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In-field pathogen detection and genotyping using CRISPR/Cas biosensing technology

  • Full or part time
  • Application Deadline
    Sunday, April 07, 2019
  • Funded PhD Project (Students Worldwide)
    Funded PhD Project (Students Worldwide)

Project Description

CRISPR/Cas systems have the potential to become the next-generation diagnostic biosensing platforms; they are sensitive, specific and can discriminate at a single DNA base-pair level of resolution. Furthermore, they can be multiplexed, enabling a single diagnostic test to identify the presence of multiple targets. Coupling of the CRISPR/Cas detection with lateral flow device-based signal readout, will allow for the highly sensitive and accurate in-field detection of pathogens.


The requirement of a rapid in-field, sensitive, specific assay which can also be quantitative, detect SNPs (Single nucleotide polymorphisms) and be multiplexed has yet to be achieved. A technology with these capabilities would have application across multiple industries, including agronomy to statutory inspection (Plant health and seeds inspectors), GM testing, food authenticity and biothreat detection. CRISPR/Cas biosensing systems have recently been developed by the Broad Institute for the detection of Zika virus and Dengue virus using a paper dip stick device to detect a single molecule in a 250 µl sample. CRISPR proteins Cas13 and Cas12a can be used to link the detection of specific target with cleavage (and induced fluorescence) of RNA or DNA based reporters, respectively. Guide RNAs are designed to be specific for the target pathogen DNA, binding to which enables Cas-based cutting of the target. This induced cutting has ‘collateral’ activity, enabling the reporter to be cut and detected (either by fluorescence, or antibody-based techniques). This system requires no expensive reagents and no special instruments, making it low cost and easily accessible for nucleic acid detection.

Full Project Description

How to apply

You must apply through the University’s online postgraduate application form. Only mandatory fields need to be completed. However, you will need to include the following information:

• insert the programme code 8020F in the programme of study section
• select ‘PhD in Biology (FT)’ as the programme of study
• insert the studentship code IAFRI-06 in the studentship/partnership reference field
• attach a covering letter and CV. The covering letter must state the title of the project, quote reference code IAFRI-06 and state how your interests and experience relate to the project
• attach degree transcripts and certificates and, if English is not your first language, a copy of your English language qualifications

You should also send a covering letter and CV to Mr Steven Hall (e-mail to )

The online application system will only allow one application for an IAFRI studentship. If you are applying for TWO projects then you will need to e-mail Postgraduate Admissions and Steven Hall with the following information:

-your applicant number (from the first project application)
-the second project title
-a two page covering letter for the second project
Please also include 'IAFRI-06' in the email header

Funding Notes

There are five studentships available from 10 projects to choose from based on the current themes.
Students will be based at either Newcastle University or Fera Science Ltd in York. Each award provides a 3 year PhD with 100% tuition fees at UK/EU rate plus an annual stipend (minimum £15,009) Successful non-EU international students will be required to make up the difference between the UK/EU fees and international fees.

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