GOHTAM: a website for ‘Genomic Origin of Horizontal Transfers, Alignment and Metagenomics’

Motivation: This website allows the detection of horizontal transfers based on a combination of parametric methods and proposes an origin by researching neighbors in a bank of genomic signatures. This bank is also used to research an origin to DNA fragments from metagenomics studies

A Benchmark of Parametric Methods for Horizontal Transfers Detection

Horizontal gene transfer (HGT) has appeared to be of importance for prokaryotic species evolution. As a consequence numerous parametric methods, using only the information embedded in the genomes, have been designed to detect HGTs. Numerous reports of incongruencies in results of the different methods applied to the same genomes were published. The use of artificial genomes in which all HGT parameters are controlled allows testing different methods in the same conditions. The results of this benchmark concerning 16 representative parametric methods showed a great variety of efficiencies. Some methods work very poorly whatever the type of HGTs and some depend on the conditions or on the metrics used. The best methods in terms of total errors were those using tetranucleotides as criterion for the window methods or those using codon usage for gene based methods and the Kullback-Leibler divergence metric. Window methods are very sensitive but less specific and detect badly lone isolated gene. On the other hand gene based methods are often very specific but lack of sensitivity. We propose using two methods in combination to get the best of each category, a gene based one for specificity and a window based one for sensitivity

Total and organic Hg concentrations in cephalopods from the North Eastern Atlantic waters: Influence of geographical origin and feeding ecology

Total (T–Hg) and organic (O–Hg) mercury concentrations and tissue distribution were examined in 20 species of cephalopods (n = 278) from the north eastern Atlantic waters, i.e. from the Bay of Biscay to the Faroe Islands. Concentrations of T–Hg in whole cephalopods showed elevated variations among species, i.e. from 40 to 3560 ng g− 1 dwt, but a low variability within each species (mean CV% = 39%). With the exception of oceanic squids, the digestive gland globally displayed higher T–Hg concentrations than the remaining tissues. In contrast, O–Hg concentrations determined in selected species were generally higher in the remaining tissues. Despite higher T–Hg concentrations, the digestive gland weakly contributed to the total body burden of both T–Hg and O–Hg ( Bay of Biscay > Faroe Islands, corresponding to the seawater Hg concentrations in these areas. In the Faroe Islands and the Celtic Sea, benthic cephalopods contained significant higher Hg concentrations compared to pelagic ones. This suggests that diet is not the main pathway of Hg uptake in cephalopods as pelagic species were expected to be more exposed to O–Hg through fish consumption than benthic ones

Characterization of ready-mixed concrete plants sludge and incorporation into mortars: Origin of pollutants, environmental characterization and impacts on mortars characteristics

International audienc

Which contamination of the seagrass Posidonia oceanica along the Provence coast (France, nw mediterranean sea) ?

International audienc

Use of skin and blubber tissues of small cetaceans to assess the trace element content of internal organs

In order to evaluate the use of biopsy samples as non-destructive tool for assessing trace element concentrations in small cetaceans, the concentrations of 14 trace elements were determined in skin, blubber, liver and kidneys of four species of small cetaceans (i.e. common dolphin Delphinus delphis, harbour porpoise Phocoena phocoena, bottlenose dolphin Tursiops truncatus and striped dolphin Stenella coeruleolba), stranded and/or by-caught along the NE Atlantic Ocean coast between 2001 and 2008. Only Cu, Fe, Hg, Mn, Ni and Zn were above the detection limit of the instruments and showed recoveries satisfactory enough to be interpreted. Among these trace elements, Hg was the only one showing a significant correlation between concentrations in and those in liver and kidneys. In consequence skin and blubber can only be used as non-invasive monitoring tissues to investigate Hg bioaccumulation in internal tissues for cetacean populations.We greatly acknowledge the stranding networks from France (Observatoire PELAGIS), Spain (CEMMA), and Portugal (SPVS) for providing us cetacean samples. We also thank A. F. Guerra and F. Read from the Instituto de Investigaciones Marinas (C.S.I.C) in Vigo, Spain, and W. Dabin from the Observatoire PELAGIS in La Rochelle, France, for the age determination of the individuals. We also wish to thank C. Pignon-Mussaud from the Cellule Géomatique (UMR LIENSs) for providing the map of the study area and M. Kalombo from the Centre Commun d’Analyses (Fédération de Recherche en Environnement pour le Développement Durable FR 3097 CNRS-IFREMER-Université de La Rochelle) for running part of the trace element analyses. This work has been funded by the CPER 13 (Contrat de Plan Etat Région) through a post-doctoral grant to AA and PMF acknowledges support from the Portuguese Foundation for Science and Technology of the Government of Portugal (SFRH/BD/36766/2007).publishe

Lead, mercury, and selenium alter physiological functions in wild caimans (Caiman crocodilus)

International audienceEnvironmental contaminants affect ecosystems worldwide and have deleterious effects on biota. Non-essentialmercury (Hg) and lead (Pb) concentrations are well documented in some taxa and are described to cause multipledetrimental effects on human and wildlife. Additionally, essential selenium (Se) is known to be toxic at highconcentrations but, at lower concentrations, Se can protect organisms against Hg toxicity. Crocodilians areknown to bioaccumulate contaminants. However, the effects of these contaminants on physiological processesremain poorly studied. In the present study, we quantified Hg, Pb and Se concentrations in spectacled caimans(Caiman crocodilus) and investigated the effects of these contaminants on several physiological processes linkedto osmoregulatory, hepatic, endocrine and renal functions measured through blood parameters in 23 individuals.Mercury was related to disruption of osmoregulation (sodium levels), hepatic function (alkaline phosphataselevels) and endocrine processes (corticosterone levels). Lead was related to disruption of hepatic functions(glucose and alanine aminotransferase levels). Selenium was not related to any parameters, but the Se:Hg molarratio was positively related to the Na+ and corticosterone concentrations, suggesting a potential protective effectagainst Hg toxicity. Overall, our results suggest that Hg and Pb alter physiological mechanisms in wild caimansand highlight the need to thoroughly investigate the consequences of trace element contamination incrocodilians