Single Particle Tracking Techniques Research Articles

4D Single-particle tracking with asynchronous read-out single-photon avalanche diode array detector

Single-particle tracking techniques enable investigation of the complex functions and interactions of individual particles in biological environments. Many such techniques exist, each demonstrating trade-offs between spatiotemporal resolution, spatial and temporal range, technical complexity, and information content. To mitigate these trade-offs, we enhanced a confocal laser scanning microscope with an asynchronous read-out single-photon avalanche diode array detector. This detector provides an image of the particle’s emission, precisely reflecting its position within the excitation volume. This localization is utilized in a real-time feedback system to drive the microscope scanning mechanism and ensure the particle remains centered inside the excitation volume. As each pixel is an independent single-photon detector, single-particle tracking is combined with fluorescence lifetime measurement. Our system achieves 40 nm lateral and 60 nm axial localization precision with 100 photons and sub-millisecond temporal sampling for real-time tracking. Offline tracking can refine this precision to the microsecond scale. We validated the system’s spatiotemporal resolution by tracking fluorescent beads with diffusion coefficients up to 10 μm2/s. Additionally, we investigated the movement of lysosomes in living SK-N-BE cells and measured the fluorescence lifetime of the marker expressed on a membrane protein. We expect that this implementation will open other correlative imaging and tracking studies.

Extreme dependence of dynamics on concentration in highly crowded polyelectrolyte solutions.

Charge-carrying species, such as polyelectrolytes, are vital to natural and synthetic processes that rely on their dynamic behavior. Through single-particle tracking techniques, the diffusivity of individual polyelectrolyte chains and overall system viscosity are determined for concentrated polylysine solutions. These studies show scaling dependences of D ~ c-6.1 and η ~ c7.2, much stronger than theoretical predictions, drawing the applicability of power law fits into question. Similar trends are observed in concentrated solutions prepared at various pH and counterion conditions. These hindered system dynamics appear universal to polyelectrolyte systems and are attributed to the large effective excluded volumes of polyelectrolyte chains inducing glassy dynamics. The framework of the Vrentas-Duda free-volume theory is used to compare polyelectrolyte and neutral systems. Supported by this theory, excluding counterion mass from total polymer mass results in all environmental conditions collapsing onto a common trendline. These results are applicable to crowded biological systems, such as intracellular environments where protein mobility is strongly inhibited.

Electrochemiluminescence-Based Single-Particle Tracking of the Biomolecules Moving along Intercellular Membrane Nanotubes between Live Cells.

Electrochemiluminescence (ECL) imaging, a rapidly evolving technology, has attracted significant attention in the field of cellular imaging. However, its primary limitation lies in its inability to analyze the motion behaviors of individual particles in live cellular environments. In this study, we leveraged the exceptional ECL properties of quantum dots (QDs) and the excellent electrochemical properties of carbon dots (CDs) to develop a high-brightness ECL nanoprobe (CDs-QDs) for real-time ECL imaging between living cells. This nanoprobe has excellent signal-to-noise ratio imaging capabilities for the single-particle tracking (SPT) of biomolecules. Our finding elucidated the enhanced ECL mechanism of CDs-QDs in the presence of reactive oxygen species through photoluminescence, electrochemistry, and ECL techniques. We further tracked the movement of single particles on membrane nanotubes between live cells and confirmed that the ECL-based SPT technique using CD-QD nanoparticles is an effective approach for monitoring the transport behaviors of biomolecules on membrane nanotubes between live cells. This opens a promising avenue for the advancement of ECL-based single-particle detection and the dynamic quantitative imaging of biomolecules.

Combined SPT and FCS methods reveal a mechanism of RNAP II oversampling in cell nuclei

Gene expression orchestration is a key question in fundamental and applied research. Different models for transcription regulation were proposed, yet the dynamic regulation of RNA polymerase II (RNAP II) activity remains a matter of debate. To improve our knowledge of this topic, we investigated RNAP II motility in eukaryotic cells by combining single particle tracking (SPT) and fluorescence correlation spectroscopy (FCS) techniques, to take advantage of their different sensitivities in order to analyze together slow and fast molecular movements. Thanks to calibrated samples, we developed a benchmark for quantitative analysis of molecular dynamics, to eliminate the main potential instrumental biases. We applied this workflow to study the diffusion of RPB1, the catalytic subunit of RNAP II. By a cross-analysis of FCS and SPT, we could highlight different RPB1 motility states and identifyed a stationary state, a slow diffusion state, and two different modes of subdiffusion. Interestingly, our analysis also unveiled the oversampling by RPB1 of nuclear subdomains. Based on these data, we propose a novel model of spatio-temporal transcription regulation. Altogether, our results highlight the importance of combining microscopy approaches at different time scales to get a full insight into the real complexity of molecular kinetics in cells.

Simultaneous single-particle tracking and fluorescence lifetime measurement with a single-photon detector array.

Fluorescence single-particle tracking (SPT) techniques are a fundamental tool for providing information on the complex functions and interactions of individual particles in biological environments. The main concern about following single particles resides mostly in how to make registered photons informative and the solution is usually optimized only to better extrapolate either the temporal or the spatial information. This tradeoff ultimately reflects into the contraposition of wide-field camera-based techniques and real-time SMT, with the latter representing the state of the art, but at the cost of high technical complexity. Furthermore, fluorescence lifetime information, despite being accessible in many cases, has yet to be measured consistently. Within the context of the BrightEyes ERC-2018-COG project, we present a real-time three-dimensional SPT implementation based on a confocal laser-scanning microscope featuring a 5×5 single-photon avalanche photodiode (SPAD) array detector capable of overcoming the above limitations due to an hybrid approach. Briefly, each sensitive element of the detector acts as a confocal pinhole, and the recorded intensity distribution mirrors the position of the particle with respect to the center of the excitation volume. The estimation is then used as input for a real-time feedback tracking system. Notably, each pixel is an independent photon counting detector, allowing for concurrent measurement of the fluorescence lifetime. The system is capable of experimentally tracking single particles with localization precision up to 30 nm with 100 photons and microsecond time resolution. The same photon stream is used to perform fluorescence lifetime measurements. The technique has been validated by tracking 20 nm fluorescent beads moved along a predetermined path and by measuring the diffusion coefficient when freely diffusing in water-glycerol solutions. As application, the movement of lysosomes in living cells has been investigated while assessing the lifetime of the GFP marker.

Nanoscopic lipid diffusion in the live cell plasma membrane revealed by ultrafast single-molecule tracking.

Membrane organization and dynamics underlie various molecular interactions required for membrane functions. Although the importance of investigating biological membranes at the nanoscale is well recognized, resolving nanoscopic structures and dynamics is technically challenging. In this work, we employ ultrafast single-particle tracking techniques to measure single phospholipid diffusion in the plasma membrane of live cells. We attach a monovalent gold nanoparticle to the headgroup of biotinylated phospholipid and record its diffusive motion on microsecond resolution and nanometer precision by advanced optical interference microscopy. We find that both saturated and unsaturated phospholipids (biotin-PEG-DSPE and biotin-PEG-DOPE, respectively) undergo anomalous subdiffusion in the length scale below 100 nm. The unsaturated lipid diffuses only slightly more freely than the saturated lipid. Moreover, the nanoscopic lipid diffusion is highly heterogeneous in space and time. With statistical analyses, we find that the apparent dual-mobility subdiffusion can describe measured diffusion. The subdiffusion agrees well with the hop diffusion model that describes a Brownian diffuser moving in periodic and partially permeable barriers created by the cytoskeleton. Inhibition of actin polymerization by the chemical drug CK-666 reduces confinement's effective size and strength. Furthermore, we examine the effect of cholesterol on lipid subdiffusion by manipulating the cholesterol concentration. Cholesterol depletion by methyl-b-cyclodextrin leads to a more restricted lipid diffusion. We attribute the more confined diffusion to the formation of solid-like gel-phase nanodomains that move slowly and act as diffusion obstacles. Lowing the system temperature shows similar effects on lipid diffusion, suggesting that the cholesterol-dependent lipid diffusion connects to the nanoscopic phase separation. Overall, this study provides experimental evidence that lipid diffusion in the cell membrane is heterogeneous at the nanoscale and regulated by the membrane cholesterol and actin cytoskeleton.

Real-Time Dissection of the Transportation and miRNA-Release Dynamics of Small Extracellular Vesicles.

Extracellular vesicles (EVs) are cell-derived membrane-enclosed structures that deliver biomolecules for intercellular communication. Developing visualization methods to elucidate the spatiotemporal dynamics of EVs' behaviors will facilitate their understanding and translation. With a quantum dot (QD) labeling strategy, a single particle tracking (SPT) platform is proposed here for dissecting the dynamic behaviors of EVs. The interplays between tumor cell-derived small EVs (T-sEVs) and endothelial cells (ECs) are specifically investigated based on this platform. It is revealed that, following a clathrin-mediated endocytosis by ECs, T-sEVs are transported to the perinuclear region in a typical three-stage pattern. Importantly, T-sEVs frequently interact with and finally enter lysosomes, followed by quick release of their carried miRNAs. This study, for the first time, reports the entire process and detailed dynamics of T-sEV transportation and cargo-release in ECs, leading to better understanding of their proangiogenic functions. Additionally, the QD-based SPT technique will help uncover more secrets of sEV-mediated cell-cell communication.

Single-Particle Tracking of Virus Entry in Live Cells.

Novel imaging technologies such as single-particle tracking provide tools to study the intricate process of virus infection in host cells. In this chapter, we provide an overview of studies in which single-particle tracking technologies were applied for the analysis of the viral entry pathways in the context of the live host cell. Single-particle tracking techniques have been dependent on advances in the fluorescent labeling microscopy method and image analysis. The mechanistic and kinetic insights offered by this technique will provide a better understanding of virus entry and may lead to a rational design of antiviral interventions.

Synthetic Stochastic Motion Platform for Testing Single Particle Tracking Microscopes.

We describe the design and implementation of a control system for testing the performance of single particle tracking microscopes with the method of synthetic motion. Single particle tracking (SPT) has become a common and powerful tool in the study of biomolecular transport in cellular biology, providing the ability to track individual biological macromolecules in their native environment. Existing methods for testing SPT techniques rely on physical simulations and there is a clear need for experimental-based schemes for both comparing different approaches and for characterizing the accuracy and precision of techniques on particular experimental setups. Synthetic motion, that is, using an actuator such as a nanopositioning stage to drive a particle along a known ground-truth trajectory, is a means for achieving these ends. However, the resolution, accuracy, and flexibility of this method is limited by the actuator static and dynamic characteristics. In this work we apply system identification and model inverse feedforward control to increase actuator bandwidth and address some common actuator nonlinearities, develop a set of dimensionless numbers that describe system limitations, and provide a set of guidelines for the practical use of synthetic motion in SPT.

Theoretical comparison of real-time feedback-driven single-particle tracking techniques.

Real-time feedback-driven single-particle tracking is a technique that uses feedback control to enable single-molecule spectroscopy of freely diffusing particles in native or near-native environments. A number of different real-time feedback-driven single-particle tracking (RT-FD-SPT) approaches exist, and comparisons between methods based on experimental results are of limited use due to differences in samples and setups. In this study, we used statistical calculations and dynamical simulations to directly compare the performance of different methods. The methods considered were the orbital method, the knight's tour (grid scan) method, and MINFLUX, and we considered both fluorescence-based and interferometric scattering (iSCAT) approaches. There is a fundamental trade-off between precision and speed, with the knight's tour method being able to track the fastest diffusion but with low precision, and MINFLUX being the most precise but only tracking slow diffusion. To compare iSCAT and fluorescence, different biological samples were considered, including labeled and intrinsically fluorescent samples. The success of iSCAT as compared to fluorescence is strongly dependent on the particle size and the density and photophysical properties of the fluorescent particles. Using a wavelength for iSCAT that is negligibly absorbed by the tracked particle allows for an increased illumination intensity, which results in iSCAT providing better tracking for most samples. This work highlights the fundamental aspects of performance in RT-FD-SPT and should assist with the selection of an appropriate method for a particular application. The approach used can easily be extended to other RT-FD-SPT methods.

Nanoparticle tracking analysis and statistical mixture distribution analysis to quantify nanoparticle–vesicle binding

Nanoparticle tracking analysis (NTA) is a single particle tracking technique that in principle provides a more direct measure of particle size distribution compared to dynamic light scattering (DLS). Here, we demonstrate how statistical mixture distribution analysis can be used in combination with NTA to quantitatively characterize the amount and extent of particle binding in a mixture of nanomaterials. The combined approach is used to study the binding of gold nanoparticles to two types of phospholipid vesicles, those containing and lacking the model ion channel peptide gramicidin A. This model system serves as both a proof of concept for the method and a demonstration of the utility of the approach in studying nano-bio interactions. Two diffusional models (Stokes–Einstein and Kirkwood–Riseman) were compared in the determination of particle size, extent of binding, and nanoparticle:vesicle binding ratios for each vesicle type. The combination of NTA and statistical mixture distributions is shown to be a useful method for quantitative assessment of the extent of binding between particles and determination of binding ratios.

In-Cell Labeling Coupled to Direct Analysis of Extracellular Vesicles in the Conditioned Medium to Study Extracellular Vesicles Secretion with Minimum Sample Processing and Particle Loss.

Extracellular vesicles (EVs) are involved in a multitude of physiological functions and play important roles in health and disease. The largest proportion of studies on EVs is based on the analysis and characterization of EVs secreted in the cell culture medium. These studies remain challenging due to the small size of the EV particles, a lack of universal EV markers, and sample loss or technical artifacts that are often associated with EV labeling for single particle tracking and/or separation techniques. To address these problems, we characterized and validated a method for in-cell EV labeling with fluorescent lipids coupled with direct analysis of lipid-labeled EVs in the conditioned medium by imaging flow cytometry (IFC). This approach significantly reduces sample processing and loss compared to established methods for EV separation and labeling in vitro, resulting in improved detection of quantitative changes in EV secretion and subpopulations compared to protocols that rely on EV separation by size-exclusion chromatography and ultracentrifugation. Our optimized protocol for in-cell EV labeling and analysis of the conditioned medium reduces EV sample processing and loss, and is well-suited for cell biology studies that focus on modulation of EV secretion by cells in culture.

Probing Allosteric Modulation of Membrane Receptor in the Native State by Data Mining-Integrated Tracking Microscopy

Probing Allosteric Modulation of Membrane Receptor in the Native State by Data Mining-Integrated Tracking Microscopy

All-optical fluorescence blinking control in quantum dots with ultrafast mid-infrared pulses.

Photoluminescence intermittency is a ubiquitous phenomenon, reducing the temporal emission intensity stability of single colloidal quantum dots (QDs) and the emission quantum yield of their ensembles. Despite efforts to achieve blinking reduction by chemical engineering of the QD architecture and its environment, blinking still poses barriers to the application of QDs, particularly in single-particle tracking in biology or in single-photon sources. Here, we demonstrate a deterministic all-optical suppression of QD blinking using a compound technique of visible and mid-infrared excitation. We show that moderate-field ultrafast mid-infrared pulses (5.5 μm, 150 fs) can switch the emission from a charged, low quantum yield grey trion state to the bright exciton state in CdSe/CdS core-shell QDs, resulting in a significant reduction of the QD intensity flicker. Quantum-tunnelling simulations suggest that the mid-infrared fields remove the excess charge from trions with reduced emission quantum yield to restore higher brightness exciton emission. Our approach can be integrated with existing single-particle tracking or super-resolution microscopy techniques without any modification to the sample and translates to other emitters presenting charging-induced photoluminescence intermittencies, such as single-photon emissive defects in diamond and two-dimensional materials.

Assessing the use of ellipsoidal microparticles for determining lipid membrane viscosity

The viscosity of lipid membranes sets the timescales of membrane-associated motions, whether driven or diffusive, and therefore influences the dynamics of a wide range of cellular processes. Techniques to measure membrane viscosity remain sparse, however, and reported measurements to date, even of similar systems, give viscosity values that span orders of magnitude. To address this, we improve a method based on measuring both the rotational and translational diffusion of membrane-anchored microparticles and apply this approach and one based on tracking the motion of phase-separated lipid domains to the same system of phase-separated giant vesicles. We find good agreement between the two methods, with inferred viscosities within a factor of two of each other. Our single-particle tracking technique uses ellipsoidal microparticles, and we show that the extraction of physically meaningful viscosity values from their motion requires consideration of their anisotropic shape. The validation of our method on phase-separated membranes makes possible its application to other systems, which we demonstrate by measuring the viscosity of bilayers composed of lipids with different chain lengths ranging from 14 to 20 carbon atoms, revealing a very weak dependence of two-dimensional viscosity on lipid size. The experimental and analysis methods described here should be generally applicable to a variety of membrane systems, both reconstituted and cellular.

High TSPAN8 expression in epithelial cancer cell-derived small extracellular vesicles promote confined diffusion and pronounced uptake.

Small extracellular vesicles (sEVs) play a key role in intercellular communication. Cargo molecules carried by sEVs may affect the phenotype and function of recipient cells. Epithelial cancer cell‐derived sEVs, particularly those enriched in CD151 or tetraspanin8 (TSPAN8) and associated integrins, promote tumour progression. The mechanism of binding and modulation of sEVs to recipient cells remains elusive. Here, we used genetically engineered breast cancer cells to derive TSPAN8‐enriched sEVs and evaluated the impact of TSPAN8 on target cell membrane's diffusion and transport properties. The single‐particle tracking technique showed that TSPAN8 significantly promoted sEV binding via confined diffusion. Functional assays indicated that the transgenic TSPAN8‐sEV cargo increased cancer cell motility and epithelial‐mesenchymal transition (EMT). In vivo, transgenic TSPAN8‐sEV promoted uptake of sEVs in the liver, lung, and spleen. We concluded that TSPAN8 encourages the sEV‐target cell interaction via forced confined diffusion and significantly increases cell motility. Therefore, TSPAN8‐sEV may serve as an important direct or indirect therapeutic target.

Study of Wound Healing Dynamics by Single Pseudo-Particle Tracking in Phase Contrast Images Acquired in Time-Lapse.

Cellular contacts modify the way cells migrate in a cohesive group with respect to a free single cell. The resulting motion is persistent and correlated, with cells’ velocities self-aligning in time. The presence of a dense agglomerate of cells makes the application of single particle tracking techniques to define cells dynamics difficult, especially in the case of phase contrast images. Here, we propose an original pipeline for the analysis of phase contrast images of the wound healing scratch assay acquired in time-lapse, with the aim of extracting single particle trajectories describing the dynamics of the wound closure. In such an approach, the membrane of the cells at the border of the wound is taken as a unicum, i.e., the wound edge, and the dynamics is described by the stochastic motion of an ensemble of points on such a membrane, i.e., pseudo-particles. For each single frame, the pipeline of analysis includes: first, a texture classification for separating the background from the cells and for identifying the wound edge; second, the computation of the coordinates of the ensemble of pseudo-particles, chosen to be uniformly distributed along the length of the wound edge. We show the results of this method applied to a glioma cell line (T98G) performing a wound healing scratch assay without external stimuli. We discuss the efficiency of the method to assess cell motility and possible applications to other experimental layouts, such as single cell motion. The pipeline is developed in the Python language and is available upon request.

3D Imaging of Lipid-Guided Vesicle Trafficking Along the Cytoskeleton.

Labeling lipids in vivo is a crucial step in exploring detailed molecular mechanisms coordinating phospholipid signaling and membrane trafficking. Using a lipid-binding domain fused with various fluorescent proteins (FPs) [such as single-colored FP, photoactivated-FP and FPs based on Förster resonance energy transfer (FRET)], lipid biosensors are used to monitor the spatiotemporal distribution, concentration, and dynamic characteristics of targeted lipids. Membrane trafficking is accompanied by rearrangement of membrane lipids and the cytoskeleton. 3D live-cell super-resolution (SR) imaging microscopy detects directional vesicle trafficking events in relation to lipids and the cytoskeleton near the plasma membrane (PM) in 3D space. 3D single-molecule co-tracking (smCo-tracking) provides time-lapse images of 3D colocalization between targeted lipids and vesicles. A dwell time pattern indicates the movement of vesicles towards exocytic sites at the PM. 3D single particle tracking (SPT) could track the overlapping trajectory of vesicles and lipids and display the distance to the cytoskeleton. Lipid biosensors provide a noninvasive and natural labeling for exploring the spatiotemporal dynamics and homeostasis of lipid in vivo. 3D live-cell SR imaging microscopy enables rapid, targeted access, deep imaging within samples at high spatial resolutions for real-time visualization of dynamic biological processes in vivo. 3D smCo-tracking analysis offers simultaneous tracking of different molecules to determine lipid-guided vesicle trafficking in a spatiotemporal organized manner. The 3D SPT technique could provide an accurate estimation of trajectories and spatiotemporal colocalization of vesicles and targeted lipids in 3D space, providing a high-precision visualization and depth track of directional vesicle trafficking. Directional vesicle trafficking is a complex and tightly organized process. Identifying specific lipids and other related regulators will contribute to the exploration of lipid vesicle–cytoskeleton interactions that drive directional delivery of cargos under various stress stimuli, particularly pathogen attacks. For 3D live-cell SR imaging microscopy, how to best balance the imaging speed, spatial-temporal resolution, and volumetric SR imaging capability remains a challenging task. Given that lipid derivatives cannot be genetically encoded, the brighter, more photostable and appropriate fluorophores visualizing the dynamic changes of targeted lipids in concentrations remain to be developed in plant cells. This work is supported by the National Natural Science Foundation of China ( 32030010 , 31900162 , 31770197 , 32000182 ), the Program of Introducing Talents of Discipline to Universities (111 project, B13007 ), and Young Elite Scientists Sponsorship Program by CAST ( 2019QNRC001 ). No interests are declared.

Determination of diffusion coefficient by image-based fluorescence recovery after photobleaching and single particle tracking system implemented in a single platform

Fluorescence recovery after photobleaching (FRAP) and single particle tracking (SPT) techniques determine the diffusion coefficient from average diffusive motion of high-concentration molecules and from trajectories of low-concentration single molecules, respectively. Lateral diffusion coefficients measured by FRAP and SPT techniques for the same biomolecule on cell membrane have exhibited inconsistent values across laboratories and platforms with larger diffusion coefficient determined by FRAP, but the sources of the inconsistency have not been investigated thoroughly. Here, we designed an image-based FRAP-SPT system and made a direct comparison between FRAP and SPT for diffusion coefficient of submicron particles with known theoretical values derived from Stokes–Einstein equation in aqueous solution. The combined [Formula: see text]FRAP-SPT technique allowed us to measure the diffusion coefficient of the same fluorescent particle by utilizing both techniques in a single platform and to scrutinize inherent errors and artifacts of FRAP. Our results reveal that diffusion coefficient overestimated by FRAP is caused by inaccurate estimation of the bleaching spot size and can be corrected by simple image analysis. Our [Formula: see text]FRAP-SPT technique can be potentially used for not only cellular membrane dynamics but also for quantitative analysis of the spatiotemporal distribution of the solutes in small scale analytical devices.

Simulation and tracking of fractional particles motion. From microscopy video to statistical analysis. A Brownian bridge approach

An ongoing rapid development in single particle tracking techniques has opened new possibilities for analysis of particles dynamics inside living cells. Assuming that the motion is governed by a fractional Brownian motion, we have generated a synthetic video resembling a real one from an experimental video of G-proteins and coupled with them receptors inside living cells. Next, we applied Brownian bridge method to study two fundamental analysis tasks on trajectory data: segmentation and classification in context of experimental data. We have shown that, depending on the method of dealing with missing data, the obtained results might vary significantly, obviously influencing the final conclusions.