ABSTRACT: Microarray data from zebrafish embryos (ZFE) exposed for 48-hr periods to oil emulsions collected from GoM shoreline sites following the Deepwater Horizon blowout.
Project description:Microarray data from zebrafish embryos (ZFE) exposed (for 48-96 hr periods and assessed 8 days post-fertilization) to oil emulsions collected from GoM shoreline sites following the Deepwater Horizon blowout.
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.
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.
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. ZFE were exposed to oil emulsions collected (July 1-4, 2010) at the shoreline in Gulfport, MS, Fort Morgan, AL and Perdido Key, FL. ZFE were exposed to emulsions, consisting of varying amounts of alkanes, polynuclear aromatic hydrocarbons (PAHs), sand and seawater that had been M-bM-^@M-^\butteredM-bM-^@M-^] on the bottom of cups, in which ZFE were suspended in zebrafish medium. ZFE development was monitored by light microscopy. M-BM- Control ZFE were suspended in zebrafish medium without emulsions. Gross developmental abnormalities, including axial changes, altered swimming patterns and yolk sac and pericardial sac swelling were noted and photographed. M-BM- M-BM- ZFE were collected at 48-hr intervals, after exposures had begun, and either placed in clean medium for up to 48 hours more, or, were collected immediately for RNA extraction. and hybridization on Affymetrix zebrafish microarrays, each containing 14,900 probe sets. We extracted RNA from all 30 ZFE in each cup for microarray analysis.
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. ZFE were exposed to oil emulsions collected (July 1-4, 2010) at the GoM shoreline. ZFE were exposed to emulsions, consisting of varying amounts of alkanes, polynuclear aromatic hydrocarbons (PAHs), sand and seawater that had been M-bM-^@M-^\butteredM-bM-^@M-^] on the bottom of cups, in which ZFE were suspended in zebrafish medium. ZFE development was monitored by light microscopy. M-BM- Control ZFE were suspended in zebrafish medium without emulsions. Gross developmental abnormalities, including axial changes, altered swimming patterns and yolk sac and pericardial sac swelling were noted and photographed. M-BM- M-BM- ZFE/larvae were collected after exposures ended, and placed in clean medium until 192 hr post-fertilization, when larvae were collected for RNA extraction and hybridization on Affymetrix zebrafish microarrays.
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.
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
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.
Project description:Purpose:To help identify the role miRNAs in molecular mechanisms and pathways potentially involved in the developmental toxicity for fish exposed to Deepwater Horizon (DWH) oil, miRNA-mRNA networks 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:miRNA profiles of 24, 48, 96 hpf mahi-mah larvae after slick and source oil exposure were generated by deep sequencing, in triplicate, using Illumina NextSeq v2. qRT–PCR validation was performed using SYBR Green assays. Results: Exposure of embryos to slick oil resulted in more DE miRNAs than source oil at all developmental stages 24hpf, 48hpf, and 96hpf. There was also an increase in the number of DE miRNA as development progressed, with 96hpf having the highest number of DE miRNAs. The expression of miRNAs and their target mRNA was further compared using advanced bioinformatics with subsequent target organ predictions based on their interactions. Gene ontology (GO) analysis on the target mRNAs was consistent with pathway analysis of miRNAs, predicting disruption of cardiovascular system development after oil exposure and showed that specific miRNA–mRNA interactions may contribute to these effects.
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.
