Biology subjects

Oosawa, C.

Publications and source records attributed to Oosawa, C..

3 recordsLinked to original sources

bioRxiv2026

Projection criteria and information risks forzero-dimensional biological dynamics across molecular,epidemic, and ecological systems

Zero-dimensional chemical master equations, ordinary differential equations, and compartmental population models replace spatial stochastic biological systems by vectors of total counts or densities. This study asks when that projection is exact and whether information retained in spatial correlations can diagnose its practical failure. Exact Markov closure is characterized by an aggregate-rate lumpability condition: for every retained transition, the sum of microscopic transition rates must be constant over all spatial configurations with the same counts. Violations are connected to BBGKY-type correlation hierarchies and to mean-field, pair, and triplet closures. Conditional rate, finite-time predictive, memory, path-space, and correlation Kullback-Leibler risks quantify distinct losses. An exactly solvable two-compartment reaction separates structural non-closure from recovery of a well-mixed law under fast hidden mixing. Copy number and a spatial mixing-interaction ratio connect concentration, volume, diffusion, and reaction parameters to practical screening, including an Escherichia coli-scale example. The same projection logic is evaluated in controlled spatial susceptible-infectious-removed and predator-prey benchmarks. Across mixed and segregated initial conditions and four mobility regimes, pair-correlation risk was strongly associated with the error of the corresponding zero-dimensional ordinary differential equations (Spearman correlations 0.95 and 1.00; pooled 0.99). A nearest-neighbour exchange sensitivity analysis preserved the positive risk-error ranking. These benchmarks do not establish a universal threshold, but support correlation information as a transferable diagnostic for selecting among count, pair, higher-order, and explicit spatial descriptions.

systems biology↗

bioRxiv2026

Covariant Biochemical Systems Theory: cBST1~cBST3 Descriptors and Quantitative Validation

Biochemical Systems Theory (BST) represents nonlinear biochemical rate laws by local power-law approximations in logarithmic concentration coordinates. First-order coefficients are elasticities, whereas higher-order derivatives describe local log-synergism and its variation. Ordinary higher derivatives, however, are not tensorial under nonlinear reparameterizations and can mix biochemical response structure with coordinate artifacts. We formulate a covariant hierarchy, cBST1-cBST3, on a positive operating-point space equipped with a declared reference connection. cBST1 recovers classical elasticities in a flat logarithmic chart, cBST2 is the covariant Hessian of the log-response, and cBST3 is the symmetrized covariant derivative of cBST2. The framework is quantitatively evaluated using three representative rate laws from the curated yeast glycolysis model BIOMD0000000064: glucose transport, glucose phosphorylation, and phosphofructokinase. For 10,000 finite log-concentration perturbations at each of five radii, cBST2 reduced the cBST1 log-rate root-mean-square error by 96.6-98.6% at the largest tested radius, and cBST3 provided a further 68.4-98.1% reduction. The contracted cBST2 and cBST3 terms strongly predicted the corresponding lower-order truncation errors. Under the nonlinear transformation qi = sinh(ui), covariant contractions agreed across coordinates to within a 95th-percentile relative error of 1.2 x 10-13, whereas ordinary higher derivatives showed order-unity coordinate mismatches. Supplementary analytic tests recovered the expected second-, third-, and fourth-order truncation-error scaling. These results show that cBST1-cBST3 are not only coordinate-consistent descriptors but also practical diagnostics of where local power-law approximations require higher-order correction.

systems biology↗

bioRxiv2025

Front-rear polarity of intracellular signaling uncovered via giant Dictyostelium cells

Intracellular signaling dynamics are often obscured by the spatial and temporal limitations of cell size. Here, we developed a method to enlarge Dictyostelium discoideum cells by partial cytokinesis inhibition, generating multinucleated yet functional giant cells. These cells retained chemotactic signaling, polarity, and motility, enabling high-resolution live-cell imaging. Using fluorescent probes for cAMP and Ca2+, we uncovered a directional, front-to-rear propagation of cAMP signaling and a biphasic Ca2+ response coordinated with actin wave dynamics. Grid-based mapping revealed asymmetric cAMP synthesis and decay kinetics, and vesicle localization suggested spatially regulated cAMP secretion. Combining giant cells with super-resolution or electron microscopy allowed detailed visualization of intracellular local structures at high resolution. Our findings demonstrate that intracellular signaling involves self-organized, spatially structured propagation events aligned with cellular polarity. The giant cell platform offers a powerful and generalizable strategy for dissecting the spatiotemporal logic of single-cell signaling.

cell biology↗