Feed restriction, but not L-carnitine infusion, affects the liver transcriptome with an evident and inhibition of energy production and sterol synthesis and increase of gluconeogenesis in mid-lactating dairy cows
Ontology highlight
ABSTRACT:
ORGANISM(S): Bos taurus
SUBMITTER: Massimo Bionaz
PROVIDER: E-GEOD-43307 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:The study investigated the acute and simultaneous response of the mammary and liver transcriptome to an intra-mammary lipopolysaccharide (LPS) challenge in early-lactating cows, and its consequences on metabolic biomarkers and liver composition. At 7 days of lactation, 7 cows served as controls (CTR) and 7 cows (LPS) received an intra-mammary E. coli LPS challenge. The mammary and liver tissues were sampled at 2.5 h from challenge for transcriptomic profiling. Liver composition was evaluated at 2.5 h and 7 d after challenge and blood biomarkers were analized at -2, 3, 7 and 14 d from challenge. In mammary tissue, the LPS challenge resulted in 189 differentially expressed gene (DEG), with 20 downregulated and 169 upregulated, while in the liver were found 107 DEG with 42 downregulated and 65 upregulated in LPS vs CTR. In the udder, the Dynamic Impact Approach (DIA) highlighted the activation of NOD-like receptor signaling, Toll-like receptor signaling, RIG-I-like receptor signaling and Apoptosis pathways, while in the liver were inhibited the Fatty acid elongation in mitochondria and activated the p53 signaling pathway. The LPS induced the alteration of liver lipid metabolism (rise of total lipid and triglyceride concentration), a systemic inflammation (rise of blood ceruloplasmin and bilirubin) and an increase of body fat mobilization. In cows subjected to intra-mammary LPS, the mammary gland responds activating mechanisms of pathogen recognition. In the liver the response likely depends by mediators coming from udder and affects the liver functionality and mainly the fatty acid metabolism. Fourteen Holstein cows entering their second or greater lactation were used. Cows were housed in a ventilated tie-stall barn and were fed a common lactation diet (Net energy of lactation = 1.69 Mcal/kg DM) as a total mixed ration once daily (0600 h) and milked twice daily (0400 and 1600 h). A bovine oligonucleotide (70-mers) microarray with >13,000 annotated sequences developed at the University of Illinois, was used for transcript profiling. Details on the development, annotation, and use of this microarray have been reported previously by Loor et al., 2007 (http://physiolgenomics.physiology.org/content/32/1/105.abstract). Methods for microarray hybridization and scanning were as reported by Loor et al. (2007). Briefly, slides were hydrated, dried, and placed in a UV Stratalinker 1800 (Stratagene, La Joya, CA) for ~5 min. Slides were washed with 0.2% SDS solution, rinsed with MilliQ (Millipore) H2O, and placed in warm prehybridization soln for 45 min at 42 C. The same amount of Cy3- or Cy5-labelled cDNA from mammary or liver and a reference standard RNA pool (made of different bovine tissues) were co-hybridized using a dye-swap design (i.e., two microarrays per sample). Slides were incubated for 48 h at 45 C prior to scanning. Criteria for evaluation of slide quality included: identification of number of spots with a minimum median signal intensity of 3 SD above background; keeping slides with a minimum of 20,000 spots with minimum median signal intensity of 3 SD above background in both Cy3 and Cy5 channels; and keeping slides with a minimum mean intensity of 400 relative fluorescent units in both Cy3 and Cy5 channels across the entire slide. Data from a total of 112 microarrays were normalized for dye and microarray effects (i.e., Lowess normalization and microarray centering) and used for statistical analysis. Data were analyzed using the Proc MIXED procedure of SAS (SAS, SAS Inst. Inc., Cary, NC). Fixed effects were treatment (LPS challenge, control (no infsuion)) and dye. Random effects included cow and microarray. Raw P values were adjusted using Benjamini and HochbergM-bM-^@M-^Ys false discovery rate (FDR). Differences in relative expression due to treatment were considered significant at an FDR-adjusted P < 0.05. For a more stringent characterization between the two treatments, a 1.5-fold difference in mRNA expression was set as threshold among differentially expressed genes.
2014-12-17 | E-GEOD-64225 | biostudies-arrayexpress
Project description:The bovine mammary epithelial cell line Mac-T has been used to study mammary gland in vitro. The reliability of this system to study mammary gland has not been tested using genomics approaches. In the present experimetn a direct transcriptomics comparison between Mac-T cells and mammary tissue at -30 and at 60 day in milk (DIM) is performed. Data indicated that Mac-T cells and mammary tissue had a substantially different transcriptome with a larger difference between Mac-T cells and lactating mammary tissue (i.e., 60 DIM) compared to non-lactating mammary tissue (i.e., -30 DIM). In addition, data indicated that the Mac-T cells substantially differ with mammary tissue in lactation-specific functions. cDNA from Mac-T cells induced in vitro into lactation for 36h (addition of prolactin) was directly hybridize in the microarray chip with cDNA from mammary tissue at -30 or 60 day in milk from 3 cows.
2013-04-30 | E-GEOD-46476 | biostudies-arrayexpress
Project description:We evaluated if a higher plane of maternal nutrition during late gestation and weaning age alters the offspringM-bM-^@M-^Ys Longissimus muscle (LM) transcriptome. A microarray analysis was performed in LM samples of early (EW) and normal weaned (NW) Angus M-CM-^W Simmental calves born from cows that were grazing endophyte-infected tall fescue/red clover pastures with no supplement (low plane of nutrition (LPN)), or supplemented with 2.3 kg of dried distillerM-bM-^@M-^Ys grains with solubles and soyhulls (70% DDGS/30% soyhulls) (medium plane of nutrition (MPN)) during the last 90 days of gestation. Biopsies were harvested at 78, 187 and 354 days of age. Bioinformatics analysis highlighted that offspring transcriptome did not respond markedly to cow plane of nutrition, resulting in only 13 differentially expressed genes. However, weaning age and a high-starch diet strongly impacted the transcriptome, especially the immediate activation of the lipogenic program in EW steers. In addition, between 78 and 187 days of age, these animals had an activation of the innate immune system due presumably to macrophage infiltration in intramuscular fat. Between 187 and 354 days of age (i.e. the fattening phase), NW steers had an activation of the lipogenic transcriptome machinery, while EW steers had a clear gene transcription inhibition. The latter appears to have occurred through the epigenetic control of histone acetylases, which were down-regulated. Higher cow plane of nutrition alone affected 35 genes in the LM of steers that underscore the presence of a mechanism of macrophage infiltration likely originating from localized oxidative stress as a result of increased levels of hypoplasia and hypertrophy in LM. A subset of 20 Angus x Simmental beef cows from the University of Illinois Dixon Springs Agriculture Center (DSAC) in Simpson, IL, were selected from a group of animals utilized in a parallel study75. Main effects evaluated were maternal plane of nutrition during late gestation and postnatal management of the offspring. Three months prior to the projected parturition date cows were assigned to treatments (low or medium plane of nutrition) in a split-plot design. Low plane of nutrition (LPN) was achieved by grazing endophyte-infected tall fescue/red clover pastures during July, August, and September with no supplement. Medium plane of nutrition cow diet (MPN) was achieved by grazing endophyte-infected tall fescue/red clover pastures supplemented with 2.3 kg of dried distillerM-bM-^@M-^Ys grains with solubles and soyhulls (70% DDGS/30% soyhulls). Angus x Simmental steer calves were randomly assigned to early or normal weaning treatments within each gestational treatment. This allowed for 10 animals for each postnatal treatment and 5 animals of each of the interactions of gestational M-CM-^W postnatal treatments. At 78 M-BM-1 2 days postpartum, early-wean offspring were weaned, transported to Urbana Beef Unit, and adapted to a high-starch diet until they had ad libitum consumption. At 187 M-BM-1 2 days postpartum, normal-wean offspring were weaned and transported to Urbana Beef Unit. All offspring were co-mingled among treatments. LM biopsies were sampled from a subset of 5 animals per gestational M-CM-^W postnatal treatment at time of early weaning (~78 days) and at time of normal weaning (~187 days), and during the last week prior to harvest (~ 354 days). After normal weaning, all offspring were placed on a common, corn grain-based high-starch finishing diet that is typical of industry management (CP% = 18.1, NDF% = 25.3, ADF% = 14.3, crude fat % = 5.1). All the offspring in the study were harvested at a commercial packing plant when they reached the selected end point target back fat thickness of 1.1 cm. Reported final body weight (BW) was calculated from hot carcass weight using a 62% dressing percentage. In the present study, we used a transcriptome-wide bovine microarray (Agilent-015354 Bovine Oligo Microarray-4x44K) that contains 21,475 unique genes and transcripts of Bos Taurus, with two probes per gene. The methods used for hybridization and scanning were according to manufacturerM-bM-^@M-^Ys protocols and Loor et al45. The microarray data were deposited in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/gds) with accession number GSE-XXXX. GeneSpring GX (Agilent Technologies) was used for data visualization and preliminary data mining. Subsequently, the entire microarray data set with associated statistical P-values were imported into Ingenuity Pathways Analysis M-BM-. (IPA, www.ingenuity.com) in order to examine the number of activated and inhibited differentially expressed genes (DEG). Entrez Gene IDs were used to identify individual sequences. Data from the microarray analysis were normalized for dye and microarray effects (i.e., Lowess normalization and array centering) and used for statistical analysis. The MIXED procedure of SAS (SAS Institute, Inc., Cary, NC, USA) was used for statistical analysis. Fixed effects were treatment (early weaning, normal weaning), diet (low and medium cow plane of nutrition), time (78, 187, and 354 days of age), first, second and third order interactions between diet, time and treatment, and dye (Cy3, Cy5) and random effects included steer and microarray. Raw P values were adjusted using Benjamini and HochbergM-bM-^@M-^Ys false discovery rate (FDR). Bioinformatics analysis of microarray data was performed using DIA 10 and information from the freely-available online databases Kyoto Encyclopedia of Genes and Genomes (KEGG) and Database for Annotation, Visualization, and Integrated Discovery (DAVID) v6.7 databases. A list of gene identifiers (Entrez Gene IDs) was uploaded all at once to extract and summarize functional annotations associated with groups of genes or with each individual gene. The significance value associated with biological processes and pathways is a measure of the likelihood that the distribution of DEG in these pathways and biological processes is due to chance. The significance is expressed as a P-value, which is calculated using the right-tailed Fisher's Exact Test and adjusted using FDR. Details of the DIA approach and its validation have been reported previously. The interpretation of the bioinformatics analysis was performed following the same approach as our previous study.
2015-02-03 | E-GEOD-65560 | biostudies-arrayexpress
Project description:Feed restriction and L-carnitine infusion are known to affect the liver metabolism of dairy cows. In the present experiment the effects on liver transcriptome of feed restriction and L-carnitine abomasal infusion and the interaction of the two in mid-lactation Holstein dairy cows was assessed. Data clearly indicated a lack of transcriptomics effect by L-carnitine but a strong effect due to feed restriction. The functional analysis identified a overall reduction of cholesterol synthesis and oxidative phosphorylation and data suggested an increase flux toward gluconeogenesis and fatty acid oxidation.
2013-01-07 | GSE43307 | GEO
Project description:The bovine transcriptome dynamics in logissimus muscle (LM) during the post-natal growth remain unknown. Biopsies of LM from Angus steers were harvested at 0, 60, 120, and 220 d from early-weaning. A 13,153 bovine oligonucleotide array was used for transcript profiling. Functional analysis of microarray data was performed using the Dynamic Impact Approach (DIA) by means of KEGG and DAVID databases. During the growing phase, most of the highly-impacted pathways (e.g. Ascorbate and aldarate metabolism, Drug metabolism - cytochrome P450 and Retinol metabolism) were inhibited. The finishing phase, was characterized with the most striking differences with 3,784 differentially expressed genes (DEG; FDR <0.01). The functional analysis of those DEG revealed that the most-impacted KEGG canonical pathway was M-bM-^@M-^\Glycosylphosphatidylinositol (GPI) - anchor biosynthesisM-bM-^@M-^]. The inhibition of this pathway suggested a unique role of GPI-anchor proteins in intracellular trafficking during the finishing phase. A mechanism regulating muscle growth during the finishing phase was uncovered in which inhibition of calpastatin and activation of tyrosine aminotransferase ubiquitination promote proteasomal degradation, while the concurrent activation of ribosomal proteins promotes protein synthesis, thus, the balance of these processes likely results in a steady state of protein turnover during the finishing phase. Overall, results underscored the importance of transcriptome dynamics in LM to support key biological functions during rapid growth. The study utilized a subset of 14 animals from a larger study encompassing 32 purebred Aberdeen Angus steers from the University of Illinois beef cattle herd. Steer calves were early-weaned (134 M-BM-1 10 d age) and after weaning were placed on a diet of 85% corn silage and 15% wet distillerM-bM-^@M-^Ys grains (as-fed basis) for 3 wk. Subsequently, one half of Angus (n = 16) steers was randomly assigned to a high-byproduct or high-grain diet for a 112 d growing phase. The high-byproduct diet contained (dry matter basis) 35% corn silage, 20% corn gluten feed, 38% soyhulls, 3% cracked corn, and 3% soybean meal (49% crude protein). The high-grain diet contained 20% corn silage, 68% cracked corn, and 11% soybean meal (49% crude protein). Both diets contained 1% limestone/dicalcium phosphate/mineral/vitamin/urea/dry molasses mixture. Calculated NEG for the high-byproduct diet was 1.19 Mcal/kg and 1.43 Mcal/kg for the high-grain diet. At the end of the growing phase, steers on each group were fed M-bM-^@M-^\step-up dietsM-bM-^@M-^] for 10 d. Step-up diet for high-byproduct-fed steers contained 1.37 Mcal NEG/kg. Step-up diet for high-grain-fed steers contained 1.43 Mcal NEG/kg but contained distillerM-bM-^@M-^Ys dried grains (16% of dry matter). After the M-bM-^@M-^\step-upM-bM-^@M-^] period, all steers were finished on a common high-grain finishing diet containing 1.44 Mcal NEG/kg (15% corn silage, 58% cracked corn, 25% dried distillerM-bM-^@M-^Ys grains, 1% limestone, and 1% urea/mineral/vitamin mixture). All diets were offered on an ad libitum basis. Steers had an individual electronic identification ear tag and individual feed intake data were collected using the GrowSafe system (GrowSafe Systems Ltd., Alberta, Canada). Cattle were harvested at approximately 13 mo age. A bovine oligonucleotide (70-mers) microarray with >13,000 annotated sequences developed at the University of Illinois, was used for transcript profiling. Details on the development, annotation, and use of this microarray have been reported previously by Loor et al., 2007 (http://physiolgenomics.physiology.org/content/32/1/105.abstract). Methods for microarray hybridization and scanning were as reported by Loor et al. (2007). Briefly, slides were hydrated, dried, and placed in a UV Stratalinker 1800 (Stratagene, La Joya, CA) for ~5 min. Slides were washed with 0.2% SDS solution, rinsed with MilliQ (Millipore) H2O, and placed in warm prehybridization soln for 45 min at 42 C. The same amount of Cy3- or Cy5-labelled cDNA from muscle and a reference standard RNA pool (made of different bovine tissues) were co-hybridized using a dye-swap design (i.e., two microarrays per sample). Slides were incubated for 48 h at 45 C prior to scanning. Criteria for evaluation of slide quality included: identification of number of spots with a minimum median signal intensity of 3 SD above background; keeping slides with a minimum of 20,000 spots with minimum median signal intensity of 3 SD above background in both Cy3 and Cy5 channels; and keeping slides with a minimum mean intensity of 400 relative fluorescent units in both Cy3 and Cy5 channels across the entire slide. Data from a total of 112 microarrays were normalized for dye and microarray effects (i.e., Lowess normalization and microarray centering) and used for statistical analysis. Data were analyzed using the Proc MIXED procedure of SAS (SAS, SAS Inst. Inc., Cary, NC). Fixed effects were treatment (high-byproduct, high-grain) and time (0, 56, 120, and 220 d), and dye. Random effects included steer and microarray. A covariate adjustment was used to assess treatment and treatment M-CM-^W time interactions, but time effects on gene expression were assessed without covariate adjustment. Raw P values were adjusted using Benjamini and HochbergM-bM-^@M-^Ys false discovery rate (FDR). Differences in relative expression due to treatment M-CM-^W time interactions were considered significant at an FDR-adjusted P < 0.25 or at P < 0.01 for time effects. qPCR data were normalized using the median of 4 suitable internal control genes, and were analyzed using the same statistical model described above. Differences were considered significant at P-value of 0.05.
2013-06-21 | E-GEOD-48136 | biostudies-arrayexpress
Project description:In dairy cows, milk production and composition are affected by numerous factors, including diet. Milk is the body fluid with the highest RNA concentration, including numerous microRNA. These microRNA presence in the different milk compartments is still poorly documented and the effect of feed restriction on milk miRNome has not been described yet. The aim of this study was to describe the effects of feed restrictions of different intensitizes on milk compartment miRNome composition. Two feed restriction trials were performed on lactating dairy cows, one of high intensity and one of moderate intensity. 2 896 mature microRNA were identified in milk, including 1 493 that were already known in bovine specie. Among the 1 095 miRNA that were abundant enough to be informative, 10% were exclusive to one milk compartment and the abundance of 155 varied between compartments, revealing a specific miRNome for each milk fraction. Feed restriction affected differently these miRNome, with microRNA in whole milk and milk extracellular vesicles being the most affected and microRNA in fat globules and exfoliated mammary epithelial cells being relatively or completely unaffected. Target prediction of known microRNA that varied under feed restriction reflected modification of some key pathways for lactation related to milk fat and protein metabolisms, cell cycle and stress responses. These findings open up opportunities for future research on the use of milk miRNA as biomarkers of energy status in dairy cows.
2023-05-31 | GSE207759 | GEO
Project description:Milk production in dairy cows is affected by numerous factors, including diet. Feed restriction is known to have little impact on milk total protein content but its effect on the fine protein composition is still poorly documented. The objective of this study was to describe the effects of two feed restriction trials of different intensities on the milk protein composition of Holstein cows. One restriction trial was short and of high intensity (SH), the second was long and of moderate intensity (LM). Feed restriction decreased the milk protein yield for caseins under the LM trial and of all six major milk proteins under the SH trial. These decreased yields lead to lower concentrations of αs1-, αs2- and β-caseins during the SH trial. The milk proteome was affected as a function of restriction intensity. Among the 345 proteins identified eight varied under the LM trial and 160 under the SH trial. Ontology analyses revealed their implication in carbohydrate, lipid and protein metabolisms as well as in the immune system. These proteins reflected adaptations of the animal and mammary gland physiology to feed restriction and constituted a signature of this change.
2022-11-10 | PXD033969 | Pride
Project description:The current situation of rising demand for animal products and sustainable resource usage, improving nutrient utilization efficiency in dairy cows is an important task. Understanding the biology of feed efficiency in dairy cows enables for the development of markers that may be used to identify and choose the best animals for animal production. Thus in this study, ten Holstein cows were evaluated for feed efficiency and adipose tissue samples from five high efficient and five low efficient dairy cows were collected for protein extraction, digestion and data were analyzed for differential abundant proteins enriched in feed efficiency pathways. Among the identified peptides, we found 110 DAPs and two protein networks significantly related to feed efficiency. Among the relative mRNA expression of genes involved in energy metabolism including transcription/translation (STAT2, DDX39A and RBM39) or protein transport (ITGAV), only RBM39 showed significant decrease in high efficient dairy cows. The findings presented here confirmed the Transferrin upregulated in pathways including acute phase response signaling, LXR/RXR activation, FXR/RXR activation of high efficient dairy cows supporting that these pathways are related to feed efficiency in dairy cows.
2022-08-12 | PXD029328 | Pride
Project description:Effect of feed restriction in mid lactation Holstein (H) and Montbéliarde (M) cows on mammary glande miRNA profil.
2021-03-10 | GSE146762 | GEO
Project description:Increased energy demands to support lactation, coupled with lowered feed intake capacity results in negative energy balance (NEB) and is typically characterized by extensive mobilization of body energy reserves in the early postpartum dairy cow. The catabolism of stored lipid leads to an increase in the systemic concentrations of nonesterified fatty acids (NEFA) and -hydroxy butyrate (BHB). Oxidation of NEFA in the liver result in the increased production of reactive oxygen species and the onset of oxidative stress and can lead to disruption of normal metabolism and physiology. The immune system is depressed in the peripartum period and early lactation and dairy cows are therefore more vulnerable to bacterial infections causing mastitis and or endometritis at this time. A bovine Affymetrix oligonucleotide array was used to determine global gene expression in the spleen of dairy cows in the early postpartum period. Spleen tissue was removed post mortem from five severe NEB (SNEB) and five medium NEB (MNEB) cows 15 days postpartum.SNEB increased systemic concentrations of NEFA and BHB, and white blood cell and lymphocyte numbers were decreased in SNEB animals. A total of 545 genes were altered by SNEB. Network analysis using Ingenuity Pathway Analysis revealed that SNEB was associated with NRF2-mediated oxidative stress, mitochondrial dysfunction, endoplasmic reticulum stress, natural killer cell signaling, p53 signaling, downregulation of IL-15, BCL-2, and IFN- ; upregulation of BAX and CHOP and increased apoptosis with a potential negative impact on innate and adaptive immunity. Multiparous Holstein-Friesian cows (n=24) were blocked 2 weeks prior to expected calving date according to parity, body condition score, and previous lactation yield (average lactation 6477M-BM-1354kg) and randomly allocated to mild (MNEB; n=12) or severe (SNEB; n=12) NEB groups. MNEB cows were fed ad lib grass silage and 8 kg day-1 concentrates and milked once daily; SNEB cows were fed 25 kg day-1 silage and 4kg day-1 concentrate and milked three times daily. Measurements of body condition score and EB were used to select cows which showed extremes in EB from each group (MNEB, n=5; SNEB, n=5). Cows were slaughtered on days 6-7 of the first follicular wave after calving (mean number of days post-partum: MNEB mean 13.6 M-BM-1 0.75, range 11M-bM-^@M-^S15; SNEB mean 14.3 M-BM-1 0.56, range 13M-bM-^@M-^S16), based on daily transrectal ultrasonography.At slaughter the entire spleen was removed and weighed, and samples weighing 1 g were dissected, rinsed in RNase-free phosphate buffer, snap frozen in liquid nitrogen, stored for 4 h in dry ice, and subsequently stored at 80M-BM-0C.
2014-04-08 | E-GEOD-56589 | biostudies-arrayexpress