Transcriptional response of adipose tissue depots to a high energy feeding regimen in Japanese Black and Holstein steers
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ABSTRACT:
ORGANISM(S): Bos taurus
PROVIDER: GSE39006 | GEO | 2012/06/30
SECONDARY ACCESSION(S): PRJNA169616
REPOSITORIES: GEO
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Project description:Three Japanese Black (JB) and 3 Holstein (HS) steers were fed a high energy diet and were slaughtered with 26 months of age. Intramuscular (IMF) and subcutaneous fat (SCF) was sampled to reveal differences in the expression profiles between the breeds and adipose depots. Pair wise comparison of JB and HS within IMF and SCF; pairwise comparision of IMF and SCF over both breeds.
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Project description:To test the hypothesis that average daily gain (ADG) and clinical parameters of steers grazing novel non-toxic (NTE) or toxic KY-31 (TE) endophyte-infected tall fescue would be improved by ad libitum intake of vitamin-mineral mixes (V-M) that contain 27 ppm Se as a 1:1 blend of SELPLEX:sodium selenite (MIX) vs. sodium selenite (ISe), 32 fescue-naïve beef steers depleted of Se were randomly assigned to ad libitum consumption ISe vs MIX for 35 d and fed enough of a NTE/alfalfa/grain diet to achieve 0.57 kg BW gain/d. Within Se-form treatments, 2 steers were randomly assigned to each of 4 NTE (ISe = 316 ± 31 kg, MIX = 315 ± 22 kg) or TE (ISe = 316 ± 37 kg, MIX = 314 ± 39 kg) paddocks for 84 d and had ad libitum access to their respective V-M. Steers were slaughtered over a 23-d period from day 90 to day 113 (August 27, 2019 to September 19, 2019) of the study and the left kidney removed.
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Project description:To test the hypothesis that average daily gain (ADG) and clinical parameters of steers grazing novel non-toxic (NTE) or toxic KY-31 (TE) endophyte-infected tall fescue would be improved by ad libitum intake of vitamin-mineral mixes (V-M) that contain 27 ppm Se as a 1:1 blend of SELPLEX:sodium selenite (MIX) vs. sodium selenite (ISe), 32 fescue-naïve beef steers depleted of Se were randomly assigned to ad libitum consumption ISe vs MIX for 35 d and fed enough of a NTE/alfalfa/grain diet to achieve 0.57 kg BW gain/d. Within Se-form treatments, 2 steers were randomly assigned to each of 4 NTE (ISe = 316 ± 31 kg, MIX = 315 ± 22 kg) or TE (ISe = 316 ± 37 kg, MIX = 314 ± 39 kg) paddocks for 84 d and had ad libitum access to their respective V-M. Steers were slaughtered over a 23-d period from day 90 to day 113 (August 27, 2019 to September 19, 2019) of the study and the left adrenal gland removed.
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Project description:Transcriptional profiling of bovine skeletal muscle comparing metabolically efficient steers to metabolically inefficient steers to ascertain what expression differences can be found in muscle tissue that might help explain differences in this economically significant phenotype. Two condition experiment, efficient versus inefficient animals. 8 efficient and 8 inefficient samples were used representing 16 unique individual animals.
2014-04-11 | E-GEOD-56705 | biostudies-arrayexpress
Project description:Transcriptional profiling of bovine skeletal muscle comparing metabolically efficient steers to metabolically inefficient steers to ascertain what expression differences can be found in muscle tissue that might help explain differences in this economically significant phenotype.
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Project description:Growing and finishing phases are two important animal production stages, which differ fundamentally in compositional growth. However, the physiological mechanisms altered concomitantly with the shift in whole-body compositional gain as cattle fatten (growing vs. finished steers), are poorly understood. Microarray analysis using the Bovine Gene 1.0 ST Array was conducted to determine shifts in hepatic genomic expression profiles of growing vs. finishing beef steers. The specific overall hypothesis tested was that genes involved in amino acid, carbohydrate and lipid metabolism, antioxidant capacity and immune responses were differentially expressed in growing vs. finishing steers.
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Project description:Growing ruminants maintained under dietary restriction for extended periods will exhibit compensatory growth when reverted to ad libitum feeding. This period of compensatory growth is associated with increased feed efficiency, lower basal energy requirements, and changes in circulating concentrations of metabolic hormones. To identify genetic mechanisms contributing to these physiological changes, 8 month-old steers were fed either ad libitum (control; n = 6) or 60-70% of intake of control animals (feed-restricted; n=6) for a period of 12 weeks. All steers were then fed ad libitum for the remaining 8 weeks of the experiment (realimentation period). Liver was biopsied from each animal at days -14, +1 and +14 relative to realimentation for RNA extraction and gene expression analysis by microarray hybridization. Steers were assigned randomly to one of two treatment groups, control or feed-restricted, and housed indoors in individual pens. Steers were acclimated to their pens for 5 d prior to starting the experimental treatments. Feed was offered once daily between 0630 and 0930 and orts from the previous day's feeding were collected and weighed to estimate actual intake. Control animals were fed ad libitum throughout the 20-wk experimental period. Feed-restricted steers were offered 60-70% of intake of control animals for 12 wks to target a limited rate of gain of approximately 0.5 kg/d. Restricted steers were then fed ad libitum for the remaining 8 wks of the experiment (realimentation period). During the first 3 d of realimentation, feed offered to both treatment groups was divided into two equal rations to gradually adjust restricted animals to full intake. Water was offered ad libitum throughout the experimental period. Approximately 200 mg of liver tissue was collected from each steer by needle biopsy using a Tru-Cut biopsy needle at -14, +1, +14 d relative to realimentation. Liver samples were immediately frozen in liquid nitrogen and stored at -80C until RNA isolation. Total RNA was isolated from 36 liver samples using TRIZOL Reagent (Invitrogen Corp., Carlsbad, CA). Samples were DNase-treated using the TURBO DNA-free kit (Ambion, Inc., Austin, TX) according to manufacturerâ??s instructions, followed by column purification using the RNeasy Mini Kit (Qiagen, Valencia, CA). Quality and concentration of RNA were assessed using a 2100 Bioanlayzer (Agilent Technologies, Palo Alto, CA) and ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). Probe labeling, hybridizations of probes to the oligo microarray, and array scanning were performed by the Roche NimbleGen Systems, Inc. Microarray Core Facility in Reykjavik, Iceland according to standard procedures (Madison, WI; http://www.nimblegen.com).
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Project description:Purpose: The goals of this study are to determine effects of castration on gene expression in longissimus dorsi muscle by comparing transcriptome profiles and to search candidate genes related with beef quality like flavor, tenderness, juiciness and fat deposition Methods: longissimus dorsi muscle mRNA profiles of 3 bulls and 3 steers of Korean cattles were generated by RNA sequencing using Illumina NextSeq 500. After quality checking, Tophat2 software was used for read mapping, and EdgeR was used to identify differentially expressed genes (DEGs) between bulls and steers. Gene ontology pathway analysis on DEGs was conducted with DAVID tool for categorization of DEGs. Results: Using an optimized data analysis workflow, we mapped about 58 million sequence reads per sample to the bovine genome (build UMD3.1) and identified 18,027 expressed genes in the longissimus dorsi muscle of bulls and steers with TopHat2 workflow. RNA-seq data confirmed 1,146 differentially expressed genes (adjusted p-value, FDR <0.05). Conclusions: We comparatively analyzed the transcriptome profile from longissimus dorsi muscle of bulls and steers of Korean cattles using NGS and identified DEGs between bulls and steers. The functional annotation analysis of DEGs found that transcriptome profile difference in longissimus dorsi muscle by castration.
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Project description:Neotyphodium coenophialum is an endophytic fungus that infects most tall fescue (Festuca arundinacea) pastures that are commonly used in animal grazing systems in the United States. Beef cattle grazing such pastures are impaired in health and production performance, resulting in a large economic loss in US food-animal production systems. Based on clinical and biochemical blood analyte profiles, hepatic targeted gene and protein analyses, and hepatic transcriptomic profiling, microarray analysis using the WT Btau 4.0 Array (version 1.0, Affymetrix, Inc., Santa Clara, CA) was conducted to determine if grazing endophyte-infected tall fescue pastures affects pituitary gene expression profiles of growing beef steers. The specific overall hypothesis tested was that grazing high endophyte-infected pasture would alter the pituitary genomic expression profiles of the same growing steers, especially genes involved in production and secretion of prolactin, growth hormone, thyroid stimulating hormone, and adrenocorticotropic hormone. Sixteen steers were assigned to graze either a low toxic endophyte tall fescue-mixed grass (LE treatment, 5.7 ha, n = 8) or a high toxic endophyte infected tall fescue (HE treatment, 5.7 ha, n = 8) pasture located in the University of Kentucky Agricultural Research Center. All steers had ad libitum access to fresh water, an industry standard mineral-vitamin supplement, and grazed respective pastures for 89 to 105 days. Whole pituitaries were collected for RNA extraction and microarray analysis.
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