bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Putative Pocket Protein Binding Site of
Autographa californica
Nucleopolyhedrovirus BV/ODV-C42 Is Required for Virus-Induced Nuclear Actin Polymerization
Authors: Li Kun , Wang Yun , Bai Huimin , Wang Qian , Song Jianhua , Zhou Yuan , Wu Chunchen , Chen Xinwen 
Published: May 2010

ABSTRACT

Nuclear filamentous actin (F-actin) is essential for nucleocapsid morphogenesis of lepidopteran nucleopolyhedroviruses. Previously, we had demonstrated that
Autographa californica
multiple nucleopolyhedrovirus (
Ac
MNPV) BV/ODV-C42 (C42) is involved in nuclear actin polymerization by recruiting P78/83, an
Ac
MNPV
orf9
-encoded N-WASP homology protein that is capable of activating an actin-related-protein 2/3 (Arp2/3) complex to initiate actin polymerization, to the nucleus. To further investigate the role of C42 in virus-induced actin polymerization, the recombinant bacmid vAc
p78/83nls-gfp
, with a
c42
knockout,
p78/83
tagged with a nuclear localization signal coding sequence, and
egfp
as a reporter gene under the control of the
Pp10
promoter, was constructed and transfected to Sf9 cells. In the nuclei of vAc
p78/83nls-gfp
-transfected cells, polymerized F-actin filaments were absent, whereas other actin polymerization elements (i.e., P78/83, G-actin, and Arp2/3 complex) were present. This
in vivo
evidence indicated that C42 actively participates in the nuclear actin polymerization process as a key element, besides its role in recruiting P78/83 to the nucleus. In order to collect
in vitro
evidence for the participation of C42 in actin polymerization, an anti-C42 antibody was used to neutralize the viral nucleocapsid, which is capable of initiating actin polymerization
in vitro
. Both the kinetics of pyrene-actin polymerization and F-actin-specific staining by phalloidin indicated that anti-C42 can significantly attenuate the efficiency of F-actin formation compared to that with control antibodies. Furthermore, we have identified the putative pocket protein binding sequence (PPBS) on C42 that is essential for C42 to exert its function in nuclear actin polymerization.
Differential Expression of the miR-200 Family MicroRNAs in Epithelial and B Cells and Regulation of Epstein-Barr Virus Reactivation by the miR-200 Family Member miR-429
Authors: Lin Zhen , Wang Xia , Fewell Claire , Cameron Jennifer , Yin Qinyan , Flemington Erik K. 
Published: May 2010

ABSTRACT
The miR-200 microRNA family is important for maintaining the epithelial phenotype, partially through suppressing ZEB1 and ZEB2. Since ZEB1 inhibits Epstein-Barr virus (EBV) reactivation, we hypothesized that expression of miR-200 family members in epithelial cells may partly account for higher levels of EBV reactivation in this tissue (relative to nonplasma B cells). Here we show that, whereas miR-200 family members are expressed in epithelial cells, their expression is low in latently infected B cells. Furthermore, the miR-200 family member miR-429 shows elevated expression in plasma cell lines and is induced by B-cell-receptor activation in Akata cells. Lastly, expression of miR-429 can break latency.
Phosphatidylinositol 3-Kinase-, Actin-, and Microtubule-Dependent Transport of Semliki Forest Virus Replication Complexes from the Plasma Membrane to Modified Lysosomes
Authors: Spuul Pirjo , Balistreri Giuseppe , Kääriäinen Leevi , Ahola Tero 
Published: May 2010

ABSTRACT
Like other positive-strand RNA viruses, alphaviruses replicate their genomes in association with modified intracellular membranes. Alphavirus replication sites consist of numerous bulb-shaped membrane invaginations (spherules), which contain the double-stranded replication intermediates. Time course studies with Semliki Forest virus (SFV)-infected cells were combined with live-cell imaging and electron microscopy to reveal that the replication complex spherules of SFV undergo an unprecedented large-scale movement between cellular compartments. The spherules first accumulated at the plasma membrane and were then internalized using an endocytic process that required a functional actin-myosin network, as shown by blebbistatin treatment. Wortmannin and other inhibitors indicated that the internalization of spherules also required the activity of phosphatidylinositol 3-kinase. The spherules therefore represent an unusual type of endocytic cargo. After endocytosis, spherule-containing vesicles were highly dynamic and had a neutral pH. These primary carriers fused with acidic endosomes and moved long distances on microtubules, in a manner prevented by nocodazole. The result of the large-scale migration was the formation of a very stable compartment, where the spherules were accumulated on the outer surfaces of unusually large and static acidic vacuoles localized in the pericentriolar region. Our work highlights both fundamental similarities and important differences in the processes that lead to the modified membrane compartments in cells infected by distinct groups of positive-sense RNA viruses.
Cross-Reactive Neutralizing Antibodies Directed against Pandemic H1N1 2009 Virus Are Protective in a Highly Sensitive DBA/2 Mouse Influenza Model
Authors: Boon Adrianus C. M. , deBeauchamp Jennifer , Krauss Scott , Rubrum Adam , Webb Ashley D. , Webster Robert G. , McElhaney Janet , Webby Richard J. 
Published: May 2010

ABSTRACTOur ability to rapidly respond to an emerging influenza pandemic is hampered somewhat by the lack of a susceptible small-animal model. To develop a more sensitive model, we pathotyped 18 low-pathogenic non-mouse-adapted influenza A viruses of human and avian origin in DBA/2 and C57BL/6 mice. The majority of the isolates (13/18) induced severe morbidity and mortality in DBA/2 mice upon intranasal challenge with 1 million infectious doses. Also, at a 100-fold-lower dose, more than 50% of the viruses induced severe weight loss, and mice succumbed to the infection. In contrast, only two virus strains were pathogenic for C57BL/6 mice upon high-dose inoculation. Therefore, DBA/2 mice are a suitable model to validate influenza A virus vaccines and antiviral therapies without the need for extensive viral adaptation. Correspondingly, we used the DBA/2 model to assess the level of protection afforded by preexisting pandemic H1N1 2009 virus (H1N1pdm) cross-reactive human antibodies detected by a hemagglutination inhibition assay. Passive transfer of these antibodies prior to infection protected mice from H1N1pdm-induced pathogenicity, demonstrating the effectiveness of these cross-reactive neutralizing antibodiesin vivo.
Upregulation of the Chemokine (C-C Motif) Ligand 2 via a Severe Acute Respiratory Syndrome Coronavirus Spike-ACE2 Signaling Pathway
Authors: Chen I-Yin , Chang Shin C. , Wu Hung-Yi , Yu Ting-Chun , Wei Wen-Chin , Lin Shiming , Chien Chung-Liang , Chang Ming-Fu 
Published: May 2010

ABSTRACT
Severe acute respiratory syndrome coronavirus (SARS-CoV) was identified to be the causative agent of SARS with atypical pneumonia. Angiotensin-converting enzyme 2 (ACE2) is the major receptor for SARS-CoV. It is not clear whether ACE2 conveys signals from the cell surface to the nucleus and regulates expression of cellular genes upon SARS-CoV infection. To understand the pathogenesis of SARS-CoV, human type II pneumocyte (A549) cells were incubated with the viral spike protein or with SARS-CoV virus-like particles containing the viral spike protein to examine cytokine modulation in lung cells. Results from oligonucleotide-based microarray, real-time PCR, and enzyme-linked immunosorbent assays indicated an upregulation of the fibrosis-associated chemokine (C-C motif) ligand 2 (CCL2) by the viral spike protein and the virus-like particles. The upregulation of CCL2 by SARS-CoV spike protein was mainly mediated by extracellular signal-regulated kinase 1 and 2 (ERK1/2) and AP-1 but not the IκBα-NF-κB signaling pathway. In addition, Ras and Raf upstream of the ERK1/2 signaling pathway were involved in the upregulation of CCL2. Furthermore, ACE2 receptor was activated by casein kinase II-mediated phosphorylation in cells pretreated with the virus-like particles containing spike protein. These results indicate that SARS-CoV spike protein triggers ACE2 signaling and activates fibrosis-associated CCL2 expression through the Ras-ERK-AP-1 pathway.
Temperature dependence of saturated vapour pressures of methyl isobutyl ketone, diisobutyl ketone, 1,1-difluorotetrachloroethane, and 1,2-difluorotetrachloroethane
Authors: Svoboda Václav , Adamcová Zdena , Kubeš Vladimír 
Published: May 2010

Temperature dependence of saturated vapour pressures of methyl isobutyl ketone, diisobutyl ketone, 1,1-difluorotetrachloroethane, and 1,2-diflurotetrachloethane was measured. A static method was used, and the measurements were carried out in the temperature range of 261 to 353 K and in the pressure range of 0.5-49 kPa.
Injury-prevention priorities according to playing position in professional rugby union players
Authors: Brooks J H M , Kemp S P T 
Published: May 2010

ObjectiveTo examine the match injury profile of professional rugby union players by individual playing position.Design4-season prospective cohort design.Setting14 English Premiership clubs.Participants899 professional players.Main outcome measureIncidence of match injury (recorded as the number of injuries/1000 player-hours of match exposure), severity of injury (recorded as the number of days of absence) and days of absence due to injury per 1000 player-hours of match exposure.Assessment of risk factorsInjury diagnosis and individual playing position during a match.Results2484 injuries were reported. While there were no significant differences in the total days of absence as a result of injury between different positions in the forwards and the backs, there were a number of significant differences in injury profile for players in individual playing positions. Although three common body locations caused a high proportion of days of absence due to match injury for forwards (shoulder, knee, ankle/heel) and backs (shoulder, hamstring, knee), there were significant differences in injury profile between individual positions.ConclusionsThe results clearly demonstrate the need for individual position-specific injury-prevention programmes in rugby union. When devising such programmes, a player's previous injury history should also be taken into account.
Reliability and validity testing of a single-item physical activity measure
Authors: Milton K , Bull F C , Bauman A 
Published: May 2010

ObjectiveTo develop and test a new single-item physical activity screening tool, suitable for assessing respondents' eligibility for behaviour change interventions.DesignTwo single-item assessment tools were developed, one using a “past week” recall period, the other using a “past month” recall period. A quota sampling system was used to recruit 480 adults from across England, Scotland and Wales. Half the sample completed the past-week question and half completed the past-month version. Test–retest reliability was assessed over a 2- to 5-day period. Concurrent validity was assessed using the Global Physical Activity Questionnaire and the UK Active People Survey. All surveys were completed via telephone interviews.ResultsBoth versions of the single-item instrument demonstrated strong reproducibility (r=0.72–0.82), using Spearman's rank correlation coefficients. The past-week recall question showed strong agreement in the classification of respondents meeting the current physical activity recommendation (kappa=0.63, 95% CI 0.54 to 0.72).Concurrent validity over the past week compared to the Global Physical Activity Questionnaire was modest (r=0.53) and slightly weaker for the past month compared to the Active People Survey (r=0.33–0.48).ConclusionBoth versions of the new single-item measure performed as well as other short physical activity tools in terms of reliability and concurrent validity. Criterion validity testing of the single-item measure is recommended to establish its ability to assess objectively measured physical activity levels. In addition, further research to assess the responsiveness of the single-item measure in detecting changes in physical activity will inform its usefulness in programme evaluation.
Ingestion of sodium citrate suppresses aldosterone level in blood at rest and during exercise
Authors: Ööpik Vahur , Timpmann Saima , Hackney Anthony C. , Kadak Kadri , Medijainen Luule , Karelson Kalle 
Published: May 2010

The purpose of this study was to determine if the ingestion of sodium citrate (CIT) alters blood levels of fluid and electrolyte regulatory hormones at rest and during exercise. Using a randomized, double-blinded, crossover design, 13 young, male well-trained runners performed continuous incremental running tests to volitional exhaustion on a treadmill 2 h after ingestion of 0.5 g·kg–1 body mass of CIT or placebo (PLC) in 1000 mL of solution. These trials were separated by 2 weeks. Baseline (before ingestion) aldosterone concentration did not differ between the 2 trials; however, it was 36.5% (p = 0.003) lower in the CIT trial compared with the PLC trial before the running test (i.e., after ingestion). The extent of the running-induced increase in aldosterone was 33% (p = 0.009) smaller in the CIT trial. There were no between-trial differences in the levels of adrenocorticotropic hormone, N-terminal pro-B-type natriuretic peptide, or renin activity at any stage of the study. However, a greater relative increase in plasma volume (mean ± SD, 6.41% ± 3.78% vs. 4.08% ± 3.33%; p = 0.042) was observed after administering the CIT compared with the PLC drink. Serum Na+ concentration increased (by 3.1 ± 1.2 mmol·L–1; p < 0.0001) after ingestion of the CIT but not the PLC drink. A higher Na+ level was observed in the CIT trial than in the PLC trial (142.4 ± 1.6 vs. 139.3 ± 1.4 mmol·L–1, p = 0.00001) after completion of the run. In conclusion, pre-exercise ingestion of CIT induces a decrease in serum aldosterone concentration in the resting condition and a blunting of the aldosterone response during incremental running exercise to volitional exhaustion. The observed effect of CIT on the serum aldosterone level may be mediated by an acute increase in plasma volume and serum Na+ concentration alterations.
Protective effects of polyphenolic compounds on oxidative stress-induced cytotoxicity in PC12 cells
Authors: Crispo James A.G. , Ansell Dominique R. , Piche Matthew , Eibl Joseph K. , Khaper Neelam , Ross Gregory M. , Tai T.C. 
Published: May 2010

To investigate the beneficial properties associated with polyphenols, we screened 12 polyphenols for their ability to increase the viability of PC12 cells subjected to oxidative stress via CoCl2 and H2O2. Cell viability data demonstrate that 50 µmol/L methyl gallate and 50 µmol/L fisetin significantly increase viability of H2O2-stressed cells. Further, viability data suggest that 100 µmol/L epigallocatechin gallate (EGCG) increases basal viability, but has no rescue effect on cells stressed with CoCl2 or H2O2. Analysis of intracellular reactive oxygen species (ROS) shows that EGCG, methyl gallate, and gallic acid are effective in reducing CoCl2-derived ROS, and that methyl gallate is effective in attenuating H2O2-derived ROS. Examination of nitric oxide concentrations shows that methyl gallate significantly increases nitric oxide, both in nonstressed and H2O2-stressed cells, whereas EGCG results are consistent with the scavenging of nitric oxide under nonstressed and stressed conditions. Furthermore, analysis of total glutathione levels reveals that EGCG, methyl gallate, and gallic acid pretreatments with and without H2O2 stress have the ability to significantly alter glutathione metabolism. These findings suggest that EGCG, methyl gallate, and gallic acid may have potential therapeutic properties.
Sex Differences in Mortality Associated With Computed Tomographic Angiographic Measurements of Obstructive and Nonobstructive Coronary Artery Disease
Authors: Shaw Leslee J. , Min James K. , Narula Jagat , Lin Fay , Bairey-Merz C. Noel , Callister Tracy Q. , Berman Daniel S. 
Published: May 2010

Background—
Sex differences exist in the prevalence and severity of obstructive coronary artery disease (CAD). Limited data are available to explore sex differences in prognosis with coronary computed tomographic angiographic (CCTA) measurements of CAD including novel nonobstructive plaque extent.

Methods and Results—

A total of 1127 consecutive patients were clinically referred to 16-slice CCTA and followed for the occurrence of all-cause death. Time to death was calculated by univariable and multivariable Cox proportional hazard models. Four-year survival (92.1%) was similar by sex (
P
=0.52). Women more often had no coronary stenosis (54%) as compared with men (28%) (
P
<0.0001). Mortality worsened for both women (
P
<0.0001) and men (
P
=0.002) by the number of vessels with ≥50% stenosis. For women, overall mortality ranged from 3.5% for no CAD to 25.0% for women with 3-vessel plus left main obstructive CAD (
P
<0.0001). For men, overall mortality ranged from 2.7% for no CAD to 17.4% for males with 3-vessel plus left main obstructive CAD (
P
=0.002). Nonobstructive disease was prevalent in women (range, 24% to 66%) and men (range, 45% to 74%) ages 45 to ≥80 years. Nonobstructive CAD extent was a significant estimator of all-cause mortality when added to a model containing pretest CAD likelihood and obstructive CAD extent (
P
=0.039). For men, in a risk-adjusted model including pretest CAD likelihood and obstructive CAD, the number of nonobstructive lesions was not a significant estimator of mortality (
P
=0.9). For women, the relative hazard for mortality, in a multivariable model, was 1.3 per nonobstructive lesion (
P
=0.003), including pretest CAD likelihood and obstructive CAD as covariates. For women, risk-adjusted median mortality ranged from 2.9% to 10.9% for none to ≥4 nonobstructive lesions (
P
<0.0001).

Conclusions—
Based on our preliminary analyses, CCTA obstructive and nonobstructive CAD adds incremental value to clinical assessment for risk stratification. Moreover, the extent of nonobstructive CAD by CCTA predicts mortality in women but not in men and may be helpful to optimize therapeutic strategies for women.
Incremental Diagnostic Value of Regional Left Ventricular Function Over Coronary Assessment by Cardiac Computed Tomography for the Detection of Acute Coronary Syndrome in Patients With Acute Chest Pain
Authors: Seneviratne Sujith K. , Truong Quynh A. , Bamberg Fabian , Rogers Ian S. , Shapiro Michael D. , Schlett Christopher L. , Chae Claudia U. , Cury Ricardo , Abbara Suhny , Brady Thomas J. , Nagurney John T. , Hoffmann Udo 
Published: May 2010

Background—
The incremental value of regional left ventricular function (LVF) over coronary assessment to detect acute coronary syndrome (ACS) is uncertain.

Methods and Results—

We analyzed 356 patients (mean age, 53±12 years; 62% men) with acute chest pain and inconclusive initial emergency department evaluation. Patients underwent 64-slice contrast-enhanced cardiac computed tomography before hospital admission. Caregivers and patients remained blinded to the results. Regional LVF and presence of coronary atherosclerotic plaque and significant stenosis (>50%) were separately assessed by 2 independent readers. Incremental value of regional LVF to predict ACS was determined in the entire cohort and in subgroups of patients with nonobstructive coronary artery disease, inconclusive assessment for stenosis (defined as inability to exclude significant stenosis due to calcium or motion), and significant stenosis. During their index hospitalization, 31 patients were ultimately diagnosed with ACS (8 myocardial infarction, 22 unstable angina), of which 74% (23 patients) had regional LV dysfunction. Adding regional LVF resulted in a 10% increase in sensitivity to detect ACS by cardiac computed tomography (87%; 95% confidence interval, 70% to 96%) and significantly improved the overall accuracy (c-statistic: 0.88 versus 0.94 and 0.79 versus 0.88, for extent of plaque and presence of stenosis, respectively; both
P
<0.03). The diagnostic accuracy of regional LVF for detection of ACS has 89% sensitivity and 86% specificity in patients with significant stenosis (n=33) and 60% sensitivity and 86% specificity in patients with inconclusive coronary computed tomographic angiography (n=33).

Conclusions—
Regional LVF assessment at rest improves diagnostic accuracy for ACS in patients with acute chest pain, especially in those with coronary artery disease and thus may be helpful to guide further management in patients at intermediate risk for ACS.

Clinical Trial Registration—

URL:
http://www.clinicaltrials.gov
. Unique identifier: NCT00990262.
Binary image representation of a ligand binding site: its application to efficient sampling of a conformational ensemble
Authors: Sung Edon , Kim Sangsoo , Shin Whanchul 
Published: May 2010

Abstract

Background
Modelling the ligand binding site of a protein is an important component of understanding protein-ligand interactions and is being actively studied. Even if the side chains are restricted to rotamers, a set of commonly-observed low-energy conformations, the exhaustive combinatorial search of ligand binding site conformers is known as NP-hard. Here we propose a new method, ROTAIMAGE, for modelling the plausible conformers for the ligand binding site given a fixed backbone structure.

Results
ROTAIMAGE includes a procedure of selecting ligand binding site residues, exhaustively searching rotameric conformers, clustering them by dissimilarities in pocket shape, and suggesting a representative conformer per cluster. Prior to the clustering, the list of conformers generated by exhaustive search can be reduced by pruning the conformers that have near identical pocket shapes, which is done using simple bit operations. We tested our approach by modelling the active-site inhibitor binding pockets of matrix metalloproteinase-1 and -13. For both cases, analyzing the conformers based on their pocket shapes substantially reduced the 'computational complexity' (10 to 190 fold). The subsequent clustering revealed that the pocket shapes of both proteins could be grouped into approximately 10 distinct clusters. At this level of clustering, the conformational space spanned by the known crystal structures was well covered. Heatmap analysis identified a few bit blocks that combinatorially dictated the clustering pattern. Using this analytical approach, we demonstrated that each of the bit blocks was associated with a specific pocket residue. Identification of residues that influenced the shape of the pocket is an interesting feature unique to the ROTAIMAGE algorithm.

Conclusions
ROTAIMAGE is a novel algorithm that was efficient in exploring the conformational space of the ligand binding site. Its ability to identify 'key' pocket residues also provides further insight into conformational flexibility with specific implications for protein-ligand interactions.