Approche statistique d'une exploitation halieutique : le cas de la pêche artisanale au Sénégal

L'activité d'une pêcherie est déterminée par l'état de la ressource, mais aussi par d'autres conditions (sociales, économiques, ...) influant sur la nature de la pêche qui est menée. Notre travail consiste à proposer une approche statistique permettant de représenter conjointement les dynamiques de la ressource exploitée et de l'effort de pêche, et de l'appliquer à la pêche artisanale sénégalaise. Après avoir exposé dans un premier chapitre le système de collecte de données, et avoir effectué une revue des modèles usuels, nous proposons dans un second chapitre, une synthèse des données à l'aide de techniques d'ACPVI. Nous reprenons ensuite un modèle couplant ressource et exploitation qui caractérise la pêcherie à l'aide de trois composantes (unités de pêche, actions de pêche, ressource), chaque composante étant définie par une typologie. Nous abordons alors le problème de l'ajustement de ce modèle aux données collectées en décrivant les différents problèmes posés, et en proposant une procédure d'ajustement. Cette procédure est mise en oeuvre dans un cinquième chapitre sur un jeu de données relatif à la pêche artisanale sénégalaise consistant en 7 séries chronologiques d'efforts de pêche et 36 séries de captures par espèce associées par quinzaine, de 1974 à 1992. Le sixième chapitre est consacré à l'évaluation pouvant être faite d'un tel modèle, avant de présenter quels apports peuvent être attendus de ce travail. (Résumé d'auteur

Influence of glass/mould interfaces on sticking

The sticking of glass on mould materials is a critical problem since it can lead to the Interruption of glass Container production. This study is a contribution to understanding the phenomena at the origin of sticking. The experiments involve loading and spreading glass gobs on flat metallic Substrates. They are performed directly on a glassmaking machine, thus the thermal conditions of the processes are simulated as closely as possible. Special attention is paid to characterizing the metal and glass surfaces before and after contact using a surface profilometer, AFM, and SEM with an EDX spectrometer. The influence on sticking of mould temperature, surface roughness and surface chemistry (nonoxidized, pre-oxidized and lubricated) is investigated

Trade-off between morphological convergence and opportunistic diet behavior in fish hybrid zone

<p>Abstract</p> <p>Background</p> <p>The invasive <it>Chondrostoma nasus nasus </it>has colonized part of the distribution area of the protected endemic species <it>Chondrostoma toxostoma toxostoma</it>. This hybrid zone is a complex system where multiple effects such as inter-species competition, bi-directional introgression, strong environmental pressure and so on are combined. Why do sympatric <it>Chondrostoma </it>fish present a unidirectional change in body shape? Is this the result of inter-species interactions and/or a response to environmental effects or the result of trade-offs? Studies focusing on the understanding of a trade-off between multiple parameters are still rare. Although this has previously been done for Cichlid species flock and for Darwin finches, where mouth or beak morphology were coupled to diet and genetic identification, no similar studies have been done for a fish hybrid zone in a river. We tested the correlation between morphology (body and mouth morphology), diet (stable carbon and nitrogen isotopes) and genomic combinations in different allopatric and sympatric populations for a global data set of 1330 specimens. To separate the species interaction effect from the environmental effect in sympatry, we distinguished two data sets: the first one was obtained from a highly regulated part of the river and the second was obtained from specimens coming from the less regulated part.</p> <p>Results</p> <p>The distribution of the hybrid combinations was different in the two part of the sympatric zone, whereas all the specimens presented similar overall changes in body shape and in mouth morphology. Sympatric specimens were also characterized by a larger diet behavior variance than reference populations, characteristic of an opportunistic diet. No correlation was established between the body shape (or mouth deformation) and the stable isotope signature.</p> <p>Conclusion</p> <p>The Durance River is an untamed Mediterranean river despite the presence of numerous dams that split the river from upstream to downstream. The sympatric effect on morphology and the large diet behavior range can be explained by a tendency toward an opportunistic behavior of the sympatric specimens. Indeed, the similar response of the two species and their hybrids implied an adaptation that could be defined as an alternative trade-off that underline the importance of epigenetics mechanisms for potential success in a novel environment.</p

Genetic manipulation of adult-born hippocampal neurons rescues memory in a mouse model of Alzheimer's disease

Richetin et al. demonstrate that retroviral expression of the transcription factor NeuroD1 in neural progenitor cells of the adult mouse hippocampus promotes differentiation, maturation and synaptic integration of newborn granule cells in vivo. When applied to a mouse model of Alzheimer's disease, the gene-targeting strategy abolishes hippocampus-dependent memory deficit

Cancer evolution: mathematical models and computational inference.

Cancer is a somatic evolutionary process characterized by the accumulation of mutations, which contribute to tumor growth, clinical progression, immune escape, and drug resistance development. Evolutionary theory can be used to analyze the dynamics of tumor cell populations and to make inference about the evolutionary history of a tumor from molecular data. We review recent approaches to modeling the evolution of cancer, including population dynamics models of tumor initiation and progression, phylogenetic methods to model the evolutionary relationship between tumor subclones, and probabilistic graphical models to describe dependencies among mutations. Evolutionary modeling helps to understand how tumors arise and will also play an increasingly important prognostic role in predicting disease progression and the outcome of medical interventions, such as targeted therapy.FM would like to acknowledge the support of The University of Cambridge, Cancer Research UK and Hutchison Whampoa Limited.This is the final published version. It first appeared at http://sysbio.oxfordjournals.org/content/early/2014/10/07/sysbio.syu081.short?rss=1

SESAME (SEquence Sorter & AMplicon Explorer): genotyping based on high-throughput multiplex amplicon sequencing

Summary: Characterizing genetic diversity through genotyping short amplicons is central to evolutionary biology. Next-generation sequencing (NGS) technologies changed the scale at which these type of data are acquired. SESAME is a web application package that assists genotyping of multiplexed individuals for several markers based on NGS amplicon sequencing. It automatically assigns reads to loci and individuals, corrects reads if standard samples are available and provides an intuitive graphical user interface (GUI) for allele validation based on the sequences and associated decision-making tools. The aim of SESAME is to help allele identification among a large number of sequences

Regulatory Features Underlying Pollination-Dependent and -Independent Tomato Fruit Set Revealed by Transcript and Primary Metabolite Profiling

Indole Acetic Acid 9 (IAA9) is a negative auxin response regulator belonging to the Aux/IAA transcription factor gene family whose downregulation triggers fruit set before pollination, thus giving rise to parthenocarpy. In situ hybridization experiments revealed that a tissue-specific gradient of IAA9 expression is established during flower development, the release of which upon pollination triggers the initiation of fruit development. Comparative transcriptome and targeted metabolome analysis uncovered important features of the molecular events underlying pollination-induced and pollination-independent fruit set. Comprehensive transcriptomic profiling identified a high number of genescommonto both types of fruit set,amongwhich only a small subset are dependent on IAA9 regulation. The fine-tuning of Aux/IAA and ARF genes and the downregulation of TAG1 and TAGL6 MADS box genes are instrumental in triggering the fruit set program. Auxin and ethylene emerged as the most active signaling hormones involved in the flower-to-fruit transition. However, while these hormones affected only a small number of transcriptional events, dramatic shifts were observed at the metabolic and developmental levels. The activation of photosynthesis and sucrose metabolism-related genes is an integral regulatory component of fruit set process. The combined results allow a far greater comprehension of the regulatory and metabolic events controlling early fruit development both in the presence and absence of pollination/fertilization

Development of 55 novel polymorphic microsatellite loci for the critically endangered L. (Actinopterygii: Perciformes: Percidae) and cross-species amplification in five other percids

International audienceBy combining biotin-enrichment protocol and next generation pyrosequencing, through 454 GS-FLX Titanium technology, 55 polymorphic microsatellites loci with perfect motif were isolated from the Rhone streber (), a critically endangered European fish species. Eight multiplex PCR kits were optimised in order to genotype a total of 58 polymorphic loci, including three previously published loci. The level of genetic diversity was assessed for 68 , 30 , 33 and four individuals. Amplification success was also assessed on and using single individuals. These markers will be useful to investigate the population structure of the highly fragmented Rhone streber. They represent a powerful tool for conservation issues and evolutionary approaches of this endemic species. Moreover, part of our markers demonstrated applicability to other percid species, allowing for potential applications to fisheries and aquaculture management

L’évaluation par indicateurs : un outil nécessaire d’aménagement urbain durable ?: Réflexions à partir de la démarche parisienne pour le géographe et l'aménageur

International audienceLes pratiques d'évaluation par indicateurs se multiplient dans les projets de durabilité urbaine, surtout en aménagement urbain durable. La Ville de Paris a notamment mis en place, depuis 2007, un tableau de bord d'indicateurs adossé au référentiel " Un aménagement durable pour Paris " pour évaluer les niveaux de performance des opérations d'aménagement au regard des objectifs de développement durable. Ce tableau de bord permet d'évaluer la prise en compte de ces objectifs dans les opérations d'aménagement, en identifiant les niveaux de performance atteints, leurs points forts et leurs points faibles en vue de les faire progresser le cas échéant. À partir de l'expérience parisienne, l'article pose la nécessité d'un débat sur la pertinence de l'évaluation par indicateurs dans l'aménagement urbain durable. Il y répond en posant des conditions d'une culture propre de l'évaluation de la durabilité et en mettant en évidence des questionnements sur l'emboîtement des modes de gouvernance, la mise en œuvre et le suivi des objectifs fixés et des temporalités, ainsi que sur l'intégration des différentes échelles territoriale

Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing

<p>Abstract</p> <p>Background</p> <p>The rapid evolution of 454 GS-FLX sequencing technology has not been accompanied by a reassessment of the quality and accuracy of the sequences obtained. Current strategies for decision-making and error-correction are based on an initial analysis by Huse <it>et al. </it>in 2007, for the older GS20 system based on experimental sequences. We analyze here the quality of 454 sequencing data and identify factors playing a role in sequencing error, through the use of an extensive dataset for Roche control DNA fragments.</p> <p>Results</p> <p>We obtained a mean error rate for 454 sequences of 1.07%. More importantly, the error rate is not randomly distributed; it occasionally rose to more than 50% in certain positions, and its distribution was linked to several experimental variables. The main factors related to error are the presence of homopolymers, position in the sequence, size of the sequence and spatial localization in PT plates for insertion and deletion errors. These factors can be described by considering seven variables. No single variable can account for the error rate distribution, but most of the variation is explained by the combination of all seven variables.</p> <p>Conclusions</p> <p>The pattern identified here calls for the use of internal controls and error-correcting base callers, to correct for errors, when available (e.g. when sequencing amplicons). For shotgun libraries, the use of both sequencing primers and deep coverage, combined with the use of random sequencing primer sites should partly compensate for even high error rates, although it may prove more difficult than previous thought to distinguish between low-frequency alleles and errors.</p