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

TrackMate is an automated tracking software used to analyze bioimages and is distributed as a Fiji plugin. Here, we introduce a new version of TrackMate. TrackMate 7 is built to address the broad spectrum of modern challenges researchers face by integrating state-of-the-art segmentation algorithms into tracking pipelines. We illustrate qualitatively and quantitatively that these new capabilities function effectively across a wide range of bio-imaging experiments.

Listeriolysin S: A bacteriocin from Listeria monocytogenes that induces membrane permeabilization in a contact-dependent manner.

Listeriolysin S (LLS) is a thiazole/oxazole-modified microcin (TOMM) produced by hypervirulent clones of Listeria monocytogenes LLS targets specific gram-positive bacteria and modulates the host intestinal microbiota composition. To characterize the mechanism of LLS transfer to target bacteria and its bactericidal function, we first investigated its subcellular distribution in LLS-producer bacteria. Using subcellular fractionation assays, transmission electron microscopy, and single-molecule superresolution microscopy, we identified that LLS remains associated with the bacterial cell membrane and cytoplasm and is not secreted to the bacterial extracellular space. Only living LLS-producer bacteria (and not purified LLS-positive bacterial membranes) display bactericidal activity. Applying transwell coculture systems and microfluidic-coupled microscopy, we determined that LLS requires direct contact between LLS-producer and -target bacteria in order to display bactericidal activity, and thus behaves as a contact-dependent bacteriocin. Contact-dependent exposure to LLS leads to permeabilization/depolarization of the target bacterial cell membrane and adenosine triphosphate (ATP) release. Additionally, we show that lipoteichoic acids (LTAs) can interact with LLS and that LTA decorations influence bacterial susceptibility to LLS. Overall, our results suggest that LLS is a TOMM that displays a contact-dependent inhibition mechanism.

An image analysis method to survey the dynamics of polar protein abundance in the regulation of tip growth.

Tip growth is critical for the lifestyle of many walled cells. In yeast and fungi, this process is typically associated with the polarized deposition of conserved tip factors, including landmarks, Rho GTPases, cytoskeleton regulators, and membrane and cell wall remodelers. Because tip growth speeds may vary extensively between life cycles or species, we asked whether the local amount of specific polar elements could determine or limit tip growth speeds. Using the model fission yeast, we developed a quantitative image analysis pipeline to dynamically correlate single tip elongation speeds and polar protein abundance in large data sets. We found that polarity landmarks are typically diluted by growth. In contrast, tip growth speed is positively correlated with the local amount of factors related to actin, secretion or cell wall remodeling, but, surprisingly, exhibits long saturation plateaus above certain concentrations of those factors. Similar saturation observed for Spitzenkörper components in much faster growing fungal hyphae suggests that elements independent of canonical surface remodelers may limit single tip growth. This work provides standardized methods and resources to decipher the complex mechanisms that control cell growth.This article has an associated First Person interview with Sarah Taheraly, joint first author of the paper.

Single-Cell Analysis of the Dps Response to Oxidative Stress.

UNLABELLED: Microorganisms have developed an elaborate spectrum of mechanisms to respond and adapt to environmental stress conditions. Among these is the expression of dps, coding for the DNA-binding protein from starved cells. Dps becomes the dominant nucleoid-organizing protein in stationary-phase Escherichia coli cells and is required for robust survival under stress conditions, including carbon or nitrogen starvation, oxidative stress, metal exposure, and irradiation. To study the complex regulation of Dps in E. coli, we utilized time-lapse fluorescence microscopy imaging to examine the kinetics, input encoding, and variability of the Dps response in single cells. In the presence of an oxidative stressor, we observed a single pulse of activation of Dps production. Increased concentrations of H2O2 led to increased intensity and duration of the pulse. While lower concentrations of H2O2 robustly activated the Dps response with little effect on the growth rate, higher concentrations of H2O2 resulted in dramatically lower and highly varied growth rates. A comparison of cells exposed to the same concentration of H2O2 revealed that increased levels of Dps expression did not confer a growth advantage, indicating that recovery from stress may rely primarily upon variation in the amount of damage caused to individual cells. IMPORTANCE: We show for the first time the response of the DNA-binding protein from starved cells (Dps) to oxidative stress in single cells of E. coli Through time-lapse fluorescence microscopy, a single pulse of Dps production is observed in cells exposed to H2O2, with a duration and intensity of induction proportional to the concentration of the applied stress. More intense Dps expression did not provide a growth benefit to the bacteria, suggesting that healing from oxidative stress may largely depend upon the amount of damage in each individual cell.

Capillarity-induced ordering of spherical colloids on an interface with anisotropic curvature.

Objects floating at a liquid interface, such as breakfast cereals floating in a bowl of milk or bubbles at the surface of a soft drink, clump together as a result of capillary attraction. This attraction arises from deformation of the liquid interface due to gravitational forces; these deformations cause excess surface area that can be reduced if the particles move closer together. For micrometer-sized colloids, however, the gravitational force is too small to produce significant interfacial deformations, so capillary forces between spherical colloids at a flat interface are negligible. Here, we show that this is different when the confining liquid interface has a finite curvature that is also anisotropic. In that case, the condition of constant contact angle along the three-phase contact line can only be satisfied when the interface is deformed. We present experiments and numerical calculations that demonstrate how this leads to quadrupolar capillary interactions between the particles, giving rise to organization into regular square lattices. We demonstrate that the strength of the governing anisotropic interactions can be rescaled with the deviatoric curvature alone, irrespective of the exact shape of the liquid interface. Our results suggest that anisotropic interactions can easily be induced between isotropic colloids through tailoring of the interfacial curvature.

Three-dimensional images reveal the impact of the endosymbiont Midichloria mitochondrii on the host mitochondria.

The hard tick, Ixodes ricinus, a main Lyme disease vector, harbors an intracellular bacterial endosymbiont. Midichloria mitochondrii is maternally inherited and resides in the mitochondria of I. ricinus oocytes, but the consequences of this endosymbiosis are not well understood. Here, we provide 3D images of wild-type and aposymbiotic I. ricinus oocytes generated with focused ion beam-scanning electron microscopy. Quantitative image analyses of endosymbionts and oocyte mitochondria at different maturation stages show that the populations of both mitochondrion-associated bacteria and bacterium-hosting mitochondria increase upon vitellogenisation, and that mitochondria can host multiple bacteria in later stages. Three-dimensional reconstructions show symbiosis-dependent morphologies of mitochondria and demonstrate complete M. mitochondrii inclusion inside a mitochondrion. Cytoplasmic endosymbiont located close to mitochondria are not oriented towards the mitochondria, suggesting that bacterial recolonization is unlikely. We further demonstrate individual globular-shaped mitochondria in the wild type oocytes, while aposymbiotic oocytes only contain a mitochondrial network. In summary, our study suggests that M. mitochondrii modulates mitochondrial fragmentation in oogenesis possibly affecting organelle function and ensuring its presence over generations.

Cytotoxicity and cellular uptake of tri-block copolymer nanoparticles with different size and surface characteristics.

BACKGROUND: Polymer nanoparticles (PNP) are becoming increasingly important in nanomedicine and food-based applications. Size and surface characteristics are often considered to be important factors in the cellular interactions of these PNP, although systematic investigations on the role of surface properties on cellular interactions and toxicity of PNP are scarce. RESULTS: Fluorescent, monodisperse tri-block copolymer nanoparticles with different sizes (45 and 90 nm) and surface charges (positive and negative) were synthesized, characterized and studied for uptake and cytotoxicity in NR8383 and Caco-2 cells. All types of PNP were taken up by the cells. The positive smaller PNP45 (45 nm) showed a higher cytotoxicity compared to the positive bigger PNP(90) (90 nm) particles including reduction in mitochondrial membrane potential (ΔΨ(m)), induction of reactive oxygen species (ROS) production, ATP depletion and TNF-α release. The negative PNP did not show any cytotoxic effect. Reduction in mitochondrial membrane potential (ΔΨ(m)), uncoupling of the electron transfer chain in mitochondria and the resulting ATP depletion, induction of ROS and oxidative stress may all play a role in the possible mode of action for the cytotoxicity of these PNP. The role of receptor-mediated endocytosis in the intracellular uptake of different PNP was studied by confocal laser scanning microscopy (CLSM). Involvement of size and charge in the cellular uptake of PNP by clathrin (for positive PNP), caveolin (for negative PNP) and mannose receptors (for hydroxylated PNP) were found with smaller PNP45 showing stronger interactions with the receptors than bigger PNP(90). CONCLUSIONS: The size and surface characteristics of polymer nanoparticles (PNP; 45 and 90 nm with different surface charges) play a crucial role in cellular uptake. Specific interactions with cell membrane-bound receptors (clathrin, caveolin and mannose) leading to cellular internalization were observed to depend on size and surface properties of the different PNP. These properties of the nanoparticles also dominate their cytotoxicity, which was analyzed for many factors. The effective reduction in the mitochondrial membrane potential (ΔΨ(m)), uncoupling of the electron transfer chain in mitochondria and resulting ATP depletion, induction of ROS and oxidative stress likely all play a role in the mechanisms behind the cytotoxicity of these PNP.

Evolutionary conservation of centriole rotational asymmetry in the human centrosome.

Centrioles are formed by microtubule triplets in a ninefold symmetric arrangement. In flagellated protists and animal multiciliated cells, accessory structures tethered to specific triplets render the centrioles rotationally asymmetric, a property that is key to cytoskeletal and cellular organization in these contexts. In contrast, centrioles within the centrosome of animal cells display no conspicuous rotational asymmetry. Here, we uncover rotationally asymmetric molecular features in human centrioles. Using ultrastructure expansion microscopy, we show that LRRCC1, the ortholog of a protein originally characterized in flagellate green algae, associates preferentially to two consecutive triplets in the distal lumen of human centrioles. LRRCC1 partially co-localizes and affects the recruitment of another distal component, C2CD3, which also has an asymmetric localization pattern in the centriole lumen. Together, LRRCC1 and C2CD3 delineate a structure reminiscent of a filamentous density observed by electron microscopy in flagellates, termed the 'acorn.' Functionally, the depletion of LRRCC1 in human cells induced defects in centriole structure, ciliary assembly, and ciliary signaling, supporting that LRRCC1 cooperates with C2CD3 to organizing the distal region of centrioles. Since a mutation in the LRRCC1 gene has been identified in Joubert syndrome patients, this finding is relevant in the context of human ciliopathies. Taken together, our results demonstrate that rotational asymmetry is an ancient property of centrioles that is broadly conserved in human cells. Our work also reveals that asymmetrically localized proteins are key for primary ciliogenesis and ciliary signaling in human cells.

The RNase J-Based RNA Degradosome Is Compartmentalized in the Gastric Pathogen Helicobacter pylori.

Posttranscriptional regulation is a major level of gene expression control in any cell. In bacteria, multiprotein machines called RNA degradosomes are central for RNA processing and degradation, and some were reported to be compartmentalized inside these organelleless cells. The minimal RNA degradosome of the important gastric pathogen Helicobacter pylori is composed of the essential ribonuclease RNase J and RhpA, its sole DEAD box RNA helicase, and plays a major role in the regulation of mRNA decay and adaptation to gastric colonization. Here, the subcellular localization of the H. pylori RNA degradosome was investigated using cellular fractionation and both confocal and superresolution microscopy. We established that RNase J and RhpA are peripheral inner membrane proteins and that this association was mediated neither by ribosomes nor by RNA nor by the RNase Y membrane protein. In live H. pylori cells, we observed that fluorescent RNase J and RhpA protein fusions assemble into nonpolar foci. We identified factors that regulate the formation of these foci without affecting the degradosome membrane association. Flotillin, a bacterial membrane scaffolding protein, and free RNA promote focus formation in H. pylori Finally, RNase J-GFP (RNase J-green fluorescent protein) molecules and foci in cells were quantified by three-dimensional (3D) single-molecule fluorescence localization microscopy. The number and size of the RNase J foci were found to be scaled with growth phase and cell volume as previously reported for eukaryotic ribonucleoprotein granules. In conclusion, we propose that membrane compartmentalization and the regulated clustering of RNase J-based degradosome hubs represent important levels of control of their activity and specificity.IMPORTANCEHelicobacter pylori is a bacterial pathogen that chronically colonizes the stomach of half of the human population worldwide. Infection by H. pylori can lead to the development of gastric pathologies such as ulcers and adenocarcinoma, which causes up to 800,000 deaths in the world each year. Persistent colonization by H. pylori relies on regulation of the expression of adaptation-related genes. One major level of such control is posttranscriptional regulation, which, in H. pylori, largely relies on a multiprotein molecular machine, an RNA degradosome, that we previously discovered. In this study, we established that the two protein partners of this machine are associated with the membrane of H. pylori Using cutting-edge microscopy, we showed that these complexes assemble into hubs whose formation is regulated by free RNA and scaled with bacterial size and growth phase. Organelleless cellular compartmentalization of molecular machines into hubs emerges as an important regulatory level in bacteria.

Modeling Embryonic Cleavage Patterns.

The division patterns of early invertebrate and vertebrate embryos are key to the specification of cell fates and embryo body axes. We here describe a generic computational modeling method to quantitatively test mechanisms which specify successive division position and orientation of eggs and early blastomeres in 3D. This approach should serve to motivate and guide future experimental work on the mechanisms controlling early embryo morphogenesis.

Asymmetric division through a reduction of microtubule centering forces.

Asymmetric divisions are essential for the generation of cell fate and size diversity. They implicate cortical domains where minus end-directed motors, such as dynein, are activated to pull on microtubules to decenter asters attached to centrosomes, nuclei, or spindles. In asymmetrically dividing cells, aster decentration typically follows a centering phase, suggesting a time-dependent regulation in the competition between microtubule centering and decentering forces. Using symmetrically dividing sea urchin zygotes, we generated cortical domains of magnetic particles that spontaneously cluster endogenous dynein activity. These domains efficiently attract asters and nuclei, yielding marked asymmetric divisions. Remarkably, aster decentration only occurred after asters had first reached the cell center. Using intracellular force measurement and models, we demonstrate that this time-regulated imbalance results from a global reduction of centering forces rather than a local maturation of dynein activity at the domain. Those findings define a novel paradigm for the regulation of division asymmetry.

Emergence of a Bilaterally Symmetric Pattern from Chiral Components in the Planarian Epidermis.

Most animals exhibit mirror-symmetric body plans, yet the molecular constituents from which they are formed are often chiral. In planarian flatworms, centrioles are arranged in a bilaterally symmetric pattern across the ventral epidermis. Here, we found that this pattern is generated by a network of centrioles with prominent chiral asymmetric properties. We identify centriole components required for establishing asymmetric connections between centrioles and balancing their effects to align centrioles along polarity fields. SMED-ODF2, SMED-VFL1, and SMED-VFL3 affect the assembly of centriole appendages that tether cytoskeletal connectors to position the centrioles. We further show that the medio-lateral polarization of centrioles relies on mechanisms that are partly distinct on the left and right sides of the planarian body. Our findings shed light on how bilaterally symmetrical patterns can emerge from chiral cellular organizations.

A Positive Feedback between Growth and Polarity Provides Directional Persistency and Flexibility to the Process of Tip Growth.

Polar cell growth is a conserved morphogenetic process needed for survival, mating, and infection [1, 2]. It typically implicates the assembly and spatial stabilization of a cortical polar domain of the active form of a small GTPase of the Rho family, such as Cdc42, which promotes cytoskeleton assembly and secretion needed for local surface expansion [3-6]. In multiple physiological instances, polarity domains may switch from being spatially unstable, exhibiting a wandering behavior around the cell surface, to being stable at a fixed cellular location [7-11]. Here, we show that the rate of surface growth may be a key determinant in controlling the spatial stability of active Cdc42 domains. Reducing the growth rate of single rod-shaped fission yeast cells using chemical, genetic, and mechanical means systematically causes polar domains to detach from cell tips and oscillate around the cell surface within minutes. Conversely, an abrupt increase in growth rate improves domain stabilization. A candidate screen identifies vesicular transport along actin cables as an important module mediating this process. Similar behavior observed in distant filamentous fungi suggests that this positive feedback between growth and polarity could represent a basal property of eukaryotic polarization, promoting persistent polar growth as well as growth redirection with respect to the mechanical environment of cells.

Size Laws and Division Ring Dynamics in Filamentous Escherichia coli cells.

Our understanding of bacterial cell size control is based mainly on stress-free growth conditions in the laboratory [1-10]. In the real world, however, bacteria are routinely faced with stresses that produce long filamentous cell morphologies [11-28]. Escherichia coli is observed to filament in response to DNA damage [22-25], antibiotic treatment [11-14, 28], host immune systems [15, 16], temperature [17], starvation [20], and more [18, 19, 21], conditions which are relevant to clinical settings and food preservation [26]. This shape plasticity is considered a survival strategy [27]. Size control in this regime remains largely unexplored. Here we report that E. coli cells use a dynamic size ruler to determine division locations combined with an adder-like mechanism to trigger divisions. As filamentous cells increase in size due to growth, or decrease in size due to divisions, its multiple Fts division rings abruptly reorganize to remain one characteristic cell length away from the cell pole and two such length units away from each other. These rules can be explained by spatiotemporal oscillations of Min proteins. Upon removal of filamentation stress, the cells undergo a sequence of division events, randomly at one of the possible division sites, on average after the time required to grow one characteristic cell size. These results indicate that E. coli cells continuously keep track of absolute length to control size, suggest a wider relevance for the adder principle beyond the control of normally sized cells, and provide a new perspective on the function of the Fts and Min systems.

Mechanosensation Dynamically Coordinates Polar Growth and Cell Wall Assembly to Promote Cell Survival.

How growing cells cope with size expansion while ensuring mechanical integrity is not known. In walled cells, such as those of microbes and plants, growth and viability are both supported by a thin and rigid encasing cell wall (CW). We deciphered the dynamic mechanisms controlling wall surface assembly during cell growth, using a sub-resolution microscopy approach to monitor CW thickness in live rod-shaped fission yeast cells. We found that polar cell growth yielded wall thinning and that thickness negatively influenced growth. Thickness at growing tips exhibited a fluctuating behavior with thickening phases followed by thinning phases, indicative of a delayed feedback promoting thickness homeostasis. This feedback was mediated by mechanosensing through the CW integrity pathway, which probes strain in the wall to adjust synthase localization and activity to surface growth. Mutants defective in thickness homeostasis lysed by rupturing the wall, demonstrating its pivotal role for walled cell survival.

Eml1 loss impairs apical progenitor spindle length and soma shape in the developing cerebral cortex.

The ventricular zone (VZ) of the developing cerebral cortex is a pseudostratified epithelium that contains progenitors undergoing precisely regulated divisions at its most apical side, the ventricular lining (VL). Mitotic perturbations can contribute to pathological mechanisms leading to cortical malformations. The HeCo mutant mouse exhibits subcortical band heterotopia (SBH), likely to be initiated by progenitor delamination from the VZ early during corticogenesis. The causes for this are however, currently unknown. Eml1, a microtubule (MT)-associated protein of the EMAP family, is impaired in these mice. We first show that MT dynamics are perturbed in mutant progenitor cells in vitro. These may influence interphase and mitotic MT mechanisms and indeed, centrosome and primary cilia were altered and spindles were found to be abnormally long in HeCo progenitors. Consistently, MT and spindle length regulators were identified in EML1 pulldowns from embryonic brain extracts. Finally, we found that mitotic cell shape is also abnormal in the mutant VZ. These previously unidentified VZ characteristics suggest altered cell constraints which may contribute to cell delamination.

Interfacial tension measured at high expansion rates and within milliseconds using microfluidics.

To understand droplet formation and stabilisation, technologies are needed to measure interfacial tension at micrometer range and millisecond scale. In this paper, microtechnology is used, and that allows us to access these ranges and derive a model for surfactant free systems. The predicting power of the model was tested, and we found that it can be used to accurately (validated with >60 experiments) describe droplet size for a wide range of flow rates, interfacial tensions, and continuous phase viscosities. The model was used next to determine interfacial tensions in a system with hexadecane and sodium dodecylsulfate (SDS) solutions, and it was found that the model can be used for droplet formation times ranging from 0.4 to 9.4ms while using a wide range of process conditions. The method described here differs greatly from standard dynamic interfacial tension methods that use quiescent, mostly diffusion-limited situations. The effects that we measured are much faster due to enhanced mass transfer; this allows us to assess the typical time scales used in industrial emulsification devices.

Manipulating and quantifying temperature-triggered coalescence with microcentrifugation.

In this paper we describe a new approach to quantify the stability and coalescence kinetics of thermally switchable emulsions using an imaging-based microcentrifugation method. We first show that combining synchronized high-speed imaging with microfluidic centrifugation allows the direct measurement of the thermodynamic stability of emulsions, as expressed by the critical disjoining pressure. We apply this to a thermoresponsive emulsion, allowing us to measure the critical disjoining pressure as a function of temperature. The same method, combined with quantitative image analysis, also gives access to droplet-scale details of the coalescence process. We illustrate this by measuring temperature-dependent coalescence rates and by analysing the temperature-induced switching between two distinct microscopic mechanisms by which dense emulsions can destabilise to form a homogeneous oil phase.

In vitro nanoparticle toxicity to rat alveolar cells and coelomocytes from the earthworm Lumbricus rubellus.

Sensitivity of immune cells (coelomocytes) of Lumbricus rubellus earthworms was investigated for exposure to selected nanoparticles, in order to obtain further insight in mechanisms of effects observed after in vivo C60 exposure. In the in vivo study, tissue damage appeared to occur without accompanying increased immune responses. Coelomocytes exposed in vitro to C60 showed no decrease of their cellular viability, but demonstrated a decrease in gene expression of the cytokine-like protein CCF-1, indicating immunosuppression. Experiments with NR8383 rat macrophage cells and tri-block copolymer nanoparticles were used to compare sensitivity and to demonstrate the usefulness of coelomocytes as a test system for nano-immunotoxicity, respectively. Overall, the results imply that sensitivity towards nanoparticles differs between cell types and nanoparticles. Moreover, this study indicates that injuries in absence of an immune response, observed after in vivo C60 exposure in our earlier work, are caused by immunosuppression rather than coelomocyte mortality.

Surface charge-specific cytotoxicity and cellular uptake of tri-block copolymer nanoparticles.

A series of monodisperse (45 ± 5 nm) fluorescent nanoparticles from tri-block copolymers (polymeric nanoparticles (PNPs)) bearing different surface charges were synthesised and investigated for cytotoxicity in NR8383 and Caco-2 cells. The positive PNPs were more cytotoxic and induced a higher intracellular reactive oxygen species production than the neutral and negative ones. The cytotoxicity of positive PNPs with quaternary ammonium groups decreased with increasing steric bulk. The intracellular uptake and cellular interactions of these different PNPs were also tested in NR8383 cells by confocal laser scanning microscopy, which revealed higher uptake for positive than for negative PNPs. Also positive PNPs were found to interact much more with cell membranes, whereas the negative PNPs were internalised mainly by lysosomal endocytosis. Uptake of positive PNPs decreased with increasing steric bulk around the positive charge. A surface charge-specific interaction of clathrin for positive PNPs and caveolin receptors for negative PNPs was observed. These findings confirm that surface charge is important for the cytotoxicity of these PNPs, while they additionally point to considerable additional effects of the steric shielding around positive charges on PNP cytotoxicity.