Food metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA314853 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3294590.fastq.gz | Fastqsanger.gz | |||
| SRR3294600.fastq.gz | Fastqsanger.gz | |||
| SRR3294610.fastq.gz | Fastqsanger.gz | |||
| SRR3294620.fastq.gz | Fastqsanger.gz | |||
| SRR3294630.fastq.gz | Fastqsanger.gz |
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Project description:Tenderness is one of the most important properties of meat quality, which is influenced by genetic and environmental factors. As an intensively studied epigenetic marker, histone methylation, occurring on arginine and lysine residues, has pivotal regulatory functions on gene expression. To examine whether histone methylation involves in beef tenderness variation, we analyzed the transcriptome and H3K4me3 enrichment profiles of muscle strips obtained from the longissimus dorsi (LD) of Angus steers previously classify to the tender or tough group. We first plotted a global bovine H3K4me3 map on chromosomes and called peak-enriched regions and genes. We found that majorities of H3K4me3 on genes were occupying the first intron and intergenic regions and its maps displayed similar patterns in tender and tough groups, with high H3K4me3 enrichment surrounding the transcription start site (TSS). We also explored the relationship of H3K4me3 and gene expression. The results showed that H3K4me3 enrichment is highly positively correlated with gene expression across the whole genome. Cluster analysis results confirmed the relationship of H3K4me3 enrichment and gene expression. By using a pathway-based approach in genes with H3K4me3 enrichment in promoter regions from the tender cluster, we revealed that those genes involved in the development of different tissues–connective tissue, skeletal and muscular system and functional tissues–; while in tough group those genes engaged in cell death, lipid metabolism and small molecule biochemistry. The results from this study provide a deep insight into understanding of the mechanisms of epigenetic regulations in meat quality and beef tenderness. Nineteen purebred Angus steers were obtained from the Wye Farm. At approximately 12 months of age, the animals were serially harvested. Immediately after harvest, samples of longissimus dorsi (LD) from the right side of the carcass were obtained and placed in RNAlater solution at -80°C. The carcass were stored at 4°C for a total of 14 days. After this period, steaks were obtained from the LD at the level of the 12th intercostal space and then frozen. For measurement of the WBSF, steaks were thawed at room temperature to an internal temperature of 4°C. Then, the steaks were cooked to a core temperature of 70°C using a George Foreman Lean Mean Fat Grilling Machine. The cooked steaks were then cooled down to room temperature. Using a sharp cylinder, especially designed for muscle, six cores (1.27 cm in diameter) were sampled parallel to the muscle fiber orientation. The Warner-Bratzler shear forces (WBSF) of the cores were obtained. The average WBSF of the six cores was calculated and used as the WBSF for the samples. From these 19 steers, 4 with the lowest WBSF values (6.77±0.56 kg) were identified as tender and 5 samples with the largest WBSF values (19.93±0.39 kg) labeled as tough. Then both groups underwent further analysis..
2015-03-31 | E-GEOD-61936 | biostudies-arrayexpress
Project description:Viral metagenomics of US store bought beef, pork, chicken
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Project description:The objective of this study was to characterize the major proteomes and metabolites present in beef exudate and determine their relationship with the color and oxidative quality of beef muscles. Beef loin (longissimus lumborum; LD) and tenderloin (psoas major; PM) muscles were cut into sections, individually vacuum-packaged, and aged for 9, 16 and 23 days. Following aging, the meat exudates were collected and analyzed for both proteomics and metabolomics profiles. Both analyses demonstrated that distinct proteins and metabolites clustered by different muscle types and aging times were detected from meat exudate, however, metabolomics profiling presented a greater capability in identifying different aging periods. The proteome profile of PM exudate exhibited a greater concentration of oxidative metabolism enzymes, while the LD exudate contained a higher abundance of glycolytic metabolism enzymes. Greater lipid, nucleotide, carnitine and glucoside metabolites were observed in LD and 23d exudates, further explaining potential postmortem energy metabolism. HSP70 and laminin proteins, together with glucosides metabolites identified in the exudates were correlated (P<0.1 and |r|>0.5) to muscle oxidative stability. The results indicated that meat exudate could be a viable analytical matrix to further understand postmortem metabolism and potentially generate unique biomarker combinations to predict meat quality attributes.
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Project description:Ceramic vessels were used to cook a mixture of milk, meat (pork and beef) and cereals (wheat and barley), and proteomic studies were conducted on the ceramics to study the absorption and subsequent extraction and identification of the proteins from th various categories of foodstuff. A novel Deep Eutectic Solvent-based extraction procedure was also trialled and its efficacy compared with the standard GuHCl-based extraction procedure.
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Project description:To find a promoter upregulated in the presence of rotten meat, we exposed B. subtilis 168 to the volatiles of rotten meat (mixed beef/pork) and performed a microarray comparing it to B. subtilis which was not exposed to the meat. The results where used to build iGEM Groningen 2012s Food Warden, a spoiled meat detector. Find more information at: 2012.igem.org/Team:Groningen One condition design; including dye swap, two technical replicates and two experimental replicates
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Project description:In this work, the effects of different sources of meat protein on liver metabolic enzymes were investigated. Rats were fed for 90 days with semisynthetic diets in which casein was fully replaced by isolated soybean, fish, chicken, pork, or beef proteins. Then, liver proteomics was performed using iTRAQ and LC−ESI−MS/MS. The results indicated that intake of meat protein diets significantly reduced the protein levels of CYP450s, GSTs, UGTs, and SULTs compared to those of the casein and soybean protein diet groups. The total antioxidant capacity and lipid peroxidation values did not differ between four meat protein diet groups and the casein diet group. However, GSH activity in the fish, chicken, and beef protein groups was significantly higher than those of the casein and soybean protein groups. The beef protein diet significantly upregulated the expression of immune-related proteins. The Keap1-Nrf2-ARE signaling pathway was suggested to involve the diet-mediated regulation of biotransformation, inflammation, and redox status.
2022-02-17 | PXD026732 | Pride
Project description:To find a promoter upregulated in the presence of rotten meat, we exposed B. subtilis 168 to the volatiles of rotten meat (mixed beef/pork) and performed a microarray comparing it to B. subtilis which was not exposed to the meat. The results where used to build iGEM Groningen 2012s Food Warden, a spoiled meat detector. Find more information at: 2012.igem.org/Team:Groningen
2013-09-04 | GSE50538 | GEO