From genes to jam: modellilng A.thaliana root growth, BBSRC Systems Biology Workshop

BBSRC Systems Biology Grantholder Workshop, University of Nottingham, 16 December 2008.

Presented by 4 people from CPIB.

Malcolm Bennett: This plant is a good choice because the morpology is simple, the development well-understood, the imaging technology required for the work is available, and multi-scale modelling is possible. Microfibrils are stopping the cells from growing radially. What are the mechanisms of plant cell expansion? Cell walls are made up of 3 components: cellulose microfibril skeleton, hemicellulose and GAX which cross-link the microfibrils, and pectins and RGI/RGII form the cell wall matrix.

Tara Holman: They divide the root into 5 developmental zones: meristem, accelerating elongation, decelerating elongation, mature, rest of root / lateral root emergence zone. The XET/XTR family function in the loosening of cell walls by allowing slippage of hemicellulose relative to cellulose microfibrils. There are two distinct clades of this family that are elongation specific (based on microarray data). They have transcriptomic data on all 5 areas, and are currently analysing it. They can track changes in expression of cell wall-related loci, such as XETs, and have a large amount of molecular-scale data.

Rosemary Dyson: But how do these changes contribute to root growth? Which factors are actually important? mechanics of root cell growth: cell has high turgor pressure, which is regulated very quickly by the osmotic potential. The TP also exerts a tension in teh cell wall, if tension is greater than a certain yield stress the wall will creep and exhibit irreversible growth. The degree of creep is controlled by varying the cell wall properties (e.g. viscosity). Current models are variations on the 1965 Lockhart model. Modelling assumptions are: approximate cell as a pressurized hollow cylinder with rigid end plates; model the cell wall as consisting of fibres embedded within a ground matrix; assume the wall is permanently yielded, therefore a viscous fluid; exploit the geometry – the cell wall is much thinner than the radius of the cell so can employ asymptotic analysis. It's just like glass blowing… 🙂 She wrote everything in terms of a moving curvilinear coordinate system, fixed within the moving sheet. Where the centre surface is and the thickness of the sheet form part of the solution. She can also decompose the total fluid velocity, U, into velocity of the centre-surface v, and the fluid velocity relative to the moving v so that U = v + u. Everything is a function of the length along the cylinder, s, and time, t, only. Initial conditions are height, radius, angle of fibres, and length of fibres. There were many more functions here, which were very nicely described, but which are impossible to reproduce in these notes 🙂

Darren Wells: takes the equation/model produced by Rosemary and validates it and looks for best-fit numbers. One of the variables that can be measured directly is turgor pressure (via a micropipette filed with silicon oil and some fancy shenanigans). Pressure is about 3 – 3.5 bar normally (about like tyre pressure). Experimental evidence shows generally that you can assume a constant turgor pressure across the 5 areas of the root, though there may be some slight variation. Conventional fixation techniques can lead to errors of up to 100% in estimation of cell wall thickness. You can solve that with Freeze Fracture, but there is no spatial localization with that. Instead, use cryo FIB-SEM and high-pressure free substitution (beautiful elecron microscopy image!). Discovered that walls are thinner when next to another cell, and thicker at the corners, so difficult to measure thickness. In terms of the growth rate (relative to tip velocity) parameter,  it requires dynamic measurement at cellular resolution. Can use confocal microscopy and image analysis techniques, which give cell lengths and diameters "for free". Vertical imaging under physiologically relevant conditions. The final parameter is viscosity, where direct measurement would require novel techniques, e.g. the development of the micro-rheometer (haven't made it, but might build it). A couple of indirect estimation techniques are possible, however. Here's where the jam comes in, with mimetic cell walls using pectin.

All 4 presenters were clear and interesting and nicely joined together, however I particularly liked the modelling section (3rd part) of this talk. Nice use of LaTex!

These are just my notes and are not guaranteed to be correct. Please feel free to let me know about any errors, which are all my fault and not the fault of the speaker. 🙂

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