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Understanding Neuroinflammation through advanced in vitro 3D modelling using human Pluripotent Stem Cells

  • Full or part time
    Dr S Cowley
    Prof W S James
  • Application Deadline
    Friday, January 25, 2019
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

Project Description

Microglia - brain-resident macrophages - carry out homeostatic surveillance functions in the brain, clearing dying cells, extracellular debris, and pruning synapses during development. However, build-up of debris, especially aggregated proteins, causes chronic microglial activation, contributing to neurodegeneration and psychiatric disorders. Microglial inflammatory damage may be direct, or mediated by astrocytes, which normally support neuronal metabolism but become damaging under instruction from microglia. Clearly, understanding the normal function of microglia, their interactions with neurons and astrocytes, and the mechanisms by which this triumvirate becomes perturbed, is crucial to our understanding of brain health, mental health and diseases of ageing - and authentic human cellular models are necessary to achieve this.

Our team have pioneered the generation of macrophages and microglia from human induced Pluripotent Stem Cells, and worked extensively with iPS-neuronal models. However, the 2D models we work with currently do not form mature, extensive synaptic networks or develop the pathological features of protein aggregation. In 3D culture, neurons mature further and aggregated protein pathology can develop. This D.Phil project will develop and exploit a relatively simple 3D triculture system, containing iPS-microglia, astrocytes and cortical neurons. The research project will expose the student to cutting-edge cell and molecular biology, imaging, biochemistry and sequencing technologies. A suite of neuronal, astrocytic and microglial assays will be deployed to assess cellular function and maturity, and for full exploitation of the 3D system, several advanced imaging methodologies can be employed, including confocal, multiphoton and Lightsheet microscopy, InCell and Opera Phoenix high-content confocal imaging systems.

The student will be primarily based at the academic partner institution, the Sir William Dunn School of Pathology, University of Oxford, with secondments to the industrial partner, Eli Lilly, as necessary. Eli Lilly is geographically very close (1 hour travel from Oxford), so the student can be seconded to the industrial partner very flexibly, according to the research progress, for periods of 1-3 weeks at a time, and for a minimum of 3 months in total across the 4 year D.Phil project. The Lilly Research Centre in Windlesham has modern biochemistry (automated liquid handling systems, AlphaLISA, MSD, SiMoA, automated Western blot systems, DLS, Flow cytometry), cell biology (Opera and Operetta Phoenix high-content imaging systems) and molecular biology (Nanostring, RT qPCR) labs, in which the student will receive appropriate professional training in support of the project work.

Attributes of suitable applicants:
The applicant should have, or be expected to achieve in the current academic year, a high-ranking in a Batchelor’s degree course in the biomedical/biosciences subject area. Experience of at least one lab-based practical research project is helpful, for the candidate to be able to demonstrate the enthusiasm, drive and tenacity needed to pursue a research degree.

How to apply:
If you are interested in applying for a BBSRC iCASE studentship please contact the named supervisor, Sally Cowley () for further information and to determine whether they would encourage you to apply. Applicants who wish to apply for a BBSRC iCASE studentship should apply directly to the Interdisciplinary Bioscience DTP via

Funding Notes

Funding notes: This project is funded for four years by the Biotechnology and Biological Sciences Research Council BBSRC. BBSRC eligibility criteria apply (View Website Annexe 1). EU nationals who do not meet BBSRC residence criteria are encouraged to contact the programme administrator to check their eligibility for BBSRC funding before submitting a formal application. Successful students will receive a stipend of no less than the standard RCUK stipend rate, currently set at £14,777 per year, which will usually be supplemented by the industrial partner.

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