Looking back on BaSyC PhD research

Lucia Baldauf, Maria Tsanai and Michele Partipilo all graduated from university in the past months and became a doctor. They now look back on their doctoral research and on their writing process and take us along in this article. We asked them:

1. What was your thesis briefly about and what was the main conclusion for BaSyC research?

Lucia took inspiration from animal cells to build a machinery that can control the shape and mechanics of synthetic cells, and ultimately drive cell division. She developed methods to build dynamic actin cortices in synthetic cells, and studied how the cortex and membrane shape each other. She found that surprisingly, very minimal actin cortices can already perform a lot of the functions we might want in a synthetic cell: the cortex self-assembles in a curvature-sensitive manner, mechanically stiffens the cell surface, and actively shapes the membrane. Furthermore, she and others developed a DNA-mediated vesicle fusion protocol to allow synthetic cells to grow, and set out a roadmap towards driving synthetic cell division with an actin cortex.

Maria her PhD research was concentrated on biomolecular condensates. Using the Martini model she was simulating different biomolecular systems, their physicochemical properties and how environmental parameters as well as post-translational modifications can regulate the condensation. The main conclusion is that although further refinement is needed on the model, we can accurately reproduce experimental findings regarding biomolecular condensate systems. Biomolecular condensates are of great importance for BaSyC since they are part of cells and they can be a useful mechanism for cell fission.

Michele his thesis focused on the reactants and in particular the enzymes suitable for the provision of reducing power in synthetic cells. He identified a shortlist of ideal compounds to ensure luminal availability of reducing equivalents and chose formate as ideal electron donor for bottom-up synthetic biology. He biochemically characterized the enzymes needed for its utilization and eventually devised a minimal enzymatic pathway for the regeneration of the redox cofactors confinable in the lumen of liposomes with different sizes.

2. What did you like the most during your PhD research and writing?

Lucia particularly enjoyed working with others from both synthetic biology and adjacent fields. This allowed her to have a much broader view of my project than she might otherwise have gotten. Also, supervising BSc and MSc students in more exploratory projects, or projects that brought together different sides of BaSyC research, brought her a lot of pleasure and inspiration.

Maria enjoyed going to conferences and workshops in and outside the Netherlands, sharing her results and network with other researchers.

Michele enjoyed the intellectual and technical challenge of integrating biochemical approaches to a multidisciplinary project as building a synthetic cell. This led him to meet and exchange opinions with amazing people with different backgrounds, allowing him to consider new different aspects of a research problem.

3. What was difficult during your PhD research and writing?

Lucia mentioned that on a technical side, her project (and probably all of those in BaSyC) was of course complex and hard to do – after all, we were trying to push research into places that have so far never been accessible. This therefore posed quite a struggle, but was worth it for her. On the conceptual level, even though she loves the ambitious nature of the project, she often found that the gap between ambition and real life possibilities was often left too far open, both in published synthetic cell work and even internally during BaSyC meetings. This was at times discouraging and left her questioning whether any of our plans could ever work, if the realities of our research progress were ignored when formulating a shared vision.

Maria mentioned that Covid lockdowns affected her mental health and also her PhD research.

Michele also mentioned that the COVID pandemic certainly has been an exceptional circumstance that we have all had to learn to deal with in order to achieve our goals. The climate of uncertainty regarding the development of the spread of the virus, the periods of isolation and the difficulties of having meetings were unprecedented experiences that undoubtedly affected his PhD.

4. What are your plans after your PhD?

Lucia is continuing her scientific research after her PhD, but moving towards a more biological system. She is now a postdoc at University College London, where she is studying how cytoskeletal networks allow tissues absorb and respond to mechanical forces. This is important for instance in our lungs, which need to expand to several times their own size as we breathe, but must avoid becoming leaky and letting pathogens enter our body. She hopes to one day combine the bottom-up expertise from her PhD with the top-down skills she is gaining in her postdoc, to study how mechanical forces drive biological assembly processes.

Maria just started a postdoc position at the University of California in Berkeley.

Michele started a postdoc position in Dirk’s group for roughly a year. He will focus on the study of membrane proteins involved in electron transfer. Maybe these proteins might find an application for synthetic biology purposes in the future!