Ontology highlight
ABSTRACT:
PROVIDER: PRJEB19387 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| milk_gatk_filtered.DP5.knowvariants_Oarv3.1-r83.VEP.vcf.gz | Vcf | |||
| milk_gatk_filtered.DP5.knowvariants_Oarv3.1-r83.VEP.vcf.gz.tbi | Vcf |
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Project description:To investigate the molecular bases of diet induced differences in milk composition, we collected milk from mid lactation dairy ewes and after 3 weeks of diet supplementation with extruded linseed. RNAs were isolated from milk somatic cells isolated from milk of 3 sheep and Illumina RNA sequencing was performed to analyze RNA synthesis in these cells.
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Project description:Transcriptome analysis in sheep Milk Somatic Cells
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Project description:This study presents a dynamic characterization of the sheep milk transcriptome aiming at achieving a better understanding of the sheep lactating mammary gland. Transcriptome sequencing (RNA-seq) was performed on total RNA extracted from milk somatic cells from ewes on days 10, 50, 120 and 150 after lambing. The experiment was performed in Spanish Churra and Assaf breeds, which differ in their milk production traits. Nearly 67% of the annotated genes in the reference genome (Oar_v3.1) were expressed in ovine milk somatic cells. For the two breeds and across the four lactation stages studied, the most highly expressed genes encoded caseins and whey proteins. We detected differentially expressed genes (DEGs) across lactation points, with the largest differences being found, between day 10 and day 150. Upregulated GO terms at late lactation stages were linked mainly to developmental processes linked to extracellular matrix remodeling. A total of 256 annotated DEGs were detected in the Assaf and Churra comparison. Some genes selectively upregulated in the Churra breed grouped under the endopeptidase and channel activity GO terms. These genes could be related to the higher cheese yield of this breed. Overall, this study provides the first integrated overview on sheep milk gene expression.
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Project description:The study reports a differential proteomic analysis of the Mediterranean buffalo milk to evaluate the changes induced by Staphylococcus spp. during a subclinical intramammary infection (IMI). A number of 12 quarter milk samples, 6 of which with somatic cell count (SCC) < 50,000 cells/mL and culture-negative, and the other 6 with SCC ˃ 3,000,000 cells/mL and culture-positive to Staphylococcus aureus (SAU, n=3), SAU, or non-aureus staphylococci (NAS, n=3) was selected. Samples were analyzed using a shotgun proteomics approach, based on filter-aided sample preparation (FASP) followed by LC-MS/MS and label-free analysis. Here, the largest buffalo milk protein dataset described so far was reported. Moreover, the results demonstrated that staphylococcal IMI mostly affected proteins involved in structural functions and in innate immune defense, with changes in their abundance that were generally more intense in SAU than in NAS samples. Further, an increase in the abundance of different cathelicidins was observed, as already reported for other animals with mastitis disease (1,2). (1) Addis MF, Pisanu S, Marogna G, Cubeddu T, Pagnozzi D, Cacciotto C, et al. Production and release of antimicrobial and immune defense proteins by mammary epithelial cells following Streptococcus uberis infection of sheep. Infect Immun. 2013;81: 3182–3197. (2) Addis MF, Tedde V, Dore S, Pisanu S, Puggioni GMG, Roggio AM, et al. Evaluation of milk cathelicidin for detection of dairy sheep mastitis. J Dairy Sci. Elsevier; 2016;99: 6446–6456. In conclusion, our results provide the first in depth characterization of buffalo milk proteins, describe the changes induced by SAU and NAS subclinical intramammary infection and suggest indications to reveal subclinical staphylococcal mastitis in buffalo by the milk proteome investigation.
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