Transcription profiling of Brassica nigra challenged by ozone, Pieris brassicae, or both ozone followed by P. brassicae feeding
ABSTRACT: Brassica nigra plants, a Brassicaceae close to Arabidopsis thaliana, was used for combined stresses experiments. In this study, we performed a whole-genome microarray analysis on five-week-old plants and compared untreated plants and plants treated with ozone at 70 ppb, larvae of Pieris brassicae or both ozone followed by P. brassicae insect.
Project description:Brassica nigra plants, a Brassicaceae close to Arabidopsis thaliana, was used for combined stresses experiments. In this study, we performed a whole-genome microarray analysis on five-week-old plants and compared untreated plants and plants treated different single or dual stresses: the larvae Pieris brassicae, egg extract of Pieris brassicae, the bacterial Xanthomonas campestris pv. raphani, the aphid Brevicoryne brassicae or by combined stresses eggs of P. brassicae / P. brassicae, X. campestris / P. brassicae, B. brassicae / P. brassicae.
Project description:Comparison between O. sativa L. indica cv. Takanari and japonica cv. Koshihikari grown under ozone for their lifetime was performed. Controls were plants grown under filtered air. Three biological replicates (4 plants in each biologicla rpelicate in each small open top chamber - seed; pooled) were used, and dye-swaped.
Project description:High ozone (O3) concentration causes serious damages in plant productivity. Climate models forecast that ground O3 level in the future will reach phytotoxic range, resulting in crop yield losses. With an ultimate goal to screen molecular factors to minimize losses of crop production by the rise of O3 level, we have started an investigation on effects of O3 on rice using rice DNA chip. Herein, we have utilized the samples of dry mature rice seeds harvested in an ozone-sensitive rice cultivar (Oryza sativa L. indica cv. Takanari) and a tolerant cultivar (Oryza sativa L. japonica cv. Koshihikari) which were fumigated with ambient air (mean O3: 32.7 ppb) in small open-top chambers (OTCs). First, we extracted total RNA from dry mature rice seeds of Takanari and Koshihikari using a modified protocol based on cethyltrimethylammonium bromide extraction buffer and phenol-chloroform-isoamylalcohol treatment. Furthermore, to perform microarray analysis using the Agilent 4x44 rice DNA Chip and the dye-swap method, we designed a balanced block design comparing seeds in an ambient air-fumigated rice cultivar and those in a filtered air-fumigated rice cultivar. Direct comparison of Koshihikari and Takanari O3 transcriptomes in seeds of rice plants fumigated with ambient O3 in OTCs successfully showed that genes encoding proteins involved in jasmonic acid, GABA biosynthesis, cell wall and membrane modification, starch mobilization, and secondary metabolite biosynthesis are differently regulated in an O3-sensitive cv. Takanari and a tolerant cv. Koshihikari. Comparison between O. sativa L. indica cv. Takanari and japonica cv. Koshihikari grown under ozone for their lifetime was performed. Controls were plants grown under filtered air. Three biological replicates (4 plants in each biological replicate in each small open top chamber - seed; pooled) were used, and dye-swaped.
Project description:Wild-type Columbia (Col-0) and rcd1-1 seeds were sown on 1:1 peat:vermiculite mixture, stratified for 2 days and grown in controlled environment chambers (Weiss Bio1300; Weiss Gallenkamp, (http://www.weiss-gallenkamp.com/) with 12-h/12-h day/night cycle, temperature 22 °C/19 °C, relative humidity 70%/90%. 1-week old plants were transplanted into individual pots (5x5cm) and subirrigated twice a week. O3 experiments (6 hours of 350 nL L-1) were performed with 3-week old plants. Control and O3-treated plants (x-10 individuals) were collected at 0, 1, 2, 4, 8 and 24h after the start of the O3 treatment. The experiment was repeated 3 times, in addition to which a fourth identical repeat was used as the common reference RNA. cDNA synthesis, sample labeling, microarray hybridization, washing of the slides as well as image scanning were performed as described in Jaspers et al. (2009; PMID:19548978). The 50-mer oligo microarrays were identical to the Jaspers et al. 2009. In prerocessing, the 50mer probes were reannoated to TAIR9 with BLASTn algorithm. Data was analysed with linear mixed models using scripts in R.
Project description:Ozone at an elevated level is an important environmental stress factor that limits plant growth and development. To test how O3-induced ROS signalling interacts with the ABA pathway we present a global characterization of O3-responsive genes in the abi1td mutant. To understand better ABA signalling and the interactions between stress-response pathways we also performed a microarray analysis of drought-treated abi1td and WT plants. Since ABA signalling is well known to mediate defined responses based on the WT and different mutants analysis in drought stress conditions, the comparison of the O3 and drought stress response in abi1td enabled the identification of new processes depending on ABA-related pathways in O3-treated plants. Altogether, our findings indicate that ABI1 plays the role of a general signal transducer linking diferrent hormone signalling pathways to O3 stress tolerance.<br><br><br><br>Key words: ROS signalling; ABA signalling; ozone stress; drought stress; environmental stress; gene knockout;
Project description:This SuperSeries is composed of the following subset Series: GSE40922: Arabidopsis thaliana wild type control (C) vs Pseudomonas syringae infected (Pseu) GSE40923: Arabidopsis thaliana wild type mechanical damage (MD) vs herbivore wounding (HW) GSE40924: Arabidopsis thaliana wild type mechanical damage (MD) vs Myzus persicae wounding (Myz) Refer to individual Series
Project description:Transcriptional profiling of Arabidopsis thaliana wild type (WT) comparing MD (mechanical damage) and HW (herbivore wounding). The differences in the biochemical responses to herbivory seen prompted us to search for less obvious differences between treatments using gene expression profiling. Biological replicates: 4 Two-condition experiment, MD vs. HW Arabidopsis leaves of WT plants. Biological replicates: 4 biological replicates.
Project description:Q fever, a zoonosis due to Coxiella burnetii infection, exhibits sexual dimorphism; men are affected more frequently and severely than women for a given exposure. Here we explore whether the severity of C. burnetii infection in mice is related to differences in male and female gene expression profiles. Mice were infected with C. burnetii for 24 hours, and gene expression was measured in liver cells using microarrays. Multiclass analysis identified 2,777 probes for which expression was specifically modulated by C. burnetti infection. Only 14% of the modulated genes were sex-independent, and the remaining 86% were differentially expressed in males and females. Castration of males and females showed that sex hormones were responsible for more than 60% of the observed gene modulation, and this reduction was most pronounced in males. Using functional annotation of modulated genes, we identified four clusters enriched in males that were related to cell-cell adhesion, signal transduction, defensins and cytokine/Jak-Stat pathways. Up-regulation of the IL-10 and Stat-3 genes may account for the high susceptibility of men with Q fever to C. burnetii infection and autoantibody production. Two clusters were identified in females, including the circadian rhythm pathway, which consists of positive (Clock, Arntl) and negative (Per) limbs of a feedback loop. We found that Clock and Arntl were down-modulated whereas Per was up-regulated; these changes may be associated with efficient bacterial elimination in females but not in males, in which an exacerbated host response would be prominent. This large-scale study revealed for the first time that circadian rhythm plays a major role in the anti-infectious response of mice, and it provides a new basis for elucidating the role of sexual dimorphism in human infections. Liver transcriptome was analyzed using whole genome microarray. Forty mice were divided into 8 groups of five mice upon three binary factors: sex, infection and castration. Four Samples were excluded from final analysis (see Data Processing for additional details).
Project description:Plant defence against insects is well known to be affected by previous exposure to cues warning of herbivory. Using Arabidopsis thaliana and the herbivore Pieris brassicae, we addressed the question whether the maintenance of the effects of the warning cue depends on its reliability. We determined the transcriptomes of Arabidopsis leaves that were treated by P. brassicae egg deposition (i) five days after oviposition, (ii) one day after removal of the eggs following the egg treatment, (iii) three days after removal of the eggs, (iv) after two days of herbivory that started one day after removal of the eggs; or that were treated by chilling (v) five days after transfer to 4°C, (vi) one day after transfering the plants to 20°C following the chilling treatment, (vii) three days after transfering the plants to 20°C, (viii) after two days of herbivory that started one day after transfering the plants to 20°C. Arabidopsis thaliana Col-0 wild type plants were grown under short day conditions (10 h/14 h light/dark) at 20°C for 7 weeks. Subsequently (i) the plants were transferred to 4°C for 5 days, or (ii) Pieris brassicae deposited ca. 40 eggs on leaf 17 where they remained for five days, or (iii) as controls plants grew untreated for five days. Next, the plants were transferred back to 20°C and the eggs were removed, respectively. Next, all plants rested for 1 day at 20°C. Next, P. brassicae larvae were allowed to feed for 2 days on leaf 17 adjacent to the former egg deposit site or at a respective leaf region of chilling-treated or untreated plants. Control plants were not exposed to larvae. From all treated and untreated plants material from a leaf region proximal to the egg deposition and/or feeding site was harvested for transcriptome analysis.