Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1000975 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25508800_1.fastq.gz | Fastqsanger.gz | |||
| SRR25508800_2.fastq.gz | Fastqsanger.gz | |||
| SRR25508801_1.fastq.gz | Fastqsanger.gz | |||
| SRR25508801_2.fastq.gz | Fastqsanger.gz | |||
| SRR25508802_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: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.
2018-06-21 | GSE116058 | GEO
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: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: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.
2022-07-31 | GSE135162 | GEO
Project description:The rumen harbors a complex mixture of archaea, bacteria, protozoa and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacteria populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen fauna. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to the initial stages of rumination, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass samples incubated in nylon bags within the rumen of cannulated dairy cows for 48 hours.
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Project description:SARST-V1 method was used to asses the effect of live yeast on the microbial population of the rumen of cows fed an acidogenic diet 3 cows were used in 3 by 3 latin-square design with 3 periods. In each period animals received either 0.5g/d of yeast, 5g/d of yeast or none. Rumen microbiota was analysed using the SARST-V1 method for each period.
2013-01-01 | E-GEOD-39206 | biostudies-arrayexpress
Project description:While dietary phosphorus (P) deprivation extending from the dry period into early lactation impairs health and productivity of cows, restricting dietary P supply during the dry period not only appears to be innocuous but rather effectively mitigates hypocalcemia during the first wk of lactation. To investigate possible negative metabolic effects of P deprivation during the dry period, the present study tested the hypothesis that restarted dietary P supply during the dry period alters the liver transcriptome of dairy cows during the periparturient period. Thirty late-pregnant multiparous Holstein-Friesian dairy cows entering their 2nd, 3rd or 4th lactation were assigned to either a dry cow ration with low (LP, 0.16% P in DM) or adequate P content (AP, 0.35% in DM) during the last 4 wk of the dry period (n = 15/group). Liver transcriptomics, which was carried out in a subset of five 2nd parity cows of each group (n = 5), and determination of selected hormones and metabolites in blood of all cows, was performed approximately one wk before calving and on d 3 postpartum. Liver tissue specimens and blood samples were obtained by a micro-invasive biopsy technique from the right 10th intercostal space and puncture of a jugular vein, respectively. 175 hepatic transcripts were expressed differentially between LP vs. AP cows in late pregnancy, and 165 transcripts differed between LP vs. AP cows in early lactation (Fold change > 1.3 and < -1.3, P < 0.05). In late pregnancy, the enriched biological processes of the up-regulated and the down-regulated transcripts were mainly related to immune processes and signal transduction (P < 0.05), respectively. In early lactation, the enriched biological processes of the up-regulated and the down-regulated transcripts were involved in mineral transport and biotransformation (P < 0.05), respectively. The plasma concentrations of the hormones and acute phase proteins (progesterone, insulin-like growth factor 1, serum amyloid alpha, haptoglobin, and 17β-estradiol) determined were not affected by P supply. These results suggest that P deprivation during the dry period moderately affects the liver transcriptome of cows in late pregnancy and early lactation, and causes no effects on important plasma hormones and acute phase proteins indicating no obvious impairment of health or metabolism of the cows.
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