Nies, G. | Search bioRxiv

bioRxiv2024

MultiMatch: Geometry-Informed Colocalization in Multi-Color Super-Resolution Microscopy

With recent advances in multi-color super-resolution light microscopy it has become possible to simultaneously visualize multiple subunits within complex biological structures at nanometer resolution. To opti-mally evaluate and interpret spatial proximity of stainings on such an image, colocalization analysis tools have to be able to integrate prior knowledge on the local geometry of the recorded biological complex. Here, we present MultiMatch to analyze the abundance and location of chain-like particle arrangements in multi-color microscopy based on multi-marginal optimal unbalanced transport methodology. Our object-based colocalization model statistically addresses the effect of incomplete labeling efficiencies enabling inference on existent, but not fully observ-able particle chains. We showcase that MultiMatch is able to consistently recover all existing chain structures in three-color STED images of DNA origami nanorulers and outperforms established geometry-uninformed triplet colocalization methods in this task in a simulation study. Further-more, MultiMatch also excels in the evaluation of simulated four-color STED images and generalizations to even more color channels can be immediately derived from our analysis. MultiMatch is provided as a user-friendly Python package comprising intuitive colocalization visual-izations and a computationally efficient network flow implementation.

bioinformatics↗

bioRxiv2023

Vimentin intermediate filaments structure and mechanically support microtubules in cells

The eukaryotic cytoskeleton is an intricate network of three types of mechanically distinct biopolymers - actin filaments, microtubules and intermediate filaments (IFs). These filamentous networks determine essential cellular functions and properties. Among them, microtubules are important for intracellular transport and establishing cell polarity during migration. Despite their intrinsic stiffness, they exhibit characteristic bending and buckling in cells due to non thermal forces acting on them. Interactions between cytoskeletal filaments have been found but are complex and diverse with respect to their effect on the mechanical behavior of the filaments and the architecture of networks. We systematically study how actin and vimentin IFs influence the network structure and local bending of microtubules by analyzing fluorescence microscopy images of mouse fibroblasts on protein micropatterns. Our automated analysis averages over large amounts of data to mitigate the effect of the considerable natural variance in biological cell data. We find that the radial orientation of microtubules in circular cells is robust and is established independently of vimentin and actin networks. Observing the local curvature of microtubules, we find highly similar average bending of microtubules in the entire cell regardless of the cytoskeletal surrounding. Small systematic differences cannot be attributed directly to vimentin and actin densities. Our results suggest that, on average, microtubules in unpolarized mouse fibroblasts are unexpectedly independent of the rest of the cytoskeleton in their global network structure and their local response to forces.

biophysics↗