Développement d’une méthodologie d’analyse de la conservation de synténie chez les plantes. Du génome d’Arabidopsis à celui du Tournesol

Le tournesol (Helianthus annuus L) est l’une des principales plantes oléagineuses cultivées. L’étude des gènes sous tendant les principaux caractères agronomiques est difficile en raison de son grand génome pour lequel peu d’informations existent. Par ailleurs, les moyens financiers et techniques sont loin d’être comparables à ceux mis en place pour les céréales ou d’autres végétaux (carte physique, séquençage en masse de génome, d’ARNm, recherche des duplications, des transposons. . .). Pour étudier l’organisation du génome du tournesol, il a donc été envisagé une approche différente basée sur la conservation de synténie avec la plante modèle Arabidopsis thaliana. Les informations relatives aux gènes de la plante modèle transférées aux séquences EST et ARNm du tournesol permettent d’optimiser l’exploitation de ces séquences. Mon travail de thèse a donc consisté à mettre au point une méthode d’analyse massive du grand nombre de séquences de tournesol puis de tester expérimentalement les résultats de cette analyse afin d’obtenir de nouvelles informations sur l’organisation du génome du tournesol et d’estimer la conservation de synténie avec Arabidopsis. La mise en place de la méthodologie a abouti à la création d’un serveur web appelé Iccare. Cet outil bioinformatique permet la comparaison et l’analyse d’un grand nombre de séquences de différents organismes végétaux ou animaux avec les séquences codantes des gènes de l’organisme modèle respectif, Homo sapiens pour les animaux et Arabidopsis thaliana pour les végétaux. Les résultats sont présentés sous forme graphique en combinant les informations de similitudes aux informations structurales des gènes de l’organisme modèle (introns, régions UTR). La combinaison de ces informations permet ainsi d’optimiser l’exploitation de ces séquences en utilisant les outils couplés à Iccare (définir des amorces ou des sondes). En complément de Iccare, Synteny Search (en cours d’achèvement) est un site web qui permet de rechercher les relations existantes entre les gènes d’Arabidopsis et du riz (conservation de synténie) ainsi que les relations de ces gènes au sein d’un même génome (ils sont uniques, dupliqués ou appartiennent à des familles multigéniques). Cet outil donne des informations complémentaires sur les gènes sélectionnés à partir d’Iccare afin de vérifier et d’interpréter les résultats expérimentaux (nombre de fragments amplifiés ou de clones BAC positifs). Iccare a permis de sélectionner, parmi 60 200 séquences de tournesol, 20 691 séquences présentant des similitudes avec 3 635 gènes d’Arabidopsis. L’organisation du génome du tournesol et la conservation de synténie avec Arabidopsis ont été étudiées en utilisant des séquences EST de tournesol qui présentaient des similitudes avec 195 gènes localisés sur le chromosome 5 de la plante modèle. Cent cinquante neuf d’entre elles ont servi à définir des sondes Overgo dans deux régions différentes. Le criblage d’une banque de clones BAC avec ces sondes présente une efficacité supérieure à 70%. Des amplifications PCR sur une quarantaine de clones BAC positifs ont permis de confirmer la présence des séquences EST. Ce criblage a aussi démontré que la banque utilisée était peu couvrante pour les régions étudiées ne permettant pas le regroupement en contig des clones BAC de sondes voisines chez la plante modèle. Par contre, le regroupement des clones BAC positifs à une même sonde montre qu’il existe plusieurs localisations pour cette sonde, conformément aux informations préalables fournies par Synteny Search. Parallèlement aux hybridations, 51 séquences EST ont servi de matrice à la définition de couples d’amorces spécifiques de régions conservées de part et d’autre d’introns. L’amplification par PCR sur différents cultivars de tournesol présente une efficacité de 90% et le taux de polymorphisme de taille observé et vérifié sur gel d’agarose est de 15%, ce qui a permis d’intégrer 7 nouveaux marqueurs moléculaires à une carte génétique issue de lignées recombinantes (Rachid Al-chaarani et al., 2004). Ces 7 marqueurs ne sont pas liés entre eux et n’ont donc pas permis de définir de conservation de synténie entre tournesol et Arabidopsis. En conclusion, Iccare permet de facilement et rapidement traiter un grand nombre de données, de transférer les informations structurelles des gènes pour faciliter et optimiser la définition d’amorces et de sondes et d’interpréter les résultats expérimentaux à l’aide de Synteny Search. En revanche, l’organisation du génome du tournesol et la synténie existant avec Arabidopsis n’ont pas pu être évaluées clairement. Les données préliminaires obtenues laissent à penser que l’espace entre les gènes du tournesol semble proportionnel à la différence de taille observée avec le génome d’Arabidopsis, expliquant ainsi la difficulté à regrouper les clones BAC en contig. Un mode d’évolution du génome du tournesol possible est donc l’augmentation de distance intergénique pouvant être due à des transposons et rétrotransposons. ABSTRACT : The sunflower (Helianthus annuus L) is one of most cultivated oil-seed plant. His great genome size makes difficult the study of gene of interest (agronomic traits) especially that few information about it are available. Others plants or crops have more technical an financial means than for sunflower (physical map, massive genome and mRNA sequencing, duplication search, transposons. . .). In order to study the sunflower genome organization, we have developped a new method based ont synteny conservation with the model plant Arabidopsis thaliana. The transfert of gene information to the EST ou mRNA sequences of the sunflower permits to optimize the sequence exploitation. My thesis works consist in developping a new methology of massive analysis of sunflower sequences then test experimentally the results in order to get new information about the genome organization of the sunflower and to estimate the degree of synteny with the Arabidopsis genome. The methodology leads to the creation of a web server called Iccare. This bioinformatic tool permits to compare and analyse a high number of sequences from differents plants or animals organisms with the coding sequences of gene from the model organism which is respectively Homo sapiens for the animals and Arabidopsis thaliana for the plants. The results are displayed according to the location of the genes on the chromosomes of the reference organism. Genes structure information and sequence similarities are combined in a graphical representation in order to optimize the sequence exploitation by designing primers or probes. The Synteny Search web site (not finished yet) complete the Iccare web server, it permits to search the relation existing between the Arabidopsis genes and those of the rice (synteny conservation) and the relation between the genes within a genome (lonely genes, duplicated genes or genes belonging to multigenic family). This tool allows the access the information about the selected genes on Iccare in order to verify and interpret the experimental results (amplified fragment number or hybrided BAC clones). The Iccare web server had permit to select among 60,200 sunflower sequences, 20,691 sequences presenting similarities with 3,635 Arabidopsis genes. The genome organization of the sunflower and the synteny conservation with Arabidopsis had been studied by using EST sequences of the sunflower wich present some similarities to 195 genes located on the chromosome 5 of the model plant. One hundred and fifty nine EST sequences had been used to design Overgo probes in two differents regions of the fifth chromosome. These probes have been screened on a BAC clones library and over 70% were efficient. PCR amplification on forty BAC clones had confirmed the screening. The screening had also shown that the BAC clones library is less covering than expected in the studied regions. Some BAC clones had been fingerprinted and contig had been made showing different location for some Overgo probes according to the Synteny Search web site results. In addition to the screening, fifty one EST sequences had been used to design primer couple on conserved exons regions on both sides of an intron. PCR amplification on different sunflower cultivar with the primer couples presents 90% of efficiency and the size polymorphism rate on agarose is about 15%. Seven primer couples are used as molecular marker and are assigned on a genetic map (Recombinant Inbreed Lines). These molecular markers are not linked and any syntenic blocks can be defined between the sunflower genome and the Arabidopsis genome. In conlusion, the Iccare web server permits to facilitate and accelerate the traitement of high number data, to transfert structural information of genes in order to optimize the primer design and the probe design and to interpret experimental results aided by the Synteny Search web site. In spite of these new tools, the genome organization of the sunflower and the synteny conservation with the Arabidopsis genome are not elucidated. The preliminary data leave with thoughts that space between the sunflower genes seems proportional to the differente genome size between the sunflower genome and the Arabidopsis genome. These data can explain the difficulty to contig BAC clones. One evolution of the sunflower genome possibility is the increase of intergenic length due to transposons and retrotransposons

The TopModL Initiative

International audienceWe believe that there is a very strong need for an environment to support research and experiments on model-driven engineering. Therefore we have started the TopModL project, an open-source initiative, with the goal of building a development community to provide: (1) an executable environment for quick and easy experimentation, (2) a set of source files and a compilation tool chain, (3) a web portal to share artefacts developed by the community. The aim of TopModL is to help the model-engineering research community by providing the quickest path between a research idea and a running prototype. In addition, we also want to identify all the possible contributions, understand how to make it easy to integrate existing components, while maintaining architectural integrity. At the time of writing we have almost completed the bootstrap phase (known as Blackhole), which means that we can model TopModL and generate TopModL with TopModL. Beyond this first phase, it is now of paramount importance to gather the best possible description of the requirements of the community involved in model-driven engineering to further develop TopModL, and also to make sure that we are able to reuse or federate existing efforts or goodwill. This paper is more intended to set up a basis for a constructive discussion than to offer definitive answers and closed solutions

Improving Prediction Accuracy of Memory Interferences for Multicore Platforms

International audienceMemory interferences may introduce important slowdowns in applications running on COTS multi-core processors. They are caused by concurrent accesses to shared hardware resources of the memory system. The induced delays are difficult to predict, making memory interferences a major obstacle to the adoption of COTS multi-core processors in real-time systems. In this article, we propose an experimental characterization of ap-plications' memory consumption to determine their sensitivity to memory interferences. Thanks to a new set of microbenchmarks, we show the lack of precision of a purely quantitative characterization. To improve accuracy, we define new metrics quantifying qualitative aspects of memory consumption and implement a profiling tool using the VALGRIND framework. In addition, our profiling tool produces high resolution profiles allowing us to clearly distinguish the various phases in applications' behavior. Using our microbenchmarks and our new characterization, we train a state-of-the-art regressor. The validation on applications from the MIBENCH and the PARSEC suites indicates significant gain in prediction accuracy compared to a purely quantitative characterization

Maximizing Parallelism without Exploding Deadlines in a Mixed Criticality Embedded System

International audienceComplex embedded systems today commonly involve a mix of real-time and best-effort applications. The recent emergence of low-cost multicore processors raises the possibility of running both kinds of applications on a single machine, with virtualization ensuring isolation. Nevertheless, memory contention can introduce other sources of delay, that can lead to missed deadlines. In this paper, we present a combined offline/online memory bandwidth monitoring approach. Our approach estimates and limits the impact of the memory contention incurred by the best-effort applications on the execution time of the real-time application. We show that our approach is compatible with the hardware counters provided by current small commodity multicore processors. Using our approach, the system designer can limit the overhead on the real-time application to under 5% of its expected execution time, while still enabling progress of the best-effort applications. I. INTRODUCTION In many embedded system domains, such as the automotive industry, it is necessary to run applications with different levels of criticality [13]. Some applications may have nearly hard real-time constraints, while others may need only best-effort access to the CPU and memory resources. A typical example is the car dashboard, which may display both critical real-time information, such as an alarm, and non critical information, such as travel maps and suggestions on how to outsmart traffic. Traditionally, multiple applications are integrated in a vehicle using a federated architecture: Every major function is implemented in a dedicated Electronic Control Unit (ECU) [28] that ensures fault isolation and error containment. This solution, however, multiplies the hardware cost, and, in an industry where every cent matters, is increasingly unacceptable. Recently, efforts have been made to develop an integrated architecture, in which multiple functions share a single ECU. AUTOSAR [16] is a consortium of actors from the automotive industry that defines a software architecture to exploit the benefits of integrated architectures by facilitating the reuse of applications. The AUTOSAR standard targets applications that control vehicle electrical systems and that are scheduled on a real-time operating system that is compliant with the AUTOSAR OS standard. Infotainment applications, however, typically target a Unix-like operating system, and thus still require the use of a federated architecture. Recent experimental small uniform memory access commodity multicore systems provide a potential path towards a complete low-cost integrated architecture. Systems such as the Freescale SABRE Lite [1] offer sufficient CPU power to run multiple applications on a single low-cost ECU. Using Virtualized architectures [8], [18], [34], multiple operatin

Understanding the Memory Consumption of the MiBench Embedded Benchmark

International audienceComplex embedded systems today commonly involve a mix of real-time and best-effort applications. The recent emergence of small low-cost commodity multi-core processors raises the possibility of running both kinds of applications on a single machine, with virtualization ensuring that the best-effort applications cannot steal CPU cycles from the real-time applications. Nevertheless, memory contention can introduce other sources of delay, that can lead to missed deadlines. In this paper, we analyze the sources of memory consumption for the real-time applications found in the MiBench embedded benchmark suite

Développement d’un procédé de revêtement zinc-Nickel répondant aux exigences du secteur aéronautique

La société MECAPROTEC Industries en collaboration avec les laboratoires CIRIMAT et ELECTRODEP, développe un procédé de dépôt ZnNi répondant aux exigences du secteur aéronautique, en vue de la substitution du cadmiage électrolytique. Ces exigences, différentes de celles du secteur automobile, imposent de nouveaux critères de choix qui viennent s’ajouter à celui du comportement en corrosion. Ainsi, pour des pièces en aciers à haute résistance mécanique, les procédés électrolytiques peuvent être à l’origine d’une fragilisation des pièces par occlusion d’hydrogène. Il est donc indispensable pour le développement de ce nouveau procédé et son application à des ensembles aéronautiques, d’évaluer ce risque à partir d’essais normalisés et d’y remédier. De plus, dans le cas d'applications sur des assemblages vissés, les caractéristiques tribologiques des alliages ZnNi devront être adaptées afin d’éviter les risques de grippage. Du point de vue anticorrosion, un post-traitement de finition par chromatation est souvent utilisé pour accroître les performances des revêtements cadmiés. Dans le cas des revêtements ZnNi, il conviendra bien sûr d’atteindre des performances identiques en utilisant un traitement de finition sans chromate. C’est ce que nous tentons de faire en développant un procédé de finition par voie sol-gel. Pour rendre compatible le procédé ZnNi avec toutes ou partie de ces contraintes, des recherches amonts sont réalisées en parallèle des nvestigations industrielles. Le but est de tendre vers une maîtrise complète du procédé et pour cela, de rechercher quels sont les paramètres opératoires qui conditionnent les aractéristiques des dépôts afin d’adapter celles-ci, à celles imposées par les exigences aéronautiques

Ten simple rules for developing visualization tools in genomics

Our following 10 simple rules are dedicated to biologists and bioinformaticians who, while already being at the crossroads of many fields, want to venture further into the land of Data Visualization (“datavis” or “dataviz” for short). They combine tips and advice that we would have wanted when we first started our own journeys, gathered from our experiences in building genomic and/or datavis tools, and the time spent with related communities. Additionally, they address current challenges in computational biology and the needs of the community

Electronic Sensors for Assessing Interactions between Healthcare Workers and Patients under Airborne Precautions

International audienceBackground: Direct observation has been widely used to assess interactions between healthcare workers (HCWs) and patients but is time-consuming and feasible only over short periods. We used a Radio Frequency Identification Device (RFID) system to automatically measure HCW-patient interactions. Methods: We equipped 50 patient rooms with fixed sensors and 111 HCW volunteers with mobile sensors in two clinical wards of two hospitals. For 3 months, we recorded all interactions between HCWs and 54 patients under airborne precautions for suspected (n=40) or confirmed (n=14) tuberculosis. Number and duration of HCW entries into patient rooms were collected daily. Concomitantly, we directly observed room entries and interviewed HCWs to evaluate their self- perception of the number and duration of contacts with tuberculosis patients. Results: After signal reconstruction, 5490 interactions were recorded between 82 HCWs and 54 tuberculosis patients during 404 days of airborne isolation. Median (interquartile range) interaction duration was 2.1 (0.8-4.4) min overall, 2.3 (0.8-5.0) in the mornings, 1.8 (0.8-3.7) in the afternoons, and 2.0 (0.7-4.3) at night (P,1024). Number of interactions/day/HCW was 3.0 (1.0-6.0) and total daily duration was 7.6 (2.4-22.5) min. Durations estimated from 28 direct observations and 26 interviews were not significantly different from those recorded by the network. Conclusions: The RFID was well accepted by HCWs. This original technique holds promise for accurately and continuously measuring interactions between HCWs and patients, as a less resource-consuming substitute for direct observation. The results could be used to model the transmission of significant pathogens. HCW perceptions of interactions with patients accurately reflected reality

Developing an acoustic-phonetic characterization of dysarthric speech in French

- ISBN: 2-9517408-6-7 - Domaines: Phonetic Databases, Phonology, Person IdentificationInternational audienceThis paper presents the rationale, objectives and advances of an on-going project (the DesPho-APaDy project funded by the French National Agency of Research) which aims to provide a systematic and quantified description of French dysarthric speech, over a large population of patients and three dysarthria types (related to the parkinson's disease, the Amyotrophic Lateral Sclerosis disease, and a pure cerebellar alteration). The two French corpora of dysarthric patients, from which the speech data have been selected for analysis purposes, are firstly described. Secondly, this paper discusses and outlines the requirement of a structured and organized computerized platform in order to store, organize and make accessible (for selected and protected usage) dysarthric speech corpora and associated patients' clinical information (mostly disseminated in different locations: labs, hospitals, ...). The design of both a computer database and a multi-field query interface is proposed for the clinical context. Finally, advances of the project related to the selection of the population used for the dysarthria analysis, the preprocessing of the speech files, their orthographic transcription and their automatic alignment are also presented