Since I am studying History, I spend most of my days behind my books or my computer. When I hear almost all my GradLife colleagues talking about «the lab», I feel this is a secret word full of mysteries. So I asked Sophie Cousineau to help me understand what she is doing exactly in her lab. Thank you Sophie!
Hi Sophie, can you present yourself?
Hi, I’m Sophie, I’m doing my PhD in the department of Microbiology & Immunology. I started as a Master’s student four years ago, and a bit over two years ago I transferred to the PhD program, where I continued the same project in the same lab.
The obvious first (and frequent) question : what is your thesis topic?
I’m doing a basic science project on the hepatitis C virus (HCV): I’m trying to figure out how HCV uses cellular RNA-binding proteins to make more copies of itself. More specifically, I’m looking at a protein called the poly(C)-binding protein 2 (PCBP2); I know from my own experiments and from what had been previously published that this protein is important for HCV replication, but I’m trying to pinpoint the exact step of the viral life cycle that needs this protein.
It’s very much a molecular biology project: I have done a lot of knockdowns or overexpressions to see how changes in the levels of my proteins of interest affect the ability of the virus to replicate in cell culture, and I have made some mutant proteins to try to figure out which parts of the protein are crucial.
How do you collect your data?
By doing lab work all day, every day (and sometimes on weekends, but I try to keep that to a minimum). All of my work involves tissue culture: I grow cells in plastic dishes in an incubator, I treat them with different reagents to knock down or overexpress my protein of interest, then I infect these cells with HCV and assess how these different conditions affected the virus.
The first step in my analysis process is always to check if my treatments actually worked, if the levels of my protein of interest changed as I wanted them to (which is not always a given). I do this by Western blot, which means that I use antibodies to see if the specific proteins that these antibodies detect were found in my samples.
I detect those antibodies with a chemical reaction that creates light, so I end up working in a dark room and developing film. The whole Western blot procedure takes 3-6 days, depending on how many proteins I need to look for.
If I see that the protein levels are what they should be, I then move on to analyze the RNA contents of my infected cells: I do this by Northern blot, which means that I use radioactive bits of DNA to check if a given piece of RNA was in my sample. That takes about 4 days to do.
And finally, to compare how my different experimental conditions affected virus production, I collect some of the media that my infected cells were growing in (and secreting virus into), dilute it to infect new cells, and after some fixing and staining steps I’m able to literally count clumps of infected cells under the microscope. This takes another 4 days to do. By repeating these experiments using different mutant viruses, I’m able to tease out different aspects.
Since all of my experiments take ~1 week to run and ~1-2 weeks to analyze, I try to organize my work so that I analyze last week’s experiment in the downtime of conducting this week’s experiment.
Is it dangerous?
I wouldn’t call it dangerous. Don’t get me wrong, there’s a certain amount of risk: if things go really wrong, I could get infected. But it’s not that easy to get infected with HCV: that virus is not airborne, it really needs to get into the bloodstream to start an infection. The only way that could happen would be through a lab injury, so we take precautions to reduce the chances of that happening. We don’t work with glass with the virus (because glass can break – we use plastic pipettes instead); we wear protective equipment (safety glasses, lab coats and gloves) and use tissue culture hoods to keep the virus away from us; and we disinfect equipment after every time we use virus. So, no.
What is a typical day for you at McGill?
I try to get in the lab around 9 (± 30 minutes). After saying hi to my labmates, I finish up things that were going on overnight: this can mean taking bacteria out of the incubator (I use bacteria as small-scale factories to make DNA that I use in my experiments), or inactivating an enzyme reaction. I then go fill my styrofoam bucket with ice, so that I can get started on thawing frozen samples; it takes a while to thaw anything on ice, so I like to get that going before I take my laptop out of my bag and check my email.
I like to get new experiments started in the morning, since most of them require pretty long incubation times (~4 hours). After I’ve treated cells with whatever I’m transfecting or infecting them with on that day, my goal is to fill the incubation time with lab work. I almost always have some Western blots going, so I’ll get started on washing those membranes (3x 5-10 minute incubations) so that I can reach a longer (~1h) incubation step in that protocol just in time to take a break for lunch.
In the afternoon, I continue what I started. Towards the end of the day, I try to assemble my data to make figures and update my electronic lab notebook. Before I leave the lab, I always make sure to make a to-do list and rough schedule for the next day in my in-lab paper notebook.
A few times a week, I shift my schedule and plan around other events like lab meeting, my weekly one-on-one meeting with my supervisor, journal club meetings, or seminars I want/need to attend.
Finally, is there anything special, difficult or funny you want to say about lab work for a non-lab student?
A lot of lab work consists of tedious and repetitive tasks – I spend a lot of time transferring tiny amounts of liquid from one tube to another, or pouring 10-20 mL of liquid out of a plastic box to pouring in a fresh slop of liquid. After doing it for years, I’ve become really good at doing these actions quickly and precisely, to the point that when I’m training a new lab member it takes me some effort to put into words what I’m actually doing.
The best description I’ve found of this is how Hope Jahren described it in her memoir Lab Girl: doing lab work is to move your brain into your hands.
Do you want to know more about the days of grad students? Tell us what kinds of studies you are intrigued by!