Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data

Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here, we present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analyzed imprinted expression to give a complete picture of the ‘allelome’ by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity to analyze lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data. We used RNA-seq data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine a biologically relevant allelic ratio cutoff, and define for the first time an entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This approach can be easily extended to analyze histone marks of active enhancers, or transcription factor binding sites and therefore provides a powerful tool to identify candidate cis regulatory elements genome wide

Observational Constraints on Red and Blue Helium Burning Sequences

We derive the optical luminosity, colors, and ratios of the blue and red helium burning (HeB) stellar populations from archival Hubble Space Telescope observations of nineteen starburst dwarf galaxies and compare them with theoretical isochrones from Padova stellar evolution models across metallicities from Z=0.001 to 0.009. We find that the observational data and the theoretical isochrones for both blue and red HeB populations overlap in optical luminosities and colors and the observed and predicted blue to red HeB ratios agree for stars older than 50 Myr over the time bins studied. These findings confirm the usefulness of applying isochrones to interpret observations of HeB populations. However, there are significant differences, especially for the red HeB population. Specifically we find: (1) offsets in color between the observations and theoretical isochrones of order 0.15 mag (0.5 mag) for the blue (red) HeB populations brighter than M_V ~ -4 mag, which cannot be solely due to differential extinction; (2) blue HeB stars fainter than M_V ~ -3 mag are bluer than predicted; (3) the slope of the red HeB sequence is shallower than predicted by a factor of ~3; and (4) the models overpredict the ratio of the most luminous blue to red HeB stars corresponding to ages <50 Myr. Additionally, we find that for the more metal-rich galaxies in our sample (Z> 0.5 Zsolar) the red HeB stars overlap with the red giant branch stars in the color magnitude diagrams, thus reducing their usefulness as indicators of star formation for ages >100 Myr.Comment: 18 pages, 11 figures, 3 table

Structural Parameters of Seven SMC Intermediate-Age and Old Star Clusters

We present structural parameters for the seven intermediate-age and old star clusters NGC121, Lindsay 1, Kron 3, NGC339, NGC416, Lindsay 38, and NGC419 in the Small Magellanic Cloud. We fit King profiles and Elson, Fall, and Freeman profiles to both surface-brightness and star count data taken with the Advanced Camera for Surveys aboard the Hubble Space Telescope. Clusters older than 1 Gyr show a spread in cluster core radii that increases with age, while the youngest clusters have relatively compact cores. No evidence for post core collapse clusters was found. We find no correlation between core radius and distance from the SMC center, although consistent with other studies of dwarf galaxies, some relatively old and massive clusters have low densities. The oldest SMC star cluster, the only globular NGC121, is the most elliptical object of the studied clusters. No correlation is seen between ellipticity and distance from the SMC center. The structures of these massive intermediate-age (1-8 Gyr) SMC star clusters thus appear to primarily result from internal evolutionary processes.Comment: 16 pages, 13 figure

Kepler-424 b: A "lonely" hot Jupiter that found a companion

Peer reviewedFinal Accepted Versio

Age Determination of Six Intermediate-age SMC Star Clusters with HST/ACS

We present a photometric analysis of the star clusters Lindsay 1, Kron 3, NGC339, NGC416, Lindsay 38, and NGC419 in the Small Magellanic Cloud (SMC), observed with the Hubble Space Telescope Advanced Camera for Surveys (ACS) in the F555W and F814W filters. Our color magnitude diagrams (CMDs) extend ~3.5 mag deeper than the main-sequence turnoff points, deeper than any previous data. Cluster ages were derived using three different isochrone models: Padova, Teramo, and Dartmouth, which are all available in the ACS photometric system. Fitting observed ridgelines for each cluster, we provide a homogeneous and unique set of low-metallicity, single-age fiducial isochrones. The cluster CMDs are best approximated by the Dartmouth isochrones for all clusters, except for NGC419 where the Padova isochrones provided the best fit. The CMD of NGC419 shows several main-sequence turn-offs, which belong to the cluster and to the SMC field. We thus derive an age range of 1.2-1.6 Gyr for NGC419. Interestingly, our intermediate-age star clusters have a metallicity spread of ~0.6 dex, which demonstrates that the SMC does not have a smooth, monotonic age-metallicity relation. We find an indication for centrally concentrated blue straggler star candidates in NGC416, while for the other clusters these are not present. Using the red clump magnitudes, we find that the closest cluster, NGC419 (~50kpc), and the farthest cluster, Lindsay 38 (~67kpc), have a relative distance of ~17kpc, which confirms the large depth of the SMC.Comment: 25 pages, 45 Figure

Why the globular cluster NGC 6752 contains no sodium-rich second-generation AGB stars

Context. Globular clusters host multiple stellar populations showing different sodium enrichments. These various populations can be observed along the main sequence, red giant and horizontal branch phases. Recently it was shown, however, that at least in the globular cluster NGC 6752, no sodium-rich stars are observed along the early asymptotic giant branch (AGB), posing an apparent problem for stellar evolution. Aims. We present an explanation for this lack of sodium-rich stars in this region of the colour–magnitude diagram. Methods. We computed models for low-mass stars following the prediction of the so-called fast rotating massive stars model for the initial composition of second-generation stars. We studied the impact of different initial helium contents on the stellar lifetimes and the evolutionary path in the Hertzsprung-Russell diagram. Results. We propose that the lack of sodium-rich stars along the early-AGB arises because sodium-rich stars were born with a high initial helium abundance, as predicted by the fast rotating massive stars scenario. Helium-rich stars have much shorter lifetimes for a given initial mass than stars with a normal helium abundance, and above a cutoff initial helium abundance that slightly depends on the mass-loss rate on the RGB they do not go through the AGB phase and evolve directly into a white dwarf stage. Within the fast rotating massive stars framework we obtained a cutoff in [Na/Fe] between the second-generation models evolving into the AGB phase and those skipping that phase between 0.18 and 0.4 dex, depending on the mass loss rate used during the red giant phase. In view of the uncertainties in abundance determinations, the cutoff obtained by the present model agrees well with the one inferred from recent observations of the cluster NGC 6752. Conclusions. The helium-sodium correlation needed to explain the lack of sodium-rich stars along the early-AGB of NGC 6752 corresponds to the one predicted by the fast rotating massive stars models. A crucial additional test of the model is the distribution of stars with various helium abundances among main-sequence stars. Our model predicts that two magnitudes below the turnoff a very large percentage of stars, about 82%, probably has a helium content lower than 0.275 in mass fraction, while only 5% of stars are expected to have helium abundances greater than 0.4

oMEGACat I: MUSE spectroscopy of 300,000 stars within the half-light radius of ω\omega Centauri

Omega Centauri ($\omega$ Cen) is the most massive globular cluster of the Milky Way and has been the focus of many studies that reveal the complexity of its stellar populations and kinematics. However, most previous studies have used photometric and spectroscopic datasets with limited spatial or magnitude coverage, while we aim to investigate it having full spatial coverage out to its half-light radius and stars ranging from the main sequence to the tip of the red giant branch. This is the first paper in a new survey of $\omega$ Cen that combines uniform imaging and spectroscopic data out to its half-light radius to study its stellar populations, kinematics, and formation history. In this paper, we present an unprecedented MUSE spectroscopic dataset combining 87 new MUSE pointings with previous observations collected from guaranteed time observations. We extract spectra of more than 300,000 stars reaching more than two magnitudes below the main sequence turn-off. We use these spectra to derive metallicity and line-of-sight velocity measurements and determine robust uncertainties on these quantities using repeat measurements. Applying quality cuts we achieve signal-to-noise ratios of 16.47/73.51 and mean metallicity errors of 0.174/0.031 dex for the main sequence stars (18 mag $\rm < mag_{F625W}<$22 mag) and red giant branch stars (16 mag $<\rm mag_{F625W}<$10 mag), respectively. We correct the metallicities for atomic diffusion and identify foreground stars. This massive spectroscopic dataset will enable future studies that will transform our understanding of $\omega$ Cen, allowing us to investigate the stellar populations, ages, and kinematics in great detail.Comment: 27 pages, 18 figures, 3 tables, accepted for publication in ApJ, the catalog will be available in the online material of the published articl

The ACS LCID project. V. The Star Formation History of the Dwarf Galaxy \objectname[]{LGS-3}: Clues for Cosmic Reionization and Feedback

We present an analysis of the star formation history (SFH) of the transition-type (dIrr/dSph) Local Group galaxy \objectname[]{LGS-3} (Pisces) based on deep photometry obtained with the {\it Advanced Camera for Surveys} onboard the {\it Hubble Space Telescope}. Our analysis shows that the SFH of \objectname[]{LGS-3} is dominated by a main episode $\sim 11.7$ Gyr ago with a duration of $\sim$ 1.4 Gyr which formed $\sim 90$ of the stars. Subsequently, \objectname[]{LGS-3} continued forming stars until the present, although at a much lower rate. The lack of early chemical enrichment is in contrast to that observed in the isolated dSph galaxies of comparable luminosity, implying that the dSphs were more massive and subjected to more tidal stripping. We compare the SFH of \objectname[]{LGS-3} with expectations from cosmological models. Most or all the star formation was produced in \objectname[]{LGS-3} after the reionization epoch, assumed to be completed at $z\sim6$ or $\sim 12.7$ Gyr ago. The total mass of the galaxy is estimated to be between 2 and $4\times 10^8$ M$_\odot$, corresponding to circular velocities between 28 km\ s$^{-1}$ to 36 km\ s$^{-1}$. These values are close to but somewhat above the limit of 30 km\ s$^{-1}$ below which the UV background is expected to prevent any star formation after reionization. Feedback from SNe associated with the initial episode of star formation (mechanical luminosity from SNe $L_w=5.3\times 10^{38}$ erg s$^{-1}$) is probably inadequate to completely blow away the gas. However, the combined effects of SN feedback and UV background heating might be expected to completely halt star formation at the reionization epoch for the low mass of \objectname[]{LGS-3}; this suggests that self-shielding is important to the early evolution of galaxies in this mass range.Comment: accepted to be published at Ap