Muscle and fat are two distinct differentiation pathways from the same precursor cells. Schirmer found that during adipogenesis muscle genes move to the nuclear envelope (NE) to be more tightly repressed while fat metabolism genes release: in myogenesis fat metabolism genes move to the NE while muscle metabolism genes release. Galloway and Hall found changes in muscle metabolism and blood metabolites following exercise and that differences in the healthy resting state relate to greater tolerance of muscle damage during exercise. Interestingly, Schirmer found that myogenic fusion genes expressed at early stages of differentiation are then recruited to the NE for tight repression while muscle damage from snake venom causes release and reactivation of these genes. Schirmer also found that treatment of a muscular dystrophy cell model with metabolic drugs improved myotube fusion and uniformity. Together these data evolved our hypothesis:
Proper segregation of fat and muscle metabolism during differentiation optimises efficient muscle function through achieving correct genome organisation in each tissue. Better understanding how this supports responses to muscle damage can lead to metabolic drug treatments based on individual genome organisation that can maximise exercise benefits, promote healthy aging, and ameliorate patient symptoms in muscular dystrophies.
Project:
Aim 1. AI relating genome organisation and metabolism changes
Student will collect muscle metabolism data (EdinOmics) from exercise volunteers (Galloway/Hall) and under experimental tissue culture conditions (Schirmer), perform fluorescence-in-situ-hybridisation (FISH) on cells, and compare metabolites/metabolic pathways altered during exercise/experiment to genomics and other data types (DamID, enhancer/function/pathway databases, FISH) using bioinformatics/AI. Gene/enhancer repositioning-metabolism correlations will also be tested for being rapid or temporary (likely after exercise), as well as in an Emery-Dreifuss muscular dystrophy (EDMD) model system.
Aim 2. Testing metabolic drugs effects on muscle function
Metabolic drug treatments dramatically improved myogenic fusion/uniformity in EDMD cells and even moderately improved control muscle cells. Guided by AI analysis of gene expression/genome organisation data for different individuals/conditions/disease mutations, drug combinations and concentrations will be compared using in vitro myogenesis assays to deliver quantitative data on myogenic fusion/uniformity, nuclear organisation (FISH), and metabolism (Seahorse metabolic analyser).
Aim 3. Do muscle metabolites alter the epigenetic landscape of metabolic genes?
Some muscle metabolites can be used in pathways adding epigenetic marks. ChIP on these genes will determine if epigenetic marks change under exercise conditions and following metabolic treatments. Metabolites upregulated in exercise will also be tested for changing the epigenetic profile important muscle genes.
For more information on the project, eligibility and how to apply for the School's PhD programme, please click on the "Visit Institution Website" link.
Please download and complete the mandatory documents from the EastBio “how to apply” website, before proceeding with your application.
Applicants should apply to the PhD in Biological Sciences with Internship programme via the University of Edinburgh’s admissions portal (Euclid) with a start date of 01 October 2026.
Important: Before applying, please send your referees the EastBio reference form to ensure reference letters are submitted using the correct format.
When completing the Euclid application, applicants should include:
- the project title
- the proposed research supervisor(s)
- anticipated funding source (i.e. EastBio/ Edinburgh Doctoral College Award)
- the completed EastBio application form, uploaded to the Research Proposal Section
- referee details or completed reference letters using the template EastBio reference form. Please note: If you submit only the referee details, they will automatically receive a link to upload their reference letter. However, the submitted letter must be using the template form, so please share this with them in advance.
The closing date for applications to be submitted to Euclid is midday on Monday 16 November 2026.
Reference letters will be accepted up to 2 weeks after the closing date.
Submitted applications will remain under consideration during the shortlisting process until 22 February 2027, when successful candidates will be invited to interview. If any information is missing from your application, we will contact you through Euclid to request this. Please check your emails and the Euclid portal regularly.
Please be aware The University reserves the right, in its sole discretion, to amend or withdraw any of the advertised scholarships, without further notice.
