More Like this

1. Topological Data Analysis Approaches to Uncovering the Timing of Ring Structure Onset in Filamentous Networks

   https://doi.org/10.1007/s11538-020-00847-3  

   Ciocanel, Maria-Veronica; Juenemann, Riley; Dawes, Adriana T.; McKinley, Scott A. (March 2021, Bulletin of Mathematical Biology)

   null (Ed.)

   Abstract In developmental biology as well as in other biological systems, emerging structure and organization can be captured using time-series data of protein locations. In analyzing this time-dependent data, it is a common challenge not only to determine whether topological features emerge, but also to identify the timing of their formation. For instance, in most cells, actin filaments interact with myosin motor proteins and organize into polymer networks and higher-order structures. Ring channels are examples of such structures that maintain constant diameters over time and play key roles in processes such as cell division, development, and wound healing. Given the limitations in studying interactions of actin with myosin in vivo, we generate time-series data of protein polymer interactions in cells using complex agent-based models. Since the data has a filamentous structure, we propose sampling along the actin filaments and analyzing the topological structure of the resulting point cloud at each time. Building on existing tools from persistent homology, we develop a topological data analysis (TDA) method that assesses effective ring generation in this dynamic data. This method connects topological features through time in a path that corresponds to emergence of organization in the data. In this work, we also propose methods for assessing whether the topological features of interest are significant and thus whether they contribute to the formation of an emerging hole (ring channel) in the simulated protein interactions. In particular, we use the MEDYAN simulation platform to show that this technique can distinguish between the actin cytoskeleton organization resulting from distinct motor protein binding parameters. 

   more » « less
2. Active cytoskeletal composites display emergent tunable contractility and restructuring

   https://doi.org/10.1039/D1SM01083B  

   Lee, Gloria; Leech, Gregor; Lwin, Pancy; Michel, Jonathan; Currie, Christopher; Rust, Michael J.; Ross, Jennifer L.; McGorty, Ryan J.; Das, Moumita; Robertson-Anderson, Rae M. (December 2021, Soft Matter)

   The cytoskeleton is a model active matter system that controls processes as diverse as cell motility and mechanosensing. While both active actomyosin dynamics and actin–microtubule interactions are key to the cytoskeleton's versatility and adaptability, an understanding of their interplay is lacking. Here, we couple microscale experiments with mechanistic modeling to elucidate how connectivity, rigidity, and force-generation affect emergent material properties in composite networks of actin, tubulin, and myosin. We use multi-spectral imaging, time-resolved differential dynamic microscopy and spatial image autocorrelation to show that ballistic contraction occurs in composites with sufficient flexibility and motor density, but that a critical fraction of microtubules is necessary to sustain controlled dynamics. The active double-network models we develop, which recapitulate our experimental findings, reveal that while percolated actomyosin networks are essential for contraction, only composites with comparable actin and microtubule densities can simultaneously resist mechanical stresses while supporting substantial restructuring. The comprehensive phase map we present not only provides important insight into the different routes the cytoskeleton can use to alter its dynamics and structure, but also serves as a much-needed blueprint for designing cytoskeleton-inspired materials that couple tunability with resilience and adaptability for diverse applications ranging from wound healing to soft robotics. 

   more » « less
3. Kinesin‐Driven De‐Mixing of Cytoskeleton Composites Drives Emergent Mechanical Properties

   https://doi.org/10.1002/marc.202401128  

   Sheung, Janet; Gunter, Christopher; Matic, Katarina; Sasanpour, Mehrzad; Ross, Jennifer L; Katira, Parag; Valentine, Megan T; Robertson‐Anderson, Rae M (April 2025, Macromolecular Rapid Communications)

   Abstract The cytoskeleton is an active composite of filamentous proteins that dictates diverse mechanical properties and processes in eukaryotic cells by generating forces and autonomously restructuring itself. Enzymatic motors that act on the comprising filaments play key roles in this activity, driving spatiotemporally heterogeneous mechanical responses that are critical to cellular multifunctionality, but also render mechanical characterization challenging. Here, we couple optical tweezers microrheology and fluorescence microscopy with simulations and mathematical modeling to robustly characterize the mechanics of active composites of actin filaments and microtubules restructured by kinesin motors. It is discovered that composites exhibit a rich ensemble of force response behaviors–elastic, yielding, and stiffening–with their propensity and properties tuned by motor concentration and strain rate. Moreover, intermediate kinesin concentrations elicit emergent mechanical stiffness and resistance while higher and lower concentrations exhibit softer, more viscous dissipation. It is further shown that composites transition from well‐mixed interpenetrating double‐networks of actin and microtubules to de‐mixed states of microtubule‐rich aggregates surrounded by relatively undisturbed actin phases. It is this de‐mixing that leads to the emergent mechanical response, offering an alternate route that composites can leverage to achieve enhanced stiffness through coupling of structure and mechanics. 

   more » « less
4. Nonlinear Cellular Mechanical Behavior Adaptation to Substrate Mechanics Identified by Atomic Force Microscope

   https://doi.org/10.3390/ijms19113461  

   Mollaeian, Keyvan; Liu, Yi; Bi, Siyu; Wang, Yifei; Ren, Juan; Lu, Meng (November 2018, International Journal of Molecular Sciences)

   Cell–substrate interaction plays an important role in intracellular behavior and function. Adherent cell mechanics is directly regulated by the substrate mechanics. However, previous studies on the effect of substrate mechanics only focused on the stiffness relation between the substrate and the cells, and how the substrate stiffness affects the time-scale and length-scale of the cell mechanics has not yet been studied. The absence of this information directly limits the in-depth understanding of the cellular mechanotransduction process. In this study, the effect of substrate mechanics on the nonlinear biomechanical behavior of living cells was investigated using indentation-based atomic force microscopy. The mechanical properties and their nonlinearities of the cells cultured on four substrates with distinct mechanical properties were thoroughly investigated. Furthermore, the actin filament (F-actin) cytoskeleton of the cells was fluorescently stained to investigate the adaptation of F-actin cytoskeleton structure to the substrate mechanics. It was found that living cells sense and adapt to substrate mechanics: the cellular Young’s modulus, shear modulus, apparent viscosity, and their nonlinearities (mechanical property vs. measurement depth relation) were adapted to the substrates’ nonlinear mechanics. Moreover, the positive correlation between the cellular poroelasticity and the indentation remained the same regardless of the substrate stiffness nonlinearity, but was indeed more pronounced for the cells seeded on the softer substrates. Comparison of the F-actin cytoskeleton morphology confirmed that the substrate affects the cell mechanics by regulating the intracellular structure. 

   more » « less
5. Encapsulation of the cytoskeleton: towards mimicking the mechanics of a cell

   https://doi.org/10.1039/C9SM01669D  

   Bashirzadeh, Yashar; Liu, Allen P. (October 2019, Soft Matter)

   The cytoskeleton of a cell controls all the aspects of cell shape changes and motility from its physiological functions for survival to reproduction to death. The structure and dynamics of the cytoskeletal components: actin, microtubules, intermediate filaments, and septins – recently regarded as the fourth member of the cytoskeleton family – are conserved during evolution. Such conserved and effective control over the mechanics of the cell makes the cytoskeletal components great candidates for in vitro reconstitution and bottom-up synthetic biology studies. Here, we review the recent efforts in reconstitution of the cytoskeleton in and on membrane-enclosed biomimetic systems and argue that co-reconstitution and synergistic interplay between cytoskeletal filaments might be indispensable for efficient mechanical functionality of active minimal cells. Further, mechanical equilibrium in adherent eukaryotic cells is achieved by the formation of integrin-based focal contacts with extracellular matrix (ECM) and the transmission of stresses generated by actomyosin contraction to ECM. Therefore, a minimal mimic of such balance of forces and quasi-static kinetics of the cell by bottom-up reconstitution requires a careful construction of contractile machineries and their link with adhesive contacts. In this review, in addition to cytoskeletal crosstalk, we provide a perspective on reconstruction of cell mechanical equilibrium by reconstitution of cortical actomyosin networks in lipid membrane vesicles adhered on compliant substrates and also discuss future perspectives of this active research area. 

   more » « less