Biology subjects

Combriat, T.

Publications and source records attributed to Combriat, T..

6 recordsLinked to original sources

bioRxiv2026

Distinguishing matrix-associated mineralization from solution-driven calcium phosphate precipitation in osteogenic culture

Mineral accumulation in osteogenic culture is often interpreted as evidence of cell-guided extracellular matrix mineralization. However, measurements could also capture calcium-phosphate precipitation outside of the organized extracellular matrix. High concentrations of {beta}-glycerophosphate ({beta}-GP) could promote nonphysiological mineral deposition. We developed a kinetic model to examine when mineral deposition occurs within the matrix and when precipitation from the medium becomes the dominant mechanism. The model couples {beta}-GP hydrolysis, medium renewal, matrix-associated precursor formation and maturation, and solution-driven precipitation. We examined model behavior using parameter sweeps, global sensitivity analysis, comparison with published mineralization time courses, and equifinality analysis to determine whether similar mineralization amounts could arise from different pathway contributions and parameter combinations. Under baseline conditions (10 mM {beta}-GP, 2-day renewal), the matrix-associated pathway activated first, followed by solution-driven precipitation about 18 h later. Once matrix capacity was approached, additional phosphate mainly increased non-matrix deposition. Parameter sets with similar total mineral gave matrix-associated fractions ranging from 0.17 to 1.00. Thus, the total amount of mineral does not necessarily indicate how much formed within the matrix, highlighting the importance of phosphate supply and medium renewal in interpreting osteogenic culture results.

bioengineering↗

bioRxiv2026

A cellular automaton model of osteogenic differentiation reveals identifiability limits of endpoint assays

Standard differentiation assays sample cell states only at discrete time points, while the underlying progression unfolds continuously and heterogeneously across cells. As a result, different combinations of proliferation, commitment, and maturation dynamics can converge to similar endpoint measurements. This many-to-one mapping between latent trajectories and observable readouts constitutes a partially observed inverse problem that limits mechanistic interpretation. Although this ambiguity is inherent to many experimental systems, it is rarely examined using models that connect cell-state dynamics to assay-level quantities. We present OsteoMin, a coarse-grained cellular automaton that links stochastic transitions between pre-osteoblast and osteoblast states to experimentally measurable readouts of alkaline phosphatase activity, collagen deposition, and mineralization. Model parameters were constrained using literature-reported kinetics and evaluated against dexamethasone and menaquinone-4 perturbations. The frame-work reproduces qualitative assay trends and enables systematic analysis of how cell-state progression, matrix maturation, and external perturbations shape differentiation outcomes. Using this framework, we quantify the identifiability limits of endpoint assays and test whether standard measurements can distinguish underlying differentiation mechanisms. Distinct perturbation families often produce similar endpoint responses (macro-F1 {approx} 0.42), indicating limited discriminative power. Incorporating temporal trajectories improves separability (macro-F1 {approx} 0.78), demonstrating that most identifiable information resides in marker dynamics rather than terminal measurements. Sobol analysis shows early markers depend on proliferation timing, whereas late mineralization is governed by nonlinear matrix maturation and parameter interactions. Together, these results show that endpoint assays constrain overall progression but do not uniquely identify underlying mechanisms. OsteoMin provides a framework linking differentiation dynamics to assay observables and a basis for assessing identifiability in endpoint-driven systems.

bioengineering↗

bioRxiv2026

Three Dimensional Dynamics of Epithelial Monolayers

Cells in epithelial monolayers are commonly quantified using a projected area and implicitly assuming constant cell volume and prism-shaped cells. These 2.5D assumptions ignore the volume and mass dynamics that may accompany density fluctuation in confluent space-filling tissues but remain inaccessible to the labelling- and intensity-based imaging techniques used to date. Here, we use time-lapse quantitative phase imaging (QPI) to obtain spatially and temporally resolved maps of height, volume, and dry mass in MDCK epithelial monolayers under physiological conditions. Three findings follow. (i) Cellular dry mass concentration is maintained to within [~] 4.5 % across the monolayer and over time, even during large-amplitude pulsations, ruling out fluid (water) transport as the dominant driver of height and area dynamics. (ii) The mean height of the monolayer increases from [~] 5.5 to [~] 9 {micro}m and the mean cell volume decreases by [~] 25 % as the cell density doubles, evidence of contact inhibition of cell size rather than constant cell volume. Cell heights vary up to 30%, oscillate with a [~] 5 h period, and follow gamma-shaped distributions. (iii) At cellular scales, both segmented-cell tracking and continuum mass-flux analysis show that projected cell volume is not conserved; mass conservation is recovered only after coarse-graining over [~] 2 cell diameters and [~] 1.6 h. Two non-exclusive mechanisms may explain this: non-prismatic cell geometry produces apparent volume fluctuations even at constant true volume, and periodic mass exchange between cells and the ECM produces genuine cyclic changes in cellular dry mass. A propagating elastic mode in the dry-mass structure factor (cs [~] 15 {micro}m/h) further indicates that the monolayer behaves as a viscoelastic active medium rather than a plug-flow fluid. Each of these results requires simultaneous, time-resolved access to height and dry mass at the cellular scale and is therefore newly visible with QPI applied to epithelial monolayers. Together, they question the common 2.5D assumptions of prism-shaped cells, constant volume, plug-flow kinematics, and argue that quantitative continuum and cell-based models of epithelial dynamics must incorporate dry-mass-density regulation and 3D cell geometry.

biophysics↗

bioRxiv2026

Quantitative Phase Imaging of Epithelial Monolayer Dynamics

This study uses two different quantitative phase imaging techniques (QPI) and for the first time measures the height, volume, and mass dynamics of Madin-Darby Canine Kidney (MDCK) monolayers. We demonstrate novel methods to determine the height of confluent monolayers of cells from 2D and 3D QPI data and validate that the two methods agree. We developed a novel cell segmentation method adapted to QPI images of confluent cell layers and present a robust measure of relative error. We also demonstrate that height statistics of cells can be obtained without segmenting the images. We obtain the following precisions of cell density (1 %), height (3 %), area (5 %) and volume (6 %). Cell height varies 15-25 % over a monolayer and increases 50-100 % when cell density doubles. The average refractive index and the dry mass fraction of the cells, on the other hand, are constant over the entire density range.

biophysics↗

bioRxiv2023

Acoustic wave-induced stroboscopic optical mechanotyping of adherent cells

In this study, we present a novel, high content technique using an innovative cylindrical acoustic transducer, stroboscopic fast imaging and homodyne detection to recover the mechanical properties (dynamic shear modulus) of living adherent cells at low ultrasonic frequencies. By analyzing the micro-oscillations of cells we were able to simultaneously mechanotype whole populations of cells with sub-cellular resolution. The technique can be combined with standard fluorescence imaging allowing to further cross-correlate biological and mechanical information. We demonstrate the potential of the technique by mechanotyping co-cultures of different cell types with significantly different mechanical properties.

biophysics↗

bioRxiv2020

Music for cells? A systematic review of studies investigating the effects of audible sound played through speaker-based systems to cell cultures.

There have been several studies investigating whether musical sound can be used as cell stimuli in recent years. We systematically searched publications to get an overview of studies that have used audible sound played through speaker-based systems to induce mechanical perturbation in cell cultures. A total of 12 studies were identified. We focused on the experimental setups, the sound materials used as stimuli, and the outcomes. The stimuli were categorized into simple and complex sounds. The effects were reported as enhanced cell migration, proliferation, colony formation, and differentiation ability. However, there are significant differences in methodologies and cell type-specific outcomes, which made it difficult to find a systematic pattern in the results. We suggest that future experiments should consider using: 1) a more controlled acoustic environment), 2) standardized sound and noise measurement methods, and 3) a more comprehensive range of controlled sound stimuli.

cell biology↗