Ontology highlight
ABSTRACT:
PROVIDER: PRJNA708307 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13925240.fastq.gz | Fastqsanger.gz | |||
| SRR13925241.fastq.gz | Fastqsanger.gz | |||
| SRR13925242.fastq.gz | Fastqsanger.gz | |||
| SRR13925243.fastq.gz | Fastqsanger.gz | |||
| SRR13925244_1.fastq.gz | Fastqsanger.gz |
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Project description:Contamination of aquatic ecosystems with anthropogenic pollutants, including pharmaceutical drugs, is a major concern worldwide. Fish are particularly at risk of exposure to pollutants but their impacts on mineralized fish tissues, particularly the scales that form a barrier between the fish and the environment, are poorly understood. The proteome data here presented support the findings reported in the associated research article “Disruption of the sea bass (Dicentrarchus labrax) skin-scale by estradiol and fluoxetine, an emerging pollutant”. Juvenile sea basses were exposed by intraperitoneal injections to: a) the antidepressant fluoxetine (FLX), a widely prescribed psychotropic drug and an emerging pollutant; b) the natural estrogen 17β-estradiol (E2) and c) coconut oil alone (control). The scale proteome profiles of fish exposed to these compounds for 5 days were analysed by the quantitative label-free proteomics technology SWATH-MS (Sequential Windowed data-independent Acquisition of the Total High-resolution-Mass Spectra). LC-MS data from pooled protein extracts from the scales of all experimental groups were acquired using information-dependent acquisition (IDA), which allowed the identification of 1,254 proteins through searches against the sea bass genome database. 715 proteins were confidently quantified by SWATH acquisition, from which 213 proteins had modified levels (p<0.05) between E2- or FLX-exposed fish and control. The main biological processes and KEGG pathways affected by E2 or FLX treatments were identified using Cytoscape/ClueGO enrichment analyses.
2022-01-11 | PXD020983 | Pride
Project description:Coral Stylophora pistillata was exposed to octocrylene at 300 and 1000 microg/L in sea water. Blank analyses are present, along with extract profiles of control and exposed corals.
2022-06-24 | MSV000089720 | MassIVE
Project description:Recent studies have unveiled the deep sea as a rich biosphere, populated by species descended from shallow-water ancestors post-mass extinctions. Research on genomic evolution and microbial symbiosis has shed light on how these species thrive in extreme deep-sea conditions. However, early adaptation stages, particularly the roles of conserved genes and symbiotic microbes, remain inadequately understood. This study examined transcriptomic and microbiome changes in shallow-water mussels Mytilus galloprovincialis exposed to deep-sea conditions at the Site-F cold seep in the South China Sea. Results reveal complex gene expression adjustments in stress response, immune defense, homeostasis, and energy metabolism pathways during adaptation. After 10 days of deep-sea exposure, shallow-water mussels and their microbial communities closely resembled those of native deep-sea mussels, demonstrating host and microbiome convergence in response to adaptive shifts. Notably, methanotrophic bacteria, key symbionts in native deep-sea mussels, emerged as a dominant group in the exposed mussels. Host genes involved in immune recognition and endocytosis correlated significantly with the abundance of these bacteria. Overall, our analyses provide insights into adaptive transcriptional regulation and microbiome dynamics of mussels in deep-sea environments, highlighting the roles of conserved genes and microbial community shifts in adapting to extreme environments.
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Project description:Black corals, ecologically important cnidarians found from shallow to deep ocean depths, form a strong yet flexible skeleton of sclerotized chitin and other biomolecules including proteins. The structure and mechanical properties of the chitin component of the skeleton have been well-characterized. However, the protein component has remained a mystery. Here we used liquid chromatography-tandem mass spectrometry to sequence proteins extracted from two species of common Red Sea black corals following either one or two cleaning steps. We detected hundreds of proteins between the two corals, nearly 70 of which are each others’ reciprocal best BLAST hit. Unlike stony corals, only a few of the detected proteins were moderately acidic (biased toward aspartic and/or glutamic acid residues) suggesting less of a role for these types of proteins in black coral skeleton formation as compared to stony corals. No distinct chitin binding domains were found in the proteins, but proteins annotated as having a role in protein and chitin modifications were detected. Our results support the integral role of proteins in black coral skeleton formation, structure, and function.
2022-06-05 | PXD032043 | Pride
Project description:Corals in nearshore marine environments are increasingly exposed to reduced water quality, which is the major local threat to coral reefs in Hawaii. Corals surviving in such conditions may have adapted to withstand sedimentation, pollutants, and other environmental stressors. Lobe coral (Porites lobata) populations from Maunalua Bay, Hawaii showed clear genetic differentiation along with distinct cellular protein expressions between the 'polluted, high-stress' nearshore site and the 'low-stress' offshore site. To understand the driving force of the observed genetic partitioning, reciprocal transplant and common-garden experiments were conducted using the nearshore and offshore colonies of P. lobata from Maunalua Bay to assess phenotypic differences between the two coral populations. Stress-related physiological and molecular responses were compared between the two populations. Proteomic responses highlighted the inherent differences in the cellular metabolic state and activities between the two populations under the same environmental conditions; nearshore corals did not significantly alter their proteome between the sites, while offshore corals responded to the nearshore transplantation with increased abundances of proteins associated with detoxification, antioxidant, and various metabolic processes. The response differences across multiple phenotypes suggest that the observed genetic partitioning was likely due to local adaptation.
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Project description:This is a dataset associated with an article in the journal Metabolomics titled "Metabolomic richness and fingerprints of deep-sea coral species and populations."
Abstract:
Introduction: From shallow water to the deep sea, corals form the basis of diverse communities with significant ecological and economic value. These communities face many anthropogenic stressors including energy and mineral extraction activities, ocean acidification and rising sea temperatures. Corals and their symbionts produce a diverse assemblage of compounds that may help provide resilience to some of these stressors. Objectives: We aim to characterize the metabolomic diversity of deep-sea corals in an ecological context by investigating patterns across space and phylogeny. Methods: We applied untargeted Liquid Chromatography-Mass Spectrometry to examine the metabolomic diversity of the deep-sea coral, Callogorgia delta, across three sites in the Northern Gulf of Mexico as well as three other deep-sea corals, Stichopathes sp., Leiopathes glaberrima, and Lophelia pertusa, and a shallow-water species, Acropora palmata. Results: Different coral species exhibited distinct metabolomic fingerprints and differences in metabolomic richness including core ions unique to each species. C. delta was generally least diverse while Lophelia pertusa was most diverse. C. delta from different sites had different metabolomic fingerprints and metabolomic richness at individual and population levels, although no sites exhibited unique core ions. Two core ions unique to C. delta were putatively identified as diterpenes and thus may possess a biologically important function. Conclusion: Deep-sea coral species have distinct metabolomic fingerprints and exhibit high metabolomic diversity at multiple scales which may contribute to their capabilities to respond to both natural and anthropogenic stressors, including climate change.
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Project description:RNASeq data on corals transplanted reciprocally into two different thermal microhabitats on Ofu Island Six individual corals transplanted into two habitats
2014-04-30 | E-GEOD-56278 | biostudies-arrayexpress
Project description:RNASeq data on corals transplanted reciprocally into two different thermal microhabitats on Ofu Island
2014-04-30 | GSE56278 | GEO