Transcriptomics

Dataset Information

4

Linkage of genomic biomarkers to whole organism endpoints in a Toxicity Identification Evaluation (TIE)


ABSTRACT: Aquatic organisms are exposed to many toxic chemicals and interpreting the cause and effect relationships between occurrence and impairment is difficult. Toxicity Identification Evaluation (TIE) provides a systematic approach for identifying responsible toxicants. TIE relies on relatively uninformative and potentially insensitive toxicological endpoints. Gene expression analysis may provide needed sensitivity and specificity aiding in the identification of primary toxicants. The current work aims to determine the added benefit of integrating gene expression endpoints into the TIE process. A cDNA library and a custom microarray were constructed for the marine amphipod Ampelisca abdita. Phase 1 TIEs were conducted using 10% and 40% dilutions of acutely toxic sediment. Gene expression was monitored in survivors and controls. An expression-based classifier was developed and evaluated against control organisms, organisms exposed to low or medium toxicity diluted sediment, and chemically selective manipulations of highly toxic sediment. The expression-based classifier correctly identified organisms exposed to toxic sediment even when little mortality was observed, suggesting enhanced sensitivity of the TIE process. The ability of the expression-based endpoint to correctly identify toxic sediment was lost concomitantly with acute toxicity when organic contaminants were removed. Taken together, this suggests that gene expression enhances the performance of the TIE process. Wild-collected Ampelisca abdita were exposed to either control (from sites in Long Island Sound, labeled LIS) sediment, toxic (from site on Elizabeth River, labeled ER) sediment, a series of mixtures of LIS and ER sediment, sediments manipulated to alter toxin bioavailability, or toxicant amended sediments. Lethality was scored, and survivors were subjected to mRNA expression analysis via oligo microarray.

ORGANISM(S): Ampelisca abdita  

SUBMITTER: Mitchell S Kostich   Mark R Reiss  M C Pelletier  mitch kostich  Kay T Ho  Lisa M Portis  Monique M Perron  Adam D Biales  Robert L Flick  David C Bencic  Robert M Burgess 

PROVIDER: E-GEOD-41463 | ArrayExpress | 2012-12-21

SECONDARY ACCESSION(S): GSE41463PRJNA177072

REPOSITORIES: GEO, ArrayExpress

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