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  Understanding structure-function relationships in the primary cilium using high content screening and super resolution microscopy


   Faculty of Biological Sciences

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Prof Michelle Peckham  No more applications being accepted  Funded PhD Project (European/UK Students Only)

About the Project

The School of Medicine (Prof. Colin Johnson - MP is co-supervisor) is seeking an enthusiastic PhD student to undertake research in molecular cell biology of a sub-cellular organelle called the primary cilium, with an emphasis on advanced imaging techniques. Cilia are finger-like projections from cells that act as a cellular “antenna” to detect and respond to chemical or mechanical cues. One important cue is fluid flow during the process of establishing asymmetry during early embryogenesis, the formation of the kidney nephron, and the formation of other tubular structures such as the neural tube. Primary cilia are regarded as cellular signalling hubs, regulating diverse signalling pathways, with particularly important roles during embryonic development. Cilia possess distinct molecular compositions and are enriched for many receptors, channels, and signaling components. In particular, the ciliary “transition zone” is a sub-compartment located at the most proximal 0.3-0.8 μm region of the cilium that is thought to control cilium composition and signalling by forming a protein diffusion barrier at the ciliary base.
The importance of the primary cilium has only become apparent in the last decade, and therefore processes involved in cilia formation and maintenance remain poorly understood. Defects in primary cilia are associated with heterogeneous inherited developmental conditions known as the ciliopathies that often present with diverse pathologies including cystic kidneys, blindness and nervous system defects. As a group, ciliopathies are comparatively common Mendelian inherited conditions with an overall estimated prevalence of 1 in 2000. By understanding the disease mechanisms for these conditions, we should gain new insights into more common diseases, including neural tube defects, retinal degeneration and obesity.
This project will use reverse genetics screening and super resolution microscopy to further characterize and understand the molecular composition and mechanisms contributing to ciliary organisation and barrier regulation. In the first instance, the student will complete a series of focused siRNA-based visual screens of cilium structure and function using high content imaging of appropriate cellular phenotypes. High content imaging will use a Perkin-Elmer “Operetta” system, based at the Leeds Institute of Biomedical and Clinical Sciences, and located at the St. James’s University Hospital campus. Potential screen hits will be confirmed by further rounds of secondary and validation screening, following by appropriate biochemical assays of function or protein-protein interaction. Detailed localization studies for ciliary proteins will then be possible with super resolution microscopy techniques, such as direct stochastic optical reconstruction microscopy (dSTORM). These studies will be based at the School of Molecular and Cellular Biology, Faculty of Biological Sciences. STORM is a single molecule sub-diffraction fluorescence imaging technique with a lateral resolution of ~20 nm and can therefore resolve components within the cilium. We envisage that this approach will provide unprecedented detail of structure-function relationships for protein trafficking and signalling processes at the primary cilium.
The student will receive training in high content imaging and biochemical techniques within the group. Prof. Peckham will be the microscopy expert supervisor, but the student will benefit from collaboration with other imaging and cell biology groups in Leeds. The Leeds group also have strong links with teams lead by Prof. Ronald Roepman at the Radboud University Medical Center, Nijmegen, and Dr. Oliver Blacque, University College Dublin.

Environment:
The student will be based at the University of Leeds in the Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, located at the St. James’s University Hospital campus. Super resolution microscopy will be based at the School of Molecular and Cellular Biology, Faculty of Biological Sciences, located on the main university campus. The student will join large research groups with expertise in the relevant techniques, with the expectation that the successful candidate will attend advanced training courses and research conferences.

Funding Notes

A full time PhD studentship: UK and EU citizens only, annual tax-free stipend of £14,273 for up to 3 years, subject to satisfactory progress. UK/EU tuition fees will be covered.
First degree: equivalent to at least a UK 2i honours degree in a relevant biomedical subject,
If your first language is not English you must provide evidence that your English language is sufficient: (See Faculty minimum requirements)

References

Reference:

Wheway G et al. (2015). An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes. Nat. Cell Biol. in press (PMID: 26167768)

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Project supervisors

Career overview

Professor Michelle Peckham graduated in Biology (Physiology of Organisms) from the University of York in 1981 and completed a PhD with Professor Roger Woledge in the Physiology Department at University College London, focusing on the energetics of muscle contraction, which she was awarded in 1984. Following her PhD, she briefly worked with Professor Woledge before moving to the Biophysics Department at King''s College London, where she collaborated with Professor Malcolm Irving from 1985 to 1987 to demonstrate the use of birefringence as a reporter of myosin cross bridge orientation in skeletal muscle. She then worked at the University of California, San Francisco, from 1987 to 1988, before returning to the Biology Department at the University of York to work with Professors David White and John Sparrow on insect flight muscle kinetics from 1988 to 1990. During this time, she engineered mutations in contractile proteins into flight muscle actin and employed advanced biophysical measurements to assess their effects on contraction, resulting in a publication in Nature in 1990. In 1990, she was awarded a Royal Society University Research Fellowship and moved to the Biophysics Department at King''s College London, where she established her own laboratory and began using molecular biology and cell culture techniques to study the cytoskeleton in cultured muscle cells. In 1997, she joined the University of Leeds as a Lecturer, progressing through the ranks to Senior Lecturer, Reader, and ultimately Professor in 2010. Her research interests expanded to include imaging and confocal microscopy, particularly developing super-resolution techniques at Leeds over the past 5 to 10 years, including the creation of Affimers for STORM imaging. Her work has also encompassed structural biology, notably the discovery and characterisation of single alpha helices in proteins, and her laboratory recently solved the structure of the shutdown state of myosin using Cryo-EM. Professor Peckham has trained over 40 postgraduate and postdoctoral researchers and served as the president of the Royal Microscopical Society from 2016 to 2019. She is currently the Executive Honorary Secretary of the RMS and a Wellcome Trust Investigator, focusing on the regulation of motor protein activity.


Research interests

Professor Peckham''s research focuses on the cytoskeleton, specifically investigating how myosins and other motor proteins function within cells and how mutations in cytoskeletal proteins can lead to disease. The laboratory employs a variety of techniques, including Cryo-electron microscopy (Cryo-EM), confocal microscopy, super-resolution imaging, and biochemical and biophysical methods to explore these areas. Significant contributions include solving the structure of the shutdown state of smooth muscle myosin, which was published in Nature in December 2020, revealing insights into how myosin transitions to this state and the role of phosphorylation in its activation. The laboratory has developed advanced imaging systems, such as a 3D PALM/STORM system and an instant structured illumination microscope (iSIM), enhancing the ability to conduct live cell imaging and achieve resolutions significantly better than conventional methods. Professor Peckham''s work also extends to collaborations aimed at developing small non-antibody binding proteins known as Affimers for improved super-resolution imaging of cytoskeletal proteins. Recent studies have utilised stimulated emission depletion (STED) microscopy to investigate structural changes in Z-discs in diseased hearts, with findings published in Frontiers in Cardiovascular Medicine in 2023. Research interests encompass the roles of myosins in diseases, including cancer, where specific myosins are found to be overexpressed in prostate cancer, and the differentiation of muscle cells in culture, focusing on the organisation of the cytoskeleton. Current PhD projects in the lab include the use of artificial intelligence to analyse super-resolution microscopy images, the development of Affimers for visualising myosins, and the impact of heart muscle diseases on protein organisation. Overall, Professor Peckham''s research integrates structural biology, advanced imaging techniques, and molecular biology to further understand the cytoskeleton''s role in health and disease.

View Professor Michelle Peckham's profile