Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA106291 | ENA |
REPOSITORIES: ENA
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Project description:- Background and Aims: Oxygen can fall to low concentrations within plant tissues, either because of environmental factors that decrease the external oxygen concentration or because the movement of oxygen through the plant tissues cannot keep pace with the rate of oxygen consumption. Recent studies document that plants can decrease their oxygen consumption in response to relative small changes in oxygen concentrations to avoid internal anoxia. The molecular mechanisms underlying this response have not been identified yet. The aim of this study was to use transcript and metabolite profiling to investigate the genomic response of Arabidopsis roots to a mild decrease in oxygen concentrations. - Methods: Arabidopsis seedlings were grown on vertical agar plates at 21, 8, 4 and 1% (v/v) external oxygen for 0.5, 2 and 48h. Roots were analyzed for changes in transcript levels using Affymetrix whole genome DNA microarrays, and for changes in metabolite levels using routine GC-MS based metabolite profiling. Root extension rates were monitored in parallel to investigate adaptive changes in growth. - Key results: Results show that root growth was inhibited and transcript and metabolite profiles were significantly altered in response to a moderate decrease in oxygen concentrations. Low oxygen leads to a preferential up-regulation of genes that might be important to trigger adaptive responses in the plant. A small but highly specific set of genes is induced very early in response to a moderate decrease in oxygen concentrations. Genes that were down-regulated mainly encoded proteins involved in energy-consuming processes. In line with this, root extension growth was significantly decreased which will ultimately save ATP and decrease oxygen consumption. This was accompanied by a differential regulation of metabolite levels at short and long term incubation at low oxygen. - Conclusions: Results show that there are adaptive changes in root extension involving large-scale reprogramming of gene expression and metabolism when oxygen concentration is decreased in a very narrow range.
2008-09-01 | GSE11558 | GEO
Project description:- Background and Aims: Oxygen can fall to low concentrations within plant tissues, either because of environmental factors that decrease the external oxygen concentration or because the movement of oxygen through the plant tissues cannot keep pace with the rate of oxygen consumption. Recent studies document that plants can decrease their oxygen consumption in response to relative small changes in oxygen concentrations to avoid internal anoxia. The molecular mechanisms underlying this response have not been identified yet. The aim of this study was to use transcript and metabolite profiling to investigate the genomic response of Arabidopsis roots to a mild decrease in oxygen concentrations. - Methods: Arabidopsis seedlings were grown on vertical agar plates at 21, 8, 4 and 1% (v/v) external oxygen for 0.5, 2 and 48h. Roots were analyzed for changes in transcript levels using Affymetrix whole genome DNA microarrays, and for changes in metabolite levels using routine GC-MS based metabolite profiling. Root extension rates were monitored in parallel to investigate adaptive changes in growth. - Key results: Results show that root growth was inhibited and transcript and metabolite profiles were significantly altered in response to a moderate decrease in oxygen concentrations. Low oxygen leads to a preferential up-regulation of genes that might be important to trigger adaptive responses in the plant. A small but highly specific set of genes is induced very early in response to a moderate decrease in oxygen concentrations. Genes that were down-regulated mainly encoded proteins involved in energy-consuming processes. In line with this, root extension growth was significantly decreased which will ultimately save ATP and decrease oxygen consumption. This was accompanied by a differential regulation of metabolite levels at short and long term incubation at low oxygen. - Conclusions: Results show that there are adaptive changes in root extension involving large-scale reprogramming of gene expression and metabolism when oxygen concentration is decreased in a very narrow range. Experiment Overall Design: Arabidopsis seedlings were grown on vertical agar plates and treated with various oxygen concentrations (1%, 4%, 8%, and 21% as a control), 350ppm CO2 and N2 (rest) for different time periods (0.5 hours, 2 hours and 2 days. At the end of the experiment, the roots of the seedlings were immediately frozen in liquid nitrogen and used for gene expression analysis.
2008-10-25 | E-GEOD-11558 | biostudies-arrayexpress
Project description:Transcript profiling of Arabidopsis epiF3 plants
| PRJNA188310 | ENA
Project description:The ALADIN protein is a component of the nuclear pore complex in higher eukaryotes. Alteration in ALADIN is the basis for the human disease called triple A syndrome (Achalasia-Addisonianism-Alacrima Syndrome). A recent report showed that ALADIN deficiency decreases the tolerance to oxidative stress in human cells and impairs their ability to proliferate. An ALADIN homologue exists in plants, but its functions are still unknown. Therefore, the role of ALADIN was investigated in Arabidopsis thaliana in link with the regulation of the cell cycle. Transcriptome profiling of the roots and shoots of the aladin mutant showed the induction of numerous transcripts linked to stress response and hormone signalling.
2015-12-30 | GSE59562 | GEO
Project description:Bisphenol compounds (BPs) have various industrial uses and can enter the environment through various sources. To evaluate the ecotoxicity of BPs and identify potential gene candidates involved in the plant toxicity, Arabidopsis thaliana was exposed to bisphenol A (BPA), BPB, BPE, BPF, and BPS at a concentration of 1, 3, 10 mg/L for a duration of 14 days, and their growth status were monitored. At day 14, roots and leaves samples were collected for internal BPs exposure concentration detection, RNA-seq, and morphological observations. As shown in the results, exposure to BPs significantly disturbed root elongation, exhibiting a trend of stimulation at low concentration and inhibition at high concentration. Additionally, BPs exhibited pronounced generation of ROS, while none of the pollutants caused significant changes in root morphology. Internal exposure concentration analysis indicate that BPs tend to accumulate in the roots, with BPS exhibiting the highest level of accumulation. The results of RNA-seq indicate that shared 211 differently expressed genes (DEGs) of these 5 exposure groups are enriched in defense response, generation of precursor metabolites, response to organic substance, response to oxygen-containing, response to hormone, oxidation-reduction process and so on. Regarding unique DEGs in each group, BPS was mainly associated with the redox pathway, BPB primarily influenced seed germination, and in BPA, BPE and BPF were primarily involved in metabolic signaling pathways. Our results provide new insights for BPs induced adverse effects on Arabidopsis thaliana and suggest that the ecological risks associated with BPA alternatives cannot be ignored. At 14 d, roots in 3 mg/kg BPA, BPB, BPE, BPF and BPS exposure groups and the control were collected for RNA-seq analysis.
2023-12-19 | GSE250123 | GEO
Project description:When grown under phosphate (Pi) deficiency, plants adjust their developmental program and metabolic activity to cope with this nutritional stress. For Arabidopsis, the developmental responses include inhibition of primary root growth and enhanced formation of lateral roots and root hairs. Pi deficiency also inhibits photosynthesis by suppressing the expression of photosynthetic genes. Interestingly, early studies showed that photosynthetic gene expression was also suppressed in roots, a non-photosynthetic tissue. The biological relevance of this phenomenon, however, is not known. In this work, we characterized an Arabidopsis mutant, hps7, which is hypersensitive to Pi deficiency; the hypersensitivity includes an increased inhibition of root growth. HPS7 encodes a tyrosylprotein sulfotransferase (TPST). Accumulation of TPST proteins, but not mRNA, is induced by Pi deficiency. Comparative RNA-Seq analyses indicated that expression of many photosynthetic genes was activated in the roots of hps7. Under Pi deficiency, the expression of the photosynthetic genes in hps7 is further increased, which leads to the enhanced accumulation of chlorophyll, starch, and reactive oxygen species. The increased inhibition of root growth in hps7 under Pi deficiency was completely reversed by growing plants in the dark. Based on these results, we propose that suppression of photosynthetic gene expression in roots is required for sustained root growth under Pi deficiency.
2014-07-28 | E-MTAB-4405 | biostudies-arrayexpress
Project description:Experiments were achieved on Arabidopsis thaliana. Transcriptional profiling of roots and shoots from plants treated with lead were compared to plants treated in similar conditions without lead. Four weeks old A. thaliana seedlings were treated in hydroponic cultures with Pb during 3 days, by adding or not 40 µM Pb(NO3)2.
2015-01-28 | GSE65333 | GEO
Project description:Single-cell RNAseq of grafted Arabidopsis plants to study transcript mobility
| PRJNA1049216 | ENA
Project description:Expression data roots of Arabidopsis plants inoculated with Verticillium longisporum
| PRJNA264365 | ENA
Project description:To explore mechanisms involved in the plant-microbe interactions, we proceeded with genome-wide transcriptome analysis of Arabidopsis roots incubated with E. coli Bl21 for 24 hours. Control plants did not receive E. coli.
2010-12-01 | GSE22277 | GEO