Mathematical modelling in microbiology and metabolism
Lead Research Organisation:
John Innes Centre
Department Name: UNLISTED
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
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.
Planned Impact
unavailable
People |
ORCID iD |
| Martin Howard (Principal Investigator) |
Publications
Flärdh K
(2012)
Regulation of apical growth and hyphal branching in Streptomyces
in Current Opinion in Microbiology
Gerdes K
(2010)
Pushing and pulling in prokaryotic DNA segregation.
in Cell
Guzzo M
(2018)
A gated relaxation oscillator mediated by FrzX controls morphogenetic movements in Myxococcus xanthus.
in Nature microbiology
Howard M
(2010)
What is the mechanism of ParA-mediated DNA movement?
in Molecular microbiology
Ietswaart R
(2014)
Competing ParA structures space bacterial plasmids equally over the nucleoid.
in PLoS computational biology
Kruse K
(2007)
An experimentalist's guide to computational modelling of the Min system.
in Molecular microbiology
Murray S
(2019)
Center Finding in E. coli and the Role of Mathematical Modeling: Past, Present and Future
in Journal of Molecular Biology
Murray SM
(2013)
Computational and genetic reduction of a cell cycle to its simplest, primordial components.
in PLoS biology
Richards DM
(2012)
Mechanistic basis of branch-site selection in filamentous bacteria.
in PLoS computational biology
Ringgaard S
(2009)
Movement and equipositioning of plasmids by ParA filament disassembly.
in Proceedings of the National Academy of Sciences of the United States of America
| 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 |