TrackMate: An open and extensible platform for single-particle tracking

Small volume platelet concentrates for neonatal use are more susceptible to shear-induced storage lesion

The impact of the biophysical environment on the platelet storage lesion (PSL) has mainly focused on reduced temperature storage, overlooking the significance of storage-induced shear stress. Shear stress in platelet storage refers to the frictional force acting parallel to the bag surface and exists solely through the implementation of agitation. This study investigates whether minimizing exposure to agitation-induced shear stress can alleviate the unexplained loss of function in stored platelet concentrates for neonatal transfusion (neonatal PCs). Using particle tracking analysis, fluid motion was measured in neonatal and adult platelet storage bags under agitation frequencies ranging from 20-60 rpm. Platelets stored at 20-60 rpm agitation over 8 days were examined by biochemical analysis, aggregation, and expression of activation markers. Results indicate that neonatal PCs experience significantly higher storage-induced shear stress compared to adult doses, leading to reduced functionality and increased activation from day 2 of storage. Adjusting the neonatal PC agitation frequency to 20 rpm improved functionality in early storage, while 40 rpm maintains this improvement throughout storage with reduced activation, compared to 60 rpm storage. This study confirms that small volume PC storage for neonatal use contributes to the PSL through the induction of shear stress, suggesting further evaluation of the recommended agitation frequency for neonatal PCs or postponement of the production of neonatal PCs until requested for neonatal transfusion.

Fluorescence microfluidic system for real-time monitoring of PS and PVC sub-micron microplastics under flowing conditions

Plastics, recognized for their convenience, disposability, and recyclability, have emerged as a significant ecological challenge, particularly with the prevalence of microplastics (MPs, 1 μm - 5 mm) and sub-micron MPs (100 - 1000 nm) in natural environments. While extensive research has focused on their occurrence and environmental impacts, quantification methods developed for MPs exhibit limitations when applied to sub-micron MPs due to their smaller size. This study addresses these limitations by introducing a novel monitoring system that integrates fluorescence labeling with a microfluidic device and particle tracking software, enabling automated quantification and size measurement of both spherical and fragmented MPs of size in the sub-micrometer range. Results showed that the developed system enabled fast quantification and size measurement of 500- and 1000-nm polystyrene (PS) sub-micron MP beads and fragmented PS and polyvinyl chloride (PVC) sub-micron MPs. Additionally, fluorescence labeling enabled the real-time discrimination of PS and PVC sub-micron MPs. Lastly, the microfluidic system allowed the monitoring of sub-micron MPs within a small quantity of water samples. This automated system has a high potential for swift and real-time monitoring of sub-micron MPs in the environment. By enhancing our ability to detect and quantify sub-micron MPs, this study contributes to a more comprehensive understanding of their presence and distribution in environmental systems.

Insights into degradation and targeting of the photoreceptor channelrhodopsin-1

In Chlamydomonas, the directly light-gated, plasma membrane-localized cation channels channelrhodopsins ChR1 and ChR2 are the primary photoreceptors for phototaxis. Their targeting and abundance is essential for optimal movement responses. However, our knowledge how Chlamydomonas achieves this is still at its infancy. Here we show that ChR1 internalization occurs via light-stimulated endocytosis. Prior or during endocytosis ChR1 is modified and forms high molecular mass complexes. These are the solely detectable ChR1 forms in extracellular vesicles and their abundance therein dynamically changes upon illumination. The ChR1-containing extracellular vesicles are secreted via the plasma membrane and/or the ciliary base. In line with this, ciliogenesis mutants exhibit increased ChR1 degradation rates. Further, we establish involvement of the cysteine protease CEP1, a member of the papain-type C1A subfamily. ΔCEP1-knockout strains lack light-induced ChR1 degradation, whereas ChR2 degradation was unaffected. Low light stimulates CEP1 expression, which is regulated via phototropin, a SPA1 E3 ubiquitin ligase and cyclic AMP. Further, mutant and inhibitor analyses revealed involvement of the small GTPase ARL11 and SUMOylation in ChR1 targeting to the eyespot and cilia. Our study thus defines the degradation pathway of this central photoreceptor of Chlamydomonas and identifies novel elements involved in its homoeostasis and targeting.

Evaluation of particle tracking codes for dispersing particles in porous media

Particle tracking (PT) is a popular technique in microscopy, microfluidics and colloidal transport studies, where image analysis is used to reconstruct trajectories from bright spots in a video. The performance of many PT algorithms has been rigorously tested for directed and Brownian motion in open media. However, PT is frequently used to track particles in porous media where complex geometries and viscous flows generate particles with high velocity variability over time. Here, we present an evaluation of four PT algorithms for a simulated dispersion of particles in porous media across a range of particle speeds and densities. Of special note, we introduce a new velocity-based PT linking algorithm (V-TrackMat) that achieves high accuracy relative to the other PT algorithms. Our findings underscore that traditional statistics, which revolve around detection and linking proficiency, fall short in providing a holistic comparison of PT codes because they tend to underpenalize aggressive linking techniques. We further elucidate that all codes analyzed show a decrease in performance due to high speeds, particle densities, and trajectory noise. However, linking algorithms designed to harness velocity data show superior performance, especially in the case of high-speed advective motion. Lastly, we emphasize how PT error can influence transport analysis.

cellPLATO - an unsupervised method for identifying cell behaviour in heterogeneous cell trajectory data

Advances in imaging, segmentation and tracking have led to the routine generation of large and complex microscopy datasets. New tools are required to process this 'phenomics' type data. Here, we present 'Cell PLasticity Analysis Tool' (cellPLATO), a Python-based analysis software designed for measurement and classification of cell behaviours based on clustering features of cell morphology and motility. Used after segmentation and tracking, the tool extracts features from each cell per timepoint, using them to segregate cells into dimensionally reduced behavioural subtypes. Resultant cell tracks describe a 'behavioural ID' at each timepoint, and similarity analysis allows the grouping of behavioural sequences into discrete trajectories with assigned IDs. Here, we use cellPLATO to investigate the role of IL-15 in modulating human natural killer (NK) cell migration on ICAM-1 or VCAM-1. We find eight behavioural subsets of NK cells based on their shape and migration dynamics between single timepoints, and four trajectories based on sequences of these behaviours over time. Therefore, by using cellPLATO, we show that IL-15 increases plasticity between cell migration behaviours and that different integrin ligands induce different forms of NK cell migration.

Early Steps of Individual Multireceptor Viral Interactions Dissected by High-Density, Multicolor Quantum Dot Mapping in Living Cells

Viral capture and entry to target cells are the first crucial steps that ultimately lead to viral infection. Understanding these events is essential toward the design and development of suitable antiviral drugs and/or vaccines. Viral capture involves dynamic interactions of the virus with specific receptors in the plasma membrane of the target cells. In the last years, single virus tracking has emerged as a powerful approach to assess real time dynamics of viral processes in living cells and their engagement with specific cellular components. However, direct visualization of the early steps of multireceptor viral interactions at the single level has been largely impeded by the technical challenges associated with imaging individual multimolecular systems at relevant spatial (nanometer) and temporal (millisecond) scales. Here, we present a four-color, high-density quantum dot spatiotemporal mapping methodology to capture real-time interactions between individual virus-like-particles (VLPs) and three different viral (co-) receptors on the membrane of primary living immune cells derived from healthy donors. Together with quantitative tools, our approach revealed the existence of a coordinated spatiotemporal diffusion of the three different (co)receptors prior to viral engagement. By varying the temporal-windows of cumulated single-molecule localizations, we discovered that such a concerted diffusion impacts on the residence time of HIV-1 and SARS-CoV-2 VLPs on the host membrane and potential viral infectivity. Overall, our methodology offers the possibility for systematic analysis of the initial steps of viral-host interactions and could be easily implemented for the investigation of other multimolecular systems at the single-molecule level.

Microvascular Engineering for the Development of a Nonembedded Liver Sinusoid with a Lumen: When Endothelial Cells Do Not Lose Their Edge

Microvascular engineering seeks to exploit known cell-cell and cell-matrix interactions in the context of vasculogenesis to restore homeostasis or disease development of reliable capillary models in vitro. However, current systems generally focus on recapitulating microvessels embedded in thick gels of extracellular matrix, overlooking the significance of discontinuous capillaries, which play a vital role in tissue-blood exchanges particularly in organs like the liver. In this work, we introduce a novel method to stimulate the spontaneous organization of endothelial cells into nonembedded microvessels. By creating an anisotropic micropattern at the edge of a development-like matrix dome using Marangoni flow, we achieved a long, nonrandom orientation of endothelial cells, laying a premise for stable lumenized microvessels. Our findings revealed a distinctive morphogenetic process leading to mature lumenized capillaries, demonstrated with both murine and human immortalized liver sinusoidal endothelial cell lines (LSECs). The progression of cell migration, proliferation, and polarization was clearly guided by the pattern, initiating the formation of a multicellular cord that caused a deformation spanning extensive regions and generated a wave-like folding of the gel, hinged at a laminin-depleted zone, enveloping the cord with gel proteins. This event marked the onset of lumenogenesis, regulated by the gradual apico-basal polarization of the wrapped cells, leading to the maturation of vessel tight junctions, matrix remodeling, and ultimately the formation of a lumen─recapitulating the development of vessels in vivo. Furthermore, we demonstrate that the process strongly relies on the initial gel edge topography, while the geometry of the vessels can be tuned from a curved to a straight structure. We believe that our facile engineering method, guiding an autonomous self-organization of vessels without the need for supporting cells or complex prefabricated scaffolds, holds promise for future integration into microphysiological systems featuring discontinuous, fenestrated capillaries.

All-Optical Trapping and Programmable Transport of Gold Nanorods with Simultaneous Orientation and Spinning Control

Gold nanorods (GNRs) are of special interest in nanotechnology and biomedical applications due to their biocompatibility, anisotropic shape, enhanced surface area, and tunable optical properties. The use of GNRs, for example, as sensors and mechanical actuators, relies on the ability to remotely control their orientation as well as their translational and rotational motion, whether individually or in groups. Achieving such particle control by using optical tools is challenging and exceeds the capabilities of conventional laser tweezers. We present a tool that addresses this complex manipulation problem by using a curve-shaped laser trap, enabling the optical capture and programmable transport of single and multiple GNRs along any trajectory. This type of laser trap combines confinement and propulsion optical forces with optical torque to transport the GNRs while simultaneously controlling their rotation (spinning) and orientation. The proposed system facilitates the light-driven control of GNRs and the quantitative characterization of their motion dynamics including transport speed, spinning frequency, orientation, and confinement strength. We experimentally demonstrate that remote control of the GNRs can be achieved both near a substrate surface (2D trapping) and deep within the sample (3D all-optical trapping). The motion dynamics of two sets of off-resonant GNRs, possessing similar aspect ratios but different resonance wavelengths, are analyzed to highlight the role played by their optical and mechanical properties in the optical manipulation process. The experimental results are supported by a theoretical model describing the observed motion dynamics of the GNRs. This optical manipulation tool can significantly facilitate applications of light-driven nanorods.

Endoplasmic reticulum exit sites are segregated for secretion based on cargo size

TANGO1, TANGO1-Short, and cTAGE5 form stable complexes at the endoplasmic reticulum exit sites (ERES) to preferably export bulky cargoes. Their C-terminal proline-rich domain (PRD) binds Sec23A and affects COPII assembly. The PRD in TANGO1-Short was replaced with light-responsive domains to control its binding to Sec23A in U2OS cells (human osteosarcoma). TANGO1-ShortΔPRD was dispersed in the ER membrane but relocated rapidly, reversibly, to pre-existing ERES by binding to Sec23A upon light activation. Prolonged binding between the two, concentrated ERES in the juxtanuclear region, blocked cargo export and relocated ERGIC53 into the ER, minimally impacting the Golgi complex organization. Bulky collagen VII and endogenous collagen I were collected at less than 47% of the stalled ERES, whereas small cargo molecules were retained uniformly at almost all the ERES. We suggest that ERES are segregated to handle cargoes based on their size, permitting cells to traffic them simultaneously for optimal secretion.

Adapting and optimizing GCaMP8f for use in Caenorhabditis elegans

Improved genetically encoded calcium indicators (GECIs) are essential for capturing intracellular dynamics of both muscle and neurons. A novel set of GECIs with ultrafast kinetics and high sensitivity was recently reported by Zhang et al. (2023). While these indicators, called jGCaMP8, were demonstrated to work in Drosophila and mice, data for Caenorhabditis elegans were not reported. Here, we present an optimized construct for C. elegans and use this to generate several strains expressing GCaMP8f (fast variant of the indicator). Utilizing the myo-2 promoter, we compare pharyngeal muscle activity measured with GCaMP7f and GCaMP8f and find that GCaMP8f is brighter upon binding to calcium, shows faster kinetics, and is not disruptive to the intrinsic contraction dynamics of the pharynx. Additionally, we validate its application for detecting neuronal activity in touch receptor neurons which reveals robust calcium transients even at small stimulus amplitudes. As such, we establish GCaMP8f as a potent tool for C. elegans research which is capable of extracting fast calcium dynamics at very low magnifications across multiple cell types.

Evolutionarily diverse fungal zoospores show contrasting swimming patterns specific to ultrastructure

Zoosporic fungi, also called chytrids, produce single-celled motile spores with flagellar swimming tails (zoospores).1,2 These fungi are key components of aquatic food webs, acting as pathogens, saprotrophs, and prey.3,4,5,6,7,8 Little is known about the swimming behavior of fungal zoospores, a crucial factor governing dispersal, biogeographical range, ecological function, and infection dynamics.6,9 Here, we track the swimming patterns of zoospores from 12 evolutionarily divergent species of zoosporic fungi from across seven orders of the Chytridiomycota and the Blastocladiomycota. We report two major swimming patterns that correlate with the cytoskeletal ultrastructure of these zoospores. Specifically, we show that species without major cytoplasmic tubulin components swim in a circular fashion, while species with prominent cytoplasmic tubulin structures swim in a pattern akin to a random walk (move-stop-redirect-move). We confirm cytoskeletal architecture by performing fluorescence confocal microscopy across all 12 species. We then treat representative species with variant swimming behaviors and cytoplasmic-cytoskeletal arrangements with tubulin-stabilizing (Taxol) and depolymerizing (nocodazole) pharmacological compounds. We observed that when treating the "random walk" species with nocodazole, their swimming behavior changed to a circular-swimming pattern. Confocal imaging of the nocodazole-treated zoospores demonstrates that these cells maintain flagellum tubulin structures but lack their characteristic cytoplasmic tubulin structures. Our data demonstrate that the capability of zoospores to perform "complex" random-walk movement is linked to the presence of prominent cytoplasmic tubulin structures and suggest a link between cytology, sensory systems, and swimming behavior in a diversity of zoosporic fungi.

Fluorescence labeling strategies for cell surface expression of TRPV1

Regulation of ion channel expression on the plasma membrane is a major determinant of neuronal excitability, and identifying the underlying mechanisms of this expression is critical to our understanding of neurons. Here, we present two orthogonal strategies to label extracellular sites of the ion channel TRPV1 that minimally perturb its function. We use the amber codon suppression technique to introduce a non-canonical amino acid (ncAA) with tetrazine click chemistry, compatible with a trans-cyclooctene coupled fluorescent dye. Additionally, by inserting the circularly permutated HaloTag (cpHaloTag) in an extracellular loop of TRPV1, we can incorporate a fluorescent dye of our choosing. Optimization of ncAA insertion sites was accomplished by screening residue positions between the S1 and S2 transmembrane domains with elevated missense variants in the human population. We identified T468 as a rapid labeling site (∼5 min) based on functional and biochemical assays in HEK293T/17 cells. Through adapting linker lengths and backbone placement of cpHaloTag on the extracellular side of TRPV1, we generated a fully functional channel construct, TRPV1exCellHalo, with intact wild-type gating properties. We used TRPV1exCellHalo in a single molecule experiment to track TRPV1 on the cell surface and validate studies that show decreased mobility of the channel upon activation. The application of these extracellular label TRPV1 (exCellTRPV1) constructs to track surface localization of the channel will shed significant light on the mechanisms regulating its expression and provide a general scheme to introduce similar modifications to other cell surface receptors.

Terminal differentiation precedes functional circuit integration in the peduncle neurons in regenerating Hydra vulgaris

Understanding how neural circuits are regenerated following injury is a fundamental question in neuroscience. Hydra is a powerful model for studying this process because it has a simple neural circuit structure, significant and reproducible regenerative abilities, and established methods for creating transgenics with cell-type-specific expression. While Hydra is a long-standing model for regeneration and development, little is known about how neural activity and behavior is restored following significant injury. In this study, we ask if regenerating neurons terminally differentiate prior to reforming functional neural circuits, or if neural circuits regenerate first and then guide the constituent naive cells toward their terminal fate. To address this question, we developed a dual-expression transgenic Hydra line that expresses a cell-type-specific red fluorescent protein (tdTomato) in ec5 peduncle neurons, and a calcium indicator (GCaMP7s) in all neurons. With this transgenic line, we can simultaneously record neural activity and track the reappearance of the terminally-differentiated ec5 neurons. Using SCAPE (Swept Confocally Aligned Planar Excitation) microscopy, we monitored both calcium activity and expression of tdTomato-positive neurons in 3D with single-cell resolution during regeneration of Hydra's aboral end. The synchronized neural activity associated with a regenerated neural circuit was observed approximately 4 to 8 hours after expression of tdTomato in ec5 neurons. These data suggest that regenerating ec5 neurons undergo terminal differentiation prior to re-establishing their functional role in the nervous system. The combination of dynamic imaging of neural activity and gene expression during regeneration make Hydra a powerful model system for understanding the key molecular and functional processes involved in neural regeneration following injury.

Optical tweezing of microparticles and cells using silicon-photonics-based optical phased arrays

Integrated optical tweezers have the potential to enable highly-compact, low-cost, mass-manufactured, and broadly-accessible optical manipulation when compared to standard bulk-optical tweezers. However, integrated demonstrations to date have been fundamentally limited to micron-scale standoff distances and, often, passive trapping functionality, making them incompatible with many existing applications and significantly limiting their utility, especially for biological studies. In this work, we demonstrate optical trapping and tweezing using an integrated OPA for the first time, increasing the standoff distance of integrated optical tweezers by over two orders of magnitude compared to prior demonstrations. First, we demonstrate trapping of polystyrene microspheres 5 mm above the surface of the chip and calibrate the trap force. Next, we show tweezing of polystyrene microspheres in one dimension by non-mechanically steering the trap by varying the input laser wavelength. Finally, we use the OPA tweezers to demonstrate, to the best of our knowledge, the first cell experiments using single-beam integrated optical tweezers, showing controlled deformation of mouse lymphoblast cells. This work introduces a new modality for integrated optical tweezers, significantly expanding their utility and compatibility with existing applications, especially for biological experiments.

Platelet activation near point-like source of agonist: Experimental insights and computational model

Disorders of hemostasis resulting in bleeding or thrombosis are leading cause of mortality in the world. Blood platelets are main players in hemostasis, providing the primary response to the vessel wall injury. In this case, they rapidly switch to the activated state in reaction to the exposed chemical substances such as ADP, collagen and thrombin. Molecular mechanisms of platelet activation are known, and detailed computational models are available. However, they are too complicated for large-scale problems (e.g. simulation of the thrombus growth) where less detailed models are required, which still should take into account the variation of agonist concentration and heterogeneity of platelets. In this paper, we present a simple model of the platelet population response to a spatially inhomogeneous stimulus. First, computational nodes modeling platelets are placed randomly in space. Each platelet is assigned the specific threshold for agonist, which determines whether it becomes activated at a given time. The distribution of the threshold value in a population is assumed to be log-normal. The model was validated against experimental data in a specially designed system, where the photorelease of ADP was caused by localized laser stimulus. In this system, a concentration of ADP obeys 2-dimensional Gaussian distribution which broadens due to the diffusion. The response of platelets to the point-like source of ADP is successfully described by the presented model. Our results advance the understanding of platelet function during hemostatic response. The simulation approach can be incorporated into larger computational models of thrombus formation.

Elucidating siRNA Cellular Delivery Mechanism Mediated by Quaternized Starch Nanoparticles

Starch-based nanoparticles are highly utilized in the realm of drug delivery taking advantage of their biocompatibility and biodegradability. Studies have utilized Quaternized starch (Q-starch) for small interfering RNA (siRNA) delivery, in which quaternary amines enable interaction with negatively charged siRNA, resulting in self-assembly complexation. Although reports present numerous applications, the demonstrated efficacy is nonetheless limited due to undiscovered cellular mechanistic delivery. In this study, a deep dive into Q-starch/siRNA complexes' cellular mechanism and kinetics at the cellular level is revealed using single-particle tracking and cell population level using imaging flow cytometry. Uptake studies depict the efficient cellular internalization via endocytosis while a significant fraction of complexes' intracellular fate is lysosome. Utilizing single-particle tracking, it is found that an average of 15% of cellular detected complexes escape the endosome which holds the potential for the integration in the cytoplasmatic gene silencing mechanism. Additional experimental manipulations (overcoming endosomal escape) demonstrate that the complex's disassembly is the rate-limiting step, correlating Q-starch's structure-function properties as siRNA carrier. Structure-function properties accentuating the high affinity of the interaction between Q-starch's quaternary groups and siRNA's phosphate groups that results in low release efficiency. However, low-frequency ultrasound (20 kHz) application may have induced siRNA release resulting in faster gene silencing kinetics.

Harnessing multifunctional collagen mimetic peptides to create bioinspired stimuli responsive hydrogels for controlled cell culture

The demand for synthetic soft materials with bioinspired structures continues to grow. Material applications range from in vitro and in vivo tissue mimics to therapeutic delivery systems, where well-defined synthetic building blocks offer precise and reproducible property control. This work examines a synthetic assembling peptide, specifically a multifunctional collagen mimetic peptide (mfCMP) either alone or with reactive macromers, for the creation of responsive hydrogels that capture aspects of soft collagen-rich tissues. We first explored how buffer choice impacts mfCMP hierarchical assembly, in particular, peptide melting temperature, fibril morphology, and ability to form physical hydrogels. Assembly in physiologically relevant buffer resulted in collagen-like fibrillar structures and physically assembled hydrogels with shear-thinning (as indicated through strain-yielding) and self-healing properties. Further, we aimed to create fully synthetic, composite peptide-polymer hydrogels with dynamic responses to various stimuli, inspired by the extracellular matrix (ECM). Specifically, we established mfCMP-poly(ethylene glycol) (PEG) hydrogel compositions that demonstrate increasing non-linear viscoelasticity in response to applied strain as the amount of assembled mfCMP content increases. Furthermore, the thermal responsiveness of mfCMP physical crosslinks was harnessed to manipulate the composite hydrogel mechanical properties in response to changes in temperature. Finally, cells relevant in wound healing, human lung fibroblasts, were encapsulated within these peptide-polymer hydrogels to explore the impact of increased mfCMP, and the resulting changes in viscoelasticity, on cell response. This work establishes mfCMP building blocks as versatile tools for creating hybrid and adaptable systems with applications ranging from injectable shear-thinning materials to responsive interfaces and synthetic ECMs for tissue engineering.

Rapid homologue juxtaposition during meiotic chromosome pairing

A central feature of meiosis is the pairing of homologous maternal and paternal chromosomes ('homologues') along their lengths1-3. Recognition between homologues and their juxtaposition in space is mediated by axis-associated recombination complexes. Also, pairing must occur without entanglements among unrelated chromosomes. Here we examine homologue juxtaposition in real time by four-dimensional fluorescence imaging of tagged chromosomal loci at high spatio-temporal resolution in budding yeast. We discover that corresponding loci come together from a substantial distance (1.8 µm) and complete pairing in a very short time, about 6 min (thus, rapid homologue juxtaposition or RHJ). Homologue loci first move rapidly together (in 30 s, at speeds of roughly 60 nm s-1) into an intermediate stage corresponding to canonical 400 nm axis coalignment. After a short pause, crossover/non-crossover differentiation (crossover interference) mediates a second short, rapid transition that ultimately gives close pairing of axes at 100 nm by means of synaptonemal complex formation. Furthermore, RHJ (1) occurs after chromosomes acquire prophase chromosome organization, (2) is nearly synchronous over thirds of chromosome lengths, but (3) is asynchronous throughout the genome. Finally, cytoskeleton-mediated movement is important for the timing and distance of RHJ onset and for ensuring its normal progression. General implications for local and global aspects of pairing are discussed.

Scaling Transition of Active Turbulence from Two to Three Dimensions

Turbulent flows are observed in low-Reynolds active fluids, which display similar phenomenology to the classical inertial turbulence but are of a different nature. Understanding the dependence of this new type of turbulence on dimensionality is a fundamental challenge in non-equilibrium physics. Real-space structures and kinetic energy spectra of bacterial turbulence are experimentally measured from two to three dimensions. The turbulence shows three regimes separated by two critical confinement heights, resulting from the competition of bacterial length, vortex size and confinement height. Meanwhile, the kinetic energy spectra display distinct universal scaling laws in quasi-2D and 3D regimes, independent of bacterial activity, length, and confinement height, whereas scaling exponents transition in two steps around the critical heights. The scaling behaviors are well captured by the hydrodynamic model we develop, which employs image systems to represent the effects of confining boundaries. The study suggests a framework for investigating the effect of dimensionality on non-equilibrium self-organized systems.

Aggregation of adult parasitic nematodes in sex-mixed groups analysed by transient anomalous diffusion formalism

Intestinal parasitic worms are widespread throughout the world, causing chronic infections in humans and animals. However, very little is known about the locomotion of the worms in the host gut. We studied the movement of Heligmosomoides bakeri, naturally infecting mice, and used as an animal model for roundworm infections. We investigated the locomotion of H. bakeri in simplified environments mimicking key physical features of the intestinal lumen, i.e. medium viscosity and intestinal villi topology. We found that the motion sequence of these nematodes is non-periodic, but the migration could be described by transient anomalous diffusion. Aggregation as a result of biased, enhanced-diffusive locomotion of nematodes in sex-mixed groups was detected. This locomotion is probably stimulated by mating and reproduction, while single nematodes move randomly (diffusive). Natural physical obstacles such as high mucus-like viscosity or villi topology slowed down but did not entirely prevent nematode aggregation. Additionally, the mean displacement rate of nematodes in sex-mixed groups of 3.0 × 10-3 mm s-1 in a mucus-like medium is in good agreement with estimates of migration velocities of 10-4 to 10-3 mm s-1 in the gut. Our data indicate H. bakeri motion to be non-periodic and their migration random (diffusive-like), but triggerable by the presence of kin.

Reduction of endocytosis and EGFR signaling is associated with the switch from isolated to clustered apoptosis during epithelial tissue remodeling in Drosophila

Epithelial tissues undergo cell turnover both during development and for homeostatic maintenance. Removal of cells is coordinated with the increase in number of newly dividing cells to maintain barrier function of the tissue. In Drosophila metamorphosis, larval epidermal cells (LECs) are replaced by adult precursor cells called histoblasts. Removal of LECs must counterbalance the exponentially increasing adult histoblasts. Previous work showed that the LEC removal accelerates as endocytic activity decreases throughout all LECs. Here, we show that the acceleration is accompanied by a mode switching from isolated single-cell apoptosis to clustered ones induced by the endocytic activity reduction. We identify the epidermal growth factor receptor (EGFR) pathway via extracellular-signal regulated kinase (ERK) activity as the main components downstream of endocytic activity in LECs. The reduced ERK activity, caused by the decrease in endocytic activity, is responsible for the apoptotic mode switching. Initially, ERK is transiently activated in normal LECs surrounding a single apoptotic LEC in a ligand-dependent manner, preventing clustered cell death. Following the reduction of endocytic activity, LEC apoptosis events do not provoke these transient ERK up-regulations, resulting in the acceleration of the cell elimination rate by frequent clustered apoptosis. These findings contrasted with the common perspective that clustered apoptosis is disadvantageous. Instead, switching to clustered apoptosis is required to accommodate the growth of neighboring tissues.

Cell dynamics revealed by microscopy advances

Cell biology emerges from spatiotemporally coordinated molecular processes. Recent advances in live-cell microscopy, fueled by a surge in optical, molecular, and computational technologies, have enabled dynamic observations from single molecules to whole organisms. Despite technological leaps, there is still an untapped opportunity to fully leverage their capabilities toward biological insight. We highlight how single-molecule imaging has transformed our understanding of biological processes, with a focus on chromatin organization and transcription in the nucleus. We describe how this was enabled by the close integration of new imaging techniques with analysis tools and discuss the challenges to make a comparable impact at larger scales from organelles to organisms. By highlighting recent successful examples, we describe an outlook of ever-increasing data and the need for seamless integration between dataset visualization and quantification to realize the full potential warranted by advances in new imaging technologies.

Clathrin-associated carriers enable recycling through a kiss-and-run mechanism

Endocytosis and recycling control the uptake and retrieval of various materials, including membrane proteins and lipids, in all eukaryotic cells. These processes are crucial for cell growth, organization, function and environmental communication. However, the mechanisms underlying efficient, fast endocytic recycling remain poorly understood. Here, by utilizing a biosensor and imaging-based screening, we uncover a recycling mechanism that couples endocytosis and fast recycling, which we name the clathrin-associated fast endosomal recycling pathway (CARP). Clathrin-associated tubulovesicular carriers containing clathrin, AP1, Arf1, Rab1 and Rab11, while lacking the multimeric retrieval complexes, are generated at subdomains of early endosomes and then transported along actin to cell surfaces. Unexpectedly, the clathrin-associated recycling carriers undergo partial fusion with the plasma membrane. Subsequently, they are released from the membrane by dynamin and re-enter cells. Multiple receptors utilize and modulate CARP for fast recycling following endocytosis. Thus, CARP represents a previously unrecognized endocytic recycling mechanism with kiss-and-run membrane fusion.

Multi-detector fusion and Bayesian smoothing for tracking viral and chromatin structures

Automatic tracking of viral and intracellular structures displayed as spots with varying sizes in fluorescence microscopy images is an important task to quantify cellular processes. We propose a novel probabilistic tracking approach for multiple particle tracking based on multi-detector and multi-scale data fusion as well as Bayesian smoothing. The approach integrates results from multiple detectors using a novel intensity-based covariance intersection method which takes into account information about the image intensities, positions, and uncertainties. The method ensures a consistent estimate of multiple fused particle detections and does not require an optimization step. Our probabilistic tracking approach performs data fusion of detections from classical and deep learning methods as well as exploits single-scale and multi-scale detections. In addition, we use Bayesian smoothing to fuse information of predictions from both past and future time points. We evaluated our approach using image data of the Particle Tracking Challenge and achieved state-of-the-art results or outperformed previous methods. Our method was also assessed on challenging live cell fluorescence microscopy image data of viral and cellular proteins expressed in hepatitis C virus-infected cells and chromatin structures in non-infected cells, acquired at different spatial-temporal resolutions. We found that the proposed approach outperforms existing methods.

The biology and chemistry of a mutualism between a soil bacterium and a mycorrhizal fungus

Arbuscular mycorrhizal (AM) fungi (e.g., Rhizophagus species) recruit specific bacterial species in their hyphosphere. However, the chemical interplay and the mutual benefit of this intricate partnership have not been investigated yet, especially as it involves bacteria known as strong producers of antifungal compounds such as Bacillus velezensis. Here, we show that the soil-dwelling B. velezensis migrates along the hyphal network of the AM fungus R. irregularis, forming biofilms and inducing cytoplasmic flow in the AM fungus that contributes to host plant root colonization by the bacterium. During hyphosphere colonization, R. irregularis modulates the biosynthesis of specialized metabolites in B. velezensis to ensure stable coexistence and as a mechanism to ward off mycoparasitic fungi and bacteria. These mutual benefits are extended into a tripartite context via the provision of enhanced protection to the host plant through the induction of systemic resistance.

Dual regulation of IP3 receptors by IP3 and PIP2 controls the transition from local to global Ca2+ signals

The spatial organization of inositol 1,4,5-trisphosphate (IP3)-evoked Ca2+ signals underlies their versatility. Low stimulus intensities evoke Ca2+ puffs, localized Ca2+ signals arising from a few IP3 receptors (IP3Rs) within a cluster tethered beneath the plasma membrane. More intense stimulation evokes global Ca2+ signals. Ca2+ signals propagate regeneratively as the Ca2+ released stimulates more IP3Rs. How is this potentially explosive mechanism constrained to allow local Ca2+ signaling? We developed methods that allow IP3 produced after G-protein coupled receptor (GPCR) activation to be intercepted and replaced by flash photolysis of a caged analog of IP3. We find that phosphatidylinositol 4,5-bisphosphate (PIP2) primes IP3Rs to respond by partially occupying their IP3-binding sites. As GPCRs stimulate IP3 formation, they also deplete PIP2, relieving the priming stimulus. Loss of PIP2 resets IP3R sensitivity and delays the transition from local to global Ca2+ signals. Dual regulation of IP3Rs by PIP2 and IP3 through GPCRs controls the transition from local to global Ca2+ signals.

Mitochondrial protein heterogeneity stems from the stochastic nature of co-translational protein targeting in cell senescence

A decline in mitochondrial function is a hallmark of aging and neurodegenerative diseases. It has been proposed that changes in mitochondrial morphology, including fragmentation of the tubular mitochondrial network, can lead to mitochondrial dysfunction, yet the mechanism of this loss of function is unclear. Most proteins contained within mitochondria are nuclear-encoded and must be properly targeted to the mitochondria. Here, we report that sustained mRNA localization and co-translational protein delivery leads to a heterogeneous protein distribution across fragmented mitochondria. We find that age-induced mitochondrial fragmentation drives a substantial increase in protein expression noise across fragments. Using a translational kinetic and molecular diffusion model, we find that protein expression noise is explained by the nature of stochastic compartmentalization and that co-translational protein delivery is the main contributor to increased heterogeneity. We observed that cells primarily reduce the variability in protein distribution by utilizing mitochondrial fission-fusion processes rather than relying on the mitophagy pathway. Furthermore, we are able to reduce the heterogeneity of the protein distribution by inhibiting co-translational protein targeting. This research lays the framework for a better understanding of the detrimental impact of mitochondrial fragmentation on the physiology of cells in aging and disease.

Low-affinity ligands of the epidermal growth factor receptor are long-range signal transmitters during collective cell migration of epithelial cells

Epidermal growth factor receptor ligands (EGFRLs) consist of seven proteins. In stark contrast to the amassed knowledge concerning the epidermal growth factor receptors themselves, the extracellular dynamics of individual EGFRLs remain elusive. Here, employing fluorescent probes and a tool for triggering ectodomain shedding of EGFRLs, we show that EREG, a low-affinity EGFRL, exhibits the most rapid and efficient activation of EGFR in confluent epithelial cells and mouse epidermis. In Madin-Darby canine kidney (MDCK) renal epithelial cells, EGFR- and ERK-activation waves propagate during collective cell migration in an ADAM17 sheddase- and EGFRL-dependent manner. Upon induction of EGFRL shedding, radial ERK activation waves were observed in the surrounding receiver cells. Notably, the low-affinity ligands EREG and AREG mediated faster and broader ERK waves than the high-affinity ligands. The integrity of tight/adherens junctions was essential for the propagation of ERK activation, implying that the tight intercellular spaces prefer the low-affinity EGFRL to the high-affinity ligands for efficient signal transmission. To validate this observation in vivo , we generated EREG-deficient mice expressing the ERK biosensor and found that ERK wave propagation and cell migration were impaired during skin wound repair. In conclusion, we have quantitatively demonstrated the distinctions among EGFRLs in shedding, diffusion, and target cell activation in physiological contexts. Our findings underscore the pivotal role of low-affinity EGFRLs in rapid intercellular signal transmission.

Calcium dynamics of skin-resident macrophages during homeostasis and tissue injury

Immune cells depend on rapid changes in intracellular calcium activity to modulate cell function. Skin contains diverse immune cell types and is critically dependent on calcium signaling for homeostasis and repair, yet the dynamics and functions of calcium in skin immune cells remain poorly understood. Here, we characterize calcium activity in Langerhans cells, skin-resident macrophages responsible for surveillance and clearance of cellular debris after tissue damage. Langerhans cells reside in the epidermis and extend dynamic dendrites in close proximity to adjacent keratinocytes and somatosensory peripheral axons. We find that homeostatic Langerhans cells exhibit spontaneous and transient changes in calcium activity, with calcium flux occurring primarily in the cell body and rarely in the dendrites. Triggering somatosensory axon degeneration increases the frequency of calcium activity in Langerhans cell dendrites. By contrast, we show that Langerhans cells exhibit a sustained increase in intracellular calcium following engulfment of damaged keratinocytes. Altering intracellular calcium activity leads to a decrease in engulfment efficiency of keratinocyte debris. Our findings demonstrate that Langerhans cells exhibit context-specific changes in calcium activity and highlight the utility of skin as an accessible model for imaging calcium dynamics in tissue-resident macrophages.

The chlamydial transcriptional regulator Euo is a key switch in cell form developmental progression but is not involved in the committed step to the formation of the infectious form

Bacteria in the genus Chlamydia are a significant health burden worldwide. They infect a wide range of vertebrate animals, including humans and domesticated animals. In humans, C. psittaci can cause zoonotic pneumonia, while C. pneumoniae causes a variety of respiratory infections. Infections with C. trachomatis cause ocular or genital infections. All chlamydial species are obligate intracellular bacteria that replicate exclusively inside of eukaryotic host cells. Chlamydial infections are dependent on a complex infection cycle that depends on transitions between specific cell forms. This cycle consists of cell forms specialized for host cell invasion, the elementary body (EB), and a form specialized for intracellular replication, the reticulate body (RB). In addition to the EB and RB, there is a transitionary cell form that mediates the transformation between the RB and the EB, the intermediate body (IB). In this study, we ectopically expressed the regulatory protein Euo and showed that high levels of expression resulted in reversible arrest of the development cycle. The arrested chlamydial cells were trapped phenotypically at an early IB stage of the cycle. These cells had exited the cell cycle but had not shifted gene expression from RB like to IB/EB like. This arrested state was dependent on continued expression of Euo. When ectopic expression was reversed, Euo levels dropped in the arrested cells which led to the repression of native Euo expression and the resumption of the developmental cycle. Our data are consistent with a model where Euo expression levels impact IB maturation to the infectious EB but not the production of the IB form.

IMPORTANCE

Bacterial species in the Chlamydiales order infect a variety of vertebrate animals and are a global health concern. They cause various diseases in humans, including genital and respiratory infections. The bacteria are obligate intracellular parasites that rely on a complex infectious cycle involving multiple cell forms. All species share the same life cycle, transitioning through different states to form the infectious elementary body (EB) to spread infections to new hosts. The Euo gene, encoding a DNA-binding protein, is involved in regulating this cycle. This study showed that ectopic expression of Euo halted the cycle at an early stage. This arrest depended on continued Euo expression. When Euo expression was reversed, the developmental cycle resumed. Additionally, this study suggests that high levels of Euo expression affect the formation of the infectious EB but not the production of the cell form committed to EB formation.

Differential roles of kinetic on- and off-rates in T-cell receptor signal integration revealed with a modified Fab'-DNA ligand

Antibody-derived T-cell receptor (TCR) agonists are commonly used to activate T cells. While antibodies can trigger TCRs regardless of clonotype, they bypass native T cell signal integration mechanisms that rely on monovalent, membrane-associated, and relatively weakly binding ligand in the context of cellular adhesion. Commonly used antibodies and their derivatives bind much more strongly than native peptide major histocompatibility complex (pMHC) ligands bind their cognate TCRs. Because ligand dwell time is a critical parameter that tightly correlates with physiological function of the TCR signaling system, there is a general need, both in research and therapeutics, for universal TCR ligands with controlled kinetic binding parameters. To this end, we have introduced point mutations into recombinantly expressed α-TCRβ H57 Fab to modulate the dwell time of monovalent Fab binding to TCR. When tethered to a supported lipid bilayer via DNA complementation, these monovalent Fab'-DNA ligands activate T cells with potencies well-correlated with their TCR binding dwell time. Single-molecule tracking studies in live T cells reveal that individual binding events between Fab'-DNA ligands and TCRs elicit local signaling responses closely resembling native pMHC. The unique combination of high on- and off-rates of the H57 R97L mutant enables direct observations of cooperative interplay between ligand binding and TCR-proximal condensation of the linker for activation of T cells, which is not readily visualized with pMHC. This work provides insights into how T cells integrate kinetic information from TCR ligands and introduces a method to develop affinity panels for polyclonal T cells, such as cells from a human patient.

Diffusion Coefficients of Coated Plasmonic Nanoparticles in Viscous Environment

The Stokes-Einstein relationship (SER) is not valid anymore in polymeric solutions for nanoparticles. It is thus important to characterize their diffusion properties to get a finer understanding of their behavior and to better tune their attributes for biomedical applications. The diffusion of gold and silver nanoparticles with citrate, hyaluronic acid, methyl-polyethylene glycol, and antibody-polyethylene glycol coatings is studied in hyaluronic-based viscous solutions. The diffusion coefficient D is estimated from the Brownian motion thanks to a cost-effective side-illumination device. It is determined that the nanoparticles (hydrodynamic radius rh: 30-135 nm) diffuse up to 4-5 times faster than expected using the SER with a macroscopic viscosity from 1 to 30 mPa·s. It is shown that the adapted Huggins equation is a good model to describe the diffusion behavior of nanoparticles using an effective viscosity ηeff given byl n ( η e f f η s ) = k ( R e f f E ) a $ln\ ( {\frac{{{{\eta }_{eff}}}}{{{{\eta }_s}}}} ) = \ k{{( {\ \frac{{{{R}_{eff}}}}{E}} )}^a}$ whereR e f f - 2 = r h - 2 + R h - 2 $R_{eff}^{ - 2} = r_h^{ - 2}\ + R_h^{ - 2}$ where E is the polymer correlation length, Rh the polymer hydrodynamic radius and ηs the solvent viscosity. The values of k and a are given and allow to obtain D with an error of 10-20%. The impact of chemical interactions on the model parameter values are also highlighted, especially due to electrostatic interactions between the polymer and the nanoparticles.

The surface interface and swimming motility influence surface-sensing responses in Pseudomonas aeruginosa

Bacterial biofilms have been implicated in several chronic infections. After initial attachment, a critical first step in biofilm formation is a cell inducing a surface-sensing response. In the Gram-negative opportunistic pathogen Pseudomonas aeruginosa, two second messengers, cyclic diguanylate monophosphate (c-di-GMP) and cyclic adenosine monophosphate (cAMP), are produced by different surface-sensing mechanisms. However, given the disparate cellular behaviors regulated by these second messengers, how newly attached cells coordinate these pathways remains unclear. Some of the uncertainty relates to studies using different strains, experimental systems, and usually focusing on a single second messenger. In this study, we developed a tricolor reporter system to simultaneously gauge c-di-GMP and cAMP levels in single cells. Using PAO1, we show that c-di-GMP and cAMP are selectively activated in two commonly used experimental systems to study surface sensing. By further examining the conditions that differentiate a c-di-GMP or cAMP response, we demonstrate that an agarose-air interface activates cAMP signaling through type IV pili and the Pil-Chp system. However, a liquid-agarose interface favors the activation of c-di-GMP signaling. This response is dependent on flagellar motility and correlated with higher swimming speed. Collectively, this work indicates that c-di-GMP and cAMP signaling responses are dependent on the surface context.

Deep learning for rapid analysis of cell divisions in vivo during epithelial morphogenesis and repair

Cell division is fundamental to all healthy tissue growth, as well as being rate-limiting in the tissue repair response to wounding and during cancer progression. However, the role that cell divisions play in tissue growth is a collective one, requiring the integration of many individual cell division events. It is particularly difficult to accurately detect and quantify multiple features of large numbers of cell divisions (including their spatio-temporal synchronicity and orientation) over extended periods of time. It would thus be advantageous to perform such analyses in an automated fashion, which can naturally be enabled using deep learning. Hence, we develop a pipeline of deep learning models that accurately identify dividing cells in time-lapse movies of epithelial tissues in vivo. Our pipeline also determines their axis of division orientation, as well as their shape changes before and after division. This strategy enables us to analyse the dynamic profile of cell divisions within the Drosophila pupal wing epithelium, both as it undergoes developmental morphogenesis and as it repairs following laser wounding. We show that the division axis is biased according to lines of tissue tension and that wounding triggers a synchronised (but not oriented) burst of cell divisions back from the leading edge.

The impacts of hypertonic conditions on Drosophila larval cool cells

Drosophila melanogaster exhibits multiple highly sophisticated temperature-sensing systems, enabling its effective response and navigation to temperature changes. Previous research has identified three dorsal organ cool cells (DOCCs) in fly larvae, consisting of two A-type and one B-type cell with distinct calcium dynamics. When subjected to hypertonic conditions, calcium imaging shows that A-type DOCCs maintain their responses to cool temperatures. In contrast, a subset of B-type DOCCs does not exhibit detectable GCaMP baseline signals, and the remaining detectable B-type DOCCs exhibit reduced temperature responses. The activation of both A-type and B-type DOCCs depends on the same members of the ionotropic receptor (IR) family: IR21a, IR93a, and IR25a. A-type DOCCs exhibit a higher somal level of IR93a than B-type DOCCs. Overexpression of Ir93a restores B-type calcium responses to cool temperatures, but not the proportion of B-type cells with a detectable GCaMP baseline, in a hypertonic environment, suggesting a selective role of IR93a in maintaining the temperature responses under hypertonic conditions. Our findings identify a novel function of B-type DOCCs in integrating temperature and tonic stimuli.

Gliding motility of the diatom Craspedostauros australis coincides with the intracellular movement of raphid-specific myosins

Raphid diatoms are one of the few eukaryotes capable of gliding motility, which is remarkably fast and allows for quasi-instantaneous directional reversals. Besides other mechanistic models, it has been suggested that an actomyosin system provides the force for diatom gliding. However, in vivo data on the dynamics of actin and myosin in diatoms are lacking. In this study, we demonstrate that the raphe-associated actin bundles required for diatom movement do not exhibit a directional turnover of subunits and thus their dynamics do not contribute directly to force generation. By phylogenomic analysis, we identified four raphid diatom-specific myosins in Craspedostauros australis (CaMyo51A-D) and investigated their in vivo localization and dynamics through GFP-tagging. Only CaMyo51B-D but not CaMyo51A exhibited coordinated movement during gliding, consistent with a role in force generation. The characterization of raphid diatom-specific myosins lays the foundation for unraveling the molecular mechanisms that underlie the gliding motility of diatoms.

Mechanical Profiling of Biopolymer Condensates through Acoustic Trapping

Characterizing the mechanical properties of single colloids is a central problem in soft matter physics. It also plays a key role in cell biology through biopolymer condensates, which function as membraneless compartments. Such systems can also malfunction, leading to the onset of a number of diseases, including many neurodegenerative diseases; the functional and pathological condensates are commonly differentiated by their mechanical signature. Probing the mechanical properties of biopolymer condensates at the single particle level has, however, remained challenging. In this study, we demonstrate that acoustic trapping can be used to profile the mechanical properties of single condensates in a contactless manner. We find that acoustic fields exert the acoustic radiation force on condensates, leading to their migration to a trapping point where acoustic potential energy is minimized. Furthermore, our results show that the Brownian motion fluctuation of condensates in an acoustic potential well is an accurate probe for their bulk modulus. We demonstrate that this framework can detect the change in the bulk modulus of polyadenylic acid condensates in response to changes in environmental conditions. Our results show that acoustic trapping opens up a novel path to profile the mechanical properties of soft colloids at the single particle level in a non-invasive manner with applications in biology, materials science, and beyond.

Condensate interfacial forces reposition DNA loci and probe chromatin viscoelasticity

Biomolecular condensates assemble in living cells through phase separation and related phase transitions. An underappreciated feature of these dynamic molecular assemblies is that they form interfaces with other cellular structures, including membranes, cytoskeleton, DNA and RNA, and other membraneless compartments. These interfaces are expected to give rise to capillary forces, but there are few ways of quantifying and harnessing these forces in living cells. Here, we introduce viscoelastic chromatin tethering and organization (VECTOR), which uses light-inducible biomolecular condensates to generate capillary forces at targeted DNA loci. VECTOR can be utilized to programmably reposition genomic loci on a timescale of seconds to minutes, quantitatively revealing local heterogeneity in the viscoelastic material properties of chromatin. These synthetic condensates are built from components that naturally form liquid-like structures in living cells, highlighting the potential role for native condensates to generate forces and do work to reorganize the genome and impact chromatin architecture.

Dynamics of Snowflakes Impacting Superhydrophobic Surfaces

Snow and ice accumulation on surfaces presents significant safety and efficiency challenges across various industries, necessitating the development of effective mitigation strategies. In this study, the dynamics and energy dissipation of natural snowflakes impacting superhydrophobic surfaces (SHS) were explored using high-speed imaging and a novel image processing method. The size, velocity (impact and bounce), and contact time of natural wet snowflakes were quantitatively analyzed, identifying two primary impact outcomes: bouncing and fragmentation. The analysis focused on bouncing to study the coefficient of restitution (COR) of snowflakes. It was found that small snowflakes (<1.40 mm in diameter) with low impact velocities (<2.90 m/s) tend to be bounced, whereas larger, faster snowflakes are more likely to be fragmented. For the first time, the contact time of natural snowflakes on SHS was also reported, introducing a dimensionless contact time (DCT) for quantifying energy dissipation during the impact. The results indicate that energy dissipation has a cubic relationship with snowflake size and a quadratic relationship with its impact velocity, demonstrating that larger and faster snowflakes dissipate more energy. It is observed that a reduction in DCT leads to an exponential increase in COR and a decrease in normalized energy dissipation, supporting the theoretical prediction that the COR approaches one and the normalized energy dissipation approaches zero as the DCT approaches zero. These results are significant for enhancing the design and efficiency of anti-icing surfaces, contributing to the development of models that simulate snow accumulation behaviors and inform better design of both active and passive snow mitigation strategies.

Dedifferentiation- and aging-induced loss of mechanical contractility and polarity in vascular smooth muscle cells: Heterogeneous changes in macroscopic and microscopic behavior of cells in serial passage culture

Dedifferentiation and aging of vascular smooth muscle cells (VSMCs) are associated with serious vascular diseases, such as arteriosclerosis and aneurysm. However, how cell dedifferentiation and aging affect cellular mechanical behaviors at the single-cell and intracellular structure levels remains unclear. An in-depth understanding of these interactions is extremely important for understanding the mechanism underlying VSMC mechanical integrity and homeostatic regulation of vascular walls. Herein, we systematically investigated changes in VSMC morphology, structure, contractility, and motility during dedifferentiation and aging induced by serial passage culture using traction force microscopy with elastic micropillar substrates, laser nanodissection of cytoskeletons, confocal fluorescence microscopy, and atomic force microscopy. We found that VSMC dedifferentiation started in the middle stage of serial passage culture, accompanied by a transient cell spreading in the cell width and decrease in contractile protein expression. Dedifferentiated VSMCs showed a significant decrease in the contraction and stiffness of individual actin stress fibers; however, their overall cell traction forces were maintained. Simultaneously, a significant increase in cell motility and the number of actin fibers was observed in dedifferentiated VSMCs, which may be associated with the enhancement of cell migration and disruption of cell/tissue integrity during the early stage of vascular diseases. As cell senescence progressed in the later stage of serial passage culture, VSMCs displayed reduced cell spreading and migration with decrease in the overall cell traction forces and drastic reduction in mechanical polarity of cell structures and forces. These results suggested that cell senescence causes loss of mechanical contractility and polarity in VSMCs, which may be an important factor in vascular disease progression. The experimental systems established in this study can be powerful tools for understanding the mechanisms underlying cellular dedifferentiation and aging from a biomechanical perspective.

Aspergillus fumigatus-derived gliotoxin impacts innate immune cell activation through modulating lipid mediator production in macrophages

Gliotoxin (GT), a secondary metabolite and virulence factor of the fungal pathogen Aspergillus fumigatus, suppresses innate immunity and supports the suppression of host immune responses. Recently, we revealed that GT blocks the formation of the chemotactic lipid mediator leukotriene (LT)B4 in activated human neutrophils and monocytes, and in rodents in vivo, by directly inhibiting LTA4 hydrolase. Here, we elucidated the impact of GT on LTB4 biosynthesis and the entire lipid mediator networks in human M1- and M2-like monocyte-derived macrophages (MDMs) and in human tissue-resident alveolar macrophages. In activated M1-MDMs with high capacities to generate LTs, the formation of LTB4 was effectively suppressed by GT, connected to attenuated macrophage phagocytic activity as well as human neutrophil movement and migration. In resting macrophages, especially in M1-MDMs, GT elicited strong formation of prostaglandins, while bacterial exotoxins from Staphylococcus aureus evoked a broad spectrum of lipid mediator biosynthesis in both MDM phenotypes. We conclude that GT impairs functions of activated innate immune cells through selective suppression of LTB4 biosynthesis, while GT may also prime the immune system by provoking prostaglandin formation in macrophages.

Transcranial focused ultrasound stimulation enhances cerebrospinal fluid movement: Real-time in vivo two-photon and widefield imaging evidence

BACKGROUND

Cerebrospinal fluid (CSF) flow is crucial for brain homeostasis and its dysfunction is highly associated with neurodegenerative diseases. Restoring CSF circulation is proposed as a key strategy for the treatment of the diseases. Among the methods to improve CSF circulation, focused ultrasound (FUS) stimulation has emerged as a promising non-invasive brain stimulation technique, with effectiveness evidenced by ex vivo studies. However, due to technical disturbances in in vivo imaging combined with FUS, direct evidence of real-time in vivo CSF flow enhancement by FUS remains elusive.

OBJECTIVE

To investigate whether FUS administered through the skull base can enhance CSF influx in living animals with various real-time imaging techniques.

METHODS

We demonstrate a novel method of applying FUS through the skull base, facilitating cortical CSF influx, evidenced by diverse in vivo imaging techniques. Acoustic simulation confirmed effective sonication of our approach through the skull base. After injecting fluorescent CSF tracers into cisterna magna, FUS was administered at the midline of the jaw through the skull base for 30 min, during which imaging was performed concurrently.

RESULTS

Enhanced CSF influx was observed in macroscopic imaging, demonstrated by the influx area and intensity of the fluorescent dyes after FUS. In two-photon imaging, increased fluorescence was observed in the perivascular space (PVS) after stimulation. Moreover, particle tracking of microspheres showed more microspheres entering the imaging field, with increased mean speed after FUS.

CONCLUSION

Our findings provide direct real-time in vivo imaging evidence that FUS promotes CSF influx and flow in the PVS.

Investigating recovery after a spontaneous intracerebral haemorrhage in zebrafish larvae

Intracerebral haemorrhage is a debilitating stroke sub-type with high morbidity and mortality rates. For survivors, rehabilitation is a long process, and with no available therapeutics to limit the immediate pathophysiology of the haemorrhage, recovery is dependent on individual neuroplasticity. We have previously shown that zebrafish larvae can be used to model spontaneous brain haemorrhage. Zebrafish exhibit innate recovery mechanisms and are often used as a model system for investigation into regeneration after injury, including injury to the nervous system. Here, we investigate the spontaneous and immediate recovery in zebrafish larvae following an intracerebral haemorrhage at 2 days post-fertilisation, during pre-protected stages and over the first 3 weeks of life. We have shown that following the onset of bleed at ∼2 days post-fertilisation zebrafish are capable of clearing the haematoma through the ventricles. Brain cell damage associated with intracerebral haemorrhage is resolved within 48 h, and this recovery is associated with survival rates equal to wildtype and non-haemorrhaged sibling control animals. Larvae express more nestin-positive neural progenitor cells 24 h after injury when the most damage is observed, and through mass spectrometry analysis, we have determined that these cells are highly proliferative and may specially differentiate into oligodendrocytes. This study provides an insight into the haematoma resolution processes in a live, intact organism, and may suggest potential therapeutic approaches to support the recovery of intracerebral haemorrhage patients.

Swashing motility: A novel propulsion-independent mechanism for surface migration in Salmonella and E. coli

Bacterial motility over surfaces is crucial for colonization, biofilm formation, and pathogenicity. Surface motility in Escherichia coli and Salmonella enterica is traditionally believed to rely on flagellar propulsion. Here, we report a novel mode of motility, termed "swashing," where these bacteria migrate on agar surfaces without functional flagella. Mutants lacking flagellar filaments and motility proteins exhibit rapid surface migration comparable to wild-type strains. Unlike previously described sliding motility, swashing is inhibited by surfactants and requires fermentable sugars. We propose that the fermentation of sugars at the colony edge produces osmolytes, creating local osmotic gradients that draw water from the agar, forming a fluid bulge that propels the colony forward. Our findings challenge the established view that flagellar propulsion is required for surface motility in E. coli and Salmonella, and highlight the role of a fermentation in facilitating bacterial spreading. This discovery expands our understanding of bacterial motility, offering new insights into bacterial adaptive strategies in diverse environments.

Anomalous relaxation of coarsening foams with viscoelastic continuous phases

We investigate the ultraslow structural relaxation of ageing foams with rheologically tunable continuous phases. We probe the bubble dynamics associated with pressure-driven foam coarsening using differential dynamic microscopy, which allows characterising the sample dynamics in reciprocal space with imaging experiments. Similar to other out-of-equilibrium jammed soft systems, these foams exhibit compressed exponential relaxations, with a ballistic-like linear dependency of the relaxation rate on the scattering wavevector. By tuning the rheology of the continuous phase, we observe changes in the relaxation shape, where stiffer matrices yield larger compression exponents. Our results corroborate recent real-space observations obtained using bubble tracking, providing a comprehensive overview of structural relaxation in these complex systems, both in direct and reciprocal space.

SARS-CoV-2 spike fusion peptide trans interaction with phosphatidylserine lipid triggers membrane fusion for viral entry

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the fusion machine for host cell entry. Still, the mechanism by which spike protein interacts with the target lipid membrane to facilitate membrane fusion during entry is not fully understood. Here, using steady-state membrane fusion and single-molecule fluorescence resonance energy transfer imaging of spike trimers on the surface of SARS-CoV-2 pseudovirion, we directly show that spike protein interacts with phosphatidylserine (PS) lipid in the target membrane for mediating fusion. We observed that the fusion peptide of the spike S2 domain interacts with the PS lipid of the target membrane. Low pH and Ca2+ trigger the spike conformational change and bring fusion peptide in close proximity to the PS lipid of the membrane. The binding of the spike with PS lipid of its viral membrane (cis interaction) impedes the fusion activation. PS on the target membrane promotes spike binding via trans interaction, prevents the cis interaction, and accelerates fusion. Sequestering or absence of PS lipid abrogates the spike-mediated fusion process and restricts SARS-CoV-2 infectivity. We found that PS-dependent interaction for fusion is conserved across all the SARS-CoV-2 spike variants of concern (D614G, Alpha, Beta, Delta, and Omicron). Our study suggests that PS lipid is indispensable for SARS-CoV-2 spike-mediated virus and target membrane fusion for entry, and restricting PS interaction with spike inhibits the SARS-CoV-2 spike-mediated entry. Therefore, PS is an important cofactor and acts as a molecular beacon in the target membrane for SARS-CoV-2 entry.

IMPORTANCE

The role of lipids in the host cell target membrane for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry is not clear. We do not know whether SARS-CoV-2 spike protein has any specificity in terms of lipid for membrane fusion reaction. Here, using in vitro reconstitution of membrane fusion assay and single-molecule fluorescence resonance energy transfer imaging of SARS-CoV-2 spike trimers on the surface of the virion, we have demonstrated that phosphatidylserine (PS) lipid plays a key role in SARS-CoV-2 spike-mediated membrane fusion reaction for entry. Membrane-externalized PS lipid strongly promotes spike-mediated membrane fusion and COVID-19 infection. Blocking externalized PS lipid with PS-binding protein or in the absence of PS, SARS-CoV-2 spike-mediated fusion is strongly inhibited. Therefore, PS is an important target for restricting viral entry and intervening spike, and PS interaction presents new targets for COVID-19 interventions.

High-Speed Atomic Force Microscopy Reveals Fluctuations and Dimer Splitting of the N-Terminal Domain of GluA2 Ionotropic Glutamate Receptor-Auxiliary Subunit Complex

α-Amino-3-hydroxy-5-methyl-4-isoxazole propionic acid glutamate receptors (AMPARs) enable rapid excitatory synaptic transmission by localizing to the postsynaptic density of glutamatergic spines. AMPARs possess large extracellular N-terminal domains (NTDs), which are crucial for AMPAR clustering at synaptic sites. However, the dynamics of NTDs and the molecular mechanism governing their synaptic clustering remain elusive. Here, we employed high-speed atomic force microscopy (HS-AFM) to directly visualize the conformational dynamics of NTDs in the GluA2 subunit complexed with TARP γ2 in lipid environments. HS-AFM videos of GluA2-γ2 in the resting and activated/open states revealed fluctuations in NTD dimers. Conversely, in the desensitized/closed state, the two NTD dimers adopted a separated conformation with less fluctuation. Notably, we observed individual NTD dimers transitioning into monomers, with extended monomeric states in the activated/open state. Molecular dynamics simulations provided further support, confirming the energetic stability of the monomeric NTD states within lipids. This NTD-dimer splitting resulted in subunit exchange between the receptors and increased the number of interaction sites with synaptic protein neuronal pentraxin 1 (NP1). Moreover, our HS-AFM studies revealed that NP1 forms a ring-shaped octamer through N-terminal disulfide bonds and binds to the tip of the NTD. These findings suggest a molecular mechanism in which NP1, upon forming an octamer, is secreted into the synaptic region and binds to the tip of the GluA2 NTD, thereby bridging and clustering multiple AMPARs. Thus, our findings illuminate the critical role of NTD dynamics in the synaptic clustering of AMPARs and contribute valuable insights into the fundamental processes of synaptic transmission.

Directional swimming patterns in jellyfish aggregations

Having a profound influence on marine and coastal environments worldwide, jellyfish hold significant scientific, economic, and public interest.1,2,3,4,5 The predictability of outbreaks and dispersion of jellyfish is limited by a fundamental gap in our understanding of their movement. Although there is evidence that jellyfish may actively affect their position,6,7,8,9,10 the role of active swimming in controlling jellyfish movement, and the characteristics of jellyfish swimming behavior, are not well understood. Consequently, jellyfish are often regarded as passively drifting or randomly moving organisms, both conceptually2,11 and in process studies.12,13,14 Here we show that the movement of jellyfish is modulated by distinctly directional swimming patterns that are oriented away from the coast and against the direction of surface gravity waves. Taking a Lagrangian viewpoint from drone videos that allows the tracking of multiple adjacent jellyfish, and focusing on the scyphozoan jellyfish Rhopilema nomadica as a model organism, we show that the behavior of individual jellyfish translates into a synchronized directional swimming of the aggregation as a whole. Numerical simulations show that this counter-wave swimming behavior results in biased correlated random-walk movement patterns that reduce the risk of stranding, thus providing jellyfish with an adaptive advantage critical to their survival. Our results emphasize the importance of active swimming in regulating jellyfish movement and open the way for a more accurate representation in model studies, thus improving the predictability of jellyfish outbreaks and their dispersion and contributing to our ability to mitigate their possible impact on coastal infrastructure and populations.

The use of ectopic volar fibroblasts to modify skin identity

Skin identity is controlled by intrinsic features of the epidermis and dermis and their interactions. Modifying skin identity has clinical potential, such as the conversion of residual limb and stump (nonvolar) skin of amputees to pressure-responsive palmoplantar (volar) skin to enhance prosthesis use and minimize skin breakdown. Greater keratin 9 (KRT9) expression, higher epidermal thickness, keratinocyte cytoplasmic size, collagen length, and elastin are markers of volar skin and likely contribute to volar skin resiliency. Given fibroblasts' capacity to modify keratinocyte differentiation, we hypothesized that volar fibroblasts influence these features. Bioprinted skin constructs confirmed the capacity of volar fibroblasts to induce volar keratinocyte features. A clinical trial of healthy volunteers demonstrated that injecting volar fibroblasts into nonvolar skin increased volar features that lasted up to 5 months, highlighting a potential cellular therapy.

Similarity Metrics for Subcellular Analysis of FRET Microscopy Videos

Understanding the heterogeneity of molecular environments within cells is an outstanding challenge of great fundamental and technological interest. Cells are organized into specialized compartments, each with distinct functions. These compartments exhibit dynamic heterogeneity under high-resolution microscopy, which reflects fluctuations in molecular populations, concentrations, and spatial distributions. To enhance our comprehension of the spatial relationships among molecules within cells, it is crucial to analyze images of high-resolution microscopy by clustering individual pixels according to their visible spatial properties and their temporal evolution. Here, we evaluate the effectiveness of similarity metrics based on their ability to facilitate fast and accurate data analysis in time and space. We discuss the capability of these metrics to differentiate subcellular localization, kinetics, and structures of protein-RNA interactions in Forster resonance energy transfer (FRET) microscopy videos, illustrated by a practical example from recent literature. Our results suggest that using the correlation similarity metric to cluster pixels of high-resolution microscopy data should improve the analysis of high-dimensional microscopy data in a wide range of applications.