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Integrated mathematical modelling and experimental research into interactions between microorganisms

  • Full or part time
    Dr J U Kreft
  • Application Deadline
    Applications accepted all year round
  • Competition Funded PhD Project (Students Worldwide)
    Competition Funded PhD Project (Students Worldwide)

Project Description

Our group aims to combine theoretical & experimental approaches to understand major problems in the ecology and evolution of microbes. We often compare well-mixed systems such as chemostats with spatially structured systems such as biofilms to work out the effect of spatial structure.

Current research in the group is focussed on the population dynamics of resistance plasmids in spatially structured systems such as biofilms and modelling the fate of antimicrobial resistance in environments such as dairy farms and urban water systems (ie sewage and sewage treatment). We study the fascinating bacterium Bdellovibrio bacteriovorus, a predator of other Gram-negative bacteria, as an alternative to the use of antibiotics. A related interest are the microbial communities living in human and animal guts (upstream of sewage). In order to study these systems, we are keen to develop microfluidics systems to study single cells and use mathematical models to predict community dynamics from these single cell level observations.

As a basis for such studies, we have been developing individual-based modelling software such as iDynoMiCS (individual-based Dynamics of Microbial Communities Simulator) and eGUT (electronic gut):

Past interests have been the evolution of metabolic division of labour, cell-cell communication and aging (damage segregation) versus damage repair in single celled organisms.

I am seeking a motivated PhD student who shares our vision that the future of biology lies in close integration of mathematical and experimental approaches since this will allow us to understand how the behaviour of complex systems emerges from the multitude of interactions of its parts.

If you are fascinated by the diversity and complexity of life, would like to work on important problems and could contribute either mathematical or experimental expertise (or of course preferably both) to strengthen a growing team of mostly friendly people based at the Centre for Computational Biology and the Institute of Microbiology and Infection at the University of Birmingham – please do apply. Your project can involve any of the above mentioned or related areas and can be tailored to your interests and experience.

Please see http://www.biosciences-labs.bham.ac.uk/kreftlab/jobs.html for current studentship and postdoc projects.

Please see http://www.biosciences-labs.bham.ac.uk/kreftlab/index.html for further information on our group and research interests (somewhat out of date).

Please see my Google Scholar page for an up to date publication list: https://scholar.google.co.uk/citations?user=hLRsYpsAAAAJ&hl=en&oi=ao

When contacting me (j.kreft at bham.ac.uk), please explain your motivation and research interest and whether you have mathematical and/or experimental expertise.

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The School of Biosciences offers a number of highly competitive UK Research Council (e.g. BBSRC, NERC, MRC) PhD studentships each year. Fully funded research council studentships are normally only available to UK nationals (or EU nationals resident in the UK) but part-funded studentships may be available to EU applicants resident outside of the UK. The deadline for applications for many research council studentships is 31 January each year but some deadlines may be earlier.

Each year we also have a few fully funded Darwin Trust Scholarships. These are provided by the Darwin Trust of Edinburgh and are for non-UK students wishing to undertake a PhD in the general area of Molecular Microbiology. The deadline for this highly competitive scheme is also 31 January each year.

For further funding details, please see the ‘Funding’ section.

Funding Notes

All applicants should indicate in their applications how they intend to fund their studies. We have a thriving community of international PhD students and encourage applications at any time from students able to find their own funding or who wish to apply for their own funding (e.g. Commonwealth Scholarship, Islamic Development Bank).

The postgraduate funding database provides further information on funding opportunities available View Website and further information is also available on the School of Biosciences website View Website

References

Kreft JU, Booth G, Wimpenny JWT (1998).
BacSim, a simulator for individual-based modelling of bacterial colony growth.
Microbiology 144: 3275-3287

Kreft JU, Picioreanu C, Wimpenny JWT, van Loosdrecht MCM (2001).
Individual-based modelling of biofilms.
Microbiology 147: 2897-2912

Kreft JU (2004).
Biofilms promote altruism.
Microbiology 150: 2751-2760

Costa E, Perez J, Kreft JU (2006).
Why is metabolic labour divided in nitrification?
Trends in Microbiology 14: 213-219

Hense BA, Kuttler C, Müller J, Rothballer M, Hartmann A, Kreft JU (2007).
Does efficiency sensing unify quorum and diffusion sensing?
Nature Reviews Microbiology 5: 230-239

Clegg RJ, Dyson RJ, Kreft JU (2014).
Repair rather than segregation of damage is the optimal unicellular aging strategy.
BMC Biology 12: 52

Hellweger FL, Clegg RJ, Clark J, Plugge CM, Kreft JU (2016).
Advancing microbial sciences by individual-based modelling.
Nature Reviews Microbiology 14: 461-471

Clegg RJ, Kreft JU (2017).
Reducing discrepancies between 3D and 2D simulations due to cell packing density.
Journal of Theoretical Biology 423: 26–30

How good is research at University of Birmingham in Biological Sciences?

FTE Category A staff submitted: 42.80

Research output data provided by the Research Excellence Framework (REF)

Click here to see the results for all UK universities

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