Biology subjects

Nakagaki, T.

Publications and source records attributed to Nakagaki, T..

7 recordsLinked to original sources

bioRxiv2026

Image-scanning light-sheet microscopy for high-speed volumetric imaging of complex biological dynamics

Volumetric fluorescence microscopy is a powerful method for studying complex biological systems because it enables comprehensive observation of structural and physiological dynamics. In particular, light-sheet microscopy (LSM) is a leading option for real-time volumetric fluorescence imaging as it combines high imaging speed, low phototoxicity, minimal photobleaching, high spatiotemporal resolution, and low computational burden. To capture fast biological events, various efforts have been made to improve the imaging speed of volumetric fluorescence microscopy, including LSM. However, existing approaches entail significant trade-offs that make routine volumetric imaging at and beyond video rates challenging under practical conditions. Here, we introduce image-scanning LSM, a method that substantially increases the volumetric imaging speed achievable with LSM while preserving key performance metrics, such as spatial resolution and photon efficiency, as well as accessibility. Our implementation, termed image-scanning oblique plane (ISOP) microscopy, enables volumetric fluorescence imaging at up to 1,000 volumes per second with submicrometer lateral spatial resolution. We demonstrate the broad utility of ISOP microscopy by recording and analyzing the dynamics of behaving and rapidly moving organisms.

bioengineering↗

bioRxiv2025

Mathematical modeling for primitive form of habituation in an amoeba

Learning abilities, once thought to be unique to higher animals, have been reported to exist in their primitive form in single-celled organisms. This has triggered a growing interest in carefully examining the nature and mechanisms of the primitive versions of learning abilities, which would provide important clues for understanding the evolution of behavioral capabilities in organisms. In this study, we focused on previous experimental studies showing that the slime mold Physarum polycephalum, a model organism for studying protist behavior, exhibits the ability to adapt to chemical environments. We propose a possible dynamic mechanism underlying this habituation, reproducing reported experimental observations with accuracy. By refining a mathematical model that was as simple as possible and based on non-specific biochemical processes within cells, we clarified a plausible mechanistic framework. Based on these results, we examined the similarities and differences between this framework and previously proposed habituation models of single-cell movement and animal neural-circuit regulation. These findings are significant because they open new avenues for research into the generality and evolutionary origins of acclimation learning.

systems biology↗

bioRxiv2025

Spiral-Sensing and Fold-Change Detection Direct Ascidian Sperm to the Egg

From microorganisms to marine sperm, successful navigation toward chemical cues relies on the integration of sensory inputs with locomotion. Ascidian sperms exhibit a robust chemotactic strategy by swimming along circular paths whose centres form large-scale spirals, guiding them toward attractant-releasing eggs. Although their intracellular Ca2+ dynamics exhibit rhythmic bursts aligned with flagellar modulation, the underlying computational principles remain unclear. Here, we propose a minimal model that captures ascidian sperm chemotaxis through a combination of swimming trajectory control and an internal signalling model with fold-change detection (FCD). This model responds to relative rather than absolute changes in the stimulus concentration, achieving scale-invariant signal processing. Concurrently, the spiral swimming path enables spatial sampling of the concentration field, allowing the cell to infer gradient direction. Our findings demonstrate that the integration of a resilient signalling module and physically structured sampling trajectory enables effective chemotaxis in complex environments.

cell biology↗

bioRxiv2025

Geometrical preference of anchoring sites in the unicellular organism Stentor coeruleus

Organisms often inhabit environments comprising complex structures across various scales. Animals rely on visual information from surrounding geometrical structures for navigation. Even at the microscale, various microsediments form complex structures in microbial habitats. The movement of microorganisms is passively affected by collisions and hydrodynamic interactions with surrounding structures. However, the influence of microenvironmental geometry on behavioral changes of unicellular organisms that lack visual perception remains unclear. Here, we developed geometrically structured chambers to investigate anchoring site preferences in the swimming ciliate Stentor coeruleus. Our experiments revealed that S. coeruleus preferentially anchored in narrow regions characterized by specific geometrical features, including corner angle, depth, and curvature at the corner end. Before anchoring, free-swimming S. coeruleus changed its behavior to move along the boundary wall of the chambers, accompanied by Ca2+-induced asymmetrical body deformation. To further investigate how S. coeruleus moves along the wall continuously, we conducted a hydrodynamic simulation and revealed that the asymmetric morphology causes asymmetric propulsive forces, explaining wall-following behavior through physical interactions with a wall. Thus, morphological change near a wall causes wall-following behavior, facilitating the identification of these narrow anchoring sites. Our findings indicate that environmental geometry drives behavioral transitions in S. coeruleus through simple biophysical processes, enabling spatial selection without visual cues. Overall, these results suggest that microgeometry plays a key role in shaping ecological niches for unicellular microorganisms. Significance StatementAnimals use various natural structures as landmarks for navigation. In microorganism habitats, microsediments also form geometrically complex environments. Is there a relationship between the geometrical features of structures and the behavior in unicellular organisms lacking visual cues? Here we report that the free-swimming unicellular organism Stentor coeruleus selects the anchoring sites based on the surrounding shapes. Further observations and numerical simulations reveal that an asymmetric morphological change causes a temporary switch from ballistic to wall-following exploration, driven by surrounding structures. These results indicate that one simple behavioral response underlies the preference of anchoring sites with specific geometrical features in non-neural unicellular organisms. The findings shed light on the role of microenvironmental geometry in forming ecological niches for microorganisms.

biophysics↗

bioRxiv2020

Basis for the phototaxis sign reversal in the green alga Chlamydomonas reinhardtii studied by high-speed observation

For organisms that respond to environmental stimuli using taxes, reversal of the tactic sign should be tightly regulated for survival. The biciliate green alga Chlamydomonas reinhardtii is an excellent model for studying reversal between positive and negative phototaxis. C. reinhardtii cells change swimming direction by modulating the balance of beating forces between their two cilia after photoreception at the eyespot; however, it remains unknown how they reverse phototactic sign. In this study, we observed cells undergoing phototactic turns with a high-speed camera and found that two key factors determine the phototactic sign: which of the two cilia beats more strongly for phototactic turning and when the strong beating starts. The timing of the strong ciliary beating is suggested to be regulated by ROS-regulated switching between the light-on and light-off responses at the eyespot, which leads to the switching between positive and negative phototaxis. This idea is supported by a mathematical model that introduces the timing of the strong ciliary beating after photoreception.

cell biology↗

bioRxiv2020

Phase transition of prion protein initiates proteinase K resistant amyloid formation

Prion diseases are characterized by accumulation of amyloid fibrils. The causative agent is an infectious amyloid that is comprised solely of misfolded prion protein (PrPSc). Prions can convert PrPC to proteinase-resistant PrP (PrP-res) in vitro; however, the intermediate steps involved in the spontaneous conversion remain unknown. We investigated whether recombinant prion protein (rPrP) can directly convert into PrP-res via liquid-liquid phase separation in the absence of PrPSc. We found that rPrP underwent liquid-liquid phase separation at the interface of the aqueous two-phase system (ATPS) of polyethylene glycol (PEG) and dextran, whereas single-phase conditions were not inducible. Fluorescence recovery assay after photobleaching revealed that the liquid-solid phase transition occurred within a short time. The aged rPrP-gel acquired proteinase-resistant amyloid accompanied by {beta}-sheet conversion, as confirmed by western blotting, Fourier transform infrared spectroscopy, and Congo red staining. The reactions required both the N-terminal region of rPrP (amino acids 23-89) and kosmotropic salts, suggesting that the kosmotropic anions may interact with the N-terminal region of rPrP to promote liquid-liquid phase separation. Thus, structural conversion via liquid-liquid phase separation and liquid-solid phase transition are intermediate steps in the conversion of prions.

biochemistry↗

bioRxiv2018

Dynamic gait transition in the Scolopendromorpha scolopocryptops rubiginosus L. Koch centipede

Crawling using locomotory waves is a common method of locomotion for limbless and many-legged invertebrates. It is generally believed that the direction of locomotory waves is fixed for a given species. However, by recording and performing detailed analyses of the gait patterns of a Scolopendromorpha scolopocryptops rubiginosus L. Koch centipede in various conditions, we found that it dynamically generated its gait to allow for locomotory waves that varied in direction. By introducing the wave-index order parameter to characterise locomotory waves, we showed that gait patterns were associated with control of stride rather than rotation frequency.

animal behavior and cognition↗