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

SAW pressure sensor on quartz membrane lapping

National audienceThe fabrication of SAW quartz-based pressure sensors has received a strong interest for many years, yielding various development using either delay lines or resonators. However, most approaches have been developed exploiting quartz machining along standard chemical or mechanical etching, rarely compatible with batch processes as used for Micro-ElectroMechanical Systems (MEMS). In this work, we propose a temperature/pressure sensor fabricated on compound Quartz/Silicon substrates obtained by Au/Au bonding at room temperature and lapping/polishing of Quartz. This approach allows for a collective and accurate production of sensors, the sensor sensitivity being controlled by the membrane thickness and diameter. As the pressure is intricately connected with temperature, an objective estimation of this parameter requires accurate temperature measurements as well. As a consequence, the proposed sensor combines a reference resonator designed to be temperature compensated (AT,X cut of quartz) together with a resonator which propagation direction is chosen according the targeted temperature coefficient of frequency in order to give access to a linear differential temperature measurement. In addition, a third resonator with propagation axis along X is placed at the right center of a circular membrane. When the membrane is bent by pressure effects, the corresponding resonance frequency drifts linearly, allowing for another differential pressure measurement. Hence, with three resonators, one can easily demonstrate the unambiguous determination of temperature and pressure at once. Until now pressure sensor based on SAW with quartz material are unity processed. This process allows us a collective manufacturing of sensors. We start by seal the quartz wafer with the silicon substrate using the thin gold layer. This process yields an homogeneous and high quality bond. It is subsequently thinned and polished to an overall thickness of 100 microns. Aluminum electrodes are deposited on the quartz to achieve three SAW resonators. Process flow based on collective manufacturing is now developed. Electrical responses of SAW resonators are done. Results show the operability of the sensors and the responses are conformed to the design. Electrical test under pressure is currently under development

Surface-wave passive sensor including an integrated antenna and medical applications using such a type of passive sensor

Patent no WO/2009/083484, International Application No PCT/EP2008/067944, 09 juillet 2009, International Filing Date 18.12.2008

The Impact of Nutritional and Environmental Stressors on the Immune Response, Oxidative Stress and Energy Use of Rainbow Trout (Oncorhynchus Mykiss)

International audienc

Etude de materiaux specifiques, l'epitaxie de semi-conducteurs composes et l'adaptation du masquage electronique a la WSI. Theme 1: epitaxie de couches atomiques

SIGLECNRS AR 11238 / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc

Table_2_Acute Stress and an Electrolyte- Imbalanced Diet, but Not Chronic Hypoxia, Increase Oxidative Stress and Hamper Innate Immune Status in a Rainbow Trout (Oncorhynchus mykiss) Isogenic Line.DOCX

<p>In aquaculture, fish may be exposed to sub-optimal rearing conditions, which generate a stress response if full adaptation is not displayed. However, our current knowledge of several coexisting factors that may give rise to a stress response is limited, in particular when both chronic and acute stressors are involved. This study investigated changes in metabolic parameters, oxidative stress and innate immune markers in a rainbow trout (Oncorhynchus mykiss) isogenic line exposed to a combination of dietary (electrolyte-imbalanced diet, DEB 700 mEq Kg^-1) and environmental (hypoxia, 4.5 mg O₂ L^-1) challenges and their respective controls (electrolyte-balanced diet, DEB 200 mEq Kg^-1 and normoxia, 7.9 or mg O₂ L^-1) for 49 days. At the end of this period, fish were sampled or subjected to an acute stressor (2 min of handling/confinement) and then sampled. Feeding trout an electrolyte-imbalanced diet produced a reduction in blood pH, as well as increases in cortisol levels, hepato-somatic index (HSI) and total energy content in the liver. The ratio between the lactate dehydrogenase (LDH) and isocitrate dehydrogenase (IDH) activities decreased in the liver of trout fed the DEB 700 diet, but increased in the heart, suggesting a different modulation of metabolic capacity by the dietary challenge. Several markers of oxidative stress in the liver of trout, mainly related to the glutathione antioxidant system, were altered when fed the electrolyte-imbalanced diet. The dietary challenge was also associated with a decrease in the alternative complement pathway activity (ACH₅₀) in plasma, suggesting an impaired innate immune status in that group. Trout subjected to the acute stressor displayed reduced blood pH values, higher plasma cortisol levels as well as increased levels of metabolic markers associated with oxidative stress in the liver. An interaction between diet and acute stressor was detected for oxidative stress markers in the liver of trout, showing that the chronic electrolyte-imbalance impairs the response of rainbow trout to handling/confinement. However, trout reared under chronic hypoxia only displayed changes in parameters related to energy use in both liver and heart. Taken together, these results suggest that trout displays an adaptative response to chronic hypoxia. Conversely, the dietary challenge profoundly affected fish homeostasis, resulting in an impaired physiological response leading to stress, which then placed constraints on a subsequent acute challenge.</p