Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.

Within the ENCODE Consortium, GENCODE aimed to accurately annotate all protein-coding genes, pseudogenes, and noncoding transcribed loci in the human genome through manual curation and computational methods. Annotated transcript structures were assessed, and less well-supported loci were systematically, experimentally validated. Predicted exon-exon junctions were evaluated by RT-PCR amplification followed by highly multiplexed sequencing readout, a method we called RT-PCR-seq. Seventy-nine percent of all assessed junctions are confirmed by this evaluation procedure, demonstrating the high quality of the GENCODE gene set. RT-PCR-seq was also efficient to screen gene models predicted using the Human Body Map (HBM) RNA-seq data. We validated 73% of these predictions, thus confirming 1168 novel genes, mostly noncoding, which will further complement the GENCODE annotation. Our novel experimental validation pipeline is extremely sensitive, far more than unbiased transcriptome profiling through RNA sequencing, which is becoming the norm. For example, exon-exon junctions unique to GENCODE annotated transcripts are five times more likely to be corroborated with our targeted approach than with extensive large human transcriptome profiling. Data sets such as the HBM and ENCODE RNA-seq data fail sampling of low-expressed transcripts. Our RT-PCR-seq targeted approach also has the advantage of identifying novel exons of known genes, as we discovered unannotated exons in ~11% of assessed introns. We thus estimate that at least 18% of known loci have yet-unannotated exons. Our work demonstrates that the cataloging of all of the genic elements encoded in the human genome will necessitate a coordinated effort between unbiased and targeted approaches, like RNA-seq and RT-PCR-seq.

Side effects of genome structural changes.

The first extensive catalog of structural human variation was recently released. It showed that large stretches of genomic DNA that vary considerably in copy number were extremely abundant. Thus it is conceivable that they play a major role in functional variation. Consistently, genomic insertions and deletions were shown to contribute to phenotypic differences by modifying not only the expression levels of genes within the aneuploid segments but also of normal copy-number neighboring genes. In this report, we review the possible mechanisms behind this latter effect.

L'argumentation de Georges Pompidou face à la crise. Une analyse textuelle des allocutions des 11 et 16 mai 1968

Les 11 et 16 mai 1968, le Premier ministre français Georges Pompidou prononce deux allocutions de crise qui ont échappé à la critique. La présente étude propose de rendre compte de leur dynamique argumentative et rhétorique à partir d'une analyse textuelle des discours politiques. Il s'agit de considérer la manière dont l'orateur construit et articule différents énoncés, les ressources qu'il exploite pour s'inscrire dans son discours et donner une place à ses allocutaires ou encore les différents procédés qui lui permettent de construire et de blâmer le tiers perturbateur pour défendre la cohésion nationale. Plus généralement, l'analyse, qui respecte le caractère séquentiel des deux discours et les considère successivement, rend compte des différentes ressources langagières que Pompidou exploite pour schématiser le monde et inviter ses allocutaires au calme. Cette étude s'adresse à toute personne intéressée par l'argumentation, la rhétorique et l'analyse linguistique du discours politique.

Next-generation sequencing of experimental mouse strains.

Since the turn of the century the complete genome sequence of just one mouse strain, C57BL/6J, has been available. Knowing the sequence of this strain has enabled large-scale forward genetic screens to be performed, the creation of an almost complete set of embryonic stem (ES) cell lines with targeted alleles for protein-coding genes, and the generation of a rich catalog of mouse genomic variation. However, many experiments that use other common laboratory mouse strains have been hindered by a lack of whole-genome sequence data for these strains. The last 5 years has witnessed a revolution in DNA sequencing technologies. Recently, these technologies have been used to expand the repertoire of fully sequenced mouse genomes. In this article we review the main findings of these studies and discuss how the sequence of mouse genomes is helping pave the way from sequence to phenotype. Finally, we discuss the prospects for using de novo assembly techniques to obtain high-quality assembled genome sequences of these laboratory mouse strains, and what advances in sequencing technologies may be required to achieve this goal.

Workgroup report: incorporating in vitro alternative methods for developmental neurotoxicity into international hazard and risk assessment strategies.

This is the report of the first workshop on Incorporating In Vitro Alternative Methods for Developmental Neurotoxicity (DNT) Testing into International Hazard and Risk Assessment Strategies, held in Ispra, Italy, on 19-21 April 2005. The workshop was hosted by the European Centre for the Validation of Alternative Methods (ECVAM) and jointly organized by ECVAM, the European Chemical Industry Council, and the Johns Hopkins University Center for Alternatives to Animal Testing. The primary aim of the workshop was to identify and catalog potential methods that could be used to assess how data from in vitro alternative methods could help to predict and identify DNT hazards. Working groups focused on two different aspects: a) details on the science available in the field of DNT, including discussions on the models available to capture the critical DNT mechanisms and processes, and b) policy and strategy aspects to assess the integration of alternative methods in a regulatory framework. This report summarizes these discussions and details the recommendations and priorities for future work.

Anxiety and severity of illicit substance use in adolescence: Evaluating the mediating role of perceived coping styles

The purpose of this study was to examine whether coping styles (Active coping, Internal coping and Withdrawal coping) mediated the relationships between anxiety and severity of illicit substance use among a sample of 110 Swiss adolescents ages 12-19 (M=16.3, SD=1.66). The current study tested two competing models of anxiety on severity of illicit substance use. In the first model, we tested the direct effect of trait anxiety (STAI-Y anxiety score) on severity of illicit substance use (ADAD drug use severity rating), while in the second models we examined the mediating role of coping styles in the link between trait anxiety and severity of illicit substance use. Path models indicated that the associations between trait anxiety and severity of illicit substance use are partially mediated by active and withdrawal coping styles. Limitations of the findings and implications for prevention of substance use in adolescence are discussed.

Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes.

The recent availability of the chicken genome sequence poses the question of whether there are human protein-coding genes conserved in chicken that are currently not included in the human gene catalog. Here, we show, using comparative gene finding followed by experimental verification of exon pairs by RT-PCR, that the addition to the multi-exonic subset of this catalog could be as little as 0.2%, suggesting that we may be closing in on the human gene set. Our protocol, however, has two shortcomings: (i) the bioinformatic screening of the predicted genes, applied to filter out false positives, cannot handle intronless genes; and (ii) the experimental verification could fail to identify expression at a specific developmental time. This highlights the importance of developing methods that could provide a reliable estimate of the number of these two types of genes.

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In this book, the authors present current research in the study of health behavior. Topics discussed include the role of fitness classes in the development of eating disorders among women; first year university female students' lifestyles and attitudes towards health risk and preventive measures; an examination of the extensive cross-sectional and longitudinal evidence that links traditional screen-time to pediatric obesity; gender issue implications on health; and health promotion messages used to inform the population about important health issues and to motivate individuals to adopt healthy behaviors and avoid unhealthy behaviors. (Imprint: Novinka)