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Mathematical modelling of actin in animals and plants. PhD in Mathematics (SWBio DTP)

  • Full or part time
  • Application Deadline
    Monday, December 02, 2019
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Lead Supervisor
Dr David Richards, Department of Mathematics, College of Engineering, Mathematics and Physical Sciences, University of Exeter

Additional Supervisors
- Dr Michael Deeks , Department of Biosciences, College of Life and Environmental Sciences, University of Exeter
- Professor Harry Mellor, School of Biochemistry, University of Bristol
- Dr Imogen Sparkes, School of Biological Sciences, University of Bristol
- Dr Helen Dawe, Department of Biosciences, College of Life and Environmental Sciences, University of Exeter
- Prof Kim Hammond-Kosack, Rothamsted Research
- Dr Kirsty Wan, Department of Mathematics, College of Engineering, Mathematics and Physical Sciences, University of Exeter

Location: University of Exeter, Streatham Campus, Exeter, EX4 4QJ

Programme Overview
The South West Biosciences Doctoral Training Partnership (SWBio DTP http://www.swbio.ac.uk/) is led by the University of Bristol, together with the Universities of Bath, Cardiff and Exeter, alongside Rothamsted Research.

For more information about the programme structure, please visit https://www.swbio.ac.uk/programme/

Funding for 2020/21
These studentships are available to UK and EU nationals who have established UK residency (EU nationals must have ordinarily lived in the UK throughout the three years preceding the start of the studentship).

The four core universities (Bath, Bristol, Cardiff and Exeter) have a very limited number of fully-funded four year studentships for EU students who do not meet the residency requirements (1-2 studentships per university)*. Please contact the relevant university for more information.

*These are not available for CASE DTP studentships or Standard DTP studentships with a collaborative partner

Project Description
The actin cytoskeleton plays a vital role in animals, plants and fungi. It forms a branched network within cells, which continually changes shape depending on the current requirements. For example, when a plant is attacked by a pathogen, the plant cells remodel their actin cytoskeleton to deliver immune proteins to the site of attack.

The rules governing how the actin network is formed are still not well-understood. They require a careful balance of filament growth, bundling, shrinking and branching. A particularly fascinating and unexplored question is how conserved these rules are across different organisms, where cells can take radically different sizes and shapes.

For example, animal cells often consist of a single, connected compartment, whereas many plant cells contain a large vacuole that forces the cytoplasm into a thin cylinder near the cell wall (see figure). How do these different geometries affect the shape of the actin network, and how do they influence the rules that govern the network?

Traditional biology tackles problems such as these with a purely experimental approach. However, much quicker progress can be made if mathematical modelling is intimately combined with experiments. This is the program you will follow during this PhD.

You will use a multidisciplinary approach that combines mathematical modelling, computer simulations, microscopy and image analysis. This will allow you to learn a wide range of different skills and techniques, ideal for a future career in academia or elsewhere. You are not expected to already know both mathematical modelling and wet-lab techniques; full training will be provided in both areas during the PhD.

In particular, during this project, you will:

1. Design a mathematical model of the actin network. This will build on our existing model for plants and will involve including filament extension, depolymerisation, branching and capping. These models will then be simulated on a computer using MATLAB or C++.

2. Take microscopy time-lapse images of the 3D shape of the actin network in both animal and plant cells. This will require using a number of state-of-the-art microscopes in both Exeter and Bristol Universities.

3. Develop image analysis software to automatically extract the actin network. This will allow quick, accurate analysis of movies from part 2, which will in turn inform the mathematical modelling in part 1. This interplay between experiment and modelling is a key part of this project and will make for a truly exciting PhD.

Eligibility
To be eligible for a fully-funded studentship, you must meet both the academic and residence criteria in line with UKRI guidelines. Please see the following webpage for further details https://www.swbio.ac.uk/programme/eligibility/.

A fully-funded four year SWBio DTP will cover

• a stipend at the standard UKRI rate; currently £15,009 per annum for 2019-2020
• research and training costs
• tuition fees (at the standard UKRI rate)
• additional funds to support fieldwork, conferences and a 3-month internship

Funding Notes

SWBio DTP funded studentship available for September 2020 entry. The studentship will provide funding of fees and a stipend which is currently £15,009 per annum for 2019-20, on a full time basis.

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