Topological data analysis for the shoot apical meristem

About the Project

Project lead: Dr John Harvey (MATHS)

Project partners: Angharad Jones (BIOSI)

The shoot apical meristem is the region of undifferentiated cells at the growing tip of a plant. Leaf and flower primordia are generated from the meristem as the plant grows. Observations show that the shape of the shoot apical meristem is affected by growing conditions such as rainfall and temperature variations. It is also expected that the shape determines future growth patterns of the plant.

Investigating these questions requires suitable shape descriptors which can be incorporated into statistical analysis and the outcomes will help ensure agricultural practices are robust to climate change, addressing Sustainability Development Goals 2 (Zero Hunger) and 13 (Climate Action).

Dr Angharad Jones (BIOSI) and Dr John Harvey (MATHS) are UKRI Future Leaders Fellows and will act as co-supervisors for a student developing and using these descriptors. Jones brings expertise in the shoot apical meristem, Harvey in topological data analysis.

While the student’s home School will be MATHS, the student will also attend fortnightly lab meetings with Jones, presenting their work and receiving updates from other group members and have the opportunity to spend time working in Jones’ lab. They will develop a clear understanding of the science underlying the mathematics, valuable skills in communicating across subject barriers and as the project progresses they will participate in experimental design, completing the full cycle of collaborative, interdisciplinary working.

EDI factors will be of importance in the student’s individual training. Harvey is Deputy Director of EDI at MATHS and played a substantial role in preparing the School’s Athena Swan Silver Award. The student will be encouraged to participate in EDI-related events at the School and directed towards relevant community networks. Both supervisors are committed to accommodating adjustments and will work with the student to empower them to contribute to the cultures of their respective groups.

Key outcomes of the studentship are

• new methods to estimate the curvature of the shoot apical meristem
• concise statistical descriptors of how curvature varies over the meristem
• curvature-informed automatic segmentation of meristem images
• analysis of the relationship between growth outcomes and curvature

The student will acquire skills in

• image processing
• plant biology
• experimental design
• geometry
• algebraic topology
• data analysis
• data visualisation
• oral and written presentation
• working across disciplinary boundaries

What we offer:

Cardiff's School of Mathematics provides an excellent postgraduate research environment including:

• research facilities at Abacws (co-designed by our PGR community),
• a vibrant research culture including a wide range of research events,
• access to national course centres in mathematics, statistics and Operational Research,
• comprehensive professional skills training offered by Cardiff’s Doctoral Academy.
• collaborations with other disciplines and with a wide range of external partners (industry and society).

The PGR community is very active in running the SIAM-IMA Student Chapter, a valuable forum for exchange of ideas and public engagement.

This studentship will be undertaken within the Mathematical Analysis research group at the School of Mathematics. The group’s members have wide-ranging interests, and offer a dynamic environment for the student to engage with experts in mathematical analysis and many other fields in mathematics and other disciplines. The group hosts a weekly seminar inviting external speakers.

Completing a PhD in mathematics opens up a range of possible next steps, from continuing an academic career to working in mathematically technical roles in industry.

The 3.5 year programme does not have any funding attached but successful applicants will receive a small Research Training Support Grant to cover costs such as research consumables, training, conferences and travel.

The possible start dates for this PhD are October, January, April or July.

What you bring:

You should have

• a 1st or upper 2nd class UK Honours degree (or equivalent) and/or a Master’s degree in mathematics or a suitable related subject.
• a strong background in coding
• an interest in learning about the mechanisms of plant development and participating in laboratory science

Applicants for whom English is not their first language must demonstrate their proficiency by obtaining an IELTS score of at least 6.5 overall, with a minimum of 5.5 in each skills component, or equivalent qualification.

Cardiff University is committed to supporting and promoting equality and diversity and to creating an inclusive research environment. We particularly welcome applications from underrepresented groups.

How to apply:

Applicants should apply through the Cardiff University online PhD application portal, for a Doctor of Philosophy in Mathematics with your desired entry point.

You must include

• Transcript(s) of your degree(s) (with certified translations if appropriate)
• Degree certificates (with certified translations if appropriate)
• References - these should be current and verifiable
• Personal statement (as part of the university application form, or as a separate attachment, if you prefer) this should provide a clear explanation of your research interest, preparation undertaken, and an understanding of the project.

Note that the 'register interest' option will not submit an application. Please follow the instructions above and submit your application via our online portal. Incomplete applications will not be considered.

Funding Notes

We welcome application from potential students who have their own sponsorship in place or are in a position to self-fund.

In the Research Proposal section of your application, please specify the project title and supervisors of this project.

In the funding section, please select that you will be self-funding and enter your source of funding.