Analysis of transient behavior in complex trajectories: application to secretory vesicle dynamics

Mapping the energy and diffusion landscapes of membrane proteins at the cell surface using high-density single-molecule imaging and Bayesian inference: application to the multiscale dynamics of glycine receptors in the neuronal membrane

Protein mobility is conventionally analyzed in terms of an effective diffusion. Yet, this description often fails to properly distinguish and evaluate the physical parameters (such as the membrane friction) and the biochemical interactions governing the motion. Here, we present a method combining high-density single-molecule imaging and statistical inference to separately map the diffusion and energy landscapes of membrane proteins across the cell surface at ~100 nm resolution (with acquisition of a few minutes). Upon applying these analytical tools to glycine neurotransmitter receptors at inhibitory synapses, we find that gephyrin scaffolds act as shallow energy traps (~3 kBT) for glycine neurotransmitter receptors, with a depth modulated by the biochemical properties of the receptor-gephyrin interaction loop. In turn, the inferred maps can be used to simulate the dynamics of proteins in the membrane, from the level of individual receptors to that of the population, and thereby, to model the stochastic fluctuations of physiological parameters (such as the number of receptors at synapses). Overall, our approach provides a powerful and comprehensive framework with which to analyze biochemical interactions in living cells and to decipher the multiscale dynamics of biomolecules in complex cellular environments.

Cdc42 controls the dilation of the exocytotic fusion pore by regulating membrane tension

On exocytosis, membrane fusion starts with the formation of a narrow fusion pore that must expand to allow the release of secretory compounds. The GTPase Cdc42 promotes fusion pore dilation in neuroendocrine cells by controlling membrane tension.

Membrane fusion underlies multiple processes, including exocytosis of hormones and neurotransmitters. Membrane fusion starts with the formation of a narrow fusion pore. Radial expansion of this pore completes the process and allows fast release of secretory compounds, but this step remains poorly understood. Here we show that inhibiting the expression of the small GTPase Cdc42 or preventing its activation with a dominant negative Cdc42 construct in human neuroendocrine cells impaired the release process by compromising fusion pore enlargement. Consequently the mode of vesicle exocytosis was shifted from full-collapse fusion to kiss-and-run. Remarkably, Cdc42-knockdown cells showed reduced membrane tension, and the artificial increase of membrane tension restored fusion pore enlargement. Moreover, inhibiting the motor protein myosin II by blebbistatin decreased membrane tension, as well as fusion pore dilation. We conclude that membrane tension is the driving force for fusion pore dilation and that Cdc42 is a key regulator of this force.

Identifying directional persistence in intracellular particle motion using Hidden Markov Models

Particle tracking is a widely used and promising technique for elucidating complex dynamics of the living cell. The cytoplasm is an active material, in which the kinetics of intracellular structures are highly heterogeneous. Tracer particles typically undergo a combination of random motion and various types of directed motion caused by the activity of molecular motors and other non-equilibrium processes. Random switching between more and less directional persistence of motion generally occurs. We present a method for identifying states of motion with different directional persistence in individual particle trajectories. Our analysis is based on a multi-scale turning angle model to characterize motion locally, together with a Hidden Markov Model with two states representing different directional persistence. We define one of the states by the motion of particles in a reference data set where some active processes have been inhibited. We illustrate the usefulness of the method by studying transport of vesicles along microtubules and transport of nanospheres activated by myosin. We study the results using mean square displacements, durations, and particle speeds within each state. We conclude that the method provides accurate identification of states of motion with different directional persistence, with very good agreement in terms of mean-squared displacement between the reference data set and one of the states in the two-state model.

Delineating cooperative responses of processive motors in living cells

Characterizing the collective functions of cytoskeletal motors is critical to understanding mechanisms that regulate the internal organization of eukaryotic cells as well as the roles various transport defects play in human diseases. Though in vitro assays using synthetic motor complexes have generated important insights, dissecting collective motor functions within living cells still remains challenging. Here, we show that the protein heterodimerization switches FKBP-rapalog-FRB can be harnessed in engineered COS-7 cells to compare the collective responses of kinesin-1 and myosinVa motors to changes in motor number and cargo size. The dependence of cargo velocities, travel distances, and position noise on these parameters suggests that multiple myosinVa motors can cooperate more productively than collections of kinesins in COS-7 cells. In contrast to observations with kinesin-1 motors, the velocities and run lengths of peroxisomes driven by multiple myosinVa motors are found to increase with increasing motor density, but are relatively insensitive to the higher loads associated with transporting large peroxisomes in the viscoelastic environment of the COS-7 cell cytoplasm. Moreover, these distinctions appear to be derived from the different sensitivities of kinesin-1 and myosinVa velocities and detachment rates to forces at the single-motor level. The collective behaviors of certain processive motors, like myosinVa, may therefore be more readily tunable and have more substantial roles in intracellular transport regulatory mechanisms compared with those of other cytoskeletal motors.

Bayesian decision tree for the classification of the mode of motion in single-molecule trajectories

Membrane proteins move in heterogeneous environments with spatially (sometimes temporally) varying friction and with biochemical interactions with various partners. It is important to reliably distinguish different modes of motion to improve our knowledge of the membrane architecture and to understand the nature of interactions between membrane proteins and their environments. Here, we present an analysis technique for single molecule tracking (SMT) trajectories that can determine the preferred model of motion that best matches observed trajectories. The method is based on Bayesian inference to calculate the posteriori probability of an observed trajectory according to a certain model. Information theory criteria, such as the Bayesian information criterion (BIC), the Akaike information criterion (AIC), and modified AIC (AICc), are used to select the preferred model. The considered group of models includes free Brownian motion, and confined motion in 2nd or 4th order potentials. We determine the best information criteria for classifying trajectories. We tested its limits through simulations matching large sets of experimental conditions and we built a decision tree. This decision tree first uses the BIC to distinguish between free Brownian motion and confined motion. In a second step, it classifies the confining potential further using the AIC. We apply the method to experimental Clostridium Perfingens [Formula: see text]-toxin (CP[Formula: see text]T) receptor trajectories to show that these receptors are confined by a spring-like potential. An adaptation of this technique was applied on a sliding window in the temporal dimension along the trajectory. We applied this adaptation to experimental CP[Formula: see text]T trajectories that lose confinement due to disaggregation of confining domains. This new technique adds another dimension to the discussion of SMT data. The mode of motion of a receptor might hold more biologically relevant information than the diffusion coefficient or domain size and may be a better tool to classify and compare different SMT experiments.

Automated characterization and parameter-free classification of cell tracks based on local migration behavior

Cell migration is the driving force behind the dynamics of many diverse biological processes. Even though microscopy experiments are routinely performed today by which populations of cells are visualized in space and time, valuable information contained in image data is often disregarded because statistical analyses are performed at the level of cell populations rather than at the single-cell level. Image-based systems biology is a modern approach that aims at quantitatively analyzing and modeling biological processes by developing novel strategies and tools for the interpretation of image data. In this study, we take first steps towards a fully automated characterization and parameter-free classification of cell track data that can be generally applied to tracked objects as obtained from image data. The requirements to achieve this aim include: (i) combination of different measures for single cell tracks, such as the confinement ratio and the asphericity of the track volume, and (ii) computation of these measures in a staggered fashion to retrieve local information from all possible combinations of track segments. We demonstrate for a population of synthetic cell tracks as well as for in vitro neutrophil tracks obtained from microscopy experiment that the information contained in the track data is fully exploited in this way and does not require any prior knowledge, which keeps the analysis unbiased and general. The identification of cells that show the same type of migration behavior within the population of all cells is achieved via agglomerative hierarchical clustering of cell tracks in the parameter space of the staggered measures. The recognition of characteristic patterns is highly desired to advance our knowledge about the dynamics of biological processes.

Ultrasensitive imaging in live cells using fluorescent quantum dots

Semiconductor quantum dots (QDs) are fluorescent nanoparticles that can be used for biological imaging. Because of their brightness and photostability, which are far superior to those of organic dyes and fluorescent proteins, they can be detected at the single-particle level over long periods of time using standard fluorescence microscopy techniques. QDs can be conjugated to biomolecules and then used to track the motion of these molecules.

Diagnosing heterogeneous dynamics in single-molecule/particle trajectories with multiscale wavelets

We describe a simple automated method to extract and quantify transient heterogeneous dynamical changes from large data sets generated in single-molecule/particle tracking experiments. Based on wavelet transform, the method transforms raw data to locally match dynamics of interest. This is accomplished using statistically adaptive universal thresholding, whose advantage is to avoid a single arbitrary threshold that might conceal individual variability across populations. How to implement this multiscale method is described, focusing on local confined diffusion separated by transient transport periods or hopping events, with three specific examples: in cell biology, biotechnology, and glassy colloid dynamics. The discussion is generalized within the framework of continuous time random walk. This computationally efficient method can run routinely on hundreds of millions of data points analyzed within an hour on a desktop personal computer.

Quantitative imaging of morphogen gradients in Drosophila imaginal discs

Cells at different positions in a developing tissue receive different concentrations of signaling molecules, called morphogens, and this influences their cell fate. Morphogen concentration gradients have been proposed to control patterning as well as growth in many developing tissues. Some outstanding questions about tissue patterning by morphogen gradients are the following: What are the mechanisms that regulate gradient formation and shape? Is the positional information encoded in the gradient sufficiently precise to determine the positions of target gene domain boundaries? What are the temporal dynamics of gradients and how do they relate to patterning and growth? These questions are inherently quantitative in nature and addressing them requires measuring morphogen concentrations in cells, levels of downstream signaling activity, and kinetics of morphogen transport. Here we first present methods for quantifying morphogen gradient shape in which the measurements can be calibrated to reflect actual morphogen concentrations. We then discuss using fluorescence recovery after photobleaching to study the kinetics of morphogen transport at the tissue level. Finally, we present particle tracking as a method to study morphogen intracellular trafficking.

Intracellular transport of insulin granules is a subordinated random walk

We quantitatively analyzed particle tracking data on insulin granules expressing fluorescent fusion proteins in MIN6 cells to better understand the motions contributing to intracellular transport and, more generally, the means for characterizing systems far from equilibrium. Care was taken to ensure that the statistics reflected intrinsic features of the individual granules rather than details of the measurement and overall cell state. We find anomalous diffusion. Interpreting such data conventionally requires assuming that a process is either ergodic with particles working against fluctuating obstacles (fractional brownian motion) or nonergodic with a broad distribution of dwell times for traps (continuous-time random walk). However, we find that statistical tests based on these two models give conflicting results. We resolve this issue by introducing a subordinated scheme in which particles in cages with random dwell times undergo correlated motions owing to interactions with a fluctuating environment. We relate this picture to the underlying microtubule structure by imaging in the presence of vinblastine. Our results provide a simple physical picture for how diverse pools of insulin granules and, in turn, biphasic secretion could arise.

Fluorescently-Labeled Estradiol Internalization and Membrane Trafficking in Live N-38 Neuronal Cells Visualized with Total Internal Reflection Fluorescence Microscopy

Estradiol is a steroid hormone that binds and activates estradiol receptors. Activation of these receptors is known to modulate neuronal physiology and provide neuroprotection, but it is not completely understood how estradiol mediates these actions on the nervous system. Activation of a sub-population of estradiol receptor-α (ERα), originally identified as a nuclear protein, localizes to the plasma membrane and appears to be a critical step in neuroprotection against brain injury and disease. Previously we showed that estradiol stimulates the rapid and transient trafficking of plasma membrane ERα in primary hypothalamic neurons, and internalization of membrane-impermeant estradiol (E6BSA-FITC) into cortical neuron endosomes in vitro. These findings support the concept that estradiol activates and down-regulates plasma membrane ERα by triggering endocytosis. Here, we use TIRFM (total internal reflection fluorescence microscopy) to image the trafficking of E6BSA-FITC, and GFP-labeled ERα, in live cells in real time. We show that activation of plasma membrane ERs by E6BSA-FITC result in internalization of the fluorescent ligand in live N-38 neurons, an immortalized hypothalamic cell line. Pretreatment with ER antagonist ICI 182,780 decreased the number of E6BSA-FITC labeled puncta observed. We also observed in live N-38 neurons that E6BSA-FITC co-localized with FM4-64 and LysoTracker fluorescent dyes that label endosomes and lysosomes. Our results provide further evidence that plasma membrane ERα activation results in endocytosis of the receptor.

Single-molecule tracking in living cells using single quantum dot applications

Revealing the behavior of single molecules in living cells is very useful for understanding cellular events. Quantum dot probes are particularly promising tools for revealing how biological events occur at the single molecule level both in vitro and in vivo. In this review, we will introduce how single quantum dot applications are used for single molecule tracking. We will discuss how single quantum dot tracking has been used in several examples of complex biological processes, including membrane dynamics, neuronal function, selective transport mechanisms of the nuclear pore complex, and in vivo real-time observation. We also briefly discuss the prospects for single molecule tracking using advanced probes.

ATP alters the diffusion mechanics of MutS on mismatched DNA

The mismatch repair (MMR) initiation protein MutS forms at least two types of sliding clamps on DNA: a transient mismatch searching clamp (∼1 s) and an unusually stable (∼600 s) ATP-bound clamp that recruits downstream MMR components. Remarkably, direct visualization of single MutS particles on mismatched DNA has not been reported. We have combined real-time particle tracking with fluorescence resonance energy transfer (FRET) to image MutS diffusion dynamics on DNA containing a single mismatch. We show searching MutS rotates during diffusion independent of ionic strength or flow rate, suggesting continuous contact with the DNA backbone. In contrast, ATP-bound MutS clamps that are visually and successively released from the mismatch spin freely around the DNA, and their diffusion is affected by ionic strength and flow rate. These observations show that ATP binding alters the MutS diffusion mechanics on DNA, which has a number of implications for the mechanism of MMR.

Optimal diffusion coefficient estimation in single-particle tracking

Single-particle tracking is increasingly used to extract quantitative parameters on single molecules and their environment, while advances in spatial and temporal resolution of tracking techniques inspire new questions and avenues of investigation. Correspondingly, sophisticated analytical methods are constantly developed to obtain more refined information from measured trajectories. Here we point out some fundamental limitations of these approaches due to the finite length of trajectories, the presence of localization error, and motion blur, focusing on the simplest motion regime of free diffusion in an isotropic medium (Brownian motion). We show that two recently proposed algorithms approach the theoretical limit of diffusion coefficient uncertainty. We discuss the practical performance of the algorithms as well as some important implications of these results for single-particle tracking.

Myrip couples the capture of secretory granules by the actin-rich cell cortex and their attachment to the plasma membrane

Exocytosis of secretory granules (SGs) requires their delivery to the actin-rich cell cortex followed by their attachment to the plasma membrane (PM). How these reactions are executed and coordinated is still unclear. Myrip, which is also known as Slac-2c, binds to the SG-associated GTPase Rab27 and is thought to promote the delivery of SGs to the PM by recruiting the molecular motor myosin Va. Myrip also interacts with actin and the exocyst complex, suggesting that it may exert multiple roles in the secretory process. By combining total internal reflection fluorescence microscopy, single-particle tracking, a photoconversion-based assay, and mathematical modeling, we show that, in human enterochromaffin cells, Myrip (1) inhibits a class of SG motion characterized by fast and directed movement, suggesting that it facilitates the dissociation of SGs from microtubules; (2) enhances their motion toward the PM and the probability of SG attachment to the PM; and (3) increases the characteristic time of immobilization at the PM, indicating that it is a component of the molecular machinery that tether SGs to the PM. Remarkably, while the first two effects of Myrip depend on its ability to recruit myosin Va on SGs, the third is myosin Va independent but relies on the C-terminal domain of Myrip. We conclude that Myrip couples the retention of SGs in the cell cortex, their transport to the PM, and their attachment to the PM, and thus promotes secretion. These three steps of the secretory process are thus intimately coordinated.

Quantum dots to tail single bio-molecules inside living cells

In the last two decades, the single particle and single molecule approach became more and more popular to investigate the activity and the mechano-chemical properties of biological molecules. The inherent limit of these assays was that the molecules of interest were observed in vitro, out of their natural environment, the cell. Several recent works have shown the possibility to overcome this limit, to extend this approach to living cells and to observe the details of many cellular processes at the molecular level. In this review we discuss the use of semiconductor quantum dots to perform single particle and single molecule tracking in the cell. We refer to other articles for the technical aspects of this method. Here, after an introduction on the advantages provided by these nanoparticles, we restrict ourselves to some examples, mainly related to intracellular transport and molecular motor activity. These will illustrate the important role played by semiconductor quantum dots as fluorescent nano-reporters in in cell single molecule approach in modern biology and biophysics.

Interactive, computer-assisted tracking of speckle trajectories in fluorescence microscopy: application to actin polymerization and membrane fusion

Analysis of particle trajectories in images obtained by fluorescence microscopy reveals biophysical properties such as diffusion coefficient or rates of association and dissociation. Particle tracking and lifetime measurement is often limited by noise, large mobilities, image inhomogeneities, and path crossings. We present Speckle TrackerJ, a tool that addresses some of these challenges using computer-assisted techniques for finding positions and tracking particles in different situations. A dynamic user interface assists in the creation, editing, and refining of particle tracks. The following are results from application of this program: 1), Tracking single molecule diffusion in simulated images. The shape of the diffusing marker on the image changes from speckle to cloud, depending on the relationship of the diffusion coefficient to the camera exposure time. We use these images to illustrate the range of diffusion coefficients that can be measured. 2), We used the program to measure the diffusion coefficient of capping proteins in the lamellipodium. We found values ∼0.5 μm(2)/s, suggesting capping protein association with protein complexes or the membrane. 3), We demonstrate efficient measuring of appearance and disappearance of EGFP-actin speckles within the lamellipodium of motile cells that indicate actin monomer incorporation into the actin filament network. 4), We marked appearance and disappearance events of fluorescently labeled vesicles to supported lipid bilayers and tracked single lipids from the fused vesicle on the bilayer. This is the first time, to our knowledge, that vesicle fusion has been detected with single molecule sensitivity and the program allowed us to perform a quantitative analysis. 5), By discriminating between undocking and fusion events, dwell times for vesicle fusion after vesicle docking to membranes can be measured.

Nuclear organization and chromatin dynamics in yeast: biophysical models or biologically driven interactions?

Over the past decade, tremendous progress has been made in understanding the spatial organization of genes and chromosomes. Nuclear organization can be thought of as information that is not encoded in DNA, but which nevertheless impacts gene expression. Nuclear organizational influences can be cell-specific and are potentially heritable. Thus, nuclear organization fulfills all the criteria necessary for it to be considered an authentic level of epigenetic information. Chromosomal nuclear organization is primarily dictated by the biophysical properties of chromatin. Diffusion models of polymers confined in the crowded nuclear space accurately recapitulate experimental observation. Diffusion is a Brownian process, which implies that the positions of chromosomes and genes are not defined deterministically but are likely to be dictated by the laws of probability. Despite the small size of their nuclei, budding yeast have been instrumental in discovering how epigenetic information is encoded in the spatial organization of the genome. The relatively simple organization of the yeast nucleus and the very high number of genetically identical cells that can be observed under fluorescent microscopy allow statistically robust definitions of the gene and chromosome positions in the nuclear space to be constructed. In this review, we will focus on how the spatial organization of the chromatin in the yeast nucleus might impact transcription. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.

Cytoskeletal control of CD36 diffusion promotes its receptor and signaling function

The mechanisms that govern receptor coalescence into functional clusters--often a critical step in their stimulation by ligand--are poorly understood. We used single-molecule tracking to investigate the dynamics of CD36, a clustering-responsive receptor that mediates oxidized LDL uptake by macrophages. We found that CD36 motion in the membrane was spatially structured by the cortical cytoskeleton. A subpopulation of receptors diffused within linear confinement regions whose unique geometry simultaneously facilitated freedom of movement along one axis while increasing the effective receptor density. Co-confinement within troughs enhanced the probability of collisions between unligated receptors and promoted their clustering. Cytoskeleton perturbations that inhibited diffusion in linear confinement regions reduced receptor clustering in the absence of ligand and, following ligand addition, suppressed CD36-mediated signaling and internalization. These observations demonstrate a role for the cytoskeleton in controlling signal transduction by structuring receptor diffusion within membrane regions that increase their collision frequency.

Analysis of molecular diffusion by first-passage time variance identifies the size of confinement zones

The diffusion of receptors within the two-dimensional environment of the plasma membrane is a complex process. Although certain components diffuse according to a random walk model (Brownian diffusion), an overwhelming body of work has found that membrane diffusion is nonideal (anomalous diffusion). One of the most powerful methods for studying membrane diffusion is single particle tracking (SPT), which records the trajectory of a label attached to a membrane component of interest. One of the outstanding problems in SPT is the analysis of data to identify the presence of heterogeneity. We have adapted a first-passage time (FPT) algorithm, originally developed for the interpretation of animal movement, for the analysis of SPT data. We discuss the general application of the FPT analysis to molecular diffusion, and use simulations to test the method against data containing known regions of confinement. We conclude that FPT can be used to identify the presence and size of confinement within trajectories of the receptor LFA-1, and these results are consistent with previous reports on the size of LFA-1 clusters. The analysis of trajectory data for cell surface receptors by FPT provides a robust method to determine the presence and size of confined regions of diffusion.

Mean square displacement analysis of single-particle trajectories with localization error: Brownian motion in an isotropic medium

We examine the capability of mean square displacement (MSD) analysis to extract reliable values of the diffusion coefficient D of a single particle undergoing Brownian motion in an isotropic medium in the presence of localization uncertainty. The theoretical results, supported by simulations, show that a simple unweighted least-squares fit of the MSD curve can provide the best estimate of D provided an optimal number of MSD points are used for the fit. We discuss the practical implications of these results for data analysis in single-particle tracking experiments.

β2-Syntrophin is a Cdk5 substrate that restrains the motility of insulin secretory granules

The molecular basis for the interaction of insulin granules with the cortical cytoskeleton of pancreatic β-cells remains unknown. We have proposed that binding of the granule protein ICA512 to the PDZ domain of β2-syntrophin anchors granules to actin filaments and that the phosphorylation/dephosphorylation of β2-syntrophin regulates this association. Here we tested this hypothesis by analyzing INS-1 cells expressing GFP-β2-syntrophin through the combined use of biochemical approaches, imaging studies by confocal and total internal reflection fluorescence microscopy as well as electron microscopy. Our results support the notion that β2-syntrophin restrains the mobility of cortical granules in insulinoma INS-1 cells, thereby reducing insulin secretion and increasing insulin stores in resting cells, while increasing insulin release upon stimulation. Using mass spectrometry, in vitro phosphorylation assays and β2-syntrophin phosphomutants we found that phosphorylation of β2-syntrophin on S75 near the PDZ domain decreases its binding to ICA512 and correlates with increased granule motility, while phosphorylation of S90 has opposite effects. We further show that Cdk5, which regulates insulin secretion, phosphorylates S75. These findings provide mechanistic insight into how stimulation displaces insulin granules from cortical actin, thus promoting their motility and exocytosis.

Versatile roles for myosin Va in dense core vesicle biogenesis and function

The motor protein myosin Va is involved in multiple successive steps in the development of dense-core vesicles, such as in the membrane remodelling during their maturation, their transport along actin filaments and the regulation of their exocytosis. In the present paper, we summarize the current knowledge on the roles of myosin Va in the different steps of dense-core vesicle biogenesis and exocytosis, and compare findings obtained from different cell types and experimental systems.

The first passage probability of intracellular particle trafficking

The first passage probability (FPP), of trafficked intracellular particles reaching a displacement L, in a given time t or inverse velocity S = t/L, can be calculated robustly from measured particle tracks. The FPP gives a measure of particle movement in which different types of motion, e.g. diffusion, ballistic motion, and transient run-rest motion, can readily be distinguished in a single graph, and compared with mathematical models. The FPP is attractive in that it offers a means of reducing the data in the measured tracks, without making assumptions about the mechanism of motion. For example, it does not employ smoothing, segmentation or arbitrary thresholds to discriminate between different types of motion in a particle track. In contrast to conventional mean square displacement analysis, FPP is sensitive to a small population of trafficked particles that move long distances (> or = 5 microm), which are thought to be crucial for efficient long range signaling in theories of network dynamics. Taking experimental data from tracked endocytic vesicles, and calculating the FPP, we see how molecular treatments affect the trafficking. We show the FPP can quantify complicated movement which is neither completely random nor completely deterministic, making it highly applicable to trafficked particles in cell biology.

Mixed microtubules steer dynein-driven cargo transport into dendrites

BACKGROUND

To establish and maintain their polarized morphology, neurons employ active transport driven by molecular motors to sort cargo between axons and dendrites. However, the basic traffic rules governing polarized transport on neuronal microtubule arrays are unclear.

RESULTS

Here we show that the microtubule minus-end-directed motor dynein is required for the polarized targeting of dendrite-specific cargo, such as AMPA receptors. To directly examine how dynein motors contribute to polarized dendritic transport, we established a trafficking assay in hippocampal neurons to selectively probe specific motor protein activity. This revealed that, unlike kinesins, dynein motors drive cargo selectively into dendrites, governed by their mixed microtubule array. Moreover, axon-specific cargos, such as presynaptic vesicle protein synaptophysin, are redirected to dendrites by coupling to dynein motors. Quantitative modeling demonstrated that bidirectional dynein-driven transport on mixed microtubules provides an efficient mechanism to establish a stable density of continuously renewing vesicles in dendrites.

CONCLUSIONS

These results demonstrate a powerful approach to study specific motor protein activity inside living cells and imply a key role for dynein in dendritic transport. We propose that dynein establishes the initial sorting of dendritic cargo and additional motor proteins assist in subsequent delivery.

Rab27a and Rab27b control different steps of the exosome secretion pathway

Exosomes are secreted membrane vesicles that share structural and biochemical characteristics with intraluminal vesicles of multivesicular endosomes (MVEs). Exosomes could be involved in intercellular communication and in the pathogenesis of infectious and degenerative diseases. The molecular mechanisms of exosome biogenesis and secretion are, however, poorly understood. Using an RNA interference (RNAi) screen, we identified five Rab GTPases that promote exosome secretion in HeLa cells. Among these, Rab27a and Rab27b were found to function in MVE docking at the plasma membrane. The size of MVEs was strongly increased by Rab27a silencing, whereas MVEs were redistributed towards the perinuclear region upon Rab27b silencing. Thus, the two Rab27 isoforms have different roles in the exosomal pathway. In addition, silencing two known Rab27 effectors, Slp4 (also known as SYTL4, synaptotagmin-like 4) and Slac2b (also known as EXPH5, exophilin 5), inhibited exosome secretion and phenocopied silencing of Rab27a and Rab27b, respectively. Our results therefore strengthen the link between MVEs and exosomes, and introduce ways of manipulating exosome secretion in vivo.

Actomyosin is the main driver of interkinetic nuclear migration in the retina

Progenitor cell nuclei in the rapidly expanding epithelium of the embryonic vertebrate central nervous system undergo a process called interkinetic nuclear migration (IKNM). Movements of IKNM are generally believed to involve smooth migration of nuclei from apical to basal and back during the G1 and G2 phases of the cell cycle, respectively. Yet, this has not been formally demonstrated, nor have the molecular mechanisms that drive IKNM been identified. Using time-lapse confocal microscopy to observe nuclear movements in zebrafish retinal neuroepithelial cells, we show that, except for brief apical nuclear translocations preceding mitosis, IKNM is stochastic rather than smooth and directed. We also show that IKNM is driven largely by actomyosin-dependent forces as it still occurs when the microtubule cytoskeleton is compromised but is blocked when MyosinII activity is inhibited.

Robustness of optimal intermittent search strategies in one, two, and three dimensions

Search problems at various scales involve a searcher, be it a molecule before reaction or a foraging animal, which performs an intermittent motion. Here we analyze a generic model based on such type of intermittent motion, in which the searcher alternates phases of slow motion allowing detection and phases of fast motion without detection. We present full and systematic results for different modeling hypotheses of the detection mechanism in space in one, two, and three dimensions. Our study completes and extends the results of our recent letter [Loverdo, Nat. Phys. 4, 134 (2008)] and gives the necessary calculation details. In addition, another modeling of the detection case is presented. We show that the mean target detection time can be minimized as a function of the mean duration of each phase in one, two, and three dimensions. Importantly, this optimal strategy does not depend on the details of the modeling of the slow detection phase, which shows the robustness of our results. We believe that this systematic analysis can be used as a basis to study quantitatively various real search problems involving intermittent behaviors.

Complexity of mitochondrial dynamics in neurons and its control by ADP produced during synaptic activity

This review focuses on different aspects of dynamics of mitochondria in neuronal cytoplasm which play an important role in the life and fate of neurons. It starts with description of the energy supply in the brain; considers the typical patterns of mitochondrial movements; relates them to the neuronal activity and in particular at the synapses; extends to the analysis of the origin of local ATP changes in the cytoplasm; considers main features of motor-assisted movements of mitochondria and their role in determining a transport velocity; describes the measurements of ATP gradients in neuronal processes and relates them to spatial variations in the mobility of mitochondria that occur in the vicinity of synapses due to the local ADP increases; considers the influence of hypoxia and intracellular signalling pathways on mitochondria movements. Finally, the recent views on the mechanisms and possible functional role of mitochondrial network as a whole in neurons are discussed and unresolved issues and future perspectives in this field of research are delineated.

Temporal analysis of active and passive transport in living cells

The cellular cytoskeleton is a fascinating active network, in which Brownian motion is intercepted by distinct phases of active transport. We present a time-resolved statistical analysis dissecting phases of directed motion out of otherwise diffusive motion of tracer particles in living cells. The distribution of active lifetimes is found to decay exponentially with a characteristic time tauA = 0.65 s. The velocity distribution of active events exhibits several peaks, in agreement with a discrete number of motor proteins acting collectively.

What do diffusion measurements tell us about membrane compartmentalisation? Emergence of the role of interprotein interactions

The techniques of diffusion analysis based on optical microscopy approaches have revealed a great diversity of the dynamic organisation of cell membranes. For a long period, two frameworks have dominated the way of representing the membrane structure: the membrane skeleton fences and the lipid raft models. Progresses in the methods of data analysis have shed light on the features and consequently the possible origin of membrane domains: Inter-protein interactions play a role in confinement. Innovative developments pushing forward the spatiotemporal resolution limits are currently emerging, which are likely to provide in the future a detailed understanding of the intimate functional dynamic organisation of the cell membrane.

Optimizing intermittent reaction paths

Various examples of biochemical reactions in cells, such as DNA/protein interactions, reveal that in extremely diluted regimes reaction paths are not always simple brownian trajectories. They can rather be qualified as intermittent, since they combine slow diffusion phases on one hand and a second mode of faster transport on the other hand, which can be either a faster diffusion mode, as in the case of DNA-binding proteins, or a ballistic mode powered by molecular motors in the case of intracellular transport. In this article, we introduce simple theoretical models which permit to calculate explicitly the reaction rates for reactions limited by intermittent transport. This approach shows quantitatively that intermittent reaction pathways are actually very efficient, since they permit to significantly increase the reaction rates, which could explain why they are observed so often. Moreover, we give theoretical arguments which suggest that intermittent transport could also be useful for in vitro chemistry. Indeed, we show that intermittent transport naturally pops up in the context of reaction at interfaces, where reactants combine surface diffusion phases and bulk excursions, and could permit to enhance reactivity. In this case, adjusting chemically the affinity of reactants with the interface makes possible to optimize the reaction rate.

Regulation of insulin granule turnover in pancreatic beta-cells by cleaved ICA512

Insulin maintains homeostasis of glucose by promoting its uptake into cells from the blood. Hyperglycemia triggers secretion of insulin from pancreatic beta-cells. This process is mediated by secretory granule exocytosis. However, how beta-cells keep granule stores relatively constant is still unknown. ICA512 is an intrinsic granule membrane protein, whose cytosolic domain binds beta2-syntrophin, an F-actin-associated protein, and is cleaved upon granule exocytosis. The resulting cleaved cytosolic fragment, ICA512-CCF, reaches the nucleus and up-regulates the transcription of granule genes, including insulin and ICA512. Here, we show that ICA512-CCF also dimerizes with intact ICA512 on granules, thereby displacing it from beta2-syntrophin. This leads to increased granule mobility and insulin release. Based on these findings, we propose a model whereby the generation of ICA512-CCF first amplifies insulin secretion. The ensuing reduction of granule stores would then increase the probability of newly generated ICA512-CCF to reach the nucleus and enhance granule biogenesis, thus allowing beta-cells to constantly adjust production of granules to their storage size and consumption. Pharmacological modulation of these feedback loops may alleviate deficient insulin release in diabetes.

Secretory granule behaviour adjacent to the plasma membrane before and during exocytosis: total internal reflection fluorescence microscopy studies

Our current notions of different granule pools, granule interaction with the plasma membrane, and ultimately granule and plasma membrane soluble N-ethylmaleimide-sensitive-factor attachment protein (SNARE) interactions, result largely from inferences based upon biochemical alterations of secretion kinetics. Another view of events comes from studies using total internal reflection fluorescence microscopy (TIRFM) to investigate granule behaviour immediately adjacent to the plasma membrane. The motions of secretory (chromaffin) granules in bovine chromaffin cells visualized by TIRFM are highly restricted, as if granules are caged or tethered. These small motions are regulated by ATP and Ca2+, two factors that increase priming of the secretory response. There is no evidence that granules decrease their motion immediately before secretion. To the contrary, there is a tendency for granules to increase their motions and travel within a few hundred milliseconds of fusion. Hence, the notion of a long-lived docked state as a prelude to fusion does not encompass the physical reality of molecular scale motions, multiple tethering states and significant travel immediately preceding the exocytotic event. Increased travel may increase the probability of granules interacting productively with the plasma membrane constituents, thereby, increasing the probability of fusion.

Sub-micromolar increase in [Ca(2+)](i) triggers delayed exocytosis of ATP in cultured astrocytes

Astrocytes release a variety of transmitter molecules, which mediate communication between glial cells in the brain and modulate synaptic transmission. ATP is a major glia-derived transmitter, but the mechanisms and kinetics of ATP release from astrocytes remain largely unknown. Here, we combined epifluorescence and total internal reflection fluorescence microscopy to monitor individual quinacrine-loaded ATP-containing vesicles undergoing exocytosis in cultured astrocytes. In resting cells, vesicles exhibited three-dimensional motility, spontaneous docking and release at low rate. Extracellular ATP application induced a Ca(2+)-dependent increase in the rate of exocytosis, which persisted for several minutes. Using UV flash photolysis of caged Ca(2+), the threshold [Ca(2+)](i) for ATP exocytosis was found to be approximately 350 nM. Subthreshold [Ca(2+)](i) transients predominantly induced vesicle docking at plasma membrane without subsequent release. ATP exocytosis triggered either by purinergic stimulation or by Ca(2+) uncaging occurred after a substantial delay ranging from tens to hundreds of seconds, with only approximately 4% of release occurring during the first 30 s. The time course of the cargo release from vesicles had two peaks centered on <or=10 s and 60 s. These results demonstrate that: (1) [Ca(2+)](i) elevations in cultured astrocytes trigger docking and release of ATP-containing vesicles; (2) vesicle docking and release have different Ca(2+) thresholds; (3) ATP exocytosis is delayed by several minutes and highly asynchronous; (4) two populations of ATP-containing vesicles with distinct (fast and slow) time course of cargo release exist in cultured astrocytes.

A 20-nm step toward the cell membrane preceding exocytosis may correspond to docking of tethered granules

In endocrine cells, plasma membrane (PM)-bound secretory granules must undergo a number of maturation stages (i.e., priming) to become fusion-competent. Despite identification of several molecules involved in binding granules to the PM and priming them, the exact nature of events occurring at the PM still largely remains a mystery. In stimulated BON cells, we used evanescent wave microscopy to study trajectories of granules shortly before their exocytoses, which provided a physical description of vesicle-PM interactions at an unprecedented level of detail, and directly lead to an original mechanistic model. In these cells, tethered (T), nonfusogenic, vesicles are prevented from converting to fusogenic, docked (D) ones in resting conditions. Upon elevation of calcium, T-vesicles perform a 21-nm step toward the PM to become D, and fuse approximately 3 s thereafter. Our ability to directly visualize different modes of PM-attachment paves the way for clarifying the exact role of various molecules implicated in attachment and priming of granules in future studies.

Computational processing and analysis of dynamic fluorescence image data

With the many modes of live cell fluorescence imaging made possible by the rapid advances of fluorescent protein technology, researchers begin to face a new challenge: How to transform the vast amounts of unstructured image data into quantitative information for the discovery of new cell behaviors and the rigorous testing of mechanistic hypotheses? Although manual and semiautomatic computer-assisted image analysis are still used extensively, the demand for more reproducible and complete image measurements of complex cellular dynamics increases the need for fully automatic computational image processing approaches for both mechanistic studies and screening applications in cell biology. This chapter provides an overview of the issues that arise with the use of computational algorithms in live cell imaging studies, with particular emphasis on the close coordination of sample preparation, image acquisition, and computational image analysis. It also aims to introduce the terminology and central concepts of computer vision to facilitate the communication between cell biologists and computer scientists in collaborative imaging projects.

Myosin va mediates docking of secretory granules at the plasma membrane

Myosin Va (MyoVa) is a prime candidate for controlling actin-based organelle motion in neurons and neuroendocrine cells. Its function in secretory granule (SG) trafficking was investigated in enterochromaffin cells by wide-field and total internal reflection fluorescence microscopy. The distribution of endogenous MyoVa partially overlapped with SGs and microtubules. Impairing MyoVa function by means of a truncated construct (MyoVa tail) or RNA interference prevented the formation of SG-rich regions at the cell periphery and reduced SG density in the subplasmalemmal region. Individual SG trajectories were tracked to analyze SG mobility. A wide distribution of their diffusion coefficient, D(xy), was observed. Almost immobile SGs (D(xy) < 5 x 10(-4) microm2 x s(-1)) were considered as docked at the plasma membrane based on two properties: (1) SGs that undergo exocytosis have a D(xy) below this threshold value for at least 2 s before fusion; (2) a negative autocorrelation of the vertical motion was found in subtrajectories with a D(xy) below the threshold. Using this criterion of docking, we found that the main effect of MyoVa inhibition was to reduce the number of docked granules, leading to reduced secretory responses. Surprisingly, this reduction was not attributable to a decreased transport of SGs toward release sites. In contrast, MyoVa silencing reduced the occurrence of long-lasting, but not short-lasting, docking periods. We thus propose that, despite its known motor activity, MyoVa directly mediates stable attachment of SGs at the plasma membrane.

Functional membrane diffusion of G-protein coupled receptors

G-protein-coupled receptor function involves interactions between the receptor, G-proteins and effectors in the cell plasma membrane. The main biochemical processes have been individually identified but the mechanisms governing the successive protein-protein interactions of this complex multi-molecular machinery have yet to be established. We discuss advances in understanding the functional dynamics of the receptor resulting from diffusion measurements, and in the context of the plasma membrane organization.

Increased motion and travel, rather than stable docking, characterize the last moments before secretory granule fusion

The state of secretory granules immediately before fusion with the plasma membrane is unknown, although the granules are generally assumed to be stably bound (docked). We had previously developed methods using total internal reflection fluorescence microscopy and image analysis to determine the position of chromaffin granules immediately adjacent to the plasma membrane with high precision, often to within approximately 10 nm, or <5% of the granule diameter (300 nm). These distances are of the dimensions of large proteins and are comparable with the unitary step sizes of molecular motors. Here we demonstrate with quantitative measures of granule travel in the plane parallel to the plasma membrane that secretory granules change position within several hundred milliseconds of nicotinic agonist-induced fusion. Furthermore, just before fusion, granules frequently move to areas that they have rarely visited. The movement of granules to new areas is most evident for granules that fuse later during the stimulus. The movement may increase the probability of productive interactions of the granule with the plasma membrane or may reflect the pull of molecular interactions between the granule and the plasma membrane that are part of the fusion process. Thus, instead of being stably docked before exocytosis, granules undergo molecular-scale motions and travel immediately preceding the fusion event.

'Should I stay or should I go?': myosin V function in organelle trafficking

Actin- and microtubule-based motors can propel different cargos along filaments. Within cells, they control the distribution of membrane-bound compartments by performing complementary tasks. Organelles make long journeys along microtubules, with class V myosins ensuring their capture and their dispersal in actin-rich regions. Myosin Va is recruited on to diverse organelles, such as melanosomes and secretory vesicles, by a mechanism involving Rab GTPases. The role of myosin Va in the recruitment of secretory vesicles at the plasma membrane reveals that the cortical actin network cannot merely be seen as a physical barrier hindering vesicle access to release sites. In neurons, myosin Va controls the targeting of IP(3) (inositol 1,4,5-trisphosphate)-sensitive Ca(2+) stores to dendritic spines and the transport of mRNAs. These defects probably account for the severe neurological symptoms observed in Griscelli syndrome due to mutations in the MYO5A gene.

The transporters GlyT2 and VIAAT cooperate to determine the vesicular glycinergic phenotype

The mechanisms that specify the vesicular phenotype of inhibitory interneurons in vertebrates are poorly understood because the two main inhibitory transmitters, glycine and GABA, share the same vesicular inhibitory amino acid transporter (VIAAT) and are both present in neurons during postnatal development. We have expressed VIAAT and the plasmalemmal transporters for glycine and GABA in a neuroendocrine cell line and measured the quantal release of glycine and GABA using a novel double-sniffer patch-clamp technique. We found that glycine is released from vesicles when VIAAT is coexpressed with either the neuronal transporter GlyT2 or the glial transporter GlyT1. However, GlyT2 was more effective than GlyT1, probably because GlyT2 is unable to operate in the reverse mode, which gives it an advantage in maintaining the high cytosolic glycine concentration required for efficient vesicular loading by VIAAT. The vesicular inhibitory phenotype was gradually altered from glycinergic to GABAergic through mixed events when GABA is introduced into the secretory cell and competes for uptake by VIAAT. Interestingly, the VIAAT ortholog from Caenorhabditis elegans (UNC-47), a species lacking glycine transmission, also supports glycine exocytosis in the presence of GlyT2, and a point mutation of UNC-47 that abolishes GABA transmission in the worm confers glycine specificity. Together, these results suggest that an increased cytosolic availability of glycine in VIAAT-containing terminals was crucial for the emergence of glycinergic transmission in vertebrates.

Characterization of sequential exocytosis in a human neuroendocrine cell line using evanescent wave microscopy and “virtual trajectory” analysis

Secretion of hormones and other bioactive substances is a fundamental process for virtually all multicellular organisms. Using total internal reflection fluorescence microscopy (TIRFM), we have studied the calcium-triggered exocytosis of single, fluorescently labeled large, dense core vesicles in the human neuroendocrine BON cell line. Three types of exocytotic events were observed: (1) simple fusions (disappearance of a fluorescent spot by rapid diffusion of the dye released to the extracellular space), (2) "orphan" fusions for which only rapid dye diffusion, but not the parent vesicle, could be detected, and (3) events with incomplete or multi-step disappearance of a fluorescent spot. Although all three types were reported previously, only the first case is clearly understood. Here, thanks to a combination of two-color imaging, variable angle TIRFM, and novel statistical analyses, we show that the latter two types of events are generated by the same basic mechanism, namely shape retention of fused vesicle ghosts which become targets for sequential fusions with deeper lying vesicles. Overall, approximately 25% of all exocytotic events occur via sequential fusion. Secondary vesicles, located 200-300 nm away from the cell membrane are as fusion ready as primary vesicles located very near the cell membrane. These findings call for a fundamental shift in current models of regulated secretion in endocrine cells. Previously, sequential fusion had been studied mainly using two-photon imaging. To the best of our knowledge, this work constitutes the first quantitative report on sequential fusion using TIRFM, despite its long running and widespread use in studies of secretory mechanisms.