High-quality SNPs from genic regions highlight introgression patterns among European white oaks (Quercus petraea and Q. robur)

International audienceIn the post-genomics era, non-model species like most Fagaceae still lack operational diversity resources for population genomics studies. Sequence data were produced from over 800 gene fragments covering ~530 kb across the genic partition of European oaks, in a discovery panel of 25 individuals from western and central Europe (11 Quercus petraea, 13 Q. robur, one Q. ilex as an outgroup). Regions targeted represented broad functional categories potentially involved in species ecological preferences, and a random set of genes. Using a high-quality dedicated pipeline, we provide a detailed characterization of these genic regions, which included over 14500 polymorphisms, with ~12500 SNPs −218 being triallelic-, over 1500 insertion-deletions, and ~200 novel di- and tri-nucleotide SSR loci. This catalog also provides various summary statistics within and among species, gene ontology information, and standard formats to assist loci choice for genotyping projects. The distribution of nucleotide diversity (θπ) and differentiation (FST) across genic regions are also described for the first time in those species, with a mean n θπ close to ~0.0049 in Q. petraea and to ~0.0045 in Q. robur across random regions, and a mean FST ~0.13 across SNPs. The magnitude of diversity across genes is within the range estimated for long-term perennial outcrossers, and can be considered relatively high in the plant kingdom, with an estimate across the genome of 41 to 51 million SNPs expected in both species. Individuals with typical species morphology were more easily assigned to their corresponding genetic cluster for Q. robur than for Q. petraea, revealing higher or more recent introgression in Q. petraea and a stronger species integration in Q. robur in this particular discovery panel. We also observed robust patterns of a slightly but significantly higher diversity in Q. petraea, across a random gene set and in the abiotic stress functional category, and a heterogeneous landscape of both diversity and differentiation. To explain these patterns, we discuss an alternative and non-exclusive hypothesis of stronger selective constraints in Q. robur, the most pioneering species in oak forest stand dynamics, additionally to the recognized and documented introgression history in both species despite their strong reproductive barriers. The quality of the data provided here and their representativity in terms of species genomic diversity make them useful for possible applications in medium-scale landscape and molecular ecology projects. Moreover, they can serve as reference resources for validation purposes in larger-scale resequencing projects. This type of project is preferentially recommended in oaks in contrast to SNP array development, given the large nucleotide variation and the low levels of linkage disequilibrium revealed

A chemical survey of exoplanets with ARIEL

Thousands of exoplanets have now been discovered with a huge range of masses, sizes and orbits: from rocky Earth-like planets to large gas giants grazing the surface of their host star. However, the essential nature of these exoplanets remains largely mysterious: there is no known, discernible pattern linking the presence, size, or orbital parameters of a planet to the nature of its parent star. We have little idea whether the chemistry of a planet is linked to its formation environment, or whether the type of host star drives the physics and chemistry of the planet’s birth, and evolution. ARIEL was conceived to observe a large number (~1000) of transiting planets for statistical understanding, including gas giants, Neptunes, super-Earths and Earth-size planets around a range of host star types using transit spectroscopy in the 1.25–7.8 μm spectral range and multiple narrow-band photometry in the optical. ARIEL will focus on warm and hot planets to take advantage of their well-mixed atmospheres which should show minimal condensation and sequestration of high-Z materials compared to their colder Solar System siblings. Said warm and hot atmospheres are expected to be more representative of the planetary bulk composition. Observations of these warm/hot exoplanets, and in particular of their elemental composition (especially C, O, N, S, Si), will allow the understanding of the early stages of planetary and atmospheric formation during the nebular phase and the following few million years. ARIEL will thus provide a representative picture of the chemical nature of the exoplanets and relate this directly to the type and chemical environment of the host star. ARIEL is designed as a dedicated survey mission for combined-light spectroscopy, capable of observing a large and well-defined planet sample within its 4-year mission lifetime. Transit, eclipse and phase-curve spectroscopy methods, whereby the signal from the star and planet are differentiated using knowledge of the planetary ephemerides, allow us to measure atmospheric signals from the planet at levels of 10–100 part per million (ppm) relative to the star and, given the bright nature of targets, also allows more sophisticated techniques, such as eclipse mapping, to give a deeper insight into the nature of the atmosphere. These types of observations require a stable payload and satellite platform with broad, instantaneous wavelength coverage to detect many molecular species, probe the thermal structure, identify clouds and monitor the stellar activity. The wavelength range proposed covers all the expected major atmospheric gases from e.g. H2O, CO2, CH4 NH3, HCN, H2S through to the more exotic metallic compounds, such as TiO, VO, and condensed species. Simulations of ARIEL performance in conducting exoplanet surveys have been performed – using conservative estimates of mission performance and a full model of all significant noise sources in the measurement – using a list of potential ARIEL targets that incorporates the latest available exoplanet statistics. The conclusion at the end of the Phase A study, is that ARIEL – in line with the stated mission objectives – will be able to observe about 1000 exoplanets depending on the details of the adopted survey strategy, thus confirming the feasibility of the main science objectives.Peer reviewedFinal Published versio

Modes ventilatoires et réglages en ventilation non invasive: retentissement sur les évènements respiratoires et implications dans leur identification

Comparé au mode invasif, la ventilation non invasive (VNI) a deux caractéristiques : sa nature non hermétique et le fait que le couple poumon–ventilateur ne peut pas être considéré comme un modèle à un seul compartiment de par l’interposition de la voie aérienne supérieure (VAS). À l’initiation de la VNI, les réglages du ventilateur sont déterminés sur la clinique et les variations de la gazométrie diurne. Cependant la VNI s’applique principalement pendant le sommeil, et une évaluation nocturne est nécessaire pour estimer la « bonne entente » patient–ventilateur. Le monitorage le plus avéré est apporté par les courbes de débit et pression au masque. Cependant, la VNI permet une large gamme de réglages. Il est nécessaire de les connaître pour comprendre l’interaction patient–ventilateur. Le mode ventilatoire, le type de déclenchement, la pente, l’utilisation d’une pression positive expiratoire et le type d’exhalation mais aussi les performances du ventilateur peuvent avoir des retentissements. Des fuites et des variations de résistance des VAS peuvent aussi modifier ces courbes. Cet article discute du matériel disponible pour la VNI, analyse l’effet des modes ventilatoires, réglages et systèmes d’exhalation sur les tracés. Son but : donner les bases nécessaires pour comprendre leur impact sur le monitorage de la VNI.Compared with invasive ventilation, non-invasive ventilation (NIV) has two unique characteristics: its non-hermetic nature and the fact that the ventilator-lung assembly cannot be considered as a single-compartment model because of the presence of variable resistance represented by the upper airways. When NIV is initiated, the ventilator settings are determined empirically based on clinical evaluation and blood gas variations. However, NIV is predominantly applied during sleep. Consequently, to assess overnight patient-machine "agreement" and efficacy of ventilation, more specific and sophisticated monitoring is needed. The effectiveness of NIV might therefore be more correctly assessed by sleep studies than by daytime assessment. The simplest monitoring can be done from flow and pressure curves from the mask or the ventilator circuit. Examination of these tracings can give useful information to evaluate if the settings chosen by the operator were the right ones for that patient. However, as NIV allows a large range of ventilatory parameters and settings, it is mandatory to have information about this to better understand patient-ventilator interaction. Ventilatory modality, mode of triggering, pressurization slope, use or not of positive end expiratory pressure and type of exhalation as well as ventilator performances may all have physiological consequences. Leaks and upper airway resistance variations may, in turn, modify these patterns. This article discusses the equipment available for NIV, analyses the effect of different ventilator modes and settings and of exhalation and connecting circuits on ventilatory traces and gives the background necessary to understand their impact on nocturnal monitoring of NIV

Dependence of catalytic activity on driving force in solution assays and protein film voltammetry: insights from the comparison of nitrate reductase mutants.

International audienc

The quest of a functional substrate access tunnel in FeFe Hydrogenase

International audienc

CO disrupts the reduced H-cluster of FeFe Hydrogenase. A combined DFT and PFV study.

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Nouvelle génération de CMO recyclables à partir de matières premières de recyclage : vers une économie circulaire (RECYCOMP)

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Interferometric Space Missions for Exoplanet Science: Legacy of Darwin/TPF

peer reviewedDarwin/TPF is a project of an infrared space-based interferometer designed to directly detect and characterize terrestrial exoplanets around nearby stars. Unlike spectrophotometric instruments observing planetary transits, an interferometer does not rely on any particular geometric constraints and could characterize exoplanets with any orbital configuration around nearby stars. The idea to use an infrared nulling interferometer to characterize exoplanets dates back to Bracewell (Nature 274:780, 1978) and was extensively studied in the 1990s and 2000s by both ESA and NASA. The project focuses on the mid-infrared regime (5-20 μm), which provides access to key features of exoplanets, such as their size, their temperature, the presence of an atmosphere, their climate structure, as well as the presence of important atmospheric molecules such as H[SUB]2[/SUB]O, CO[SUB]2[/SUB], O[SUB]3[/SUB], NH[SUB]3[/SUB], and CH[SUB]4[/SUB]. This wavelength regime also provides a favorable planet/star contrast to detect the thermal emission of temperate (˜300 K) exoplanets (10[SUP]7[/SUP] vs 10[SUP]10[/SUP] in the visible). In this chapter, we first review the scientific rationale of a mid-infrared nulling interferometer and present how it would provide an essential context for interpreting detections of possible biosignatures. Then, we present the main technological challenges identified during the ESA and NASA studies, and how they have progressed over the last 10 years. Finally, we discuss which technologies remain to be developed before flying such an instrument and possible ways to make D arwin/TPF a reality in the midterm future