Meta-analysis of muscle transcriptome data using the MADMuscle database reveals biologically relevant gene patterns

<p>Abstract</p> <p>Background</p> <p>DNA microarray technology has had a great impact on muscle research and microarray gene expression data has been widely used to identify gene signatures characteristic of the studied conditions. With the rapid accumulation of muscle microarray data, it is of great interest to understand how to compare and combine data across multiple studies. Meta-analysis of transcriptome data is a valuable method to achieve it. It enables to highlight conserved gene signatures between multiple independent studies. However, using it is made difficult by the diversity of the available data: different microarray platforms, different gene nomenclature, different species studied, etc.</p> <p>Description</p> <p>We have developed a system tool dedicated to muscle transcriptome data. This system comprises a collection of microarray data as well as a query tool. This latter allows the user to extract similar clusters of co-expressed genes from the database, using an input gene list. Common and relevant gene signatures can thus be searched more easily. The dedicated database consists in a large compendium of public data (more than 500 data sets) related to muscle (skeletal and heart). These studies included seven different animal species from invertebrates (<it>Drosophila melanogaster, Caenorhabditis elegans</it>) and vertebrates (<it>Homo sapiens, Mus musculus, Rattus norvegicus, Canis familiaris, Gallus gallus</it>). After a renormalization step, clusters of co-expressed genes were identified in each dataset. The lists of co-expressed genes were annotated using a unified re-annotation procedure. These gene lists were compared to find significant overlaps between studies.</p> <p>Conclusions</p> <p>Applied to this large compendium of data sets, meta-analyses demonstrated that conserved patterns between species could be identified. Focusing on a specific pathology (Duchenne Muscular Dystrophy) we validated results across independent studies and revealed robust biomarkers and new pathways of interest. The meta-analyses performed with MADMuscle show the usefulness of this approach. Our method can be applied to all public transcriptome data.</p

Effet d'un choc hypotonique sur le volume cellulaire et sur la concentration intracellulaire de calcium des cellules branchiales de truite arc-en-ciel

La branchie étant un organe à structure complexe, il était impossible d'étudier l'effet d'un choc hypotonique sur les cellules branchiales in situ. Une culture primaire de branchie de truite a donc été mise au point et l'effet d'une dilution du milieu extracellulaire sur ces cellules en culture a été étudié. Les cellules branchiales en culture primaire forment un épithélium à confluence après 5 à 7 jours de culture. Ces cellules présentent les caractéristiques morphologiques des cellules respiratoires de la branchie. Les mesures du volume cellulaire, lors d'un choc hypotonique, sont effectuées sur des populations isolées de cellules respiratoires, à l'aide du système Coulter counter. Lors de la dilution aux 2/3 du milieu externe, les cellules gonflent pour atteindre un volume moyen de 130% en 5 minutes. Ensuite, les cellules régulent lentement leur volume. Après 30 minutes dans les conditions hypotoniques, le gonflement cellulaire ne représente plus que 110% du volume initial. Lors d'un choc hypotonique, nous avons mesuré, à l'aide d'une sonde fluorescente sensible au calcium (le Fura-2), une augmentation de la concentration intracellulaire de calcium des cellules respiratoires en culture primaire

Mechanosensitive calcium entry and mobilization in renal A6 cells

International audienc

Absence of tiGh effect on adaptability to brackish water in Tilapia (Oreochromis niloticus)

The aim of this study was to investigate the possible role of growth hormone in the adaptation of tilapia (Oreochromis niloticus) to brackish water and to analyze its interactions with prolactin in this process. Plasma levels of growth hormone do not change upon transfer to brackish water. Treatment of intact tilapia in fresh water with growth hormone prior to transfer did not enable the fish to preadapt to brackish water: the duration of the hydromineral imbalance after transfer was the same in treated animals and controls. The major osmoregulatory role of prolactin in fresh water led us to test the hypothesis that prolactin might antagonize the effect of growth hormone on adaptation to brackish water. Growth-hormone-treated hypophysectomized animals, however, exhibited no increased osmoregulatory capacity as compared to hypophysectomized controls, confirming the absence of a growth-hormone-related osmoregulatory effect. When prolactin and growth hormone were coinjected, growth hormone also proved unable to oppose the Na+ retaining effect of prolactin, in both brackish and fresh water. Surprisingly, hypophysectomized animals adapt better to brackish water than do sham-operated animals. This result is discussed in light of the effects of prolactin and cortisol on osmoregulation in brackish water and we suggest that an important event which allows O. niloticus to adapt to hyperosmotic environment is the reduction of plasma PRL upon transfer to brackish water

Global assessment of the response to chronic stress in European sea bass

Stress modifies energy allocation in fishes by redirecting energy from growth and reproduction to coping mechanisms. However, these adjustments become inappropriate when the challenge consists of sustained or repeated stressors, with the animal entering a maladaptive state. Capacities to cope with additional threats are then altered and compromise survival. The characterization of the responses to chronic stress in fishes helps better understanding the physiological limits in an aquaculture or ecological context. Here, we investigate the coping capacities of European sea bass to multiple and diverse stressors applied over a 3-weeks period. Multiple behavioural (group dispersion and swimming activity) and physiological responses (blood cortisol, osmoregulatory mechanisms, stress-related gene expression, etc.) were evaluated in resting fish or in fish exposed to additional challenges. Resilience to the chronic stress protocol was evaluated 4 months after the end of the chronic stress. Chronically stressed individuals showed reduced growth, lower cortisol response, increased chloride and sodium concentration in the plasma and modified gill gene expression translating osmoregulatory dysfunctions. Chronic stress had no significant effect on plasmatic calcium, lysozyme concentration and osmotic pressure. Increased thigmotaxic behaviour was observed in a new environment behavioural test. Four months after the chronic stress, no significant difference was observed in growth performances and in plasma parameters. Altogether, gills and more generally osmoregulatory functions were found to be the most sensitive to the chronic stress, while only limited changes in growth, activity of the HPI axis, immunity and swimming behaviour were observed when assessed individually. This work demonstrates the necessity of using multiple and diverse endpoints related to different functions to properly assess health and welfare in fishes

Xenobiotic and Steroid Biotransformation Activities in Rainbow Trout Gill Epithelial Cells in Culture.

Abstract not availableJRC.(EI)-Environment Institut