Ontology highlight
ABSTRACT:
PROVIDER: PRJNA682184 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13190224_1.fastq.gz | Fastqsanger.gz | |||
| SRR13190224_2.fastq.gz | Fastqsanger.gz | |||
| SRR13190225_1.fastq.gz | Fastqsanger.gz | |||
| SRR13190225_2.fastq.gz | Fastqsanger.gz | |||
| SRR13190226_1.fastq.gz | Fastqsanger.gz |
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Project description:The objective of this study was to identify metabolic regulatory mechanisms affected by choline availability in rainbow trout (Oncorhynchus mykiss) broodstock diets associated with increased offspring growth performance. Three customized diets were formulated to have different levels of choline: (a) 0% choline supplementation (Low Choline: 2065 ppm choline), (b) 0.6% choline supplementation (Medium Choline: 5657 ppm choline), and (c) 1.2% choline supplementation (High Choline: 9248 ppm choline). Six all-female rainbow trout families were fed experimental diets beginning 18 months post-hatch until spawning; their offspring were fed a commercial diet. Experimental broodstock diet did not affect overall choline, fatty acid, or amino acid content in the oocytes (p > 0.05), apart from tyrosine (p ≤ 0.05). Offspring body weights from the High and Low Choline diets did not differ from those in the Medium Choline diet (p > 0.05); however, family-by-diet and sire-by-diet interactions on offspring growth were detected (p ≤ 0.05). The High Choline diet did not improve growth performance in the six broodstock families at final harvest (520-days post-hatch, or dph). Numerous genes associated with muscle development and lipid metabolism were identified, including myosin, troponin C, and fatty acid binding proteins, which were associated with key signaling pathways of lipid metabolism, muscle cell development, muscle cell proliferation, and muscle cell differentiation. These findings indicate that supplementing broodstock diets with choline does regulate expression of genes related to growth and nutrient partitioning but does not lead to growth benefits in rainbow trout families selected for disease resistance.
2024-02-09 | GSE243186 | GEO
Project description:Rainbow trout (Oncorhynchus mykiss) were fed during 4 weeks with either a control diet or an immunostimulant diet and then injected with LPS to investigate the effect of dietary immunostimulation in the portals of entry, intestine and gills, using a salmonid-specific microarray platform enriched with immune-related genes. IS-diet feeding significantly changed transcriptomic expression profiles in response to LPS: significant changes in genes and functional GO categories related to remodeling processes and antigen presentation were different for both diets. The results revealed that one of the main effects of IS-diets in trout is the increase of genes involved in antigen recognition and in adaptive immunity. Keywords: gills, intestine, immunostimulats, transcriptomic response, trout
2008-10-02 | GSE12961 | GEO
Project description:The objective of this paper was to determine whether shifts in the methylome in rainbow trout (Oncorhynchus mykiss) are correlated with transcriptomic changes during early development in response to maternal dietary choline intake. Three experimental diets were formulated to have different levels of choline: (a) 2065 ppm choline (Low Choline, 0% supplementation), (b) 5657 ppm choline (Medium Choline, 0.6% supplementation), and (c) 9248 ppm choline (High Choline, 1.2% choline supplementation). Six rainbow trout families were fed experimental diets beginning 18 months post-hatch until spawning; their offspring were fed a commercial diet. Reduced representational bisulfite sequencing (RRBS) was utilized to measure genome-wide methylation differences in offspring immediately after hatching. When comparing to the Medium Choline offspring, differential DNA methylation occurred more in the Low Choline offspring than High Choline, especially in genic features like promoters. The differentially methylated CpGs (q ≤ 0.01) were identified evenly between CpG islands and shores in the genome, mostly found in the introns of genes. Genes such as fabp2 and leap2B associated with protein binding, fatty acid binding, DNA binding, and response to bacteria were differentially methylated and detected as differentially regulated genes by previous RNA-seq analysis. Although these findings indicate that levels of dietary choline available in broodstock diets alters offspring DNA methylation; most differentially expressed genes were not associated with differential DNA methylation, suggesting additional mechanisms playing a role in regulating gene expression in response to maternal choline intake.
2024-11-21 | GSE269087 | GEO
Project description:The sustainable growth of fish aquaculture will require the procurement of non-marine feed sources. Glycerol is a potential feed supplement whose metabolism may spare the catabolism of dietary amino acids, thereby extending the use of the feed protein to other physiological functions such as growth. In the present study, the effects of dietary glycerol supplementation on the muscle and liver metabolomes of rainbow trout (Oncorhynchus mykiss) and European seabass (Dicentrarchus labrax) were evaluated. Fish juveniles were fed diets with 0%, 2.5%, and 5% glycerol. Muscle and liver aqueous fractions were extracted and 1H NMR spectra were acquired. Metabolite profiles derived from the 1H NMR signals were assessed using univariate and multivariate statistical analyses. The adenylate energy charge was determined in the muscle. For both species, the muscle metabolite profile showed more variability compared to that of the liver and was most perturbed by the 5.0% glycerol diet. For the liver metabolite profile, rainbow trout showed fewer differences compared to European seabass. No differences were observed in energy charge between experimental groups for either species. Thus, rainbow trout appeared to be less susceptible to tissue metabolite perturbations, compared to seabass, when the diet was supplemented with up to 5% glycerol.
2020-02-24 | MTBLS832 | MetaboLights
Project description:A 10-week feeding trial was conducted to determine an appropriate carbohydrate source evaluating growth performance, feed utilization, hepatic activity, whole-body fatty/amino acid composition, liver transcriptomics and gut microbiome for Florida pompano (Trachinotus carolinus). Five isonitrogenous (46.67% crude protein), iso-lipidic (15.15% crude lipid) and isocaloric (385Kcal/100g digestible energy) diets were formulated containing 14% of different source of carbohydrates: whole wheat grain flour (WG), wheat starch (WS), whole corn grain flour (CG), corn starch (CS) and dextrinized corn starch (DCS). The results indicated that: highest percentage weight gain (PWG) and specific growth rate (SGR) were found in fish fed with whole wheat grain flour (WG) diet, the highest feed efficiency (FE) was shown in WG and WS diets, lowest conversion index (CI) was observed in fish fed with WG diet and the highest protein efficiency ratio (PER) was shown in in WS diet. The poorest values were observed in fish fed with CS and DCS diets. The whole-body crude protein and total amino acid and fatty acids composition was not significantly affected by different sources of carbohydrates in the diets. In fish fed with the WG diet, glucose levels in plasma and liver were significantly low while liver glycogen content was statistically high compared to the other diets. Liver transcriptomics analysis revealed differentially expressed genes (DEGs) and gene ontology (GO) enrichment analysis highlighting up/down regulated biological functions depending on the carbohydrate source. The microbial community presented high diversity and richness among treatments. Overall, results indicated that whole wheat grain flour is the more adequate dietary carbohydrate source based on production performance, physio-biochemical and molecular approaches. These data are critical when formulating a complete commercial feed for sustainable and profitable culturing of Florida pompano
2025-07-23 | GSE266429 | GEO
Project description:Rainbow trout (Oncorhynchus mykiss) and other salmonids are piscivorous fish. In aquaculture, fish-based feed ingredients are rapidly becoming unsustainable due to increased demand and diminishing supply. Total replacement of fishmeal with plant proteins causes severe intestinal enteritis, leading to reduced growth and lower feed efficiency. Through selective breeding, we have developed a strain of rainbow trout that does not develop distal intestine enteritis when reared on a high soy plant protein-based feed and also shows increased growth compared to other strains. Since central metabolism plays a major role in dietary alterations, and as growth was a major factor in the selection program, both muscle and liver gene expression were examined for differential regulation between commercial and selected trout strains when fed alternative diets. After three months of rearing on either a fishmeal (FM) or plant protein-based (PM) diet, muscle and liver tissues from a domestic non-selected strain (House Creek; develops enteritis) and the selected strain (ARS-KO; no enteritis) were extracted and prepped for Illumina RNA-seq. Raw reads were screened for quality then aligned to the rainbow trout transcriptome. Read-counts were used to assess differential expression between strains and treatments. Significant differentially expressed genes between comparisons were assessed.
2017-09-05 | GSE79531 | GEO
Project description:We used fish from two divergent lines of rainbow trout, selected for low or high muscle fat content (respectively L and F lines) and fed two different diets, containing either 10% (LE diet) or 23% (HE diet) lipids. For more details about experimental fish and diets, see Kolditz et al.,Am J Physiol Regul Integr Comp Physiol 294: R1154–R1164, 2008. There are 4 experimental conditions: L-LE, L-HE, F-LE and F-HE. This experiment contain the data derived from the hybridization of the RNA extracted from individual liver of these fish. for each membrane, spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array. Keywords: Nutritional genomics, response to divergent selection for muscle fattening, liver metabolism, rainbow trout
2008-09-01 | GSE12031 | GEO
Project description:In rainbow trout (Oncorhynchus mykiss), the effect of a paternal and a maternal "high carbohydrate/low protein" diet was assessed on progeny. To this purpose, two-year old males and females rainbow trout were fed either a control diet or a "high carbohydrate/low protein" diet for an entire reproductive cycle for females and for 5 months for males. Crossed-fertilizations were carried out in order to obtain 4 groups of offspring. Offspring were fed with a commercial diet until they reached a market size. At this stage, hepatic transcriptomes were compared to detect any impact of the parental diet on offspring metabolism.
2021-08-16 | GSE169001 | GEO
Project description:The whole-body transcriptome of trout alevins was characterized to investigate the effects of long-term feeding of rainbow trout broodstock females a diet free of fishmeal (FM) and fish oil (FO) on the metabolic capacities of progeny. Effects were studied before first feeding and after 3 weeks of feeding with diets containing different proportions of marine and plant ingredients. We showed that that maternal diet history did not significantly affect expression of any gene before the first feeding. We found an effect of maternal nutritional history on gene expression in alevins after 3 weeks of feeding. The major differences in the transcriptome of alevins from VEG-fed females compared to those from COM-fed females were: (i) a down-regulation of genes involved in muscle growth/contraction and (ii) a higher level of expression of genes involved in carbohydrate and energy metabolism related to the delay in growth/ development observed with plant-based diets. Our findings also showed an effect of the first-feeding diets, irrespective of maternal nutritional history. Specifically, the introduction of plant ingredients resulted in up-regulation of genes involved in AA/protein and cholesterol metabolism and in differences in the expression of genes related to carbohydrate metabolism.
2016-10-03 | GSE74271 | GEO