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EASTBIO Investigating the role of microtubule cytoskeleton in building the neuronal connectome


School of Biological Sciences

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Dr D Cheerambathur , Dr Tony Ly No more applications being accepted Competition Funded PhD Project (Students Worldwide)

About the Project

The central nervous system is a complex network of neurons and supporting cells that form the information relaying unit of an organism. During neural development, pioneer neurons extend axons in response to guidance cues from other neurons and non-neuronal cells to establish the framework that build the neural circuits. The assembly of this circuit is a highly orchestrated event that initiates with the pioneer axon outgrowth which is followed by fasciculation (axon bundling) and synapse formation with the axons of follower neurons. How these organizational features emerge during development is poorly understood.
This project will focus on how the microtubule cytoskeleton function within the pioneer neurons to facilitate the assembly of neural circuits. Microtubules, polymers of alpha and beta-tubulin are critical to the structure and function of all types of neurons. Several microtubule related proteins are linked to mutations that underlie neurological and brain development disorders. Despite the central role of the microtubule in the neurons, little is known about the identity and function of microtubule cytoskeleton in specific neuronal subtypes such as the pioneer neurons. To tackle this problem, the project will draw on the expertise of the Cheerambathur-lab expertise in studying neurodevelopmental mechanisms using C. elegans and Ly-lab expertise in developing novel quantitative tools to study dynamic changes in cellular proteomes.
Overall the goal of the project is to build a proteomic profile of the developing pioneer neurons in C. elegans to identify key microtubule factors required for pioneer neuron function. Quantitative mass spectrometry-based proteomics have largely been restricted to sample types where cells are in abundance. Recently, Ly lab developed a sample processing method, ‘in cell digest’, obtaining proteome depths of >6,000 proteins from 2,000 cells and detection of hundreds of proteins from single cells. We aim to develop and apply this method to obtain detailed proteomic profiles of the developing pioneer neurons in C. elegans. Its highly invariant and synchronous developmental program and simple and well-characterized neuronal tissue will highly aid this analysis.
The student will combine cutting-edge quantitative whole-organism proteomics with in vivo fluorescent cell labelling techniques to isolate pioneer neurons from developing embryos and profile the microtubule neuronal proteome. Promising candidates will be analyzed using genetic and microscopy-based approaches to determine the relation of the microtubule factors and neural circuit assembly. The student will also be trained state-of-the-art in vivo high-resolution live microscopy, image analysis tools (e.g. Image J), genetics and molecular biology techniques, cutting-edge mass spectrometry-based proteomics. Taken together, the student will develop experience in quantitative cell biology using the latest proteomic, genetic and imaging tools to tackle questions related to neuronal development. Additionally, this collaborative effort will allow the student to work in labs with complementing expertise and access the state-of-the-art research and training environment offered by the two institutions, the Wellcome Centre for Cell Biology in Edinburgh and the School of Life Sciences in Dundee.

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Funding Notes

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership http://www.eastscotbiodtp.ac.uk/how-apply-0. This opportunity is open to UK and International students and provides funding to cover stipend and UK level tuition fees. The fee difference will be covered by the University of Edinburgh for successful international applicants. Please refer to UKRI website (https://www.ukri.org/our-work/developing-people-and-skills/find-studentships-and-doctoral-training/get-a-studentship-to-fund-your-doctorate/) and Annex B of the UKRI Training Grant Terms and Conditions (https://www.ukri.org/wp-content/uploads/2020/10/UKRI-291020-guidance-to-training-grant-terms-and-conditions.pdf) for full eligibility criteria.
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