Lemna gibba
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA158035 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11734583_1.fastq.gz | Fastqsanger.gz | |||
| SRR11734583_2.fastq.gz | Fastqsanger.gz | |||
| SRR11734584_1.fastq.gz | Fastqsanger.gz | |||
| SRR11734584_2.fastq.gz | Fastqsanger.gz | |||
| SRR11734585_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 36 |
Similar Datasets
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
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
Project description:Duckweeds are small, rapidly growing aquatic flowering plants. Due to their ability for biomass production at high rates they represent promising candidates for biofuel feedstocks. Duckweeds are also excellent model organisms because they can be maintained in well-defined liquid media, usually reproduce asexually, and because genomic resources are becoming increasingly available. To establish a framework for quantitative metabolic research in duckweeds we derived a central carbon metabolism network model of Lemna gibba based on its draft genome. Lemna gibba fronds were grown in a photomixotrophic mode in liquid media under continuous light with 13C-labeled glucose as a carbon source. Two different conditions (nitrate vs. glutamine as nitrogen source) were compared by quantification of growth kinetics, metabolite levels, metabolic flux and transcript abundance.
2023-09-14 | GSE153602 | GEO
Project description:Lemna gibba SA-induced flowering
| PRJNA631155 | ENA
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
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
Project description:Lemna gibba strain:D0289 Genome sequencing and assembly
| PRJNA374943 | ENA
Project description:Lemna gibba strain:G3 Genome sequencing
| PRJNA180986 | ENA
Project description:BackgroundDuckweeds are small, rapidly growing aquatic flowering plants. Due to their ability for biomass production at high rates they represent promising candidates for biofuel feedstocks. Duckweeds are also excellent model organisms because they can be maintained in well-defined liquid media, usually reproduce asexually, and because genomic resources are becoming increasingly available. To demonstrate the utility of duckweed for integrated metabolic studies, we examined the metabolic adaptation of growing Lemna gibba cultures to different nutritional conditions.ResultsTo establish a framework for quantitative metabolic research in duckweeds we derived a central carbon metabolism network model of Lemna gibba based on its draft genome. Lemna gibba fronds were grown with nitrate or glutamine as nitrogen source. The two conditions were compared by quantification of growth kinetics, metabolite levels, transcript abundance, as well as by 13C-metabolic flux analysis. While growing with glutamine, the fronds grew 1.4 times faster and accumulated more protein and less cell wall components compared to plants grown on nitrate. Characterization of photomixotrophic growth by 13C-metabolic flux analysis showed that, under both metabolic growth conditions, the Calvin-Benson-Bassham cycle and the oxidative pentose-phosphate pathway are highly active, creating a futile cycle with net ATP consumption. Depending on the nitrogen source, substantial reorganization of fluxes around the tricarboxylic acid cycle took place, leading to differential formation of the biosynthetic precursors of the Asp and Gln families of proteinogenic amino acids. Despite the substantial reorganization of fluxes around the tricarboxylic acid cycle, flux changes could largely not be associated with changes in transcripts.ConclusionsThrough integrated analysis of growth rate, biomass composition, metabolite levels, and metabolic flux, we show that Lemna gibba is an excellent system for quantitative metabolic studies in plants. Our study showed that Lemna gibba adjusts to different nitrogen sources by reorganizing central metabolism. The observed disconnect between gene expression regulation and metabolism underscores the importance of metabolic flux analysis as a tool in such studies.
| S-EPMC10546790 | biostudies-literature