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Lytic polysaccharide (mono)oxygenases (LPMOs) perform oxidative cleavage of polysaccharides, and are key enzymes in biomass processing and the global carbon cycle. It has been shown that LPMO reactions may be driven by light, using photosynthetic pigments or photocatalysts, but the mechanism behind this highly attractive catalytic route remains unknown. Here, prompted by the discovery that LPMOs catalyze a peroxygenase reaction more efficiently than a monooxygenase reaction, we revisit these light-driven systems, using an LPMO from Streptomyces coelicolor (ScAA10C) as model cellulolytic enzyme. By using coupled enzymatic assays, we show that H2O2 is produced and necessary for efficient light-driven activity of ScAA10C. Importantly, this activity is achieved without addition of reducing agents and proportional to the light intensity. Overall, the results highlight the importance of controlling fluxes of reactive oxygen species in LPMO reactions and demonstrate the feasibility of light-driven, tunable enzymatic peroxygenation to degrade recalcitrant polysaccharides., Lytic polysaccharide (mono)oxygenases (LPMOs) perform oxidative cleavage of polysaccharides. Here, the authors showed that the light-driven activity of LPMOs is dependent on hydrogen peroxide availability and can be controlled via the light intensity provided.

Session : Systèmes d'élevages, environnement et durabilité; Approche de l'aquaponie par bilan de masse : étude des flux de matière et caractérisation de la capacité épuratoire d'un système aquaponique truite arc-en-ciel (oncorhynchus mykiss) salade (Lactuca sativa). 6. Journées de la Recherche Filière Piscicole

Proper carbon (C) supply is essential for nitrogen (N) assimilation especially when plants are grown under ammonium (NH4+) nutrition. However, how C and N metabolic fluxes adapt to achieve so remains uncertain. In this work, roots of wheat (Triticum aestivum L.) plants grown under exclusive NH4+ or nitrate (NO3−) supply were incubated with isotope-labelled substrates (15NH4+, 15NO3−, or [13C]Pyruvate) to follow the incorporation of 15N or 13C into amino acids and organic acids. Roots of plants adapted to ammonium nutrition presented higher capacity to incorporate both 15NH4+ and 15NO3− into amino acids, thanks to the previous induction of the NH4+ assimilative machinery. The 15N label was firstly incorporated into [15N]Gln vía glutamine synthetase; ultimately leading to [15N]Asn accumulation as an optimal NH4+ storage. The provision of [13C]Pyruvate led to [13C]Citrate and [13C]Malate accumulation and to rapid [13C]2-OG consumption for amino acid synthesis and highlighted the importance of the anaplerotic routes associated to tricarboxylic acid (TCA) cycle. Taken together, our results indicate that root adaptation to ammonium nutrition allowed efficient assimilation of N thanks to the promotion of TCA cycle open flux modes in order to sustain C skeleton availability for effective NH4+ detoxification into amino acids.

Le nombre croissant de déchets d’équipements électriques et électroniques (DEEE) et le renforcement des législations relatives à leur collecte et leur traitement développent l’intérêt porté à la gestion de ces déchets. En Belgique, outre le système conventionnel de collecte-traitement géré par les organismes officiels mis en place par les producteurs d’équipements électroniques afin de se conformer à l’obligation de reprise imposée par l’Europe, d’autres acteurs de collecte et de traitement existent. Parmi eux se retrouvent les entreprises d’économie sociale (ES) actives dans le réemploi et le démantèlement manuel. Si certaines d’entre elles sont impliquées dans la filière conventionnelle, d’autres ont développé leur propre filière de fin de vie des DEEE.Bien que le recyclage et le tri des déchets ne fassent pas partie des secteurs principaux investis par les entreprises d’ES, ils constituent pour elles un domaine important pour trois raisons principales. Premièrement, le secteur du recyclage et de la récupération est une activité historique des entreprises d’ES qui y ont été des pionnières. Deuxièmement, le recyclage, la récupération ainsi que, plus largement, le développement durable et l’économie circulaire sont des secteurs d’activité et des concepts gourmands en main-d’oeuvre qui offrent de ce fait de grandes perspectives en matière de création d’emplois. Le secteur du recyclage et du tri des déchets, ne nécessitant généralement pas une main-d’oeuvre très qualifiée, est donc investi par des entreprises se positionnant dans l’insertion par l’emploi. Troisièmement, les entreprises d’ES poursuivent différents objectifs parmi lesquels se retrouvent la préservation de l’environnement et la favorisation du développement durable. Le recyclage et la récupération y sont incontestablement attachés. Il existe donc un lien inhérent entre les entreprises d’ES et la gestion des déchets. Cette constatation amène à se demander si ces entreprises génèrent des impacts environnementaux spécifiques liés à leur gestion des DEEE.Ce travail s’intéresse plus particulièrement à la gestion de fin de vie de deux types de DEEE :les tours d’ordinateurs de bureau et les panneaux photovoltaïques de première génération. Pour ces deux flux, les différentes filières de collecte et de traitement sont tout d’abord mises en évidence sur la base de données de la littérature et de contact avec des acteurs actifs dans la fin de vie des DEEE. Ensuite, une analyse des flux de matières est réalisée pour déterminer les quantités de DEEE générés en Belgique francophone et leur répartition dans les différentes filières. Enfin, une analyse de cycle de vie permet de déterminer les impacts spécifiques des entreprises d’ES, avec une attention particulière pour l’épuisement des ressources abiotiques.Les résultats obtenus montrent que les entreprises d’ES actives dans la fin de vie des deux flux étudiés, grâce au réemploi et à la récupération plus importante de matériaux permise par le démantèlement manuel, contribuent positivement à l’impact environnemental global de cette fin de vie. En particulier, dans le cas d’étude dédié aux ordinateurs, les bénéfices environnementaux relatifs à l’épuisement des ressources sont près de 30% plus importants dans la filière de l’ES que dans la conventionnelle. Pour une tonne d’ordinateurs traitée, cette différence correspond à des bénéfices équivalents aux émissions de trois européens. L’importance de cette contribution positive est toutefois conditionnée par les quantités captées par les entreprises d’ES et le potentiel de démantèlement qu’offre le DEEE.La comparaison des deux cas d’étude permet de mettre en évidence que l’implication des entreprises d’ES dans la gestion de fin de vie d’un DEEE dépend de critères législatifs et technico-économiques. Sur cette base, des recommandations peuvent être dégagées pour soutenir les entreprises d’ES. Ainsi, les inclure dans la législation relative aux DEEE ou favoriser leur inclusion via l’utilisation d’indicateurs de recyclage effectif et des clauses sociales dans les appels d’offre permettrait à ces entreprises d’occuper une place plus importante dans la gestion des DEEE en Belgique francophone et en améliorerait le bilan environnemental global., Doctorat en Sciences, info:eu-repo/semantics/nonPublished

Metabolic network reconstruction is a new critical step to connect massive sequencing and biochemical data with metabolic information contained in databases. In this context, the aim of this internship was to reconstruct the metabolic network of the Tisochrysis lutea (T. lutea) microalgae through a workflow developed by the Dyliss team. This workflow combines several methods such as genomic annotation based reconstruction and orthology based reconstruction. It allows the gap-filling and manual curation as well as the analysis of the flux of these networks. The metabolic network reconstruction of T. lutea was carried out on one hand, from the combination of two distinct annotations, one obtained experimentally and the other in silico, on the other hand from the orthology informations of four organisms (Arabidopsis thaliana, Chlamydomonas reinhardtii, Ectocarpus siliculosus et Synechocystis sp. PCC 6803). The metabolic network obtained grows on its growth medium. Following this, a verification of this network was carried out on the analysis of a specific biosynthetic pathway: the carnosine biosynthesis pathway. The resulting figure is part of an article in preparation which co-authors I figure among.; La reconstruction de réseau métabolique est une nouvelle étape essentielle pour faire le lien entre les données issues du séquençage massif et les informations biochimiques et métaboliques renfermées dans des bases de données. En ce sens, ce stage a eu pour but de reconstruire de manière automatique le réseau métabolique de la microalgue Tisochrysis lutea (T. lutea) au travers du workflow AuReMe développé par l'équipe Dyliss. Ce workflow combine plusieurs méthodes telles que la reconstruction basée sur l'annotation génomique et la reconstruction basée sur l'orthologie. Il permet aussi bien le remplissage des lacunes (gap-filling) et la curation manuelle que l'analyse du flux de ces réseaux. Le processus de reconstruction automatique du réseau métabolique de T. lutea a été réalisé en partant de deux annotations de génomes de deux protéomes, l'un expérimental et l'autre in silico, et de quatre réseaux métaboliques connus (Arabidopsis thaliana, Chlamydomonas reinhardtii, Ectocarpus siliculosus et Synechocystis sp. PCC 6803). Le réseau métabolique obtenu croît sur son milieu de culture. Suite à cela, une vérification de ce réseau a été effectuée sur l'analyse d'une voie de biosynthèse spécifique : la voie de biosynthèse de la carnosine. La figure résultat fait partie d'un article en préparation dont je figure parmi des co-auteurs.

The production of medium chain length polyhydroxyalkanoates by Pseudomonas putida KT2440 from fatty acids leads to the loss of a large proportion of carbon. We studied the possibility of a shift of potentially available energy and carbon towards monitored residual growth during the production phase. A Fed-Batch culture achieving 125.6 g/L of total biomass containing 54.4% (g/g) of medium chain length polyhydroxyalkanoates was carried out leading to an overall experimental carbon yield of 0.7 Cmole/Cmole. The analysis of modeling fluxes deduced from experimental data indicated how carbon and reduced cofactors (NADH and FADH(2)) were managed to conclude that part of the carbon and reduced cofactors made available by polymer production were used in anabolic pathways. The strategy which consisted in coupled growth and medium chain length polyhydroxyalkanoate production enhanced the global yields compared to growth followed by a production phase. The understanding of carbon and energy fluxes distribution allowed deducing optimized culture strategy to perform the highest reported in the literature.

Highlights:• Many forests have an heterogeneous structure not accounted for in models.• We developed NOTG, a 3D, individual-based model of carbon and water budgets.• The model was parameterized for a mixed Mediterranean forest.• 3D simulation was more consistent with observations than 1D simulation.• Results show the importance of above- and below-ground spatial structures.Abstract:Many natural terrestrial ecosystems, agroforestry systems, and, increasingly, forest plantations, are made of a mixture of species and display significant structural heterogeneity. Yet most carbon-based biophysical models are limited to homogeneous, monospecific canopies. We explored whether the spatial structure at the Font-Blanche experimental site, located in a mixed Mediterranean forest of Aleppo pine and holm oak in south-east France, could affect the components of the carbon and water cycles. We used NOTG, a new 3D, process-based, and individual-based model specifically developed to study the importance of the spatial structure on the carbon and water cycles of complex ecosystems. It incorporates processes involved in the energy, carbon, and water cycles at the tree (radiation interception, photosynthesis, phenology, allocation, senescence, transpiration), and soil (soil moisture, soil organic matter decomposition) levels. It is designed to handle various plant phenological types (deciduous, non opportunistic evergreen, and opportunistic evergreen), and a comprehensive description of plant C pools. The model is designed to study water and carbon fluxes at the stand scale over one to a few years. In this study, NOTG was parameterized for the Font-Blanche forest and two five-year simulations were made using either the full 3D representation, or a simplified 1D representation. Comparison of model outputs against observations at the tree, soil, and ecosystem scales, showed a much better accuracy when using the 3D representation. This illustrates the dependence of plant and ecosystem function to the above- and below-ground spatial structures, and the usefulness of such detailed models when dealing with structurally complex ecosystems.

A large number of organic matter degradation, CO2 transport and dissolved organic matter models have been developed during the last decades. However, organic matter degradation models are in many cases strictly hard-coded in terms of organic pools, degradation kinetics and dependency on environmental variables. The scientific input of the model user is typically limited to the adjustment of input parameters. In addition, the coupling with geochemical soil processes including aqueous speciation, pH-dependent sorption and colloid-facilitated transport are not incorporated in many of these models, strongly limiting the scope of their application. Furthermore, the most comprehensive organic matter degradation models are combined with simplified representations of flow and transport processes in the soil system. We illustrate the capability of generic reactive transport codes to overcome these shortcomings. The formulations of reactive transport codes include a physics-based continuum representation of flow and transport processes, while biogeochemical reactions can be described as equilibrium processes constrained by thermodynamic principles and/or kinetic reaction networks. The flexibility of these type of codes allows for straight-forward extension of reaction networks, permits the inclusion of new model components (e.g.: organic matter pools, rate equations, parameter dependency on environmental conditions) and in such a way facilitates an application-tailored implementation of organic matter degradation models and related processes. A numerical benchmark involving two reactive transport codes (HPx and MIN3P) demonstrates how the process-based simulation of transient variably saturated water flow (Richards equation), solute transport (advection-dispersion equation), heat transfer and diffusion in the gas phase can be combined with a flexible implementation of a soil organic matter degradation model. The benchmark includes the production of leachable organic matter and inorganic carbon in the aqueous and gaseous phases, as well as different decomposition functions with first-order, linear dependence or nonlinear dependence on a biomass pool. In addition, we show how processes such as local bioturbation (bio-diffusion) can be included implicitly through a Fickian formulation of transport of soil organic matter. Coupling soil organic matter models with generic and flexible reactive transport codes offers a valuable tool to enhance insights into coupled physico-chemical processes at different scales within the scope of C-biogeochemical cycles, possibly linked with other chemical elements such as plant nutrients and pollutants.

Chapitre 13; Analysis of Fouling and Flux Behavior in Cross-Flow Microfiltration of Nonalcoholic Beer by Ceramic Membrane

International audience; In this paper we illustrate the use of qualitative reasoning models to assess the consistency of a hypothesis about the functioning of a black box system.To that purpose we have built a qualitativemodel of a mechanism for the periodic spring of Fontestorbes (Ariège, France) based on the siphon's hypothesis. The spring, called fountain locally,is a black box system because the mechanism is not accessible. Our model exhibits a cyclic behaviour that matches well with the periodic flow observed at Fontestorbes. It also generates the unexpected behaviour that was used to challenge the consistency of the hypothesis. The simulation of the expected behaviours appears to be a necessary condition to assert the consistency of the hypothesis while the generation of unexpected behaviours provide directions to challenge it. The mechanism at work characterizes a nonlinear relaxation oscillator,its modelling is our contribution to the modelling of natural phenomena.

Background 13C metabolic flux analysis is one of the pertinent ways to compare two or more physiological states. From a more theoretical standpoint, the structural properties of metabolic networks can be analysed to explore feasible metabolic behaviours and to define the boundaries of steady state flux distributions. Elementary flux mode analysis is one of the most efficient methods for performing this analysis. In this context, recent approaches have tended to compare experimental flux measurements with topological network analysis. Results Metabolic networks describing the main pathways of central carbon metabolism were set up for a bacteria species (Corynebacterium glutamicum) and a plant species (Brassica napus) for which experimental flux maps were available. The structural properties of each network were then studied using the concept of elementary flux modes. To do this, coefficients of flux efficiency were calculated for each reaction within the networks by using selected sets of elementary flux modes. Then the relative differences - reflecting the change of substrate i.e. a sugar source for C. glutamicum and a nitrogen source for B. napus - of both flux efficiency and flux measured experimentally were compared. For both organisms, there is a clear relationship between these parameters, thus indicating that the network structure described by the elementary flux modes had captured a significant part of the metabolic activity in both biological systems. In B. napus, the extension of the elementary flux mode analysis to an enlarged metabolic network still resulted in a clear relationship between the change in the coefficients and that of the measured fluxes. Nevertheless, the limitations of the method to fit some particular fluxes are discussed. Conclusion This consistency between EFM analysis and experimental flux measurements, validated on two metabolic systems allows us to conclude that elementary flux mode analysis could be a useful tool to complement 13C metabolic flux analysis, by allowing the prediction of changes in internal fluxes before carbon labelling experiments.