Biology subjects

Shelley, M. J.

Publications and source records attributed to Shelley, M. J..

9 recordsLinked to original sources

bioRxiv2026

Geometric optics organizes organelle interactions and positioning

Microtubule asters are central to positioning organelles and organizing intracellular architectures. We show that the multi-stage choreography of microtubule asters which positions pronuclei during the first cell division in Caenorhabditis elegans, is governed by a cellular analog of geometric optics. Large-scale electron tomography reveals that astral microtubules reach cortical and pronuclear surfaces largely along line-of-sight trajectories, leaving complementary regions shadowed and inaccessible. Laser ablation identifies surface-anchored motors pulling on microtubules as the dominant drivers of motion. We develop a biophysical model incorporating dynamic terminator curves that separate microtubule-accessible and -inaccessible surfaces, and quantitatively recapitulate aster separation, pronuclear migration, centering, and rotation in control and genetically perturbed embryos. More broadly, robust positioning emerges from a feedback loop wherein intracellular geometry gates microtubule access, thus sculpting the distribution and magnitude of pulling forces, which in turn reshape that geometry.

cell biology↗

bioRxiv2025

Cell size reduction scales spindle elongation but not chromosome segregation in C. elegans

How embryos adapt their internal cellular machinery to reductions in cell size during development remains a fundamental question in cell biology1-11. Here, we use high-resolution lattice light-sheet fluorescence microscopy and automated image analysis to quantify lineage-resolved mitotic spindle and chromosome segregation dynamics from the 2-to 64-cell stages in Caenorhabditis elegans embryos. While spindle length scales with cell size across both wild-type and size-perturbed embryos, chromosome segregation dynamics remain largely invariant, suggesting that distinct mechanisms govern these mitotic processes. Combining femtosecond laser ablation12,13 with large-scale electron tomography14, we find that central spindle microtubules mediate chromosome segregation dynamics and remain uncoupled from cell size across all stages of early development. In contrast, spindle elongation is driven by cortically anchored motor proteins and astral microtubules, rendering it sensitive to cell size12,13,15-17. Incorporating these experimental results into an extended stoichiometric model for both the spindle and chromosomes, we find that allowing only cell size and microtubule catastrophe rates to vary reproduces elongation dynamics across development. The same model also accounts for centrosome separation and pronuclear positioning in the one-cell C. elegans embryo18, spindle-length scaling across nematode species spanning ~100 million years of divergence17, and spindle rotation in human cells19. Thus, a unified stoichiometric framework provides a predictive, mechanistic account of spindle and nuclear dynamics across scales and species.

cell biology↗

bioRxiv2025

Collective multicellular patterns arising from cadherin-linked cytoskeletal domains

I.In multicellular systems, adhesion complexes, such as those composed of E-cadherin and associated catenins, mechanically couple neighboring cells by directly linking their actin-based cytoskeletal assemblies. However, the mechanics of how forces are transmitted across these adhesions remains largely unstudied. Here, we introduce a biophysical model that explicitly couples adhesion complex dynamics to intracellular mechanics across cell boundaries. A cadherin dimer plus associated catenins connecting two cells is represented as a spring whose ends experience drag with respect to the moving actin cytoskeleton. The cytoskeleton is modeled as a contractile gel driven by myosin activity in its bulk and forces from adhesion on its boundaries. Our model captures this bidirectional coupling via a coarse-grained continuum framework and reveals a range of observed cell- and tissue-scale behaviors. These include global cell polarization of the multicellular collective, other polarization patterns and oscillatory dynamics, spontaneously formed actin rings within cells, and supracellular stress chains. Many of these features arise from modeling the direct mechanical coupling between cytoskeleton and adhesion. This model can be extended to other adhesion-cytoskeleton feedback systems and used to advance our understanding of multicellular tissue dynamics, particularly during development.

biophysics↗

bioRxiv2024

A first-principles geometric model for dynamics of motor-driven centrosomal asters

The centrosomal aster is a mobile and adaptable cellular organelle that exerts and transmits forces necessary for tasks such as nuclear migration and spindle positioning. Recent experimental and theoretical studies of nematode and human cells demonstrate that pulling forces on asters by cortically anchored force generators are dominant during such processes. Here we present a comprehensive investigation of a first-principles model of aster dynamics, the S-model (S for stoichiometry), based solely on such forces. The model evolves the astral centrosome position, a probability field of cell-surface motor occupancy by centrosomal microtubules (under an assumption of stoichiometric binding), and free boundaries of unattached, growing microtubules. We show how cell shape affects the stability of centering of the aster, and its transition to oscillations with increasing motor number. Seeking to understand observations in single-cell nematode embryos, we use highly accurate simulations to examine the nonlinear structures of the bifurcations, and demonstrate the importance of binding domain overlap to interpreting genetic perturbation experiments. We find a generally rich dynamical landscape, dependent upon cell shape, such as internal constant-velocity equatorial orbits of asters that can be seen as traveling wave solutions. Finally, we study the interactions of multiple asters which we demonstrate an effective mutual repulsion due to their competition for surface force generators. We find, amazingly, that centrosomes can relax onto the vertices of platonic and non-platonic solids, very closely mirroring the results of the classical Thomson problem for energy-minimizing configurations of electrons constrained to a sphere and interacting via repulsive Coulomb potentials. Our findings both explain experimental observations, providing insights into the mechanisms governing spindle positioning and cell division dynamics, and show the possibility of new nonlinear phenomena in cell biology.

cell biology↗

bioRxiv2023

Flow Physics Explains Morphological Diversity of Ciliated Organs

Organs that pump fluids by the coordinated beat of motile cilia through the lumen are integral to animal physiology. Such organs include the human air-ways, brain ventricles, and reproductive tracts. Although cilia organization and duct morphology vary drastically in the animal kingdom, ducts are typically classified as either carpet or flame designs. The reason behind this di-chotomy and how duct design relates to fluid pumping remain unclear. Here, we demonstrate that two structural parameters - lumen diameter and cilia-to-lumen ratio - organize the observed duct diversity into a continuous spectrum that connects carpets to flames across all animal phyla. Using a unified fluid model, we show that carpet and flame designs maximize flow rate and pressure generation, respectively. We propose that convergence of ciliated organ designs follows functional constraints rather than phylogenetic distance, along with universal design rules for ciliary pumps.

biophysics↗

bioRxiv2022

Euchromatin activity enhances segregation and compaction of heterochromatin in the cell nucleus

The large-scale organization of the genome inside the cell nucleus is critical for the cells function. Chromatin - the functional form of DNA in cells - serves as a substrate for active nuclear processes such as transcription, replication and DNA repair. Chromatins spatial organization directly affects its accessibility by ATP-powered enzymes, e.g., RNA polymerase II in the case of transcription. In differentiated cells, chromatin is spatially segregated into compartments - euchromatin and heterochromatin - the former being largely transcriptionally active and loosely packed, the latter containing mostly silent genes and densely compacted. The euchromatin/heterochromatin segregation is crucial for proper genomic function, yet the physical principles behind it are far from understood. Here, we model the nucleus as filled with hydrodynamically interacting active Zimm chains - chromosomes - and investigate how large heterochromatic regions form and segregate from euchromatin through their complex interactions. Each chromosome presents a block copolymer composed of heterochromatic blocks, capable of crosslinking that increases chromatins local compaction, and euchromatic blocks, subjected to stochastic force dipoles that capture the microscopic stresses exerted by nuclear ATPases. These active stresses lead to a dynamic self-organization of the genome, with its coherent motions driving the mixing of chromosome territories as well as large-scale heterochromatic segregation through crosslinking of distant genomic regions. We study the stresses and flows that arise in the nucleus during the heterochromatic segregation, and identify their signatures in Hi-C proximity maps. Our results reveal the fundamental role of active mechanical processes and hydrodynamic interactions in the kinetics of chromatin compartmentalization and in the emergent large-scale organization of the nucleus.

biophysics↗

bioRxiv2021

Laser Ablation and Fluid Flows Show a Single Force Mechanism Governs Spindle Positioning

Few techniques are available for elucidating the nature of forces that drive subcellular behaviors. Here we develop two complementary ones: 1) femtosecond stereotactic laser ablation (FESLA), which rapidly creates complex cuts of subcellular structures, thereby allowing precise dissection of when, where, and in what direction forces are generated; and 2) assessment of subcellular fluid flows, by comparing direct flow measurements, using microinjected fluorescent nanodiamonds, to large-scale fluid-structure simulations of different models of force transduction. We apply these to study centrosomes in Caenorhabditis elegans early embryos, and use the data to construct a biophysically-based model of centrosome dynamics. Taken together, we demonstrate that cortical pulling forces provide a general explanation for many behaviors mediated by centrosomes, including pronuclear migration/centration and rotation, metaphase spindle positioning, asymmetric spindle elongation and spindle oscillations. In sum, this work establishes new methodologies for disentangling the forces responsible for cell biological phenomena.

biophysics↗

bioRxiv2020

Swirling Instability of the Microtubule Cytoskeleton

In the cellular phenomena of cytoplasmic streaming, molecular motors carrying cargo along a network of microtubules entrain the surrounding fluid. The piconewton forces produced by individual motors are sufficient to deform long microtubules, as are the collective fluid flows generated by many moving motors. Studies of streaming during oocyte development in the fruit fly D. melanogaster have shown a transition from a spatially-disordered cytoskeleton, supporting flows with only short-ranged correlations, to an ordered state with a cell-spanning vortical flow. To test the hypothesis that this transition is driven by fluid-structure interactions we study a discrete-filament model and a coarse-grained continuum theory for motors moving on a deformable cytoskeleton, both of which are shown to exhibit a swirling instability to spontaneous large-scale rotational motion, as observed.

biophysics↗

bioRxiv2018

Extensile motor activity drives coherent motions in a model of interphase chromatin

The 3D spatiotemporal organization of the human genome inside the cell nucleus remains a major open question in cellular biology. In the time between two cell divisions, chromatin - the functional form of DNA in cells - fills the nucleus in its uncondensed polymeric form. Recent in-vivo imaging experiments reveal that the chromatin moves coherently, having displacements with long-ranged correlations on the scale of microns and lasting for seconds. To elucidate the mechanism(s) behind these motions, we develop a novel coarse-grained active-polymer model where chromatin is represented as a confined flexible chain acted upon by molecular motors, which perform work by exerting dipolar forces on the system. Numerical simulations of this model account for steric and hydrodynamic interactions as well as internal chain mechanics. These demonstrate that coherent motions emerge in systems involving extensile dipoles and are accompanied by large-scale chain reconfigurations and nematic ordering. Comparisons with experiments show good qualitative agreement and support the hypothesis that self-organizing long-ranged hydrodynamic couplings between chromatin-associated active motor proteins are responsible for the observed coherent dynamics.

biophysics↗