Galactic Chemical Evolution and the abundances of lithium, beryllium and boron

A LiBeB evolution model including Galactic Cosmic Ray nucleosynthesis, the $\nu$-process, novae, AGB and C-stars is presented. We have included Galactic Cosmic Ray Nucleosynthesis (GCRN) in a complete Chemical Evolution Model that takes into account 76 stable isotopes from hydrogen to zinc. Any successful LiBeB evolution model should also be compatible with other observational constraints like the age-metallicity relation, the G-dwarf distribution or the evolution of other elements. At the same time, we have checked how different would be a model that took into account the last observations by Wakker et al. (1999) of metal-enriched clouds falling onto the disk, from a primordial infall model.Comment: 2 pages, 2 figures. To appear in `Cosmic Evolution' Conference at IAp, Paris 13-17 Nov 200

Asterias: a parallelized web-based suite for the analysis of expression and aCGH data

Asterias (\url{http://www.asterias.info}) is an integrated collection of freely-accessible web tools for the analysis of gene expression and aCGH data. Most of the tools use parallel computing (via MPI). Most of our applications allow the user to obtain additional information for user-selected genes by using clickable links in tables and/or figures. Our tools include: normalization of expression and aCGH data; converting between different types of gene/clone and protein identifiers; filtering and imputation; finding differentially expressed genes related to patient class and survival data; searching for models of class prediction; using random forests to search for minimal models for class prediction or for large subsets of genes with predictive capacity; searching for molecular signatures and predictive genes with survival data; detecting regions of genomic DNA gain or loss. The capability to send results between different applications, access to additional functional information, and parallelized computation make our suite unique and exploit features only available to web-based applications.Comment: web based application; 3 figure

Galactic Cosmic Rays from Superbubbles and the Abundances of Lithium, Beryllium, and Boron

In this article we study the galactic evolution of the LiBeB elements within the framework of a detailed model of the chemical evolution of the Galaxy that includes galactic cosmic ray nucleosynthesis by particles accelerated in superbubbles. The chemical composition of the superbubble consists of varying proportions of ISM and freshly supernova synthesized material. The observational trends of 6 LiBeB evolution are nicely reproduced by models in which GCR come from a mixture of 25% of supernova material with 75% of ISM, except for 6 Li, for which maybe an extra source is required at low metallicities. To account for 7 Li evolution several additional sources have been considered (neutrino-induced nucleosynthesis, nova outbursts, C-stars). The model fulfills the energetic requirements for GCR acceleration.Comment: 25 pages, 9 figures. Accepted for publication in the Astrophysical Journa

Chemical evolution of local galaxies in a hierarchical model

We investigate the chemical properties of local galaxies within a cosmological framework in the hierarchical picture of galaxy formation. To this aim, we use a hierarchical semi-analytic model which includes the contribution from (i) low and intermediate mass stars, (ii) type Ia Supernovae (SNe) and (iii) massive stars. - Abridged - We compare our predictions with available observations in the Milky Way (MW), in local dwarf galaxies and in local ellipticals. For Milky-Way-like galaxies, we can successfully reproduce the [O-Fe] vs [Fe/H] relation observed in disc stars and the stellar metallicity distribution (SMD). For dwarf galaxies, the stellar metallicity vs mass relation is reproduced by assuming that a substantial fraction of the heavy elements is lost through metal-enhanced outflows and a type Ia SN realization probability lower than the one of MW-like galaxies. - Abridged - In ellipticals, the observations indicate higher [alpha/Fe] values in larger galaxies. - Abridged - Our results computed with a standard Salpeter initial mass function (IMF) indicate a flat [alpha/Fe]-sigma relation. However, we suggest a possible solution to this problem and show how, by assuming a star formation-dependent IMF with a slope x=1.35 in systems with star formation rates < 100 M_sun/yr and slightly flatter (i.e. with x=1) in object with stronger star formation, the observed correlation between [alpha/Fe] and sigma can be accounted for on a large velocity dispersion range. Fundamental roles are played also by interaction-triggered starbursts and AGN.Comment: MNRAS, accepted, 27 pages, 22 figure

PaLS: filtering common literature, biological terms and pathway information

Many biological experiments and their subsequent analysis yield lists of genes or proteins that can potentially be important to the prognosis or diagnosis of certain diseases (e.g. cancer). Nowadays, information about the function of those genes or proteins may be already gathered in some databases, but it is essential to understand if some of the members of those lists have a function in common or if they belong to the same metabolic pathway. To help researchers filter those genes or proteins that have such information in common, we have developed PaLS (pathway and literature strainer, http://pals.bioinfo.cnio.es). PaLS takes a list or a set of lists of gene or protein identifiers and shows which ones share certain descriptors. Four publicly available databases have been used for this purpose: PubMed, which links genes with those articles that make reference to them; Gene Ontology, an annotated ontology of terms related to the cellular component, biological process or molecular function where those genes or proteins are involved; KEGG pathways and Reactome pathways. Those descriptors among these four sources of information that are shared by more members of the list (or lists) are highlighted by PaLS

MicroRNA-224 Targets SMAD Family Member 4 to Promote Cell Proliferation and Negatively Influence Patient Survival

10.1371/journal.pone.0068744PLoS ONE87-POLN

Evolution of interstellar dust and stardust in the solar neighbourhood

The abundance evolution of interstellar dust species originating from stellar sources and from condensation in molecular clouds in the local interstellar medium of the Milky Way is studied and the input of dust material to the Solar System is determined. A one-zone chemical evolution model of the Milky Way for the elemental composition of the disk combined with an evolution model for its interstellar dust component similar to that of Dwek (1998) is developed. The dust model considers dust-mass return from AGB stars as calculated from synthetic AGB models combined with models for dust condensation in stellar outflows. Supernova dust formation is included in a simple parameterized form which is gauged by observed abundances of presolar dust grains with supernova origin. For dust growth in the ISM a simple method is developed for coupling this with disk and dust evolution models. The time evolution of the abundance of the following dust species is followed in the model: silicate, carbon, silicon carbide, and iron dust from AGB stars and from SNe as well as silicate, carbon, and iron dust grown in molecular clouds. It is shown that the interstellar dust population is dominated by dust accreted in molecular clouds; most of the dust material entering the Solar System at its formation does not show isotopic abundance anomalies of the refractory elements, i.e., inconspicuous isotopic abundances do not point to a Solar System origin of dust grains. The observed abundance ratios of presolar dust grains formed in SN ejecta and in AGB star outflows requires that for the ejecta from SNe the fraction of refractory elements condensed into dust is 0.15 for carbon dust and is quite small ($\sim10^{-4}$) for other dust species.Comment: 29 pages, 19 figure

Using a structural and logics systems approach to infer bHLH–DNA binding specificity determinants

Numerous efforts are underway to determine gene regulatory networks that describe physical relationships between transcription factors (TFs) and their target DNA sequences. Members of paralogous TF families typically recognize similar DNA sequences. Knowledge of the molecular determinants of protein–DNA recognition by paralogous TFs is of central importance for understanding how small differences in DNA specificities can dictate target gene selection. Previously, we determined the in vitro DNA binding specificities of 19 Caenorhabditis elegans basic helix-loop-helix (bHLH) dimers using protein binding microarrays. These TFs bind E-box (CANNTG) and E-box-like sequences. Here, we combine these data with logics, bHLH–DNA co-crystal structures and computational modeling to infer which bHLH monomer can interact with which CAN E-box half-site and we identify a critical residue in the protein that dictates this specificity. Validation experiments using mutant bHLH proteins provide support for our inferences. Our study provides insights into the mechanisms of DNA recognition by bHLH dimers as well as a blueprint for system-level studies of the DNA binding determinants of other TF families in different model organisms and humans.National Institute of General Medical Sciences (U.S.) (DK068429)National Institute of General Medical Sciences (U.S.) (HG003985)European Union (PROSPECTS HEALTH-F4-2008-201648