Transcriptional Assessment by Microarray Analysis and Large-Scale Meta-analysis of the Metabolic Capacity of Cardiac and Skeletal Muscle Tissues to Cope With Reduced Nutrient Availability in Gilthead Sea Bream (Sparus aurata L.)

The effects of nutrient availability on the transcriptome of cardiac and skeletal muscle tissues were assessed in juvenile gilthead sea bream fed with a standard diet at two feeding levels: (1) full ration size and (2) 70 % satiation followed by a finishing phase at the maintenance ration. Microarray analysis evidenced a characteristic transcriptomic profile for each muscle tissue following changes in oxidative capacity (heart > red skeletal muscle > white skeletal muscle). The transcriptome of heart and secondly that of red skeletal muscle were highly responsive to nutritional changes, whereas that of glycolytic white skeletal muscle showed less ability to respond. The highly expressed and nutritionally regulated genes of heart were mainly related to signal transduction and transcriptional regulation. In contrast, those of white muscle were enriched in gene ontology (GO) terms related to proteolysis and protein ubiquitination. Microarray meta-analysis using the bioinformatic tool Fish and Chips (http://fishandchips.genouest.org/index.php) showed the close association of a representative cluster of white skeletal muscle with some of cardiac and red skeletal muscle, and many GO terms related to mitochondrial function appeared to be common links between them. A second round of cluster comparisons revealed that mitochondria-related GOs also linked differentially expressed genes of heart with those of liver from cortisol-treated gilthead sea bream. These results show that mitochondria are among the first responders to environmental and nutritional stress stimuli in gilthead sea bream, and functional phenotyping of this cellular organelle is highly promising to obtain reliable markers of growth performance and well-being in this fish species. © 2014 Springer Science+Business Media New York.This work was funded by the EU seventh Framework Programme by the AQUAEXCEL (Aquaculture Infrastructures for Excellence in European Fish Research, FP7/2007-2012; grant agreement no. 262336) project. Additional funding was obtained from the Generalitat Valenciana (research grant PROMETEO 2010/006) and the Spanish Government through AQUAGENOMICS project (Consolider-Ingenio-2010 Programme).Peer Reviewe

Mitochondria as key responders of metabolic and hormonal disturbances in fish. Meta-analysis flowchart of transcriptomic data in gilthead sea bream (Sparus aurata)

Trabajo presentado en el 17th International Congress of Comparative Endocrinology celebrado en Barcelona del 15 al 19 de julio de 2013The application of genomic technologies in aquaculture is providing a growing number of valuable information about the metabolic mechanisms controlling key traits for optimal performance in cultured fish. For instance, development of fish-specific microarrays has allowed researchers to monitor the simultaneous expression of thousands of genes on a vast diversity of experimental conditions. Nevertheless, an integration of the heterogeneous data generated to detect common patterns of gene activity for particular traits is still far to be achieved. On this issue, the integrated meta-analyses of functional genomics data have enormous potential for identifying phenotype-associated genes. To achieve this goal, the bioinformatic tool Fish and Chips (http://fishandchips.genouest.org), specifically designed for the meta-analysis of fish-related microarray experiments, has been constructed. It involves an automatic re-normalization and re-analysis of the included datasets from fish species of interest in aquaculture and in basic research (355 stored to date, from public repositories and private experiments) to identify clusters of co-expressed genes that are functionally annotated. Meta-analysis of a group of differentially expressed genes in white skeletal muscle samples of gilthead sea bream from a feed restriction trial showed a close relationship with other clusters from aerobic muscles (heart and red skeletal muscle) derived from the same experience, and many gene ontology (GO) terms related to mitochondria function appeared as common links among clusters. More interestingly, a second round of cluster profile comparison revealed that mitochondria-related GOs were also linking differentially expressed genes from heart samples of the feed restriction trial with liver samples of gilthead sea bream with cortisol-treated fish. These results evidence that mitochondria are among the first responders to various stress challenging homeostasis of the cell and organism, and further characterization in fish of this cellular organelle is desirable in order to obtain reliable markers of optimal growth and performance in aquaculture.Peer Reviewe

Milk Antibody Collection

Milk Antibody Collection. Biopolymères' 2010 Matrices alimentaires : Construction, déconstruction, propriétés sensorielles et nutritionnelle

Milk Antibody Collection

Milk Antibody Collection. Biopolymères' 2010 Matrices alimentaires : Construction, déconstruction, propriétés sensorielles et nutritionnelle

Transcriptional assessment by microarray analysis and large-scale meta-analysis of the metabolic capacity of cardiac and skeletal muscle tissues to cope with reduced nutrient availability in Gilthead Sea Bream [i](Sparus aurata L.).[/i]

The effects of nutrient availability on the transcriptome of cardiac and skeletal muscle tissues were assessed in juvenile gilthead sea bream fed with a standard diet at two feeding levels: (1) full ration size and (2) 70 % satiation followed by a finishing phase at the maintenance ration. Microarray analysis evidenced a characteristic transcriptomic profile for each muscle tissue following changes in oxidative capacity (heart > red skeletal muscle > white skeletal muscle). The transcriptome of heart and secondly that of red skeletal muscle were highly responsive to nutritional changes, whereas that of glycolytic white skeletal muscle showed less ability to respond. The highly expressed and nutritionally regulated genes of heart were mainly related to signal transduction and transcriptional regulation. In contrast, those of white muscle were enriched in gene ontology (GO) terms related to proteolysis and protein ubiquitination. Microarray meta-analysis using the bioinformatic tool Fish and Chips ( http://fishandchips.genouest.org/index.php ) showed the close association of a representative cluster of white skeletal muscle with some of cardiac and red skeletal muscle, and many GO terms related to mitochondrial function appeared to be common links between them. A second round of cluster comparisons revealed that mitochondria-related GOs also linked differentially expressed genes of heart with those of liver from cortisol-treated gilthead sea bream. These results show that mitochondria are among the first responders to environmental and nutritional stress stimuli in gilthead sea bream, and functional phenotyping of this cellular organelle is highly promising to obtain reliable markers of growth performance and well-being in this fish species

A common gene signature across multiple studies relate biomarkers and functional regulation in tolerance to renal allograft

International audiencePatients tolerant to a kidney graft display a specific blood cell transcriptional pattern but results from five different studies were inconsistent, raising the question of relevance for future clinical application. To resolve this, we sought to identify a common gene signature, specific functional and cellular components, and discriminating biomarkers for tolerance following kidney transplantation. A meta-analysis of studies identified a robust gene signature involving proliferation of B and CD4 T cells, and inhibition of CD14 monocyte related functions among 96 tolerant samples. This signature was further supported through a cross-validation approach, yielding 92.5% accuracy independent of the study of origin. Experimental validation, performed on new tolerant samples and using a selection of the top-20 biomarkers, returned 91.7% of good classification. Beyond the confirmation of B-cell involvement, our data also indicated participation of other cell subsets in tolerance. Thus, the use of the top 20 biomarkers, mostly centered on B cells, may provide a common and standardized tool towards personalized medicine for the monitoring of tolerant or low-risk patients among kidney allotransplant recipients. These data point to a global preservation of genes favoring the maintenance of a homeostatic and 'healthy' environment in tolerant patients and may contribute to a better understanding of tolerance maintenance mechanisms