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EASTBIO Non-invasive Mapping of Oxygen Extraction Fraction in Human: Development of Novel Multi-Parametric Magnetic Resonance Relaxometry Imaging Methods.

School of Medicine, Medical Sciences & Nutrition

Dr J He , Prof V Speirs , Dr Yazan Masannat Wednesday, January 06, 2021 Competition Funded PhD Project (Students Worldwide)

About the Project


Dr Jiabao He (University of Aberdeen)

Professor Valerie Speirs (University of Aberdeen)

Dr Yazan Masannat (University of Aberdeen)

This project aims to develop and optimise quantitative oxygen extraction fraction mapping based on oxygen enriched air inspiration and magnetic resonance (MR) relaxometry imaging for the investigation of aerobic glycolysis. This underpinning bioimaging method will be pivotal in the the understanding of in vivo mitochondrial function and surrounding cellular environment, fundamental in discerning the of hypoxia in cellular expression.

Oxygen is essential to the aerobic energy production, while anaerobic energy production is employed under insufficient oxygen supply. The anaerobic pathway is not only inefficient in terms of amount of energy produced, but also alters the pH affecting skeletal muscle performance. Deteriorated musculoskeletal function associated with fatigue, present compromised skeletal muscle energy regulation and inadequate pH handling. Our previous work has shown that single dose of dietary nitrate (in the form of 7cl concentrated beetroot juice) can reduce skeletal muscle oxygen deficit1, underscoring its sports performance enhancement function.

MR imaging is a promising powerful non-invasive method for assessing tissue oxygen level. Since deoxyhaemoglobin is paramagnetic, generating local field disturbance inside MR scanner, both the rate of signal dissipation (R2*) and the rate of tissue re-magnetisation (R1*) increases with the concentration of deoxyhaemoglobin. However, these methods are qualitative in nature, with R1* measurement influenced by hardware imperfection. Recently, a method based on the employment of inspiration of oxygen enriched air in conjunction with the observation of R1* was successfully developed and demonstrated, allowing quantitative assessment of oxygen extraction fraction2. However, R1* measurement is lengthy compared to R2* assessment, limiting the observation to static system. While several acceleration methods are available (namely Look-Locker, fast reordering and DESPOT1 methods)3.

We are seeking a highly motivated student, with a background in quantitative discipline, to join our vibrant multidisciplinary team. The successful candidate will conduct literature review, three main workpackages and thesis writing. The workpackages include:
• development and optimisation of R1* and R2* acquisition schemes to establish accuracy and robustness,
• development and optimisation of data feature extraction algorithms for the effective combination of R1* and R2* data,
• implementation and validation of this new acquisition approach on our state of the art MR scanner.

Aberdeen has a long tradition in bioimaging, and has the infrastructure for in vivo imaging with sophisticated experimental setup. The multidisciplinary investigation team has extensive experience and strong track record in the development and application of novel MR methods, in vivo imaging application, cellular biology, and scanner hardware analysis and programming. The successful candidate will be guided by Dr Jiabao He on imaging science, Prof Valerie Speirs on cellular biology, and Dr Yazan Masannat on impact generation.

The student will receive training in:
• theory of MRI and relaxometry, a rapidly expanding area essential for in vivo human biological research,
• implementation of imaging acquisition methodologies and analysis approaches, highly sought after skillsets,
• large data management, visualisation and information extraction, critical in modern biology,
• mitochondrial function and the oxygen consumption pathways,
• generic skills of academic writing, presentation and project management.

Application Procedure:

Please send your completed EASTBIO application form, along with academic transcripts to Alison McLeod at . Two references should be provided by the deadline using the EASTBIO reference form. Please advise your referees to return the reference form to .

Funding Notes

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership View Website. This opportunity is open to UK and International students and provides funding to cover stipend and UK level tuition (limited funding is available to provide international tuition fees). Please refer to UKRI website and Annex B of the UKRI Training Grant Terms and Conditions for full eligibility criteria.

Candidates should have (or expect to achieve) a minimum of a 2:1 UK Honours degree, or the equivalent qualifications gained outside the UK, in a relevant subject.


1. Bentley, R., Gray, S. R., Schwarzbauer, C., et al. (2014). Dietary nitrate reduces skeletal muscle oxygenation response to physical exercise: a quantitative muscle functional MRI study. Physiological Reports, 2(7), e12089–e12089.
2. Beeman, S. C., Shui, Y.-B., Perez-Torres, C. J., Engelbach, J. A., Ackerman, J. J. H., & Garbow, J. R. (2016). O2 -sensitive MRI distinguishes brain tumor versus radiation necrosis in murine models. Magnetic Resonance in Medicine, 75(6), 2442–2447.
3. Eldeniz, C., Finsterbusch, J., Lin, W., & An, H. (2016). TOWERS: T-One with Enhanced Robustness and Speed. Magnetic Resonance in Medicine, 76(1), 118–126.

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