The root and the PIN-mediated reflux-loop. (A): Cross-section of a root containing the stem cell niche and quiescent centre (QC) (blue), and the meristem (MZ, yellow), elongation (EZ, green) and differentiation (DZ, white) zone. (B): In silico root segment used for simulations (here the most distal 1200 μm is shown of the simulated 3 mm long segment). The distinct cell types treated in the simulations are: vascular, red; pericycle, orange; endodermis, yellow; cortex, green (dark in MZ, light in EZ); epidermis, blue; quiescent cells, grey; and columella tiers, cyan. A cell wall/apoplast (black) of 0.5 μm surrounds all cells. Cell lengths change for all cell types from 16 μm in the MZ, to 60 μm in the EZ. Cell widths differ slightly, according to experimental images. Note that for the unidirectional transport mechanism, only the vascular and pericycle tissue are considered, together with the QC. (C): PIN localisation is specified in a tissue-dependent manner, based on experimentally observed distributions [see ]. PIN-mediated permeability follows the observed PIN expression levels, and was set to either
=5μm/s (corresponding to ‘weak’ expression levels, indicated in blue), or
=20μm/s (‘strong’ expression, indicated in red). Where PINs are not observed experimentally, a background permeability of
=1μm/s is assumed. Diffusion occurs within cells with a default value of 600 μm2/s, and in the cell wall with a 15-times reduced coefficient of 40 μm2/s. Influx is considered to be apolar in all cells, with
=20 μm/s. (D): Resulting auxin reflux-loop through the root tissue. Colours show direction and magnitude of fluxes, as indicated by the colour circle to the left. For more details regarding choice of root layout, expression levels and parameters, see  and . Scale bar 100 μm (A,B,D).