Profile

I’m a wee quine makin her fae Scotland livin’ in the big city of London. When I’m not too busy saving the world from diseases, I spend my time saving Hyrule or completing side quests on the Witcher. When I have a difficult day I go to art as my creative release, or martial arts as my physical release. If you’re wondering who my role model is, my go to is Buffy the Vampire Slayer.

Illustration of macrophage cells eating a bacteria cell

Martial arts training

Portrait of one of my supervisors who mentors me on computational biology

So below is a story all about how my life got flip-turned upside down, so I’d like to take a minute, I’ll tell you how I became the queen of computational biology…

I grew up in a small city in Scotland where I attended a local state school. I was always interested in science, biology, chemistry, and even the dreaded physics, but this didn’t stop me from exploring other non-sciencey subjects like art and PE. It was always difficult to find opportunities for young people to engage with my hobbies and interests, but I soon found out that through curiosity and determination you can make great things happen.

At the end of school I packed my bags, donned my kilt, and was ready to start my university experience at the University of Edinburgh. For the first time I met likeminded people who weren’t shy about showing their enthusiasm for science. I worked hard and landed a place on the study abroad scheme. I readied my haggis and set off again, this time to the far East: Singapore. After going through the culture shock of a completely different country, I met the professors who would shape my career. Not only did they introduce me to the world of infectious diseases, but they provided me with the network to land a PhD at Imperial College London.

Back in Edinburgh I wrapped up my time in undergrad, packed my bagpipes, and headed to London. Currently, I’m a PhD student in the departments of Life Sciences and Medicine at Imperial.

I work with a bacteria called mycobacterium tuberculosis (Mtb). Mtb is found all over the world, and is thought to have infected 1/4 of the world’s population, but most of the time it stays hidden inside human lungs. When a person is infected with Mtb and develops the disease called Tuberculosis, they might breathe/sneeze/cough in the air and pass on the bacteria to another person. If someone breathes the bacteria into their lungs, the bacteria will try to infect an immune cell called a macrophage. This cell usually parades round the body, eating any invaders that shouldn’t be there to kill them. Unfortunately, when Mtb gets eaten it turns on several lines of defence to keep it alive inside the macrophage cell. There are lots of other immune cells which also help to kill Mtb, like T cells or B cells, and in my work I want to look at how Mtb interacts with all these different immune cells.

I have 2 different aspects of my work, the lab side and the computer side. You can skip to whichever section is more interesting for you below:

First, the lab stuff.
At the start of my PhD I was always in the lab. I spent most days taking blood from my colleagues (your blood has lots of immune cells in it) to grow the bacteria, Mtb, in it. Then, I take the blood and bacteria and ‘extract’ all the RNA from it – RNA is a way of looking at which genes (encoded in your DNA) are actually switched on or off. I then send the RNA to a sequencing company which ‘sequences’ it. After a few months the company sends me files on my computer which encode all the RNA from my sample and I analyse it.

I also do other things with the blood, like measure how many, and which, immune cells are in it by labelling them with fluorescent colours. I need to know this because when the blood is infected by Mtb the immune cells might change. The bacteria might kill some of the cells, or it could cause some cells to multiply to try and fight it.

Now, the computer stuff, called bioinformatics.

I’m a few years into my PhD now, so most of my time is spent looking at data. I do this in lots of different ways, for example with the RNA from the infected blood I look at what genes are being expressed in the blood cells and the bacteria. The immune cells in the blood will express some genes more than usual, and these genes will encode molecules and proteins which will help the cell fight the bacteria. On the other hand, the bacteria will express genes which will create molecules or proteins which will help it stay alive in the blood. The genes that are increased, or decreased, are what I’m interested in finding out.

I also work on lots of other projects that involve computational biology, or bioinformatics, all on the same bacteria. There are different types of Mtb all over the world and one of my projects tries to understand why that is through using their DNA and metabolites (small molecules made by the bacteria that perform lots of tasks like helping it survive in the lungs).  I also work with scientists across the world to create a new test which will tell doctors if a patient has tuberculosis (caused by Mtb infection) or not using RNA.

During the pandemic things have changed a little, so now I work from home with my flatmates. In the morning we have breakfast together, lots of tea, and then I get my desk set up for the day.

The first thing I do is check my emails, then check my Slack chat (this is like a whatsapp app for work which I use to talk to my supervisors and the rest of the bioinformatics team). After answering any emails or messages I start with opening my computer programming software called R. This is what I use to do almost all of my work in. Using R is like learning another language – a computer’s language – and understanding how I can tell it what I want it to do with all the data I have. The data I work on are really really big so I need something like R to be able to help me understand it better. R can look at the data for me, it can make changes to it, take away or add in things, and can also make really pretty pictures so other scientists can understand my data too.

There are other programming languages that you can use to do this work but almost everyone in my team uses R so if we get stuck with anything there’s always someone we can ask for help. So, I spend most of my day trying to understand what my data really means.