Ghostbusters: PhD student Lara Cassidy
Lara Cassidy, PhD student and researcher at the Smurfit Institute of Genetics

Contributing to human understanding is the most fulfilling part of being a researcher

21 Jul 2016

Ghostbusters has been out in theatres for over a week now, and the world hasn’t fallen down around our ears.

Much was made of the fact that this reboot of the 1984 classic would be anathema to good taste, simply because it was led by an all-female team of scientists (and ghostbusters). And yet, by all accounts – and coming as a surprise to few – the gender of the leading characters has had no effect on the final product.

To coincide with the release of the movie, we’re profiling some of the real-life female researchers and scientists at work in Ireland. Here, Lara Cassidy, a PhD student at the Smurfit Institute of Genetics, Trinity College Dublin (TCD), tells us about her work in prehistory.

What is your role at Smurfit Institute of Genetics?

I’m a PhD student in Dan Bradley’s Molecular Population Genetics lab, heading into my final year. At the moment, the lab’s main focus is ancient DNA (aDNA) research and my project deals specifically with Irish human prehistory.

My overarching aim is the cataloguing and analysis of Irish human genome variation throughout the island’s prehistory. The resulting dataset will hopefully be an invaluable resource in the study of the demographic and evolutionary processes that have shaped modern Irish genetics.

From an archaeological perspective, we can also use these genomes to explore burial kinship dynamics, examine the extent to which migration and admixture accompanied various cultural shifts, and even establish phenotypic traits such as hair colour or blood type.

If there is such a thing, can you describe a typical day in the job?

I suppose the ‘typical day’ completely depends on what phase of the project you are in.

It is a pretty long process, sourcing suitable skeletal material and turning it into data on a screen – data which we then must analyse inside out and upside down.

This means that, some weeks, I may be poring over archaeological literature, meeting up with ever-helpful archaeologists, and spending days carefully going through boxes of bones in museum archives (field-trips to the actual sites are a bonus!).

Other months, the focus of my days will be drilling the bones, extracting DNA from the powder and prepping the extracts for sequencing. This is a meticulous process, all of which is conducted in our basement anti-contamination facilities, away from the rest of the lab. It can get a bit lonely down there in your boiler-suit!

After the DNA is sequenced, most of the day is spent at your desk, processing the data, reconstructing the genome, calling variants, carrying out analyses that allow you to compare your ancient individuals to other modern and ancient data and, most importantly, interpreting your results. This is by far the longest part of the process, but also the most creative and definitely my favourite. It is also the part that requires the most teamwork.

Then there are the times when you are sourcing, drilling, processing and analysing all at once. Those days are hectic.

What types of project do you work on?

My main focus is my own PhD project, but I also get the opportunity to collaborate with other aDNA projects, inside and outside the lab. Outside our lab, these usually involve carrying out specific types of analysis on other researchers’ data, for which you already have a pipeline set up for and are familiar with.

As for within the lab, it’s hard not to get involved with the other projects going on here, even informally. The lab is also working on the ancient genomes of domesticated species (cow, sheep and goat), as well as other human projects.

We are a pretty talkative bunch, discussing new results, airing our frustrations, untangling bioinformatics problems, knocking around our thoughts on the big, confusing questions of prehistory, and constantly holding unofficial lab meetings around someone’s desk. Although each of us has our own focus, we are very much a team.

What skills do you use on a daily basis?

Honestly, I think the most important skills I use (or at least try use) are organisational skills. There is a lot of multitasking and jumping from one thing to another. It can be difficult to keep on top of things if you don’t have structure.

If you are organised, you will have the time and clear-headedness to develop and implement your other skill sets – such as problem-solving, communication, programming, wet lab work, presenting, writing, and not chopping your finger off with the diamond-edged saw while drilling the bones.

What is the hardest part of your working day?

Starting and stopping. It usually takes me a little while to pick up the previous day’s threads and get productive in the mornings, particularly if I’m feeling a bit overwhelmed. The flip side of this is that it can be difficult to let go of the threads in the evening and turn your head off until tomorrow (especially if you have access to the lab server at home on your laptop).

Do you have any productivity tips that help you through the working day?

To-do lists, to-do lists and more to-do lists. My desk is covered in brightly coloured Post-its. Writing out exactly what needs to be done immediately makes you feel more in control and allows you to easily prioritise. Without them, I always have this vague nagging feeling I’ve forgotten something terribly important.

When you first started this job, what were you most surprised to learn was important in the role?

Honestly, the amount of cleaning!

Modern contamination is a constant threat when working in human ancient DNA. Our lab work requires us to continuously use bleach, DNAoff (a spray for eliminating all trace DNA), ethanol and UV light on all surfaces and tools we use. Cleaning probably takes up more of our time than actual bench-work. I should have added it to my list of skills, actually!

How has this role changed as your area has grown and evolved?

I’ve only been in the field a few years, but I suppose one of the biggest changes I’ve seen, even in this short amount of time, is the explosion in data.

When I first started, there were only a handful of published ancient genomes. Now there are hundreds. I used to have a single external hard-drive (3TB), now I have nine. It’s challenging dealing with this ever-increasing amount of information, but it does really force you to keep constantly improving your bioinformatic and data-handling skills.

What do you enjoy most about the job?

Learning something I didn’t know the day before. Sometimes, if I’m lucky, it’s something that nobody in the whole world knew the day before. Being part of that discovery process and contributing in some small way to our understanding of the world is definitely the most fulfilling part of being a researcher.

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