Biology subjects

Raguin, E.

Publications and source records attributed to Raguin, E..

6 recordsLinked to original sources

bioRxiv2026

Crystallization of magnesium calcite otoconia in the inner ear of the developing quail

Otolith organs are specialized structures of the vertebrate inner ear that provide the inertial mass required for maintaining equilibrium. Mammals possess two otolithic organs, the utricle and the saccule, whereas birds and other non-mammalian vertebrates also retain a third one, the lagena, whose development remains poorly understood and whose function is still debated. In birds, the lagena contains thousands of calcium carbonate biomineral particles, termed otoconia. Here, we reconstruct the developmental crystallization of lagena otoconia in the Japanese quail (Coturnix japonica) throughout embryogenesis. We combine multiscale imaging with structural, compositional, and crystallographic analyses across length scales. We show that lagena mineralization precedes cranial bone formation and proceeds predominantly through the growth of existing otoconia rather than continued nucleation. Otoconia develop through progressive particle growth, alignment, and fusion within a pre-existing organic compartment while maintaining a persistent central core, ultimately forming magnesium calcite biominerals. This maturation is accompanied by progressive nanoscale densification, transforming early mineral deposits into mature hierarchical crystals. This work establishes a developmental model of avian otoconia formation and provides new insights into how hierarchical calcium carbonate crystals are assembled during vertebrate development. Statement of significanceOtoliths are the only calcite based biomineral in our body that has a physiological function, yet their developmental assembly remain incompletely understood. While the utricle and saccule have been extensively investigated across vertebrates, the lagena, a third otolithic organ lost during mammalian evolution, has received comparatively little attention. Here, we combine multiscale imaging and materials characterization to reconstruct the developmental crystallization of lagena otoconia in the Japanese quail. We establish how hierarchical magnesium calcite biominerals emerge through coordinated mineral growth, structural maturation, and crystallization, providing a developmental framework for avian otoconia formation and new insights into the assembly of vertebrate calcium carbonate crystals.

developmental biology↗

bioRxiv2026

Intracellular photonic crystals in photosynthetic sea slugs form via a kidney-mediated biomineralisation pathway

Sea slugs in the Sacoglossa superorder are some of the few animals capable of photosynthesising by isolating and maintaining functional chloroplasts within their body1,2. While this ability allows some species in this superorder, such as Elysia viridis, to appear green, camouflaging themselves within their surroundings3,4, this species is marked by extremely bright, coloured regions. Here, we show that these animals produce a yet undiscovered class of photonic structure consisting of intracellular mixed amorphous CaCO3 and calcite spherical nanoparticles organised in non-closed-packed face-centred cubic (FCC) lattices and photonic glasses5. By mapping the distribution of the cells containing such architectures, we suggest that their colour is linked both to their function and to their biological formation via the animals renal system. Using a combination of different optical methods and cryo-electron microscopy, we reveal that the biomineralisation pathway proceeds through stages of calcium ion concentration in the kidney, transport via internal vessels, and precipitation from a dense liquid-like precursor, culminating in the formation of monodisperse nanoparticles, which are the building blocks of these photonic structures.

biophysics↗

bioRxiv2026

Mineralization kinetics during embryonic avian bone growth: a three-dimensional multiscale and cryogenic imaging approach

Bone formation during embryonic development requires the rapid and sustained delivery of large amounts of calcium to mineralizing tissue. In avian embryos, this process coincides with a unique physiological transition in calcium supply, shifting from limited yolk reserves to massive mobilization from the eggshell. To address the question of how calcium transport responds to the increasing mineral demand during this transition, we combine micro computed tomography with three-dimensional cryogenic FIB-SEM imaging at different embryonic stages in the developing quail femur. Over this developmental period, bone mineralized volume increases rapidly through periosteal expansion. We observe that bone forming cells consistently contain numerous membrane-bound carriers loaded with mineral precursors throughout all growth stages. By integrating measurements across length scales, we calculate the intracellular velocities required to sustain the observed mineral deposition in the successive developmental stages. Surprisingly, these velocities remain within a similar range across development, despite the significant difference of bone formation rates, and are consistent with active transport by molecular motors. The increasing mineral demand corresponds to the expansion of mineralizing surfaces, which leads to an increasing number of cells, while the transport capacity of individual cells remains similar. Our work reveals a perfect tuning between the calcium transport capacity and bone growth, even in a situation where the skeletal growth is accelerating in the quail embryo. Significance statementDespite the importance of bone mineralization for the integrity of the skeleton, surprisingly little is known about how calcium is transported across the organic matrix to the mineralization sites during embryonal development. Using an avian model, where the main source of calcium shifts from a limited contribution from the yolk to the massive reservoir in the eggshell, we quantify bone mineral deposition using tissue level characterization together with three-dimensional cryogenic nanoscale imaging. We discover that intracellular vesicles containing mineral precursors are transported at similar speed, although the overall mineral deposition rate is increasing six-fold from embryonal day 10 to 14. This shows that the acceleration in mineralization activity is due to an increased number of bone cells rather than to a larger workload for individual cells. These findings demonstrate that rapid bone development is regulated to synchronize growth rates and mineral transport.

physiology↗

bioRxiv2026

E. coli extracellular matrix: a tunable composite with hierarchical structure

Escherichia coli (E. coli) biofilms consist of bacteria, an extracellular matrix (ECM) mainly made of curli amyloid fibers, phosphoethanolamine-modified cellulose (pEtN-cellulose), and water. While curli amyloid fibers contribute to biofilm rigidity, pEtN-cellulose contributes to their cohesion. This work explores the interplay between these fibers, and how their interaction influence biofilm structure and mechanical properties. We performed a multiscale analysis on E. coli biofilms grown using strains producing curli and pEtN-cellulose, and only curli and only pEtN-cellulose in co-seeded ratios. Micro-indentation experiments, confocal microscopy, and cryo-FIBSEM 3D imaging revealed a composite-like behavior of the biofilm, where its mechanical properties depend on ECM composition and organization. Spectroscopic analysis of the extracted fibers showed that their biophysical properties are influenced by their pEtN-cellulose to curli ratio and assembly. We propose that pEtN-cellulose swelling is contrained by its interactions with rigid curli fibers. The reference E. coli strain maximizes this effect by assembling a curli/pEtN-cellulose hybrid material at the sub-micron scale, where its composition, interactions, and architecture can explain biofilm emergent properties. This knowledge on microbial ECM assembly opens new avenues for engineering living materials, especially for the use of bacterial biofilms as a source of bio-sourced materials.

biophysics↗

bioRxiv2023

Logistics of Bone Mineralization in the Chick Embryo Studied by 3D Cryo FIB-SEM Imaging

During skeletal development, bone growth and mineralization require transport of substantial amounts of calcium, while maintaining very low concentration. How an organism overcomes this major logistical challenge remains mostly unexplained. To shed some light on the dynamics of this process, we use cryogenic Focused Ion Beam-Scanning Electron Microscopy (cryo-FIB/SEM) to image forming bone tissue at day 13 of a chick embryo femur. We visualize both cells and matrix in 3D and observe calcium-rich intracellular vesicular structures. Counting the number of these vesicles per unit volume and measuring their calcium content based on the electron back-scattering signal, we are able to estimate the intracellular velocity at which these vesicles need to travel to transport all the calcium required for the mineral deposited in one day within the collagenous tissue. We estimate this velocity at 0.27 m/s, which is too large for a diffusion process and rather suggests active transport through the cellular network. We conclude that calcium logistics is hierarchical and based on several transport mechanisms: first through the vasculature using calcium-binding proteins and the blood flow, then active transport over tens of micrometers through the network of osteoblasts and osteocytes and, finally, diffusive transport over the last one or two microns.

systems biology↗

bioRxiv2022

Induced mineralization in Escherichia coli biofilms: the key role of bacterial alkaline phosphatase

Biofilms appear when bacteria colonize a surface and synthesize and assemble extracellular matrix components. In addition to the organic matrix, some biofilms precipitate mineral particles such as calcium phosphate. While calcified biofilms induce diseases like periodontitis in physiological environments, they also inspire the engineering of living composites. Understanding mineralization mechanisms in biofilms will thus provide key knowledge for either inhibiting or promoting mineralization in these research fields. The enzyme alkaline phosphatase (ALP) plays a key role in calcium phosphate precipitation in mammalian bone tissue. Produced by eukaryotic cells, ALP catalyzes the hydrolysis of monophosphates starting from different precursors (e.g., alkaloids, proteins) and makes phosphate ions readily available for the precipitation with calcium. Bacterial ALPs are expressed by the well-characterized gram-negative and gram-positive bacteria E. coli and S. aureus as well as a large number of marine and soil bacteria. While it was recently proposed that bacterial ALPs induce mineral precipitation, their role in biofilm mineralization is not fully understood. In this work, we address this question using the biofilm-forming E. coli K-12 strain W3110, which expresses periplasmic ALP from the phoA gene. We first identify the mineralization conditions of biofilms grown on nutritive agar substrates supplemented with calcium ions and {beta}-glycerophosphate. We then localize the mineral phase at different scales, using light and scanning electron microscopy as well as X-ray microtomography. Wide-angle X-ray scattering enables us to further identify the mineral as being hydroxyapatite. Finally, growing E. coli cells on mineralizing medium supplemented with an ALP inhibitor demonstrates that ALP is essential for biofilm mineralization. This is confirmed with a bacteria-free model, where the deposition of a drop of bacterial ALP solution on calcium and {beta}-glycerophosphate containing agar substrate is sufficient to induce mineralization. Overall, these results will benefit the development of strategies against diseases involving calcified biofilms as well as the engineering of biofilm-based living composites.

microbiology↗