AmelHap: Leveraging drone whole-genome sequence data to create a honey bee HapMap

Honey bee, Apis mellifera, drones are typically haploid, developing from an unfertilized egg, inheriting only their queen’s alleles and none from the many drones she mated with. Thus the ordered combination or ‘phase’ of alleles is known, making drones a valuable haplotype resource. We collated whole-genome sequence data for 1,407 drones, including 45 newly sequenced Scottish drones, collectively representing 19 countries, 8 subspecies and various hybrids. Following alignment to Amel_HAv3.1, variant calling and quality filtering, we retained 17.4 M high quality variants across 1,328 samples with a genotyping rate of 98.7%. We demonstrate the utility of this haplotype resource, AmelHap, for genotype imputation, returning >95% concordance when up to 61% of data is missing in haploids and up to 12% of data is missing in diploids. AmelHap will serve as a useful resource for the community for imputation from low-depth sequencing or SNP chip data, accurate phasing of diploids for association studies, and as a comprehensive reference panel for population genetic and evolutionary analyses.For the purpose of open access, the author has applied a Creative Commons Attribution (CC BY) licence to any Author Accepted Manuscript version arising from this submission. This work was supported by a grant from the CB Dennis British Beekeepers’ Research Trust awarded to MB and DW, and through strategic investment funding to the Roslin Institute from the Biotechnology and Biological Sciences Research Council (BBS/E/D/30002276). MP was supported by a Basque Government grant (IT1233-19)

Etude de couches limites oscillantes par vélocimétrie laser Doppler

International audienceLe transport sédimentaire induit par les vagues à l'approche de la côte est piloté par des processus non linéaires et turbulents. Les non-linéarités des vagues se caractérisent par une dissymétrie de vitesse (les crêtes hautes des vagues sont de courte durée et les creux peu profonds de longue durée) et une asymétrie de vitesse (ou dissymétrie d'accélération, caractérisant la raideur des fronts). Des études récentes indiquent que des fronts raides (vagues asymétriques) produisent des vitesses dissymétriques dans la couche limite. Ainsi, pour développer des formules de prédiction de transport des sédiments, la compréhension détaillée de la dynamique de la couche limite de fond et des contraintes de cisaillement sous les ondes de surface apparaît essentielle. Ceci justifie de chercher à réaliser des mesures de vitesse dans les tous premiers millimètres au-dessus du lit.Par ailleurs, la caractérisation de la turbulence sous les vagues déferlantes reste une question ouverte, en particulier pour chercher à évaluer la part provenant de la vague déferlée de celle produite par frottement au fond.Actuellement, l’essentiel de notre connaissance des couches limites oscillantes est issu de mesures réalisées sur des fonds fixes horizontaux. En laboratoire, l’évolution des non-linéarités des vagues, lors de leur propagation et de leur déferlement, a été principalement étudiée pour des plages de pentes relativement fortes (> 1:40). Cependant, des études de terrain récentes sur des plages réelles de pentes moins raides (1:80) ont montré que certains processus non-linéaires sont différents par rapport aux cas des plages de pentes relativement raides (> 1:40). Cette constatation a motivé le lancement d’une série d'expériences de laboratoire dans le cadre du projet européen GLOBEX sur une plage à fond fixe de pente 1:80

On the thermodynamics of the Swift–Hohenberg theory

We present the microbalance including the microforces, the first- and second-order microstresses for the Swift–Hohenberg equation concomitantly with their constitutive equations, which are consistent with the free-energy imbalance. We provide an explicit form for the microstress structure for a free-energy functional endowed with second-order spatial derivatives. Additionally, we generalize the Swift–Hohenberg theory via a proper constitutive process. Finally, we present one highly resolved three-dimensional numerical simulation to demonstrate the particular form of the resulting microstresses and their interactions in the evolution of the Swift–Hohenberg equation

Downregulation of the Drosophila Immune Response by Peptidoglycan-Recognition Proteins SC1 and SC2

Peptidoglycan-recognition proteins (PGRPs) are evolutionarily conserved molecules that are structurally related to bacterial amidases. Several Drosophila PGRPs have lost this enzymatic activity and serve as microbe sensors through peptidoglycan recognition. Other PGRP family members, such as Drosophila PGRP-SC1 or mammalian PGRP-L, have conserved the amidase function and are able to cleave peptidoglycan in vitro. However, the contribution of these amidase PGRPs to host defense in vivo has remained elusive so far. Using an RNA-interference approach, we addressed the function of two PGRPs with amidase activity in the Drosophila immune response. We observed that PGRP-SC1/2–depleted flies present a specific over-activation of the IMD (immune deficiency) signaling pathway after bacterial challenge. Our data suggest that these proteins act in the larval gut to prevent activation of this pathway following bacterial ingestion. We further show that a strict control of IMD-pathway activation is essential to prevent bacteria-induced developmental defects and larval death

Genetic control of resistance to salmonellosis and to Salmonella carrier-state in fowl: a review

<p>Abstract</p> <p>Salmonellosis is a frequent disease in poultry stocks, caused by several serotypes of the bacterial species <it>Salmonella enterica </it>and sometimes transmitted to humans through the consumption of contaminated meat or eggs. Symptom-free carriers of the bacteria contribute greatly to the propagation of the disease in poultry stocks. So far, several candidate genes and quantitative trait loci (QTL) for resistance to carrier state or to acute disease have been identified using artificial infection of <it>S. enterica </it>serovar Enteritidis or <it>S. enterica </it>serovar Typhimurium strains in diverse genetic backgrounds, with several different infection procedures and phenotypic assessment protocols. This diversity in experimental conditions has led to a complex sum of results, but allows a more complete description of the disease. Comparisons among studies show that genes controlling resistance to <it>Salmonella </it>differ according to the chicken line studied, the trait assessed and the chicken's age. The loci identified are located on 25 of the 38 chicken autosomal chromosomes. Some of these loci are clustered in several genomic regions, indicating the possibility of a common genetic control for different models. In particular, the genomic regions carrying the candidate genes <it>TLR4 </it>and <it>SLC11A1</it>, the Major Histocompatibility Complex (MHC) and the QTL <it>SAL1 </it>are interesting for more in-depth studies. This article reviews the main <it>Salmonella </it>infection models and chicken lines studied under a historical perspective and then the candidate genes and QTL identified so far.</p

An Asymptotic Preserving Scheme for the Euler equations in a strong magnetic field

This paper is concerned with the numerical approximation of the isothermal Euler equations for charged particles subject to the Lorentz force. When the magnetic field is large, the so-called drift-fluid approximation is obtained. In this limit, the parallel motion relative to the magnetic field direction splits from perpendicular motion and is given implicitly by the constraint of zero total force along the magnetic field lines. In this paper, we provide a well-posed elliptic equation for the parallel velocity which in turn allows us to construct an Asymptotic-Preserving (AP) scheme for the Euler-Lorentz system. This scheme gives rise to both a consistent approximation of the Euler-Lorentz model when epsilon is finite and a consistent approximation of the drift limit when epsilon tends to 0. Above all, it does not require any constraint on the space and time steps related to the small value of epsilon. Numerical results are presented, which confirm the AP character of the scheme and its Asymptotic Stability

Impact of different destocking strategies on the resilience of dry rangelands

Half of the world's livestock live in (semi-)arid regions, where a large proportion of people rely on animal husbandry for their survival. However, overgrazing can lead to land degradation and subsequent socio-economic crises. Sustainable management of dry rangeland requires suitable stocking strategies and has been the subject of intense debate in the last decades. Our goal is to understand how variations in stocking strategies affect the resilience of dry rangelands. We describe rangeland dynamics through a simple mathematical model consisting of a system of coupled differential equations. In our model, livestock density is limited only by forage availability, which is itself limited by water availability. We model processes typical of dryland vegetation as a strong Allee effect, leading to bistability between a vegetated and a degraded state, even in the absence of herbivores. We study analytically the impact of varying the stocking density and the destocking adaptivity on the resilience of the system to the effects of drought. By using dynamical systems theory, we look at how different measures of resilience are affected by variations in destocking strategies. We find that the following: (1) Increasing stocking density decreases resilience, giving rise to an expected trade-off between productivity and resilience. (2) There exists a maximal sustainable livestock density above which the system can only be degraded. This carrying capacity is common to all strategies. (3) Higher adaptivity of the destocking rate to available forage makes the system more resilient: the more adaptive a system is, the bigger the losses of vegetation it can recover from, without affecting the long-term level of productivity. The first two results emphasize the need for suitable dry rangeland management strategies, to prevent degradation resulting from the conflict between profitability and sustainability. The third point offers a theoretical suggestion for such a strategy

A genome scan for quantitative trait loci affecting the Salmonella carrier-state in the chicken

Selection for increased resistance to Salmonella colonisation and excretion could reduce the risk of foodborne Salmonella infection. In order to identify potential loci affecting resistance, differences in resistance were identified between the N and 61 inbred lines and two QTL research performed. In an F2 cross, the animals were inoculated at one week of age with Salmonella enteritidis and cloacal swabs were carried out 4 and 5 wk post inoculation (thereafter called CSW4F2 and CSW4F2) and caecal contamination (CAECF2) was assessed 1 week later. The animals from the (N × 61) × N backcross were inoculated at six weeks of age with Salmonella typhimurium and cloacal swabs were studied from wk 1 to 4 (thereafter called CSW1BC to CSW4BC). A total of 33 F2 and 46 backcross progeny were selectively genotyped for 103 and 135 microsatellite markers respectively. The analysis used least-squares-based and non-parametric interval mapping. Two genome-wise significant QTL were observed on Chromosome 1 for CSW2BC and on Chromosome 2 for CSW4F2, and four suggestive QTL for CSW5F2 on Chromosome 2, for CSW5F2 and CSW2BC on chromosome 5 and for CAECF2 on chromosome 16. These results suggest new regions of interest and the putative role of SAL1

Open-Angle Glaucoma and Paraoptic Cyst: First Description of a Series of 11 Patients

International audienceWe report 11 patients who were referred to our institution for severe open-angle glaucoma who had a paraoptic cyst on MR imaging. All cysts were extraoptic and retrolaminar; most were deforming the adjacent optic nerve. Cysts had a high signal on T2 and FLAIR sequences, and a variable signal on T1 and variable echogenicity, suggesting different proteinaceous content. Arterial vascularization of the optic nerve was normal. Cyst volumes were inversely correlated with the severity of glaucoma on the same eye (P < .01-.05, Spearman correlation coefficient). We hypothesized that such cysts may reflect a valve mechanism, which would allow preservation of the translamina cribrosa pressure and thus could preserve visual function. The rarity of this association, together with the frequent mass effect of the cyst on the optic nerve, stresses the necessity of long-term follow-up in these patients