In vivo biophysics of signaling and behavior

Group leader: Prof. dr. Tom Shimizu

We are searching for motivated students and postdocs to join our group

Living cells sense and respond to their environment by an intricate web of molecular interactions. Inasmuch as their designs are dictated by the problems they solve, such networks can be considered primitive algorithms derived by natural selection.

We aim to link the temporal dynamics of intracellular signaling networks to the constraints imposed by behavioral performance and evolution.  Can naturally evolved systems be understood in the same language that engineers use to design machines for a specific purpose? Or are there fundamental design principles peculiar to the continuously evolving biological world? How plastic are these signaling algorithms over evolutionary time scales? Microbes can serve as an excellent vehicle for probing such questions, as the time scales involved in signaling, behavior and evolution are all amenable to laboratory experiments.

Group Members

We combine experiment with theory to tackle these problems. Fluorescence microscopy and spectroscopy techniques allow us to probe molecular responses to dynamically varying chemical stimuli in living cells. Such physiological measurements constrain mechanistic models of signaling, the parameter space of which can be explored again experimentally by genetic alterations of the organism. We are also designing microfluidic chambers in which behavior of individual cells and populations can be interrogated by video microscopy, to link specific signaling network topologies and parameter sets to behavioral performance.

  • Personality and mood swings in bacteria

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  • Bacteriën vertonen stemmingen en persoonlijkheid

    Bacteriën gebruiken een signaalnetwerk van eiwitmoleculen om te bepalen waar ze naar toe willen. Wetenschappers van AMOLF hebben een microscopiemethode ontwikkeld waarmee ze kunnen zien hoe individuele bacteriën dit netwerk …

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  • New 3D tracking technique “for the masses” reveals individuality of bacterial behavior

    Microscopy techniques used to study the movement of swimming microbes are limited to two dimensions (2D) or require sophisticated devices. In a paper to be published online on 2 November, …

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  • Tom Shimizu appointed professor at VU University Amsterdam

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