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Stressor mRNA expression profiling of three different stressors in the water flea Daphnia magna

ABSTRACT: Microarray analyses were used to evaluate patterns of gene transcription following exposure of the waterflea Daphnia magna to two natural and one anthropogenic stressor. cDNA microarrays compiled of three life stage specific and three stressor-specific EST libraries, yielding 1734 different EST sequences, were used. We exposed the water flea Daphnia magna to three stressors known to exert strong selection in natural populations of this species i.e. a sublethal concentration of the pesticide carbaryl, infective spores of the endoparasite Pasteuria ramosa, and fish predation risk mimicked by exposure to fish kairomones. A total of 148 gene fragments were differentially expressed compared to the control. Most gene fragments were downregulated under stress (82.4% downregulation compared to 17.6% upregulation) irrespective of the treatment. In approximately 5% of the cases up- or downregulation depended on stressor identity. Based on a PCA, we could identify two different groups within our exposure treatments: small and big gene expression differences compared to the control condition. The treatments parasite 96h exposure, carbaryl 144h of exposure and fish 144h of exposure are combined in the high stress group.

ORGANISM(S): Daphnia magna

PROVIDER: GSE24322 | GEO | 2013/09/01

SECONDARY ACCESSION(S): PRJNA132847

REPOSITORIES: GEO

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Project description:Microarray analyses were used to evaluate patterns of gene transcription following exposure of the waterflea Daphnia magna to two natural and one anthropogenic stressor. cDNA microarrays compiled of three life stage specific and three stressor-specific EST libraries, yielding 1734 different EST sequences, were used. We exposed the water flea Daphnia magna to three stressors known to exert strong selection in natural populations of this species i.e. a sublethal concentration of the pesticide carbaryl, infective spores of the endoparasite Pasteuria ramosa, and fish predation risk mimicked by exposure to fish kairomones. A total of 148 gene fragments were differentially expressed compared to the control. Most gene fragments were downregulated under stress (82.4% downregulation compared to 17.6% upregulation) irrespective of the treatment. In approximately 5% of the cases up- or downregulation depended on stressor identity. Based on a PCA, we could identify two different groups within our exposure treatments: small and big gene expression differences compared to the control condition. The treatments parasite 96h exposure, carbaryl 144h of exposure and fish 144h of exposure are combined in the high stress group. 26 samples x 2 biological replicates were analysed in a carriage wheel design (Khanin & Wit, 2005; Knapen et al., 2009) with a reference sample composed of a clutch of non-exposed D. magna that were collected at different time points ranging from 0-24h until three weeks old. The 26 samples included: 4 treatments (control, carbaryl, fish and parasite exposure) x three time points (48h, 96h and 144h) x 2 replicates + 2 start samples (non-exposed individuals younger than 24h old). This led to 52 different microarray hybridizations: 26 hybridizations for the inner part of the wheel, where every sample is hybridized against the reference, and another 26 for the outer part. Color flip experiments were incorporated per sample to fulfill the conditions of technical replicates on the level of labelling; every stressor-time combination was included at least once in red and once in green. One hybridization in the outer part of the wheel had technical problems, and is not included here.

Project description:"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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Stressor mRNA expression profiling of three different stressors in the water flea Daphnia magna

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