Modelling of the TICS Catalyse : Definition of a basic vocabulary

International audienceThe thinking launched since the creation of "Catalyse" tools led in 2008 to the necessity of integrating the tools of quantitative, qualitative and spatial analysis in an information system managing the contents from data collection to results publishing according to actor's use. Within the framework of these information systems so-called TICS "Territorial Intelligence Community Systems" conception, an action of modelling started in 2009. After definition of first models, which describe the data manipulated by the existing tools of the "Valise Catalyse", we realized that it was important and essential, to define the vocabulary allowing territorial intelligence specialists and computing specialists to communicate. Reminding of realised works in the modelling action we present in this article this last aspect of our work.La réflexion lancée depuis la création des outils " Catalyse " a abouti en 2008 à la nécessité d'intégrer les outils d'analyse quantitative, qualitative et spatiale dans un système d'information gérant les contenus de la collecte des données à la publication des résultats en respectant les usages des acteurs. Dans le cadre de la conception de ces systèmes d'information appelés SCIT " Systèmes Communautaires d'Intelligence Territoriale ", une action de modélisation a été lancée dès 2009. Après la définition de premiers modèles décrivant les données manipulées par les outils existants de la valise Catalyse, nous nous sommes rendus compte qu'il était important de définir le vocabulaire permettant aux spécialistes de l'intelligence territoriale et aux informaticiens de communiquer. Après un rappel des travaux réalisés dans le cadre de cette action, nous présentons dans cet article ce dernier aspect de notre travail

: Dans cet article, une étude visant à définir des métadonnées pour la CAENTI est présentée. Le standard du Dublin Core est le plus connu des standards de métadonnées pour la description de ressources. Ce standard est détaillé et illustré par un exemple. Ensuite une discussion montre quels raffinements doivent être ajoutés au Dublin Core pour caractériser les resources de la CAENTI.

International audienceIn this article, a study to define metadata for the CAENTI resources is presented. The Dublin Core standard is the most know for metadata standards to describe resources. This standard is detailed and illustrated by an example. Then a discussion shows which refinements must be added to the Dublin Core to characterize the CAENTI resources

Étude comparative des plateformes parallèles pour systèmes multi-agents

International audienceLa simulation est devenue un outil indispensable à la recherche pour explorer les systèmes sans avoir recours à l'expérience. En fonction des caractéristiques du système la méthode de modélisation utilisée pour représenter le système varie. Les systèmes multi-agents sont ainsi souvent utilisés pour modéliser et simuler les systèmes complexes. Quel que soit le type de modélisation utilisée, l'augmentation de la taille et de la précision du modèle fait croître le nombre des calculs, rendant nécessaire l'utilisation de systèmes parallèles. Dans cet article, nous nous intéressons aux plateformes de simulation multi-agent parallèles. Notre contribution est une étude comparative de ces différentes plateformes, dans un contexte de calcul intensif. Nous présentons une analyse qualitative, à partir de critères que nous avons définis, puis un comparatif de performance, sur la base d'un modèle agent que nous avons implémenté sur chaque plateforme

Predictive toxicology using systemic biology and liver microfluidic "on chip" approaches: Application to acetaminophen injury

International audienceWe have analyzed transcriptomic, proteomic and metabolomic profiles of hepatoma cells cultivated inside a microfluidic biochip with or without acetaminophen (APAP). Without APAP, the results show an adaptive cellular response to the microfluidic environment, leading to the induction of anti-oxidative stress and cytoprotective pathways. In presence of APAP, calcium homeostasis perturbation, lipid peroxidation and cell death are observed. These effects can be attributed to APAP metabolism into its highly reactive metabolite. N-acetyl-p-benzoquinone imine (NAPQI). That toxicity pathway was confirmed by the detection of GSH-APAP, the large production of 2-hydroxybutyrate and 3-hydroxybutyrate, and methionine, cystine, and histidine consumption in the treated biochips. Those metabolites have been reported as specific biomarkers of hepatotoxicity and glutathione depletion in the literature. In addition, the integration of the metabolomic, transcriptomic and proteomic collected profiles allowed a more complete reconstruction of the APAP injury pathways. To our knowledge, this work is the first example of a global integration of microfluidic biochip data in toxicity assessment. Our results demonstrate the potential of that new approach to predictive toxicology

Insights on the virulence of swine respiratory tract mycoplasmas through genome-scale metabolic modeling

Background: The respiratory tract of swine is colonized by several bacteria among which are three Mycoplasma species: Mycoplasma flocculare, Mycoplasma hyopneumoniae and Mycoplasma hyorhinis. While colonization by M. flocculare is virtually asymptomatic, M. hyopneumoniae is the causative agent of enzootic pneumonia and M. hyorhinis is present in cases of pneumonia, polyserositis and arthritis. The genomic resemblance among these three Mycoplasma species combined with their different levels of pathogenicity is an indication that they have unknown mechanisms of virulence and differential expression, as for most mycoplasmas. Methods: In this work, we performed whole-genome metabolic network reconstructions for these three mycoplasmas. Cultivation tests and metabolomic experiments through nuclear magnetic resonance spectroscopy (NMR) were also performed to acquire experimental data and further refine the models reconstructed in silico. Results: Even though the refined models have similar metabolic capabilities, interesting differences include a wider range of carbohydrate uptake in M. hyorhinis, which in turn may also explain why this species is a widely contaminant in cell cultures. In addition, the myo-inositol catabolism is exclusive to M. hyopneumoniae and may be an important trait for virulence. However, the most important difference seems to be related to glycerol conversion to dihydroxyacetone-phosphate, which produces toxic hydrogen peroxide. This activity, missing only in M. flocculare, may be directly involved in cytotoxicity, as already described for two lung pathogenic mycoplasmas, namely Mycoplasma pneumoniae in human and Mycoplasma mycoides subsp. mycoides in ruminants. Metabolomic data suggest that even though these mycoplasmas are extremely similar in terms of genome and metabolism, distinct products and reaction rates may be the result of differential expression throughout the species. Conclusions: We were able to infer from the reconstructed networks that the lack of pathogenicity of M. flocculare if compared to the highly pathogenic M. hyopneumoniae may be related to its incapacity to produce cytotoxic hydrogen peroxide. Moreover, the ability of M. hyorhinis to grow in diverse sites and even in different hosts may be a reflection of its enhanced and wider carbohydrate uptake. Altogether, the metabolic differences highlighted in silico and in vitro provide important insights to the different levels of pathogenicity observed in each of the studied species

Metabolites

The study of the metabolome within tissues, organisms, cells or biofluids can be carried out by several bioanalytical techniques. Among them, nuclear magnetic resonance (NMR) is one of the principal spectroscopic methods. This is due to a sample rotation technique, high-resolution magic angle spinning (HR-MAS), which targets the analysis of heterogeneous specimens with a bulk sample mass from 5 to 10 mg. Recently, a new approach, high-resolution micro-magic angle spinning (HR-μMAS), has been introduced. It opens, for the first time, the possibility of investigating microscopic specimens (<500 μg) with NMR spectroscopy, strengthening the concept of homogeneous sampling in a heterogeneous specimen. As in all bioanalytical approaches, a clean and reliable sample preparation strategy is a significant component in designing metabolomics (or -omics, in general) studies. The sample preparation for HR-μMAS is consequentially complicated by the μg-scale specimen and has yet to be addressed. This report details the strategies for three specimen types: biofluids, fluid matrices and tissues. It also provides the basis for designing future μMAS NMR studies of microscopic specimens

Metabolic Investigation of the Mycoplasmas from the Swine Respiratory Tract

International audienceBackgroundThe respiratory tract of swine is colonized by several bacteria among which are three Mycoplasma species: Mycoplasma flocculare, Mycoplasma hyopneumoniae and Mycoplasma hyorhinis. While colonization by M. flocculare is virtually asymptomatic, M. hyopneumoniae is the causative agent of enzootic pneumonia and M. hyorhinis is present in cases of pneumonia, polyserositis and arthritis. The genomic resemblance among these three Mycoplasma species combined with their different levels of pathogenicity is an indication that they have unknown mechanisms of virulence and differential expression, as for most mycoplasmas.MethodsIn this work, we performed whole-genome metabolic network reconstructions for these three mycoplasmas. Cultivation tests and metabolomic experiments through nuclear magnetic resonance spectroscopy (NMR) were also performed to acquire experimental data and further refine the models reconstructed in silico.ResultsEven though the refined models have similar metabolic capabilities, interesting differences include a wider range of carbohydrate uptake in M. hyorhinis, which in turn may also explain why this species is a widely contaminant in cell cultures. In addition, the myo-inositol catabolism is exclusive to M. hyopneumoniae and may be an important trait for virulence. However, the most important difference seems to be related to glycerol conversion to dihydroxyacetone-phosphate, which produces toxic hydrogen peroxide. This activity, missing only in M. flocculare, may be directly involved in cytotoxicity, as already described for two lung pathogenic mycoplasmas, namely Mycoplasma pneumoniae in human and Mycoplasma mycoides subsp. mycoides in ruminants. Metabolomic data suggest that even though these mycoplasmas are extremely similar in terms of genome and metabolism, distinct products and reaction rates may be the result of differential expression throughout the species.ConclusionsWe were able to infer from the reconstructed networks that the lack of pathogenicity of M. flocculare if compared to the highly pathogenic M. hyopneumoniae may be related to its incapacity to produce cytotoxic hydrogen peroxide. Moreover, the ability of M. hyorhinis to grow in diverse sites and even in different hosts may be a reflection of its enhanced and wider carbohydrate uptake. Altogether, the metabolic differences highlighted in silico and in vitro provide important insights to the different levels of pathogenicity observed in each of the studied species

The Essential Role for Laboratory Studies in Atmospheric Chemistry

Laboratory studies of atmospheric chemistry characterize the nature of atmospherically relevant processes down to the molecular level, providing fundamental information used to assess how human activities drive environmental phenomena such as climate change, urban air pollution, ecosystem health, indoor air quality, and stratospheric ozone depletion. Laboratory studies have a central role in addressing the incomplete fundamental knowledge of atmospheric chemistry. This article highlights the evolving science needs for this community and emphasizes how our knowledge is far from complete, hindering our ability to predict the future state of our atmosphere and to respond to emerging global environmental change issues. Laboratory studies provide rich opportunities to expand our understanding of the atmosphere via collaborative research with the modeling and field measurement communities, and with neighboring disciplines

Métabolomics

International audienc