Liver profiles of mid-lactating goats using Agilent Array
Ontology highlight
ABSTRACT:
ORGANISM(S): Capra hircus
SUBMITTER: Dong Haibo
PROVIDER: E-GEOD-50448 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Cattle are often fed high concentrate diets to increase energy intake and improve overall animal performance. Such diets also cause changes in fermentation patterns and epithelial function. However, the molecular mechanisms involved in regulating epithelial function for cattle fed high concentrate diets have not been elucidated. In this study, we aimed to gain a broad overview of the involved molecular mechanisms by detecting differentially expressed genes (DEG) in rumen tissue from dairy cows fed a low concentrate (LC; 8%) compared to a high concentrate (HC; 64%) diet using a bovine-specific microarray platform containing 16,846 unique gene loci and 5,943 ESTs from the bovine genome. Feeding the HC diet increased the total volatile fatty acid concentration and markedly reduced ruminal pH, suggesting that the dietary treatments used did induce changes in ruminal fermentation. In response to changes in the ruminal environment, a total of 5,200 elements were detected as DEG in ruminal tissue with >1.5-fold expression change (P < 0.05) for cows fed HC relative to LC. Of the 5,200 DEG, 2,233 and 2,967 were up- and down-regulated, respectively. The GENECODIS analysis elucidated that relationships among the DEG represented 19 annotations characterized with GO molecular function and KEGG pathways with 26 DEG identified in multiple annotations such as calcium signaling and gap junction pathways. Among those DEG that were identified numerous times, catalytic subunit of cAMP-dependent protein kinase (PRKACB) was down-regulated in ruminal tissue from cows fed HC, suggesting that this gene may have important roles including regulation of cell proliferation and differentiation, and intracellular pH regulation. Two-condition experiment, High concentrate vs. Low concentrate diets. Biological replicates: 5 high concentrate fed, 5 low concentrate, independently grown and harvested. Two replicates per array.
2010-10-02 | E-GEOD-19802 | biostudies-arrayexpress
Project description:Dairy ruminants are often fed high grain diets to meet the energy demand for high milk production. As a result, body metabolism occurs change and milk quality was suppression. As the vital organ that controls metabolism, the liver contributes to the input of substrate precursors to the mammary gland. To further investigate the role of genes in feeding high concentrate diet metabolic characters, a comparison of mRNA expression profiles in liver of feeding high-concentrate diet (60% concentrate of dry matter, HC) and low-concentrate diet (40% concentrate of dry matter, LC) was carried out.When compaired with LC goats, 43 genes were significantly down-regulated and 112 genes were significantly up-regulated (fold change >2 and p value < 0.01) in the liver of HC among the 115 probes. Through Co-expression network analysis to find K-core regulatory factors (genes). These genes were mainly involved in immune and inflammatory responses (n = 8), lipid metabolism (n = 5), protein metabolism (n = 26), carbohydrate metabolism (n = 7). These results were further described in the unpublished paper
2014-08-29 | GSE50448 | GEO
Project description:Impaired resistance to insulin, the key defect in type 2 diabetes (T2D), is associated with a low capacity to adapt fuel oxidation to fuel availability, i.e., metabolic inflexibility. The hampered metabolic adaptability triggers a further damage of insulin signaling. Since skeletal muscle is the main site of glucose uptake, effectiveness of T2D treatment depends in large on the improvement of insulin sensitivity and metabolic adaptability of the muscle. We have shown previously in mice fed an obesogenic high-fat diet that a combination treatment using n-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA) and thiazolidinedione (TZD) anti-diabetic drugs preserved metabolic health and synergistically improved muscle insulin sensitivity. We investigated here whether TZD rosiglitazone could elicit the additive beneficial effects on metabolic flexibility when combined with n-3 LC-PUFA. Adult male C57BL/6N mice were fed an obesogenic corn oil-based high-fat diet (cHF) for 8 weeks, or randomly assigned to various dietary treatments: (i) cHF+F, cHF with n-3 LC-PUFA concentrate replacing 15% of dietary lipids; (ii) cHF+ROSI, cHF with 10 mg rosiglitazone/kg diet; and (iii) cHF+F+ROSI, or chow-fed. Indirect calorimetry demonstrated superior preservation of metabolic flexibility to carbohydrates in response to the combination treatment. Metabolomic and gene expression analyses in the muscle suggested distinct and complementary effects of the single treatments, with rosiglitazone augmenting insulin sensitivity by the modulation of branched-chain amino acid metabolism, and n-3 LC PUFA supporting complete oxidation of fatty acids in mitochondria. These beneficial metabolic effects were associated with the activation of the switch between glycolytic and oxidative muscle fibers, especially in the cHF+F+ROSI mice. Our results further support the idea that the combination treatment using n-3 LC-PUFA and TZDs could improve the efficacy of the treatment of obese and diabetic patients. Male C57BL/6N mice had free access to water and Chow. Three-month-old mice were randomly assigned (8 animals per group) to cHF diet (lipid content ~35% wt/wt) or to the following 'treatments' by isocaloric cHF-based diets, namely (i) cHF+F, cHF diet supplemented with n-3 LC-PUFA concentrate (46% DHA, 14% EPA, wt/wt, as triglycerides; product EPAX 1050 TG), which replaced 15% wt/wt of dietary lipids; (ii) cHF+ROSI, cHF diet supplemented with 10 mg rosiglitazone/kg diet; and (iii) cHF+F+ROSI, cHF diet supplemented with both n-3 LC-PUFA concentrate and rosiglitazone. cHF+ROSI at a higher dose, namely 100 mg rosiglitazone/kg diet was also included in the study, but not in the final microarray analysis. The treatment lasted for 8 weeks, whereafter the animals were first fasted for 10 hours during the light phase of the day (between 8.00hr and 18.00hr), than re-fed Chow (starting at 18.00hr), and killed the following day by cervical dislocation under pentobarbital anesthesia (between 9.00hr and 11.00hr); the so-called 'diet-switch protocol'. Gastrocnemius muscle was isolated and used for total RNA isolation.
2012-09-07 | E-GEOD-36716 | biostudies-arrayexpress
Project description:Nutrition affects milk composition influencing its nutritional properties. Nutrition also modifies the expression of mammary genes, whose regulation is not completely known. MicroRNAs (miRNA) are small non-coding RNA that work as important post-transcriptional gene expression regulators by targeting messenger RNAs. Our goal was to characterize miRNA whose expression is regulated by nutrition in the lactating goat mammary gland, and which may give clues to decipher the regulations of milk components biosynthesis and secretion. Using high-throughput sequencing technology, miRNomes of the lactating mammary gland have been established from 4 goats fed ad libitum and 6 goats food deprived during 48h. Food deprivation affected the expression of 30 miRNA (padj<0.1), 16 were downregulated and 14 were upregulated. Prediction tools Diana-microT suggests a potential role of several nutriregulated miRNA in the lipid metabolism. Among putative targets 19 differently expressed genes (DEG) previously identified in the same sample, were found. Functions of these 19 DEG revealed their involvement in tissue remodeling. This study constitutes the first evidence of nutriregulated miRNA in the ruminant mammary gland. The characterization of these 30 miRNA could contribute to a better understanding of genes regulations in the mammary gland in response to nutrition. MicroRNA profiles of mammary glands from 10 Alpine goats at the peak of lactation (48 ± 2 days post-partum) generated by a HiSeq 2500 using Illumina Solexa technic.
2015-07-01 | E-GEOD-61025 | biostudies-arrayexpress
Project description:Cattle are often fed high concentrate diets to increase energy intake and improve overall animal performance. Such diets also cause changes in fermentation patterns and epithelial function. However, the molecular mechanisms involved in regulating epithelial function for cattle fed high concentrate diets have not been elucidated. In this study, we aimed to gain a broad overview of the involved molecular mechanisms by detecting differentially expressed genes (DEG) in rumen tissue from dairy cows fed a low concentrate (LC; 8%) compared to a high concentrate (HC; 64%) diet using a bovine-specific microarray platform containing 16,846 unique gene loci and 5,943 ESTs from the bovine genome. Feeding the HC diet increased the total volatile fatty acid concentration and markedly reduced ruminal pH, suggesting that the dietary treatments used did induce changes in ruminal fermentation. In response to changes in the ruminal environment, a total of 5,200 elements were detected as DEG in ruminal tissue with >1.5-fold expression change (P < 0.05) for cows fed HC relative to LC. Of the 5,200 DEG, 2,233 and 2,967 were up- and down-regulated, respectively. The GENECODIS analysis elucidated that relationships among the DEG represented 19 annotations characterized with GO molecular function and KEGG pathways with 26 DEG identified in multiple annotations such as calcium signaling and gap junction pathways. Among those DEG that were identified numerous times, catalytic subunit of cAMP-dependent protein kinase (PRKACB) was down-regulated in ruminal tissue from cows fed HC, suggesting that this gene may have important roles including regulation of cell proliferation and differentiation, and intracellular pH regulation.
2010-10-02 | GSE19802 | GEO
Project description:Impaired resistance to insulin, the key defect in type 2 diabetes (T2D), is associated with a low capacity to adapt fuel oxidation to fuel availability, i.e., metabolic inflexibility. The hampered metabolic adaptability triggers a further damage of insulin signaling. Since skeletal muscle is the main site of glucose uptake, effectiveness of T2D treatment depends in large on the improvement of insulin sensitivity and metabolic adaptability of the muscle. We have shown previously in mice fed an obesogenic high-fat diet that a combination treatment using n-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA) and thiazolidinedione (TZD) anti-diabetic drugs preserved metabolic health and synergistically improved muscle insulin sensitivity. We investigated here whether TZD rosiglitazone could elicit the additive beneficial effects on metabolic flexibility when combined with n-3 LC-PUFA. Adult male C57BL/6J mice were fed an obesogenic corn oil-based high-fat diet (cHF) for 8 weeks, or randomly assigned to various dietary treatments: (i) cHF+F, cHF with n-3 LC-PUFA concentrate replacing 15% of dietary lipids; (ii) cHF+ROSI, cHF with 10 mg rosiglitazone/kg diet; and (iii) cHF+F+ROSI, or chow-fed. Indirect calorimetry demonstrated superior preservation of metabolic flexibility to carbohydrates in response to the combination treatment. Metabolomic and gene expression analyses in the muscle suggested distinct and complementary effects of the single treatments, with rosiglitazone augmenting insulin sensitivity by the modulation of branched-chain amino acid metabolism, and n-3 LC PUFA supporting complete oxidation of fatty acids in mitochondria. These beneficial metabolic effects were associated with the activation of the switch between glycolytic and oxidative muscle fibers, especially in the cHF+F+ROSI mice. Our results further support the idea that the combination treatment using n-3 LC-PUFA and TZDs could improve the efficacy of the treatment of obese and diabetic patients. Male C57BL/6N mice had free access to water and Chow. Three-month-old mice were randomly assigned (8 animals per group) to cHF+ROSI diet (lipid content ~35% wt/wt) supplemented with 10 mg rosiglitazone/kg diet, or cHF+F+ROSI in which n-3 LC-PUFA concentrate (46% DHA, 14% EPA, wt/wt, as triglycerides; product EPAX 1050 TG) replaced 15% wt/wt of dietary lipids. The treatment lasted for 8 weeks, whereafter the animals were first fasted for 10 hours during the light phase of the day (between 8.00hr and 18.00hr), than re-fed Chow (starting at 18.00hr), and killed the following day by cervical dislocation under pentobarbital anesthesia (between 9.00hr and 11.00hr); the so-called 'diet-switch protocol'. Gastrocnemius muscle was isolated and used for total RNA isolation.
2012-09-07 | E-GEOD-36717 | biostudies-arrayexpress
Project description:The cardioprotective effects of long chain (LC) 3PUFA can be achieved at the gene expression level, notably in liver. However, the complexity of biological pathways modulations and the nature of the bioactive molecules are still under investigation. The present study aimed to investigate the dose-response effects of LC 3PUFA on the production of peroxidated metabolites and on global gene expression in liver. The intake of LC ?3PUFA increased, in a dose-dependent manner, their incorporation in liver phospholipids but also the hepatic production of 4-HHE. Pathways related to inflammation were dose-dependently associated with the 3 groups but Group 2 was rather associated with inflammatory effects while Group 3 was anti-inflammatory. LC ?3PUFA had no effect on PPAR-controlled genes. However, they modified, in a dose-dependent manner, the expression of major genes related to lipoprotein metabolism (LDLR, VLDLR, INSIG1 and MTTP), possibly through the FXR signaling pathway. In conclusion, the effect of LC ?3PUFA is dependent on the dose possibly because of the production of peroxidated metabolites such as 4-HHE. New-Zealand white rabbits were fed (7 wk) a high cholesterol diet and received by daily oral gavages either oleic acid rich oil or a mixture of oils providing 0.1% (Group 1), 0.5% (Group 2) or 1% (Group 3) of energy as docosahexaenoic acid. Specific peroxidated metabolite issued from LC 3PUFA (4-hydroxyhexenal or 4-HHE) were measured by GC/MS/MS and transcription profiling was conducted in liver. Differentially expressed genes were identified using Bioconductor (Moderated p<0.05, Fold Change>1.20) and clustered into pathways (Ingenuity Pathway Analysis 7.0).
2011-06-04 | E-GEOD-27621 | biostudies-arrayexpress
Project description:Early life nutritional imbalances are risk factors for metabolic dysfunctions in adulthood, but the effects of perinatal exposure to high versus low protein diets are poorly understood. We exposed C57BL/6 offspring to a high protein/low carbohydrate (HP/LC) or low protein/high carbohydrate (LP/HC) diet during gestation and lactation, and measured metabolic phenotypes between birth and ten months of age in male offspring. Perinatal HP/LC and LP/HC exposures resulted in a decreased ability to clear glucose in the offspring, with reduced baseline insulin and glucose levels in the LP/HC group and a reduced insulin response post-glucose challenge in the HP/LC group. The LP/HC diet group also showed reduced weight at birth and at weaning age, whereas the HP/LC offspring showed an increased weight at weaning and increased adiposity after 5 months of age. Gene expression profiling of hypothalamic and liver tissues indicated alterations of diverse molecular pathways by both diets. Specifically, hypothalamic transcriptome and pathway analyses indicate perturbations of MAPK and hedgehog signaling, processes associated with neural restructuring and transmission, and phosphate metabolism by perinatal protein imbalances. Liver transcriptome data revealed changes in purine and phosphate metabolism, hedgehog signaling, and circadian rhythm pathways. Our results support that maternal protein imbalances perturb molecular pathways in central and peripheral metabolic tissues and predispose offspring to metabolic dysfunctions.
2018-10-01 | GSE120548 | GEO
Project description:The objective of this study was to examine changes in muscle gene expression of growing steers during a period of dietary energy restriction followed by a period of realimentation. Crossbred Aberdeen Angus x Holstein Friesian (n = 24) steers were assigned to one of two feeding treatments. Over a 99 d period, 1 group (n=12) was offered a high energy control diet consisting of concentrates ad libitum and 7 kg of grass silage per head daily. The second group (n=12) was offered an energy restricted diet consisting of grass silage ad libitum plus 0.5 kg of concentrate per head per day. From the end of the differential feeding period (99 d), both groups of animals were offered a total mixed ration (grass silage:concentrate ratio of 80:20). This period, which lasted 200 d, was known as the realimentation period. All animals were slaughtered on d 299 of the study. Muscle biopsies were collected at 2 time points (end of the differential feeding period (d 99) and during the realimentation period (d131). RNA was extracted and muscle gene expression was examined using RNA-seq technology and bioinformatic analysis. During the differential feeding period, 17 over-represented pathways were identified, including the peroxisome proliferator activated receptor signalling, glycolysis/ gluconeogenesis and metabolic pathways controlling the metabolism of lipids and lipoproteins which indicate reduced energy intake and fat tissue accumulation occurring in muscle tissue during the restriction phase. During the realimentation period, 164 differentially expressed genes were annotated to 9 over-represented pathways including starch and sucrose metabolism, carbohydrate digestion and absorption and TGF-β signalling pathway. It is hypothesised that the signalling effects of the TGF-β pathway were reduced thereby promoting accelerated cell growth and proliferation in muscle tissue of animals experiencing compensatory growth. This information can be exploited in genomic breeding programmes to assist selection of cattle with a greater ability to compensate following a period dietary restriction. 24 muscle RNA samples were analysed in total. 6 samples were from muscle biopsies collected at the end of a period of dietary restriction (d99) and 6 samples were from muscle biopsies collected at the peak of compensatory growth (d131). In addition, RNA was also analysed from 6 samples collected from animals fed ad libitum at each of these two timepoints.
2015-01-07 | E-GEOD-48481 | biostudies-arrayexpress
Project description:The general acclimation of cyanobacteria to low carbon (LC) conditions includes coordinated alterations of gene expression and metabolism. To analyze possible signals for LC sensing and compensating reactions, we compared wild-type (WT) cells with two mutants of Synechocystis, the carboxysome-less mutant ccmM and the photorespiratory mutant ΔglcD1/D2. Metabolic phenotyping revealed that the mutant ΔccmM accumulated high 2-phosphoglycolate (2PG) levels while the ΔglcD1/D2 mutant accumulated glycolate, indicating oxygenase activity of RubisCO at high carbon (HC). The changes in the metabolite spectrum were compared to alterations in the global gene expression pattern. Cells of HC-grown mutants ΔccmM and ΔglcD1/D2 showed altered mRNA levels for many genes involved in photosynthesis, high light stress, and N-assimilation, while LC-specific genes such as those for inorganic carbon (Ci) transporters were not increased. After a shift to LC, mutant ΔglcD1/D2 revealed gene expression changes similar to WT cells, while mutant ΔccmM showed no differential expression of most LC-induced genes under identical conditions. In fact, none of the genes for Ci transporters or other components of the carbon concentrating mechanism (CCM) displayed higher transcript levels in the ΔccmM mutant. This finding renders a direct role for 2PG as a metabolic signal component for the induction of CCM during LC acclimation less likely. Because, the transcription pattern of ΔglcD1/D2 under LC showed specific differences compared to WT, a potential role for glycolate as a signal molecule that may trigger expression of parts of the CCM is proposed. Transcriptional profiling of carboxysomal and photorespiratory mutants of Synechocystis sp. PCC 6803 under high carbon (HC) and low carbon (LC) conditions relative to the wildtype response.
2011-12-30 | E-GEOD-31672 | biostudies-arrayexpress