Supervisors:
Julian Hibberd
Johannes Kromdijk
Yiliang Ding (John Innes Centre)
Overview:
The aim is to create minimal, tuneable genetic circuits for precise control of gene expression in mesophyll cells. Hibberd has contributed to international efforts to engineer C4 photosynthesis into C3 crops to improve yield (1). To enable cell-specific expression of C4 genes, his group developed computational and experimental pipelines to identify minimal DNA elements driving expression in defined cells. This approach allows both specificity and tunable expression in the bundle sheath of Arabidopsis (2) and rice (3,4) but is slow. Ding developed RNA (5) and now DNA Foundation Models (unpub), that outperform existing tools in predicting regulatory function.
Objectives:
To combine AI-based prediction with functional testing to accelerate discovery of regulators controlling mesophyll expression. Full C4 engineering is beyond scope, but this work will generate key tools supporting that goal. Aims are to (1) predict and identify regulators of mesophyll expression in Arabidopsis and rice, and (2) modify sequences for adjustable expression. The outcome will be a toolkit for tuneable, mesophyll-specific gene control.
Approach:
Existing datasets will be analysed using Ding’s RNA/DNA Foundation Models to predict motifs controlling mesophyll expression. Search space will be refined using open-chromatin data. Predicted transcription factors and cis-elements will be tested with a high-throughput effector system in Arabidopsis and rice. Oligomerisation of cis-elements will enable graded expression. Top candidates will be validated in stable transformants for cell specificity and expression strength. Prime editing will be preferred, though transgenes can be used if required. Hibberd's lab has expertise in transforming both species, and promising elements may be tested in wheat via the JIC transformation facility.
Novelty and Timelines:
Despite mesophyll cells forming ~80% of leaf tissue and housing most chloroplasts, no transcription factors or cis-elements specific to this cell type are known. This project combines AI and experimental validation to remove that barrier.
Expected Outcomes:
The first components enabling mesophyll-specific expression will be developed. Shared regulators across Arabidopsis and rice will have broad crop relevance. The student will gain skills in AI, synthetic biology, and functional genomics to design and validate minimal genetic circuits controlling expression in a defined cell type.
The Programme:
PhD in Plant BioDesign (4 years)
Plant BioDesign is a doctoral programme that will train the next generation of scientists to design and engineer plants to tackle global challenges in food security, clean growth, and environmental sustainability. The programme brings together world-leading researchers at the universities of York, Cambridge and Bristol and the John Innes Centre.
Plant BioDesign offers a unique four-year PhD training programme in plant engineering biology incorporating interdisciplinary research with training in engineering principles, advanced lab techniques, non-academic collaboration and professional and leadership development.
Plant BioDesign is part of the TechExpert pilot providing an enhanced annual stipend of £31,000. PGRs will participate in TechExpert activities each year, including outreach to promote tech careers, networking with the TechFirst community and engagement with the tech industry. The aim of the TechExpert pilot is to strengthen the UK’s innovation pipeline and build a more inclusive, resilient and high-impact research ecosystem.
The School of Biological Sciences is a diverse community conducting ground-breaking research. We are committed to fostering inclusive excellence and enthusiastically welcome applications from all ethnic, socioeconomic, cultural, and belief backgrounds and from all genders and sexual orientations. We seek to recruit students from all backgrounds, including those who may not have previously considered Cambridge. If you have the talent and motivation, then Cambridge is for people like you.
Entry Requirements:
You can apply if you have, or are expecting to gain, at least an upper second class honours degree or equivalent. You should have a background in biological, chemical or physical science or mathematics, be passionate about plant engineering biology and keen to develop your research and innovation skills to tackle global challenges. Open to UK (home) students only.
Plant BioDesign is committed to recruiting future engineering biologists regardless of age, ethnicity, gender, gender identity, disability, sexual orientation or career pathway to date. We welcome applicants from all backgrounds, particularly those under-represented in science, who have curiosity, creativity and a drive to help grow the UK’s capability in engineering biology.
The aim of the TechExpert pilot is to strengthen the UK’s innovation pipeline and build a more inclusive, resilient and high-impact research ecosystem, retaining talented graduates in research roles at doctoral level to upskill for future tech careers and providing a viable way back into these roles for those who are employed.
Plant BioDesign will hold a webinar at 2.30 pm on Wed 10th December to provide more information on the programme and recruitment process. Please register if you wish to attend.
Start Date: 1st Oct 2026
How to apply:
To submit your application, complete our application form. You can apply for up to two Plant BioDesign projects (which can be at different institutions).
We advise you to read the questions in the form before submitting your application. Inside the form there is a link to a document for you to see the questions in advance.
Please note that students who need a visa to study in the UK are not eligible to apply for this project.
Click here to read about this project on Find-A-PhD.
If you have questions about the application process, please email plant-biodesign-network@york.ac.uk
How we allocate:
Shortlisting will take place shortly after the closing date and successful applicants will be notified promptly. If you're shortlisted, you'll be invited for an online interview on 27th February 2026. You'll be notified shortly after the interview dates whether your application has been successful, placed on a reserve list or unsuccessful. If you are successful, you'll be offered a visit to the offering institution and asked to confirm your intention to accept the studentship within 14 days.
Application deadline: 5pm on Monday 19th January 2026
