Biology subjects

Fukamachi, S.

Publications and source records attributed to Fukamachi, S..

4 recordsLinked to original sources

bioRxiv2026

Computational Design for Engineering Layered Tissue Architectures via Cell-Cell Interfacial Tension Modulation

The spatial arrangement of cells is fundamental to the mechanical and functional integrity of three-dimensional (3D) tissues, yet engineering spatially well-controlled tissue architectures remains challenging. Here, we computationally investigated how layered tissue architectures can be designed by modulating cell-cell interfacial tension. We performed simulations using a 3D vertex model and systematically varied interfacial tension magnitudes. The simulations generated a range of layered tissue architectures, including planar monolayers, bilayers, and structurally stratified states. In homogeneous cell populations, increasing interfacial tension drove transitions from monolayer to structurally stratified configurations. In heterogeneous populations, differential interfacial tensions induced out-of-plane cell sorting and the formation of compositionally sorted multilayers. Moreover, a recursive tension design strategy enabled hierarchical organization of multiple cell types into separate layers. Notably, this recursive scheme uses only two tension levels (high vs. low) assigned across interfaces and can, in principle, be extended to specify layered architectures with an arbitrary number of layers. Together, these results identify cell-cell interfacial tension as a tunable mechanical parameter for regulating layered tissue architecture and provide design principles for layered tissue engineering and regenerative medicine.

bioengineering↗

bioRxiv2025

A New Look at Medaka: Surprising Deep Diving Behavior Uncovered in the Lab

Medaka (Oryzias latipes and O. sakaizumii) are small freshwater fish native to East Asia, commonly found in shallow waters. However, their presence and behavior in deeper habitats remain poorly understood due to observational challenges. Here, we introduce a novel experimental system--a 9-meter-tall cylindrical tank made from vertically connected transparent PVC pipes--that enables direct observation of medaka diving behavior. Our results demonstrate that medaka voluntarily dive to depths of up to 9 meters and remain at the bottom for extended periods, a behavior contrasting with that of zebrafish (Danio rerio), which rarely reached such depths. Moreover, when fish were introduced from the bottom of the tank, zebrafish exhibited repeated vertical movements, ascending and descending but rarely reaching the water surface, whereas medaka consistently remained at the bottom. While primarily descriptive, these findings represent a significant and previously unrecognized aspect of medaka ecology, challenging the traditional view of them as purely surface-dwelling fish. This study provides a unique tool and foundational insight that opens new avenues for ecological and physiological investigations of fish depth preferences.

animal behavior and cognition↗

bioRxiv2024

Epithelium Stratifies via Nucleation and Growth Induced by Foam-Geometric Instability

The epithelium undergoes stratification, transitioning from a monolayer to a multilayer structure, across broad phenomena. Recent studies have identified several cell behaviors as triggers, including junctional tension, cell density and geometry, and topological defects. However, how these factors drive stratification throughout the entire epithelium remains poorly understood. Here, we report a mechanism underlying epithelial stratification that mirrors the physics of phase transition. Combining cell culture with three-dimensional vertex modeling, we demonstrate that epithelial stratification is analogous to a structural phase transition driven by the nucleation-growth process, i.e., multilayer origins dispersedly appear and expand across the epithelium via unordered intermediate states. This transition is induced by a mechanical instability inherent in the foam-like geometry of the epithelium. Moreover, the nucleation-growth concept applies to embryonic skin development and intestinal cancer transformation. These findings conceptualize epithelial stratification as a form of a phase transition governed by foam mechanics, offering a physical perspective on various epithelial developments.

biophysics↗

bioRxiv2023

Multicellular dynamics on 3D scaffolds: Stress concentration is a key to controlling complex microtissue morphology on engineered surfaces

Tissue engineers have utilized a variety of three-dimensional (3D) scaffolds for controlling multicellular dynamics and the resulting tissue microstructures. In particular, cutting-edge microfabrication technologies, such as 3D bioprinting, provide increasingly complex structures. However, unpredictable microtissue detachment from scaffolds, which ruins desired tissue structures, is becoming an evident problem. To overcome this issue, we elucidated the mechanism underlying collective cellular detachment by combining a new computational simulation method with quantitative tissue-culture experiments. We first quantified the stochastic processes of cellular detachment shown by vascular smooth muscle cells on model curved scaffolds and found that microtissue morphologies vary drastically depending on cell contractility, substrate curvature, and cell-substrate adhesion strength. To explore this mechanism, we developed a new particle-based model that explicitly describes stochastic processes of multicellular dynamics, such as adhesion, rupture, and large deformation of microtissues on structured surfaces. Computational simulations using the developed model successfully reproduced characteristic detachment processes observed in experiments. Crucially, simulations revealed that cellular contractility-induced stress is locally concentrated at the cell-substrate interface, subsequently inducing a catastrophic process of collective cellular detachment, which can be suppressed by modulating cell contractility, substrate curvature, and cell-substrate adhesion. These results show that the developed computational method is useful for predicting engineered tissue dynamics as a platform for prediction-guided scaffold design.

biophysics↗