Figure 1.
Confocal microscopy image of the A. thaliana root tip.
The stem-cell niche (SCN) with the quiescent cells (QC, in green) and surrounding stem cells, the cell proliferation domain (CPD) with actively proliferating cells, the transition domain (TD) and the elongation zone (EZ), where cells do not proliferate, are indicated. The SCN, CPD and TD comprise the RAM.
Figure 2.
Simplified scheme of the cell cycle.
The four main phases and the expression of two key cyclins are indicated.
Figure 3.
Histological drawing of the A. thaliana root tip.
Here we show the SCN and the same domains as shown in Fig. 1 are indicated along the root apical-basal axis, as well as an schematic representation of the processes that are included in the cellular model and their interactions.
Figure 4.
Typical initial configuration of cells after the Voronoi tessellation of random generating points.
Figure 5.
Configuration of cells after 2000 time iterations.
(A) The points in Fig. 4 once they have attained equilibrium using the potential (See Video S3). (B) Final configuration of the cells in the RAM. Observe the regularity of the shapes and sizes of the cells. (C) 2D profile of the field after relaxation. Observe that it is not constant, but there are three well defined sections (See Video S4).
Figure 6.
Typical numerical integration of Eq. 7 showing the formation of auxin gradients.
(A) All gates are open (no PIN action). (B) Including the logical rules to open the gates to model the PIN action.
Figure 7.
Variation of two-type cyclins concentrations and typical oscillations from the Lotka-Volterra model.
Relative expression data of D-type cyclins (purple triangles) and B-type cyclins (green rhombuses) were taken from analysis of gene expression profiles using aphidicolin synchronization on Ref. [76], and are available on GENEVESTIGATOR web page. The oscillations from the Lotka-Volterra model of the inhibitor (blue dashed line) and the activator (red line) are also shown.
Figure 8.
Flow-chart diagram of the program used for the numerical simulations.
We show the parameters in red and the initial conditions in blue at the top of the diagram.
Figure 9.
Typical calculation of the dynamical growth of the root using the model described.
We show four snapshots of the configuration at 400, 1400, 2400 and 3400 time steps. The color code represents the concentration of auxins, red for the maximum and blue for the minimum. See Video S5.
Figure 10.
Plots of local potential, auxin concentration and cell cycle, after coupling dynamics.
The normalized local potential (dashed-blue), the auxin concentration (red) and the advance of the cycle clock (dotted-black) as functions of the distance from the tip (), at
time steps, corresponding to seven days.
Figure 11.
Histogram of the number of cell divisions obtained along the root when
. The potential profile is shown as red dots. Observe that there are no cell divisions beyond
, meaning that the meristem has attained a stationary length.
Figure 12.
Comparisons between results obtained with the model and experimental data.
(A) Cell proliferation rate as a function of the distance from the quiescent centre; calculation from Fig. 9 after six days of growth. The red line and dots are the experimental points reported in Ref. [64]. (B) Frequency distribution for cell length. Experimental data were taken from our laser microscope image of Fig. 1. (C) Average cell length as a function of the distance from the quiescent centre; calculation from Fig. 9 after six days of growth. The red line is the experimental result reported in Ref. [64]. (D) Average cell proliferation velocity as a function of the distance from the quiescent centre; calculation from Fig. 9 after six days of growth. The red line is the experimental result reported in Ref. [64].
Figure 13.
Log-log plot of the maximum RAM as a function of the parameter .
Numerical results are blue rhombuses, and the red line is the best fit with a function of the form with R
.