Data on European seabass fed with methionine supplemented diets obtained through label free shotgun proteomics
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Dicentrarchus Labrax
TISSUE(S): Liver
SUBMITTER: 
Ana Paula Farinha
LAB HEAD: Pedro Miguel Rodrigues
PROVIDER: PXD019610 | Pride | 2020-12-02
REPOSITORIES: pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 10_13_I.mzid.gz | Mzid | |||
| 10_13_I.mzid_10_13_I.MGF | Mzid | |||
| 10_13_I.raw | Raw | |||
| 10_14_I.mzid.gz | Mzid | |||
| 10_14_I.mzid_10_14_I.MGF | Mzid |
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Project description:Plant-based protein sources play an important role in aquaculture by dwindling fish meal to sustainable levels. However, the use of such feedstuffs requires nutrient supplementation to fulfil fish nutritional requirements. This work addressed the response in the liver of farmed fish to dietary methionine (Met), assessing at the same time the growth performance. Fish were fed at suboptimal levels of dietary Met (0.77% w/w; M0.65 diet), within (1% w/w Met; M0.85 diet)and above(1.36 % w/w Met (M1.25 diet); 1.66% w/w Met(M1.5 diet)) the estimated requirement for this species, in a total of four tested conditions. The impact of dietary methionine supplementation in seabass juvenile’s performance was assessed through 85 days of trial, between May and August of 2018. Fish were reared in triplicate tanks and three liver samples/tank (9 per treatment) were collected for liver proteome analysis at the end of the trial i.e., after 85 days of feeding.
2020-11-25 | PXD019622 | Pride
Project description:The aim of this experiment was to explore transcriptomic changes in the distal gut of Altantic salmon fed five experimental and two control diets. The experimental diets were isonitrogenous, isolipidic and isocaloric. They had similar content of fish meal (~22%) and similar total plant protein content (~45%), but differed in the contents of soya protein concentrate (SPC) and bean protein concentrate (BPC). These two ingredients were used to replace each other (either partially or fully) at the levels of incorporation ranging from 0 to 45%, with ~11% increments. As a result, the experimental diets contained either 45% SPC and 0% BPC (S45), 34% SPC and 11% BPC (S34B11), 22% SPC and 22% BPC (S22B22), 11% SPC and 34% BPC (S11B34) or 0% SPC and 45% BPC (B45). The S45 and B45 diets were single plant protein diets, while the others (S34B11, S22B22 and S11B34) were mixed plant protein diets. The control diets were enriched with fish meal (FM diet) or soybean meal (SBM diet) to provide negative and positive controls for gut inflammation (enteritis), respectively. The study was conducted at EWOS Innovation Research Facility in Dirdal (Norway) Atlantic salmon (Salmo salar L.) of the SalmoBreed strain were supplied as fertilized eggs and hatched on site. Mixed-sex juvenile salmon in groups of ~150 fish were transferred to 26 indoor tanks (0.6 x 0.6 x 0.6 m), with ~60 L of freshwater flowing at a rate of 3.9 L/min and continuous aeration. The temperature of water was regulated at 13°C and all animals were exposed to a constant light regime (24 h light/day). Fish were fed a commercial EWOS Start 1 diet and acclimated to the experimental conditions for 2 weeks, after which (at body mass ~1.5 g) they were subjected to a 56-day feeding trial. Tanks were randomly assigned to the dietary treatments, with 4 replicate tanks per each experimental diet (S45, S34B11, S22B22, S11B34 and B45) and 3 replicate tanks per each control diet (FM and SBM diets). Fish were fed to satiation prior to the feeding trial and during the dietary manipulation using automatic band feeders (Holland Technology, Norway). During the feeding trial, all fish in each tank had their biomass recorded on days 0 (start of experiment), 14, 28, 42 and 56 (end of experiment) for evaluation of growth performance.
2016-02-01 | E-MTAB-3613 | biostudies-arrayexpress
Project description:We used DNA microarrays to identify discriminative gene signatures for the purpose of classifying n-3 PUFA-fed, carcinogen injected Sprague Dawley rats at the initiation and progression stages. Animals were assigned to three dietary treatments differeing only in the type of fat (corn oi/n-6 PUFA, fish oil/n-3 PUFA, or olive oli/n-9 monounsaturated fatty acid). The effects of diet on colonic mucosal gene expression signatures during tumor initiation with the progression of colon cancer. Each dietary lipid source exhibited its own unique transcriptional profile, as assessed by linear discriminant analysis. Applying this novel approach we identified the single genes and the two- to three-gene combinations that best distinguished the dietary treatment groups. For the chemoprotective fish oil diet, mediators of stem cell homeostasis, e.g., ephrin B1 and bone morphogenic protein 4, were the top-permorming gene classifiers. keywords: diet analysis 29 samples were analyzed. 10 samples had repeat arrays. No control or reference samples were included.
2010-12-09 | E-GEOD-25912 | biostudies-arrayexpress
Project description:Dietary zinc is routinely supplemented to promote growth, boost the immune system, protect against diabetes or aid recovery from diarrhoea. We exploited the zebrafish (Danio rerio) gill as a unique vertebrate ion transporting epithelium model to study the time-dependent regulatory networks of gene-expression leading to homeostatic control during zinc supplementation. This organ forms a conduit for zinc uptake whilst exhibiting conservation of zinc trafficking components. Fish were maintained with zinc supplemented water (4.0 uM) and diet (2023 mg zinc kg-1) or in un-amended water and diet, containing Zn2+ at 0.25 µM and 233 mg zinc kg-1 respectively. Gill tissues were harvested at five time points (8 hours to 14 days) and transcriptome changes analysed in quintuplicate using a 16K microarray. Global transcript levels were measured in zebrafish gills using a oligonucleotide array either zinc-adequate or zinc-supplemented diet. Gill samples were collected at five time points and transcriptome changes analysed in quintuplicate using a 16K oligonucleotide array
2010-05-20 | E-GEOD-21907 | biostudies-arrayexpress
Project description:Since the liver is the central organ of metabolism, changes in diet have a great impact on this organ and overall on health with aging. It is well known that dietary fat source strongly influences many parameters of the hepatic mitochondria. These changes includes modification of lipid composition of mitochondrial membrane, affecting the mtETC functions, oxidative stress and mtDNA alterations. We used microarrays to detail the changes in gene expression provides by feeding lifelong on different dietary fat sources, and identified distinct classes of up and down-regulated genes during aging under different dietary conditions. Rats were fed lifelong on a normolipidic diet (4% w/w) with virgin olive, sunflower or fish oil as dietary fat source. At 6 and 24 months, animals were killed and liver were removed for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain changes in gene expression due to both aging and dietary conditions. There were 6 experimental groups (virgin olive oil at 6 months, sunflower oil at 6 months, fish oil at 6 months, virgin olive oil at 24 months, sunflower oil at 24 months and fish oil at 24 months. 3 animals were studied of each experimental group, so a total of 18 samples were analyzed.
2014-03-26 | E-GEOD-56166 | biostudies-arrayexpress
Project description:The inclusion of intact phospholipids in the diet is essential during larval development and can improve culture performance of many fish species. The effects of supplementation of dietary phospholipid from marine (krill) or plant (soy lecithin) sources were investigated in Atlantic salmon, Salmo salar. First feeding fry were fed diets containing either krill oil supplying phospholipid at 2.6% of diet (named K2.6) or soybean lecithin supplying phospholipid at 2.6 % (S2.6), 3.6 % (S3.6) of diet. A control diet (B) without supplemented phospholipid was also supplied. Fish were sampled at ~ 2.5 g (~1990 ˚ day post fertilization, dpf) and ~10 g (2850 ˚dpf). By comparison of the intestinal transcriptome in specifically chosen contrasts, it was determined that by 2850˚dpf fish possessed a profile that resembled that of mature and differentiated intestinal cell types with a number of changes specific to glycerophospholipid metabolism. It was shown that intact phospholipids and particularly phosphatidylcholine are essential during larval development and that this requirement is associated with the inability of enterocytes in young fry to endogenously synthesize sufficient phospholipid for the efficient export of dietary lipid. In the immature phase (~1990 ˚dpf), the dietary phospholipid content as well as its class composition impacted on several biochemical and morphological parameters including growth, but these differences were not associated with differences in intestinal transcriptomes. The results of this study have made an important contribution to our understanding of the mechanisms associated with lipid transport and phospholipid biosynthesis in early life stages of fish.
2015-08-20 | E-MTAB-3673 | biostudies-arrayexpress
Project description:Previous works in the framework of EU ARRAINA Project evidenced a pro-inflammatory condition in gilthead sea bream (Sparus aurata) fed extremely low fish meal/fish oil diets, and this effect was mostly reversed by butyrate supplementation. The hypothesis of work is that these nutritionally-mediated changes can be extensive to intestinal mucus proteome and gut microbiota, which in turn could modify disease outcome.s If so, the prevalence and progression of the disease might be also modified by diet composition and feed additives. Gilthead sea bream fingerlings were fed with control and experimental diets formulated by BioMar until two year-old. FM was added at 25% in the control diet (D1) and at 5% in the other three diets (D2-D4). Added oil was either FO (D1 control diet) or a blend of vegetable oils, replacing the 58% (D2) and the 84% (D3-D4 diets) of FO. A commercial sodium butyrate preparation (NOREL, BP70) was added to the D4 diet at 0.4%. At month 20, 6 fish per each dietary treatment were sampled for iTRAQ profiling and fingerprinting of intestinal mucus proteome. Mucus collected from anterior and posterior intestine segments was trypsin digested, labelled with iTRAQ reagents, isoelectrofocused and resolved by LC-MS/MS. More than 1000 proteins were unequivocally annotated and principal component analysis clearly separated anterior and posterior segments. The diet effect with changes in the abundance of approximately 120 proteins was restricted to anterior section with a reversion of the pattern of the extreme diet (D3 fish) with dietary butyrate supplementation. Butyrate supplementation also reversed the decrease of microbiotay diversity associated with D3 feeding, and led to a improvement the disease outcomes in fish challenged with Photobacterium damselae and the intestinal parasite Enteromyxum leei.
2018-10-24 | PXD006183 | Pride
Project description:Background: The decreasing availability of fishmeal as a protein source in aquaculture diets will require aquaculture to develop an econmoical and sustainable protien replacement. Plant proteins are readily available and are being tested as a promising alternative to replace a substantial portion of fishmeal which currently provides most of the protein content in aquaculture diets. The types of plant protein feasible for incorporation into aquaculture diets will likely contain various anti-nutritional compounds, carbohydrates, fiber, and a different amino acid profile than what is found in fishmeal. Substantial genetic variation was previously observed for growth on plant based dits in rainbow trout Hence, it will be beneficial to identify metabolic and physiologic pathways related to enhanced plant protein utilization which will aid in identifying genes that contribute to this genetic variation. Results: Microarray analysis of liver samples from two families of rainbow trout that differed in their growth responses when compared between individuals grown on a fish meal or plant protein based diet. Differential expression relating to dietary utilization between the two families found significant changes in expression of 33 ESTs. Eight of the differntially expressed ESTs had identified mammalian homologs that had been previously researched with identified cellular interactions and functions. Conclusions: Utilizing pathway analysis software to analyze sequences annotated with known mammalian genes were were ablet o map gene pathway and process interactions. From this information we were able to infer that the metabolic changes associated with utilization of plant protein versus fishmeal were associated with differential reaulation of genes related to cell oxidative stress, proliferation, growth, and survival. Furthermore, we inferred from the changes we observed in immune response genes expression that ingestion of this plant based diet upregulated the expression of genes involved in immunoregulatroy processes. Genotyped samples linked to families that had 4 or more members sampled on each diet were identified and ranked according to average family weight on each diet. Size rankings corresponded to large (>750 g), medium (600-640 g), and small (<500 g). From these identified groups 2 families were chosen for microarray expression analysis that demonstrated individuals with growth differences between the two diets. Data for the two families used for analysis and slide arrangements are listed in table 3. The families compared for growth differences between diets used for this study only differed by one growth range, large fish on fish meal compared to medium fish on plant-based diet and medium sized fish on fishmeal diet compared to small fish on plant-based diet. This strategy to use size separation within family was an attempt to identify gene changes more specific to diet utilization than specific for growth differences.
2011-04-01 | E-GEOD-28310 | biostudies-arrayexpress
Project description:A common-garden experiment was carried out to compare two genetically distinct strains of Atlantic salmon (Salmo salar) fed diets formulated with either high (CHO) or low (NoCHO) carbohydrate (starch). Twenty salmon from either a commercial farmed strain or a land-locked population were placed in two tanks (10 fish of each population in each tank) and fed either CHO or NoCHO feeds for 32 days. At the end of the experimental period fish were fasted for 8 h, euthanized and samples of blood and liver collected. Both diet and population had an effect on circulating glucose levels with land-locked salmon showing hypoglycaemia and dietary starch increasing this parameter. In contrast, land-locked salmon showed increased plasma triacylglycerol levels regardless of dietary treatment. This enhanced ability to metabolise dietary starch in land-locked compared to farmed salmon stock was also reflected at a molecular (gene) level as most of the metabolic pathways evaluated in the present study were mainly affected by the factor population rather than by diet. In particular, lower expression of genes for mitochondrial metabolism in land-locked salmon reflects drastic differences in energy metabolism between the populations. The liver transcriptome analysis highlighted some new gene candidates such as elovl6 to evaluate in future studies assessing the capacity of salmonids to cope with feeds containing higher levels of dietary starch.
2018-12-31 | E-MTAB-6188 | biostudies-arrayexpress
Project description:Dietary supplementation with ω-3 polyunsaturated fatty acids (ω-3 PUFAs), specifically the fatty acids docosahexaenoic acid (DHA; 22:6 ω-3) and eicosapentaenoic acid (EPA; 20:5 ω-3), is known to have beneficial health effects including improvements in glucose and lipid homeostasis and modulation of inflammation. To evaluate the efficacy of two different sources of ω-3 PUFAs, we performed gene expression profiling in the liver of mice fed diets supplemented with either fish oil or krill oil. We found that ω-3 PUFA supplements derived from a phospholipid krill fraction (krill oil) downregulated the activity of pathways involved in hepatic glucose production as well as lipid and cholesterol synthesis. The data also suggested that krill oil-supplementation increases the activity of the mitochondrial respiratory chain. Surprisingly, an equimolar dose of EPA and DHA derived from fish oil modulated fewer pathways than a krill oil-supplemented diet and did not modulate key metabolic pathways regulated by krill oil, including glucose metabolism, lipid metabolism and the mitochondrial respiratory chain. Moreover, fish oil upregulated the cholesterol synthesis pathway, which was the opposite effect of krill supplementation. Neither diet elicited changes in plasma levels of lipids, glucose or insulin, probably because the mice used in this study were young and were fed a low fat diet. Further studies of krill oil supplementation using animal models of metabolic disorders and/or diets with a higher level of fat may be required to observe these effects. Twenty-one microarrays: three diets (CO, FO, KO) x seven mice per diet x one microarray per mouse
2011-07-21 | E-GEOD-29572 | biostudies-arrayexpress