Life in the lab as a present-day Victorian

This summer I went back in time, literally, although only by ~8 hours, as I jetted off to Victoria, BC in the South-West of Canada to spend 10 weeks working in Dr John Burke’s lab at the University of Victoria. The lab focuses on understanding the regulation of proteins involved in lipid signalling and use a variety of techniques from X-ray crystallography to Hydrogen-Deuterium Exchange-Mass Spectrometry (HDX-MS) to achieve this. During my time there I got to experience these different biophysical techniques to further understand the protein PI3K-gamma and its regulatory partners.

Figure 1: Turns out I actually went to a mystery island called Canad.

The biochemistry

Initially I got trained on the mass spectrometer. This involved learning how to operate it, run samples and retrieve data to be analysed. The mass spectrometer is used for mass spectrometry (MS), an analytical technique for determining the mass to charge ratio of ions. It is often used as a “detective” technique to identify what compounds, such as proteins, are in a sample. In our case, we already knew which protein was present. Instead what we were interested in was the dynamics of the protein – this can be determined through coupling the MS to HDX. In HDX, your protein is first exposed to deuterium, the heavier isotope of hydrogen and regions of proteins more flexible are more likely to exchange their hydrogen to deuterium. This heavier deuterium isotope can then be identified using MS and hence dynamic regions of proteins can be identified.

Figure 2: Me and the mass spec.

Besides HDX-MS, I also ran standard samples to identify regions of the protein that were phosphorylated. Figure 3 depicts part of the analytical process to quantify the levels of phosphorylation of the protein in different conditions – I liked to think of it as Painting by Numbers, Mass Spec style;

Figure 3: Painting by numbers, Mass Spec style

Met my favourite piece of lab equipment

Despite the amount of time I spent with it, its cost and capability, the mass spectrometer only made it to second place as my favourite piece of lab equipment. Coming in first was of course “The Belly Dancer”, a groovy, hip-hopping piece of lab tech for letting protein gels soak in staining dye and later for washing.

The cycling remained

Like in Cambridge, cycling is big in Victoria and was the easiest way for me to get to work each day. This involved me buying one second hand (or more likely, multiple hands down). Day 1, bike 1, I got a flat tyre. Since the bike was already too small, I resold it somehow and bought another. This bike was much bigger, much comfier and way cooler with flames to finish and dice for valve stoppers – I had never received so many compliments..- and nothing could beat cruising down-hill on McKenzie Avenue on my ride back home in the sun.

Back to the future

When I return to Cambridge I will begin my PhD at Cancer Research UK. The lab and life experience I have gained whilst at UVic has been the perfect way of taking a break whilst learning further lab skills. Moreover, international experience is invaluable for a future in academic research, since it depends so heavily on international collaborations and sharing of knowledge. I am very grateful to the Burke lab who have trained me well and provided a mass-spectacular experience I will never forget!


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