Digital expression profiling of novel diatom transcripts provides insight into their biological functions

Background: Diatoms represent the predominant group of eukaryotic phytoplankton in the oceans and are responsible for around 20% of global photosynthesis. Two whole genome sequences are now available. Notwithstanding, our knowledge of diatom biology remains limited because only around half of their genes can be ascribed a function based onhomology-based methods. High throughput tools are needed, therefore, to associate functions with diatom-specific genes. Results: We have performed a systematic analysis of 130,000 ESTs derived from Phaeodactylum tricornutum cells grown in 16 different conditions. These include different sources of nitrogen, different concentrations of carbon dioxide, silicate and iron, and abiotic stresses such as low temperature and low salinity. Based on unbiased statistical methods, we have catalogued transcripts with similar expression profiles and identified transcripts differentially expressed in response to specific treatments. Functional annotation of these transcripts provides insights into expression patterns of genes involved in various metabolic and regulatory pathways and into the roles of novel genes with unknown functions. Specific growth conditions could be associated with enhanced gene diversity, known gene product functions, and over-representation of novel transcripts. Comparative analysis of data from the other sequenced diatom, Thalassiosira pseudonana, helped identify several unique diatom genes that are specifically regulated under particular conditions, thus facilitating studies of gene function, genome annotation and the molecular basis of species diversity. Conclusions: The digital gene expression database represents a new resource for identifying candidate diatom-specific genes involved in processes of major ecological relevance

Addressing the Childhood Asthma Crisis in Harlem: The Harlem Children’s Zone Asthma Initiative

Objectives. We determined the prevalence of asthma and estimated baseline asthma symptoms and asthma management strategies among children aged 0–12 years in Central Harlem. Methods. The Harlem Children’s Zone Asthma Initiative is a longitudinal, community-based intervention designed for poor children with asthma. Children aged 0–12 years who live or go to school in the Harlem Children’s Zone Project or who participate in any Harlem Children’s Zone, Inc, program were screened for asthma. Children with asthma or asthma-like symptoms were invited to participate in an intensive intervention. Results. Of the 1982 children currently screened, 28.5% have been told by a doctor or nurse that they have asthma, and 30.3% have asthma or asthma-like symptoms. To date, 229 children are enrolled in the Harlem Children’s Zone Asthma Initiative; at baseline, 24.0% had missed school in the last 14 days because of asthma. Conclusion. The high prevalence of asthma among children in the Harlem Children’s Zone Project is consistent with reports from other poor urban communities. Intensive efforts are under way to reduce children’s asthma symptoms and improve their asthma management strategies

Toward a smoke-free Harlem: engaging families, agencies, and community-based programs

The aim of this collaborative public health study was to engage families, agencies, and programs in reducing secondhand smoke exposure in Central Harlem, New York City. Baseline interviews (n=657) and focus groups (n=4) were conducted with adult members of households with children who had asthma and asthma-like symptoms in the Harlem Children's Zone Asthma Initiative. The interviews concerned the prevalence and determinants of exposure of enrolled children to secondhand smoke. Key findings were that participants: (1) were generally aware of the hazards of secondhand smoke; (2) used strategies to reduce exposure to secondhand smoke in their homes; (3) believed that outdoor pollutants are sometimes just as bad for the health of their children as secondhand smoke; and (4) used smoking to provide stress relief and help diffuse otherwise volatile situations in their homes. The Harlem Smoke-Free Home Campaign was launched in October 2007 based in part on these findings

Finishing the euchromatic sequence of the human genome

International audienc

Complete DNA sequence of Kuraishia capsulata illustrates novel genomic features among budding yeasts (Saccharomycotina)

The numerous yeast genome sequences presently available provide a rich source of information for functional as well as evolutionary genomics but unequally cover the large phylogenetic diversity of extant yeasts. We present here the complete sequence of the nuclear genome of the haploid-type strain of Kuraishia capsulata (CBS1993(T)), a nitrate-assimilating Saccharomycetales of uncertain taxonomy, isolated from tunnels of insect larvae underneath coniferous barks and characterized by its copious production of extracellular polysaccharides. The sequence is composed of seven scaffolds, one per chromosome, totaling 11.4 Mb and containing 6,029 protein-coding genes, 13.5% of which being interrupted by introns. This GC-rich yeast genome (45.7%) appears phylogenetically related with the few other nitrate-assimilating yeasts sequenced so far, Ogataea polymorpha, O. parapolymorpha, and Dekkera bruxellensis, with which it shares a very reduced number of tRNA genes, a novel tRNA sparing strategy, and a common nitrate assimilation cluster, three specific features to this group of yeasts. Centromeres were recognized in GC-poor troughs of each scaffold. The strain bears MAT alpha genes at a single MAT locus and presents a significant degree of conservation with Saccharomyces cerevisiae genes, suggesting that it can perform sexual cycles in nature, although genes involved in meiosis were not all recognized. The complete absence of conservation of synteny between K. capsulata and any other yeast genome described so far, including the three other nitrate-assimilating species, validates the interest of this species for long-range evolutionary genomic studies among Saccharomycotina yeasts.Sequencing was supported by CEA/Genoscope and performed/nusing HPC resources from GENCI-TGCC (Grants 2012076389 and 2013036389). Data analysis and experimental aspects of the work were supported in part 1) by contract DYGEVO from ANR (2011SVSE6) to B.D., 2) by the/nSpanish ministry of Economy and Competitiveness(BIO2012-37161) and the European Research Council (Grant Agreement n ERC-2012-StG-310325) to T.G., and 3) by the/nQatar National Research Fund grant (NPRP 5-298-3-086) to T.B. and T.G

Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate

International audienceGenomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on the level of genome plasticity. It also illuminates issues as fundamental as the mechanisms of intron gain

Data from: Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate

Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on the level of genome plasticity. It also illuminates issues as fundamental as the mechanisms of intron gain