Gautam Dey studied cell biology at the National Centre for Biological Sciences, Bangalore, India, where he worked with Satyajit Mayor and Mukund Thattai on genome-scale screens for endocytosis. He then joined Tobias Meyer's lab at Stanford University and earned his PhD in 2015 for studying the evolution of human gene regulatory modules. Gautam then moved to the MRC Laboratory for Molecular Cell Biology at University College London for his postdoc with Buzz Baum, where he used comparative approaches in fission yeast and the archaeon Sulfolobus to understand the evolution of the nucleus and cell division. In 2021, Gautam became a group leader at EMBL in Heidelberg, Germany, where his lab investigates the fundamental organisational principles and evolutionary dynamics of the nuclear compartment across eukaryotes.

Gautam Dey. Image credit: Kinga Lubowiecka, EMBL.

How did you decide to become a scientist in the first place?

I wish I had a single eureka moment to share, but in my case it was really just a series of fortunate coincidences until one day I thought ‘Oh, I guess I'm a scientist'. I had great science teachers in high school, so that was a really big factor, and my parents were also very keen that their kids read widely and deeply about the world.

And then later, how did you end up in the field of evolutionary cell biology?

I did my PhD in a systems biology department, and at the time everyone was very excited about the possibility of reverse engineering biological systems after quantifying as many phenotypic parameters as we could. However, the more parameters we measured, the more complex our resulting regulatory network – the infamous ‘hairballs’ of systems biology – became, and the less we understood. Just generating more data would clearly not be enough – we needed ways to reduce dimensionality in ever more complex datasets. So, I focused instead on developing an approach to reconstruct the evolutionary history of regulatory networks as a way to disentangle species-specific adaptations from the fundamental components of the system. I thought it was a very exciting time to bring an evolutionary perspective to cell biological questions, and Buzz Baum's lab was quickly becoming the perfect place to do this – which is why I moved to London to join him as a postdoc.

What is your lab working on at the moment?

I'm fortunate to already have quite a diverse group. Roughly half of the lab is using budding and fission yeast to study fundamental mechanisms of nuclear remodelling through the cell cycle, and the other half is studying ‘weird bugs’ – bringing the tools of quantitative cell biology to different emerging and non-model systems to better understand the phenotypic diversity of nuclear dynamics across the eukaryotic tree.

Are there any new techniques you are adapting to your work?

Expansion microscopy (ExM), which has been a game changer for the study of ultrastructure in tiny cells. In physically expanding protein complexes at the nanoscale, ExM also greatly increases antibody accessibility and labelling efficiency. We use it almost daily across all our experimental models, including fission yeast. Another technique we're really excited about is experimental evolution, brought to the lab by a postdoc, Jana Helsen. Using this approach, we can perturb certain aspects of the mitotic process or nuclear integrity and function, and evolve budding or fission yeast in the subsequent 100–150 generations to compensate for the resulting growth defect. We then use whole-genome sequencing and phenotyping to figure out how the cells solved the challenge we posed them.

Could you tell us about the new, highly interdisciplinary and collaborative project in which you will be studying planktonic diversity using expansion microscopy?

EMBL and Tara Oceans are leading a big pan-European coastline expedition in 2023 – the Traversing European Coastlines (TREC) expedition – extending all the way from the Arctic Circle down to the bottom of the Mediterranean, with the aim of comprehensively mapping coastal ecosystem diversity as well as the impact of climate change and human intervention on these critical ecosystems. EMBL will send a custom-built mobile services truck to marine stations all along the expedition route, bringing high-pressure freezers, confocal microscopes and imaging flow sorters to field sites for the first time. Amongst many international collaborative projects, our contribution will be to build an atlas of subcellular architecture in marine protists using ExM for ultrastructure imaging and 18S rRNA FISH for species identification. This is a highly collaborative effort – we're partnering with Omaya Dudin at EPFL, Lausanne, our close collaborator on several projects; Paul Guichard and Virginie Hamel at the University of Geneva; and Yannick Schwab and Sinem Saka's groups at EMBL. We also expect that our ExM atlas will nicely complement electron microscopy studies of plankton samples from TREC.

You've told me before that interacting with scientists is one of your favourite parts of the job. Is this key to collaborating and doing interdisciplinary research successfully?

Science is an essentially human activity, in which we view fundamental ground truths about the universe – if they exist – through the eyes of people who dedicate their lives to investigating them. This is truer than ever in modern biology, which demands interdisciplinary and collaborative team science efforts – you can't really tackle a really hard problem without bringing diverse perspectives to the table. Moreover, science is just more fun with friends – I love learning from other people and discussing new ideas over a coffee or beer, and it's not a coincidence that most of my collaborations were scientific friendships first.

“Moreover, science is just more fun with friends – I love learning from other people and discussing new ideas over a coffee or beer, and it's not a coincidence that most of my collaborations were scientific friendships first.”

The Dey lab in 2021. Image credit: ©Alice Bernal, Université de Paris; reproduced with permission.

The Dey lab in 2021. Image credit: ©Alice Bernal, Université de Paris; reproduced with permission.

What do you feel has been the most challenging part of being a new PI?

Of course COVID has made some aspects of the job difficult, including recruiting a group of – very brave, I must say – early-career researchers to a new country, new institute, new life and brand-new lab in the middle of a bitter lockdown winter. I feel that a generally challenging aspect of being a new PI is dealing with the fragmentation of time and balancing multiple personal and professional responsibilities. At this career stage it's also very difficult to say no to opportunities or service requests, and, given my personality, this is especially true for me. I often end up with way too much on my plate!

Is there any advice you would give to someone who is seeking to start their own group?

One piece of advice I consistently received as a PhD student and postdoc was to develop a deep expertise and understanding of a specific problem in biology, but I have to admit I completely ignored it! So, perhaps instead my advice to people about to go on the job market would be to be very honest with yourself about the type of scientist you are, and with other people about how you want to run your lab. There's no point in convincing yourself that you will study one protein complex for 40 years and figure out everything there is to know about it if that's not the kind of research question that keeps you up at night.

You've not only worked on various research questions, but have also been involved in different initiatives related to preprints. Could you tell us a bit about these?

With preLights, I've participated in the curated, community-led discussion of preprints, particularly as a way to amplify the voices of early-career researchers as both authors and peer reviewers. I've also worked with ASAPbio to help promote preprint uptake and peer review evolution through advocacy, policy changes or working with funders. My role at ASAPbio has evolved over the years – it started off with community-level involvement; I then joined their fellowship programme, and most recently their advisory board, which is an exciting opportunity for me to help shape the organisation's future directions.

“Preprints are a democratising force in science – you have the same opportunity to share your science regardless of whether you're at a small university in a developing country or at a high-profile institute in the USA.”

Why is advocating for preprints so important to you?

Preprints are a democratising force in science – you have the same opportunity to share your science regardless of whether you're at a small university in a developing country or at a high-profile institute in the USA. Preprints really open up and speed up the dissemination and sharing of research; they are not a one-stop solution to all the problems with science publishing, but are certainly a critical piece. Therefore, advocating for the adoption of preprints has been a really important part of my time as a postdoc; this is when momentum grew in a huge way, and by now in my research communities it's nearly a solved problem. But having said that, I'm also aware of the bubble effect here, and that many life science communities – and especially countries outside of Europe, North America and Australia – haven't adopted this ecosystem as openly and quickly as we might have liked.

Based on your personal experience, how can actively engaging on social media – such as Twitter – benefit young researchers?

Twitter is another democratising force, opening up the discussion around the key scientific issues of our time. I also use Twitter as a way to discover new research. And then finally, of course, it's a way to create visibility for my work and occasional personal perspectives. But this is also a bit of a double-edged sword, because everything that you say or do on Twitter can be amplified and taken out of context, without the space for a nuanced argument. I know that many early-career researchers are wary of engaging too much on Twitter because they're worried about how they will be perceived. This is a completely valid concern, as people tend to make assumptions easily, so it's important to carefully curate what you share. But overall, Twitter has been a very positive tool for me for identifying opportunities and collaborations, linking me up with people that I wouldn't have met otherwise, and giving me visibility at a time in my career when I needed it. Will I move to Mastodon now? No clue!

As an organiser of both virtual seminar series and in-person conferences, what's your take on the future of conferences?

I am more convinced than I was before of the importance of bringing scientists together in the same physical space, as this nucleates new ideas and conversations. In order to balance this key benefit against all the other factors, such as accessibility, equality of opportunity and the environmental cost, we need some sort of compromise. The best solution that I can think of is that we focus on attending smaller, local in-person meetings, where interactions and discussions are prioritised over presentations; big meetings, used for disseminating the latest research to lots of people, could be moved to virtual formats with a local hub component, meaning that people could still gather in different places for the personal interactions.

Finally, what is something people wouldn't know about you by just looking at your CV?

I used to do a lot of theatre and thought I was going to have a career in it one day, but that never panned out. I'm also a half-decent photographer, and I most enjoy taking photos of people.

Gautam Dey’s contact details: EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.


Gautam Dey was interviewed by Máté Pálfy, Features & Reviews Editor at Journal of Cell Science. This piece has been edited and condensed with approval from the interviewee.