PhD student profiles

     
     

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Graeme Smith
Wellcome Trust 4-year Interdisciplinary PhD Programme, beginning in Autumn 2012

Project title
Genome-wide analysis of ageing in fission yeast

Principal investigator: Prof Jürg Bähler, ISMB, UCL
Co-investigator: Prof Christine Orengo, ISMB, UCL

   
Background
From 2004 to 2010, I studied biology, computer science, and statistics through the Open University whilst working full-time to fund my studies.  After graduating with a BSc in Life Sciences, I received BBSRC funding to do an MSc in Bioscience Technology at the University of York.  My motivation in undertaking this master’s course was to gain in-depth knowledge and hands-on experience of a variety of practical techniques in preparation for a PhD.

During my MSc I did an industrial placement with AstraZeneca where I used high-throughput screening methods to investigate the role of the membrane transporter OCTN2 in drug-induced cardiotoxicity.  I first became interested in ageing research whilst working as a Research Support Technician in Dr Lynne Cox’s lab at the University of Oxford, which specializes in the molecular basis of ageing. I chose the Wellcome Trust ISMB PhD programme as I believe modern research increasingly requires a multi-disciplinary approach.
 

Rotations
Rotation 1
Dr Bibek Gooptu and Dr Konstantinos Thalassinos: Subcellular proteomic studies of endoplasmic reticulum stress in a model conformational disease.

Rotation 2
Prof Jürg Bähler: Characterisation of Intron Sequences and Regulation in Fission Yeast.

Rotation 3
Prof Ivan Gout: Unpublished work

 
PhD Project
My PhD project uses the fission yeast Schizosaccharomyces pombe as a model organism to investigate the molecular basis of cellular ageing.  A well-established model of ageing is the chronological lifespan, defined as the survival time of non-dividing cells.  In fission yeast a non-dividing state can be induced by either glucose depletion or nitrogen starvation (See Figure).

Why use fission yeast to investigate chronological ageing? 
There are several age-related pathways, such as TORC1, which are conserved from yeast to man, calorific restriction modulates lifespan in mammalian models as well as yeast, and pharmacological interventions which modulate life span are widely conserved over divergent organisms.  In using S. pombe as a model organism to investigate cellular ageing, we hope to better understand the mechanisms underlying age-related human diseases. Additional advantages are that S. pombe is easily cultured and shows a short lifespan.

Experimental Approach
Ageing of S. pombe cells is done as described in the figure below.  Once samples are obtained across the cell culture’s lifespan, techniques such as RNA-seq or proteomic analysis can be used to investigate ageing specific cellular mechanisms.

 

figure 1a

 

figure 1b

 

Figure 1: This diagram of the S. pombe cell cycle shows the two emerging models used in cellular ageing studies.
1) S. pombe cells depleted for glucose arrest in a G2 stage where they can survive for several days.
2) Under nitrogen starvation S. pombe cells enter a G0 like quiescent state which allows the cells to survive for > 2 months providing that the media is exchanged frequently to replenish glucose and remove the build-up of toxic by-products. 
Our experimental approach is to induce non-dividing cells via either of these methods and then maintain two cultures, a wildtype to act as control, and a long-lived mutant as identified by a screen within the Bähler lab.  These samples are then aged while collecting regular samples for subsequent RNA-Seq analysis.   During this process the viability of the cultures can be monitored by plating a known volume of cells onto a plate and counting the colonies formed.

 
Publications

Widespread exon-skipping triggers degradation by nuclear RNA surveillance in fission yeast. Danny A. Bitton, Sophie R. Atkinson, Charalampos Rallis, Graeme C. Smith, David A. Ellis, Daniel C. Jeffares, Yuan Yi Constance Chen, Michal Malecki, Sandra Codlin, Michal S. Lubas, François Bachand, Cristina Cotobal, Samuel Marguerat, Juan Mata, Torben H. Jensen, and Jürg Bähler (2015), Published online April 16, 2015, in advance of the print journal, Genome Research

LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq Genome Research. Danny A. Bitton, Charalampos Rallis, Daniel C. Jeffares, Graeme C. Smith, Yuan Y.C. Chen, Sandra Codlin, Samuel Marguerat, and Jürg Bähler  (2014), Genome Research 24(7), 1169–79.

 

 

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