Sélection de variables pour la classification par mélanges gaussiens pour prédire la fonction des gènes orphelins

Biologists are interested in predicting the gene functions of sequenced genome organisms according to microarray transcriptome data. The microarray technology development allows one to study the whole genome in different experimental conditions. The information abundance may seem to be an advantage for the gene clustering. However, the structure of interest can often be contained in a subset of the available variables. The currently available variable selection procedures in model-based clustering assume that the irrelevant clustering variables are all independent or are all linked with the relevant clustering variables. A more versatile variable selection model is proposed, taking into account three possible roles for each variable: The relevant clustering variables, the redundant variables and the independent variables. A model selection criterion and a variable selection algorithm are derived for this new variable role modelling. The interest of this new modelling for discovering the function of orphan genes is highlighted on a transcriptome dataset for the arabidopsis thaliana plant.Les biologistes s’attachent actuellement à prédire la fonction des gènes d’organismes de génome séquence à partir de données transcriptomes, issues de l’utilisation des puces à ADN. Le d´développement de cette technologie permet de tester l’expression de l’ensemble du génome dans de nombreuses conditions expérimentales. Cette quantité d’information peut alors sembler être un atout pour la classification des gènes. Pourtant il est courant que seul un sous-ensemble contienne l’information pertinente pour la classification. Les procédures de sélection des variables en classification non supervisée par mélanges gaussiens supposent généralement que les variables non informatives pour la classification sont soit toutes indépendantes, soit liées à des variables informatives. Nous proposons une nouvelle modélisation du rôle des variables plus polyvalente : les variables sont soit informatives pour la classification, soit redondantes, soit totalement indépendantes. Nous proposons un critère de sélection des variables et un algorithme pour cette nouvelle modélisation. L’intérêt de cette nouvelle modélisation pour la prédiction de la fonction des gènes orphelins est illustrée sur un ensemble de données transcriptomes obtenues chez Arabidopsis thaliana

Impacts environnementaux associés au traitement biologique et à l'utilisation agricole des déchets organiques. Bilan des connaissances en vue de l'évaluation environnementale globale des filières

National audienceFace à l'accroissement des exigences sociales et environnementales, les pays européens s'engagent de plus en plus dans une politique de gestion des déchets organiques tournée vers les filières de traitement biologique de ces déchets et leur utilisation agricole. Ces filières de gestion, qui mettent en jeu des phénomènes biologiques et physico-chimiques spécifiques et complexes, demandent encore à être confortées quant à leur coût, leur efficacité et leur impact environnemental. Cet article nous présente ici la démarche et les résultats d'une étude de synthèse bibliographique visant à rassembler les connaissances de base nécessaires à la réalisation d'évaluations environnementales de ces filières

Quantification des impacts environnementaux associés au traitemant biologique et à l'utilisation agricole des produits organiques - bilan des connaissances

National audienc

Environmental impacts of biological waste management of organic waste

International audienc

GEM2Net: from gene expression modeling to -omics networks, a new CATdb module to investigate Arabidopsis thaliana genes involved in stress response

publié Epub 2014 Nov 11CATdb (http://urgv.evry.inra.fr/CATdb) is a database providing a public access to a large collection of transcriptomic data, mainly for Arabidopsis but also for other plants. This resource has the rare advantage to contain several thousands of microarray experiments obtained with the same technical protocol and analyzed by the same statistical pipelines. In this paper, we present GEM2Net, a new module of CATdb that takes advantage of this homogeneous dataset to mine co-expression units and decipher Arabidopsis gene functions. GEM2Net explores 387 stress conditions organized into 18 biotic and abiotic stress categories. For each one, a model-based clustering is applied on expression differences to identify clusters of co-expressed genes. To characterize functions associated with these clusters, various resources are analyzed and integrated: Gene Ontology, subcellular localization of proteins, Hormone Families, Transcription Factor Families and a refined stress-related gene list associated to publications. Exploiting protein-protein interactions and transcription factors-targets interactions enables to display gene networks. GEM2Net presents the analysis of the 18 stress categories, in which 17,264 genes are involved and organized within 681 co-expression clusters. The meta-data analyses were stored and organized to compose a dynamic Web resource

Scavenging iron: a novel mechanism of plant immunity activation by microbial siderophores

Siderophores are specific ferric iron chelators synthesized by virtually all microorganisms in response to iron deficiency. We have previously shown that they promote infection by the phytopathogenic enterobacteria Dickeya dadantii and Erwinia amylovora. Siderophores also have the ability to activate plant immunity. We have used complete Arabidopsis transcriptome microarrays to investigate the global transcriptional modifications in roots and leaves of Arabidopsis (Arabidopsis thaliana) plants after leaf treatment with the siderophore deferrioxamine (DFO). Physiological relevance of these transcriptional modifications was validated experimentally. Immunity and heavy-metal homeostasis were the major processes affected by DFO. These two physiological responses could be activated by a synthetic iron chelator ethylenediamine-di(o-hydroxyphenylacetic) acid, indicating that siderophores eliciting activities rely on their strong iron-chelating capacity. DFO was able to protect Arabidopsis against the pathogenic bacterium Pseudomonas syringae pv tomato DC3000. Siderophore treatment caused local modifications of iron distribution in leaf cells visible by ferrocyanide and diaminobenzidine-H2O2 staining. Metal quantifications showed that DFO causes a transient iron and zinc uptake at the root level, which is presumably mediated by the metal transporter iron regulated transporter1 (IRT1). Defense gene expression and callose deposition in response to DFO were compromised in an irt1 mutant. Consistently, plant susceptibility to D. dadantii was increased in the irt1 mutant. Our work shows that iron scavenging is a unique mechanism of immunity activation in plants. It highlights the strong relationship between heavy-metal homeostasis and immunity

Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis

72 ref. http://www.plantcell.org/cgi/doi/10.1105/tpc.104.022236International audienc

Reassessment of the size of the Scopoli's Shearwater population at its main breeding site resulted in a tenfold increase: implications for the species conservation

International audienceScopoli's Shearwater (Calonectris diomedea) is a Procellariiform endemic to the Mediterranean Basin which is considered to be vulnerable in Europe due to recent local declines and its susceptibility to both marine and terrestrial threats. In the 1970s-1980s, its population size was estimated at 57,000-76,000 breeding pairs throughout the Mediterranean Basin, with the largest colony, estimated at 15,000-25,000 pairs, found on Zembra Island, Tunisia. The objectives of our study were to re-estimate the size of the breeding population on Zembra Island, to reassess the global population size of the species, and to analyse the implications of these findings on status and conservation of this species in the Mediterranean. Using distance sampling, we estimated the Zembra breeding population to be 141,780 pairs (95 % confidence interval 113,720-176,750 pairs). A review of the most recent data on populations of this species throughout the Mediterranean Basin led us to estimate its new global population size at 141,000-223,000 breeding pairs. Using the demographic invariant and potential biological removal approaches, we estimated the maximum number of adults which could be killed annually by all non-natural causes without causing a population decline to be 8800 (range 7700-9700) individuals, of which could be 3700 breeders. Although these results are less alarming in the context of species conservation than previously thought, uncertainties associated with global population size, trends and major threats still raise questions on the future of this species. More generally, we show how a monitoring strategy for a bird supposed to be relatively well known overall can be potentially misleading due to biases in survey design. The reduction of such biases would therefore appear to be an unavoidable prerequisite in cryptic species monitoring before any reliable inference on the conservation status of the species can be drawn

Safety and Outcome of Carotid Dissection Stenting During the Treatment of Tandem Occlusions: A Pooled Analysis of TITAN and ETIS

International audienceBackground and Purpose: The efficacy of endovascular therapy in patients with acute ischemic stroke due to tandem occlusion is comparable to that for isolated intracranial occlusion in the anterior circulation. However, the optimal management of acute cervical internal carotid artery lesions is unknown, especially in the setting of carotid dissection, but emergency carotid artery stenting (CAS) is frequently considered. We investigated the safety and efficacy of emergency CAS for carotid dissection in patients with acute stroke with tandem occlusion in current clinical practice. Methods: We retrospectively analyzed a prospectively maintained database composed of 2 merged multicenter international observational real-world registries (Endovascular Treatment in Ischemic Stroke and Thrombectomy in Tandem Lesion). Data from endovascular therapy performed in the treatment of tandem occlusions related to acute cervical carotid dissection between January 2012 and January 2019 at 24 comprehensive stroke centers were analyzed. Results: The study assessed 136 patients with tandem occlusion due to dissection, including 65 (47.8%) treated with emergency CAS and 71 (52.2%) without. The overall rates of favorable outcome (90-day modified Rankin Scale score, 0–2) and successful reperfusion (modified Thrombolysis in Cerebral Infarction, 2b–3) were 58.0% (n=76 [95% CI, 49.6%–66.5%]) and 77.9% (n=106 [95% CI, 71.0%–85.0%]), respectively. In subgroup analyses, the rate of successful reperfusion (89.2% versus 67.6%; adjusted odds ratio, 2.24 [95% CI, 1.33–3.77]) was higher after CAS, whereas the 90-day favorable outcome (54.3% versus 61.4%; adjusted odds ratio, 0.84 [95% CI, 0.58–1.22]), symptomatic intracerebral hemorrhage (sICH; 10.8% versus 5.6%; adjusted odds ratio, 1.59 [95% CI, 0.79–3.17]), and 90-day mortality (8.0% versus 5.8%; adjusted odds ratio, 1.00 [95% CI, 0.48–2.09]) did not differ. In sensitivity analyses of patients with successful intracranial reperfusion, CAS was not associated with an improved clinical outcome. Conclusions: Emergency stenting of the dissected cervical carotid artery during endovascular therapy for tandem occlusions seems safe, whatever the quality of the intracranial reperfusion

Recanalization Treatments for Pediatric Acute Ischemic Stroke in France

International audienceImportance: There is to date limited evidence that revascularization strategies are associated with improved functional outcome in children with acute ischemic stroke (AIS).Objectives To report clinical outcomes and provide estimates of revascularization strategy safety and efficacy profiles of intravenous thrombolysis (IVT) and/or endovascular treatment (EVT) in children with AIS.Design, Setting, and Participants The KidClot multicenter nationwide cohort study retrospectively collected data of children (neonates excluded) with AIS and recanalization treatment between January 1, 2015, and May 31, 2018. Data analysis was performed from January 1, 2015, to May 31, 2019.Exposure: IVT and/or EVT.Main Outcomes and Measures Primary outcome was day 90 favorable outcome (modified Rankin Scale [mRs] 0-2, with 0 indicating no symptoms and 6 indicating death). Secondary end points included 1-year favorable outcome (mRs, 0-2), mortality, and symptomatic intracerebral hemorrhage. Other measures included the Pediatric National Institutes of Health Stroke Scale (pedNIHSS), with pedNIHSS 0 indicating no symptoms, 1 to 4 corresponding to a minor stroke, 5 to 15 corresponding to a mild stroke, greater than 15 to 20: severe stroke, and the adult Alberta Stroke Program Early CT Score (ASPECTS), which provides segmental assessment of the vascular territory, with 1 point deducted from the initial score of 10 for every region involved (from 10 [no lesion] to 0 [maximum lesions]).Results: Overall, 68 children were included in 30 centers (IVT [n = 44]; EVT [n = 40]; 44 boys [64.7%]; median [IQR] age, 11 [4-16] years; anterior circulation involvement, 57 [83.8%]). Median (IQR) pedNIHSS score at admission was 13 (7-19), higher in the EVT group at 16 (IQR, 10-20) vs 9 (6-17) in the IVT only group (P < .01). Median time from stroke onset to imaging was higher in the EVT group at 3 hours and 7 minutes (IQR, 2 hours and 3 minutes to 6 hours and 24 minutes) vs 2 hours and 39 minutes (IQR, 1 hour and 51 minutes to 4 hours and 13 minutes) (P = .04). Median admission ASPECTS score was 8 (IQR, 6-9). The main stroke etiologies were cardioembolic (21 [30.9%]) and focal cerebral arteriopathy (17 [25.0%]). Median (IQR) time from stroke onset to IVT was 3 hours and 30 minutes (IQR, 2 hours and 33 minutes to 4 hours and 28 minutes). In the EVT group, the rate of postprocedure successful reperfusion (≥modified Treatment in Cerebral Infarction 2b) was 80.0% (32 of 40). Persistent proximal arterial stenosis was more frequent in focal cerebral arteriopathy (P < .01). Death occurred in 3 patients (4.4%). Median pedNIHSS reduction at 24 hours was 4 (IQR, 0-9) points. Intracerebral hemorrhage occurred in 4 patients and symptomatic intracerebral hemorrhage occurred in 1 patient, all in the EVT group. The median mRS was 2 (IQR, 0-3) at day 90 and 1 (IQR, 0-2) at 1 year, which was not significantly different between EVT and IVT only groups, although different in initial severity.Conclusions and Relevance: The findings of this cohort study suggest that use of EVT and/or IVT is safe in children with AIS