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GSE19275
Sus scrofa
67 Downloadable Samples
Affymetrix Porcine Genome Array (porcine)
Description
Background: Marketing products with added-value characteristics is a current trend in livestock production systems. Regarding meat, selection for intramuscular fat and muscular fatty acid composition is a way to improve the palatability and juiciness of meat while assuring a healthy fat content. This represents selecting animal with a different muscular metabolic profile with respect to the extended selection of lean animals. Results: The present study has analysed the muscular gene expression profiles of 68 commercial Duroc pigs belonging to two groups with extreme phenotypes for traits strongly related with lipid deposition and composition. This has allowed us to compare the physiological and metabolic implications of selecting for each of these extreme groups. Rather than upregulation of a single pathway, the main differences lied on the transcriptional levels of genes related with lipogenesis and lipolysis, revealing the existence of a cycle where triacylglycerols are continuously synthesized and degraded. Most strikingly, several genes which enhanced fatty acid -oxidation and favoured insulin signalling and glucose uptake were upregulated in the fattest animals, indicating that the events leading to peripheral insulin resistance in humans with increased levels of intramuscular fat and obesity do not take place in these pigs. Moreover, neither was detected the well-characterised low-grade inflammatory state observed in overweighed humans. Conclusion: As a whole, our data suggest that selection for increasing intramuscular fat content in pigs would lead to a shift but not a disruption of the metabolic homeostasis of muscle cells. Future studies on the post-translational changes affecting protein activity or expression as well as information about protein location within the cell would be needed to fully understand how lipid deposition affects muscle physiology in pigs.
Publication Title
Muscle transcriptomic profiles in pigs with divergent phenotypes for fatness traits.
Sample Metadata Fields
Age, Specimen part
View Samples- Sus scrofa
- 56 Downloadable Samples
- Affymetrix Porcine Genome Array (porcine)
Description
A mRNA expression study has been performed 20-25 minutes postmortem obtained samples from Longissimus dorsi muscle of 59 Duroc x LD/LW pigs to search for gene sequences related to meat quality (pH24, pH45, Lab colour coordinates, curing yield and exudation at three different times) or to meat composition (intramuscular fat, content of several fatty acid (C16:0, C18:0, C18:1 and C18:2), ratio of saturated, monounsaturated and polyunsaturated fatty acids, and protein and humidity contents) traits in order to find targets for selection. Gene ontology analysis, biological pathways and gene networks studies all show, that many more differentially expressed genes (506 vs 279) are related to meat quality (Group P, or perimortem characters) than to meat composition traits (Group L, or whole life traits). The difference between the number of GO terms annotated, biological pathways and gene networks in groups P and L is notable due to the differences in the complexity of the generation process of P-traits and the involvement of other tissues or organs in the generation of variability of L-traits. Also, interactions between a list of differentially expressed genes were found in ECM-receptor interaction, TGF-beta signaling pathway, fatty acid elongation in mitochondria and adipocytokine signalling pathway indicating that a substantial fraction of the gene networks could be associated with interactions between differential expressed genes related to traits under study. A high number of the most overexpressed genes are related to muscle development and functionality and repair mechanisms; they could be good candidates for breeding programs whose main goal is to enhance meat quality.
Publication Title
Early postmortem gene expression and its relationship to composition and quality traits in pig Longissimus dorsi muscle.
Sample Metadata Fields
Age, Specimen part
View Samples- Rattus norvegicus
- 35 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
retinal ganglion cells die after optic nerve injury, either crush or transection. The molecular causesunderlying this degeneration are largely unkwon
Publication Title
Time course profiling of the retinal transcriptome after optic nerve transection and optic nerve crush.
Sample Metadata Fields
No sample metadata fields
View Samples- Escherichia coli k-12
- 18 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
Although protein acetylation is widely observed, it has been associated with few specific regulatory functions making it poorly understood. To interrogate its functionality, we analyzed the acetylome in Escherichia coli knockout mutants of cobB, the only known sirtuin-like deacetylase, and patZ, the best-known protein acetyltransferase. For four growth conditions, more than 2,000 unique acetylated peptides, belonging to 809 proteins, were identified and differentially quantified. Nearly 65% of these proteins are related to metabolism. The global activity of CobB contributes to the deacetylation of a large number of substrates and has a major impact on physiology. Apart from the regulation of acetyl-CoA synthetase, we found that CobB-controlled acetylation of isocitrate lyase contributes to the fine-tuning of the glyoxylate shunt. Acetylation of the transcription factor RcsB prevents DNA binding, activating flagella biosynthesis and motility, and increases acid stress susceptibility. Surprisingly, deletion of patZ increased acetylation in acetate cultures, which suggests that it regulates the levels of acetylating agents. The results presented offer new insights into functional roles of protein acetylation in metabolic fitness and global cell regulation.
Publication Title
Protein acetylation affects acetate metabolism, motility and acid stress response in Escherichia coli.
Sample Metadata Fields
No sample metadata fields
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