Transverse Fluctuations Control the Assembly of Semiflexible Filaments.

The kinetics of the assembly of semiflexible filaments through end-to-end annealing is key to the structure of the cytoskeleton, but is not understood. We analyze this problem through scaling theory and simulations, and uncover a regime where filaments' ends find each other through bending fluctuations without the need for the whole filament to diffuse. This results in a very substantial speedup of assembly in physiological regimes, and could help with understanding the dynamics of actin and intermediate filaments in biological processes such as wound healing and cell division.

Next-generation ABACUS biosensors reveal cellular ABA dynamics driving root growth at low aerial humidity.

The plant hormone abscisic acid (ABA) accumulates under abiotic stress to recast water relations and development. To overcome a lack of high-resolution sensitive reporters, we developed ABACUS2s-next-generation Förster resonance energy transfer (FRET) biosensors for ABA with high affinity, signal-to-noise ratio and orthogonality-that reveal endogenous ABA patterns in Arabidopsis thaliana. We mapped stress-induced ABA dynamics in high resolution to reveal the cellular basis for local and systemic ABA functions. At reduced foliar humidity, root cells accumulated ABA in the elongation zone, the site of phloem-transported ABA unloading. Phloem ABA and root ABA signalling were both essential to maintain root growth at low humidity. ABA coordinates a root response to foliar stresses, enabling plants to maintain foraging of deeper soil for water uptake.

Generic stress rectification in nonlinear elastic media.

Stress propagation in nonlinear media is crucial in cell biology, where molecular motors exert anisotropic force dipoles on the fibrous cytoskeleton. While the force dipoles can be either contractile or expansile, a medium made of fibers which buckle under compression rectifies these stresses towards a biologically crucial contraction. A general understanding of this rectification phenomenon as a function of the medium's elasticity is however lacking. Here we use theoretical continuum elasticity to show that rectification is actually a very general effect in nonlinear materials subjected to anisotropic internal stresses. We analytically show that both bucklable and constitutively linear materials subjected to geometrical nonlinearities rectify small forces towards contraction, while granular-like materials rectify towards expansion. Using simulations, we moreover show that these results extend to larger forces. Beyond fiber networks, these results could shed light on the propagation of stresses in brittle or granular materials following a local plastic rearrangement.

Image Reconstruction in Light-Sheet Microscopy: Spatially Varying Deconvolution and Mixed Noise.

We study the problem of deconvolution for light-sheet microscopy, where the data is corrupted by spatially varying blur and a combination of Poisson and Gaussian noise. The spatial variation of the point spread function of a light-sheet microscope is determined by the interaction between the excitation sheet and the detection objective PSF. We introduce a model of the image formation process that incorporates this interaction and we formulate a variational model that accounts for the combination of Poisson and Gaussian noise through a data fidelity term consisting of the infimal convolution of the single noise fidelities, first introduced in L. Calatroni et al. (SIAM J Imaging Sci 10(3):1196-1233, 2017). We establish convergence rates and a discrepancy principle for the infimal convolution fidelity and the inverse problem is solved by applying the primal-dual hybrid gradient (PDHG) algorithm in a novel way. Numerical experiments performed on simulated and real data show superior reconstruction results in comparison with other methods.

Epidemiological Study of Multiple Zoonotic Mosquito-Borne Alphaviruses in Horses in Queensland, Australia (2018-2020).

The increased frequency of extreme weather events due to climate change has complicated the epidemiological pattern of mosquito-borne diseases, as the host and vector dynamics shift to adapt. However, little is known about the seroprevalence of common mosquito-borne virus infections in horses in Australia. In this study, serological surveys for multiple alphaviruses were performed on samples taken from 622 horses across two horse populations (racehorses and horses residing on The University of Queensland (UQ) campus) in Queensland using the gold standard virus neutralization test. As is the case in humans across Australia, Ross River virus (RRV) is the most common arbovirus infection in horses, followed by Barmah Forest virus, with an overall apparent seroprevalence of 48.6% (302/622) and 4.3% (26/607), respectively. Horses aged over 6 years old (OR 1.86, p = 0.01) and residing at UQ (OR 5.8, p < 0.001) were significantly associated with seroconversion to RRV. A significant medium correlation (r = 0.626, p < 0.001) between RRV and Getah virus (GETV) neutralizing antibody titers was identified. Collectively, these results advance the current epidemiological knowledge of arbovirus exposure in a susceptible host in Australia. The potential use of horses as sentinels for arbovirus monitoring should be considered. Furthermore, since GETV is currently exotic to Australia, antibodies cross-reactivity between RRV and GETV should be further investigated for cross-protection, which may also help to inform vaccine developments.

Identification of a canine coronavirus in Australian racing Greyhounds.

Coronavirus infection can cause a range of syndromes, which in dogs can include mild-to-severe enteritis that generally resolves rapidly. Fatalities can occur from coinfection with other pathogens, including canine parvovirus. Between late December 2019 and April 2020, canine coronavirus (CCoV) was detected in Australian racing Greyhounds that displayed signs of gastrointestinal disease. The CCoV was genotyped using high-throughput sequencing, recovering 98.3% of a type IIb CCoV, generally thought to cause a mild but highly contagious enteric disease. The Australian CCoV was almost identical (99.9%, whole-genome sequence) to another CCoV associated with an outbreak of severe vomiting in dogs in the United Kingdom at the same time (December 2019-March 2020).

Passive coupling of membrane tension and cell volume during active response of cells to osmosis.

During osmotic changes of their environment, cells actively regulate their volume and plasma membrane tension that can passively change through osmosis. How tension and volume are coupled during osmotic adaptation remains unknown, as their quantitative characterization is lacking. Here, we performed dynamic membrane tension and cell volume measurements during osmotic shocks. During the first few seconds following the shock, cell volume varied to equilibrate osmotic pressures inside and outside the cell, and membrane tension dynamically followed these changes. A theoretical model based on the passive, reversible unfolding of the membrane as it detaches from the actin cortex during volume increase quantitatively describes our data. After the initial response, tension and volume recovered from hypoosmotic shocks but not from hyperosmotic shocks. Using a fluorescent membrane tension probe (fluorescent lipid tension reporter [Flipper-TR]), we investigated the coupling between tension and volume during these asymmetric recoveries. Caveolae depletion and pharmacological inhibition of ion transporters and channels, mTORCs, and the cytoskeleton all affected tension and volume responses. Treatments targeting mTORC2 and specific downstream effectors caused identical changes to both tension and volume responses, their coupling remaining the same. This supports that the coupling of tension and volume responses to osmotic shocks is primarily regulated by mTORC2.

Local structure of DNA toroids reveals curvature-dependent intermolecular forces.

In viruses and cells, DNA is closely packed and tightly curved thanks to polyvalent cations inducing an effective attraction between its negatively charged filaments. Our understanding of this effective attraction remains very incomplete, partly because experimental data is limited to bulk measurements on large samples of mostly uncurved DNA helices. Here we use cryo electron microscopy to shed light on the interaction between highly curved helices. We find that the spacing between DNA helices in spermine-induced DNA toroidal condensates depends on their location within the torus, consistent with a mathematical model based on the competition between electrostatic interactions and the bending rigidity of DNA. We use our model to infer the characteristics of the interaction potential, and find that its equilibrium spacing strongly depends on the curvature of the filaments. In addition, the interaction is much softer than previously reported in bulk samples using different salt conditions. Beyond viruses and cells, our characterization of the interactions governing DNA-based dense structures could help develop robust designs in DNA nanotechnologies.

Chiral Active Hexatics: Giant Number Fluctuations, Waves, and Destruction of Order.

Active materials, composed of internally driven particles, have properties that are qualitatively distinct from matter at thermal equilibrium. However, the most spectacular departures from equilibrium phase behavior are thought to be confined to systems with polar or nematic asymmetry. In this Letter, we show that such departures are also displayed by more symmetric phases such as hexatics if, in addition, the constituent particles have chiral asymmetry. We show that chiral active hexatics whose rotation rate does not depend on density have giant number fluctuations. If the rotation rate depends on density, the giant number fluctuations are suppressed due to a novel orientation-density sound mode with a linear dispersion which propagates even in the overdamped limit. However, we demonstrate that beyond a finite but large length scale, a chirality and activity-induced relevant nonlinearity invalidates the predictions of the linear theory and destroys the hexatic order. In addition, we show that activity modifies the interactions between defects in the active chiral hexatic phase, making them nonmutual. Finally, to demonstrate the generality of a chiral active hexatic phase we show that it results from the melting of chiral active crystals in finite systems.

Anisotropic ESCRT-III architecture governs helical membrane tube formation.

ESCRT-III proteins assemble into ubiquitous membrane-remodeling polymers during many cellular processes. Here we describe the structure of helical membrane tubes that are scaffolded by bundled ESCRT-III filaments. Cryo-ET reveals how the shape of the helical membrane tube arises from the assembly of two distinct bundles of helical filaments that have the same helical path but bind the membrane with different interfaces. Higher-resolution cryo-EM of filaments bound to helical bicelles confirms that ESCRT-III filaments can interact with the membrane through a previously undescribed interface. Mathematical modeling demonstrates that the interface described above is key to the mechanical stability of helical membrane tubes and helps infer the rigidity of the described protein filaments. Altogether, our results suggest that the interactions between ESCRT-III filaments and the membrane could proceed through multiple interfaces, to provide assembly on membranes with various shapes, or adapt the orientation of the filaments towards the membrane during membrane remodeling.

Reversal of contractility as a signature of self-organization in cytoskeletal bundles.

Bundles of cytoskeletal filaments and molecular motors generate motion in living cells, and have internal structures ranging from very organized to apparently disordered. The mechanisms powering the disordered structures are debated, and existing models predominantly predict that they are contractile. We reexamine this prediction through a theoretical treatment of the interplay between three well-characterized internal dynamical processes in cytoskeletal bundles: filament assembly and disassembly, the attachement-detachment dynamics of motors and that of crosslinking proteins. The resulting self-organization is easily understood in terms of motor and crosslink localization, and allows for an extensive control of the active bundle mechanics, including reversals of the filaments' apparent velocities and the possibility of generating extension instead of contraction. This reversal mirrors some recent experimental observations, and provides a robust criterion to experimentally elucidate the underpinnings of both actomyosin activity and the dynamics of microtubule/motor assemblies in vitro as well as in diverse intracellular structures ranging from contractile bundles to the mitotic spindle.

Swimmer Suspensions on Substrates: Anomalous Stability and Long-Range Order.

We present a comprehensive theory of the dynamics and fluctuations of a two-dimensional suspension of polar active particles in an incompressible fluid confined to a substrate. We show that, depending on the sign of a single parameter, a state with polar orientational order is anomalously stable (or anomalously unstable), with a nonzero relaxation (or growth) rate for angular fluctuations, not parallel to the ordering direction, at zero wave number. This screening of the broken-symmetry mode in the stable state does lead to conventional rather than giant number fluctuations as argued by Bricard et al., Nature 503, 95 (2013), but their bend instability in a splay-stable flock does not exist and the polar phase has long-range order in two dimensions. Our theory also describes confined three-dimensional thin-film suspensions of active polar particles as well as dense compressible active polar rods, and predicts a flocking transition without a banding instability.

A super-resolution platform for correlative live single-molecule imaging and STED microscopy.

Super-resolution microscopy offers tremendous opportunities to unravel the complex and dynamic architecture of living cells. However, current super-resolution microscopes are well suited for revealing protein distributions or cell morphology, but not both. We present a super-resolution platform that permits correlative single-molecule imaging and stimulated emission depletion microscopy in live cells. It gives nanoscale access to the positions and movements of synaptic proteins within the morphological context of growth cones and dendritic spines.

Spontaneous rotation can stabilise ordered chiral active fluids.

Active hydrodynamic theories are a powerful tool to study the emergent ordered phases of internally driven particles such as bird flocks, bacterial suspension and their artificial analogues. While theories of orientationally ordered phases are by now well established, the effect of chirality on these phases is much less studied. In this paper, we present a complete dynamical theory of orientationally ordered chiral particles in two-dimensional incompressible systems. We show that phase-coherent states of rotating chiral particles are remarkably stable in both momentum-conserved and non-conserved systems in contrast to their non-rotating counterparts. Furthermore, defect separation-which drives chaotic flows in non-rotating active fluids-is suppressed by intrinsic rotation of chiral active particles. We thus establish chirality as a source of dramatic stabilisation in active systems, which could be key in interpreting the collective behaviors of some biological tissues, cytoskeletal systems and collections of bacteria.

Considerations for Imaging and Analyzing Neural Structures by STED Microscopy.

STED microscopy images of live or fixed brain tissue contain a wealth of geometric information about cellular structures down to the scale of individual dendritic spines and axonal structures. To extract such morphological data in a credible way, several considerations regarding image acquisition and analysis must be taken into account. This chapter highlights the parameters of primary importance for acquiring and analyzing STED images and interpreting STED microscopy data.

Fiber plucking by molecular motors yields large emergent contractility in stiff biopolymer networks.

The mechanical properties of the cell depend crucially on the tension of its cytoskeleton, a biopolymer network that is put under stress by active motor proteins. While the fibrous nature of the network is known to strongly affect the transmission of these forces to the cellular scale, our understanding of this process remains incomplete. Here we investigate the transmission of forces through the network at the individual filament level, and show that active forces can be geometrically amplified as a transverse motor-generated force "plucks" the fiber and induces a nonlinear tension. In stiff and densely connected networks, this tension results in large network-wide tensile stresses that far exceed the expectation drawn from a linear elastic theory. This amplification mechanism competes with a recently characterized network-level amplification due to fiber buckling, suggesting that that fiber networks provide several distinct pathways for living systems to amplify their molecular forces.

Stress-dependent amplification of active forces in nonlinear elastic media.

The production of mechanical stresses in living organisms largely relies on localized, force-generating active units embedded in filamentous matrices. Numerical simulations of discrete fiber networks with fixed boundaries have shown that buckling in the matrix dramatically amplifies the resulting active stresses. Here we extend this result to a continuum elastic medium prone to buckling subjected to an arbitrary external stress, and derive analytical expressions for the active, nonlinear constitutive relations characterizing the full active medium. Inserting these relations into popular "active gel" descriptions of living tissues and the cytoskeleton will enable investigations into nonlinear regimes previously inaccessible due to the phenomenological nature of these theories.