Ontology highlight
ABSTRACT:
PROVIDER: PRJNA780472 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16947335_1.fastq.gz | Fastqsanger.gz | |||
| SRR16947335_2.fastq.gz | Fastqsanger.gz | |||
| SRR16947336_1.fastq.gz | Fastqsanger.gz | |||
| SRR16947336_2.fastq.gz | Fastqsanger.gz | |||
| SRR16947337.fastq.gz | Fastqsanger.gz |
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Project description:The purpose of this research was to investigate the causes and consequences of pHu variations in beef cattle. For that, were evaluated 176 Nellore beef cattle, and classified into two different pHu groups: High (≥6.0, N=17) and Normal (<5.8, N=159). Plasma concentrations of cortisol and adrenocorticotropic hormone, lactate and glycogen muscular content, meat color, shear force and Longissimus thoracis muscle proteomic profile were evaluated and compared between pHu groups. Muscle glycogen content, meat color and shear force statistically differed between pHu groups. Label-free quantitative proteomic analysis revealed ten differentially abundant proteins between pHu groups, involved in metabolic processes and muscle contraction. Thirty-six and 31 proteins were exclusively present in Normal and High pHu group, respectively, which were related to TCA cycle, cortisol production, calcium regulation, and antioxidant function. The MYH7, UGP2, and VDAC3 were identified as potential indicators of pHu variations. CALM and NNT appeared to be interesting proteins to better understand the metabolic pathways behind pHu.
2018-07-11 | PXD009320 | Pride
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Project description:It has been proved that intramuscular fat (IMF) or marbling in beef improves palatability. Recently, consumers have considered not only the degree of marbling but also the size and distribution of marbling flecks for their health and appetizing looking of beef. Computer image analysis (CIA) systems have been developed to assess various characteristics of marbling particles (MPs) such as the number, size, and distribution (fineness or coarseness) objectively. Some CIA indexes about MPs indicating how MPs are distributed evenly had significant positive relationship with price which represents consumers’ interest. RNA-seq research about formation of fine MPs in the longissimus thoracis (LT) muscle tissue of cattle have not yet been tried in transcriptome level. This study was conducted to reveal the DEGs between groups which have high or low number of fine MPs in the Longissimus thoracis muscle of Korean beef cattle and to understand molecular events associated with marbling fineness.
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Project description:The intramuscular fat (IMF) content of different beef cattle breeds varies greatly, which plays an important role in taste and nutritional value. However, the molecular mechanism of fat metabolism and deposition in beef cattle is still not very clear. In this study, the meat quality traits of Angus cattle and Chinese Simmental cattle were compared, the transcriptome of the longissimus dorsi muscle (LD) between Angus cattle and Chinese Simmental cattle was then analyzed to identify key genes related to fat metabolism and adipogenesis by high-throughput RNA-seq technology. In the current study conducted a comprehensive analysis on the transcriptome of the longissimus dorsi muscle (LD) of Angus and Simmental cattle, and identified differentially expressed genes related to lipid metabolism，which may have a great impact on on the formation of IMF.
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Project description:The objective of this project is identifying differentially expressed (DE) genes which are associated with higher omega-3 fatty acids deposition in beef cows. Omega-3 fatty acids have been found to influence meat flavor and are beneficial to human health. Supplementation of livestock diets with flaxseed, a rich source of ë±-linolenic acid, is the most common means of producing omega-3 fatty acid-enriched animal products. Towards the goal of enhancing beef fatty acid composition, 64 crossbred cull cows (~30 months of age) with similar breed composition were randomized by weight/body condition, and fed one of four 50:50 forage:concentrate diets on a DM basis (16 cows/treatment), containing ground barley grain with either hay or silage, supplemented with 0 or 15% ground flaxseed (DM basis). Cows were slaughtered after spending 140 days on the treatment diets. Five cows from each of the four diets were selected for transcriptional analysis based on FA profiles of the kidney fat collected at slaughter. RNA was isolated from Longissimus thoracis muscle, subcutaneous and kidney fat of each cow (20 samples/tissue) and hybridized in duplicate to BOMC 24K 60-mer microarrays. Differential gene expression between flax-fed and non-flax-fed cows as well as identifying those genes associated with fatty acid metabolism were studied.
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Project description:Black cattle is a new breed of beef cattle developed by combining modern biotechnologies such as somatic cell cloning and conventional breeding methods. To provide new ideas for improving meat quality and generating new breeds of cattle, the important candidate genes affecting fat deposition in two kinds of cattle were identified. Eighteen months Black cattles and Luxi cattles were randomly assigned into two environmental. The longissimus dorsi muscle were collected on Black cattle and Luxi cattle,for analyses including fatty acid determinationrs, high-throughput sequencing metagenomics, qRT-PCR expression profile and western blot.The ratio of unsaturated fatty acids to saturated fatty acids was 1.37:1 and 1.24:1 in the muscle tissues of Black cattle and Luxi cattle, respectively. The results of RNA-Seq analysis revealed 1,415 DEGs(fold change ≥ ± 2, P<0.05) between the longissimus dorsi of Black cattle and yellow cattle. A total of 939 genes were upregulated, and the other 476 genes were downregulated. With GO enrichment analysis, it was found that the identified DEGs were significantly enriched in biological regulation, regulation of the Wnt signaling pathway, negative regulation of the Wnt signaling pathway, cAMP metabolic process, fat cell differentiation, and brown fat cell differentiation, among other functions. Regulation of lipolysis in adipocytes, AMPK signaling pathway, adipocytokine signaling pathway and PPAR signaling pathway in the KEGG pathway database were significantly enriched. PPI network analysis showed that the downregulated genes FABP4, ADIPOQ, PLIN1, PLIN2 and LIPE were closely linked to other DEGs and were the key sites of multiple metabolic pathways. Combined with qRT-PCR and protein expression profile analysis, the expression level of fat acid metabolism related genes (FABP4, ADIPOQ) in black cattle was high and the difference was significant. Changes in the expression of fatty acid metabolism-related genes in Black cattle and Luxi cattle were analyzed and important candidate marker genes (such as ADIPOQ and FABP4) that affect fat deposition were identified in order to provide a genetic basis for the efficient breeding of production performance, establish a molecular marker database for local cattle breeds and support the cultivation of new breeds.
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Project description:Arouquesa breed is an autochthonous Portuguese breed produced under a traditional mountain system. It is known for its Arouquesa PDO beef, a high-quality product with valued organoleptic characteristics. There is a need to improve production systems without affecting beef quality. The aim of this work is to compare the proteomics profile from the Longissimus thoracis muscle from Arouquesa animals produced under different systems. Sixty weaners were produced under the following systems: traditional (TF) and traditional with starter feed supplementation (TF+S1) with weaning and slaughtering at 8 months, the S1+S2 (weaning at 5 months and grower supplement until slaughter) and two rearing periods with finishing supplementation (TF+S3 and S3). Upon slaughter, samples of L. thoracis were taken and analyzed using a shotgun proteomics workflow. Several putative biomarkers of beef quality for the Arouquesa breed were identified: VIM, FSCN1, SERPINH1, ALDH1A1, NDUFB5, ANXA1, PDK4, CEMIP2, NDUFB9, PDLIM1, OXCT1, MYH4. These proteins were involved in actin binding, skeletal muscle development and in the mitochondrial respiratory chain and they can influence mostly meat tenderness and color. Our results demonstrate the link between production practices and putative meat quality signatures, that have potential to improve traceability of certified products.
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Project description:This study aimed to evaluate the effect of including soybean molasses (SM) on performance, blood parameters, carcass traits, meat quality, fatty acid and muscle (longissimus thoracis) transcriptomic profiles of castrated lambs. Twenty Dorper × Santa Inês lambs (20.06 ± 0.76 kg BW) were assigned to a randomized block design, stratified by BW, with the following treatments: CON - 0 g/kg of SM and SM20 - 200 g/kg of SM on DM basis, allocated in individual pens. The diet consisted of 840 g/kg concentrate and 160 g/kg corn silage for 76 days, with the first 12 days as an adaptation period and the remaining 64 days on the finishing diet. The SM20 diet increased blood urea concentration (P = 0.03) while reduced glucose concentration (P = 0.04). Lambs fed SM showed higher subcutaneous fat deposition (P = 0.04) and higher subcutaneous adipocyte diameter (P < 0.01), in addition to reduced meat lipid oxidation (P < 0.01). Soybean molasses reduced the quantity of branched-chain fatty acids in longissimus thoracis (P = 0.05) and increased the quantity of saturated fatty acids (P = 0.01). In the transcriptomic analysis, 294 genes were identified as differentially expressed, which belong to pathways such as oxidative phosphorylation, citric acid cycle, and monosaccharide metabolic process. In conclusion, diet with SM increased carcass fat deposition, reduced lipid oxidation, and changed the energy metabolism, supporting its use in ruminant nutrition.
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Project description:In order to establish the correlation between biological processes and the mechanisms of gene expression controlling beef traits formation in bovine, microarray analysis was performed to capture the differences in gene expression related to beef traits profile in Longissimus Dorsi muscle tissue between 1-month and 24-month Chinese Red Steppes. 1282 (5.6%) probes showed significant differences at the two stages in the experiment, and 1008 differential gene annotations were obtained using Capitalbio molecule annotation system. BLAST analysis revealed that 1001(78.1%) probe genes shared significant similarity in amino acid sequence with other functional genes (As of June 2009). 126 genes showing strong correlation with beef traits were gained by the GO analysis. With the KEGG analysis, 63 pathways were found to be related to beef traits which involved 73 genes. 28 genes were found in a single pathway, while 35 genes were found in 2-16 pathways respectively. The panels of transcripts and gene pathways analysis in different growth stages may be helpful for the study on beef traits formation, and the gene expression profile construction in Longissimus Dorsi muscle tissues, would make a foundation for screening candidate genes which have genetic effect on meat quality in bovine. Keywords: Microarray analysis; Beef traits; Differences of gene expression; Longissimus Dorsi muscle tissue; Chinese Red Steppe
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