Gene expression profiling in Daphnia magna, Part III: Uncovering Biomarkers for Metal and ORC exposures
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ABSTRACT:
ORGANISM(S): Daphnia magna
PROVIDER: GSE13169 | GEO | 2008/10/16
SECONDARY ACCESSION(S): PRJNA109639
REPOSITORIES: GEO
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Project description:To determine toxicant specific effects of Ordnance Related Compound (ORC) exposure we performed microarray hybridizations with RNA isolated from Daphnia magna following different ORC exposures at the 1/10 LC50. The gene expression profiles revealed toxicant specific gene expression profiles allowed for the identification of specific biomarkers of exposure. Keywords: ecotoxicogenomic exposure study We exposed Daphnia magna the 1/10 LC50 of different Ordnance Related Compounds (Cu, Zn, Pb, WO4, RDX, TNT, 2-ADNT, 2-ADNT, TNB, DNB, 2,4-DNT, and 2,6-DNT) for 24 hours. For each exposure condition, we performed 3 exposures and 2 technical replicates (as dye swap) for each exposure (6 microarrays total, except TNT and Cu). All exposures were compared to a unexposed laboratory control (MHRW media).
2010-05-18 | E-GEOD-13169 | biostudies-arrayexpress
Project description:Background: Toxicogenomics provides new opportunities for innovative and proactive approaches to chemical screening, risk assessment, and predictive toxicology. If applied to ecotoxicology, genomics tools could greatly enhance the ability to detect toxicants and understand the modes of toxicity in an environmental setting. However, few studies have yet to illustrate the potential of genomic techniques in ecotoxicology. Objective: Therefore, our objective was to demonstrate the potential utility of gene expression profiling in ecotoxicology using Daphnia magna, a standard aquatic ecotoxicity test organism. Methods: D. magna were exposed to copper, cadmium, and zinc at the 1/10 LC50 for 24 hours. Following each exposure, RNA was isolated, reverse transcribed, and the cDNA was hybridized to a 5000 clone cDNA microarray for D. magna. Differentially expressed cDNAs were sequenced and homology searches revealed each gene product's potential function. Real time PCR was used to verify the differential expression of several genes, and enzyme assays were used to assess the significance of these changes. Results: We identified distinct expression profiles in response to acute copper, cadmium, and zinc exposures and discovered specific biomarkers of exposure including two probable metallothioneins, and a ferritin mRNA with a functional IRE. The gene expression patterns support known mechanisms of metal toxicity and reveal novel modes of action including zinc inhibition of chitinase activity. Conclusions: Using a cDNA microarray for traditional ecotoxicology organism, D. magna, we have identified novel biomarkers of exposure and revealed possible modes of toxicity, providing experimental support for the utility of ecotoxicogenomics. Keywords: comparative toxicant exposure
2006-12-22 | GSE4759 | GEO
Project description:To determine dose-dependent effects of metal exposure we performed microarray hybridizations with RNA isolated from Daphnia magna following Cu, Cd, and Zn exposures over a range of concentrations that included a tolerated concentration, a sublethal concentration, and a highly toxic concentration. The gene expression profiles revealed effects to digestion related genes, immune related genes, metallothioneins, and oxidative stress genes at the higher concentrations. We also observed that the highest concentrations produced less specific gene expression profiles than the lower concentrations suggesting a more general stress response at the higher concentrations. The lowest concentration tested, representing tolerated concentrations of the metals, caused differential expression of only a few genes and were distinct from the expression profiles of the higher concentrations. This result provides support for the presence of a No Observed Transcriptional Effect Level (NOTEL) for metal exposure in D. magna and suggests that gene expression analysis may offer a strategy for distinguishing between toxic and nontoxic concentrations of metals in the environment. Keywords: ecotoxicogenomic exposure study
2008-06-09 | GSE7668 | GEO
Project description:Cadmium (Cd) is a toxic metal causing sublethal and chronic effects in crustaceans. Omic technologies offer unprecedented opportunities to better understand modes of toxicity by providing a holistic view of the molecular changes underlying physiological disruption. We sought to use gene expression and metabolomic analyses to reveal the processes leading to chronic Cd toxicity in the indicator species, Daphnia magna, after a 24-h sublethal exposure (18 ug/L, corresponding to 1/10 LC50). We first confirmed that metabolites can be detected and identified in small volumes (~3-6 ul) of D. magna hemolymph using Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry and NMR spectroscopy. We then compared the altered metabolite levels from a mass spectrometry metabolomics study to differentially expressed genes identified by a D. magna 44k oligonucleotide microarray. Metabolomics identified several essential amino acids, nucleotides and fatty acids as decreased in D. magna hemolymph following Cd exposure. Transcriptional changes included decreased levels of digestive enzymes and increased expression of genes related to embryonic development. The integration of metabolomic and transcriptomic profiles, as well as incorporation of results from previous studies, has enabled construction of a conceptual model detailing how sublethal Cd disrupts energy reserves and reproduction resulting in chronic toxicity.
2010-12-31 | GSE20218 | GEO
Project description:The use of chemical flame-retardants (FR) in consumer products has steadily increased over the last 30 years. Toxicity data exist for legacy FRs such as pentabromodiphenyl ether (pentaBDE), but less is known about effects of new formulations. To address this issue, the toxicity of seven FR chemicals and formulations was assessed on the freshwater crustacean Daphnia magna. Acute 48-h nominal LC50 values for penta- and octabromodiphenyl ether (pentaBDE, octaBDE), Firemaster 550 (FM550), Firemaster BZ-54 (BZ54), bis(2-ethylhexyl) tetrabromophthalate (BEH-TEBP), triphenyl phosphate (TPhP), and nonbrominated BEH-TEBP analog bis(2-ethylhexyl) phthalate (BEHP) ranged from 0.058 mg/L (pentaBDE) to 3.96 mg/L (octaBDE). mRNA expression, (1)H NMR-based metabolomic and lipidomic profiling at 1/10 LC50 revealed distinct patterns of molecular response for each exposure, suggesting pentaPBDE affects transcription and translation, octaBDE and BEH-TEBP affect glycosphingolipid biosynthesis and BZ54 affects Wnt and Hedgehog signal pathways as well as glycosaminoglycan degradation. Brominated components of FM550 (i.e., BZ54) were significantly higher in Daphnia after 48 h following 1/10 LC50 exposure. FM550 elicited significant mRNA changes at five concentrations across a range from 1/10^6 LC50 to 1/2 LC50. Analyses suggest FM550 impairs nutrient utilization or uptake in Daphnia.
2015-11-06 | GSE74736 | GEO
Project description:Cadmium (Cd) is a toxic metal causing sublethal and chronic effects in crustaceans. Omic technologies offer unprecedented opportunities to better understand modes of toxicity by providing a holistic view of the molecular changes underlying physiological disruption. We sought to use gene expression and metabolomic analyses to reveal the processes leading to chronic Cd toxicity in the indicator species, Daphnia magna, after a 24-h sublethal exposure (18 ug/L, corresponding to 1/10 LC50). We first confirmed that metabolites can be detected and identified in small volumes (~3-6 ul) of D. magna hemolymph using Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry and NMR spectroscopy. We then compared the altered metabolite levels from a mass spectrometry metabolomics study to differentially expressed genes identified by a D. magna 44k oligonucleotide microarray. Metabolomics identified several essential amino acids, nucleotides and fatty acids as decreased in D. magna hemolymph following Cd exposure. Transcriptional changes included decreased levels of digestive enzymes and increased expression of genes related to embryonic development. The integration of metabolomic and transcriptomic profiles, as well as incorporation of results from previous studies, has enabled construction of a conceptual model detailing how sublethal Cd disrupts energy reserves and reproduction resulting in chronic toxicity. Daphnia magna were exposed to 18 micrograms/L Cadmium sulfate for 24 hours. RNA was extracted and hybridized to a custom Daphnia magna microarray to determine genes differentially expressed by the treatment. Two treament experiment:Unexposed and Cd treatment, 6 replicates for each condition
2010-12-31 | E-GEOD-20218 | biostudies-arrayexpress
Project description:The aim of this study was to measure chronic sublethal effects of the flame retardant Tris(2-butoxyethyl)phosphate (TBEP) on gene expression, associated protein activity and life-history endpoints (reproduction, development) in the freshwater crustacean Daphnia magna. We exposed <24h old D. magna neonates for 21 days to culture medium (control) and to 3 sublethal doses of TBEP: 14.7, 147 and 1470 µg/L. Exposure doses were chosen from 48h acute toxicity testing and represent 1/10000, 1/1000 and 1/100 of the LC50, respectively. Each condition (control and the 3 different doses) were performed on 3 independant biological replicates, with 10 individuals each. We used a custom 15000 sequences D. magna microarray to measure transcriptional effect of each of the TBEP doses in comparison to unexposed controls.
2014-02-19 | GSE55132 | GEO
Project description:The use of chemical flame-retardants (FR) in consumer products has steadily increased over the last 30 years. Toxicity data exist for legacy FRs such as pentabromodiphenyl ether (pentaBDE), but less is known about effects of new formulations. To address this issue, the toxicity of seven FR chemicals and formulations was assessed on the freshwater crustacean Daphnia magna. Acute 48-h nominal LC50 values for penta- and octabromodiphenyl ether (pentaBDE, octaBDE), Firemaster 550 (FM550), Firemaster BZ-54 (BZ54), bis(2-ethylhexyl) tetrabromophthalate (BEH-TEBP), triphenyl phosphate (TPhP), and nonbrominated BEH-TEBP analog bis(2-ethylhexyl) phthalate (BEHP) ranged from 0.058 mg/L (pentaBDE) to 3.96 mg/L (octaBDE). mRNA expression, (1)H NMR-based metabolomic and lipidomic profiling at 1/10 LC50 revealed distinct patterns of molecular response for each exposure, suggesting pentaPBDE affects transcription and translation, octaBDE and BEH-TEBP affect glycosphingolipid biosynthesis and BZ54 affects Wnt and Hedgehog signal pathways as well as glycosaminoglycan degradation. Brominated components of FM550 (i.e., BZ54) were significantly higher in Daphnia after 48 h following 1/10 LC50 exposure. FM550 elicited significant mRNA changes at five concentrations across a range from 1/10^6 LC50 to 1/2 LC50. Analyses suggest FM550 impairs nutrient utilization or uptake in Daphnia. Seven flame retardant formulations and equal volume solvent (DMSO) controls for each; four exposed and three or four biological replicates per condition.
2015-11-06 | E-GEOD-74736 | biostudies-arrayexpress
Project description:The aim of this study was to measure chronic sublethal effects of the flame retardant Tris(2-butoxyethyl)phosphate (TBEP) on gene expression, associated protein activity and life-history endpoints (reproduction, development) in the freshwater crustacean Daphnia magna. We exposed <24h old D. magna neonates for 21 days to culture medium (control) and to 3 sublethal doses of TBEP: 14.7, 147 and 1470 M-BM-5g/L. Exposure doses were chosen from 48h acute toxicity testing and represent 1/10000, 1/1000 and 1/100 of the LC50, respectively. Each condition (control and the 3 different doses) were performed on 3 independant biological replicates, with 10 individuals each. We used a custom 15000 sequences D. magna microarray to measure transcriptional effect of each of the TBEP doses in comparison to unexposed controls. We exposed <24h old Daphnia magna to culture medium (unexposed controls) and 3 sublethal doses of TBEP (14.7M-BM-5g/L, 147M-BM-5g/L and 1470M-BM-5g/L) for 21 days. We used 3 biological replicates of 10 individuals for each condition.
2014-02-19 | E-GEOD-55132 | biostudies-arrayexpress