New Publication for Mike Stout

Congratulations to Mike Stout (and many other friends and colleagues) on his recent publication:

Dyson RJ, Vizcay-Barrena G, Band LR, Fernandes AN, French AP, Fozard JA, Hodgman TC, Kenobi K, Pridmore TP, Stout M, Wells DM, Wilson MH, Bennett MJ, Jensen OE (2014). Mechanical modelling quantifies the functional importance of outer tissue layers during root elongation and bending. New Phytologist. doi: 10.1111/nph.12764.


Root elongation and bending require the coordinated expansion of multiple cells of different types. These processes are regulated by the action of hormones that can target distinct cell layers. We use a mathematical model to characterise the influence of the biomechanical properties of individual cell walls on the properties of the whole tissue. Taking a simple constitutive model at the cell scale which characterises cell walls via yield and extensibility parameters, we derive the analogous tissue-level model to describe elongation and bending. To accurately parameterise the model, we take detailed measurements of cell turgor, cell geometries and wall thicknesses. The model demonstrates how cell properties and shapes contribute to tissue-level extensibility and yield. Exploiting the highly organised structure of the elongation zone (EZ) of the Arabidopsis root, we quantify the contributions of different cell layers, using the measured parameters. We show how distributions of material and geometric properties across the root cross-section contribute to the generation of curvature, and relate the angle of a gravitropic bend to the magnitude and duration of asymmetric wall softening. We quantify the geometric factors which lead to the predominant contribution of the outer cell files in driving root elongation and bending.





New Publication: Modelling Plasmid Regulatory Systems

Springer have brought out on on-line encyclopedia on Molecular Life Sciences and my contribution has just been published:

Stekel D.: Modelling Plasmid Regulatory Systems. In: Bell E., Bond J., Klinman J., Masters B., Wells R. (Ed.) Molecular Life Sciences: An Encyclopedic Reference: SpringerReference ( Springer-Verlag Berlin Heidelberg, 2013.


The success of plasmids as stably inherited, autonomously replicating units depends on control circuits that ensure that positive events such as replication occur efficiently at a set average frequency and that the genetic load carried by the plasmid is at minimal metabolic cost to the host.  While selective pressure has ensured that natural plasmids do achieve this, the wish to exploit plasmids or interfere with their survival mechanisms for biotechnological applications means that we need to understand the critical features that are needed for success.  Mathematical modelling of the intracellular control circuits can help to explore different systems and to distinguish between key parameters and those whose variation will have little effect on the system.  The relatively low complexity of plasmids makes them ideal systems to model and they also provide suitable systems to test prediction from the models.  In the past, plasmid modelling has particularly focussed on the ColE1 and R1 plasmids, using both deterministic and stochastic approaches; more recent work has started to address plasmids with more complex regulatory architectures, such as RK2. This has developed our understanding of the contrasting regulatory mechanisms found in high and low copy number plasmids. The combination of mathematical modelling with robust statistical methods for parameter estimation can integrate experimental data into the model, leading to more realistically parameterized mathematical models. These have greater predictive power and are likely to play a crucial future role in the rational design of plasmids for use in biotechnology and bioprocessing.