Current PhD Projects
Developing a novel technology platform to map endogenous gene expression in vivo for correlation to life course heart health in murine models
Mammalian Utrophin and Dystrophin are paralogous genes that are important for skeletal and cardiac muscle function, but are expressed sequentially during ontogeny. We will study the processes that regulate this switch in gene expression, using new mouse models to image gene expression in development and to profile epigenetic modifications that curtail Utrophin expression. We aim to explore whether epigenetic interventions are useful in Duchenne's Muscular Dystrophy. MRes Project 1 will use RT-PCR and RNA sequence analysis to examine gene expression in muscle samples throughout development. This data is used to identify critical time points where Utrophin is silenced in favour of Dystrophin; bisulphite sequencing and histone ChIP analysis will be used to evaluate relevant chromatin-based changes at the Utrophin locus at these times. MRes Project 2 will exploit two new mouse reporter lines where Utrophin and Dystrophin expression will be detected using luciferase and LacZ read out, with photoacoustic imaging and optical projection tomography. The subsequent multidisciplinary PhD project based between the CSC and the Physics Department will build upon data generated by projects 1 and 2 to investigate whether epigenetic drug treatment can be used to prolong the expression of Utrophin into adulthood.
Professor Amanda Fisher and Dr Mathew Van de Pette - MRC Clinical Sciences Centre
Professor Paul French and Dr James McGinty - Photonics Group, Physics Department, Imperial College London.
Multidimensional imaging and spectroscopy of diamond photoluminescence
This MSc+PhD project would be undertaken within the EPSRC funded Centre for Doctoral Training on Diamond Science and Technology, which is led and co-ordinated by the University of Warwick. The PhD project would be supervised by Paul French, Chris Dunsby and Mark Neil and the MSc year would include miniprojects supervised by Philip Martineau (De Beers Technologies, DTC Research Centre) on the characterisation of photoluminescence lifetime parameters of diamond and by Oliver Williams (Cardiff University) on the optical characterisation of nanodiamond luminescence. The PhD project aims to develop and apply photonics technology for time resolved luminescence studies, including fluorescence lifetime imaging (FLIM) microscopy and spectroscopy using tunable supercontinuum sources, femtosecond Ti:Sapphire lasers and "two colour-two photon" nonlinear excitation below 340 nm, i.e. near and above the bandgap. Characterising the spectro-temporal properties of diamond photoluminescence and mapping these properties to correlate them with structural images, including super-resolved images from our STED microscope, could provide new means to contrast different types and states of diamond for: (a) contrasting different forms of diamond including natural and synthetic gemstones, monocrystalline and polycrystalline diamond, bulk diamond and nanodiamond, (b) studying diamond materials that have experienced different levels of stress, and (c) studying emission properties of nanodiamonds for potential biomedical imaging applications. This project would require a student with a background in physics or materials science with strong experimental and programming skills and knowledge of optical physics.
Development and application of novel 3-D microscope
Oblique Plane Microscopy (OPM) is a novel (patented) microscopy technique that is capable of video-rate 3-D imaging of fluorescently labelled biological samples. OPM works by illuminating the sample with a tilted sheet of laser light and employs correction optics that allow the focal plane of the microscope system to be tilted so that the focal plane is overlapped with the plane of illumination. OPM is therefore similar to the technique of selective plane illumination microscopy (SPIM), but can be implemented as an add-on to a standard fluorescence microscope and only requires a single objective lens to both illuminate and collect light from the specimen. The advantages of OPM include minimal exposure of the specimen to illumination light, as only the plane being imaged is illuminated at any given time. This minimizes the undesirable effects of photobleaching (optically induced destruction of fluorophores) and phototoxicity (optically induced killing) of sensitive biological specimens. As it can be implemented on a conventional microscope, OPM is also readily compatible with high throughput imaging of multiwell plate arrays, e.g. for screening developing embryos in developmental biology studies. This interdisciplinary project will include the construction of OPM systems, experimental measurements of their resolution and performance, and a comparson of this performance with theory. New illumination and detection geometries will also be explored. During the project, the OPM system will be applied to imaging dynamic biological samples such as imaging calcium wave propagation in electrically paced cardiac myocytes and the development of c. elegans and zebrafish embryos expressing the intrinsic green fluorescent protein (GFP). More information on OPM can be found here.