Soft Matter

Vertebrate gastrulating mesoderm is a prototypic example of a mesenchymal-like tissue undergoing extensive remodelling. While the tissue may be globally represented as a viscoelastic material, the actual biological material is intrinsically complex. To get to a real understanding of its properties, one needs to move to the mesoscale, linking cellular properties to collective phenomena. Vertebrate embryos also display a remarkable variability in mechanical properties, despite which they robustly complete gastrulation. This study attempts to explore these aspects by dissecting Xenopus mesoderm cell behaviour in a minimal system, using aspiration through a microfluidic system to impose controlled stress to a mesoderm aggregate. We show that beyond estimating global rheology at the tissue scale, it is possible to infer a wealth of information based on cell morphology and dynamics. Our data are consistent with collective behaviour being mostly dictated by the balance between the capacity of cells to stretch and the resistance to cell-cell contacts, which limits cell-cell intercalation and thus tissue remodelling. Importantly, tissues are not only able to transmit stress over a distance, they also clearly react to it through actively reinforcing cell-cell mechanical coupling. This adaptative property is found through a broad range of tissue stiffness, and adhesion strength appears to scale with the elastic modulus, suggesting that cell stiffness may ultimately be the key parameter setting mesoderm rheology and accounting for the large differences observed between embryo batches.

Flow and extensional deformation of mucin networks are fundamental in mucus biophysics, governing how mucus functions as a protective and lubricating, and transport-facilitating layer. While the shear and oscillatory rheology of mucin solutions have been characterized in considerable detail, their behavior under extensional deformation remains comparatively understudied. Here, we report a concentration-dependent transition in extensional flow response of mucin solutions using a bespoke dripping-onto-substrate extensional rheometer. We show that mucin solutions at the lower concentrations undergo linear filament thinning, whereas semidilute mucin solutions form highly extensible filaments, with radius decaying exponentially in time, consistent with the elastocapillary thinning observed in solutions of high molecular weight synthetic polymers. Remarkably, at higher mucin concentrations inter-chain mucin associations produce a sudden reduction in the apparent elastocapillary relaxation time. We demonstrate how increasing macromolecular concentration redistributes the balance between viscous and elastic stresses during capillary thinning in a biopolymer network and reveal a concentration-driven reduction in mucin filament extensibility. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/725541v2_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@1f593acorg.highwire.dtl.DTLVardef@1b23686org.highwire.dtl.DTLVardef@119add3org.highwire.dtl.DTLVardef@e31908_HPS_FORMAT_FIGEXP M_FIG C_FIG

The interactions of droplets and filaments can lead to mutual deformations and complex combined behavior. Such interactions also occur within the cell, where biomolecular condensates, distinct liquid phases often composed of proteins, have been observed to structure and affect the organization of the cytoskeleton. In particular, biomolecular condensates have been shown to undergo characteristic deformations when cytoskeletal filaments are fully embedded within them. However, a full understanding of the underlying physical mechanisms is still missing. Here, we combine experiments with coarse-grained molecular dynamics simulations and analytical models to uncover the physical mechanisms that define emerging shapes of droplets containing filaments. We find that the surface tension of the liquid phase and the bending energy of the filament(s) suffice to accurately capture emerging shapes if the length of the filament is small compared to the liquid volume. As the volume fraction of filament(s) increases, wetting effects become increasingly important, setting physical constraints within which surface and bending energies compete to define the droplet shapes. We find that mutual deformations of condensate and filament extend accessible shapes beyond classical stability considerations, leading to structuring and entrapment of contained filaments. Shape deformations may further affect ripening dynamics that favor certain geometries. Our findings provide a physical framework for a better understanding of the possible roles of biomolecular condensates in cytoskeletal organization.

Cells are mechanosensitive, responding to external mechanical stimulation. Nanovibrational stimulation has been shown to enhance cell contractility and actin stress fibre formation. These changes in morphology occur quickly, alongside associated mechanical changes. Here, the relationship between acute morphological and mechanical changes in NIH 3T3 fibroblastic cells in response to nanovibrational stimulation is presented. A 1 kHz, 30 nm vibration is applied continuously for 72 hours. Atomic force microscopy (AFM) quantifies mechanical properties of the nucleus and cytoplasm at multiple timepoints, while immunofluorescence tracks morphological changes. Within 3 hours of stimulation, both nuclear and cytoplasmic stiffness increase significantly, accompanied by a decrease in the cellular fluid exponent, suggesting a shift of the cell towards more solid-like behaviour. These changes correlate with increased nuclear area. Actin polymerisation also increases within 24 hours, although variably. To understand the role of the cytoskeleton, actin polymerisation and contraction are inhibited using cytochalasin D and blebbistatin. Results show that inhibition prevents stiffness increases and results in a higher fluid exponent, indicating a more fluid-like state. These findings demonstrate that actin-myosin dynamics mediate cell stiffening under nanovibrational stimulation. Interestingly, prolonged stimulation appears to reverse this effect, suggesting that temporal optimisation of stimulation may enhance long-term mechanotransducive responses.

Saturated fatty acids such as stearic acid (SA) can exhibit both antimicrobial and growth-promoting effects on bacteria, depending on their concentration and chemical structure. However, the physical properties of the bacterial cell envelope in response to such molecules remain under-explored compared to their biochemical pathways. In this study, a comprehensive investigation is presented on the interaction of SA with the Gram-positive bacterium, Staphylococcus epider-midis (S. epi). SA alters bacterial growth, reflected in a higher maximum specific growth rate, a shorter lag phase, and an extended exponential phase, consistent with a prebiotic effect. Using fluorescence correlation spectroscopy and fluorescence lifetime imaging microscopy, we show that SA incorporation leads to significant fluidization of the lipid membrane, characterized by enhanced lateral diffusion and reduced membrane viscosity. Coarse-grained molecular dynamics (CG-MD) simulations demonstrate spontaneous insertion of SA into the membrane and a significant increase in mean-square displacement after insertion, supporting our experimental observations. Importantly, atomic force microscopy measurements show an increase in cell-envelope stiffness, reflected by a higher Youngs modulus which can be attributed to modulations in the glycan-peptide linkage density based on earlier studies that correlate stiffness changes to peptidoglycan (PG) crosslinking in Gram-positive strains [1]. These results provide direct evidence linking membrane fluidization induced by SA and increased cell wall stiffness due to transport modifications in the membrane mediated PG synthesis pathways to enhance bacterial cell viability.

In mammalian cells, lipid monolayers support the integrity of lipid droplets (LDs), organelles that function as storage for neutral lipids. Liver-targeting illnesses such as liver cancer interrupt normal LD metabolism and prompt changes in the chemical content of these organelles, which can have effects on structural and organizational behavior of the lipids. In LDs, liver cancer induces concentric crystalline phases of cholesteryl esters (CEs) and triglycerides near the NL-monolayer interface, which become more pronounced as CE concentration increases. Yet, there is little known about how this phenomenon may link to persistence of undigested LDs in liver cancer patients. To shed light on this, all-atom molecular dynamics simulations were used to model LD micropipette aspiration experiments and gain insight into the effect of CE concentration on partitioning, structural, and mechanical properties of LDs. We successfully model micropipette aspiration by application of constant surface tension laterally, which stretches lipid bilayers and monolayers as the magnitude increased. The results show increased phospholipid packing due to insertion of CE fatty tails into the monolayer. Increasing CE concentration induces a non-linear change in surface packing defects on the LDs, notable rigidification, and stiffness. Taken together, these insights improve our understanding of the physical properties at the LD monolayer-core interface during liver cancer progression.

Building on a complex between a tubulin protofilament (PF) and a fragment of the Tau protein containing residues 169 to 367, we investigate the dynamics of the disordered elements of the system, namely the tubulin C-terminal tails (CTTs) and the Tau protein, using classical all-atom molecular dynamics simulations. Our results show that CTTs adopt a hook-like dynamic pattern on the bare PF while remaining highly mobile. The binding of Tau on the PF surface alters the dynamics of the I-CTTs in a sequence-dependent manner. While the repeat domains of Tau are mostly maintained on the PF by weak and strong binding patches with the tubulin cores, the Proline-Rich Region (PRR) relies on the wrapping phenomenon of I-CTTs to fuzzily stabilize its interaction with the PF. Our study thus provides a deep dive into the dynamic interplay between the Tau protein and the CTTs of microtubules, the latter being characterized extensively using a variety of disorder-adapted metrics. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/721901v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@b3f985org.highwire.dtl.DTLVardef@1c2bf70org.highwire.dtl.DTLVardef@a66b95org.highwire.dtl.DTLVardef@1e138e0_HPS_FORMAT_FIGEXP M_FIG C_FIG

The apparent pKa of ionizable lipids in lipid nanoparticles (LNPs) is a key determinant of RNA encapsulation during formulation and endosomal release after cellular uptake. However, it is difficult to predict the effective pKa of a given ionizable lipid solely from its solution pKa, because it is sensitive to the membranes composition, as well as solution conditions such as the salt concentration. We developed a simple continuum electrostatics model, based on Gouy-Chapman theory, to predict the shift in effective pKa for ionizable lipids in lipid bilayers as a function of salt concentration and membrane composition. We derive equations for the surface potential and fraction of lipids charged, which are solved self-consistently as a function of solution pH to extract the titration curve and effective pKa. The model shows that the shift in effective pKa is largest when the concentration of titratable lipid is high, and the effect is diminished by increasing salt concentration. We provide a python implementation of the model and an interactive notebook that will allow users to further easily explore the predicted pKa shifts as a function of formulation variables.

A broad range of cellular functions involve transient or persistent changes in the morphology of lipid membranes, from the organellar to the molecular scale. By and large, the thermodynamics of these remodeling processes remain to be understood. Molecular Dynamics simulations enhanced by advanced sampling methods are uniquely suited to examine and quantitate these phenomena. Here, we focus on the cellular process known as mechanosensation and use the Multi-Map simulation method to quantify how applied lateral tension impacts the energetics of both global and localized membrane perturbations induced extrinsically. We also examine how tension impacts the dynamics of lipid molecules. We find that the conformational energetics of the membrane clearly differs when it is stretched, and that this difference increases with the magnitude of the applied tension. The reason is not that tension alters the mechanical properties of the lipid bilayer, such as its bending modulus, but rather that it opposes any reduction in the projected area of the membrane relative to that at rest, while the opposite is favored. It follows that tension may shift a conformational equilibrium of a protein that deforms the membrane differently in alternative functional states, if that difference also entails a change in the projected membrane area. Conversely, we find that stretch has little to no effect on the dynamics of lipids at the single-molecule level, implying it would also have no bearing on the lifetime of specific protein-lipid interactions. Finally, we show how changes in lipid composition that result in global membrane thinning can mimic the effect of lateral stretch without any applied tension. Statement of SignificanceCells have evolved the ability to sense mechanical forces, such as pressure or stretch, through specialized proteins embedded in their membranes. How exactly the membrane transduces these stimuli to the proteins therein has been unclear. Using state-of-the-art computer simulations, we show that stretching a membrane does not result in forces that pull or push on the individual lipid molecules that constitute the membrane. Instead, lateral tension alters the energetics of reshaping the membrane. This shift in plasticity explains why several well-known force-sensing proteins switch between active and inactive states at specific tension values observed experimentally. We also show that altering the lipid composition of the membrane can produce the same effect as lateral stretch, without any applied force.

Lipid nanoparticles (LNPs) are the most successful drug delivery carrier to date, but optimizing lipid formulations to improve membrane fusion capabilities for effective drug release has been challenging due to lack of a quantitative measure for fusogenicity. Here we introduce a new framework based on small angle X-ray scattering to experimentally measure [Formula] for lipids used in LNP formulations such as glycerol monooleate (GMO) and ionizable lipids (SM-102 and ALC-0315). Q intrinsically captures spontaneous curvature (J0), which is traditionally used to assess fusogenicity. The change of cubic lattice parameters with temperature was measured for GMO-containing lipid mixtures, and the Q extracted quantitatively correlated with LNP fusogenicity power validated by fluorescence-based fusion assays and cryogenic electron microscopy. Fusogenicity of SM-102 and ALC-0315 was quantified by adding them to host membranes and assessing change in Q. This framework provides researchers with the ability to optimize the fusogenicity of LNP formulations for potent drug release and enhances understanding of parameters governing fusion in all biomembranes.

-Synuclein (Syn) remodels cellular membranes through interactions that involve both its structured, membrane-binding N-terminal domain (NTD) and intrinsically disordered C-terminal domain (CTD). While the amphipathic NTD helix is known to insert into lipid bilayers and generate curvature, the contribution of the acidic CTD remains unclear. Here, we dissect the individual and cooperative roles of these domains using Supported Bilayers with Excess Membrane Reservoir (SUPER) templates to quantify membrane remodeling via membrane fission and membrane morphological deformations (i.e., membrane budding and tubulation). We show that both the NTD and CTD independently remodel membranes, while full-length Syn exhibits greater remodeling ability than either the NTD or CTD in isolation. This result demonstrates a synergistic amplification between helix insertion of the NTD and the tethered, disordered CTD. To further probe the mechanism of membrane remodeling by the CTD, we modulated the chain length of the protein, the bulk ionic strength of the solution (i.e., charge screening), and applied relevant polymer scaling laws for disordered proteins. Our results suggest that the membrane remodeling mechanism for the disordered CTD is electrostatic in nature, stemming from protein-protein repulsion at elevated binding densities. Together, our findings reveal a cooperative energetic mechanism in which N-terminal helix insertion biases membrane curvature and the disordered, C-terminal domain adds an additional electrostatic component that helps to overcome the free energy barrier for membrane bending.

Tau and -Synuclein (Syn) frequently co-aggregate in various neurodegenerative disorders. Recently, Tau has been shown to form dynamic, liquid-like condensates that can recruit Syn, and potentially serve as a precursor to pathological aggregation. However, the quantitative impact of Syn on the material properties of these condensates remains elusive. Here, we measure the viscosity and interfacial tension of Tau condensates and determine how these properties are modulated by Syn monomers and fibril seeds. We find that while both forms of Syn partition efficiently into Tau condensates, they exert vastly different effects on the condensates material state. The viscosity of Tau condensates remains unchanged in the presence of Syn monomers at concentrations up to 200 {micro}M, accompanied by a moderate reduction in the condensates interfacial tension. In contrast, the addition of only 5 {micro}M Syn fibril seeds triggers rapid solidification of Tau condensates, manifested by a nearly 100-fold increase in condensate viscosity within one hour. These findings provide quantitative insights into condensate mechanics, highlighting the unique capacity of Syn seeds to drive the liquid-to-solid transition of Tau condensates that may underlie the formation of pathological aggregates.

Significant cellular processes, including protein sorting, signal transduction, and pathogen entry, amongst others, are associated with membrane microdomains, also known as lipid rafts. Lipid rafts, due to their unique biophysical properties compared to their surrounding environment, which stem from their distinct lipid and protein profiles, have garnered interest in methods and techniques that tune their coexisting liquid-ordered/liquid-disordered state, aiming to disrupt or destabilize them. Since cholesterol stabilizes the membrane domain, cholesterol-depleting compounds like cyclodextrin can be used to destabilize and disrupt the membrane rafts. Overall, given the membrane rafts importance in biological processes, it is crucial to understand the biophysical factors that influence its stability. In this study, we present a new method for disrupting and dissolving lipid rafts in a model system of phase-separated supported lipid bilayer (SLB) patches composed of DOPC, DPPC, and cholesterol. Using fluorescence microscopy to monitor the liquid ordered (Lo) and liquid disordered (Ld) phases of the SLB patches, we observed that adding DOPC liposomes causes a transformation of the co-existing Ld and Lo phases into a single-phase bilayer. On the other hand, adding liposomes that match the lipid content of the phase-separated SLB patch increase the areas of the existing Ld and Lo phases. This work also offers a new method for redistributing raft-localized molecules, confirmed by tracking the redistribution of cholera toxin bound to GM1 after domain dissolution with DOPC liposomes. The work describes an alternative method for dynamically altering membrane composition and dissolving domains via liposome addition, rather than lipid depletion or exchange.

Although organelles are often studied one at a time, whole-cell imaging studies show that organelles take up a large part of the cell volume such that they are crowded together. Here we use whole cell soft X-ray tomography imaging to investigate how such crowding affects organelle size scaling, position, and shape, focusing on the nucleus and vacuole of budding yeast. We find that as the vacuole becomes larger, the nucleus loses its normal scaling relation with respect to cell volume, becomes displaced from its normal position near the cell center, and becomes progressively deformed from a sphere into a pancake shape. Using a whole-cell integrated modeling framework, we find that these changes are statistically correlated and give rise to distinct modes in cell organization space. Using a simplified mechanical model for two initially spherical compartments contained inside a confined intracellular space, we are able to recapitulate the effects seen in the experimental data, indicating that these observations are consistent with a purely mechanical interaction. Taken together, our work indicates that, in addition to the well-known protein-based organelle-organelle interactions, physical steric packing of organelles inside a limited cellular volume also plays a large role in the inter-organelle relationships and the overall geometry of the cell.

Cerebrospinal fluid (CSF) is a Newtonian fluid that bathes the brain and spinal cord and oscillates in response to the physiological periodic changes in brain volume, of which the cardiac cycle is a major driver. Understanding this motion is essential for clarifying its contribution to solute transport, waste clearance, and drug delivery. In this work, we study oscillatory and steady streaming flow in the cranial subarachnoid space using a lubrication-based theoretical framework. The model represents the cranial CSF compartment as a thin fluid layer bounded internally by the brain surface and externally by the dura, driven by time-dependent brain surface displacements. We first derive simplified governing equations for flow over an arbitrary smooth sphere-like brain surface and obtain analytical solutions for an idealised spherical geometry with uniform displacements. We then incorporate realistic displacement fields reconstructed from MRI measurements in healthy subjects and solve the reduced equations numerically. The results show that oscillatory forcing produces a steady streaming component that may enhance solute transport compared with diffusion alone. This work provides a mechanistic description of the flow generated by physiological brain motion and highlights the potential presence of steady streaming in cranial subarachnoid fluid dynamics.

Motile cells can sense and exert forces on the extracellular environment through dynamic actin networks. Increased stress against the polymerizing barbed ends of branched actin networks has been shown to lead to an increase in the density of these networks through a force feedback mechanism, though this phenomenon has not been explored through the examination of real-time responses of endogenous actin networks in cells. Here, we utilize mouse embryonic fibroblast CRISPR knock-in lines with labeled ARP2/3 complex to identify cellular and extracellular conditions that regulate branched actin density and enrichment at the leading edge of lamellipodial protrusions. A common theme shared among all branched actin density-increasing conditions is higher levels of interface stress between the plasma membrane and the barbed ends of the lamellipodial actin network. Among these conditions, we find that ARP2/3 is specifically required for robust spreading and protrusion in response to increased extracellular viscosity. Interestingly, time-lapse traction force microscopy of ARP2/3-dependent viscosity responses show significantly reduced changes in strain energy applied to the substrate when compared to spreading and motility through cell-matrix adhesion. In addition, we find that increased extracellular viscosity can bypass the need for extracellular matrix proteins to support lamellipodial protrusion driven by optogenetic Rac activation. Our studies provide strong support for in vitro models of branched actin force feedback responses and further characterize an essential role for branched actin in mediating dramatic cell shape changes in response to increased extracellular viscosity.

We develop a self-consistent free-energy framework in which membrane shape and osmotic pressure are determined simultaneously in a finite reservoir by minimizing bending elasticity and solute entropy. Solute conservation makes osmotic pressure a thermodynamic variable rather than an externally prescribed parameter, producing a nonlinear coupling between membrane mechanics and solvent entropy. This coupling modifies the classical stability condition for spherical vesicles: instability emerges from global free-energy competition rather than the linear Helfrich stability criterion. The resulting critical pressures differ by orders of magnitude from Helfrich predictions and agree with simulations for small and large unilamellar vesicles. The framework is relevant to cellular environments involving biomolecular condensate confinement as well as synthetic vesicles and the development of osmotic-pressure-driven encapsulation platforms.

Colorectal cancer (CRC) is the second most common cause of cancer-related mortality. At the molecular level, CRC is associated with genetic mutations and epigenetic modifications that dysregulate various signaling networks. From the biophysical viewpoint, invasive and metastatic cell migration need to be empowered by mechanical forces. In this study, we analyze the dynamic deformation of patient-derived CRC organoids in Fourier space and demonstrate how organoids with protooncogene BRAF mutation exhibit deformation phenotypes at an early stage. The organoids with BRAFmut have significantly lower elasticity and higher viscosity than those with BRAFWT, which mathematically indicated as the weakening of cell-cell adhesion. Immunohistochemical images, qRT-PCR, and TCGA data analysis confirm the downregulation of E-cadherin (CDH1) in BRAFmut organoids as well as in BRAFmut CRC, suggesting that the decrease in cell-cell adhesion in BRAFmut CRC facilitates invasive and metastatic migration. Notably, the recovery of CDH1 expression by pharmacological inhibition of DNA methylation can quantitatively be detected as the change in mechanical properties, suggesting that the complementary combination of dynamic phenotyping, mathematical modelling, and molecular-level analyses has a potential to unravel the mechanistic causality of the critical gene mutation and CRCs prognosis and the response to therapeutic interventions.

In tissue engineering, it is important to conceive and construct artificial bio-mimetic scaffolds able to foster cell migration as this is a fundamental process in wound healing and tissue regeneration. In order to do that, cubically symmetric and triply periodic porous structures have been identified as promising candidates for instance for the reconstruction of artificial cartilages and bones, also due to their tunable mechanical characteristics and highly inter-connected porous architectures that mimic the trabecular bone hyperboloidal topography. We propose here a mathematical approach that might be helpful to identify what are the best geometrical characteristics of such scaffolds, in order to promote cell migration into the porous structures and speed-up their re-population. The method is based on the observation that cell nucleus deformations should be avoided, yet assuring a good possibility for the cell to reach the wall of the porous structure. Mathematically speaking, this leads to the problem of identifying the size of the largest sphere that can pass, without being stuck, through the pores of the bio-mimetic scaffold.

Artificial ovarian scaffolds represent a promising therapeutic strategy for preserving reproductive health in patients. However, current in vitro approaches are limited by inadequate biomimicry of the native tissue microenvironment, leading to poor development of in vitro ovarian models. In this study, we developed region-specific hydrogel scaffolds incorporating solubilized decellularized ovarian extracellular matrix (dECM) with mechanically tuned properties to enhance the functionality of engineered 3D ovarian models. Ovine ovarian dECM was isolated by mechanical and chemical decellularization methods and subsequently solubilized and incorporated in varying concentrations in homogenous alginate (0.5%) and a composite mixture of 1% gelatin with 0.5% alginate (1:1). The synthesized hydrogels were characterized for rheological properties, including Youngs modulus, pore size, and viscosity, and cytocompatibility assays were conducted using Chinese hamster ovary (CHO) cells. The study demonstrated that both 0.5% alginate and the composite gelatin-alginate hydrogels successfully replicated the mechanical properties of native human ovarian cortical and medullary tissue, with Youngs modulus of 0.84 {+/-} 0.16 kPa, pore size (60-150 nm), and toughness of 0.4Pa, respectively. Zonal hydrogel scaffolds incorporating ovarian dECM demonstrated significantly enhanced cell viability compared to hydrogels supplemented with dECM. The study emphasises the critical role of integrating both mechanical and biochemical attributes while developing functional artificial ovarian constructs for transplantation and regenerative medicine applications. This work contributes to advancing strategies for creating physiologically relevant in vitro models of ovarian tissue.