Available PhDs

EASTBIO (College of Medicine and Veterinary Medicine) 

Understanding the contribution of reduced niche oxygenation on haematopoiesis during healthy ageing

Applications accepted up till Monday 15th December, 2025.  Competition funded PhD Project. 

Supervisors: Dr Ananda Mirchandani (The University of Edinburgh), Dr Tony Ly (The University of Dundee) 

About the Project

As we age, a common phenomenon across tissues is the loss of capillaries and capillarisation. These tiny vessels are essential for the delivery of oxygen to tissues, as oxygen can only be accessed through its passive diffusion from an area with a higher partial pressure of oxygen, to a lower one. (doi:10.14336/AD.2017.0430). The ageing bone marrow is no different to other organs in this process. A number of key changes have been observed in both the circulating cells and bone marrow composition of healthily ageing individuals. These changes include an increase in the neutrophil:lymphocyte ratio (NLR) (https://doi.org/10.1182/blood-2022-170882), as well as an increase in multipotent stem cell numbers, however the function of these stem cells appears to be defective. Importantly, these observed changes are conserved across species, including in the mouse, making the aged mouse model a useful means to understand and identify the molecular mechanisms that drive this process (doi: 10.1038/s41586-024-07238-x.). 

Data from our lab has identified some overlapping changes induced by acute hypoxia  exposure in young mice, with these ageing changes, including a skewing towards myelopoiesis and a reduction of lymphopoiesis (unpublished) raising the possibility that hypoxia itself could be an important driver of the ageing bone marrow phenotype. Healthy tissue oxygenation has been largely overlooked as an important niche factor, but less so in the bone marrow, where stem cells are known to reside in less oxygenated niches enabling them to maintain quiescence (doi: 10.1038/nature13034). 

This PhD will offer the applicant the opportunity to use mouse models and human bone marrow samples, alongside both in-vivo and ex-vivo oxygen availability manipulation systems, to dissect the contribution of reduced oxygen availability to the ageing bone marrow immune phenotype. To obtain crucial new insights, the PhD student will utilize cutting edge single cell assays that will characterize gene expression and proteome changes with spatial and temporal resolution to understand bone marrow evolution during ageing. The successful candidate will assess the interplay between niche vascularity, oxygen availability and haematopoiesis to determine the molecular mechanisms that drive the changing circulating immune landscape in healthy ageing.

Funding Notes

UKRI-funded studentships are open to students worldwide and will cover tuition fees at the UK rate, plus a stipend to support living costs and an annual research grant of £5,000 for the first three years of the PhD research. The proportion of international students appointed through the EASTBIO DTP is capped at 30%.  All students must meet the eligibility criteria as outlined in the UKRI guidance on UK, EU and international candidates. This guidance should be read in conjunction with the UKRI Training Grant Terms and Conditions

Apply Now 

EASTBIO Webpage (to download the documents required for email application process, detailed below) 

• EASTBIO Application
• Equality, Diversity and Inclusion (EDI) survey
• Reference Forms can be downloaded via link above

Please send your completed EASTBIO Application Form and EDI survey along with a copy of your academic transcripts to CIR.Postgraduate@ed.ac.uk before the deadline. You should also ensure that two references have been sent to CIR.Postgraduate@ed.ac.uk by the deadline using the EASTBIO Reference Form.

The EASTBIO team will run a series of 1-hour online sessions in November/December 2025, open to applicants who have queries about the application process. Please view EASTBIO How to Apply webpage for details. 

Unfortunately due to workload constraints, we cannot consider incomplete applications.

EASTBIO (College of Medicine and Veterinary Medicine) 

Cellular responses to fluid forces: Phases across the ages

Applications accepted up till Monday 15th December, 2025.  Competition funded PhD Project. 

Supervisors: Dr Carsten Gram Hansen (The University of Edinburgh), Dr Tyler Shendruk (The University of Edinburgh), Dr Pierre Bagnaninchi (The University of Edinburgh) 

About the Project

Water is essential for life and the most abundant molecule in the human body, accounting for more than 50% of body weight. Around 15–20% of this is extracellular, mainly interstitial fluid. These fluids, and the hydrostatic pressures they exert, are central to cellular processes in development, inflammation, regeneration, and homeostasis. Fluid forces and phases therefore play vital roles across biology.
This project will uncover how fluids influence biological structures and functions across scales, and how ageing alters these interactions. By combining intrinsic cellular ageing with ageing-induced changes in the microenvironment, we will explore how these stressors impair cellular capacity to respond to stimuli.

Research Challenge

The key challenge is to decipher the heterogeneity in how dynamic fluids influence cells. Such parameters have been difficult to study, but recent advances now allow us to do so. We will combine bioimaging, modelling, and advanced imaging platforms to analyse dynamic cellular behaviours at single-cell resolution.

Objectives

1. Develop imaging pipelines to stratify responses to fluid dynamics.
   We will extract cellular features from confocal and label-free images, enabling classification of cell types and states under different fluidic conditions.
2. Assess responses to microenvironmental change.
   Using models of young and aged microenvironments, we will analyse how cells adapt and correlate these behaviours with genetic and proteomic profiles.
3. Integrate proteomics, modelling, and imaging to identify modular nodes

By linking molecular signatures to phenotypic features captured through bioimaging, we will identify potential targets for genetic or therapeutic intervention.

Approach

The project will be delivered through an interdisciplinary, team-based framework built around these three objectives. We will combine microfluidics, phase-change systems, bioengineering, label-free quantitative phase imaging, and high-content imaging with diverse cellular models. Experimental data will be integrated with fluid simulations to enable predictive and iterative modelling.

Training and Environment

The student will join a supportive interdisciplinary environment, gaining expertise in:

• Biomedical image analysis, omics, genome editing, and molecular biology
• High-content and label-free imaging
• Tissue culture, microfluidics, and bioengineering methods
• Programming with Python/Matlab

The training programme will prepare the candidate for a broad range of career paths in academia, industry, and beyond. They will also participate in outreach, including Science Festivals and Open Doors events, and benefit from professional development workshops offered by the Institute for Academic Development (IAD).

Research Culture

The collaborative setting of the Institute for Regeneration and Repair (IRR; CGH/PB) and the Institute for Condensed Matter and Complex Systems will provide a positive, inclusive research culture. The project’s interdisciplinary and team-focused design ensures the candidate develops both deep technical expertise and cross-disciplinary collaboration skills, equipping them for future success.

Funding Notes

UKRI-funded studentships are open to students worldwide and will cover tuition fees at the UK rate, plus a stipend to support living costs and an annual research grant of £5,000 for the first three years of the PhD research. The proportion of international students appointed through the EASTBIO DTP is capped at 30%.  All students must meet the eligibility criteria as outlined in the UKRI guidance on UK, EU and international candidates. This guidance should be read in conjunction with the UKRI Training Grant Terms and Conditions

Apply Now 

EASTBIO Webpage (to download the documents required for email application process, detailed below) 

• EASTBIO Application
• Equality, Diversity and Inclusion (EDI) survey
• Reference Forms can be downloaded via link above

Please send your completed EASTBIO Application Form and EDI survey along with a copy of your academic transcripts to CIR.Postgraduate@ed.ac.uk before the deadline. You should also ensure that two references have been sent to CIR.Postgraduate@ed.ac.uk by the deadline using the EASTBIO Reference Form.

The EASTBIO team will run a series of 1-hour online sessions in November/December 2025, open to applicants who have queries about the application process. Please view EASTBIO How to Apply webpage for details. 

Unfortunately due to workload constraints, we cannot consider incomplete applications.

EASTBIO (College of Medicine and Veterinary Medicine) 

Establish proximity labelling strategies in zebrafish to capture cellular interactions in vivo 

Applications accepted up till Monday 15th December, 2025.  Competition funded PhD Project. 

Supervisors: Dr Yi Feng (The University of Edinburgh), Dr Mattias Malaguti (The University of Edinburgh)

About the Project

Unravelling the outcomes of cell–cell interactions is fundamental to understanding biological processes. The ability to visualise and track these interactions in vivo greatly enhances our capacity to dissect contact-dependent communication. Synthetic biology approaches, such as the engineered synNotch system, have been successfully applied in models including mouse and fly. Zebrafish larvae, with their translucency, provide a powerful platform for live imaging of cell–cell interactions at subcellular resolution. Using lineage-specific fluorescent reporter fish, we have observed close interactions between oncogene-expressing cells and innate immune cells in vivo and demonstrate that host innate immune cells support early tumour development. However, direct contacts and interactions between emerging oncogene-expressing cells and their immediate neighbours have not yet been visualised in vivo, despite the likelihood that these interactions influence mutant cell progression, either positively or negatively. This project aims to address this gap by generating a suite of proximity-labelling transgenic zebrafish tools including the synNotch system for live imaging of neighbouring cell interactions at tumour initiation. These tools will provide broadly applicable resources for uncovering fundamental mechanisms of cell–cell communication in both development and tumourigenesis.

Funding Notes

UKRI-funded studentships are open to students worldwide and will cover tuition fees at the UK rate, plus a stipend to support living costs and an annual research grant of £5,000 for the first three years of the PhD research. The proportion of international students appointed through the EASTBIO DTP is capped at 30%.  All students must meet the eligibility criteria as outlined in the UKRI guidance on UK, EU and international candidates. This guidance should be read in conjunction with the UKRI Training Grant Terms and Conditions

Apply Now 

EASTBIO Webpage (to download the documents required for email application process, detailed below) 

• EASTBIO Application
• Equality, Diversity and Inclusion (EDI) survey
• Reference Forms can be downloaded via link above

Please send your completed EASTBIO Application Form and EDI survey along with a copy of your academic transcripts to CIR.Postgraduate@ed.ac.uk before the deadline. You should also ensure that two references have been sent to CIR.Postgraduate@ed.ac.uk by the deadline using the EASTBIO Reference Form.

The EASTBIO team will run a series of 1-hour online sessions in November/December 2025, open to applicants who have queries about the application process. Please view EASTBIO How to Apply webpage for details. 

Unfortunately due to workload constraints, we cannot consider incomplete applications.

EASTBIO (College of Medicine and Veterinary Medicine) 

The impact of diet-microbiome-immune interactions on intestinal function

Applications accepted up till Monday 15th December, 2025.  Competition funded PhD Project. 

Supervisors: Dr Chengcan Yao (The University of Edinburgh), Dr Laura Glendinning (The University of Edinburgh), Dr Cecile Benezech (The University of Edinburgh)

About the Project

Maintenance of gut health is determined by a balance among epithelial cell function, proper immune response, and symbiotic microbiota. A disruption in this balance can result in uncontrolled pathological epithelial dysfunction and diseases such as inflammatory bowel disease (IBD) and cancer. Environmental factors and life style, such as diet, smoking, and exercise, significantly impact gut health, although the underlying mechanisms have yet to be fully elucidated. Diets, especially dietary fats, have long been known to influence the gut microbiota and, consequently, both gut resident and systemic immune responses. Metabolites of dietary fats, once digested by gut commensal bacteria, can either directly stimulate host cells or act as procurers for the generation of small molecular lipid mediators such as prostaglandins (PGs). PGs play critical physiological and pathological roles in both health and disease, for example, by mediating bone development, regulating immune cell function, and driving inflammatory responses such as fever and pain. Notably, PGs are crucial in maintaining gut epithelial homeostasis, possibly through modulating host cell function and the microbiota.

In this PhD project, we will investigate the effects of dietary fats on the modulation of intestinal health and their roles in systemic metabolic functions. The main objectives of the project include examining how dietary fats modulate the gut microbiota and intestinal immune function, the effects of the microbiota on fatty acid metabolism in intestinal cells, and the roles of fatty acid metabolites in modulating gut immune cell function. We will utilise cutting-edge immunological, pharmacological, genetic and systems biological approaches to examine the interactions among intestinal immune cells, epithelial cells and the gut microbiota in response to the consumption of dietary fatty acids. Techniques such as flow cytometry, single-cell RNA-seq, and in vitro cell culture systems will be applied for profiling intestinal immune cell and assessment of epithelial function. Microbial RNA sequencing will be used for profiling the gut microbiota and identifying functional bacterial pathways, which will be validated by manipulation (i.e. depletion and transplantation) of the microbiota. Fatty acid metabolism and PG production in immune cells will be examined through immuno-metabolic phenotyping and lipidomics. The impact of lipid mediators will also be examined using pharmacological reagents and gene-modified animals. Upon completion of this project, we expect to gain a comprehensive understanding of how dietary fatty acids interact with the gut microbiome and the host immune system, and how these interactions fundamentally regulate gut health.

Funding Notes

UKRI-funded studentships are open to students worldwide and will cover tuition fees at the UK rate, plus a stipend to support living costs and an annual research grant of £5,000 for the first three years of the PhD research. The proportion of international students appointed through the EASTBIO DTP is capped at 30%.  All students must meet the eligibility criteria as outlined in the UKRI guidance on UK, EU and international candidates. This guidance should be read in conjunction with the UKRI Training Grant Terms and Conditions

Apply Now 

EASTBIO Webpage (to download the documents required for email application process, detailed below) 

• EASTBIO Application
• Equality, Diversity and Inclusion (EDI) survey
• Reference Forms can be downloaded via link above

Please send your completed EASTBIO Application Form and EDI survey along with a copy of your academic transcripts to CIR.Postgraduate@ed.ac.uk before the deadline. You should also ensure that two references have been sent to CIR.Postgraduate@ed.ac.uk by the deadline using the EASTBIO Reference Form.

The EASTBIO team will run a series of 1-hour online sessions in November/December 2025, open to applicants who have queries about the application process. Please view EASTBIO How to Apply webpage for details. 

Unfortunately due to workload constraints, we cannot consider incomplete applications.