In silico identification and molecular characterization of genes predominantly expressed in the fish oocyte

Background: In fish, molecular mechanisms that control follicle-enclosed oocyte progression throughout oogenesis and oocyte developmental competence acquisition remain poorly understood. Existing data in mammals have indicated that the so called "oocyte-specific" genes play an important role in oogenesis, fertilization, and early embryo development. In teleost species, very little is known about "oocyte-specific" genes. The present study therefore aimed at identifying and characterizing oocyte-specific genes in fish. Results: Using digital differential display PCR, mouse ESTs exhibiting an oocyte-predominant expression were identified. Those murine ESTs were subsequently used to identify cognate rainbow trout (Oncorhynchus mykiss) ESTs using a reciprocal Blast search strategy. In the present study we report the identification of five previously uncharacterized rainbow trout cDNAs exhibiting a oocyte-specific, oocyte-predominant, or gonad-specific expression: zygote arrest 1 (zar1), v-mos Moloney murine sarcoma viral oncogene-like protein (mos), B-cell translocation gene (btg3), growth differentiation factor 9 (gdf9), and mutS homolog 4 (msh4). The orthology relationship of each of these genes with vertebrate counterparts was verified by phylogenetic analysis. Among those five genes, three had never been characterized in any fish species. In addition, we report the oocyte-predominant expression of btg3 for the first time in any vertebrate species. Finally, those five genes are present in unfertilized eggs as maternally-inherited mRNAs thus suggesting that they could participate in ovarian folliculogenesis as well as early embryonic development. Conclusion: The expression patterns of zar1, mos, btg3, gdf9 and msh4 in rainbow trout and the functions of their orthologs in higher vertebrates strongly suggest that they might play an important role in follicle-enclosed oocyte development, meiosis control and early embryonic development in fish. Future investigations are however required to unravel the participation of those strong candidates in the molecular processes that control folliculogenesis and/or oocyte developmental competence in fish

In silico identification and molecular characterization of genes predominantly expressed in the fish oocyte

<p>Abstract</p> <p>Background</p> <p>In fish, molecular mechanisms that control follicle-enclosed oocyte progression throughout oogenesis and oocyte developmental competence acquisition remain poorly understood. Existing data in mammals have indicated that the so called "oocyte-specific" genes play an important role in oogenesis, fertilization, and early embryo development. In teleost species, very little is known about "oocyte-specific" genes. The present study therefore aimed at identifying and characterizing oocyte-specific genes in fish.</p> <p>Results</p> <p>Using digital differential display PCR, mouse ESTs exhibiting an oocyte-predominant expression were identified. Those murine ESTs were subsequently used to identify cognate rainbow trout (<it>Oncorhynchus mykiss</it>) ESTs using a reciprocal Blast search strategy. In the present study we report the identification of five previously uncharacterized rainbow trout cDNAs exhibiting a oocyte-specific, oocyte-predominant, or gonad-specific expression: zygote arrest 1 (<it>zar1</it>), v-mos Moloney murine sarcoma viral oncogene-like protein (<it>mos</it>), B-cell translocation gene (<it>btg3</it>), growth differentiation factor 9 (<it>gdf9</it>), and mutS homolog 4 (<it>msh4</it>). The orthology relationship of each of these genes with vertebrate counterparts was verified by phylogenetic analysis. Among those five genes, three had never been characterized in any fish species. In addition, we report the oocyte-predominant expression of <it>btg3 </it>for the first time in any vertebrate species. Finally, those five genes are present in unfertilized eggs as maternally-inherited mRNAs thus suggesting that they could participate in ovarian folliculogenesis as well as early embryonic development.</p> <p>Conclusion</p> <p>The expression patterns of <it>zar1</it>, <it>mos</it>, <it>btg3</it>, <it>gdf9 </it>and <it>msh4 </it>in rainbow trout and the functions of their orthologs in higher vertebrates strongly suggest that they might play an important role in follicle-enclosed oocyte development, meiosis control and early embryonic development in fish. Future investigations are however required to unravel the participation of those strong candidates in the molecular processes that control folliculogenesis and/or oocyte developmental competence in fish.</p

Browsing repeats in genomes: Pygram and an application to non-coding region analysis

BACKGROUND: A large number of studies on genome sequences have revealed the major role played by repeated sequences in the structure, function, dynamics and evolution of genomes. In-depth repeat analysis requires specialized methods, including visualization techniques, to achieve optimum exploratory power. RESULTS: This article presents Pygram, a new visualization application for investigating the organization of repeated sequences in complete genome sequences. The application projects data from a repeat index file on the analysed sequences, and by combining this principle with a query system, is capable of locating repeated sequences with specific properties. In short, Pygram provides an efficient, graphical browser for studying repeats. Implementation of the complete configuration is illustrated in an analysis of CRISPR structures in Archaea genomes and the detection of horizontal transfer between Archaea and Viruses. CONCLUSION: By proposing a new visualization environment to analyse repeated sequences, this application aims to increase the efficiency of laboratories involved in investigating repeat organization in single genomes or across several genomes

Modeling local repeats on genomic sequences

This paper deals with the specification and search of repeats of biological interest, i.e. repeats that may have a role in genomic structures or functions. Although some particular repeats such as tandem repeats have been well formalized, models developed so far remain of limited expressivity with respect to known forms of repeats in biological sequences. This paper introduces new general and realistic concepts characterizing potentially useful repeats in a sequence: Locality and several refinements around the Maximality concept. Locality is related to the distribution of occurrences of repeated elements and characterizes the way occurrences are clustered in this distribution. The associated notion of neighborhood allows to indirectly exhibit words with a distribution of occurrences that is correlated to a given distribution. Maximality is related to the contextual delimitation of the repeated units. We have extended the usual notion of maximality, working on the inclusion relation between repeats and taking into account larger contexts. Mainly, we introduced a new repeat concept, largest maximal repeats, looking for the existence of a subset of maximal occurrences of a repeated word instead of a global maximization. We propose algorithms checking for local and refined maximal repeats using at the conceptual level a suffix tree data structure. Experiments on natural and artificial data further illustrate various aspects of this new setting. All programs are available on the genouest platform, at http://genouest.org/modulome

Single-cell scattering and auto-fluorescence-based fast antibiotic susceptibility testing for gram-negative and gram-positive bacteria

In this study, we assess the scattering of light and auto-fluorescence from single bacterial cells to address the challenge of fast (&lt;2 h), label-free phenotypic antimicrobial susceptibility testing (AST). Label-free flow cytometry is used for monitoring both the respiration-related auto-fluorescence in two different fluorescence channels corresponding to FAD and NADH, and the morphological and structural information contained in the light scattered by individual bacteria during incubation with or without antibiotic. Large multi-parameter data are analyzed using dimensionality reduction methods, based either on a combination of 2D binning and Principal Component Analysis, or with a one-class Support Vector Machine approach, with the objective to predict the Susceptible or Resistant phenotype of the strain. For the first time, both Escherichia coli (Gram-negative) and Staphylococcus epidermidis (Gram-positive) isolates were tested with a label-free approach, and, in the presence of two groups of bactericidal antibiotic molecules, aminoglycosides and beta-lactams. Our results support the feasibility of label-free AST in less than 2 h and suggest that single cell auto-fluorescence adds value to the Susceptible/Resistant phenotyping over single-cell scattering alone, in particular for the mecA+ Staphylococcus (i.e., resistant) strains treated with oxacillin

Climatic risks and impacts in South Asia: extremes of water scarcity and excess

This paper reviews the current knowledge of climatic risks and impacts in South Asia associated with anthropogenic warming levels of 1.5°C to 4°C above pre-industrial values in the 21st century. It is based on the World Bank Report “Turn Down the Heat, Climate Extremes, Regional Impacts and the Case for Resilience” (2013). Many of the climate change impacts in the region, which appear quite severe even with relatively modest warming of 1.5–2°C, pose significant hazards to development. For example, increased monsoon variability and loss or glacial meltwater will likely confront populations with ongoing and multiple challenges. The result is a significant risk to stable and reliable water resources for the region, with increases in peak flows potentially causing floods and dry season flow reductions threatening agriculture. Irrespective of the anticipated economic development and growth, climate projections indicate that large parts of South Asia’s growing population and especially the poor are likely to remain highly vulnerable to climate change

Modes guidés dans un milieu stratifié perturbé

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La dynamique d’émergence d’un standard industriel : proposition d’une grille d’analyse théorique

International audienceThe goal of this paper is to present a model aimed at analyzing battles for technological standards. It is based mainly on evolutionist economy and innovation sociology. These approaches are combined in a strategic management frame, which leads us to analyze the ability to win battles of standards as a dynamic capability.Cet article vise à présenter une grille d’analyse des batailles de standards industriels issue principalement de l’économie évolutionniste (concept de rendements croissants d’adoption) et de la sociologie de l’innovation. Le but est d’intégrer ces différents éléments à une démarche de management stratégique. Nous montrons que la capacité à imposer un standard peut alors être analysée comme une capacité dynamique

Changement climatique et risques du rayonnement UV

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