Applications are welcomed for two fully funded, four-year, full-time PhD positions at University College Dublin, Ireland.

PhD Project area: Reconstructing animal immune system evolution.

PhD supervisor: Dr Anthony Redmond

Proposed Start Date: Early 2025 (TBC).

Location: School of Medicine, University College Dublin, Ireland

Positions: 2x 4-year, Full-time PhD studentships (One University College Dublin Ad Astra PhD Studentship and one Royal Society-Research Ireland PhD studentship).

Stipend: €22,000 per annum tax-free plus tuition fees.

Summary of Project(s): The immune system is a complex evolutionary marvel. Although the system is very well studied in humans, and in some key model organisms, the early formation of the animal immune system is poorly understood. This has been complicated by a combination of issues, including: i) poor availability of high-quality genomes for some of our most distantly related animal relatives, ii) the fast-evolving nature of immune genes rendering homology difficult to identify across vast time periods, and iii) uncertainty in the relationships of the major animal lineages. Fortunately, high-quality genome sequences are now available for representatives of the major animal lineages, while combining wet lab and ‘omics’ approaches means that genes responding to immune challenges can be more readily identified, providing an unprecedented opportunity to counteract the key issues outlined above.

Both studentships will involve collection and maintenance of phylogenetically important marine invertebrates in the lab for use in immune challenge trials paired with and various ‘omics’ and imaging approaches, to identify the array of immune-associated genes in key lineages. This will reveal both novel immune genes, as well as homologs of known immune genes found in traditional model species. Together with phylogenetic investigation of immune genes from across animal diversity this approach will guide reconstruction of the key steps in immune system evolution.

The proposed projects are intertwined in approach and share the overarching aim of understanding the origins and evolution of the animal immune system, but diverge in that one studentship will focus on the early evolution of the bilaterian immune system and the other on immune evolution in non-bilaterian animals.

These interdisciplinary projects intersect evolutionary genetics, invertebrate zoology, immunology, and bioinformatics. Appropriate training and/or opportunities to gain experience will be provided in skills spanning these areas, including in fieldwork and husbandry of marine invertebrates, wetlab techniques, as well as in phylogenetics, bioinformatics and ‘omics’ approaches. Both students will have the opportunity to publish in leading scientific journals and to attend international conferences.

Research Team and Environment: The successful candidates will join the newly established Redmond lab in University College Dublin’s School of Medicine. The group focuses primarily on understanding the evolutionary history of animals, with particular interests in genome evolution, immune systems, and resolving the tree of life, as well as the development of new methodological approaches that this research agenda calls for. Both studentships will benefit from opportunities to contribute to other projects as well as from planned local and international collaborations to ensure the success of this project.

Requirements Qualifications/Expertise: Applications are sought from inquisitive and dedicated candidates with interest in scientific methodology and discovery. Candidates should have, or expect to soon be awarded, a BSc (grade 2.1 or above), or an MSc, in the area of biology (especially: genetics, immunology, zoology or related fields) and/or computer science.

To apply for these positions: Please send your CV, a cover letter, and the contact details of at least two referees to anthony.redmond@ucd.ie by 30th November 2024. Informal enquiries in relation to the position are welcome and encouraged. All applicants will be considered for both positions unless otherwise requested in the cover letter.

Relevant publications:

Redmond, A.K., 2024. Acoelomorph flatworm monophyly is a long-branch attraction artefact obscuring a clade of Acoela and Xenoturbellida. Proceedings of the Royal Society B: Biological Sciences, 291(2031).

Matz, H., Taylor, R.S., Redmond, A.K., Hill, T.M., Daniels, R.R., Beltran, M., Henderson, N.C., Macqueen, D.J. and Dooley, H., 2023. Organized B cell sites in cartilaginous fishes reveal the evolutionary foundation of germinal centers. Cell reports, 42(7).

Redmond, A.K., Pettinello, R., Bakke, F.K. and Dooley, H., 2022. Sharks provide evidence for a highly complex TNFSF repertoire in the jawed vertebrate ancestor. The Journal of Immunology, 209(9), pp.1713-1723.

Tan, M., Redmond, A.K., Dooley, H., Nozu, R., Sato, K., Kuraku, S., Koren, S., Phillippy, A.M., Dove, A.D. and Read, T., 2021. The whale shark genome reveals patterns of vertebrate gene family evolution. Elife, 10, p.e65394.

Redmond, A.K. and McLysaght, A., 2021. Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding. Nature communications, 12(1), p.1783.

Redmond, A.K., Zou, J., Secombes, C.J., Macqueen, D.J. and Dooley, H., 2019. Discovery of all three types in cartilaginous fishes enables phylogenetic resolution of the origins and evolution of interferons. Frontiers in immunology, 10, p.467824.

Redmond, A.K., Macqueen, D.J. and Dooley, H., 2018. Phylotranscriptomics suggests the jawed vertebrate ancestor could generate diverse helper and regulatory T cell subsets. BMC Evolutionary Biology, 18, pp.1-19.

Applications are invited from suitably qualified candidates for (a full funding with fees and stipend is pending), 4-year full-time PhD position at the UCD Charles Institute of Dermatology, University College Dublin, Dublin, Ireland.

This projects seeks to deepen mechanistic insights on extracellular matrix and integrins across different temporal, molecular, and structural scales in human skin fibrosis. Multiparametric approaches will be employed to thoroughly profile fibrotic human skin tissues and to understand how different skin cells use different integrins to respond to fibrotic skin extracellular matrices across various time points. The results from this project will greatly contribute to expand biological insights in skin fibrosis and potentially unravel novel therapeutic targets for different stages of skin fibrosis.

The PhD candidate will use combined in vitro and ex vivo experiments to characterize skin cells and tissues. The candidate will work with various techniques/tools including proteomics, qPCR, electron microscopy, confocal microscopy, and atomic force microscopy to study spatiotemporal matrix biology in skin fibrosis. The candidate will join a group under the supervision of Dr. Seungkuk Ahn (Associate Professor of Cutaneous Biology at UCD Charels Institute of Dermatology).

Qualifications / Expertise: Only EU applicants are eligible due to the funding regulation. Applicants should have a Bachelor’s or Master’s degree in Biomedical Sciences or Cell Biology or a related discipline. The ideal candidate should have experience in as many of the following techniques as possible: mammalian cell culture; molecular biology; extracellular matrix; protein and gene analysis; immunohistochemistry. The candidate should have excellent communication and organisational skills; be highly motivated and have strong written, oral and interpersonal skills. The candidate should be able to work independently and as a part of team.

Funding: The PhD studentship covers EU tuition fees and a tax free stipend of €22,000 per year.

Starting date: The candidate must start in January 2025 or latest by 1 May 2025.

How to apply: Please send a cover letter (1 page max), CV, academic transcript, and referee’s contact details (2 referees min) to Dr Seungkuk Ahn (seungkuk.ahn@ucd.ie) no later than 17 Dec  2024