Évaluation de la durabilité du régime québécois d'autorisation de prélèvements d'eau souterraine

Un nouveau régime d’autorisation de prélèvements d’eau est entré en vigueur dans la province de Québec au mois d’août 2014. Il est venu remplacer le Règlement sur le captage des eaux souterraines par l’ajout de dispositions plus spécifiques concernant la protection des puits et le renforcement de la protection des sources. L’objectif de l’essai est d’exécuter une évaluation générale de la durabilité du régime spécifiquement pour l’eau souterraine. Elle permet d’examiner si son application répond à deux enjeux qui sont d’assurer une quantité et une qualité de l’eau aux générations actuelles et futures. L’outil d’évaluation proposé est une grille multicritère élaborée à partir de quatorze critères répartis parmi quatre piliers du développement durable : environnement, social, économique et gouvernance. Un diagnostic de durabilité attribue au régime un indice de rendement durable à trois niveaux : rendement faible, rendement moyen, rendement élevé. L’évaluation des critères se fait de façon systémique à partir de principes énumérés dans la Loi sur le développement durable, de dix-sept indicateurs environnementaux et d’actions prévues par la juridiction du régime. Les résultats de l’analyse démontrent que l’indice de rendement durable de l’enjeu sur la quantité d’eau est « moyen », alors qu’il est « élevé » pour l’enjeu sur la qualité de l’eau. En définitive, l’indice de rendement durable total du régime est « moyen ». La démarche d’analyse effectuée indique que dans sa forme actuelle le régime n’est pas conçu pour surveiller les quantités disponibles à l’échelle des aquifères, mettant plutôt l’accent sur les débits extraits localement et sur la qualité de l’eau en périphérie des sites de prélèvement. Les conclusions constatent que le régime doit être bonifié pour avoir un rendement plus durable. Par contre, il ne peut pas assurer à lui seul la durabilité de la ressource. Des outils additionnels de gestion doivent s’y greffer. L’essai se termine par l’énumération de dix-sept recommandations durables. Elles consistent essentiellement à développer un système officiel d’indicateurs environnementaux; à considérer la connectivité des eaux souterraines avec les eaux de surfaces; à intégrer de nouvelles dispositions en aménagement du territoire pour soutenir la protection des aires d’alimentation des aquifères; à développer des outils complémentaires permettant de mesurer et de surveiller le niveau des nappes en temps réel; à attribuer une valeur monétaire à la ressource en considérant les biens et services écologiques produits par l’aquifère; à procéder à une reddition de compte des usages de l’eau souterraine aux cinq ans; et à adopter des mesures de gestion adaptative pour pallier les effets des changements climatiques sur les aquifères

Disruption of Mycobacterium avium subsp. paratuberculosis-specific genes impairs in vivo fitness

Background: Mycobacterium avium subsp. paratuberculosis (MAP) is an obligate intracellular pathogen that infects many ruminant species. The acquisition of foreign genes via horizontal gene transfer has been postulated to contribute to its pathogenesis, as these genetic elements are absent from its putative ancestor, M. avium subsp. hominissuis (MAH), an environmental organism with lesser pathogenicity. In this study, high-throughput sequencing of MAP transposon libraries were analyzed to qualitatively and quantitatively determine the contribution of individual genes to bacterial survival during infection. Results: Out of 52384 TA dinucleotides present in the MAP K-10 genome, 12607 had a MycoMarT7 transposon in the input pool, interrupting 2443 of the 4350 genes in the MAP genome (56%). Of 96 genes situated in MAP-specific genomic islands, 82 were disrupted in the input pool, indicating that MAP-specific genomic regions are dispensable for in vitro growth (odds ratio = 0.21). Following 5 independent in vivo infections with this pool of mutants, the correlation between output pools was high for 4 of 5 (R = 0.49 to 0.61) enabling us to define genes whose disruption reproducibly reduced bacterial fitness in vivo. At three different thresholds for reduced fitness in vivo, MAP-specific genes were over-represented in the list of predicted essential genes. We also identified additional genes that were severely depleted after infection, and several of them have orthologues that are essential genes in M. tuberculosis. Conclusions: This work indicates that the genetic elements required for the in vivo survival of MAP represent a combination of conserved mycobacterial virulence genes and MAP-specific genes acquired via horizontal gene transfer. In addition, the in vitro and in vivo essential genes identified in this study may be further characterized to offer a better understanding of MAP pathogenesis, and potentially contribute to the discovery of novel therapeutic and vaccine targets. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-415) contains supplementary material, which is available to authorized users

Evaluating the performance of commercial whole-genome marker sets for capturing common genetic variation

<p>Abstract</p> <p>Background</p> <p>New technologies have enabled genome-wide association studies to be conducted with hundreds of thousands of genotyped SNPs. Several different first-generation genome-wide panels of SNPs have been commercialized. The total amount of common genetic variation is still unknown; however, the coverage of commercial panels can be evaluated against reference population samples genotyped by the International HapMap project. Less information is available about coverage in samples from other populations.</p> <p>Results</p> <p>In this study we compare four commercial panels: the HumanHap 300 and HumanHap 550 Array Sets from the Illumina Infinium series and the Mapping 100 K and Mapping 500 K Array Sets from the Affymetrix GeneChip series. Tagging performance is compared among HapMap CEPH (CEU), Asian (JPT, CHB) and Yoruba (YRI) population samples. It is also evaluated in an Estonian population sample with more than 1000 individuals genotyped in two 500-kbp ENCODE regions of chromosome 2: ENr112 on 2p16.3 and ENr131 on 2p37.1.</p> <p>Conclusion</p> <p>We found that in a non-reference Caucasian population, commercial SNP panels provide levels of coverage similar to those in the HapMap CEPH population sample. We present the proportions of universal and population-specific SNPs in all the commercial platforms studied.</p

A human ALDH1A2 gene variant is associated with increased newborn kidney size and serum retinoic acid

Nephron number varies widely between 0.3 and 1.3 million per kidney in humans. During fetal life, the rate of nephrogenesis is influenced by local retinoic acid (RA) level such that even moderate maternal vitamin A deficiency limits the final nephron number in rodents. Inactivation of genes in the RA pathway causes renal agenesis in mice; however, the impact of retinoids on human kidney development is unknown. To resolve this, we tested for associations between variants of genes involved in RA metabolism (ALDH1A2, CYP26A1, and CYP26B1) and kidney size among normal newborns. Homozygosity for a common (1 in 5) variant, rs7169289(G), within an Sp1 transcription factor motif of the ALDH1A2 gene, showed a significant 22% increase in newborn kidney volume when adjusted for body surface area. Infants bearing this allele had higher umbilical cord blood RA levels compared to those with homozygous wild-type ALDH1A2 rs7169289(A) alleles. Furthermore, the effect of the rs7169289(G) variant was evident in subgroups with or without a previously reported hypomorphic RET 1476(A) proto-oncogene allele that is critical in determining final nephron number. As maternal vitamin A deficiency is widespread in developing countries and may compromise availability of retinol for fetal RA synthesis, our study suggests that the ALDH1A2 rs7169289(G) variant might be protective for such individuals

An Evaluation of the Performance of Tag SNPs Derived from HapMap in a Caucasian Population

The Haplotype Map (HapMap) project recently generated genotype data for more than 1 million single-nucleotide polymorphisms (SNPs) in four population samples. The main application of the data is in the selection of tag single-nucleotide polymorphisms (tSNPs) to use in association studies. The usefulness of this selection process needs to be verified in populations outside those used for the HapMap project. In addition, it is not known how well the data represent the general population, as only 90–120 chromosomes were used for each population and since the genotyped SNPs were selected so as to have high frequencies. In this study, we analyzed more than 1,000 individuals from Estonia. The population of this northern European country has been influenced by many different waves of migrations from Europe and Russia. We genotyped 1,536 randomly selected SNPs from two 500-kbp ENCODE regions on Chromosome 2. We observed that the tSNPs selected from the CEPH (Centre d'Etude du Polymorphisme Humain) from Utah (CEU) HapMap samples (derived from US residents with northern and western European ancestry) captured most of the variation in the Estonia sample. (Between 90% and 95% of the SNPs with a minor allele frequency of more than 5% have an r (2) of at least 0.8 with one of the CEU tSNPs.) Using the reverse approach, tags selected from the Estonia sample could almost equally well describe the CEU sample. Finally, we observed that the sample size, the allelic frequency, and the SNP density in the dataset used to select the tags each have important effects on the tagging performance. Overall, our study supports the use of HapMap data in other Caucasian populations, but the SNP density and the bias towards high-frequency SNPs have to be taken into account when designing association studies

Rain-on-Snow and Ice Layer Formation Detection Using Passive Microwave Radiometry: An Arctic Perspective

No abstract availabl

An Extremes of outcome strategy provides evidence that multiple sclerosis severity is determined by alleles at the <i>HLA-DRB1</i> locus

Multiple sclerosis (MS) is a common inflammatory disease of the central nervous system unsurpassed for variability in disease outcome. A cohort of sporadic MS cases (n=63), taken from opposite extremes of the distribution of long-term outcome, was used to determine the role of the HLA-DRB1 locus on MS disease severity. Genotyping sets of benign and malignant MS patients showed that HLA-DRB1*01 was significantly underrepresented in malignant compared with benign cases. This allele appears to attenuate the progressive disability that characterizes MS in the long term. The observation was doubly replicated in (i) Sardinian benign and malignant patients and (ii) a cohort of affected sibling pairs discordant for HLA-DRB1*01. Among the latter, mean disability progression indices were significantly lower in those carrying the HLA-DRB1*01 allele compared with their disease-concordant siblings who did not. The findings were additionally supported by similar transmission distortion of HLA-DRB1*04 subtypes closely related to HLA-DRB1*01. The protective effect of HLA-DRB1*01 in sibling pairs may result from a specific epistatic interaction with the susceptibility allele HLA-DRB1*1501. A high-density (&gt;700) SNP examination of the MHC region in the benign and malignant patients could not identify variants differing significantly between the two groups, suggesting that HLA-DRB1 may itself be the disease-modifying locus. We conclude that HLA-DRB1*01, previously implicated in disease resistance, acts as an independent modifier of disease progression. These results closely link susceptibility to long-term outcome in MS, suggesting that shared quantitative MHC-based mechanisms are common to both, emphasizing the central role of this region in pathogenesis