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International audience; Brassinosteroids (BRs) are steroid hormones that coordinate fundamental developmental programs in plants. In this study we show that in addition to the well established roles of BRs in regulating cell elongation and cell division events, BRs also govern cell fate decisions during stomata development in Arabidopsis thaliana. In wild-type A. thaliana, stomatal distribution follows the one-cell spacing rule; that is, adjacent stomata are spaced by at least one intervening pavement cell. This rule is interrupted in BR-deficient and BR signaling-deficient A. thaliana mutants, resulting in clustered stomata. We demonstrate that BIN2 and its homologues, GSK3/Shaggy-like kinases involved in BR signaling, can phosphorylate the MAPK kinases MKK4 and MKK5, which are members of the MAPK module YODA-MKK4/5-MPK3/6 that controls stomata development and patterning. BIN2 phosphorylates a GSK3/Shaggy-like kinase recognition motif in MKK4, which reduces MKK4 activity against its substrate MPK6 in vitro. In vivo we show that MKK4andMKK5act downstream of BR signaling because their overexpression rescued stomata patterning defects in BR-deficient plants. A model is proposed in which GSK3-mediated phosphorylation of MKK4 and MKK5 enables for a dynamic integration of endogenous or environmental cues signaled by BRs into cell fate decisions governed by the YODA-MKK4/5-MPK3/6 module.

International audience; In 2005, Demange and Paschos proposed in [M. Demange, V.Th. Paschos, On-line vertex-covering, Theoret. Comput. Sci. 332 (2005) 83-108] an online algorithm (noted LR here) for the classical vertex cover problem. They shown that, for any graph of maximum degree Δ, LR constructs a vertex cover whose size is at most Δ times the optimal one (this bound is tight in the worst case). Very recently, two of the present authors have shown in [F. Delbot, C. Laforest, A better list heuristic for vertex cover, Inform. Process. Lett. 107 (2008) 125-127] that LR has interesting properties (it is a good "list algorithm" and it can easily be distributed). In addition, LR has good experimental behavior in spite of its Δ approximation (or competitive) ratio and the fact that it can be executed without the knowledge of the full instance at the beginning. In this paper we analyze it deeper and we show that LR has good "average" performances: we prove that its mean approximation ratio is strictly less than 2 for any graph and is equal to 1+e−2≈1.13 in paths. LR is then a very interesting algorithm for constructing small vertex covers, despite its bad worst case behavior.

It is known since Kellerer (1972) that for any peacock process there exist mar-tingales with the same marginal laws. Nevertheless, there is no general method for finding such martingales that yields diffusions. Indeed, Kellerer's proof is not constructive: finding the dynamics of processes associated to a given peacock is not trivial in general. In this paper we are interested in the uniform peacock that is, the peacock with uniform law at all times on a generic time-varying support [a(t), b(t)]. We derive explicitly the corresponding Stochastic Differential Equations (SDEs) and prove that, under certain conditions on the boundaries a(t) and b(t), they admit a unique strong solution yielding the relevant diffusion process. We discuss the relationship between our result and the previous derivation of diffusion processes associated to square-root and linear time-boundaries, emphasizing the cases where our approach adds strong uniqueness, and study the local time and activity of the solution processes. We then study the peacock with uniform law at all times on a constant support [−1, 1] and derive the SDE of an associated mean-reverting diffusion process with uniform margins that is not a martingale. For the related SDE we prove existence of a solution in [0, T ]. Finally, we provide a numerical case study showing that these processes have the desired uniform behaviour. These results may be used to model random probabilities, random recovery rates or random correlations.

International audience; Amongst iron-oxidizing bacteria playing a key role in the natural attenuation of arsenic in acid mine drainages (AMDs), members of the Ferrovum genus were identified in mine effluent or water treatment plants, and were shown to dominate biogenic precipitates in field pilot experiments. In order to address the question of the in situ activity of the uncultivated Ferrovum sp. CARN8 strain in the Carnoul es AMD, we assembled its genome using metagenomic and metatranscriptomic sequences and we determined standardized expression values for protein-encoding genes. Our results showed that this microorganism was indeed metabolically active and allowed us to sketch out its metabolic activity in its natural environment. Expression of genes related to the respiratory chain and carbon fixation suggests aerobic energy production coupled to ferrous iron oxidation and chemolithoautotrophic growth. Notwithstanding the presence of nitrogenase genes in its genome, expression data also indicated that Ferrovum sp. CARN8 relied on ammonium import rather than nitrogen fixation. The expression of flagellum and chemotaxis genes hints that at least a proportion of this strain population was motile. Finally, apart from some genes related to metal resistance showing surprisingly low expression values, genes involved in stress response were well expressed as expected in AMDs.

Some plants are able to grow in nitrogen-poor soils because they can establish symbiosis with rhizobia or frankia (actinobacteria) bacteria, which are able to reduce the non-limiting atmospheric gaseous nitrogen (N2) to NH3 to the benefit of their host. The capacity to establish this symbiosis, also called root nodule symbiosis (RNS), is confined to the Rosid I clade, including actinorhizal plants, Parasponia and legumes [1]. RNS has been extensively studied using legume–rhizobia symbiosis as a model, and generally requires specific signaling between both organisms, with excretion of flavonoids in the rhizosphere by the plant and production of specific lipo-chitooligosaccharides (LCOs or Nod factors for the RNS) by the rhizobia that are recognized by plant-specific receptors belonging to the LysM kinase receptor family (LysM-RLK) [2]. Genetic studies have highlighted the central role of the Nod factor-dependent signaling in most of the legume–rhizobia interactions, even if variations around this theme exist [3]. RNS requires organogenesis, and leads to the formation of the nodule organ (generally on the root), which hosts the symbiotic bacteria and in which nitrogen reduction takes place. Actinorhizal nodules present a single central vascular bundle that makes them resemble modified lateral roots [4,5]. Legume nodules are divided in two main types, depending on the presence or absence of an apical meristem (indeterminate versus determinate nodules), and have peripheral vascular tissues surrounding the central infected tissues.

International audience; Salinity severely hampers crop productivity worldwide and plant growth promoting bacteria could serve as a sustainable solution to improve plant growth under salt stress. However, the molecular mechanisms underlying salt stress tolerance promotion by beneficial bacteria remain unclear. In this work, six bacterial isolates from four different desert plant species were screened for their biochemical plant growth promoting traits and salinity stress tolerance promotion of the unknown host plant Arabidopsis thaliana. Five of the isolates induced variable root phenotypes but could all increase plant shoot and root weight under salinity stress. Inoculation of Arabidopsis with five isolates under salinity stress resulted in tissue-specific transcriptional changes of ion transporters and reduced Na+/K+ shoot ratios. The work provides first insights into the possible mechanisms and the commonality by which phylogenetically diverse bacteria from different desert plants induce salinity stress tolerance in Arabidopsis. The bacterial isolates provide new tools for studying abiotic stress tolerance mechanisms in plants and a promising agricultural solution for increasing crop yields in semi-arid regions.

International audience; Microbial communities from cheeses contribute to the development of typical organoleptic properties. Metatranscriptomic analyses can be used to provide a global picture of the functioning of these communities. Our objective was to evaluate the efficiency of RNA extraction from various cheese types and to evaluate mRNA enrichment procedures for metatranscriptomic analyses. For the 32 tested cheese brands, corresponding to five cheese types, the extraction yield varied from 1 µg to 363 µg RNA per gram of cheese and, overall, the yield was lower for fresh cheeses and for the core of pressed cooked cheeses than for the other cheese types. Pressed cooked cheeses also had a lower RNA integrity than the other cheese types. For total RNA extracts from four cheeses, approximately 99% of the sequencing reads corresponded to ribosomal RNA, and mRNA enrichment by RiboPOOL and FastSelect kits decreased this percentage to a range of 75 to 97% and of 53 to 76%, respectively. Comparison of RNA libraries after mRNA enrichment with libraries of undepleted total RNA showed that the FastSelect mRNA enrichment had a lower impact on the gene expression profiles of five target cheese species than the riboPOOL kit and the oligo (dT) selection method. The procedures that we describe in the present study may be useful for metatranscriptomic analysis of various cheese types.

Several statistical approaches based on reproducing kernels have been proposed to detect abrupt changes arising in the full distribution of the observations and not only in the mean or variance. Some of these approaches enjoy good statistical properties (oracle inequality, consistency). Nonetheless, they have a high computational cost both in terms of time and memory. This makes their application difficult even for small and medium sample sizes ( n 1 0 4 ). This computational issue is addressed by first describing a new efficient procedure for kernel multiple change-point detection with an improved worst-case complexity that is quadratic in time and linear in space. It is based on an exact optimization algorithm and deals with medium size signals (up to n ≈ 1 0 5 ). Second, a faster procedure (based on an approximate optimization algorithm) is described. It relies on a low-rank approximation to the Gram matrix and is linear in time and space. The resulting procedure can be applied to large-scale signals ( n ≥ 1 0 6 ). These two procedures (based on the exact or approximate optimization algorithms) have been implemented in R and C for various kernels. The computational and statistical performances of these new algorithms have been assessed through empirical experiments. The runtime of the new algorithms is observed to be faster than that of other considered procedures. Finally, simulations confirmed the higher statistical accuracy of kernel-based approaches to detect changes that are not only in the mean. These simulations also illustrate the flexibility of kernel-based approaches to analyze complex biological profiles made of DNA copy number and allele B frequencies.

International audience; Viruses are obligate parasites that replicate intracellularly in many living organisms, including plants. Consequently, no chemicals are available that target only the virus without impacting host cells or vector organisms. The use of natural resistant varieties appears as the most reliable control strategy and remains the best and cheapest option in managing virus diseases, especially in the current ecological context of preserving biodiversity and environment in which the use of phytosanitary products becomes limited. Common bean is a grain legume cultivated mainly in Africa and Central-South America. Virus diseases of common bean have been extensively studied both by breeders to identify natural resistance genes in existing germplasms and by pathologists to understand the molecular bases of plant-virus interactions. Here we present a critical review in which we synthesize previous and recent information concerning 1) main viruses causing diseases in common bean, 2) genetic resistance to viruses in common bean, 3) the different resistance phenotypes observed and more particularly the effect of temperature, 4) the molecular bases of resistance genes to viruses in common bean, and 5) future prospects using transgenic-engineered resistant lines.

Bacteria rely on allosteric transcription factors (aTFs) to sense a wide range of chemicals. The variety of effectors has contributed in making aTFs the most used input system in synthetic biological circuits. Considering their enabling role in biotechnology, an important question concerns the size of the chemical space that can potentially be detected by these biosensors. From digging into the ever changing repertoire of natural regulatory circuits, to advances in aTF engineering, we review here different strategies that are pushing the boundaries of this chemical space. We also review natural and synthetic cases of indirect sensing, where aTFs work in combination with metabolism to enable detection of new molecules.

International audience; This work presents the synthesis and the characterization of hybrid material thin films obtained by the combination of two processes. The electrochemical grafting of organic layers made of carboxyphenyl moieties is carried out from the reduction of a diazonium salt on tin dioxide (SnO2) thin films previously deposited on Si substrates by metal organic chemical vapor deposition (MOCVD). Since the MOCVD experimental parameters impact the crystal growth of the SnO2 layer (i.e. its morphology and its texturation), various electrochemical grafting models can occur, producing different hybrid materials. In order to evidence the efficiency of the electrochemical grafting of the carboxyphenyl moieties, X-ray Photoelectron Spectroscopy (XPS) is used to characterize the first nanometers in depth of the synthesized hybrid material layer. Then three electrochemical grafting models are proposed.

The aim of this article is to propose a novel kernel estimator of the baseline function in a general high-dimensional Cox model, for which we derive non-asymptotic rates of convergence. To construct our estimator, we first estimate the regression parameter in the Cox model via a Lasso procedure. We then plug this estimator into the classical kernel estimator of the baseline function, obtained by smoothing the so-called Breslow estimator of the cumulative baseline function. We propose and study an adaptive procedure for selecting the bandwidth, in the spirit of Gold-enshluger and Lepski (2011). We state non-asymptotic oracle inequalities for the final estimator, which reveal the reduction of the rates of convergence when the dimension of the covariates grows.

This paper studies the corrosion behaviour of non-sensitized stainless steels in oxidizing environments, where they can suffer intergranular corrosion. In this case, corrosion rate estimated by gravimetric measurement is not constant as a function of time. This paper proposes a quantitative modelling of the IGC kinetics. Two models were developed: the first one is based on the geometrical simulation of the groove penetration; the second one uses a semi-empirical approach based on the typical shape of the corrosion kinetics. Both models reproduce successfully the experimental corrosion kinetics observed for a AISI 310L stainless steel corroded in nitric acid containing oxidizing ions.

International audience; We report in this paper an original way to covalently bind the macrocyclic ligand, 1,4,8,11-tetraazacyclotetradecane (cyclam), through diazonium salt chemistry, on the surface of carbon screen-printed electrodes (SPEs). The in situ synthesis of the diazonium salt obtained from the amine precursor derived from the cyclam and its electrografting are described. X-ray Photoelectron Spectroscopy was used to characterize this functionalized surface. Owing to the strong cyclam–Cu(II) affinity, the so called SPE-cyclam can be used as electrochemical sensors for Cu(II) determination at trace levels. The influence of electroanalysis parameters such as the accumulation time and the pH of the medium were investigated. An interference study was carried out with numerous metallic cations and few interference was found for Cu(II) quantification. The described method provided a limit of detection and a limit of quantification of 1.3×10−8M and 4.0×10−8M, respectively. Interference study and performances show that SPE-cyclam could be considered as efficient sensors for environmental analysis.

Modelling heterogeneity in large datasets of counts under the presence of covariates demands advanced clustering methods. Towards this direction a mixture of Poisson regressions is proposed. Conditionally on the covariates and a cluster, the multivariate distribution is a product of independent Poisson distributions. A variety of different parameterizations is taken into account for the slope of the conditional log-means. Also considered is the case of partitioning the response variables into sets of replicates sharing the same conditional log-mean up to an additive constant. Model parameters are estimated via an Expectation Maximization algorithm with Newton Raphson steps. In particular, an efficient initialization is introduced in order to improve the inference: a splitting scheme is combined with a Small-EM strategy. Simulations and application on two real high-throughput sequencing datasets highlight improvements of parameter estimations. The proposed methodology is implemented in the R package poisson glm. mix, available on CRAN.

International audience; Electrodeposited birnessite thin films have remarkable properties for spontaneous degradation of organic pollutants until mineralization via a complex mechanism of charge transfer reactions. But, birnessite may be transformed into passivated material by reaction with Mn(II) species generated during the reduction of birnessite due to oxidation of organic pollutants. Such modification could imply a possible inhibition of the degradation process, a depreciated condition for future applications. This paper focuses on the determination of the real robustness of electrodeposited birnessite thin films and their quality for innovative wastewater treatment. Systematical studies were performed with solutions containing different Mn(II) concentrations in presence and in absence of oxygen to have unfavorable conditions. Samples were characterized at macroscopic scales (SEM and XRD) in addition to a focused study on the chemical modification at the extreme near surface by XPS. Open circuit potential (OCP) was also followed to complete the study. Similar characterizations were performed after interaction with organic pollutants solutions. As a result, nature and structure of the bulk and the near surface of birnessite stay unchanged after long times even in absence of oxygen or in presence of organic pollutants at high concentrations, proving their very good robustness and real interests for future applications.

Summary Bacterial lipo-chitooligosaccharides (LCOs) are key mediators of the nitrogen-fixing root nodule symbiosis (RNS) in legumes. The isolation of LCOs from arbuscular mycorrhizal fungi suggested that LCOs are also signaling molecules in arbuscular mycorrhiza (AM). However, the corresponding plant receptors have remained uncharacterized. Here we show that petunia and tomato mutants in the LysM receptor-like kinases LYK10 are impaired in AM formation. Petunia and tomato LYK10 proteins have a high affinity for LCOs (Kd in the nM range) comparable to that previously reported for a legume LCO receptor essential for the RNS. Interestingly, the tomato and petunia LYK10 promoters, when introduced into a legume, were active in nodules similarly to the promoter of the legume orthologous gene. Moreover, tomato and petunia LYK10 coding sequences restored nodulation in legumes mutated in their orthologs. This combination of genetic and biochemical data clearly pinpoints Solanaceous LYK10 as part of an ancestral LCO perception system involved in AM establishment, which has been directly recruited during evolution of the RNS in legumes., Highlights • Mutants in Solanaceaous LysM receptors LYK10 are impaired in arbuscular mycorrhiza • LYK10 proteins have a high affinity for lipo-chitooligosaccharidic signal molecules • LYK10 promoter is expressed in arbuscule-containing cells in tomato roots • Solanaceaous LYK10 can restore nodulation in legumes mutated in their orthologs, Soil rhizobial bacteria and arbuscular mycorrhizal (AM) fungi produce lipo-chitooligosaccharidic (LCO) signal molecules. Girardin et al. show that plant LCO receptors are involved in establishment of the ancient AM symbiosis and have been recruited during evolution for establishment of the nitrogen-fixing root nodule symbiosis with rhizobia.

International audience; This study investigates the oxidative dissolution of Fe monosulfide (FeS) as a function of sample pretreatment. The dissolution rates of FeS (troilite) either untreated or pretreated with water (FeS#1) or 1 M HCl (FeS#2) were determined at 25 °C and initial pH 2.0 in aerated solutions. Fourier Transform Infrared Spectroscopy and Differential Scanning Calorimetry analyses show that, compared to the initial sample (FeS#0), pretreated FeS samples contain an excess of sulfur and ferric oxyhydroxides which form external amorphous layers. For FeS#1, the external layer is rich in ferric oxyhydroxides. A diminution of dissolved amount of FeS#2 and FeS#1 compared to FeS#0 occurs after only 3 h of reaction. This dissolution inhibition was also confirmed by electrochemical measurements (potentiodynamic polarization measurements and Electrochemical Impedance Spectroscopy).

The development and application of biotechnology-based strategies has had a great socio-economical impact and is likely to play a crucial role in the foundation of more sustainable and efficient industrial processes. Within biotechnology, metabolic engineering aims at the directed improvement of cellular properties, often with the goal of synthesizing a target chemical compound. The use of computer-aided design (CAD) tools, along with the continuously emerging advanced genetic engineering techniques have allowed metabolic engineering to broaden and streamline the process of heterologous compound-production. In this work, we review the CAD tools available for metabolic engineering with an emphasis, on retrosynthesis methodologies. Recent advances in genetic engineering strategies for pathway implementation and optimization are also reviewed as well as a range of bionalytical tools to validate in silico predictions. A case study applying retrosynthesis is presented as an experimental verification of the output from Retropath, the first complete automated computational pipeline applicable to metabolic engineering. Applying this CAD pipeline, together with genetic reassembly and optimization of culture conditions led to improved production of the plant flavonoid pinocembrin. Coupling CAD tools with advanced genetic engineering strategies and bioprocess optimization is crucial for enhanced product yields and will be of great value for the development of non-natural products through sustainable biotechnological processes.

A high-throughput screening for the identification of nitrilases demonstrating activity towards alpha-aminonitriles is reported. A LC–MS assay giving access to both conversion and enantiospecificity was developed. 588 candidate enzymes were screened as cell lysates against six alpha-aminonitriles in 96-well microplates. The candidate enzymes were selected following two criteria, their sequence identity with a set of known nitrilases or their phylogenetic position among the nitrilase superfamily. Five enzymes were identified and found to hydrolyse alpha-aminonitrile into the corresponding alpha-aminoacid. The substrate range was found to be very narrow as only two different alpha-aminonitriles, 2-aminovaleronitrile and 2-amino-2-phenylacetonitrile, were found to be substrates. The biocatalytic capabilities of three enzymes were further investigated and the best result was obtained with an enzyme from Burkholderia xenovorans catalysing the enantiospecific hydrolysis of 2-aminovaleronitrile into (S)-norvaline with excellent conversion and enantiomeric excess.

Ever since plants colonized land, they evolved mechanisms to respond to changing environmental conditions and settle in extreme habitats. Recent studies show that several plant species require microbial associations for stress tolerance and survival. Although many plants lack the adaptive capability to adapt to stress conditions, the ability of a variety of plants to adapt to stress conditions often appears to depend on their association with certain microbes, raising a number of questions: What distinguishes the microbes and plants that can adapt to extreme environmental conditions? Can all plants improve stress tolerance when associated with appropriate microbial partners? Answers to these questions should modify our concepts of plant physiology and could lead to new ways towards a sustainable agriculture.

International audience; In order to shed light on the fragmentation mechanisms occurring during the collision induced dissociation (CID) of peptides in the gas phase, we have studied a model system, the N-formylalanylamide (HCO-Ala-NH2), by coupling experimental and theoretical methods. In particular, we have addressed two different questions arising in such experiments: (i) what is (are) the structure(s) of the ion before collision, and (ii) what are the fragmentation mechanisms occurring after collision with the target gas. For the first question, we coupled the potential energy surface (PES) study done by means of density functional theory (DFT), with Infra Red Multiple Photon Dissociation (IRMPD) spectroscopy. For the second problem, which is actually the main topic of the present work, we coupled quantum mechanics plus molecular mechanics (QM + MM) direct chemical dynamics simulations with tandem mass spectrometry (MS/MS). In addition, in order to better delineate the fragmentation mechanisms and validate those proposed by simulations, isotopic labeling experiments using 2H and 13C were performed. Thanks to the interplay between simulations and experiments, it was possible to successfully identify the fragmentation pathways leading to b1, y1, a1 and immonium ions. Our mechanisms support the "mobile proton" picture that is supposed to trigger the peptide fragmentation in the gas phase, confirming, from a chemical dynamics point of view, previous theoretical and experimental studies on similar systems.

International audience; De novo biosynthetic pathways are designed, assembled and optimized to produce high-value compounds such as drugs and chemical building blocks from renewable resources. Microorganisms are used as synthetic platforms of systems biology where biochemical pathways are engineered into the host metabolic network. Retrosynthetic biology offers a creative pathway design concept that has gained interest because of its potential to identify novel metabolic ways for therapeutic production. Retrosynthetic biology uses the backward search of retrosynthetic analysis to devise and optimize tailor-made pathways. The retrosynthetic process can be seamlessly integrated into a complete circuitry system for therapeutic applications where production, sensing and delivery act as constitutive interconnecting parts. The aim of this review is to highlight recent efforts toward synthetic design for therapeutic development.

We present the variable length local decoding, a method which augments the alphabet of a sequence or a set of sequences. Roughly speaking, the approach distinguishes several types of symbols/nucleotides according to their contexts in the sequences. These contexts have variable lengths and are defined from a prefix code.We first give an original algorithm computing the decoding with a complexity linear both in time and memory space. Next, the approach is applied to alignment-free sequence comparison. We give a heuristic way to select context lengths relevant to this question. The comparison of sequences itself is based on the composition in “augmented” symbols of their variable length local decodings. The results of this comparison are illustrated on a biological alignment.

International audience; In Arabidopsis thaliana, the putative RNA-helicase SDE3 assists posttranscriptional-gene-silencing (PTGS) amplification by RNA-dependent-RNA-polymerase-6 (RDR6). SDE3 homologs in Drosophila, worm and human contribute to silence viruses, transposons or recently duplicated genes but the underlying mechanisms remain largely unknown. Here, we demonstrate that SDE3 is present with the PTGS effectors AGO1 and AGO2 in higher-order protein complexes owing to a specialized GW-repeat-containing C-terminal domain. We uncover an essential contribution of the RNA-helicase activity and a facilitating role for AGO binding in SDE3 action, which occurs downstream of RDR6. We show that these biochemical properties underpin dual roles for SDE3 in antiviral defense and, unexpectedly, in transposon silencing via a hitherto unanticipated pathway that correlates with DNA methylation, suggesting a continuum of action between PTGS and chromatin-level silencing. We identified endogenous SDE3 targets corresponding to nonconserved intergenic regions, transposons and recently evolved pseudogenes, unraveling striking functional convergences among plant and metazoan SDE3 pathways.

International audience; In clinical cancer research, high throughput genomic technologies are increasingly used to identify copy number aberrations. However, the admixture of tumor and stromal cells and the inherent karyotypic heterogeneity of most of the solid tumor samples make this task highly challenging. Here, we propose a robust two-step strategy to detect copy number aberrations in such a context. A spatial mixture model is first used to fit the preprocessed data. Then, a calling algorithm is applied to classify the genomic segments in three biologically meaningful states (copy loss, copy gain and modal copy). The results of a simulation study show the good properties of the proposed procedure with complex patterns of genomic aberrations. The interest of the proposed procedure in clinical cancer research is then illustrated by the analysis of real lung adenocarcinoma samples.

International audience; In the present work we have investigated the gas phase reactivity of protonated urea after collision with the diatomic inert gas N2, by studying the energy transfer and fragmentation induced by collisions. We first developed an analytical pair potential to describe the interaction between the projectile and the ion, and then performed QM/MM direct chemical dynamics simulations of the collision between the projectile and protonated urea in its two most stable isomers. In particular, the effect of the diatomic projectile, and the role of its initial rotational state, were compared with the fragmentation and energy transfer obtained previously (J. Phys. Chem. A 2009, 113, 13853) for the monoatomic projectile Ar. The diatomic projectile was found to be less efficient in energy transfer compared to the monoatomic projectile. In addition, rotational activation of UreaH+ is dependent on the initial rotational quantum number of N2. Finally, we investigated the UreaH+ gas phase reactivity as a function of its rovibrational activation by means of chemical dynamics simulations where the initial structure for the simulations is the transition state (TS) that the system can reach after collisional activation of the most stable isomer. The simulation time-length is not able to directly access this TS from the most stable isomer since its lifetime is notably longer, of about two order of magnitude in time.

International audience; In plants and animals, innate immunity is triggered through pattern recognition receptors (PRRs) in response to microbe-associated molecular patterns (MAMPs) to provide the first line of inducible defense. Plant receptor protein kinases (RPKs) represent the main plasma membrane PRRs perceiving diverse MAMPs. RPKs also recognize secondary danger-inducible plant peptides and cell-wall signals. Both types of RPKs trigger rapid and convergent downstream signaling networks controlled by calcium-activated PKs and mitogen-activated PK (MAPK) cascades. These PK signaling networks serve specific and overlapping roles in controlling the activities and synthesis of a plethora of transcription factors (TFs), enzymes, hormones, peptides and antimicrobial chemicals, contributing to resistance against bacteria, oomycetes and fungi.

International audience; The detection of oligosaccharides at the single-molecule level was investigated using a protein nanopore device. Neutral oligosaccharides of various molecular weights were translocated through a single α-hemolysin nanopore and their nano-transit recorded at the single-molecule level. The translocation of maltose and dextran oligosaccharides featured by 1 → 4 and 1 → 6 glycosidic bonds respectively was studied in an attempt to discriminate oligosaccharides according to their polymerization degree and glycosidic linkages. Oligosaccharides were translocated through a free diffusion regime indicating that they adopted an extended conformation during their translocation in the nanopore. The dwell time increased with molecular mass, suggesting the usefulness of nanopore as a molecular sizing device.

International audience; Microarray technology is widely used for gene expression research targeting the development of new drug treatments. In the case of a two-color microarray, the process starts with labeling DNA samples with fluorescent markers (cyanine 635 or Cy5 and cyanine 532 or Cy3), then mixing and hybridizing them on a chemically treated glass printed with probes, or fragments of genes. The level of hybridization between a strand of labeled DNA and a probe present on the array is measured by scanning the fluorescence of spots in order to quantify the expression based on the quality and number of pixels for each spot. The intensity data generated from these scans are subject to errors due to differences in fluorescence efficiency between Cy5 and Cy3, as well as variation in human handling and quality of the sample. Consequently, data have to be normalized to correct for variations which are not related to the biological phenomena under investigation. Among many existing normalization procedures, we have implemented the quantile adjustment method using the python computer language, and produced a module which can be run via an HTML dynamic form. This module is composed of different functions for data files reading, intensity and ratio computations and visualization. The current version of the HTML form allows the user to visualize the data before and after normalization. It also gives the option to subtract background noise before normalizing the data. The output results of this module are in agreement with the results of other normalization tools. Published by Elsevier B.V.

Host plant resistance is an efficient and environmentally friendly means of controlling insects, including aphids, but resistant-breaking biotypes have occurred in several plant–aphid systems. Our review of the genetic and molecular bases of aphid resistance in crop species emphasizes the limited number of aphid resistance genes and alleles. Inheritance of aphid resistance may be monogenic (dominant or recessive genes) or polygenic. Two dominant, aphid resistance genes have been isolated to date. They both encode NBS-LRR proteins involved in the specific recognition of aphids. Strategies to ensure aphid resistance effectiveness and durability are discussed. Innovative research activities are proposed., La résistance génétiquement déterminée des plantes est un moyen efficace et respectueux de l’environnement de lutter contre les pucerons. Cependant, des biotypes de pucerons, capables de contourner les résistances, sont apparus dans plusieurs systèmes plantes–pucerons. Dans cet article, sur les bases génétiques et moléculaires des résistances aux pucerons chez les espèces cultivées, nous insistons sur le nombre de gènes de résistance aux pucerons disponibles est limité. Les résistances aux pucerons sont contrôlées par des gènes majeurs (dominants ou récessifs) aussi bien que par des facteurs génétiques quantitatifs. Deux gènes de résistance aux pucerons ont été clonés jusqu’à présent, chez la tomate et le melon. Ils codent pour des protéines NBS-LRR, qui sont impliquées dans la reconnaissance spécifique des pucerons. Les stratégies de gestion dura

International audience; Pyrite dissolution and interaction with Fe(II), Co(II), Eu(III) and U(VI) have been studied under anoxic conditions by solution chemistry and spectroscopic techniques. Aqueous data show a maximal cation uptake above pH 5.5. Iron (II) uptake can explain the non-stoichiometric [S]aq/[Fe]aq ratios often observed during dissolution experiments. Protonation data corrected for pyrite dissolution resulted in a proton site density of 9±3sitesnm−2. Concentration isotherms for Eu(III) and U(VI) sorption on pyrite indicate two different behaviours which can be related to the contrasted redox properties of these elements. For Eu(III), sorption can be explained by the existence of a unique site with a saturation concentration of 1.25×10−6molg−1. In the U(VI) case, sorption seems to occur on two different sites with a total saturation concentration of 4.5×10−8molg−1. At lower concentration, uranium reduction occurs, limiting the concentration of dissolved uranium to the solubility of UO2(s).Scanning electron microscopy and micro-Raman spectrometry of U(VI)-sorbed pyrite indicate a heterogeneous distribution of U at the pyrite surface and a close association with oxidized S. X-ray photoelectron spectroscopy confirms the partial reduction of U and the formation of a hyperstoichiometric UO2+x(s). Our results are consistent with a chemistry of the pyrite surface governed not by Fe(II)-bound hydroxyl groups, but by S groups which can either sorb cations and protons, or sorb and reduce redox-sensitive elements such as U(VI).

International audience; In this paper, we define a class of Petri nets, called Petri nets with counters, that can be seen as place/transition Petri nets enriched with a vector of integer variables on which linear operations may be applied. Their semantics usually leads to huge or infinite reachability graphs. Then, a more compact representation for this semantics is defined as a symbolic state graph whose nodes possibly encode infinitely many values for the variables. Both representations are shown behaviourally equivalent.

International audience; We review the current status of expression of heterologous systems for bioenergy and bioproduction in bacteria using a model-based approach. As an aim for synthetic biology, it requires mathematical models of genetic modules that could be characterized independently of their context. This fastens the design of metabolic circuits using a combinatorial design approach, where given pathways could be optimized for maximal bioproduction, while being nontoxic for the chassis. We show how recent characterization of genetic parts, such as promoters, RBS or sRNAs could be used to fine-tune the expression of individual genes to achieve that goal. We also present lists of enzymes that are used for bioproduction, enlarging such set of biological parts.

International audience; The formalism of hybrid functional petri nets (HFPN) has proved its convenience for simulating biological systems. The drawback of the noticeable expressiveness of HFPN is the difficulty to perform formal verifications of dynamical properties. In this article, we propose a model-checking procedure for timed hybrid petri nets (THPN), a sub-class of HFPN. This procedure is based on the translation of the THPN model and of the studied property into real-time automata. It is applied to model enzymatic competitions existing in amphibian metamorphosis.

International audience; This paper presents a new strategy for formation control of multiple mobile robots to capture a target including self organization. A decentralized formation control is proposed to make the system more reliable and fault-tolerant. Acting on a hostile environnement, each robot of the formation has to avoid an obstacle. For that, we propose a new technique that modifies the trajectory behavior while preserving the formation convergence. LaSalle's theorem is applied to construct the proposed smooth continuous feedback control, to surround the target. The validity of convergence and obstacle avoidance is supported by computer simulation.

Bioinformatique et génomique (Resp. Hadi Quesneville); International audience; Transposable elements (TEs) are ubiquitous components of eukaryotic genomes that impact many aspects of genome function. TE detection in genomic sequences is typically performed using similarity searches against a set of reference sequences built from previously identified TEs. Here, we demonstrate that this process can be improved by designing reference sets that incorporate key aspects of the structure and evolution of TEs and by combining these sets with Repbase Update (RU), which is composed mainly of consensus sequences. Using the Arabidopsis genome as a test case, our approach leads to the detection of an extra 12.4% of TE sequences. These correspond to novel TE fragments as well as to the extension of TE fragments already detected by RU. Significantly, we find that TE detection could be readily optimized using only two reference sets, one containing true consensus sequences and the other mosaic sequences that capture the structural diversity of TE copies within a family.

International audience; This paper presents the various stages for the construction of a two wheeled riding simulator. Despite its simplicity, the particularity of this simulator comes from the possibility to reproduce most of the movements and the inertial effects allowing to perceive sensations close to reality cases. This simulator has been developed for three purposes: * as a training tool for new riders in normal traffic environment * sensibilization for dangerous riding situations (avoidance, emergency braking, failling, etc.) * to study riders behaviours in such situations Our studies have lead to an original 5 degrees of freedom (DOF) mechanical platform including a double haptic feedback on the handlebar. The choices of the platform movements and the system actuation are motivated and described. Also, a detailed kinematics and dynamics modeling will be presented. Some results are shown, validating the actutation requirements and platform control.

Stratified institutions and elementary homomorphisms; International audience; For conventional logic institutions, when one extends the sentences to contain open sentences, their satisfaction is then parameterized. For instance, in the first-order logic, the satisfaction is parameterized by the valuation of unbound variables, while in modal logics it is further by possible worlds. This paper proposes a uniform treatment of such parameterization of the satisfaction relation within the abstract setting of logics as institutions, by defining the new notion of stratified institutions. In this new framework, the notion of elementary model homomorphisms is defined independently of an internal stratification or elementary diagrams. At this level of abstraction, a general Tarski style study of connectives is developed. This is an abstract unified approach to the usual Boolean connectives, to quantifiers, and to modal connectives. A general theorem subsuming Tarski's elementary chain theorem is then proved for stratified institutions with this new notion of connectives.

International audience; In this article, we present a game theory based framework, named games network, for modeling biological interactions. After introducing the theory, we more precisely describe the methodology to model biological interactions. Then we apply it to the plasminogen activator system (PAs) which is a signal transduction pathway involved in cancer cell migration. The games network theory extends game theory by including the locality of interactions. Each game in a games network represents local interactions between biological agents. The PAs system is implicated in cytoskeleton modifications via regulation of actin and microtubules, which in turn favors cell migration. The games network model has enabled us a better understanding of the regulation involved in the PAs system.

International audience; Since rewriting logic has been introduced, it has shown its adequateness both as a semantic and a logical framework. But the numerous applications of the rewriting logic in the above two areas has shown the importance of increasing its expressive power. Therefore, in order to facilitate this work, we will study in this paper how to generalize the transformation that from the equational logic has resulted in the rewriting logic. To achieve this purpose, we will show that there exists a valid and useful notion of rewriting logic associated to any rewriting theory fitting an abstract framework developed by two of the authors in previous papers.

To describe the solvation properties of polar or charged species, and the reaction free-energy of charge transfers, we propose a generalization of the Marcus electrostatic polarization free-energy functional which accounts for the molecular nature of the solvent. The proposed generic free energy functional relies crucially on the knowledge of the direct correlation function of the homogeneous solvent. For the case of a dipolar solvent, we show how this fundamental quantity can be extracted directly from molecular dynamics simulations of the pure solvent instead of the traditional route of integral equation theories. The direct correlation function computed from simulation is compared to approximate ones obtained from linearized and quadratic HNC integral closures. The performance of the corresponding density functionals is assessed, in comparison to “exact” molecular dynamics results, for the solvation free-energies and the solvent density profiles around simple molecular solutes.

In the framework of waste management strategy for future fusion reactor, it has been demonstrated that one of the major issue is to reduce the high level waste. The tritium activity strongly contributes to the waste classification. A better knowledge of the mechanisms involved in tritium trapping and desorption will allow to choose the most appropriate procedure to reduce the tritium constraint. This paper deals with the management of tritiated steels and the way to reduce tritium transfer. This experimental work concerns steel obtained by remelting under vacuum of tritiated austenitic stainless steel wastes. The goal of this study is to develop heat treatments in solid phase to lower the residual tritium concentration and its desorption kinetics at room temperature. The surface activity, the desorption of residual tritium at room temperature and the residual concentration have been measured for each condition (temperature, time, atmosphere, etc.). For reheating temperatures below 600 °C, the surface activity increases by one or two orders of magnitude; this is the consequence of the formation of a tritium rich oxide layer. After a 20 h annealing above 300 °C and removing of the tritium rich oxide layer, the surface activity is strongly reduced (80%) when compared with the value measured before annealing. For such annealing conditions, the amount of desorbed tritium is reduced by a factor 25 and the desorption kinetics yield a reduction factor of 40–50 after annealing at 400 °C for 20 h.

International audience; The natural speciation of Mn (0.19 g/kg), Ni (46 mg/kg), and Zn (42 mg/kg) in the argillic horizon (120 cm depth, pH = 5.6) of an Ultisol from a paddy soil in northern Taiwan was investigated by advanced X-ray synchrotron techniques. Microchemical associations were imaged by synchrotron-based X-ray microfluorescence, host minerals were identified by standard and micrometer-resolved X-ray diffraction, and the local coordination environment of Mn, Ni, and Zn was probed using extended X-ray absorption fine structure (EXAFS) spectroscopy on a powdered sample and a soil thin section, and polarized EXAFS spectroscopy on a highly textured self-supporting clay film from the < 2 mu m fraction of the soil. Manganese was concentrated in Fe-Mn soft mottles (44.4 g/kg) as turbostratic hexagonal birnessite and lithiophorite having Mn3+/Mn4+ atomic ratios of similar to 20% and 50%, respectively. Quantitative analysis of high-order scattering paths of the EXAFS spectrum for natural and synthetic (Al0.67Li0.32)(Mn0.684+Mn0.323+)O-2(OH)(2) lithiophorite revealed that Mn3+ and Mn4+ are ordered in the [(Mn0.684+Mn0.323+)O-2](0.32-) layer. A structural model is proposed, in which Mn4+ and Mn3+ are ordered similarly to Al and Li in the [(A(0.67)(3+)Li(0.32)(+))(OH2)O-2](0.32+) layer, with Mn3+ cations being surrounded by six Mn4+, and Mn4+ cations by three Mn3+ and three Mn. Similar cation ordering in the manganese and aluminum layers likely provides a more homogeneous local balance of the excess and deficit of charges in each layer and increases the stability of lithiophorite. Ni (r = 0.70 angstrom) substitutes for Mn (r(Mn4+) = 0.54 angstrom, r(Mn3+) = 0.65 angstrom) in the manganese layer in the natural lithiophorite. In contrast, Zn (r = 0.74 angstrom) fills vacant sites in the gibbsitic layer of natural lithiophorite, in a similar manner as lithium (r = 0.74 angstrom) in synthetic lithiophorite. The partitioning of Ni and Zn between the two layers is a result of the general preference of Ni, whose size is intermediate between those of Mn3+ and Li+, for slightly smaller sites. In contrast with nickel, which is detected only where there is lithiophorite, the Zn-lithiophorite association found in Fe-Mn mottles is not representative of the bulk soil. The combined use of X-ray diffraction, and powder and polarized EXAFS spectroscopy revealed that Zn is predominantly bound to hydroxy-Al interlayers sandwiched between 2:1 vermiculite layers in the fine soil matrix. The incorporation of Zn in the gibbsitic layer of both lithiophorite and vermiculite helps increase the stability of these minerals by providing positive charge to balance the negative charge from the 2:1 phyllosilicate layer and the [(Mn0.684+Mn0.323+)O-2](0.32-) layer of lithiophorite. This binding environment for zinc is probably the main mechanism by which zinc is sequestered in acidic to near-neutral aluminum-rich clayey soils.

International audience; We present a model of microbial information processing that contains characteristic features of the phenomenon of physiological adaptation. The backbone of the model is the "`adaptive event"' in which energy-converting subsystems of the cell interact with the changing environment. In this process, the subsystems pass, via an adaptive operation mode, from one adapted state to the next. An adaptive operation mode takes place when an adapted state is disturbed by an environmental alteration. These two manifestations of an adaptive event were differently treated in the simulation, based on an application of linear irreversible thermodynamics to the energy transduction of adaptive subsystems. In adapted states, the conductivity coefficients of the flow-force relationships employed remained constant, whereas during an adaptive operation mode, these coefficients were altered in a directional manner during the simulation. An example dealing with the complex relationship between phosphate uptake and cyanobacterial growth is given. In this example, the simulation of adapted states of two subsystems of the incorporating machinery, namely the phosphate carrier in the cell membrane and the F-ATPase in the thylakoid membrane, was in accordance with the measured uptake kinetics, and when fixed, predetermined conductivity coefficients were used. In the adaptive operation mode, however, the simulated behavior was in agreement with experimental observations when the program was able to interpret its own performance in the light of environmental phosphate fluctuations, experienced by the cell in the past, and to reconstruct the two subsystems according to this interpretation. Via transitions between adapted states and adaptive modes, information is transferred from one adaptive event to the next: the latter inherits the results of former interpretations. By appropriating them selectively, it is entering into a future in which its own interpretation is passed on to the following adaptive event. The model is discussed with respect to the concept of autopoiesis.

International audience; We study the problem of minimizing the average weighted completion time on a single machine under the additional constraint that the sum of completion times does not exceed a given bound B (1|ΣCj ≤ B| ΣωjCj) for which we propose a (2,1)-approximation algorithm. We also address the problem 1|ΣcjCj ≤ B|ΣωjCj for which we present a (2,2)-approximation algorithm. After showing that the problem of minimizing two different sums of weighted completion times is intractable, we present an algorithm which computes a (2(1 + ε), 1) (respectively (2(1 + ε), 2))-approximate Pareto curve for the problem 1∥(ΣCj, ΣωjCj) (respectively 1∥(ΣcjCj,ΣωjCj).

Integrated formal description techniques are a promising approach for the specification of multi-aspect systems. In this context, we have proposed a formalism, called Extended State Diagrams (ESD), combining in an homogeneous framework state diagrams and formal data description languages. Our purpose is here to enhance the implicit ESD communication mechanisms with explicit descriptions of communications, which is achieved using synchronization vectors. The use of interaction diagrams is also discussed.

An efficient and simple one-pot procedure for selective etherification of 2-aryl-ethylalcohols has been achieved through Amberlyst 15-catalyzed reaction in dimethyl carbonate (DMC). Moreover, the polymer catalyst could be recovered and reused with no effect on its activity. The reaction mechanism involves the formation of phenonium ion which has been demonstrated by a C-C bond forming reaction. Theoretical studies are in agreement with and thus explain experimental results. (C) 2013 Elsevier Ltd. All rights reserved.

International audience; Human functional MRI studies frequently reveal the joint activation of parietal and of lateral and mesial frontal areas during various cognitive tasks. To analyze the geometrical organization of those networks, we used an automatized clustering algorithm that parcels out sets of areas based on their similar profile of task-related activations or deactivations. This algorithm allowed us to reanalyze published fMRI data (Simon, O., Mangin, J.F., Cohen, L., Le Bihan, D., Dehaene, S., 2002. Topographical layout of hand, eye, calculation, and language-related areas in the human parietal lobe. Neuron 33, 475-487) and to reproduce the previously observed geometrical organization of activations for saccades, attention, grasping, pointing, calculation, and language processing in the parietal lobe. Further, we show that this organization extends to lateral and mesial prefrontal regions. Relative to the parietal lobe, the prefrontal functional geometry is characterized by a partially symmetrical anteroposterior ordering of activations, a decreased representation of effector-specific tasks, and a greater emphasis on higher cognitive functions of attention, higher-order spatial representation, calculation, and language. Anatomically, our results in humans are closely homologous to the known connectivity of parietal and frontal regions in the macaque monkey.

Cell motility and division are complex mechanisms that involve drastic cell shape changes. A crucial role is played by the actin cortex, which, together with the molecular motor myosin, regulates the production of cellular tension (1). A better understanding of the interplay between actin network dynamics and myosin-driven contractility is necessary to elucidate the detailed mechanism of contraction in a dynamic, out of equilibrium, constantly polymerizing and depolymerizing actin structure. In order to dissect this dual actin-myosin contribution we make advantage of biomimetic systems: cell-sized liposomes indeed offer the possibility to retain only the essential players involved in contraction mechanisms and to finely control the physical and biochemical conditions to mimic cell-like shape changes (2).Particularly we study acto-myosin contraction mechanisms on cell-sized doublets, which enable overcoming the spherical symmetry of single liposomes: with this geometry, shape changes, and hence tension build-up, can be fully characterised by recording contact angle variations. A polymerizing actin network is built at the outer surface of doublets. A fluorescently labelled actin is used and simultaneous detection of phase contrast and fluorescence images allow following actin cortex dynamics and further shape changes induced by the addition of myosin motors (3). A micropipette aspiration technique is also adopted to further characterize these cell-like shape changes (4).This reconstituted doublet system allows us to decouple biochemical and physical aspects of actin network dynamics and fully dissect the dual role of actin and myosin contractility, thus significantly improving our understanding of acto-myosin driven cell shape changes.1.Blanchoin L et al. Physiol Rev 2014, 94:235-263.2.Murrell M et al. Nat Rev Mol Cell Biol. 2015, 16(8):486-98.3.Carvalho K et al. Proc Natl Acad Sci U S A. 2013, 110(41):16456-16461.4.Campillo C et al. Biophys J 2013, 104:1248-1256.