Aix-Marseille University

About: Aix-Marseille University is a education organization based out in Marseille, France. It is known for research contribution in the topics: Population & Galaxy. The organization has 24326 authors who have published 54240 publications receiving 1455416 citations. The organization is also known as: University Aix-Marseille & université d'Aix-Marseille.

The COSMOS2015 galaxy stellar mass function . Thirteen billion years of stellar mass assembly in ten snapshots

Abstract: We measure the stellar mass function (SMF) and stellar mass density of galaxies in the COSMOS field up to z ~ 6. We select them in the near-IR bands of the COSMOS2015 catalogue, which includes ultra-deep photometry from UltraVISTA-DR2, SPLASH, and Subaru/Hyper Suprime-Cam. At z > 2.5 we use new precise photometric redshifts with error σ_z = 0.03(1 + z) and an outlier fraction of 12%, estimated by means of the unique spectroscopic sample of COSMOS (~100 000 spectroscopic measurements in total, more than one thousand having robust z_(spec)> 2.5). The increased exposure time in the DR2, along with our panchromatic detection strategy, allow us to improve the completeness at high z with respect to previous UltraVISTA catalogues (e.g. our sample is >75% complete at 10^(10)M⊙ and z = 5). We also identify passive galaxies through a robust colour–colour selection, extending their SMF estimate up to z = 4. Our work provides a comprehensive view of galaxy-stellar-mass assembly between z = 0.1 and 6, for the first time using consistent estimates across the entire redshift range. We fit these measurements with a Schechter function, correcting for Eddington bias. We compare the SMF fit with the halo mass function predicted from ΛCDM simulations, finding that at z > 3 both functions decline with a similar slope in thehigh-mass end. This feature could be explained assuming that mechanisms quenching star formation in massive haloes become less effective at high redshifts; however further work needs to be done to confirm this scenario. Concerning the SMF low-mass end, it shows a progressive steepening as it moves towards higher redshifts, with α decreasing from -1.47^(+0.02)_(-0.02) at z ≃ 0.1 to -2.11^(+0.30)_(-0.13) at z ≃ 5. This slope depends on the characterisation of the observational uncertainties, which is crucial to properly remove the Eddington bias. We show that there is currently no consensus on the method to quantify such errors: different error models result in different best-fit Schechter parameters.

Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations

Abstract: Disturbance of the beneficial gut microbial community is a potential collateral effect of antibiotics, which have many uses in animal agriculture (disease treatment or prevention and feed efficiency improvement). Understanding antibiotic effects on bacterial communities at different intestinal locations is essential to realize the full benefits and consequences of in-feed antibiotics. In this study, we defined the lumenal and mucosal bacterial communities from the small intestine (ileum) and large intestine (cecum and colon) plus feces, and characterized the effects of in-feed antibiotics (chlortetracycline, sulfamethazine and penicillin (ASP250)) on these communities. 16S rRNA gene sequence and metagenomic analyses of bacterial membership and functions revealed dramatic differences between small and large intestinal locations, including enrichment of Firmicutes and phage-encoding genes in the ileum. The large intestinal microbiota encoded numerous genes to degrade plant cell wall components, and these genes were lacking in the ileum. The mucosa-associated ileal microbiota harbored greater bacterial diversity than the lumen but similar membership to the mucosa of the large intestine, suggesting that most gut microbes can associate with the mucosa and might serve as an inoculum for the lumen. The collateral effects on the microbiota of antibiotic-fed animals caused divergence from that of control animals, with notable changes being increases in Escherichia coli populations in the ileum, Lachnobacterium spp. in all gut locations, and resistance genes to antibiotics not administered. Characterizing the differential metabolic capacities and response to perturbation at distinct intestinal locations will inform strategies to improve gut health and food safety.

Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations

Abstract: Thanks to genome-scale diversity data, present-day studies can provide a detailed view of how natural and cultivated species adapt to their environment and particularly to environmental gradients. However, due to their sensitivity, up-to-date studies might be more sensitive to undocumented demographic effects such as the pattern of migration and the reproduction regime. In this study, we provide guidelines for the use of popular or recently developed statistical methods to detect footprints of selection. We simulated 100 populations along a selective gradient and explored different migration models, sampling schemes and rates of self-fertilization. We investigated the power and robustness of eight methods to detect loci potentially under selection: three designed to detect genotype–environment correlations and five designed to detect adaptive differentiation (based on FST or similar measures). We show that genotype– environment correlation methods have substantially more power to detect selection than differentiation-based methods but that they generally suffer from high rates of false positives. This effect is exacerbated whenever allele frequencies are correlated, either between populations or within populations. Our results suggest that, when the underlying genetic structure of the data is unknown, a number of robust methods are preferable. Moreover, in the simulated scenario we used, sampling many populations led to better results than sampling many individuals per population. Finally, care should be taken when using methods to identify genotype–environment correlations without correcting for allele frequency autocorrelation because of the risk of spurious signals due to allele frequency correlations between populations.

The radial and azimuthal profiles of Mg II absorption around 0,5 <z <0,9 zCosmos galaxies of different colors, masses, and environments

Abstract: We map the radial and azimuthal distribution of Mg II gas within ~ 200 kpc (physical) of ~ 4000 galaxies at redshifts 0.5 1. We investigate the variation of Mg II rest-frame equivalent width (EW) as a function of the radial impact parameter for different subsets of foreground galaxies selected in terms of their rest-frame colors and masses. Blue galaxies have a significantly higher average Mg II EW at close galactocentric radii as compared to the red galaxies. Among the blue galaxies, there is a correlation between Mg II EW and galactic stellar mass of the host galaxy. We also find that the distribution of Mg II absorption around group galaxies is more extended than that for non-group galaxies, and that groups as a whole have more extended radial profiles than individual galaxies. Interestingly, these effects can be satisfactorily modeled by a simple superposition of the absorption profiles of individual member galaxies, assuming that these are the same as those of non-group galaxies, suggesting that the group environment may not significantly enhance or diminish the Mg II absorption of individual galaxies. We show that there is a strong azimuthal dependence of the Mg II absorption within 50 kpc of inclined disk-dominated galaxies, indicating the presence of a strongly bipolar outflow aligned along the disk rotation axis. There is no significant dependence of Mg II absorption on the apparent inclination angle of disk-dominated galaxies.

RSAT 2015: Regulatory Sequence Analysis Tools

Abstract: RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding motif analysis (quality assessment, comparisons and clustering), (iii) comparative genomics and (iv) analysis of regulatory variations. Nine new programs have been added to the 43 described in the 2011 NAR Web Software Issue, including a tool to extract sequences from a list of coordinates (fetch-sequences from UCSC), novel programs dedicated to the analysis of regulatory variants from GWAS or population genomics (retrieve-variation-seq and variation-scan), a program to cluster motifs and visualize the similarities as trees (matrix-clustering). To deal with the drastic increase of sequenced genomes, RSAT public sites have been reorganized into taxon-specific servers. The suite is well-documented with tutorials and published protocols. The software suite is available through Web sites, SOAP/WSDL Web services, virtual machines and stand-alone programs at http://www.rsat.eu/.