Imaging and Sensing the Interactions Between Bacteria and Viruses Using Cutting Edge Optical Techniques - Physics - EPSRC DTP funded PhD Studentship

About the award
This project is one of a number funded by the Engineering and Physical Sciences Research Council (EPSRC) Doctoral Training Partnership to commence in September 2018. This project is in direct competition with others for funding; the projects which receive the best applicants will be awarded the funding.

The studentships will provide funding for a stipend which is currently £14,553 per annum for 2017-2018. It will provide research costs and UK/EU tuition fees at Research Council UK rates for 42 months (3.5 years) for full-time students, pro rata for part-time students.

Please note that of the total number of projects within the competition, up to 15 studentships will be filled.

Location
Streatham Campus, Exeter

Project Description
Bacteria and their viruses (phage) are engaged in a never-ending arms race. The CRISPR-Cas adaptive immune system plays a key role in defending bacteria against their viral predators. However, some viruses can overcome bacterial immunity using anti-CRISPR genes that block the host immune system. This project will use state of the art microscopy techniques to monitor the interaction between the bacterial immune system and viral anti-CRISPR proteins.

Understanding bacteria-virus infection dynamics is vital across multiple research domains, from predicting impact on biogeochemical cycles to using phage therapy as an alternative to antibiotics. However, the current tools for studying host-virus interactions mostly relies on bulk assays, which lacks the resolution to link macroscopic processes to the underlying molecular and individual-level interactions.

The student will use microscopy techniques to address key questions concerning the interactions between bacteria with CRISPR resistance and phage encoding anti-CRISPR genes. Specifically, the student will use a combination of photolithography (Physics Department) and soft lithography techniques to fabricate microfluidic devices to be interfaced and programmed in the microfluidic facility in Biosciences. This will allow the student to trap up to thousands of Escherichia coli or Pseudomonas aeruginosa bacteria and fully control the microfluidic environment around them. He/she will then introduce a known concentration of fluorescently labelled phages via microfluidics and image in real time the different phases of bacteria-phage interaction with both single-bacterium and single-phage resolution. He/she will perform quantitative image analysis to extract information about phage invasion. This will allow us to obtain information on the dynamics of phage invasion and propagation and measure host mortality and phage replication rates.

The student will also learn how to design, fabricate and handle state of the art optical micro-sensors (whispering gallery modes sensors), to detect bacteria and monitor their interactions with a phage (1, 2). The label-free method is applied to monitor the different stages of the infection cycle, from the entry of the virus, virus replication, to the lysis of individual hosts. Analysis of the phage-bacteria dynamics allows us to characterise the adaptive immunity of CRISPR-Cas at a systems level, and complements the fluorescence imaging studies with label-free sensor data. Without the need for a label, the native host-phage interactions can be studied for prolonged times and over multiple infection cycles and with a high temporal resolution. The whispering gallery mode detection technology may also lead the development of next generation of bacterial biochips, for the rapid detection of virus particles with a detection specificity that can be programmed by CRISPR-Cas.

This interdisciplinary project encompassing microbiology, biophysics, label-free sensing/imaging and engineering aims to develop lab-on-a-chip and bio-sensing technologies with the specific goal of quantifying phage-bacteria interactions.
During this 3.5 year studentship, the PhD student will benefit from supervision from Prof Vollmer’s, who recently developed the label free sensing techniques, Dr Pagliara’s who developed microfluidic devices and protocols to investigate bacterial response to environmental perturbation (for example exposure to antibiotics) with single-cell resolution, and Dr Westra who has been studying molecular and evolutionary aspects of CRISPR-Cas immune systems for the past decade.

Entry Requirements
The majority of the studentships are available for applicants who are ordinarily resident in the UK and are classed as UK/EU for tuition fee purposes. If you have not resided in the UK for at least 3 years prior to the start of the studentship, you are not eligible for a maintenance allowance so you would need an alternative source of funding for living costs. To be eligible for fees-only funding you must be ordinarily resident in a member state of the EU.

Applicants who are classed as International for tuition fee purposes are NOT eligible for funding. International students interested in studying at the University of Exeter should search our funding database for alternative options.