PhD Studentship: Tracking virus-induced shifts in cellular ultrastructure: Developing novel 3D correlative imaging pipelines to anticipate and track the effect of viral infections within living cells

Given the rapid cell-cell and tissue-tissue communication pathways within a living organism, any single cell within can be viewed as a potential indicator of the health of that organism and can do so through its particular biochemistry and morphology. Often, the internal landscape of cells is difficult to decipher and assess to high spatial resolution and for that reason our analysis is limited to molecular indicators alone. We have now at our disposal a novel nanometer resolution 3D correlative imaging pipeline that combines light and X-rays and allows us to utilise the cellular landscape as a useful tool for analysis. Ultrastructural analysis of mammalian cells gives important insights into cellular physiology and, most interestingly, cellular heterogeneity, even within common-ancestor cell lines with identical genomes. Within the context of a recently awarded ERC grant that promises to deliver diagnostic capabilities using micron-sized biopsies assessed through ultrastructural cellular features we will tackle immediate knowledge requirements in infection biology such as:

• Why do some cells within a population get infected while others don’t?
• What is the effect of the circadian cycle to the healthy and pathological states of cells?
• How do cellular features restructure throughout an infection?
• Do neighbouring cells change their ultrastructure in response to their neighbours’ state of health?

Using the automated imaging pipeline for correlative ultra-high resolution 3D imaging of mammalian cells developed for the beamline B24 at the UK synchrotron Diamond Light Source, we will study influenza infection in standardised model systems such as A549 cells. We have successfully produced a toolbox of fluorescently labelled influenza viruses, including spherical strains (A/WSN/33) and filamentous strains (A/Udorn/72) which allow us to track infection presence and progression of distinct types of the same virus and assess their effect in the target cells and their neighbours. Importantly, given that a known factor influencing cellular heterogeneity and infection of cells by viruses is the cellular circadian clock, we will also attempt to map and correlate the circadian variation in ultrastructure to viral infection potency and persistence using fluorescence circadian phase markers and synchronised “phased” cultures.

Such combined approach will allow the thorough investigation of infection effects on cellular ultrastructure and give rise to physiologically relevant insights into the life of a prominent human pathogen.

Specific objectives:

1. Setup an analysis pipeline for medium throughput correlative fluorescence and soft-X ray imaging
2. Generate a model of mammalian cell infection with influenza virus and characterise the time-course of ultrastructural changes.
3. Assign structural variability profiles given a comprehensive range of variables such as temporal states and viral strains.

Taken together, this will produce a body of data that can then be used to develop diagnostic biomedical applications.

Please get in touch with Maria Harkiolaki (Maria.Harkiolaki@warwick.ac.uk), Nicole Robb (Nicole.Robb@warwick.ac.uk) or Robert Dallmann (r.dallmann@warwick.ac.uk) for more information.

Funding 

The scholarship will cover full tuition fees at the UK/Home fee level and will also provide an annual stipend for 3 years at the UKRI rate.

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