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

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.

Statin-treated RBC dynamics in a microfluidic porous-like network

The impact of therapeutic interventions on red blood cell (RBC) deformability and microscale transport is investigated, using statins as an exemplar. Human RBCs were treated in vitro with two commonly prescribed statins, atorvastatin and rosuvastatin, at clinically relevant concentrations. Changes in RBC deformability were quantified using a microfluidic-based ektacytometer and expressed in terms of the elongation index. Dilute suspensions of the statin-treated RBCs were then perfused through a microfluidic pillar array, at a constant flow rate and negligible inertia, and imaged. Particle Tracking Velocimetry (PTV) was applied to track RBCs, identify preferential paths and estimate their velocities, whereas image processing was used to estimate cell dynamics, perfusion metrics and distributions. The findings were compared against those of healthy, untreated cells. Statins enhanced RBC deformability in agreement with literature. The extent of enhancement was found to be statin-dependent. The softer statin-treated cells were found to flow in straight, less tortuous paths, spend more time inside the pillar array and exhibit lower velocities compared to healthy RBCs, attributed to their enhanced deformation and longer shape recovery time upon impact with the array posts. The in vitro microfluidic approach demonstrated here may serve as a monitoring tool to personalise and maximise the outcome of a therapeutic treatment.

Roles for the canonical polarity machinery in the de novo establishment of polarity in budding yeast spores

The yeast Saccharomyces cerevisiae buds at sites predetermined by cortical landmarks deposited during prior budding. During mating between haploid cells in the lab, external pheromone cues override the cortical landmarks to drive polarization and cell fusion. By contrast, in haploid gametes (called spores) produced by meiosis, a predetermined polarity site drives initial polarized morphogenesis independent of mating partner location. Spore membranes are made de novo so existing cortical landmarks were unknown, as were the mechanisms by which the spore polarity site is made and how it works. We find that the landmark canonically required for distal budding, Bud8, stably marks the spore polarity site along with Bud5, a GEF for the GTPase Rsr1 that canonically links cortical landmarks to the conserved Cdc42 polarity machinery. Cdc42 and other GTPase regulators arrive at the site during its biogenesis, after spore membrane closure but apparently at the site where membrane synthesis began, and then these factors leave, pointing to the presence of discrete phases of maturation. Filamentous actin may be required for initial establishment of the site, but thereafter Bud8 accumulates independent of actin filaments. These results suggest a distinct polarization mechanism that may provide insights into gamete polarization in other organisms.

The primary cilium gene CPLANE1 is required for peripheral nervous system development

Ciliopathies are a group of neurodevelopmental disorders characterized by the dysfunction of the primary cilium. This small protrusion from most cells of our body serves as a signaling hub for cell-to-cell communication during development. Cell proliferation, differentiation, migration, and neural circuit formation have been demonstrated to depend on functional primary cilia. In the context of ciliopathies, the focus has been on the development of the central nervous system, while the peripheral nervous system has not been studied in depth. In line with phenotypes seen in patients, the absence of a functional primary cilium was shown to affect the migration of cranial and vagal neural crest cells, which contribute to the development of craniofacial features and the heart, respectively. We show here that the ciliopathy gene Cplane1 is required for the development of the peripheral nervous system. Loss of Cplane1 function in chicken embryos induces defects in dorsal root ganglia, which vary in size and fail to localize symmetrically along the spinal cord. These defects may help to understand the alteration in somatosensory perceptions described in some ciliopathy patients.

Co-zorbs: Motile, multispecies biofilms aid transport of diverse bacterial species

Biofilms are three-dimensional structures containing one or more bacterial species embedded in extracellular polymeric substances. Although most biofilms are stationary, Flavobacterium johnsoniae forms a motile spherical biofilm called a zorb, which is propelled by its base cells and contains a polysaccharide core. Here, we report the formation of spatially organized, motile, multispecies biofilms, designated "co-zorbs," that are distinguished by a core-shell structure. F. johnsoniae forms zorbs whose cells collect other bacterial species and transport them to the zorb core, forming a co-zorb. Live imaging revealed that co-zorbs also form in zebrafish, thereby demonstrating a different type of bacterial movement in vivo. This finding opens different avenues for understanding community behaviors, the role of biofilms in bulk bacterial transport, and collective strategies for microbial success in various environments.

Microtubule inner proteins of Plasmodium are essential for transmission of malaria parasites

Microtubule inner proteins (MIPs) are microtubule-associated proteins that bind to tubulin from the luminal side. MIPs can be found in axonemes to stabilize flagellar beat or within cytoplasmic microtubules. Plasmodium spp. are the causative agents of malaria that feature different parasite forms across a complex life cycle with both unique and divergent microtubule-based arrays. Here, we investigate four MIPs in a rodent malaria parasite for their role in transmission to and from the mosquito. We show by single and double gene deletions that SPM1 and TrxL1, MIPs associated with subpellicular microtubules, are dispensable for transmission from the vertebrate host to the mosquito and back. In contrast, FAP20 and FAP52, MIPs associated with the axonemes of gametes, are essential for transmission to mosquitoes but only if both genes are deleted. In the absence of both FAP20 and FAP52, the B-tubule of the axoneme partly detaches from the A-tubule, resulting in the deficiency of axonemal beating and hence gamete formation and egress. Our data suggest that a high level of redundancy ensures microtubule stability in the transmissive stages of Plasmodium, which is important for parasite transmission.

TapeTech microfluidic connectors: adhesive tape-enabled solution for organ-on-a-chip system integration

A longstanding challenge in microfluidics has been the efficient delivery of fluids from macro-scale pumping systems into microfluidic devices, known as the "world-to-chip" problem. Thus far, the entire industry has accepted the use of imperfect, rigid tubing and connectors as the ecosystem within which to operate, which, while functional, are often cumbersome, labor-intensive, prone to errors, and ill-suited for high-throughput experimentation. In this paper, we introduce TapeTech microfluidics, a flexible and scalable solution designed to address the persistent "world-to-chip" problem in microfluidics, particularly in organ-on-a-chip (OoC) applications. TapeTech offers a streamlined alternative, utilizing adhesive tape and thin-film polymers to create adaptable, integrated multi-channel ribbon connectors that simplify fluidic integration with pumps and reservoirs. Key features of TapeTech include reduced pressure surges, easy priming, rapid setup, easy multiplexing, and broad compatibility with existing devices and components, which are essential for maintaining stable fluid dynamics and protecting sensitive cell cultures. Furthermore, TapeTech is designed to flex around the lids of Petri dishes, enhancing sterility and transportability by enabling easy transfer between incubators, biosafety cabinets (BSCs), and microscopes. The rapid design-to-prototype iteration enabled by TapeTech allows users to quickly develop connectors for a wide range of microfluidic devices. Importantly, we showcase the utility of TapeTech in OoC cultures requiring fluid flow. We also highlight other utilities, such as real-time microscopy and a well-plate medium exchanger. The accessibility of this technology should enable more laboratories to simplify design and setup of microfluidic experiments, and increase technology adoption.

Cyanobacteria and Chloroflexota cooperate to structure light-responsive biofilms

Microbial mats are stratified communities often dominated by unicellular and filamentous phototrophs within an exopolymer matrix. It is challenging to quantify the dynamic responses of community members in situ as they experience steep gradients and rapid fluctuations of light. To address this, we developed a binary consortium using two representative isolates from hot spring mats: the unicellular oxygenic phototrophic cyanobacterium Synechococcus OS-B' (Syn OS-B') and the filamentous anoxygenic phototroph Chloroflexus MS-CIW-1 (Chfl MS-1). We quantified the motility of individual cells and entire colonies and demonstrated that Chfl MS-1 formed bundles of filaments that moved in all directions with no directional bias to light. Syn OS-B' was slightly less motile but exhibited positive phototaxis. This binary consortium displayed cooperative behavior by moving further than either species alone and formed ordered arrays where both species aligned with the light source. No cooperative motility was observed when a nonmotile pilB mutant of Syn OS-B' was used instead of Syn OS-B'. The binary consortium also produced more adherent biofilm than individual species, consistent with the close interspecies association revealed by electron microscopy. We propose that cyanobacteria and Chloroflexota cooperate in forming natural microbial mats by colonizing new niches and building robust biofilms.

The cell cycle oscillator and spindle length set the speed of chromosome separation in Drosophila embryos

Anaphase is tightly controlled spatiotemporally to ensure proper separation of chromosomes.1,2,3 The mitotic spindle, the self-organized microtubule structure driving chromosome segregation, scales in size with the available cytoplasm.4,5,6,7 Yet, the relationship between spindle size and chromosome movement remains poorly understood. Here, we address this relationship during the cleavage divisions of the Drosophila blastoderm. We show that the speed of chromosome separation gradually decreases during the four nuclear divisions of the blastoderm. This reduction in speed is accompanied by a similar reduction in spindle length, ensuring that these two quantities are tightly linked. Using a combination of genetic and quantitative imaging approaches, we find that two processes contribute to controlling the speed at which chromosomes move in anaphase: the activity of molecular motors important for microtubule depolymerization and sliding and the cell cycle oscillator. Specifically, we found that the levels of multiple kinesin-like proteins important for microtubule depolymerization, as well as kinesin-5, contribute to setting the speed of chromosome separation. This observation is further supported by the scaling of poleward flux rate with the length of the spindle. Perturbations of the cell cycle oscillator using heterozygous mutants of mitotic kinases and phosphatases revealed that the duration of anaphase increases during the blastoderm cycles and is the major regulator of chromosome velocity. Thus, our work suggests a link between the biochemical rate of mitotic exit and the forces exerted by the spindle. Collectively, we propose that the cell cycle oscillator and spindle length set the speed of chromosome separation in anaphase.

Differential impact of lymphatic outflow pathways on cerebrospinal fluid homeostasis

Dysfunctional lymphatic drainage from the central nervous system (CNS) has been linked to neuroinflammatory and neurodegenerative disorders, but our understanding of the lymphatic contribution to CNS fluid autoregulation remains limited. Here, we studied forces that drive the outflow of the cerebrospinal fluid (CSF) into the deep and superficial cervical lymph nodes (dcLN and scLN) and tested how the blockade of lymphatic networks affects CNS fluid homeostasis. Outflow to the dcLN occurred spontaneously in the absence of lymphatic pumping and was coupled to intracranial pressure (ICP), whereas scLN drainage was driven by pumping. Impaired dcLN drainage led to elevated CSF outflow resistance and delayed CSF-to-blood efflux despite the recruitment of the nasal-to-scLN pathway. Fluid regulation was better compensated after scLN obstruction. The dcLN pathway exhibited steady, consistent drainage across conditions, while the nasal-to-scLN pathway was dynamically activated to mitigate perturbances. These findings highlight the complex physiology of CSF homeostasis and lay the groundwork for future studies aimed at assessing and modulating CNS lymphatic function.

Balancing limited resources in actin network competition

In cells, multiple actin networks coexist in a dynamic manner. These networks compete for a common pool of actin monomers and actin-binding proteins. Interestingly, all of these networks manage to coexist despite the strong competition for resources. Moreover, the coexistence of networks with various strengths is key to cell adaptation to external changes. However, a comprehensive view of how these networks coexist in this competitive environment, where resources are limited, is still lacking. To address this question, we used a reconstituted system, in closed microwells, consisting of beads propelled by actin polymerization or micropatterns functionalized with lipids capable of initiating polymerization close to a membrane. This system enabled us to build dynamic actin architectures, competing for a limited pool of proteins, over a period of hours. We demonstrated the importance of protein turnover for the coexistence of actin networks, showing that it ensures resource distribution between weak and strong networks. However, when competition becomes too intense, turnover alone is insufficient, leading to a selection process that favors the strongest networks. Consequently, we emphasize the importance of competition strength, which is defined by the turnover rate, the amount of available protein, and the number of competing structures. More generally, this work illustrates how turnover allows biological populations with various competition strengths to coexist despite resource constraints.

Hybrid model to simulate host cell biomechanics and infection spread during intracellular infection of epithelial monolayers

Mechanical signals are crucial in regulating the response of cells in a monolayer to both physiological and pathological stressors, including intracellular bacterial infections. In particular, during intracellular infection of epithelial cells in monolayer with the food-borne bacterial pathogen Listeria monocytogenes, cellular biomechanics dictates the degree of bacterial dissemination across the monolayer. This occurs through a process whereby surrounder uninfected cells mechanically compete and eventually extrude infected cells. However, the plethora of physical mechanisms involved and their temporal dynamics are still not fully uncovered, which could inform whether they benefit or harm the host. To further investigate these mechanisms, we propose a two-dimensional hybrid computational model that combines an agent-based model with a finite element method to simulate the kinematics and dynamics of epithelial cell monolayers in the absence or presence of infection. The model accurately replicated the impact of cell density on the mechanical behaviour of uninfected monolayers, showing that increased cell density reduces cell motility and coordination of motion, cell fluidity and monolayer stresses. Moreover, when simulating the intercellular spread of infection, the model successfully reproduced the mechanical competition between uninfected and infected cells. Infected cells showed a reduction in cell area, while the surrounder cells migrated towards the infection site, exerting increased monolayer stresses, consistent with our in vitro observations. This model offers a powerful tool for studying epithelial monolayers in health and disease, by providing in silico predictions of cell shapes, kinematics and dynamics that can then be tested experimentally.

Pilin antigenic variants impact gonococcal lifestyle and antibiotic tolerance by modulating interbacterial forces

Type 4 pili (T4P) are multifunctional filaments involved in adhesion, surface motility, biofilm formation, and horizontal gene transfer. These extracellular polymers are surface-exposed and, therefore, act as antigens. The human pathogen Neisseria gonorrhoeae uses pilin antigenic variation to escape immune surveillance, yet it is unclear how antigenic variation impacts most other functions of T4P. Here, we addressed this question by replacing the major pilin of a laboratory strain with pilins from clinical isolates. We reveal that the resulting strains vary substantially in their attractive forces. Strongly interacting bacteria form microcolonies while weakly interacting bacteria retain a planktonic lifestyle. In mixed microcolonies, different variant strains segregate in agreement with the differential strength of adhesion hypothesis. By combining structural predictions and laser tweezers experiments, we show that the C-terminal region of the pilin is crucial for attraction. Lifestyle affects growth kinetics and antibiotic tolerance. In the presence of ceftriaxone or ciprofloxacin, the killing kinetics indicate strongly increased tolerance of aggregating strains. We propose that pilin antigenic variation produces a mixed population containing variants optimized for growth, colonization, or survivability under external stress. Different environments select different variants, ensuring the survival and reproduction of the population as a whole.

Nanodevice-Mediated Immune Cell Recruitment: Targeting Senescent Cells via MMP-3-Responsive CXCL12-Coated Nanoparticles

Senescent cells are involved in age-related disorders in different organs and are therapeutic targets for fibrotic and chronic pathologies. Immune-modulating agents, able to enhance senescent cell detection and elimination by endogenous immune cells, have emerged as pharmacological strategies. We report herein a nanoparticle for immune cell-mediated senolytic therapy designed to recruit immune cells in response to specific enzymatic matrix metalloproteinase-3 (MMP-3) activity in the senescence-associated secretory phenotype. For this, mesoporous silica nanoparticles (MSNs) are coated with a peptide substrate of the metalloproteinase MMP-3, and the peptide is decorated with chemokine CXCL12 that enhances immune cell recruitment (NPs@CXCL12). Controlled release studies confirmed the progressive and specific release of CXCL12 in the presence of MMP-3. The ability of immune cell recruitment in response to a senescent microenvironment (senescent WI-38 fibroblasts) is confirmed by Transwell migration assays with green fluorescent Jurkat T-cells, showing NPs@CXCL12 has an enhanced chemotaxis effect toward senescent cells compared to free CXCL12 (2-fold). Moreover, the cytotoxic capacity of human primary natural killer (NK) cells over senescent WI-38 is also confirmed, and their migration trajectories in response to NPs@CXCL12 or free CXCL12 are monitored by using a microfluidic device. Results confirm the ability of NPs@CXCL12 to generate a chemotactic gradient able to attract NK cells. When compared with free CXCL12, the NPs@CXCL12 system showed a reduction of up to 15.56% in the population of NK cells migrating toward free CXCL12 under competitive conditions. This study demonstrates the potential of designing nanoparticles to recruit immune cells under specific responses to eliminate senescent cells. Results confirm that NPs@CXCL12 can effectively establish a chemotactic gradient to attract NK cells.

Early onset of septal FtsK localization allows for efficient DNA segregation in SMC-deleted Corynebacterium glutamicum strains

Structural maintenance of chromosomes (SMC) are ubiquitously distributed proteins involved in chromosome organization. Deletion of smc causes severe growth phenotypes in many organisms. Surprisingly, smc can be deleted in Corynebacterium glutamicum, a member of the Actinomycetota phylum, without any apparent growth phenotype. SMC in C. glutamicum is loaded in a ParB-dependent fashion to the chromosome and functions in replichore cohesion. The unexpected absence of a growth phenotype in the smc mutant prompted us to screen for synthetic interactions within C. glutamicum. We generated a high-density Tn5 library from wild-type and smc-deleted C. glutamicum strains. Transposon sequencing data revealed that the DNA translocase FtsK is essential in an smc-deletion strain. In wild-type cells, FtsK localized to the septa and cell poles, showing polar enrichment during the earlier stages of the life cycle and relocating to the septum in the later stages. However, deletion of smc resulted in an earlier onset of pole-to-septum FtsK relocation, suggesting that prolonged FtsK complex activity is both required and sufficient to compensate for the absence of SMC, thus achieving efficient chromosome segregation in C. glutamicum. Deletion of ParB increases SMC and FtsK mobility. While the change in SMC dynamics aligns with previous data showing ParB's role in SMC loading on DNA, the change in FtsK mobility suggests defects in chromosome segregation. Based on our data, we propose an efficient mechanism for reliable DNA segregation in the absence of replichore arm cohesion in smc mutant cells.IMPORTANCEFaithful DNA segregation is of fundamental importance for life. Bacteria have developed efficient systems to coordinate chromosome compaction, DNA segregation, and cell division. A key factor in DNA compaction is the SMC complex that is found to be essential in many bacteria. In members of the Actinomycetota, smc is dispensable, but the reason for the lack of an smc phenotype in these bacteria remained unclear. We show here that the divisome-associated DNA pump FtsK can compensate for SMC loss and the subsequent loss in correct chromosome organization. In cells with distorted chromosomes, FtsK is recruited and stabilized earlier to the septum, allowing for DNA segregation for a larger part of the cell cycle, until chromosomes are segregated.

High-throughput Mucus Microrheology for Phenotyping and Disease Modeling

Mucus plays an integral role for the barrier function of many epithelial tissues. In the human airways, mucus is constantly secreted to capture inhaled microbes and pollutants and cleared away through concerted ciliary motion. Many important respiratory diseases exhibit altered mucus flowability and impaired clearance, contributing to respiratory distress and increased risk of infections. Understanding how mucus rheology changes during disease progression and in response to treatments is thus of great interest for subtyping patients and tailoring treatments, probing disease mechanisms, and tailoring therapies; however, basic research of mucus rheology is greatly hampered by the lack of scalable and user-friendly rheometry assays for the small volumes of mucus typically produced by in vitro respiratory models and in clinical ex vivo settings. To address this challenge, we developed a streamlined, high-throughput protocol leveraging Differential Dynamic Microscopy (DDM) to reliably measure the frequency-dependent microrheology of minuscule (3-10 µ L) mucus samples using standard epifluorescence microscopy. Our method does not require time-consuming user-interventions common in particle tracking routines and measures microrheology at the time scale of mucus relaxation (1-20s), hence greatly reducing assay time. We demonstrate the successful application of our method in mucus samples harvested from state-of-the-art air-liquid-interface (ALI) human respiratory cultures to assess mucus rheology in airway disease models and different culture conditions. To show that our approach equally applies to other types and sources of human mucus, we also validated our method with clinical samples of cervical mucus. We envision that our method can be seamlessly adopted by non-expert users, without the need for specialized equipment or extensive training, to study diseases and their treatments in the respiratory, intestinal, reproductive and other mucosal organ systems. This advancement opens up new avenues for large-scale studies, providing new insights into the role of mucus rheology which was previously limited by data accessibility and resource constraints.

Extracellular volume expansion drives vertebrate axis elongation

The vertebrate bauplan is primarily established via the formation of embryonic tissues in a head-to-tail progression. The mechanics of this elongation, which requires the presomitic mesoderm (PSM), remain poorly understood. Here, we find that avian PSM explants can elongate autonomously when physically confined in vitro, producing a pushing force promoting posterior elongation of the embryo. This tissue elongation is caused by volumetric expansion, which results from an increase in the extracellular fraction accompanied by graded cellular motility. We show that fibroblast growth factor (FGF) signaling promotes glycolysis-dependent production of hyaluronic acid (HA), which is required for expansion of the posterior PSM. Our findings link body axis elongation to tissue expansion through the metabolic control of extracellular matrix production downstream of FGF signaling.

Multifunctional Microflowers for Precise Optoacoustic Localization and Intravascular Magnetic Actuation In Vivo

Efficient drug delivery remains a significant challenge in modern medicine and pharmaceutical research. Micrometer-scale robots have recently emerged as a promising solution to enhance the precision of drug administration through remotely controlled navigation within microvascular networks. Real-time tracking is crucial for accurate guidance and confirmation of target arrival. However, deep-tissue monitoring of microscopic structures in vivo is limited by the sensitivity and spatiotemporal resolution of current bioimaging techniques. In this study, biocompatible microrobots are synthesized by incorporating indocyanine green and iron oxide nanoparticles onto copper phosphate microflowers using a layer-by-layer approach, enhancing optoacoustic contrast and enabling magnetic navigation. Magnetic control of these particles under optoacoustic guidance is demonstrated in vivo. Furthermore, super-resolution optoacoustic imaging, achieved through individual particle tracking, is shown to enable the characterization of microvascular structures and quantification of blood flow. The combination of the microflowers' high carrying capacity, in vivo actuation, and high-resolution tracking capabilities opens new opportunities for precise microvascular targeting and localized administration of theranostic agents via intravascular routes.

Integrating Particle Motion Tracking into Thermal Gel Electrophoresis for Label-Free Sugar Sensing

Bioanalytical sensors are adept at quantifying target analytes from complex sample matrices with high sensitivity, but their multiplexing capacity is limited. Conversely, analytical separations afford great multiplexing capacity but typically require analyte labeling to increase sensitivity. Here, we report the development of a separation-based sensor to sensitively quantify unlabeled polysaccharides using particle motion tracking within a microfluidic electrophoresis platform. Carboxymethyl dextran (20 kDa) was spiked into Pluronic thermal gel along with fluorescent nanoparticles (200 nm diameter) and loaded into single-channel microfluidic devices. Upon voltage application, the soluble sugar enriched into a concentrated band that induced motion of the insoluble particles as it passed. Bead displacement was tracked over time to produce electropherograms where peak areas were proportional to analyte concentrations. Key studies herein established the range of acceptable operating conditions (e.g., gel concentration, temperature) to characterize how the temperature-dependent rigidity of thermal gel influenced the analysis. Data processing strategies were then evaluated to identify conditions (e.g., exposure intervals, particle averaging, motion directionality) to maximize sensitivity. The quantitative response of the method was evaluated over a broad concentration range (0.5-5000 nM) where detection limits were found to be 520 pM for the 20 kDa sugar, providing a 106-fold superior mass LOD than a gold standard UV-vis absorbance method. Studies into the detection mechanism found that sensitivity was dependent on the molecular weight of the sugar as larger sugars produced greater responses. Collectively, these studies established best practices for integrating particle sensing into thermal gel separations for label-free polysaccharide quantitation.

Active Nematics Reinforce the Ratchet Flow in Dense Environments Without Jamming

The past decade witnessed a surge in discoveries where biological systems, such as bacteria or living cells, inherently portray active polar or nematic behavior: they prefer to align with each other and form local order during migration. Although the underlying mechanisms remain unclear, utilizing their physical properties to achieve controllable cell-layer transport will be of fundamental importance. In this study, the ratchet effect is harnessed to control the collective motion of neural progenitor cells (NPCs) in vitro. NPCs travel back-and-forth and do not specify head or tail, and therefore regarded as nematics alike liquid crystals. Ratchet and splay-shaped confinements are crafted to modulate collective cell dynamics in dense environments, while jamming is not explicitly spotted. The adaptation of an agent-based simulation further revealed how the ratchet's asymmetry and active forces from nematic order synergistically reinforce the directional cell flow. These findings provide insights into topotaxis in cell populations when restricted to crowded 2D ratchets and the mechanisms that regulate collective behavior of the cells.

Characterizing and targeting glioblastoma neuron-tumor networks with retrograde tracing

Glioblastomas are invasive brain tumors with high therapeutic resistance. Neuron-to-glioma synapses have been shown to promote glioblastoma progression. However, a characterization of tumor-connected neurons has been hampered by a lack of technologies. Here, we adapted retrograde tracing using rabies viruses to investigate and manipulate neuron-tumor networks. Glioblastoma rapidly integrated into neural circuits across the brain, engaging in widespread functional communication, with cholinergic neurons driving glioblastoma invasion. We uncovered patient-specific and tumor-cell-state-dependent differences in synaptogenic gene expression associated with neuron-tumor connectivity and subsequent invasiveness. Importantly, radiotherapy enhanced neuron-tumor connectivity by increased neuronal activity. In turn, simultaneous neuronal activity inhibition and radiotherapy showed increased therapeutic effects, indicative of a role for neuron-to-glioma synapses in contributing to therapeutic resistance. Lastly, rabies-mediated genetic ablation of tumor-connected neurons halted glioblastoma progression, offering a viral strategy to tackle glioblastoma. Together, this study provides a framework to comprehensively characterize neuron-tumor networks and target glioblastoma.

Multi-SpinX: An advanced framework for automated tracking of mitotic spindles and kinetochores in multicellular environments

SpinX, an AI-guided spindle tracking software, allows the 3-dimensional (3D) tracking of metaphase spindle movements in mammalian cells. Using over 900 images of dividing cells, we create the Multi-SpinX framework to significantly expand SpinX's applications: a) to track spindles and cell cortex in multicellular environments, b) to combine two object tracking (spindle with kinetochores marked by centromeric probes) and c) to extend spindle tracking beyond metaphase to prometaphase and anaphase stages where spindle morphology is different. We have used a human-in-the-loop approach to assess our optimisation steps, to manually identify challenges and to build a robust computational pipeline for segmenting kinetochore pairs and spindles. Spindles of both H1299 and RPE1 cells have been assessed and validated for use through Multi-SpinX, and we expect the tool to be versatile in enabling quantitative studies of mitotic subcellular dynamics.

Gradients in cell density and shape transitions drive collective cell migration into confining environments

Epithelial cell collectives migrate through tissue interfaces and crevices to orchestrate development processes, tumor invasion, and wound healing. Naturally, the traversal of cell collective through confining environments involves crowding due to narrowing spaces, which seems tenuous given the conventional inverse relationship between cell density and migration. However, the physical transitions required to overcome such epithelial densification for migration across confinements remain unclear. Here, in a system of contiguous microchannels of varying confinements, we show that epithelial (MCF10A) monolayers accumulate higher cell density and undergo fluid-like shape transitions before entering narrower channels. However, overexpression of breast cancer oncogene ErbB2 did not require such accumulation of cell density to migrate across matrix confinement. While wild-type MCF10A cells migrated faster in narrow channels, this confinement sensitivity was reduced after +ErbB2 mutation or with constitutively active RhoA. This physical interpretation of collective cell migration as density and shape transitions in granular matter could advance our understanding of complex living systems.

Spatially restricted and ontogenically distinct hepatic macrophages are required for tissue repair

Our understanding of the functional heterogeneity of resident versus recruited macrophages in the diseased liver is limited. A population of recruited lipid-associated macrophages (LAMs) has been reported to populate the diseased liver alongside resident Kupffer cells (KCs). However, the precise roles of these distinct macrophage subsets remain elusive. Here, using proteogenomics, we have identified LAMs in multiple models of liver injury. Moreover, we found that this phenotype is not specific to recruited macrophages, as a subset of resident KCs can also adopt a LAM-like phenotype in the mouse and human liver. By combining genetic mouse models targeting the distinct populations, we determined that both recruited LAMs and resident LAM-like KCs play crucial roles in tissue repair. Specifically, triggering receptor expressed on myeloid cells 2 (TREM2) expression on either resident or recruited macrophages is required for the efficient clearance of dying cells, enhancing repair and preventing exacerbated fibrosis.

Obesity increases DNA damage in the breast epithelium

Obesity is a modifiable risk factor for breast cancer. Yet, how obesity contributes to cancer initiation is not fully understood. The goal of this study was to determine if the body mass index (BMI) and metabolic hallmarks of obesity are related to DNA damage in normal breast tissue. In a mouse model of diet-induced obesity, weight gain was associated with elevated levels of DNA double-strand breaks in the mammary gland. We also found a positive correlation between BMI and DNA breaks in the breast epithelium of premenopausal women (but not postmenopausal women). High BMI was associated with elevated systemic and tissue-level oxidative DNA damage across the lifespan, and we propose that the breast epithelium undergoing menstruous proliferation waves is particularly prone to the generation of DNA breaks from oxidative lesions. Ancestry was an important modulator of the obesity-DNA break connection. Compared to non-Hispanic Whites, women identifying as African Americans had higher levels of DNA breaks, as well as elevated leptin and IGF-1. In 3D cultures of breast acini, both leptin and IGF-1 caused an accumulation of DNA damage. The results highlight a connection between premalignant genomic alterations in the breast epithelium and metabolic health modulated by obesity and ancestry. They call for attention on biological determinants of breast cancer risk disparities.

Piscis: a novel loss estimator of the F1 score enables accurate spot detection in fluorescence microscopy images via deep learning

Single-molecule RNA fluorescence in situ hybridization (RNA FISH)-based spatial transcriptomics methods have enabled the accurate quantification of gene expression at single-cell resolution by visualizing transcripts as diffraction-limited spots. While these methods generally scale to large samples, image analysis remains challenging, often requiring manual parameter tuning. We present Piscis, a fully automatic deep learning algorithm for spot detection trained using a novel loss function, the SmoothF1 loss, that approximates the F1 score to directly penalize false positives and false negatives but remains differentiable and hence usable for training by deep learning approaches. Piscis was trained and tested on a diverse dataset composed of 358 manually annotated experimental RNA FISH images representing multiple cell types and 240 additional synthetic images. Piscis outperforms other state-of-the-art spot detection methods, enabling accurate, high-throughput analysis of RNA FISH-derived imaging data without the need for manual parameter tuning.

StretchView - A Multi-Axial Cell-Stretching Device for Long-Term Automated Videomicroscopy of Living Cells

Incorporating mechanical stretching of cells in tissue culture is crucial for mimicking (patho)-physiological conditions and understanding the mechanobiological responses of cells, which can have significant implications in areas like tissue engineering and regenerative medicine. Despite the growing interest, most available cell-stretching devices are not compatible with automated live-cell imaging, indispensable for characterizing alterations in the dynamics of various important cellular processes. In this work, StretchView is presented, a multi-axial cell-stretching platform compatible with automated, time-resolved live-cell imaging. Using StretchView, long-term image acquisition of cells in the relaxed and stretched states is shown for the first time (experimental time of 12 h) without the need for human intervention. Homogeneous and stable strain fields are demonstrated for 18 h of cyclic stretching, highlighting the platform's versatility and robustness. As proof-of-principle, the effect of stretching on cell kinematics and spatiotemporal localization of the cell-cell adhesion protein E-cadherin is examined for MDCK cells in monolayer. First evidence of a monotonic increase in junctional E-cadherin localization upon exposure to stretch is presented using live-cell imaging data acquired during cyclic stretching, suggestive of an increase in barrier integrity of the monolayer. These findings highlight the potential of StretchView in providing insights into cell mechanobiology and beyond.

Phenotypic analysis of complex bioengineered 3D models

With advances in underlying technologies such as complex multicellular systems, synthetic materials, and bioengineering techniques, we can now generate in vitro miniaturized human tissues that recapitulate the organotypic features of normal or diseased tissues. Importantly, these 3D culture models have increasingly provided experimental access to diverse and complex tissues architectures and their morphogenic assembly in vitro. This review presents an analytical toolbox for biological researchers using 3D modeling technologies through which they can find a collation of currently available methods to phenotypically assess their 3D models in their normal state as well as their response to therapeutic or pathological agents.

The IQGAP-related RasGAP IqgC regulates cell-substratum adhesion in Dictyostelium discoideum

Proper adhesion of cells to their environment is essential for the normal functioning of single cells and multicellular organisms. To attach to the extracellular matrix (ECM), mammalian cells form integrin adhesion complexes consisting of many proteins that together link the ECM and the actin cytoskeleton. Similar to mammalian cells, the amoeboid cells of the protist Dictyostelium discoideum also use multiprotein adhesion complexes to control their attachment to the underlying surface. However, the exact composition of the multiprotein complexes and the signaling pathways involved in the regulation of adhesion in D. discoideum have not yet been elucidated. Here, we show that the IQGAP-related protein IqgC is important for normal attachment of D. discoideum cells to the substratum. Mutant iqgC-null cells have impaired adhesion, whereas overexpression of IqgC promotes directional migration. A RasGAP C-terminal (RGCt) domain of IqgC is sufficient for its localization in the ventral adhesion focal complexes, while RasGAP activity of a GAP-related domain (GRD) is additionally required for the proper function of IqgC in adhesion. We identify the small GTPase RapA as a novel direct IqgC interactor and show that IqgC participates in a RapA-regulated signaling pathway targeting the adhesion complexes that include talin A, myosin VII, and paxillin B. On the basis of our results, we propose that IqgC is a positive regulator of adhesion, responsible for the strengthening of ventral adhesion structures and for the temporal control of their subsequent degradation.

Configuration of electrical synapses filters sensory information to drive behavioral choices

Synaptic configurations underpin how the nervous system processes sensory information to produce a behavioral response. This is best understood for chemical synapses, and we know far less about how electrical synaptic configurations modulate sensory information processing and context-specific behaviors. We discovered that innexin 1 (INX-1), a gap junction protein that forms electrical synapses, is required to deploy context-specific behavioral strategies underlying thermotaxis behavior in C. elegans. Within this well-defined circuit, INX-1 couples two bilaterally symmetric interneurons to integrate sensory information during migratory behavior across temperature gradients. In inx-1 mutants, uncoupled interneurons display increased excitability and responses to subthreshold sensory stimuli due to increased membrane resistance and reduced membrane capacitance, resulting in abnormal responses that extend run durations and trap the animals in context-irrelevant tracking of isotherms. Thus, a conserved configuration of electrical synapses enables differential processing of sensory information to deploy context-specific behavioral strategies.

Roles for the canonical polarity machinery in the de novo establishment of polarity in budding yeast spores

The yeast Saccharomyces cerevisiae buds at sites pre-determined by cortical landmarks deposited during prior budding. During mating between haploid cells in the lab, external pheromone cues override the cortical landmarks to drive polarization and cell fusion. By contrast, in haploid gametes (called spores) produced by meiosis, a pre-determined polarity site drives initial polarized morphogenesis independent of mating partner location. Spore membranes are made de novo so existing cortical landmarks were unknown, as were the mechanisms by which the spore polarity site is made and how it works. We find that the landmark canonically required for distal budding, Bud8, stably marks the spore polarity site along with Bud5, a GEF for the GTPase Rsr1 that canonically links cortical landmarks to the conserved Cdc42 polarity machinery. Cdc42 and other GTPase regulators arrive at the site during its biogenesis, after spore membrane closure but apparently at the site where membrane synthesis began, and then these factors leave, pointing to the presence of discrete phases of maturation. Filamentous actin may be required for initial establishment of the site, but thereafter Bud8 accumulates independent of actin filaments. These results suggest a distinct polarization mechanism that may provide insights into gamete polarization in other organisms.

Divergent endothelial mechanisms drive arteriovenous malformations in Alk1 and SMAD4 loss-of-function

Hereditary hemorrhagic telangiectasia is an autosomal dominant disorder caused by mutations in the bone morphogenetic protein signaling pathway, leading to arteriovenous malformations. While previously thought to share molecular and cellular dysregulation, this study reveals highly distinct mechanisms depending on whether mutations occur in Alk1 or SMAD4. Loss of SMAD4 enhances endothelial cell responses to flow, including flow-regulated transcription and cell migration against blood flow, causing excessive pruning of capillaries and the formation of single large shunts. Conversely, Alk1 deficiency disrupts endothelial flow responses, including cell polarization and directional migration, leading to a dense vascular network and the persistence of a malformation nidus. In vivo cell population tracking of mutant cells validates unique endothelial cell migration defects. Mosaic cell culture models further illustrate that mutant cells co-opt wild-type cells driving distinct Alk1 or SMAD4 mutant-like behavioral defects. These findings demonstrate that arteriovenous malformations develop through fundamentally different cellular mechanisms based on the specific genetic mutation emphasizing the need for tailored diagnostic and therapeutic strategies.

Dietary amino acids promote glucagon-like hormone release to generate global calcium waves in adipose tissues in Drosophila

Propagation of intercellular calcium waves through tissues has been found to coordinate different multicellular responses. Nevertheless, our understanding of how calcium waves operate remains limited. In this study, we explore the real-time dynamics of intercellular calcium waves in Drosophila adipose tissues. We identify Adipokinetic Hormone (AKH), the fly functional homolog of glucagon, as the key factor driving Ca2+ activities in adipose tissue. We find that AKH, which is released into the hemolymph from the AKH-producing neurosecretory cells, stimulates calcium waves in the larval fat by a previously unrecognized gap-junction-independent mechanism to promote lipolysis. In the adult fat body, however, gap-junction-dependent intercellular calcium waves are triggered by a presumably uniformly diffused AKH. Additionally, we discover that amino acids activate the AKH-producing neurosecretory cells, leading to increased intracellular Ca2+ and AKH secretion. Altogether, we show that dietary amino acids regulate the AKH release from the AKH-producing neurosecretory cells in the brain, which subsequently stimulates gap-junction-independent intercellular calcium waves in adipose tissue, enhancing lipid metabolism.

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.

Dynamic interplay of autophagy and membrane repair during Mycobacterium tuberculosis Infection

Autophagy plays a crucial role in the host response to Mycobacterium tuberculosis (Mtb) infection, yet the dynamics and regulation of autophagy induction on Mtb-containing vacuoles (MCVs) remain only partially understood. We employed time-lapse confocal microscopy to investigate the recruitment of LC3B (LC3), a key autophagy marker, to MCVs at the single cell level with our newly developed workflow for single cell and single MCV tracking and fluorescence quantification. We show that approximately 70% of MCVs exhibited LC3 recruitment but that was lost in about 40% of those MCVs. The LC3 recruitment to MCVs displayed a high variability in timing that was independent of the size of the MCV or the bacterial burden. Most notably, the LC3-positive MCVs did not acidify, indicating that LC3 recruitment does not necessarily lead to the formation of mature autophagolysosomes. Interferon-gamma pre-treatment did not affect LC3 recruitment frequency or autophagosome acidification but increased the susceptibility of the macrophage to Mtb-induced cell death. LC3 recruitment and lysotracker staining were mutually exclusive events, alternating on some MCVs multiple times thus demonstrating a reversible aspect of the autophagy response. The LC3 recruitment was associated with galectin-3 and oxysterol-binding protein 1 staining, indicating a correlation with membrane damage and repair mechanisms. ATG7 knock-down did not impact membrane repair, suggesting that autophagy is not directly involved in this process but is coregulated by the membrane damage of MCVs. In summary, our findings provide novel insights into the dynamic and variable nature of LC3 recruitment to the MCVs over time during Mtb infection. Our data does not support a role for autophagy in either cell-autonomous defense against Mtb or membrane repair of the MCV in human macrophages. In addition, the combined dynamics of LC3 recruitment and Lysoview staining emerged as promising markers for investigating the damage and repair processes of phagosomal membranes.

Measurements of neurite extension and nucleokinesis in an iPSC-derived model system following microtubule perturbation

In neurons, patterns of different microtubule types are essential for neurite extension and nucleokinesis. Cellular model systems such as rodent primary cultures and induced pluripotent stem cells (iPSC)-derived neurons have provided key insights into how these patterns are created and maintained through the action of microtubule-associated proteins, motor proteins, and regulatory enzymes. iPSC-derived models show tremendous promise but lack benchmarking and validation relative to rodent primary cultures. Here we have characterized a recent iPSC-derived model, in which doxycycline-induced expression of Neurogenin-2 drives consistent transdifferentiation into the neuronal state (EBiSC-NEUR1 neurons, referred to as NGN2 neurons below). We developed a suite of open-access, semiautomated methods to measure neurite extension and nucleokinesis of NGN2 neurons, which compare favorably to published data from other models. Then, we challenged NGN2 neurons with a panel of drugs that perturb microtubule physiology. NGN2 neurons extension and nucleokinesis were significantly perturbed by two microtubule-targeting drugs, namely a taxane (paclitaxel) and a vinca alkaloid (DZ-2384). In contrast, inhibition of microtubule severing (spastazoline) or of deacetylation (trichostatin A) had a limited effect on nucleokinesis only. Our results support the primary importance of microtubule dynamics in neuronal development and demonstrate the power of NGN2 neurons as a model system.

Substrate stiffness-dependent activation of Hippo pathway in cancer associated fibroblasts

The tumor microenvironment (TME) comprises a heterogenous cell population within a complex three-dimensional (3D) extracellular matrix (ECM). Stromal cells within this TME are altered by signaling cues from cancer cells to support uncontrolled tumor growth and invasion events. Moreover, the ECM also plays a fundamental role in tumor development through pathological remodeling, stiffening and interaction with TME cells. In healthy tissues, Hippo signaling pathway actively contributes to tissue growth, cell proliferation and apoptosis. However, in cancer, the Hippo signaling pathway is highly dysregulated, leading to nuclear translocation of the YAP/TAZ complex, which directly contributes to uncontrolled cell proliferation and tissue growth, and ECM remodeling and stiffening processes. Here, we compare the effect of increasing cell culture substrate stiffness, derived from tumor progression, upon the dysregulation of the Hippo signaling pathway in colorectal cancer-associated fibroblasts (CAFs) and normal colorectal fibroblasts (NFs). We correlate the dysregulation of Hippo pathway with the magnitude of the traction forces exerted by healthy and malignant stromal cells. We found that ECM stiffening is crucial in Hippo pathway dysregulation in CAFs, but not in normal fibroblasts.

BETA CELL DYSFUNCTION OCCURS INDEPENDENTLY OF INSULITIS IN TYPE 1 DIABETES PATHOGENESIS

During type 1 diabetes (T1D) progression, beta cells become dysfunctional and exhibit reduced first-phase insulin release. While this period of beta cell dysfunction is well established, its cause and underlying mechanism remain unknown. To address this knowledge gap, live human pancreas tissue slices were prepared from autoantibody-negative organ donors without diabetes (ND), donors positive for one or more islet autoantibodies (AAb+), and donors with T1D within 0-4 years of diagnosis (T1D+). Dynamic imaging and physiological secretion studies were conducted to assess the extent and impact of T cell infiltration on beta cell function through immunolabeling, Ca2+ imaging, and perifusion assays for insulin secretion. Beta cells were identified in living slices by ENTPD3 cell surface staining. Beta cells from both ND and AAb+ donors exhibited normal cytosolic Ca2+ mobilization in response to high glucose and KCl. Beta cells from donors with T1D had significantly diminished Ca2+ responses to high glucose but preserved responses to KCl. In T1D, glucose responsiveness was impaired in both T cell-infiltrated and non-infiltrated insulin positive islets, supporting the concept that beta cell dysfunction is independent of close spatial association between beta cells and T cells. Fixed tissue staining and gene expression profiling of laser-capture microdissected islets revealed significant decreases in markers of glucose metabolism to ATP in beta cells from donors with T1D but no changes in endoplasmic reticulum (ER) stress markers. From these data, we posit that functional defects occur in beta cells during T1D pathogenesis independent of local T cell infiltration and beta cell destruction. Additionally, these beta cell metabolic defects contribute to the clinical manifestation of dysglycemia at T1D diagnosis despite a remaining mass of beta cells.

Density-dependent flow generation in active cytoskeletal fluids

The actomyosin cytoskeleton, a protein assembly comprising actin fibers and the myosin molecular motor, drives various cellular dynamics through contractile force generation at high densities. However, the relationship between the density dependence of the actomyosin cytoskeleton and force-controlled ordered structure remains poorly understood. In this study, we measured contraction-driven flow generation by varying the concentration of cell extracts containing the actomyosin cytoskeleton and associated nucleation factors. We observed continuous actin flow toward the center at a critical actomyosin density in cell-sized droplets. The actin flow exhibited an emergent oscillation in which the tracer advection in the bulk solution periodically changed in a stop-and-go fashion. In the vicinity of the actomyosin density where oscillatory dynamics occur, the velocity of tracer particle motion decreases with actomyosin density but exhibits superdiffusive motion. Furthermore, the increase or decrease in myosin activity causes the oscillatory flow generation to become irregular, indicating that the density-dependent flow generation of actomyosin is driven by an interplay between actin density and myosin force generation.

Quantitative Live Imaging Reveals Phase Dependency of PDAC Patient-Derived Organoids on ERK and AMPK Activity

Patient-derived organoids represent a novel platform to recapitulate the cancer cells in the patient tissue. While cancer heterogeneity has been extensively studied by a number of omics approaches, little is known about the spatiotemporal kinase activity dynamics. Here we applied a live imaging approach to organoids derived from 10 pancreatic ductal adenocarcinoma (PDAC) patients to comprehensively understand their heterogeneous growth potential and drug responses. By automated wide-area image acquisitions and analyses, the PDAC cells were non-selectively observed to evaluate their heterogeneous growth patterns. We monitored single-cell ERK and AMPK activities to relate cellular dynamics to molecular dynamics. Furthermore, we evaluated two anti-cancer drugs, a MEK inhibitor, PD0325901, and an autophagy inhibitor, hydroxychloroquine (HCQ), by our analysis platform. Our analyses revealed a phase-dependent regulation of PDAC organoid growth, where ERK activity is necessary for the early phase and AMPK activity is necessary for the late stage of organoid growth. Consistently, we found PD0325901 and HCQ target distinct organoid populations, revealing their combination is widely effective to the heterogeneous cancer cell population in a range of PDAC patient-derived organoid lines. Together, our live imaging quantitatively characterized the growth and drug sensitivity of human PDAC organoids at multiple levels: in single cells, single organoids, and individual patients. This study will pave the way for understanding the cancer heterogeneity and promote the development of new drugs that eradicate intractable cancer.

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.

Hybrid Cell Membrane-Engineered Nanocarrier for Triple-Action Strategy to Address Pseudomonas aeruginosa Infection

Bacterial infections resistant to antimicrobial treatments, particularly those caused by Pseudomonas aeruginosa (P. aeruginosa), frequently lead to elevated mortality rates. Tackling this resistance using therapeutic combinations with varied mechanisms has shown considerable promise. In this study, a bioinspired nanocarrier is successfully designed and engineered for targeted antibiotic delivery and toxin/bacteria clearance. This is achieved by encapsulating antibiotic-loaded framework nucleic acids with hybrid cell membranes acquired from neutrophils and platelets. By coating the hybrid membrane outside the shell, nanocarriers are endowed with the function of neutrophil-like chemotaxis and platelet-like bacteria adhesion to achieve the first stage of inflammation targeting. Based on the specific binding of bacteria toxin to the hybrid membrane, the release of antibiotic-loaded framework nucleic acids is triggered by toxin-mediated membrane lysis to fulfill the second stage of toxin neutralization and bacteria killing. Meanwhile, the immunomodulation potential of framework nucleic acids enables nanocarriers to accomplish the third stage of reversing the immunosuppressive microenvironment. In mouse models of acute and chronic P. aeruginosa pneumonia, the nanocarriers can reduce bacterial burden at a low dosage and decrease mortality with negligible toxicity. In sum, these findings have illustrated the remarkable capability of nanocarriers in treating recalcitrant bacterial infections.

Hormone-responsive progenitors have a unique identity and exhibit high motility during mammary morphogenesis

Hormone-receptor-positive (HR+) luminal cells largely mediate the response to estrogen and progesterone during mammary gland morphogenesis. However, there remains a lack of consensus on the precise nature of the precursor cells that maintain this essential HR+ lineage. Here we refine the identification of HR+ progenitors and demonstrate their unique regenerative capacity compared to mature HR+ cells. HR+ progenitors proliferate but do not expand, suggesting rapid differentiation. Subcellular resolution, 3D intravital microscopy was performed on terminal end buds (TEBs) during puberty to dissect the contribution of each luminal lineage. Surprisingly, HR+ TEB progenitors were highly elongated and motile compared to columnar HR- progenitors and static, conoid HR+ cells within ducts. This dynamic behavior was also observed in response to hormones. Development of an AI model for motility dynamics analysis highlighted stark behavioral changes in HR+ progenitors as they transitioned to mature cells. This work provides valuable insights into how progenitor behavior contributes to mammary morphogenesis.

The plant retromer components SNXs bind to ATG8 and CLASP to mediate autophagosome movement along microtubules

In eukaryotic cells, autophagosomes are double-membrane vesicles that are highly mobile and traffic along cytoskeletal tracks. While core autophagy-related proteins (ATGs) and other regulators involved in autophagosome biogenesis in plants have been extensively studied, the specific components regulating plant autophagosome motility remain elusive. In this study, using TurboID-based proximity labeling, we identify the retromer subcomplex comprising sorting nexin 1 (SNX1), SNX2a, and SNX2b as interacting partners of ATG8. Remarkably, SNX proteins decorate ATG8-labeled autophagosomes and facilitate their coordinated movement along microtubules. Depletion of SNX proteins restricts the motility of autophagosomes in the cytoplasm, resulting in decreased autophagic flux. Furthermore, we show that the microtubule-associated protein CLASP is a bridge, connecting the SNX-ATG8-decorated autophagosomes to the microtubules. Genetically, the clasp-1 mutant phenotype resembles that of plants with disrupted SNXs or microtubule networks, displaying diminished autophagosome motility and reduced autophagic flux. Collectively, our study unveils a hitherto unanticipated role of the SNXs subcomplex in connecting autophagosomes with microtubules to promote autophagosome mobility in Arabidopsis.

ThirdPeak is a flexible tool designed for the robust analysis of two- and three-dimensional tracking data

Biological processes, though often imaged and visualized in two dimensions, inherently occur in at least three-dimensional space. As time-resolved volumetric imaging becomes increasingly accessible, there emerges a necessity for tools that empower non-specialists to process and interpret intricate datasets. We introduce ThirdPeak, an open-source tool tailored for the comprehensive analysis of two- and three-dimensional track data across various scales. Its versatile import and export options ensure seamless integration into established workflows, while the intuitive user interface allows for swift visualization and analysis of the data. When applied to live-cell diffusion data, this software demonstrates the benefits of integrating both 2D and 3D analysis, yielding valuable insights into the understanding of biological processes.

Protocol for live-cell imaging of immune synapse formation and activation of CAR T cells against cancer cells

Immune synapse (IS) formation determines T cell antitumor activity. Here, we present a protocol for characterizing the IS formation between chimeric antigen receptor (CAR) T cells and tumor cells by measuring the IS size and calcium flux by live-cell imaging. We describe steps for CAR T cell manufacturing, sample preparation, image acquisition, and data analysis. For complete details on the use and execution of this protocol, please refer to Chockley et al.,1 Ibanez et al.,2 and Zoine et al.3.

ECM-dependent regulation of septin 7 in focal adhesions promotes mechanosensing and functional response in fibroblasts

Fibroblasts are adherent cells that maintain tissue homeostasis by sensing and responding to the extracellular matrix (ECM). Focal adhesions (FAs) link these ECM changes to actomyosin dynamics through changes in its composition, influencing cellular response. Septin-7 (Sept-7) has previously been found in FA proteomics studies and shown to influence ECM sensing. Using total internal reflection microscopy, we found that ECM-mediated integrin activation regulates spatially distinct Sept-7 structures in FAs. In perinuclear regions, ECM binding stabilized Sept-7 bundles at the back of FAs, while in the core of peripheral FAs high integrin activation promoted elongation of Sept-7 structures. Ventral Sept-7 structures were crucial for ECM sensing, impacting region-specific FA elongation, stabilization, and contributing to fibroblast mechanosensitivity. Taken together, our results suggest that ECM and integrin-dependent regulation of ventral Sept-7 structures plays a pivotal role in fibroblast ECM sensing and mechanotransduction through its recruitment and assembly into FA subpopulations.

The scramblases VMP1 and TMEM41B are required for primitive endoderm specification by targeting WNT signaling

The ER-resident proteins VMP1 and TMEM41B share a conserved DedA domain, which confers lipid scramblase activity. Loss of either gene results in embryonic lethality in mice and defects in autophagy and lipid droplet metabolism. To investigate their role in pluripotency and lineage specification, we generated Vmp1 and Tmem41b mutations in mouse embryonic stem cells (ESCs). We observed that ESCs carrying mutations in Vmp1 and Tmem41b show robust self-renewal and an unperturbed pluripotent expression profile but accumulate LC3-positive autophagosomes and lipid droplets consistent with defects in autophagy and lipid metabolism. ESCs carrying combined mutations in Vmp1 and Tmem41b can differentiate into a wide range of embryonic cell types. However, differentiation into primitive endoderm-like cells in culture is impaired, and the establishment of extra-embryonic endoderm stem (XEN) cells is delayed. Mechanistically, we show the deregulation of genes that are associated with WNT signaling. This is further confirmed by cell surface proteome profiling, which identified a significant reduction of the WNT-receptor FZD2 at the plasma membrane in Vmp1 and Tmem41b double mutant ESCs. Importantly, we show that transgenic expression of Fzd2 rescues XEN differentiation. Our findings identify the role of the lipid scramblases VMP1 and TMEM41B in WNT signaling during extra-embryonic endoderm development and characterize their distinct and overlapping functions.

Lipid Membrane Domains Control Actin Network Viscoelasticity

The mammalian cell membrane is embedded with biomolecular condensates of protein and lipid clusters, which interact with an underlying viscoelastic cytoskeleton network to organize the cell surface and mechanically interact with the extracellular environment. However, the mechanical and thermodynamic interplay between the viscoelastic network and liquid-liquid phase separation of 2-dimensional (2D) lipid condensates remains poorly understood. Here, we engineer materials composed of 2D lipid membrane condensates embedded within a thin viscoelastic actin network. The network generates localized anisotropic stresses that deform lipid condensates into triangular morphologies with sharp edges and corners, shapes unseen in many 3D composite gels. Kinetic coarsening of phase-separating lipid condensates accelerates the viscoelastic relaxation of the network, leading to an effectively softer composite material over intermediate time scales. We dynamically manipulate the membrane composition to control the elastic-to-viscous crossover of the network. Such viscoelastic composite membranes may enable the development of coatings, catalytic surfaces, separation membranes, and other interfaces with tunable spatial organization and plasticity mechanisms.

The cell cycle oscillator and spindle length set the speed of chromosome separation in Drosophila embryos

Anaphase is tightly controlled in space and time to ensure proper separation of chromosomes. The mitotic spindle, the self-organized microtubule structure driving chromosome segregation, scales in size with the available cytoplasm. Yet, the relationship between spindle size and chromosome movement remains poorly understood. Here, we address how the movement of chromosomes changes during the cleavage divisions of the Drosophila blastoderm. We show that the speed of chromosome separation gradually decreases during the 4 nuclear divisions of the blastoderm. This reduction in speed is accompanied by a similar reduction in the length of the spindle, thus ensuring that these two quantities are tightly linked. Using a combination of genetic and quantitative imaging approaches, we find that two processes contribute to controlling the speed at which chromosomes move at mitotic exit: the activity of molecular motors important for microtubule depolymerization and sliding, and the cell cycle oscillator. Specifically, we found that the levels of Klp10A, Klp67A, and Klp59C, three kinesin-like proteins important for microtubule depolymerization, and the level of microtubule sliding motor Klp61F (kinesin-5) contribute to setting the speed of chromosome separation. This observation is supported by quantification of microtubule dynamics indicating that poleward flux rate scales with the length of the spindle. Perturbations of the cell cycle oscillator using heterozygous mutants of mitotic kinases and phosphatases revealed that the duration of anaphase increases during the blastoderm cycles and is the major regulator of chromosome velocity. Thus, our work suggests a potential link between the biochemical rate of mitotic exit and the forces exerted by the spindle. Collectively, we propose that the cell cycle oscillator and spindle length set the speed of chromosome separation in anaphase.