**PLEASE NOTE – the deadline for requesting a funding pack from Darwin Trust has now passed and completed funding applications must be submitted to Darwin Trust by 19th January. We can still accept applications for this project from self-funding students.
Fungi control their growth to thrive in varied environments. Fungal pathogens are a major worldwide health burden, killing more people each year than malaria or tuberculosis. We hypothesize that conserved RNA binding proteins (RBPs) have a major role in controlling fungal growth in response to the environment, by allowing precise temporal and spatial control of protein production within fungal cells. For example, the Ssd1 protein binds the messenger RNAs encoding some protein components of the fungal cell wall, probably to control their translation near the growing tip of the cell.
This project is an interdisciplinary mixture of lab-based molecular biology and computational studies, that will use quantitative methods to study how RBPs regulate protein production from messenger RNA. Using rapid cross-linking and cDNA analysis (CRAC) the student will generate RNAseq libraries that will give high resolution datasets (in time and sequence space) of changing RNA-protein interactions over environmental responses. We will use bioinformatic analysis to identify motifs within RNA that these RBPs recognize, and test these predictions by genetic engineering and assays such as fluorescence microscopy. There will be opportunities to use available fungal genome sequences to study the evolution of both protein and its regulatory targets. There will be further opportunities to develop structural bioinformatics and analysis skills through interactions with the Cook Lab, to develop molecular-level hypotheses of protein function. Overall, the work will give a mechanistic insight into how fungal growth responds to the environment in budding yeast and pathogenic fungal models.
The successful candidate will be excited to combine experimental (yeast, RNA, proteins) with computational (bioinformatics, statistics, structural modeling, phylogenetic) methods. You will have demonstrated basic skills in at least one of wet and dry work, and during the PhD will be trained to a high level in both. You will join a thriving research collaboration, in a vibrant research environment focused on fundamental cell biology and bioinformatics. Both the Wallace and Cook groups will support your career development including laboratory, programming, presentation and writing skills. You will be encouraged to build a network of scientific colleagues in Edinburgh and more widely, including presenting your work at conferences.
This project will be supervised by Edward Wallace (https://ewallace.github.io/) and Atlanta Cook (http://cook.bio.ed.ac.uk/). Interested candidates should enquire in teh first instance to us by email, describing your interest in this project in specific terms (see https://www.ed.ac.uk/informatics/postgraduate/apply/contacting-supervisors).
Please indicate why you are interested in the subject matter (i.e. some combination of fungi, pathogens, RNA, translational control, big data or bioinformatics), and also briefly describe your experimental and computational skills.
The School of Biological Sciences is committed to Equality & Diversity: https://www.ed.ac.uk/biology/equality-and-diversity
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