TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines

Advancing in vitro cell migration studies: a review of open-source analytical platforms for cancer and wound healing research

A single cell or cell population exhibits the fundamental phenomenon of cell migration during developmental processes or disease progression. Vast literature suggests that, in vitro 2-dimensional or 3-dimensional cell migration assay is one of the most commonly used assays in cancer, wound healing research, and developmental biology research. The data obtained from this assay are often analyzed using various proprietary or open-source programs. Proprietary software are costly and not always accessible to everyone. Whereas the open-source programs are free, easy to access, and user friendly. However, not all researchers are aware of these open-source programs. Despite the increasing availability of these programs, many researchers still rely on proprietary software, due to a lack of comparative analyses and practical guidance on their implementation. Hence, this review aims to provide insights into these open-source tools and serves as a practical guide to both biologists and computational researchers for their specific analytical needs.

Perspectives on label-free microscopy of heterogeneous and dynamic biological systems

Significance

Advancements in label-free microscopy could provide real-time, non-invasive imaging with unique sources of contrast and automated standardized analysis to characterize heterogeneous and dynamic biological processes. These tools would overcome challenges with widely used methods that are destructive (e.g., histology, flow cytometry) or lack cellular resolution (e.g., plate-based assays, whole animal bioluminescence imaging).

Aim

This perspective aims to (1) justify the need for label-free microscopy to track heterogeneous cellular functions over time and space within unperturbed systems and (2) recommend improvements regarding instrumentation, image analysis, and image interpretation to address these needs.

Approach

Three key research areas (cancer research, autoimmune disease, and tissue and cell engineering) are considered to support the need for label-free microscopy to characterize heterogeneity and dynamics within biological systems. Based on the strengths (e.g., multiple sources of molecular contrast, non-invasive monitoring) and weaknesses (e.g., imaging depth, image interpretation) of several label-free microscopy modalities, improvements for future imaging systems are recommended.

Conclusion

Improvements in instrumentation including strategies that increase resolution and imaging speed, standardization and centralization of image analysis tools, and robust data validation and interpretation will expand the applications of label-free microscopy to study heterogeneous and dynamic biological systems.

Semi-synthetic fibrous fibrin composites promote 3D microvascular assembly, survival, and host integration of endothelial cells without mesenchymal cell support

Vasculogenic assembly of 3D capillary networks remains a promising approach to vascularizing tissue-engineered grafts, a significant outstanding challenge in tissue engineering and regenerative medicine. Current approaches for vasculogenic assembly rely on the inclusion of supporting mesenchymal cells alongside endothelial cells, co-encapsulated within vasculo-conducive materials such as low-density fibrin hydrogels. Here, we established a material-based approach to circumvent the need for supporting mesenchymal cells and report that the inclusion of synthetic matrix fibers in dense (>3 mg mL-1) 3D fibrin hydrogels can enhance vasculogenic assembly in endothelial cell monocultures. Surprisingly, we found that the addition of non-cell-adhesive synthetic matrix fibers compared to cell-adhesive synthetic fibers best encouraged vasculogenic assembly, proliferation, lumenogenesis, a vasculogenic transcriptional program, and additionally promoted cell-matrix interactions and intercellular force transmission. Implanting fiber-reinforced prevascularized constructs to assess graft-host vascular integration, we demonstrate additive effects of enhanced vascular network assembly during in vitro pre-culture, fiber-mediated improvements in endothelial cell survival and vascular maintenance post-implantation, and enhanced host cell infiltration that collectively enabled graft vessel integration with host circulation. This work establishes synthetic matrix fibers as an inexpensive alternative to sourcing and expanding secondary supporting cell types for the prevascularization of tissue constructs.

CCSer2 gates dynein activity at the cell periphery

Cytoplasmic dynein-1 (dynein) is a microtubule-associated, minus end-directed motor that traffics hundreds of different cargos. Dynein must discriminate between cargos and traffic them at the appropriate time from the correct cellular region. How dynein's trafficking activity is regulated in time or cellular space remains poorly understood. Here, we identify CCSer2 as the first known protein to gate dynein activity in the spatial dimension. CCSer2 promotes the migration of developing zebrafish primordium cells, macrophages, and cultured human cells by facilitating the trafficking of cargos that are acted on by peripherally localized dynein. Our data suggest that CCSer2 disfavors the interaction between dynein and its regulator Ndel1 at the cell edge, resulting in localized dynein activation. These findings support a model where the spatial specificity of dynein is achieved by the localization of proteins that trigger Ndel1's release from dynein. We propose that CCSer2 defines a broader class of proteins that activate dynein in distinct microenvironments via regulating Ndel1-dynein interaction.

Neural crest cells are sensitive to radiation-induced DNA damage

Radiation-induced DNA damage introduces mutations that have various deleterious effects, which may lead to apoptosis and carcinogenesis. Different tissues and cell types exhibit varying degrees of sensitivity to radiation-induced DNA damage, which is often attributed to the frequency of cell division. In this study, we showed that irradiation affects early zebrafish embryos in a manner that is not explained by direct DNA damage and repair nor by the frequency of cell division. Zebrafish embryos irradiated at 2 h post fertilization showed drastic apoptosis, mainly in the head region, during organogenesis. Herein, we show that these apoptotic cells did not show aneuploidy or micronuclei, and that not all descendants of the same cells with the same DNA damage were necessarily apoptotic. Finally, we demonstrate that apoptotic cells have various origins and that neural crest cells have a sensitive cell fate. Our results suggest the existence of a radiation damage response mechanism other than those previously described, the elucidation of which may inform strategies for greater protection against radiation injury.

Microglial pro-inflammatory mechanisms induced by monomeric C-reactive protein are counteracted by soluble epoxide hydrolase inhibitors

Monomeric C-reactive protein (mCRP) is a pro-inflammatory molecule generated by the dissociation of native CRP. Clinical and experimental studies suggest that mCRP deposition in the brain induces Alzheimer's disease (AD) pathology and cognitive loss. Pathological neuroinflammation is increasingly suggested as relevant in AD. Innovative therapies against neuroinflammation are desperately needed, and inhibitors of the enzyme soluble epoxide hydrolase (sEH) are a promising new generation of anti-inflammatory drugs. Mouse primary microglia and BV2 cell line cultures were exposed to mCRP to analyze its pro-inflammatory mechanisms. sEH inhibitors, both newly synthesized UB-SCG-55 and UB-SCG-65, and the reference agent TPPU, were tested for their anti-inflammatory action against mCRP. Phenotypic changes were analyzed through cell imaging techniques, as well as molecular analysis of inflammatory mediators and gene activation pathways. Results show that mCRP triggers a pro-inflammatory response through three main inflammatory pathways: iNOS, NLRP3, and COX-2, followed by increased cytokine generation. Polarization of microglia toward a M1-like phenotype was confirmed by morphological analysis. Also, mCRP can bind to and cross the cell membrane, providing further insight into its mechanisms of action. sEH inhibitors were effective against mCRP induction of a reactive microglial phenotype. The first-line compound UB-SCG-55 emerged as the most potent anti-inflammatory against mCRP injury. Therefore, the direct activation of microglia by mCRP provides evidence of its role in triggering and exacerbating neurodegenerative diseases with a neuroinflammatory component, such as AD. Furthermore, the protection given by inhibitors of sEH confirms its potential as innovative drugs against deleterious effects of neuroinflammation.

A responsive living material prepared by diffusion reveals extracellular enzyme activity of cyanobacteria

Stimuli-responsive engineered living materials (ELMs) can respond to environmental or biochemical cues and have broad utility in biological sensors and machines, but have traditionally been limited to biocompatible scaffolds. This is because they are typically made by mixing cells into a precursor solution before crosslinking. Here, we demonstrate a diffusion mechanism for incorporating cells of the cyanobacterium Synechococcus elongatus sp. PCC 7942 (S. elongatus) into nanoclay-poly-N-isopropylacrylamide (NC-PNIPAm), a hydrogel with a cytotoxic precursor, by exploiting its temperature-dependent shape-morphing behavior. Subsequent growth of S. elongatus caused a decrease in the bending curvature and stiffness (local Young's modulus) of NC-PNIPAm due to partial degradation by an unannotated enzyme. Creation and observation of this cyanobacteria-hydrogel ELM showcases a method for diffusing cells into a hydrogel as well as characterizing an extracellular enzyme.

Waveguide Evanescent Field Fluorescence Microscopy Images of Osteoblast Cells: The Effect of Trypsin and Image Processing Using TrackMate

Waveguide evanescent field fluorescence microscopy (WEFF) is an evanescent-based microscopy that utilizes a confined thin film of light, around 100 nm, to image the plasma membrane of cells attached to a waveguide. Low photobleaching and low background besides its high axial resolution allows time-lapse imaging to investigate changes in cell morphology in the presence or absence of chemical agents. Both large field of view (FOV) and uniform illumination are very important while imaging cell-substrate contacts with an evanescent field. In the current study, we demonstrate that the WEFF microscope is capable of large FOVs with a uniform illumination source and imaging over a very long time period with a simple and inexpensive experimental setup. The interaction of the trypsin with plasma membranes of live osteoblast cells is investigated. To analyze cell images (250 images), instead of relying on manual tracking, which is time-consuming and can introduce numerous errors, we performed image processing using TrackMate to investigate the dynamic response of cells upon exposure to trypsin. This helps to save time and increase the accuracy of the analysis. The powerful tracking and analysis capabilities of the TrackMate plugin in ImageJ are used to automatically detect the cells border and trace each cluster of cells. The reduction in cell area is accompanied by a notable increase in mean intensity, reflecting changes in the intracellular environment. However, the background did not change during the experiment, which proves that the fluorescence material remains attached to the cell membrane and does not leak into the cell medium.

The biochemical mechanism of Rho GTPase membrane binding, activation and retention in activity patterning

Rho GTPases form plasma membrane-associated patterns that control the cytoskeleton during cell division, morphogenesis, migration, and wound repair. Their patterning involves transitions between inactive cytosolic and active membrane-bound states, regulated by guanine nucleotide exchange factors (GEFs), GTPase-activating proteins (GAPs), and guanine nucleotide dissociation inhibitors (GDIs). However, the relationships between these transitions and role of different regulators remain unclear. We developed a novel reconstitution approach to study Rho GTPase patterning with all major GTPase regulators in a biochemically defined system. We show that Rho GTPase dissociation from RhoGDI is rate-limiting for its membrane association. Rho GTPase activation occurs after membrane insertion, which is unaffected by GEF activity. Once activated, Rho GTPases are retained at the membrane through effector interactions, essential for their enrichment at activation sites. Thus, high cytosolic levels of RhoGDI-bound GTPases ensure a constant supply of inactive GTPases for the membrane, where GEF-mediated activation and effector binding stabilize them. These results delineate the route by which Rho GTPase patterns are established and define stage-dependent roles of its regulators.

Unifying Structure and Function Towards a Comprehensive Macular Evaluation in Eye Disorders: A Multi-Modal Approach Using Microperimetry and Optical Coherence Tomography

OBJECTIVE

We present a new automatic and comprehensive framework to evaluate retinal sub-layer thickness and visual sensitivity at precise retinal locations through multi-modal registration of confocal scanning laser ophthalmoscope (cSLO) images obtained separately from an optical coherence tomography (OCT) device and a microperimeter.

METHODS

We map consecutive B-scans onto the cSLO images after accounting for eye motion. Next, we coarsely register the SLO-microperimetry and cSLO-OCT images using SIFT, followed by precise elastic image registration. Subsequently, we ensure the quality of the co-registered images through single-particle and object tracking of the warped microperimetry test locations. Finally, the retinal thickness is queried from the segmented retinal layers in the co-registered space. A manual mode involving projective transformation accounting for perspective distortions in the images arising from the two modalities is also included.

RESULTS

Validation using retinal images of 8 adults with albinism, 16 adults with amblyopia, 3 adults with macular diseases, and 15 visually healthy adults showed results with excellent reliability.

CONCLUSION

The proposed framework enables the evaluation of retinal thickness by utilizing precise structural and functional relationships of the eye through a self-assessing multi-tiered approach.

SIGNIFICANCE

Our framework lays the foundation towards a comprehensive structure-function assessment of the macular region in various eye disorders.

aquaDenoising: AI-enhancement of in situ liquid phase STEM video for automated quantification of nanoparticles growth

Automatic processing and full analysis of in situ liquid phase scanning transmission electron microscopy (LP-STEM) acquisitions are yet to be achievable with available techniques. This is particularly true for the extraction of information related to the nucleation and growth of nanoparticles (NPs) in liquid as several parasitic processes degrade the signal of interest. These degradations hinder the use of classical or state-of-the-art techniques making the understanding of NPs formation difficult to access. In this context, we propose aquaDenoising, a novel simulation-based deep neural framework to address the challenges of denoising LP-STEM images and videos. Trained on synthetic pairs of clean and noisy images obtained from kinematic-model-based simulations, we show that our model is able to achieve a fifteen-fold improvement in the signal-to-noise ratio of videos of gold NPs growing in water. The enhanced data unleash unprecedented possibilities for automatic segmentation and extraction of structures at different scales, from assemblies of objects down to the individual NPs with the same precision as manual segmentation performed by experts, but with higher throughput. The present denoising method can be easily adapted to other nanomaterials imaged in liquid media. All the codes developed in the present work are open and freely available.

Effects of nocodazole and latrunculin B on locomotion of amoeboid cells of Rhizochromulina sp. strain B44 (Heterokontophyta, Dictyochophyceae)

Rhizochromulina is a genus of unicellular dictyochophycean algae (Heterokontophyta), comprising a single species R. marina and numerous strains. Recently, we described the first arctic rhizochromuline-Rhizochromulina sp. strain B44. Amoeboid cells of this algae are able to transform into flagellates, and this transition can be triggered by prolonged mechanical disturbance. Thin branching pseudopodia of the neighboring rhizochromuline cells fuse to form a meroplasmodium. The pseudopodia contain microtubules, but do not contain actin microfilaments; actin forms the cytoplasmic cytoskeleton and extends only to the bases of the pseudopodia. Microtubule-driven pseudopodia are characteristic to a plethora of eukaryotes, but the role of microtubular and actin cytoskeleton in locomotion of these organisms remains poorly understood. We conducted a series of experiments where amoeboid cells of Rhizochromulina sp. B44 were treated with either 10 µM nocodazole, 10 µM latrunculin B, or both drugs simultaneously. Cellular locomotion was captured on camera, tracked, and then analyzed with the help of the generalized additive mixed model. The obtained results indicate that both drugs, when applied separately, decrease the motility of the studied cells. Unexpectedly, the combined treatment had the opposite effect, as the cells became more motile. The analysis also revealed a non-linear pattern of relationship between motility of amoeboid cells of rhizochromulines and density of their population.

Mitochondria-plasma membrane contact sites regulate the ER-mitochondria encounter structure

Cells form multiple, molecularly distinct membrane contact sites (MCSs) between organelles. Despite knowing the molecular identity of several of these complexes, little is known about how MCSs are coordinately regulated in space and time to promote organelle function. Here, we examined two well-characterized mitochondria-endoplasmic reticulum (ER) MCSs - the ER-mitochondria encounter structure (ERMES) and the mitochondria-ER-cortex anchor (MECA) in Saccharomyces cerevisiae. We report that loss of MECA results in a substantial reduction in the number of ERMES contacts. Rather than reducing ERMES protein levels, loss of MECA results in an increase in the size of ERMES contacts. Using live-cell microscopy, we demonstrate that ERMES contacts display several dynamic behaviors, such as de novo formation, fusion and fission, that are altered in the absence of MECA or by changes in growth conditions. Unexpectedly, we find that the mitochondria-plasma membrane (PM) tethering, and not the mitochondria-ER tethering, function of MECA regulates ERMES contacts. Remarkably, synthetic tethering of mitochondria to the PM in the absence of MECA is sufficient to rescue the distribution of ERMES foci. Overall, our work reveals how one MCS can influence the regulation and function of another.

Phylogenetic analysis of pathogenic algae reveals lineage-dependent patterns of phagocytosis

Prototheca is an unusual genus of algae that lack chlorophyll and are obligate heterotrophs. To date, six paraphyletic pathogenic species have been identified in the context of vertebrates, principally in cattle-associated and human-associated infections. Together with the genus Auxenochlorella and Helicosporidium, rDNA sequence analysis currently favors grouping Prototheca under a clade known as the Auxenochlorella, Helicosporidium and Prototheca (AHP) lineage. Most studies so far have focused only on Prototheca bovis and Prototheca ciferrii as cattle-associated species and on Prototheca wickerhamii as a human-associated species. However, such studies remain limited in scope as they focus on only three species of Prototheca, which is not representative of the total number of species within the AHP lineage. In this study, we employ a phylogenetics approach based on five new organelle-encoded genes to delineate higher-level relationships within the AHP lineage. We use the resultant data to then guide a live-cell imaging-based investigation of aspects of the mammalian innate immune response to 11 Prototheca species and four Auxenochlorella species. Our data reveal varying patterns of phagocytosis dynamics that are both host cell type- and algal species-dependent. Together, these findings reveal the interaction between pathogen phylogeny and host immune response, revealing ways to identify new therapeutic targets in the future.

IMPORTANCE

Protothecosis is a rare algal infection caused by members of the genus Prototheca, which is comprised of unusual non-photosynthetic algae. Six pathogenic species have been identified so far that can cause infection in vertebrates, primarily cattle and humans. The phylogeny of this genus remains obscure and has been revised multiple times recently. However, this phylogeny has largely been based on only three species of Prototheca. To resolve this phylogenetic conundrum, here, we employ a phylogenetics approach based on five new organelle-encoded genes. We then use these data to perform live-cell imaging of a selected range of Prototheca species co-cultured with mammalian immune cells. Visualizing these phagocytic interactions in this context helps delineate both host cell-type- and species-dependent differences in phagocytic uptake, thereby providing novel insight into lineage-based differences.

A transient contractile seam promotes epithelial sealing and sequential assembly of body segments

In embryos, epithelial sealing proceeds with progressive zipping eventually leading to a scar-free epithelium and ensuring the assembly of body segments in insects and neural tube in mammals. How zipping is mechanically controlled to promote tissue fusion on long distances, remains unclear. Combining physical modeling with genetic and mechanical perturbations, we reveal the existence of a transient contractile seam that generates forces to reduce the zipping angle by force balance, consequently promoting epidermal sealing during Drosophila embryogenesis. The seam is formed by the adhesion of two tissues, the epidermis and amnioserosa, and is stabilized by the tensions generated by the segment boundaries. Once a segment is zipped, the seam disassembles concurrently with the inactivation of the Jun kinase pathway. Thus, we show that epithelial sealing is promoted by a transient actomyosin contractile seam allowing sequential segment assembly.

Microfluidic cell unroofing for the in situ molecular analysis of organelles without membrane permeabilization

Molecular networks of organelle membranes are involved in many cell processes. However, the nature of plasma membrane as a barrier to various analytical tools, including antibodies, makes it challenging to examine intact organelle membranes without affecting their structure and functions via membrane permeabilization. Therefore, in this study, we aimed to develop a microfluidic method to unroof cells and observe the intrinsic membrane molecules in organelles. In our method, single cells were precisely arrayed on the bottom surface of microchannels in a light-guided manner using a photoactivatable cell-anchoring material. At sufficiently short cell intervals, horizontal stresses generated by the laminar flow instantly fractured the upper cell membranes, without significantly affecting some organelles inside the fractured cells. Subsequently, nucleus and other organelles in unroofed cells were observed via confocal fluorescence and scanning electron microscopy. Furthermore, distribution of the mitochondrial membrane protein, translocase of outer mitochondrial membrane 20, on the mitochondrial membrane was successfully observed via immunostaining without permeabilization. Overall, the established cell unroofing method shows great potential to examine the localization, functions, and affinities of proteins on intact organelle membranes.

Mechanism of bacterial outer membrane exchange revealed by quantitative microscopy

Kin recognition, the ability to distinguish self from nonself at the cellular level is critical to multicellular life. Myxococcus xanthus is a multicellular bacterium that cooperates among genetically-related cells and reduces exploitation by nonkin through outer membrane exchange (OME) of common goods and toxins. The polymorphic cell surface receptor called TraA and its partner protein TraB mediate kin recognition by OME, but its molecular mechanism remains unknown. Here we used quantitative microscopy techniques to characterize the stoichiometry of the intracellular TraAB complexes and the intercellular TraA-TraA interactions. We visualized the OME of single protein particles between cells and revealed that OME depends on the free diffusion of outer membrane (OM) contents. Based on the predicted structures, we propose a model that TraAB overcomes the repulsion between OMs by stressing the membranes and reducing the contact area, analogous to the eukaryotic soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs), which mediate plasma membrane fusion. Our working model provides a novel pathway that leads to an underlying conserved mechanism for membrane fusion that is a foundation process for multicellularity.

CellPhePy: A python implementation of the CellPhe toolkit for automated cell phenotyping from microscopy time-lapse videos

We previously developed the CellPhe toolkit, an open-source R package for automated cell phenotyping from ptychography time-lapse videos. To align with the growing adoption of python-based image analysis tools and to enhance interoperability with widely used software for cell segmentation and tracking, we developed a python implementation of CellPhe, named CellPhePy. CellPhePy preserves all of the core functionality of the original toolkit, including single-cell phenotypic feature extraction, time-series analysis, feature selection and cell type classification. In addition, CellPhePy introduces significant enhancements, such as an improved method for identifying features that differentiate cell populations and extended support for multiclass classification, broadening its analytical capabilities. Notably, the CellPhePy package supports CellPose segmentation and TrackMate tracking, meaning that a set of microscopy images are the only required input with segmentation, tracking and feature extraction fully automated for downstream analysis, without reliance on external applications. The workflow's increased flexibility and modularity make it adaptable to different imaging modalities and fully customisable to address specific research questions. CellPhePy can be installed via PyPi or GitHub, and we also provide a CellPhePy GUI to aid user accessibility.

Role of a single MCP in evolutionary adaptation of Shewanella putrefaciens for swimming in planktonic and structured environments

Bacteria can adapt to their environments by changing phenotypic traits by mutations. However, improving one trait often results in the deterioration of another one, a trade-off that limits the degree of adaptation. The gammaproteobacterium Shewanella putrefaciens CN-32 has an elaborate motility machinery comprising two distinct flagellar systems and an extensive chemotaxis array with 36 methyl-accepting chemotaxis sensor proteins (MCPs). In this study, we performed experimental selection on S. putrefaciens for increased spreading through a porous environment. We readily obtained a mutant that showed a pronounced increase in covered distance. This phenotype was almost completely caused by a deletion of 24 bp from the chromosome, which leads to a moderately enhanced production of a single MCP. Accordingly, chemotaxis assays under free-swimming conditions and cell tracking in soft agar showed that the mutation improved navigation through nutritional gradients. In contrast, further increased levels of the MCP negatively affected spreading. The study demonstrates how moderate differences in the abundance of a single MCP can lead to an efficient upgrade of chemotaxis in specific environments at a low expense of cellular resources.IMPORTANCEExperimental evolution experiments have been used to determine the trade-offs occurring in specific environments. Several studies that have used the spreading behavior of bacteria in structured environments identified regulatory mutants that increase the swimming speed of the cells. While this results in a higher chemotaxis drift, the growth fitness decreases as the higher swimming speed requires substantial cellular resources. Here we show that rapid chemotaxis adaptation can also be achieved by modifying the chemotaxis signal input at a low metabolic cost for the cell.

Border-zone cardiomyocytes and macrophages regulate extracellular matrix remodeling to promote cardiomyocyte protrusion during cardiac regeneration

Despite numerous advances in our understanding of zebrafish cardiac regeneration, an aspect that remains less studied is how regenerating cardiomyocytes invade and replace the collagen-containing injured tissue. Here, we provide an in-depth analysis of the process of cardiomyocyte invasion. We observe close interactions between protruding border-zone cardiomyocytes and macrophages, and show that macrophages are essential for extracellular matrix remodeling at the wound border zone and cardiomyocyte protrusion into the injured area. Single-cell RNA-sequencing reveals the expression of mmp14b, encoding a membrane-anchored matrix metalloproteinase, in several cell types at the border zone. Genetic mmp14b mutation leads to decreased macrophage recruitment, collagen degradation, and subsequent cardiomyocyte protrusion into injured tissue. Furthermore, cardiomyocyte-specific overexpression of mmp14b is sufficient to enhance cardiomyocyte invasion into the injured tissue and along the apical surface of the wound. Altogether, our data provide important insights into the mechanisms underlying cardiomyocyte invasion of the collagen-containing injured tissue during cardiac regeneration.

A tension-induced morphological transition shapes the avian extra-embryonic territory

The segregation of the extra-embryonic lineage is one of the earliest events and a key step in amniote development. Whereas the regulation of extra-embryonic cell fate specification has been extensively studied, little is known about the morphogenetic events underlying the formation of this lineage. Here, taking advantage of the amenability of avian embryos to live and quantitative imaging, we investigate the cell- and tissue-scale dynamics of epiboly, the process during which the epiblast expands to engulf the entire yolk. We show that tension arising from the outward migration of the epiblast border on the vitelline membrane stretches extra-embryonic cells, which reversibly transition from a columnar to a squamous morphology. The propagation of this tension is strongly attenuated in the embryonic territory, which concomitantly undergoes fluid-like motion, culminating in the formation of the primitive streak. We formulate a simple viscoelastic model in which the epiblast responds elastically to isotropic stress but, on a similar timescale, flows in response to shear stress, and we show that it recapitulates the flows and deformation of both embryonic and extra-embryonic tissues. Together, our results clarify the mechanical basis of early avian embryogenesis and provide a framework unifying the divergent mechanical behaviors observed in the contiguous embryonic and extra-embryonic territories that make up the epiblast.

Influence of Myosin Regulatory Light Chain and Myosin Light Chain Kinase on the Physiological Function of Inner Ear Hair Cells

PURPOSE

In the receptor organs of the inner ear, hair cells detect mechanical stimuli such as sounds and accelerations by deflection of their hair bundles. Myosin regulatory light chain (RLC) and non-muscle myosin II (NM2) are expressed at the apical surfaces of hair cells, and NM2 and the phosphorylation of RLC by myosin light chain kinase (MLCK) have earlier been shown to regulate the shapes of hair cells' apical surfaces in rodents. The aim of our study was to elucidate the function of myosin molecules on hair cell physiology.

METHODS

We investigated the expression of NM2 and RLC in the bullfrog's saccule by immunostaining. Using NM2 and MLCK inhibitors, we measured the stiffness, spontaneous oscillation, and resting open probability of frog hair bundles. Six to ten saccules from pleural animals were used in each experiment. In addition, we recorded auditory brainstem responses in ten mice after transtympanic injection of an MLCK inhibitor.

RESULTS

We confirmed the expression of NM2A/B and MYL9 on the apical surfaces of hair cells and of NM2A and MYL12A in hair bundles. We found that NM2 and MLCK inhibitors reduce the stiffness of hair bundles from the bullfrog's saccule. Moreover, MLCK inhibition inhibits the spontaneous oscillation of hair bundles and increases the resting open probability of transduction channels. In addition, MLCK inhibition elevates hearing thresholds in mice.

CONCLUSION

We conclude that NM2 and the phosphorylation of RLC modulate the physiological function of hair cells and thereby help to set the normal operating conditions of hair bundles.

A central role for CCR2 in monocyte recruitment and blood-brain barrier disruption during Usutu virus encephalitis

Usutu virus (USUV) is an emerging neurotropic flavivirus capable of causing encephalitis in humans. Here, our main goal was to characterize the innate immune response in the brain during USUV encephalitis and to identify strategies to control disease severity. Using an immunocompetent mouse model of USUV encephalitis, we showed that microglia activation, blood-brain barrier (BBB) disruption and inflammatory monocyte recruitment are hallmarks of disease 6 days post infection. Activated microglia were in close association to USUV-infected cells, concomitantly with elevated levels of IL-6, IFN-γ, CCL2, CCL5, CXCL10 and CXCL1 in the brain. Monocyte recruitment was CCR2-dependent and driven by IFN-γ and CCL2 production beneath the brain vasculature. Moreover, CCR2 deficiency inhibited microglia activation and BBB disruption, showing the central role of CCR2 in USUV encephalitis. Accordingly, treatment with dexamethasone prevented pro-inflammatory mediator production and reduced leukocyte recruitment significantly, restraining encephalitis severity. Concluding, USUV encephalitis is driven by CCR2-mediated monocyte recruitment and BBB disruption, and blocked therapeutically by glucocorticoids.

UFMTrack, an Under-Flow Migration Tracker enabling analysis of the entire multi-step immune cell extravasation cascade across the blood-brain barrier in microfluidic devices

The endothelial blood-brain barrier (BBB) strictly controls immune cell trafficking into the central nervous system (CNS). In neuroinflammatory diseases such as multiple sclerosis, this tight control is, however, disturbed, leading to immune cell infiltration into the CNS. The development of in vitro models of the BBB combined with microfluidic devices has advanced our understanding of the cellular and molecular mechanisms mediating the multistep T-cell extravasation across the BBB. A major bottleneck of these in vitro studies is the absence of a robust and automated pipeline suitable for analyzing and quantifying the sequential interaction steps of different immune cell subsets with the BBB under physiological flow in vitro. Here, we present the under-flow migration tracker (UFMTrack) framework for studying immune cell interactions with endothelial monolayers under physiological flow. We then showcase a pipeline built based on it to study the entire multistep extravasation cascade of immune cells across brain microvascular endothelial cells under physiological flow in vitro. UFMTrack achieves 90% track reconstruction efficiency and allows for scaling due to the reduction of the analysis cost and by eliminating experimenter bias. This allowed for an in-depth analysis of all behavioral regimes involved in the multistep immune cell extravasation cascade. The study summarizes how UFMTrack can be employed to delineate the interactions of CD4+ and CD8+ T cells with the BBB under physiological flow. We also demonstrate its applicability to the other BBB models, showcasing broader applicability of the developed framework to a range of immune cell-endothelial monolayer interaction studies. The UFMTrack framework along with the generated datasets is publicly available in the corresponding repositories.

Med12 cooperates with multiple differentiation signals to facilitate efficient lineage transitions in embryonic stem cells

Cell differentiation results from coordinated changes in gene transcription in response to combinations of signals. Fibroblast growth factor (FGF), Wnt and mammalian target of rapamycin (mTOR) signals regulate the differentiation of pluripotent mammalian cells towards embryonic and extraembryonic lineages, but how these signals cooperate with general transcriptional regulators is not fully resolved. Here, we report a genome-wide CRISPR screen that reveals both signaling components and general transcriptional regulators for differentiation-associated gene expression in mouse embryonic stem cells (mESCs). Focusing on the Mediator subunit-encoding Med12 gene as one of the strongest hits in the screen, we show that it regulates gene expression in parallel to FGF and mTOR signals. Loss of Med12 is compatible with differentiation along both the embryonic epiblast and the extraembryonic primitive endoderm lineage but impairs pluripotency gene expression and slows down transitions between pluripotency states. These findings suggest that Med12 helps pluripotent cells to efficiently execute transcriptional changes during differentiation, thereby modulating the effects of a broad range of signals.

Drosophila complement-like Mcr acts as a wound-induced inflammatory chemoattractant

Sterile tissue injury is accompanied by an acute inflammatory response whereby innate immune cells rapidly migrate to the site of injury guided by pro-inflammatory chemotactic damage signals released at the wound. Understanding this immune response is key to improving human health, and recent advances in imaging technology have allowed researchers using different model organisms to observe this inflammatory response in vivo. Over recent decades, offering a unique combination of live time-lapse microscopy and genetics, the fruit fly Drosophila has emerged as a powerful model system to study inflammatory cell migration within a living animal.1,2,3,4 However, we still know relatively little regarding the identity of the earliest signals that drive this immune cell recruitment and the mechanisms by which they act within the complex, in vivo setting of a multicellular organism. Here, we couple the powerful genetics and live imaging of Drosophila with mathematical modeling to identify the fly complement ortholog-macroglobulin complement-related (Mcr)-as an early, wound-induced chemotactic signal responsible for the inflammatory recruitment of immune cells to injury sites in vivo. We show that epithelial-specific knockdown of Mcr suppresses the recruitment of macrophages to wounds and combine predictive mathematical modeling with in vivo genetics to understand macrophage migration dynamics following manipulation of this chemoattractant. We propose a model whereby Mcr operates alongside hydrogen peroxide to ensure a rapid and efficient immune response to damage, uncovering a novel function for this protein that parallels the chemotactic role of the complement component C5a in mammals.

Auxin and tryptophan trigger common responses in the streptophyte alga Penium margaritaceum

Auxin is a signaling molecule that regulates multiple processes in the growth and development of land plants. Research gathered from model species, particularly Arabidopsis thaliana, has revealed that the nuclear auxin pathway controls many of these processes through transcriptional regulation. Recently, a non-transcriptional pathway based on rapid phosphorylation mediated by kinases has been described, complementing the understanding of the complexity of auxin-regulated processes. Phylogenetic inferences of both pathways indicate that only some of these components are conserved beyond land plants. This raises fundamental questions about the evolutionary origin of auxin responses and whether algal sisters share mechanistic features with land plants. Here, we explore auxin responses in the unicellular streptophyte alga Penium margaritaceum. By assessing physiological, transcriptomic, and cellular responses, we found that auxin triggers cell proliferation, gene regulation, and acceleration of cytoplasmic streaming. Notably, all these responses are also triggered by the structurally related tryptophan. These results identify shared auxin response features among land plants and algae and suggest that less chemically specific responses preceded the emergence of auxin-specific regulatory networks in land plants.

Scale selection and machine learning based cell segmentation and tracking in time lapse microscopy

Monitoring and tracking of cell motion is a key component for understanding disease mechanisms and evaluating the effects of treatments. Time-lapse optical microscopy has been commonly employed for studying cell cycle phases. However, usual manual cell tracking is very time consuming and has poor reproducibility. Automated cell tracking techniques are challenged by variability of cell region intensity distributions and resolution limitations. In this work, we introduce a comprehensive cell segmentation and tracking methodology. A key contribution of this work is that it employs multi-scale space-time interest point detection and characterization for automatic scale selection and cell segmentation. Another contribution is the use of a neural network with class prototype balancing for detection of cell regions. This work also offers a structured mathematical framework that uses graphs for track generation and cell event detection. We evaluated cell segmentation, detection, and tracking performance of our method on time-lapse sequences of the Cell Tracking Challenge (CTC). We also compared our technique to top performing techniques from CTC. Performance evaluation results indicate that the proposed methodology is competitive with these techniques, and that it generalizes very well to diverse cell types and sizes, and multiple imaging techniques. The code of our method is publicly available on https://github.com/smakrogi/CSTQ_Pub/ , (release v.3.2).

Tissue-like multicellular development triggered by mechanical compression in archaea

The advent of clonal multicellularity is a critical evolutionary milestone, seen often in eukaryotes, rarely in bacteria, and only once in archaea. We show that uniaxial compression induces clonal multicellularity in haloarchaea, forming tissue-like structures. These archaeal tissues are mechanically and molecularly distinct from their unicellular lifestyle, mimicking several eukaryotic features. Archaeal tissues undergo a multinucleate stage followed by tubulin-independent cellularization, orchestrated by active membrane tension at a critical cell size. After cellularization, tissue junction elasticity becomes akin to that of animal tissues, giving rise to two cell types-peripheral (Per) and central scutoid (Scu) cells-with distinct actin and protein glycosylation polarity patterns. Our findings highlight the potential convergent evolution of a biophysical mechanism in the emergence of multicellular systems across domains of life.

Tonotopic Specialization of MYO7A Isoforms in Auditory Hair Cells

1. Mutations in Myo7a cause Usher syndrome type 1B and non-syndromic deafness, but the precise function of MYO7A in sensory hair cells remains unclear. We identify and characterize a novel isoform, MYO7A-N, expressed in auditory hair cells alongside the canonical MYO7A-C. Isoform-specific knock-in mice reveal that inner hair cells primarily express MYO7A-C, while outer hair cells express both isoforms in opposing tonotopic gradients. Both localize to the upper tip-link insertion site, consistent with a role in the tip link for mechanotransduction. Loss of MYO7A-N leads to outer hair cell degeneration and progressive hearing loss. Cryo-EM structures reveal isoform-specific differences at actomyosin interfaces, correlating with distinct ATPase activities. These findings reveal an unexpected layer of molecular diversity within the mechanotransduction machinery. We propose that MYO7A isoform specialization enables fine-tuning of tip-link tension, thus hearing sensitivity, and contributes to the frequency-resolving power of the cochlea.

Axial asymmetry organizes division plane orthogonality in Neisseria gonorrhoeae

For rod-shaped bacterial model organisms, the division plane is defined by the geometry of the cell. However, for Neisseria gonorrhoeae, a coccoid organism that most commonly exists as a diplococcus and that possesses genes coding for rod-based cell division systems, the relationship between cell geometry and division is unclear. Here, we characterized the organization of N. gonorrhoeae division using a combination of fluorescent probes, genetics, and time-lapse microscopy. We found that the planes of successive cell divisions are orthogonal and temporally overlapping, thereby maintaining diplococcal morphology. Division takes place perpendicular to a long axis in each coccus. In keeping with the ParABS and the MinCDE systems reading the more pronounced long axis of rod-shaped bacteria, in the coccoid N. gonorrhoeae, ParB segregates along this long axis and cells lacking minCDE suffer severe morphological consequences, including an inability to perform orthogonal division and aberrant assembly of the division plane at the cell poles. Taken together, this stresses the central role of even slight dimensional asymmetry as a general organizational principle in coccoid bacterial cell division.

Development and Characterization of a Primary Ciliated Porcine Airway Model for the Evaluation of In Vitro Mucociliary Clearance and Mucosal Drug Delivery

Background/Objectives: In vitro models play a crucial role in preclinical respiratory research, enabling the testing and screening of mucosal formulations, dosage forms, and inhaled drugs. Mucociliary clearance (MCC) is an essential defense mechanism in mucosal drug delivery but is often impaired in respiratory diseases. Despite its importance, standardized in vitro MCC assays are rarely reported. Furthermore, many published methods primarily measure cilia beat frequency (CBF), which requires high-speed cameras that are not accessible to all laboratories. Therefore, this study aimed to develop a physiologically relevant, differentiated in vitro model of the respiratory epithelium that incorporates both beating cilia and functional MCC. We chose porcine airway mucosa as an alternative to human tissue due to ethical considerations and limited availability. The established model is designed to provide a reproducible and accessible method for a broad range of research laboratories. Methods: The previously published tracheal mucosal primary cell (TMPC DS) model, derived from porcine tissue, lacked the presence of beating cilia, which are crucial for effective MCC analysis. For accurate MCC assessment, beating cilia are essential as they play a key role in mucus clearance. To address this limitation, the here-described ciliated tracheal mucosal primary cell (cTMPC) model was developed. cTMPCs were isolated from porcine tissue and cultured under air-liquid interface (ALI) conditions for 21 days to promote differentiation. This model was evaluated for cell morphology, tight junction formation, ciliated and mucus-producing cells, barrier function, gene expression, and tracer/IgG transport. MCC and the model's suitability for standardized MCC assays were assessed using an inverted microscope. In contrast to the TMPC DS model, which lacked beating cilia and thus could not support MCC analysis, the cTMPC model allows for comprehensive MCC studies. Results: The developed differentiated in vitro model demonstrated key structural and functional features of the respiratory epithelium, including well-differentiated cell morphology, tight junction integrity, ciliated and mucus-producing cells, and effective barrier function. Functional MCC was observed, confirming the model's potential for standardized clearance assays. Conclusions: This differentiated in vitro model closely replicates the structural and functional characteristics of in vivo airways. It provides a valuable platform for studying mucociliary clearance, toxicology, drug uptake, and evaluating mucosal formulations and dosage forms in respiratory research.

The aPBP-type cell wall synthase PBP1b plays a specialized role in fortifying the Escherichia coli division site against osmotic rupture

A multi-protein system called the divisome promotes bacterial division. This apparatus synthesizes the peptidoglycan (PG) cell wall layer that forms the daughter cell poles and protects them from osmotic lysis. In the model Gram-negative bacterium Escherichia coli , PG synthases called class A penicillin-binding proteins (aPBPs) have been proposed to play crucial roles in division. However, there is limited experimental support for aPBPs playing a specialized role in division that is distinct from their general function in the expansion and fortification of the PG matrix. Here, we present in situ cryogenic electron tomography data indicating that the aPBP-type enzyme PBP1b is required to produce a wedge-like density of PG at the division site. Furthermore, atomic force and live cell microscopy showed that loss of this structure weakens the division site and renders it susceptible to lysis. Surprisingly, we found that the lipoprotein activator LpoB needed to promote the general function of PBP1b was not required for normal division site architecture or its integrity. Additionally, we show that of the two PBP1b isoforms produced in cells, it is the one with an extended cytoplasmic N-terminus that functions in division, likely via recruitment by the FtsA component of the divisome. Altogether, our results demonstrate that PBP1b plays a specialized, LpoB-independent role in E. coli cell division involving the biogenesis of a PG structure that prevents osmotic rupture. The conservation of aPBPs with extended cytoplasmic N-termini suggests that other Gram-negative bacteria may use similar mechanisms to reinforce their division site.

Enteric glutamatergic interneurons regulate intestinal motility

The enteric nervous system (ENS) controls digestion autonomously via a complex neural network within the gut wall. Enteric neurons expressing glutamate have been identified by transcriptomic studies as a distinct subpopulation, and glutamate can affect intestinal motility by modulating enteric neuron activity. However, the nature of glutamatergic neurons, their position within the ENS circuit, and their function in regulating gut motility are unknown. We identify glutamatergic neurons as longitudinally projecting descending interneurons in the small intestine and colon and as a novel class of circumferential neurons only in the colon. Both populations make synaptic contact with diverse neuronal subtypes and signal with multiple neurotransmitters and neuropeptides in addition to glutamate, including acetylcholine and enkephalin. Knocking out the glutamate transporter VGLUT2 from enkephalin neurons disrupts gastrointestinal transit, while ex vivo optogenetic stimulation of glutamatergic neurons initiates colonic propulsive motility. Our results posit glutamatergic neurons as key interneurons that regulate intestinal motility.

Unraveling the metastasis-preventing effect of miR-200c in vitro and in vivo

Advanced breast cancer, as well as ineffective treatments leading to surviving cancer cells, can result in the dissemination of these malignant cells from the primary tumor to distant organs. Recent research has shown that microRNA 200c (miR-200c) can hamper certain steps of the invasion-metastasis cascade. However, it is still unclear whether miR-200c expression alone is sufficient to prevent breast cancer cells from metastasis formation. Hence, we performed a xenograft mouse experiment with inducible miR-200c expression in MDA-MB 231 cells. The ex vivo analysis of metastatic sites in a multitude of organs, including lung, liver, brain, and spleen, revealed a dramatically reduced metastatic burden in mice with miR-200c-expressing tumors. A fundamental prerequisite for metastasis formation is the motility of cancer cells and, therefore, their migration. Consequently, we analyzed the effect of miR-200c on collective- and single-cell migration in vitro, utilizing MDA-MB 231 and MCF7 cell systems with genetically modified miR-200c expression. Analysis of collective-cell migration revealed confluence-dependent motility of cells with altered miR-200c expression. Additionally, scratch assays showed an enhanced predisposition of miR-200c-negative cells to leave cell clusters. The in-between stage of collective- and single-cell migration was validated using transwell assays, which showed reduced migration of miR-200c-positive cells. Finally, to measure migration at the single-cell level, a novel assay on dumbbell-shaped micropatterns was performed, which revealed that miR-200c critically determines confined cell motility. All of these results demonstrate that sole expression of miR-200c impedes metastasis formation in vivo and migration in vitro and highlights miR-200c as a metastasis suppressor in breast cancer.

Quantitative measurement of morphometric indicators of skeletal muscle cell behaviour and quality

In vitro culturing of effective human-induced pluripotent stem cell-derived skeletal muscle cells (hiPSC-SMCs) has proven to be challenging. Progress is hindered by the limited range of metrics applied to assess experimental success. We present a semi-automated workflow for segmenting, tracking and quantifying migration and fusion behaviour in live and static images of myoblast and myotube cells. Workflow outputs are validated against manually labelled images and the metrics applied to images from case studies of in vitro cultures of primary mouse muscle cells under varying culture media conditions, mouse primary cells undergoing optogenetic stimulation and hiPSC-SMC. We show culture media-dependent differences in cell fusion dynamics and increased acetylcholine receptors in myonuclei under optogenetic stimulation. We show that myoblasts have greater persistence and proliferation in primary mouse cells than hiPSC, and cell-cell fusion occurred earlier but at a steadier rate in primary mouse cells.

A ternary complex of MIPs in the A-tubule of basal bodies and axonemes depends on RIB22 and the EF-hand domain of RIB72A in Tetrahymena cilia

The lumens of the highly stable microtubules that make up the core of basal bodies, cilia, and flagella are coated with a network of proteins known as MIPs, or microtubule inner proteins. MIPs are hypothesized to enhance the rigidity and stability of these microtubules, but how they assemble and contribute to cilia function is poorly understood. Here we describe a ciliate specific MIP, RIB22, in Tetrahymena thermophila. RIB22 is a calmodulin-like protein found in the A-tubule of doublet and triplet microtubules in cilia and basal bodies. Its localization is dependent on the conserved MIP RIB72. Here we use cryogenic electron tomography (cryoET) to examine RIB22 and its interacting partners in axonemes and basal bodies. RIB22 forms a ternary complex with the C-terminal EF-hand domain of RIB72A and another MIP, FAM166A. Tetrahymena strains lacking RIB22 or the EF-hand domain of RIB72A showed impaired cilia function. CryoET on axonemes from these strains demonstrated an interdependence of the three proteins for stabilization within the structure. Deletion of the RIB72A EF-hand domain resulted in the apparent loss of multiple MIPs in the region. These findings emphasize the intricacy of the MIP network and the importance of understanding MIPs' functions during cilium assembly and regulation.

PLK1 inhibition delays mitotic entry revealing changes to the phosphoproteome of mammalian cells early in division

Polo-like kinase 1 (PLK1) is a conserved regulator of cell division. During mitotic prophase, PLK1 contributes to the activation of the cyclin-dependent kinase 1 (CDK1). However, the exact functions of PLK1 in prophase remain incompletely understood. Here, we show that PLK1 inhibition in synchronous G2 cell populations of multiple mammalian cell lines delays or prevents mitotic entry with high variability between individual cells. Using a mathematical model, we recapitulate this phenomenon and provide an explanation for the observed phenotypic variability. We show that PLK1-inhibited cells are delayed in a prophase-like state with low CDK1 activity that increases slowly and gradually over hours. These cells display progressively condensing chromosomes, increased microtubule dynamics, and reorganization of the actin cortex, while the nuclear envelope remains intact. We characterize this state further by phosphoproteomics, revealing phosphorylation of regulators of chromatin organization and the cytoskeleton consistent with the cellular phenotypes. Together, our results indicate that PLK1 inhibition stabilizes cells in a prophase-like state with low CDK1 activity displaying a specific set of early mitotic phosphorylation events.

MSP-tracker: A versatile vesicle tracking software tool used to reveal the spatial control of polarized secretion in Drosophila epithelial cells

Understanding how specific secretory cargoes are targeted to distinct domains of the plasma membrane in epithelial cells requires analyzing the trafficking of post-Golgi vesicles to their sites of secretion. We used the RUSH (retention using selective hooks) system to synchronously release an apical cargo, Cadherin 99C (Cad99C), and a basolateral cargo, the ECM protein Nidogen, from the endoplasmic reticulum and followed their movements to the plasma membrane. We also developed an interactive vesicle tracking framework, MSP-tracker and viewer, that exploits developments in computer vision and deep learning to determine vesicle trajectories in a noisy environment without the need for extensive training data. MSP-tracker outperformed other tracking software in detecting and tracking post-Golgi vesicles, revealing that Cad99c vesicles predominantly move apically with a mean speed of 1.1µm/sec. This is reduced to 0.85 µm/sec by a dominant slow dynein mutant, demonstrating that dynein transports Cad99C vesicles to the apical cortex. Furthermore, both the dynein mutant and microtubule depolymerization cause lateral Cad99C secretion. Thus, microtubule organization plays a central role in targeting apical secretion, suggesting that Drosophila does not have distinct apical versus basolateral vesicle fusion machinery. Nidogen vesicles undergo planar-polarized transport to the leading edge of follicle cells as they migrate over the ECM, whereas most Collagen is secreted at trailing edges. The follicle cells therefore bias secretion of different ECM components to opposite sides of the cell, revealing that the secretory pathway is more spatially organized than previously thought.

Practical considerations for data exploration in quantitative cell biology

Data exploration is an essential step in quantitative cell biology, bridging raw data and scientific insights. Unlike polished, published figures, effective data exploration requires a flexible, hands-on approach that reveals trends, identifies outliers and refines hypotheses. This Opinion offers simple, practical advice for building a structured data exploration workflow, drawing on the authors' personal experience in analyzing bioimage datasets. In addition, the increasing availability of generative artificial intelligence and large language models makes coding and improving data workflows easier than ever before. By embracing these practices, researchers can streamline their workflows, produce more reliable conclusions and foster a collaborative, transparent approach to data analysis in cell biology.

Development of label-free cell tracking for discrimination of the heterogeneous mesenchymal migration

Image-based cell phenotyping is fundamental in both cell biology and medicine. As cells are dynamic systems, phenotyping based on static data is complemented by dynamic data extracted from time-dependent cell characteristics. We developed a label-free automatic tracking method for phase contrast images. We examined the possibility of using cell motility-based discrimination to identify different types of mesenchymal migration in invasive malignant cancer and non-cancer cells. These cells were cultured in plastic tissue culture vessels, using motility parameters from cell trajectories extracted with label-free tracking. Correlation analysis with these motility parameters identified characteristic parameters for cancer HT1080 fibrosarcoma and non-cancer 3T3-Swiss fibroblast cell lines. The parameter "sum of turn angles," combined with the "frequency of turns" at shallow angles and "migration speed," proved effective in highlighting the migration characteristics of these cells. It revealed differences in their mechanisms for generating effective propulsive forces. The requirements to characterize these differences included the spatiotemporal resolution of segmentation and tracking, capable of detecting polarity changes associated with cell morphological alterations and cell body displacement. With the segmentation and tracking method proposed here, a discrimination curve computed using quadratic discrimination analysis from the "sum of turn angles" and "frequency of turns below 30°" gave the best performance with a 94% sensitivity. Cell migration is a process related not only to cancer but also to tissue healing and growth. The proposed methodology is easy to use, enabling anyone without professional skills in image analysis, large training datasets, or special devices. It has the potential for application not only in cancer cell discrimination but also in a broad range of applications and basic research. Validating the expandability of this method to characterize cell migration, including the scheme of propulsive force generation, is an important consideration for future study.

Mycobacterium tuberculosis phagosome Ca2+ leakage triggers multimembrane ATG8/LC3 lipidation to restrict damage in human macrophages

The role of canonical autophagy in controlling Mycobacterium tuberculosis (Mtb), referred to as xenophagy, is understood to involve targeting Mtb to autophagosomes, which subsequently fuse with lysosomes for degradation. Here, we found that Ca2+ leakage after Mtb phagosome damage in human macrophages is the signal that triggers autophagy-related protein 8/microtubule-associated proteins 1A/1B light chain 3 (ATG8/LC3) lipidation. Unexpectedly, ATG8/LC3 lipidation did not target Mtb to lysosomes, excluding the canonical xenophagy. Upon Mtb phagosome damage, the Ca2+ leakage-dependent ATG8/LC3 lipidation occurred on multiple membranes instead of single or double membranes excluding the noncanonical autophagy pathways. Mechanistically, Ca2+ leakage from the phagosome triggered the recruitment of the V-ATPase-ATG16L1 complex independently of FIP200, ATG13, and proton gradient disruption. Furthermore, the Ca2+ leakage-dependent ATG8/LC3 lipidation limited Mtb phagosome damage and restricted Mtb replication. Together, we uncovered Ca2+ leakage as the key signal that triggers ATG8/LC3 lipidation on multiple membranes to mitigate Mtb phagosome damage.

Generative frame interpolation enhances tracking of biological objects in time-lapse microscopy

Object tracking in microscopy videos is crucial for understanding biological processes. While existing methods often require fine-tuning tracking algorithms to fit the image dataset, here we explored an alternative paradigm: augmenting the image time-lapse dataset to fit the tracking algorithm. To test this approach, we evaluated whether generative video frame interpolation can augment the temporal resolution of time-lapse microscopy and facilitate object tracking in multiple biological contexts. We systematically compared the capacity of Latent Diffusion Model for Video Frame Interpolation (LDMVFI), Real-time Intermediate Flow Estimation (RIFE), Compression-Driven Frame Interpolation (CDFI), and Frame Interpolation for Large Motion (FILM) to generate synthetic microscopy images derived from interpolating real images. Our testing image time series ranged from fluorescently labeled nuclei to bacteria, yeast, cancer cells, and organoids. We showed that the off-the-shelf frame interpolation algorithms produced bio-realistic image interpolation even without dataset-specific retraining, as judged by high structural image similarity and the capacity to produce segmentations that closely resemble results from real images. Using a simple tracking algorithm based on mask overlap, we confirmed that frame interpolation significantly improved tracking across several datasets without requiring extensive parameter tuning and capturing complex trajectories that were difficult to resolve in the original image time series. Taken together, our findings highlight the potential of generative frame interpolation to improve tracking in time-lapse microscopy across diverse scenarios, suggesting that a generalist tracking algorithm for microscopy could be developed by combining deep learning segmentation models with generative frame interpolation.

Functional morphology of gliding motility in benthic diatoms

Diatoms, a highly successful group of photosynthetic algae, contribute to a quarter of global primary production. Many species are motile, despite having no appendages and a completely rigid cell body. Cells move to seek out nutrients, locate mating partners, and undergo vertical migration. To explore the natural diversity of diatom motility, we perform a comparative study across five common biofilm-forming species. Combining morphological measurements with high-resolution cell tracking, we establish how gliding movements relate to the morphology of the raphe-a specialized slit in the cell wall responsible for motility generation. Our detailed analyses reveal that cells exhibit a rich but species-dependent phenotype, switching stochastically between four stereotyped motility states. We model this behavior and use stochastic simulations to predict how heterogeneity in microscale navigation patterns leads to differences in long-time diffusivity and dispersal. In a representative species, we extend these findings to quantify diatom gliding in complex, naturalistic 3D environments, suggesting that cells may exploit these distinct motility signatures to achieve niche segregation in nature.

Suppressing parasitic flow in membraneless diffusion-based microfluidic gradient generators

Diffusion-based microfluidic gradient generators (DMGGs) are essential for various in vitro studies due to their ability to provide a convection-free concentration gradient. However, these systems, often referred to as membrane-based DMGGs, exhibit delayed gradient formation due to the incorporated flow-resistant membrane. This limitation substantially hinders their application in dynamic and time-sensitive studies. Here, we accelerate the gradient response in DMGGs by removing the membrane and implementing new geometrical configurations to compensate for the membrane's role in suppressing parasitic flows. We introduce these novel configurations into two microfluidic designs: the H-junction and the Y-junction. In the H-junction design, parasitic flow is redirected through a bypass channel following the gradient region. The Y-junction design features a shared discharge channel that allows converging discharge flow streams, preventing the buildup of parasitic pressure downstream of the gradient region. Using hydraulic circuit analysis and fluid dynamics simulations, we demonstrate the effectiveness of the H-junction and Y-junction designs in suppressing parasitic pressure flows. These computational results, supported by experimental data from particle image velocimetry, confirm the capability of our designs to generate a highly stable, accurate, and convection-free gradient with rapid formation. These advantages make the H-junction and Y-junction designs ideal experimental platforms for a wide range of in vitro studies, including drug testing, cell chemotaxis, and stem cell differentiation.

Imaging and Tracking RNA in Live Mammalian Cells via Fluorogenic Photoaffinity Labeling

Cellular RNA labeling using light-up aptamers that bind to and activate fluorogenic molecules has gained interest in recent years as an alternative to protein-based RNA labeling approaches. Aptamer-based systems are genetically encodable and cover the entire visible spectrum. However, the inherently temporary nature of the noncovalent aptamer-fluorogen interaction limits the utility of these systems in that imaging does not withstand dye washout, and dye dissociation can compromise RNA tracking. We propose that these limitations can be averted through covalent RNA labeling. Here, we describe a photoaffinity approach in which the aptamer ligand is functionalized with a photoactivatable diazirine reactive group such that irradiation with UV light results in covalent attachment to the RNA of interest. In addition to the robustness of the covalent linkage, this approach benefits from the ability to achieve spatiotemporal control over RNA labeling. To demonstrate this approach, we incorporated a photoaffinity linker into malachite green and fused a single copy of the malachite green aptamer to a Cajal body-associated small nuclear RNA of interest as well as a cytoplasmic mRNA. We observed improved sensitivity for live cell imaging of the target RNA upon UV irradiation and demonstrated visualization of RNA dynamics over a time scale of minutes. The covalent attachment uniquely enables these time-resolved experiments, whereas in noncovalent approaches, the dye molecule can be transferred between different RNA molecules, compromising tracking. We envision future applications of this method for a wide range of investigations into the cellular localization, dynamics, and protein-binding properties of cellular RNAs.

KAT6B overexpression in mice causes aggression, anxiety, and epilepsy

Loss of the gene encoding the histone acetyltransferase KAT6B (MYST4/MORF/QKF) causes developmental brain abnormalities as well as behavioral and cognitive defects in mice. In humans, heterozygous variants in the KAT6B gene cause two cognitive disorders, Say-Barber-Biesecker-Young-Simpson syndrome (SBBYSS; OMIM:603736) and genitopatellar syndrome (GTPTS; OMIM:606170). Although the effects of KAT6B homozygous and heterozygous mutations have been documented in humans and mice, KAT6B gain-of-function effects have not been reported. Here, we show that overexpression of the Kat6b gene in mice caused aggression, anxiety, and spontaneous epilepsy. Kat6b overexpression led to an increase in histone H3 lysine 9 acetylation and upregulation of genes driving nervous system development and neuronal differentiation. Kat6b overexpression additionally promoted neural stem cell proliferation and favored neuronal over astrocyte differentiation in vivo and in vitro. Our results suggest that, in addition to loss-of-function alleles, gain-of-function KAT6B alleles may be detrimental for brain development.

4D light sheet imaging, computational reconstruction, and cell tracking in mouse embryos

As light sheet fluorescence microscopy (LSFM) becomes widely available, reconstruction of time-lapse imaging will further our understanding of complex biological processes at cellular resolution. Here, we present a comprehensive workflow for in toto capture, processing, and analysis of multi-view LSFM experiments using the ex vivo mouse embryo as a model system of development. Our protocol describes imaging on a commercial LSFM instrument followed by computational analysis in discrete segments, using open-source software. Quantification of migration and morphodynamics is included. For complete details on the use and execution of this protocol, please refer to Dominguez et al.1.

Multiplexed dynamic control of temperature to probe and observe mammalian cells

Temperature is an important biological stimulus, yet there is a lack of approaches to modulate the temperature of biological samples in a dynamic and high-throughput manner. The thermoPlate is a device for programmable control of temperature in a 96-well plate, compatible with cell culture and microscopy. The thermoPlate maintains feedback control of temperature independently in each well, with minutes-scale heating and cooling through ΔT = 15-20°C. We first used the thermoPlate to characterize the rapid temperature-dependent phase separation of a synthetic elastin-like polypeptide (ELP53). We then examined stress granule (SG) formation in response to dynamic heat stress, revealing adaptation of SGs to persistent heat and formation of a memory of stress that prevented SG formation in response to subsequent heat shocks. The capabilities and open-source nature of the thermoPlate will empower the study and engineering of a wide range of thermoresponsive phenomena. A record of this paper's transparent peer review process is included in the Supplemental information.