BBSRC South West Biosciences Doctoral Training Partnership (SWBio) studentships

Applications are invited for fully funded 4 years (FTE) PhD studentship. The studentship is due to start in October 2025.

Applications for October 2025 are now open
Application deadline: Midnight (23:59pm GMT), Wednesday 11 December 2024
The BBSRC-funded SWBio DTP involves a partnership of world-renown universities, research institutes and industry, based mainly across the South West and Wales.
This partnership has established international, national, and regional scientific networks, and widely recognised research excellence and facilities.
We aim to provide you with outstanding interdisciplinary bioscience research training, underpinned by transformative technologies.
Standard DTP studentship with associate partner
These projects are jointly hosted between a core and associate partner within SWBio DTP partnership.
Supervisor details: Each project has a listed lead supervisor at each of the partner institutions involved.
Location: You will spend time at each of the partner institutions.
Registration: You will be registered at one of the partner universities of the lead supervisors. Your registered university will be confirmed by the DTP following the interview stage of the selection process. The lead supervisor at the registered university will be responsible for monitoring your academic progress.
Placement: You will be required to undertake a PIPS placement which will be for 3 months during your second or third year of your PhD. This placement will outside of an academic research environment and will not be directly related to your PhD project.

Projects available with the University of Plymouth

Developmental specificity of subcellular dynamic responses to Colletotrichum higginsianum infection of Arabidopsis thaliana

Lead Supervisor (associate partner): Dr George Littlejohn , University of Plymouth
Lead Supervisor (core partner): Dr Imogen Sparkes, University of Bristol
Project summary
Pathogens are responsible for reducing global crop yields of major crops by around 20% annually. Fungal pathogens of the Colletotrichum species complexes are the causative agents of anthracnose in several crop species including orchard fruits, coffee and chili and have been responsible for 95% losses in individual Colombian coffee plantations. During the infection process phytopathogens alter positioning and movement of organelles including the nucleus and chloroplasts. For example, changes in chloroplast morphology and position are currently being investigated in the rice Magnaporthe oryzae pathosystem in Dr Littlejohn’s research group. In addition, host susceptibility to pathogens is related to leaf developmental stage. Here, we will assess how Colletotrichum higginsianum affects organelle dynamics and whether we can alter susceptibility to the pathogen by introducing genetic tools which control organelle movement. We will observe subcellular dynamics in juvenile and mature leaves and assess whether there is a relationship between infection rate, leaf age and changes in organelle movement. Work will be carried out in the model organism Arabidopsis.
Dr Sparkes’ group focuses on molecular mechanisms underpinning organelle movement including myosins and membrane contract sites.
Dr Littlejohn’s group has expertise in plant-pathogen interactions.
Dr Fouracre is an expert in plant development.
Dr Plessis has expertise in complex quantitative analysis of plants.
The student will be registered at Bristol University where they will initially be based before moving to Plymouth University to carry out pathogen studies. They will be trained in plant cell biology, confocal microscopy, plant pathology and plant developmental biology.

Investigating novel interactions of the Merlin gene in cell behaviour

Lead Supervisor (Associate Partner): Professor David Parkinson , University of Plymouth
Lead Supervisor (Core Partner): Professor Benjamin Housden, University of Exeter
Project summary
The aim of this project is to investigate the functions of the Merlin/NF2 protein using a combination of Drosophila, mouse and human resources and approaches, giving the student on this project a huge range of expertise with many different techniques and model organisms. This project is important because the Merlin protein is a key scaffolding protein, which controls many aspects of cell growth, adhesion, proliferation, differentiation and migration as well as being dysregulated in many tumour types and tumour syndromes.
While the function of NF2/Merlin in regulating Hippo signalling is relatively well characterised, there is evidence that the protein has multiple other functions that have not been fully explored. Understanding these alternate roles of the protein as well as completely unknown functions will lead to a better understanding of how basic cell behaviour is controlled during tissue development and disease. The wide range of mutations within the NF2/Merlin gene in disease also gives us ideal models to track such new interactions.
In this project, the student will use a combination of Drosophila, mouse and human model systems to investigate novel functions of the NF2/Merlin protein. We will start by investigating the genetic interactions of the NF2/Merlin gene in Drosophila cells, which will provide insight into gene function. This will identify genes that depend on NF2/Merlin to fulfil their own functions and, combined with statistical enrichment analysis of the genetic interactions, will provide new knowledge into the various biological pathways that are dysregulated by NF2/Merlin loss.
Next, the identified pathways will be investigated in human cell lines and primary cells to assess the conservation of the newly identified functions of NF2/Merlin. Finally, mouse models will be used to test the new functions of NF2/Merlin using an in vivo system.
By the end of the project, we expect to have uncovered new functions of the NF2/Merlin gene that will improve our understanding of how cells control their growth, proliferation and behaviour. Given the important role of this gene in disease, we expect that this new knowledge will lead to the discovery of new therapies for NF2/Merlin related tumours in the future.
This project will combine cell culture, molecular biology, biochemistry, statistical analysis and in vivo experiments. This broad range of experience and skills will provide a strong basis for the successful candidate’s future career development.

Establishment and Characterisation of a Novel self-renewing, non-transformed Chicken Macrophage Cell Line for the Study of Innate Immunity

Lead Supervisor (Associate Partner): Dr Gyorgy Fejer , University of Plymouth
Lead Supervisor (Core Partner): Professor Shahriar Behboudi, University of Bristol
Project summary
Introduction
Macrophages are a heterogeneous population of immune cells critical for host defense against pathogens. While essential for understanding innate immunity, there is a paucity of suitable chicken macrophage models. Current models, such as bone marrow-derived macrophages, exhibit limited lifespan and may not accurately reflect the phenotype of tissue-resident macrophages. Our preliminary data demonstrate the potential of generating self-renewing, non-transformed macrophages from chicken fetal liver, offering a promising tool to study the innate immune response.
Aims and objectives
This studentship aims to comprehensively characterise a novel macrophage cell line derived from neonatal chicken hepatic stem cells. By comparing these cells to bone marrow-derived macrophages, we will elucidate their differential phenotypic, functional, and molecular properties.
Specific objectives include:
  1. To comprehensively characterise novel macrophage cell lines: Conduct a comparative analysis of phenotypic, functional, and molecular properties between the novel hepatic-derived macrophage cell line and bone marrow-derived macrophages. Utilise a battery of techniques, including flow cytometry, microscopy, ELISA, RNA-seq, RT-PCR, and proteomics, to assess lineage-specific markers, cytokine production, gene expression, and protein profiles, both in basal conditions and upon stimulation with toll-like receptor ligands.
  2. Functional validation of differentially expressed genes: Following the comparative analysis in Objective 1, the student will identify genes or proteins with significant expression differences between the cell lines. The data will be utilised to investigate the functional roles of selected genes using RNA interference, lentiviral overexpression, and CRISPR/Cas9-mediated gene editing. Finally, the student will assess the impact of gene manipulation on the functional abilities of the macrophages, employing the same methods described in Objectives 1 and 3.
  3. Evaluation of antimicrobial function: Assess the differential ability of the self-renewing macrophages and bone marrow derived macrophages to control Salmonella infection in vitro using the gentamicin protection assay. Determine the contribution of specific genes identified in objectives 1 and 2 to the antimicrobial response through CRISPR/Cas9-mediated gene manipulation.
This project offers an exceptional opportunity for the student to acquire a comprehensive skill set in both experimental methodologies and immunological concepts. By engaging in a comparative analysis of macrophage subtypes, the student will gain proficiency in a wide range of techniques, including flow cytometry, microscopy, ELISA, RNA-seq, RT-PCR, and proteomics. Furthermore, the project provides hands-on experience in gene editing technologies such as RNA interference, lentiviral overexpression, and CRISPR/Cas9. This multidisciplinary approach will equip the student with a strong foundation in immunology and prepare them for a successful career in research.

Standing up to threats: Understanding the neural mechanisms underpinning threat-related changes in balance control

Main Supervisor: Dr Jennifer Davies, Cardiff University
2nd Supervisor: Professor Jonathan Marsden , University of Plymouth
Project summary
Fear of falling is common, particularly among older individuals and clinical populations, such as people with arthritis, osteoporosis or Parkinson's disease. It is linked to increased physical decline, frailty and deconditioning. Being fearful of falling changes the way that a person controls their balance when they are standing still and when they are moving. Paradoxically, some of these changes (e.g., increased movement variability) can increase the risk of falling. Understanding how and why these changes in movement occur will enable us to design ways to prevent unhelpful movement strategies and reduce the number of falls. Specifically, this studentship seeks to understand how fear of falling alters the neural and sensorimotor control of balance.
Virtual reality (VR) technology can be used create a simulated environment in which to induce threat and fear in a safe and controlled environment. We (Ellmers) have shown that a novel VR environment that simulates the experience of standing on an elevated surface reliably induces postural threat and fear of falling, and associated changes in behaviour.
The successful applicant will combine this VR environment with a bespoke toolbox of cutting-edge neurophysiology equipment that allows them to probe the sensorimotor control of balance at multiple levels of the nervous system. They will have the opportunity to use transcranial magnetic stimulation (TMS), a type of non-invasive brain stimulation, to probe the connection between brain and muscles. We (Davies) have developed a highly novel system, unique in the UK, to deliver TMS during standing and walking, allowing study of how the brain is involved in controlling muscle activity during dynamic, full-body activities. In addition, peripheral nerve stimulation allows study of the transmission of information through networks of neurones in the spinal cord, and high-density surface electromyography allows study of the firing of individual spinal motor neurones that project to muscles involved in the control of balance. These techniques will provide the first thorough neurophysiological exploration of the mechanisms driving fear-related changes in balance.
The successful applicant will be supported to codevelop their own research questions to apply these highly novel, internationally unique capabilities to probe the neural mechanisms that contribute to threat-related changes in balance control during standing and walking. This work will advance our understanding of how the human sensorimotor system functions, particularly the interaction between psychological and physiological variables.

Engineering Optogenetic Systems in Rice Blast Fungus to Elucidate the Role of Timing in Effector Delivery and Pathogenesis

Main Supervisor: Professor John Love, University of Exeter
2nd Supervisor: Dr George Littlejohn , University of Plymouth
Project summary
Are you interested in cutting-edge research at the intersection of synthetic biology and fungal biotechnology? This exciting PhD project aims to explore how specific wavelengths of light can be used to fine-tune biosynthetic pathways in filamentous fungi through optogenetic regulation. This project offers a unique opportunity to develop a broad skill set in molecular biology, bioinformatics, synthetic biology and plant pathology while contributing to innovative research with real-world applications.
You will aim to characterise and investigate the potential of light-sensitive promoters to control gene expression in fungi, with the ultimate goal of understanding the timing of effector delivery during pathogenesis in Magnaporthe oryzae, the causative agent of Rice Blast disease. In addition to increasing our understanding of metabolic regulation and timing in the establishment of fungal pathology, this research has wide-ranging implications for developing alternative solutions to countering crop diseases globally.
Research requires adaptability and resilience, and this PhD will enable you to develop these traitsas you navigate the diverse challenges of this project. You will acquire a wide range of cutting-edge skills that will prepare you for success in a wide range of career paths in Academia or Industry, including experimental design, genetic sequencing, bioinformatics, recombinant DNA technologies, fungal culture and engineering, advanced biological imaging and analysis by flowcytometry and confocal microscopy, and communication skills.
Additionally, this PhD will help you develop strong problem-solving abilities and refine your project management skills, learning how to plan, prioritize, and manage multiple tasks and deadlines effectively.
You will regularly present your research findings, both in written and oral formats, to diverse audiences, improving your ability to convey complex ideas clearly and confidently. Working within an interdisciplinary research team and at two Universities, will enhance your collaboration and teamwork skills helping you to exchange ideas effectively. The technical and professional skills acquired in this project will prepare you for success in a wide range of careers in science, industry, or other sectors.

Application deadline

The deadline for applications is on 11 December 2024, midnight (GMT)
The studentship will start 1 October 2025.
Your application must be submitted to the Core Partner