187 research outputs found

    Swiss EMBnet node web server

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    EMBnet is a consortium of collaborating bioinformatics groups located mainly within Europe (http://www.embnet.org). Each member country is represented by a ‘node', a group responsible for the maintenance of local services for their users (e.g. education, training, software, database distribution, technical support, helpdesk). Among these services a web portal with links and access to locally developed and maintained software is essential and different for each node. Our web portal targets biomedical scientists in Switzerland and elsewhere, offering them access to a collection of important sequence analysis tools mirrored from other sites or developed locally. We describe here the Swiss EMBnet node web site (http://www.ch.embnet.org), which presents a number of original services not available anywhere els

    Longitudinal associations of skipping breakfast with ethnicity and cardiometabolic risk: the Determinants of Adolescence, now young Adults, Social well-being and Health Study (DASH)

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    Ethnic inequalities in cardiometabolic disease(1,2) may be explained by differences in diet and lifestyle. Poor dietary habits, such as skipping breakfast and consumption of fizzy drinks and fast foods are more common amongst ethnic minority children and adolescents(3,4) . The long-term effects of these childhood behaviours on adult cardiometabolic risk factors have not yet been investigated in an ethnically diverse population. We aimed to assess ethnic patterns in adolescent and young adult breakfast skipping and its influence on cardiometabolic risk in young adulthood amongst a diverse UK cohort. The DASH cohort was recruited in 2002/03 and consisted of 6643 11–13 year olds, sampled to represent the main ethnic groups of the UK population. The ‘DASH 10 years on’ study is a longitudinal follow-up of a subset of the cohort who are now young adults (21–23 years). Participants had anthropometric measures (weight, BMI, waist circumference), blood pressure, total and HDL-cholesterol and HbA1c assessed and completed a short dietary behaviours questionnaire indicating how frequently they consume breakfast (daily, 3–4 days a week, 1–2 days a week, never/hardly ever). The cohort consisted of 311 males (age 22·8 (95 % CI 22·7, 22·9) years; BMI 24·7 (95 % CI 24·3, 25·2) kg/m2 ) and 316 females (age 22·7 (95 % CI 22·6, 22·8) years; BMI 24·9 (95 % CI 24·3, 25·5) kg/m2 ). A total of 107 White British, 102 Black Caribbean, 132 Black African, 99 Indian, 111 Bangladeshi or Pakistani and 115 Other (mainly mixed) were included in the follow-up. In young adulthood regular breakfast skipping was reported by 56 % of participants; Black African participants were more likely to skip breakfast than White British (OR: 1·81, 1·04 to 3·17, p = 0·004). The highest proportion of breakfast skipping occurred amongst the Black Caribbean (66 %) and Black African (64 %) groups and the lowest amongst Indian participants (46 %). The impact of skipping breakfast during both adolescence and young adulthood on cardiometabolic risk factors during young adulthood were investigated using multivariate regression modelling. Skipping breakfast at 11–13 years was a significant determinant of BMI at 21–23 years (1·45 (95 % CI 0·61, 2·29), p = 0·001) as was skipping breakfast at 21–23 years, although the effect was slightly attenuated in this age group (0·92 (95 % CI 0·1, 1·73), p = 0·027). Skipping breakfast at both 11–13 years and 21–23 years were also important determinants of total cholesterol levels (11–13 years: 0·17 (95 % CI 0·01, 0·33), p = 0·041; 21–23 years: 0·23 (95 % CI 0·07, 0·38), p = 0·003). This is the first longitudinal assessment of breakfast skipping and its impact on cardiometabolic risk factors amongst an ethnically diverse cohort of young adults in the UK. In this work we have recognised the detrimental impact of childhood breakfast skipping on cardiometabolic risk factors, such as BMI and cholesterol concentrations, in young adulthood. Furthermore we have identified distinct ethnic patterns in breakfast skipping, such that skipping breakfast is most prevalent amongst Black African and Caribbean groups and less common amongst Indians. Our findings provide a useful insight into dietary behaviours that health promotion campaigns could target in aiming to improve the diets of young people, and highlights the importance of targeting interventions to improve dietary behaviours such as breakfast consumption at specific groups of young adults in the population. 1. Becker E et al. (2006) National Centre for Social Research. 2. Zhang Q et al. (2009) Ethnicity & Health 14(5): 439–57. 3. Harding S et al. (2008) Int J Epi 37(1): 162–72. 4. Nicklas TA et al. (1998) J Am Diet Assoc 98(12): 1432–8

    Aerobic capacity and skeletal muscle characteristics in glycogen storage disease IIIa: an observational study

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    Background: Individuals with glycogen storage disease IIIa (GSD IIIa) (OMIM #232400) experience muscle weakness and exercise limitation that worsen through adulthood. However, normative data for markers of physical capacity, such as strength and cardiovascular fitness, are limited. Furthermore, the impact of the disease on muscle size and quality is unstudied in weight bearing skeletal muscle, a key predictor of physical function. We aim to produce normative reference values of aerobic capacity and strength in individuals with GSD IIIa, and to investigate the role of muscle size and quality on exercise impairment. Results: Peak oxygen uptake (V̇O2peak) was lower in the individuals with GSD IIIa than predicted based on demographic data (17.0 (9.0) ml/kg/min, 53 (24)% of predicted, p = 0.001). Knee extension maximum voluntary contraction (MVC) was also substantially lower than age matched predicted values (MVC: 146 (116) Nm, 57% predicted, p = 0.045), though no difference was found in MVC relative to body mass (1.88 (2.74) Nm/kg, 61% of predicted, p = 0.263). There was a strong association between aerobic capacity and maximal leg strength (r = 0.920; p = 0.003). Substantial inter-individual variation was present, with a high physical capacity group that had normal leg strength (MVC), and relatively high V̇O2peak, and a low physical capacity that display impaired strength and substantially lower V̇O2peak. The higher physical capacity sub-group were younger, had larger Vastus Lateralis (VL) muscles, greater muscle quality, undertook more physical activity (PA), and reported higher health-related quality of life. Conclusions: V̇O2peak and knee extension strength are lower in individuals with GSD IIIa than predicted based on their demographic data. Patients with higher physical capacity have superior muscle size and structure characteristics and higher health-related quality of life, than those with lower physical capacity. This study provides normative values of these important markers of physical capacity

    The Specificity of Peptides Bound to Human Histocompatibility Leukocyte Antigen (HLA)-B27 Influences the Prevalence of Arthritis in HLA-B27 Transgenic Rats

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    Human histocompatibility leukocyte antigen B27 is highly associated with the rheumatic diseases termed spondyloarthropathies, but the mechanism is not known. B27 transgenic rats develop a spontaneous disease resembling the human spondyloarthropathies that includes arthritis and colitis. To investigate whether this disease requires the binding of specific peptides to B27, we made a minigene construct in which a peptide from influenza nucleoprotein, NP383-391 (SRYWAIRTR), which binds B27 with high affinity, is targeted directly to the ER by the signal peptide of the adenovirus E3/gp19 protein. Rats transgenic for this minigene, NP1, were made and bred with B27 rats. The production of the NP383-391 peptide in B27+NP1+ rats was confirmed immunologically and by mass spectrometry. The NP1 product displaced ∼90% of the 3H-Arg-labeled endogenous peptide fraction in B27+NP1+ spleen cells. Male B27+NP1+ rats had a significantly reduced prevalence of arthritis, compared with B27+NP− males or B27+ males with a control construct, NP2, whereas colitis was not significantly affected by the NP1 transgene. These findings support the hypothesis that B27-related arthritis requires binding of a specific peptide or set of peptides to B27, and they demonstrate a method for efficient transgenic targeting of peptides to the ER

    Engineering substrate promiscuity in halophilic alcohol dehydrogenase (HvADH2) by in silico design

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    An alcohol dehydrogenase from the halophilic archaeon Haloferax volcanii (HvADH2) has been engineered by rational design to broaden its substrate scope towards the conversion of a range of aromatic substrates, including flurbiprofenol, that is an intermediate of the non-steroidal anti-inflammatory drug, flurbiprofen. Wild-type HvADH2 showed minimal activity with flurbiprofenol (11.1 mU/mg). A homology model of HvADH2 was built and docking experiments with this substrate revealed that the biphenyl rings of flurbiprofenol formed strong interactions with residues F85 and F108, preventing its optimal binding in the active site. Mutations at position 85 however did not increase activity. Site directed mutagenesis at position F108 allowed the identification of three variants showing a significant (up to 2.3-fold) enhancement of activity towards flurbiprofenol, when compared to wild-type HvADH2. Interestingly, F108G variant did not show the classic inhibition in the presence of (R)-enantiomer when tested with rac-1-phenylethanol, underling its potential in racemic resolution of secondary alcohols

    Influence of Sequence Changes and Environment on Intrinsically Disordered Proteins

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    Many large-scale studies on intrinsically disordered proteins are implicitly based on the structural models deposited in the Protein Data Bank. Yet, the static nature of deposited models supplies little insight into variation of protein structure and function under diverse cellular and environmental conditions. While the computational predictability of disordered regions provides practical evidence that disorder is an intrinsic property of proteins, the robustness of disordered regions to changes in sequence or environmental conditions has not been systematically studied. We analyzed intrinsically disordered regions in the same or similar proteins crystallized independently and studied their sensitivity to changes in protein sequence and parameters of crystallographic experiments. The observed changes in the existence, position, and length of disordered regions indicate that their appearance in X-ray structures dramatically depends on changes in amino acid sequence and peculiarities of the crystallographic experiment. Our study also raises general questions regarding protein evolution and the regulation of protein structure, dynamics, and function via variations in cellular and environmental conditions

    A barley cysteine-protease inhibitor reduces teh performance of two aphid species in artificial diets and transgenic arabidopsis plants

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    Cystatins from plants have been implicated in plant defense towards insects, based on their role as inhibitors of heterologous cysteine-proteinases. We have previously characterized thirteen genes encoding cystatins (HvCPI-1 to HvCPI-13) from barley (Hordeum vulgare), but only HvCPI-1 C68 → G, a variant generated by direct-mutagenesis, has been tested against insects. The aim of this study was to analyze the effects of the whole gene family members of barley cystatins against two aphids, Myzus persicae and Acyrthosiphon pisum. All the cystatins, except HvCPI-7, HvCPI-10 and HvCPI-12, inhibited in vitro the activity of cathepsin L- and/or B-like proteinases, with HvCPI-6 being the most effective inhibitor for both aphid species. When administered in artificial diets, HvCPI-6 was toxic to A. pisum nymphs (LC50 = 150 μg/ml), whereas no significant mortality was observed on M. persicae nymphs up to 1000 μg/ml. The effects of HvCPI-6 ingestion on A. pisum were correlated with a decrease of cathepsin B- and L-like proteinase activities. In the case of M. persicae, there was an increase of these proteolytic activities, but also of the aminopeptidase-like activity, suggesting that this species is regulating both target and insensitive enzymes to overcome the effects of the cystatin. To further analyze the potential of barley cystatins as insecticidal proteins against aphids, Arabidopsis plants expressing HvCPI-6 were tested against M. persicae. For A. pisum, which does not feed on Arabidopsis, a combined diet-Vicia faba plant bioassay was performed. A significant delay in the development time to reach the adult stage was observed in both species. The present study demonstrates the potential of barley cystatins to interfere with the performance of two aphid specie

    The Protein Model Portal

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    Structural Genomics has been successful in determining the structures of many unique proteins in a high throughput manner. Still, the number of known protein sequences is much larger than the number of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. Thereby, experimental structure determination efforts and homology modeling complement each other in the exploration of the protein structure space. One of the challenges in using model information effectively has been to access all models available for a specific protein in heterogeneous formats at different sites using various incompatible accession code systems. Often, structure models for hundreds of proteins can be derived from a given experimentally determined structure, using a variety of established methods. This has been done by all of the PSI centers, and by various independent modeling groups. The goal of the Protein Model Portal (PMP) is to provide a single portal which gives access to the various models that can be leveraged from PSI targets and other experimental protein structures. A single interface allows all existing pre-computed models across these various sites to be queried simultaneously, and provides links to interactive services for template selection, target-template alignment, model building, and quality assessment. The current release of the portal consists of 7.6 million model structures provided by different partner resources (CSMP, JCSG, MCSG, NESG, NYSGXRC, JCMM, ModBase, SWISS-MODEL Repository). The PMP is available at http://www.proteinmodelportal.org and from the PSI Structural Genomics Knowledgebase
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