Sparus aurata
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ABSTRACT:
PROVIDER: PRJNA147777 | ENA |
REPOSITORIES: ENA
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Project description:This study describes the development and validation of the Aquagenomic Sparus aurata oligonucleotide-microarray (SAQ) based on the Agilent Technology system (eArray) to provide a platform for studies on the gene expression of gilthead seabream. The platform developed used all available public ESTs stored and annotated in the Aquagenomic Consortium seabream library (10K). In fish, lipopolysaccharide (LPS) gives a robust cytokine response that is stimulated by crude LPS preparations, some component of the LPS complex are responsible for this stimulation. Peptidoglycan (PGN) is a component of G-negative bacteria (found as a contaminant of crude LPS preparations) able to be recognized by macrophages inducing depth transcriptional modulations and a strong inflammatory response. For microarray analysis, head kidney macrophage cultures were used (N = 36 fish). Each cell culture was stimulated with equal concentrations of PGN and LPS from E. coli O111:B4 strain (10 ug/mL): non-stimulated cell cultures (control n = 9 fish), stimulated during 6 h with LPS (n = 9), and stimulated during 1 h (n = 9), and 6 h (n = 9) with PGN. A loop microarray design approach was used for the study. All experimental RNA samples were labelled with a single colour dye (Cy3) and each stimulated sample was compared to the control sample (pool without stimulation) labelled with the same dye (Cy3). Our microarray analyses identified differential transcriptional modulations in macrophages stimulated with both LPS and PGN at the level of differentially activated RNA transcripts related with the regulation of transcriptional program, prostaglandin synthesis or highlighting the expression of responsive gene-cassettes tightly related to LPS-PGN host recognition.
2011-04-23 | GSE28610 | GEO
Project description:Circadian rythms of gene expression in a continuosly growing fish larva
| PRJNA271259 | ENA
Project description:Sparus aurata Assembly of transcripts of genes related to fish mitochondrial bioenergetics
| PRJNA175023 | ENA
Project description:Fish in aquaculture farms frequently face unfavarouble husbandry conditions and other unpredictable situations, which are sometimes part of routine procedures. However, managing stress originated from these situations is crucial to ensure the sustainability of the production. When fish is exposed to prolonged stress, and overload of the physiological systems can occur and the fish may no longer be able to adapt and restore homeostasis, and this can impair the animal performance, such as growth and immunity, and consequently fish welfare. In this study the genes and gene families responsible for the molecular stress response to different challenges in gilthead seabream was assessed. Gilthead seabream adults were exposed to overcrowding, net-handling and hypoxia, in separate trials, each against a control group. Overcrowding and net-handling trials lasted for a month and half (chronic stress) and hypoxia for 48h (acute stress). The liver was the chosen organ for this transcriptomics analysis as this plays a crucial role in stress adaptation. The characterization of stress adaptation mechanisms provides valuable knowledge for the future selective breeding of more resilient commercial species that can thrive under changing conditions and adapt well to life in captivity, while ensuring high welfare standards.
2023-04-30 | E-MTAB-12842 | biostudies-arrayexpress
Project description:This study describes the development and validation of the Aquagenomic Sparus aurata oligonucleotide-microarray (SAQ) based on the Agilent Technology system (eArray) to provide a platform for studies on the gene expression of gilthead seabream. The platform developed used all available public ESTs stored and annotated in the Aquagenomic Consortium seabream library (10K). In fish, lipopolysaccharide (LPS) gives a robust cytokine response that is stimulated by crude LPS preparations, some component of the LPS complex are responsible for this stimulation. Peptidoglycan (PGN) is a component of G-negative bacteria (found as a contaminant of crude LPS preparations) able to be recognized by macrophages inducing depth transcriptional modulations and a strong inflammatory response. For microarray analysis, head kidney macrophage cultures were used (N = 36 fish). Each cell culture was stimulated with equal concentrations of PGN and LPS from E. coli O111:B4 strain (10 ug/mL): non-stimulated cell cultures (control n = 9 fish), stimulated during 6 h with LPS (n = 9), and stimulated during 1 h (n = 9), and 6 h (n = 9) with PGN. A loop microarray design approach was used for the study. All experimental RNA samples were labelled with a single colour dye (Cy3) and each stimulated sample was compared to the control sample (pool without stimulation) labelled with the same dye (Cy3). Our microarray analyses identified differential transcriptional modulations in macrophages stimulated with both LPS and PGN at the level of differentially activated RNA transcripts related with the regulation of transcriptional program, prostaglandin synthesis or highlighting the expression of responsive gene-cassettes tightly related to LPS-PGN host recognition. A total of 43,398 oligonucleotide probes were used to construct a high-density seabream microarray based on the Agilent 4 × 44 K design format. Microarray hybridization validation was made by analyzing the gene expression profiles in primary cultures of seabream macrophages (MC). 7,285 transcripts with annotated sequences were spotted in triplicate onto the slide (total probes 21,855), as well as 8,377 ESTs without annotation, 183 enriched sequences (gene bank) with 15 replicated probes (total probes 2,745), and finally 1,417 internal control probes of Agilent (N = 43,398).
2011-04-22 | E-GEOD-28610 | biostudies-arrayexpress
Project description:This study characterizes the liver stress proteome of fish submitted to overcrowding (OC), repeated net-handling (NET) and hypoxia (HYP). Fish trials were conducted in triplicate tanks and two fish per tank were randomly sampled for MS analysis. This work aims to disclose most significant changes in signaling and metabolic pathways involved in the stress response. This data-driven knowledge may ultimately contribute for the improvement of species-specific welfare management protocols, towards a sustainable aquaculture.
2022-12-13 | PXD036392 | Pride
Project description:This study aimed at the identification of minimally invasive stress biomarkers in the skin mucus of fish submitted to distinct intensities (mild and most intense) of different types of stress i.e., overcrowding (OC), repeated net-handling (NET) and hypoxia (HYP). Fish trials were conducted in triplicate tanks and four fish per tank were randomly sampled for MS analysis. This work also aimed to disclose most significant changes in signaling and metabolic pathways involved in the stress response in this immunity related biofluid. The presented data-driven knowledge study may ultimately contribute for the improvement of species-specific welfare management protocols, towards a sustainable aquaculture.
2023-04-20 | PXD038712 | Pride
Project description:A longer on-land rearing period of Gilthead seabream Sparus aurata before transfer to sea-cages would allow the farmer to benefit from exercise-enhanced growth and resilience as induced by increasing water flow in the tanks. In this study, the physiological effects of flow-conditioning were investigated by subjecting large groups of experimental fish to minimal flow or to flow regimes inducing swimming exercise at 1 or 2 Body Length (BL) s-1 for a period of 8 months (Feb.-Oct.) in 1,500 l RAS tanks. Fish size after eight months of flow conditioning was 92 ± 27 g body weight (BW) for fish under minimal flow; 106 ± 24 g BW (+15%) at 1 BL s-1, and 125 ± 27 g BW (+36%) at 2 BL s-1. Although flow enhanced growth linearly with swimming speed, the number of malformed fish was significantly higher for swimming at 2 BL s-1 indicating that the mechanical load imposed by exercise was too high for a developing juvenile. Fish representing the three treatment groups were then used for: (1) a stress challenge netting test and plasma cortisol measurement (baseline, peaking and recovery levels); (2) blood plasma measurements of glucose, triglycerides, lactate, cholesterol, growth hormone (GH) and insulin-like growth factor I (IGF-I), and heart and muscle gene expression of the GH and IGF-I receptors and the muscle transcriptome by deep RNA sequencing (RNAseq). Flow conditioning at 1 BL s-1 provided optimal conditions for growth and stress coping without energetic depletion and morphological deformation. The absence of important differences in plasma GH and IGF-I, and expression levels of the receptors in heart and white skeletal muscle, indicated that other factors may be involved in growth enhancement. RNAseq of the white skeletal muscle showed that transcription regulators play an important role. Also expression of immune genes is strongly up-regulated. Whereas muscle of fish conditioned at 1 BL s-1 shows up-regulated expression of structural genes such as troponins and myosins, muscle of fish conditioned at 2 BL s-1 shows up-regulated expression of skeletal genes instead which may reflect the mechanism behind morphological deformations.
2020-11-26 | GSE151668 | GEO