Biology subjects

Bidan, C. M.

Publications and source records attributed to Bidan, C. M..

13 recordsLinked to original sources

bioRxiv2026

Charged agar surfaces affect E. coli biofilm properties by balancing curli amyloid quantity and quality

Biofilm extracellular matrix (ECM) varies with environmental conditions and substrate properties. Understanding the surface-biofilm relationship helps to perfect antibacterial strategies and to design new engineered living materials (ELMs). In this work, we studied how cationic and anionic polyelectrolyte coatings affect macroscopic features of Escherichia coli curli-producing biofilms, as well as the properties of their curli amyloid fibers. Cationic coatings limited biofilm spreading, increased their surface density and water absorption, which correlated with a higher yield of curli amyloid fibers with looser structure. In contrast, anionic surfaces allowed for standard biofilm spreading, with a lower fiber yield but a more compact and chemically stable fiber structure. Higher biofilm rigidity and adhesion were measured on both types of charged surfaces. Thus, we propose that the differences in biofilm macroscopic properties result from a trade-off between curli quantity and quality in the ECM, namely fiber density and molecular packing, as well as their interaction with water. Our findings provide insights on how the biophysical properties of the ECM can be controlled by tuning the substrate physico-chemical characteristics with charged coatings. This work opens up new avenues for developing antimicrobial strategies, as well as tailoring the properties of amyloid-based ELMs. TOC figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/721109v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@191cd79org.highwire.dtl.DTLVardef@148f914org.highwire.dtl.DTLVardef@1d8c2f8org.highwire.dtl.DTLVardef@1e84eaf_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2026

Biophysical properties of material-colonizing fungal biofilms: multiscale structural and mechanical characterization

Black extremotolerant fungi form persistent biofilms on a wide range of natural and engineered substrates. Able to weather minerals, affect stone monument surfaces, and colonize solar panels, they demonstrate a strong capacity to interact with and modify material surfaces, even under most extreme conditions. In this study, we establish a methodological workflow for the structural and mechanical characterization of melanized biofilms formed by the black fungus Knufia petricola. This species represents a broader group of resilient surface colonizers and provides a model for in-depth investigation. When grown on solid agar/air interface, this species predominantly forms a compact biofilm, composed of spherical cells, while retaining the capacity for filamentous growth, providing a suitable framework to explore morphology-dependent biomechanical responses. The proposed toolbox combines complementary analytical techniques spanning multiple spatial scales, including shear-rheology to quantify bulk viscoelastic behavior, micro-indentation to resolve local stiffness of the biofilm surface, micro-computed tomography for non-destructive three-dimensional visualization of biofilm architecture, and cryogenic preparation methods and electron microscopy for high-resolution ultrastructural analysis. As a case study, we applied this workflow to compare biofilms grown on two nitrogen sources (NO3- vs. NH4+). Our results reveal that the nitrogen source plays a key role in biofilm morphology across multiple hierarchical levels - ranging from cell division patterns and distribution of extracellular polymeric substances (EPS) to overall mechanical properties, where NO3- leads to budding-dominated growth and increased stiffness, whereas NH4+ promotes meristematic growth and softer biofilms. The successful transfer and integration of methods originally developed for bacterial biofilm research highlights the feasibility of quantitative mechanical analyses in fungal systems. This multiscale toolbox provides a foundation for advancing the mechanistic understanding of fungal biofilms and biofilm-material interactions, with implications for geomicrobiology, material biodeterioration, and the design of bio-inspired functional materials. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=147 SRC="FIGDIR/small/720134v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@7fd08borg.highwire.dtl.DTLVardef@15476c2org.highwire.dtl.DTLVardef@40be50org.highwire.dtl.DTLVardef@8e9410_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2026

Osmotic pressure gradients in E. coli biofilms revealed by in-situ sensors

Osmotic pressure has been known to play essential roles in living systems from single cells to complex tissues. However, direct in-situ measurements of osmotic pressures in biosystems have remained challenging, especially in complicated heterogeneous systems in which osmotic pressure gradients could exist and induce directed forces. Bacterial biofilms -- organized communities of bacteria encased in a self-produced extracellular matrix -- are a major mode of bacterial life. It has, however, remained unexplored how the osmotic pressure is distributed in the biofilm and how this distribution contributes to biofilm growth and activity. Here, liposomal nano-sensors are developed for the in-situ mapping of osmotic pressures at an unprecedented microscale resolution in real time using Escherichia coli. biofilm as a model system that develops at the surface of a hydrogel containing the nutrients. The measurements reveal osmotic pressure gradients with a radially increasing trend from the inner regions to the outer regions of the biofilm, which is associated with biofilm formation, morphology, and metabolism. The gradients likely contribute to mechanical properties, internal stresses, and nutrient transport. The sensor readouts also show that there is an osmotic pressure difference between the biofilm and the adjacent medium, which may promote biofilm expansion through matrix swelling and bacteria growth via water and nutrient uptake from the surroundings. Our novel approach based on in-situ osmotic pressure mapping in a growing biofilm reveals a sophisticated spatial regulation of physical forces, which may inspire new models and approaches in the field of mechanobiology.

biophysics↗

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↗

bioRxiv2025

Cortical Tension Links Curvature to Tissue Growth in the Cellular Potts Model

The growth of biological tissue is sensitive to the physical properties of the environment. For example, the growth rate of contractile tissue under geometric confinement is proportional to local curvature as a result of tissue surface tension. It is not known how local cell behavior is coordinated to give rise to such behavior. Here, we use computer simulations based on the Cellular Potts Model (CPM) to investigate the role of cell adhesion and cortical contractility for curvature-dependent tissue growth. Our results show that tension-dependent local proliferation leads to the observed macroscopic curvature-driven growth kinetics via tissue surface tension, independent of soluble growth factors.

biophysics↗

bioRxiv2025

Mechanical comparison of Escherichia coli biofilms with altered matrix composition: a study combining shear-rheology and microindentation

The mechanical properties of bacterial biofilms depend on the composition and micro-structure of their extracellular matrix (ECM), which constitutes a network of extracellular proteins and polysaccharide fibers. In particular, E. coli macrocolony biofilms were suggested to present tissue-like elasticity due to a dense fiber network consisting of amyloid curli and phosphoethanolamine-modified cellulose (pEtN-cellulose). To understand the contribution of these two main ECM components to the emergent mechanical properties of E. coli biofilms, we performed shear-rheology and microindentation experiments on biofilms grown from E. coli strains that produce different ECM. We measured that biofilms containing curli fibers are stiffer in compression than curli-deficient biofilms. We further quantitatively demonstrate the crucial contribution of pEtN-cellulose, and especially of the pEtN modification, to the stiffness and structural stability of biofilms when associated with curli fibers. To compare the differences observed between the two methods, we also investigated how the structure and mechanical properties of biofilms with different ECM compositions are affected by the sample preparation method used for shear-rheology. We found that biofilm homogenization, used prior to shear-rheology, destroys the macroscale structure of the biofilm while the microscopic ECM architecture may remain intact. The resulting changes in biofilm mechanical properties highlight the respective advantages and limitations of the two complementary mechanical characterization techniques in the context of biofilm research. As such, our work does not only describe the role of the ECM on the mechanical properties of E. coli biofilms. It also informs the biofilm community on considering sample preparation when interpreting mechanical data of biofilm-based materials.

biophysics↗

bioRxiv2023

Nutrient availability influences E. coli biofilm properties and the structure of purified curli amyloid fibers

Bacterial biofilms are highly adaptable and resilient to challenges. Nutrient availability can induce changes in biofilm growth, biomass, morphology, architecture and mechanical properties. Bacterial extracellular matrix plays a major role in achieving biofilm stability under different environmental conditions. Curli amyloid fibers are determining for the architecture and stiffness of E. coli biofilms, but how this major matrix component adapts to different environmental cues remains unclear. Here, we investigated for the first time the effect of nutrient availability on both i) biofilm materials properties and ii) the structure and properties of curli amyloid fibers extracted from the biofilms. For this, we cultured E. coli W3110, which main matrix component is curli fibers. We quantified the size, mass and water content of the resulting biofilms and estimated their mechanical properties by microindentation. The curli amyloid fibers were then purified from the biofilms and their molecular structure and properties were studied by spectroscopic techniques. Our results show that the availability of nutrients in the substrate influences the yield of curli fibers, their structural composition and chemical stability, and suggest that these molecular features contribute to the stiffness of the biofilms. Biofilms grown on substrates with high nutrient concentration are softer, contain less curli fibers, and these fibers exhibit low {beta}-sheet content and chemical stability. Our multiscale study sheds new light on the relationship between the molecular structure of bacterial matrix and the macroscopic properties of biofilms. This knowledge will benefit the development of both anti-biofilm strategies and biofilm-based materials. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=60 SRC="FIGDIR/small/556686v2_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@ab9469org.highwire.dtl.DTLVardef@9c8f61org.highwire.dtl.DTLVardef@895de8org.highwire.dtl.DTLVardef@74433d_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2023

Twisted plywood-like tissue formation in vitro. Does curvature do the twist?

Little is known about the contribution of 3D surface geometry on the development of multi-layered tissues containing fibrous extracellular matrix components such as those found in bone. Here we elucidate the role of curvature in the formation of chiral, twisted plywood-like structures. Tissues consisting of murine pre-osteoblast cells (MC3T3-E1) were grown on 3D scaffolds with constant mean curvature and negative Gaussian curvature for up to 32 days. Using 3D fluorescence microscopy, the influence of surface curvature on actin stress-fiber alignment and chirality was investigated. To gain mechanistic insights, also MC3T3-E1 cells deficient in nuclear A-type lamins or treated with drugs targeting cytoskeleton proteins were used in our study. We find that wild type cells grow multilayered tissue with fibers predominantly aligned along directions of negative curvature, but where subsequent layers twist in orientation with respect to older tissues with time. Fiber orientation is conserved below the tissue surface thus creating a twisted plywood like material. We further show that this directional organization strongly depends on structural components of the cells (A-type lamins, actin and myosin). Our data indicate the importance of substrate curvature in the formation of 3D tissues and provides new insights into the emergence of chirality. Significance StatementBiological tissues (like compact bone) often consist of multiple fibrous layers which are staggered with a twisting angle relative to each other, thereby improving mechanical performance. The underlying principles of how such tissues are formed and what determines the fiber direction are still debated. Here we report the formation of a twisted plywood-like tissue grown in vitro on constant mean and negative Gaussian curvature substrates and present evidence that for tissue consisting of pre-osteoblast like cells, surface curvature is a main determinant for fiber orientation.

biophysics↗

bioRxiv2022

Curli fibers in Escherichia coli biofilms: the influence of water availability on amyloid structure and properties

E. coli biofilms consist of bacteria embedded in a self-produced matrix mainly made of protein fibers and polysaccharides. The curli amyloid fibers found in the biofilm matrix are promising versatile building blocks to design sustainable bio-sourced materials. To exploit this potential, it is crucial to understand i) how environmental cues during biofilm growth influence the molecular structure of these amyloid fibers, and ii) how this translates at higher length scales. To explore these questions, we studied the effect of water availability during biofilm growth on the conformation and functions of curli. We used microscopy and spectroscopy to characterize the amyloid fibers purified from biofilms grown on nutritive substrates with different water contents, and micro-indentation to measure the rigidity of the respective biofilms. The purified curli amyloid fibers present differences in the yield, structure and functional properties upon biofilm growth conditions. Fiber packing and {beta}-sheets content correlate with their hydrophobicity and chemical stability, and with the rigidity of the biofilms. Our study highlights how E. coli biofilm growth conditions impact curli structure and functions contributing to macroscopic materials properties. These fundamental findings infer an alternative strategy to tune curli structure, which will ultimately benefit to engineer hierarchical and functional curli-based materials. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=169 SRC="FIGDIR/small/517345v3_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@124ddd2org.highwire.dtl.DTLVardef@15f234dorg.highwire.dtl.DTLVardef@106a65forg.highwire.dtl.DTLVardef@194c53f_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

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↗

bioRxiv2022

Influence of metal cations on the viscoelastic properties of Escherichia coli biofilms

Biofilms frequently cause complications in various areas of human life, e.g. in medicine and in the food industry. More recently, biofilms are discussed as new types of living materials with tuneable mechanical properties. In particular, Escherichia coli produces a matrix composed of amyloid-forming curli and phosphoethanolamine-modified cellulose fibres in response to suboptimal environmental conditions. It is currently unknown how the interaction between these fibres contributes to the overall mechanical properties of the formed biofilms and if extrinsic control parameters can be utilized to manipulate these properties. Using shear rheology, we show that biofilms formed by the E. coli K-12 strain AR3110 stiffen by a factor of two when exposed to the trivalent metal cations Al(III) and Fe(III) while no such response is observed for the bivalent cations Zn(II) and Ca(II). Strains producing only one matrix component did not show any stiffening response to either cation or even a small softening. No stiffening response was further observed when strains producing only one type of fibre were co-cultured or simply mixed after biofilm growth. These results suggest that the E. coli biofilm matrix is a uniquely structured composite material when both matrix fibres are produced from the same bacterium. While the exact interaction mechanism between curli, phosphoethanolamine-modified cellulose and trivalent metal cations is currently not known, our results highlight the potential of using extrinsic parameters to understand and control the interplay between biofilm structure and mechanical properties. This will ultimately aid the development of better strategies for controlling biofilm growth. Table of Contents Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/510089v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@12fdd08org.highwire.dtl.DTLVardef@1583efborg.highwire.dtl.DTLVardef@8ef241org.highwire.dtl.DTLVardef@c28dca_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2018

Surface tension determines tissue shape and growth kinetics

The growth of tissue is an essential process controlling morphogenesis and regeneration of organs [1]. In general tissue forming cells are interactive and motile [2], which can give rise to emergent physical properties such as viscous fluid behaviour as has been shown for epithelial monolayers during embryogenesis [3, 4], and for cell-agglomerates [5] with a measurable surface tension [6]. However, the mechanical integrity of tissues is provided by extracellular matrices (ECM) that turn tissues into solids with well-defined elastic properties [7]. Paradoxically, it has been shown by in-vitro experiments that even osteoid-like tissue with large amounts of ECM grows according to rules reminiscent of fluid behavior [8, 9]. Motivated by this conundrum, we show here quantitatively, by constraining growing tissues to surfaces of con ...

biophysics↗

bioRxiv2017

Magneto-active substrates for local mechanical stimulation of living cells

Cells are able to sense and react to their physical environment by translating a mechanical cue into an intracellular biochemical signal that triggers biological and mechanical responses. This process, called mechanotransduction, controls essential cellular functions such as proliferation and migration. The cellular response to an external mechanical stimulation has been investigated with various static and dynamic systems, so far limited to global deformations or to local stimulation through discrete substrates. To apply local and dynamic mechanical constraints at the single cell scale through a continuous surface, we have developed and modelled magneto-active substrates made of magnetic micro-pillars embedded in an elastomer. Constrained and unconstrained substrates are analysed to map surface stress resulting from the magnetic actuation of the micro-pillars and the adherent cells. These substrates have a rigidity in the range of cell matrices, and the magnetic micro-pillars generate local forces in the range of cellular forces, both in traction and compression. As an application, we followed the protrusive activity of cells subjected to dynamic stimulations. Our magneto-active substrates thus represent a new tool to study mechanotransduction in single cells, and complement existing techniques by exerting a local and dynamic stimulation, traction and compression, through a continuous soft substrate.

biophysics↗