Project description:To see the function of CERK1 receptor-like kinase in the chitin elicitor signaling in Arabidopsis, we compared the gene expression profiles in the chitin oligosaccharide treated seedlings of wild type A. thaliana and CERK1 knock-out mutant. Keywords: Defense response
Project description:Transcriptional profiling of Arabidopsis thaliana seedlings treated with goniothalamin, highlighting to the physiological function of phytochemicals by observing early response of gene expressions in Arabidopsis seedlings.
Project description:Transcriptional profiling of Arabidopsis thaliana seedlings treated with cyanamid, highlighting to the physiological function of phytochemicals by observing early response of gene expressions in Arabidopsis seedlings
Project description:Purpose: The purpose of this experiment was to identify the gene expression changes in Arabidopsis thaliana seedlings induced by 1 h of 100 µM NAE 18:3 treatment. Methods: mRNA profiles of 4-day-old Arabidopsis thaliana seedling were generated by deep sequencing, in triplicate, using Illumina HiSeq. The sequence reads that passed quality filters were analyzed at the transcript level using TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays
Project description:We evaluated the effect of a pre-treatment at 38°C on the early response (30 min) of Arabidopsis thaliana seedlings to a 43°C treatment
Project description:Transcriptional profiling of Arabidopsis thaliana seedlings treated with safranal, highlighting to the physiological function of plant volatile chemicals by observing early response of gene expressions in Arabidopsis seedlings.
Project description:Plant roots located in the upper soil layers are prone to experience high temperatures. To gain insight into the effect of high temperature on root development and functioning, we exposed five-day-old Arabidopsis thaliana seedlings grown on agar plates to 30 °C for 48 hours, and compared the gene expression profile in the root tip with that from seedlings that remained at 22 °C.
Project description:Flis2015 - Plant clock gene circuit
(P2011.1.2 PLM_71 ver 1)
This model is described in the article:
Defining the robust
behaviour of the plant clock gene circuit with absolute RNA
timeseries and open infrastructure.
Flis A, Fernández AP, Zielinski
T, Mengin V, Sulpice R, Stratford K, Hume A, Pokhilko A, Southern
MM, Seaton DD, McWatters HG, Stitt M, Halliday KJ, Millar
AJ.
Open Biol 2015 Oct; 5(10):
Abstract:
Our understanding of the complex, transcriptional feedback
loops in the circadian clock mechanism has depended upon
quantitative, timeseries data from disparate sources. We
measure clock gene RNA profiles in Arabidopsis thaliana
seedlings, grown with or without exogenous sucrose, or in
soil-grown plants and in wild-type and mutant backgrounds. The
RNA profiles were strikingly robust across the experimental
conditions, so current mathematical models are likely to be
broadly applicable in leaf tissue. In addition to providing
reference data, unexpected behaviours included co-expression of
PRR9 and ELF4, and regulation of PRR5 by GI. Absolute RNA
quantification revealed low levels of PRR9 transcripts (peak
approx. 50 copies cell(-1)) compared with other clock genes,
and threefold higher levels of LHY RNA (more than 1500 copies
cell(-1)) than of its close relative CCA1. The data are
disseminated from BioDare, an online repository for focused
timeseries data, which is expected to benefit mechanistic
modelling. One data subset successfully constrained clock gene
expression in a complex model, using publicly available
software on parallel computers, without expert tuning or
programming. We outline the empirical and mathematical
justification for data aggregation in understanding highly
interconnected, dynamic networks such as the clock, and the
observed design constraints on the resources required to make
this approach widely accessible.
cL_m_degr, param m1, modified to ensure light rate > dark rate.
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