SCALE Science Lunch Seminar – Prof. Dr. Yvonne Stahl and Dr. Thomas Sokolowski

  • 2024-05-29
  • 12:30 am
  • Lecture Hall, Max Planck Institute of Biophysics and via ZOOM

Multiscale functional imaging of plant stem cell regulation (Yvonne Stahl)

Dynamic protein interactions are crucial for many cellular processes. In plant research, there is a growing focus on investigating in vivo protein-protein interactions (PPIs) by techniques such as Förster resonance energy transfer fluorescence lifetime imaging (FRET-FLIM) and the dynamics of proteins of interest. FRET-FLIM allows the visualization of PPIs at subcellular resolution, preserving spatio-temporal details. As the study of higher-order protein complexes becomes increasingly important, traditional PPI techniques are often insufficient. Therefore, combining various advanced fluorescence methods provides deeper insights into the complex protein compositions. New analytical methods further enhance the identification of higher-order protein complex compositions and their binding affinities.
Our focus is on key receptors and transcription factors (TFs) that regulate stem cell homeostasis in the plant roots by forming (higher-order) complexes. Here, intrinsically disordered regions and prion-like domains are necessary for distinct subcellular localizations and complex formation, possibly involving liquid-liquid phase separation. This seminar will highlight the use of advanced fluorescence imaging techniques to study in vivo dynamic complex formation and their roles in plant stem cell homeostasis.

The tale of the mouse and the fly: Multiscale modeling, optimization and inference for elucidating distinct developmental strategies (Thomas Sokolowski)

For different organisms, early development unfolds under very different circumstances and time scales, but always impaired by biological noise resulting from the inherently stochastic nature of the underlying processes. To cope with this, various developmental strategies and
mechanisms evolved, shaped by the constraints imposed by physical laws and their natural environments. In spite of intense research, we are still lacking theories that explain these processes in a truly mechanistic fashion, even for paradigmatic organisms. Ubiquitous computational
resources have recently enabled construction of genuinely spatial-stochastic developmental models with ever increasing complexity. However, since experimental reports on microscopic cell-physical quantities are scarce, the parametrization of such models becomes a key problem itself and posits a new frontier in multiscale modeling. I will contrast two distinct strategies for parametrizing biophysical models in
development and beyond: optimization of normative theories, and Bayesian inference, which in principle can operate even in a model-free regime. I will first highlight a mathematical framework that unifies both approaches in a rigorous way and allows smooth transition between them. I will then present our results on elucidating early development of two distinct organisms while making use of both strategies: (1.) optimization of a biophysic-rooted spatial-stochastic model of the gap-gene system in the early fruit fly, and (2.) characterization of the spatial regulatory processes driving early cell-fate assignment in the early mouse embryo via AI-driven SBI (simulation-based inference). Our results exemplify how optimization of normative models and inference strategies can be combined for sucessfully determining complex spatial-stochastic models, and at the same time highlight how distinct developmental strategies emerged under the significantly different circumstances faced by the fly and mouse embryos.

The SCALE lunch seminar will take place in a hybrid form. All interested are invited to attend in person at the lecture hall of the MPI-BP with coffee and a light lunch in the atrium afterwards. At the same time, the lecture will also be streamed online via ZOOM.

Zoom link: https://uni-frankfurt.zoom.us/j/97193552271?pwd=Q1hMU0IwTzVoUmlpN3o1cjZ5VVlxUT09

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