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

  • ️Fri Jan 01 2010

Continuous-time modeling of cell fate determination in Arabidopsis flowers

Simon van Mourik et al. BMC Syst Biol. 2010.

Abstract

Background: 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.

Results: 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.

Conclusions: 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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Figures

Figure 1
Figure 1

The ABCDE model for flower organ determination in Arabidopsis. The figure has to be read column-wise. E.g., in the sepal-whorl 1, genes A and E are dominantly expressed.

Figure 2
Figure 2

Graphical representation of the interactions in Table 1.

Figure 3
Figure 3

Simulated dynamics of the decoupled model (5) (solid lines) of the monomers, together with the data points for the four organs.

Figure 4
Figure 4

Simulated dynamics of the coupled network (1)-(2) (solid lines) of the concentrations of proteins that are part of dimer complexes, together with the data points for the four organs.

Figure 5
Figure 5

Mean relative error between simulation and experiment as defined in equation (13). The horizontal axis corresponds to the variables [x1, .., x6].

Figure 6
Figure 6

Simulated dynamics for the AP3 = 0 mutant: the second whorls grow sepals, and the third whorl grows carpels. The data points denote the wild-type expression levels, and they are shown to compare the mutant dynamics with.

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