Transcriptome profiling reveals that feeding live zooplankton to larval Atlantic cod (Gadus morhua) influences suites of genes involved in oxidation-reduction, mitosis, and selenium homeostasis.
Ontology highlight
ABSTRACT:
ORGANISM(S): Gadus morhua
PROVIDER: GSE68792 | GEO | 2015/10/06
SECONDARY ACCESSION(S): PRJNA283846
REPOSITORIES: GEO
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Project description:Lipid metabolism is essential in maintaining energy homeostasis in multicellular organisms. In vertebrates, the peroxisome proliferator-activated receptors (PPARs, NR1C) regulate the expression of many genes involved in these processes. Four Ppar subtypes from Atlantic cod (Gadus morhua) were recently cloned and characterized. However, the downstream regulatory role of Ppars in cod lipid metabolism is presently not well understood or described. Here we study the involvement of Atlantic cod Ppar subtypes in systemic regulation of lipid metabolism using the model agonists WY14,643, GW501516, and tetradecylthioacetic acid, employing a multiple omics approach after an in vivo exposure situation.
2022-09-20 | PXD031739 | Pride
Project description:Larval nutrition and growth are key issues for wild and cultured cod. While it was shown previously that larval cod fed wild zooplankton grow faster than those fed only rotifers, the mechanisms involved in this enhanced growth are not completely understood. We used microarrays to identify larval cod transcripts that respond to feeding with small amounts of wild zooplankton (5-10 % of live prey items). The larval transcriptome was compared between 3 treatment groups [fed rotifers (RA), rotifers with protein hydrolysate (RA-PH), or rotifers with zooplankton (RA-Zoo)] at 9-10 mm length [26-30 days post-hatch (dph)] to identify a robust suite of zooplankton-responsive genes (i.e. differentially expressed between RA-Zoo and both other groups).The microarray experiment identified 147 significantly up-regulated and 156 significantly down-regulated features in RA-Zoo compared with both RA and RA-PH. Gene ontology terms overrepresented in the RA-Zoo responsive gene set included "response to selenium ion" and several related to cell division and oxidation-reduction. Ten selenoprotein-encoding genes, and 2 genes involved in thyroid hormone generation, were up-regulated in RA-Zoo compared with both other groups. Hierarchical clustering of RA-Zoo responsive genes involved in oxidation-reduction and selenium homeostasis demonstrated that only the zooplankton treatment had a considerable and consistent impact on the expression of these genes. Fourteen microarray-identified genes were selected for QPCR involving 9-13 mm larvae, and 13 of these were validated as differentially expressed between RA-Zoo and both other groups at ~9 mm. In contrast, in age-matched (34-35 dph; ~11 mm RA and RA-PH, ~13 mm RA-Zoo) and size-matched (~13 mm) older larvae, only 2 and 3 genes, respectively, showed the same direction of RA-Zoo-responsive change as in ~9 mm larvae.The modulation of genes involved in selenium binding, redox homeostasis, and thyroid hormone generation in ~9 mm RA-Zoo larvae in this study may be in response to the relatively high levels of selenium, iodine, and LC-PUFA (potentially causing oxidative stress) in zooplankton. Nonetheless, only a subset of zooplankton-responsive genes in ~9 mm larvae remained so in older larvae, suggesting that the observed transcriptome changes are largely involved in initiating the period of growth enhancement.
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Project description:Early life stage mortality is an important issue for Atlantic cod aquaculture. The impact of the cod maternal (egg) transcriptome on egg quality and mortality during embryonic development is poorly understood. In the present work we studied embryonic mortality and maternal transcript expression using 15 females within an Atlantic cod broodstock development program. Cumulative mortality at 7 days post-fertilization (segmentation stage) and percent hatch were used to assess embryonic survival as an indicator of egg quality. A 20,000 probe (20K) microarray experiment compared the 7 hour post-fertilization (7 hpf, ~ 2-cell stage) egg transcriptome of the two lowest quality females (both with less than 1 percent hatch) to that of the highest quality female (greater than 50 percent hatch).
2014-12-31 | GSE54233 | GEO
Project description:Methylmercury (MeHg) is a highly toxic environmental pollutant. To understand the mechanisms of toxicity of the compound and possibly to discover new biomarkers for environmental monitoring, we have conducted toxicogenomics studies. We designed 126k-cod-oligonucleotide arrays and performed genome-wide gene expression assays in liver samples from juvenile cod treated with MeHg (0.5 and 2 mg/kg body weight). Microarray analysis showed MeHg differentially regulated hundreds of genes. Gene Ontology and pathway analyses of differentially regulated genes revealed that MeHg modulated mainly genes involved in immune response, oxidative stress response, tissue remodelling, and energy pathways such as lipid, carbohydrate and amino acid metabolism. The results provide insights into the mechanisms of toxicity of MeHg and provide candidate biomarkers of exposure to MeHg for further evaluation.
2013-01-22 | GSE38746 | GEO
Project description:Male and female Atlantic cod (Gadus morhua) liver transcriptome analysis following in vivo waterborne PAH, AP and phenol exposure
2011-03-24 | E-MTAB-121 | biostudies-arrayexpress
Project description:This study was performed to validate the newly developed CGP Atlantic cod 20K oligonucleotide microarray. Atlantic cod (Gadus morhua) received an intraperitoneal injection of either formalin-killed, atypical Aeromonas salmonicida (Asal) or PBS and transcriptional profiles of spleen tissues from Asal-injected fish were compared to those from pre-injection control fish and PBS-injected control fish. Gene expression profiles resulting from this study were compared to those from suppression subtractive hybridization library studies, that were previously performed on the same samples, and to literature. Gene expression patterns of single genes were confirmed by QPCR analysis. This study has shown that the newly developed CGP Atlantic cod 20K oligo microarray platform is a valuable tool for cod genomic research.
2010-11-05 | GSE22312 | GEO
Project description:This experiment was designed to investigate the impacts of non-lethal increases in temperature on the anti-viral transcriptomic response of Atlantic cod. Selected genes identified as differentially expressed between samples injected with pIC but held at different temperatures were validated using QPCR.
2011-10-01 | GSE27299 | GEO
Project description:BackgroundHemoglobin (Hb) polymorphism, assessed by protein gel electrophoresis, has been used almost exclusively to characterize the genetic structure of Atlantic cod (Gadus morhua) populations and to establish correlations with phenotypic traits such as Hb oxygen binding capacity, temperature tolerance and growth characteristics. The genetic system used to explain the results of gel electrophoresis entails the presence of one polymorphic locus with two major alleles (HbI-1; HbI-2). However, vertebrates have more than one gene encoding Hbs and recent studies have reported that more than one Hb gene is present in Atlantic cod. These observations prompted us to re-evaluate the number of Hb genes expressed in Atlantic cod, and to perform an in depth search for polymorphisms that might produce relevant phenotypes for breeding programs.ResultsAnalysis of Expressed Sequence Tags (ESTs) led to the identification of nine distinct Hb transcripts; four corresponding to the alpha Hb gene family and five to the beta Hb gene family. To gain insights about the Hb genes encoding these transcripts, genomic sequence data was generated from heterozygous (HbI-1/2) parents and fifteen progeny; five of each HbI type, i.e., HbI-1/1, HbI-1/2 and HbI-2/2. beta Hb genes displayed more polymorphism than alpha Hb genes. Two major allele types (beta1A and beta1B) that differ by two linked non-synonymous substitutions (Met55Val and Lys62Ala) were found in the beta1 Hb gene, and the distribution of these beta1A and beta1B alleles among individuals was congruent with that of the HbI-1 and HbI-2 alleles determined by protein gel electrophoresis. RT-PCR and Q-PCR analysis of the nine Hb genes indicates that all genes are expressed in adult fish, but their level of expression varies greatly; higher expression of almost all Hb genes was found in individuals displaying the HbI-2/2 electrophoretic type.ConclusionThis study indicates that more Hb genes are present and expressed in adult Atlantic cod than previously documented. Our finding that nine Hb genes are expressed simultaneously in adult fish suggests that Atlantic cod, similarly to fish such as rainbow trout, carp, and goldfish, might be able to respond to environmental challenges such as chronic hypoxia or long-term changes in temperature by altering the level of expression of these genes. In this context, the role of the non-conservative substitution Lys62Ala found in the beta1 Hb gene, which appears to explain the occurrence of the HbI-1 and HbI-2 alleles described by gel electrophoresis, and which was found to be present in other fish such as eel, emerald rockcod, rainbow trout and moray, requires further investigation.
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Project description:In the North Sea and adjacent North Atlantic coastal areas fish experience relatively high levels of persistent organic pollutants. The aim of this study is to compare the mode of actions of environmentally relevant concentrations of halogenated compounds and their mixtures in Atlantic cod. Juvenile male cod were fed mixtures of chlorinated (PCBs, DDT analogs, chlordane, lindane and toxaphene), brominated (PBDEs) and fluorinated (Perfluorooctanesulfonate/PFOS) compounds for one month. One group received a mixture of all three compounds. Transcriptome analysis of liver samples was performed to identify the main affected pathways. Accumulated levels of chemicals in cod liver reflected concentrations found in wild fish. Pathway analysis revealed that the treatment effects by each of the three groups of chemicals (chlorinated, brominated and fluorinated) converged on activation of the unfolded protein response (UPR). The results of our transcriptomics analysis suggest that the UPR pathway is a sensitive common target of halogenated organic environmental pollutants
2023-01-04 | E-MTAB-12338 | biostudies-arrayexpress
Project description:Microarray analyses were performed to assess temporal profiles of maternal and zygotic transcripts and their developmental roles. Results revealed the presence of multiple transcripts involved in patterning and development of tissues and organs long before activation of the zygotic genome. The switch from maternal to zygotic developmental programs is associated with large-scale modification of chromosomes. Analyses included unfertilized and newly fertilized oocytes, mid blastulas and embryos at different stages of segmentation. Pooled organs of adult cod were used as common reference.
2014-06-12 | E-GEOD-58392 | biostudies-arrayexpress