Ever wondered what our scientists are getting up to inside EI? Our Day in the Life of series delves into the researchers’ daily lives of decoding living systems.
We start with Post Doctoral scientist Ross Low in the Hall Group, who we speak to about seeking out global antimicrobial resistance to fight disease by investigating genome evolution, how ‘gut-interplay’ is on his study bucket list and Japanese martial arts helps him unwind.
My interest in genomics started during my undergraduate degree in Biochemistry. Genomes come in all shapes and sizes but at the end of the day it all comes down to A’s T’s C’s and G’s (and occasionally U’s). It’s also an exciting field of research with new sequencing technologies and analysis programmes emerging all the time.
Goliaths like the Human Genome Project have paved the way for genomics to be a powerful tool for many labs. As soon as genome sequencing becomes available on the NHS, they’ll need all the bioinformaticians they can get. I came to EI because it is a centre for genomics research. They also offered me a place on a really exciting project which I just couldn’t say no to.
My role revolves loosely around evolutionary genomics, but that’s a pretty broad term. I’m a postdoc and I mainly work on analysing multi-genomic data for clues about how they have evolved. This may be just to understand how they have come to be like they are, or it could be a more focused question, like why does this group of organisms cause disease and these others don’t?
I work a lot with intestinal organisms that are linked to disease. My motivation for this work is simple; helping to diagnose, treat or understand disease is a precursor to developing methods which have a real impact on human (and sometimes animal) lives.
My typical day entails mostly working at my computer, albeit a really nice computer and a comfy chair; so it’s not so bad, with brief breaks for sustenance. Kidding aside, the nature of my work means that no two days are exactly alike. As each project progresses, I am able to follow it on to the next stage of analysis.
Having multiple projects on the go is also a bonus which helps to keep things interesting. For example, I have just finished the ‘assembly phase’ of a project whereby I was attempting to optimise the DNA assemblies for a number of bacterial genomes. Next, I must annotate them and compare the gene repertoires, then the real fun can begin. Occasionally, I may set aside a whole day to dedicate to a particular task but mostly I get to jump between projects.
... don’t try to annotate a genome manually, trust me, it’s not worth it.
My main project is working on the analysis of 10,000 Salmonella genomes from around the world. The project takes a global approach to understanding the epidemiology, transmission and virulence of Salmonella.
The genomes have been collected from 52 countries around the world and I’m working on searching through these to find clues about what bestows antimicrobial resistance (AMR) on a particular group of stains, what differentiates environmental strains from epidemic strains and the variations between invasive and non-invasive infections. Other projects involve investigating the evolutionary history of deep-branching protists as well as how other intestinal bacteria are linked to intestinal disorders.
My favourite part of the day has to be getting results. They don’t even have to be ‘good’ results, just being the first to see something is exciting, like staring into the bare face of discovery. And chatting at coffee breaks …
"All of us are the result of successful survival and reproduction in an unbroken chain leading right back to bacteria and the origin of all life."
I’m fairly early in my career so my proudest moment was passing my PhD viva. Hopefully, I’ll be able to top that in the very near future. One thing I would do differently; don’t try to annotate a genome manually, trust me, it’s not worth it.
My ideal research project would be a metagenomic project investigating the interactions between the human, bacterial, protist and viral components of the intestinal microbiome. Traditionally, in this type of investigation, the first thing you do is take an organism of interest out of the gut environment and study it in isolation, thereby losing all of the information about how it's actually behaving in its natural environment. More and more, it looks as though the answer to these questions revolves around the interplay between the organism of interest and all the other things floating around in your guts. We are only now developing technology advanced enough to make projects like this feasible.
During my undergraduate degree, I spent a year working as a research technician in a lab in Chicago. That was a baptism of fire for working in science. Not only did I get first-hand, hands-on experience of working in a real research lab, but I also had to cope with being in a different country. Little things, like buying toothpaste became a challenge; do you go to Trader Joes? Or Target? Or Walgreens? On the plus side, I was introduced to spray-on cheese and Potbelly (google it)!
I take my inspiration from our own evolutionary history as self-indulgent as that sounds. All of us is the result of successful survival and reproduction in an unbroken chain leading back - past your parents and grandparents, past the common ancestor we share with chimps, past our common ancestors with other animals, insects, plants - right back to bacteria and on to the origin of all life. One unbroken chain.
When I’m not at work, I like to relax by playing computer games (I’m a PlayStation man all the way), but when I need time not looking at a screen, I’m also a qualified Jiu Jitsu instructor. Jiu Jitsu is a traditional Japanese martial art that has been adapted to modern situations. Think fewer swords and more knives and nightclubs. This takes me up and down the country both training at different clubs and competing at national events. On a regular week though it’s just fun to chuck some people around and then go to the pub.
My dream is to prove something in a text book wrong. Something innocuous that everyone takes for granted because that’s where the fame and fortune lies. But in five years, I’ll settle for coming to the end of my second or third postdoc and looking to advance my career by founding my own research group.
Learn how to code. Perl, python, tcl (pronounced ‘tickle’), whatever language takes your fancy. Sequencing is now very cheap, which means that it’s not uncommon to have to deal with huge amounts of data. Just imagine how long it would take to change the names of 10,000 files by hand. Knowing how to handle and process data on the command line is an invaluable skill.
