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Potential biomarker genes for crowding stress in rainbow trout Oncorhynchus mykiss

ABSTRACT: Stocking density is considered as a key factor determining the productivity of fish aquaculture systems. The transcriptomic response to crowding stress is, however, still poorly investigated. We aimed at the identification of potential biomarker genes via microarray analyses to get insight into molecular pathways modulated through density-induced stress in farmed rainbow trout Oncorhynchus mykiss. Transcriptome profiling in liver, kidney, and gills was complemented with behaviarol observation and analysis of classical plasma parameters. Individuals of two trout strains were exposed for eight days to definite stocking densities, 1 kg/m³ (low density); 10 kg/m³ (moderate); 18 kg/m³ (elevated); and 35 kg/m³ (high). Whereas stocking density had no significant effect on cortisol levels, plasma glucose levels were elevated in trout kept at high density. Pathway enrichment analyses confirmed the upregulation of HIF1a signaling in liver contributing to glucose homeostasis during stress conditions, while mTOR and PI3K/AKT signaling pathways were downregulated. Further perturbed hepatic pathways were involved in protein ubiquitination and the biosynthesis of cholesterol, retinol and glutathione.

ORGANISM(S): Salmo salar Oncorhynchus mykiss

PROVIDER: GSE74332 | GEO | 2015/10/24

SECONDARY ACCESSION(S): PRJNA299696

REPOSITORIES: GEO

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Potential biomarker genes for crowding stress in rainbow trout Oncorhynchus mykiss

Project description:Stocking density is considered as a key factor determining the productivity of fish aquaculture systems. The transcriptomic response to crowding stress is, however, still poorly investigated. We aimed at the identification of potential biomarker genes via microarray analyses to get insight into molecular pathways modulated through density-induced stress in farmed rainbow trout Oncorhynchus mykiss. Transcriptome profiling in liver, kidney, and gills was complemented with behaviarol observation and analysis of classical plasma parameters. Individuals of two trout strains were exposed for eight days to definite stocking densities, 1Â kg/mÂ³ (low density); 10Â kg/mÂ³ (moderate); 18Â kg/mÂ³ (elevated); and 35Â kg/mÂ³ (high). Whereas stocking density had no significant effect on cortisol levels, plasma glucose levels were elevated in trout kept at high density. Pathway enrichment analyses confirmed the upregulation of HIF1a signaling in liver contributing to glucose homeostasis during stress conditions, while mTOR and PI3K/AKT signaling pathways were downregulated. Further perturbed hepatic pathways were involved in protein ubiquitination and the biosynthesis of cholesterol, retinol and glutathione. Three stocking density conditions were investigated: an uncrowded âmoderateâ density (MD: 10Â kg trout/mÂ³) , an elevated density (ED: 18Â kg/mÂ³ ), and high density (HD: 35Â kg/mÂ³). The experiment was performed twice with two strains of Steelhead rainbow trout (Troutlodge and Born trout), randomly assigned to identical glass tanks with MD (30 and 34 individuals), ED (60 and 64 individuals), and HD (120 and 140 individuals). Trout were sampled 8 d after experimental onset.

2015-10-24 | E-GEOD-74332 | biostudies-arrayexpress

Potential biomarker genes for crowding stress in maraena whitefish Coregonus lavaretus

Project description:Stress represents a major factor negatively affecting fish welfare in aquaculture. The objective of the present study was to identify and evaluate informative indicators for the welfare and particular health status of maraena whitefish (Coregonus maraena) farmed at four different stocking densities. Transcriptome profiling revealed that numerous stress-related signaling pathways were activated in liver and kidney under ED and HD conditions, such as ERK/MAPK, mTOR, glucocorticoid receptor, SAPK/JNK and JAK/Stat signalling, as well as p38 and p53 signalling. Moreover, several stress-relevant effector pathways were found to be overexpressed including glycolysis and glycogen degradation. Strikingly, a high number of upregulated genes in kidney and in liver of fish kept at HD (compared to MD fish) were related to immunological processes, such as Acute-phase response signalling, B cell receptor signaling, CD28 signaling in T helper cells, and Interleukin-6 signaling. Four stocking density conditions were investigated: an uncrowded âmoderateâ density (MD: 33Â kg trout/mÂ³) , an elevated density (ED: 60Â kg/mÂ³ ), a low density (LD: 10Â kg/mÂ³ ), and high density (HD: 100Â kg/mÂ³). The experiment was performed twice, randomly assigned to identical glass tanks with MD (100 individuals), ED (180 individuals), LD (30 individuals), and HD (300 individuals). Trout were sampled 8 d after experimental onset.

2016-01-06 | E-GEOD-76543 | biostudies-arrayexpress

Microarray-predicted marker genes and molecular pathways indicating combined crowding and thermal stress in rainbow trout (Oncorhynchus mykiss)

Project description:Stress represents a major factor negatively affecting fish welfare in aquaculture. The objective of the present study was to identify and evaluate informative indicators for the welfare of rainbow trout Oncorhynchus mykiss exposed to (A) a critical water temperature of 27 °C and (B) acute crowding of 100 kg/m3 combined with water temperature of 27 °C. In order to make an approximate assessment of the overall condition, we determined health index, spleen-somatic index and haematocrit and recorded the blood concentrations of haemoglobin, cortisol and glucose of rainbow trout under challenging versus control conditions. Moreover, we analysed the transcriptomic profiles of the spleen of the two stress-treatment and the reference groups to identify gene sets, which are specific for temperature stress alone or combined temperature and crowding stress.

2019-04-04 | GSE129271 | GEO

RNA sequencing identifies sub-clinical hepatic response to stocking density

Project description:We report the hepatic response of broiler chickens to an increase in stocking density. Here we compare gene expression profiles of liver cells via RNA-seq of broiler chicken raised under a high stocking density to broiler chickens raised under a lower stocking density with the objective of this study being to identify biomarkers of stress before the clinical and economic impacts are observed. We found that increasing stocking density seems to have a unique impact on hepatic gene expression prior to eliciting common clinical signs associated with stress. The cellular functions that are most affected appear to be those involved in steroidogenesis and cell movement/migration as identified by RNA-seq analysis of the liver transcriptome. These results could provide a baseline of information that future research to identify genes or molecules that could aid in the detection of negative effects of stressors such as stocking density prior to negative clinical and economic signs presenting themselves.

2021-04-12 | GSE171864 | GEO

Potential biomarker genes for crowding stress in maraena whitefish Coregonus maraena

2016-01-06 | GSE76543 | GEO

Dietary germinated paddy rice and stocking density affect egg performance, serum biochemical properties, and proteomic and transcriptomic response of laying hens exposed to chronic heat stress

Project description:Germinated paddy rice (GPR) could be a good alternative feed source for poultry with stocking density and heat stress problems. 72 Hy-line Brown laying hens raised under low (LSD, 0.12 m2/bird) and high stocking densities (HSD, 0.06 m2/bird) were investigated. Three dietary GPR levels (0, 74 and 148 g/kg) were used. It was found that average daily feed intake, hen-day egg production and egg mass significantly decreased in the HSD group. The levels of serum glucose (GLU), phosphorous (P), corticosterone (CORT), total Ig, lysozyme (LZY) and superoxide dismutase activities (SOD) in the HSD group were higher than those in the LSD group. Dietary GPR significantly affected GLU, P, alternative complement haemolytic 50 (ACH50), total Ig, and LZY. Moreover, CORT level was significantly decreased in 74 and 148 g/kg dietary GPR groups, whereas SOD significantly increased only in the 148 g/kg dietary GPR group. Serum samples were analyzed using liquid chromatography-tandem mass spectrometry, and 8607 proteins were identified. Proteome analysis revealed 19 proteins which were enriched in different stocking densities and dietary GPR levels. Quantitative real-time Reverse Transcription-PCR technique was successfully used to verify the differentiated abundant protein profile changes. The proteins identified in this study could serve as appropriate biomarkers.

2021-11-04 | PXD029557 | JPOST Repository

Project description:Micro Stocking Density

| PRJNA527780 | ENA

Golden Pompano (Trachinotus blochii) improves tolerance to acute hypoxic stress by changing the mode of glucose and lipid metabolism

Project description:Due to the increase in stocking density, eutrophication of water quality, and high-temperature conditions aggravate the possibility of hypoxia, and inevitably lead to hypoxic stress, affecting the development of its aquaculture industry. We simulated severe hypoxia stress conditions and constructed two different hypoxia tolerance groups. We used next-generation sequencing to analyze the mRNA expression profiles of the brain and liver under hypoxia to clarify the main pathways and metabolic pathways involved in hypoxia, to systematically reveal the reasons for the differences in hypoxia tolerance among different groups.

2021-12-31 | GSE163685 | GEO

Duck liver TMT - Proteome and microbiota analysis reveals alterations of liver-gut axis under different stocking density of Peking ducks

Project description:The aim of this project is to investigate the effect of stocking density on duck liver proteome.

2018-11-04 | PXD010952 | Pride

Identification of differentially expressed Oncorhynchus mykiss microRNA in plasma, mucus, and water following acute stress using high throughput sequencing.

Project description:Circulating plasma microRNAs (miRNAs) are well established as biomarkers of several diseases in humans and have recently been used as indicators of environmental exposures in fish. However, the role of plasma miRNAs in regulating acute stress responses in fish is largely unknown. Tissue and plasma miRNAs have recently been associated with excreted miRNAs in humans however external miRNAs have never been measured in fish. The objective of this study was to characterize the plasma miRNA profile in response to acute stress in rainbow trout (Oncorhynchus mykiss), as well as miRNA profiles in novel external samples, (fish epidermal mucus and the surrounding water). RNA was extracted and sequenced from plasma, mucus, and water collected from rainbow trout and their surrounding environment prior to and one-hour following a three-minute air exposure, a known inducer of an acute stress response in fish. Following small RNA-Seq and pathway analysis, we identified differentially expressed plasma miRNAs that targeted biosynthetic, degradation, and metabolic pathways. We successfully isolated miRNA from trout mucus and the surrounding water and detected differences in miRNA expression one-hour post air stress. The altered miRNA profiles in mucus and water were unique to the altered plasma miRNA profile, indicating that the plasma miRNA response was not associated with or immediately reflected in external samples. This research expands our understanding of the role of plasma miRNA in the acute stress response of fish and is the first study to report on the successful isolation and profiling of miRNA from fish mucus and water samples. Measurements of miRNA from plasma, mucus, and water can be further studied and have the potential to be applied in environmental monitoring as non-lethal indicators of acute stress in fish.

2020-12-28 | GSE151138 | GEO

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