elPrep: high-performance preparation of sequence alignment/map files for variant calling

elPrep is a high-performance tool for preparing sequence alignment/map files for variant calling in sequencing pipelines. It can be used as a replacement for SAMtools and Picard for preparation steps such as filtering, sorting, marking duplicates, reordering contigs, and so on, while producing identical results. What sets elPrep apart is its software architecture that allows executing preparation pipelines by making only a single pass through the data, no matter how many preparation steps are used in the pipeline. elPrep is designed as a multithreaded application that runs entirely in memory, avoids repeated file I/O, and merges the computation of several preparation steps to significantly speed up the execution time. For example, for a preparation pipeline of five steps on a whole-exome BAM file (NA12878), we reduce the execution time from about 1: 40 hours, when using a combination of SAMtools and Picard, to about 15 minutes when using elPrep, while utilising the same server resources, here 48 threads and 23GB of RAM. For the same pipeline on whole-genome data (NA12878), elPrep reduces the runtime from 24 hours to less than 5 hours. As a typical clinical study may contain sequencing data for hundreds of patients, elPrep can remove several hundreds of hours of computing time, and thus substantially reduce analysis time and cost

Perspectives for integrating human and environmental risk assessment and synergies with socio-economic analysis

International audienceFor more than a decade, the integration of human and environmental risk assessment (RA) has become an attractive vision. At the same time, existing European regulations of chemical substances such as REACH (EC Regulation No. 1907/2006), the Plant Protection Products Regulation (EC regulation 1107/2009) and Biocide Regulation (EC Regulation 528/2012) continue to ask for sector-specific RAs, each of which have their individual information requirements regarding exposure and hazard data, and also use different methodologies for the ultimate risk quantification. In response to this difference between the vision for integration and the current scientific and regulatory practice, the present paper outlines five medium-term opportunities for integrating human and environmental RA, followed by detailed discussions of the associated major components and their state of the art. Current hazard assessment approaches are analyzed in terms of data availability and quality, and covering non-test tools, the integrated testing strategy (ITS) approach, the adverse outcome pathway (AOP) concept, methods for assessing uncertainty, and the issue of explicitly treating mixture toxicity. With respect to exposure, opportunities for integrating exposure assessment are discussed, taking into account the uncertainty, standardization and validation of exposure modeling as well as the availability of exposure data. A further focus is on ways to complement RA by a socio-economic assessment (SEA) in order to better inform about risk management options. In this way, the present analysis, developed as part of the EU FP7 project HEROIC, may contribute to paving the way for integrating, where useful and possible, human and environmental RA in a manner suitable for its coupling with SEA

The role of atmospheric deposition in the biogeochemistry of the Mediterranean Sea

Estimates of atmospheric inputs to the Mediterranean (MED) and some coastal areas are reviewed, and uncertainities in these estimates considered. Both the magnitude and the mineralogical composition of atmospheric dust inputs indicate that eolian deposition is an important (50%) or prevailing (>80%) contribution to sediments in the offshore waters of the entire Mediterranean (MED) basin. Model data for trace metals and nutrients indicate that the atmosphere delivers more than half the lead and nitrogen, one-third of total phosphorus, and 10% of the zinc entering the entire basin. Measured data in sub-basins, such as the north-western MED and northern Adriatic indicate an even greater proportion of atmospheric versus riverine inputs. When dissolved fluxes are compared (the form most likely to impinge on surface water biogeochemical cycles), the atmosphere is found to be 5 to 50 times more important than rivers for dissolved Zn and 15 to 30 times more important for Pb fluxes. Neglecting co-limitation by other nutrients, new production supported by atmospheric nitrogen deposition ranges from 2-4 g C m-2 yr-1, whereas atmospheric phosphorus deposition appears to support less than 1 g C m-2 yr-1. In spite of the apparently small contribution of atmospheric deposition to overall production in the basin it has been suggested that certain episodes of phytoplankton blooms are triggered by atmospheric deposition of N, P or Fe. Future studies are needed to clarify the extent and causal links between these episodic blooms and atmospheric/oceanographic forcing functions. A scientific program aimed at elucidating the possible biogeochemical effects of Saharan outbreaks in the MED through direct sampling of the ocean and atmosphere before and after such events is therefore highly recommended

Identification of Genomic Regions Associated with Phenotypic Variation between Dog Breeds using Selection Mapping

Peer reviewe

Di-and Triblock Copolymers Based on Polyethylene and Polyisobutene Blocks. Toward New Thermoplastic Elastomers

International audienc

Effects of timing of artificial insemination and treatment of semen with a Slo3 potassium channel blocker on fertility of dairy heifers subjected to the 5-day CIDR-Synch protocol

International audienc

Global, regional, and cryptic population structure in a high gene-flow transatlantic fish

Lumpfish (Cyclopterus lumpus) is a transatlantic marine fish displaying large population sizes and a high potential for dispersal and gene-flow. These features are expected to result in weak population structure. Here, we investigated population genetic structure of lumpfish throughout its natural distribution in the North Atlantic using two approaches: I) 4,393 genome wide SNPs and 95 individuals from 10 locations, and II) 139 discriminatory SNPs and 1,669 individuals from 40 locations. Both approaches identified extensive population genetic structuring with a major split between the East and West Atlantic and a distinct Baltic Sea population, as well as further differentiation of lumpfish from the English Channel, Iceland, and Greenland. The discriminatory loci displayed ~2–5 times higher divergence than the genome wide approach, revealing further evidence of local population substructures. Lumpfish from Isfjorden in Svalbard were highly distinct but resembled most fish from Greenland. The Kattegat area in the Baltic transition zone, formed a previously undescribed distinct genetic group. Also, further subdivision was detected within North America, Iceland, West Greenland, Barents Sea, and Norway. Although lumpfish have considerable potential for dispersal and gene-flow, the observed high levels of population structuring throughout the Atlantic suggests that this species may have a natal homing behavior and local populations with adaptive differences. This fine-scale population structure calls for consideration when defining management units for exploitation of lumpfish stocks and in decisions related to sourcing and moving lumpfish for cleaner fish use in salmonid aquaculture.publishedVersio