Whole proteome analyses on Ruminiclostridium cellulolyticum show a modulation of the cellulolysis machinery in response to cellulosic materials with subtle differences in chemical and structural properties

Lignocellulosic materials from municipal solid waste emerge as attractive resources for anaerobic digestion biorefinery. To increase the knowledge required for establishing efficient bioprocesses, dynamics of batch fermentation by the cellulolytic bacterium Ruminiclostridium cellulolyticum were compared using three cellulosic materials, paper handkerchief, cotton discs and Whatman filter paper. Fermentation of paper handkerchief occurred the fastest and resulted in a specific metabolic profile: it resulted in the lowest acetate-to-lactate and acetate-to-ethanol ratios. By shotgun proteomic analyses of paper handkerchief and Whatman paper incubations, 151 proteins with significantly different levels were detected, including 20 of the 65 cellulosomal components, 8 non-cellulosomal CAZymes and 44 distinct extracytoplasmic proteins. Consistent with the specific metabolic profile observed, many enzymes from the central carbon catabolic pathways had higher levels in paper handkerchief incubations. Among the quantified CAZymes and cellulosomal components, 10 endoglucanases mainly from the GH9 families and 7 other cellulosomal subunits had lower levels in paper handkerchief incubations. An in-depth characterization of the materials used showed that the lower levels of endoglucanases in paper handkerchief incubations could hypothetically result from its lower crystallinity index (50%) and degree of polymerization (970). By contrast, the higher hemicellulose rate in paper handkerchief (13.87%) did not result in the enhanced expression of enzyme with xylanase as primary activity, including enzymes from the xyl-doc cluster. It suggests the absence, in this material, of molecular structures that specifically lead to xylanase induction. The integrated approach developed in this work shows that subtle differences among cellulosic materials regarding chemical and structural characteristics have significant effects on expressed bacterial functions, in particular the cellulolysis machinery, resulting in different metabolic patterns and degradation dynamics.This work was supported by a grant [R2DS 2010-08] from Conseil Regional d'Ile-de-France through DIM R2DS programs (http://www.r2ds-ile-de-france.com/). Irstea (www.irstea.fr/) contributed to the funding of a PhD grant for the first author. The funders provided support in the form of salaries for author [NB], funding for consumables and laboratory equipment, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. Omics Services provided support in the form of salaries for authors [VS, MD], but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors [NB, VS, MD] are articulated in the 'author contributions' section.info:eu-repo/semantics/publishedVersio

Présentation du Challenge ROSE : robotique et capteurs au service d’Ecophyto

National audienc

Structuration de la diversité métabolique chez escherichia coli (Intégration du réseau métabolique, du protéome, des paramètres enzymatiques et des phénotypes de croissance)

Les microorganismes sont remarquablement adaptés à des environnements divers, changeants et imprévisibles. Escherischia coli est une bactérie d'importance en santé publique et compte parmi les plus versatiles. Sa diversité génétique intra-spécifique a été très étudiée et indique l'existence d'une plasticité du génome et d'une structure en phylogroupes. Alors que le métabolisme détermine la capacité d'une bactérie à exploiter les ressources, la diversité métabolique de l'espèce est mal connue. Pour comprendre le rôle des facteurs écologiques dans l'évolution de cette espèce, nous avons étudié l'importance et la structure de la diversité pour trois caractères métaboliques : la présence/absence de réactions au sein du réseau métabolique, la capacité à utiliser différentes sources de carbone et la variation des concentrations des protéines dans différents milieux. Nous avons montré que les réseaux métaboliques partagent un large noyau de réactions communes, et que leur part variable est structurée en fonction de la phylogénie. Toutefois, les phénotypes métaboliques ne sont pas liés aux phylogroupes et E. coli constitue un unique groupe phénotypique, ce qui suggère l'absence de spécialisation pour l'utilisation de source de carbone. Ce travail révèle l'importance de la diversité métabolique intra-spécifique et suggère de nouvelles hypothèses à propos des relations génotype/phénotype. La diversité métabolique intra-spécifique étant très structurée par les ressources en interaction avec les souches mais peu par la phylogénie de l'espèce ou le mode de vie, elle pourrait brouiller le signal phylogénétique. En perspective, l'intégration des données expérimentales dans les modèles métaboliques permettrait de mettre en relation les concentrations des enzymes avec les taux de croissance.Microorganisms are remarkably adapted to diverse, changing and unpredictable environments. Although metabolism is directly linked to the bacterial ability to grow in an ecological niche, the intra-species metabolic diversity is poorly known. Escherichia coli is one of the most versatile medically important species. Its intra-species genetic diversity has been thoroughly studied showing its genome plasticity and phylogroup structure. In order to better understand the role of ecological factors in the species evolution, we studied the extent and structure of metabolic diversity throughout the species for three metabolic traits: the presence/absence of reactions in the metabolic networks, the ability to grow on different carbon sources and the variation of protein concentrations in different environments. We found that metabolic networks share a large core of common reactions, and that its variable part is structured according to the species phylogeny. Nevertheless, metabolic phenotypes are not linked to phylogroups and E. coli constitutes a single phenotypic group, which suggests that no specialization occurred for carbon source usage within the species. This work reveals the extent of the intra-species metabolic diversity and suggests new hypotheses about genotype-phenotype relationships that could blur the phylogenetic signal. The main emerging picture is that the intra-species metabolic diversity is highly structured by the resources in interaction with the strains but weakly by the strain phylogeny or lifestyle. Further prospects consist in integrating these experimental data into metabolic models to relate variation of enzyme concentrations to growth rates.ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF

Le cervelet comme predicteur

ISBN : 978-2-9532965-0-1Le cervelet a une structure uniforme, consistant en la répétition d'une même boucle neuronale. On ignore encore si les diverses fonctions motrices et cognitives auxquelles le cervelet participe reposent sur une unique computation basique implémentée par cette boucle ou bien reflètent la capacité de cette boucle à produire plusieurs computations dédiées. Nous avons testé la première hypothèse avec l'exemple du contrôle moteur en simulant les propriétés dynamiques d'un modèle de la boucle cérébelleuse basique qui inclue (i) la copie des commandes motrices et les retours sensoriels sur leurs effets dans les entrées délivrées aux cellules de Purkinje (CP, l'unique voie de sortie du cortex cérebelleux) par les fibres parallèles (FP, l'une des deux entrées du cervelet) (ii) la capacité des cellules de Purkinje (CP) à produire une trace électrique de durée adaptive en réponse à une commande motrice phasique (iii) les rebonds de potentiel des neurones des noyaux cérebelleux profonds (NCP) à l'interruption de leur inhibition par les CP (iv) la plasticité des connexions FP?CP et CP?NCP, supervisée par les signaux de l'olive inférieure (OI, la seconde entrée du cervelet). Soumis à une séquence de commandes aléatoires (mimant une activité exploratoire par tâtonnement), le modèle apprend à associer correctement les retours sensoriels informant des changements d'état, malgré un retard du aux délais de conduction et de pré-traitement de ces informations, aux commandes motrices qui les ont déclenchés. Dans le modèle, après apprentissage les neurones excitateurs des NCP (la sortie du cervelet) produisent une estimation robuste de l'état courant des variables d'état. Ces résultats obtenus dans le cadre du contrôle moteur démontrent pour la première fois que, grâce à son architecture et aux propriétés actives de ses neurones, le cervelet peut implémenter la fonction de prédicteur de changements de variables d'état postulée par les théories fonctionnelles du cervelet

Late-life reproduction in an insect: terminal investment, reproductive restraint or senescence

1. The Terminal Investment, Reproductive Restraint or Senescence theories may explain individual late-life patterns of reproduction. The terminal investment hypothesis predicts that individuals increase reproductive allocation late in life as prospects for future survival decrease. The other two hypotheses predict reduced reproduction late in life, but for different reasons. Under the Reproductive Restraint hypothesis, individuals restrain their reproductive effort to sustain future survival and gain more time for reproducing, whereas under the Senescence process, reproduction is constrained because of somatic deterioration. While these hypotheses imply that reproduction is costly, they should have contrasted implications in terms of survival after late reproduction and somatic maintenance. 2. Testing these hypotheses requires proper consideration of the effects of age-dependent reproductive effort on post-reproduction survival and age-related somatic functions. We experimentally tested these three hypotheses in females of the mealworm beetle, Tenebrio molitor, an iteroparous and income breeder insect. We manipulated their age-specific allocation into reproduction and observed the effects of this manipulation on their late life- fecundity, post-reproduction survival and immunocompetence as a measurement of somatic protection. 3. We found that females exhibit age-related declines in fecundity and that this reproductive senescence is accelerated by a cost of early reproduction. The cost of reproduction had no significant effect on female longevity and their ability to survive a bacterial infection, despite that some immune cells were depleted by reproduction. We found that female post-infection survival deteriorated with age, which could be partly explained by a decline in some immune parameters. Importantly, females did not increase their reproductive effort late in life at the expense of their late-life post-reproduction survival. 4. Late-life reproduction in T. molitor females is senescing and not consistent with a terminal investment strategy. Rather, our results suggest that females allocate resources according to a priority scheme favouring longevity at the expense of reproduction, which is in line with the reproductive restraint hypothesis. 5. Such a priority scheme also shows that a relatively short-lived insect can evolve life history strategies hitherto known only in long-lived animals. This puts in perspective the role of longevity in the evolution of life history strategies.The file JAE_fecundity _longevity corresponds to females for which we manipulated reproductions and measured their fecundity and longevity. The file JAE_imunity corresponds to the females for which we also manipulated the reproduction in the same way and measured their immunity via hemolymphe sampling

Drainage par injection à l’aide des forages absorbants. (Périmètre d’irrigation de la plaine des Doukkalas, Maroc)

Injection drainage by means of absorption wells. — Doukkalas Plain irrigation area (Morocco). The problem was to dispose of surplus runoff from an irrigation area covering roughly 1,000 hectares. Geological prospections, boreholes and tests were carried out in order to ascertain the possibility of draining the water off into absorption wells. The results of water absorption tests carried out in Pliocene sandstone were interpreted, and the point permeability rates and transmitting capacities were calculated. The final stage was a transition from the reconnaissance work to the construction of the final structures, the operation and layout of which are described in this report.Problème de l'évacuation des eaux de colature d'un casier d'irrigation de 1 000 hectares environ. Etudes géologiques, campagne de sondages de reconnaissance et essais destinés à déterminer la possibilité d'évacuer ces eaux à l'aide de forages absorbants. Interprétation d'essais d'absorption d'eau réalisée dans un grès Pliocène et calcul des perméabilités et transmissivités ponctuelles. Passage du stade reconnaissance aux ouvrages définitifs. Disposition et comportement de ces derniers.Ambroggi R., Moullard L., Hazan R., Sabarly F. Drainage par injection à l’aide des forages absorbants. (Périmètre d’irrigation de la plaine des Doukkalas, Maroc). In: L'hydraulique souterraine. Compte rendu des sixièmes journées de l'hydraulique, Nancy, 28-30 juin 1960. Tome 1, 1961