Dataset Information

Improving the proteome coverage of Daphnia magna

ABSTRACT: To improve proteome coverage in Daphnia, we established an easy-to-use procedure based on the LC-MS/MS of whole daphnids and dissected daphnia guts separately. Using a comprehensive spectral library, generated by gas-phase fractionation (GPF) and a data-independent acquisition method, we identified in total > 6000 proteins, demonstrating the effectiveness of our approach.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Daphnia Magna Sus Scrofa Domesticus (domestic Pig)

TISSUE(S): Gut, Whole Body

DISEASE(S): Duchenne Muscular Dystrophy

SUBMITTER: Thomas Fröhlich

LAB HEAD: Thomas Fröhlich

PROVIDER: PXD029198 | Pride | 2022-11-17

REPOSITORIES: Pride

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Improving the proteome coverage of Daphnia magna - implications for future ecotoxicoproteomics studies.

Wilde Magdalena V MV Brehm Julian J Schwarzer Michael M Stöckl Jan B JB Laforsch Christian C Fröhlich Thomas T

Proteomics 20220220 10

Aquatic pollution is an increasing problem and requires extensive research efforts to understand associated consequences and to find suitable solutions. The crustacean Daphnia is a keystone species in lacustrine ecosystems by connecting primary producers with higher trophic levels. Therefore, Daphnia is perfectly suitable to investigate biological effects of freshwater pollution and is frequently used as an important model organism in ecotoxicology. The field of ecotoxicoproteomics has become in ...[more]

PMID: 35143708

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Project description:The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in juvenile daphnids (daphnia magna) as aquatic vertebrate non-target model exposed to sub lethal concentrations of Fipronil. Fipronil is a widely used insecticide applied for crop protection against field pests and Ectoparasites. The Insecticide Resistance Action Committee (IRAC) classified Fipronil after its mode of action (MoA) in the target organism as a GABA-gated chloride channel blocker (Group 2). The goal is to identify toxicogenomic profiles with predictive character and identify potential molecular key events (KE) explaining upstream adverse effects. 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 acute immobilisation test (OECD 202), 50 juvenile Daphnids were exposed to two sub lethal concentrations of Fipronil for 48 hours under static conditions. Each test comprised of a low exposure (LE), high exposure (HE) and a negative control (NC) group and was performed in triplicates. At 48 hours after introducing the daphnids into the test solutions, RNA and protein was extracted from living daphnids with NucleoSpin RNA/Protein kit (Macherey-Nagel). RNA quality was assessed with a 2100 Bioanalyzer system (Agilent) before messenger 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. magna reference genome (daphmag2.4) using 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 count 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 juvenile daphnids (daphnia magna) as aquatic vertebrate non-target model exposed to sub lethal concentrations of Imidacloprid. Imidacloprid is is a popular insecticide widely applied in agriculture and by veterinarians against ectoparasites.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 4). The goal is to identify toxicogenomic profiles with predictive character and identify potential molecular key events (KE) explaining upstream adverse effects. 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 acute immobilisation test (OECD 202), 50 juvenile Daphnids were exposed to two sub lethal concentrations of Imidacloprid for 48 hours under static conditions. Each test comprised of a low exposure (LE), high exposure (HE) and a negative control (NC) group and was performed in triplicates. At 48 hours after introducing the daphnids into the test solutions, RNA and protein was extracted from living daphnids with NucleoSpin RNA/Protein kit (Macherey-Nagel). RNA quality was assessed with a 2100 Bioanalyzer system (Agilent) before messenger 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. magna reference genome (daphmag2.4) using 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 count normalization and differential gene expression analysis with DESeq2.

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Dataset Information

Improving the proteome coverage of Daphnia magna

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Publications

Improving the proteome coverage of Daphnia magna - implications for future ecotoxicoproteomics studies.

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