Large scale statistical analysis of GEO datasets

The problem addressed here is that of simultaneous treatment of several gene expression datasets, possibly collected under different experimental conditions and/or platforms. Using robust statistics, a large scale statistical analysis has been conducted over $20$ datasets downloaded from the Gene Expression Omnibus repository. The differences between datasets are compared to the variability inside a given dataset. Evidence that meaningful biological information can be extracted by merging different sources is provided

Jacques Logie 1938-2007

Dans la nuit du 3 au 4 septembre 2007 s’éteignait, le cœur foudroyé, Jacques Logie dans sa demeure de Plancenoit au cœur du champ de bataille de Waterloo. La veille de sa mort, comme président de la commission provinciale du patrimoine de la province de Brabant wallon, il avait pu se réjouir de voir accepté un de ses projets, l’extension du classement du site de la bataille dans la perspective du bicentenaire de 2015. Jacques Logie était né à Louvain, fils d’un officier combattant de la premi..

Time course analysis of RNA stability in human placenta

<p>Abstract</p> <p>Background</p> <p>Evaluation of RNA quality is essential for gene expression analysis, as the presence of degraded samples may influence the interpretation of expression levels. Particularly, qRT-PCR data can be affected by RNA integrity and stability. To explore systematically how RNA quality affects qRT-PCR assay performance, a set of human placenta RNA samples was generated by two protocols handlings of fresh tissue over a progressive time course of 4 days. Protocol A consists of a direct transfer of tissue into RNA-stabilizing solution (RNAlater™) solution. Protocol B uses a dissection of placenta villosities before bio banking. We tested and compared RNA yields, total RNA integrity, mRNA integrity and stability in these two protocols according to the duration of storage.</p> <p>Results</p> <p>A long time tissue storage had little effect on the total RNA and mRNA integrity but induced changes in the transcript levels of stress-responsive genes as TNF-alpha or COX2 after 48 h. The loss of the RNA integrity was higher in the placental tissues that underwent a dissection before RNA processing by comparison with those transferred directly into RNA later™ solution. That loss is moderate, with average RIN (RNA Integration Numbers) range values of 4.5–6.05, in comparison with values of 6.44–7.22 in samples directly transferred to RNAlater™ (protocol A). Among the house keeping genes tested, the B2M is the most stable.</p> <p>Conclusion</p> <p>This study shows that placental samples can be stored at + 4°C up to 48 h before RNA extraction without altering RNA quality. Rapid tissue handling without dissection and using RNA-stabilizing solution (RNAlater™) is a prerequisite to obtain suitable RNA integrity and stability.</p

A critical appraisal of guidelines for the management of knee osteoarthritis using Appraisal of Guidelines Research and Evaluation criteria

Clinical practice guidelines have been elaborated to summarize evidence related to the management of knee osteoarthritis and to facilitate uptake of evidence-based knowledge by clinicians. The objectives of the present review were summarizing the recommendations of existing guidelines on knee osteoarthritis, and assessing the quality of the guidelines using a standardized and validated instrument – the Appraisal of Guidelines Research and Evaluation (AGREE) tool. Internet medical literature databases from 2001 to 2006 were searched for guidelines, with six guidelines being identified. Thirteen clinician researchers participated in the review. Each reviewer was trained in the AGREE instrument. The guidelines were distributed to four groups of three or four reviewers, each group reviewing one guideline with the exception of one group that reviewed two guidelines. One independent evaluator reviewed all guidelines. All guidelines effectively addressed only a minority of AGREE domains. Clarity/presentation was effectively addressed in three out of six guidelines, scope/purpose and rigour of development in two guidelines, editorial independence in one guideline, and stakeholder involvement and applicability in none. The clinical management recommendation tended to be similar among guidelines, although interventions addressed varied. Acetaminophen was recommended for initial pain treatment, combined with exercise and education. Nonsteroidal anti-inflammatory drugs were recommended if acetaminophen failed to control pain, but cautiously because of gastrointestinal risks. Surgery was recommended in the presence of persistent pain and disability. Education and activity management interventions were superficially addressed in most guidelines. Guideline creators should use the AGREE criteria when developing guidelines. Innovative and effective methods of knowledge translation to health professionals are needed

Swine influenza: Epidemiological situation in France

Serological and virus identification studies have been carried out in France to assess the epidemiological situation of the swine population. At the end of the 70’s, the serological profile in pig farms was dominated by the presence of A/H3N2 antibodies, associated with epidemics of human influenza. Since then, epizootic outbreaks have succeeded one another in the pig. The disease is now both enzootic and epizootic. Since the early 2000s, swine influenza in France occurs mainly in Brittany, where pig density is the highest. Its economic impact is considerable in pig farms of that area. The disease is caused by the influenza A/H1 virus of avian origin (A/H1N1) or by reassortants (A/H1N2). As influenza viruses are unstable, detection tools need permanent updating to guarantee an effective epidemiological surveillance.La situation épidémiologique du cheptel porcin français est appréhendée au travers d'études sérologiques ainsi que de recherches virales. À la fin des années 1970,le profil sérologique des élevages est dominé par la présence d'anticorps A/H3N2 correspondant à des épidémies de grippe humaine. Par la suite, des vagues épizootiques ont déferlé. La maladie se présente désormais sous une forme enzootique et épizootique. Depuis le début des années 2000, la grippe du porc en France concerne avant tout les élevages de Bretagne, où la densité porcine est la plus élevée. Elle a un impact économique considérable dans les élevages de cette région. L'activité grippale est le fait de virus A/H1 d'origine aviaire (A/H1N1) ou de réassortants (A/H1N2). L'instabilité des virus grippaux suppose d'adapter régulièrement les outils de détection afin de permettre une épidémiosurveillance efficace

Intestinal antiinflammatory effect of 5-aminosalicylic acid is dependent on peroxisome proliferator–activated receptor-γ

5-aminosalicylic acid (5-ASA) is an antiinflammatory drug widely used in the treatment of inflammatory bowel diseases. It is known to inhibit the production of cytokines and inflammatory mediators, but the mechanism underlying the intestinal effects of 5-ASA remains unknown. Based on the common activities of peroxisome proliferator–activated receptor-γ (PPAR-γ) ligands and 5-ASA, we hypothesized that this nuclear receptor mediates 5-ASA therapeutic action. To test this possibility, colitis was induced in heterozygous PPAR-γ+/− mice and their wild-type littermates, which were then treated with 5-ASA. 5-ASA treatment had a beneficial effect on colitis only in wild-type and not in heterozygous mice. In epithelial cells, 5-ASA increased PPAR-γ expression, promoted its translocation from the cytoplasm to the nucleus, and induced a modification of its conformation permitting the recruitment of coactivators and the activation of a peroxisome-proliferator response element–driven gene. Validation of these results was obtained with organ cultures of human colonic biopsies. These data identify PPAR-γ as a target of 5-ASA underlying antiinflammatory effects in the colon

Evaluation des besoins et des activités. Problématique de leur localisation. Critères, méthodes et applications pour la révision des plans de secteur. Problématique pour la mise en oeuvre des zones d'aménagement différé

Rapport final de la subvention 2001, Cinquième Volum

RÔLE DE L'OCCUPATION DU SOL VIS À VIS DE LA MODÉLISATION DES FLUX ENERGÉTIQUES ET HYDRIQUES EN MILIEU URBAIN ET PÉRIURBAIN

National audienceLe projet Rosenhy vise à étudier l’impact de l’occupation du sol sur la modélisation météorologique et hydrologique en termes de flux énergétiques et hydriques, en milieu urbain et périurbain. Trois sites appartenant aux observatoires français OTHU et ONEVU sont au centre de ce projet. Le quartier urbain hétérogène du Pin sec (Nantes), imperméabilisé à environ 45%, a fait l’objet d’une campagne expérimentale durant le mois de juin 2012, visant à estimer les flux de chaleur sensible et latente avec une haute résolution spatiale et temporelle par rapport aux mesures réalisées en continu sur ce site depuis 5 ans. Deux bassins versant périurbains (La Chézine à Nantes et l’Yzeron à Lyon), avec un taux d’imperméabilisation moins important (environ 10%) mais grandissant depuis plusieurs décennies, sont aussi étudiés. Ces deux derniers sites bénéficient d’un suivi hydrométéorologique depuis 10 ans pour la Chézine et 15 ans pour l’Yzeron. Sur ces trois sites, différentes sources de données d’occupation du sol à différentes résolutions sont disponibles :différentes bases de données géographiques communément utilisées par la communauté scientifique et les collectivités et des données télédétectées (multispectrales et hyperspectrales). L’utilisation de ces données en entrée de différents modèles météorologiques et hydrologiques implique un travail d’analyse et de classification pour adapter les informations aux besoins des modèles. Dans ce projet, les différents modèles adaptés au milieu urbain ou périrubain sont évalués et améliorés. Ainsi, les modèles hydrologiques périrubains sont en développement pour prendre en compte les différentes pratiques de gestion des eaux pluviales existantes (noues, toitures végétalisées, ...). L’utilisation conjointe des données simulées par les différents modèles aidera à déterminer le rôle de la part des surfaces naturelles et artificielles sur les bilans énergétique et hydrique en milieu plus ou moins urbanisé. Le milieu périurbain étant en évolution, le projet s’intéressera aussi à des scénarios d’urbanisation prospectifs en regardant d’une part l’impact de la densification sur les scénarios construits pour l’Yzeron lors du projet AVuPUR (ANR-VMCS, 2008-2011) et d’autre part, en réfléchissant conjointement avec Nantes Métropole, aux possibles voies d’évolution sur le bassin de la Chézine

The Testis-Specific Factor CTCFL Cooperates with the Protein Methyltransferase PRMT7 in H19 Imprinting Control Region Methylation

Expression of imprinted genes is restricted to a single parental allele as a result of epigenetic regulation—DNA methylation and histone modifications. Igf2/H19 is a reciprocally imprinted locus exhibiting paternal Igf2 and maternal H19 expression. Their expression is regulated by a paternally methylated imprinting control region (ICR) located between the two genes. Although the de novo DNA methyltransferases have been shown to be necessary for the establishment of ICR methylation, the mechanism by which they are targeted to the region remains unknown. We demonstrate that CTCFL/BORIS, a paralog of CTCF, is an ICR-binding protein expressed during embryonic male germ cell development, coinciding with the timing of ICR methylation. PRMT7, a protein arginine methyltransferase with which CTCFL interacts, is also expressed during embryonic testis development. Symmetrical dimethyl arginine 3 of histone H4, a modification catalyzed by PRMT7, accumulates in germ cells during this developmental period. This modified histone is also found enriched in both H19 ICR and Gtl2 differentially methylated region (DMR) chromatin of testis by chromatin immunoprecipitation (ChIP) analysis. In vitro studies demonstrate that CTCFL stimulates the histone-methyltransferase activity of PRMT7 via interactions with both histones and PRMT7. Finally, H19 ICR methylation is demonstrated by nuclear co-injection of expression vectors encoding CTCFL, PRMT7, and the de novo DNA methyltransferases, Dnmt3a, -b and -L, in Xenopus oocytes. These results suggest that CTCFL and PRMT7 may play a role in male germline imprinted gene methylation