Impact of sucrose on the tolerance of phenanthrene-phytoremediation
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE48181 | GEO | 2013/06/28
SECONDARY ACCESSION(S): PRJNA209331
REPOSITORIES: GEO
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Project description:au10-04_phytoremediation; impact of sucrose on the tolerance of phenanthrene Effect of phenanthrene and sucrose - We test 3 conditions plants non-treated (C or t0), plants treated with phenanthrene (P) and plants tread with phenanthrene and sucrose (S). The plants were grown on MS/2 media for 17 days and then transferred on the corresponding condition. We took a sample of 30 plants at different times (0, 30 min, 2h, 4h, 8h and 24h). 22 dye-switch - treated vs untreated comparison
2013-06-28 | E-GEOD-48181 | biostudies-arrayexpress
Project description:Background: Polycyclic aromatic hydrocarbons (PAHs) are toxic, widely-distributed, environmentally persistent, and carcinogenic byproducts of carbon-based fuel combustion. Previously, plant studies have shown that PAHs induce oxidative stress, reduce growth, and cause leaf deformation as well as tissue necrosis. To understand the transcriptional changes that occur during these processes, we performed microarray experiments on Arabidopsis thaliana L. under phenanthrene treatment, and compared the results to published Arabidopsis microarray data representing a variety of stress and hormone treatments. In addition, to probe hormonal aspects of PAH stress, we assayed transgenic ethylene-inducible reporter plants as well as ethylene pathway mutants under phenanthrene treatment. Results: Microarray results revealed numerous perturbations in signaling and metabolic pathways that regulate reactive oxygen species (ROS) and responses related to pathogen defense. A number of glutathione S-transferases that may tag xenobiotics for transport to the vacuole were upregulated. Comparative microarray analyses indicated that the phenanthrene response was closely related to other ROS conditions, including pathogen defense conditions. The ethylene-inducible transgenic reporters were activated by phenanthrene. Mutant experiments showed that PAH inhibits growth through an ethylene-independent pathway, as PAH-treated ethylene-insensitive etr1-4 mutants exhibited a greater growth reduction than WT. Further, phenanthrene-treated, constitutive ethylene signaling mutants had longer roots than the untreated control plants, indicating that the PAH inhibits parts of the ethylene signaling pathway. Conclusions: This study identified major physiological systems that participate in the PAH-induced stress response in Arabidopsis. At the transcriptional level, the results identify specific gene targets that will be valuable in finding lead compounds and engineering increased tolerance. Collectively, the results open a number of new avenues for researching and improving plant resilience and PAH phytoremediation.
2010-04-15 | GSE20009 | GEO
Project description:Background: Polycyclic aromatic hydrocarbons (PAHs) are toxic, widely-distributed, environmentally persistent, and carcinogenic byproducts of carbon-based fuel combustion. Previously, plant studies have shown that PAHs induce oxidative stress, reduce growth, and cause leaf deformation as well as tissue necrosis. To understand the transcriptional changes that occur during these processes, we performed microarray experiments on Arabidopsis thaliana L. under phenanthrene treatment, and compared the results to published Arabidopsis microarray data representing a variety of stress and hormone treatments. In addition, to probe hormonal aspects of PAH stress, we assayed transgenic ethylene-inducible reporter plants as well as ethylene pathway mutants under phenanthrene treatment. Results: Microarray results revealed numerous perturbations in signaling and metabolic pathways that regulate reactive oxygen species (ROS) and responses related to pathogen defense. A number of glutathione S-transferases that may tag xenobiotics for transport to the vacuole were upregulated. Comparative microarray analyses indicated that the phenanthrene response was closely related to other ROS conditions, including pathogen defense conditions. The ethylene-inducible transgenic reporters were activated by phenanthrene. Mutant experiments showed that PAH inhibits growth through an ethylene-independent pathway, as PAH-treated ethylene-insensitive etr1-4 mutants exhibited a greater growth reduction than WT. Further, phenanthrene-treated, constitutive ethylene signaling mutants had longer roots than the untreated control plants, indicating that the PAH inhibits parts of the ethylene signaling pathway. Conclusions: This study identified major physiological systems that participate in the PAH-induced stress response in Arabidopsis. At the transcriptional level, the results identify specific gene targets that will be valuable in finding lead compounds and engineering increased tolerance. Collectively, the results open a number of new avenues for researching and improving plant resilience and PAH phytoremediation. Arabidopsis thaliana (ecotype Columbia) plants were long-day grown with +/- 0.25 mM phenanthrene in sterile plates at 23C for 21d before harvest. At least 20 plants were pooled prior to each mRNA extraction.
2010-04-27 | E-GEOD-20009 | biostudies-arrayexpress
Project description:For RNA-seq, new cuttings from 3-week-old in vivo plants were cultured on the solid Woody Plant Medium (WPM) containing 20 g/L sucrose and 3 g/L Gelrite (Duchefa). After 5 days of culture, the root primordium formed cuttings were transferred to modified liquid WPM containing 10 μM or 200 μM KH2PO4, and harvested the basal ends of stem cuttings containing root primordium with its surrounding tissues using 11# scalpel after 2h, 4h, 8h, 12h and 24h culture. Samples were collected from two biological replicates (50 cuttings each).
2022-08-16 | GSE174726 | GEO
Project description:Polycyclic aromatic hydrocarbons are common pollutants in soil, have negative effects on soil ecosystems, and are potentially carcinogenic. The Springtail (Collembola) Folsomia candida is often used as an indicator species for soil toxicity. Here we report a toxicogenomic study that translates the ecological effects of the polycyclic aromatic hydrocarbon phenanthrene in soil to the early transcriptomic responses in Folsomia candida. Microarrays were used to examine two different exposure concentrations of phenanthrene, namely the EC10 (24.95 mg kg-1 soil) and EC50 (45.80 mg kg-1 soil) on reproduction of this springtail, which evoked 405 and 251 differentially expressed transcripts, respectively. Fifty transcripts were differential in response to either concentration. Many transcripts encoding xenobiotic detoxification and biotransformation enzymes (phases I, II, and III) were upregulated in response to either concentration. Furthermore, indications of general and oxidative stress were found in response to phenanthrene. Chitin metabolism appeared to be disrupted particularly at the low concentration, and protein translation appeared suppressed at the high concentration of phenanthrene; most likely in order to reallocate energy budgets for the detoxification process. Finally, an immune response was evoked especially in response to the high effect concentration, which was also described in a previous transcriptomic study using the same effect concentration (EC50) of cadmium. Our study provides new insights in the molecular mode of action of the important polluting class of polycyclic aromatic hydrocarbons in soil animals. Furthermore, we present a fast, sensitive, and specific soil toxicity test which enhances traditional tests and may help to improve current environmental risk assessments and monitoring of potentially polluted sites. Folsomia candida was exposed to phenanthrene spiked soil or untreated (reference/control) soil for 2 days. Two different concentrations of phenanthrene were used, 24.95 and 45.80 mg/kg soil which represent the EC10 and EC50 on reproduction, respectively. For each concentration treatment 4 biological replicates were used, replicate samples consisted of total RNA extracted from ~30 animals exposed in the same jar to either reference or phenanthrene spiked soil. Phenanthrene treated samples were always hybridized to reference samples in an evenly distributed dye-swap manner, which resulted in total in 8 hybridizations of 16 samples.
2010-05-18 | E-GEOD-14207 | biostudies-arrayexpress
Project description:FHMs were exposed to three concentrations of phenanthrene (average measured 29, 287, 1006 ng/L) and fish were sampled after 48hr.
2013-08-27 | GSE44839 | GEO
Project description:FHMs were exposed to three concentrations of phenanthrene (average measured 29, 287, 1006 ng/L) and fish were sampled after 48hr. There were 20 samples analyzed 5) control liver tissues 5) 29 ng/L phenanthrene exposed liver tissues 5) 287 ng/L phenanthrene exposed liver tissues 5)1006 ng/L phenanthrene exposed liver tissues. There was a total of 20 microarrays processed. In this study, gene expression to a 'dose-response' was investigated after in vivo exposure of fish to phenanthrene.
2013-08-27 | E-GEOD-44839 | biostudies-arrayexpress
Project description:We used HeLa cells expressing GFP-tagged SRSF5 and the rapid depletion plasmid hGRAD from genomic loci. SRSF5 depletion was started after addition of Doxycyclin and was allowed for 2h, 8h and 16h. One hour before harvesting, cells were incubated with 4-sU for exactly 1 hour to label newly transcribed RNAs. 4-sU-labelled RNAs were biotinylated and purified over streptavidin beads and transformed into an RNA-seq library. We compared differential expression and intron retention between T0 and the other time points.
2023-12-11 | GSE229324 | GEO
Project description:Polycyclic aromatic hydrocarbons are common pollutants in soil, have negative effects on soil ecosystems, and are potentially carcinogenic. The Springtail (Collembola) Folsomia candida is often used as an indicator species for soil toxicity. Here we report a toxicogenomic study that translates the ecological effects of the polycyclic aromatic hydrocarbon phenanthrene in soil to the early transcriptomic responses in Folsomia candida. Microarrays were used to examine two different exposure concentrations of phenanthrene, namely the EC10 (24.95 mg kg-1 soil) and EC50 (45.80 mg kg-1 soil) on reproduction of this springtail, which evoked 405 and 251 differentially expressed transcripts, respectively. Fifty transcripts were differential in response to either concentration. Many transcripts encoding xenobiotic detoxification and biotransformation enzymes (phases I, II, and III) were upregulated in response to either concentration. Furthermore, indications of general and oxidative stress were found in response to phenanthrene. Chitin metabolism appeared to be disrupted particularly at the low concentration, and protein translation appeared suppressed at the high concentration of phenanthrene; most likely in order to reallocate energy budgets for the detoxification process. Finally, an immune response was evoked especially in response to the high effect concentration, which was also described in a previous transcriptomic study using the same effect concentration (EC50) of cadmium. Our study provides new insights in the molecular mode of action of the important polluting class of polycyclic aromatic hydrocarbons in soil animals. Furthermore, we present a fast, sensitive, and specific soil toxicity test which enhances traditional tests and may help to improve current environmental risk assessments and monitoring of potentially polluted sites.
2009-05-21 | GSE14207 | GEO
Project description:In this study, female fathead minnows (FHM) were exposed to waterbourne phenanthrene (201.8 µg/L) or a solvent control for 7 weeks. Fish were tested for behavioral differences in a modified behavioral test prior to euthansia. Hypothalami were excised and stored for microarray analyses. Fish were exposed to one dose of phenanthrene. Female and male hypothalami were analyzed (n=8 per group, control vs. treatment); liver was also analyzed. N=7 control and 8 phenanthrene. In this study, a subchronic exposure to phenanthrene was investigated
2016-08-25 | E-GEOD-85993 | biostudies-arrayexpress