The Bloomsbury Colleges | PhD Studentships | Studentships 2020 | Dissecting the non-coding transcriptome of pathogenic mycobacteria
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Dissecting the non-coding transcriptome of pathogenic mycobacteria

Principal supervisor: Dr Irilenia Nobeli (Birkbeck)

Co-Supervisor: Dr Sharon Kendall (RVC)

Award includes tuition fees and a stipend of £17,009 including London Weighting (at 2019/20 rates, so slightly higher for 2020 entry)

100% FTE for 3 years, from September 2020.

Project Description:

Project Description

Members of the Mycobacterium tuberculosis complex are among the most successful pathogens. A complex regulation of when genes are switched on and off plays a significant role in this success. Traditionally, proteins were thought of as the mediators of gene expression regulation but more recently, non-coding (nc) RNAs (antisense, short, long non-coding RNAs and parts of the untranslated regions of mRNA transcripts) have been shown to play important regulatory roles in mycobacteria (Arnvig et al. 2014; Golby et al. 2013).

In this project, we will test the hypothesis that mutations in ncRNA regulators across human- and animal-adapted pathogens are linked to host specificity and zoonosis (disease spread to humans via animal pathogens). Understanding this link could lead to the identification of mycobacterial targets for novel therapies. Importantly, the principles of ncRNA regulation extend to many diverse species and thus studying this poorly understood part of gene expression regulation has implications beyond mycobacterial research.

The study’s main aim is to further our knowledge of gene expression regulation by non-coding elements in mycobacterial genomes. The bulk of the initial work will be computational, developing and using bioinformatics methods for mining public genomic/trancriptomic data. Hypotheses generated by this computational analysis will then be tested in the lab.

Candidate requirements

We invite applications from students with good Science undergraduate degrees ((1st class or upper second), preferably with some Biology component. Postgraduate training in bioinformatics is highly desirable but alternative working experience or self-taught skills will be considered.

Training

The project offers opportunities for training in a very wide range of bioinformatics skills, including the analysis of next-generation sequencing data, unix shell programming, programming in R and python, as well as more general bioinformatics training on sequence and structure analysis of proteins and nucleic acids. The student will be encouraged to attend relevant modules of the MSc Bioinformatics at Birkbeck, especially Statistics.

The collaboration with the RVC-based supervisor will offer the opportunity to acquire skills in basic molecular biology and in working with Mycobacteria. The student will gain experience in basic Microbiology and Molecular Biology techniques.

Subject Areas/Keywords:

Bioinformatics, non-coding  RNA, mycobacteria, zoonosis, next-generation sequencing, genomics, transcriptomics,, RNA-seq, Tn-seq, microbiology, molecular biology.

Key References:

Arnvig et al. (2014) DOI: 10.1128/microbiolspec.MGM2-0029-2013.

Golby et al. (2013) DOI: 10.1186/1471-2164-14-710

Ozuna et al. (2019) DOI: 10.1093/bioinformatics/btz643

Further details about the project may be obtained from:

Principal Supervisor: Dr Irilenia Nobeli (i.nobeli@bbk.ac.uk)

Co-Supervisor: Dr Sharon Kendall (skendall@rvc.ac.uk)

Further information about PhDs at Birkbeck (Biological Sciences) is available from:

http://www.bbk.ac.uk/study/2019/phd/programmes/RMPBIOLG

Application forms and details about how to apply are available from:

http://www.bbk.ac.uk/study/2019/phd/programmes/RMPBIOLG/#how-to-apply

Please note that you do not need to write your own research proposal. Instead, please state clearly in your application that you are applying for this specific project and use the Supporting Statement in the application to explain what attracted you to the project and why you are a suitable candidate for it.

The successful applicant will be affiliated with the BBSRC-funded London Interdisciplinary Doctoral (LIDo) programme in biosciences (http://lido-dtp.ac.uk/index.html). As part of LIDo the student will undertake two 4-month rotations in the first year (in the labs of the first and second supervisor), will follow the LIDo training programme (including the SysMIC course) and will take part in the annual retreat and other LIDo events, in addition to events organised for Bloomsbury-funded PhD students. The student will not be expected to take part in the Professional Internship for PhD Students scheme.

Closing date for applications is:      
2 March 2020