pinecone/core-2020-05-10-deduplication huggingface dataset:
Molecular Characterization of Menangle Virus, a Novel Paramyxovirus which Infects Pigs, Fruit Bats, and Humans

AbstractMenangle virus (MenV), isolated in August 1997 following an outbreak of reproductive disease in a piggery in New South Wales, is the second previously unclassified member of the family Paramyxoviridae to be identified in Australia since 1994. Similar to Hendra virus (HeV), MenV appears to be a virus of fruit bats (flying foxes) in the genus Pteropus. No serological cross-reactivity was detected between MenV and other known paramyxoviruses and to facilitate virus classification a cDNA subtraction method was used to obtain viral-specific cDNA from MenV-infected cells. Cloning and sequencing of the products enabled the entire sequences of the NP, P/V, M, F, and HN genes to be determined. Comparison of the nucleotide and deduced amino acid sequences for each gene with members of the family Paramyxoviridae, determination of the P gene mRNA editing strategy, and phylogenetic analyses confirmed that MenV is a new member of the genus Rubulavirus. However the deduced protein sequence of MenV HN exhibited only limited sequence homology when compared with attachment proteins of other paramyxoviruses. Key differences within the amino acid residues considered important determinants of neuraminidase activity suggest MenV HN is unlikely to possess the same degree of neuraminidase activity characteristic of other rubulavirus and respirovirus HN proteins
Chimeric Subgroup A Respiratory Syncytial Virus with the Glycoproteins Substituted by Those of Subgroup B and RSV without the M2-2 Gene Are Attenuated in African Green Monkeys

AbstractUsing the existing reverse genetics system developed for the subgroup A respiratory syncytial virus (RSV), a chimeric virus (designated rA-GBFB) that expresses subgroup B-specific antigens was constructed by replacing the G and F genes of the A2 strain with those of the 9320 strain of subgroup B RSV. rA-GBFB grew well in tissue culture, but it was attenuated in the respiratory tracts of cotton rats and African green monkeys. To further attenuate this chimeric RSV, the M2-2 open reading frame was removed from rA-GBFB. rA-GBFBΔM2-2 was highly attenuated in replication in the respiratory tracts of the infected monkeys, but it provided complete protection against wild-type subgroup B RSV challenge following two doses of infection. In this study, rA2ΔM2-2 (a recombinant A2 RSV that lacks the M2-2 gene) was also evaluated in African green monkeys. The replication of rA2ΔM2-2 was highly restricted in both the upper and lower respiratory tracts of the infected monkeys and it induced titers of serum anti-RSV neutralizing antibody that were slightly lower than those induced by wild-type rA2. When rA2ΔM2-2-infected monkeys were challenged with wild-type A2 virus, the replication of the challenge virus was reduced by approximately 100-fold in the upper respiratory tract and 45,000-fold in the lower respiratory tracts. rA2ΔM2-2 and rA-GBFBΔM2-2 could represent a bivalent RSV vaccine composition for protection against multiple strains from the two RSV subgroups
Hepatitis C Virus Core Protein Enhances FADD-Mediated Apoptosis and Suppresses TRADD Signaling of Tumor Necrosis Factor Receptor

AbstractHepatitis C virus (HCV) core protein has been shown to interact with the death domain (DD) of tumor necrosis factor receptor-1 (TNFR1). In this study, we further examined the interaction of the core protein with the signaling molecules of TNFR1, including FADD, TRADD, and TRAF2, in a human embryonic kidney cell line, HEK-293, that overexpresses the HCV core protein. This core protein-expressing cell line exhibited enhanced sensitivity to TNF-induced apoptosis. By in vitro binding and in vivo coimmunoprecipitation assays, we showed that the HCV core protein interacted with the DD of FADD and enhanced apoptosis induced by FADD overexpression. This enhancement could be blocked by a dominant-negative mutant of FADD. In contrast, the core protein did not directly interact with the DD of TRADD, but could disrupt the binding of TRADD to TNFR1. TRAF2 recruitment to the TNFR1 signaling complex was also disrupted by the core protein. Correspondingly, TRAF2-dependent activation of the protein kinase JNK was suppressed in the core protein-expressing cells. However, NFκB activation by TNF was not significantly altered by the HCV core protein, suggesting the existence of TRAF2-independent pathways for NFκB activation. These results combined indicate that the HCV core protein sensitizes cells to TNF-induced apoptosis primarily by facilitating FADD recruitment to TNFR1. The inhibition of JNK activation by the HCV core protein may also contribute to the increased propensity of cells for apoptosis. These results, in comparison with other published studies, suggest that the effects of the HCV core protein and their underlying mechanisms vary significantly among cells of different origins
Functional Activity of HERV-K-T47D-Related Long Terminal Repeats

AbstractThe human genome contains a family of endogenous retroviruses, HERV-K(HML-4), that comprises the full-length provirus HERV-K-T47D, five related elements, and hundreds of solitary long terminal repeats (LTRs). We here show that HERV-K-T47D-related LTRs are dispersed over all human chromosomes and have arisen after the divergence of Old and New World monkeys. By screening a cDNA library derived from the human mammary carcinoma cell line T47D with a HERV-K-T47D LTR probe, we isolated several clones containing LTR/cellular gene chimeras and assessed the transcriptional activity of these LTRs in transient transfection experiments. All LTRs were able to drive the expression of a reporter gene, thereby displaying distinct activities in different cell lines. We found that sequences located downstream of the LTR-U3 region modulate the level of gene expression. Based on the impact of the R region we distinguished between three different LTR types; the activity of type I LTRs was enhanced in the presence of the LTR-R region in all cell lines tested, whereas a type II LTR was downregulated. Type III LTRs are characterized by lacking or having a varying influence of the R region that was dependent on the cell line used. Finally, our results attribute to LTR-U5-gag sequences a role in determining LTR activity
Carbohydrate Modifications of the NDV Fusion Protein Heptad Repeat Domains Influence Maturation and Fusion Activity

AbstractThe amino acid sequence of the fusion protein (F) of Newcastle disease virus (NDV) has six potential N-linked glycosylation addition sites, five in the ectodomain (at amino acids 85, 191, 366, 447, and 471) and one in the cytoplasmic domain at amino acid 542. Two of these sites, at positions 191 and 471, are within heptad repeat (HR) domains implicated in fusion activity of the protein. To determine glycosylation site usage as well as the function of added carbohydrate, each site was mutated by substituting alanine for the serine or threonine in the addition signal. The sizes of the resulting mutant proteins, expressed in Cos cells, showed that sites at amino acids 85, 191, 366, and 471 are used. This conclusion was verified by comparing sizes of mutant proteins missing all four used sites with that of unglycosylated F protein. The role of each added oligosaccharide in the structure and function of the F protein was determined by characterizing stability, proteolytic cleavage, surface expression, and fusion activity of the mutant proteins. Elimination of the site in F2 at amino acid 85 had the most detrimental effect, decreasing cleavage, stability, and surface expression as well as fusion activity. The protein missing the site at 191, at the carboxyl terminus of the HR1 domain, also showed modestly reduced surface expression and negligible fusion activity. Proteins missing sites at 366 and 471 (within HR2) were expressed at nearly wild-type levels but had decreased fusion activity. These results suggest that all carbohydrate side chains, individually, influence the folding or activity of the NDV F protein. Importantly, carbohydrate modifications of the HR domains impact fusion activity of the protein
Analysis of a Three-Dimensional Structure of Potato leafroll virus Coat Protein Obtained by Homology Modeling

AbstractViruses of the family Luteoviridae are ssRNA plant viruses that have particles that exhibit icosahedral symmetry. To identify the residues that might be exposed on the surface of the Potato leafroll virus (PLRV; genus Polerovirus, family Luteoviridae) capsid, and therefore involved in biological interactions, we performed a structural analysis of the PLRV coat protein (CP) on the basis of comparisons with protein sequences and known crystal structures of CPs of other viruses. The CP of PLRV displays 33% sequence similarity with that of Rice yellow mottle virus (genus Sobemovirus) when the sequences were aligned by using the hidden Markov model method. A structure model for PLRV CP was designed by protein homology modeling, using the crystal structure of RYMV as a template. The resulting model is consistent with immunological and site-directed mutagenesis data previously reported. On the basis of this model it is possible to predict some surface properties of the PLRV CP and also speculate about the structural evolution of small icosahedral viruses
Long-Distance Movement and Replication Maintenance Functions Correlate with Silencing Suppression Activity of Potyviral HC-Pro

AbstractThe tobacco etch potyviral protein, HC-Pro, is a multifunctional proteinase required for long-distance movement in plants and maintenance of genome replication at the single-cell level. It also functions in a counterdefensive capacity as a suppressor of posttranscriptional gene silencing (PTGS). To determine whether the requirements for HC-Pro during long distance movement and replication maintenance are due to the silencing suppressor function of the protein, a series of HC-Pro alanine scanning and other site-directed mutants were analyzed. Using a transient silencing suppression assay in Agrobacterium-injected leaf tissue, several suppression-defective mutants were identified. Each of six HC-Pro mutations, which were shown previously to confer long-distance movement and replication maintenance defects, conferred PTGS suppression defects. Interestingly, the genes encoding these defective HC-Pro derivatives were themselves susceptible targets of PTGS, resulting in low levels of mRNA and protein accumulation. Mutations that inactivated the proteinase domain active site had no effect on PTGS suppression function. The results are consistent with the hypothesis that the role of HC-Pro in long-distance movement and genome replication depends on PTGS suppression function and that this function is independent of HC-Pro proteolytic activity
Herpes Simplex Virus 1 ICP27 Is Required for Transcription of Two Viral Late (γ2) Genes in Infected Cells

AbstractThe herpes simplex virus infected cell protein 27 (ICP27) is required for the expression of certain early viral proteins and for many late proteins during productive infection. Expression of at least one late (γ2) gene, that encoding glycoprotein C, is severely restricted in the absence of functional ICP27. The exact mode of action by which ICP27 induces late gene expression is not known, but the effect is apparent at the mRNA level as demonstrated by Northern blot analysis. To determine whether ICP27 activates late genes via transcriptional or posttranscriptional mechanisms, we initially used nuclear run-on assays to measure transcription of viral genes in Vero cells infected with wild-type (WT) virus or an ICP27 nonsense mutant virus, n504. We observed a 4-fold reduction in the nuclear run-on signal from the coding strand of the gC gene for n504-infected cells compared to that of WT-infected cells. However, interpretation of the results was complicated by the observation of a significant signal from the noncoding strand in these experiments. To obviate the problem of symmetrical transcription, we utilized in vivo RNA pulse-labeling to measure the amount of transcription of viral genes in cells infected with either WT virus or n504 virus. We found a 5- to 10-fold reduction in the transcription of the gC and UL47 genes, two late genes, in cells infected with n504 compared to that in cells infected with WT virus. In contrast, transcription of the ICP8 gene, an early gene, was similar in WT and n504 virus-infected cells. We also examined the stability of the gC and UL47 gene transcripts in n504-infected cells, and we found it to be comparable to that in WT virus-infected cells, further supporting an effect on transcription. Transcription of the gC and UL47 genes by n504 was normal in a cell line that expresses WT ICP27. From these results we conclude that ICP27 is required for transcription of the late gC and UL47 genes during productive infection
Use of VSV-G Pseudotyped Retroviral Vectors to Target Murine Osteoprogenitor Cells

AbstractMarrow stromal cells (MSC) and neonatal calvarial cells have the potential to differentiate and express markers of mature osteoblasts. Furthermore, MSCs can generate multiple differentiated connective tissue phenotypes. These properties and their ability to be expanded ex vivo make them good models for ex vivo gene therapy. In this study we examined the ability of vesicular stomatitis virus (VSV-G) pseudotyped retroviral vectors to transduce osteoprogenitor cells derived from bone marrow and from neonatal calvaria. Retrovectors encoding either β-galactosidase or green fluorescent protein (eGFP) were used for transduction of primary murine marrow stromal and primary neonatal calvarial cell cultures. High infection efficiency was demonstrated by fluorescence-activated cell analysis when GFP was used as a marker or by estimating the number of β-galactosidase-positive cells. Expression of markers of differentiated bone cells, including Col1a1, bone sialoprotein, and osteocalcin mRNA and alkaline phosphatase activity was not impaired by retroviral transduction. Our data suggest that VSV-G pseudotypes retroviral vectors are suitable for introducing genes into osteoprogenitor cells without affecting osteoprogenitor lineage progression
A CCR5/CXCR4-Independent Coreceptor Pathway on Human Macrophages Supports Efficient SIV Env-Mediated Fusion but Not Infection: Implications for Alternative Pathways of Viral Entry

AbstractSeveral coreceptors in addition to CCR5 and CXCR4 support immunodeficiency virus entry in transfected cells, but whether they could play a role in HIV-1 pathogenesis is uncertain. To probe whether human macrophages express potentially functional alternative entry pathways, we analyzed cell–cell fusion and infection of primary macrophage by several SIVmac Envs. All Envs fused with normal macrophages. One, SIVmac316, also fused efficiently with macrophages lacking CCR5. CCR5-independent fusion was not mediated by CXCR4 and was CD4 dependent, while CCR5-mediated fusion was partly independent of CD4. However, pseudotype virions carrying the SIVmac316 Env and HIV-1 core could not infect macrophages through the CCR5-independent pathway, although they did infect wild-type macrophages. Thus, human macrophages possess an alternative coreceptor pathway that mediates SIV Env fusion but does not support infection. Macrophage entry pathways other than CCR5 and CXCR4 may have limited potential in pathogenesis given their restricted capacity for infection despite efficient fusion
Interactions of Single and Combined Human Immunodeficiency Virus Type 1 (HIV-1) DNA Vaccines

AbstractDNA immunization permits evaluation of possible antagonistic or synergistic effects between the encoded components. The protein expression capacity in vitro was related to the immunogenicity in vivo of plasmids encoding the HIV-1 regulatory genes tat rev, and nef. Neither Tat nor Rev expression was influenced by co-expression in vitro of all three proteins, while Nef expression was slightly inhibited. With the combination of genes, the T-cellular responses of mice against Rev and Nef were inhibited compared with those when single gene immunization was used. No interference was detected for the Tat T-cell response. Thus, co-immunization with certain genes may result in inhibition of specific immune responses
Identification of a Novel Occlusion Derived Virus-Specific Protein in Spodoptera exigua Multicapsid Nucleopolyhedrovirus

AbstractUnderstanding the molecular basis of the distinct biological properties of Spodoptera exigua multicapsid nucleopolyhedrovirus (SeMNPV), such as its narrow host range and high virulence, requires detailed information on the temporal expression and subcellular localization of SeMNPV gene products. The expression of two unique SeMNPV ORFs, 116 (Se116) and 117 (Se117), which show 45% amino acid similarity, was analyzed. Se116 and Se117 were expressed both in cultured cells and in larvae of S. exigua as polyadenylated transcripts of 0.80 and 0.75 kb, respectively. These transcripts initiated from ATCA(G/T)T promoter motifs, commonly found for baculovirus early genes. Se116 transcripts were detected with increasing abundance from 8 to 48 h p.i., whereas Se117 transcripts were present from 4 h p.i. and most abundantly at 24 h p.i. Western blot analysis of infected Se301 cells revealed 27- and 23-kDa proteins for Se116 and Se117, respectively. C-terminal GFP–fusion proteins of Se116 and Se117 were primarily localized in the nucleus of Se301 cells. When Se301 cells were infected with SeMNPV, both GFP–fusion proteins were localized in the virogenic stroma of the nucleus. While the function of the Se116 protein is still enigmatic, the Se117 protein appeared to be a structural protein associated with nucleocapsids of occlusion-derived SeMNPV virions but not of budded virus
Recombinant Equine Arteritis Virus as an Expression Vector

AbstractEquine arteritis virus (EAV) is the prototypic member of the family Arteriviridae, which together with the Corona- and Toroviridae constitutes the order Nidovirales. A common trait of these positive-stranded RNA viruses is the 3′-coterminal nested set of six to eight leader-containing subgenomic mRNAs which are generated by a discontinuous transcription mechanism and from which the viral open reading frames downstream of the polymerase gene are expressed. In this study, we investigated whether the unique gene expression strategy of the Nidovirales could be utilized to convert them into viral expression vectors by introduction of an additional transcription unit into the EAV genome directing the synthesis of an extra subgenomic mRNA. To this end, an expression cassette consisting of the gene for a green fluorescent protein (GFP) flanked at its 3′ end by EAV-specific transcription-regulating sequences was constructed. This genetic module was inserted into the recently obtained mutant infectious EAV cDNA clone pBRNX1.38-5/6 (A. A. F. de Vries, et al., 2000, Virology 270, 84–97) between the genes for the M and the GL proteins. Confocal fluorescence microscopy of BHK-21 cells electroporated with capped RNA transcripts derived from the resulting plasmid (pBRNX1.38-5/6-GFP) demonstrated that the GFP gene was expressed in the transfected cells, while the gradual spread of the infection through the cell monolayer showed that the recombinant virus was replication competent. The development of the cytopathic effect was, however, much slower than in cells that had received equivalent amounts of pBRNX1.38-5/6 RNA, indicating that the vector virus had a clear growth disadvantage compared to its direct precursor. Immunoprecipitation analyses of proteins from metabolically labeled BHK-21 cells infected with supernatant of the transfected cultures confirmed that the recombinant virus vector was viable and expressed viral genes as well as the GFP gene. Reverse transcription-PCR of the viral mRNAs extracted from cells infected with the vector virus revealed that it directed the synthesis of nine instead of eight different EAV RNAs. These findings were corroborated by hybridization analyses. Mapping of the leader-to-body junctions of the ninth mRNA indicated that the 3′ part of the GFP gene contains cryptic transcription signals which gave rise to at least five different RNA species ranging in size from 1277 to 1439 nt [without oligo(A) tract]. Furthermore, translation of the unintended mRNA resulted in the production of an extended version of the EAV M protein. Serial passage of the recombinant virus vector led to its gradual replacement by viral mutants carrying deletions in the GFP gene. The reduction in viral fitness associated with the insertion of the expression cassette into the EAV genome apparently caused genetic instability of the recombinant virus
First Outbreak of Callitrichid Hepatitis in Germany: Genetic Characterization of the Causative Lymphocytic Choriomeningitis Virus Strains

AbstractCallitrichid hepatitis (CH) is a highly fatal, rodent-borne zoonosis of New World primates (family Callitrichidae) caused by lymphocytic choriomeningitis virus (LCMV). It is unclear whether virulence in Callitrichidae is associated with specific genetic or phylogenetic markers of the virus as only a partial S RNA sequence of a single CH-associated isolate is known. In a period of 10 months, three pygmy marmosets (Cebuella pygmaea) and one Goeldi's monkey (Callimico goeldii) died from CH in a German zoo. LCMV was most likely transmitted by wild mice. Infection was associated with characteristic histopathological lesions in liver, brain, and lymphoid tissue. Virus sequences from all callitrichids and a captured mouse were ≥99.2% identical. LCMV strains from a pygmy marmoset and the Goeldi's monkey were isolated in cell culture and the 3.4-kb S RNA was completely sequenced. Both strains differed considerably in their genetic and phylogenetic characteristics from known LCMV strains, including the previously described CH-associated strain. These data show that CH is widespread and can be caused by distantly related LCMV strains
Assessment of Recombinants That Arise from the Use of a TMV-Based Transient Expression Vector

AbstractA potential use of virus-based transient expression vectors is the large-scale production of commercial specialty products, which would require the inoculation of many acres of plants with the viral vector. However, there are several concerns about the widespread use of virus-based vectors. Among these are the spread of the engineered virus to susceptible plants and the generation and persistence of recombinant viruses in the environment. Using a Tobacco mosaic virus (TMV)-based transient gene expression vector, 30B, which expresses the jellyfish green fluorescent protein (30B-GFP), we describe the predominant types of hybrid viruses that developed in plants. In general, the recombinants deleted the foreign gene and repeated sequences, retaining only those sequences required for optimal replication and movement. In pathogenicity studies and challenge experiments designed to make a comparative assessment of the competitiveness of the recombinants with the parent virus, the recombinants had reduced vigor and were less competitive and pathogenic than TMV, a virus which is already present in the areas where tobacco is grown