Time-Resolved Scanning Ion Conductance Microscopy for Three-Dimensional Tracking of Nanoscale Cell Surface Dynamics

Label-Free Techniques for Probing Biomolecular Condensates

Biomolecular condensates play important roles in a wide array of fundamental biological processes, such as cellular compartmentalization, cellular regulation, and other biochemical reactions. Since their discovery and first observations, an extensive and expansive library of tools has been developed to investigate various aspects and properties, encompassing structural and compositional information, material properties, and their evolution throughout the life cycle from formation to eventual dissolution. This Review presents an overview of the expanded set of tools and methods that researchers use to probe the properties of biomolecular condensates across diverse scales of length, concentration, stiffness, and time. In particular, we review recent years' exciting development of label-free techniques and methodologies. We broadly organize the set of tools into 3 categories: (1) imaging-based techniques, such as transmitted-light microscopy (TLM) and Brillouin microscopy (BM), (2) force spectroscopy techniques, such as atomic force microscopy (AFM) and the optical tweezer (OT), and (3) microfluidic platforms and emerging technologies. We point out the tools' key opportunities, challenges, and future perspectives and analyze their correlative potential as well as compatibility with other techniques. Additionally, we review emerging techniques, namely, differential dynamic microscopy (DDM) and interferometric scattering microscopy (iSCAT), that have huge potential for future applications in studying biomolecular condensates. Finally, we highlight how some of these techniques can be translated for diagnostics and therapy purposes. We hope this Review serves as a useful guide for new researchers in this field and aids in advancing the development of new biophysical tools to study biomolecular condensates.

The target region focused imaging method for scanning ion conductance microscopy

Scanning ion conductance microscopy (SICM) has developed rapidly and has wide applications in biomedicine, single-cell science and other fields. SICM scanning speed is limited by the conventional raster-type scanning method, which spends most of time on imaging the substrate and does not focus enough on the target area. In order to solve this problem, a target region focused (TRF) method is proposed, which can effectively avoid the scanning of unnecessary substrate areas and enables SICM to image the target area only to achieve high-speed and effective local scanning. TRF method and conventional hopping mode scanning method are compared in the experiments using breast cancer cells and rat basophilic leukemia cells as experimental materials. It was demonstrated that our method can reduce the scanning time for a single sample image significantly without losing scanning information or compromising the quality of imaging. The TRF method developed in this paper can provide an efficient and fast scanning strategy for improving the imaging performance of SICM systems, which can be applied to the dynamic features of cell samples in the fields of biology and pharmacology analysis.

Open-source microscope add-on for structured illumination microscopy

Super-resolution techniques expand the abilities of researchers who have the knowledge and resources to either build or purchase a system. This excludes the part of the research community without these capabilities. Here we introduce the openSIM add-on to upgrade existing optical microscopes to Structured Illumination super-resolution Microscopes (SIM). The openSIM is an open-hardware system, designed and documented to be easily duplicated by other laboratories, making super-resolution modality accessible to facilitate innovative research. The add-on approach gives a performance improvement for pre-existing lab equipment without the need to build a completely new system.

Rapid scanning method for SICM based on autoencoder network

Scanning Ion Conductance Microscopy (SICM) enables non-destructive imaging of living cells, which makes it highly valuable in life sciences, medicine, pharmacology, and many other fields. However, because of the uncertainty retrace height of SICM hopping mode, the time resolution of SICM is relatively low, which makes the device fail to meet the demands of dynamic scanning. To address above issues, we propose a fast-scanning method for SICM based on an autoencoder network. Firstly, we cut under-sampled images into small image lists. Secondly, we feed them into a self-constructed primitive-autoencoder super-resolution network to compute high-resolution images. Finally, the inferred scanning path is determined using the computed images to reconstruct the real high-resolution scanning path. The results demonstrate that the proposed network can reconstruct higher-resolution images in various super-resolution tasks of low-resolution scanned images. Compared to existing traditional interpolation methods, the average peak signal-to-noise ratio improvement is greater than 7.5823 dB, and the average structural similarity index improvement is greater than 0.2372. At the same time, using the proposed method for high-resolution image scanning leads to a 156.25% speed improvement compared to traditional methods. It opens up possibilities for achieving high-time resolution imaging of dynamic samples in SICM and further promotes the widespread application of SICM in the future.

Aptamer Renaissance for Neurochemical Biosensing

Unraveling the complexities of brain function, which is crucial for advancing human health, remains a grand challenge. This endeavor demands precise monitoring of small molecules such as neurotransmitters, the chemical messengers in the brain. In this Perspective, we explore the potential of aptamers, selective synthetic bioreceptors integrated into electronic affinity platforms to address limitations in neurochemical biosensing. We emphasize the importance of characterizing aptamer thermodynamics and target binding to realize functional biosensors in biological systems. We focus on two label-free affinity platforms spanning the micro- to nanoscale: field-effect transistors and nanopores. Integration of well-characterized structure-switching aptamers overcame nonspecific binding, a challenge that has hindered the translation of biosensors from the lab to the clinic. In a transformative era driven by neuroscience breakthroughs, technological innovations, and multidisciplinary collaborations, an aptamer renaissance holds the potential to bridge technological gaps and reshape the landscape of diagnostics and neuroscience.

Scanning ion conductance microscopy revealed cisplatin-induced morphological changes related to apoptosis in single adenocarcinoma cells

The studies of drug-induced apoptosis play a vital role in the identification of potential drugs that could treat diseases such as cancer. Alterations in the native morphology of cancer cells following treatment with anticancer drugs serve as one of the indicators that reveal drug efficacy. Various techniques such as optical microscopy, electron microscopy (EM), and atomic force microscopy (AFM) have been used to map the three dimensional (3D) morphological changes in cells induced with drugs. However, caution should be exercised when interpreting morphological data from techniques that might alter the native morphology of cells, caused by phototoxicity, electron beam invasiveness, intrusive sample preparation, and cell membrane deformation. Herein, we have used scanning ion conductance microscopy (SICM) to study the 3D morphology and roughness of A549 adenocarcinoma cells under physiological conditions before and after cisplatin induced apoptosis, where we observed an increase in height, overall shrinkage of the cells, and irregular features form on the cell membrane. Tracking the morphology of the same single A549 cells exposed to cisplatin unveiled heterogeneity in response to the drug, formation of membrane blebs, and an increase in membrane roughness. We have also demonstrated the use of SICM for studying the effect of cisplatin on the dynamic changes in the volume of A549 cells over days. SICM is demonstrated as a technique for studying the effect of drug induced apoptosis in the same cells over time, and for multiple different single cells.

A review of innovative electrochemical strategies for bioactive molecule detection and cell imaging: Current advances and challenges

Cellular heterogeneity poses a major challenge for tumor theranostics, requiring high-resolution intercellular bioanalysis strategies. Over the past decades, the advantages of electrochemical analysis, such as high sensitivity, good spatio-temporal resolution, and ease of use, have made it the preferred method to uncover cellular differences. To inspire more creative research, herein, we highlight seminal works in electrochemical techniques for biomolecule analysis and bioimaging. Specifically, micro/nano-electrode-based electrochemical techniques enable real-time quantitative analysis of electroactive substances relevant to life processes in the micro-nanostructure of cells and tissues. Nanopore-based technique plays a vital role in biosensing by utilizing nanoscale pores to achieve high-precision detection and analysis of biomolecules with exceptional sensitivity and single-molecule resolution. Electrochemiluminescence (ECL) technology is utilized for real-time monitoring of the behavior and features of individual cancer cells, enabling observation of their dynamic processes due to its capability of providing high-resolution and highly sensitive bioimaging of cells. Particularly, scanning electrochemical microscopy (SECM) and scanning ion conductance microscopy (SICM) which are widely used in real-time observation of cell surface biological processes and three-dimensional imaging of micro-nano structures, such as metabolic activity, ion channel activity, and cell morphology are introduced in this review. Furthermore, the expansion of the scope of cellular electrochemistry research by innovative functionalized electrodes and electrochemical imaging models and strategies to address future challenges and potential applications is also discussed in this review.

Application and outlook of electrochemical technology in single-cell analysis

Cellular heterogeneity, especially in some important diseased cells like tumor cells, acts as an invisible driver for disease development like cancer progression in the tumor ecosystem, contributing to differences in the macroscopic and microscopic detection of disease lesions like tumors. Traditional analysis techniques choose group information masked by the mean as the analysis sample, making it difficult to achieve precise diagnosis and target treatment, on which could be shed light via the single-cell level determination/bioanalysis. Hence, in this article we have reviewed the special characteristic differences among various kinds of typical single-cell bioanalysis strategies and electrochemical techniques, and then focused on the recent advance and special bio-applications of electrochemiluminescence and micro-nano electrochemical sensing mediated in single-cell bioimaging & bioanalysis. Especially, we have summarized the relevant research exploration of the possibility to establish the in-situ single-cell electrochemical methods to detect cell heterogeneity through determination of specific biomolecules and bioimaging of some important biological processes. Eventually, this review has explored some important advances of electrochemical single-cell detection techniques for the real-time cellular bioimaging and diagnostics of some disease lesions like tumors. It raises the possibility to provide the specific in-situ platform to exploit the versatile, sensitive, and high-resolution electrochemical single-cell analysis for the promising biomedical applications like rapid tracing of some disease lesions or in vivo bioimaging for precise cancer theranostics.

A high-bandwidth voltage amplifier for driving piezoelectric actuators in high-speed atomic force microscopy

High-speed atomic force microscopy (HS-AFM) is a technique capable of revealing the dynamics of biomolecules and living organisms at the nanoscale with a remarkable temporal resolution. The phase delay in the feedback loop dictates the achievable speed of HS-AFM instruments that rely on fast nanopositioners operated predominantly in conjunction with piezoelectric actuators (PEAs). The high capacitance and high operating voltage of PEAs make them difficult to drive. The limited bandwidth of associated high-voltage piezo-amplifiers is one of the bottlenecks to higher scan speeds. In this study, we report a high-voltage, wideband voltage amplifier comprised of a separate amplification and novel voltage-follower power stage, requiring no global feedback. The reported amplifier can deliver a current over ±2 amps, offers a small-signal bandwidth of 1 MHz, and exhibits an exceptionally low phase lag, making it particularly well suited for the needs of next-generation HS-AFMs. We demonstrate its capabilities by reporting its achievable bandwidth under various PEA loads and showcasing its merit for HS-AFM by imaging tubulin protofilament dynamics at sub-second frame rates.

Spatially multiplexed single-molecule translocations through a nanopore at controlled speeds

In current nanopore-based label-free single-molecule sensing technologies, stochastic processes influence the selection of translocating molecule, translocation rate and translocation velocity. As a result, single-molecule translocations are challenging to control both spatially and temporally. Here we present a method using a glass nanopore mounted on a three-dimensional nanopositioner to spatially select molecules, deterministically tethered on a glass surface, for controlled translocations. By controlling the distance between the nanopore and glass surface, we can actively select the region of interest on the molecule and scan it a controlled number of times and at a controlled velocity. Decreasing the velocity and averaging thousands of consecutive readings of the same molecule increases the signal-to-noise ratio by two orders of magnitude compared with free translocations. We demonstrate the method's versatility by assessing DNA-protein complexes, DNA rulers and DNA gaps, achieving down to single-nucleotide gap detection.

Nanopipette Fabrication Guidelines for SICM Nanoscale Imaging

Scanning ion conductance microscopy (SICM) is a promising tool for visualizing the dynamics of nanoscale cell surface topography. However, there are still no guidelines for fabricating nanopipettes with ideal shape consisting of small apertures and thin glass walls. Therefore, most of the SICM imaging has been at a standstill at the submicron scale. In this study, we established a simple and highly reproducible method for the fabrication of nanopipettes with sub-20 nm apertures. To validate the improvement in the spatial resolution, we performed time-lapse imaging of the formation and disappearance of endocytic pits as a model of nanoscale time-lapse topographic imaging. We have also successfully imaged the localization of the hot spot and the released extracellular vesicles. The nanopipette fabrication guidelines for the SICM nanoscale topographic imaging can be an essential tool for understanding cell-cell communication.

Large Range Atomic Force Microscopy with High Aspect Ratio Micropipette Probe for Deep Trench Imaging

Atomic force microscopy (AFM) has been adopted in both industry and academia for high-fidelity, full-profile topographic characterization. Typically, the tiny tip of the cantilever and the limited traveling range of the scanner restrict AFM measurement to relatively flat samples (recommend 1 µm). The primary objective of this work is to address these limitations using a large-range AFM (measuring height >10 µm) system consisting of a novel repairable high aspect ratio probe (HARP) with a nested-proportional-integral-derivative (nested-PID) AFM system. The HARP is fabricated using a reliable, cost-efficient bench-top process. The tip is then fused by pulling the end of the micropipette cantilever with a length up to hundreds of micrometers and a tip diameter of 30 nm. The design, simulation, fabrication, and performance of the HARP are described herein. This instrument is then tested using polymer trenches which reveals superior image fidelity compared to standard silicon tips. Finally, a nested-PID system is developed and employed to facilitate 3D characterization of 50-µm-step samples. The results demonstrate the efficacy of the proposed bench-top technique for the fabrication of low-cost, simple HAR AFM probes that facilitate the imaging of samples with deep trenches.

Label-Free Long-Term Methods for Live Cell Imaging of Neurons: New Opportunities

Time-lapse light microscopy combined with in vitro neuronal cultures has provided a significant contribution to the field of Developmental Neuroscience. The establishment of the neuronal polarity, i.e., formation of axons and dendrites, key structures responsible for inter-neuronal signaling, was described in 1988 by Dotti, Sullivan and Banker in a milestone paper that continues to be cited 30 years later. In the following decades, numerous fluorescently labeled tags and dyes were developed for live cell imaging, providing tremendous advancements in terms of resolution, acquisition speed and the ability to track specific cell structures. However, long-term recordings with fluorescence-based approaches remain challenging because of light-induced phototoxicity and/or interference of tags with cell physiology (e.g., perturbed cytoskeletal dynamics) resulting in compromised cell viability leading to cell death. Therefore, a label-free approach remains the most desirable method in long-term imaging of living neurons. In this paper we will focus on label-free high-resolution methods that can be successfully used over a prolonged period. We propose novel tools such as scanning ion conductance microscopy (SICM) or digital holography microscopy (DHM) that could provide new insights into live cell dynamics during neuronal development and regeneration after injury.

Charge Mapping of Pseudomonas aeruginosa Using a Hopping Mode Scanning Ion Conductance Microscopy Technique

Scanning ion conductance microscopy (SICM) is a topographic imaging technique capable of probing biological samples in electrolyte conditions. SICM enhancements have enabled surface charge detection based on voltage-dependent signals. Here, we show how the hopping mode SICM method (HP-SICM) can be used for rapid and minimally invasive surface charge mapping. We validate our method usingPseudomonas aeruginosaPA14 (PA) cells and observe a surface charge density of σ_PA = -2.0 ± 0.45 mC/m² that is homogeneous within the ∼80 nm lateral scan resolution. This biological surface charge is detected from at least 1.7 μm above the membrane (395× the Debye length), and the long-range charge detection is attributed to electroosmotic amplification. We show that imaging with a nanobubble-plugged probe reduces perturbation of the underlying sample. We extend the technique to PA biofilms and observe a charge density exceeding -20 mC/m². We use a solid-state calibration to quantify surface charge density and show that HP-SICM cannot be quantitatively described by a steady-state finite element model. This work contributes to the body of scanning probe methods that can uniquely contribute to microbiology and cellular biology.

Mapping Nanomechanical Properties of Basal Surfaces in Metastatic Intestinal 3D Living Organoids with High-Speed Scanning Ion Conductance Microscopy

Studying mechanobiology is increasing of scientific interests in life science and nanotechnology since its impact on cell activities (e.g., adhesion, migration), physiology, and pathology. The role of apical surface (AS) and basal surface (BS) of cells played in mechanobiology is significant. The mechanical mapping and analysis of cells mainly focus on AS while little is known about BS. Here, high-speed scanning ion conductance microscope as a powerful tool is utilized to simultaneously reveal morphologies and local elastic modulus (E) of BS of genotype-defined metastatic intestinal organoids. A simple method is developed to prepare organoid samples allowing for long-term BS imaging. The multiple nano/microstructures, i.e., ridge-like, stress-fiber, and E distributions on BS are dynamically revealed. The statistic E analysis shows softness of BS derived from eight types of organoids following a ranking: malignant tumor cells > benign tumor cells > normal cells. Moreover, the correlation factor between morphology and E is demonstrated depending on cell types. This work as first example reveals the subcellular morphologies and E distributions of BS of cells. The results would provide a clue for correlating genotype of 3D cells to malignant phenotype reflected by E and offering a promising strategy for early-stage diagnosis of cancer.

In Situ Visualization of Dynamic Cellular Effects of Phospholipid Nanoparticles via High-Speed Scanning Ion Conductance Microscopy

Phospholipid nanoparticles have been actively employed for numerous biomedical applications. A key factor in ensuring effective and safe applications of these nanomaterials is the regulation of their interactions with target cells, which is significantly dependent on an in-depth understanding of the nanoparticle-cell interactions. To date, most studies investigating these nano-bio interactions have been performed under static conditions and may lack crucial real-time information. It is, however, noteworthy that the nanoparticle-cell interactions are highly dynamic. Consequently, to gain a deeper insight into the cellular effects of phospholipid nanoparticles, real-time observation of cellular dynamics after nanoparticle introduction is necessary. Herein, a proof-of-concept in situ visualization of the dynamic cellular effects of sub-100 nm phospholipid nanoparticles using high-speed scanning ion conductance microscopy (HS-SICM) is reported. It is revealed that upon introduction into the cellular environment, within a short timescale of hundreds of seconds, phospholipid nanoparticles can selectively modulate the edge motility and surface roughness of healthy fibroblast and cancerous epithelial cells. Furthermore, the dynamic deformation profiles of these cells can be selectively altered in the presence of phospholipid nanoparticles. This work is anticipated to further shed light on the real-time nanoparticle-cell interactions for improved formulation of phospholipid nanoparticles for numerous bioapplications.

Start Me Up: How Can Surrounding Gangliosides Affect Sodium-Potassium ATPase Activity and Steer towards Pathological Ion Imbalance in Neurons?

Gangliosides, amphiphilic glycosphingolipids, tend to associate laterally with other membrane constituents and undergo extensive interactions with membrane proteins in cis or trans configurations. Studies of human diseases resulting from mutations in the ganglioside biosynthesis pathway and research on transgenic mice with the same mutations implicate gangliosides in the pathogenesis of epilepsy. Gangliosides are reported to affect the activity of the Na⁺/K⁺-ATPase, the ubiquitously expressed plasma membrane pump responsible for the stabilization of the resting membrane potential by hyperpolarization, firing up the action potential and ion homeostasis. Impaired Na⁺/K⁺-ATPase activity has also been hypothesized to cause seizures by several mechanisms. In this review we present different epileptic phenotypes that are caused by impaired activity of Na⁺/K⁺-ATPase or changed membrane ganglioside composition. We further discuss how gangliosides may influence Na⁺/K⁺-ATPase activity by acting as lipid sorting machinery providing the optimal stage for Na⁺/K⁺-ATPase function. By establishing a distinct lipid environment, together with other membrane lipids, gangliosides possibly modulate Na⁺/K⁺-ATPase activity and aid in “starting up” and “turning off” this vital pump. Therefore, structural changes of neuronal membranes caused by altered ganglioside composition can be a contributing factor leading to aberrant Na⁺/K⁺-ATPase activity and ion imbalance priming neurons for pathological firing.

Mechanics of migrating platelets investigated with scanning ion conductance microscopy

Platelets are small blood cells involved in hemostasis, wound healing, and immune response. After adhesion and spreading, platelets can migrate at sites of injury inducing an early immune response to inflammation or infection. Platelet migration requires fibrinogen-integrin binding and fibrinogen depletion from the substrate inducing a self-generated ligand gradient guiding the direction of migration. This type of cellular motion is referred to as haptotactic migration. The underlying mechanisms of haptotactic platelet migration have just recently been discovered, but the connection to platelet mechanics has remained unknown yet. Using scanning ion conductance microscopy (SICM), we investigated the three-dimensional morphology and mechanics of platelets during haptotactic migration for the first time. Migrating platelets showed a polarized, anisotropic shape oriented in the direction of migration. This polarization goes hand in hand with a characteristic subcellular stiffness distribution showing a region of increased stiffness at the leading edge. Moreover, the mechanical properties of the leading edge revealed a highly dynamic stiffening and softening process with rapid changes of the elastic modulus by a factor of up to 5× per minute. Inhibition of actin polymerization stopped the dynamic stiffening and softening process and halted the migration. By combining SICM with confocal fluorescence microscopy, we found that the increased stiffness and mechanical dynamics at the leading edge coincided with an increased volumetric F-actin density. Our data provide a connection between platelet mechanics and the cytoskeletal contribution to the migration process of platelets.