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MRNA-Seq of Lemna minor exposed to different concentrations of the herbicide bentazon against untreated control groups

ABSTRACT: mRNA-Seq of Lemna minor exposed to different concentrations of the herbicide bentazon against untreated control groups

PROVIDER: PRJEB51082 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	ERR8701960.fastq.gz	Fastqsanger.gz
	ERR8701961.fastq.gz	Fastqsanger.gz
	ERR8701962.fastq.gz	Fastqsanger.gz
	ERR8701963.fastq.gz	Fastqsanger.gz
	ERR8701964.fastq.gz	Fastqsanger.gz

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mRNA-Seq of Lemna minor exposed to different concentrations of the herbicide bentazon against untreated control groups

Project description:In this study, Lemna minor was used to investigate ecotoxic modes-of-action (MoA) at the gene expression level. For this purpose, mRNA sequencing was applied to plant RNA extracted from L. minor exposed to the herbicide bentazon in a shortened version of the OECD guideline test No. 221 (OECD TG 221). L. minor is commonly used as a non-target model organism to determine ecotoxicological effects of xenobiotics. As bentazon is one of the five most frequently detected pesticides in European groundwater, it is known for its environmental impact. Therefore, aquatic organisms, especially plants like L. minor, may be affected by its photosynthesis inhibition. The aim of our study was to determine a molecular fingerprint of the substance in order to identify potential biomarkers for its MoA. Therefore, we applied bioinformatics approaches to functionally annotate the previously unannotated reference genome of L. minor. Our functional annotation pipeline is in principle applicable to any organism with an available reference genome and thus greatly facilitates the identification of gene functions for poorly annotated organisms. The observed effects at the molecular level showed promising results for the development of OMICs as screening methods as well as for the identification of biomarkers for the toxicity of bentazon in L. minor.

2022-07-15 | E-MTAB-11460 | biostudies-arrayexpress

mRNA-Seq of Lemna minor exposed to different concentrations of the pharmaceutical atorvastatin against untreated control groups

Project description:In this study, Lemna minor was used to investigate ecotoxic modes-of-action (MoA) at the gene expression level. For this purpose, mRNA sequencing was applied to plant RNA extracted from L. minor exposed to the pharmaceutical atorvastatin in a shortened version of the OECD guideline test No. 221 (OECD TG 221). L. minor is commonly used as a non-target model organism to determine ecotoxicological effects of xenobiotics. Since atorvastatin (and statins in general) are frequently used pharmaceuticals, they can be found in the aquatic environment. In humans, they are used as cholesterol-lowering agents due to their hydroxymethylglutaryl-CoA reductase (HMGR) inhibitory effect. Analogously, in L. minor, atorvastatin can also inhibit the plant’s HMGR, which is involved in phytosterol synthesis. The aim of our study was to determine a molecular fingerprint of the substance in order to identify potential biomarkers for its MoA. Therefore, we applied bioinformatics approaches to functionally annotate the previously unannotated reference genome of L. minor. Our functional annotation pipeline is in principle applicable to any organism with an available reference genome and thus greatly facilitates the identification of gene functions for poorly annotated organisms. The observed effects at the molecular level showed promising results for the development of OMICs as screening methods as well as for the identification of biomarkers for the toxicity of atorvastatin in L. minor.

2022-07-15 | E-MTAB-11459 | biostudies-arrayexpress

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Proteomic profiling of Lemna minor exposed to Bentazon

Project description:Lemna minor a small aquatic plant has been used extensively in ecotoxicolgical testing to elucidate substance-related effects to freshwater plants. They are free-floating freshwater macrophyte, very sensitive towards chemical exposure and easy to cultivate thus makes the plant suitable for laboratory testing. Here we present a rapid and reproducible data dependent proteomics approach for identifying growth related molecular signatures in lemna minor as an alternative to algae testing. For this, we have analyzed the proteome of lemna minor exposed to bentazon as a model substances for identifying growth related molecular perturbations. These fingerprints allow for a definition of potential biomarkers as tools in screening approaches and for integration in plant growth inhibition studies, for identifying suspect substances, such as in the Lemna sp. growth inhibition test (OECD TG 221).

2022-08-15 | PXD031679 | Pride

Proteomic profiling of Lemna minor exposed to Atorvastatin

Project description:Lemna minor a small aquatic plant has been used extensively in ecotoxicolgical testing to elucidate substance-related effects to freshwater plants. They are free-floating freshwater macrophyte, very sensitive towards chemical exposure and easy to cultivate thus makes the plant suitable for laboratory testing. Here we present a rapid and reproducible data dependent proteomics approach for identifying growth related molecular signatures in lemna minor as an alternative to algae testing. For this, we have analyzed the proteome of lemna minor exposed to atorvastatin as a model substances for identifying growth related molecular perturbations. These fingerprints allow for a definition of potential biomarkers as tools in screening approaches and for integration in plant growth inhibition studies (OECD TG 221), for identifying suspect substances.

2022-08-15 | PXD031680 | Pride

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