Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data

<p>Abstract</p> <p>Background</p> <p>Genome-scale metabolic models are powerful tools to study global properties of metabolic networks. They provide a way to integrate various types of biological information in a single framework, providing a structured representation of available knowledge on the metabolism of the respective species.</p> <p>Results</p> <p>We reconstructed a constraint-based metabolic model of <it>Acinetobacter baylyi </it>ADP1, a soil bacterium of interest for environmental and biotechnological applications with large-spectrum biodegradation capabilities. Following initial reconstruction from genome annotation and the literature, we iteratively refined the model by comparing its predictions with the results of large-scale experiments: (1) high-throughput growth phenotypes of the wild-type strain on 190 distinct environments, (2) genome-wide gene essentialities from a knockout mutant library, and (3) large-scale growth phenotypes of all mutant strains on 8 minimal media. Out of 1412 predictions, 1262 were initially consistent with our experimental observations. Inconsistencies were systematically examined, leading in 65 cases to model corrections. The predictions of the final version of the model, which included three rounds of refinements, are consistent with the experimental results for (1) 91% of the wild-type growth phenotypes, (2) 94% of the gene essentiality results, and (3) 94% of the mutant growth phenotypes. To facilitate the exploitation of the metabolic model, we provide a web interface allowing online predictions and visualization of results on metabolic maps.</p> <p>Conclusion</p> <p>The iterative reconstruction procedure led to significant model improvements, showing that genome-wide mutant phenotypes on several media can significantly facilitate the transition from genome annotation to a high-quality model.</p

Modélisation et analyse, globale et locale, de réseaux d'interactions biologiques hétérogènes (RIBH) appliqué à la Levure.

This work studies biological in silico networks. It assess the question of integration, formalism and model of biological networks and subnetworks. First, an integration tool called Cyclone was developed to simplify the access and analyse biological information of the Biocyc database. Then, a graph model framework to analyse heterogeneous networks, MIB (for Biological Interaction Model) is presented. Finally, on one hand, these methods were used to study how subnetworks were linked together and to study network motifs in larger networks, and on the other hand, to study and model the metabolic pathway of galactose in yeast (Saccharomyces cerevisiae) that includes a heterogeneous feedback loop made of protein-protein interaction and transcriptional regulation.Le travail présenté s'articule autour de l'étude in silico des réseaux biologiques en abordant aussi bien les aspects d'intégration, de formalisation et de modélisation des réseaux et sous-réseaux biologiques. Dans ce contexte, les travaux ont porté dans un premier temps, sur le développement d'un outil d'intégration Cyclone à même d'assurer un accès et une exploitation simplifiés des données présentes dans la base de données BioCyc puis, dans un second temps, sur le développement d'un cadre de modélisation des graphes particulièrement adapté à l'étude de réseaux d'interactions hétérogènes, MIB (pour Modèle d'Interaction Biologique). Enfin, ces développements ont été mis à profit afin d'une part, de caractériser et d'étudier la présence et le mode de connexion de sous-réseaux ou motifs à l'intérieur de réseaux plus vastes et d'autre part, d'étudier et de modéliser la voie métabolique du galactose chez la levure Saccharomyces cerevisiae en tant que boucle de rétroaction impliquant régulation transcriptionnelle et interaction protéine-protéine

Decentralised Approach to Provision of Home Services

This paper introduces an approach that addresses interoperability in AAL domain, the Decentralised Service Delivery Architecture. The approach was developed Within the Advanced Support for Independent Living; Human Lifecycle Approach in Senior Housing (Lily) project, funded in the Ambient Assisted Living Joint Programme. The approach has a decentralised architecture and therefore differsfrom traditional approaches where services are provisioned via central nodes as via service portals or hubs, dedicated home platforms or systems. The idea of the architecture is to use linked descriptions of samples of service-product continuum that can be discovered using certain criteria, and thus provisioned to inhabitants of intelligent environments. The paper describes the Smart Living concept under which the architecture takes a place, presents some particularities of the architecture and systems that utilise it - HoviMestari and VisAge, and introduces Integration Levels and service templates with respect to the architecture

CycSim - an online genome-scale metabolic model simulator and browser, integrated with pathways databases

International audienceCycSim is a web-based application dedicated to analyses with genome-scale metabolic models coupled to the exploration of knowledge from BioCyc and KEGG. Specifically, CycSim supports the design of knockout experiments: simulation of growth phenotypes of single or multiple gene deletions mutants on specified media, comparison of these predictions with experimental phenotypes, and direct visualization of both on metabolic maps. The web interface is designed for simplicity, putting constraint-based modeling techniques within easier reach of biologists. CycSim also functions as an online repository of constraint-based models devoted to metabolic networks and can be used to produce training data for metabolic network inference methods

The SWEET-HOME Project: Audio Technology in Smart Homes to improve Well-being and Reliance

4 pagesInternational audienceThe SWEET-HOME project aims at providing audio-based interaction technology that lets the user have full control over their home environment, at detecting distress situations and at easing the social inclusion of the elderly and frail population. This paper presents an overview of the project focusing on the multimodal sound corpus acquisition and labelling and on the investigated techniques for speech and sound recognition. The user study and the recognition performances show the interest of this audio technology

The SWEET-HOME Project: Audio Technology in Smart Homes to improve Well-being and Reliance

International audienc