bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simian Immunodeficiency Virus Variants That Differ in Pathogenicity Differ in Fitness under Rapid Cell Turnover Conditions
Authors: Voronin Yegor , Overbaugh Julie , Emerman Michael 
Published: November 2005

ABSTRACT
Simian immunodeficiency virus (SIV) has been shown to progress through a number of changes that lead to the emergence of pathogenic viral variants in macaques initially infected with a mildly cytopathic variant, SIVMneCL8. One of these late-stage isolates, SIVMne170, replicates to high levels in vivo and causes a rapid disease course when reintroduced into naïve macaques, resulting in a viral set point up to 3,000-fold higher than the set point of the parental virus, SIVMneCL8. However, in cell culture both viruses replicate with similar kinetics. One major difference between in vivo and in vitro cultures is the life span of the infected cells. Here, we manipulated the life span of infected cells in vitro, and we show that the fitness of SIVMne170 in cultures with a limited cell life span dramatically increased compared to its fitness in cultures with a nonlimited life span of cells. The increase in fitness was at least partially due to the fact that the rapid turnover system eliminates the negative influence of the cytopathic effects associated with replication of SIVMne170. Because the relative fitness of SIVMneCL8 and SIVMne170 observed in the rapid turnover system more accurately reflects their fitness in vivo, the system represents an improved approach to comparing relative fitness of viruses.
Clade Replacements in Dengue Virus Serotypes 1 and 3 Are Associated with Changing Serotype Prevalence
Authors: Zhang Chunlin , Mammen Mammen P. , Chinnawirotpisan Piyawan , Klungthong Chonticha , Rodpradit Prinyada , Monkongdee Patama , Nimmannitya Suchitra , Kalayanarooj Siripen , Holmes Edward C. 
Published: November 2005

ABSTRACT
The evolution of dengue virus (DENV) is characterized by phylogenetic trees that have a strong temporal structure punctuated by dramatic changes in clade frequency. To determine the cause of these large-scale phylogenetic patterns, we examined the evolutionary history of DENV serotype 1 (DENV-1) and DENV-3 in Thailand, where gene sequence and epidemiological data are relatively abundant over a 30-year period. We found evidence for the turnover of viral clades in both serotypes, most notably in DENV-1, where a major clade replacement event took place in genotype I during the mid-1990s. Further, when this clade replacement event was placed in the context of changes in serotype prevalence in Thailand, a striking pattern emerged; an increase in DENV-1 clade diversity was associated with an increase in the abundance of this serotype and a concomitant decrease in DENV-4 prevalence, while clade replacement was associated with a decline in DENV-1 prevalence and a rise of DENV-4. We postulate that intraserotypic genetic diversification proceeds at times of relative serotype abundance and that replacement events can result from differential susceptibility to cross-reactive immune responses.
Blockade of Neutrophil Elastase Attenuates Severe Liver Injury in Hepatitis B Transgenic Mice
Authors: Takai Shinji , Kimura Kiminori , Nagaki Masahito , Satake Shinichi , Kakimi Kazuhiro , Moriwaki Hisataka 
Published: November 2005

ABSTRACTSerine proteinases produced by polymorphonuclear neutrophils play important roles in neutrophil-mediated tissue injury at inflammatory sites. Although neutrophil recruitment to the liver has been shown to be involved in the exacerbation of liver inflammation, the function of neutrophil elastase (NE) in liver injury remains unclear. Here, we found that administration of an NE inhibitor (NEI) reduced serum alanine aminotransferase (sALT) activity and inflammatory cell infiltration into the liver from 8 to 24 h after injection of antigen-specific cytotoxic T lymphocytes (CTLs) into hepatitis B virus transgenic mice. Furthermore, the NEI treatment reduced the expressions of inflammatory cytokines and chemokines in the liver and tumor necrosis factor alpha production by macrophages. In addition, the NEI treatment suppressed the mRNA expressions of CC chemokine ligand 3 (CCL-3), CCL-4, and macrophage inflammatory protein 2 (MIP-2) in neutrophils in the liver at 8 h after the CTL injection. In support of these results, we confirmed that administration of anti-CCL-3, anti-CCL-4, and anti-MIP-2 monoclonal antibodies suppressed sALT activity and leukocyte migration into the liver. In conclusion, the present results suggest that NE contributes to the early step of the inflammatory cascade in acute viral hepatitis and that NEIs may have potential as therapeutic drugs against acute severe viral hepatitis.
Transcription Program of Red Sea Bream Iridovirus as Revealed by DNA Microarrays
Authors: Lua Dang Thi , Yasuike Motoshige , Hirono Ikuo , Aoki Takashi 
Published: November 2005

ABSTRACT

Red sea bream iridovirus (RSIV) has been identified as the causative agent of a serious disease in red sea bream and at least 30 other marine fish species. We developed a viral DNA microarray containing 92 putative open reading frames of RSIV to monitor the viral gene transcription program over the time course of an in vitro infection and to classify RSIV transcripts into temporal kinetic expression classes. The microarray analysis showed that viral genes commenced expression as early as 3 h postinfection (p.i.) and this was followed by a rapid escalation of gene expression from 8 h p.i. onwards. Based on the expression of some enzymes associated with viral DNA replication, the DNA replication of RSIV appeared to begin at around 8 h p.i. in infected cells in vitro. Using a de novo protein synthesis inhibitor (cycloheximide) and a viral DNA replication inhibitor (phosphonoacetic acid), 87 RSIV transcripts could be classified into three temporal kinetic classes: nine immediate-early (IE), 40 early (E), and 38 late (L) transcripts. The gene expression of RSIV occurred in a temporal kinetic cascade with three stages (IE, E, and L). Although the three classes of transcripts were distributed throughout the RSIV genome, E transcripts appeared to cluster in at least six discrete regions and L transcripts appeared to originate from seven discrete regions. The microarray data were statistically confirmed by using a
t
test, and were also clustered into groups based on similarity in the gene expression patterns by using a cluster program.
Rotavirus Glycoprotein NSP4 Is a Modulator of Viral Transcription in the Infected Cell
Authors: Silvestri Lynn S. , Tortorici M. Alejandra , Vasquez-Del Carpio Rodrigo , Patton John T. 
Published: November 2005

ABSTRACT
The outer shell of the rotavirus triple-layered virion is lost during cell entry, yielding a double-layered particle (DLP) that directs synthesis of viral plus-strand RNAs. The plus-strand RNAs act as templates for synthesis of the segmented double-stranded RNA (dsRNA) genome in viral inclusion bodies (viroplasms). The viral endoplasmic reticulum (ER)-resident glycoprotein NSP4 recruits progeny DLPs formed in viroplasms to the ER, where the particles are converted to triple-layered particles (TLPs) via budding. In this study, we have used short interfering RNAs to probe the role of NSP4 in the viral life cycle. Our analysis showed that knockdown of NSP4 expression had no marked effect on the expression of other viral proteins or on the replication of the dsRNA genome segments. However, NSP4 loss of function suppressed viroplasm maturation and caused a maldistribution of nonstructural and structural proteins that normally accumulate in viroplasms. NSP4 loss of function also inhibited formation of packaged virus particles, instead inducing the accumulation of empty particles. Most significant was the observation that NSP4 knockdown led to dramatically increased levels of viral transcription late in the infection cycle. These findings point to a multifaceted role for NSP4 in virus replication, including influencing the development of viroplasms, linking genome packaging with particle assembly, and acting as a modulator of viral transcription. By recruiting transcriptionally active or potentially active DLPs to the ER for conversion to quiescent TLPs, NSP4 acts as a feedback inhibitor down-regulating viral transcription when adequate levels of plus-strand RNAs are available to allow for productive infection.
RDR6 Has a Broad-Spectrum but Temperature-Dependent Antiviral Defense Role in
Nicotiana benthamiana
Authors: Qu Feng , Ye Xiaohong , Hou Guichuan , Sato Shirley , Clemente Thomas E. , Morris T. Jack 
Published: November 2005

ABSTRACT

SDE1/SGS2/RDR6, a putative RNA-dependent RNA polymerase (RdRP) from
Arabidopsis thaliana
, has previously been found to be indispensable for maintaining the posttranscriptional silencing of transgenes, but it is seemingly redundant for antiviral defense. To elucidate the antiviral role of this RdRP in a different host plant and to evaluate whether plant growth conditions affect its role, we down-regulated expression of the
Nicotiana benthamiana
homolog, NbRDR6, and examined the plants for altered susceptibility to various viruses at different growth temperatures. The results we describe here clearly show that plants with reduced expression of NbRDR6 were more susceptible to all viruses tested and that this effect was more pronounced at higher growth temperatures. Diminished expression of NbRDR6 also permitted efficient multiplication of tobacco mosaic virus in the shoot apices, leading to serious disruption with microRNA-mediated developmental regulation. Based on these results, we propose that NbRDR6 participates in the antiviral RNA silencing pathway that is stimulated by rising temperatures but suppressed by virus-encoded silencing suppressors. The relative strengths of these two factors, along with other plant defense components, critically influence the outcome of virus infections.
Upregulation of Protein Phosphatase 2Ac by Hepatitis C Virus Modulates NS3 Helicase Activity through Inhibition of Protein Arginine Methyltransferase 1
Authors: Duong Francois H. T. , Christen Verena , Berke Jan Martin , Penna Sabina Hernandez , Moradpour Darius , Heim Markus H. 
Published: November 2005

ABSTRACT
Hepatitis C virus (HCV) is a major cause of chronic liver disease, cirrhosis, and hepatocellular carcinoma worldwide. HCV has a positive-strand RNA genome of about 9.4 kb in size, which serves as a template for replication and for translation of a polyprotein of about 3,000 amino acids. The polyprotein is cleaved co- and posttranslationally by cellular and viral proteases into at least 10 different mature proteins. One of these proteins, nonstructural protein 3 (NS3), has serine protease and NTPase/RNA helicase activity. Arginine 467 in the helicase domain of NS3 (arginine 1493 in the polyprotein) can be methylated by protein arginine methyltransferase 1 (PRMT1). Here we report that the methylation of NS3 inhibits the enzymatic activity of the helicase. Furthermore, we found that PRMT1 activity itself is regulated by protein phosphatase 2A (PP2A). PP2A inhibits PRMT1 enzymatic activity and therefore increases the helicase activity of NS3. This is important, because we found an increased expression of PP2A in cell lines with inducible HCV protein expression, in transgenic mice expressing HCV proteins in hepatocytes, and in liver biopsy samples from patients with chronic hepatitis C. Interestingly, up-regulation of PP2A not only modulates the enzymatic activity of an important viral protein, NS3 helicase, but also interferes with the cellular defense against viruses by inhibiting interferon-induced signaling through signal transducer and activator of transcription 1 (STAT1). We conclude that up-regulation of PP2A might be crucial for the efficient replication of HCV and propose PP2A as a potential target for anti-HCV treatment strategies.
Activation of the ATR Pathway by Human Immunodeficiency Virus Type 1 Vpr Involves Its Direct Binding to Chromatin In Vivo
Authors: Lai Maoyi , Zimmerman Erik S. , Planelles Vicente , Chen Junjie 
Published: November 2005

ABSTRACT

The human immunodeficiency virus type 1 (HIV-1) protein Vpr (viral protein R) arrests cells in the G
2
phase of the cell cycle, a process that requires activation of the ATR (ataxia-telangiectasia and Rad3-related) pathway. In this study we demonstrate that the expression of Vpr does not cause DNA double-strand breaks but rather induces ATR activation, as indicated by induction of Chk1 phosphorylation and the formation of γ-H2AX and 53BP1 nuclear foci. We define a C-terminal domain containing repeated H(F/S)RIG sequences required for Vpr-induced activation of ATR. Further investigation of the mechanism by which Vpr activates the ATR pathway reveals an increase in chromatin binding of replication protein A (RPA) upon Vpr expression. Immunostaining shows that RPA localizes to nuclear foci in Vpr-expressing cells. Furthermore, we demonstrate direct binding of Vpr to chromatin in vivo, whereas Vpr C-terminal domain mutants lose this chromatin-binding activity. These data support a mechanism whereby HIV-1 Vpr induces ATR activation by targeting the host cell DNA and probably interfering with normal DNA replication.
Recombination in the Genesis and Evolution of Hepatitis B Virus Genotypes
Authors: Simmonds Peter , Midgley Sofie 
Published: November 2005

ABSTRACT
Hepatitis B virus (HBV) infection is widely distributed in both human and ape populations throughout the world and is a major cause of human morbidity and mortality. HBV variants are currently classified into the human genotypes A to H and species-associated chimpanzee and gibbon/orangutan groups. To examine the role of recombination in the evolution of HBV, large-scale data retrieval and automated phylogenetic analysis (TreeOrder scanning) were carried out on all available published complete genome sequences of HBV. We detected a total of 24 phylogenetically independent potential recombinants (different genotype combinations or distinct breakpoints), eight of which were previously undescribed. Instances of intergenotype recombination were observed in all human and ape HBV variants, including evidence for a novel gibbon/genotype C recombinant among HBV variants from Vietnam. By recording sequence positions in trees generated from sequential fragments across the genome, violations of phylogeny between trees also provided evidence for frequent intragenotype recombination between members of genotypes A, D, F/H, and gibbon variants but not in B, C, or the Asian B/C recombinant group. In many cases, favored positions for both inter- and intragenotype recombination matched positions of phylogenetic reorganization between the human and ape genotypes, such as the end of the surface gene and the core gene, where sequence relationships between genotypes changed in the TreeOrder scan. These findings provide evidence for the occurrence of past, extensive recombination events in the evolutionary history of the currently classified genotypes of HBV and potentially in changes in its global epidemiology and associations with human disease.
How evidence based is the management of two common sports injuries in a sports injury clinic?
Authors: Murray I R , Murray S A , MacKenzie K , Coleman S 
Published: November 2005

Objectives:To examine the diagnosis and management of adults attending a sports injury clinic, to establish to what extent the management of the two most common injuries treated at this clinic is evidence based, and to explore factors that affect management.Methods:A retrospective examination of 100 random case notes extracted age, sex, sport, type and site of injury, treatment, and outcome. Systematic literature reviews examined the extent and quality of scientific evidence for the management of the two most commonly presenting injuries. A clinical attachment period and practitioner interviews allowed recognition of factors impinging on management decisions.Results:Patellofemoral pain syndrome (PFPS; 10% of all injuries) and Achilles tendinopathy (6% of all injuries) were the most commonly presenting injuries. The mean (SD) number of treatments used for PFPS was 2.8 (0.9). The mean number of treatments used for Achilles tendinopathy was 3.7 (1.0). Clinicians reported that personal experience formed the basis of management plans in 44% of PFPS cases and 59% of Achilles tendinopathy cases, and that primary research evidence only accounted for 24% of management plans in PFPS and 14% in Achilles tendinopathy. Practitioners were unaware of literature supporting over 50% of the treatment modalities they used. However, clinicians were often using evidence based treatments, unaware of the supporting research data.Conclusions:This study highlights a lack of evidence base, a lack of knowledge of the research evidence, and a lack of management based on the current evidence that is available for these conditions. Practitioners practised evidence based medicine in under 50% of cases.
Specificity of V˙o2max and the ventilatory threshold in free swimming and cycle ergometry: comparison between triathletes and swimmers
Authors: Roels B , Schmitt L , Libicz S , Bentley D , Richalet J-P , Millet G 
Published: November 2005

Objectives:To compare maximal heart rate (HRmax), maximal oxygen consumption (V˙o2max), and the ventilatory threshold (VT; %V˙o2max) during cycle ergometry and free swimming between swimmers and triathletes.Methods:Nine swimmers and ten triathletes completed an incremental swimming and cycling test to exhaustion. Whole body metabolic responses were determined in each test.Results:The swimmers exhibited a significantly higher V˙o2maxin swimming than in cycling (58.4 (5.6)v51.3 (5.1) ml/kg/min), whereas the opposite was found in the triathletes (53.0 (6.7)v68.2 (6.8) ml/kg/min). HRmaxwas significantly different in the maximal cycling and swimming tests for the triathletes (188.6 (7.5)v174.8 (9.0) beats/min). In the maximal swimming test, HRmaxwas significantly higher in the swimmers than in the triathletes (174.8 (9.0)v184.6 (9.7) beats/min). No significant differences were found for VT measured in swimming and cycling in the triathletes and swimmers.Conclusion:This study confirms that the exercise testing mode affects the V˙o2maxvalue, and that swimmers have very specific training adaptations even compared with triathletes. This may be a function of acute physiological responses combined with the specialist training status of the different athletes influencing maximal cardiac output or oxygen extraction. In contrast, the different training regimens do not seem to influence the VT, as this variable did not differ between the two testing modes in either group.
Effects of mycorrhizal inoculant, N:P supply ratio, and water depth on the growth and biomass allocation of three wetland plant species
Authors: Fraser Lauchlan H. , Feinstein Larry M. 
Published: November 2005

In the greenhouse, we investigated the growth and biomass allocation of three juvenile wetland species ( Carex tribuloides Wahl., Phalaris arundinacea L., and Rumex orbiculatus Gray) under three different water depths (–4, 0, and +2 cm relative to the soil surface), three N:P supply ratios (1:30, 1:1, 30:1), and two mycorrhizal inoculant treatments (arbuscular mycorrhizal (AM) fungi present, absent). After 6 weeks, the plants were harvested, separated to above- and below-ground parts, oven-dried, and weighed. The mycorrhizal inoculant significantly increased plant growth and reduced root:shoot ratios. At an N:P supply ratio of 30:1, plants with AM fungi had significantly greater biomass than those plants without AM fungi. However, at 1:1 N:P supply ratio, plants without AM fungi had greater biomass. Plants without AM fungi had higher root:shoot ratios at 0 and –4 cm water depth than plants with AM fungi. In general, C. tribuloides had the lowest growth, and unlike P. arundinacea and R. orbiculatus, was not affected by the water depth treatment. Growth of the wetland plants was limited more by nitrogen than by phosphorus. Our results suggest that at high N:P nutrient supply ratios and non-flooded conditions the growth of wetland seedlings can benefit by being inoculated with AM fungi.
Spatial and temporal dynamicsof Puccinia andropogonisonComandra umbellataandAndropogon gerardiiin a native prairie
Authors: Barnes Charles W. , Kinkel Linda L. , Groth James V. 
Published: November 2005

The rust Puccinia andropogonis (Schwein.) was studied on its aecial and telial plant hosts, comandra ( Comandra umbellata L. Nutt.) and big bluestem ( Andropogon gerardii Vitman), respectively, in a native prairie to investigate the influence of aecial host proximity on disease severity of the telial host in a natural system. Both hosts were mapped to measure distances from comandra clones to selected big bluestem plants in a Minnesota prairie. Mean rust severity on big bluestem was regressed on the number of aecia on comandra (aecial density) within eight distance intervals from big bluestem plants. Distance intervals were analyzed both inclusive and exclusive of other distance intervals. There was a significant positive relationship between aecial density on comandra and rust severity on big bluestem that decreased with increasing distance in accordance with the power law model, becoming nonsignificant at distances >40 m. To establish whether the genetic background of big bluestem influenced the relationship between rust severity and the distance to comandra, a common garden was planted with a representative big bluestem plant population. The low coefficient of determination (r2) between mean rust severities of individual plants from one year to another suggests there is not a strong genetic component in the host determining disease severity.
A General Method of Incorporating Forecast Cost and Loss in Value Scores
Authors: Briggs William 
Published: November 2005

Abstract
In this note, the author shows how to incorporate cost for correct forecasts in the skill score statistical test developed by Briggs and Ruppert and how to extend this result to another value score developed by Wilks. It is then shown that both of these methods are special cases of a more general complete value score, where the loss and costs are allowed to be completely general.
Misocyclone Characteristics along Florida Gust Fronts during CaPE
Authors: Friedrich Katja , Kingsmill David E. , Young Carl R. 
Published: November 2005

Abstract
Multiple-Doppler radar and rawinsonde data are used to examine misocyclone characteristics along gust fronts observed during the Convection and Precipitation/Electrification (CaPE) project in Florida. The objective of this study is to investigate the observational representativeness of previous numerical simulations of misocyclones by employing a consistent analysis strategy to 11 gust fronts observed in the same region. The investigation focuses on the intensity range of misocyclones and their organization along gust fronts; the relationship between misocyclone intensity and horizontal wind shear, vertical wind shear, and static stability; and the relationship between misocyclones and convection initiation.
The intensity of misocyclones, as indicated by the maximum values of vertical vorticity, varied from 2.8 × 10−3 to 13.9 × 10−3 s−1, although all but one case exhibited values less than 6.4 × 10−3 s−1. Organized misocyclone patterns were only found along small segments of gust fronts. Within those segments misocyclones were spaced between 3 and 7 km. Results show that the intensity of misocyclones was most closely related to the strength of horizontal wind shear across the gust front. The relationship between misocyclone intensity and vertical wind shear and static stability was not as clear. Although convection was initiated along the gust front in 7 of the 11 cases, those regions were not collocated with or in close proximity to misocyclones.