Transcription profiling by array of A. Thaliana Wild-type (Col-0) and mutant plants (adg1-1, tpt-2, adg1-1/tpt-2) to investigate response to low and high light stress
ABSTRACT: Wild-type (Col-0) and mutant plants (adg1-1, tpt-2, adg1-1/tpt-2) were grown for 28 days under low light conditions and were then transferred to HL. Leaf samples for transcriptional profiling were taken at time 0 (before transfer to high light) and 4 hours and 48 hours (2 days) after transfer to high light.
Retrograde signals from chloroplasts are thought to control the expression of nuclear genes associated with plastidial processes such as acclimation to varying light conditions. Arabidopsis mutants altered in the day and night path of photoassimilate export from the chloroplasts served as tools to study the involvement of carbohydrates in high light (HL) acclimation. A double mutant impaired in the triose phosphate/phosphate translocator (TPT) and ADP-glucose pyrophosphorylase (AGPase) (adg1-1/t ...[more]
Project description:To identify YehT-regulated genes, the transcriptome profiles of E. coli cells overproducing either the response regulator (RR) YehT or the RR KdpE (control) were comparatively analyzed. The expression level of 32 genes varied more than 8-fold.
Project description:To identify YpdB-regulated genes, the transcriptome profiles of E. coli cells overproducing either the response regulator (RR) YpdB or the RR YehS (control) were comparatively analyzed. The expression level of 15 genes varied more than 1.9-fold.
Project description:Redox Responsive Transcription Factor1 (RRTF1) in Arabidopsis is rapidly and transiently upregulated by H202, as well as biotic and abiotic induced redox signals. Inactivation of RRTF1 restricts and overexpression promotes reactive oxygen species (ROS) accumulation in response to stress. Overexpressor (oe) lines are impaired in root and shoot development, light sensitive and susceptible to Alternaria brassicae infection. These symptoms are diminished by the beneficial root endophyte Piriformospora indica which reduces ROS accumulation locally in roots and systemically in shoots, and by antioxidants and ROS inhibitors which scavenge ROS. More than 850 stress-, redox-, ROS regulated-, ROS scavenging-, defense-, cell death- and senescence-related genes are regulated by RRTF1, ~ 30% of them have ROS related functions. Bioinformatic analyses and in vitro DNA binding assays demonstrate that RRTF1 binds to GCC-box and GCC-box like sequences in the promoter of RRTF1-responsive genes. Upregulation of RRTF1 by stress stimuli as well as H2O2 requires WRKY18/40/60. RRTF1 is co-regulated with the phylogenetically related RAP2.6, which contains GCC-box like sequene in its promoter, but RAP2.6 oe lines do not accumulate higher ROS levels. RRTF1 stimulates systemic ROS accumulation in distal non-stressed leaves. We conclude that the highly conserved RRTF1 rapidly, transiently and systemically induce ROS accumulation in response to ROS and ROS-producing abiotic and biotic stress signals. Necrotrophs stimulate RRTF1 expression, while symbiotic interactions of Arabidopsis with (hemi)-biotrophs and P. indica do not affect or repress RRTF1 expression. Mature leaves of 5 weeks-old Col-0 wild type and RRTF1-overexpressor Arabidopsis (called oe18), which were grown on soil under short-day condition at 20˚C, were subjected to RNA extraction and Affymetrix microarray analysis. Three biological independent experiments for both Col-0 and oe18 were performed.
Project description:We have used a microarray approach to study the effects of the Potato Virus X Potexvirus (PVX)-specific P25 VRS protein on the transcript profile of tobacco plants, when expressed as a transgene in these plants.
Project description:Agilent 4x44k tobacco micro array of wild type tobacco, empty vector control, and HC-Pro transgenic tobacco plants. Both 1-month old leaves and flowers were analyzed. Three biological replicates were performed of each sample.
Project description:Agilent 4x44k tobacco micro array of wild type tobacco (WT) and whole tobacco mosaic virus (TMV) containing transgenic tobacco plants. The transgenic plants before resistance break (BRB-6 weeks), after resistance break (ARB-8 weeks) and wild type tobacco plants infected with TMV (TMVi-9weeks) leaves were analyzed. Three biological replicates were performed for each sample.
Project description:Stochastic changes in cytosine methylation are a source of heritable epigenetic and phenotypic diversity in plants. Using the model plant Arabidopsis thaliana, we derive robust estimates of the rate at which methylation is spontaneously gained (forward epimutation) or lost (backward epimutation) at individual cytosines and construct a comprehensive picture of the epimutation landscape in this species. We demonstrate that the dynamic interplay between forward and backward epimutations is modulated by genomic context and show that subtle contextual differences have profoundly shaped patterns of methylation diversity in A. thaliana natural populations over evolutionary timescales. Theoretical arguments indicate that the epimutation rates reported here are high enough to rapidly uncouple genetic from epigenetic variation, but low enough for new epialleles to sustain long-term selection responses. Our results provide new insights into methylome evolution and its population-level consequences. MethylC-seq of Arabidopsis thaliana
Project description:Dowling-Meara type epidermolysis bullosa simplex (EBS-DM) is a severe blistering disease, caused by dominant mutations in either the keratin-5 (K5) or keratin-14 (K14) gene. K5 and K14 are the major components of the intermediate filament (IF) network in basal keratinocytes. Due to the dominant nature of EBS-DM, misfolded K5 or K14 proteins are incorporated into intermediate filaments, rendering them sensitive to mechanical stress. Upon trauma, these filaments disrupt and the keratinocytes lyse, leading to intra-epidermal blistering. The dominant nature of K5 and K14 mutations in EBS-DM represents a challenge to gene therapeutic approaches. Therefore, we investigated the gene expression profile of a K14 mutant keratinocyte cell line (KEB7) and compared it to the gene expression profile of a wild-type keratinocyte cell line (NEB1). The aim of this study was to identify differentially regulated genes as potential therapeutic targets for the development of new therapies.
Project description:The development of whole-genome bisulfite sequencing (WGBS) has led to a number of exciting discoveries about how genomes utilize DNA methylation and has led to a plethora of novel testable hypotheses. Methods for constructing sodium bisulfite-converted and amplified libraries have recently excelled to the point that the bottleneck for experiments that use WGBS has shifted to data analysis and interpretation. Here we present empirical evidence for an over-representation of methylated DNA from WGBS. This enrichment for methylated DNA is exacerbated by higher cycles of PCR and is influenced by the type of uracil-insensitive DNA polymerase used for amplifying the sequencing library. Future efforts to computationally correct for this enrichment bias will be essential to increasing the accuracy of determining methylation levels for individual cytosines. MethylC-Seq of Arabidopsis thaliana
Project description:Autophagy is activated in pancreatic ductal adenocarcinoma (PDAC) and is currently being considered a promising therapeutic target in clinical trials. PDAC is a highly lethal disease with incidence rate equalling mortality rate. Main reasons for PDAC lethality are late-stage diagnosis, high agressiveness and metastatic rate, lack of effective treatments as well as specific diagnostic markers. Here we show that varying levels of the Autophagy related gene 5 (Atg5) determine pancreatic tumor formation and malignancy. While homozygous deletion of Atg5 blocks tumor progression in an in vivo model of PDAC, heterozygous deletion increases tumor aggressiveness and metastasis. Further analyses reveal that monoallelic loss of Atg5 affects mitochondrial homeostasis, changes intracellular calcium oscillations, heightens extracellular cathepsin activities , and promotes a pro-tumorigenic inflammatory microenvironment collectively enhancing tumor cell migration, invasion, and metastasis. Future treatments should take into account that variations in the autophagy pathway may have opposing effects on pancreatic tumor load, especially considering the multitude of autophagy inhibitors currently tested in clinical trials.