Tell me about your experience on the internship programme
I learned a lot about specific techniques, especially relating to nanobody purification since that was repeated several times during my work! However, I think the most valuable thing I gained from the internship was general lab experience and building confidence in the lab, because I did about as much lab time over the internship as I had done over the preceding two years of my degree. I spent eight weeks working five days a week in a lab, and whenever I was confused about something I could ask experienced researchers for advice; not just about how to perform the technique, but about subtleties that it’s difficult to cover in a teaching lab, whether because they are done for you by technicians or because there are only so many demonstrators available.
I’ve also improved my understanding of fundamental procedures in biochemistry, such as Western blotting. The whole process for this takes a full day to do, so it’s not possible to follow the process all the way through in a teaching lab. In working through it myself in the internship, I learned how much had been done for me and my classmates in the teaching labs by technicians – not least washing everything up afterwards! In the same vein, it was useful to learn how much time and effort in biochemical research goes into just making the materials before you can do the experiment. At school and university level, you’re either using reagents that can be easily mass-produced or the technicians make them up for you in advance; that means you get limited opportunities to practice those skills, so it was great to get the opportunity to put the theory I’d learned into practice.
As far as direct utility for my career goes, when I apply for internships with companies in the coming year (which I do intend to do!), the experience I gained during this internship is likely to be very helpful in boosting my chances of getting one, as well as improving my performance if I do. It’s also valuable for my career beyond that, in terms of understanding how a research lab runs, but also in terms of knowing how to plan your experiment when parts aren’t done for you in a teaching lab, and how to deal with experiments going wrong (which happens very often in the real world!). Of course, experiments go wrong in the teaching lab too; but you don’t usually have the opportunity to try to fix them, which is something I got quite a bit of experience with in weeks 3-5.
Overall it was a great experience, I learned a huge amount, and am very happy to have gotten to do it.
What impact has it had on your studies?
As well as lab work, I also did a significant amount of reading and understanding papers and research, trying to build a picture of how something works from the literature. We do some of this in our degree studies, but this was more intensive than I’d done previously. For example, around weeks 3 to 5 the amount of lab work I could do was limited because I was waiting for cultures to grow. I had a side project reading through a previous DPhil student’s thesis (which had been completed, but had yet to be published) in order to identify areas where further work could be done, and in order to identify data that might be useful for a short paper the lab wanted to write to describe the tools developed in the thesis so that others could use them. I picked out from the thesis the data that I needed and areas of work that were unfinished, then compiled them into a format that I could present to my supervisor. It wasn’t that different to standard degree work, really; but it was useful in the sense that it helped me practice the other side of research work, writing things up and extracting coherent insights from bodies of data.
Mostly, what I learned is useful for my future career, rather than my current studies. However, there is some crossover, and the skills I acquired will certainly be very useful for my fourth-year research project!
What was your key takeaway?
Research is messy. When you learn things in theory it sounds like everything is clean and clear cut, and it isn’t. You often have setbacks and complications, you often have to improvise. Obviously, you don’t want to improvise too much, because you risk biasing your results – but when you’re just producing materials, or doing preliminary investigations to get a qualitative handle on what’s going on rather than trying to get quantitative data, it’s often necessary.
As an example, we originally planned to further purify the nanobodies with size-exclusion chromatography after the affinity purification step; but some of my nanobodies initially failed to express, so we found ourselves with less time than expected. However, the eluate from affinity purification was unexpectedly pure, pure enough that we decided it made more sense to use it directly rather than spend the time putting it through SEC (and taking the risk that there might not be enough nanobody left afterwards!). In an ideal world, we would have used SEC, and made more nanobody if we didn’t have enough; but in reality, time is limited, and since the results were qualitative in any case it was better to use what we had. (The important thing, of course, is to keep track of what you changed so that anyone looking at your results later isn’t misled!)
Would you recommend the internship to others?
Absolutely. If you possibly can, do it. It’s an incredibly valuable experience, and will be very useful for me for fourth year in terms of knowing how things work already. It represents an incredible opportunity to work with researchers working in the field. It’s hard to overstate how valuable that experience is.
So, finally, tell us about your project
My project was characterising a panel of nanobodies against a protein (the guidance receptor) involved in neural migration, with the goal of identifying nanobodies that might be useful for modulating the interactions between that and another protein (the ligand). I’d originally contacted the Seiradake lab to ask for an internship because I’d read about previous work they’d done that used nanobodies to modulate the interaction between another pair of proteins, GPC3 and Unc5D, and mentioned that work in my email. At the time, I was completely unaware that they had more they wanted to explore, so it was something of a serendipitous encounter!
To explain some of those terms, the Seiradake lab works mainly on neural migration, a process during early development where neural progenitor cells migrate in a controlled manner to form the various layers of the brain. The guidance receptor sits in the membrane of those progenitor cells; it interacts with the ligand, which sits in the membrane of a different cell, to help direct neural migration. Nanobodies are antibody fragments; they’re single-domain proteins consisting of the variable domain from the heavy chain of heavy-chain-only antibodies produced by camelids (camels, alpacas, llamas, and so on) and also sharks, though for obvious reasons we tend not to use those as a source! They’re convenient tools in molecular biology, because they’re smaller than full antibodies, so they’re less interfering and more of them can bind to a single target; they’re more stable than antibodies, and therefore easier to handle; and they’re much easier to grow, since they can be expressed in bacteria instead of needing insect or mammalian cells.
I spent the first 4-5 weeks expressing and purifying the nanobodies I needed. I also got to do some tissue culture in order to produce the guidance receptor protein that I needed, which was a very valuable experience, albeit a stressful one! (Mammalian cell cultures are expensive and extremely susceptible to contamination; cultures in vitro have no immune defences, so a single bacterium or fungal spore is all it takes to ruin the entire culture.) There were some setbacks with the nanobody expression, but in the end I had all the nanobodies purified by the end of week 5. I extracted them using osmotic shock, purified them on a nickel-NTA column, and tested the purity. Since (unexpectedly!) they were almost completely pure, we elected to use them as they were rather than go through the additional purification step we’d originally planned. I spent the remaining three weeks doing pulldowns to investigate their binding affinity to the guidance receptor and their ability to alter the binding of the receptor to the ligand. The results weren’t as clear as they could have been – there was an unexpected background signal from some of the pulldowns – but overall I more or less accomplished the goal of my project.
