Developmental and Anatomical Constraints on Vertebrate Genome Evolution

Pendant ma thèse de doctorat, j'ai utilisé des espèces modèles, comme la souris et le poisson-zèbre, pour étudier les facteurs qui affectent l'évolution des gènes et leur expression. Plus précisément, j'ai montré que l'anatomie et le développement sont des facteurs clés à prendre en compte, car ils influencent la vitesse d'évolution de la séquence des gènes, l'impact sur eux de mutations (i.e. la délétion du gène est-elle létale ?), et leur tendance à se dupliquer. Où et quand il est exprimé impose à un gène certaines contraintes ou au contraire lui donne des opportunités d'évoluer. J'ai pu comparer ces tendances aux modèles classiques d'évolution de la morphologie, que l'on pensait auparavant refléter directement les contraintes s'appliquant sur le génome. Nous avons montré que les contraintes entre ces deux niveaux d'organisation ne peuvent pas être transférées simplement : il n'y a pas de lien direct entre la conservation du génotype et celle de phénotypes comme la morphologie. Ce travail a été possible grâce au développement d'outils bioinformatiques. Notamment, j'ai travaillé sur le développement de la base de données Bgee, qui a pour but de comparer l'expression des gènes entre différentes espèces de manière automatique et à large échelle. Cela implique une formalisation de l'anatomie, du développement et de concepts liés à l'homologie grâce à l'utilisation d'ontologies. Une intégration cohérente de données d'expression hétérogènes (puces à ADN, marqueurs de séquence exprimée, hybridations in situ) a aussi été nécessaire. Cette base de données est mise à jour régulièrement et disponible librement. Elle devrait contribuer à étendre les possibilités de comparaison de l'expression des gènes entre espèces pour des études d'évo-devo (évolution du développement) et de génomique. During my PhD, I used model species of vertebrates, such as mouse and zebrafish, to study factors affecting the evolution of genes and their expression. More precisely I have shown that anatomy and development are key factors to take into account, influencing the rate of gene sequence evolution, the impact of mutations (i.e. is the deletion of a gene lethal?), and the propensity of a gene to duplicate. Where and when genes are expressed imposes constraints, or on the contrary leaves them some opportunity to evolve. We analyzed these patterns in relation to classical models of morphological evolution in vertebrates, which were previously thought to directly reflect constraints on the genomes. We showed that the patterns of evolution at these two levels of organization do not translate smoothly: there is no direct link between the conservation of genotype and phenotypes such as morphology. This work was made possible by the development of bioinformatics tools. Notably, I worked on the development of the database Bgee, which aims at comparing gene expression between different species in an automated and large-scale way. This involves the formalization of anatomy, development, and concepts related to homology, through the use of ontologies. A coherent integration of heterogeneous expression data (microarray, expressed sequence tags, in situ hybridizations) is also required. This database is regularly updated and freely available. It should contribute to extend the possibilities for comparison of gene expression between species in evo-devo and genomics studies.

Current genetic data do not improve the prediction of type 2 diabetes mellitus: the CoLaus study.

CONTEXT: Several genetic risk scores to identify asymptomatic subjects at high risk of developing type 2 diabetes mellitus (T2DM) have been proposed, but it is unclear whether they add extra information to risk scores based on clinical and biological data. OBJECTIVE: The objective of the study was to assess the extra clinical value of genetic risk scores in predicting the occurrence of T2DM. DESIGN: This was a prospective study, with a mean follow-up time of 5 yr. SETTING AND SUBJECTS: The study included 2824 nondiabetic participants (1548 women, 52 ± 10 yr). MAIN OUTCOME MEASURE: Six genetic risk scores for T2DM were tested. Four were derived from the literature and two were created combining all (n = 24) or shared (n = 9) single-nucleotide polymorphisms of the previous scores. A previously validated clinic + biological risk score for T2DM was used as reference. RESULTS: Two hundred seven participants (7.3%) developed T2DM during follow-up. On bivariate analysis, no differences were found for all but one genetic score between nondiabetic and diabetic participants. After adjusting for the validated clinic + biological risk score, none of the genetic scores improved discrimination, as assessed by changes in the area under the receiver-operating characteristic curve (range -0.4 to -0.1%), sensitivity (-2.9 to -1.0%), specificity (0.0-0.1%), and positive (-6.6 to +0.7%) and negative (-0.2 to 0.0%) predictive values. Similarly, no improvement in T2DM risk prediction was found: net reclassification index ranging from -5.3 to -1.6% and nonsignificant (P ≥ 0.49) integrated discrimination improvement. CONCLUSIONS: In this study, adding genetic information to a previously validated clinic + biological score does not seem to improve the prediction of T2DM.

Bases de dades multimedia

Aquest treball vol fer conèixer d'una manera més o menys acurada el concepte de base de dades multimèdia i tot el que hi està relacionat. Amb aquesta finalitat, el treball s'ha estructurat de manera que el lector conegui els conceptes fonamentals de les bases de dades en general i de les multimèdia en concret, com també les tecnologies disponibles per a gestionar-les, saber com funcionen, què ofereixen, etc.

Construcción y explotación de un almacén de datos para el análisis de información inmobiliaria

L'objectiu fonamental d'aquest TFC és la creació i posada en funcionament d'un magatzem de dades, partint de la informació procedent de bases de dades transaccionals.

Generació, actualització y consulta de bases de dades relacionals utilitzant XML (Servei d'emmagatzemament de dades a internet)

El que es vol, en aquest projecte, és generar una sèrie d'eines que permetin a una entitat externa d'interactuar en una base de dades relacional sense necessitat de coneixements específics sobre bases de dades. Quan es diu interactuar, s'hi inclou des de la creació de la base de dades fins a la consulta de la informació, passant per l'actualització d'aquesta base de dades.

The UniProtKB/Swiss-Prot Tox-Prot program: A central hub of integrated venom protein data.

Animal toxins are of interest to a wide range of scientists, due to their numerous applications in pharmacology, neurology, hematology, medicine, and drug research. This, and to a lesser extent the development of new performing tools in transcriptomics and proteomics, has led to an increase in toxin discovery. In this context, providing publicly available data on animal toxins has become essential. The UniProtKB/Swiss-Prot Tox-Prot program (http://www.uniprot.org/program/Toxins) plays a crucial role by providing such an access to venom protein sequences and functions from all venomous species. This program has up to now curated more than 5000 venom proteins to the high-quality standards of UniProtKB/Swiss-Prot (release 2012_02). Proteins targeted by these toxins are also available in the knowledgebase. This paper describes in details the type of information provided by UniProtKB/Swiss-Prot for toxins, as well as the structured format of the knowledgebase.

The effectiveness of brief alcohol interventions in primary care settings: A systematic review

Numerous studies have reported that brief interventions delivered in primary care are effective in reducing excessive drinking. However, much of this work has been criticised for being clinically unrepresentative. This review aimed to assess the effectiveness of brief interventions in primary care and determine if outcomes differ between efficacy and effectiveness trials. Approach. A pre-specified search strategy was used to search all relevant electronic databases up to 2006. The authors also hand-searched the reference lists of key articles and reviews. They included randomised controlled trials (RCT) involving patients in primary care who were not seeking alcohol treatment and who received brief intervention. Two authors independently abstracted data and assessed trial quality. Random effects meta-analyses, subgroup and sensitivity analyses and meta-regression were conducted.This resource was contributed by The National Documentation Centre on Drug Use.

Summer School Programme

The Summer School aims to enable and foster a climate of inquiry for critical thinking, quantitative analysis and explore existing relevant data sources. We aim to develop the concepts and tools associated with quantitative research related to child health and wellbeing. Building on participants’ existing knowledge of research, policy and practice, we will focus on the quantitative skills necessary to mine and critique relevant national databases, conduct basic quantitative research and apply these skills to work. The SPSS workshops will provide  participants with a basic understanding of a statistical programme for analysing empirical data and the open clinics will allow participants to discuss their own research issues with experts.

Bases de datos Multimedia

Aquest treball mira d'aproximar-se a la situació actual de les bases de dades multimèdia. Per a fer-ho, s'ha optat per un enfocament múltiple que té en compte diferents aspectes del producte multimèdia: els aspectes econòmics, és a dir, la situació del mercat (nombre de bases de dades, volum de negoci, creixement, etc.), els aspectes tècnics, és a dir, l'eina emprada, la seva evolució, les seves limitacions i problemes, i les seves aplicacions i serveis en diferents àrees (amb un interès especial en el camp de la documentació i la formació i la recerca).

Interventions to achieve long-term weight loss in obese older people: A systematic review and meta-analysis

The prevalence of obesity is rapidly increasing in older adults. Information is required about what interventions are effective in reducing obesity and influencing health outcomes in this age group. Thirteen databases were searched, earliest date 1966 to December 2008, including Medline, CINAHL, PsycINFO, the Cochrane database and EMBASE.

Interventions to achieve long-term weight loss in obese older people: A systematic review and meta-analysis

Purpose: the prevalence of obesity is rapidly increasing in older adults. Information is required about what interventions are effective in reducing obesity and influencing health outcomes in this age group. Design: systematic review and meta-analysis. Data sources: thirteen databases were searched, earliest date 1966 to December 2008, including Medline, CINAHL, PsycINFO, the Cochrane database and EMBASE. Study selection: we included studies with participants�۪ mean age 60 years and mean body mass index 30 kg/m2, with outcomes at a minimum of 1 year. Data were independently extracted by two reviewers and differences resolved by consensus. Data extraction: nine eligible trials were included. Study interventions targeted diet, physical activity and mixed approaches. Populations included patients with coronary artery disease, diabetes mellitus and osteoarthritis. Results: meta-analysis (seven studies) demonstrated a modest but significant weight loss of 3.0 kg [95% confidence interval (CI) 5.1���0.9] at 1 year. Total cholesterol (four studies) did not show a significant change: ���0.36 mmol/l (95% CI ���0.75 to 0.04). There was no significant change in high-density lipoprotein, low-density lipoprotein or triglycerides. In one study, recurrence of hypertension or cardiovascular events was significantly reduced (hazard ratio 0.65, 95% CI 0.50���0.85). Six-minute walk test did not significantly change in one study. Health-related quality of life significantly improved in one study but did not improve in a second study. Conclusions: although modest weight reductions were observed, there is a lack of high-quality evidence to support the efficacy of weight loss programmes in older people. ��Keywords: obesity, older, weight loss, meta-analysis, elderly, systematic review

Analysis of expressed sequence tags from Trypanosoma cruzi amastigotes

A total of 880 expressed sequence tags (EST) originated from clones randomly selected from a Trypanosoma cruzi amastigote cDNA library have been analyzed. Of these, 40% (355 ESTs) have been identified by similarity to sequences in public databases and classified according to functional categorization of their putative products. About 11% of the mRNAs expressed in amastigotes are related to the translational machinery, and a large number of them (9% of the total number of clones in the library) encode ribosomal proteins. A comparative analysis with a previous study, where clones from the same library were selected using sera from patients with Chagas disease, revealed that ribosomal proteins also represent the largest class of antigen coding genes expressed in amastigotes (54% of all immunoselected clones). However, although more than thirty classes of ribosomal proteins were identified by EST analysis, the results of the immunoscreening indicated that only a particular subset of them contains major antigenic determinants recognized by antibodies from Chagas disease patients.

Inequalities in Old Age: The impact of the recession on older people in Ireland, North and South CARDI Grants

Inequalities in Old Age: the impact of the recession on older people in Ireland, North and SouthAbout the research:This research, led by Professor Paddy Hillyard, Emeritus Professor Queen’s University Belfast, was carried out with funding from CARDI’s Grants Programme Call 2. The purpose of the study was to analyse the impact of the recession on older people in Northern Ireland (NI) and the Republic of Ireland (ROI) and the extent to which inequalities within the older population have been affected by the economic crisis.Research Brief:This brief, authored by CARDI staff, is based on the findings of the research project and also contains additional information of interest.Research Team:Professor Paddy Hillyard, Emeritus Professor Queen’s University Belfast - lead researcher;Dr Francesca Lundstr̦m, Research Consultant;Dr Demi Patsios, Policy Research Consultant;Sarah Machniewski, Researcher;David Taylor, Chartered Accountant and Management Consultant;Dr Maureen Lyons, Research Manager, School of Social Justice, UCD.Methodology and availability of data:Several methods were used in the research, including:�� a review of relevant literature;����a detailed analysis of many databases relevant to older people’s incomes and lives;��building a model to assess the impact of the recession on older people;surveys of financial advisers in voluntary, private and public sectors;��six focus groups, three each in NI and RoI.Availability of data:Despite the huge amount of information which is officially collected and published in NI and RoI, very little is directly comparable. ��The development of a mechanism to encourage the production of more comparable data North and South would be very beneficial.��For example, this study identified a basket of 25 factors that can be used to compare the living standards of older people in NI and RoI and to monitor changes in future yearsTo access the full report please click on the following link:Inequalities in Old Age: the impact of the recession on older people in Ireland, North and SouthPlease find the presentation from the launch below:Inequalities, Pensions and the Recession by Prof Paddy Hillyard, Queen’s University Belfast and Dr Demi Patsios, Policy Research Consultant, Dr Francesca Lundstr̦m, Research Consultant.��������

Interventions to achieve long-term weight loss in obese older people

Purpose: the prevalence of obesity is rapidly increasing in older adults. Information is required about what interventions are effective in reducing obesity and influencing health outcomes in this age group. Design: systematic review and meta-analysis. Data sources: thirteen databases were searched, earliest date 1966 to December 2008, including Medline, CINAHL, PsycINFO, the Cochrane database and EMBASE. Study selection: we included studies with participants�۪ mean age 60 years and mean body mass index 30 kg/m2, with outcomes at a minimum of 1 year. Data were independently extracted by two reviewers and differences resolved by consensus. Data extraction: nine eligible trials were included. Study interventions targeted diet, physical activity and mixed approaches. Populations included patients with coronary artery disease, diabetes mellitus and osteoarthritis. Results: meta-analysis (seven studies) demonstrated a modest but significant weight loss of 3.0 kg [95% confidence interval (CI) 5.1���0.9] at 1 year. Total cholesterol (four studies) did not show a significant change: ���0.36 mmol/l (95% CI ���0.75 to 0.04). There was no significant change in high-density lipoprotein, low-density lipoprotein or triglycerides. In one study, recurrence of hypertension or cardiovascular events was significantly reduced (hazard ratio 0.65, 95% CI 0.50���0.85). Six-minute walk test did not significantly change in one study. Health-related quality of life significantly improved in one study but did not improve in a second study. Conclusions: although modest weight reductions were observed, there is a lack of high-quality evidence to support the efficacy of weight loss programmes in older people. ��Keywords: obesity, older, weight loss, meta-analysis, elderly, systematic review��

Social support group interventions in people with dementia and mild cognitive impairment: a systematic review of the literature

Abstract Despite the large number of studies evaluating social support groups for people with dementia, there are no systematic reviews of current evidence.The aim of this study was to evaluate the effectiveness of social support group interventions for people with dementia and mild cognitive impairment.A systematic review was performed. We searched electronic databases for randomised controlled trials. Two reviewers worked independently to select trials, extract data and assess risk of bias. A total of 546 studies were identified of which two met the inclusion criteria. We were not able to pool data for further analyses, as the interventions tested in the studies meeting the inclusion criteria were too dissimilar in content.The first trial (n = 136) showed a benefit of early-stage memory loss social support groups for depression and quality of life in people with dementia.The second trial (n = 33) showed that post-treatment self-reported self-esteem was higher in the group receiving a multicomponent intervention of social support compared with that in the no intervention control group.Limited data from two studies suggest that support groups may be of psychological benefit to people with dementia by reducing depression and improving quality of life and self-esteem.These findings need to be viewed in light of the small number, small sample size and heterogeneous characteristics of current trials, indicating that it is difficult to draw any conclusions. More multicentre randomised controlled trials in social support group interventions for people with dementia are needed.������������