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Applications of an atlas of protein nanoscale organisation for understanding immune cell function

Principal Supervisor: Professor Dylan Owen

Secondary Supervisor(s): Dr Daniel Nieves

University of Registration: University of Birmingham

BBSRC Research Themes: Understanding the Rules of Life (Immunology, Systems Biology)

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Deadline: 4 January, 2024


Project Outline

Taking the analogy of gene sequence databases, these have allowed the development of the field of genomics - the analysis of gene sequences and genomes between cells, between species, between individuals and between conditions (e.g. health and disease). This includes recent advances in GWAS – Genome Wide Association Studies, which correlate genetic markers with disease predisposition. However, current descriptions of cellular systems are incomplete. They can be characterised at the genomic, transcriptomic and proteomic level, but there is a final level: How those proteins are organised in 3D space.

We have recently established a unique database of protein nanoscale organisation containing data from super-resolution single molecule microscopy – the method for which the 2014 Nobel Prize in Chemistry was awarded. The aim of this project is to develop “spatial nano-omics” – the systematic study of the way molecules are organised in cells and to understand what we can learn when given access to a large database of diverse protein organisations. Based on our own expertise, the initial focus of this PhD project will be the organisation of membrane proteins on the surface of T cells.

Components of the T cell receptor signalling pathway are known to display a variety of nano- and microclustering behaviour. These proteins include the TCR complex itself, kinases such as Lck and ZAP70, phosphatases like CD45 and Lyp and adaptor proteins, for example LAT and SLP76. Clustering behaviour is context dependent, with many proteins rearranging their organisation after stimulation. The clustering behaviour serves to regulate the signalling pathways and set thresholds for T cell activation. Aberrant nanoscale organisation has been linked to pathology, however, the degree of nanoscale organisational diversity of T cell signalling proteins is not known.

The objectives of this PhD are:

  1. To develop the language, concepts and analysis methods to compare and contrast different protein nanoscale organisations.
  2. To interrogate the database (and to acquire your own imaging data) to define the diversity of protein nanoscale organisation it contains.
  3. To determine how the nanoscale organisation of receptors on the surface of T cells varies in health and disease, between different T cell sub-types and between individuals.

The methods used will be:

  1. Super-resolution fluorescence microscopy
  2. Cell culture
  3. Coding and data analysis in Matlab, R, Python or C

Techniques

  • Cell culture
  • Super-resolution fluorescence microscopy
  • Data analysis (R, Matlab, Python or C depending on the student preference)
  • Bioinformatics, data curation and interaction with public databases