2014 - Present: PhD, University of Warwick
"Functional Electrochemical Mapping of Immune Cells"
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2013 - 2014: MSc, Mathematical Biology and Biophysical Chemistry (Distinction), University of Warwick
Miniproject 1 (Theoretical) - "Analysis of TCR sequencing data".
Supervisor - Dr. Sascha Ott
Thesis Abstract: A preliminary analysis of over 5 million sequences from the T cell receptor beta (TRB) locus was performed, identifying previously unknown levels of expression from the sub-dominant TRB allele. It is now thought to be transcribed at a comparable rate to the functional allele. Non-functional sequences can be identiﬁed via recognition of one of two ’putative V segments’ found during this project, a lack of a J segment, or failure to contain an open reading frame. The strategies presented here allow a more accurate interpretation of β-chain sequences which could lead to the identiﬁcation of speciﬁc T cell receptor (TCR) clones for the recognition of antigens associated with many diseases, including cancer.
Software was developed to manage the large data ﬁles generated by high-throughput sequencing, permitting the characterisation of observed frequencies of each V and J seg-ment, as well as each V/J combination. This software can be used on future analyses and provides a base for the development of more advanced software that may be required in light of the numerous improvements to both the experimental protocol and computational pipeline proposed as a result of this project.
Miniproject 2 (Experimental Biology) - "Accelerated directed evolution of gene expression regulation".
Supervisor - Prof. Alfonso Jaramillo
Poster Abstract: Directed evolution is now firmly established as one of the main methods of protein engineering in the laboratory. However, one round of discrete directed evolution involves mutation, expression, selection and amplification steps and can often take days with frequent human intervention. In 2011, Liu et al. developed a new technique, phage assisted continuous evolution (PACE), that allows many rounds of direction evolution over a significantly shorter time period (~200 in 8 days). Here we replace the phage in Liu’s work with a synthetic phagemid, allowing evolution much faster still.
Miniproject 3 (Physical Chemistry) - "Surface Charge Detection with Bias Modulated Scanning Ion
Supervisor - Prof. Patrick Unwin
Paper Abstract: In this contribution, bias-modulated scanning ion conductance microscopy (SICM) is used to simultaneously map both the topography and surface charge of a substrate. At low electrolyte concentrations (10mM) the direct ion current, driven by a potential applied between a bulk quasireference counter electrode (QRCE) and a QRCE in the nanopipette probe is shown to be sensitive to heterogeneities in the surface charge as a result of the relatively thick diffuse double layer at the interface.
Furthermore, the alternating current (AC) phase is also shown to act as a feedback mechanism, with characteristic shifts at different interfacial charges. The myriad potential applications for the ability to simultaneously image topography and activity are as diverse as to include both materials science and proteomics, where an ability to map surface charge could provide detailed studies of protein activity in a membrane-bound environment.
2010 - 2013: BSc (Hons), Mathematics (First Class), University of Warwick
I graduated from Warwick University in the summer of 2013 with a First Class Honours degree in Mathematics, with broad interests including topology, combinatorics and astrophysics.
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