BackgroundAnimal’s efficiency in converting feed into lean gain is a critical issue for the profitability of meat industries. This study aimed to describe shared and specific molecular responses in different tissues of pigs divergently selected over eight generations for residual feed intake (RFI).ResultsPigs from the low RFI line had an improved gain-to-feed ratio during the test period and displayed higher leanness but similar adiposity when compared with pigs from the high RFI line at 132 days of age. Transcriptomics data were generated from longissimus muscle, liver and two adipose tissues using a porcine microarray and analyzed for the line effect (n = 24 pigs per line). The most apparent effect of the line was seen in muscle, whereas subcutaneous adipose tissue was the less affected tissue. Molecular data were analyzed by bioinformatics and subjected to multidimensional statistics to identify common biological processes across tissues and key genes participating to differences in the genetics of feed efficiency. Immune response, response to oxidative stress and protein metabolism were the main biological pathways shared by the four tissues that distinguished pigs from the low or high RFI lines. Many immune genes were under-expressed in the four tissues of the most efficient pigs. The main genes contributing to difference between pigs from the low vs high RFI lines were CD40, CTSC and NTN1. Different genes associated with energy use were modulated in a tissue-specific manner between the two lines. The gene expression program related to glycogen utilization was specifically up-regulated in muscle of pigs from the low RFI line (more efficient). Genes involved in fatty acid oxidation were down-regulated in muscle but were promoted in adipose tissues of the same pigs when compared with pigs from the high RFI line (less efficient). This underlined opposite line-associated strategies for energy use in skeletal muscle and adipose tissue. Genes related to cholesterol synthesis and efflux in liver and perirenal fat were also differentially regulated in pigs from the low vs high RFI lines.ConclusionsNon-productive functions such as immunity, defense against pathogens and oxidative stress contribute likely to inter-individual variations in feed efficiency.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3639-0) contains supplementary material, which is available to authorized users.

Genome-scale metabolic models have become the tool of choice for the global analysis of microorganism metabolism, and their reconstruction has attained high standards of quality and reliability. Improvements in this area have been accompanied by the development of some major platforms and databases, and an explosion of individual bioinformatics methods. Consequently, many recent models result from “à la carte” pipelines, combining the use of platforms, individual tools and biological expertise to enhance the quality of the reconstruction. Although very useful, introducing heterogeneous tools, that hardly interact with each other, causes loss of traceability and reproducibility in the reconstruction process. This represents a real obstacle, especially when considering less studied species whose metabolic reconstruction can greatly benefit from the comparison to good quality models of related organisms. This work proposes an adaptable workspace, AuReMe, for sustainable reconstructions or improvements of genome-scale metabolic models involving personalized pipelines. At each step, relevant information related to the modifications brought to the model by a method is stored. This ensures that the process is reproducible and documented regardless of the combination of tools used. Additionally, the workspace establishes a way to browse metabolic models and their metadata through the automatic generation of ad-hoc local wikis dedicated to monitoring and facilitating the process of reconstruction. AuReMe supports exploration and semantic query based on RDF databases. We illustrate how this workspace allowed handling, in an integrated way, the metabolic reconstructions of non-model organisms such as an extremophile bacterium or eukaryote algae. Among relevant applications, the latter reconstruction led to putative evolutionary insights of a metabolic pathway.

Increasing amounts of sequence data are becoming available for a wide range of non-model organisms. Investigating and modelling the metabolic behaviour of those organisms is highly relevant to understand their biology and ecology. As sequences are often incomplete and poorly annotated, draft networks of their metabolism largely suffer from incompleteness. Appropriate gap-filling methods to identify and add missing reactions are therefore required to address this issue. However, current tools rely on phenotypic or taxonomic information, or are very sensitive to the stoichiometric balance of metabolic reactions, especially concerning the co-factors. This type of information is often not available or at least prone to errors for newly-explored organisms. Here we introduce , a tool dedicated to the topological gap-filling of genome-scale draft metabolic networks. reformulates gap-filling as a qualitative combinatorial optimization problem, omitting constraints raised by the stoichiometry of a metabolic network considered in other methods, and solves this problem using Answer Set Programming. Run on several artificial test sets gathering 10,800 degraded Escherichia coli networks was able to efficiently identify essential reactions missing in networks at high degradation rates, outperforming the stoichiometry-based tools in scalability. To demonstrate the utility of we applied it to two case studies. Its application to recent metabolic networks reconstructed for the brown algal model Ectocarpus siliculosus and an associated bacterium Candidatus Phaeomarinobacter ectocarpi revealed several candidate metabolic pathways for algal-bacterial interactions. Then was used to reconstruct, from transcriptomic and metabolomic data, the first metabolic network for the microalga Euglena mutabilis. These two case studies show that is a versatile tool to complete draft genome-scale metabolic networks produced from heterogeneous data, and to suggest relevant reactions that explain the metabolic capacity of a biological system.

Abstract. -Substitutions are combinatorial objects (one replaces a letter by a word) which produce sequences by iteration. They occur in many mathematical fields, roughly as soon as a repetitive process appears. In the present monograph we deal with topological and geometric properties of substitutions, i.e., we study properties of the Rauzy fractals associated to substitutions.To be more precise, let σ be a substitution over the finite alphabet A. We assume that the incidence matrix of σ is primitive and its dominant eigenvalue is a unit Pisot number (i.e., an algebraic integer greater than one whose norm is equal to one and all of whose Galois conjugates are of modulus strictly smaller than one). It is well-known that one can attach to σ a set T which is now called central tile or Rauzy fractal of σ. Such a central tile is a compact set that is the closure of its interior and decomposes in a natural way in n = #A subtiles T (1), . . . , T (n). The central tile as well as its subtiles are graph directed self-affine sets that often have fractal boundary.Pisot substitutions and central tiles are of high relevance in several branches of mathematics like tiling theory, spectral theory, Diophantine approximation, the construction of discrete planes and quasicrystals as well as in connection with numeration like generalized continued fractions and radix representations. The questions coming up in all these domains can often be reformulated in terms of questions related to the topology and geometry of the underlying central tile.After a thorough survey of important properties of unit Pisot substitutions and their associated Rauzy fractals the present monograph is devoted to the investigation of a variety of topological properties of T and its subtiles. Our approach is an algorithmic one. In particular, we dwell upon the question whether T and its subtiles induce a tiling, calculate the Hausdorff dimension of their boundary, give criteria for their connectivity and homeomorphy to a disk and derive properties of their fundamental group.The basic tools for our criteria are several classes of graphs built from the description of the tiles T (i) (1 ≤ i ≤ n) as graph directed iterated function systems and from the structure of the tilings induced by these tiles. These graphs are of interest in their own right. For instance, they can be used to construct the boundaries ∂T as well as ∂T (i) (1 ≤ i ≤ n) and all points where two, three or four different tiles of the induced tilings meet.When working with central tiles in one of the above mentioned contexts it is often useful to know such intersection properties of tiles. In this sense the present monograph also aims at providing tools for "everyday's life" when dealing with topological and geometric properties of substitutions.Many examples are given throughout the text in order to illustrate our results. Moreover, we give perspectives for further directions of research related to the topics discussed in this monograph.

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Female gamete production relies on coordinated molecular and cellular processes that occur in the ovary throughout oogenesis. In fish, as in other vertebrates, these processes have been extensively studied both in terms of endocrine/paracrine regulation and protein expression and activity. The role of small non-coding RNAs in the regulation of animal reproduction remains however largely unknown and poorly investigated, despite a growing interest for the importance of miRNAs in a wide variety of biological processes. Here, we analyzed the role of miR-202, a miRNA predominantly expressed in male and female gonads in several vertebrate species. We studied its expression in the medaka ovary and generated a mutant line (using CRISPR/Cas9 genome editing) to determine its importance for reproductive success with special interest for egg production. Our results show that miR-202-5p is the most abundant mature form of the miRNA and that it is expressed in granulosa cells and in the unfertilized egg. The knock out (KO) of mir-202 gene resulted in a strong phenotype both in terms of number and quality of eggs produced. Mutant females exhibited either no egg production or produced a dramatically reduced number of eggs that could not be fertilized, ultimately leading to no reproductive success. We quantified the size distribution of the oocytes in the ovary of KO females and performed a large-scale transcriptomic analysis approach to identified dysregulated molecular pathways. Together, cellular and molecular analyses indicate that the lack of miR-202 impairs the early steps of oogenesis/folliculogenesis and decreases the number of large (i.e. vitellogenic) follicles, ultimately leading to dramatically reduced female fecundity. This study sheds new light on the regulatory mechanisms that control the early steps of follicular development, including possible targets of miR-202-5p, and provides the first in vivo functional evidence that a gonad-predominant microRNA may have a major role in female reproduction.

Cyanorak v2.1 (http://www.sb-roscoff.fr/cyanorak) is an information system dedicated to visualizing, comparing and curating the genomes of Prochlorococcus, Synechococcus and Cyanobium, the most abundant photosynthetic microorganisms on Earth. The database encompasses sequences from 97 genomes, covering most of the wide genetic diversity known so far within these groups, and which were split into 25,834 clusters of likely orthologous groups (CLOGs). The user interface gives access to genomic characteristics, accession numbers as well as an interactive map showing strain isolation sites. The main entry to the database is through search for a term (gene name, product, etc.), resulting in a list of CLOGs and individual genes. Each CLOG benefits from a rich functional annotation including EggNOG, EC/K numbers, GO terms, TIGR Roles, custom-designed Cyanorak Roles as well as several protein motif predictions. Cyanorak also displays a phyletic profile, indicating the genotype and pigment type for each CLOG, and a genome viewer (Jbrowse) to visualize additional data on each genome such as predicted operons, genomic islands or transcriptomic data, when available. This information system also includes a BLAST search tool, comparative genomic context as well as various data export options. Altogether, Cyanorak v2.1 constitutes an invaluable, scalable tool for comparative genomics of ecologically relevant marine microorganisms.

On montre que la condition combinatoire de fortes coïncidences est suffisante pour qu'un système substitutif de type Pisot soit isomorphe en mesureà unéchange de morceaux dans un compact autosimilaire de mesure non nulle dans le produit d'un espace euclidien et d'extensions finies de corps p-adiques. En particulier, tout système substitutif de type Pisot est une extension finie de son facteuréquicontinu maximal ; en règle générale, ce dernier contient une translation p-adique si et seulement si la matrice d'incidence de la substitution est nilpotente modulo p.Abstract. The combinatorial condition of strong coincidence is proved to be a sufficient condition for the dynamical system associated with a non-unimodular substitution of Pisot type to be measure-theoretically isomorphic with an exchange of domain on a set called the Rauzy fractal of the substitution. The Rauzy fractal is a self-similar compact subset of the product of an Euclidean space with finite extensions of p-adic fields. As a consequence, every substitutive dynamical system of Pisot type is a finite extension of its maximal equicontinuous factor. We prove that this maximal factor contains a p-adic translation if and only if the incidence matrix of the substitution is nilpotent modulo p. 1248A. SiegelUne réponse complète aété obtenue durant les années 1960-1970 concernant les substitutions de longueur constante (voir en particulier [Kam72, Mar73, Dek78]) : le facteuréquicontinu maximal d'un système substitutif de longueur constante l est une translation sur le produit direct du groupe des entiers l-adiques Z l et d'un groupe fini ; il y a de plus un isomorphisme mesurable entre un système substitutif de longueur constante et son facteuréquicontinu maximal si et seulement si la substitution vérifie une condition combinatoire simple dite de coïncidences [Dek78].Concernant l'étude des substitutions de longueur non constante, un pas significatif fut de montrer que les fonctions propres des systèmes substitutifs primitifs sont continues ([Hos86], voir aussi [FMN96]). Ainsi, très opportunément, les deux principales classifications dynamiques que sont la classification par isomorphisme mesurable et celle par isomorphisme topologique sontéquivalentes dans le cas des systèmes substitutifs primitifs. De plus, le spectre discret d'un système substitutif se divise en deux parties : la première, d'origine arithmétique, provient de la matrice d'incidence de la substitution ; la seconde, combinatoire, est liée aux mots de retour associés au point fixe de la substitution. Des conditions partielles, certaines suffisantes, d'autres nécessaires, pour qu'un système substitutif soità spectre discret, ontété obtenuesà partir des méthodes développées dans [Hos86] (voir [Hos92, Sol92, Liv92, FMN96] en particulier).Pour les substitutions de type Pisot unimodulaires, la partie arithmétique du spectre est entièrement déterminée :étant convenu que les valeur propres seront toujours notées additivement, le spectre arithmétique est engendré par les fréquences d'apparition des let...