Dr S Holden
Dr Boguslaw Obara
No more applications being accepted
Competition Funded PhD Project (European/UK Students Only)
We are looking for an outstanding physical/ computational scientist to develop cutting edge microscopy and quantitative imaging tools for high resolution imaging of bacterial biofilms.
Biofilms are dense, spatially complex communities of bacteria enclosed in a polymer matrix. Over 65% of all human infections are estimated to be biofilm-related, include cystic-fibrosis related Pseudomonas aeruginosa lung infections and Escherichia coli urinary tract infections. Although the complex structure of biofilms is responsible for their remarkable robustness, our understanding of the developmental and physical principles which determine biofilm structure is currently very limited. One important reason for this is that it is currently difficult to observe the development of a biofilm at sufficient resolution. To solve this, we need to build tools to observe how a micron sized bacterium multiplies and differentiates into a highly structured millimetre scale community.
During this PhD you will establish widely useful microscopy and image processing tools for biofilm imaging. You will perform single cell resolution microscopy of biofilms as they grow and develop. You will then develop open source image analysis tools and software for high resolution 3D bacterial cell segmentation and lineage tracing using deep learning to achieve high robustness and sensitivity.
The outcome of this project will be widely useful open source software & open science protocols for tracing bacterial development in structured biofilm communities via microscopy.
What will you be doing for your PhD research?
You will perform highly interdisciplinary work, working on both quantitative bioimaging (biophysics & computer science) and microbiology. This will include using advanced microscopy and microfluidics to image the development of biofilms at single cell resolution, and developing new image processing methods for three dimensional single cell lineage tracing of growing bacteria in space and time.
This work will be primarily be performed between the Holden lab at Newcastle (https://blogs.ncl.ac.uk/seamusholden/), experts in advanced microscopy & biophysics, and the Obara lab at Durham (http://community.dur.ac.uk/boguslaw.obara/), experts in image processing & computer science. This work will be performed in collaboration with excellent biofilm biologists: Dr Nick Jakubowics (Newcastle), Professor Miguel Camara (Nottingham), Dr Jo Fothergill (Liverpool).
What training will you receive?
You will join an exciting multidisciplinary collaboration with expertise in advanced microscopy, image processing, machine learning and biofilm microbiology. You will gain experience of each of these disciplines, with primary focus on advanced microscopy, image processing and machine learning.
Is this project right for you?
We are seeking someone from the physical or computational sciences (eg. physics, computer science, engineering) with an interest in software and hardware development and a good degree (BSc/MSci 2(1) or above, or MSc). Enthusiasm for working in interdisciplinary environments, and a desire to learn about biological systems is a must. However, previous experience in the biological sciences is not required.
This project could also suit someone from the biological sciences with demonstrable strong interdisciplinary expertise (eg in computer science, biophysics or software development).
Benefits of being in the DiMeN DTP:
This project is part of the Discovery Medicine North Doctoral Training Partnership (DiMeN DTP), a diverse community of PhD students across the North of England researching the major health problems facing the world today. Our partner institutions (Universities of Leeds, Liverpool, Newcastle and Sheffield) are internationally recognised as centres of research excellence and can offer you access to state-of the-art facilities to deliver high impact research.
We are very proud of our student-centred ethos and committed to supporting you throughout your PhD. As part of the DTP, we offer bespoke training in key skills sought after in early career researchers, as well as opportunities to broaden your career horizons in a range of non-academic sectors.
Being funded by the MRC means you can access additional funding for research placements, international training opportunities or internships in science policy, science communication and beyond. See how our current DiMeN students have benefited from this funding here: http://www.dimen.org.uk/overview/student-profiles/flexible-supplement-awards
Further information on the programme can be found on our website:
Studentships are fully funded by the Medical Research Council (MRC) for 3.5yrs
Stipend at national UKRI standard rate
Research training and support grant (RTSG)
Studentships commence: 1st October 2019.
To qualify, you must be a UK or EU citizen who has been resident in the UK/EU for 3 years prior to commencement. Applicants must have obtained, or be about to obtain, at least a 2.1 honours degree (or equivalent) in a relevant subject. All applications are scored blindly based on merit. Please read additional guidance here: https://goo.gl/8YfJf8
• Seamus Holden, Thomas Pengo, Karin Meibom, Carmen Fernandez-Fernandez, Justine Collier, Suliana Manley. High throughput 3D super-resolution microscopy reveals Caulobacter crescentus in vivo Z-ring organization. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, 111, 4566-4571 (2014).
• C. Willcocks, P. T. G. Jackson, C. J. Nelson, A. Nasrulloh, and B. Obara, "Interactive GPU Active Contours for Segmenting Inhomogeneous Objects," JOURNAL OF REAL-TIME IMAGE PROCESSING, pp. 1-14, 2017.
• Rampioni, Giordano, Falcone, Marilena, Heeb, Stephan, Frangipani, Emanuela, Fletcher, Matthew P., Dubern, Jean-Frederic, Visca, Paolo, Leoni, Livia, Camara, Miguel and Williams, Paul, 2016. Unravelling the Genome-Wide Contributions of Specific 2-Alkyl-4-Quinolones and PqsE to Quorum Sensing in Pseudomonas aeruginosa PLOS PATHOGENS. 12(11), 6029-6029
How good is research at Newcastle University in Biological Sciences?
FTE Category A staff submitted: 30.60
Research output data provided by the Research Excellence Framework (REF)
Click here to see the results for all UK universities