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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Differential response of hepatic transcriptome of post-smolt Atlantic salmon (Salmo salar) to dietary DHA alone or in combination with other LC-PUFA

ABSTRACT: This study compared the transcriptome of salmon fed diets with different levels and/or composition of LC_PUFA. Feeds were formulated with either DHA (Docosahexaenoic acid) alone (either 1% of the diet or 2% of the diet) or with a combination of DHA and EPA (Eicosapentaenoic acid) or DHA and ARA (Arachidonic acid). NOTE: Two treatments used in this trial (1% DHA and 2% DHA) were also used in an experiment previously submitted (E-MTAB-3180). Specifically, arrays 62_3, 69_1, 67_1, 62_2, 70_4, 65_2, 76_4, 66_3, 73_3, 70_2.

ORGANISM(S): Salmo salar

SUBMITTER: Christian De Santis

PROVIDER: E-MTAB-3840 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Regression analysis of response of hepatic transcriptome to dietary docosahexaenoic acid in post-smolt Atlantic salmon (Salmo salar)

Project description:The present study aimed to determine the impact of dietary docosahexaenoic acid (DHA) on the metabolism of Atlantic salmon (Salmo salar). The effects of diets containing increasing levels of DHA (1 g kg-1, 5 g kg-1, 10 g kg-1, 15 g kg-1 and 20 g kg-1) on the liver transcriptome of post-smolt salmon was determined using regression analysis to elucidate patterns of gene expression and responses of specific metabolic pathways. Total RNA was isolated from liver of individual fish and analyzed using a custom 44K Atlantic salmon oligo-microarray. The expression of up to 911 unique annotated genes was significantly affected by dietary DHA inclusion relative to a low DHA reference diet. Using regression analysis, 797 unique genes were found with a significant linear correlation between expression level and dietary DHA. Gene-Set Enrichment Analysis (GSEA) identified a range of pathways that were significantly affected by dietary DHA content. Pathways that showed a significant response to dietary DHA level included those for long-chain polyunsaturated fatty acid biosynthesis, fatty acid elongation, steroid biosynthesis, glycan biosynthesis, protein export and protein processing in the endoplasmic reticulum. These findings suggest that in addition to clear roles in influencing lipid metabolic pathways, DHA also has key functional roles in other biosynthetic pathways distinct from lipid metabolism.

2015-08-20 | E-MTAB-3180 | biostudies-arrayexpress

Evaluation of a high-EPA oil from transgenic Camelina sativa in feeds for Atlantic salmon (Salmo salar L.): Effects on tissue fatty acid composition, histology and gene expression

Project description:Currently, the only sustainable alternatives for dietary fish oil (FO) in aquafeeds are vegetable oils (VO) that are devoid of omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFA). Entirely new sources of n-3 LC-PUFA such as eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids through de novo production is a potential solution to fill the gap between supply and demand of these important nutrients. Camelina sativa,was metabolically engineered to produce a seed oil (ECO) with > 20 % EPA and its potential to substitute for FO in Atlantic salmon feeds was tested. Fish were fed one of three experimental diets containing FO, wild-type camelina oil (WCO) or ECO as the sole lipid sources for 7-weeks. Inclusion of ECO did not affect any of the performance parameters studied and enhanced apparent digestibility of individual n-6 and n-3 PUFA compared to dietary WCO. High levels of EPA were maintained in brain, liver and intestine (pyloric caeca), and levels of DPA and DHA were increased in liver and intestine of fish fed ECO compared to fish fed WCO likely due to increased LC-PUFA biosynthesis based on up-regulation of the genes. Fish fed WCO and ECO showed slight lipid accumulation within hepatocytes similar to that with WCO, although not significantly different to fish fed FO. The regulation of a small number of genes could be attributed to the specific effect of ECO (311 features) with metabolism being the most affected category. The EPA oil from transgenic Camelina (ECO) could be used as a substitute for FO, however it is a hybrid oil containing both FO (EPA) and VO (18:2n-6) fatty acid signatures that resulted in similarly mixed metabolic and physiological responses.

2016-03-01 | E-MTAB-3268 | biostudies-arrayexpress

Nutritional evaluation of an EPA-DHA oil from transgenic Camelina sativa in feeds for post-smolt Atlantic salmon (Salmo salar L.)

Project description:Vegetable oils (VO) are possible substitutes for fish oil in aquafeeds but are limited by their lack of omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFA). However, oilseed crops can be modified to produce n-3 LC-PUFA such as eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids, representing a potential option to fill the gap between supply and demand of these important nutrients. Camelina sativa was metabolically engineered to produce a seed oil with around 15 % total n-3 LC-PUFA to potentially substitute for fish oil in salmon feeds. Post-smolt Atlantic salmon (Salmo salar) were fed for 11-weeks with one of three experimental diets containing either fish oil (FO), wild-type Camelina oil (WCO) or transgenic Camelina oil (DCO) as added lipid source to evaluate fish performance, nutrient digestibility, tissue n-3 LC-PUFA, and metabolic impact determined by liver transcriptome analysis. The DCO diet did not affect any of the performance or health parameters studied and enhanced apparent digestibility of EPA and DHA compared to the WCO diet. The level of total n-3 LC-PUFA was higher in all the tissues of DCO-fed fish than in WCO-fed fish with levels in liver similar to those in fish fed FO. Endogenous LC-PUFA biosynthetic activity was observed in fish fed both the Camelina oil diets as indicated by the liver transcriptome and levels of intermediate metabolites such as docosapentaenoic acid, with data suggesting that the dietary combination of EPA and DHA inhibited desaturation and elongation activities. Expression of genes involved in phospholipid and triacylglycerol metabolism followed a similar pattern in fish fed DCO and WCO despite the difference in n-3 LC-PUFA contents.

2016-12-05 | E-MTAB-4621 | biostudies-arrayexpress

An EPA and DHA rich oil as a replacement to fish oil in Atlantic salmon aquafeeds: Effects on liver and pyloric caeca transcriptome

Project description:Facing a bottleneck in the growth of aquaculture, and a gap in the supply and demand of the highly beneficial omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFA), sustainable alternatives to the traditional feeds are much needed. Therefore, in this trial, an oil extracted from newly designed plant, Camelina sativa, was tested for its n-3 replacement capabilities, using three different groups of post-smolt Atlantic salmon (Salmo salar) which were fed for 12 weeks three experimental diets; a control diet containing a blend of fish oil (5 %) and rapeseed oil (15 %) (FO), a wild-type Camelina (20 %) (WCO) and the transgenic Camelina oil (20 %) (DCO), all of them having the same basal composition. By comparing them, an overall evaluation of fish performance, fatty acid profile, feeds digestibility and gene expression was done. In the context of the new transgenic diet, there were no negative effects on the growth, survival rate or health of the fish. The whole fish n-3 levels were highest in the DCO-fed fish with EPA+DHA levels almost double compared to FO-fed fish and more than double when compared to WCO-fed ones, clearly suggesting the efficiency of the Camelina oil in providing competitive levels of n-3 LC-PUFA compared to the commercial “gold standard”.

2019-11-30 | E-MTAB-6228 | biostudies-arrayexpress

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Project description:The use of high levels of marine fish oil in aquafeeds is a non-sustainable practice. However, more sustainable oils sources from terrestrial plants do not contain long-chain polyunsaturated fatty acids (LC-PUFA). Consequently, feeds based on conventional vegetable oils reduce n-3 LC-PUFA levels in farmed fish. Therefore, the aquaculture industry desperately requires new, sustainable oil sources that contain high levels of n-3 LC-PUFA in order to supply the increasing demand for fish and seafood while maintaining the high nutritional quality of the farmed product. One approach to the renewable supply of n-3 LC-PUFA is metabolic engineering oilseed crops with the capacity to synthesize these essential fatty acids in seeds. In the present study, the oilseed Camelina sativa has been transformed with algal genes encoding the n-3 biosynthetic pathway and expression restricted to the seeds via seed-specific promoters to produce an oil containing > 20% eicosapentaenoic acid (EPA). This oil was investigated as a replacement for marine fish oil in feeds for post-smolt Atlantic salmon. In addition, this study with EPA-rich oil will contribute to our understanding of the biochemical and molecular mechanisms involved in the control and regulation of docosahexaenoic acid (DHA) production from EPA, and will thus better inform our understanding of this key part of the LC-PUFA biosynthetic pathway.

2015-12-21 | E-MTAB-2855 | biostudies-arrayexpress

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Project description:The natural food for Atlantic salmon (Salmo salar) in freshwater has relatively lower levels of omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFA) than found in prey for post-smolt salmon in seawater. Land-locked salmon such as the GullspÃ¥ng population feed exclusively on freshwater type lipids during its entire life cycle, a successful adaptation derived from divergent evolution. Studying land-locked populations may provide insights into the molecular and genetic control mechanisms that determine and regulate n-3 LC-PUFA biosynthesis and retention in Atlantic salmon. A two factorial study was performed comparing land-locked and farmed salmon parr fed diets formulated with fish or rapeseed oil for 8 weeks. The land-locked parr had higher capacity to synthesise n-3 LC-PUFA as indicated by higher expression and activity of desaturase and elongase enzymes. The data suggested that the land-locked salmon had reduced sensitivity to dietary fatty acid composition and that dietary docosahexaenoic acid (DHA) did not appear to suppress expression of LC-PUFA biosynthetic genes or activity of the biosynthesis pathway, probably an evolutionary adaptation to a natural diet lower in DHA. Increased biosynthetic activity did not translate to enhanced n-3 LC-PUFA contents in the flesh and diet was the only factor affecting this parameter. Additionally, high lipogenic and glycolytic potentials were found in land-locked salmon, together with decreased lipolysis which in turn could indicate increased use of carbohydrates as an energy source and a sparing of lipid.

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2015-08-19 | E-MTAB-3835 | biostudies-arrayexpress

Influence of dietary inclusion of a wet processed faba bean protein concentrate on post-smolt Atlantic salmon (Salmo salar)

Project description:In the present study, a faba bean protein isolate (wBPC) with almost ~80 % crude protein produced by a wet process was investigated in feeds for Atlantic salmon in seawater. Four dietary treatments were tested including one treatment with high inclusion of fishmeal (400 g kg-1, named FM) and three treatments with low fishmeal (216 g kg-1) and increasing inclusions of faba bean protein concentrate (0, 70 and 140 g kg-1) substituting soy protein concentrate (236, 125 and 45 g kg-1), named SPC, BPC7 and BPC14 respectively.

2016-04-20 | E-MTAB-4661 | biostudies-arrayexpress

The response to substitution of soybean with faba bean protein concentrate on hepatic transcriptome of Atlantic salmon (Salmo salar)

Project description:The production of carnivorous fish such as Atlantic salmon (Salmo salar) is dependent on the availability of high quality protein required as a sustainable substitute for the formulation of the feeds. Plants have arguably the greatest potential, however a major limitation is associated with the presence of anti-nutritional factors. Investigating novel raw materials involves understanding the physiological consequences of the substitution. The primary aim of the present study was to assess the metabolic response of salmon to increasing inclusion of air-classified faba bean protein concentrate (BPC) in feeds as a replacement for soy (SPC). Specifically, we focused on the hepatic transcriptome response to dietary BPC inclusion over a range including commercially relevant levels (e.g. 11-22%) to levels giving impaired performance (45 %). The present investigation provided a profile of the salmon hepatic response to BPC indicating that fish tolerated moderate substitution of dietary SPC with BPC with no evident negative effects on the hepatic physiology of the fish. The analysis of extreme levels of substitution provided insights into physiological mechanisms that are significantly altered providing the basis for further investigation and improvement.

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