Lab meeting with the Żylicz Lab

Where is the lab?

reNEW, University of Copenhagen, Denmark

Lab website: https://renew.ku.dk/research/reseach-groups/zylicz-group/

Research summary

Jan Żylicz: Our primary focus is on unravelling the intricate molecular mechanisms through which chromatin and metabolism regulate early mammalian development. The team explores fundamental questions such as how global changes in metabolism lead to specific outcomes, the causal relationship between chromatin and gene expression alterations during lineage specification, and the biological significance of the coupling between metabolism and epigenetics.

Lab roll call

Sandra Bages Arnal: Lab Manager – I take care of the general things in the lab, like ordering, organization, mice colony management, etc. And I help people with their projects when needed.

Arnau Casoliba Melich: PhD student – I study the role of metabolism in promoting and maintaining the trophoblast lineage in mouse models using degron systems and CRISPR interference.

Antar Drews: PhD student – My interest lies in uncovering novel epigenetic regulators of lineage fate in the early human embryo, with a particular focus on the trophectoderm.

Eleni Kafkia: PostDoc – My scientific interests lie in understanding the metabolic architecture routings during pluripotent state transitions and how these are specifically intertwined with chromatin alterations. To elucidate this, I am employing a combination of ¹³C-isotope metabolic flux analyses, chemoproteomic profiling and CRISPRi/a technologies.

Viktoria Lavro: PhD student – I am using single-cell sequencing techniques to investigate the causes behind embryo failure and the fidelity of in vitro models in recapitulating key features of development.

David Pladevall Morera: PostDoc – I use CRISPR interference and high-throughput microscopy to decipher the role of metabolic enzymes in regulating chromatin and cell states during early embryonic development, specifically at the stage of embryo implantation.

Nikolaos Stamidis: PhD student – I am using in vivo and in vitro approaches to understand the role of histone acetylation in early mouse development, especially with regards to regulation of chromatin and gene expression.

Karlien van Nerum: PhD student – I am trying to understand the influence of the interaction between metabolism and epigenetics during trophectoderm specification and differentiation, but mostly I just like to culture cells.

Anne Wenzel: Bioinformatician – Steering clear from the wet lab at all times, I try to make sense of the data that gets generated by my teammates. I integrate various omics data or assisting my lab mates in their data analyses.

Jan Żylicz: PI – I take care of people, grants, ethics and papers; also, I tend to occupy people’s benches when I want to show that he can still do experiments.

Favourite technique, and why?

Jan Żylicz: Definitely ChIP-seq, beautiful peaks give me great satisfaction and I can explore them for days. This process typically serves as the initial step in formulating a detailed hypothesis, which can later be tested functionally.

Apart from your own research, what are you most excited about in developmental and stem cell biology?

Jan Żylicz: The role of mechanics in every aspect of a cell’s functioning never ceases to amaze me! I am excited when previously unanticipated perspectives of developmental biology emerge. Our field is rapidly progressing in this direction. Indeed, last years have demonstrated clear couplings between cell and tissue mechanics with transcription, chromatin, and even metabolism. Despite these exciting discoveries, the molecular understanding of these inter-modal couplings remains poorly understood and lacks integration into in silico modeling. I can’t wait for this to actually happen!

How do you approach managing your group and all the different tasks required in your job?

Jan Żylicz: I consider my primary responsibility to be taking care of the entire team. I provide support in various aspects, such as encouraging them to generate ideas, assisting in troubleshooting, aiding with writing tasks, and helping them plan for their future steps. However, in practice, it can become challenging to manage multiple tasks simultaneously. Given my inherent disorganization, I rely on many tools to keep things organized and on track.

What is the best thing about where you work?

Arnau Casoliba Melich: The people and specially labmates are very supportive. We all go through similar experiences and knowing people are there for you is very reassuring.

Antar Drews: Having labmates that help me with (and sometimes prevent me from) consuming concerning amounts of gummy bears in the office.

Eleni Kafkia: I really appreciate the supportive and collaborative atmosphere within and across the labs at the institute.

Viktoria Lavro: The environment is very supportive, not just within my group, but also across other research labs. On top of that, I really appreciate our central location in the city, in a lively area of beautiful Copenhagen.

David Pladevall Morera: The collaborative environment across labs in our institute and the always supportive colleagues.

Nikolaos Stamidis: The individuals from the institute are the ones who create an environment that you truly want to work in. Additionally, I would like to highlight the institute’s incredible facilities and its central location in the heart of Copenhagen, which places it at the center of Denmark’s scientific community.

Karlien van Nerum: The international treats when our colleagues return from holidays.

Anne Wenzel: We have a highly interdisciplinary and international environment with ample opportunities for exchange in scientific and social settings, such as the ChatBPC (BioinformaticsPeerCommunity) meetings and “Friday Hygge”.

Jan Żylicz: Our institute has a close-knit atmosphere, where you get to know everyone personally. Additionally, due to our shared use of similar tools and approaches, we frequently collaborate with labs located right next door.

What’s there to do outside of the lab?

Sandra Bages Arnal: During summer there is plenty of live music around the city, some for free, and in general there is a very nice atmosphere everywhere.

Arnau Casoliba Melich: You have plenty to do in Copenhagen, from cute cafés to great parks, there is always a new thing to do. I specially like the climbing gyms around the city.

Antar Drews: Although Copenhagen is not famous for having great weather, there are plenty of cozy cafés and bars to hide from the rain! Also, people are very sporty and there is a large running community here, which I personally find very motivating.

Eleni Kafkia: The concentration and diversity of museums, galleries, events, and activities make Copenhagen a city with incredibly rich cultural offerings. This, in combination with Copenhagen’s international atmosphere that melds local traditions with foreign influences, contributes to its distinct cultural uniqueness.

Viktoria Lavro: When the weather is good, the city truly comes alive as everyone takes the opportunity to enjoy being outdoors and there are endless events to check out. But you can also always find something fun to do on rainy days, I particularly enjoy attending concerts and playing board games in cafés.

David Pladevall Morera: I love Copenhagen in general and how international the city is. Particularly, I enjoy trying the many different restaurants that the city offers. Although it is a small city, as a capital, you can find great cultural and sport events all year around.

Nikolaos Stamidis: I truly believe that Copenhagen is one of the best cities to live in. The quality of life is very high. Despite the Scandinavian weather, there are many parks around the city where people can be seen exercising throughout the entire year. On top of that, there are always events to attend, and people are always up for going out for a beer.

Karlien van Nerum: As a capital city, Copenhagen is very vibrant and international. You can always find something unique to do and go on little adventures.

Anne Wenzel: Copenhagen is a very livable city. Despite its small size, which means that one can easily get everywhere by bike, it’s still the capital and offers all kinds of entertainment, lots of concerts etc.

Jan Żylicz: The food scene in Copenhagen is truly phenomenal! From street and comfort food to extravagant new Scandinavian cuisine we are spoiled for choice.

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