2024

Which rotation did you decide to pursue for your PhD project and why did you choose it? My PhD project explores the metastatic tumour microenvironment within the lymph nodes of patients with oesophageal adenocarcinoma. This project combines elements of both my first and third rotation projects, allowing me to directly apply the skills I developed during my first year to the remainder of my PhD. I am part of an interdisciplinary team led by Professors Underwood and Walters, working closely at the interface between scientific advancement and clinical practice. I have particularly enjoyed the translational aspect of my work and the opportunity to collaborate with clinicians treating patients with oesophageal adenocarcinoma.

What skills have you developed so far? During the first year of the iPhD, I have developed a wide range of skills across different areas. I have consolidated and expanded my bioinformatics knowledge and applied it across all three of my rotation projects. I have also strengthened academic skills such as critical thinking, academic writing, and research governance. In addition, I have gained experience working in diverse scientific environments, collaborating with different research groups, engaging school pupils in scientific discussions, and presenting at conferences. These experiences have given me both the confidence and the ability to communicate my research effectively to a variety of audiences, while ensuring my key message remains clear and consistent.

How have you found the mathematic/computational component of the DTP? Before joining the University of Southampton, I had some experience in bioinformatics, although most of it was self-taught due to the breadth of the field. The computational component of the course in Southampton has helped me to understand the wider context of bioinformatics—how it works and how it is applied in research. It has also enabled me to strengthen my coding skills, particularly in R, despite already having a reasonable level of prior experience.

What have you enjoyed most about your experience so far? What have you found challenging? A highlight for me has been the freedom to shape the direction of my research career. I have been able to focus entirely on bioinformatics while applying it to a range of disease contexts, including cancer and inflammatory disease. One of the main challenges has been balancing rotation projects, taught modules, and other responsibilities simultaneously. However, this experience has been valuable in preparing for the demands of my full PhD project.

Which rotation did you decide to pursue for your PhD project and why did you choose it? From three really enjoyable rotations and equally fascinating projects, I chose to pursue my third rotation in the lab of Dr Cara Croft, focusing on glial contributions to tau pathology and clearance. 

What skills have you developed so far? My rotations focused on Alzheimer’s disease but from three very different angles, so I was lucky to develop a variety of skills in microbiology, bioinformatics, rodent behaviour, tissue culture, molecular biology, and microscopy. It is really exciting to have had an introduction to such a range of research skills so that I can think about how to apply these to my project throughout my PhD. 

How have you found the mathematic/computational component of the DTP? I entered the DTP with minimal experience in computational biology, but the introduction offered in the DTP was really effective and enjoyable. The instructors in the Quantitative Cell Biology module were clear and helpful in their explanations and I feel so much more confident now approaching computational techniques in the future.  

What have you enjoyed most about your experience so far? What have you found challenging? The most enjoyable aspect of the DTP is being able to pursue your interests surrounded by such supportive and encouraging colleagues. Truly, everyone wants you to succeed and find a research area that suits you and your interests. It also goes without saying that being part of a DTP and having immediate friends in the form of your cohort is a great aspect that helps you feel supported. The first semester of the rotation year is probably the most challenging time (it is smooth-sailing after that!) because you are just starting to get your bearings, you have several modules, and you are settling into your first rotation. But the organisers of the DTP and other students in years 2/3/4 are super helpful, supportive, and encouraging, and overall the experience couldn’t have been better. 

Which rotation did you decide to pursue for your PhD project and why did you choose it? I choose to pursue a rotation with Professor Stephanie Kermorgant within the Tumour Biology team at Bart’s Cancer Institute. For my project I will be investigating a mutant variant of the receptor tyrosine kinase Met in lung cancer, characterising the relationship between its protein trafficking and downstream signalling. The mutant Exon 14 Met protein presents a driver mutation that is sufficient to initiate tumorigenesis in isolation, and clinical application is significant given that in addition to Met-addicted tumours, aberrant Met gene activity may promote acquired resistance to classical kinase inhibition. The project therefore really appealed to me as a means to explore my interests in fundamental signalling biology with clinical implication.

What skills have you developed so far? I have developed some classical wet lab techniques particularly focusing around western blotting, tissue culture and immunofluorescence, with the additional benefit of rotations allowing me to get to grips with more bespoke techniques such as PhosTag gels. In addition I will be using the bioinformatics skills I gained through the Southampton Course to perform phosphoproteomic analysis for signalling pathway analysis.

How have you found the mathematic/computational component of the DTP? As someone with very little prior experience I found the computational aspect challenging but certainly worth it, it is catered for beginners and whilst the learning curve is steep it is an essential skill for modern biologists.

What have you enjoyed most about your experience so far? What have you found challenging? I most enjoyed the rotational aspect as it provided me with an insight into PhD-level research in multiple laboratories, allowing me to see how I handle different lab environments and what kind of supervision for example I find most helpful. I think the timings for the MRes component can be challenging at times as you have to juggle several responsibilities whilst learning something brand new in the QCB module but I am glad I did it.

What is your PhD project? My PhD project with Professor Mark Cragg, Professor Stephen Beers and Dr Robert Oldham is to investigate the key mediators of antibody dependent cellular phagocytosis. Antibody dependent cellular phagocytosis is one of the most important mechanisms involved in the depletion of cancer cells when a patient receives antibody-based immunotherapy. The activating Fc gamma receptors that are expressed on many immune cells control this process. Using mouse models with conditional knock-out of Fc gamma receptor surface expression and activating receptor signalling, I will investigate the importance of different cell types and tissues in the antibody dependent depletion of various circulatory cells. I also hope to investigate anti-tumour therapy in the absence of activating Fc gamma receptor signalling. My project also aims to investigate the target cell intrinsic mediators of phagocytosis.

What skills have you developed so far? I have learnt a variety of laboratory skills so far during my PhD. I have gained experience in cell culture, flow cytometry, molecular biology and in vivo mouse handling and procedures. As well as laboratory skills I have also had the opportunity to develop transferable skills such as critical analysis of papers, presenting data and public speaking.  

How have you found the mathematic/computational component of the DTP? Before the start of the course, I had very limited experience in computer programming and bioinformatics. The Quantitative Cell Biology module provided me with a strong foundational understanding of bioinformatics, RNA sequencing and coding in R. The Research Skills for Biomedical Science module was very useful in strengthening my understanding of statistics and how to present data.

What have you enjoyed most about your experience so far? What have you found challenging? I have getting to know and working with the amazing people who work at the CCI. The wide variety of research that is being undertaken is very inspiring. I have also enjoyed being able to design and carry out my own research. Initially, the most challenging aspect was balancing the taught modules and laboratory research. However, throughout the year I developed my time management skills.