103 research outputs found
Ăvaluation de la durabilitĂ© du rĂ©gime quĂ©bĂ©cois d'autorisation de prĂ©lĂšvements d'eau souterraine
Un nouveau rĂ©gime dâautorisation de prĂ©lĂšvements dâeau est entrĂ© en vigueur dans la province de QuĂ©bec au mois dâaoĂ»t 2014. Il est venu remplacer le RĂšglement sur le captage des eaux souterraines par lâajout de dispositions plus spĂ©cifiques concernant la protection des puits et le renforcement de la protection des sources. Lâobjectif de lâessai est dâexĂ©cuter une Ă©valuation gĂ©nĂ©rale de la durabilitĂ© du rĂ©gime spĂ©cifiquement pour lâeau souterraine. Elle permet dâexaminer si son application rĂ©pond Ă deux enjeux qui sont dâassurer une quantitĂ© et une qualitĂ© de lâeau aux gĂ©nĂ©rations actuelles et futures. Lâoutil dâĂ©valuation proposĂ© est une grille multicritĂšre Ă©laborĂ©e Ă partir de quatorze critĂšres rĂ©partis parmi quatre piliers du dĂ©veloppement durable : environnement, social, Ă©conomique et gouvernance. Un diagnostic de durabilitĂ© attribue au rĂ©gime un indice de rendement durable Ă trois niveaux : rendement faible, rendement moyen, rendement Ă©levĂ©.
LâĂ©valuation des critĂšres se fait de façon systĂ©mique Ă partir de principes Ă©numĂ©rĂ©s dans la Loi sur le dĂ©veloppement durable, de dix-sept indicateurs environnementaux et dâactions prĂ©vues par la juridiction du rĂ©gime. Les rĂ©sultats de lâanalyse dĂ©montrent que lâindice de rendement durable de lâenjeu sur la quantitĂ© dâeau est « moyen », alors quâil est « Ă©levĂ© » pour lâenjeu sur la qualitĂ© de lâeau. En dĂ©finitive, lâindice de rendement durable total du rĂ©gime est « moyen ». La dĂ©marche dâanalyse effectuĂ©e indique que dans sa forme actuelle le rĂ©gime nâest pas conçu pour surveiller les quantitĂ©s disponibles Ă lâĂ©chelle des aquifĂšres, mettant plutĂŽt lâaccent sur les dĂ©bits extraits localement et sur la qualitĂ© de lâeau en pĂ©riphĂ©rie des sites de prĂ©lĂšvement.
Les conclusions constatent que le rĂ©gime doit ĂȘtre bonifiĂ© pour avoir un rendement plus durable. Par contre, il ne peut pas assurer Ă lui seul la durabilitĂ© de la ressource. Des outils additionnels de gestion doivent sây greffer. Lâessai se termine par lâĂ©numĂ©ration de dix-sept recommandations durables. Elles consistent essentiellement Ă dĂ©velopper un systĂšme officiel dâindicateurs environnementaux; Ă considĂ©rer la connectivitĂ© des eaux souterraines avec les eaux de surfaces; Ă intĂ©grer de nouvelles dispositions en amĂ©nagement du territoire pour soutenir la protection des aires dâalimentation des aquifĂšres; Ă dĂ©velopper des outils complĂ©mentaires permettant de mesurer et de surveiller le niveau des nappes en temps rĂ©el; Ă attribuer une valeur monĂ©taire Ă la ressource en considĂ©rant les biens et services Ă©cologiques produits par lâaquifĂšre; Ă procĂ©der Ă une reddition de compte des usages de lâeau souterraine aux cinq ans; et Ă adopter des mesures de gestion adaptative pour pallier les effets des changements climatiques sur les aquifĂšres
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 90â120 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 (>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
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