Fundulus heteroclitus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA104605 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We used the mummichog (Fundulus heteroclitus) array we developed to test whether our arrays could be used to monitor the efficacy of remediation at an estuarine Superfund site. Shipyard Creek is a chromium-contaminated Superfund site in Charleston, SC undergoing remediation, therefore it provides a unique opportunity to study the efficacy of arrays as a molecular biomarker in of toxicant effects in mummichogs. Mummichogs were captured in Shipyard Creek in Charleston, SC prior to remediation (2000), after remediation began (2003), and as remediation further progressed (2005). Simultaneously, mummichogs were collected from a reference site at the Winyah-Bay National Estuarine Research Reserve (NERR). The hepatic gene expression pattern of fish captured at Shipyard Creek showed wide differences from the fish captured at NERR in 2000. As remediation progressed the gene expression pattern of fish captured at Shipyard Creek became increasingly similar to fish captured at NERR, and the number of genes differently expressed dropped from 22 to 4. The magnitude of differential gene expression of the individual genes also decreased during remediation. The recovering gene expression profile is associated with lower chromium bioavailability, demonstrated through significantly decreased body burden and sediment concentrations. For example, sediment concentrations at Shipyard Creek were 80-fold greater than NERR in 2000, 51-fold greater in 2003, and only 8-fold greater in 2005. However, hydraulic dredging in 2005 stirred up the sediments and increased body burden of chromium even though chromium sediment concentrations continued to drop. Therefore, the number of differentially expressed genes increased to 9. Overall, the data supports our hypothesis that arrays can be used to monitor site mitigation, as the number of genes differentially expressed mimics the body burden and also indicates when on-site remediation is increasing bioavailability. Keywords: Field site
2006-09-01 | GSE4212 | GEO
Project description:We used the mummichog (Fundulus heteroclitus) array we developed to test whether our arrays could be used to monitor the efficacy of remediation at an estuarine Superfund site. Shipyard Creek is a chromium-contaminated Superfund site in Charleston, SC undergoing remediation, therefore it provides a unique opportunity to study the efficacy of arrays as a molecular biomarker in of toxicant effects in mummichogs. Mummichogs were captured in Shipyard Creek in Charleston, SC prior to remediation (2000), after remediation began (2003), and as remediation further progressed (2005). Simultaneously, mummichogs were collected from a reference site at the Winyah-Bay National Estuarine Research Reserve (NERR). The hepatic gene expression pattern of fish captured at Shipyard Creek showed wide differences from the fish captured at NERR in 2000. As remediation progressed the gene expression pattern of fish captured at Shipyard Creek became increasingly similar to fish captured at NERR, and the number of genes differently expressed dropped from 22 to 4. The magnitude of differential gene expression of the individual genes also decreased during remediation. The recovering gene expression profile is associated with lower chromium bioavailability, demonstrated through significantly decreased body burden and sediment concentrations. For example, sediment concentrations at Shipyard Creek were 80-fold greater than NERR in 2000, 51-fold greater in 2003, and only 8-fold greater in 2005. However, hydraulic dredging in 2005 stirred up the sediments and increased body burden of chromium even though chromium sediment concentrations continued to drop. Therefore, the number of differentially expressed genes increased to 9. Overall, the data supports our hypothesis that arrays can be used to monitor site mitigation, as the number of genes differentially expressed mimics the body burden and also indicates when on-site remediation is increasing bioavailability. Keywords: Field site
2006-09-01 | GSE4211 | GEO
Project description:We used the mummichog (Fundulus heteroclitus) array we developed to test whether our arrays could be used to monitor the efficacy of remediation at an estuarine Superfund site. Shipyard Creek is a chromium-contaminated Superfund site in Charleston, SC undergoing remediation, therefore it provides a unique opportunity to study the efficacy of arrays as a molecular biomarker in of toxicant effects in mummichogs. Mummichogs were captured in Shipyard Creek in Charleston, SC prior to remediation (2000), after remediation began (2003), and as remediation further progressed (2005). Simultaneously, mummichogs were collected from a reference site at the Winyah-Bay National Estuarine Research Reserve (NERR). The hepatic gene expression pattern of fish captured at Shipyard Creek showed wide differences from the fish captured at NERR in 2000. As remediation progressed the gene expression pattern of fish captured at Shipyard Creek became increasingly similar to fish captured at NERR, and the number of genes differently expressed dropped from 22 to 4. The magnitude of differential gene expression of the individual genes also decreased during remediation. The recovering gene expression profile is associated with lower chromium bioavailability, demonstrated through significantly decreased body burden and sediment concentrations. For example, sediment concentrations at Shipyard Creek were 80-fold greater than NERR in 2000, 51-fold greater in 2003, and only 8-fold greater in 2005. However, hydraulic dredging in 2005 stirred up the sediments and increased body burden of chromium even though chromium sediment concentrations continued to drop. Therefore, the number of differentially expressed genes increased to 9. Overall, the data supports our hypothesis that arrays can be used to monitor site mitigation, as the number of genes differentially expressed mimics the body burden and also indicates when on-site remediation is increasing bioavailability. Keywords: Field site
2006-09-01 | GSE4210 | GEO
Project description:The Atlantic killifish (Fundulus heteroclitus) is an ideal model species to study physiological and toxicological adaptations to stressors. Killifish inhabiting the PCB-contaminated Superfund site in New Bedford Harbor, MA (NBH) have evolved resistance to toxicity and activation of the aryl hydrocarbon receptor (AHR) signaling pathway after exposure to PCBs and other AHR agonists. Until recently, a lack of genomic information has limited efforts to understand the molecular mechanisms underlying environmental adaptation to stressors. The advent of high throughput sequencing has facilitated an unbiased assessment of coding as well as non-coding RNAs in any species of interest. Among non-coding RNAs, microRNAs (miRNAs) are important regulators of gene expression and play crucial roles in development and physiology. The objective of this study is to catalog the miRNAs in killifish and determine their expression patterns in the embryos from contaminated (NBH) and pristine (Scorton Creek, MA (SC)) sites. Embryos from NBH and SC were collected daily from 1 to 15 days post-fertilization and RNA from pooled samples from each site was sequenced using SOLiD sequencing. We obtained 7.5 and 11 million raw reads from pooled SC and NBH samples, respectively. Analysis of the sequencing data identified 216 conserved mature miRNA sequences that are expressed during development. Using the draft killifish genome, we retrieved the miRNA precursor sequences. Based on the capacity of these putative precursor sequences to form the characteristic hairpin loop (assessed using RNAfold), we identified 197 conserved miRNA sequences in the genome.
2015-07-20 | GSE70953 | GEO
Project description:Gene expression throughout vertebrate embryogenesis
| PRJNA126081 | ENA
Project description:Fundulus heteroclitus Transcriptome or Gene expression
| PRJNA201069 | ENA
Project description:Fundulus heteroclitus Transcriptome or Gene expression
| PRJNA177696 | ENA
Project description:Fundulus heteroclitus Transcriptome or Gene expression
| PRJNA269174 | ENA