Délégation Régionale Nord Ouest

Pour la realisation d’ouvrages de stockage enterres des eaux pluviales, un ensemble de solutions techniques et de materiaux sont disponibles : canalisations surdimensionnees, ouvrages en genie civil, tunnels de stockage, materiaux poreux. Parmi ceux-ci, les structures alveolaires ultralegeres (SAUL) constituent une famille de materiaux adaptee a la rarete et au cout du foncier en milieu urbain dense. Employes depuis pres d’une vingtaine d’annees en France, ils sont mis en oeuvre pour la realisation de bassins de retenue, de tranchees, de chaussees a structure reservoir et de puits d’infiltration. Cependant, peu de retours d’experiences sont encore disponibles sur les choix de conception, le fonctionnement et la maintenance de ces ouvrages enterres de stockage des eaux pluviales. Apres une presentation des caracteristiques de ces materiaux et des resultats d’une enquete nationale, sont detailles des retours d’experience issus d’amenagements neufs et de renovation urbaine ayant fait appel a des SAUL. Des recommandations sont ensuite formulees, relevant essentiellement des choix de conception qui determinent par la suite les conditions d’exploitation.

Intersex is the condition whereby both testicular and ovarian tissues are observed within the same gonad. The phenomenon traduces the exposure to endocrine-disrupting chemicals and can predict adverse reproductive effects for wild fish and populations. The occurence of intersex is documented in several aquatic ecosystem around the world but few data is available in French rivers. Also, due to the ecological relevance of this parameter, a large monitoring campaign is performed. For this purpose, wild Cyprinid fish were electrofished in rivers characterised by various levels of contamination and impact in fish population. Gonads were dissected and prepared for histological analysis. During microscopic observations, fish gender is noticed and sex-ratio is determined. For intersex fish, the ovotestis severity index previously developed in European flounder and recommended by OSPAR is calculated. Preliminary results of this large monitoring campaign will be presented. First results obtained in 13 sites show that intersex is observed in 8 rivers where 4 to 38% of fish are affected. To complete, two sites exposed to industrial presures, levels of occurence up to 50% are observed. Complementary works are in progress to analyse intersex occurence in other sampled sites (n=15) and to explore relationships between intersex and environmental pressures or fish assemblage quality.

Point sur les travaux menés par le laboratoire EMMS sur les réactions de gonflement interne.

Currently, for environmental risk assessment, multi-biomarker approach based on complementary parameters in term of substances, measured effect and biological integration levels were developed with some biochemical biomarkers, such as ethoxyresorufine-o-deethylase (EROD), glutathione-S-transferase (GST), glutathione peroxidase (GPx), lipid peroxidation (TBARS) and acetylcholinesterase (AChE). This approach allows integration of each environmental factor by restitution of qualitative and quantitative exposure variation. Nevertheless, use of these biochemical parameters was not enough to obtain clear information about fish and ecosystem health. Now, components of the fish immune system are considered as an attractive non-specific marker for environmental biomonitoring which integrate measure of exposure over time and may reflect the combined results of simultaneous contamination to several chemicals. Moreover, immune parameters were attractive due to their ecological importance by direct implications in individual fitness and population growth. In this way, the present work proposed the use of fish immunomarkers (i.e. apoptosis, necrosis and respiratory burst activity) together with more current biochemical biomarkers (i.e. EROD, GST, GPx, TBARS and AChE) to better evaluate fish health. The determination of a relationship between fish immune capacities and Fish Based Index (FBI), a useful indicator of ecosystem health by monitoring fish population, were also search. This work demonstrated that selected immune and biochemical biomarkers were able to discriminate sites in function of contaminant effect since sampling conditions were optimized to reduce biomarker variability and increase parameters robustness. In the multiple discriminant analysis, the sites were highly correlated with apoptosis, respiratory burst, GST and EROD activity. Moreover, the use together of biochemical and immune markers increase the percentage of fish correctly classed in each site (from 45 % with only biochemical data to 68 % with immune/biochemical values) and enhanced site separation (increase of dotted line from 5.51 to 11.71 after agglomerative hierarchical clustering). The relationship between immune capacities and FBI must further be demonstrated. So, this study argues for attractive utilization of immunomarkers for determination of environmental risk assessment in addition with a set of biochemical biomarkers currently used.

Le developpement durable est aujourd’hui inscrit dans les discours et politiques publiques, notamment la politique de l’eau. Ayant emerge recemment sur les scenes internationale et francaise, ce concept peut encore apparaitre comme un concept au perimetre incertain et au contenu imprecis. Comment analyser et situer un projet au regard du developpement durable, c’est-a-dire concilier la protection et la mise en valeur de l’environnement, le developpement economique et le progres social ? Pour faciliter cette traduction, une grille d’analyse multicritere a ete concue par le Reseau scientifique et technique du ministere en charge de l’ecologie. Cette grille RST, basee sur les principes enonces dans la declaration de Rio de 1992, s’applique a differentes echelles : programmes d’action, operations d’amenagement, equipements et ouvrages. Elle a ete declinee a la gestion du cycle de l’eau. Apres avoir rappele les fondements du developpement durable et ses enjeux pour la gestion de l’eau et des milieux aquatiques, cet article presente les domaines d’emploi et principes d’utilisation de la grille, puis illustre sa mise en oeuvre a deux echelles : l’etude d’un schema d’hydraulique viticole et la realisation d’une station d’epuration par marais construit.

Flooding is frequent on the Nantes ring road and disrupts users dependent on this mode of transport directly or indirectly. To deal with them, the road operator has defined preventive and curative measures based essentially on the flow of the river involved in the submergence of the roadway. The RESIIST (Resilience of Interconnected Infrastructures and Systems) research project aims to develop a methodology and tools to assess the resilience of Critical Infrastructures (within the meaning of European Directive 2008/114/EC), of which we find the ring road. In order to test them, a scenario will be used to simulate the events likely to cause flooding, characterise the disturbances caused by these events and the interactions with adjacent road infrastructures and present a decision aiding based on the road operator's criteria. RESIIST can contribute to improving the resilience of critical infrastructures by enabling stakeholders to continuously monitor data from the context, to interpret them and deduce the disruption's risks on infrastructure and territory and finally to benefit from proposals for solutions adapted and corresponding to their decision criteria. More modestly, this scenario could serve as a support in discussions on possible work concerning the ring road and the crisis management protocols.

Multi-biomarker approach is extensively used to characterize the effects of ecosystem contamination on fish health. In order to measure multi-biomarker responses in freshwater ecosystems, numerous wild fish species have been used. However, the geographical distribution of these extensively characterized fish species did not allow a large sampling for ecotoxicological application and justifies the research of novel sentinel species for biomonitoring. The aim of this study is to characterize the potential of the European bullhead (Cottus sp.) as sentinel fish species to assess the effects of pollution using a set of biochemical biomarkers. This fish is widespread throughout Europe, and it's sedentary fish that allows assessing local disturbances conversely to migratory or mobile fish species. The selected biomarkers included biotransformation enzyme (i.e 7-ethoxyresorufin-O-deethylase, EROD), oxidative stress (i.e glutathione peroxidase, GPx and lipoperoxidation, TBARS) and neurotoxic parameters (i.e acetylcholinesterase, AChE). To evaluate the potential of European bullhead for biomonitoring, laboratory and field experiments were conducted. Laboratory investigations were performed to characterize chemical-induced variations of biomarkers using reference chemical compounds. For this purpose, bullheads were exposed to beta-naphtoflavone (BNF), fenitrothion and copper in order to evaluate respectively EROD, AChE and GPx activities as well as TBARS data. BNF generated a rapid induction of liver EROD activity in bullhead. Fenitrothion had no effect on the AChE activities. In field, wild bullheads were sampled, in the North of France, between September and October 2008 at seven sites considered as benchmark by the Water Framework Directive, and five contaminated sites. The selected set of biomarkers was measured in fish from sites exhibiting various contamination levels to evaluate discriminant power of this tool and to characterize response profiles in a multicontamination context. The response profile of AChE allowed a good discrimination between reference area exhibiting low AChE levels and contaminated sites with high AChE levels.

Légumineuse au rendement exceptionnel et aux grandes vertus nutritionnelles, le soja a été testé dans tous les microclimats ivoiriens depuis 1968. Il a même été cultivé à grande échelle dans le nord-ouest de la Côte d'Ivoire à titre expérimental. Contrairement à de nombreuses autres cultures vivrières, la culture du soja en Côte d'Ivoire n'a pas encore fait l'objet d'études historiques. Cet article contribue à combler cette lacune historiographique sur la base de sources imprimées et d'entretiens avec des témoins de la première phase (jusqu'en 1979), en mettant en lumière le processus d'introduction de la culture du soja en Côte d'Ivoire. Après les premiers essais de culture réussis depuis 1968, le soja a été introduit en 1974 comme culture de diversification. La poursuite des essais de confirmation a montré que les départements de Touba et d'Odienné, dans le nord-ouest de la Côte d'Ivoire, constituaient la zone la plus propice à la culture du soja. Un premier projet de soja y a été lancé en 1979, mais il a finalement échoué et a été abandonné en 1984.

In freshwater ecosystems, a large number of chemical substances are able to disturb homeostasis and adaptative responses of fish organisms by modulating different physiological functions including immune system. In order to characterize the early biological effects of environmental contaminants on fish health status, some immune-related cellular and biochemical responses were proposed as immunotoxicological biomarkers. The aim of the present study was to evaluate immune status of European bullhead, Cottus sp., natural populations, living in different field contexts characterized by various chemical environmental pressures. In Champagne region (France), five sites of the Vesle watershed in the North East of France were selected with urban (Muizon), intensive agricultural (Bouy and Prunay) or viticultural (Serzy and Prunay) influences. For each location, adult fish were caught by electrofishing in spring, summer and autumn and splenic leucocyte parameters (leucocyte sub populations, cell mortality and phagocytosis) were carried out by flow cytometry. Fish biometric characteristics, such as length and weight, have no impact on immune parameters. Seasonal variations in immune responses depended on the tested immune function without discrepancy between studied sites. For example, the lymphocyte percentages were higher in summer whereas leucocyte mortalities were strongly increased in spring and phagocytosis percentages in autumn. Nevertheless, independently of seasonal variations, environmental characteristics of each site seem to disturb selected immune markers. The highest immune modulations were observed in sites situated in areas with intensive agriculture or viticulture, Bouy, Prunay and Serzy respectively. These first results may indicate possible immunotoxicological impacts of agri-viticultural practices on bullhead natural populations living in Vesle watershed. It is sure that further observations, on many years, have to be done to verify observed immunomodulations. Moreover, data are needed to better characterize the effects of biotic and abiotic confounding factors on these biomarker base levels and to define their natural variability ranges for assessment of wild fish health.

Many branches of the tree of life still lack high‑quality, well‑annotated reference genomes. This limitation makes it difficult to apply reference‑based genomic methods, and researchers often resort to using distant reference genomes instead. While convenient, this approach can introduce substantial biases when the evolutionary distance between the taxon or taxa of study and the reference is large. ConSenStruct was developed to address this challenge by generating reference‑free, local consensus sequences from short‑read sequencing data. Its workflow is designed for datasets containing various individuals of one or multiple taxa, potentially with varying levels of divergence, and is particularly well suited for target enrichment (gene‑capture) datasets and resequencing projects where targets were originally defined from transcriptomic resources, while enrichment was performed on genomic DNA. The input of ConSenStruct consists of one or several multifasta (.fasta) files, containing either one gene/region of interest per file, or a single file with a concatenation of several genes/regions. Each line in such multifasta files typically represents data of one specimen, but data could also consist of up to n lines per specimen, where n represents the ploidy level of each specimen. Such multifasta files can be developed in several ways, but for target enrichment data it is often generated by assembling quality-controlled reads with HybPiper (Johnson et al. 2016) resulting in a 'supercontig' per gene/region of interest. The output of HybPiper, consisting of a supercontig for each gene/region of interest, with the resulting multifasta file containing all assembled sequences across samples, can directly be used as input for ConSenStruct. ConSenStruct will then reconstruct a high‑quality consensus sequence for each gene/region of interest. The original target sequence (usually the transcript that was used during probe design) can be included in the multifasta and marked with a prefix -p. This -p option allows ConSenSTruct to leverage the original target sequence for optional annotation with Exonerate (Slater and Birney, 2005). Before launching ConSenSTruct on your data, removes all ambiguous bases (N) from the supercontigs (a script called fasta_removeNNN.py is provided), to ensure that depth estimation, region detection, and consensus construction are not biased by low‑quality or missing data introduced during assembly or by HybPiper's intron scaffolding. The resulting accurate, localized consensus sequences can subsequently be leveraged as genomic reference, that can then be used in downstream reference‑based analyses, reducing bias and improving the reliability of genomic inference.

International audience

Many branches of the tree of life still lack high‑quality, well‑annotated reference genomes. This limitation makes it difficult to apply reference‑based genomic methods, and researchers often resort to using distant reference genomes instead. While convenient, this approach can introduce substantial biases when the evolutionary distance between the taxon or taxa of study and the reference is large. ConSenStruct was developed to address this challenge by generating reference‑free, local consensus sequences from short‑read sequencing data. Its workflow is designed for datasets containing various individuals of one or multiple taxa, potentially with varying levels of divergence, and is particularly well suited for target enrichment (gene‑capture) datasets and resequencing projects where targets were originally defined from transcriptomic resources, while enrichment was performed on genomic DNA. The input of ConSenStruct consists of one or several multifasta (.fasta) files, containing either one gene/region of interest per file, or a single file with a concatenation of several genes/regions. Each line in such multifasta files typically represents data of one specimen, but data could also consist of up to n lines per specimen, where n represents the ploidy level of each specimen. Such multifasta files can be developed in several ways, but for target enrichment data it is often generated by assembling quality-controlled reads with HybPiper (Johnson et al. 2016) resulting in a 'supercontig' per gene/region of interest. The output of HybPiper, consisting of a supercontig for each gene/region of interest, with the resulting multifasta file containing all assembled sequences across samples, can directly be used as input for ConSenStruct. ConSenStruct will then reconstruct a high‑quality consensus sequence for each gene/region of interest. The original target sequence (usually the transcript that was used during probe design) can be included in the multifasta and marked with a prefix -p. This -p option allows ConSenSTruct to leverage the original target sequence for optional annotation with Exonerate (Slater and Birney, 2005). Before launching ConSenSTruct on your data, removes all ambiguous bases (N) from the supercontigs (a script called fasta_removeNNN.py is provided), to ensure that depth estimation, region detection, and consensus construction are not biased by low‑quality or missing data introduced during assembly or by HybPiper's intron scaffolding. The resulting accurate, localized consensus sequences can subsequently be leveraged as genomic reference, that can then be used in downstream reference‑based analyses, reducing bias and improving the reliability of genomic inference.