Comprehensive Identification of RNA-Binding Domains in Human Cells

Mammalian cells harbor more than a thousand RNA-binding proteins (RBPs), with half of these employing unknown modes of RNA binding. We developed RBDmap to determine the RNA-binding sites of native RBPs on a proteome-wide scale. We identified 1,174 binding sites within 529 HeLa cell RBPs, discovering numerous RNA-binding domains (RBDs). Catalytic centers or protein-protein interaction domains are in close relationship with RNA-binding sites, invoking possible effector roles of RNA in the control of protein function. Nearly half of the RNA-binding sites map to intrinsically disordered regions, uncovering unstructured domains as prevalent partners in protein-RNA interactions. RNA-binding sites represent hot spots for defined posttranslational modifications such as lysine acetylation and tyrosine phosphorylation, suggesting metabolic and signal-dependent regulation of RBP function. RBDs display a high degree of evolutionary conservation and incidence of Mendelian mutations, suggestive of important functional roles. RBDmap thus yields profound insights into native protein-RNA interactions in living cells

Evolution with Stochastic Fitness and Stochastic Migration

Migration between local populations plays an important role in evolution - influencing local adaptation, speciation, extinction, and the maintenance of genetic variation. Like other evolutionary mechanisms, migration is a stochastic process, involving both random and deterministic elements. Many models of evolution have incorporated migration, but these have all been based on simplifying assumptions, such as low migration rate, weak selection, or large population size. We thus have no truly general and exact mathematical description of evolution that incorporates migration.We derive an exact equation for directional evolution, essentially a stochastic Price equation with migration, that encompasses all processes, both deterministic and stochastic, contributing to directional change in an open population. Using this result, we show that increasing the variance in migration rates reduces the impact of migration relative to selection. This means that models that treat migration as a single parameter tend to be biassed - overestimating the relative impact of immigration. We further show that selection and migration interact in complex ways, one result being that a strategy for which fitness is negatively correlated with migration rates (high fitness when migration is low) will tend to increase in frequency, even if it has lower mean fitness than do other strategies. Finally, we derive an equation for the effective migration rate, which allows some of the complex stochastic processes that we identify to be incorporated into models with a single migration parameter.As has previously been shown with selection, the role of migration in evolution is determined by the entire distributions of immigration and emigration rates, not just by the mean values. The interactions of stochastic migration with stochastic selection produce evolutionary processes that are invisible to deterministic evolutionary theory

Theory of channel simulation and bounds for private communication

We review recent results on the simulation of quantum channels, the reduction of adaptive protocols (teleportation stretching), and the derivation of converse bounds for quantum and private communication, as established in PLOB [Pirandola, Laurenza, Ottaviani, Banchi, arXiv:1510.08863]. We start by introducing a general weak converse bound for private communication based on the relative entropy of entanglement. We discuss how combining this bound with channel simulation and teleportation stretching, PLOB established the two-way quantum and private capacities of several fundamental channels, including the bosonic lossy channel. We then provide a rigorous proof of the strong converse property of these bounds by adopting a correct use of the Braunstein-Kimble teleportation protocol for the simulation of bosonic Gaussian channels. This analysis provides a full justification of claims presented in the follow-up paper WTB [Wilde, Tomamichel, Berta, arXiv:1602.08898] whose upper bounds for Gaussian channels would be otherwise infinitely large. Besides clarifying contributions in the area of channel simulation and protocol reduction, we also present some generalizations of the tools to other entanglement measures and novel results on the maximum excess noise which is tolerable in quantum key distribution

Varying Herbivore Population Structure Correlates with Lack of Local Adaptation in a Geographic Variable Plant-Herbivore Interaction

Local adaptation of parasites to their hosts due to coevolution is a central prediction of many theories in evolutionary biology. However, empirical studies looking for parasite local adaptation show great variation in outcomes, and the reasons for such variation are largely unknown. In a previous study, we showed adaptive differentiation in the arctiid moth Utetheisa ornatrix to its host plant, the pyrrolizidine alkaloid-bearing legume Crotalaria pallida, at the continental scale, but found no differentiation at the regional scale. In the present study, we sampled the same sites to investigate factors that may contribute to the lack of differentiation at the regional scale. We performed field observations that show that specialist and non-specialist polyphagous herbivore incidence varies among populations at both scales. With a series of common-garden experiments we show that some plant traits that may affect herbivory (pyrrolizidine alkaloids and extrafloral nectaries) vary at the regional scale, while other traits (trichomes and nitrogen content) just vary at the continental scale. These results, combined with our previous evidence for plant population differentiation based on larval performance on fresh fruits, suggest that U. ornatrix is subjected to divergent selection even at the regional scale. Finally, with a microsatellite study we investigated population structure of U. ornatrix. We found that population structure is not stable over time: we found population differentiation at the regional scale in the first year of sampling, but not in the second year. Unstable population structure of the herbivore is the most likely cause of the lack of regional adaptation

RHOMEO Axe B, rapport final de la 1ère phase (2011-2012)

In 2000, the European Water Framework Directive introduced the concept of "good status of water bodies." Associated wetlands, participating in achieving good state must also be qualified. This is why the Water Agency RMC since 2005 reflects the establishment of a monitoring and analysis of the status of wetlands based on biological indicators. A first operational phase of two years took place in 2011-12, which aimed to develop methodologies to build the future Observatory areas wet the Rhone Mediterranean Basin, including assessment tools in good condition wetlands (indicators, protocols etc..) in the south.En 2000, la Directive européenne Cadre sur l’Eau a introduit la notion de « bon état des masses d’eau ». Les zones humides associées, participant à l’atteinte du bon état, doivent également pouvoir être qualifiées. C’est pourquoi l’Agence de l’Eau RMC réfléchit depuis 2005 à la mise en place d’un outil de suivi et d’analyse de l’état des zones humides basé sur les indicateurs biologiques. Une première phase opérationnelle de 2 ans s’est déroulée en 2011-12, qui visait à développer les méthodologies permettant de construire le futur Observatoire des zones humides du bassin Rhône-Méditerranée, et notamment les outils d’évaluation du bon état des zones humides (indicateurs, protocoles etc.) dans le sud

The positive effect of workplace accommodations on employment five years after a cancer diagnosis

International audienceBackground:Each year, almost 400,000 new individuals are diagnosed with cancer in France and nearly half of them are in the working age. The disease was found to have a negative impact on professional life, especially for the most vulnerable cancer survivors. Literature reviews have pointed out the lack of studies focusing on the evaluation of interventions. In France, workstation layouts are recommended by the French law, but not mandatory to facilitate return to work. The aim of this study was to explore the effect of having a workstation layout after a cancer diagnosis on maintenance in employment five years after diagnosis. Methods:We used the French VICAN survey carried out in 2015/2016 on living conditions five years after a cancer diagnosis. Using propensity score matching, we matched two subsamples (with and without workstation layout) to investigate the effect of workstation layout taking into account the characteristics associated with the access to these arrangements. Results:Among the 1,514 individuals aged between 18 and 54 at diagnosis and employed in a salaried job at this time, three in five (61.2%) had a workstation layout within the five years following the diagnosis: 35.5% had a position type layout, 41.5% had a schedule layout, and 49.2% had a working time layout. Among those who had a workstation layout, 89.7% were still in employment five years after diagnosis against only 77.8% of those who did not so (p.value<0,001). After matching, having a workstation layout increased maintenance in employment from 77.8% to 95.0% (Average workstation layout effect on the treated of 0.172, 95% CI = [0.114; 0.229]). Conclusions: Having a workstation layout after a cancer diagnosis strongly increases maintenance in employment of five years cancer survivors. More research is needed to better understand the differences in access to these arrangements and the related selection effect. Key messages: Workstation layout increases maintenance in employment of survivors five years after a cancer diagnosis. Therefore, it should be used more systematically to facilitate work with a chronic disease. Having a workstation layout may constitute a disadvantageous selection bias for more vulnerable workers. It can also lead to discrimination feelings

RhoMéO Axe B : rapport final

En 2009, l’Agence s’est rapprochée des gestionnaires de zones humides du Bassin Rhône-Méditerranée pour la concrétisation d’un tel outil. Suite à son démarrage en Rhône-Alpes en 2009, le programme RhoMéO s’est ensuite déployé sur l’ensemble du Bassin en collaboration étroite avec les acteurs des autres régions. Ce programme devait répondre à deux objectifs : Peut-on définir des méthodes opérationnelles et valides de suivi de l'état et des pressions des zones humides, pour fournir aux acteurs locaux des outils clefs en main ? Quels sont les indicateurs (hydrologiques, chimiques, biologiques) les plus appropriés de l’état et des fonctions des zones humides, et susceptibles d'intégrer un réseau de surveillance à l'échelle du bassin Rhône-Méditerranée