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| Status |
Public on Dec 07, 2007 |
| Title |
Whole Daphnia_20microg/L Cadmium_48hr |
| Organism |
Daphnia pulex |
| Experiment type |
Expression profiling by array
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| Summary |
"Gene response profiles for Daphnia pulex exposed to the environmental stressor cadmium reveals novel crustacean metallothioneins." Joseph.R.Shaw, John.K.Colbourne, Jennifer.C.Davey, Stephen.P.Glaholt, Thomas.H.Hampton, Celia.Y.Chen, Carol.L.Folt, Joshua.W.Hamilton (BMC Genomics 2007).
Genomic research tools such as microarrays are proving to be important resources to study the complex regulation of genes that respond to environmental perturbations. A first generation cDNA microarray was developed for the environmental indicator species Daphnia pulex, to identify genes whose regulation is modulated following exposure to the metal stressor cadmium. Our experiments revealed interesting changes in gene transcription that suggest their biological roles and their potentially toxicological features in responding to this important environmental contaminant.
Our microarray identified genes reported in the literature to be regulated in response to cadmium exposure, suggested functional attributes for genes that share no sequence similarity to proteins in the public databases, and pointed to genes that are likely members of expanded gene families in the Daphnia genome. Genes identified on the microarray also were associated with cadmium induced phenotypes and population-level outcomes that we experimentally determined. A subset of genes regulated in response to cadmium exposure was independently validated using quantitative-realtime (Q-RT)-PCR. These microarray studies led to the discovery of three genes coding for the metal detoxication protein metallothionein (MT). The gene structures and predicted translated sequences of D. pulex MTs clearly place them in this gene family. Yet, they share little homology with previously characterized MTs.
The genomic information obtained from this study represents an important first step in characterizing microarray patterns that may be diagnostic to specific environmental contaminants and give insights into their toxicological mechanisms, while also providing a practical tool for evolutionary, ecological, and toxicological functional gene discovery studies. Advances in Daphnia genomics will enable the further development of this species as a model organism for the environmental sciences.
Keywords: cDNA microarrays, stress response, expressed sequence tags (EST), Daphnia Genomics Consortium, Arthropod, Gene Expression Profiling, Gene Expression Regulation
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| Overall design |
Microarrays were used to discover genes that were differentially expressed following sub-lethal cadmium exposure (LC01; 20microg/L, 48-h) in D. pulex. They utilized RNA isolated from three independent and concurrently replicated exposures of Daphnia to cadmium and control conditions. RNA was applied to three microarrays using a standard, control vs. treated design that included dye swaps.
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| Contributor(s) |
Shaw JR, Colbourne JK, Davey JC, Glaholt SP, Hampton TH, Chen CY, Folt CL, Hamilton JW |
| Citation(s) |
18154678 |
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| Submission date |
Dec 02, 2007 |
| Last update date |
Jun 06, 2019 |
| Contact name |
Joseph R Shaw |
| E-mail(s) |
joeshaw@indiana.edu
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| Organization name |
Indiana University
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| Department |
The School of Public and Environmental Affairs
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| Lab |
Shaw Lab
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| Street address |
1315 E. Tenth Street
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| City |
Bloomington |
| State/province |
IN |
| ZIP/Postal code |
47405 |
| Country |
USA |
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| Platforms (1) |
| GPL6195 |
IU/UNH/DU Daphnia pulex Generation 2.4 (3.1K) |
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| Samples (3) |
| GSM246093 |
Whole Daphnia_20microg/LCadmium_48hr_rep1 |
| GSM246094 |
Whole Daphnia_20microg/LCadmium_48hr_rep2 |
| GSM246095 |
Whole Daphnia_20microg/LCadmium_48hr_rep3 |
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| Relations |
| BioProject |
PRJNA103667 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE9746_RAW.tar |
2.5 Mb |
(http)(custom) |
TAR (of GPR, TXT) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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