Gastruloids and DNA replication – PhD defense Vincent van Batenburg

Embryo model

During the first part of his PhD, Van Batenburg worked on gastruloids. These are clumps of stem cells in the lab that closely resemble the early stages of an embryo. Therefore, they can be used for research into the first steps of embryonic development. “Research with real embryos is complicated,” says Van Batenburg. “But gastruloids can be produced in large numbers from stem cells, and resemble real embryos enough to learn a lot from them. This reduces the need for embryos for research.”

Van Batenburg discovered that somite formation occurs in gastruloids, just like in real embryos. This process involves the formation of small ‘blocks’ of tissue that ultimately form various parts of the body, such as the vertebrae. “I hope that research with gastruloids can at some point contribute to a deeper understanding of early embryonic development, and also why it goes wrong in some cases,” says Van Batenburg.

Speed ​​measurement in the cell

Van Batenburg’s second project was developing a technique to study DNA replication in detail. DNA replication occurs before a cell divides. The DNA is copied, so that both new cells receive a complete set of genetic information. Van Batenburg developed a technique that for the first time allowed scientists to determine the speed of DNA replication in single cells. Previously, such a speed measurement could only be performed in a large bulk collection of cells, which obscured differences between individual cells. This made it difficult to determine which factors influence DNA replication.

The new technique makes it possible to look at a single cell level and identify such factors. Van Batenburg and his colleagues discovered, for example, that DNA replication slows down in regions where transcription occurs. In these areas, genes are transcribed, ultimately producing proteins that carry out various cellular processes. If transcription and replication occur simultaneously in the same location, they are in each other’s way, slowing down DNA replication.

Good discussions and hard work

Looking back on his PhD, Van Batenburg has fond memories of the daily discussions with colleagues. “Learning from such motivated and inspiring people feels like a privilege,” he says. A scientific highlight was the first time he saw evidence of somite formation in his gastruloids. “That was quite a special feeling, a mix of relief and excitement, and simultaneously the stress of making sure I saved the files correctly, because I knew it was important data.” Of course, there were also less enjoyable aspects of his PhD. For example, doing cell culture in the weekend was his least preferred task, from which he gladly steered away in the later years of his PhD. His advice to future PhD students is to try to enjoy the process as much as possible. “Things can be though, so it’s not a job you should do if you don’t at least enjoy it from time to time.”