BBSRC SWBio DTP PhD studentship: Novel microfluidic technologies for single bacterium RNA-sequencing Ref: 2334

About the award


The South West Biosciences Doctoral Training Partnership

The South West Biosciences Doctoral Training Partnership (SWBio DTP) is a BBSRC-funded PhD training programme in the biosciences, delivered by a consortium comprising the Universities of Bristol (lead), Bath, Cardiff, Exeter, and Rothamsted Research. Together, these institutions present a distinctive cadre of bioscience research staff and students with established international, national and regional networks and widely recognised research excellence. The partnership has a strong track record in advancing knowledge through high quality research and teaching in partnership with industry and government.

The aim of the SWBio DTP is to produce highly motivated and excellently trained postgraduates in the BBSRC priority areas of Agriculture & Food Security (AFS) and World-Class Underpinning Bioscience (WCUB). These are growth areas of the biosciences and for which there will be considerable future demand.


The award

This project is one of a number that are in competition for funding from the South West Biosciences Doctoral Training Partnership (SWBio DTP).  Up to 4 fully-funded studentships are being offered to start in September 2017 at the University of Exeter.

For UK/EU nationals who meet the residency requirements outlined by the BBSRC, the studentship will cover funding for 4 years (48 months) as follows.  These awards might be available to part-time students, but only in exceptional circumstances, in which case the funding will be paid on a pro-rata basis.

•    a stipend at the standard Research Council UK rate; currently £14,296 per annum for 2016-2017

•    research and training costs

•    tuition fees (at the standard Research Councils UK rate

•    additional funds to support fieldwork, conferences and a 3-month internship


Further information about eligibility can be found in the BBSRC Guide to Studentship Eligibility.   


Academic Supervisors:

Main supervisor: Dr Stefano Pagliara, University of Exeter

Co-supervisor:  Dr Thomas Connor, University of Cardiff

Co-supervisor: Prof John Love, University of Exeter

Co-supervisor: Dr Konrad Paszkiewicz, University of Exeter



University of Exeter, Streatham Campus, Exeter


Project Description:

We have recently begun to understand that there is considerable variation in phenotype between bacterial cells in a population – even when they share a common genetic heritage. For example, across a population of a bacterium commonly found in our intestine, some cells grow much more slowly than others while some cells are able to survive antibiotic drugs that kill the rest of the population. The basis of this variation is not understood as our ability to compare individual cells is still limited. This project aims to change that.

The transcriptome is the set of all messenger RNA molecules in a cell and determines the function of each cell. If we want to be able to understand variation in phenotype between otherwise identical cells, we need to study the transcriptome of individual cells. This is currently possible for eukaryotic cells with single-cell RNA-sequencing (Kolodziejczyk 2015, Mol Cell 58:610) and the help of a commercially available instrument based on integrated fluidic circuits ( Unfortunately, there is not an equivalent instrument for studying prokaryotic cells, thus limiting our understanding to population transcriptomic measurements that mask the features of rare but important subsets of cells.

Dr Pagliara’s laboratory has extensive experience in microfluidics (Pagliara 2014, Nat Mater 13:638) and is currently using the microfluidic mother machine technology ( to image individual Escherichia coli bacteria and study the expression of selected genes of interest by using reporter-gene fusions. You will build on this expertise to develop microfluidic devices capable of capturing single bacteria and prepare their lysate for off chip RNA-sequencing. This will allow us to obtain unprecedented understanding on the heterogeneity in gene expression in bacterial cells and how this links with cell-to-cell phenotypic differences in growth and resistance to stress, such as antibiotic exposure.

You will receive a unique and comprehensive training including fabrication of devices with micrometer features, handling of microfluidics, fluorescence-activated cell sorting technologies, imaging via bright- field and fluorescence microscopy, programming image analysis software, handling microbial cultures, constructing reporter-gene fusions, extracting nucleic acids and preparing cDNA libraries, transcriptomic analysis and bioinformatics.


Entry requirements:

Applicants should have obtained, or be about to obtain, a First or Upper Second Class UK Honours degree, or the equivalent qualifications gained outside the UK, in an appropriate area of science or technology.  Applicants with a Lower Second Class degree will be considered if they also have Masters degree or have significant relevant non-academic experience. In addition, due to the strong mathematical component of the taught course in the first year and the quantitative emphasis in our projects, a minimum of a grade B in A-level Maths or an equivalent qualification or experience is required.  If English is not your first language you will need to have achieved at least 6.5 in IELTS and no less than 6.5 in any section by the start of the project.  Alternative tests may be acceptable, please see

Students from EU countries who do not meet the residency requirements may still be eligible for a fees-only award but no stipend.  Applicants who are classed as International for tuition fee purposes are not eligible for funding.  Further information about eligibility can be found in the following document:


Selection process

Please note, the studentship selection process will take place in two stages:

1.     The project supervisors will consider your application and may invite you to visit for an informal interview. You can apply for more than one BBSRC SWBio DTP project, although supervisors may take into account your interest and commitment to their particular project.  If you apply for multiple projects, please indicate your preferred project choice in your letter of application.  Each application for an individual project will be considered separately by the project supervisors.

2.     After closure of applications, each supervisory team will then nominate their preferred applicant.  A shortlist will be selected from these nominations and shortlisted applicants will be invited for interview on a selection day at the University of Exeter.  Please note that nomination by a project supervisor therefore does not guarantee the award of a studentship.


Application deadline:5th December 2016
Value:£14,296 per annum for 2016-17
Duration of award:per year
Contact: CLES PGR Team +44 (0) 1392 725150 /

How to apply


Click here to apply


Please be aware you will be asked to upload the following documents:

•         CV

•         Letter of application outlining your academic interests, prior research experience and reasons for wishing to undertake the project.  Please indicate your preferred project choice if applying for multiple BBSRC SWBio DTP projects.

•         Transcript(s) giving full details of subjects studied and grades/marks obtained.  This should be an interim transcript if you are still studying.

•         If you are not a national of a majority English-speaking country you will need to submit evidence of your proficiency in English (see entry requirements above)

You will be asked to name 2 referees as part of the application process however we will not contact these people until the shortlisting stage. Your referees should not be from the prospective supervisory team.


The closing date for applications is midnight on Monday, 5 December 2016. Interviews will be held at the University of Exeter in early February 2017.


If you have any general enquiries about the application process please email or phone +44 (0)1392 725150 / 723706. Project-specific queries should be directed to the primary supervisor.