Over the past 6 months, a post-doc and I have had the ominous task of setting up a brand new piece of equipment never before used in the lab: a chemostat. Before it fell into our hands it had been sat in a box, taking up space, for four years waiting to be opened – so our boss decided it was time for it to finally get an outing.
Firstly, a quick intro about the chemostat, so you can grasp why we have had so much difficulty:
A chemostat is a device that allows you to maintain bacteria at a steady state within their exponential growth phase, without them using up their growth media or poisoning themselves. It works by constantly diluting the culture with new media, whilst removing old media at the same rate, so keeping a constant density of bacteria within a constant volume. You control the dilution/removal rate, the gas mixture pumped through, the rate of mixing and the media that you grow it with, giving the chance to investigate the impact of different variables on your sample. As you might be able to guess, this is not the simplest piece of equipment. The company that we bought it from turned out to provide very minimal instructions, and had no mention of any control measures to ensure sterility – something that is essential in microbiology. Over the course of half a year we came across unique problems with different aspects of the equipment, at every stage from making the media to taking samples to keeping a constant gas flow. But now we think we may finally be in a position to get some real results.
After all that work, and now that we’ve finally reached the stage of getting something back for our efforts, I felt it only fair to share some of my tips for setting up something from scratch in the lab.
I think that a big factor in our eventual success was, as the saying says, that two heads are better than one. Having two of us working together meant that we had twice the brainpower to think about our problems, and we could throw ideas back and forth until we came up with a plausible solution to our problem. I went to a seminar on site a few months ago where the speaker spoke about spending entire weeks “just thinking”. I thought that spending that much time thinking seemed a bit far-fetched, but it turned out that one of the best ideas we had came out of spending an entire afternoon thinking about and discussing the problem. Roping in other lab members, or fellow PhDs over lunchtimes was also great for getting new ideas or solutions to problems we hadn’t thought of yet. The same goes for looking back at the literature – even the older stuff. We found our supervisor’s PhD thesis to have some essential parameters for our initial set up – despite it being decades since his PhD.
Any biologist can tell you that things often won’t work first time, and when coming up with solutions to our problems we definitely had a few failures. The chemostat took two weeks to complete an entire run, and we had a couple of times when we lost the entire fortnight because one of our ‘solutions’ turned out to be completely wrong. However, these mistakes often led us to coming up with something better, or made us go back and start thinking about it from scratch. My favourite example of this was when we spent an entire afternoon attempting to create a custom one-way valve using random things found in the lab, only to realise that there was a much more simple way to circumvent the problem we were having.
My final, and possibly most important piece of advice is to ensure you document everything you do, and every change to the protocol that you make. Sometimes the smallest change can make a big difference, so making sure it is all written down can be very important – as is using controls to make sure that the change you made is definitely the change you need. We kept a checklist which we updated as needed, to make sure that every time we ran the chemostat we did everything we needed – from cleaning each piece to making sure we had all the ingredients for our media in the correct amounts. Even though the chemostat is taking a break at the moment whilst we concentrate on other experiments, we are both sure that when we return to it, the checklist will help us be certain that we have set it up with everything we need.
I hope these few tips have given you a bit of an insight to the months of struggle that our lab had over our equipment, but have also given you a bit of hope that if you have to do the same one day, it is possible to get things right. If you do ever get put in the situation of running an experiment this complicated, I wish you luck and say this: don’t give up without a fight – it might just be worth it.
By Izzy Webb – a second year PhD student in Phil Poole’s group