De <i>novo </i>transcriptomes of 14 gammarid individuals for proteogenomic analysis of seven taxonomic groups

Gammarids are amphipods found worldwide distributed in fresh and marine waters. They play an important role in aquatic ecosystems and are well established sentinel species in ecotoxicology. In this study, we sequenced the transcriptomes of a male individual and a female individual for seven different taxonomic groups belonging to the two genera Gammarus and Echinogammarus: Gammarus fossarum A, G. fossarum B, G. fossarum C, Gammarus wautieri, Gammarus pulex, Echinogammarus berilloni, and Echinogammarus marinus. These taxa were chosen to explore the molecular diversity of transcribed genes of genotyped individuals from these groups. Transcriptomes were de novo assembled and annotated. High-quality assembly was confirmed by BUSCO comparison against the Arthropod dataset. The 14 RNA-Seq-derived protein sequence databases proposed here will be a significant resource for proteogenomics studies of these ecotoxicologically relevant non-model organisms. These transcriptomes represent reliable reference sequences for whole-transcriptome and proteome studies on other gammarids, for primer design to clone specific genes or monitor their specific expression, and for analyses of molecular differences between gammarid species

Shotgun lipidomics and mass spectrometry imaging unveil diversity and dynamics in Gammarus fossarum lipid composition

Sentinel species are playing an indispensable role in monitoring environmental pollution in aquatic ecosystems. Many pollutants found in water prove to be endocrine disrupting chemicals that could cause disruptions in lipid homeostasis in aquatic species. A comprehensive profiling of the lipidome of these species is thus an essential step toward understanding the mechanism of toxicity induced by pollutants. Both the composition and spatial distribution of lipids in freshwater crustacean Gammarus fossarum were extensively examined herein. The baseline lipidome of gammarids of different sex and reproductive stages was established by high throughput shotgun lipidomics. Spatial lipid mapping by high resolution mass spectrometry imaging led to the discovery of sulfate-based lipids in hepato-pancreas and their accumulation in mature oocytes. A diverse and dynamic lipid composition in G. fossarum was uncovered, which deepens our understanding of the biochemical changes during development and which could serve as a reference for future ecotoxicological studies.Approches Protéomique et Lipidomique pour la compréhension des mécanismes moléculaires de toxicité en lien avec l'altération du métabolisme lipidique chez l'espèce sentinelle Gammarus fossarum durant le cycle de reproductio

Modèles ecologiques pour l'extrapolation des effets écotoxicologiques enregistrés lors de biotests in situ cheZ Gammarus

[Departement_IRSTEA]Eaux [TR1_IRSTEA]BELCAInternational audienceEvaluating the effects of chemical contamination on populations and ecological communities still constitutes a challenging necessity in environmental management. However the toxic effects of contaminants are commonly measured by means of organism-level responses. Linking such effects measures with ecological models is a promising way to apprehend population-level impacts. In this way, population models are currently increasingly used in predictive risk assessment procedures, but their use in environmental diagnostic framework remains limited due to their lack of ecological realism. The present study with the crustacean amphipod Gammarus fossarum, a sentinel species in freshwater monitoring, combines a dual field and laboratory experimental approach with a population modelling framework. In this way, we developed an ecologically-relevant periodic matrix population model for Gammarus. This model allowed us to capture the population dynamics in the field, and to understand the particular pattern of demographic sensitivities induced by Gammarus life-history phenology. The model we developed provided a robust population-level assessment of in situ-based effects measures recorded during a biomonitoring program on a French watershed impacted by past mining activities. Thus, our study illustrates the potential of population modelling when seeking to decipher the role of environmental toxic contamination in ecological perturbations

Development and Validation of a Risk Score for Chronic Kidney Disease in HIV Infection Using Prospective Cohort Data from the D:A:D Study

Ristola M. on työryhmien DAD Study Grp ; Royal Free Hosp Clin Cohort ; INSIGHT Study Grp ; SMART Study Grp ; ESPRIT Study Grp jäsen.Background Chronic kidney disease (CKD) is a major health issue for HIV-positive individuals, associated with increased morbidity and mortality. Development and implementation of a risk score model for CKD would allow comparison of the risks and benefits of adding potentially nephrotoxic antiretrovirals to a treatment regimen and would identify those at greatest risk of CKD. The aims of this study were to develop a simple, externally validated, and widely applicable long-term risk score model for CKD in HIV-positive individuals that can guide decision making in clinical practice. Methods and Findings A total of 17,954 HIV-positive individuals from the Data Collection on Adverse Events of Anti-HIV Drugs (D:A:D) study with >= 3 estimated glomerular filtration rate (eGFR) values after 1 January 2004 were included. Baseline was defined as the first eGFR > 60 ml/min/1.73 m2 after 1 January 2004; individuals with exposure to tenofovir, atazanavir, atazanavir/ritonavir, lopinavir/ritonavir, other boosted protease inhibitors before baseline were excluded. CKD was defined as confirmed (>3 mo apart) eGFR In the D:A:D study, 641 individuals developed CKD during 103,185 person-years of follow-up (PYFU; incidence 6.2/1,000 PYFU, 95% CI 5.7-6.7; median follow-up 6.1 y, range 0.3-9.1 y). Older age, intravenous drug use, hepatitis C coinfection, lower baseline eGFR, female gender, lower CD4 count nadir, hypertension, diabetes, and cardiovascular disease (CVD) predicted CKD. The adjusted incidence rate ratios of these nine categorical variables were scaled and summed to create the risk score. The median risk score at baseline was -2 (interquartile range -4 to 2). There was a 1: 393 chance of developing CKD in the next 5 y in the low risk group (risk score = 5, 505 events), respectively. Number needed to harm (NNTH) at 5 y when starting unboosted atazanavir or lopinavir/ritonavir among those with a low risk score was 1,702 (95% CI 1,166-3,367); NNTH was 202 (95% CI 159-278) and 21 (95% CI 19-23), respectively, for those with a medium and high risk score. NNTH was 739 (95% CI 506-1462), 88 (95% CI 69-121), and 9 (95% CI 8-10) for those with a low, medium, and high risk score, respectively, starting tenofovir, atazanavir/ritonavir, or another boosted protease inhibitor. The Royal Free Hospital Clinic Cohort included 2,548 individuals, of whom 94 individuals developed CKD (3.7%) during 18,376 PYFU (median follow-up 7.4 y, range 0.3-12.7 y). Of 2,013 individuals included from the SMART/ESPRIT control arms, 32 individuals developed CKD (1.6%) during 8,452 PYFU (median follow-up 4.1 y, range 0.6-8.1 y). External validation showed that the risk score predicted well in these cohorts. Limitations of this study included limited data on race and no information on proteinuria. Conclusions Both traditional and HIV-related risk factors were predictive of CKD. These factors were used to develop a risk score for CKD in HIV infection, externally validated, that has direct clinical relevance for patients and clinicians to weigh the benefits of certain antiretrovirals against the risk of CKD and to identify those at greatest risk of CKD.Peer reviewe

Effects of metals on feeding rate and digestive enzymes in Gammarus fossarum: an in situ experiment

International audienceThe feeding activity and afterward the assimilation of the products resulting of the food digestion, allow organisms to obtain energy useful for growth, maintenance and reproduction. These biological parameters may be studied to assess the impact of contaminants on the energy metabolism of organisms, which could induce potential effects at an individual level. The studied species was an amphipod Gammarus fossarum, which has a high ecological relevance since it is widespread in European streams and plays a major role in the breakdown of leaf litter. Thus some G. fossarum were transplanted in four sites of a river characterized by metal contamination (Amous River, France). The following parameters were studied: digestive enzymes activities (esterase, β-glucosidase, β-galactosidase, amylase and endoglucanase), feeding rate, metal bioaccumulation and survival. Results showed a strong relationship between digestive enzymes activities, feeding rate and metal contents

Approaching a closer surrogate for the biologically effective dose with subcellular partitioning-based toxicokinetic models

International audienceA general concept in risk assessment is that a threshold of exposure exists above which adverse effects are initiated. Toxicity is related to the target-site concentration or the biologically active dose. Although it is often a huge challenge to measure the specific dose metric of metal toxicity, significant progress has been obtained to approach closer to the target-site concentration. Such developments are reviewed in the present study. In addition, a general framework to simulate the subcellular metal partitioning, which is supposed to account for the internal metal sequestration, is developed and applied to various metals. The framework allows for delineating mechanisms of internal metal sequestration. Moreover, the specificity in these mechanisms, which varies among metals, species, and exposure conditions, might explain the complicated relationship between the internal concentration and metal toxicity. Attention should be paid to the data requirements as the high number of unknown parameters might be accompanied by potential uncertainties. In addition, future efforts should focus on linking the concentration of metals in sensitive fractions and toxicological effects

Impact des pressions toxiques multiples sur les écosystèmes aquatiques du Bassin Versant du Rhône

Cette fiche est la synthèse du projet de recherche "IPOTOMUS", lauréat de l'appel à projet de recherche du LabEx DRIIHM et de l'OHM vallée du Rhône. Elle a vocation à porter à connaissance les principaux résultats scientifiques de cette recherche, la plus-value pour le territoire et les perspectives ouvertes.L’impact écologique potentiel des pressions toxiques multiples exercées sur l’écosystème aquatique a été caractérisé via un indice unique évalué le long du corridor rhodanien. Certaines substances inventoriées n’ont cependant pas pu être incluses du fait d’un manque de connaissances sur leur écotoxicité (cas des polychlorobiphényles - PCB). L’impact écologique résulterait principalement de la présence de certains métaux traces (cuivre, nickel, vanadium et zinc) qui proviennent à la fois de l’érosion des roches et de l’activité humaine. La contribution de chacune de ces sources reste à estimer. La prise en compte des substances très faiblement quantifiées montre que les dichlorodiphényl-trichloroéthanes (DDT) et les hydrocarbures aromatiques polycycliques (HAP) peuvent contribuer de manière non négligeable. Finalement, la variation spatio-temporelle de l’indice est faible et surtout liée à l’hétérogénéité des jeux de données