PhD Opportunity: Geospatial modelling the spread of antimicrobial resistance in the environment

We are looking for an excellent candidate for a PhD in Geospatial modelling the spread of antimicrobial resistance in the environment, funded by the NERC Envision doctoral training programme, supervised jointly by myself, Stuart Marsh (Nottingham Geospatial Institute), Malcolm Bennett (School of Veterinary Medicine and Science) and Andrew Singer (Centre for Ecology and Hydrology). Details of the project are below. Please apply by 6th January on

Project Description

Antimicrobial resistance (AMR) is a major global challenge. It is estimated that globally 700,000 human deaths per year are due to AMR, predicted to rise to 10 million by 2050. While much research is in medical/agricultural contexts, the spread of AMR in the environment is often neglected. Antimicrobials and antimicrobial resistant genes (ARGs) and organisms have sources in agriculture and wastewater treatment plants (WWTP), which are spread on land through slurry, manures or sewage sludge, or released directly into rivers. Soil and water polluted by antimicrobials and resistant bacteria can impact crops, animals and humans. Thus, AMR presents both an environmental and human health hazard.

Our vision is to develop mathematical models that can predict AMR spread in the environment. Such modelling will require numerous factors, including: prevalence of ARGs and the relative role of different AMR sources, pathways, drivers and receptors. These models would be used to inform policy on the priorities for controlling AMR in agriculture and the wider natural environment and on the most appropriate specific actions following an outbreak of an AMR pathogen. They will also help prioritise AMR surveillance. Most mathematical modelling for the environmental spread of AMR operates locally, e.g. in a slurry tank, field soil or a WWTP, or a smaller still, e.g. a biofilm. A challenge is to develop predictive models at much larger environmental scales.

This PhD project will begin to address this challenge, by following four novel modelling approaches: incorporation of the heterogeneity of AMR agents; using a combination of deterministic and stochastic models to account for both microscopic and population level scales; up-scaling the current approaches to an environmental scale by using methods developed for geospatial modelling of pollutants; and calibrating the models with geospatially explicit environmental AMR surveillance data from our projects and those of our collaborators.

Funding Notes

Applicants should hold a minimum of a UK Honours Degree at 2:1 level or equivalent in any relevant scientific discipline with considerable quantitative component (mathematics, physics, computer science, engineering). They must be able to evidence excellent mathematical and computer programming skills, a willingness to work across multi-disciplinary boundaries, including physical geography and microbiology.

Full studentships are available to UK/EU candidates who’ve been ordinarily resident in the UK throughout the 3-year period immediately preceding the date of an award. EU candidates who’ve not been resident in the UK for the last 3-years are eligible for “tuition fees-only” awards (no maintenance grant).

PhD opportunity: Tunable zinc responsive bacterial promoters for controlled gene expression


Tunable zinc responsive bacterial promoters for controlled gene expression

Supervisory Team: Dr Jon Hobman (School of Biosciences), Dr Phil Hill (School of Biosciences), Dr Dov Stekel (School of Biosciences).

Applications are invited for this 4-year PhD project which is part of a University-funded Doctoral Training Programme (DTP) in Synthetic Biology and associated with Nottingham’s new BBSRC/EPSRC Synthetic Biology Research Centre. Students will benefit from a diverse range of training opportunities, including specialist workshops, lectures and seminars, as well as participation in Nottingham’s yearly BBSRC DTP Spring School event.

Zinc is an essential metal, required in ~30% of bacterial proteins, but is toxic at higher intracellular concentrations. Bacteria such as E. coli have evolved sophisticated zinc import and export systems controlled by transcription factors that repress the expression of genes encoding importer proteins (regulator Zur) or activate expression of zinc efflux (regulator ZntR). These regulators and the promoters they control represent a good example of fine tuning of cellular response to external zinc concentrations (1) and different Zur and ZntR regulated promoters have different affinities and transcription levels. The aim of this PhD will be to study the levels of expression from engineered Zur and ZntR regulated promoters in response to zinc, so that a suite of promoters can be used to finely control gene expression in response to zinc levels in growth media. These promoters will be used to control gene expression in engineered bacteria using cheap zinc inducers and zinc chelators, and will allow tuned expression of industrially useful synthetic pathways in E. coli and other Gram-negative bacteria. These tunable promoters could have potential impact in a range of biotechnology/biosynthesis contexts.

The project is available from 1st October 2016 and is open to UK and EU students with a 2(i) degree or above in microbiology, genetics, biochemistry, or a related discipline. The work will be based at the School of Biosciences in Nottingham.

The supervision team for this project is multi-disciplinary, enabling training in a wide-range of subjects and techniques in microbiology, molecular biology, cell engineering, reporter gene systems, mathematical modelling, data analysis, and cell metabolism.

Applicants should submit a covering letter, CV and the names of two academic referees addressed to: Rob Johnston School Administrator

Closing date for applications: 31st July 2016

Informal enquiries to Dr Jon Hobman ( )

(1)       Takahashi et al (2015). Journal of the Royal Society Interface 12: 20150069


PhD opportunities at the University of Nottingham

The University of Nottingham and the Rothamsted Research Institute are now advertising for 42 fully funded four-year PhD places in their Doctoral Training Partnership. For applicants with a maths, physics or computing background interested in mathematical / computational biology, there are opportunities in all three themes to become involved in world-leading bioscience research. There are three projects on which I would be a second / third supervisor.

  1. Bayesian Inference for Dynamical Systems: From Parameter Estimation to Experimental Design with Theodore Kypraios (maths) as main supervisor. This project will be entirely mathematical / computational.
  2. The role of a novel zinc uptake system (C1265-7) in uropathogenic E. coli, with Jon Hobman as main supervisor. This project will be mostly experimental, but could involve a mathematical modelling component should the student be interested.
  3. Tunable zinc responsive bacterial promoters for controlled gene expression in E. coli, with Phil Hill as main supervisor. This project will be mostly experimental, but could involve a mathematical modelling component should the student be interested.

For more information, please visit the advert site on