Project description:Immune responses in plants are triggered in part by conserved microbe-associated molecular pattern (MAMP) molecules such as bacterial flagellin. Upon MAMP perception, plants rapidly turn on the induction of numerous defense-related genes. We have identified a novel type of plant innate immunity elicitor, protease IV from Pseudomonas aeruginosa. Genome-wide transcriptomic profiles obtained with Affymetrix Arabidopsis ATH1 GeneChips® of 10-day old Arabidopsis seedlings treated with 20 nM purified protease IV for 1 hour were compared to published bacterial flagellin- and oligogalacturonide-triggered responses. We used microarrays to characterize the global transcriptomic changes in Arabidopsis seedlings upon protease IV treatment.
Project description:Early stages of host microbe adaptations involve 'system status changes' (rewiring of pre-existing cellular signaling networks and components) of the host and microbe. We posited that under certain environmental conditions these changes leads to maladaptations and favor emergence of new infectious diseases, and these adaptations will have characteristic signatures representative of the adaptation. Here using Arabidopsis seedlings in a submerged environment treated with P. aerugionsa, we show one such rewired regulation where the master two-component regulator GacA (previously shown to act upstream of quorum sensing, including the regulator LasR, that in turn controls a subset of virulence factors) is completely dispensable. The gacA mutant behaves similar to wild type P. aeruginosa (strain PA14) by a number of read-outs. Consistent with that, the gene expression data here indicates that the transcriptome pattern of the host is identical when treated with wild type PA14 or PA14-gacA mutant. Single time point (10 day old Arabidopsis seedlings infected with wild type PA14 or mutant bacteria PA14DgacA, and analyzed 24h after infection) with two independent experimenal replicates per treatment
Project description:Transcript profiling analysis of vfb (Vier F-Box) mutant seedlings compared to wild type using Arabidopsis ATH1 GeneChip array. Keywords: 10 day old light grown seedlings, wild type and mutant
Project description:Differential transcriptomic analysis of 10-day-old Arabidopsis seedlings treated with 50 μM ABA, PA, or DPA. 10-day-old Arabidopsis seedlings grown on MS medium was treated with 50 μM ABA, PA, or DPA. Total RNA was extracted from biological duplicates, Illumina RNAseq was performed on each sample.
Project description:We performed Illumina sequencing of ribosome depletion RNA libraries prepared from 10-day-old seedlings in Arabidopsis. SE is required for transposon reactivation in atxr5 atxr6 mutant.
Project description:Identification of new and unpredicted full length Arabidopsis genes. Examination of cRNA prepared from Arabidopsis thaliana ecotype Columbia light grown 7-day old seedlings, light grown 7-day old seedlings treated at 4 degrees C for 24hrs, and etiolated 7-day old seedlings using pilot genome tiling arrays. Total RNA was isolated from seedlings with the TRIzol reagent procedure of Invitrogen, then poly(A)+ RNA was purified with Qiagen oligotex. One microgram poly(A)+ RNA was converted into ds-cDNA using T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions using ENZO labeling kit, fragmented and then 20 micrograms of fragmented cRNA were hybridized to the arrays according to Affymetrix instructions. Keywords: other
