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EASTBIO Mechanisms and functions of RNA interference in Cryptococcus neoformans


School of Biological Sciences

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Dr E Bayne , Dr E Wallace No more applications being accepted Competition Funded PhD Project (Students Worldwide)
Edinburgh United Kingdom Genetics Microbiology Molecular Biology

About the Project

RNA interference is a fundamental mechanism of genome regulation mediated by small RNAs and conserved across eukaryotes. It can operate at both transcriptional and post-transcriptional levels, and plays important roles in controlling gene expression and genome stability. Recent studies suggest that RNAi can also play significant roles in host-pathogen interactions.

Our lab has recently begun to investigate RNAi pathways in Cryptococcus neoformans, an opportunistic fungal pathogen that is responsible for ~1 million cases of meningitis per year in immunocompromised people. The C. neoformans genome encodes two of each of the core RNAi pathway components, Dicer and Argonaute, and our preliminary analyses of deletion mutants suggest that these proteins are involved in regulation of distinct sets of genomic loci. However, the mechanisms of regulation and their biological significance remain poorly understood.

The aim of this project is to further investigate RNAi function in Cryptococcus. We will examine the nature of the loci regulated by RNAi, and the regulatory mechanisms involved, determining whether regulation occurs at transcriptional and/or post-transcriptional levels, and identifying and characterising additional factors required for the process. We will also assess the phenotypic consequences of disrupting RNAi-mediated regulation, including testing whether RNAi is involved in changes in gene expression associated with pathogenicity. We may also look for any evidence of cross-kingdom RNAi, i.e. transfer of functional small RNAs between Cryptococcus and host cells.

The project will provide training in a broad range of molecular biology techniques including CRISPR-Cas9 genome editing, DNA, RNA and protein analyses, chromatin-IP, proteomics, and next-generation sequencing approaches such as RNA-seq and ChIP-seq. Communication, presentation and critical thinking skills will be developed through regular participation in lab meetings, journal clubs and seminars.

The School of Biological Sciences is committed to Equality & Diversity: https://www.ed.ac.uk/biology/equality-and-diversity

How to Apply:
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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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