First isolation of Clostrioides difficile from smoked and dried freshwater fish in Cambodia

In Cambodia, freshwater aquaculture is the most important source of food production. Fresh fish meat is considered a highly perishable food that requires the use of different manipulations and preservation techniques to inhibit the proliferation of undesirable bacteria. These bacteria are naturally present in the raw product or could be acquired during manipulation by cross-contamination. Many studies worldwide have investigated the epidemiology of Clostridioides difficile (C. difficile) in food, but to date, there are no publications about the bacterium in ready-to-eat fish or descriptions in Cambodia. The objective of this study was to assess the presence of C. difficile in one of the main food supplies of this country, smoked freshwater fish, originating from different provinces. A total of 25 samples were collected directly from local markets, yielding 4 C. difficile isolates and an overall recovery rate of 16%. Most of the isolates were toxigenic and classified as rare PCR profiles, and they were resistant to clindamycin. These findings indicate contamination during handling and/or contamination of the raw fish, followed by insufficient heat treatment to kill the spores. The presence of C. difficile in smoked and dried fish implies a potential risk of human exposure, contamination and infection

Mechanisms and Evolutionary Patterns of Mammalian and Avian Dosage Compensation

A large-scale comparative gene expression study reveals the different ways in which the chromosome-wide gene dosage reductions resulting from sex chromosome differentiation events were compensated during mammalian and avian evolution

Successful transmission and transcriptional deployment of a human chromosome via mouse male meiosis

Most human aneuploidies originate maternally, due in part to the presence of highly stringent checkpoints during male meiosis. Indeed, male sterility is common among aneuploid mice used to study chromosomal abnormalities, and male germline transmission of exogenous DNA has been rarely reported. Here we show that, despite aberrant testis architecture, males of the aneuploid Tc1 mouse strain produce viable sperm and transmit human chromosome 21 to create aneuploid offspring. In these offspring, we mapped transcription, transcriptional initiation, enhancer activity, non-methylated DNA, and transcription factor binding in adult tissues. Remarkably, when compared with mice derived from female passage of human chromosome 21, the chromatin condensation during spermatogenesis and the extensive epigenetic reprogramming specific to male germline transmission resulted in almost indistinguishable patterns of transcriptional deployment. Our results reveal an unexpected tolerance of aneuploidy during mammalian spermatogenesis, and the surprisingly robust ability of mouse developmental machinery to accurately deploy an exogenous chromosome, regardless of germline transmission.This research was supported by Cancer Research UK (CE, CK, FC, TFR, ML, DTO), the European Molecular Biology Laboratory (NE), the Wellcome Trust (106563/Z/14/A: SJA and 098024/Z/11/Z: RJK) and the European Research Council (DTO)

Large scale assessment of regulatory evolution and transcriptome complexity in mammals

AbstractIn addition to genetic changes affecting the function of gene products, changes in gene expression have been suggested to underlie many or even most of the phenotypic differences among mammals. However, detailed gene expression comparisons were, until recently, restricted to closely related species, owing to technological limitations. Thus, we took advantage of the latest technologies (RNA-Seq) to generate extensive qualitative and quantitative transcriptome data for a unique collection of somatic and germline tissues from representatives of all major mammalian lineages (placental mammals, marsupials and monotremes) and birds, the evolutionary outgroup.In the first major project of my thesis, we performed global comparative analyses of gene expression levels based on these data. Our analyses provided fundamental insights into the dynamics of transcriptome change during mammalian evolution (e.g., the rate of expression change across species, tissues and chromosomes) and allowed the exploration of the functional relevance and phenotypic implications of transcription changes at a genome-wide scale (e.g., we identified numerous potentially selectively driven expression switches).In a second project of my thesis, which was also based on the unique transcriptome data generated in the context of the first project we focused on the evolution of alternative splicing in mammals. Alternative splicing contributes to transcriptome complexity by generating several transcript isoforms from a single gene, which can, thus, perform various functions. To complete the global comparative analysis of gene expression changes, we explored patterns of alternative splicing evolution. This work uncovered several general and unexpected patterns of alternative splicing evolution (e.g., we found that alternative splicing evolves extremely rapidly) as well as a large number of conserved alternative isoforms that may be crucial for the functioning of mammalian organs.Finally, the third and final project of my PhD consisted in analyzing in detail the unique functional and evolutionary properties of the testis by exploring the extent of its transcriptome complexity. This organ was previously shown to evolve rapidly both at the phenotypic and molecular level, apparently because of the specific pressures that act on this organ and are associated with its reproductive function. Moreover, my analyses of the amniote tissue transcriptome data described above, revealed strikingly widespread transcriptional activity of both functional and nonfunctional genomic elements in the testis compared to the other organs. To elucidate the cellular source and mechanisms underlying this promiscuous transcription in the testis, we generated deep coverage RNA-Seq data for all major testis cell types as well as epigenetic data (DNA and histone methylation) using the mouse as model system. The integration of these complete dataset revealed that meiotic and especially post-meiotic germ cells are the major contributors to the widespread functional and nonfunctional transcriptome complexity of the testis, and that this "promiscuous" spermatogenic transcription is resulting, at least partially, from an overall transcriptionally permissive chromatin state. We hypothesize that this particular open state of the chromatin results from the extensive chromatin remodeling that occurs during spermatogenesis which ultimately leads to the replacement of histones by protamines in the mature spermatozoa. Our results have important functional and evolutionary implications (e.g., regarding new gene birth and testicular gene expression evolution).Generally, these three large-scale projects of my thesis provide complete and massive datasets that constitute valuables resources for further functional and evolutionary analyses of mammalian genomes

Phénoménologie et modélisation d'écoulements aérodynamiques instationnaires décollés pour la prévision des phénomènes aéroélastiques liés au tremblement des avions civils

L'objectif de ces travaux décrits dans ce mémoire est la modélisation du phénomène de tremblement susceptible d'être provoqué sur avions quadrimoteurs par un décollement à l'intrados de la voilure, côté interne de l'installation motrice externe. Cette étude doit permettre, à terme de mieux prédire le risque de vibration de ce type d'avions dans leur domaine de vol. La méthode retenue consiste à proposer un modèle semi-empirique des efforts instationnaires liés aux zones décollées, ces grandeurs restant inaccessibles, pour le moment, à la simulation numérique. Ces efforts sont ensuite appliqués en tant que forces extérieures à un modèle représentant le comportement dynamique de l'avion. Les décollements de bord d'attaque d'intrados voilure sur plusieurs quadrimoteurs sont, pour cela, étudiés grâce à l'analyse de nombreux essais en soufflerie et en vol. La capacité des codes de calcul à prédire ce type de décollement est également testée. Les nombreux cas étudiés au cours de cette thèse ont montré que les caractéristiques des fluctuations de pression dans ces zones décollées sont assez génériques dès lors qu'elles sont adimensionnées en pression dynamique et en fréquence réduite. Le modèle semi-empirique des fluctuations de pression repose alors sur l'interpolation d'un nombre limité de spectres en fréquence mesurés en soufflerie, sur des fonctions de coorrélation spatiale analytiques et sur la dimension des zones décollées fournie par les calculs numériques stationnaires. Il permet finalement d'estimer, par intégration des fluctuations de pression modélisées, les efforts provoqués par le décollement. Les calculs vibratoires réalisés pour estimer la réponse de l'avion à ces efforts modélisés ont apporté une première validation de la méthodologie retenue. Les caractéristiques spectrales et amplitude des vibrations observées sur avion ont en effet été reproduites.TOULOUSE-ISAE (315552318) / SudocSudocFranceF

Improvement of livestock breeding strategies using physiologic and functional genomic information of the muscle regulatory factors gene family for skeletal muscle development

A defined number of skeletal muscle fibers are formed in two separate waves during prenatal development, while postnatal growth is restricted to hypertrophic muscle fiber growth. The genes of the MRF (muscle regulatory factors) gene family, consisting of 4 structurally related transcription factors - myogenin, MyoD1, myf-5, and MRF4 - regulate both skeletal muscle fiber development and postnatal hypertrophic growth. In meat producing animals, skeletal muscle tissue becomes meat after slaughtering. Skeletal muscle fibers are the major cell type of meat mass. Thus, differences in the activity of the MRF gene family may be very important for the amount of meat deposited in these animals, which is of major economic importance. Therefore, the MRF genes can be considered as potential candidate genes to investigate the relation between genomic variation in these genes and skeletal muscle mass, and thus meat mass. In this review we discuss the MRF gene family in relation to meat production, and show that information of genomic variation in these functional genes, and variation in their expression provide information that can be used in commercial breeding. Furthermore, we will review experiments that show that hormones, growth factors, and specific drugs can affect the expression of these genes, thus potentially affecting skeletal muscle mass and thus meat mass, offering several potential strategies for steering of meat production, and showing the power of functional genomics. Using the genetic information available from these experiments, ways to speed up genetic improvement of livestock breeding and future research directions will be highlighted