Biology subjects

Graedel, B.

Publications and source records attributed to Graedel, B..

5 recordsLinked to original sources

bioRxiv2025

Optogenetic SH3 nanoclustering of SRC and HCK uncovers the functional specificity of these redundant kinases in macrophages.

Understanding redundancy among Src Family Kinases (SFKs) challenges how cells achieve signaling specificity using closely related enzymes, and paves the way to revisit a basic property of any cell signaling network. Optogenetic control of the adaptor properties of the most redundant SFK members, SRC and HCK, was used to examine their potential specificity in macrophages. Uncoupling their kinase and adaptor functions uncovers an unique mechanism driven by oligomerized- and SH3-dependent specific binding that enables inducing distinct signaling outputs for each kinase. OptoSRC and optoHCK probes revealed that SRC and HCK can trigger specific cellular responses, despite only supposed overlapping functions. The specificity of optoHCK even unveils a novel role in activating polarized clathrin hotspots essential for directional migration. Redundancy could be rebuilt within optoHCK through stepwise optogenetic reconstruction of adaptor modules revealing the essential role of both membrane anchoring and SH2-domain. This deconstructive approach of SFK activation elucidated the molecular basis of their shared and unique signaling activities and supports a model of cooperative functional entanglement between SFK members, rather than simple redundancy.

cell biology↗

bioRxiv2025

Real-time feedback control microscopy for automation of optogenetic targeting

Optogenetics has revolutionized our ability to study cellular signaling by enabling the precise control of cellular functions with light. Most classical implementations rely on fixed or manually updated illumination patterns, limiting their ability to accommodate living systems that move, change shape or rapidly adapt their signaling states. Here, we present an experimental platform for Feedback Adaptive Real-time Optogenetics (FARO) that combines automated image segmentation, tracking, feature extraction, and adaptive hardware control to dynamically adjust optogenetic stimulation based on live cell behavior. By continuously analyzing biosensor signals, FARO updates illumination patterns in real time across biological scales; from maintaining stimulation on specific subcellular regions, to selectively activating single cells in deforming tissue. This fully automated, Python-based framework is built on open standards for data management and microscope control and data handling, supporting large-scale experiments and long-term timelapse studies, compatible with different microscope hardware. Eliminating the need for human intervention to reposition light patterns or select target cells enables reproducible, systematic and high-throughput interrogation of spatiotemporal signaling. We show how automated and adaptive optogenetic perturbations are a powerful tool to study how local signaling events shape cellular behavior, from subcellular dynamics and single-cell migration up to emergent tissue-level processes.

cell biology↗

bioRxiv2025

Interplay between Rac1/RhoA and actin waves in giant epithelial cells : experiment and theory

The acto-myosin cytoskeleton is a key driver of cellular shape changes in vivo and in vitro. Acto-myosin organization results from actin assembly and interactions between actin and myosin, which are both regulated by small Rho GTPases like Rac1 and RhoA. To uncover principles governing cytoskeletal organization, we analyzed actin patterns using live microscopy and theory. In giant Madin-Darby Canine Kidney (MDCK) epithelial cells and REF52 fibroblasts, we observed acto-myosin stress fibres and propagating waves. Stress fibres were stationary and correlated with homogeneous distributions of Rac and RhoA activity. Waves propagated at {approx} 1m/min and were associated with density variations of actin, Rac and active RhoA. Some waves transported cellular components or generated protrusions at the cell edge. Essential features of wave propagation are captured by a polar reaction-diffusion system for actin and Rac. Notably, two colliding waves annihilate each other. In cells, myosin activity was not required for the emergence of waves, but tended to suppress them. Consistently, local activation of RhoA slowed down or stopped and broke waves. These results highlight how the coupling between acto-myosin and Rho GTPase generates a variety of cytoskeletal structures and dynamics. O_TEXTBOXSIGNIFICANCEThe cytoskeleton shapes cells in vitro and in vivo. Its molecular mechanisms have been extensively documented, but the mesoscopic structures resulting from the interplay between the activator and the motor activity have been poorly characterized. Here we show that two structures are conserved in two systems, stress fibres with RhoA activity and diffusion actin waves regulated by Rac1. The annihilation of waves and the alteration of the wave dynamics are reproduced by a minimal model based on a polar reaction-diffusion model. This approach could pave the way to a generic description of regulated active gels in cells with potential biological functions, such as stress generation for fibres and probing of space and homogenization of the cortex by actin waves. C_TEXTBOX

biophysics↗

bioRxiv2025

Teach your microscope how to print: Low-cost and rapid-iteration microfabrication for biology

The application of traditional microfabrication techniques to biological research is hindered by their reliance on clean rooms, expensive or toxic materials, and slow iteration cycles. We present an accessible microfabrication workflow that addresses these challenges by integrating consumer 3D printing techniques and repurposing standard fluorescence microscopes equipped with DMDs for maskless photolithography. Our method achieves micrometer-scale precision across centimeter-sized areas without clean room infrastructure, using affordable and readily available consumables. We demonstrate the versatility of this approach through four biological applications: inducing cytoskeletal protrusions via 1 m-resolution surface topographies; micropatterning to standardize cell and tissue morphology; fabricating multilayer microfluidic devices for confined cell migration studies; imprinting agar chambers for long-time tracking of C. elegans. Our protocol drastically reduces material costs compared to conventional methods and enables design-to-device turnaround within a day. By leveraging open-source microscope control software and existing lab equipment, our workflow lowers the entry barrier to micro-fabrication, enabling labs to prototype custom solutions for diverse experimental needs while maintaining compatibility with soft lithography and downstream biological assays.

cell biology↗

bioRxiv2024

Convpaint - Universal framework for interactive pixel classification using pretrained neural networks

We develop Convpaint, a universal computational framework for interactive pixel classification. Convpaint utilizes pretrained convolutional neural networks (CNNs) or vision transformers (ViTs) for feature extraction and enables easy segmentation across a wide variety of tasks. Available within the Python-based napari software ecosystem, Convpaint integrates seamlessly with other plugins into image processing pipelines, which we demonstrate with three workflows across different data modalities.

bioinformatics↗