Welcome to Michelle Baker and Henry Todman

We are delighted to welcome two new lab members this month, Michelle Baker and Henry Todman. Both Michelle and Henry are joint appointments with the School of Mathematics, co-supervised with Theo Kypraios.

Michelle has rejoined our lab, following a post-doc with Jamie Twycross and Liz Sockett. Michelle’s previous stint with us was very productive, leading to our first AMR slurry modelling paper, which I am sure contributed to our grant success. Michelle will be with us for two years. Michelle writes:

I am a post-doctoral researcher in the field of mathematical biology, and am particularly interested in the study of bacteria and antibiotic resistance. I work in the EVAL-FARMS project using mathematical modelling to investigate the risk of emergence of antibiotic resistance from agricultural slurries. This interdisciplinary project allows me to work alongside experts from a wide range of disciplines to tackle the problem in an integrated way and to produce high quality research.

I completed my PhD in Mathematics here at the University of Nottingham, focussed on cytokine dynamics in arthritic disease. After completing my PhD I took up a research position supervised by Prof Liz Sockett and Dr Jamie Twycross, investigating the potential of predatory bacteria to be used as ‘living antibiotics’.

Henry Todman has joined us as a four year PhD student associated with the EVAL-FARMS project. Henry writes:

I am a mathematical modelling PhD student working with Dov, Theo Kypraios and Michelle Baker. My PhD research will primarily look at developing new mathematical models to assess the risks of bacterial population carrying antimicrobial resistance genes and fitting these models to experimental data produced from the EVAL-FARMS project. 

Prior to beginning my PhD, I studied Mathematics at the University of Warwick for my undergraduate degree, and also completed an MSc in Mathematical Medicine and Biology at the University of Nottingham. Over the course of my MSc I was exposed to a wide range of current research topics in mathematical biology, however, it was antimicrobial resistance that immediately captured my interest. This led me to complete my dissertation on the phage-mediated spread of AMR, and I am now eager to pursue this topic even further in my PhD.

Outside of work, I am a keen climber and you will often find me hanging off some rock in the Peak District, or taking part in bouldering competitions around the country.



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 Robert.Johnston@nottingham.ac.uk

Closing date for applications: 31st July 2016

Informal enquiries to Dr Jon Hobman ( Jon.Hobman@nottingham.co.uk )

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


Welcome to Anna Swan, Mengyuan Yu and Sophie Patel

Three new people have joined the laboratory recently.

Anna Swan is in the final year of her PhD. Anna writes of herself:

I am currently a PhD student, having started in 2010, working on the bioinformatics analysis of omics data from models of articular cartilage with the aim to identify biomarkers for Osteoarthritis. I have focussed largely on the analysis of proteomics data, generated by mass spectrometry, and the application of machine learning to such data. Machine learning, particularly rule-based methods, have been used for both classification of samples and identification of putative biomarkers. I am funded by a BBSRC Case studentship and Waltham Centre for Pet Nutrition (Mars).

Prior to starting my PhD, I completed a BSc in Biological Sciences at the University of Reading (2009) and an MSc in Applied Bioinformatics at Cranfield University (2010). I also spent some time working at Genetix (now Molecular Sciences) as a laboratory scientist, working in mammalian cell culture and on the development of a cell imaging platform.

Mengyuan Yu and Sophie Patel join the lab as undergraduate project students. Both Mengyuan and Sophie are final year students studying Environmental Science. Mengyuan will be modelling production and flow of nitrates in dairy slurry, making use of the dairy farm at Sutton Bonington. Sophie will be analyzing camera trap data from the Malaysian rain forest, based on data she has captured from a summer project with Ahimsa Campos-Arceiz at the University of Nottingham, Malaysia.

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 findaphd.com