Development and implementation of eco-genomic tools for aquatic ecosystem biomonitoring: the SYNAQUA French-Swiss program

The effectiveness of environmental protection measures is based on the early identification and diagnosis of anthropogenic pressures. Similarly, restoration actions require precise monitoring of changes in the ecological quality of ecosystems, in order to highlight their effectiveness. Monitoring the ecological quality relies on bioindicators, which are organisms revealing the pressures exerted on the environment through the composition of their communities. Their implementation, based on the morphological identification of species, is expensive because it requires time and experts in taxonomy. Recent genomic tools should provide access to reliable and high-throughput environmental monitoring by directly inferring the composition of bioindicators’ communities from their DNA (metabarcoding). The French-Swiss program SYNAQUA (INTERREG France-Switzerland 2017–2019) proposes to use and validate the tools of environmental genomic for biomonitoring and aims ultimately at their implementation in the regulatory bio-surveillance. SYNAQUA will test the metabarcoding approach focusing on two bioindicators, diatoms, and aquatic oligochaetes, which are used in freshwater biomonitoring in France and Switzerland. To go towards the renewal of current biomonitoring practices, SYNAQUA will (1) bring together different actors: scientists, environmental managers, consulting firms, and biotechnological companies, (2) apply this approach on a large scale to demonstrate its relevance, (3) propose robust and reliable tools, and (4) raise public awareness and train the various actors likely to use these new tools. Biomonitoring approaches based on such environmental genomic tools should address the European need for reliable, higher-throughput monitoring to improve the protection of aquatic environments under multiple pressures, guide their restoration, and follow their evolution.     

Non-invasive fetal genotyping for maternal alleles with droplet digital PCR: A comparative study of analytical approaches

Objectives

To develop a flexible droplet digital PCR (ddPCR) workflow to perform non-invasive prenatal diagnosis via relative mutation dosage (RMD) for maternal pathogenic variants with a range of inheritance patterns, and to compare the accuracy of multiple analytical approaches.

Methods

Cell free DNA (cfDNA) was tested from 124 archived maternal plasma samples: 88 cases for sickle cell disease and 36 for rare Mendelian conditions. Three analytical methods were compared: sequential probability ratio testing (SPRT), Bayesian and z-score analyses.

Results

The SPRT, Bayesian and z-score analyses performed similarly well with correct prediction rates of 96%, 97% and 98%, respectively. However, there were high rates of inconclusive results for each cohort, particularly for z-score analysis which was 31% overall. Two samples were incorrectly classified by all three analytical methods; a false negative result predicted for a fetus affected with sickle cell disease and a false positive result predicting the presence of an X-linked IDS variant in an unaffected fetus.

Conclusions

ddPCR can be applied to RMD for diverse conditions and inheritance patterns, but all methods carry a small risk of erroneous results. Further evaluation is required both to reduce the rate of inconclusive results and explore discordant results in more detail.     

Adaptation to climate change and freshwater resources in Vusama village,Viti Levu,Fiji

Regional Environmental Change - Changing precipitation patterns including more intense and prolonged dry periods have become a growing concern for people living in the Pacific Island region. People...     

Abdominopelvic injuries due to road traffic accidents: Characteristics in a registry of 162,695 victims

Objective: Road traffic accidents (RTAs) are the first cause of abdominopelvic injuries (APIs). The objective of this study was to describe the characteristics and severity of APIs due to traffic accidents in a large French trauma registry and to identify risk factors for API.

Methods: All victims from the French Rhône registry of victims of RTAs were analyzed from 1996 to 2013. This registry contained data that were issued over a 20-year period from 245 medical departments, from prehospital care until re-adaptation, and forensic medicine departments. All APIs, defined as an injury between the diaphragm and the pelvic bone, were extracted and studied.

Results: Among 162,695 victims, 10,165 had an API (6.7%). Accidents frequently involved young men and 2 cars. Mean Injury Severity Score (ISS) was 8.7. Mortality rate was 5.6%. Soft tissue injuries largely predominated (n = 6,388; 54.4% of patients). Overall, 2,322 victims had a pelvic bone injury. Internal abdominal organs were involved in 2,425 patients; the most frequent were the spleen, liver, and kidney. Wearing of the seat belt appeared to be a significant protective factor in API, including serious injuries. A partial analysis over the past 2 years among the most severe patients hospitalized in the intensive care unit indicated that nonoperative management was carried out in two thirds of the wounded. In uni- or multivariate analysis, sex, age, type of user, antagonist, time of occurrence, associated severe lesions, or wearing of the seat belt were statistically associated with the occurrence of API, highlighting a more dangerous user profile.

Conclusions: Abdominopelvic injuries concern a minority of road traffic injuries, but they are responsible for significant mortality. Large solid organs are the most frequently affected. Women drivers wearing a seat belt and driving in town during the day appear to be more protected against API.     

Social network analysis and valid Markov chain Monte Carlo tests of null models

Analyses of animal social networks derived from group-based associations often rely on randomisation methods developed in ecology (Manly, Ecology 76:1109–1115, 1995) and made available to the animal behaviour community through implementation of a pair-wise swapping algorithm by Bejder et al. (Anim Behav 56:719–725, 1998). We report a correctable flaw in this method and point the reader to a wider literature on the subject of null models in the ecology literature. We illustrate the importance of correcting the method using a toy network and use it to make a preliminary analysis of a network of associations among eagle rays.

Perceptions of climate change risks in primary resource use industries: a survey of the Canadian mining sector

A survey documenting how climate change is perceived, experienced, and responded to in the Canadian mining sector was administered to industry practitioners at the Prospectors & Developers Association of Canada annual meeting. Nine key findings from the survey are discussed: (1) The Canadian mining sector is sensitive to climate-related conditions. (2) Climate change is perceived to be having a negative impact on mining operations. (3) Companies are taking action to manage the current impacts. (4) Cost and uncertainty are commonly identified barriers to adapting to current climate change. (5) Future climate change is expected to have impacts for the industry. (6) Climate change projections are perceived as threats by the majority of respondents. (7) Despite the perceived threat, companies are not currently taking action to plan for future impacts. (8) Cost and uncertainty are commonly identified barriers to adapting to future climate change impacts. (9) The mining sector is currently making efforts to reduce greenhouse gas emissions. The survey is exploratory in nature, establishing a baseline for targeted research to assess in greater detail the vulnerability of mining to climate change.     

Courtship and reproduction in<Emphasis Type="Italic"> Carybdea sivickisi</Emphasis> (Cnidaria: Cubozoa)

Courtship and fertilization events in cubozoans have received little attention from biologists, and much of what we know about these processes is based on conjecture or scant anecdotal evidence. I set out to describe these processes in the cubozoan Carybdea sivickisi by observing mature medusae in vitro. Mature adults engage in courtship during which spermatophores are transferred from the male to the female, who then inserts the gametes into her manubrium. Females accepted multiple spermatophores from multiple males, and only produced one embryo strand. This study also provides evidence that the presence of conspicuous velar spots on the females bell margin is a signal of sexual maturity, and that sexual maturity was not reached in either sex until individuals had a bell diameter of at least 5 mm.Communicated by R.J. Thompson, St. Johns