Mathematical modelling in microbiology and metabolism

Lead Research Organisation: John Innes Centre
Department Name: Contracts Office

Abstract

The aim of this project is to use mathematical modelling to understand key processes in bacteria and also the dynamics of metabolism in plants. A particular interest has been modelling spatiotemporal protein dynamics inside individual bacterial cells, including the MinCDE system regulating cell division positioning in E. coli. Current work in this area focuses on the dynamics of the ParABC system regulating low copy number plasmid partitioning in E. coli, and on uncovering the dynamics of DivIVA regulating branch morphogenesis in Streptomyces. A further topic of current interest is the dynamics of starch metabolism in Arabidopsis. Techniques used include ordinary/partial differential equation models, often in the form of reaction-diffusion equations, as well as Langevin equations. Stochastic simulations are frequently employed, typically using Monte-Carlo methods. Close collaboration with experimental groups both at the John Innes Centre and elsewhere is a key element of our approach.

Publications

10 25 50
 
Description This grant helped to fund a variety of fundamental mechanistic investigations into various aspects of microbial dynamics and plant metabolism. For the latter, we investigated the build up and decay of starch during the day/night in Arabidopsis. We found that the plants were able to efficiently manage these resources by performing an arithmetic division calculation such that starch resources would run out at the time of expected dawn. In microbiology, we uncovered the mechanistic basis of how low copy number plasmids could be regularly spaced over the nucleoid by a reaction-diffusion type mechanism. We also made significant progress in dissecting the basis of asymmetric cell cycle progression in Caulobacter, as well as in how branching patterns were regulated in Streptomyces by the polar protein DivIVA.
Exploitation Route The research findings were fundamental mechanistic understanding of processes such as branching morphogenesis, asymmetric cell cycle control and plasmid segregation in bacteria, as well as metabolic resource allocation in plants.The latter work could be taken forwards by working to verify many of our model predictions, such as identifying predicted proteins involved in the arithmetic division computation in Arabidopsis starch metabolism.
Sectors Agriculture, Food and Drink

 
Description The research findings were fundamental mechanistic understanding of processes such as branching morphogenesis, asymmetric cell cycle control and plasmid segregation in bacteria, as well as metabolic resource allocation in plants. The latter may have important applications in agriculture though it may take some years for this knowledge to percolate through.
Sector Agriculture, Food and Drink
 
Description Collaboration on plasmid positioning with Gerdes lab 
Organisation Newcastle University
Department Centre for Bacterial Cell Biology
Country United Kingdom 
Sector Academic/University 
PI Contribution We collaborated with the lab of Prof. Kenn Gerdes from Newcastle University to investigate plasmid spacing in E. coli bacteria.
Collaborator Contribution Member Florian Szardenings performed experiments relevant to this project.
Impact paper in PLoS computational biology as indicated in publications section.
Start Year 2010
 
Description Patrick Viollier 
Organisation University of Geneva
Country Switzerland 
Sector Academic/University 
PI Contribution Mathematical modelling of the asymmetric Caulobacter crescentus cell cycle.
Collaborator Contribution Experimental genetic and imaging approaches to Caulobacter.
Impact Multi-disciplinary: experimental microbiology together with mathematical modelling
Start Year 2010