Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Exposure of zebrafish embryos to organic solvents, dimethylformamide and dimethyl sulfoxide

ABSTRACT: Current aquatic chemical testing guidelines recognise that solvents can potentially interfere with the organism or environmental conditions of aquatic ecotoxicity tests and therefore recommend concentration limits for their use. These recommendations are based on evidence of adverse solvent effects in apical level tests. The growing importance of sub-apical and chronic endpoints in future test strategies, however, suggests the limits may need re-assessment. To address this concern, microarrays were used to determine the effects of organic solvents, dimethylformamide (DMF) and dimethyl sulfoxide (DMSO), upon the transcriptome of zebrafish (Danio rerio) embryos. Embryos were exposed for 48 h to 0.025 and 0.1 ml/L DMF or DMSO. Effects on survival and development after 24 and 48 h were assessed microscopically with no effects on mortality or morphology. However, analysis of 48-h embryonic RNA revealed large numbers of differentially expressed genes for both solvent at both concentrations. The enrichment of differentially expressed genes was found for metabolic, development and other key biological processes, some of which could be linked to observed morphological effects at higher solvent concentrations. These findings emphasise the need to remove or lower as far as possible, the concentrations of solvent carriers in ecotoxicology tests. Balanced loop design consisting of five separate conditions - two exposure concentrations for each of the two solvents and a control treatment - using four replicates for each condition all of which were dye swapped, resulting in a total of twenty independant samples on twenty arrays.

ORGANISM(S): Danio rerio

SUBMITTER: Catherine Turner

PROVIDER: E-GEOD-32593 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Project description:Cellular stress responses are frequently presumed to be more sensitive than traditional ecotoxicological life cycle endpoints such as survival and growth. Yet, the focus to reduce test duration and to generate more sensitive endpoints has caused transcriptomics studies to be performed at low doses during short exposures, separately and independently from traditional ecotoxicity tests, making comparisons with life cycle endpoints indirect. Therefore we aimed to directly compare the effects on growth, survival and gene expression of the non-biting midge Chironomus riparius. To this purpose, we analyzed simultaneously life cycle and transcriptomics responses of chironomid larvae exposed to four model toxicants. We observed that already at the lowest test concentrations many transcripts were significantly differentially expressed, while the life cycle endpoints of C. riparius were hardly affected. Analysis of the differentially expressed transcripts showed that at the lowest test concentrations substantial and biologically relevant cellular stress was induced and that many transcripts responded already maximally at these lowest test concentrations. The direct comparison between molecular en life cycle responses after fourteen days of exposure revealed that gene expression is more sensitive to toxicant exposure than life cycle endpoints, underlining the potential of transcriptomics for ecotoxicity testing and environmental risk assessment. Cellular stress responses are frequently presumed to be more sensitive than traditional ecotoxicological life cycle endpoints such as survival and growth. Yet, the focus to reduce test duration and to generate more sensitive endpoints has caused transcriptomics studies to be performed at low doses during short exposures, separately and independently from traditional ecotoxicity tests, making comparisons with life cycle endpoints indirect. Therefore we aimed to directly compare the effects on growth, survival and gene expression of the non-biting midge Chironomus riparius. To this purpose, we analyzed simultaneously life cycle and transcriptomics responses of chironomid larvae exposed to four model toxicants. We observed that already at the lowest test concentrations many transcripts were significantly differentially expressed, while the life cycle endpoints of C. riparius were hardly affected. Analysis of the differentially expressed transcripts showed that at the lowest test concentrations substantial and biologically relevant cellular stress was induced and that many transcripts responded already maximally at these lowest test concentrations. The direct comparison between molecular en life cycle responses after fourteen days of exposure revealed that gene expression is more sensitive to toxicant exposure than life cycle endpoints, underlining the potential of transcriptomics for ecotoxicity testing and environmental risk assessment. Four 14-day Chironomus riparius sediment toxicity tests were conducted, one with each toxicant. The surviving larvae were individually flash frozen in liquid nitrogen. For each toxicant we analyzed the gene expression of larvae exposed to low, intermediate and high concentrations. We also included a control and a solvent control. For each treatment we analyzed 10 replicates (individual larvae).

Project description:The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish (Danio rerio) embryos as aquatic vertebrate non-target model exposed to sub lethal concentrations of the heavily used organophosphate insecticide Fipronil (CAS 2921-88-2). The Insecticide Resistance Action Committee (IRAC) classified Fipronil after its mode of action (MoA) in the target organism as an acetylcholinesterase (AChE) inhibitor (Group 1B). The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events (KE) explaining upstream adverse effects in aquatic non-target organisms. This will provide useful information to refine and improve existing adverse outcome pathways (AOP). Furthermore, integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects, based on similarly altered transcriptomic and proteomic profiles. In a modified version of the zebrafish embryo toxicity test (OECD 236), 15 fertilized eggs were exposed to two different sub lethal concentrations of Fipronil for 96 hours under semi-static conditions. Each test comprised of a low exposure (LE, 0.075 mg/L), high exposure (HE, 0.3 mg/L) and negative control (NC) group and was performed in triplicates. At 96 hours post fertilization (hpf), 10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit (Macherey-Nagel). RNA quality was assessed with a 2100 Bioanalyzer system (Agilent) before coding RNA was purified (PolyA selection with TruSeq RNA Library Prep Kit v2) and sequenced on an Illumina HiSeq 4000 System (Illumina) in 50 bp single read mode, producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.

Project description:The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish (Danio rerio) embryos (96 hpf) as aquatic vertebrate non-target model exposed to sub lethal concentrations of the carbamate insecticide Carbaryl (CAS 63-25-2). The Insecticide Resistance Action Committee (IRAC) classified Carbaryl after its mode of action (MoA) in the target organism as an acetylcholinesterase (AChE) inhibitor (Group 1A). The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events (KE) explaining upstream adverse effects in aquatic non-target organisms. This will provide useful information to refine and improve existing adverse outcome pathways (AOP). Furthermore, integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects, based on similarly altered transcriptomic and proteomic profiles. In a modified version of the zebrafish embryo toxicity test (OECD 236), 15 fertilized eggs were exposed to two different sub lethal concentrations of Carbaryl for 96 hours under semi-static conditions. Each test comprised of a low exposure (LE, 275 µg/L), high exposure (HE, 1100 µg/L) and negative control (NC) group and was performed in triplicates. At 96 hours post fertilization (hpf), 10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit (Macherey-Nagel). RNA quality was assessed with a 2100 Bioanalyzer system (Agilent) before coding RNA was purified (PolyA selection with TruSeq RNA Library Prep Kit v2) and sequenced on an Illumina HiSeq 4000 System (Illumina) in 50 bp single read mode, producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.

Project description:The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish (Danio rerio) embryos as aquatic vertebrate non-target model exposed to sub lethal concentrations of the heavily used neonicotinoid insecticide Imidacloprid (CAS 138261-41-3). The Insecticide Resistance Action Committee (IRAC) classified Imidacloprid after its mode of action (MoA) in the target organism as a nicotinic acetylcholine receptor (nAChR) competitive modulator (Group 4A) The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events (KE) explaining upstream adverse effects in aquatic non-target organisms. This will provide useful information to refine and improve existing adverse outcome pathways (AOP). Furthermore, integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects, based on similarly altered transcriptomic and proteomic profiles. In a modified version of the zebrafish embryo toxicity test (OECD 236), 15 fertilized eggs were exposed to two different sub lethal concentrations of Imidacloprid for 96 hours under semi-static conditions. Each test comprised of a low exposure (LE, 0.015 mg/L), medium exposure (ME, 0.03 mg/L), high exposure (HE, 0.06 mg/L) and negative control (NC) group and was performed in triplicates. At 96 hours post fertilization (hpf), 10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit (Macherey-Nagel). RNA quality was assessed with a 2100 Bioanalyzer system (Agilent) before coding RNA was purified (PolyA selection with TruSeq RNA Library Prep Kit v2) and sequenced on an Illumina HiSeq 4000 System (Illumina) in 50 bp single read mode, producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for data normalization and differential gene expression analysis with DESeq2.

Project description:The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish (Danio rerio) embryos as aquatic vertebrate non-target model exposed to sub lethal concentrations of the heavily used organophosphate insecticide Chlorpyrifos (CAS 2921-88-2). The Insecticide Resistance Action Committee (IRAC) classified Chlorpyrifos after its mode of action (MoA) in the target organism as an acetylcholinesterase (AChE) inhibitor (Group 1B). The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events (KE) explaining upstream adverse effects in aquatic non-target organisms. This will provide useful information to refine and improve existing adverse outcome pathways (AOP). Furthermore, integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects, based on similarly altered transcriptomic and proteomic profiles. In a modified version of the zebrafish embryo toxicity test (OECD 236), 15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for 96 hours under semi-static conditions. Each test comprised of a low exposure (LE, 0.75 mg/L), high exposure (HE, 3 mg/L) and negative control (NC) group and was performed in triplicates. At 96 hours post fertilization (hpf), 10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit (Macherey-Nagel). RNA quality was assessed with a 2100 Bioanalyzer system (Agilent) before coding RNA was purified (PolyA selection with TruSeq RNA Library Prep Kit v2) and sequenced on an Illumina HiSeq 4000 System (Illumina) in 50 bp single read mode, producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for data normalization and differential gene expression analysis with DESeq2.

Project description:The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish (Danio rerio) embryos as aquatic vertebrate non-target model exposed to sub lethal concentrations of Abamectin (CAS 71751-41-2). Abamectin is a heavily used insecticide applied for crop protection against sucking insects (i.e. Acari). The Insecticide Resistance Action Committee (IRAC) classified Abamectin after its mode of action (MoA) in the target organism as a Glutamate-gated chloride channel (GluCl) allosteric modulator (Group 6). In vertebrates, GluCl do not exist, but they are closely related to vertebrate glycine receptors (Wolstenholme 2012). The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events (KE) explaining upstream adverse effects in aquatic non-target organisms. This will provide useful information to refine and improve existing adverse outcome pathways (AOP). Furthermore, integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects, based on similarly altered transcriptomic and proteomic profiles. In a modified version of the zebrafish embryo toxicity test (OECD 236), 15 fertilized eggs were exposed to two different sub lethal concentrations of Abamectin for 96 hours under semi-static conditions. Each test comprised of a low exposure (LE, 0.11 mg/L), mid exposure (ME, 0.22 mg/L), high exposure (HE, 0.44 mg/L) and negative control (NC) group and was performed in triplicates. At 96 hours post fertilization (hpf), 10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit (Macherey-Nagel). RNA quality was assessed with a 2100 Bioanalyzer system (Agilent) before coding RNA was purified (PolyA selection with TruSeq RNA Library Prep Kit v2) and sequenced on an Illumina HiSeq 4000 System (Illumina) in 50 bp single read mode, producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.

Project description:The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish (Danio rerio) embryos as aquatic vertebrate non-target model exposed to sub lethal concentrations of synthetic organochloride insecticide Methoxychlor (CAS 72-43-5). It is structurally highly similar to its precursor molecule DDT (Dichlorodiphenyltrichloroethane). Like its precursor, today Methoxychlor is banned from the use as pesticide in the United States and the European Union due to its acute toxicity, high bioaccumulation potential and endocrine disruption activity. The Insecticide Resistance Action Committee (IRAC) classified Methoxychlor after its mode of action (MoA) in the target organism as a sodium channel modulator (Group 3B). Our goal is to identify toxicogenomic profiles with predictive character and potential molecular key events (KE) explaining upstream adverse effects in aquatic non-target organisms for this substance of particularly high environmental concern. This will provide useful information to refine and improve existing adverse outcome pathways (AOP). Furthermore, integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects, based on similarly altered transcriptomic and proteomic profiles. In a modified version of the zebrafish embryo toxicity test (OECD 236), 15 fertilized eggs were exposed to two different sub lethal concentrations of Methoxychlor for 96 hours under semi-static conditions. Each test comprised of a low exposure (LE, 20 µg/L), mid exposure (ME, 60 µg/L), high exposure (HE, 180 µg/L) and negative control (NC) group and was performed in triplicates. At 96 hours post fertilization (hpf), 10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit (Macherey-Nagel). RNA quality was assessed with a 2100 Bioanalyzer system (Agilent) before coding RNA was purified (PolyA selection with TruSeq RNA Library Prep Kit v2) and sequenced on an Illumina HiSeq 4000 System (Illumina) in 50 bp single read mode, producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.