Identification of genes
Ontology highlight
ABSTRACT:
ORGANISM(S): Salmo salar
SUBMITTER: 
Odd-Helge Romarheim Margareth Øverland Fabian Grammes Thor Landsverk Felipe Reveco Liv-Trunn Mydland
PROVIDER: E-GEOD-44978 | ArrayExpress | 2013-05-30
SECONDARY ACCESSION(S): GSE44978PRJNA193318
REPOSITORIES: GEO, ArrayExpress
Similar Datasets
Project description:Identifying genes that show differential cardiac expression by comparing Atlantic salmon fed with a tetradecylthioacetic acid (TTA) supplemented diet to those fed a control diet for two sampling time points. Comparing cardiac gene expression from Atlantic salmon with 2 different diets (TTA and control) and sampled at 2 time points. 6 biological replicates (individuals), totally 24 arrays.
2011-07-31 | E-GEOD-25305 | ArrayExpress
Project description:Background: Commercial Atlantic salmon is fed diets with high fat levels to promote fast and cost-effective growth. To avoid negative impact of obesity, food additives that stimulate fat metabolism and immune function are of high interest. TTA, tetradecylthioacetic acid, is a synthetic fatty acid that stimulates mitochondrial β -oxidation most likely by activation of peroxysome proliferator-activated receptors (PPARs). PPARs are important transcription factors regulating multiple functions including fat metabolism and immune responses. Atlantic salmon experiments have shown that TTA supplemented diets significantly reduce mortality during natural outbreaks of viral diseases, suggesting a modulatory role of the immune system. Results: To gain new insights into TTA effects on the Atlantic salmon immune system, a factorial, high-throughput microarray experiment was conducted using a 44K oligo nucleotide salmon microarray SIQ2.0 and the Atlantic salmon macrophage-like cell line ASK. The experiment was used to determine the transcriptional effects of TTA, the effects of TTA in poly(I:C) elicited cells and the effects of pretreating the cells with TTA. The expression patterns revealed that a large proportion of genes regulated by TTA were related to lipid metabolism and increased mitochondrial β -oxidation. In addition we found that for a subset of genes TTA antagonized the transcriptional effects of poly(I:C). This, together with the results from qRT-PCR showing an increased transcription of anti-inflammatory IL10 by TTA, indicates anti-inflammatory effects. Conclusions: We demonstrate that TTA has significant effects on macrophage-like salmon cells that are challenged by the artificial dsRNA poly(I:C). The immune stimulatory effect of TTA in macrophages involves increased lipid metabolism and suppressed inflammatory status. Thus, suggesting that TTA directs the macrophage-like cells towards alternative, anti-inflammatory, activation. This has positive implications for TTA as a feed additive. Factorial designed experiment: factor pretreatment = 2 levels (Control, TTA); factor treatment = 4 levels (Control, TTA, polyIC, TTA+polyIC). Experiment was performed with 2 biological replicates (different passages). 1 array hybridization failed and was excluded from the dataset. Therefore total number of arrays =15
2011-07-31 | E-GEOD-25328 | ArrayExpress
Project description:Single cell proteins, such as Candida utilis, are known to have immunomodulating effects in the distal intestine (DI) of Atlantic salmon, whereas soybean meal (SBM) can cause soybean meal induce enteritis (SBMIE). Inflammatory or immunomodulatory stimuli at the local level in the intestine may alter the plasma protein profile of Atlantic salmon. These changes can be helpful tools in diagnosis for fish diseases and indicators for fish health. The present work aimed to identify local intestinal tissue responses and changes in plasma protein profiles of Atlantic salmon fed C. utilis yeast, SBM, or combined diets. Fish meal (FM) based diet was used as a control diet and the six experimental diets were: FM diet with 200 g/kg C. utilis (FM200CU) and five diets containing 200 g/kg SBM together with 0 (SBM group), 25, 50, 100 or 200 g/kg C. utilis (SBM25CU, SBM50CU, SBM100CU and SBM200CU groups, respectively). Intestine morphology of fish fed FM200CU where not affected whereas SBM group presented changes characteristic of SBMIE. Low inclusion of C. utilis in SBM diet showed a modulation of immune cell populations, but did not alleviate inflammatory symptom.
2020-05-18 | PXD012051 | Pride
Project description:Intestinal inflammation, caused by impaired intestinal homeostasis, is a serious condition in both animals and humans. The use of conventional extracted soybean meal (SBM) in diets for Atlantic salmon and several other fish species is known to induce enteropathy in the distal intestine, a condition often referred to as SBM induced enteropathy (SBMIE). In the present study, we investigated the potential of different microbial ingredients to alleviate SBMIE in Atlantic salmon, as a model of feed-induced inflammation. The dietary treatments consisted of a negative control based on fish meal (FM), a positive control based on 20% SBM, and four experimental diets combining 20% SBM with either one of the three yeasts Candida utilis (CU), Kluyveromyces marxianus (KM), Saccharomyces cerevisiae (SC) or the microalgae Chlorella vulgaris (CV). Histopathological examination of the distal intestine showed that all fish fed the SC or SBM diets developed characteristic signs of SBMIE, while those fed the FM, CV or CU diets showed a healthy intestine. Fish fed the KM diet showed intermediate signs of SBMIE. Corroborating results were obtained when measuring the relative length of PCNA positive cells in the crypts of the distal intestine. Gene set enrichment analysis revealed decreased expression of amino acid, fat and drug metabolism pathways as well as increased expression of the pathways for NOD-like receptor signalling and chemokine signalling in both the SC and SBM groups while CV and CU were similar to FM and KM was intermediate. Gene expression of antimicrobial peptides was reduced in the groups showing SBMIE. The characterisation of microbial communities using PCR-DGGE showed a relative increased abundance of Firmicutes bacteria in fish fed the SC or SBM diets. Overall, our results show that both CU and CV were highly effective to counteract SBMIE, while KM had less effect and SC had no functional effects.
2013-01-01 | S-EPMC3873917 | BioStudies
Project description:The inclusion of plant meals in diets of farmed Atlantic salmon can elicit inflammatory responses in the distal intestine (DI). For the present work, fish were fed a standard fish meal (FM) diet or a diet with partial replacement of FM with solvent-extracted camelina meal (CM) (8, 16, or 24 % CM inclusion) during a 16-week feeding trial. A significant decrease in growth performance was seen in fish fed all CM inclusion diets (Hixson et al. in Aquacult Nutr 22:615-630, 2016). A 4x44K oligonucleotide microarray experiment was carried out and significance analysis of microarrays (SAM) and rank products (RP) methods were used to identify differentially expressed genes between the DIs of fish fed the 24 % CM diet and those fed the FM diet. Twelve features representing six known transcripts and two unknowns were identified as CM responsive by both SAM and RP. The six known transcripts (including thioredoxin and ependymin), in addition to tgfb, mmp13, and GILT, were studied using qPCR with RNA templates from all four experimental diet groups. All six microarray-identified genes were confirmed to be CM responsive, as was tgfb and mmp13. Histopathological analyses identified signs of inflammation in the DI of salmon fed CM-containing diets, including lamina propria and sub-epithelial mucosa thickening, infiltration of eosinophilic granule cells, increased goblet cells and decreased enterocyte vacuolization. All of these were significantly altered in 24 % CM compared to all other diets, with the latter two also altered in 16 % CM compared with 8 % CM and control diet groups. Significant correlation was seen between histological parameters as well as between five of the qPCR analyzed genes and histological parameters. These molecular biomarkers of inflammation arising from long-term dietary CM exposure will be useful in the development of CM-containing diets that do not have deleterious effects on salmon growth or physiology.
2016-01-01 | S-EPMC4911373 | BioStudies
Project description:This study was performed to investigate assess the impacts of CO and/or CM containing diets on Atlantic salmon hepatic gene expression in order to identify candidate molecular biomarkers of responses to camelina-containing diets. Atlantic salmon were fed diets with complete or partial replacement of FO and/or FM with camelina oil (CO) and/or camelina meal (CM) in a 16-week trial (Control diet: FO; Test diet: 100% FO replacement with CO, with solvent-extracted FM and inclusion of 10% CM (100COSEFM10CM). A 44K microarray experiment identified liver transcripts that responded to 100COSEFM10CM (associated with reduced growth) compared to FO controls at week 16. Atlantic salmon were fed for 16 weeks with the FO or 100COSEFM10CM diet (three tanks per diet). Liver samples were taken from 7 fish from each tank at week 16. A universal reference design was used for the microarray experiment. For the test samples, RNA was used from individual livers of fish from the 2 treatment groups: FO and 100COSEFM10CM. For each treatment group we used 9 biological replicates (3 fish from each of 3 tanks). All test samples were labeled with Cy5. The common reference was a pool of 18 RNA samples from livers of fish from all individuals invovled in microarray experiment. The common reference was labeled with Cy3. Each individual test sample was hybridized together with the common reference sample on an array, so the experiment consisted of 18 arrays
2015-05-12 | E-GEOD-56784 | ArrayExpress
Project description:Fish were fed a standard fish meal (FM) diet or a diet with partial replacement of FM with solvent extracted camelina meal (CM) (8%, 16% or 24% CM inclusion) during a 16-week feeding trial. A significant decrease in growth performance was seen in fish fed the CM inclusion diets. A 44k oligonucleotide array experiment was used to identify any differentially expressed transcripts in the distal intestine of the fish fed the 24% CM diet compared to the control. The expression level of these genes was validated using quantitative polymerase chain reaction, which was also used to measure transcript expression in the fish fed the 8% CM and 16% CM diets. Histopathological analysis was used to quantify any physical signs in inflammation in the distal intestine of the Atlantic salmon fed the CM-containing diets. Overall design: Two condition experiment, 0% CM vs 24% CM, Biological replicates: 9 control replicates, 9 expermiental replicates
| GSE68732 | GEO
Project description:Atlantic salmon was fed with diets based on five plant protein sources combined with soyabean saponins. Diets with corn gluten, sunflower, rapeseed and horsebean produced minor effects while combination of saponins with pea protein concentrate caused enteritis and major transcriptome changes in the distal intestine. Microarray analyses were perfromed in distant intestine. Individual samples from fish that received saponing were hybridized to pools from salmon fed with the same feeds without saponins.
2011-12-21 | E-GEOD-34578 | ArrayExpress
Project description:There is an urgent need to find alternative feed resources that can further substitute fishmeal in Atlantic salmon diets without compromising health and food quality, in particular during the finishing feeding period when the feed demand is highest and flesh quality effects are most significant. This study investigates efficacy of substituting a isoprotein (35 %) and isolipid (35 %) low fishmeal diet (FM, 15 %) with Antarctic krill meal (KM, 12 %) during 3 months with growing finishing 2·3 kg salmon (quadruplicate sea cages/diet). Final body weight (3·9 (se 0·04) kg) was similar in the dietary groups, but the KM group had more voluminous body shape, leaner hearts and improved fillet integrity, firmness and colour. Ectopic epithelial cells and focal Ca deposits in intestine were only detected in the FM group. Transcriptome profiling by microarray of livers showed dietary effects on several immune genes, and a panel of structural genes were up-regulated in the KM group, including cadherin and connexin. Up-regulation of genes encoding myosin heavy chain proteins was the main finding in skeletal muscle. Morphology examination by scanning electron microscopy and secondary structure by Fourier transform IR spectroscopy revealed more ordered and stable collagen architecture of the KM group. NEFA composition of skeletal muscle indicated altered metabolism of n-3, n-6 and SFA of the KM group. The results demonstrated that improved health and meat quality in Atlantic salmon fed krill meal were associated with up-regulation of immune genes, proteins defining muscle properties and genes involved in cell contacts and adhesion, altered fatty acid metabolism and fat deposition, and improved gut health and collagen structure.
2020-01-01 | S-EPMC7369378 | BioStudies
Project description:The present study aimed to investigate whether alternative dietary protein sources modulate the microbial communities in the distal intestine (DI) of Atlantic salmon, and whether alterations in microbiota profiles are reflected in modifications in host intestinal function and health status. A 48-day feeding trial was conducted, in which groups of fish received one of five diets: a reference diet in which fishmeal (diet FM) was the only protein source and four experimental diets with commercially relevant compositions containing alternative ingredients as partial replacements of fishmeal, i.e., poultry meal (diet PM), a mix of soybean meal and wheat gluten (diet SBMWG), a mix of soy protein concentrate and poultry meal (diet SPCPM), and guar meal and wheat gluten (diet GMWG). Samples were taken of DI digesta and mucosa for microbial profiling using high-throughput sequencing and from DI whole tissue for immunohistochemistry and expression profiling of marker genes for gut health. Regardless of diet, there were significant differences between the microbial populations in the digesta and the mucosa in the salmon DI. Microbial richness was higher in the digesta than the mucosa. The digesta-associated bacterial communities were more affected by the diet than the mucosa-associated microbiota. Interestingly, both legume-based diets (SBMWG and GMWG) presented high relative abundance of lactic acid bacteria in addition to alteration in the expression of a salmon gene related to cell proliferation (pcna). It was, however, not possible to ascertain the cause-effect relationship between changes in bacterial communities and the host's intestinal responses to the diets.IMPORTANCE The intestine of cultivated Atlantic salmon shows symptoms of compromised function, which are most likely caused by imbalances related to the use of new feed ingredients. Intestinal microbiota profiling may become in the future a valuable endpoint measurement in order to assess fish intestinal health status and effects of diet. The present study aimed to gain information about whether alternative dietary protein sources modulate the microbial communities in the Atlantic salmon intestine and whether alterations in microbiota profiles are reflected in alterations in host intestinal function and health status. We demonstrate here that there are substantial differences between the intestinal digesta and mucosa in the presence and abundance of bacteria. The digesta-associated microbiota showed clear dependence on the diet composition, whereas mucosa-associated microbiota appeared to be less affected by diet composition. Most important, the study identified bacterial groups associated with diet-induced gut dysfunction that may be utilized as microbial markers of gut health status in fish.
2017-01-01 | S-EPMC5311410 | BioStudies