Defining Pax9 driven endodermal networks that shape or break aortic arch development.

About the Project

Project overview

Congenital heart defects are among the most common birth abnormalities, yet the developmental pathways that shape the early cardiovascular system remain only partly understood. This PhD will explore one of the most intriguing and understudied aspects of this process: how a specialised epithelial tissue in the embryo, the pharyngeal endoderm, orchestrates the formation of the major arteries of the heart. Working at the interface of developmental biology, genetics, imaging and computational analysis, this project offers an exciting opportunity to uncover the molecular networks that ensure the aortic arch arteries form correctly, and to understand why they sometimes do not.

What the student will do

You will combine cutting-edge single-cell and spatial transcriptomics, advanced in situ imaging, and mechanistic cell-based assays to reveal how the transcription factor Pax9 regulates communication between the pharyngeal endoderm and neighbouring cells. Using existing single-nucleus RNA-sequencing datasets, you will map key endodermal signalling pathways during normal arch artery development. You will then validate these pathways in mouse embryos using RNAscope and confocal imaging, before testing the underlying mechanisms in a tractable epithelial model that closely resembles embryonic endoderm. By integrating data-rich discovery with targeted functional assays, including inducible gene knockdown, pathway-response analyses and ChIP-seq, you will build a mechanistic picture of how developmental signalling competence is established and maintained.

Why this project is ideal for a PhD student

This studentship provides outstanding opportunities for training across multiple high-value skill sets:

• Single-cell bioinformatics (R/Python, Seurat, LIANA, Monocle/scVelo)
• Advanced imaging (RNAscope, immunofluorescence, confocal microscopy)
• Mouse developmental biology (embryo dissection, tissue processing)
• Cell and molecular biology (cell culture, lentiviral transduction, luciferase assays)
• Epigenomics (FLAG-Pax9 ChIP-seq)

You will join a collaborative, supportive environment spanning three research groups, with day-to-day access to experienced postdocs and current PhD students, as well as Newcastle University’s state-of-the-art Bioimaging, Genomics and Bioinformatics facilities.

Who should apply?

This project will appeal to applicants with backgrounds in biological sciences, developmental biology, genetics, biochemistry, biomedical sciences, physiology, or related disciplines. No single technique is assumed as full training will be provided. Curiosity, motivation, and enthusiasm for interdisciplinary research are more important than prior specialist experience.

The bigger picture

By revealing how early embryonic tissues coordinate cardiovascular development, this work adds crucial insight into the origins of congenital heart defects. The project will suit students who want to contribute to impactful biomedical research while gaining strong, future-proof skills for careers in academia, industry, or translational science.

Funding

Students who have, or are expecting to attain, at least an upper second-class honours degree (or equivalent) in a relevant subject, are invited to apply. Funding is available for Home (UK) students to cover tuition fees, a tax-free stipend at the UKRI rate (indicative amount in year 1 in 2026-27, £21,805) and research costs, for four years. Applicants normally required to cover International fees will have to cover the difference between the Home and the International tuition fee rates. There is no additional funding available to cover NHS Immigration Health Surcharge (IHS) costs, visa costs, flights etc.

Funding for this studentship is awarded on a competitive basis and is not guaranteed; availability will depend on the outcome of the selection process and subject to final approval by the University.

HOW TO APPLY

Please complete the following application form – Google Form

Applicants can only apply for 1 project; any additional applications will not be accepted.

Applicants should send the following documents to FMSstudentships@newcastle.ac.uk:

• a CV (including contact details of at least two academic (or other relevant) referees).
• a Cover letter – stating your project choice, as well as including additional information you feel is pertinent to your application.
• copies of your relevant undergraduate degree transcripts and certificates.
• a copy of your IELTS or TOEFL English language certificate (where required)
• a copy of your passport (photo page).

A GUIDE TO THE FORMAT REQUIRED FOR THE APPLICATION DOCUMENTS IS AVAILABLE

Please submit your documents in the following format only:

• each document should be submitted as a separate attachment and should be named as follows: candidate surname, candidate name – document type. For example: Jones, Jamie – CV; Jones, Jamie – cover letter.
• Please submit .pdf documents where possible for your CV, cover letter, transcripts and certificates. Do not submit photos of certificates.
• Do not combine documents into one pdf. You may zip separate documents into a zip file to send via email if required.
• When emailing your application, please use the email subject header: FMS PhD Application 2026

Applications not meeting these criteria may be rejected.

Informal enquiries may be made to the lead supervisor of the project you are interested in.

The deadline for all applications is 12 noon BST (UK time) on Wednesday 20th May 2026.