Theoretical biology and biophysics

Hermsen lab

The Hermsen lab is lead by Rutger Hermsen.  It is part of the Theoretical Biology and Bioinformatic group and the Institute for Biodynamics & Biocomplexity at Utrecht University in The Netherlands. 

Currently, our research focusses on the physiology of bacterial cells and a broad range of topics in evolutionary biology.  For more details, see Research and  Publications.

Just out:

Multiscale selection in spatially structured populations

June, 2024

Finally, this long-awaited article has been published! Many congratulations to Hilje Doekes, the first author.

The spatial structure of populations is key to many (eco-)evolutionary processes. In such cases, the strength and sign of selection on a trait may depend on the spatial scale considered. An example is the evolution of altruism: selection in local environments often favours cheaters over altruists, but this can be outweighed by selection at larger scales, favouring clusters of altruists over clusters of cheaters. For populations subdivided into distinct groups, this effect is described formally by multilevel selection theory. However, many populations do not consist of non-overlapping groups but rather (self-)organize into other ecological patterns. We therefore present a mathematical framework for multiscale selection. This framework decomposes natural selection into two parts: local selection, acting within environments of a certain size, and interlocal selection, acting among them. Varying the size of the local environments subsequently allows one to measure the contribution to selection of each spatial scale. To illustrate the use of this framework, we apply it to models of the evolution of altruism and pathogen transmissibility. The analysis identifies how and to what extent ecological processes at different spatial scales contribute to selection and compete, thus providing a rigorous underpinning to eco-evolutionary intuitions.

Read the article here!

Multiscale selection in spatially structured populations

HM Doekes, R Hermsen - Proceedings of the Royal Society B, 2024.

Just started: Charlotte de Vries

February, 2024

We are very happy to announce that Charlotte (Lotte) de Vries has joined our group as a senior postdoc!

Lotte is an evolutionary demographer who uses demographic models to study eco-evolutionary processes and life-history evolution. She recently was awarded the prestigious NWO VENI grant for research on the impact of aging on evolutionary transitions towards multi-cellularity and eusociality. This topic  dovetails perfectly with the research in the group on transitions of individuality.

Read more on Lotte's personal website.

Just out in Cell Reports:
The interplay between metabolic stochasticity and cAMP-CRP regulation in single E. coli cells

October 20, 2023

We're very happy to finally see this article online. Many congratulations to the lead authors, Martijn Wehrens and Laurens Krah!

In collaboration with the group of Sander Tans at AMOLF, we combined measurements of gene expression and growth in individual bacteria with advanced mathematical models of growing bacteria. We found that a known regulatory feedback mechanism not only responds to external conditions, but also continuously reacts to metabolic fluctuations unique to each individual bacterium.  The study yields new insights into cellular homeostasis and regulatory interactions.

Read the article here!

The interplay between metabolic stochasticity and cAMP-CRP regulation in single E. coli cells.
Martijn Wehrens, Laurens Krah, et al.
Cell Reports, Volume 42, ISSUE 10, 113284, October 31, 2023

S4S Grant for Bryan Verhoef:
Extending the lifespan of antibiotics

September 1, 2023

We congratulate Bryan Verhoef for winning a Science for Science for Sustainability Graduate Program grant, which allows him to pursue a PhD based on his own project proposal.

Bryan wants to learn more about how bacteria develop resistance to antibiotics, so that the lifespan of existing antibiotics can be extended. He aims to build a computer model of bacterial colonies developing resistance when they are exposed to the antibiotic. The model can then be used to study how specific factors, such as spatial structure of the colony and inhomogeneous exposure effect the development of resistance. 

Bryam will be jointly supervised by Joost de Graaf (Institute for Theoretical Physics) and Rutger Hermsen (Theoretical Biology). 

Worth checking out:

Visualization of translation and protein biogenesis at the ER membrane

February 1, 2023

In this research article just published in Nature, Gemmer, Chaillet, van Loenhout et al  use cryo-electron tomography, extensive classification and molecular modelling to visualize of translation and protein maturation at the ER in amazing detail. We are grateful for the acknowledgement of our help with a small part of the statistics used .

Gemmer, M., Chaillet, M.L., van Loenhout, J. et al. Visualization of translation and protein biogenesis at the ER membrane. Nature 614, 160–167 (2023). 
Hermsen Movie2 S.mp4

Just out:
Emergent Multilevel Selection in a Simple Spatial Model of the Evolution of Altruism

October 25, 2022

Our newest article just appeared online at PLOS Computational Biology!

Theories on the evolutionary origins of altruistic behavior have a long history and have become a canonical part of the theory of evolution. Nevertheless, the mechanisms that allow altruism to appear and persist are still incompletely understood. It is well known, however, that the spatial structure of populations is an important determinant. In both theoretical and experimental studies, much attention has been devoted to populations that are subdivided into discrete groups. Such studies typically imposed the structure and dynamics of the groups by hand. Here, we instead present a simple individual-based model in which altruistic organisms spontaneously self-organize into spatially separated colonies that themselves reproduce by binary fission and hence behave as Darwinian entities in their own right. 

Read the article here!

Emergent Multilevel Selection in a Simple Spatial Model of the Evolution of Altruism.
Rutger Hermsen
PLOS Computational Biology 18, no. 10 (October 25, 2022): e1010612.