PhD Opportunities

Supervisor: Dr Richard Gill, Dept. of Life Sciences, Silwood Park, Imperial College London (ICL)

Co-supervisors & collaborators: Prof. Ian Barnes (NHM London), Dr Gavin Broad (NHM London), Dr Alan Buddie (CABI), Dr Peter Graystock (ICL)

Project Title: Fungal disease risks under landscape homogenisation: tracking fungal transmission across plant-pollinator networks using contemporary and historic museum specimens

Project Description: Mapping how microbial pathogens are vectored through ecological networks is important to understand how direct and indirect species interactions contribute to transmission dynamics. In the case of plant-pollinator networks, however, we understand little about how flowers act as pathogen transmission hubs and how pollinators act as pathogen vectors through complex networks. Furthermore, we know little about how fungal pathogens are transmitted through networks despite fungi posing significant risks to plant crop, wildflower, and insect pollinator brood health.

How landscape context can increase fungal transmission across modules of plant-pollinator networks is an important outstanding question. For example, landscape homogenisation now epitomises widespread habitat change driven primarily by agricultural intensification. This can lead to functional homogenisation across plant and pollinator communities, increasing the likelihood of pollinators sharing plant hosts and vice versa that may not have occurred historically (Fig. 1). This project will first ask whether transmission of fungal species previously restricted within specific pollinator taxonomic clades has become more prevalent across more distant evolutionary related clades. For instance, could fungal pathogens normally restricted to transmission between beetle pollinators hypothetically spill-over to bee clades? Second, could such an increased ‘reach’ of fungal pathogens across the pollinator community increase transmission risk to wildflowers and important flowering food crops?

This PhD will assess how fungal species are associated with plants and pollinators in contemporary networks when sampled across a landscape homogenisation gradient (varying levels of agricultural intensification). Then, through targeted sampling of museum specimens, we will determine historic fungal species prevalence in populations before major land-use transitions in agricultural intensification occurred (i.e., early 1900s). Evolutionary relationships between hosts will be considered to develop a more predictive framework and lay the foundation for exploring how fungal species that have evolved to increase transmission under increasingly functionally homogenised communities.

The student will be able to learn a variety of skills, including employing modern DNA sequencing approaches and ancient DNA-techniques, handling big data, script writing and developing bioinformatic pipelines, conduct fieldwork sampling and surveys of plant-pollinator networks, and working with museum collections. The student would join the Leverhulme Centre for the Holobiont (www.imperial.ac.uk/holobiont/), a multi-institutional research centre devoted to understanding interactions between microbes and their multicellular hosts.

The student would join the Leverhulme Centre for the Holobiont (www.imperial.ac.uk/holobiont/), a multi-institutional research centre devoted to understanding interactions between multicellular hosts and their microbial symbionts.

Informal enquiries are welcomed and should be sent to Dr Richard Gill (r.gill@imperial.ac.uk)

How to apply:

Please email Dr Richard Gill (r.gill@imperial.ac.uk) and include in your application:

• - Statement of purpose (max. 2 pages A4, Arial/Calibri font size 11)
• - CV
• - Please arrange for two academic reference letters to be sent directly to Dr Gill.

Full applications made before 30th April 2024 will be considered at any time.

Funding and eligibility:

A fully funded 4 years Leverhulme Studentship, including tuition fees and a standard research council stipend (£19,668). The fees and stipend cover UK home applicants and standard research council eligibility criteria apply: https://www.ukri.org/what-we-offer/developing-people-and-skills/find-studentships-and-doctoral-training/get-a-studentship-to-fund-your-doctorate/

The successful applicant must hold or be expected to complete a Masters (MRes or MSc) or a four-year MSci with a grade of at least 2:1 level (or equivalent experience) in a relevant subject area, e.g., ecology, evolution, genetics, or microbiology.

Development of Novel Binding Partners for the Identification and Quantification of Small Molecules: Differentiable protein design for small molecule binding.

Dr James Murray and Prof Geoff Baldwin have been awarded a Defence Science and Technology Laboratory 4-year PhD to start in Oct 2024. This studentship includes stipend and tuition fees for UK students paid at the UKRI level.

The project is to design protein-based small molecule binding partners, for the purposes of detection, identification and quantitation of small molecules. We will create de novo protein binders with computational protein design, using a diffusion deep-learning generative models, and then synthesise and test them. There has recently been a quantum leap in the capabilities of protein design, due to the development of deep-learning based tools, kick-started by the release of AlphaFold2 in 2021. An important application of protein design is to bind small molecules for detection. Such proteins have usually been raised as antibodies or produced by screening libraries, but these processes are unreliable and labour-intensive. Here we propose to put together an entirely differentiable pipeline, where the binding energy of the ligand is another parameter to be optimised in a deep-learning protein design pathway. The student will design ligand binding proteins, then express and purify them.  We will then characterise the designs for binding to the target ligand, and then optimise the designs in an iterative process. Ligand binding will be tested via biochemical assays, including tryptophan based fluorescence and ELISAs.

Training will be gained in computational protein design, protein generative models, protein expression, purification and characterization. The project would suit a computationally oriented biochemist, or someone with a computational/physical science background and an interest in protein design.

Funding Notes and Eligibility: 

This project is funded by Dstl. Funding includes payment of college fees and a tax-free stipend for four years starting from October 2024.Please note that the nature of the sponsor means that only UK nationals, UK dual nationals, EU nationals with settled status, or foreign nationals with indefinite leave to remain are eligible. You will have an appropriate undergraduate  degree with a 2:1 result or better. Additionally, a Masters degree with Merit or better in a relevant topic will be preferred.

Informal enquires can be made to Dr James Murray (j.w.murray@imperial.ac.uk)

How to apply:

Please email Dr James Murray (j.w.murray@imperial.ac.uk and include in your application:

- Personal Statement (max. 2 pages A4, Arial/Calibri font size 11)

- CV

- Please arrange for two academic reference letters to be sent directly to Dr James Murray

Full applications made before 30^th June 2024 will be considered at any time.