ABSTRACT: 35S::AtOFP1-GR seeds were directly sown on MS/G plates without or with 10 uM DEX and stratified at 4C in dark for 2 days. Imbibed seeds were then transferred to growth conditions (23°C with 14/10 hr photoperiod at approximately 120 umol m-2 s-1) and grown for 7d.
BACKGROUND: The Arabidopsis genome contains 18 genes that are predicted to encode Ovate Family Proteins (AtOFPs), a protein family characterized by a conserved OVATE domain, an approximately 70-amino acid domain that was originally found in tomato OVATE protein. Among AtOFP family members, AtOFP1 has been shown to suppress cell elongation, in part, by suppressing the expression of AtGA20ox1, AtOFP4 has been shown to regulate secondary cell wall formation by interact with KNOTTED1-LIKE HOMEODOMAI ...[more]
Project description:imbibed Col-0 seeds were sown on ? X MS medium supplemented with 0.8% agar and 1% sucrose. The plates were first exposed to continuous light for 12 h to stimulate germination and then wrapped with two layers of aluminum foil and placed in the growth chamber for 5 d. Once the plant material was uniformly germinated, the experimental conditions were applied. 5-d-old, dark-grown seedlings were washed seven times with sterile water followed by a wash with ? X MS liquid medium without sucrose to remove residual exogenous sugar and the plant material was kept in ? X MS liquid without sucrose in the dark for all subsequent steps. Cultures were shaken at 140 rpm at 22 C for 24 h and then treated with ? X MS without glucose or ½ X MS supplemented with BR (100 nM), glucose (3%), or glucose (3%) + BR (100 nM) for 3 h. Seedlings were harvested after 3h and preceded for RNA isolation and microarray analysis.
Project description:This experiment was designed to study the interactions between Medicago truncatula and the charcoal rot pathogen Macrophomina phaeolina. Two-week-old plants grown in Magenta boxes supplied with 1/2 MS salt and 1% sucrose were inoculated with M. phaseolina covered wheat seeds, and roots were harvested at 24, 36 and 48 hours after inoculation. Control plants were mock inoculated with a sterile wheat seed, and roots were harvest 24 hours later. Pooled RNAs were used in the array experiment using Affymetrix GeneChip(r) Medicago Genome Array.
Project description:Arabidopsis plants expressing DEX-inducible version of the developmental regulator FIL were exposed to DEX or a solution lacking DEX and changes in gene expression assessed after 4h and 8h using microarray analysis.
Project description:This study analyzes transcriptome profiles in pre-germinated seeds and hypoxia-treated seedlings of Arabidopsis thaliana wild type (Col-0) and homozygous mutants (prt6-1 and ate1 ate2). This dataset includes CEL files, RMA signal values and MAS5 P/M/A calls. For pre-germinated seeds, seeds imbibed for 24 h were used for total RNA extraction. For hypoxia treatment, 7-d-old seedlings were incubated in a hypoxia chamber for 2 h and the entire seedling was subjected to RNA extraction. Quantitative profiling of cellular mRNAs was accomplished with the Affymetrix ATH1 platform. Changes in the transcriptome during early seed germination stage and in response to hypoxia in seedlings were evaluated. The data led to identification of mRNAs with abundance regulated by PRT6 and ATE1 / ATE2, which are essential components for the N-end rule pathway of targeted proteolysis (NERP). A combination of genetic, biochemical and molecular analyses reveal that NERP coordinates the stability of key ethylene responsive factor (ERF) family transcription factors, which regulate expression of core hypoxia response genes and tolerance to low oxygen stress. This indicates that the NERP functions as a homeostatic sensor of low oxygen in plants. Pre-germinated seeds; 2 genotypes (Col-0 and prt6-1) x 3 independent biological replicate experiments: Hypoxia treated seedlings; 3 genotypes (Col-0, prt6-1, and ate1 ate2) x 2 treatments (2h aerobic and 2h hypoxia) x 2 independent biological replicate experiments.
Project description:Histone acetylation is involved in the regulation of gene expression in plants and eukaryotes. Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl groups from histones, which is associated with the repression of gene expression. To study the role of histone acetylation in the regulation of gene expression during seed germination, trichostatin A (TSA), a specific inhibitor of histone deacetylase, was used to treat imbibing Arabidopsis thaliana seeds. GeneChip arrays were used to show that TSA induces up-regulation of 45 genes and down-regulation of 27 genes during seed germination. Eight TSA-up-regulated genes were selected for further analysis - RAB18, RD29B, ATEM1, HSP70 and four late embryogenesis abundant protein genes (LEA). A gene expression time course shows that these eight genes are expressed at high levels in the dry seed and repressed upon seed imbibition at an exponential rate. In the presence of TSA, the onset of repression of the eight genes is not affected but the final level of repressed expression is elevated. Chromatin immunoprecipitation and HDAC assays show that there is a transient histone deacetylation event during seed germination at one day after imbibition, which serves as a key developmental signal that affects the repression of the eight genes. Experiment Overall Design: Three samples: Unimbibed seeds, untreated imbibed seeds, TSA-treated imbibed seeds.
Project description:Arabidopsis thaliana seeds after imbibition were inoculated in ½ MS medium supplemented with 0.8% agar and 1% sucrose. Once the plant material was uniformly germinated, the experimental conditions were applied. 5d old light-grown uniformly germinated seedlings were washed seven times with sterile water with last wash given by ½ MS liquid medium without sucrose to remove residual exogenous sugar and the plant material was kept in ½ MS liquid without sucrose in the dark for all subsequent steps. Cultures were shaken at 140 rpm at 22oC for 24 h and then 3 h treatment was given with liquid ½ MS without glucose and liquid ½ MS supplemented with BR (0.1 ?M EBR), glucose (3%), glucose (3%) + BR (0.1 ?M EBR). Seedlings were harvested after 3h and preceded for RNA isolation and Microarray analysis.
Project description:Seeds were plated on sterilized membranes and grown under a 16h/8h light/dark regime at 21ﾰC. After 2 days of germination and 5 days of growth, the membrane was transferred to MS medium containing 0.3 ?g/ml bleomycin for 24 h. Triplicate batches of root meristem material seedlings were harvested for total RNA preparation.
Project description:Microarray experiments of the abi5 seeds were performed by analyzing the samples obtained from two different alleles (both for wild-type and mutant). For the analysis of gene expression profiles in abi5-1 seeds, RNA from Ws seeds was used. For the analysis of gene expression profiles in abi5-7 seeds, RNA from Col seeds was used.
Project description:Microarray experiments of the abi3 seeds were performed by analyzing the samples obtained from two different alleles (both for wild-type and mutant).For the analysis of gene expression profiles in abi3-1 seeds, RNA from Ler seeds was used. For the analysis of gene expression profiles in abi3-6 seeds, RNA from Col seeds was used.