Gérer ou gouverner la ressource en eau ? Modélisation en temps réel et gestion de la pénurie au sein de la rivière Crocodile (Afrique du Sud)

Nous analysons dans cet article trois dispositifs sociotechniques de gestion de la pénurie en eau mis en oeuvre sur la rivière Crocodile en Afrique du Sud : un processus de réallocation de la ressource (compulsory licensing), un modèle informatisé de gestion en temps réel et une détermination plus précise du débit environnemental. Cette analyse est l'occasion de mettre en évidence à quel point ces dispositifs sociotechniques, loin de se contenter de gérer, d'un point de vue purement technique, la ressource en eau, se sont transformés en instruments de gouvernement de celle-ci, neutralisant certaines dispositions réglementaires et certains objectifs de politiques publiques au coeur de l'agenda de transformation du pays. En outre, nous démontrons que cette pénurie est tout autant sinon plus un construit, découlant des choix de gestion, qu'une réelle fatalité sur la Crocodile. (Résumé d'auteur

Factor Analysis for Multiple Testing (FAMT): An R Package for Large-Scale Significance Testing under Dependence

The R package FAMT (factor analysis for multiple testing) provides a powerful method for large-scale significance testing under dependence. It is especially designed to select differentially expressed genes in microarray data when the correlation structure among gene expressions is strong. Indeed, this method reduces the negative impact of dependence on the multiple testing procedures by modeling the common information shared by all the variables using a factor analysis structure. New test statistics for general linear contrasts are deduced, taking advantage of the common factor structure to reduce correlation and consequently the variance of error rates. Thus, the FAMT method shows improvements with respect to most of the usual methods regarding the non discovery rate and the control of the false discovery rate (FDR). The steps of this procedure, each of them corresponding to R functions, are illustrated in this paper by two microarray data analyses. We first present how to import the gene ex- pression data, the covariates and gene annotations. The second step includes the choice of the optimal number of factors, the factor model fitting, and provides a list of selected genes according to a preset FDR control level. Finally, diagnostic plots are provided to help the user interpret the factors using available external information on either genes or arrays.

Microsatellite diversity and broad scale geographic structure in a model legume: building a set of nested core collection for studying naturally occurring variation in Medicago truncatula

BACKGROUND: Exploiting genetic diversity requires previous knowledge of the extent and structure of the variation occurring in a species. Such knowledge can in turn be used to build a core-collection, i.e. a subset of accessions that aim at representing the genetic diversity of this species with a minimum of repetitiveness. We investigate the patterns of genetic diversity and population structure in a collection of 346 inbred lines representing the breadth of naturally occurring diversity in the Legume plant model Medicago truncatula using 13 microsatellite loci distributed throughout the genome. RESULTS: We confirm the uniqueness of all these genotypes and reveal a large amount of genetic diversity and allelic variation within this autogamous species. Spatial genetic correlation was found only for individuals originating from the same population and between neighbouring populations. Using a model-based clustering algorithm, we identified four main genetic clusters in the set of individuals analyzed. This stratification matches broad geographic regions. We also identified a set of "admixed" individuals that do not fit with this population structure scheme. CONCLUSION: The stratification inferred is discussed considering potential historical events like expansion, refuge history and admixture between neighbouring groups. Information on the allelic richness and the inferred population structure are used to build a nested core-collection. The set of inbred lines and the core collections are publicly available and will help coordinating efforts for the study of naturally occurring variation in the growing Medicago truncatula community

Fidgetin-Like1 Is a Strong Candidate for a Dynamic Impairment of Male Meiosis Leading to Reduced Testis Weight in Mice

Chantier qualité GAInternational audienceBACKGROUND: In a previous work, using an interspecific recombinant congenic mouse model, we reported a genomic region of 23 Mb on mouse chromosome 11 implicated in testis weight decrease and moderate teratozoospermia (∼20-30%), a Quantitative Trait Locus (QTL) called Ltw1. The objective of the present study is to identify the gene underlying this phenotype. RESULTS: In the present study, we refined the QTL position to a 5 Mb fragment encompassing only 11 genes. We showed that the low testis weight phenotype was due to kinetic alterations occurring during the first wave of the spermatogenesis where we could point out to an abnormal lengthening of spermatocyte prophase. We identify Fidgetin-like 1 (Fignl1) as the gene underlying the phenotype, since if fulfilled both the physiological and molecular characteristics required. Indeed, amongst the 11 positional candidates it is the only gene that is expressed during meiosis at the spermatocyte stage, and that presents with non-synonymous coding variations differentiating the two mouse strains at the origin of the cross. CONCLUSIONS: This work prompted us to propose Fignl1 as a novel actor in mammal's male meiosis dynamics which has fundamental interest. Besides, this gene is a new potential candidate for human infertilities caused by teratozoospermia and blockades of spermatogenesis. In addition this study demonstrates that interspecific models may be useful for understanding complex quantitative traits

A framework for human-like behavior in an immersive virtual world

Just as readers feel immersed when the story-line adheres to their experiences, users will more easily feel immersed in a virtual environment if the behavior of the characters in that environment adheres to their expectations, based on their life-long observations in the real world. This paper introduces a framework that allows authors to establish natural, human-like behavior, physical interaction and emotional engagement of characters living in a virtual environment. Represented by realistic virtual characters, this framework allows people to feel immersed in an Internet based virtual world in which they can meet and share experiences in a natural way as they can meet and share experiences in real life. Rather than just being visualized in a 3D space, the virtual characters (autonomous agents as well as avatars representing users) in the immersive environment facilitate social interaction and multi-party collaboration, mixing virtual with real

Ecological niche modelling for predicting the risk of cutaneous leishmaniasis in the Neotropical moist forest biome

A major challenge of eco-epidemiology is to determine which factors promote the transmission of infectious diseases and to establish risk maps that can be used by public health authorities. The geographic predictions resulting from ecological niche modelling have been widely used for modelling the future dispersion of vectors based on the occurrence records and the potential prevalence of the disease. The establishment of risk maps for disease systems with complex cycles such as cutaneous leishmaniasis (CL) can be very challenging due to the many inference networks between large sets of host and vector species, with considerable heterogeneity in disease patterns in space and time. One novelty in the present study is the use of human CL cases to predict the risk of leishmaniasis occurrence in response to anthropogenic, climatic and environmental factors at two different scales, in the Neotropical moist forest biome (Amazonian basin and surrounding forest ecosystems) and in the surrounding region of French Guiana. With a consistent data set never used before and a conceptual and methodological framework for interpreting data cases, we obtained risk maps with high statistical support. The predominantly identified human CL risk areas are those where the human impact on the environment is significant, associated with less contributory climatic and ecological factors. For both models this study highlights the importance of considering the anthropogenic drivers for disease risk assessment in human, although CL is mainly linked to the sylvatic and peri-urban cycle in Meso and South America. © 2019 Chavy et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

A transcriptome multi-tissue analysis identifies biological pathways and genes associated with variations in feed efficiency of growing pigs

International audienceBackground - Animal's efficiency in converting feed into lean gain is a critical issue for the profitability of meat industries. This study aimed to describe shared and specific molecular responses in different tissues of pigs divergently selected over eight generations for residual feed intake (RFI). Results - Pigs from the low RFI line had an improved gain-to-feed ratio during the test period and displayed higher leanness but similar adiposity when compared with pigs from the high RFI line at 132 days of age. Transcriptomics data were generated from longissimus muscle, liver and two adipose tissues using a porcine microarray and analyzed for the line effect (n = 24 pigs per line). The most apparent effect of the line was seen in muscle, whereas subcutaneous adipose tissue was the less affected tissue. Molecular data were analyzed by bioinformatics and subjected to multidimensional statistics to identify common biological processes across tissues and key genes participating to differences in the genetics of feed efficiency. Immune response, response to oxidative stress and protein metabolism were the main biological pathways shared by the four tissues that distinguished pigs from the low or high RFI lines. Many immune genes were under-expressed in the four tissues of the most efficient pigs. The main genes contributing to difference between pigs from the low vs high RFI lines were CD40, CTSC and NTN1. Different genes associated with energy use were modulated in a tissue-specific manner between the two lines. The gene expression program related to glycogen utilization was specifically up-regulated in muscle of pigs from the low RFI line (more efficient). Genes involved in fatty acid oxidation were down-regulated in muscle but were promoted in adipose tissues of the same pigs when compared with pigs from the high RFI line (less efficient). This underlined opposite line-associated strategies for energy use in skeletal muscle and adipose tissue. Genes related to cholesterol synthesis and efflux in liver and perirenal fat were also differentially regulated in pigs from the low vs high RFI lines. Conclusions - Non-productive functions such as immunity, defense against pathogens and oxidative stress contribute likely to inter-individual variations in feed efficiency

Alix is required for activity-dependent bulk endocytosis at brain synapses

In chemical synapses undergoing high frequency stimulation, vesicle components can be retrieved from the plasma membrane via a clathrin-independent process called activitydependent bulk endocytosis (ADBE). Alix (ALG-2-interacting protein X/PDCD6IP) is an adaptor protein binding to ESCRT and endophilin-A proteins which is required for clathrinindependent endocytosis in fibroblasts. Alix is expressed in neurons and concentrates at synapses during epileptic seizures. Here, we used cultured neurons to show that Alix is recruited to presynapses where it interacts with and concentrates endophilin-A during conditions triggering ADBE. Using Alix knockout (ko) neurons, we showed that this recruitment, which requires interaction with the calcium-binding protein ALG-2, is necessary for ADBE. We also found that presynaptic compartments of Alix ko hippocampi display subtle morphological defects compatible with flawed synaptic activity and plasticity detected electrophysiologically. Furthermore, mice lacking Alix in the forebrain undergo less seizures during kainate-induced status epilepticus and reduced propagation of the epileptiform activity. These results thus show that impairment of ADBE due to the lack of neuronal Alix leads to abnormal synaptic recovery during physiological or pathological repeated stimulations

TEFM variants impair mitochondrial transcription causing childhood-onset neurological disease

Mutations in the mitochondrial or nuclear genomes are associated with a diverse group of human disorders characterized by impaired mitochondrial respiration. Within this group, an increasing number of mutations have been identified in nuclear genes involved in mitochondrial RNA biology. The TEFM gene encodes the mitochondrial transcription elongation factor responsible for enhancing the processivity of mitochondrial RNA polymerase, POLRMT. We report for the first time that TEFM variants are associated with mitochondrial respiratory chain deficiency and a wide range of clinical presentations including mitochondrial myopathy with a treatable neuromuscular transmission defect. Mechanistically, we show muscle and primary fibroblasts from the affected individuals have reduced levels of promoter distal mitochondrial RNA transcripts. Finally, tefm knockdown in zebrafish embryos resulted in neuromuscular junction abnormalities and abnormal mitochondrial function, strengthening the genotype-phenotype correlation. Our study highlights that TEFM regulates mitochondrial transcription elongation and its defect results in variable, tissue-specific neurological and neuromuscular symptoms