Identification of Candidate Biomarkers for Quality Assessment of Hatchery-reared Mussel Larvae Via GC/MS-based Metabolomics

To ensure environmental and economic sustainability of future aquaculture growth, large-scale hatchery production of mollusc larvae is required. However, variation in larval quality currently limits potential maximum yields. Identification of biomarkers which reflect the immediate physiological condition of larvae during hatchery production could help monitor and determine causes of variation. Metabolomics is well-suited to this task due to its capacity for providing an instantaneous snapshot of the physiology of an organism through analysis of its metabolite profile. As a test, we applied GC/MS-based metabolomics for this purpose. Using a variety of univariate and multivariate feature selection methods, we identified four metabolite–metabolite ratios involving levels of succinate, glycine, alanine, pyroglutamate and myristic acid as candidate biomarkers for assessing mussel larval quality. These metabolites are known to have roles in energy metabolism, osmotic regulation, immune function and cell–cell communication. We anticipate that further investigation of these metabolites and their associated biochemical pathways will yield a more complete understanding of the factors responsible for larval production variability

Formation des adultes, formation des enseignants? Entretien avec Jean-Marie Barbier

Docteur Honoris Causa de l'Université Catholique de Louvain (Belgique), Jean-Marie Barbier est Professeur au Conservatoire National des Arts et Métiers (Cnam, Paris-France) où il forme des professionnels et des chercheurs dans le domaine de la formation des adultes. Il est également directeur du Centre de Recherche sur la Formation (CRF) du Cnam. En 2009, avec Étienne Bourgeois, il a fondé l'Institut Européen de Recherche sur la Formation et l'Analyse des Activités (IERFA). Il co-dirige la collection de recherche «Action et Savoir» chez l'Harmattan et la collection «Formation et pratiques professionnelles» aux Presses Universitaires de France (PUF)

Jogos didáticos: um estudo de representações sociais

The present article, drawing on the general theory of social representations, is based on a research developed with a group of undergraduates of a History course at a private University in São Paulo. It was the research’s basic intention to identify the constitutive elements of the didactic game’s semantic universe in the interface between cognitive and affective aspects of social representations with the daily needs by questioning the polarization between cognition and emotion. In order to approach such semantic universe, instruments based on methods of compilation, organization, and interrogation were used. Results showed the existence of a complex and unstable organization, operating by means of a contradictory logic (which, although, was not an excluding one), composing the semantic universe of the didactic game.Elaborado con base en la teoría general de las representaciones sociales, este artículo presenta los datos de una investigación desarrollada con un grupo de estudiantes del curso de Historia de una institución de educación superior de la Grande São Paulo, con el objetivo de identificar los elementos que constituyen el universo semántico de los juegos didácticos en la interfaz de los aspectos cognitivos, afectivos y exigencias de la vida cotidiana, cuestionando la polarización entre la cognición y la emoción. Para ello, hace uso de instrumentos basados en los métodos de compilación, de organización de contenido y interrogativo. Los resultados mostraron la existencia de una organización compleja e inestable de elementos que, funcionando por medio de una lógica contradictoria, pero no exclusiva, conforman el universo semántico del juego didáctico.Elaborado com base na teoria geral das representações sociais, este artigo apresenta os dados de uma pesquisa desenvolvida com um grupo de graduandos do curso de História de uma instituição de ensino superior da Grande São Paulo com o objetivo de identificar os elementos que constituem o universo semântico do jogo didático na interface com aspectos cognitivos, afetivos e demandas do cotidiano, questionando a polarização entre cognição e emoção. Para isso, faz uso de instrumentos baseados em métodos de compilação, de organização de conteúdo e interrogativos. Os resultados obtidos demonstraram a existência de uma organização complexa e instável em torno de elementos que, operando por meio de uma lógica contraditória, mas não excludente, compõem o universo semântico do jogo didático

Algorithms to infer metabolic flux ratios from fluxomics data

In silico cell simulation approaches based in the use of genome-scale metabolic models (GSMMs) and constraint-based methods such as Flux Balance Analysis are gaining importance, but methods to integrate these approaches with omics data are still greatly needed. In this work, the focus relies on fluxomics data that provide valuable information on the intracellular fluxes, although in many cases in an indirect, incomplete and noisy way. The proposed framework enables the integration of fluxomics data, in the form of 13C labeling distribution for metabolite fragments, with GSMMs enriched with carbon atom transition maps. The algorithms implemented allow to infer labeling distributions for fragments/metabolites not measured and to build expressions for the relevant flux ratios that can be then used to enrich constraint-based methods for flux determination. This approach does not require any assumptions on the metabolic network and reaction reversibility, allowing to compute ratios originating from coupled joint points of the network. Also, when enough data do not exist, the system tries to infer ratio bounds from the measurements

Metabolic footprint analysis of recombinant Escherichia coli strains during fed-batch fermentations

Metabolic footprinting has become a valuable analytical approach for the characterization of phenotypes and the distinction of specific metabolic states resulting from environmental and/or genetic alterations. The metabolic impact of heterologous protein production in Escherichia coli cells is of particular interest, since there are numerous cellular stresses triggered during this process that limit the overall productivity. Because the knowledge on the metabolic responses in recombinant bioprocesses is still scarce, metabolic footprinting can provide relevant information on the intrinsic metabolic adjustments. Thus, the metabolic footprints generated by Escherichia coli W3110 and the ΔrelA mutant strain during recombinant fed-batch fermentations at different experimental conditions, were measured and interpreted. The IPTG-induction of the heterologous protein expression resulted in the rapid accumulation of inhibitors of the glyoxylate shunt in the culture broth, suggesting the clearance of this anaplerotic route to replenish the TCA intermediaries withdrawn for the additional formation of heterologous protein. Nutritional shifts were also critical in the recombinant cellular metabolism, indicating that cells employ diverse strategies to counteract imbalances in the cellular metabolism, including the secretion of certain metabolites that are, most likely, used as a metabolic relief to survival processes.The authors thank to Raphael Aggio for assisting in the automatic refinement and correction of the GC-MS data. This work was supported in part by the research project Bridging Systems and Synthetic Biology for the development of Improved Microbial Cell Factories (MIT-Pt/BS-BB/0082/2008) and HeliSysBio-Molecular Systems Biology Helicobacter pylori (FCT PTDC/EBB-EBI/104235/2008), both financed by the Portuguese Fundacao para a Ciencia e Tecnologia. Sonia Carneiro was also supported by a PhD grant from the same institution (ref. SFRH/BD/22863/2005)

Applying a metabolic footprinting approach to characterize the impact of the recombinant protein production in Escherichia coli

In this study metabolic footprinting was applied to evaluate the metabolic consequences of protein overproduction at slow growth conditions (μ = 0.1 h-1). The extracellular metabolites detected by gas chromatography-mass spectrometry characterized the metabolic footprints before and after the induction of the recombinant protein production (i.e. pre- and post-induction phases). Metabolic footprinting enabled the discrimination between the two growth phases and ex-posed significant metabolic alterations in the extracellular milieu during the re-combinant processes.This work is partly funded by the Portuguese FCT (Fundacao para a Ciencia e Tecnologia) funded MIT-Portugal Program in Bioengineering (MIT-Pt/BSBB/0082/2008). The work of Sonia Carneiro is supported by a PhD grant from FCT (ref. SFRH/BD/22863/2005)

Influence of the RelA activity on E. coli metabolism by metabolite profiling of glucose-limited chemostat cultures

Metabolite profiling of E. coli W3110 and the isogenic ∆relA mutant cells was used to characterize the RelA-dependent stringent control of metabolism under different growth conditions. Metabolic profiles were obtained by gas chromatography–mass spectrometry (GC-MS) analysis and revealed significant differences between E. coli strains grown at different conditions. Major differences between the two strains were assessed in the levels of amino acids and fatty acids and their precursor metabolites, especially when growing at the lower dilution rates, demonstrating differences in their metabolic behavior. Despite the fatty acid biosynthesis being the most affected due to the lack of the RelA activity, other metabolic pathways involving succinate, lactate and threonine were also affected. Overall, metabolite profiles indicate that under nutrient-limiting conditions the RelA-dependent stringent response may be elicited and promotes key changes in the E. coli metabolism.The authors thank to Raphael Aggio for assisting in the automatic refinement and correction of the GC-MS data, Katie Smart for performing acetate analyses and Clark Ehlers for his support with the bioreactor set up. This work was supported by the Portuguese FCT (Fundacao para a Ciencia e Tecnologia) funded MIT-Portugal Program in Bioengineering (MIT-Pt/BS-BB/0082/2008) and by ERDF-European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness) and by National Funds through the FCT (Portuguese Foundation for Science and Technology) within the project FCOMP-01-0124-FEDER-009707 (HeliSysBio. molecular Systems Biology in Helicobacter pylori). The work was also supported by a PhD grant from FCT (ref. SFRH/BD/22863/2005)

Genome-scale metabolic network of the central carbon metabolism of Enterococcus faecalis

The profound advance in experimental high throughput techniques (generally referred to as omics techniques) has enabled the analysis of a large number of components within a living cell. The vast amount of data obtained from the different omics (genomics, proteomics, fluxomics, metabolomics, transcriptomics) demands the use of bioinformatics tools. These methods comprise the development of comparative tools and maintenance of databases for the analysis of genomics data, in addition to the construction of models for the analysis and integration of data in a system-wide approach. Enterococcus faecalis is a gram-positive bacterium that is getting more attention due to its two-face behavior. This natural inhabitant of the mammalian gastrointestinal tract is also an opportunist pathogen responsible for urinary tract infections, nosocomial infections, bacteremia and infective endocarditis. Besides, its intrinsic physiological properties such as inherent antibiotic resistance and exceptional ability to adapt to harsh conditions provide this organism with an enormous advantage in the infection processes. Here, we propose to reconstruct the genome scale metabolic network of the central carbon metabolism of Enterococcus faecalis using genome sequencing information available on different databases as well as proteomics and metabolomics data. The first metabolic model generated for this bacterium will allow correlating metabolite levels and fluxes which enables identification of key control points in its metabolism. As it has been previously shown for other organisms, the metabolic network reconstruction may serve as a valuable tool to predict the phenotypic behaviour under various genetic and environmental conditions.Supported by a PhD grant from the FCT (Portuguese Science Foundation): SFRH/BD/47016/2008 and funding from HRC (Health Research Council of New Zealand)

Genome scale metabolic network reconstruction of pathogen – Enterococcus faecalis

Enterococcus faecalis is a Gram-positive bacterium that is getting more attention due to its “two-face” behavior. This natural inhabitant of the gastrointestinal mammalian tract is also an opportunist pathogen responsible for urinary tract infections, nosocomial infections, bacteremia and infective endocarditis (1). Since the metabolic reconstruction of Haemophilus influenzae was published in 1999 (2), many other researchers have focused their attention into the possibilities that the new era of genome-scale metabolic models could bring to the scientific scene, both in prokaryotic and eukaryotic organisms