Capping protein is dispensable for polarized actin network growth and actin-based motility.

Heterodimeric capping protein (CP) binds the rapidly growing barbed ends of actin filaments and prevents the addition (or loss) of subunits. Capping activity is generally considered to be essential for actin-based motility induced by Arp2/3 complex nucleation. By stopping barbed end growth, CP favors nucleation of daughter filaments at the functionalized surface where the Arp2/3 complex is activated, thus creating polarized network growth, which is necessary for movement. However, here using an in vitro assay where Arp2/3 complex-based actin polymerization is induced on bead surfaces in the absence of CP, we produce robust polarized actin growth and motility. This is achieved either by adding the actin polymerase Ena/VASP or by boosting Arp2/3 complex activity at the surface. Another actin polymerase, the formin FMNL2, cannot substitute for CP, showing that polymerase activity alone is not enough to override the need for CP. Interfering with the polymerase activity of Ena/VASP, its surface recruitment or its bundling activity all reduce Ena/VASP's ability to maintain polarized network growth in the absence of CP. Taken together, our findings show that CP is dispensable for polarized actin growth and motility in situations where surface-directed polymerization is favored by whatever means over the growth of barbed ends in the network.

Interdisciplinary Research in Artificial Intelligence: Challenges and Opportunities.

The use of artificial intelligence (AI) in a variety of research fields is speeding up multiple digital revolutions, from shifting paradigms in healthcare, precision medicine and wearable sensing, to public services and education offered to the masses around the world, to future cities made optimally efficient by autonomous driving. When a revolution happens, the consequences are not obvious straight away, and to date, there is no uniformly adapted framework to guide AI research to ensure a sustainable societal transition. To answer this need, here we analyze three key challenges to interdisciplinary AI research, and deliver three broad conclusions: 1) future development of AI should not only impact other scientific domains but should also take inspiration and benefit from other fields of science, 2) AI research must be accompanied by decision explainability, dataset bias transparency as well as development of evaluation methodologies and creation of regulatory agencies to ensure responsibility, and 3) AI education should receive more attention, efforts and innovation from the educational and scientific communities. Our analysis is of interest not only to AI practitioners but also to other researchers and the general public as it offers ways to guide the emerging collaborations and interactions toward the most fruitful outcomes.

Actin shells control buckling and wrinkling of biomembranes.

Global changes of cell shape under mechanical or osmotic external stresses are mostly controlled by the mechanics of the cortical actin cytoskeleton underlying the cell membrane. Some aspects of this process can be recapitulated in vitro on reconstituted actin-and-membrane systems. In this paper, we investigate how the mechanical properties of a branched actin network shell, polymerized at the surface of a liposome, control membrane shape when the volume is reduced. We observe a variety of membrane shapes depending on the actin thickness. Thin shells undergo buckling, characterized by a cup-shape deformation of the membrane that coincides with the one of the actin network. Thick shells produce membrane wrinkles, but do not deform their outer layer. For intermediate micrometer-thick shells, wrinkling of the membrane is observed, and the actin layer is slightly deformed. Confronting our experimental results with a theoretical description, we determine the transition between buckling and wrinkling, which depends on the thickness of the actin shell and the size of the liposome. We thus unveil the generic mechanism by which biomembranes are able to accommodate their shape against mechanical compression, through thickness adaptation of their cortical cytoskeleton.

Myosin 1b is an actin depolymerase.

The regulation of actin dynamics is essential for various cellular processes. Former evidence suggests a correlation between the function of non-conventional myosin motors and actin dynamics. Here we investigate the contribution of myosin 1b to actin dynamics using sliding motility assays. We observe that sliding on myosin 1b immobilized or bound to a fluid bilayer enhances actin depolymerization at the barbed end, while sliding on myosin II, although 5 times faster, has no effect. This work reveals a non-conventional myosin motor as another type of depolymerase and points to its singular interactions with the actin barbed end.

Probing the Interplay between Dendritic Spine Morphology and Membrane-Bound Diffusion.

Dendritic spines are protrusions along neuronal dendrites that harbor the majority of excitatory postsynapses. Their distinct morphology, often featuring a bulbous head and small neck that connects to the dendritic shaft, has been shown to facilitate compartmentalization of electrical and cytoplasmic signaling stimuli elicited at the synapse. The extent to which spine morphology also forms a barrier for membrane-bound diffusion has remained unclear. Recent simulations suggested that especially the diameter of the spine neck plays a limiting role in this process. Here, we examine the connection between spine morphology and membrane-bound diffusion through a combination of photoconversion, live-cell superresolution experiments, and numerical simulations. Local photoconversion was used to obtain the timescale of diffusive equilibration in spines and followed by global sparse photoconversion to determine spine morphologies with nanoscopic resolution. These morphologies were subsequently used to assess the role of morphology on the diffusive equilibration. From the simulations, we could determine a robust relation between the equilibration timescale and a generalized shape factor calculated using both spine neck width and neck length, as well as spine head size. Experimentally, we found that diffusive equilibration was often slower, but rarely faster than predicted from the simulations, indicating that other biological confounders further reduce membrane-bound diffusion in these spines. This shape-dependent membrane-bound diffusion in mature spines may contribute to spine-specific compartmentalization of neurotransmitter receptors and signaling molecules and thereby support long-term plasticity of synaptic contacts.

A Method for Molecular Dynamics on Curved Surfaces.

Dynamics simulations of constrained particles can greatly aid in understanding the temporal and spatial evolution of biological processes such as lateral transport along membranes and self-assembly of viruses. Most theoretical efforts in the field of diffusive transport have focused on solving the diffusion equation on curved surfaces, for which it is not tractable to incorporate particle interactions even though these play a crucial role in crowded systems. We show here that it is possible to take such interactions into account by combining standard constraint algorithms with the classical velocity Verlet scheme to perform molecular dynamics simulations of particles constrained to an arbitrarily curved surface. Furthermore, unlike Brownian dynamics schemes in local coordinates, our method is based on Cartesian coordinates, allowing for the reuse of many other standard tools without modifications, including parallelization through domain decomposition. We show that by applying the schemes to the Langevin equation for various surfaces, we obtain confined Brownian motion, which has direct applications to many biological and physical problems. Finally we present two practical examples that highlight the applicability of the method: 1) the influence of crowding and shape on the lateral diffusion of proteins in curved membranes; and 2) the self-assembly of a coarse-grained virus capsid protein model.

Role of charge regulation and size polydispersity in nanoparticle encapsulation by viral coat proteins.

Nanoparticles can be encapsulated by virus coat proteins if their surfaces are functionalized to acquire a sufficiently large negative charge. A minimal surface charge is required to overcome (i) repulsive interactions between the positively charged RNA-binding domains on the proteins and (ii) the loss of mixing and translational entropy of RNA and capsid coat proteins. Here, we present a model describing the encapsulation of spherical particles bearing weakly acidic surface groups and investigate how charge regulation and size polydispersity impact upon the encapsulation efficiency of gold nanoparticles by model coat proteins. We show that the surface charge density of these particles cannot be assumed fixed, but that it adjusts itself to minimize electrostatic repulsion between the charges on them and maximize the attractive interaction with the RNA binding domains on the proteins. Charge regulation in combination with the natural variation of particle radii has a large effect on the encapsulation efficiency: it makes it much more gradual despite its inherently cooperative nature. Our calculations rationalize recent experimental observations on the coassembly of gold nanoparticles by brome mosaic virus coat proteins.

Confinement without boundaries: anisotropic diffusion on the surface of a cylinder.

Densely packed systems of thermal particles in curved geometries are frequently encountered in biological and microfluidic systems. In 2D systems, at sufficiently high surface coverage, diffusive motion is widely known to be strongly affected by physical confinement, e.g., by the walls. In this work, we explore the effects of confinement by shape, not rigid boundaries, on the diffusion of discs by confining them to the surface of a cylinder. We find that both the magnitude and the directionality of lateral diffusion is strongly influenced by the radius of the cylinder. An anisotropy between diffusion in the longitudinal and circumferential direction of the cylinder develops. We demonstrate that the origin of this effect lies in the fact that screw-like packings of mono- and oligodisperse discs on the surface of a cylinder induce preferential collective motions in the circumferential direction, but also show that even in polydisperse systems lacking such order an intrinsic finite size confinement effect increases diffusivity in the circumferential direction.

Barriers in the brain: resolving dendritic spine morphology and compartmentalization.

Dendritic spines are micron-sized protrusions that harbor the majority of excitatory synapses in the central nervous system. The head of the spine is connected to the dendritic shaft by a 50-400 nm thin membrane tube, called the spine neck, which has been hypothesized to confine biochemical and electric signals within the spine compartment. Such compartmentalization could minimize interspinal crosstalk and thereby support spine-specific synapse plasticity. However, to what extent compartmentalization is governed by spine morphology, and in particular the diameter of the spine neck, has remained unresolved. Here, we review recent advances in tool development - both experimental and theoretical - that facilitate studying the role of the spine neck in compartmentalization. Special emphasis is given to recent advances in microscopy methods and quantitative modeling applications as we discuss compartmentalization of biochemical signals, membrane receptors and electrical signals in spines. Multidisciplinary approaches should help to answer how dendritic spine architecture affects the cellular and molecular processes required for synapse maintenance and modulation.

Forced transport of deformable containers through narrow constrictions.

We study, numerically and analytically, the forced transport of deformable containers through a narrow constriction. Our central aim is to quantify the competition between the constriction geometry and the active forcing, regulating whether and at which speed a container may pass through the constriction and under what conditions it gets stuck. We focus, in particular, on the interrelation between the force that propels the container and the radius of the channel, as these are the external variables that may be directly controlled in both artificial and physiological settings. We present lattice Boltzmann simulations that elucidate in detail the various phases of translocation and present simplified analytical models that treat two limiting types of these membrane containers: deformational energy dominated by the bending or stretching contribution. In either case we find excellent agreement with the full simulations, and our results reveal that not only the radius but also the length of the constriction determines whether or not the container will pass.

Impact of morphology on diffusive dynamics on curved surfaces.

Diffusive processes on nonplanar substrates are deeply relevant for cellular function and transport and increasingly used to probe and characterize the behavior of proteins in membranes. We present analytical and numerical analyses of in-plane diffusion of discrete particles on curved geometries reflecting various generic motifs in biology and explore, in particular, the effect that the shape of the substrate has on the characteristic time scales of diffusive processes. To this end, we consider both collective measures (the relaxation of concentration profiles towards equilibrium) and single-particle measures (escape rates and first passage times of individual diffusing molecules): the first relevant for the correct interpretation of FRAP experiments in curved environments; the second, for single-particle tracking probes. Each of these measures is sensitively affected by the morphology of the substrate, and we find that the exit rate out of a domain is not uniquely set by the size of its boundary, illustrating the general principle we reveal: By varying the shape of a substrate, Nature can control the diffusive time scales in a microenvironment without changing the bare substrate properties.

Shape-induced asymmetric diffusion in dendritic spines allows efficient synaptic AMPA receptor trapping.

Dendritic spines are the primary postsynaptic sites of excitatory neurotransmission in the brain. They exhibit a remarkable morphological variety, ranging from thin protrusions, to stubby shapes, to bulbous mushroom shapes. The remodeling of spines is thought to regulate the strength of the synaptic connection, which depends vitally on the number and the spatial distribution of AMPA-type glutamate receptors (AMPARs). We present numerical and analytical analyses demonstrating that this shape strongly affects AMPAR diffusion. We report a pronounced suppression of the receptor exit rate out of spines with decreasing neck radius. Thus, mushroomlike spines become highly effective at retaining receptors in the spine head. Moreover, we show that the postsynaptic density further enhances receptor trapping, particularly in mushroomlike spines local exocytosis in the spine head, in contrast to release at the base, provides rapid and specific regulatory control of AMPAR concentration at synapses.

Digit somatotopy in the human cerebellum: a 7T fMRI study.

The representation of the human body in the human cerebellum is still relatively unknown, compared to the well-studied homunculus in the primary somatosensory cortex. The investigation of the body representation in the cerebellum and its somatotopic organisation is complicated because of the relatively small dimensions of the cerebellum, compared to the cerebrum. Somatotopically organised whole-body homunculi have previously been reported in both humans and rats. However, whether individual digits are represented in the cerebellum in a somatotopically organised way is much less clear. In this study, the high spatial resolution and high sensitivity to the blood oxygenation level dependent (BOLD) signal of 7T fMRI were employed to study the BOLD responses in the human cerebellum to the stroking of the skin of individual digits, the hand and forearm. For the first time, a coarse somatotopic organisation of the digits, ordered from D1-D5, could be visualised in individual human subjects in both the anterior (lobule V) and the posterior (lobule VIII) lobes of the cerebellum using a somatosensory stimulus. The somatotopic gradient in lobule V was found consistently in the posterior to anterior direction, with the thumb most posterior, while the direction of the somatotopic gradient in lobule VIII differed between subjects. No somatotopic organisation was found in Crus I. A comparison of the digit patches with the hand patch revealed that the digit regions are completely covered by the hand region in both the anterior and posterior lobes of the cerebellum, in a non-somatotopic manner. These results demonstrate the promise of ultra-high field, high-resolution fMRI for studies of the cerebellum.