Noninvasive population genetics: a review of sample source, diet, fragment length and microsatellite motif effects on amplification success and genotyping error rates

Noninvasive population genetics has found many applications in ecology and conservation biology. However, the technical difficulties inherent to the analysis of low quantities of DNA generally tend to limit the efficiency of this approach. The nature of samples and loci used in noninvasive population genetics are important factors that may help increasing the potential success of case studies. Here we reviewed the effects of the source of DNA (hair vs. faeces), the diet of focal species, the length of mitochondrial DNA fragments, and the length and repeat motif of nuclear microsatellite loci on genotyping success (amplification success and rate of allelic dropout). Locus-specific effects appeared to have the greatest impact, amplification success decreasing with both mitochondrial and microsatellite fragments' length, while error rates increase with amplicons' length. Dinucleotides showed best amplification success and lower error rates compared to longer repeat units. Genotyping success did not differ between hair- versus faeces-extracted DNA, and success in faeces-based analyses was not consistently influenced by the diet of focal species. While the great remaining variability among studies implies that other unidentified parameters are acting, results show that the careful choice of genetic markers may allow optimizing the success of noninvasive approache

On-the-field calibration of an array of sensors

International audienceWe address the problem of the calibration of an array of sensors by investigating theoretically and experimentally the case of 2 three-axis sensors. Our focus is on magnetometers that can be used in a low-cost inertial navigation system. Usual errors (misalignments, non-orthogonality, scale factors, biases) are accounted for. The proposed calibration method requires no specific calibration hardware. Instead, we solely use the fact that, if the sensor is properly calibrated, the norm of the sensed field must remain constant irrespective of the sensors orientation. Several strategies of calibration for an array of sensors are described along with the impact of (unavoidable) field disturbances. Experiments conducted with a couple of magneto-resistive magnetometers and data fusion results illustrate the relevance of the approach

Method to geometrically personalize a detailed finite element model of the spine

To date, developing geometrically personalized and detailed solid finite element models of the spine remains a challenge, notably due to multiple articulations and complex geometries. To answer this problem, a methodology based on a free form deformation technique (kriging) was developed to deform a detailed reference finite element mesh of the spine (including discs and ligaments) to the patient-specific geometry of 10 and 82-year old asymptomatic spines. Different kriging configurations were tested: with or without smoothing, and control points on or surrounding the entire mesh. Based on the results, it is recommended to use surrounding control points and smoothing. The mean node to surface distance between the deformed and target geometries was 0.3 mm ± 1.1. Most elements met the mesh quality criteria (95%) after deformation, without interference at the articular facets. The method’s novelty lies in the deformation of the entire spine at once, as opposed to deforming each vertebra separately, with surrounding control points and smoothing. This enables the transformation of reference vertebrae and soft tissues to obtain complete and personalized FEMs of the spine with minimal post-processing to optimize the mesh. Biomechanics

Temporal sampling helps unravel the genetic structure of naturally occurring populations of a phytoparasitic nematode. 2. Separating the relative effects of gene flow and genetic drift

International audienceStudying wild pathogen populations in natural ecosystems offers the opportunity to better understand the evolutionary dynamics of biotic diseases in crops and to enhance pest control strategies. We used simulations and genetic markers to investigate the spatial and temporal population genetic structure of wild populations of the beet cyst nematode Heterodera schachtii on a wild host plant species, the sea beet (Beta vulgaris spp. maritima), the wild ancestor of cultivated beets. Our analysis of the variation of eight microsatellite loci across four study sites showed that (i) wild H. schachtii populations displayed fine-scaled genetic structure with no evidence of substantial levels of gene flow beyond the scale of the host plant, and comparisons with simulations indicated that (ii) genetic drift substantially affected the residual signals of isolation-by-distance processes, leading to departures from migration–drift equilibrium. In contrast to what can be suspected for (crop) field populations, this showed that wild cyst nematodes have very low dispersal capabilities and are strongly disconnected from each other. Our results provide some key elements for designing pest control strategies , such as decreasing passive dispersal events to limit the spread of virulence among field nematode populations

Iterative calibration method for inertial and magnetic sensors

International audienceWe address the problem of three-axis sensor calibration. Our focus is on magnetometers. Usual errors (misalignment, non-orthogonality, scale factors, biases) are accounted for. We consider a method where no specific calibration hardware is required. We solely use the fact that the norm of the sensed field must remain constant irrespective of the sensors orientation. The proposed algorithm is iterative. Its convergence is studied. Experiments conducted with MEMS sensors (magnetometers) stress the relevance of the approach