a modest effect on virus infectivity. A similarly mutated virus based on the HXB2 clone of HIV was not infectious. Mutational analysis of NL4-3 NC residues demonstrated that NC polymorphisms modulated the phenotype of NC mutations. Conservative amino acid differences between HXB2 and NL4-3 NCs were sufficient to explain the difference in infectivity of viruses carrying the R10A and K11A mutations
Enhanced Immunogenicity of HPV 16 E7 Fusion Proteins in DNA Vaccination

AbstractDNA vaccination is a promising approach for inducing both humoral and cellular immune responses. For immunotherapy of HPV-16-associated diseases the E7 protein is considered a prime candidate, as it is expressed in all HPV-16-positive tumors. Unfortunately, the E7 protein is a very poor inducer of a cytotoxic T-cell response, when being used as antigen in DNA vaccination. Here we demonstrate that after fusion to protein export/import signals such as the herpes simplex virus ferry protein VP22, E7 can translocate in vitro from VP22-E7-expressing cells to neighboring cells that do not carry the VP22-E7 gene. In vivo, the VP22-E7 fusion shows significantly increased efficiency in inducing a cytotoxic T-cell response. Our data suggest that the export function of VP22 plays a major role in this phenomenon, since VP22 can be replaced by classical protein export signals, without impairing the induction of the E7-specific cellular immune response. However, all E7 fusion constructs showed significantly elevated protein steady-state levels, which might also account for the observed boost in immunogenicity
Nontemplated Base Addition by HIV-1 RT Can Induce Nonspecific Strand Transfer in Vitro

AbstractAfter minus-strand strong-stop DNA (−sssDNA) synthesis, the RNA template is degraded by the RNase H activity of reverse transcriptase (RT), generating a single-stranded DNA. The genomes of some retroviruses contain sequences that could lead to self-priming of their −sssDNA. Self-priming was prevented by annealing a DNA oligonucleotide to the 3′ end of model DNAs that corresponded to the 3′ ends of the −sssDNAs (−R ssDNA) from human immunodeficiency virus type 1 (HIV-1), type 2 (HIV-2), and human T-cell leukemia virus type 1 (HTLV-1) but nonspecific strand transfer to ssDNA molecules in solution was induced in vitro (18). This nonspecific strand transfer involved the addition of a nontemplated base to the 3′ end of −R ssDNAs that was part of a blunt-ended duplex. In the case of HIV-2 −R ssDNA, A and C were added more efficiently than G and T. Strand transfer to ssDNA in solution occurred only if the nontemplated base could form a basepair with the last base at the 3′ end of the ssDNA. If there was a mismatch, strand transfer did not occur. There was no detectable strand transfer to internal sites in the target ssDNA except to the second position from the 3′ end of the DNA acceptor when the sequences at the 3′ ends of the two DNAs allowed the formation of two basepairs. The nontemplated base addition and the one-basepair strand transfer were both affected by the salt concentration in the reaction, the nature of the reverse transcriptase (HIV-1 versus Moloney murine leukemia virus), and the sequence at the 3′ end of −R ssDNA. NC reduced the efficiency of nonspecific strand transfer in vitro, suggesting that NC may have a role in reducing nonspecific strand transfer in vivo
Spliced and Prematurely Polyadenylated Jaagsiekte Sheep Retrovirus-Specific RNAs from Infected or Transfected Cells

AbstractJaagsiekte sheep retrovirus (JSRV) is the etiologic agent of a contagious lung cancer of sheep, ovine pulmonary adenocarcinoma (OPA). In this study, we characterized the virus-specific RNAs in 293T cells transiently transfected with a human cytomegalovirus promoter-driven JSRV expression plasmid, in productively infected OHH1.LU deer lung cells, and in OPA tumors from field isolates. Typical unspliced (presumably for gag, pro, and pol) and singly spliced env mRNAs were detected. In addition, six other virus-specific RNAs were detected that resulted from the use of alternate splice acceptor sites and two premature polyadenylation sites (located in gag and in env). The orf-x gene of the virus appears to be expressed from two singly spliced subgenomic mRNAs of 3.2 kb that would encode an independent orf-x protein of 179 amino acids. In addition, the results suggested that there may also be an internal promoter for orf-x
Dugbe Nairovirus S Segment: Correction of Published Sequence and Comparison of Five Isolates

AbstractThe sequence of the S (small) RNA segment of the ArD 44313 isolate of Dugbe nairovirus (DUG) has been redetermined, and a number of apparent errors in the previously reported sequence (V. K. Ward, A. C. Marriott, A. A. El-Ghorr, and P. A. Nuttall, 1990, Virology 175, 518–524) were revealed. Our results indicate that the S RNA is 1716 nucleotides (nt) in length and contains one large open reading frame spanning 1449 nt. This can encode a 483 amino acid polypeptide, Mr 53.9 kDa, corresponding to the viral nucleocapsid protein N. The DUG N protein is thus similar in length to the N proteins of Hazara (HAZ) and Crimean–Congo haemorrhagic fever (CCHF) nairoviruses, which are 485 and 482 amino acids in length, respectively. S segment RNA sequences were also determined for DUG isolates IbAr 1792, IbH 11480, ArD 16095, and KT 281/75; only the KT 281/75 sequence differed markedly from that of ArD 44313. Phylogenetic trees were constructed for these nairovirus S segment sequences
Conformational Changes Accompanying Self-Assembly of the Hepatitis C Virus Core Protein

AbstractAlthough a number of recent studies have suggested that the function of the hepatitis C virus (HCV) core protein may be both to package the viral genome and to modulate host cellular processes, little is known of the structure of the core protein necessary to accomplish these functions. Using in vitro assembled particles that mimic essential features of native HCV nucleocapsids, we report the earliest structural information of the HCV core protein and its nucleocapsid. The core protein is proteinase-resistant when assembled into nucleocapsid-like particles or complexed with nucleic acid in vitro. In contrast, the highly basic amino terminus of the free core protein is sensitive to proteolytic digestion. The hydrophobic carboxyl-terminal region of the core protein stabilizes the structure of the free core protein but is not required to stabilize core protein assembled into nucleocapsid-like particles or complexed to nucleic acid. Significantly, the carboxyl-terminal region is sufficient, but not necessary, to fold the core protein into a stable structure. These data are consistent with a model of a partially flexible HCV core protein that undergoes extensive conformational changes upon binding to nucleic acid and assembling into nucleocapsid particles. In addition, the susceptibility of nucleocapsid particles to RNase digestion suggests that RNA–core interactions may stabilize HCV nucleocapsids
Kinetic Analysis of Glycoprotein C of Herpes Simplex Virus Types 1 and 2 Binding to Heparin, Heparan Sulfate, and Complement Component C3b

AbstractGlycoprotein C (gC) from herpes simplex virus (HSV) facilitates virus entry by attaching the virion to host cell-surface heparan sulfate (HS). Although gC from HSV-1 (gC1) and from HSV-2 (gC2) bind to heparin, gC2 is believed to play a less significant role than gC1 in attachment of virus to cells. This attachment step is followed by the binding of gD to one of several cellular receptors. gC also plays an important role in immune evasion by binding to the C3b fragment of the third component of the host complement system. Yet, although both gC1 and gC2 protect HSV against complement-mediated neutralization, only gC on HSV-1-infected cells acts as a receptor for C3b. We used optical biosensor technology to quantitate the affinities (KD) and the stabilities (koff) between both serotypes of gC with heparin, HS, and C3b to address three questions concerning gC interactions. First, can differences in affinity or stability account for differences between the contributions of HSV-1 and HSV-2 gC in attachment? Our data show that the gC2–HS complex is highly unstable (koff = 0.2 s−1) compared to the gC1–HS complex (koff = 0.003 s−1), suggesting why gC2 may not play an important role in attachment of virus to cells as does gC1. Second, does gC2 have a lower affinity for C3b than does gC1, thereby explaining the lack of C3b-receptor activity on HSV-2 infected cells? Surprisingly, gC2 had a 10-fold higher affinity for C3b compared to gC1, so this functional difference in serotypes cannot be accounted for by affinity. Third, do differences in gC–HS and gD-receptor affinities support a model of HSV entry in which the gC–HS interaction is of lower affinity than the gD-receptor interaction? Our biosensor results indicate that gC has a higher affinity for HS than gD does for cellular receptors HveA (HVEM) and HveC (nectin-1)
Complementation of a Defective Human Adenovirus by an Otherwise Incompatible Ovine Adenovirus Recombinant Carrying a Functional E1A Gene

AbstractAll known human adenoviruses are classified as mastadenoviruses, while the ovine adenovirus (OAdV) serotype 7 is the prototype of the atadenoviruses, a proposed new genus. OAdV replicates abortively in human cell types and has potential as a gene transfer vector. However, the function of OAdV nonstructural genes is poorly understood and it is unclear whether OAdV replication might be complemented by a replicating human AdV in coinfected cells. To investigate possible interactions three human cell lines were singly infected with OAdV or human AdV5 or doubly infected. The development of a cytopathic effect and genome replication was monitored over three passages in each cell type. No significant OAdV replication occurred in any of the cell types examined either in the presence or in the absence of replicating AdV5. No aberrant AdV5 genome products were detected in coinfected cells. In contrast, in coinfected cells an OAdV recombinant that expressed the AdV5 E1A gene was able to promote the replication of an AdV5 E1A-deficient mutant, demonstrating trans-complementation between appropriate viruses. These findings have implications for the biosafety of OAdV vectors and their possible utility for enhancing gene delivery
RNA Helicase Activity of the Plant Virus Movement Proteins Encoded by the First Gene of the Triple Gene Block

AbstractCell-to-cell and long-distance transport of some plant viruses requires coordinated action of three movement proteins encoded by triple gene block (TGB). The largest of TGB proteins, TGBp1, is a member of the superfamily I of DNA/RNA helicases and possesses a set of conserved helicase sequence motifs necessary for virus movement. A recombinant His-tagged form of TGBp1 of two hordeiviruses and potato virus X, a potexvirus, produced in Escherichia coli had unwinding activity on a partially duplexed RNA, but not DNA substrate. The helicase activity of these proteins was dependent on Mg2+ and ATP. The isolated C-terminal half of the PSLV TGBp1 retaining all helicase motifs was also able to unwind RNA duplex
Matrix Protein Mutations Contribute to Inefficient Induction of Apoptosis Leading to Persistent Infection of Human Neural Cells by Vesicular Stomatitis Virus

AbstractIn a model system to study factors involved in the establishment of a persistent viral infection that may lead to neurodegenerative diseases, Indiana and New Jersey variants of vesicular stomatitis virus (VSV) with different capacities to infect and persist in human neural cells were studied. Indiana matrix (M) protein mutants and the wild-type New Jersey strain persisted in the human neural cell line H4 for at least 120 days. The Indiana wild-type virus (HR) and a non-M mutant (TP6), both unable to persist, induced apoptosis more strongly than all the other variants tested, as indicated by higher levels of DNA fragmentation and caspase-3-like activity. Transfection of H4 cells with mRNA coding for the VSV M protein confirmed the importance of this protein in the induction of apoptosis. Furthermore, the pan-caspase inhibitor ZVAD-fmk maintained cell survival to about 80%, whereas inhibition of caspase-8, caspase-9, or both only partially protected the cells against death, consistent with the fact that anti-apoptotic molecules from the Bcl-2 family also protect cells from death only partially. These results suggest that VSV activates many pathways of cell death and that an inefficient induction of caspase-3-related apoptosis participates in the establishment of a persistent infection of human neural cells by less virulent VSV variants
Transcription Mapping as a Tool in Phage Genomics: The Case of the Temperate Streptococcus thermophilus Phage Sfi21

AbstractFor the lytic growth cycle of the temperate cos-site Streptococcus thermophilus phage Sfi21 a transcription map was developed on the basis of systematic Northern blot hybridizations. All deduced 5′ ends were confirmed by primer extension analysis. Three time classes of transcripts were observed. Early transcripts were identified in four different genome regions. One prominent early mRNA of 4.8 kb length covered a group of 12 genes located between the origin of replication and the cos-site. Two short early mRNAs represented a single gene from the direct vicinity of the cos-site and the superinfection immunity gene from the lysogeny module, respectively. A fourth early transcript covered a group of four genes located between the lysin and the integrase gene. Middle transcripts of 2.1 and 5.8 kb length covered cro-like and ant-like repressor genes and the DNA replication module, respectively. Four types of late transcripts were identified. The transcripts covered the likely DNA packaging genes, the head morphogenesis module plus the major tail gene, the remainder of the tail genes, and the putative tail fiber plus lysis genes, respectively. Only the transcript from the head morphogenesis genes yielded defined late mRNA species. The transcription map concurred with most of the in silico predictions for the genome organization of phage Sfi21 except for the separation of the DNA replication module from a possible transcription regulation module. Most 5′ ends of the transcripts determined in primer-extension experiments were not preceded by a consensus promoter sequence. The involvement of phage-encoded regulators for middle and late transcription was suggested by chloramphenicol-inhibition experiments
Characterization of Nontypeable Rotavirus Strains from the United States: Identification of a New Rotavirus Reassortant (P2A[6],G12) and Rare P3[9] Strains Related to Bovine Rotaviruses

AbstractAmong 1316 rotavirus specimens collected during strain surveillance in the United States from 1996 to 1999, most strains (95%) belonged to the common types (G1 to G4 and G9), while 5% were mixed infections of common serotypes, rare strains, or not completely typeable. In this report, 2 rare (P[9],G3) and 2 partially typeable (P[6],G?; P[9],G?) strains from that study were further characterized. The P[6] strain was virtually indistinguishable by hybridization analysis in 10 of its 11 gene segments with recently isolated P2A[6],G9 strains (e.g., U.S.1205) from the United States, but had a distinct VP7 gene homologous (94.7% aa and 90.2% nt) to the cognate gene from P1B[4],G12 reference strain L26. Thus, this serotype P2A[6],G12 strain represents a previously unrecognized reassortant. Three P3[9] strains were homologous (97.8–98.2% aa) in the VP8 region of VP4 to the P3[9],G3 feline-like reference strain AU-1, but had a high level of genome homology to Italian bovine-like, P3[9],G3 and P3[9],G6 rotavirus strains. Two of the U.S. P3[9] strains were confirmed to be type G3 (97.2–98.2% VP7 aa homology with reference G3 strain AU-1), while the other was most similar to Italian bovine-like strain PA151 (P3[9],G6), sharing 99.0% aa homology in VP7. Cross-neutralization studies confirmed all serotype assignments and represented the first detection of these rotavirus serotypes in the United States. The NSP4 genes of all U.S. P3[9] strains and rotavirus PA151 were most closely related to the bovine and equine branch within the DS-1 lineage, consistent with an animal origin. These results demonstrate that rare strains with P and G serotypes distinct from those of experimental rotavirus vaccines circulate in the United States, making it important to understand whether current vaccine candidates protect against these strains
Birnavirus VP1 Proteins Form a Distinct Subgroup of RNA-Dependent RNA Polymerases Lacking a GDD Motif

AbstractWe have cloned and characterized the Drosophila X virus (DXV) genome segment B and its encoded VP1, the putative RNA-dependent RNA polymerase (RdRp) present in the virion. The 2991-bp open reading frame encodes the largest birnavirus VP1 at 977 aa, with a calculated Mr of 112.8 kDa. As with the VP1 proteins of the type species of the other two genera in the family Birnaviridae, namely, infectious pancreatic necrosis virus (genus Aquabirnavirus) and infectious bursal disease virus (genus Avibirnavirus), the DXV (genus Entomobirnavirus) VP1 protein contains a consensus GTP-binding site and appears to possess self-guanylylation activity. All of the birnavirus VP1 proteins contain conserved RdRp motifs that reside in the catalytic “palm” domain of all classes of polymerases. However, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps. All three birnavirus RdRps do contain downstream DD motifs that could function as part of the catalytic triad. These motifs are, however, located in spatially distinct regions of the various birnavirus VP1 proteins. These results suggest that the VP1 proteins of birnaviruses form a defined subgroup of polymerases that either are lacking the conserved RdRp motif VI or have repositioned this motif to different structural regions
Identification of a Conserved HLA-A2-Restricted Decapeptide from the IE1 Protein (pUL123) of Human Cytomegalovirus

AbstractControl of human cytomegalovirus (HCMV) infection is predominantly mediated by cytolytic CD8+ T lymphocytes (CTL). Among the roughly 200 HCMV-encoded polypeptides, the tegument protein pp65 (ppUL83) and the nonstructural IE1 protein are considered to be dominant CTL targets. Yet the importance of CTL against IE1 for protective immunity against HCMV reactivation and disease has remained elusive. Analyses have been difficult, as all MHC class I presented peptides of IE1 defined so far are located in parts of the protein that are variable between viral strains. In this study a conserved decameric peptide from IE1 (P6, IE1354–363) that bound to HLA-A2 was identified. Using peptide-pulsed, HLA-matched stimulator cells, CTL lines which recognized P6 after exogenous loading as well as after endogenous processing could repeatedly be generated. However, memory CTL directed against P6 were not readily detectable by ex vivo ELISPOT analysis in peripheral blood mononuclear cells of healthy seropositive individuals, indicating that this peptide represents a quantitatively subdominant determinant during latent HCMV infection. Using the conserved HLA-A2 presented peptide P6 will enable more detailed studies on the role of IE1-specific CTL in patients suffering from various HCMV-related disease conditions and investigation of the role of such cells for immune control of HCMV. Since IE1 is the first viral protein to be expressed after reactivation from latency, P6 may also serve as an important component of a future recombinant HCMV vaccine