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Differentially expressed genes (DEGs) were grouped by gene ontology functional categories ... In slow muscle, functional categories altered by LPS administration included mitochondrion and electron transport (both up-regulated at 72 h), cytoskeleton, muscle development (up-regulated at 24 h but down-regulated at 72 h), glycolysis (down-regulated at 24 and 72 h) and immune response (up-regulated at 72 h) (Figure 2). In fast muscle, LPS administration caused changes in the expression of functional categories related to carbohydrate metabolism (e.g., glycolyis; down-regulated at 24 h but up-regulated at 72 h), protein metabolism (e.g., protein biosynthesis and modification), muscle development (up-regulated at 24 and 72 h), nuclear activity and transcription, apoptosis and immune response (up-regulated at 72 h) (Figure 3). Within these differentially expressed functional categories, the LY294002 nmr individual value and direction of change for representative genes are detailed in Table 2 and the full list of DEGs in slow and fast muscle at 24 and 72 h after LPS administration can be found in Tables S2 to S5, respectively. Table 2 Differentially expressed genes representative of various physiological processes in slow and fast skeletal muscle at 24 and 72 h after lipopolysaccharide administration in rainbow trout a. Within the functional category of carbohydrate metabolism we observed a significant (p Lapatinib mw dehydrogenase), and gluconeogenesis (glucose-6-phosphate isomerase) in fast muscle at 72 h after LPS administration that was preceded by a significant down-regulation of most of these genes at 24 h after LPS administration (Table 2, Tables S4 and S5). The mRNA expression levels of 6-phosphofructokinase (6-PFK), a key glycolytic enzyme, were decreased by LPS administration in fast muscle at both 24 and 72 h, suggesting a tight regulation of this metabolic pathway during endotoxin treatment as in the mammalian muscle [34]. In contrast, in slow muscle we observed a marked down-regulation, S6 Kinase particularly at 72 h, of DEGs involved in carbohydrate metabolism including several important genes involved in glycolysis (e.g., beta-enolase, glyceraldehyde-3-phosphate dehydrogenase and 6-PFK) (Table 2, Tables S2 and S3). LPS administration in trout also caused significant changes in the mRNA expression levels of genes involved in protein metabolism, as shown by the large number of DEGs involved in protein biosynthesis as well as in protein modification and catabolism. In particular, this functional category included DEGs coding for several ribosomal proteins (e.g., 40S, 60S) in both types of muscle.