One panel to rule them all: DArTcap genotyping for population structure, historical demography, and kinship analyses, and its application to a threatened shark

With recent advances in sequencing technology, genomic data are changing how important conservation management decisions are made. Applications such as Close‐Kin Mark‐Recapture demand large amounts of data to estimate population size and structure, and their full potential can only be realised through ongoing improvements in genotyping strategies. Here we introduce DArTcap, a cost‐efficient method that combines DArTseq and sequence capture, and illustrate its use in a high resolution population analysis of Glyphis garricki , a rare, poorly known and threatened euryhaline shark. Clustering analyses and spatial distribution of kin pairs from four different regions across northern Australia and one in Papua New Guinea, representing its entire known range, revealed that each region hosts at least one distinct population. Further structuring is likely within Van Diemen Gulf, the region that included the most rivers sampled, suggesting additional population structuring would be found if other rivers were sampled. Coalescent analyses and spatially explicit modelling suggest that G. garricki experienced a recent range expansion during the opening of the Gulf of Carpentaria following the conclusion of the Last Glacial Maximum. The low migration rates between neighbouring populations of a species that is found only in restricted coastal and riverine habitats show the importance of managing each population separately, including careful monitoring of local and remote anthropogenic activities that may affect their environments. Overall we demonstrated how a carefully chosen SNP panel combined with DArTcap can provide highly accurate kinship inference and also support population structure and historical demography analyses, therefore maximising cost‐effectiveness

Analyse des semences par vision artificielle

Les outils développés et les travaux réalisés permettent de disposer des prototypes d’acquisition d’images à haut débit et des algorithmes de traitement des images. Ces outils permettent des caractérisations d’échantillons de semences et la validation des applications souhaitées.</p

Ossau-Iraty原产地名号保护干酪生产地区生鲜羊乳中乳酸乳球菌的含量, 基因型和特性

International audienc

Analysis of plasticizers in PVC medical devices: performance comparison of eight analytical methods.

International audienceA wide variety of medical devices (MDs) used in hospitals are made of flexible plasticized polyvinylchloride (PVC). Different plasticizers are present in variable amounts in the PVC matrix of the devices and can leach out into the infused solutions and may enter into contact with the patients. The ARMED1 project aims to assess the migration of these plasticizers from medical devices and therefore the level of exposure in patients. For the first task of the project, eight methods were developed to directly detect and quantify the plasticizers in the PVC matrix of the MDs. We compared the overall performances of the analytical methods using standardized and validated criteria in order to provide the scientific community with the guidance and the technical specifications of each method for the intended application. We have shown that routine rapid screening could be performed directly on the MDs using the FTIR technique, with cost-effective analyses. LC techniques may also be used, but with limits and only with individual quantification of the main plasticizers expected in the PVC matrix. GC techniques, especially GC–MS, are both more specific and more sensitive than other techniques. NMR is a robust and specific technique to precisely discriminate all plasticizers in a MD but is limited by its cost and its low ability to detect and quantify plasticizer contamination, e.g. by DEHP. All these results have been confirmed by a real test, called the " blind test " carried out on 10 MD samples

Premières journées francophones des utilisateurs de système d’aide à la décision en pharmacie clinique : retour d’expériences et perspectives [First French-speaking days of users of decision support system in clinical pharmacy: Feedback and perspectives]

Clinical decision support systems (CDSS) are tools that have been used for several years by clinical pharmacy teams to support pharmaceutical analysis, with a perspective of contributing to the quality of care in collaboration with the other health care team members. These tools require both technical, logistical and human resources. The growing use of these systems in different establishments in France and in Europe gave birth to the idea of meeting to share our experiences. The days organized in Lille in September 2021 aimed at proposing a time of exchange and reflection on the use of these CDSS in clinical pharmacy. A first session was devoted to feedback from each establishment. These tools are essentially used to optimize pharmaceutical analysis and to secure patient medication management. This session outlined the clear advantages and common limitations of these CDSS. Two research projects were also presented to put the use of these tools into perspective. The second session of these days, in the form of workshops, addressed 4 themes that surround the implementation of CDSS: their usability, the legal aspect, the creation of rules and their possible valorization. Common problems were raised, the resolution of which requires close collaboration. This is a first step proposing a beginning of harmonization and sharing that should be deepened in order not to lose the dynamics created between the different centers. This event ended with the proposal to set up two working groups around these systems: the creation and structuring of rules for the detection of risk situations and the common valorization of the work

Global genetic diversity and historical demography of the Bull Shark

International audienceAim: Biogeographic boundaries and genetic structuring have important effects on the inferences and interpretation of effective population size (Ne) temporal variations, a key genetics parameter. We reconstructed the historical demography and divergence history of a vulnerable coastal high-trophic shark using population genomics and assessed our ability to detect recent bottleneck events.Location: Western and Central Indo-Pacific (IPA), Western Tropical Atlantic (WTA) and Eastern Tropical Pacific (EPA).Taxon: Carcharhinus leucas (Müller & Henle, 1839).Methods: A DArTcap™ approach was used to sequence 475 samples and assess global genetic structuring. Three demographic models were tested on each population, using an ABC-RF framework coupled with coalescent simulations, to investigate within-cluster structure. Divergence times between clusters were computed, testing multiple scenarios, with fastsimcoal. Ne temporal variations were reconstructed with STAIRWAYPLOT. Coalescent simulations were performed to determine the detectability of recent bottleneck under the estimated historical trend for datasets of this size.Results: Three genetic clusters corresponding to the IPA, WTA and EPA regions were identified, agreeing with previous studies. The IPA presented the highest genetic diversity and was consistently identified as the oldest. No significant within-cluster structuring was detected. Ne increased globally, with an earlier onset in the IPA, during the last glacial period. Coalescent simulations showed that weak and recent bottlenecks could not be detected with our dataset, while old and/or strong bottlenecks would erase the observed ancestral expansion.Main Conclusions: This study further confirms the role of marine biogeographic breaks in shaping the genetic history of large mobile marine predators. Ne historical increases in Ne are potentially linked to extended coastal habitat availability. The limited within-cluster population structuring suggests that Ne can be monitored over ocean basins. Due to insufficient amount of available genetic data, it cannot be concluded whether overfishing is impacting Bull Shark genetic diversity, calling for whole-genome sequencing

From rivers to ocean basins: The role of ocean barriers and philopatry in the genetic structuring of a cosmopolitan coastal predator

The Bull Shark (Carcharhinus leucas) faces varying levels of exploitation around the world due to its coastal distribution. Information regarding population connectivity is crucial to evaluate its conservation status and local fishing impacts. In this study, we sampled 922 putative Bull Sharks from 19 locations in the first global assessment of population structure of this cosmopolitan species. Using a recently developed DNA-capture approach (DArTcap), samples were genotyped for 3400 nuclear markers. Additionally, full mitochondrial genomes of 384 Indo-Pacific samples were sequenced. Reproductive isolation was found between and across ocean basins (eastern Pacific, western Atlantic, eastern Atlantic, Indo-West Pacific) with distinct island populations in Japan and Fiji. Bull Sharks appear to maintain gene flow using shallow coastal waters as dispersal corridors, whereas large oceanic distances and historical land-bridges act as barriers. Females tend to return to the same area for reproduction, making them more susceptible to local threats and an important focus for management actions. Given these behaviors, the exploitation of Bull Sharks from insular populations, such as Japan and Fiji, may instigate local decline that cannot readily be replenished by immigration, which can in turn affect ecosystem dynamics and functions. These data also supported the development of a genetic panel to ascertain the population of origin, which will be useful in monitoring the trade of fisheries products and assessing population-level impacts of this harvest