PyMorph: Automated Galaxy Structural Parameter Estimation using Python

We present a new software pipeline -- PyMorph -- for automated estimation of structural parameters of galaxies. Both parametric fits through a two dimensional bulge disk decomposition as well as structural parameter measurements like concentration, asymmetry etc. are supported. The pipeline is designed to be easy to use yet flexible; individual software modules can be replaced with ease. A find-and-fit mode is available so that all galaxies in a image can be measured with a simple command. A parallel version of the Pymorph pipeline runs on computer clusters and a Virtual Observatory compatible web enabled interface is under development.Comment: 15 pages, 12 figures, 1 table, accepted for publication in MNRA

Mitochondrial effects of dexamethasone imply both membrane and cytosolic-initiated pathways in HepG2 cells

Glucocorticoid treatment is often linked to increased whole-body energy expenditure and hypermetabolism. Glucocorticoids affect mitochondrial energy production, notably in the liver, where they lead to mitochondrial uncoupling reducing the efficacy of oxidative phosphorylation. However, the signaling pathways involved in these phenomena are poorly understood. Here we treated HepG2 cells with dexamethasone for different times and, by using different combinations of inhibitors, we showed that dexamethasone treatment leads to recruitment of two main signaling pathways. The first one involves a G-protein coupled membrane glucocorticoid binding site and rapidly decreases complexes I and II activities while complex III activity is upregulated in a p38MAPK dependent mechanism. The second one implies the classical cytosolic glucocorticoid receptor and triggers long-term transcriptional increases of respiration rates and of complex IV activity and quantity. We concluded that mitochondria are the target of multiple dexamethasone-induced regulatory pathways that are set up gradually after the beginning of hormone exposure and that durably influence mitochondrial oxidative phosphorylation

Mutations in Conserved Residues of the C. elegans microRNA Argonaute ALG-1 Identify Separable Functions in ALG-1 miRISC Loading and Target Repression

microRNAs function in diverse developmental and physiological processes by regulating target gene expression at the post-transcriptional level. ALG-1 is one of two Caenorhabditis elegans Argonautes (ALG-1 and ALG-2) that together are essential for microRNA biogenesis and function. Here, we report the identification of novel antimorphic (anti) alleles of ALG-1 as suppressors of lin-28(lf) precocious developmental phenotypes. The alg-1(anti) mutations broadly impair the function of many microRNAs and cause dosage-dependent phenotypes that are more severe than the complete loss of ALG-1. ALG-1(anti) mutant proteins are competent for promoting Dicer cleavage of microRNA precursors and for associating with and stabilizing microRNAs. However, our results suggest that ALG-1(anti) proteins may sequester microRNAs in immature and functionally deficient microRNA Induced Silencing Complexes (miRISCs), and hence compete with ALG-2 for access to functional microRNAs. Immunoprecipitation experiments show that ALG-1(anti) proteins display an increased association with Dicer and a decreased association with AIN-1/GW182. These findings suggest that alg-1(anti) mutations impair the ability of ALG-1 miRISC to execute a transition from Dicer-associated microRNA processing to AIN-1/GW182 associated effector function, and indicate an active role for ALG/Argonaute in mediating this transition

Applying dissipative dynamical systems to pseudorandom number generation: Equidistribution property and statistical independence of bits at distances up to logarithm of mesh size

The behavior of a family of dissipative dynamical systems representing transformations of two-dimensional torus is studied on a discrete lattice and compared with that of conservative hyperbolic automorphisms of the torus. Applying dissipative dynamical systems to generation of pseudorandom numbers is shown to be advantageous and equidistribution of probabilities for the sequences of bits can be achieved. A new algorithm for generating uniform pseudorandom numbers is proposed. The theory of the generator, which includes proofs of periodic properties and of statistical independence of bits at distances up to logarithm of mesh size, is presented. Extensive statistical testing using available test packages demonstrates excellent results, while the speed of the generator is comparable to other modern generators.Comment: 6 pages, 3 figures, 3 table

Improving the population genetics toolbox for the study of the African malaria vector Anopheles nili: microsatellite mapping to chromosomes

<p>Abstract</p> <p>Background</p> <p><it>Anopheles nili </it>is a major vector of malaria in the humid savannas and forested areas of sub-Saharan Africa. Understanding the population genetic structure and evolutionary dynamics of this species is important for the development of an adequate and targeted malaria control strategy in Africa. Chromosomal inversions and microsatellite markers are commonly used for studying the population structure of malaria mosquitoes. Physical mapping of these markers onto the chromosomes further improves the toolbox, and allows inference on the demographic and evolutionary history of the target species.</p> <p>Results</p> <p>Availability of polytene chromosomes allowed us to develop a map of microsatellite markers and to study polymorphism of chromosomal inversions. Nine microsatellite markers were mapped to unique locations on all five chromosomal arms of <it>An. nili </it>using fluorescent <it>in situ </it>hybridization (FISH). Probes were obtained from 300-483 bp-long inserts of plasmid clones and from 506-559 bp-long fragments amplified with primers designed using the <it>An. nili </it>genome assembly generated on an Illumina platform. Two additional loci were assigned to specific chromosome arms of <it>An. nili </it>based on <it>in silico </it>sequence similarity and chromosome synteny with <it>Anopheles gambiae</it>. Three microsatellites were mapped inside or in the vicinity of the polymorphic chromosomal inversions <it>2Rb </it>and <it>2Rc</it>. A statistically significant departure from Hardy-Weinberg equilibrium, due to a deficit in heterozygotes at the <it>2Rb </it>inversion, and highly significant linkage disequilibrium between the two inversions, were detected in natural <it>An. nili </it>populations collected from Burkina Faso.</p> <p>Conclusions</p> <p>Our study demonstrated that next-generation sequencing can be used to improve FISH for microsatellite mapping in species with no reference genome sequence. Physical mapping of microsatellite markers in <it>An. nili </it>showed that their cytological locations spanned the entire five-arm complement, allowing genome-wide inferences. The knowledge about polymorphic inversions and chromosomal locations of microsatellite markers has been useful for explaining differences in genetic variability across loci and significant differentiation observed among natural populations of <it>An. nili</it>.</p

Métabolomique et spectrométrie de masse : de nouvelles perspectives en analyse biomédicale

Metabolomics is defined as an integrative approach consisting in the comprehensive analysis of all of the small molecules of a biological system (the "metabolome"). The main objective of metabolomics in medecine is to discover metabolic biomarkers for diseases. Mass spectrometry (MS) coupled to liquid or gas chromatography is amongst major analytical tools used in metabolomics. However, the holistic approach used in metabolomics requires very good performances of the analytical system (chromatographic column and MS equipment) and the use of non-conventional validation strategies. Metabolomics workflow can be divided in three main steps: sample preparation, MS data acquisition and processing, and statistical analysis. Processing of the "raw" data (obtained after MS acquisition) is mostly required to normalise chromatographic conditions and to carry out accurate quantification of MS features. Features resulting from this processing may be identified later. The statistical analyses include typically multivariate techniques such as supervised and non-supervised methods. Supervised methods make use of the response variable (e.g., case/control) for model construction while non-supervised methods do not use this piece of information. When the study is focused on a particular set of metabolites, targeted metabolomics could be an interesting alternative to the holistic approach since it may allow absolute quantitation and be associated with a reduced cost

Searches for neutrinoless double beta decay

Neutrinoless double beta decay is a lepton number violating process whose observation would also establish that neutrinos are their own anti-particles. There are many experimental efforts with a variety of techniques. Some (EXO, Kamland-Zen, GERDA phase I and CANDLES) started take data in 2011 and EXO has reported the first measurement of the half life for the double beta decay with two neutrinos of $^{136}$Xe. The sensitivities of the different proposals are reviewed.Comment: 8 pages, prepared for TAUP 201

The Morphological Content of Ten EDisCS Clusters at 0.5 < z < 0.8

We describe Hubble Space Telescope (HST) imaging of 10 of the 20 ESO Distant Cluster Survey (EDisCS) fields. Each ~40 square arcminute field was imaged in the F814W filter with the Advanced Camera for Surveys Wide Field Camera. Based on these data, we present visual morphological classifications for the ~920 sources per field that are brighter than I_auto=23 mag. We use these classifications to quantify the morphological content of 10 intermediate-redshift (0.5 < z < 0.8) galaxy clusters within the HST survey region. The EDisCS results, combined with previously published data from seven higher redshift clusters, show no statistically significant evidence for evolution in the mean fractions of elliptical, S0, and late-type (Sp+Irr) galaxies in clusters over the redshift range 0.5 < z < 1.2. In contrast, existing studies of lower redshift clusters have revealed a factor of ~2 increase in the typical S0 fraction between z=0.4 and z=0, accompanied by a commensurate decrease in the Sp+Irr fraction and no evolution in the elliptical fraction. The EDisCS clusters demonstrate that cluster morphological fractions plateau beyond z ~ 0.4. They also exhibit a mild correlation between morphological content and cluster velocity dispersion, highlighting the importance of careful sample selection in evaluating evolution. We discuss these findings in the context of a recently proposed scenario in which the fractions of passive (E,S0) and star-forming (Sp,Irr) galaxies are determined primarily by the growth history of clusters.Comment: 18 pages, 7 figures; To be published in ApJ; minor changes made to table label

Searches for neutrinoless double beta decay

Neutrinoless double beta decay is a lepton number violating process whose observation would also establish that neutrinos are their own anti-particles. There are many experimental efforts with a variety of techniques. Some (EXO, Kamland-Zen, GERDA phase I and CANDLES) started take data in 2011 and EXO has reported the first measurement of the half life for the double beta decay with two neutrinos of $^{136}$Xe. The sensitivities of the different proposals are reviewed.Comment: 8 pages, prepared for TAUP 201