360 Intrusions in a Miniature Volcano: Birth, Growth, and Evolution of an Analog Edifice

Most volcanoes throughout the world have been monitored with geophysical data (seismology and geodesy) for no more than three decades, a relatively short time compared to their overall life. The consequence is that we lack a long observation of volcanic growth and behavior to get a more complete picture of the interaction between edifice stress state and magma transfer. Here we present the birth and evolution of a 83 x 83 cm analog model, where we reproduce for the first time volcanic growth over 360 successive intrusions (15 mL every half hour, at a rate of 3 mL/min) in an analog elasticity-dominated material (pigskin gelatine). By observing the development of this model volcano, we hope to provide insights to the study of long-term volcanic activity. In particular, we are interested in stress accumulation/release cycles and their role in the triggering of distant eruptions. Our model volcano started as a flat topography and ended 3.82 cm in height at the summit. It displayed cyclic eruptive patterns with alternating phases of eruptive and purely intrusive behavior. Alike to many intraplate volcanoes in nature, main dyke swarms produced in the experiment were disposed in a three-branched radial pattern centered above the injection source (“volcanic rift zones”). They were accompanied by two radial sill networks, at source depth and edifice base. Long-term radial compressive stress building during dyke swarming was likely compensated by radial compressive stress release during sill emplacement. Near-surface stresses, deduced from the main orientation eruptive fissures and “dry” fractures, became more localized as the volcano grew. At the end of the experiment, the shallow stress field was interpreted as generally extensional radial at the summit, extensional tangential on the flanks, and compressive radial in distal areas. This experiment showcases the potential of studying long-term stress permutations in volcanic edifices in the understanding of their morphology and successive activity phases

Using Model Types to Support Contract-Aware Model Substitutability

International audienceModel typing brings the benefit associated with well-defined type systems to model-driven development (MDD) through the assignment of specific types to models. In particular, model type systems enable reuse of model manipulation operations (e.g., model transformations), where manipulations defined for models of a supertype can be used to manipulate models of subtypes. Existing model typing approaches are limited to structural typing defined in terms of object-oriented metamodels (e.g., MOF) in which the only structural (well-formedness) constraints are those that can be expressed directly in metamodeling notations (e.g., multiplicity and element containment constraints). In this paper we describe an extension to model typing that takes into consideration structural invariants, other than those that can be expressed directly in metamodeling notation, and specifications of behaviors associated with model types. The approach supports contract-aware substitutability, where contracts are defined in terms of invariants and pre-/postconditions expressed using OCL. Support for behavioral typing paves the way for behavioral substitutability. We also describe a technique to rigorously reason about model type substitutability as supported by contracts and apply the technique in use cases from the optimizing compiler community

Coat colour in dogs: identification of the Merle locus in the Australian shepherd breed

BACKGROUND: Coat colours in canines have many natural phenotypic variants. Some of the genes and alleles involved also cause genetic developmental defects, which are also observed in humans and mice. We studied the genetic bases of the merle phenotype in dogs to shed light on the pigmentation mechanisms and to identify genes involved in these complex pathways. The merle phenotype includes a lack of eumelanic pigmentation and developmental defects, hearing impairments and microphthalmia. It is similar to that observed in microphthalmia mouse mutants. RESULTS: Taking advantage of the dog as a powerful genetic model and using recently available genomic resources, we investigated the segregation of the merle phenotype in a five-generation pedigree, comprising 96 sampled Australian shepherd dogs. Genetic linkage analysis allowed us to identify a locus for the merle phenotype, spanning 5.5 megabases, at the centromeric tip of canine chromosome 10 (CFA10). This locus was supported by a Lod score of 15.65 at a recombination fraction θ = 0. Linkage analysis in three other breeds revealed that the same region is linked to the merle phenotype. This region, which is orthologous to human chromosome 12 (HSA12 q13-q14), belongs to a conserved ordered segment in the human and mouse genome and comprises several genes potentially involved in pigmentation and development. CONCLUSION: This study has identified the locus for the merle coat colour in dogs to be at the centromeric end of CFA10. Genetic studies on other breeds segregating the merle phenotype should allow the locus to be defined more accurately with the aim of identifying the gene. This work shows the power of the canine system to search for the genetic bases of mammalian pigmentation and developmental pathways

Model-Driven Engineering and Optimizing Compilers: A bridge too far?

International audienceA primary goal of Model Driven Engineering (MDE) is to reduce the cost and effort of developing complex software systems using techniques for transforming abstract views of software to concrete implementations. The rich set of tools that have been developed, especially the growing maturity of model transformation technologies, opens the possibility of applying MDE technologies to transformation-based problems in other domains. In this paper, we present our experience with using MDE technologies to build and evolve compiler infrastructures in the optimizing compiler domain.We illustrate, through our two ongoing research compiler projects for C and a functional language, the challenging aspects of optimizing compiler research and show how mature MDE technologies can be used to address them.We also identify some of the pitfalls that arise from unrealistic expectations of what can be accomplished using MDE and discuss how they can lead to unsuccessful and frustrating application of MDE technologies

FEELnc : a tool for long non-coding RNA annotation and its application to the dog transcriptome

Whole transcriptome sequencing (RNA-seq) has become a standard for cataloguing and monitoring RNA populations. One of the main bottlenecks, however, is to correctly identify the different classes of RNAs among the plethora of reconstructed transcripts, particularly those that will be translated (mRNAs) from the class of long non-coding RNAs (lncRNAs). Here, we present FEELnc (FlExible Extraction of LncRNAs), an alignment-free program that accurately annotates lncRNAs based on a Random Forest model trained with general features such as multi k-mer frequencies and relaxed open reading frames. Benchmarking versus five state-of-the-art tools shows that FEELnc achieves similar or better classification performance on GENCODE and NONCODE data sets. The program also provides specific modules that enable the user to fine-tune classification accuracy, to formalize the annotation of lncRNA classes and to identify lncRNAs even in the absence of a training set of non-coding RNAs. We used FEELnc on a real data set comprising 20 canine RNA-seq samples produced by the European LUPA consortium to substantially expand the canine genome annotation to include 10 374 novel lncRNAs and 58 640 mRNA transcripts. FEELnc moves beyond conventional coding potential classifiers by providing a standardized and complete solution for annotating lncRNAs and is freely available at https://github.com/tderrien/FEELnc.Peer reviewe

When RNA and protein degradation pathways meet

RNA silencing has become a major focus of molecular and biomedical research in the last decade. This mechanism, which is conserved in most eukaryotes, has been extensively studied and is associated to various pathways implicated in the regulation of development, in the control of transposition events, heterochromatin maintenance and also playing a role in defense against viruses. Despite of its importance, the regulation of the RNA silencing machinery itself remains still poorly explored. Recently several reports in both plants and metazoans revealed that key components of RNA silencing, such as RNA-induced silencing complex component ARGONAUTE proteins, but also the endonuclease Dicer are subjected to proteasomal and autophagic pathways. Here we will review these post-translational proteolytic regulations with a special emphasis on plant research and also discuss their functional relevance

Le complexe ClpP de Chlamydomonas reinhardtii (Contribution à l'étude biochimique et fonctionnelle d'une protéase atypique du chloroplaste)

La protéase Clp est une protéase à sérine ubiquitaire. Dans les mitochondries et la plupart des bactéries, elle associe une peptidase homo-oligomérique (ClpP) et des chaperonnes Clp/HSP100. Dans les cyanobactéries et les plastes, la peptidase ClpP est un hétéro-oligomère constitué, essentiellement, de sous-unités ClpP (actives) et ClpR (Homologues inactifs des ClpP). Suite à l endosymbiose, les gènes codant ces sous-unités ont subi une évolution remarquable qui a engendré une famille multigénique extrêmement diversifiée. Chez Chlamydomonas reinhardtii, ClpP est composé des produits de 8 gènes nucléaires (CLPP3, P4 et P5 et CLPR1, R2, R3, R4 et R6) et d un unique gène chloroplastique essentiel (clpP1). Du fait de cette complexité, de la faible abondance et de l aspect essentiel de ces protéines, la caractérisation des protéases Clp chloroplastiques est bien moins avancée que celle de leurs homologues bactériens et mitochondriaux. Les résultats présentés dans ce manuscrit apportent des informations originales et déterminantes pour la caractérisation biochimique et fonctionnelle du complexe ClpP chloroplastique : des expériences de mutagenèse dirigée sur la sous unité ClpP1 ont permis d élucider sa biogenèse particulière et de purifier le complexe ClpP chloroplastique natif et actif ; l étude préliminaire de ce complexe apporte des informations capitales sur sa composition et sa structure et ouvre de nouvelles perspectives dans l étude de cette protéase atypique. Enfin, l étude de souches dans lesquelles l accumulation de ClpP est réduite de 60% a permis de montrer que cette protéase intervient dans la régulation de l expression de gènes du chloroplaste.PARIS-BIUSJ-Physique recherche (751052113) / SudocSudocFranceF

One-step Affinity Purification of the Chloroplast ClpP Complex from the Green Alga Chlamydomonas reinhardtii Using the Strep-tagII Epitope Tag

This protocol describes the affinity purification of the chloroplast ClpP complex from Chlamydomonas reinhardtii. To this purpose, we have created a Chlamydomonas reinhardtii strain in which the chloroplast encoded ClpP1 subunit of the ClpP complex is tagged at its C-terminal end by a strep-tagII peptide