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MRC DiMeN Doctoral Training Partnership: New treatments for antimicrobial resistant TB via modulation of innate immunity

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  • Full or part time
    Dr P Elks
    Prof S Renshaw
    Dr V See
  • Application Deadline
    No more applications being accepted
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Neutrophils are the most abundant white blood cell type and are able to directly kill invading pathogens using a powerful artillery at their disposal. However, they are classically seen as being a blunt tool against infection that can cause surrounding tissue damage and chronic inflammatory diseases.
Our disease of interest is tuberculosis (TB), a bacterial infection on the rise due to the increasing prevalence of antimicrobial resistance. The roles of the neutrophil in TB control remain unclear. We use the zebrafish embryo infected with Mycobacterium marinum (Mm, fish TB) in combination with a tailfin inflammation model to understand how infection and inflammation are managed in an individual organism in vivo.

Our lab has a focus on genetic hypoxia signalling (via the transcription factor Hif-alpha). Hif-1alpha stabilisation protects against infection but also leads to prolonged neutrophil inflammation, negatively affecting inflammation and tissue remodelling (Elks et al., 2013. Two Hif-alpha variants, Hif-1alpha and Hif-2alpha, have opposing effects on neutrophil antimicrobial activity but have a similar effects on neutrophil behaviour during inflammation.

In this project we aim to understand whether neutrophils can be molecularly tuned, by modulating Hif-1alpha and Hif-2alpha appropriately, to better kill infection while not causing excess inflammation.
Specifically, we aim to address:
1. How Hif-alpha signalling alters neutrophil migratory behaviours and decision making to sites of a wound or infection in the same individual in a dual infection and inflammation model.
2. Whether Hif-alpha variants can be modulated to improve infection outcomes without negative inflammatory effects.
The dual infection and inflammation model is recently developed in the lab and has so far produced exciting results that require a PhD student to take it forwards. Neutrophil migratory behaviour will be assessed in the in vivo zebrafish using timelapse fluorescence microscopy to observe decision making between infection and wounds after Hif-alpha variant manipulation. Links between Hif-alpha signalling and neutrophil phenomena including neutrophil swarming and NET (neutrophil extracellular trap) formation will be explored to uncover novel molecular mechanisms.
Hif-1alpha and Hif-2alpha will be modulated using dominant constructs and novel neutrophil specific CRISPRi (CRISPR mediated interference) to assess the outcomes of infection and inflammation in the dual model. The downstream targets of Hif-1alpha and Hif-2alpha will be assessed by FACs sorting of neutrophils from Hif-alpha modulated embryos and performing RNAseq analysis.
The findings from these studies will identify which Hif-alpha isoforms and downstream effectors in neutrophils are potential therapeutic targets against antimicrobial resistant TB.

This work will take place in a young and vibrant research group ( The student will be trained in a variety of lab techniques including molecular biology and microscopy, with further diverse training opportunities via the DTP.

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 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, attending international training opportunities and internships in science policy, science communication and beyond.
See how our current DiMeN students have benefitted from this funding here:
Further information on the programme can be found on our website:

Funding Notes

Studentships are fully funded by the Medical Research Council (MRC) for 3.5yrs
Stipend at national UKRI standard rate
Tuition fees
Research training and support grant (RTSG)
Travel allowance
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 these additional guidance here:
Good luck.


1. Ogryzko N, Lewis A, Wilson HL, Meijer AH, Renshaw SR, Elks PM (2018) Hif-1alpha induced expression of Il-1beta protects against mycobacterial infection in zebrafish. JI in press, (available on BioRXiv,

2. Ellett F, Elks PM, Robertson AL, Ogryzko NV, Renshaw SA (2015) Defining the phenotype of neutrophils following reverse migration in zebrafish. J Leukoc Biol. 2015 Jun 12. pii: jlb.3MA0315-105R.

3. Elks PM, Brizee S, van der Vaart M, Walmsley SR, van Eeden FJ, Renshaw SA, Meijer AH (2013) Hypoxia inducible factor signaling modulates susceptibility to mycobacterial infection via a nitric oxide dependent mechanism.. PLoS Pathog, 9(12), e1003789.

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