bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analyses of Genotypic Diversity among North, South, and Central American Isolates ofSugarcane Yellow Leaf Virus: Evidence for Colombian Origins and for Intraspecific Spatial Phylogenetic Variation
Authors: Moonan Francis , Mirkov T. Erik 
Published: October 2010

ABSTRACTWe have analyzed the genotypic diversity ofSugarcane yellow leaf virus(SCYLV) collected from North, South, and Central America by fingerprinting assays and selective cDNA cloning and sequencing. One group of isolates from Colombia, designated the C-population, has been identified as residing at the root node between a separable superpopulation structure of SCYLV and other members of the familyLuteoviridae, indicating that the progenitor viruses of the North, South, and Central American isolates of the SCYLV superpopulation most likely arose from a C-population structure. From a model of intrafamilial evolution (F. Moonan et al., Virology 269:156–171, 2000), a prediction could be made that within the SCYLV species, the capacity of genomic sequence divergence would range from lowest in the capsid protein open reading frame 3 (ORF 3) to highest in a region spanning across the carboxy-terminal end of the RNA-dependent RNA polymerase ORF. We have demonstrated the validity and applicability of this intrafamilial model for the prediction of intraspecies SCYLV diversity. Analysis of spatial phylogenetic variation (SPV) within the SCYLV isolates could not be assessed by application of a “partial likelihoods assessed through optimization” (PLATO)-derived intraspecies model alone. However, application of a PLATO-derived intrafamilial model with the intraspecies-derived model allowed distinction of three forms of SPV. Two of the SPV forms identified correspond to the extremes in a continuum of sequence evolution displayed in a SCYLV superpopulation structure, and the third form was diagnostic of a C-population structure. The application of these types of models has value in terms of predicting the types of SCYLV intraspecies diversity that may exist worldwide, and in general, may be useful in application for more informed design of transgenes for use in the elicitation of homology-dependent virus resistance mechanisms in transgenic plants.
Oncoviral Bovine Leukemia Virus G4 and Human T-Cell Leukemia Virus Type 1 p13
II
Accessory Proteins Interact with Farnesyl Pyrophosphate Synthetase
Authors: Lefèbvre Laurent , Vanderplasschen Alain , Ciminale Vincenzo , Heremans Hubertine , Dangoisse Olivier , Jauniaux Jean-Claude , Toussaint Jean-François , Zelnik Vlado , Burny Arsène , Kettmann Richard , Willems Luc 
Published: October 2010

ABSTRACT

G4 and p13
II
are accessory proteins encoded by the X region of bovine leukemia virus and human T-cell leukemia virus type 1 (HTLV-1), respectively. Disruption of the G4 and p13
II
open reading frames interferes with viral spread in animal model systems, indicating that the corresponding proteins play a key role in viral replication. In addition, G4 is oncogenic in primary cell cultures and is absolutely required for efficient onset of leukemogenesis in sheep. To gain insight into the function of these proteins, we utilized the yeast two-hybrid system to identify protein partners of G4. Results revealed that G4 interacts with farnesyl pyrophosphate synthetase (FPPS), a protein involved in the mevalonate/squalene pathway and in synthesis of FPP, a substrate required for prenylation of Ras. The specificity of the interaction was verified by glutathione
S
-transferase (GST) pull-down assays and by coimmunoprecipitation experiments. Furthermore, confocal microscopy showed that the subcellular localization of G4 was profoundly affected by FPPS. The G4 protein itself was not prenylated, at least in rabbit reticulocyte lysate-based assays. The domain of G4 required for binding to FPPS was restricted to an amphipathic α-helix rich in arginine residues. Subtle mutation of this α-helix abrogated G4 oncogenic potential in vitro, providing a biological relevance for FPPS-G4 complex formation in cells. Finally, HTLV-1 p13
II
was also found to specifically interact with FPPS (in yeast as well as in GST pull-down assays) and to colocalize with G4 in mitochondria, suggesting a functional analogy between these oncoviral accessory proteins. Identification of FPPS as a molecular partner for p13
II
and G4 accessory proteins opens new prospects for treatment of retrovirus-induced leukemia.
Heterologous Gene Expression from Transmissible Gastroenteritis Virus Replicon Particles
Authors: Curtis Kristopher M. , Yount Boyd , Baric Ralph S. 
Published: October 2010

ABSTRACT

We have recently isolated a transmissible gastroenteritis virus (TGEV) infectious construct designated TGEV 1000 (B. Yount, K. M. Curtis, and R. S. Baric, J. Virol. 74:10600–10611, 2000). Using this construct, a recombinant TGEV was constructed that replaced open reading frame (ORF) 3A with a heterologous gene encoding green fluorescent protein (GFP). Following transfection of baby hamster kidney (BHK) cells, a recombinant TGEV (TGEV-GFP2) was isolated that replicated efficiently and expressed GFP. Replicon constructs were constructed that lacked either the ORF 3B and E genes or the ORF 3B, E, and M genes [TGEV-Rep(
Avr
II) and TGEV-Rep(
Eco
NI), respectively]. As the E and M proteins are essential for TGEV virion budding, these replicon RNAs should replicate but not result in the production of infectious virus. Following cotransfection of BHK cells with the replicon RNAs carrying
gfp
, GFP expression was evident by fluorescent microscopy and leader-containing transcripts carrying
gfp
were detected by reverse transcription-PCR (RT-PCR). Subsequent passage of cell culture supernatants onto permissive swine testicular (ST) cells did not result in the virus, GFP expression, or the presence of leader-containing subgenomic transcripts, demonstrating the single-hit nature of the TGEV replicon RNAs. To prepare a packaging system to assemble TGEV replicon particles (TGEV VRP), the TGEV E gene was cloned into a Venezuelan equine encephalitis (VEE) replicon expression vector and VEE replicon particles encoding the TGEV E protein were isolated [VEE-TGEV(E)]. BHK cells were either cotransfected with TGEV-Rep(
Avr
II) (E gene deletion) and VEE-TGEV(E) RNA transcripts or transfected with TGEV-Rep(
Avr
II) RNA transcripts and subsequently infected with VEE VRPs carrying the TGEV E gene. In both cases, GFP expression and leader-containing GFP transcripts were detected in transfected cells. Cell culture supernatants, collected ∼36 h posttransfection, were passed onto fresh ST cells where GFP expression was evident ∼18 h postinfection. Leader-containing GFP transcripts containing the ORF 3B and E gene deletions were detected by RT-PCR. Recombinant TGEV was not released from these cultures. Under identical conditions, TGEV-GFP2 spread throughout ST cell cultures, expressed GFP, and formed viral plaques. The development of infectious TGEV replicon particles should assist studies of TGEV replication and assembly as well as facilitate the production of novel swine candidate vaccines.
The Herpes Simplex Virus Type 2 R1 Protein Kinase (ICP10 PK) Blocks Apoptosis in Hippocampal Neurons, Involving Activation of the MEK/MAPK Survival Pathway
Authors: Perkins D. , Pereira E. F. R. , Gober M. , Yarowsky P. J. , Aurelian L. 
Published: October 2010

ABSTRACTHerpes simplex virus type 1 (HSV-1) and HSV-2 trigger or counteract apoptosis by a cell-specific mechanism. Our studies are based on previous findings that the protein kinase (PK) domain of the large subunit of HSV-2 ribonucleotide reductase (ICP10) activates the Ras/MEK/MAPK pathway (Smith et al., J. Virol. 74:10417, 2000). Because survival pathways can modulate apoptosis, we used cells that are stably or transiently transfected with ICP10 PK, an HSV-2 mutant deleted in ICP10 PK (ICP10ΔPK) and the MEK-specific inhibitor U0126 to examine the role of ICP10 PK in apoptosis. Apoptosis was induced by staurosporine ord-mannitol in human (HEK293) cells or HEK293 cells stably transfected with the ICP10 PK-negative mutant p139 (JHL15), as determined by morphology, DNA fragmentation, terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling (TUNEL), caspase-3 activation, and poly(ADP-ribose) polymerase (PARP) cleavage. HEK293 cells stably transfected with ICP10 (JHLa1) were protected from apoptosis. ICP10 but not p139 protected neuronally differentiated PC12 cells from death due to nerve growth factor withdrawal, and apoptosis (determined by TUNEL) and caspase-3 activation were seen in primary hippocampal cultures infected with ICP10ΔPK but not with HSV-2 or a revertant virus [HSV-2(R)]. The data indicate that ICP10 has antiapoptotic activity under both paradigms and that it requires a functional PK activity. The apoptotic cells in primary hippocampal cultures were neurons, as determined by double immunofluorescence with fluorescein-labeled dUTP (TUNEL) and phycoerythrin-labeled antibodies specific for neuronal proteins (TuJ1 and NF-160). Protection from apoptosis was associated with MEK/MAPK activation, as evidenced by (i) increased levels of activated (phosphorylated) MAPK in HSV-2- but not ICP10ΔPK-infected cultures and (ii) inhibition of MAPK activation by the MEK-specific inhibitor U0126. MEK and MAPK were activated by infection with UV-inactivated but not antibody-neutralized HSV-2, suggesting that activation requires cellular penetration but is independent of de novo viral protein synthesis.
Adenovirus E1A N-Terminal Amino Acid Sequence Requirements for Repression of Transcription In Vitro and In Vivo Correlate with Those Required for E1A Interference with TBP-TATA Complex Formation
Authors: Boyd Janice M. , Loewenstein Paul M. , Tang Qing-quan , Yu Li , Green Maurice 
Published: October 2010

ABSTRACT
The adenovirus (Ad) E1A 243R oncoprotein encodes an N-terminal transcription repression domain that is essential for early viral functions, cell immortalization, and cell transformation. The transcription repression function requires sequences within amino acids 1 to 30 and 48 to 60. To elucidate the roles of the TATA-binding protein (TBP), p300, and the CREB-binding protein (CBP) in the mechanism(s) of E1A repression, we have constructed 29 amino acid substitution mutants and 5 deletion mutants spanning the first 30 amino acids within the E1A 1-80 polypeptide backbone. These mutant E1A polypeptides were characterized with regard to six parameters: the ability to repress transcription in vitro and in vivo, to disrupt TBP-TATA box interaction, and to bind TBP, p300, and CBP. Two regions within E1A residues 1 to 30, amino acids 2 to 6 and amino acid 20, are critical for E1A transcription repression in vitro and in vivo and for the ability to interfere with TBP-TATA interaction. Replacement of 6Cys with Ala in the first region yields the most defective mutant. Replacement of 20Leu with Ala, but not substitutions in flanking residues, yields a substantially defective phenotype. Protein binding assays demonstrate that replacement of 6Cys with Ala yields a mutant completely defective in interaction with TBP, p300, and CBP. Our findings are consistent with a model in which the E1A repression function involves interaction of E1A with p300/CBP and interference with the formation of a TBP-TATA box complex.
E4orf6 Variants with Separate Abilities To Augment Adenovirus Replication and Direct Nuclear Localization of the E1B 55-Kilodalton Protein
Authors: Orlando Joseph S. , Ornelles David A. 
Published: October 2010

ABSTRACT
The E4orf6 protein of group C adenovirus is an oncoprotein that, in association with the E1B 55-kDa protein and by E1B-independent means, promotes virus replication. An arginine-faced amphipathic α-helix in the E4orf6 protein is required for the E4orf6 protein to direct nuclear localization of the E1B 55-kDa protein and to enhance replication of an E4 deletion virus. In this study, E4orf6 protein variants containing arginine substitutions in the amphipathic α-helix were analyzed. Two of the six arginine residues within the α-helix, arginine-241 and arginine-243, were critical for directing nuclear localization of the E1B 55-kDa protein. The four remaining arginine residues appear to provide a net positive charge for the E4orf6 protein to direct nuclear localization of the E1B 55-kDa protein. The molecular determinants of the arginine-faced amphipathic α-helix that were required for the functional interaction between the E4orf6 and E1B 55-kDa proteins seen in the transfected cell differed from those required to support a productive infection. Several E4orf6 protein variants with arginine-to-glutamic acid substitutions that failed to direct nuclear localization of the E1B 55-kDa protein restored replication of an E4 deletion virus. Additionally, a variant containing an arginine-to-alanine substitution at position 243 that directed nuclear localization of the E1B 55-kDa protein failed to enhance virus replication. These results indicate that the ability of the E4orf6 protein to relocalize the E1B 55-kDa protein to the nucleus can be separated from the ability of the E4orf6 protein to support a productive infection.
Increased p50/p50 NF-κB Activation in Human Papillomavirus Type 6- or Type 11-Induced Laryngeal Papilloma Tissue
Authors: Vancurova Ivana , Wu Rong , Miskolci Veronika , Sun Shishinn 
Published: October 2010

ABSTRACTWe have observed elevated NF-κB DNA-binding activity in nuclear extracts from human papillomavirus type 6- and 11-infected laryngeal papilloma tissues. The predominant DNA-binding species is the p50/p50 homodimer. The elevated NF-κB activity could be correlated with a reduced level of cytoplasmic IκBβ and could be associated with the overexpression of p21CIP1/WAF1in papilloma cells. Increased NF-κB activity and cytoplasmic accumulation of p21CIP1/WAF1might counteract death-promoting effects elicited by overexpressed PTEN and reduced activation of Akt and STAT3 previously noted in these tissues.
Integrin αvβ1 Is a Receptor for Foot-and-Mouth Disease Virus
Authors: Jackson Terry , Mould A. Paul , Sheppard Dean , King Andrew M. Q. 
Published: October 2010

ABSTRACT

Infection by field strains of
Foot-and-mouth disease virus
(FMDV) is initiated by binding to certain species of arginine-glycine-aspartic acid (RGD)-dependent integrin including αvβ3 and the epithelial integrin αvβ6. In this report we show that the integrin αvβ1, when expressed as a human/hamster heterodimer on transfected CHOB2 cells, is a receptor for FMDV. Virus binding and infection mediated by αvβ1 was inefficient in the presence of physiological concentrations of calcium and magnesium but were significantly enhanced by reagents that activate the integrin and promote ligand binding. The ability of chimeric α5/αv integrin subunits, in association with the β1 chain, to bind FMDV and mediate infection matched the ligand binding specificity of αvβ1, not α5β1, thus providing further evidence for the receptor role of αvβ1. In addition, data are presented suggesting that amino acid residues near the RGD motif may be important for differentiating between the binding specificities of αvβ1 and αvβ6.
Dissociation of Genome Dimerization from Packaging Functions and Virion Maturation of Human Immunodeficiency Virus Type 1
Authors: Sakuragi Jun-ichi , Iwamoto Aikichi , Shioda Tatsuo 
Published: October 2010

ABSTRACT
The dimer initiation site/dimer linkage sequence (DIS/DLS) region of the human immunodeficiency virus type 1 (HIV-1) RNA genome is thought to play important roles at various stages of the virus life cycle. Recently we showed that the DIS/DLS region affects RNA-RNA interaction in intact virus particles, by demonstrating that duplication of the region in viral RNA caused the production of virus particles containing partially monomeric RNAs. We have extended this finding and succeeded for the first time in creating mutant particles which contain only monomeric RNAs without modifying any viral proteins. In terms of RNA encapsidation ability, virion density, and protein processing, the mutant particles were comparable to wild-type particles. The level of production of viral DNA by the mutant virus construct in infected cells was also comparable to that of the constructs that produced exclusively dimeric RNA, indicating that monomeric viral RNA could be the template for strand transfer. These results indicated that the RNA dimerization of HIV-1 could be separated from viral RNA packaging and was not absolutely required for RNA packaging, virion maturation, and reverse transcription.
Viral Dynamics during Structured Treatment Interruptions of Chronic Human Immunodeficiency Virus Type 1 Infection
Authors: Frost Simon D. W. , Martinez-Picado Javier , Ruiz Lidia , Clotet Bonaventura , Leigh Brown Andrew J. 
Published: October 2010

ABSTRACTAlthough antiviral agents which block human immunodeficiency virus (HIV) replication can result in long-term suppression of viral loads to undetectable levels in plasma, long-term therapy fails to eradicate virus, which generally rebounds after a single treatment interruption. Multiple structured treatment interruptions (STIs) have been suggested as a possible strategy that may boost HIV-specific immune responses and control viral replication. We analyze viral dynamics during four consecutive STI cycles in 12 chronically infected patients with a history (>2 years) of viral suppression under highly active antiretroviral therapy. We fitted a simple model of viral rebound to the viral load data from each patient by using a novel statistical approach that allows us to overcome problems of estimating viral dynamics parameters when there are many viral load measurements below the limit of detection. There is an approximate halving of the average viral growth rate between the first and fourth STI cycles, yet the average time between treatment interruption and detection of viral loads in the plasma is approximately the same in the first and fourth interruptions. We hypothesize that reseeding of viral reservoirs during treatment interruptions can account for this discrepancy, although factors such as stochastic effects and the strength of HIV-specific immune responses may also affect the time to viral rebound. We also demonstrate spontaneous drops in viral load in later STIs, which reflect fluctuations in the rates of viral production and/or clearance that may be caused by a complex interaction between virus and target cells and/or immune responses.
Hepatitis C Virus Genotype 1b Core Protein Does Not Exert Immunomodulatory Effects on Virus-Induced Cellular Immunity
Authors: Liu Zhang-Xu , Nishida Hiroshi , He Jian-Wen , Lai Michael M. C. , Feng Ni , Dennert Gunther 
Published: October 2010

ABSTRACTThe hepatitis C virus (HCV) core protein is among the most conserved proteins in HCV and is known to induce sensitization of cytotoxic T lymphocytes (CTL). Therefore, it is a prime candidate for a component of a potential HCV vaccine. The HCV core protein has, however, been reported to exert multiple effects on cell functions, raising questions as to its suitability for this purpose. This question was investigated here with mice into which replication-deficient adenoviruses expressing core protein of an HCV genotype 1b isolate were injected. We show that induction of cytokines in response to the infection, infiltration of lymphocytes into the infected liver, priming of virus-specific CTL, and liver injury are not modulated by expression of the core protein in the liver. Moreover, no changes in the sensitivity to tumor necrosis factor alpha- or Fas-mediated liver injury are demonstrable. A similar lack of demonstrable effects of the core protein on immune functions has also been obtained using transgenic mice expressing another HCV genotype 1b core protein. It is concluded that the HCV core protein of genotype 1b has no modulatory effects on induction of virus-specific immune responses and may therefore be a suitable component of an HCV vaccine.
Metabolome-Proteome Differentiation Coupled to Microbial Divergence
Authors: Wilmes Paul , Bowen Benjamin P. , Thomas Brian C. , Mueller Ryan S. , Denef Vincent J. , VerBerkmoes Nathan C. , Hettich Robert L. , Northen Trent R. , Banfield Jillian F. 
Published: October 2010

ABSTRACT
Tandem high-throughput proteomics and metabolomics were employed to functionally characterize natural microbial biofilm communities. Distinct molecular signatures exist for each analyzed sample. Deconvolution of the high-resolution molecular data demonstrates that identified proteins and detected metabolites exhibit organism-specific correlation patterns. These patterns are reflective of the functional differentiation of two bacterial species that share the same genus and that co-occur in the sampled microbial communities. Our analyses indicate that the two species have similar niche breadths and are not in strong competition with one another.

IMPORTANCE
Natural microbial assemblages represent dynamic consortia that exhibit extensive complexity at all levels. In the present study, we demonstrate that correlations between protein and metabolite abundances allow the deconvolution of complex molecular data sets into shared and organism-specific contingents. We demonstrate that evolutionary divergence is associated with the restructuring of cellular metabolic networks, which in turn allows bacterial species to occupy distinct ecological niches. The apparent lack of interspecific competition may explain the extensive population-level genetic heterogeneity observed extensively within microbial communities. The reported findings have broad implications for the in-depth investigation of the ecology and evolution of distinct microbial community members and for leveraging the solution of cryptic metabolic processes in the future.
Alcohol based tissue fixation as an alternative for formaldehyde: influence on immunohistochemistry
Authors: van Essen Hendrik F , Verdaasdonk Marina A M , Elshof Sabrina M , de Weger Roel A , van Diest Paul J 
Published: October 2010

BackgroundFormaldehyde is commonly used in histopathology to fix tissue. Not only are the carcinogenic properties of this solution a hazard to the people in the workplace, it is also a major burden on the environment, and it crosslinks molecular groups that hinder immunohistochemistry.AimsThe influence of two new alcohol based non-crosslinking fixatives on immunohistochemical staining properties was tested on various tissues.MethodsFresh tissue samples were cut into three equal pieces, which were then fixed in the alcohol based fixatives Boonfix or RCL2, or in neutral buffered formaldehyde (NBF) as control. After fixation, tissue was routinely processed to paraffin sections. Deparaffinised slides were blocked for endogenous peroxidase and subsequently submitted to the usual NBF based immunohistochemical protocols for 85 different common antibodies either not requiring antigen retrieval (AR), or AR in citrate buffer, EDTA or pepsin.ResultsNBF fixed tissues provided significantly better immunostaining results (84% good staining) than RCL2 (66% good) and Boonfix (60%). The lesser performance of RCL2 and Boonfix was especially caused by pepsin AR which caused significant tissue damage. Omission of pepsin AR resulted in better immunostaining for these antibodies for RCL2 fixed tissues which were overall no longer significantly worse than NBF fixed tissue.ConclusionTissues fixed in non-crosslinking alcohol based fixatives can successfully be immunohistochemically stained for most antibodies following the usual NBF based protocols. Omission of pepsin pretreatment seems to be important to retain proper morphology of immunostained tissues preserved in alcohol based fixatives. Therefore, when switching to less toxic and non-carcinogenic alcohol-based fixatives like RCL2, no major changes in the daily routine of immunohistochemistry are anticipated.