Biology subjects

Siri, M.

Publications and source records attributed to Siri, M..

8 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

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

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↗

bioRxiv2024

Photoswitchable endocytosis of biomolecular condensates in giant vesicles

Interactions between membranes and biomolecular condensates can give rise to complex phenomena such as wetting transitions, mutual remodeling, and endocytosis. In this study, we demonstrate a light-triggered manipulation of condensate engulfment using giant vesicles containing photoswitchable lipids. UV irradiation increases the membrane area, facilitating a rapid condensate endocytosis, which can be reverted by blue light. The affinity of the protein-rich condensates to the membrane and the reversibility of the engulfment processes is quantified from confocal microscopy images. The degree of engulfment, whether partial or complete, depends on the initial membrane excess area and the relative sizes of vesicles and condensates. Theoretical estimates suggest that utilizing the light-induced excess area to increase the vesicles-condensate adhesion interface is energetically more favorable than the energy gain from folding the membrane into invaginations and tubes. Our overall findings demonstrate that membrane-condensate interactions can be easily and quickly modulated via light, providing a versatile system for building platforms to control cellular events and design intelligent drug delivery systems for cell repair.

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

Wetting by biomolecular condensates increases membrane lipid packing and dehydration

Membrane wetting by biomolecular condensates recently emerged as a key phenomenon in cell biology, playing an important role in a diverse range of processes across different organisms. However, an understanding of the molecular mechanisms behind condensate formation and interaction with lipid membranes is still missing. To study this, we exploited the properties of the dyes ACDAN and LAURDAN as nano-environmental sensors in combination with phasor analysis of hyperspectral and lifetime imaging microscopy. Using glycinin as a model condensate-forming protein and giant vesicles as model membranes, we obtained vital information on the process of condensate formation and membrane wetting. Our results reveal that glycinin condensates display differences in water dynamics when changing the salinity of the medium as a consequence of rearrangements in the secondary structure of the protein. Remarkably, analysis of membrane-condensates interaction with protein as well as polymer condensates indicated a correlation between increased wetting affinity and enhanced lipid packing. This is demonstrated by a decrease in the dipolar relaxation of water across all membrane-condensate systems, suggesting a general mechanism to tune membrane packing by condensate wetting.

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↗

bioRxiv2019

Effect of structure in ionized albumin - based nanoparticle: Characterisation, Emodin interaction, and in vitro cytotoxicity

A {gamma}-irradiated bovine albumin serum based nanoparticle was characterised structurally, and functionally. The nanoparticle was characterised by A.F.M, D.L.S, zeta potential, T.E.M., gel-electrophoresis, spectroscopy (UV-Vis, Fluorescence, FT-IR, and CD). Its stability was studied under adverse experimental conditions: pH values, chaotropic agents, and ionic strength and stability studies against time were mainly carried out by fluorescence spectroscopy following the changes in the tryptophan environment in the nanoparticle. Its function was studied by the interaction of the NP with the hydrophobic drug Emodin was studied. The binding and kinetic properties of the obtained complex were tested by biophysical methods as well as its toxicity in tumour cells.\n\nAccording to its biophysics, the nanoparticle is a spherical nanosized vehicle with a hydrodynamic diameter of 70 nm. Data obtained describe the nanoparticle alone as nontoxic for cancer cell lines. When combined with Emodin, the bioconjugate proved to be more active on MCF-7 and PC-3 cancer cell lines than the nanoparticle alone. No haemolytic activity was found when tested against ex vivo red blood cells. The stability of the albumin nanoparticle is based on a competition between short-range attraction forces and long-range repulsion forces. The nanoparticle showed similar behaviour as albumin against pH while improving its stability in urea and tween 80. It was stable up to 15 days and presented no protein degradation in solutions up to 2 M salt concentration. Significantly, the albumin aggregate preserves the main activity-function of albumin and improved characteristics as an excellent carrier of molecules.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC=\"FIGDIR/small/631788v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (44K):\norg.highwire.dtl.DTLVardef@154a680org.highwire.dtl.DTLVardef@7f32b2org.highwire.dtl.DTLVardef@d97fdeorg.highwire.dtl.DTLVardef@159ee36_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗