Transcriptome analysis of gilthead sea bream Sparus aurata liver upon exposure to low temperature
Ontology highlight
ABSTRACT:
ORGANISM(S): Sparus aurata
PROVIDER: GSE51442 | GEO | 2014/08/27
SECONDARY ACCESSION(S): PRJNA223176
REPOSITORIES: GEO
Similar Datasets
Project description:A gilthead sea bream (Sparus aurata) microarray platform was developed to identify brain gene expression profiles in response to environmental concentrations of human pharmaceuticals.
2014-05-22 | GSE38195 | GEO
Project description:Analysis of the gene expression profiles of Sparus aurata head kidney after infection with Photobaterium damselae piscicida. The expression levels of 21,497 sea bream transcripts, on both directions, 24 and 48 hours post-infection, were compared with the levels detected in uninfected individuals.
2013-02-22 | GSE26651 | GEO
Project description:We report the proteomic characterization of livers from Sparus aurata exposed to cold temperatures. In this study, mimicking the winter challenge conditions, a 8 week feeding trial was carried out on gilthead sea bream juveniles reared in RAS systems at a temperature ramp made of two phases of four weeks each: a cooling phase from 18°C 8 (t0) to 11°C (t1) and a cold maintenance phase at 11°C (t2). Sparus aurata livers, after exposure to the three temperature phases (t0, t1 and t2), were collected and analyzed using a shotgun proteomics approach based on filter-aided sample preparation followed by tandem mass spectrometry, peptide identification carried out using Sequest-HT as search engine within the Proteome Discoverer informatic platform, and label-free differential analysis. Along the whole trial, sea breams underwent several changes occurring upon thermal stress in liver protein abundance. These occurred mostly during the cooling phase, when catabolic processes were mainly observed. These included protein and lipid degradation and a decrease in protein synthesis and amino acid metabolism. A decrease in protein mediators of oxidative stress protection was also seen. Liver protein profiles showed less marked changes during cold maintenance, although pathways such as the methionine cycle and sugar metabolism were significantly affected. This study provided useful hints on the dynamics and extent of the metabolic shift occurring in sea bream liver with decreasing water temperature, helping the development of feeds aimed at compensating the thermal stress encountered by fish in offshore farming conditions.
2019-05-28 | PXD011059 | Pride
Project description:Sparicotylosis is an endemic parasitic disease across the Mediterranean Sea caused by the polyopisthocotylean monogenean Sparycotyle chrysophrii, which affects the gills of gilthead sea bream (Sparus aurata). Current disease-management, mitigation and treatment strategies are scarce against sparicotylosis. In order to successfully develop more efficient therapeutic strategies against this disease, understanding which molecular mechanisms and metabolic pathways are altered in the host is critical. This study aims to elucidate how S. chrysophrii infection modulates giltheadd seea bream physiological status and to identify the main altered biological processes through plasma proteomics of the host.
2022-10-14 | PXD034541 | Pride
Project description:In Sparus aurata, seasonal temperature variations outside the normal thermal range, may trigger physiological responses leading to pathologies and death. In the present study two groups of wild sea bream were exposed for 21 days to two temperature regimes: 16 ± 0.3 °C (control group) and 6.8 ± 0.3 °C (cold-exposed group). Samples were collected during the acute phase (0, 6 and 24 hours after temperature drop) and upon chronic exposure (21 days). A comparative analysis of gene expression was conducted between S. aurata exposed to 6.8°C. Two groups of wild sea breams (120±16 g body weight; 21±1 cm total length) caught in Valle Bonello were kept in duplicate groups in four 5 m3 circular recycling tanks and acclimated over one month at 16 °C (Di Marco et al. 2010). Fish were then exposed for 21 days to two different temperature treatments: 16 ± 0.3 °C (control groups) and 6.8 ± 0.3 °C (cold groups). Both groups were fasted during the trial. Warm and cold water temperature conditions were maintained by supplying tanks with two separate re-circulating systems equipped with mechanical and biological filters. Cold water conditions were achieved by inducing two consecutive temperature drops: water was firstly gradually cooled from 16 °C to 12 °C at a rate of 1°C day -1 and then reduced from 12 °C to 6.8 °C within 24 h. This temperature was then kept for 21 days. Ten fish per treatment were sampled at different intervals during acute: 0 (T1), 6 (T2) and 24 hours (T3), and chronic exposure (21 days; T4) to low temperature. Fish were firstly anaesthetized in a solution of tricaine methanesulphonate (300 mg/l; MS 222, Finquel) in a 30-litre bucket and then euthanized by severing their spinal cord. Liver samples (about 30 mg) were collected from each specimen, incubated in RNA later at 4 °C for 24 h and then stored at -20 °C. Total RNA was extracted from tissue samples using the RNAeasy Mini Kit (Qiagen, Hilden, Germany). RNA concentration was determined using a UV-Vis spectrophotometer NanoDrop® ND-1000 (NanoDrop Technologies, Wilmington, USA). RNA integrity and quality was evaluated by means of Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) and Expert software according to Ferraresso et al. (2008). RNA integrity number (RIN) index was calculated for each sample that provides a numerical assessment of RNA integrity. This value facilitates the standardization of the quality interpretation; only RNAs with RIN >8 were used for further microarray experiments. Once single RNA samples were extracted and measured, 3 pools (Pool_A consisting of four individuals, Pool_B and _C of three) per each sampling-time point were prepared. This was aimed at getting a sufficient statistical power which is reached by a minimum of three biological replicates per analysed point and at reducing microarray analysis cost. To perform DNA microarray analyses has been used the microarray platform GPL6467 (Ferraresso et al. 2008). Sample labelling and hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol. For each of 24 liver pools 500 ng of total RNA were linearly amplified and labelled with Cy3-dCTP, using the Low RNA Input Linear Amplification Kit PLUS one-color (Agilent Technologies). A total of 24 Agilent 4 x 44K sea bream microarrays (12 samples from both control and cold groups) were then hybridized. An Agilent G2565BA DNA microarray scanner was used to scan arrays at 5 µm resolution, Feature Extraction Software 9.5.1 was then used to process and analyse array images. The software returns a series of spot quality measures in order to evaluate the goodness and the reliability of spot intensity estimates. Filtering and cyclic lowess normalization were performed using R statistical software (http://www.r-project.org/).
2014-08-27 | E-GEOD-51442 | biostudies-arrayexpress
Project description:A gilthead sea bream (Sparus aurata) microarray platform was developed to identify brain gene expression profiles in response to environmental concentrations of human pharmaceuticals. Comparative analysis of gene expression profiles was conducted among brain of gilthead seabream exposed to Acetaminophen (APAP; analgesic), Carbamazepine (CBZ; anti-epileptic) and Atenolol (AT; β-blocker). All groups of samples were also compared with brain of control individuals.
2014-05-22 | E-GEOD-38195 | biostudies-arrayexpress
Project description:Analysis of the gene expression profiles of Sparus aurata head kidney after infection with Photobaterium damselae piscicida. The expression levels of 21,497 sea bream transcripts, on both directions, 24 and 48 hours post-infection, were compared with the levels detected in uninfected individuals. Sea bream individuals were exposed by immersion in 100 l of aereated sea water containing 2.89x108 CFU of a virulent Photobacterium damselae piscidida strain (249/ittio99) for 30 min. After pathogen exposure, all fish were returned to one tank. A challenge in the absence of pathogen was carried out with the same experimental procedure. For both infected and uninfected group, four (4) fish were collected at 24h and 48h post challenge and euthanized by over anesthetization, for a total of 16 individuals. Samples of head kidney were taken and stored in RNA later at -20°C until RNA extraction. Gene expression profiling was then performed using the Agilent-027679 Sparus aurata Oligo Microarray platform based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.6 used XDR ID to link the pairs of scans together automatically when extracting data.
2013-02-22 | E-GEOD-26651 | biostudies-arrayexpress
Project description:Euryhaline teleosts can live in a wide range of environmental salinities. Transcriptomic analysis in important osmoregulatory and non-osmoregulatory tissues (liver, gills and hypothalamus) by means of a specific oligo-microarray revealed new aspects related to the osmoregulatory processes mediated by different canonical pathways after hypo- or hyper-omotic challenges in gilthead sea bream (Sparus aurata) juveniles. Liver was the most responsive tissue to salinity changes. In addition, around 24 %, 8 % and 12 % of the total genes differentially expressed were affected and regulated in the same way (up- or down-regulated) by both hyper- and hypo-osmotic challenges in liver, gills and hypothalamus, respectively. In liver and gills, functional analysis of the differentially expressed genes established 2 major clusters of canonical pathways related to i) Energy Metabolism and ii) Oxidative Stress: Damage and Repair, whereas for hypothalamus only a main clusters linked to Oxidative Stress: Damage and Repair was identified. Further, this common cluster presents different sub-nodes in all analyzed tissues, with a clear dualism between liver and gills in those pathways involved in nitrogenous turnover, as well as between gills and hypothalamus in cell stress processes. In addition, several sub-nodes related to cell and tissue architecture was only found in hypothalamus. Moreover, only genes involved in xenobiotic metabolism signaling canonical pathway were differentially regulated by both hypo- and/or hyper-salinity transfer in the three tissues considered. Our results indicated that hepatic, branchial and hypothalamic transcriptome of the sea bream clearly responded after 7 days in different environmental salinities, when mainly metabolic and different cell functions are activated to reach homeostasis, or even return to their basal levels.
2017-02-10 | GSE73872 | GEO
Project description:Transcriptome analysis of gilthead sea bream Sparus aurata liver upon exposure to low temperature
| PRJNA223176 | ENA
Project description:In this study, gilthead sea bream (Sparus aurata) fast muscle myoblasts were stimulated with two pro-growth treatments, amino acids (AA) and insulin-like growth factor 1 (Igf-1), to analyze the transcriptional response of genes, microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) and their regulatory network. AA had a higher impact on gene transcription (1795 genes significantly changed) compared to Igf-1 (385 genes significantly changed). Both treatments stim-ulated the transcription of genes related to muscle differentiation (GO:0042692) and sarcomere components (GO:0030017), but AA stimulated more the DNA replication and cell division (GO:0007049). Notably, four miRNAs (miR-21, miR-146, miR-22b and miR-206) dominated the landscape among 403 expressed miRNAs. Both pro-growth treatments altered the transcription of over 100 miRNAs, including muscle-specific miRNAs (myomiRs) such as miR-133a/b, miR-206, miR-499, miR-1, and miR 27a. Among 111 detected lncRNAs (> 1 FPKM), only 30 were significantly changed by AA and 11 by Igf-1. Eight lncRNAs exhibited strong negative correlations with several mRNAs, suggesting direct regulation; while 30 lncRNAs showed strong correlations and interac-tions with several miRNAs, suggesting their function as miRNA’s sponges. This work is the first step in the identification of ncRNAs network controlling muscle development and growth in gilthead sea bream, pointing out potential regulatory mechanisms in response to pro-growth signals.
2024-04-17 | GSE246573 | GEO