Long-tip high-speed atomic force microscopy for nanometer-scale imaging in live cells

Nano-Scale Video Imaging of Motility Machinery by High-Speed Atomic Force Microscopy

Motility is a vital aspect of many forms of life, with a wide range of highly conserved as well as highly unique systems adapted to the needs of various organisms and environments. While many motility systems are well studied using structural techniques like X-ray crystallography and electron microscopy, as well as fluorescence microscopy methodologies, it is difficult to directly determine the relationship between the shape and movement of a motility system due to a notable gap in spatiotemporal resolution. Bridging this gap as well as understanding the dynamic molecular movements that underpin motility mechanisms has been challenging. The advent of high-speed atomic force microscopy (HS-AFM) has provided a new window into understanding these nano-scale machines and the dynamic processes underlying motility. In this review, we highlight some of the advances in this field, ranging from reconstituted systems and purified higher-order supramolecular complexes to live cells, in both prokaryotic and eukaryotic contexts.

A look beyond topography: Transient phenomena of Escherichia coli cell division captured with high-speed in-line force mapping

Life on the nanoscale has been made accessible in recent decades by the development of fast and noninvasive techniques. High-speed atomic force microscopy (HS-AFM) is one such technique that shed light on single protein dynamics. Extending HS-AFM to effortlessly incorporate mechanical property mapping while maintaining fast imaging speed allows a look deeper than topography and reveal details of nanoscale mechanisms that govern life. Here, we present high-speed in-line force mapping (HS-iFM) to record mechanical properties and topography maps with high spatiotemporal resolution. Using HS-iFM, a comprehensive study of the nanoscale mechanical properties of living Escherichia coli revealed localized stiffening and details during cell division, formation and diffusion of pores in the membrane, and the impact of depressurization of a cell. The frame time was as low as 15 seconds with a spatial resolution of 5.5 nanometers per pixel in topography and 22 nanometers per pixel in force maps, allowing the capture of transient phenomena on bacterial surfaces in striking detail.

Membrane Ruffles: Composition, Function, Formation and Visualization

Membrane ruffles are cell actin-based membrane protrusions that have distinct structural characteristics. Linear ruffles with columnar spike-like and veil-like structures assemble at the leading edge of cell membranes. Circular dorsal ruffles (CDRs) have no supporting columnar structures but their veil-like structures, connecting from end to end, present an enclosed ring-shaped circular outline. Membrane ruffles are involved in multiple cell functions such as cell motility, macropinocytosis, receptor internalization, fluid viscosity sensing in a two-dimensional culture environment, and protecting cells from death in response to physiologically compressive loads. Herein, we review the state-of-the-art knowledge on membrane ruffle structure and function, the growth factor-induced membrane ruffling process, and the growth factor-independent ruffling mode triggered by calcium and other stimulating factors, together with the respective underlying mechanisms. We also summarize the inhibitors used in ruffle formation studies and their specificity. In the last part, an overview is given of the various techniques in which the membrane ruffles have been visualized up to now.

Biophysical Modeling of Synaptic Plasticity

Dendritic spines are small, bulbous compartments that function as postsynaptic sites and undergo intense biochemical and biophysical activity. The role of the myriad signaling pathways that are implicated in synaptic plasticity is well studied. A recent abundance of quantitative experimental data has made the events associated with synaptic plasticity amenable to quantitative biophysical modeling. Spines are also fascinating biophysical computational units because spine geometry, signal transduction, and mechanics work in a complex feedback loop to tune synaptic plasticity. In this sense, ideas from modeling cell motility can inspire us to develop multiscale approaches for predictive modeling of synaptic plasticity. In this article, we review the key steps in postsynaptic plasticity with a specific focus on the impact of spine geometry on signaling, cytoskeleton rearrangement, and membrane mechanics. We summarize the main experimental observations and highlight how theory and computation can aid our understanding of these complex processes.

An Efficient Method for Isolating and Purifying Nuclei from Mice Brain for Single-Molecule Imaging Using High-Speed Atomic Force Microscopy

Nuclear pore complexes (NPCs) on the nuclear membrane surface have a crucial function in controlling the movement of small molecules and macromolecules between the cell nucleus and cytoplasm through their intricate core channel resembling a spiderweb with several layers. Currently, there are few methods available to accurately measure the dynamics of nuclear pores on the nuclear membranes at the nanoscale. The limitation of traditional optical imaging is due to diffraction, which prevents achieving the required resolution for observing a diverse array of organelles and proteins within cells. Super-resolution techniques have effectively addressed this constraint by enabling the observation of subcellular components on the nanoscale. Nevertheless, it is crucial to acknowledge that these methods often need the use of fixed samples. This also raises the question of how closely a static image represents the real intracellular dynamic system. High-speed atomic force microscopy (HS-AFM) is a unique technique used in the field of dynamic structural biology, enabling the study of individual molecules in motion close to their native states. Establishing a reliable and repeatable technique for imaging mammalian tissue at the nanoscale using HS-AFM remains challenging due to inadequate sample preparation. This study presents the rapid strainer microfiltration (RSM) protocol for directly preparing high-quality nuclei from the mouse brain. Subsequently, we promptly utilize HS-AFM real-time imaging and cinematography approaches to record the spatiotemporal of nuclear pore nano-dynamics from the mouse brain.

Technical advances in high-speed atomic force microscopy

It has been 30 years since the outset of developing high-speed atomic force microscopy (HS-AFM), and 15 years have passed since its establishment in 2008. This advanced microscopy is capable of directly visualizing individual biological macromolecules in dynamic action and has been widely used to answer important questions that are inaccessible by other approaches. The number of publications on the bioapplications of HS-AFM has rapidly increased in recent years and has already exceeded 350. Although less visible than these biological studies, efforts have been made for further technical developments aimed at enhancing the fundamental performance of HS-AFM, such as imaging speed, low sample disturbance, and scan size, as well as expanding its functionalities, such as correlative microscopy, temperature control, buffer exchange, and sample manipulations. These techniques can expand the range of HS-AFM applications. After summarizing the key technologies underlying HS-AFM, this article focuses on recent technical advances and discusses next-generation HS-AFM.

Contact resonance atomic force microscopy using long elastic tips

In this work, a new theoretical model for contact resonance atomic force microscopy, which incorporates the elastic dynamics of a long sensing tip is presented. The model is based on the Euler-Bernoulli beam theory and includes coupling effects from the two-beam structure, also known as an 'L-shaped' beam in the literature. Here, high-accuracy prediction of the sample stiffness, using several vibration modes with a relative error smaller than 10% for practical working ranges, is demonstrated. A discussion on the model's capability to predict the dynamic phenomena of eigenmode veering and crossing, as the force applied to the sample increases, is presented. The L-shaped beam model presented here is also applicable for structural applications such as: micro-electro-mechanical systems, energy harvesting, and unmanned aerial vehicle landing gear.

Hybridization of papain molecules and DNA-wrapped single-walled carbon nanotubes evaluated by atomic force microscopy in fluids

Although various conjugates of single-walled carbon nanotubes (SWNTs) and biomolecules, such as nanobiosensors and nanobiodevices, have been reported, the conjugation of papain and SWNTs have not been reported because of the formation of unexpected aggregates. In this study, atomic force microscopy (AFM) in liquid was used to investigate the interactions between papain and DNA-wrapped SWNTs (DNA-SWNTs) at two different pH values (pH 3.0 and 10.5). The direct AFM observation of the mixture of papain and DNA-SWNTs confirmed the aggregation of papain molecules with DNA-SWNTs in the buffer solutions. The numerous and non-uniform adsorption of papain molecules onto DNA-SWNTs was more pronounced at pH 3.0 than that at pH 10.5. Furthermore, thick conjugates appeared when papain and DNA-SWNTs were simultaneously mixed. The near-infrared photoluminescence spectra of the SWNTs drastically changed when the papain molecules were injected into the DNA-SWNT suspension at pH 3.0. Thus, the regulation of electrostatic interactions is a key aspect in preparing optimal conjugates of papain and DNA-SWNTs. Furthermore, although previous papers reported AFM images of dried samples, this study demonstrates the potential of AFM in liquid in evaluating individual bioconjugates of SWNTs.

Recent advances in sensing the inter-biomolecular interactions at the nanoscale - A comprehensive review of AFM-based force spectroscopy

Biomolecular interactions underpin most processes inside the cell. Hence, a precise and quantitative understanding of molecular association and dissociation events is crucial, not only from a fundamental perspective, but also for the rational design of biomolecular platforms for state-of-the-art biomedical and industrial applications. In this context, atomic force microscopy (AFM) appears as an invaluable experimental technique, allowing the measurement of the mechanical strength of biomolecular complexes to provide a quantitative characterization of their interaction properties from a single molecule perspective. In the present review, the most recent methodological advances in this field are presented with special focus on bioconjugation, immobilization and AFM tip functionalization, dynamic force spectroscopy measurements, molecular recognition imaging and theoretical modeling. We expect this work to significantly aid in grasping the principles of AFM-based force spectroscopy (AFM-FS) technique and provide the necessary tools to acquaint the type of data that can be achieved from this type of experiments. Furthermore, a critical assessment is done with other nanotechnology techniques to better visualize the future prospects of AFM-FS.

A cryogen-free superconducting magnet based scanning tunneling microscope for liquid phase measurement

Scanning tunneling microscopes (STMs) that work in ultra-high vacuum and low temperatures are commonly used in condensed matter physics, but an STM that works in a high magnetic field to image chemical molecules and active biomolecules in solution has never been reported. Here, we present a liquid-phase STM for use in a 10 T cryogen-free superconducting magnet. The STM head is mainly constructed with two piezoelectric tubes. A large piezoelectric tube is fixed at the bottom of a tantalum frame to perform large-area imaging. A small piezoelectric tube mounted at the free end of the large one performs high-precision imaging. The imaging area of the large piezoelectric tube is four times that of the small one. The high compactness and rigidity of the STM head make it functional in a cryogen-free superconducting magnet with huge vibrations. The performance of our homebuilt STM was demonstrated by the high-quality, atomic-resolution images of a graphite surface, as well as the low drift rates in the X-Y plane and Z direction. Furthermore, we successfully obtained atomic-resolution images of graphite in solution conditions while sweeping the field from 0 to 10 T, illustrating the new STM's immunity to magnetic fields. The sub-molecular images of active antibodies and plasmid DNA in solution conditions show the device's capability of imaging biomolecules. Our STM is suitable for studying chemical molecules and active biomolecules in high magnetic fields.

Tip-scan high-speed atomic force microscopy with a uniaxial substrate stretching device for studying dynamics of biomolecules under mechanical stress

High-speed atomic force microscopy (HS-AFM) is a powerful tool for studying the dynamics of biomolecules in vitro because of its high temporal and spatial resolution. However, multi-functionalization, such as combination with complementary measurement methods, environment control, and large-scale mechanical manipulation of samples, is still a complex endeavor due to the inherent design and the compact sample scanning stage. Emerging tip-scan HS-AFM overcame this design hindrance and opened a door for additional functionalities. In this study, we designed a motor-driven stretching device to manipulate elastic substrates for HS-AFM imaging of biomolecules under controllable mechanical stimulation. To demonstrate the applicability of the substrate stretching device, we observed a microtubule buckling by straining the substrate and actin filaments linked by α-actinin on a curved surface. In addition, a BAR domain protein BIN1 that senses substrate curvature was observed while dynamically controlling the surface curvature. Our results clearly prove that large-scale mechanical manipulation can be coupled with nanometer-scale imaging to observe biophysical effects otherwise obscured.

Guide to studying intrinsically disordered proteins by high-speed atomic force microscopy

Intrinsically disordered proteins (IDPs) are partially or entirely disordered. Their intrinsically disordered regions (IDRs) dynamically explore a wide range of structural space by their highly flexible nature. Due to this distinct feature largely different from structured proteins, conventional structural analyses relying on ensemble averaging is unsuitable for characterizing the dynamic structure of IDPs. Therefore, single-molecule measurement tools have been desired in IDP studies. High-speed atomic force microscopy (HS-AFM) is a unique tool that allows us to directly visualize single biomolecules at 2-3 nm lateral and ∼ 0.1 nm vertical spatial resolution, and at sub-100 ms temporal resolution under near physiological conditions, without any chemical labeling. HS-AFM has been successfully used not only to characterize the shape and motion of IDP molecules but also to visualize their function-related dynamics. In this article, after reviewing the principle and current performances of HS-AFM, we describe experimental considerations in the HS-AFM imaging of IDPs and methods to quantify molecular features from captured images. Finally, we outline recent HS-AFM imaging studies of IDPs.

3D nanomechanical mapping of subcellular and sub-nuclear structures of living cells by multi-harmonic AFM with long-tip microcantilevers

Recent developments such as multi-harmonic Atomic Force Microscopy (AFM) techniques have enabled fast, quantitative mapping of nanomechanical properties of living cells. Due to their high spatiotemporal resolution, these methods provide new insights into changes of mechanical properties of subcellular structures due to disease or drug response. Here, we propose three new improvements to significantly improve the resolution, identification, and mechanical property quantification of sub-cellular and sub-nuclear structures using multi-harmonic AFM on living cells. First, microcantilever tips are streamlined using long-carbon tips to minimize long-range hydrodynamic interactions with the cell surface, to enhance the spatial resolution of nanomechanical maps and minimize hydrodynamic artifacts. Second, simultaneous Spinning Disk Confocal Microscopy (SDC) with live-cell fluorescent markers enables the unambiguous correlation between observed heterogeneities in nanomechanical maps with subcellular structures. Third, computational approaches are then used to estimate the mechanical properties of sub-nuclear structures. Results are demonstrated on living NIH 3T3 fibroblasts and breast cancer MDA-MB-231 cells, where properties of nucleoli, a deep intracellular structure, were assessed. The integrated approach opens the door to study the mechanobiology of sub-cellular structures during disease or drug response.

A Single Shot of Vesicles

Bacteria communicate through signaling molecules that coordinate group behavior. Hydrophobic signals that do not diffuse in aqueous environments are used as signaling molecules by several bacteria. However, limited information is currently available on the mechanisms by which these molecules are transported between cells. Membrane vesicles (MVs) with diverse functions play important roles in the release and delivery of hydrophobic signaling molecules, leading to differences in the dynamics of signal transportation from those of free diffusion. Studies on Paracoccus denitrificans, which produces a hydrophobic long-chain N-acyl homoserine lactone (AHL), showed that signals were loaded into MVs at a concentration with the potential to trigger the quorum sensing (QS) response with a "single shot" to the cell. Furthermore, stimulating the formation of MVs increased the release of signals from the cell; therefore, a basic understanding of MV formation is important. Novel findings revealed the formation of MVs through different routes, resulting in the production of different types of MVs. Methods such as high-speed atomic force microscopy (AFM) phase imaging allow the physical properties of MVs to be analyzed at a nanometer resolution, revealing their heterogeneity. In this special minireview, we introduce the role of MVs in bacterial communication and highlight recent findings on MV formation and their physical heterogeneity by referring to our research. We hope that this minireview will provide basic information for understanding the functionality of MVs in ecological systems.

Quantifying molecular- to cellular-level forces in living cells

Mechanical cues have been suggested to play an important role in cell functions and cell fate determination, however, such physical quantities are challenging to directly measure in living cells with single molecule sensitivity and resolution. In this review, we focus on two main technologies that are promising in probing forces at the single molecule level. We review their theoretical fundamentals, recent technical advancements, and future directions, tailored specifically for interrogating mechanosensitive molecules in live cells.

The emerging role of mechanical and topographical factors in the development and treatment of nervous system disorders: dark and light sides of the force

Nervous system diseases are the subject of intensive research due to their association with high mortality rates and their potential to cause irreversible disability. Most studies focus on targeting the biological factors related to disease pathogenesis, e.g. use of recombinant activator of plasminogen in the treatment of stroke. Nevertheless, multiple diseases such as Parkinson’s disease and Alzheimer’s disease still lack successful treatment. Recently, evidence has indicated that physical factors such as the mechanical properties of cells and tissue and topography play a crucial role in homeostasis as well as disease progression. This review aims to depict these factors’ roles in the progression of nervous system diseases and consequently discusses the possibility of new therapeutic approaches. The literature is reviewed to provide a deeper understanding of the roles played by physical factors in nervous system disease development to aid in the design of promising new treatment approaches.

An ultra-wide scanner for large-area high-speed atomic force microscopy with megapixel resolution

High-speed atomic force microscopy (HS-AFM) is a powerful tool for visualizing the dynamics of individual biomolecules. However, in single-molecule HS-AFM imaging applications, x,y-scanner ranges are typically restricted to a few hundred nanometers, preventing overview observation of larger molecular assemblies, such as 2-dimensional protein crystal growth or fibrillar aggregation. Previous advances in scanner design using mechanical amplification of the piezo-driven x,y-positioning system have extended the size of HS-AFM image frames to several tens of micrometer, but these large scanners may suffer from mechanical instabilities at high scan speeds and only record images with limited pixel numbers and comparatively low lateral resolutions (> 20–100 nm/pixel), complicating single-molecule analysis. Thus, AFM systems able to image large sample areas at high speeds and with nanometer resolution have still been missing. Here, we describe a HS-AFM sample-scanner system able to record large topographic images (≤ 36 × 36 µm²) containing up to 16 megapixels, providing molecular resolution throughout the image frame. Despite its large size, the flexure-based scanner features a high resonance frequency (> 2 kHz) and delivers stable operation even at high scans speeds of up to 7.2 mm/s, minimizing the time required for recording megapixel scans. We furthermore demonstrate that operating this high-speed scanner in time-lapse mode can simultaneously identify areas of spontaneous 2-dimensional Annexin A5 crystal growth, resolve the angular orientation of large crystalline domains, and even detect rare crystal lattice defects, all without changing scan frame size or resolution. Dynamic processes first identified from overview scans can then be further imaged at increased frame rates in reduced scan areas after switching to conventional HS-AFM scanning. The added ability to collect large-area, high-resolution images of complex samples within biological-relevant time frames extends the capabilities of HS-AFM from single-molecule imaging to the study of large dynamic molecular arrays. Moreover, large-area HS-AFM scanning can generate detailed structural data sets from a single scan, aiding the quantitative analysis of structurally heterogenous samples, including cellular surfaces.

How did correlative atomic force microscopy and super-resolution microscopy evolve in the quest for unravelling enigmas in biology?

With the invention of the Atomic Force Microscope (AFM) in 1986 and the subsequent developments in liquid imaging and cellular imaging it became possible to study the topography of cellular specimens under nearly physiological conditions with nanometric resolution. The application of AFM to biological research was further expanded with the technological advances in imaging modes where topographical data can be combined with nanomechanical measurements, offering the possibility to retrieve the biophysical properties of tissues, cells, fibrous components and biomolecules. Meanwhile, the quest for breaking the Abbe diffraction limit restricting microscopic resolution led to the development of super-resolution fluorescence microscopy techniques that brought the resolution of the light microscope comparable to the resolution obtained by AFM. The instrumental combination of AFM and optical microscopy techniques has evolved over the last decades from integration of AFM with bright-field and phase-contrast imaging techniques at first to correlative AFM and wide-field fluorescence systems and then further to the combination of AFM and fluorescence based super-resolution microscopy modalities. Motivated by the many developments made over the last decade, we provide here a review on AFM combined with super-resolution fluorescence microscopy techniques and how they can be applied for expanding our understanding of biological processes.

Nano-Surveillance: Tracking Individual Molecules in a Sea of Chromatin

Chromatin is the epigenomic platform for diverse nuclear processes such as DNA repair, replication, transcription, telomere, and centromere function. In cancer cells, mutations in key processes result in DNA amplification, chromosome translocations, and chromothripsis, severely distorting the natural chromatin state. In normal and diseased states, dozens of chromatin effectors alter the physical integrity and dynamics of chromatin at the level of both single nucleosomes and arrays of nucleosomes folded into 3-dimensional shapes. Integrating these length scales, from the 10 nm sized nucleosome to mitotic chromosomes, whilst jostling within the crowded environment of the cell, cannot yet be achieved by a single technology. In this review, we discuss tools that have proven powerful in the investigation of nucleosome and chromatin fiber dynamics. We also provide a deeper focus into atomic force microscopy (AFM) applications that can bridge diverse length and time scales. Using time course AFM, we observe that chromatin condensation by H1.5 is dynamic, whereas using nano-indentation force spectroscopy we observe that both histone variants and nucleosome binding partners alter material properties of individual nucleosomes. Finally, we demonstrate how high-speed AFM can visualize plasmid DNA dynamics, intermittent nucleosome-nucleosome contacts, and changes in nucleosome phasing along a contiguous chromatin fiber. Altogether, the development of innovative technologies holds the promise of revealing the secret lives of nucleosomes, potentially bridging the gaps in our understanding of how chromatin works within living cells and tissues.

Cytoskeleton induced the changes of microvilli and mechanical properties in living cells by atomic force microscopy

The cytoskeleton acts as a scaffold for membrane protrusion, such as microvilli. However, the relationship between the characteristics of microvilli and cytoskeleton remains poorly understood under the physiological state. To investigate the role of the cytoskeleton in regulating microvilli and cellular mechanical properties, atomic force microscopy (AFM) was used to detect the dynamic characteristics of microvillus morphology and elastic modulus of living HeLa cells. First, HeLa and MCF-7 cell lines were stained with Fluor-488-phalloidin and microtubules antibody. Then, the microvilli morphology was analyzed by high-resolution images of AFM in situ. Furthermore, changes in elastic modulus were investigated by the force curve of AFM. Fluorescence microscopy and AFM results revealed that destroyed microfilaments led to a smaller microvilli size, whereas the increase in the aggregation and number of microfilaments led to a larger microvilli size. The destruction and aggregation of microfilaments remarkably affected the mechanical properties of HeLa cells. Microtubule-related drugs induced the change of microtubule, but we failed to note significant differences in microvilli morphology and mechanical properties of cells. In summary, our results unraveled the relationship between microfilaments and the structure of microvilli and Young's modulus in living HeLa cells, which would contribute to the further understanding of the physiological function of the cytoskeleton in vivo.

Review: Cantilever-Based Sensors for High Speed Atomic Force Microscopy

This review critically summarizes the recent advances of the microcantilever-based force sensors for atomic force microscope (AFM) applications. They are one the most common mechanical spring-mass systems and are extremely sensitive to changes in the resonant frequency, thus finding numerous applications especially for molecular sensing. Specifically, we comment on the latest progress in research on the deflection detection systems, fabrication, coating and functionalization of the microcantilevers and their application as bio- and chemical sensors. A trend on the recent breakthroughs on the study of biological samples using high-speed atomic force microscope is also reported in this review.

Nanomechanical mapping of soft materials with the atomic force microscope: methods, theory and applications

Fast, high-resolution, non-destructive and quantitative characterization methods are needed to develop materials with tailored properties at the nanoscale or to understand the relationship between mechanical properties and cell physiology. This review introduces the state-of-the-art force microscope-based methods to map at high-spatial resolution the elastic and viscoelastic properties of soft materials. The experimental methods are explained in terms of the theories that enable the transformation of observables into material properties. Several applications in materials science, molecular biology and mechanobiology illustrate the scope, impact and potential of nanomechanical mapping methods.

High-Speed Atomic Force Microscopy to Study Myosin Motility

High-speed atomic force microscopy (HS-AFM) is a unique tool that enables imaging of protein molecules during their functional activity at sub-100 ms temporal and submolecular spatial resolution. HS-AFM is suited for the study of highly dynamic proteins, including myosin motors. HS-AFM images of myosin V walking on actin filaments provide irrefutable evidence for the swinging lever arm motion propelling the molecule forward. Moreover, molecular behaviors that have not been noticed before are also displayed on the AFM movies. This chapter describes the principle, underlying techniques and performance of HS-AFM, filmed images of myosin V, and mechanistic insights into myosin motility provided from the filmed images.

Nanorheology of living cells measured by AFM-based force-distance curves

Mechanobiology aims to establish functional relationships between the mechanical state of a living a cell and its physiology. The acquisition of force-distance curves with an AFM is by far the dominant method to characterize the nanomechanical properties of living cells. However, theoretical simulations have shown that the contact mechanics models used to determine the Young's modulus from a force-distance curve could be off by a factor 5 from its expected value. The semi-quantitative character arises from the lack of a theory that integrates the AFM data, a realistic viscoelastic model of a cell and its finite-thickness. Here, we develop a method to determine the mechanical response of a cell from a force-distance curve. The method incorporates bottom-effect corrections, a power-law rheology model and the deformation history of the cell. It transforms the experimental data into viscoelastic parameters of the cell as a function of the indentation frequency. The quantitative agreement obtained between the experiments performed on living fibroblast cells and the analytical theory supports the use of force-distance curves to measure the nanorheological properties of cells.

High-Speed SICM for the Visualization of Nanoscale Dynamic Structural Changes in Hippocampal Neurons

Dynamic reassembly of the cytoskeleton and structural changes represented by dendritic spines, cargo transport, and synapse formation are closely related to memory. However, the visualization of the nanoscale topography is challenging because of the diffraction limit of optical microscopy. Scanning ion conductance microscopy (SICM) is an effective tool for visualizing the nanoscale topography changes of the cell surface without labeling. The temporal resolution of SICM is a critical issue of live-cell time-lapse imaging. Here, we developed a new scanning method, automation region of interest (AR)-mode SICM, to select the next imaging region by predicting the location of a cell, thus improving the scanning speed of time-lapse imaging. The newly developed algorithm reduced the scanning time by half. The time-lapse images provided not only novel information about nanoscale structural changes but also quantitative information on the dendritic spine and synaptic bouton volume changes and formation process of the neural network that are closely related to memory. Furthermore, translocation of plasmalemmal precursor vesicles (ppvs), for which fluorescent labeling has not been established, were also visualized along with the rearrangement of the cytoskeleton at the growth cone.

Integration of sharp silicon nitride tips into high-speed SU8 cantilevers in a batch fabrication process

Employing polymer cantilevers has shown to outperform using their silicon or silicon nitride analogues concerning the imaging speed of atomic force microscopy (AFM) in tapping mode (intermittent contact mode with amplitude modulation) by up to one order of magnitude. However, tips of the cantilever made out of a polymer material do not meet the requirements for tip sharpness and durability. Combining the high imaging bandwidth of polymer cantilevers with making sharp and wear-resistant tips is essential for a future adoption of polymer cantilevers in routine AFM use. In this work, we have developed a batch fabrication process to integrate silicon nitride tips with an average tip radius of 9 ± 2 nm into high-speed SU8 cantilevers. Key aspects of the process are the mechanical anchoring of a moulded silicon nitride tip and a two-step release process. The fabrication recipe can be adjusted to any photo-processable polymer cantilever.

High-speed force spectroscopy: microsecond force measurements using ultrashort cantilevers

Complete understanding of the role of mechanical forces in biological processes requires knowledge of the mechanical properties of individual proteins and living cells. Moreover, the dynamic response of biological systems at the nano- and microscales span over several orders of magnitude in time, from sub-microseconds to several minutes. Thus, access to force measurements over a wide range of length and time scales is required. High-speed atomic force microscopy (HS-AFM) using ultrashort cantilevers has emerged as a tool to study the dynamics of biomolecules and cells at video rates. The adaptation of HS-AFM to perform high-speed force spectroscopy (HS-FS) allows probing protein unfolding and receptor/ligand unbinding up to the velocity of molecular dynamics (MD) simulations with sub-microsecond time resolution. Moreover, application of HS-FS on living cells allows probing the viscoelastic response at short time scales providing deep understanding of cytoskeleton dynamics. In this mini-review, we assess the principles and recent developments and applications of HS-FS using ultrashort cantilevers to probe molecular and cellular mechanics.

OBSERVER-BASED CONTROL OF A DUAL-STAGE PIEZOELECTRIC SCANNER

Despite its proven success in a wide variety of applications, the atomic force microscope (AFM) remains limited by its slow imaging rate. One approach to overcome this challenge is to rely on algorithmic approaches that reduce the imaging time not by scanning faster but by scanning less. Such schemes are particularly useful on older instruments as they can provide significant gains despite the existing (slow) hardware. At the same time, algorithms for sub-sampling can yield even greater improvements in imaging rate when combined with advanced scanners that can be retrofitted into the system. In this work, we focus on the use of a dual-stage piezoelectric scanner coupled with a particular scanning algorithm known as Local Circular Scan (LCS). LCS drives the tip of the AFM along a circular trajectory while using feedback to center that circle on a sample edge and to move the circle along the feature, thus reducing imaging time by concentrating the samples to the region of interest. Dual-stage systems are well-suited to LCS as the algorithm is naturally described in terms of a high-frequency, short range path (the scanning circle) and a slower, long range path (the track along the sample). However, control of the scanner is not straightforward as the system is multi-input, single-output. Here we establish controllability and observability of the scanning stage, allowing us to develop individual controllers for the long-range and short-range actuators through the principle of separation. We then use an internal model controller for the short range actuator to track a sinusoidal input (to generate the circular motion) and a state-space set-point tracking controller for the long range actuator. The results are demonstrated through simulation.

Spatial high resolution of actin filament organization by PeakForce atomic force microscopy

Objectives

To investigate the heterogeneous feature of actin filaments (ACFs) associated with the cellular membrane in HeLa and HCT‐116 cells at the nanoscale level.

Materials and Methods

Fluorescence microscopy coupled with atomic force microscopy (AFM) was used to identify and characterize ACFs of cells. The distribution of ACFs was detected by Fluor‐488‐phalloidin–labelled actin. The morphology of the ACFs was probed by AFM images. The spatial correlation of the microvilli and ACFs was explored with different forces of AFM loading on cells.

Results

Intricate but ordered structures of the actin cytoskeletons associated with cellular membrane were characterized and revealed. Two different layers of ACFs with distinct structural organizations were directly observed in HCT‐116 and HeLa cells. Bundle‐shaped ACFs protruding the cellular membrane forming the microvilli, and the network ACFs underneath the cellular membrane were resolved with high resolution under near‐physiological conditions. Approximately 14 nm lateral resolution was achieved when imaging single ACF beneath the cellular membrane. On the basis of the observed spatial distribution of the ultrastructure of the ACF organization, a model for this organization of ACFs was proposed.

Conclusions

We revealed the two layers of the ACF organization in Hela and HCT‐116 cells. The resolved heterogeneous structures at the nanoscale level provide a spatial view of the ACFs, which would contribute to the understanding of the essential biological functions of the actin cytoskeleton.

Unraveling the Macromolecular Pathways of IgG Oligomerization and Complement Activation on Antigenic Surfaces

IgG antibodies play a central role in protection against pathogens by their ability to alert and activate the innate immune system. Here, we show that IgGs assemble into oligomers on antigenic surfaces through an ordered, Fc domain-mediated process that can be modulated by protein engineering. Using high-speed atomic force microscopy, we unraveled the molecular events of IgG oligomer formation on surfaces. IgG molecules were recruited from solution although assembly of monovalently binding molecules also occurred through lateral diffusion. Monomers were observed to assemble into hexamers with all intermediates detected, but in which only hexamers bound C1. Functional characterization of oligomers on cells also demonstrated that C1 binding to IgG hexamers was a prerequisite for maximal activation, whereas tetramers, trimers, and dimers were mostly inactive. We present a dynamic IgG oligomerization model, which provides a framework for exploiting the macromolecular assembly of IgGs on surfaces for tool, immunotherapy, and vaccine design.

High-speed atomic force microscope with a combined tip-sample scanning architecture

A high-speed atomic force microscope (HS-AFM) based on a tip-sample combined scanning architecture is presented. In this system, the X-scanner, which is separated from the AFM head, carries the sample and scans along the fast-axis. The Y and Z scanners integrated in the AFM head oscillate an ultrashort cantilever probe and scan in the other two dimensions. The optical beam deflection method is improved to enable the laser to track the probe over a wide scan range. A novel probe holder realizes easy exchange and alignment of the probe. Due to the separation of the X and Y scanners, both appear with better dynamic performance and carrying capacity. Experiments show that the HS-AFM established in this work can achieve a line rate of up to 100 Hz with the basic proportional-integral-derivative control algorithm and linear driving. The permissible sample size and mass can be as large as several centimeters and above 40 g.

High-speed near-field fluorescence microscopy combined with high-speed atomic force microscopy for biological studies

BACKGROUND

High-speed atomic force microscopy (HS-AFM) has successfully visualized a variety of protein molecules during their functional activity. However, it cannot visualize small molecules interacting with proteins and even protein molecules when they are encapsulated. Thus, it has been desired to achieve techniques enabling simultaneous optical/AFM imaging at high spatiotemporal resolution with high correlation accuracy.

METHODS

Scanning near-field optical microscopy (SNOM) is a candidate for the combination with HS-AFM. However, the imaging rate of SNOM has been far below that of HS-AFM. We here developed HS-SNOM and metal tip-enhanced total internal reflection fluorescence microscopy (TIRFM) by exploiting tip-scan HS-AFM and exploring methods to fabricate a metallic tip on a tiny HS-AFM cantilever.

RESULTS

In tip-enhanced TIRFM/HS-AFM, simultaneous video recording of the two modalities of images was demonstrated in the presence of fluorescent molecules in the bulk solution at relatively high concentration. By using fabricated metal-tip cantilevers together with our tip-scan HS-AFM setup equipped with SNOM optics, we could perform simultaneous HS-SNOM/HS-AFM imaging, with correlation analysis between the two overlaid images being facilitated.

CONCLUSIONS

This study materialized simultaneous tip-enhanced TIRFM/HS-AFM and HS-SNOM/HS-AFM imaging at high spatiotemporal resolution. Although some issues remain to be solved in the future, these correlative microscopy methods have a potential to increase the versatility of HS-AFM in biological research.

GENERAL SIGNIFICANCE

We achieved an imaging rate of ~3 s/frame for SNOM imaging, more than 100-times higher than the typical SNOM imaging rate. We also demonstrated ~39 nm resolution in HS-SNOM imaging of fluorescently labeled DNA in solution.

Thermoelectric stack sample cooling modification of a commercial atomic force microscopy

Enabling temperature dependent experiments in Atomic Force Microscopy is of great interest to study materials and surface properties at the nanoscale. By studying Curie temperature of multiferroic materials, temperature dependent phase transitions on crystalline structures or resistive switching phenomena are only a few examples of applications. We present an equipment capable of cooling samples using a thermoelectric cooling stage down to -61.4 °C in a 15 × 15 mm² sample plate. The equipment uses a four-unit thermoelectric stack to achieve maximum temperature range, with low electrical and mechanical noise. The equipment is installed into a Keysight 5500LS Atomic Force Microscopy maintaining its compatibility with all Electrical and Mechanical modes of operation. We study the contribution of the liquid cooling pump vibration into the cantilever static deflection noise and the temperature dependence of the cantilever deflection. A La_0.7Sr_0.3MnO_3-y thin film sample is used to demonstrate the performance of the equipment and its usability by analyzing the resistive switching phenomena associated with this oxide perovskite.

The 2018 correlative microscopy techniques roadmap

Developments in microscopy have been instrumental to progress in the life sciences, and many new techniques have been introduced and led to new discoveries throughout the last century. A wide and diverse range of methodologies is now available, including electron microscopy, atomic force microscopy, magnetic resonance imaging, small-angle x-ray scattering and multiple super-resolution fluorescence techniques, and each of these methods provides valuable read-outs to meet the demands set by the samples under study. Yet, the investigation of cell development requires a multi-parametric approach to address both the structure and spatio-temporal organization of organelles, and also the transduction of chemical signals and forces involved in cell-cell interactions. Although the microscopy technologies for observing each of these characteristics are well developed, none of them can offer read-out of all characteristics simultaneously, which limits the information content of a measurement. For example, while electron microscopy is able to disclose the structural layout of cells and the macromolecular arrangement of proteins, it cannot directly follow dynamics in living cells. The latter can be achieved with fluorescence microscopy which, however, requires labelling and lacks spatial resolution. A remedy is to combine and correlate different readouts from the same specimen, which opens new avenues to understand structure-function relations in biomedical research. At the same time, such correlative approaches pose new challenges concerning sample preparation, instrument stability, region of interest retrieval, and data analysis. Because the field of correlative microscopy is relatively young, the capabilities of the various approaches have yet to be fully explored, and uncertainties remain when considering the best choice of strategy and workflow for the correlative experiment. With this in mind, the Journal of Physics D: Applied Physics presents a special roadmap on the correlative microscopy techniques, giving a comprehensive overview from various leading scientists in this field, via a collection of multiple short viewpoints.

Photothermal Off-Resonance Tapping for Rapid and Gentle Atomic Force Imaging of Live Cells

Imaging living cells by atomic force microscopy (AFM) promises not only high-resolution topographical data, but additionally, mechanical contrast, both of which are not obtainable with other microscopy techniques. Such imaging is however challenging, as cells need to be measured with low interaction forces to prevent either deformation or detachment from the surface. Off-resonance modes which periodically probe the surface have been shown to be advantageous, as they provide excellent force control combined with large amplitudes, which help reduce lateral force interactions. However, the low actuation frequency in traditional off-resonance techniques limits the imaging speed significantly. Using photothermal actuation, we probe the surface by directly actuating the cantilever. Due to the much smaller mass that needs to be actuated, the achievable measurement frequency is increased by two orders of magnitude. Additionally, photothermal off-resonance tapping (PORT) retains the precise force control of conventional off-resonance modes and is therefore well suited to gentle imaging. Here, we show how photothermal off-resonance tapping can be used to study live cells by AFM. As an example of imaging mammalian cells, the initial attachment, as well as long-term detachment, of human thrombocytes is presented. The membrane disrupting effect of the antimicrobial peptide CM-15 is shown on the cell wall of Escherichia coli. Finally, the dissolution of the cell wall of Bacillus subtilis by lysozyme is shown. Taken together, these evolutionarily disparate forms of life exemplify the usefulness of PORT for live cell imaging in a multitude of biological disciplines.

Algal Viruses: The (Atomic) Shape of Things to Come

Visualization of algal viruses has been paramount to their study and understanding. The direct observation of the morphological dynamics of infection is a highly desired capability and the focus of instrument development across a variety of microscopy technologies. However, the high temporal (ms) and spatial resolution (nm) required, combined with the need to operate in physiologically relevant conditions presents a significant challenge. Here we present a short history of virus structure study and its relation to algal viruses and highlight current work, concentrating on electron microscopy and atomic force microscopy, towards the direct observation of individual algae⁻virus interactions. Finally, we make predictions towards future algal virus study direction with particular focus on the exciting opportunities offered by modern high-speed atomic force microscopy methods and instrumentation.

Morphological changes of plasma membrane and protein assembly during clathrin-mediated endocytosis

Clathrin-mediated endocytosis (CME) proceeds through a series of morphological changes of the plasma membrane induced by a number of protein components. Although the spatiotemporal assembly of these proteins has been elucidated by fluorescence-based techniques, the protein-induced morphological changes of the plasma membrane have not been fully clarified in living cells. Here, we visualize membrane morphology together with protein localizations during CME by utilizing high-speed atomic force microscopy (HS-AFM) combined with a confocal laser scanning unit. The plasma membrane starts to invaginate approximately 30 s after clathrin starts to assemble, and the aperture diameter increases as clathrin accumulates. Actin rapidly accumulates around the pit and induces a small membrane swelling, which, within 30 s, rapidly covers the pit irreversibly. Inhibition of actin turnover abolishes the swelling and induces a reversible open–close motion of the pit, indicating that actin dynamics are necessary for efficient and irreversible pit closure at the end of CME.

Cells communicate with their environments via the plasma membrane and various membrane proteins. Clathrin-mediated endocytosis (CME) plays a central role in such communication and proceeds with a series of multiprotein assembly, deformation of the plasma membrane, and production of a membrane vesicle that delivers extracellular signaling molecules into the cytoplasm. In this study, we utilized our home-built correlative imaging system comprising high-speed atomic force microscopy (HS-AFM) and confocal fluorescence microscopy to simultaneously image morphological changes of the plasma membrane and protein localization during CME in a living cell. The results revealed a tight correlation between the size of the pit and the amount of clathrin assembled. Actin dynamics play multiple roles in the assembly, maturation, and closing phases of the process, and affects membrane morphology, suggesting a close relationship between endocytosis and dynamic events at the cell cortex. Knock down of dynamin also affected the closing motion of the pit and showed functional correlation with actin.

High-speed atomic force microscopy and its future prospects

Various techniques have been developed and used to investigate how proteins produce complex biological architectures and phenomena. Among these techniques, high-speed atomic force microscopy (HS-AFM) holds a unique position. It is only HS-AFM that allows the simultaneous assessment of structure and dynamics of single protein molecules in action. This new microscopy tool has been successfully applied to a variety of proteins, from motor proteins to membrane proteins, antibodies, enzymes, and even to intrinsically disordered proteins. And yet there still remain many biomolecular phenomena that cannot be addressed by HS-AFM in its current form. Here, I present a brief history of HS-AFM development, describe the current state of HS-AFM, and then discuss which new biological scanning probe microscopy techniques will be coming up next.

Receptor-mediated endocytosis generates nanomechanical force reflective of ligand identity and cellular property

Whether environmental (thermal, chemical, and nutrient) signals generate quantifiable, nanoscale, mechanophysical changes in the cellular plasma membrane has not been well elucidated. Assessment of such mechanophysical properties of plasma membrane may shed lights on fundamental cellular process. Atomic force microscopic (AFM) measurement of the mechanical properties of live cells was hampered by the difficulty in accounting for the effects of the cantilever motion and the associated hydrodynamic force on the mechanical measurement. These challenges have been addressed in our recently developed control-based AFM nanomechanical measurement protocol, which enables a fast, noninvasive, broadband measurement of the real-time changes in plasma membrane elasticity in live cells. Here we show using this newly developed AFM platform that the plasma membrane of live mammalian cells exhibits a constant and quantifiable nanomechanical property, the membrane elasticity. This mechanical property sensitively changes in response to environmental factors, such as the thermal, chemical, and growth factor stimuli. We demonstrate that different chemical inhibitors of endocytosis elicit distinct changes in plasma membrane elastic modulus reflecting their specific molecular actions on the lipid configuration or the endocytic machinery. Interestingly, two different growth factors, EGF and Wnt3a, elicited distinct elastic force profiles revealed by AFM at the plasma membrane during receptor-mediated endocytosis. By applying this platform to genetically modified cells, we uncovered a previously unknown contribution of Cdc42, a key component of the cellular trafficking network, to EGF-stimulated endocytosis at plasma membrane. Together, this nanomechanical AFM study establishes an important foundation that is expandable and adaptable for investigation of cellular membrane evolution in response to various key extracellular signals.

High-speed atomic force microscopy and its future prospects

Various techniques have been developed and used to investigate how proteins produce complex biological architectures and phenomena. Among these techniques, high-speed atomic force microscopy (HS-AFM) holds a unique position. It is only HS-AFM that allows the simultaneous assessment of structure and dynamics of single protein molecules in action. This new microscopy tool has been successfully applied to a variety of proteins, from motor proteins to membrane proteins, antibodies, enzymes, and even to intrinsically disordered proteins. And yet there still remain many biomolecular phenomena that cannot be addressed by HS-AFM in its current form. Here, I present a brief history of HS-AFM development, describe the current state of HS-AFM, and then discuss which new biological scanning probe microscopy techniques will be coming up next.

High-speed atomic force microscopy imaging of live mammalian cells

Direct imaging of morphological dynamics of live mammalian cells with nanometer resolution under physiological conditions is highly expected, but yet challenging. High-speed atomic force microscopy (HS-AFM) is a unique technique for capturing biomolecules at work under near physiological conditions. However, application of HS-AFM for imaging of live mammalian cells was hard to be accomplished because of collision between a huge mammalian cell and a cantilever during AFM scanning. Here, we review our recent improvements of HS-AFM for imaging of activities of live mammalian cells without significant damage to the cell. The improvement of an extremely long (~3 μm) AFM tip attached to a cantilever enables us to reduce severe damage to soft mammalian cells. In addition, a combination of HS-AFM with simple fluorescence microscopy allows us to quickly locate the cell in the AFM scanning area. After these improvements, we demonstrate that developed HS-AFM for live mammalian cells is possible to image morphogenesis of filopodia, membrane ruffles, pits open-close formations, and endocytosis in COS-7, HeLa cells as well as hippocampal neurons.

Directly watching biomolecules in action by high-speed atomic force microscopy

Proteins are dynamic in nature and work at the single molecule level. Therefore, directly watching protein molecules in dynamic action at high spatiotemporal resolution must be the most straightforward approach to understanding how they function. To make this observation possible, high-speed atomic force microscopy (HS-AFM) has been developed. Its current performance allows us to film biological molecules at 10-16 frames/s, without disturbing their function. In fact, dynamic structures and processes of various proteins have been successfully visualized, including bacteriorhodopsin responding to light, myosin V walking on actin filaments, and even intrinsically disordered proteins undergoing order/disorder transitions. The molecular movies have provided insights that could not have been reached in other ways. Moreover, the cantilever tip can be used to manipulate molecules during successive imaging. This capability allows us to observe changes in molecules resulting from dissection or perturbation. This mode of imaging has been successfully applied to myosin V, peroxiredoxin and doublet microtubules, leading to new discoveries. Since HS-AFM can be combined with other techniques, such as super-resolution optical microscopy and optical tweezers, the usefulness of HS-AFM will be further expanded in the near future.

Plasmonic Microcantilever with Remarkably Enhanced Photothermal Responses

Plasmonic nanostructures exhibit abundant optoelectronic properties. We explore here the technological potentials of plasmonic nanostructures as active component to actuate microcantilever sensors. We find that the photothermal excitation of microcantilevers can be greatly enhanced by Au nanoparticle (NPs). A detailed investigation reveals that the enhancement is wavelength dependent and can be attributed to selective excitation of localized surface plasmon resonance (LSPR). The associated effects are discussed based on a thorough examination of the geometric aspects of Au NPs, microcantilever lengths, and incident optical power. Some technological advantages offered by this method are also discussed.