Transcriptome response to the Deepwater Horizon oil spill identifies novel candidate genes for oil tolerance in natural populations of the foundation plant Spartina alterniflora
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PROVIDER: PRJNA472011 | ENA |
REPOSITORIES: ENA
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Project description:Genome-wide expression assay of S. alterniflora individuals from populations (4 from Louisiana, 2 from Mississippi) either exposed or unexposed to the Deepwater Horizon oil spill
2018-05-19 | GSE114635 | GEO
Project description:Deepwater Horizon oil spill sediments Metagenome
| PRJNA796582 | ENA
Project description:Catastrophic events offer unique opportunities to study rapid population response to stress in natural settings. In concert with genetic variation, epigenetic mechanisms may allow populations to persist through severe environmental challenges. In 2010, the Deepwater Horizon oil spill devastated large portions of the coastline along the Gulf of Mexico. However, the foundational salt marsh grass, Spartina alterniflora, showed high resilience to this strong environmental disturbance. Following the spill, we simultaneously examined the genetic and epigenetic structure of recovering populations of S. alterniflora to oil exposure. We quantified genetic and DNA methylation variation using amplified fragment length polymorphism and methylation sensitive fragment length polymorphism (MS-AFLP) to test the hypothesis that response to oil exposure in S. alterniflora resulted in genetically and epigenetically based population differentiation. We found high genetic and epigenetic variation within and among sites and found significant genetic differentiation between contaminated and uncontaminated sites, which may reflect nonrandom mortality in response to oil exposure. Additionally, despite a lack of genomewide patterns in DNA methylation between contaminated and uncontaminated sites, we found five MS-AFLP loci (12% of polymorphic MS-AFLP loci) that were correlated with oil exposure. Overall, our findings support genetically based differentiation correlated with exposure to the oil spill in this system, but also suggest a potential role for epigenetic mechanisms in population differentiation.
| S-EPMC5680422 | biostudies-literature
Project description:Purpose:To help identify molecular regulatory mechanisms of developmental toxicity for fish exposed to Deepwater Horizon (DWH) oil, microRNA profiles in red drum larvae exposed to different DWH oils (source/mass and artificially weathered oil) were evaluated using High Throughput Sequencing (HTS). Methods:Total microRNA profiles of 48 hpf red drum larvae after source oil (0.135%, 0.27%, and 0.54%) and slick oil (1.25%, 2.5% and 5%) exposure were generated by deep sequencing, in triplicate, using Illumina NextSeq 500. Results: Source and slick oil significantly dysregulated the expression of miR-18a, miR-27b, and miR-203a across all exposure concentrations. The target genes of these miRNAs were predominantly involved in the neuro-cardio system development processes and associated key signaling pathways such as axonal guidance signaling, CREB signaling in neurons, synaptic long-term potentiation pathway, calcium signaling and role of NFAT in cardiac hypertrophy.
2019-01-09 | GSE120670 | GEO
Project description:Purpose: To help identify molecular regulatory mechanisms of developmental toxicity for fish exposed to Deepwater Horizon (DWH) oil, microRNA profiles in mahi-mahi (Coryphaena hippurus) larvae exposed to different DWH oils (source/mass and artificially weathered oil) were evaluated using High Throughput Sequencing (HTS). Methods: Total microRNA profiles of 48 hpf mahi-mah larvae after slick (0.5%, 1%, and 2%) and source/mass oil (0.125%, 0.25% and 5%) exposure were generated by deep sequencing, in triplicate, using Illumina NextSEQ v2. Results: Among over 100 significant DE miRNAs, DE miRNAs that were inversely correlated with target mRNAs after slick and source oil exposure were identfied. miR-34b, miR-181b, miR-23b, and miR-203a responsive to both slick and source oil exposure were further filtered to predict downstream biological functions. The target genes of these four miRNAs were involved AhR signaling, Cardiac β-adrenergic signaling, nNOS signaling in neurons, xenobiotic metabolism signaling, p53 signaling, cell cycle regulation, etc., as well as potential diseases including cardiovascular disease, neurological disease, developmental disorder, ophthalmic disease, metabolism disease, etc.
2019-02-20 | GSE116711 | GEO
Project description:Purpose:To help identify molecular mechanisms and pathways potentially involved in the developmental toxicity for estuary fish exposed to different concentrations of Deepwater Horizon (DWH) oil, transcriptomic profiles in red drum (Sciaenops ocellatus) embryos exposed to different DWH oils (source/mass and artificially weathered oil) were evaluated using High Throughput Sequencing (HTS). Methods:Total mRNA profiles of 48 hpf red drum larvae after slick (1.25%, 2.5%, and 5%) and source/mass oil (0.135%, 0.27% and 0.54%) exposure were generated by deep sequencing, in triplicate, using Illumina NextSEQ v2. Results:To determine the potential biological impact of oil exposure at system level, a gene ontology (GO) term analysis on biological processes (BPs) was conducted by analyzing the DEGs using DAVID. After exposure to source oil, the top enriched biological processes were terms associated with oxidation-reduction process, metabolic process (e.g. steroid), and organism development. Similar biological processes were also among the most significant biological processes by slick oil exposure. Among the top biological process list a significant number of nervous system related terms were highly enriched by both source and slick oil exposure, including midbrain development, motor neuron axon guidance, nervous system development, eye development, neuron development, neuron differentiation etc.
2019-01-09 | GSE119934 | GEO
Project description:Purpose:To help identify molecular mechanisms and pathways potentially involved in the developmental toxicity for fish exposed to Deepwater Horizon (DWH) oil, transcriptomic profiles in mahi-mahi (Coryphaena hippurus) embryos exposed to different DWH oils (source and artificially weathered oil) were evaluated at different critical windows of development using High Throughput Sequencing (HTS). Methods:Total mRNA profiles of 24, 48, 96 hpf mahi-mahi larvae after slick and source oil exposure were generated by deep sequencing, in triplicate, using Illumina HiSeq2500. qRTâPCR validation was performed using SYBR Green assays. Results: Exposure to slick oil induced more pronounced changes in gene expression over time than did exposure to source oil. Predominant transcriptomic responses included alteration of E1F2 signaling, steroid biosynthesis, ribosome biogenesis, perturbation in eye development and peripheral nervous, and activation of P450 pathway. Comparisons of changes of cardiac / Ca2+-associated genes with phenotypic responses revealed reduced heart rate and increased pericardial edema in larvae exposed to slick oil but not source oil. Total mRNA profiles of 24, 48, 96 hpf mahi-mahi larvae after slick and source (mass) oil exposure were generated by deep sequencing, in triplicate, using Illumina HiSeq2500.
2016-07-07 | E-GEOD-79675 | biostudies-arrayexpress
Project description:Purpose:To help identify molecular mechanisms and pathways potentially involved in the developmental toxicity for fish exposed to Deepwater Horizon (DWH) oil, transcriptomic profiles in mahi-mahi (Coryphaena hippurus) embryos exposed to different DWH oils (source and artificially weathered oil) were evaluated at different critical windows of development using High Throughput Sequencing (HTS). Methods:Total mRNA profiles of 24, 48, 96 hpf mahi-mahi larvae after slick and source oil exposure were generated by deep sequencing, in triplicate, using Illumina HiSeq2500. qRT–PCR validation was performed using SYBR Green assays. Results: Exposure to slick oil induced more pronounced changes in gene expression over time than did exposure to source oil. Predominant transcriptomic responses included alteration of E1F2 signaling, steroid biosynthesis, ribosome biogenesis, perturbation in eye development and peripheral nervous, and activation of P450 pathway. Comparisons of changes of cardiac / Ca2+-associated genes with phenotypic responses revealed reduced heart rate and increased pericardial edema in larvae exposed to slick oil but not source oil.
2016-07-07 | GSE79675 | GEO
Project description:Zebrafish embryos/larvae are a choice model system for studying early stages of vertebrate development and how these stages can be perturbed by environmental stressors. Petrochemical combustion products elicit developmental toxicity that is associated with transcriptome changes in zebrafish embryos (ZFE). We used microarrays to characterize transcriptome changes in ZFE that had been exposed in the laboratory to oil emulsions collected from the GoM shoreline, ~9 weeks after the Deepwater Horizon blowout.
2013-12-03 | GSE52873 | GEO
Project description:Purpose:To help identify molecular mechanisms and pathways potentially involved in the developmental toxicity for fish exposed to different concentrations of Deepwater Horizon (DWH) oil, transcriptomic profiles in mahi-mahi (Coryphaena hippurus) embryos exposed to different DWH oils (source and artificially weathered oil) were evaluated using High Throughput Sequencing (HTS). Methods:Total mRNA profiles of 48 hpf mahi-mah larvae after slick (0.5%, 1%, and 2%) and source/mass oil (0.125%, 0.25% and 5%) exposure were generated by deep sequencing, in triplicate, using Illumina NextSEQ v2. Results:To determine the potential biological impact of oil exposure at system level, a gene ontology (GO) term analysis on biological processes (BPs) was conducted by analyzing the DEGs using ToppGene. The profile of BPs was dose- and oil type- dependent. After exposure to 0.125% slick oil, the top enriched biological processes were RNA processing and RNA metabolism terms. Metabolic and catabolic process and terms associated with embryo development were some of the most enriched BPs at 0.25% slick oil. The top enriched BPs at 0.5% slick oil were organic acid metabolic process and cardiovascular system development. For source oil, cell cycle process, metabolic process, and RNA processing were the most enriched by 0.125% source oil exposure, which were also highly enriched by 0.25% source oil exposure, while more ‘response’ BPs were enriched by 0.25% source oil exposure, such as regulation of response to stress, response to endogenous stimulus, response to hormone, cellular response to light stimulus, etc. The most significantly enrich BP by 0.5% source oil was cardiovascular system development followed by organic acid metabolic process and cell junction assembly.
2019-02-20 | GSE116639 | GEO