Biology subjects

Funamoto, K.

Publications and source records attributed to Funamoto, K..

5 recordsLinked to original sources

bioRxiv2026

Microscopic collisions govern macroscopic aerotactic spreading through emergent transport coefficients

Collective migration is often attributed to complex cell-cell communication, yet coordinated multicellular dynamics can also emerge in organisms lacking social interactions. Continuum descriptions successfully capture such behaviors but generally rely on phenomenological transport coefficients whose microscopic origin remains elusive. Here we show that these coefficients emerge from cell-cell collisions and can be independently determined from experiments. We investigate the aerotactic dispersal of confined colonies of the solitary amoeba Acanthamoeba castellanii, in which oxygen consumption continuously reshapes the local environment to generate self-organized guidance cues. Combining quantitative videomicroscopy, oxygen mapping with phosphorescent sensing films, and oxygen-controlled microfluidics, we directly measure both the oxygen landscape and the aerotactic response governing colony expansion. We then develop a Patlak-Keller-Segel (PKS) -type drift-diffusion model whose transport coefficients are entirely determined from independent experiments and microscopic-to-macroscopic modeling approach, without adjustable parameters. The model quantitatively reproduces the observed dynamics, including the coexistence of a fast ballistic front and a trailing transient accumulation band. We show that both diffusion and aerotactic transport are modulated by the same collision-controlled mechanism through density-dependent changes in cell persistence. More generally, our results establish transport coefficients as measurable emergent properties bridging microscopic cell dynamics and macroscopic collective behavior, providing a predictive framework for oxygen-guided migration in living active matter.

biophysics↗

bioRxiv2025

Dictyostelium discoideum chemotaxis is altered by hypoxia to orient streaming toward higher oxygen level independently of aerotaxis.

BackgroundDictyostelium discoideum (Dd) exhibits a unique life cycle marked by its transition from single-cell amoeboid movement to multicellular development in response to environmental stimuli. While its chemotactic response to cyclic adenosine monophosphate (cAMP) has been extensively studied, experiments are usually carried out in a high oxygen environment (21% O2, also called normoxia) that might not reflect the natural condition for a soil amoeba as hypoxia is common underground. Our recent research has unveiled a novel phenomenon termed aerotaxis, wherein Dd cells migrate towards oxygen-rich environments under low oxygen (hypoxia). ResultsWe tested Dd response when submitted to two different stress sources: starvation and hypoxia. While both stresses induce a motile response, namely chemotaxis and aerotaxis, we were able to decoupled both type of responses to explore potential shared mechanisms. Importantly, aerotaxis appears to be operated independently of known chemotactic pathways, demonstrating unique signaling pathways and cellular responses. Aerotaxis contributes to Dd developmental processes by letting cells escape from acute hypoxia. Even though chemotactic response can occur at less than 2% O2, it does not lead to well organized or stable streaming. Furthermore, in an oxygen gradient, aggregation center for chemotactic response appears preferentially at higher O2 level. RT-qPCR analysis show that hypoxia only slightly reduces the expression of genes required for chemotactic response, suggesting that the bias toward high O2 might occur at another level. Reoxygenation of cells that have been starved in hypoxic condition for 18h allow rapid aggregation but require de novo protein synthesis. ConclusionAerotaxis and chemotaxis mechanisms do not interact directly. However, when cells are exposed to both hypoxia and starvation, both mechanisms can be combined to direct the migration of cells toward place with higher oxygen level. As hypoxia is frequent in the soil where Dd usually grow, formation of aggregation centers at, or close to the soil surface, where oxygen is abundant, will be advantageous. Low O2 level does not preclude cells to participate to streaming but seems to reduce or delay their ability to produce stable aggregation centers, resulting into bias favoring centers that form at higher oxygen level.

cell biology↗

bioRxiv2025

Cell-cultured PDMS vascular model to allow placement of implant devices

BackgroundA stent maintains normal blood flow by expanding a stenotic artery from the inside. Stents currently in clinical use are mechanically sub-optimized and, therefore, exert excessive mechanical stimuli on the vascular wall. This can lead to arterial inflammation and potentially in-stent restenosis. To optimize the force exerted by a stent on the vascular wall, we should understand, reproduce, and analyze in detail the mechanical field to which the stented vessel is exposed. However, to date, no in vitro model has been established that can adequately evaluate the mechanical effects of a stent on the vascular wall and be constructed without relying on a laboratorys know-how. This study aims to develop a three-dimensional in vitro vascular model that allows stent placement and to provide the details of its construction method. MethodsPolydimethylsiloxane (PDMS) was used to mimic the adventitial structure of arteries. Human carotid artery endothelial cells (HCtAECs) were then seeded on the luminal surface and cultured for 24 h to form a confluent monolayer (intima). The constructed model was installed in the flow-exposure culturing system, and hemodynamic stimulation (two types of shear stress (SS); 0.5 Pa and 2.3 Pa) was applied to the HCtAECs inside to reproduce the physiological state of blood vessels. In addition, a self-expanding stent was placed in the model during perfusion culture. ResultsWe examined the performance of the developed model based on quantitative evaluations of endothelial morphology in response to SS and in-stent endothelialization. Exposure to SS for 24 and 48 h caused endothelial orientation and elongation in the direction of flow, confirming the physiological responses of blood vessels. We were also able to quantitatively evaluate endothelial migration (endothelialization) to the stent. DiscussionOur model can reproduce the mechanical field inside the stented blood vessel, including hemodynamic stimuli. Based on the results obtained, the developed cell-cultured vascular model has sufficient performance to be used not only for quantitative evaluation of in-stent endothelialization but also for optimization of the mechanical fields in the stented vessel.

bioengineering↗

bioRxiv2022

Stiffness of primordial germ cells is required for their extravasation in avian embryos

During metastasis intravascularly circulating cancer cells undergo extravasation, which frequently takes place in vascular capillary beds 1-3. It remains poorly understood how the extravasation in the capillary beds is regulated. To address this question, chicken primordial germ cells (PGCs) serve as a powerful model since they circulate in blood stream and extravasate at a specific site of capillary bed near the forming gonad 4-6. The extravasation consists of two steps, the intravascular arrest of cells and their subsequent transmigration through the endothelial lining. We here demonstrate with live imaging at a single cell level in vivo that the arrest of PGCs is predominantly governed by occlusion at a narrow path in the capillary bed. In addition, this occlusion is enabled by a hightened stiffness of the PGCs, revealed by atomic force microscopy indentation analyses. The PGCs stiffness is regulated by actin polymerization: inhibition of the actin function causes not only a failure of PGC occlusion in the capillary bed, but also a failure of PGC colonization in the gonads at later stages. Following the occlusion, PGCs reset their stiffness to soften in order to squeeze through the endothelial lining as they transmigrate. The discovery of F-actin-mediated stiffness in pre-extravasating cells provides a model for understanding of dynamic mechanism by which other cells, including metastasizing cancer cells, extravasate in capillary beds.

developmental biology↗

bioRxiv2020

Hypoxia triggers collective aerotactic migration in Dictyostelium discoideum

It is well known that eukaryotic cells can sense oxygen (O2) and adapt their metabolism accordingly. It is less known that they can also move towards regions of higher oxygen level (aerotaxis). Using a self-generated hypoxic assay, we show that the social amoeba Dictyostelium discoideum displays a spectacular aerotactic behavior. When a cell colony is covered by a coverglass, cells quickly consume the available O2 and the ones close to the periphery move directionally outward forming a dense ring keeping a constant speed and density. To confirm that O2 is the main molecular player in this seemingly collective process, we combined two technological developments, porphyrin based O2 sensing films and microfluidic O2 gradient generators. We showed that Dictyostelium cells exhibit aerotactic and aerokinetic (increased speed at low O2) response in an extremely low range of O2 concentration (0-1.5%) indicative of a very efficient detection mechanism. The various cell behaviors under self-generated or imposed O2 gradients were modeled with a very satisfactory quantitative agreement using an in silico cellular Potts model built on experimental observations. This computational model was complemented with a parsimonious Go or Grow partial differential equation (PDE) model. In both models, we found that the collective migration of a dense ring can be explained by the interplay between cell division and the modulation of aerotaxis, without the need for cell-cell communication.

biophysics↗