Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1211861 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32402435_1.fastq.gz | Fastqsanger.gz | |||
| SRR32402435_2.fastq.gz | Fastqsanger.gz | |||
| SRR32402436_1.fastq.gz | Fastqsanger.gz | |||
| SRR32402436_2.fastq.gz | Fastqsanger.gz | |||
| SRR32402437_1.fastq.gz | Fastqsanger.gz |
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Project description:Nitrogen (N) emissions became a huge topic under environmental and nutrient concerns in dairy farming. Nitrogen is metabolized in cows as a consequence of feed crude protein digestion which is either recycled or excreted via urine, faeces and/or milk. In dairy cows differences between cows in N-recycling and N-emissions have been postulated. This study investigated 24 Holstein dairy cows in late lactation. The experimental design comprises two dietary groups (low (LP) vs normal (NP) crude protein) and two groups of milk urea content, high (HMU) vs low (LMU). Transcriptomic profiles of the liver, rumen, mammalian gland and kidney tissues were comparatively assessed by mRNA sequencing.
2024-11-30 | E-MTAB-9901 | biostudies-arrayexpress
Project description:The transition to lactation challenges dairy cows metabolically. Immune dysfunction and infectious disease risk is the hallmark of this transition period. Transcriptome data of PBMC shows differentially expressed pathways postpartum. Metabolically stressed cows show upregulation of innate immune pathways and inflammation.
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Project description:In the present study, transcript profiling was carried out in the liver samples from wk 5 of lactation in order to identify genes and pathways regulated by rumen-protected CLA during early lactation. The first wks after parturition represent a critical phase in the productive cycle of high-yielding dairy cows because the liver experiences pronounced metabolic and inflammatory stress which increases the risk to develop liver-associated diseases, such as fatty liver and ketosis.
2016-09-28 | GSE87391 | GEO
Project description:The severity of negative energy balance (NEB) in high-producing dairy cows has a high incidence among health diseases. The periparturient period is crucial for the health status and reproductive performance of dairy cows. During this period, dairy cows experience a transition from a pregnant, non-lactating state to a non-pregnant, lactating state. At the beginning of lactation, the energy needs for milk production are higher than the available energy consumed from feed intake, resulting in a negative energy balance (NEB)]. While in a NEB, cows mobilise their reserves from adipose tissue, resulting in elevated plasma concentrations of non-esterified fatty acids (NEFAs), which are used as a fuel source by peripheral tissues and the mammary gland for milk fat synthesis. Thus, white adipose tissue is one of the main tissue involved in the energy production during this transition period. So the objectives of our study were to dentify mRNA differentially expressed in white adipose before and after calving in dairy cow fed with low (LE) and high (HE) energy diet.
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Project description:We performed single-cell RNA-sequencing on the rumen epithelium of dairy cows to construct an epithelial single-cell map of the rumen.
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Project description:In dairy cows, administration of high dosages of niacin (NA) was found to cause anti-lipolytic effects, which are mediated by the NA receptor hydroxyl-carboxylic acid receptor 2 (HCAR2) in white adipose tissue (WAT), and thereby to an altered hepatic lipid metabolism. However, almost no attention has been paid to possible direct effects of NA in cattle liver, despite showing that HCAR2 is expressed also in the liver of cattle and is even more abundant than in WAT. Due to this, we hypothesized that feeding of rumen-protected NA to dairy cows influences critical metabolic and/or signaling pathways in the liver through inducing changes in the hepatic transcriptome. In order to identify these pathways, we applied genome-wide transcript profiling in liver biopsies obtained at 1 wk postpartum (p.p.) from dairy cows of a recent study (Zeitz et al., 2018) which were fed a total mixed ration without (control group) or with rumen-protected NA from 21 d before calving until 3 wk p.p. Hepatic transcript profiling revealed that a total of 487 transcripts were differentially expressed [filter criteria fold change (FC) > 1.2 or FC < -1.2 and P < 0.05] in the liver at 1 wk p.p. between cows fed NA and control cows. Substantially more transcripts were down-regulated (n = 338), while only 149 transcripts were up-regulated by NA in the liver of cows. Gene set enrichment analysis (GSEA) for the up-regulated transcripts revealed that the most enriched gene ontology (GO) biological process terms were exclusively related to immune processes, such as leukocyte differentiation, immune system process, leukocyte differentiation, activation of immune response and acute inflammatory response. In line with this, the plasma concentration of the acute phase protein haptoglobin tended to be increased in dairy cows fed rumen-protected NA compared to control cows (P < 0.1). GSEA of the down-regulated transcripts showed that the most enriched biological process terms were related to metabolic processes, such as cellular metabolic process, small molecule metabolic process, lipid catabolic process, organic cyclic compound metabolic process, small molecule biosynthetic process and cellular lipid catabolic process. In conclusion, hepatic transcriptome analysis shows that rumen-protected NA induces genes which are involved mainly in immune processes including acute phase response and stress response in dairy cows at wk 1 p.p. These findings indicate that supplementation of rumen-protected NA to dairy cows in the periparturient period may induce or amplify the systemic inflammation-like condition which is typically observed in the liver of high-yielding dairy cows in the p.p. period.
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Project description:Multi-omics integration analysis of rumen microorganisms isolated from cows fed either an ad lib or restricted diet, and comparing this with methane emission rates for the cows.
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Project description:<p><strong>BACKGROUND:</strong> Lactation is extremely important for dairy cows; however, the understanding of the underlying metabolic mechanisms is very limited. This study was conducted to investigate the inherent metabolic patterns during lactation using the overall biofluid metabolomics and the metabolic differences from non-lactation periods, as determined using partial tissue-metabolomics. We analyzed the metabolomic profiles of four biofluids (rumen fluid, serum, milk and urine) and their relationships in six mid-lactation Holstein cows and compared their mammary gland (MG) metabolomic profiles with those of six non-lactating cows by using gas chromatography-time of flight/mass spectrometry. </p><p><strong>RESULTS:</strong> In total, 33 metabolites were shared among the four biofluids, and 274 metabolites were identified in the MG tissues. The sub-clusters of the hierarchical clustering analysis revealed that the rumen fluid and serum metabolomics profiles were grouped together and highly correlated but were separate from those for milk. Urine had the most different profile compared to the other three biofluids. Creatine was identified as the most different metabolite among the four biofluids (VIP=1.537). Five metabolic pathways, including gluconeogenesis, pyruvate metabolism, the tricarboxylic acid cycle (TCA cycle), glycerolipid metabolism, and aspartate metabolism, showed the most functional enrichment among the four biofluids (false discovery rate<0.05, fold enrichment >2). Clear discriminations were observed in the MG metabolomics profiles between the lactating and non-lactating cows, with 54 metabolites having a significantly higher abundance (P<0.05, VIP>1) in the lactation group. Lactobionic acid, citric acid, orotic acid and oxamide were extracted by the S-plot as potential biomarkers of the metabolic difference between lactation and non-lactation. The TCA cycle, glyoxylate and dicarboxylate metabolism, glutamate metabolism and glycine metabolism were determined to be pathways that were significantly impacted (P<0.01, impact value >0.1) in the lactation group. Among them, the TCA cycle was the most up-regulated pathway (P<0.0001), with 7 of the 10 related metabolites increased in the MG tissues of the lactating cows. </p><p><strong>CONCLUSIONS:</strong> The overall biofluid and MG tissue metabolic mechanisms in the lactating cows were interpreted in this study. Our findings are the first to provide an integrated insight and a better understanding of the metabolic mechanism of lactation, which is beneficial for developing regulated strategies to improve the metabolic status of lactating dairy cows.</p>
2018-03-16 | MTBLS411 | MetaboLights
Project description:The objective of this study was to characterize the mRNA expression profile in rumen epithelium from Holstein dairy cows fed high or low concentrate dits.
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Project description:Liver and mammary gland are among the most prominent organs during lactation in dairy cows. With the purpose to understand 1) the adaptation of liver and mammary to different levels of forage/concentrate ration (60:40 vs. 40:60) and 2) the crosstalk between the two organs during lactation, a transcriptome analysis was performed on liver and mammary tissues of 10 primiparous dairy cows in mid-lactation. The analysis was performed using a 4x44K Bovine Agilent microarray chip. The mammary and liver samples were obtained from a subset of animals from a larger experiment where cows were fed two different levels of forage/concentrare ration (Archives of Animal Nutrition, 68:1, 63-71).
2017-02-14 | GSE73980 | GEO