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The study of Atlantic cod (Gadus morhua) spleen global gene expression response to intraperitoneal injection with formalin-killed atypical Aeromonas salmonicida.

ABSTRACT: 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.

ORGANISM(S): Gadus morhua

PROVIDER: GSE22312 | GEO | 2010/11/05

SECONDARY ACCESSION(S): PRJNA127377

REPOSITORIES: GEO

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The study of Atlantic cod (Gadus morhua) spleen global gene expression response to intraperitoneal injection with formalin-killed atypical Aeromonas salmonicida.

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. Fish were assigned to 1 of 3 groups: Asal group, PBS group or 'undisturbed control' group (the latter were not handled during the experiment). These groups were kept in 3 separate tanks. For the test samples, RNA was used from individual spleen samples that were taken from 6 fish from each of 4 treatment groups: PBS group pre-injection (0H PBS), Asal group pre-injection (0H Asal), PBS group 24 hours post-injection (24HPI PBS) and Asal group 24 hours post-injection (24HPI Asal). All test samples were labeled with AlexaFluor 647. For the universal reference sample, RNA from 31 'undisturbed control' fish was pooled, with each individual contributing an equal amount, and labeled with AlexaFluor 555. Each individual test sample was hybridized together with the universal reference sample on an array. For one sample from the 0H PBS group the array failed. This study therefore includes 6 biological replicates for 0H Asal, 24HPI Asal and 24HPI PBS groups and 5 biological replicates for the 0H PBS group.

2010-11-05 | E-GEOD-22312 | biostudies-arrayexpress

A multi-omics approach to study peroxisome proliferator-activated receptor mediated regulation of lipid metabolism in Atlantic cod (Gadus morhua)

Project description:Lipid metabolism is essential in maintaining energy homeostasis in multicellular organisms. In vertebrates, a group of nuclear receptor transcription factors named peroxisome proliferator-activated receptors (PPARs, NR1C) regulate the expression of many genes involved in these processes. We have recently cloned the four Ppars in Atlantic cod (Gadus morhua), including Ppara1 and Ppara2, Pparb/d, and Pparg, and studied their tissue specific transcription and ligand activation characteristics. However, the downstream regulative role of Ppars in cod lipid metabolism is not well understood or described. In this study, activation of Atlantic cod Ppar by the fibrate drug WY-14,643 (pirinixic acid) and the performance enhancing drug GW501516 (Cardarine) were first studied using ligand-binding luciferase reporter assays in vitro. Based on the agonist activities found in vitro, juvenile Atlantic cod was injected twice over four days with WY-14,643 and GW501516 in vivo, and sampled seven days after the last injection. Using multiple omics methods, including RNA sequencing, quantitative proteomics, and lipidomics, liver and plasma samples from male cod were analyzed. The resulting multi-omics dataset provides novel insights into the systemic regulation of lipid metabolism in Atlantic cod.

2022-02-28 | MTBLS2131 | MetaboLights

RNA-Seq of Atlantic cod (Gadus morhua) liver treated with WY-14,643 and GW501516 in vivo

Project description:The aim of the exposure was to study the effects of activation of peroxisome proliferator-activated receptors (PPARs) in Atlantic cod (Gadus morhua), by injecting the fish with the compounds WY-14,643 and GW501516. Using luciferase reporter assay in vitro, we have shown that WY-14,643 activate Atlantic cod Ppara1 and Ppara2, while GW501516 activate Ppara1, Ppara2, and Pparb. The experimental set-up was as follows: Immature cod were injected at day 0 and day 4 with either high dose (40 mg/kg WY-14,643 and 4.0 mg/kg GW501516), low dose (4.0 mg/kg WY-14,643 and 0.4 mg/kg GW501516), or solvent control (10 % DMSO, 90 % teleost saline (2.41 mM KCl, 133.5 mM NaCl, 1.5 mM CaCl2, 0.79 mM MgSO4, 1 mM NaHCO3, 0.5 mM Na2HPO4)). At day 11, liver samples were collected from 9-12 male fish from each group (total of 50 samples). Total RNA was isolated from 50 mg of each sample using TRI reagent (Sigma), and 0.4 μg RNA were sequenced at the Genomics Core Facility at the University of Bergen on Illumina HiSeq 4000 (Illumina, Inc., San Diego, CA, USA).

2022-03-06 | E-MTAB-11490 | biostudies-arrayexpress

Atlantic Cod Early Development

Project description:Gene expression profiling of Atlantic cod (Gadus morhua) embryogenesis

2011-06-15 | E-TABM-1156 | biostudies-arrayexpress

Responses of Atlantic cod to high water temperature and bacterial infection

Project description:Aquaculture is one of the fastest growing food production sectors in the world and further expansion is expected throughout the 21st century. However, climate change is threatening the development of the sector and action is needed to prepare the industry for the coming challenges. Using downscaled temperature projections based on the Intergovernmental Panel on Climate Change (IPCC) climate projection (Shared Socioeconomic Pathway, SSP2-4.5), we analysed potential future temperatures at a selected Atlantic cod (Gadus morhua L.) farm site in Northern Norway. Results showed that the farming area may experience increased temperatures the next 10–15 years, including more days with temperatures above 17°C. Based on the predicted future conditions, we designed a study with Atlantic cod (Gadus morhua L.) to evaluate effects from high temperature alone and in combination with Fransicella noatunensis infection. Fish were kept at 12°C and 17°C for eight weeks and samples of skin and spleen collected at different timepoints were analysed with transcriptomics, histology, scanning electron microscopy and immunohistochemistry.

2023-08-01 | GSE233737 | GEO

Diverse transcriptome response to salinity change in cod subpopulations from the Baltic Sea

Project description:The Atlantic cod (Gadus morhua L.) is one of the most important species in the Baltic Sea with high ecological and economical value. To explore the differences in adaptation to salinity between Baltic cod subpopulation: western (Kiel Bight) and eastern (Gdańsk Bay) samples were analyzed through genome-wide oligonucleotide microarray.

2022-02-02 | GSE195878 | GEO

Microarray analysis of gene expression of Atlantic cod from different Baltic Sea regions

Project description:The Atlantic cod (Gadus morhua L.) is one of the most important species in the Baltic Sea with high ecological and economical value. To explore the differences in adaptation to salinity between Baltic cod from different regions, western (Kiel Bight) and eastern (Gdańsk Bay) samples were analyzed through oligonucleotide microarray.

2019-01-21 | GSE122988 | GEO

The impact of chronic temperature elevation on the spleen anti-viral transcriptomic response in Atlantic cod (Gadus morhua)

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. This was a common reference design. For the common reference each individual sample analyzed in the microarray experiment contributed with equal amounts of RNA to a pool. Sixty individuals were analyzed representing 6 biological replicates from 10 different experimental groups. Two separate control groups were used. Non-injected groups at the final temperatures (i.e. 10°C and 16°C) were used as prior to injection controls. At each time-point and temperatures there was also a sham-injected time matched control (injected with phosphate buffered saline [PBS]). The time points were 6 and 24 hours post-injection. Immunostimulated fish were injected with a weight-based dose of poly (I:C)(2 µg per g of wet body mass).

2011-09-30 | E-GEOD-27299 | biostudies-arrayexpress

Quantitative proteomics of liver from PCB 153 exposed Atlantic cod

Project description:In order to investigate the underlying mechanisms of PCB 153 mediated toxicity to Atlantic cod (Gadus morhua), we analyzed the liver proteome of fish exposed to various doses of PCB 153 (0, 0.5, 2 and 8mg/kg body weight) for two weeks and examined the effects on expression of liver proteins using quantitative proteomics. Label-free mass spectrometry enabled quantification of 1272 proteins, and 78 were differentially regulated between PCB 153 treated samples and controls. Two proteins downregulated due to PCB 153 treatment, Glutathione S-transferase theta 1 (GSTT1) and sulfotransferase family protein 1 (ST2B1), were verified using selected reaction monitoring (SRM). Supported by bioinformatics analyses, we concluded that PCB 153 perturbs lipid metabolism in the Atlantic cod liver and that increased levels of lipogenic enzymes indicate increased synthesis of fatty acids and triglycerides.

2017-01-17 | PXD004362 | Pride

Quantitative proteomics of liver from methylmercury-exposed Atlantic cod

Project description:In order to investigate the underlying mechanisms of methylmecury (MeHg)-mediated toxicity to Atlantic cod (Gadus morhua), we analyzed the liver proteome of fish exposed in vivo to MeHg (0, 0.5, 2 mg/kg body weight) for 2 weeks. Label-free quantitative mass spectrometry enabled quantification of 1143 proteins, and 125 were differentially regulated between MeHg-treated samples and controls. Six proteins among the top differentially regulated (T23O, GLNA EPS8L2, APOA4, RAP1B, CZTZ) were analyzed using selected reaction monitoring (SRM). Supported by bioinformatics analyses, we conclude that MeHg disrupts mainly redox homeostasis and energy generating metabolic pathways in cod liver, the latter potentially modulated through MeHg-induced oxidative stress.

2016-08-09 | PXD004311 | Pride

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