Letters from my PhD (II)

It’s funny how ideas work. Sometimes a bunch of them come to you at once, and although you may manage to write some down, you usually end up forgetting most of them. Once in a while you are able to turn one of these ideas into a post, and sometimes you even think it might become something regular, like a series. Then two years later you read that post again and you smile at how naively optimist you were. But then you decide to give it a second chance. One and a half months into my PhD at UCL I wrote what I thought would “start a new section in my blog: a place where once a month(ish) I’ll try to write about how this PhD thingy is going”. Two years later, it is time for part two.


A first year of rotations

In 2016 I joined the Wellcome Trust 4-Year PhD in Neuroscience at UCL, and now that I think of it, the last think I told you was that we visited 83 labs. The hard part was to choose the three where we would carry out the 3-month rotations that make up the first year of the programme. Looking back, I am really happy about my choices. I studied astrocyte glutamate-uptake currents using patch-clamp recordings in acute hippocampal slices in Prof. David Attwell’s group, investigated the connectivity of inhibitory neurons in a midbrain circuit computing innate defensive behaviours in Dr. Tiago Branco’s group, and explored the brain areas involved in homeostatic sleep regulation in zebrafish in Dr. Jason Rihel’s group. Each rotation taught me something different. I got to learn several techniques, work with different animal models, and experience various ways in which research groups approach science. It was a very formative year, and I would encourage anyone to apply to a programme (here are some) that includes rotations to explore, learn, and figure out which environment will suit you best and allow you learn and grow as a scientist.

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The wavy path to the Upgrade

Towards the end of the first year of rotations, the time comes for another big decision: the one that will set the topic and the research group on which you will invest the 3+ years of your PhD. Once that is settled, you and your now PhD supervisor craft a PhD proposal that will need to be approved by the 4-year PhD Committee. And so the PhD begins. Fast forward another year, you have probably build a rig (or several), did a bunch of experiments that turned out to be useless or totally wrong, learned a lot from your mistakes, did your best to kinda supervise a Master student, and hopefully gathered some useful preliminary data. You might also have attended a course or summer school to learn a specific technique, or even presented in a small meeting related to your topic. It is time for you to Upgrade.

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In the UK, you start off your PhD as being registered for an MPhil degree, and it is not until the end of your first year since you joined the research group and started your PhD project that you transition, or upgrade, to a PhD degree. Every University will have specific guidelines for this, but you are usually required to write a ~20-pages report summarising the background of your project, the methods used, your progress or results so far, and the plan for the remaining two years. The report is then read by a small committee formed by your second supervisor and another faculty member from your department, with whom you eventually have a mini viva to go over what you have done and what the next steps are going to be. Finally, you might or might not need to give a talk at your department seminar series. In my case, the Upgrade implied two months of data analysis, reading, and writing that helped me to put order in my project and carefully think about the next steps. It was also a great opportunity to discuss my research with two senior group leaders and get feedback on the work done so far, and on what to focus next. Once Upgraded, life goes on, and so you resume experiments with a bureaucratic weight lifted from your shoulders, and a slightly clearer idea of where you are headed.


My first preprint

During my rotation in Dr. Jason Rihel’s group I worked closely with Sabine Reichert on a project to identify which areas in the larval zebrafish brain are more active during (and putatively involved on) homeostatic rebound sleep. Sabine had developed a pharmacological assay that allowed her to monitor the effects that different pharmacological compounds had on the sleep/wake cycle of zebrafish larva, and found that compounds that increased neuronal activity such as caffeine induced a homeostatic rebound sleep (something similar to what happens when you stay awake until late for fun or work and you wake up at lunch time on the next day, “catching up” on sleep). Under her guidance and with the invaluable help from Marcus Ghosh I combined her assay with whole-brain activity mapping to identify rebound sleep-active neurons following pharmacologically induced increases in neuronal activity. I am extremely happy that the results from these experiments contributed a bit to the fantastic project Sabine carried out, which you can now read in full on bioRxiv.

Reichert et al. 2018


Is scientific research a hobbyless venture?

This is the last thing I’d like to write about today. And the answer is a big no it’s not. Definitely not. I may not have written as many “Letters from my PhD” as I originally thought, but I have certainly been writing about many different things and explored various topics and formats, from interviews, short stories and image competitions, to interesting reads, podcasts and overviews of scientific meetings. I may have not been playing guitar that much, and I am definitely not even a tiny bit closer to being able to play Bohemian Rhapsody as I was two years ago, but I have been training Judo regularly, got involved with the Judo Club as treasurer and now president, and have even done a couple of competitions. I have also been busy collaborating as a Section Editor for Bright Brains, and have helped organise a couple of symposiums on Cross-species Conversations and the Quantum of Neural Computation. It’s certainly been an intense couple of years, but it’s also been a very fun and enriching experience.

So invest some time in trying new things, and stick to the ones that make you happy. Ideally do this from the beginning, although it is never too late to start. It doesn’t really matter what you do, as long as you want to do it and have fun doing it. It might just be that thing that makes you smile when you think about it, or that moment of the week that allows you to precisely not think about anything else. But never force yourself to do it, we have enough pressure and deadlines from work already. Be it a sport, building things from wood, dancing, or drawing, have something you look forward to and do it whenever you fancy doing it. These activities, and the people you meet while doing them, are the things that will help you keep your feet on the ground and will make your research and PhD experience more enjoyable along the way. Take care people!

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