Continuous-time modeling of cell fate determination in Arabidopsis flowers.

BMC Systems Biology
Simon van MourikJaap Molenaar

Abstract

The genetic control of floral organ specification is currently being investigated by various approaches, both experimentally and through modeling. Models and simulations have mostly involved boolean or related methods, and so far a quantitative, continuous-time approach has not been explored. We propose an ordinary differential equation (ODE) model that describes the gene expression dynamics of a gene regulatory network that controls floral organ formation in the model plant Arabidopsis thaliana. In this model, the dimerization of MADS-box transcription factors is incorporated explicitly. The unknown parameters are estimated from (known) experimental expression data. The model is validated by simulation studies of known mutant plants. The proposed model gives realistic predictions with respect to independent mutation data. A simulation study is carried out to predict the effects of a new type of mutation that has so far not been made in Arabidopsis, but that could be used as a severe test of the validity of the model. According to our predictions, the role of dimers is surprisingly important. Moreover, the functional loss of any dimer leads to one or more phenotypic alterations.

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Citations

Jan 15, 2014·PloS One·Mochamad ApriJaap Molenaar
Feb 12, 2014·BMC Systems Biology·Charles C N WangJeffrey J P Tsai
Jan 11, 2011·Trends in Plant Science·Joost J B KeurentjesBart P H J Thomma
May 15, 2012·Plant Signaling & Behavior·Simon van MourikJaap Molenaar
Jun 11, 2014·Journal of Experimental Botany·Alice PajoroGerco C Angenent
Feb 27, 2015·PloS One·Felipe Leal ValentimAalt D J van Dijk
Mar 29, 2011·Annals of Botany·K GeutenV F Irish
Jun 20, 2013·Plant, Cell & Environment·Joost J B KeurentjesBas J Zwaan

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Software Mentioned

Matlab
lsqnonlin

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