Liquid-liquid phase separation of type II diabetes-associated IAPP initiates hydrogelation and aggregation.

Amyloidoses (misfolded polypeptide accumulation) are among the most debilitating diseases our aging societies face. Amyloidogenesis can be catalyzed by hydrophobic-hydrophilic interfaces (e.g., air-water interface in vitro [AWI]). We recently demonstrated hydrogelation of the amyloidogenic type II diabetes-associated islet amyloid polypeptide (IAPP), a hydrophobic-hydrophilic interface-dependent process with complex kinetics. We demonstrate that human IAPP undergoes AWI-catalyzed liquid-liquid phase separation (LLPS), which initiates hydrogelation and aggregation. Insulin modulates these processes but does not prevent them. Using nonamyloidogenic rat IAPP, we show that, whereas LLPS does not require the amyloidogenic sequence, hydrogelation and aggregation do. Interestingly, both insulin and rat sequence delayed IAPP LLPS, which may reflect physiology. By developing an experimental setup and analysis tools, we show that, within the whole system (beyond the droplet stage), macroscopic interconnected aggregate clusters form, grow, fuse, and evolve via internal rearrangement, leading to overall hydrogelation. As the AWI-adsorbed gelled layer matures, its microviscosity increases. LLPS-driven aggregation may be a common amyloid feature and integral to pathology.

Polar Fluctuations Lead to Extensile Nematic Behavior in Confluent Tissues.

How can a collection of motile cells, each generating contractile nematic stresses in isolation, become an extensile nematic at the tissue level? Understanding this seemingly contradictory experimental observation, which occurs irrespective of whether the tissue is in the liquid or solid states, is not only crucial to our understanding of diverse biological processes, but is also of fundamental interest to soft matter and many-body physics. Here, we resolve this cellular to tissue level disconnect in the small fluctuation regime by using analytical theories based on hydrodynamic descriptions of confluent tissues, in both liquid and solid states. Specifically, we show that a collection of microscopic constituents with no inherently nematic extensile forces can exhibit active extensile nematic behavior when subject to polar fluctuating forces. We further support our findings by performing cell level simulations of minimal models of confluent tissues.

Incompressible Polar Active Fluids with Quenched Random Field Disorder in Dimensions d>2.

We present a hydrodynamic theory of incompressible polar active fluids with quenched random field disorder. This theory shows that such fluids can overcome the disruption caused by the quenched disorder and move coherently, in the sense of having a nonzero mean velocity in the hydrodynamic limit. However, the scaling behavior of this class of active systems cannot be described by linearized hydrodynamics in spatial dimensions between 2 and 5. Nonetheless, we obtain the exact dimension-dependent scaling exponents in these dimensions.

Packed Swarms on Dirt: Two-Dimensional Incompressible Flocks with Quenched and Annealed Disorder.

We show that incompressible polar active fluids can exhibit an ordered, coherently moving phase even in the presence of quenched disorder in two dimensions. Unlike such active fluids with annealed disorder (i.e., time-dependent random white noise) only, which behave like equilibrium ferromagnets with long-range interactions, this robustness against quenched disorder is a fundamentally nonequilibrium phenomenon. The ordered state belongs to a new universality class, whose scaling laws we calculate using three different renormalization group schemes, which all give scaling exponents within 0.02 of each other, indicating that our results are quite accurate. Our predictions can be quantitatively tested in readily available artificial active systems and imply that biological systems such as cell layers can move coherently in vivo, where disorder is inevitable.

Moving, Reproducing, and Dying Beyond Flatland: Malthusian Flocks in Dimensions d>2.

We show that "Malthusian flocks"-i.e., coherently moving collections of self-propelled entities (such as living creatures) which are being "born" and "dying" during their motion-belong to a new universality class in spatial dimensions d>2. We calculate the universal exponents and scaling laws of this new universality class to O(ε) in an ε=4-d expansion, and find these are different from the "canonical" exponents previously conjectured to hold for "immortal" flocks (i.e., those without birth and death) and shown to hold for incompressible flocks in d>2. Our expansion should be quite accurate in d=3, allowing precise quantitative comparisons between our theory, simulations, and experiments.

Physics of active emulsions.

Phase separating systems that are maintained away from thermodynamic equilibrium via molecular processes represent a class of active systems, which we call active emulsions. These systems are driven by external energy input, for example provided by an external fuel reservoir. The external energy input gives rise to novel phenomena that are not present in passive systems. For instance, concentration gradients can spatially organise emulsions and cause novel droplet size distributions. Another example are active droplets that are subject to chemical reactions such that their nucleation and size can be controlled, and they can divide spontaneously. In this review, we discuss the physics of phase separation and emulsions and show how the concepts that govern such phenomena can be extended to capture the physics of active emulsions. This physics is relevant to the spatial organisation of the biochemistry in living cells, for the development of novel applications in chemical engineering and models for the origin of life.

Critical Motility-Induced Phase Separation Belongs to the Ising Universality Class.

A collection of self-propelled particles with volume exclusion interactions can exhibit the phenomenology of a gas-liquid phase separation, known as motility-induced phase separation (MIPS). The nonequilibrium nature of the system is fundamental to the phase transition; however, it is unclear whether MIPS at criticality contributes a novel universality class to nonequilibrium physics. We demonstrate here that this is not the case by showing that a generic critical MIPS belongs to the Ising universality class with conservative dynamics.

Chemical-Reaction-Controlled Phase Separated Drops: Formation, Size Selection, and Coarsening.

Phase separation under nonequilibrium conditions is exploited by biological cells to organize their cytoplasm but remains poorly understood as a physical phenomenon. Here, we study a ternary fluid model in which phase-separating molecules can be converted into soluble molecules, and vice versa, via chemical reactions. We elucidate using analytical and simulation methods how drop size, formation, and coarsening can be controlled by the chemical reaction rates, and categorize the qualitative behavior of the system into distinct regimes. Ostwald ripening arrest occurs above critical reaction rates, demonstrating that this transition belongs entirely to the nonequilibrium regime. Our model is a minimal representation of the cell cytoplasm.

Insights into the Origin of Distinct Medin Fibril Morphologies Induced by Incubation Conditions and Seeding.

Incubation conditions are an important factor to consider when studying protein aggregation in vitro. Here, we employed biophysical methods and atomic force microscopy to show that agitation dramatically alters the morphology of medin, an amyloid protein deposited in the aorta. Agitation reduces the lag time for fibrillation by ~18-fold, suggesting that the rate of fibril formation plays a key role in directing the protein packing arrangement within fibrils. Utilising preformed sonicated fibrils as seeds, we probed the role of seeding on medin fibrillation and revealed three distinct fibril morphologies, with biophysical modelling explaining the salient features of experimental observations. We showed that nucleation pathways to distinct fibril morphologies may be switched on and off depending on the properties of the seeding fibrils and growth conditions. These findings may impact on the development of amyloid-based biomaterials and enhance understanding of seeding as a pathological mechanism.

Interface stability, interface fluctuations, and the Gibbs-Thomson relationship in motility-induced phase separations.

Minimal models of self-propelled particles with short-range volume exclusion interactions have been shown to exhibit the signatures of phase separation. Here I show that the observed interfacial stability and fluctuations in motility-induced phase separations (MIPS) can be explained by modeling the microscopic dynamics of the active particles in the interfacial region. In addition, I demonstrate the validity of the Gibbs-Thomson relationship in MIPS, which provides a functional relationship between the size of a condensed drop and its surrounding vapor concentration. As a result, the late-stage coarsening dynamics of MIPS at vanishing supersaturation follows the classic Lifshitz-Slyozov scaling law.

Thermodynamic costs of information processing in sensory adaptation.

Biological sensory systems react to changes in their surroundings. They are characterized by fast response and slow adaptation to varying environmental cues. Insofar as sensory adaptive systems map environmental changes to changes of their internal degrees of freedom, they can be regarded as computational devices manipulating information. Landauer established that information is ultimately physical, and its manipulation subject to the entropic and energetic bounds of thermodynamics. Thus the fundamental costs of biological sensory adaptation can be elucidated by tracking how the information the system has about its environment is altered. These bounds are particularly relevant for small organisms, which unlike everyday computers, operate at very low energies. In this paper, we establish a general framework for the thermodynamics of information processing in sensing. With it, we quantify how during sensory adaptation information about the past is erased, while information about the present is gathered. This process produces entropy larger than the amount of old information erased and has an energetic cost bounded by the amount of new information written to memory. We apply these principles to the E. coli's chemotaxis pathway during binary ligand concentration changes. In this regime, we quantify the amount of information stored by each methyl group and show that receptors consume energy in the range of the information-theoretic minimum. Our work provides a basis for further inquiries into more complex phenomena, such as gradient sensing and frequency response.

Designing non-native iron-binding site on a protein cage for biological synthesis of nanoparticles.

In biomineralization processes, a supramolecular organic structure is often used as a template for inorganic nanomaterial synthesis. The E2 protein cage derived from Geobacillus stearothermophilus pyruvate dehydrogenase and formed by the self-assembly of 60 subunits, has been functionalized with non-native iron-mineralization capability by incorporating two types of iron-binding peptides. The non-native peptides introduced at the interior surface do not affect the self-assembly of E2 protein subunits. In contrast to the wild-type, the engineered E2 protein cages can serve as size- and shape-constrained reactors for the synthesis of iron nanoparticles. Electrostatic interactions between anionic amino acids and cationic iron molecules drive the formation of iron oxide nanoparticles within the engineered E2 protein cages. The work expands the investigations on nanomaterial biosynthesis using engineered host-guest encapsulation properties of protein cages.

The air-water interface determines the outcome of seeding during amyloidogenesis.

Amyloid formation is a hallmark of protein misfolding diseases (e.g. Type II diabetes mellitus). The energetically unfavourable nucleation step of amyloidogenesis can be accelerated by seeding, during which pre-formed aggregates act as templates for monomer recruitment. Hydrophobic-hydrophilic interfaces [e.g. AWI (air-water interface)] can also catalyse amyloidogenesis due to the surfactant properties of amyloidogenic polypeptides. Using thioflavin T fluorescence and electron microscopy, we demonstrate that the outcome of seeding on human islet amyloid polypeptide amyloidogenesis is dependent upon whether the AWI is present or absent and is dictated by seed type. Seeding significantly inhibits (with AWI) or promotes (without AWI) plateau height compared with seedless controls; with short fibrils being more efficient seeds than their longer counterparts. Moreover, promotion of nucleation by increasing monomer concentrations can only be observed in the absence of an AWI. Using biophysical modelling, we suggest that a possible explanation for our results may reside in lateral interactions between seeds and monomers determining the fibril mass formed in seeded reactions at steady-state. Our results suggest that in vivo hydrophobic-hydrophilic interfaces (e.g. the presence of membranes and their turnover rate) may dictate the outcome of seeding during amyloidogenesis and that factors affecting the size of the pre-aggregate may be important.

Machine learning topological defects in confluent tissues.

Active nematics is an emerging paradigm for characterizing biological systems. One aspect of particularly intense focus is the role active nematic defects play in these systems, as they have been found to mediate a growing number of biological processes. Accurately detecting and classifying these defects in biological systems is, therefore, of vital importance to improving our understanding of such processes. While robust methods for defect detection exist for systems of elongated constituents, other systems, such as epithelial layers, are not well suited to such methods. Here, we address this problem by developing a convolutional neural network to detect and classify nematic defects in confluent cell layers. Crucially, our method is readily implementable on experimental images of cell layers and is specifically designed to be suitable for cells that are not rod shaped, which we demonstrate by detecting defects on experimental data using the trained model. We show that our machine learning model outperforms current defect detection techniques and that this manifests itself in our method as requiring less data to accurately capture defect properties. This could drastically improve the accuracy of experimental data interpretation while also reducing costs, advancing the study of nematic defects in biological systems.

Dynamics of packed swarms: Time-displaced correlators of two-dimensional incompressible flocks.

We analytically calculate the scaling exponents of a two-dimensional KPZ-like system: coherently moving incompressible polar active fluids. Using three different renormalization group approximation schemes, we obtain values for the roughness exponent χ and anisotropy exponent ζ that are extremely near the known exact results. This implies our prediction for the previously unknown dynamic exponent z is likely to be quantitatively accurate.

Combined effects of agitation, macromolecular crowding, and interfaces on amyloidogenesis.

Amyloid formation and accumulation is a hallmark of protein misfolding diseases and is associated with diverse pathologies including type II diabetes and Alzheimer's disease (AD). In vitro, amyloidogenesis is widely studied in conditions that do not simulate the crowded and viscous in vivo environment. A high volume fraction of most biological fluids is occupied by various macromolecules, a phenomenon known as macromolecular crowding. For some amyloid systems (e.g. α-synuclein) and under shaking condition, the excluded volume effect of macromolecular crowding favors aggregation, whereas increased viscosity reduces the kinetics of these reactions. Amyloidogenesis can also be catalyzed by hydrophobic-hydrophilic interfaces, represented by the air-water interface in vitro and diverse heterogeneous interfaces in vivo (e.g. membranes). In this study, we investigated the effects of two different crowding polymers (dextran and Ficoll) and two different experimental conditions (with and without shaking) on the fibrilization of amyloid-ß peptide, a major player in AD pathogenesis. Specifically, we demonstrate that, during macromolecular crowding, viscosity dominates over the excluded volume effect only when the system is spatially non homogeneous (i.e. an air-water interface is present). We also show that the surfactant activity of the crowding agents can critically influence the outcome of macromolecular crowding and that the structure of the amyloid species formed may depend on the polymer used. This suggests that, in vivo, the outcome of amyloidogenesis may be affected by both macromolecular crowding and spatial heterogeneity (e.g. membrane turn-over). More generally, our work suggests that any factors causing changes in crowding may be susceptibility factors in AD.

Spatial organization of the cell cytoplasm by position-dependent phase separation.

During asymmetric cell division, cytoplasmic components are segregated to opposite sides of the cell. We discuss how the observed segregation can be achieved by a position-dependent phase separation mechanism controlled by a protein concentration gradient. We show that effects of even a weak gradient can be amplified by the phase transition to achieve strong segregation. We compare our theory to the segregation of germ granules observed during the divisions in the C. elegans embryo. Our study demonstrates how liquid-liquid phase separation can play a key role in the organization of the cytoplasm.

Model of inverse bleb growth explains giant vacuole dynamics during cell mechanoadaptation.

Cells can withstand hostile environmental conditions manifest as large mechanical forces such as pressure gradients and/or shear stresses by dynamically changing their shape. Such conditions are realized in the Schlemm's canal of the eye where endothelial cells that cover the inner vessel wall are subjected to the hydrodynamic pressure gradients exerted by the aqueous humor outflow. These cells form fluid-filled dynamic outpouchings of their basal membrane called giant vacuoles. The inverses of giant vacuoles are reminiscent of cellular blebs, extracellular cytoplasmic protrusions triggered by local temporary disruption of the contractile actomyosin cortex. Inverse blebbing has also been first observed experimentally during sprouting angiogenesis, but its underlying physical mechanisms are poorly understood. Here, we hypothesize that giant vacuole formation can be described as inverse blebbing and formulate a biophysical model of this process. Our model elucidates how cell membrane mechanical properties affect the morphology and dynamics of giant vacuoles and predicts coarsening akin to Ostwald ripening between multiple invaginating vacuoles. Our results are in qualitative agreement with observations from the formation of giant vacuoles during perfusion experiments. Our model not only elucidates the biophysical mechanisms driving inverse blebbing and giant vacuole dynamics, but also identifies universal features of the cellular response to pressure loads that are relevant to many experimental contexts.

Enrichment of amyloidogenesis at an air-water interface.

The aggregation of proteins or peptides into amyloid fibrils is a hallmark of protein misfolding diseases (e.g., Alzheimer's disease) and is under intense investigation. Many of the experiments performed are in vitro in nature and the samples under study are ordinarily exposed to diverse interfaces, e.g., the container wall and air. This naturally raises the question of how important interfacial effects are to amyloidogenesis. Indeed, it has already been recognized that many amyloid-forming peptides are surface-active. Moreover, it has recently been demonstrated that the presence of a hydrophobic interface can promote amyloid fibrillization, although the underlying mechanism is still unclear. Here, we combine theory, surface property measurements, and amyloid fibrillogenesis assays on islet amyloid polypeptide and amyloid-ß peptide to demonstrate why, at experimentally relevant concentrations, the surface activity of the amyloid-forming peptides leads to enriched fibrillization at an air-water interface. Our findings indicate that the key that links these two seemingly different phenomena is the surface-active nature of the amyloid-forming species, which renders the surface concentration much higher than the corresponding critical fibrillar concentration. This subsequently leads to a substantial increase in fibrillization.