Using chromosomal-level genome assemblies to discover missing links in neuropeptide evolution
We are seeking applicants for the following PhD opportunity. The successful applicant will join a student cohort in Environment, Biodiversity and Genomics, training together, following an exciting programme designed to inspire the next generation of environmental experts, managers and leaders. They will be equipped to address some of the toughest challenges of our time.
The School of Biological and Behavioural Sciences at Queen Mary is one of the UK’s elite research centres, according to the 2014 Research Excellence Framework (REF). We offer a multi-disciplinary research environment and have approximately 160 PhD students working on projects in the biological and psychological sciences. Our students have access to a variety of research facilities supported by experienced staff, as well as a range of student support services.
This project will be co-supervised by Prof. Maurice Elphick and Dr. Alex De Mendoza. Prof Elphick is an expert on the evolution and comparative physiology of neuropeptide signalling systems. See here for further details of Prof. Elphick's research interests and publications. See here for details of Dr De Mendoza's research interests and publications.
Training and development
Our PhD students become part of Queen Mary’s Doctoral College which provides training and development opportunities, advice on funding, and financial support for research. Our students also have access to a Researcher Development Programme designed to help recognise and develop key skills and attributes needed to effectively manage research, and to prepare and plan for the next stages of their career.
Specific training will provided for 1. computational comparative analysis of genomic/transcriptomic sequence data to enable identification of genes/transcripts encoding precursors of neuropeptides as candidate ligands for orphan G-protein coupled receptors. 2. Use of in vitro cell based assays to test neuropeptides as candidate ligands for orphan neuropeptide receptors.
Neuropeptides are key regulators of physiological/behavioural processes that exert effects by binding to specific receptor proteins. Accordingly, neuropeptide receptors are targets for therapeutics in humans (morphine) and potential novel targets for pesticides. Our knowledge of the evolution and diversity of neuropeptide signalling systems has been advanced tremendously in recent years by genome/transcriptome sequencing (Elphick et al. 2018; https://doi.org/10.1242/jeb.151092). However, discovery of orthologous neuropeptides in distantly related taxa is often difficult because they are typically short peptides (e.g. 3-15 residues).
We are now entering a new era in genomics where chromosomal-level assemblies of genomes are being obtained for species from an ever-growing diversity of taxa (https://www.darwintreeoflife.org, including the starfish Asterias rubens led by Elphick). Furthermore, analysis of these data is revealing that some extant taxa exhibit a remarkable level of conservation of the predicted karyotype of the common ancestor of bilaterian animals (Simakov et al., 2020; https://www.nature.com/articles/s41559-020-1156-z). Importantly, this provides a framework for gene synteny-based discovery of genes encoding neuropeptide orthologs in distantly related taxa.
Accordingly, the aim of this project will investigate the evolution and orthology of genes encoding neuropeptides and neuropeptide receptors. Informed by analysis gene synteny at the chromosomal level and gene/protein sequences/structures in a variety of phyla, novel candidate ligands for neuropeptide receptors will be discovered. Then cell-based receptor assays will be used to test predicted neuropeptide-receptor partners.
Identifying these ‘missing links’ will facilitate reconstruction of the evolution of neuropeptide signalling in the Bilateria in unprecedented detail, leading to high profile publications in top rank journals. The project will be co-supervised by Prof. Maurice Elphick, who is an expert on the evolution and comparative physiology of neuropeptide signalling systems, and Dr Alex de Mendoza, who is an expert on comparative genomics/bioinformatics.
This studentship is open to Mexican students applying for CONACyT funding. CONACyT will provide a contribution towards your tuition fees each year and Queen Mary will waive the remaining fee. CONACyT will pay a stipend towards living costs to its scholars.
Eligibility and applying
Applications are invited from outstanding candidates with or expecting to receive a first or upper-second class honours degree and a masters degree in an area relevant to the project. A masters degree that includes training in one or more of the following is desirable: bioinformatics/computational biology/biochemistry/molecular biology/genetics/cell biology/evolutionary biology/comparative physiology/pharmaceutical chemistry.
Applicants are required to provide evidence of their English language ability. Please see our English language requirements page for details.
Applicants will need to complete an online application form by this date to be considered, including a CV, personal statement and qualifications. Shortlisted applicants will be invited for a formal interview by the project supervisor. Those who are successful in their application for our PhD programme will be issued with an offer letter which is conditional on securing a CONACyT scholarship (as well as any academic conditions still required to meet our entry requirements).
Once applicants have obtained their offer letter from Queen Mary they should then apply to CONACyT for the scholarship as per their requirements and deadlines, with the support of the project supervisor.
Only applicants who are successful in their application to CONACyT can be issued an unconditional offer and enrol on our PhD programme.
- Tinoco AB, Barreiro-Iglesias A, Yañez Guerra LA, Delroisse J, Zhang Y, Gunner EF, Zampronio CG, Jones AM, Egertová M, Elphick MR (2021) Ancient role of sulfakinin/cholecystokinin-type signalling in inhibitory regulation of feeding processes revealed in an echinoderm. Elife. 10:e65667. doi: 10.7554/eLife.65667.
- Yañez-Guerra LA, Zhong X, Moghul I, Butts T, Zampronio CG, Jones AM, Mirabeau O, Elphick MR. (2020) Echinoderms provide missing link in the evolution of PrRP/sNPF-type neuropeptide signalling. Elife. 2020 9:e57640. doi: 10.7554/eLife.57640.
- Odekunle EA, Semmens DC, Martynyuk N, Tinoco AB, Garewal AK, Patel RR, Blowes LM, Zandawala M, Delroisse J, Slade SE, Scrivens JH, Egertová M, Elphick MR (2019) Ancient role of vasopressin/oxytocin-type neuropeptides as regulators of feeding revealed in an echinoderm. BMC Biology 17(1):60.
- Elphick MR, Mirabeau O, Larhammar D. (2018) Evolution of neuropeptide signalling systems. J Exp Biol. 221(Pt 3) doi: 10.1242/jeb.151092.
- Semmens DC, Mirabeau O, Moghul I, Pancholi MR, Wurm Y, Elphick MR (2016) Transcriptomic identification of starfish neuropeptide precursors yields new insights into neuropeptide evolution. Open Biology Vol 6(2) 150224 doi.org/10.1098/rsob.150224.
- de Mendoza, A., Poppe, D., Buckberry, S. et al. The emergence of the brain non-CpG methylation system in vertebrates. Nat Ecol Evol 5, 369–378 (2021).
- de Mendoza, A., Hatleberg, W.L., Pang, K. et al. Convergent evolution of a vertebrate-like methylome in a marine sponge. Nat Ecol Evol 3, 1464–1473 (2019).