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KESS2 East PhD in Rapid Pathogen Detection: Universal sample preparation platform for rapid diagnosis of infection

This funding opportunity has expired.

Key facts

Application deadline 31 July 2019
Start date 1 October 2019
Duration 3 years
Funding body KESS
Level of study Postgraduate research
Award type PhD studentship
Number of studentships One

This PhD studentship will focus on the development of a rapid microwave based system to extract DNA from clinical samples.

Background

In order to make biomarkers available for detection, target DNA must be extracted from the clinical sample. Sputum is a complex mixture of organic material which contains a mixture of mucus, food debris and lung derived cells some of which contain bacteria trapped within.

The distribution of these bacteria in the sample is uneven, making it challenging to detect the presence of target DNA. Indeed, increasing the amount of sample processed increases the chance of detecting the biomarker.

Project aims and methods

To address this issue, we will develop a sample processing cartridge which will employ ultrasound to homogenize the sample, followed by exposure to pulsed microwaves of around 10 W rms power to release the DNA biomarkers from bacteria containing cells into the surrounding medium.

In this part of the extraction process, the duty cycle of the pulsed microwaves will be used to prevent heating, which might otherwise denature the target DNA. The released single stranded DNA will then be captured by specific DNA probes chemically linked to the surface of magnetite beads (a streptavidin/biotin system).

An electromagnet will then be used to recover the beads and their DNA cargo from the organic material. Following washing to remove extraneous organic material, the retained beads will be heated to 60°C to cause detachment of the target DNA. This detachment could be performed via directed microwave heating, or use conventional heating methods.

To achieve the objective, we have identified the following three work packages (WP):

  • WP1. Design the sample processing  cartridge and create prototypes
  • WP2. Identify the nanoparticle DNA probe combinations which maximise the recovery of target DNA from microwaved samples.
  • WP3. Identify the cartridge/ nanoparticle combination which maximises target DNA recovery in a form compatible with a lateral flow assay

The outputs from WP1 and WP2 will be combined to identify the approach which maximises the recovery of target DNA. This will be determined using simulated clinical samples spiked with known concentrations of Mycobacteria. The level of sensitivity achieved will be compared to that seen using stand microscopy based screening (ZN).

The industrial partner Microchip will support the activities in WP 1 and WP2 ensuring manufacturability and suitability for volume assembly. They will also support the design and assembly of microwave control and actuation.

Contact

Professor Les Baillie

Professor Les Baillie

Professor of Microbiology

Email:
bailliel@cardiff.ac.uk
Telephone:
+44 (0)29 2087 5535

Funding details

Tuition fee support Full UK/EU tuition fees
Maintenance stipend A stipend of at least £14,628 per year for PhD studentships (exact figures subject to confirmation of start date) will be offered.
Additional funding offered £3,000 per year for consumables, training, travel and small equipment costs.

Eligibility criteria

Residency UK Research Council eligibility conditions apply
Academic criteria

You are expected to have one or both of:

  • a first degree, normally with class 2:1 or higher, or equivalent in a relevant subject
  • a relevant Master's qualification or equivalent

You must:

  • have a home or work address in the East Wales at the time of your application for KESS2 funding and your enrolment for the course of study
  • have a legal right to live and work in the UK for the duration of the KESS2 support, and the right to take up paid work in the East Wales region on completion of the scholarship
  • classified as a ‘home’ or ‘EU’ student.

You must be able to provide documentary evidence of a home or work address in the East Wales region of Wales at the time of your KESS2 application and enrolment for study.

The ‘East Wales’ region is made up of the following seven local authorities: Flintshire, Wrexham, Powys, Monmouthshire, Newport, Cardiff and Vale of Glamorgan.

Contact

Professor Les Baillie

Professor Les Baillie

Professor of Microbiology

Email:
bailliel@cardiff.ac.uk
Telephone:
+44 (0)29 2087 5535

Consideration is automatic on applying for the PhD in Pharmacy and Pharmaceutical Sciences with a start date of October 2019.

In the 'Research proposal and Funding' section of your online application, please specify the project title and supervisors of this project and copy the project description in the text box provided.

Please select 'No, I am not self-funding my research' when asked whether you are self-funding your research.

Please add 'KESS2 East PhD in Rapid Pathogen Detection: Universal sample preparation platform for rapid diagnosis of infection' when asked 'Please provide the name of the funding you are applying for'.

We reserve the right to close applications early should sufficient applications be received.

Contact

Professor Les Baillie

Professor Les Baillie

Professor of Microbiology

Email:
bailliel@cardiff.ac.uk
Telephone:
+44 (0)29 2087 5535

Eligible research programmes