Adapting atomic force microscopy for cell biology

Atomic force microscopy applied to interrogate nanoscale cellular chemistry and supramolecular bond dynamics for biomedical applications

Understanding biological interactions at a molecular level grants valuable information relevant to improving medical treatments and outcomes. Among the suite of technologies available, Atomic Force Microscopy (AFM) is unique in its ability to quantitatively probe forces and receptor-ligand interactions in real-time. The ability to assess the formation of supramolecular bonds and intermediates in real-time on surfaces and living cells generates important information relevant to understanding biological phenomena. Combining AFM with fluorescence-based techniques allows for an unprecedented level of insight not only concerning the formation and rupture of bonds, but understanding medically relevant interactions at a molecular level. As the ability of AFM to probe cells and more complex models improves, being able to assess binding kinetics, chemical topographies, and garner spectroscopic information will likely become key to developing further improvements in fields such as cancer, nanomaterials, and virology. The rapid response to the COVID-19 crisis, producing information regarding not just receptor affinities, but also strain-dependent efficacy of neutralizing nanobodies, demonstrates just how viable and integral to the pre-clinical development of information AFM techniques are in this era of medicine.

A review of focused ion beam applications in optical fibers

Focused ion beam (FIB) technology has become a promising technique in micro- and nano-prototyping due to several advantages over its counterparts such as direct (maskless) processing, sub-10 nm feature size, and high reproducibility. Moreover, FIB machining can be effectively implemented on both conventional planar substrates and unconventional curved surfaces such as optical fibers, which are popular as an effective medium for telecommunications. Optical fibers have also been widely used as intrinsically light-coupled substrates to create a wide variety of compact fiber-optic devices by FIB milling diverse micro- and nanostructures onto the fiber surface (endfacet or outer cladding). In this paper, the broad applications of the FIB technology in optical fibers are reviewed. After an introduction to the technology, incorporating the FIB system and its basic operating modes, a brief overview of the lab-on-fiber technology is presented. Furthermore, the typical and most recent applications of the FIB machining in optical fibers for various applications are summarized. Finally, the reviewed work is concluded by suggesting the possible future directions for improving the micro- and nanomachining capabilities of the FIB technology in optical fibers.

Atomic Force Microscopy-Based Force Spectroscopy and Multiparametric Imaging of Biomolecular and Cellular Systems

During the last three decades, a series of key technological improvements turned atomic force microscopy (AFM) into a nanoscopic laboratory to directly observe and chemically characterize molecular and cell biological systems under physiological conditions. Here, we review key technological improvements that have established AFM as an analytical tool to observe and quantify native biological systems from the micro- to the nanoscale. Native biological systems include living tissues, cells, and cellular components such as single or complexed proteins, nucleic acids, lipids, or sugars. We showcase the procedures to customize nanoscopic chemical laboratories by functionalizing AFM tips and outline the advantages and limitations in applying different AFM modes to chemically image, sense, and manipulate biosystems at (sub)nanometer spatial and millisecond temporal resolution. We further discuss theoretical approaches to extract the kinetic and thermodynamic parameters of specific biomolecular interactions detected by AFM for single bonds and extend the discussion to multiple bonds. Finally, we highlight the potential of combining AFM with optical microscopy and spectroscopy to address the full complexity of biological systems and to tackle fundamental challenges in life sciences.

Characterization of cytoplasmic viscosity of hundreds of single tumour cells based on micropipette aspiration

Cytoplasmic viscosity (μ c) is a key biomechanical parameter for evaluating the status of cellular cytoskeletons. Previous studies focused on white blood cells, but the data of cytoplasmic viscosity for tumour cells were missing. Tumour cells (H1299, A549 and drug-treated H1299 with compromised cytoskeletons) were aspirated continuously through a micropipette at a pressure of -10 or -5 kPa where aspiration lengths as a function of time were obtained and translated to cytoplasmic viscosity based on a theoretical Newtonian fluid model. Quartile coefficients of dispersion were quantified to evaluate the distributions of cytoplasmic viscosity within the same cell type while neural network-based pattern recognitions were used to classify different cell types based on cytoplasmic viscosity. The single-cell cytoplasmic viscosity with three quartiles and the quartile coefficient of dispersion were quantified as 16.7 Pa s, 42.1 Pa s, 110.3 Pa s and 74% for H1299 cells at -10 kPa (n cell = 652); 144.8 Pa s, 489.8 Pa s, 1390.7 Pa s, and 81% for A549 cells at -10 kPa (n cell = 785); 7.1 Pa s, 13.7 Pa s, 31.5 Pa s, and 63% for CD-treated H1299 cells at -10 kPa (n cell = 651); and 16.9 Pa s, 48.2 Pa s, 150.2 Pa s, and 80% for H1299 cells at -5 kPa (n cell = 600), respectively. Neural network-based pattern recognition produced successful classification rates of 76.7% for H1299 versus A549, 67.0% for H1299 versus drug-treated H1299 and 50.3% for H1299 at -5 and -10 kPa. Variations of cytoplasmic viscosity were observed within the same cell type and among different cell types, suggesting the potential role of cytoplasmic viscosity in cell status evaluation and cell type classification.

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.

Biomechanical Characterization at the Cell Scale: Present and Prospects

The rapidly growing field of mechanobiology demands for robust and reproducible characterization of cell mechanical properties. Recent achievements in understanding the mechanical regulation of cell fate largely rely on technological platforms capable of probing the mechanical response of living cells and their physico–chemical interaction with the microenvironment. Besides the established family of atomic force microscopy (AFM) based methods, other approaches include optical, magnetic, and acoustic tweezers, as well as sensing substrates that take advantage of biomaterials chemistry and microfabrication techniques. In this review, we introduce the available methods with an emphasis on the most recent advances, and we discuss the challenges associated with their implementation.

Topographic analysis by atomic force microscopy of proteoliposomes matrix vesicle mimetics harboring TNAP and AnxA5

Atomic force microscopy (AFM) is one of the most commonly used scanning probe microscopy techniques for nanoscale imaging and characterization of lipid-based particles. However, obtaining images of such particles using AFM is still a challenge. The present study extends the capabilities of AFM to the characterization of proteoliposomes, a special class of liposomes composed of lipids and proteins, mimicking matrix vesicles (MVs) involved in the biomineralization process. To this end, proteoliposomes were synthesized, composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-dipalmitoyl-sn-glycero-3-phospho-l-serine (DPPS), with inserted tissue-nonspecific alkaline phosphatase (TNAP) and/or annexin V (AnxA5), both characteristic proteins of osteoblast-derived MVs. We then aimed to study how TNAP and AnxA5 insertion affects the proteoliposomes' membrane properties and, in turn, interactions with type II collagen, thus mimicking early MV activity during biomineralization. AFM images of these proteoliposomes, acquired in dynamic mode, revealed the presence of surface protrusions with distinct viscoelasticity, thus suggesting that the presence of the proteins induced local changes in membrane fluidity. Surface protrusions were measurable in TNAP-proteoliposomes but barely detectable in AnxA5-proteoliposomes. More complex surface structures were observed for proteoliposomes harboring both TNAP and AnxA5 concomitantly, resulting in a lower affinity for type II collagen fibers compared to proteoliposomes harboring AnxA5 alone. The present study achieved the topographic analysis of lipid vesicles by direct visualization of structural changes, resulting from protein incorporation, without the need for fluorescent probes.

Characterizing the Nano-Bio Interface Using Microscopic Techniques: Imaging the Cell System is Just as Important as Imaging the Nanoparticle System

The rapid growth of nanotechnology and its industries has elevated the need to understand the risks associated with handling, using, and disposing of nanomaterials. These risks can be assessed through exposure measurement and hazard identification. One of the common challenges associated with quantifying nanomaterials in products, waste, humans, or the environment is the lack of tools available to measure concentration. The ability of refined tools and techniques to qualitatively detect nanoparticles in complex matrices has been demonstrated. For biological and ecological tests systems, dose can be represented as initial concentration in the applied matrix, concentration administered during the route of exposure, concentration at the target organ, and intake concentration at the cellular level. Each of these concentration measurements requires different sets of tools to perform accurate analyses. Advances in microscopy techniques provide new opportunities for reporting observations occurring at the interaction of a nanoparticle with a biomolecular entity of similar size within a biological test(s) system. This protocol outlines the steps to image nanomaterials within cell-based systems. © 2017 by John Wiley & Sons, Inc.

Sensing of Streptococcus mutans by microscopic imaging ellipsometry

Microscopic imaging ellipsometry is an optical technique that uses an objective and sensing procedure to measure the ellipsometric parameters ? and ? in the form of microscopic maps. This technique is well known for being noninvasive and label-free. Therefore, it can be used to detect and characterize biological species without any impact. Microscopic imaging ellipsometry was used to measure the optical response of dried Streptococcus mutans cells on a glass substrate. The ellipsometric ? and ? maps were obtained with the Optrel Multiskop system for specular reflection in the visible range ( ? = 450 to 750 nm). The ? and ? images at 500, 600, and 700 nm were analyzed using three different theoretical models with single-bounce, two-bounce, and multibounce light paths to obtain the optical constants and height distribution. The obtained images of the optical constants show different aspects when comparing the single-bounce analysis with the two-bounce or multibounce analysis in detecting S. mutans samples. Furthermore, the height distributions estimated by two-bounce and multibounce analyses of S. mutans samples were in agreement with the thickness values measured by AFM, which implies that the two-bounce and multibounce analyses can provide information complementary to that obtained by a single-bounce light path.

Atomic Force Microscopy Mechanical Mapping of Micropatterned Cells Shows Adhesion Geometry-Dependent Mechanical Response on Local and Global Scales

In multicellular organisms, cell shape and organization are dictated by cell-cell or cell-extracellular matrix adhesion interactions. Adhesion complexes crosstalk with the cytoskeleton enabling cells to sense their mechanical environment. Unfortunately, most of cell biology studies, and cell mechanics studies in particular, are conducted on cultured cells adhering to a hard, homogeneous, and unconstrained substrate with nonspecific adhesion sites, thus far from physiological and reproducible conditions. Here, we grew cells on three different fibronectin patterns with identical overall dimensions but different geometries (▽, T, and Y), and investigated their topography and mechanics by atomic force microscopy (AFM). The obtained mechanical maps were reproducible for cells grown on patterns of the same geometry, revealing pattern-specific subcellular differences. We found that local Young's moduli variations are related to the cell adhesion geometry. Additionally, we detected local changes of cell mechanical properties induced by cytoskeletal drugs. We thus provide a method to quantitatively and systematically investigate cell mechanics and their variations, and present further evidence for a tight relation between cell adhesion and mechanics.

Force nanoscopy of cell mechanics and cell adhesion

Cells are constantly exposed to mechanical stimuli in their environment and have several evolved mechanisms to sense and respond to these cues. It is becoming increasingly recognized that many cell types, from bacteria to mammalian cells, possess a diverse set of proteins to translate mechanical cues into biochemical signalling and to mediate cell surface interactions such as cell adhesion. Moreover, the mechanical properties of cells are involved in regulating cell function as well as serving as indicators of disease states. Importantly, the recent development of biophysical tools and nanoscale methods has facilitated a deeper understanding of the role that physical forces play in modulating cell mechanics and cell adhesion. Here, we discuss how atomic force microscopy (AFM) has recently been used to investigate cell mechanics and cell adhesion at the single-cell and single-molecule levels. This knowledge is critical to our understanding of the molecular mechanisms that govern mechanosensing, mechanotransduction, and mechanoresponse in living cells. While pushing living cells with the AFM tip provides a means to quantify their mechanical properties and examine their response to nanoscale forces, pulling single surface proteins with a functionalized tip allows one to understand their role in sensing and adhesion. The combination of these nanoscale techniques with modern molecular biology approaches, genetic engineering and optical microscopies provides a powerful platform for understanding the sophisticated functions of the cell surface machinery, and its role in the onset and progression of complex diseases.

Quantification of intracellular mitochondrial displacements in response to nanomechanical forces

Mechanical stress affects various aspects of cell behavior, including cell growth, morphology, differentiation, and genetic expression. Here, we describe a method to quantify the intracellular mechanical response to an extracellular mechanical perturbation, specifically the displacement of mitochondria. A combined fluorescent-atomic force microscope (AFM) was used to simultaneously produce well-defined nanomechanical stimulation to a living cell while optically recording the real-time displacement of fluorescently labeled mitochondria. A single-particle tracking (SPT) approach was then applied in order to quantify the two-dimensional displacement of mitochondria in response to local forces.

An Approach to Visualize the Deformation of the Intermediate Filament Cytoskeleton in Response to Locally Applied Forces

The intermediate filament (IF) cytoskeleton plays an important role in integrating biomechanical pathways associated with the actin and microtubule cytoskeleton. Vimentin is a type III IF protein commonly found in fibroblast cells and plays a role in transmitting forces through the cytoskeleton. Employing simultaneous laser scanning confocal and atomic force microscopy (AFM), we developed a methodology to quantify the deformation of the GFP-vimentin-labeled IF cytoskeleton as a function of time in response to force application by the AFM. Over short times (seconds), IFs deformed rapidly and transmitted force throughout the entire cell in a highly complex and anisotropic fashion. After several minutes, mechanically induced displacements of IFs resemble basal movements. In well-adhered cells the deformation of IFs is highly anisotropic as they tend to deform away from the longitudinal axis of the cell. This study demonstrates that simultaneous AFM and LSCM can be employed to track the deformation and dissipation of force through the IF cytoskeleton.

Force transduction and strain dynamics in actin stress fibres in response to nanonewton forces

It is becoming clear that mechanical stimuli are crucial factors in regulating the biology of the cell, but the short-term structural response of a cell to mechanical forces remains relatively poorly understood. We mechanically stimulated cells transiently expressing actin-EGFP with controlled forces (0-20 nN) in order to investigate the structural response of the cell. Two clear force-dependent responses were observed: a short-term (seconds) local deformation of actin stress fibres and a long-term (minutes) force-induced remodelling of stress fibres at cell edges, far from the point of contact. By photobleaching markers along stress fibres we were also able to quantify strain dynamics occurring along the fibres throughout the cell. The results reveal that the cell exhibits complex heterogeneous negative and positive strain fluctuations along stress fibres in resting cells that indicate localized contraction and stretch dynamics. The application of mechanical force results in the activation of myosin contractile activity reflected in an ~50% increase in strain fluctuations. This approach has allowed us to directly observe the activation of myosin in response to mechanical force and the effects of cytoskeletal crosslinking on local deformation and strain dynamics. The results demonstrate that force application does not result in simplistic isotropic deformation of the cytoarchitecture, but rather a complex and localized response that is highly dependent on an intact microtubule network. Direct visualization of force-propagation and stress fibre strain dynamics have revealed several crucial phenomena that take place and ultimately govern the downstream response of a cell to a mechanical stimulus.

Stability enhancement of an atomic force microscope for long-term force measurement including cantilever modification for whole cell deformation

Atomic force microscopy (AFM) is widely used in the study of both morphology and mechanical properties of living cells under physiologically relevant conditions. However, quantitative experiments on timescales of minutes to hours are generally limited by thermal drift in the instrument, particularly in the vertical (z) direction. In addition, we demonstrate the necessity to remove all air-liquid interfaces within the system for measurements in liquid environments, which may otherwise result in perturbations in the measured deflection. These effects severely limit the use of AFM as a practical tool for the study of long-term cell behavior, where precise knowledge of the tip-sample distance is a crucial requirement. Here we present a readily implementable, cost effective method of minimizing z-drift and liquid instabilities by utilizing active temperature control combined with a customized fluid cell system. Long-term whole cell mechanical measurements were performed using this stabilized AFM by attaching a large sphere to a cantilever in order to approximate a parallel plate system. An extensive examination of the effects of sphere attachment on AFM data is presented. Profiling of cantilever bending during substrate indentation revealed that the optical lever assumption of free ended cantilevering is inappropriate when sphere constraining occurs, which applies an additional torque to the cantilevers "free" end. Here we present the steps required to accurately determine force-indentation measurements for such a scenario. Combining these readily implementable modifications, we demonstrate the ability to investigate long-term whole cell mechanics by performing strain controlled cyclic deformation of single osteoblasts.

DISEASED RED BLOOD CELLS STUDIED BY ATOMIC FORCE MICROSCOPY

In recent years, many mammalian cells, especially erythrocytes because of simpleness of their membrane surfaces, were widely studied by atomic force microscopy. In our study, diseased erythrocytes were taken from patients of lung cancer, myelodisplastic syndrome (MDS), and so on. We obtained many clear topographical images of numerous erythrocytes, single erythrocyte, and ultramicrostructure of erythrocyte membrane surfaces from normal persons and patients. By studying the red cells of lung cancer patients, we found that many erythrocytes of lung cancer patient have changed into echinocytes. One erythrocyte has 10–20 short projections, most of which, with a mean width of 589.0 nm and a length of 646.7 nm, are on the edge of cell. The projections in the center of echinocytes are lodged and embedded, but in conventional model of echinocytes, the projections in the center stretch outside cell membrane, so a novel model of erythrocytes was designed in our paper. After observation of microstructure of MDS patient's erythrocyte membrane surface, we found that many apertures with different diameters of tens to hundreds nanometers appeared on the surface of cell membrane. It can be concluded that AFM may be widely applied in clinic pathological inspection.

High-speed force load in force measurement in liquid using scanning probe microscope

This article presents an inversion-based iterative feedforward-feedback (II-FF/FB) approach to achieve high-speed force load in force measurement of soft materials in liquid using scanning probe microscope (SPM). SPM force measurement under liquid environment is needed to interrogate a wide range of soft materials, particularly live biological samples. Moreover, when dynamic evolution of the sample occurs during the measurement, and/or measuring the rate-dependent viscoelasticity of the sample, the force measurement also needs to be acquired at high-speed. Precision force load in liquid, however, is challenged by adverse effects including the thermal drift effect, the reduction of the signal to noise ratio, the distributive hydrodynamic force effect, and the hysteresis and vibrational dynamics effects of the piezoelectric actuators (for positioning the probe relative to the sample), particularly during high-speed measurement. Thus, the main contribution of the article is the development of the II-FF/FB approach to tackle these challenges. The proposed method is illustrated through an experimental implementation to the force-curve measurement of a poly (dimethylsiloxane) sample in liquid at high-speed.

Indirect identification and compensation of lateral scanner resonances in atomic force microscopes

Improving the imaging speed of atomic force microscopy (AFM) requires accurate nanopositioning at high speeds. However, high speed operation excites resonances in the AFM's mechanical scanner that can distort the image, and therefore typical users of commercial AFMs elect to operate microscopes at speeds below which scanner resonances are observed. Although traditional robust feedforward controllers and input shaping have proven effective at minimizing the influence of scanner distortions, the lack of direct measurement and use of model-based controllers have required disassembling the microscope to access lateral scanner motion with external sensors in order to perform a full system identification experiment, which places excessive demands on routine microscope operators. Further, since the lightly damped instrument dynamics often change from experiment to experiment, model-based controllers designed from offline system identification experiments must trade off high speed performance for robustness to modeling errors. This work represents a new way to automatically characterize the lateral scanner dynamics without addition of lateral sensors, and shape the commanded input signals in such a way that disturbing dynamics are not excited. Scanner coupling between the lateral and out-of-plane directions is exploited and used to build a minimal model of the scanner that is also sufficient to describe the nature of the distorting resonances. This model informs the design of an online input shaper used to suppress spectral components of the high speed command signals. The method presented is distinct from alternative approaches in that neither an information-complete system identification experiment nor microscope modification are required. Because the system identification is performed online immediately before imaging, no tradeoff of performance is required. This approach has enabled an increase in the scan rates of unmodified commercial AFMs from 1-4 lines s(-1) to over 40 lines s(-1).

Note: Seesaw actuation of atomic force microscope probes for improved imaging bandwidth and displacement range

The authors describe a method of actuation for atomic force microscope (AFM) probes to improve imaging speed and displacement range simultaneously. Unlike conventional piezoelectric tube actuation, the proposed method involves a lever and fulcrum "seesaw" like actuation mechanism that uses a small, fast piezoelectric transducer. The lever arm of the seesaw mechanism increases the apparent displacement range by an adjustable gain factor, overcoming the standard tradeoff between imaging speed and displacement range. Experimental characterization of a cantilever holder implementing the method is provided together with comparative line scans obtained with contact mode imaging. An imaging bandwidth of 30 kHz in air with the current setup was demonstrated.

Biophysical characterization of G-protein coupled receptor-peptide ligand binding

G-protein coupled receptors (GPCRs) are ubiquitous membrane proteins allowing intracellular responses to extracellular factors that range from photons of light to small molecules to proteins. Despite extensive exploitation of GPCRs as therapeutic targets, biophysical characterization of GPCR-ligand interactions remains challenging. In this minireview, we focus on techniques that have been successfully used for structural and biophysical characterization of peptide ligands binding to their cognate GPCRs. The techniques reviewed include solution-state nuclear magnetic resonance (NMR) spectroscopy, solid-state NMR, X-ray diffraction, fluorescence spectroscopy and single-molecule fluorescence methods, flow cytometry, surface plasmon resonance, isothermal titration calorimetry, and atomic force microscopy. The goal herein is to provide a cohesive starting point to allow selection of techniques appropriate to the elucidation of a given GPCR-peptide interaction.

Bone cell elasticity and morphology changes during the cell cycle

The mechanical properties of cells are reported to be regulated by a range of factors including interactions with the extracellular environment and other cells, differentiation status, the onset of pathological states, as well as the intracellular factors, for example, the cytoskeleton. The cell cycle is considered to be a well-ordered sequence of biochemical events. A number of processes reported to occur during its progression are inherently mechanical and, as such, require mechanical regulation. In spite of this, few attempts have been made to investigate the putative regulatory role of the cell cycle in mechanobiology. In the present study, Atomic Force Microscopy (AFM) was employed to investigate the elastic modulus of synchronised osteoblasts. The data obtained confirm that osteoblast elasticity is regulated by cell cycle phase; specifically, cells in S phase were found to have a modulus approximately 1.7 times that of G1 phase cells. Confocal microscopy studies revealed that aspects of osteoblast morphology, namely F-actin expression, were also modulated by the cell cycle, and tended to increase with phase progression from G0 onwards. The data obtained in this study are likely to have implications for the fields of tissue- and bio-engineering, where prior knowledge of cell mechanobiology is essential for the effective replacement and repair of tissue. Furthermore, studies focused on biomechanics and the biophysical properties of cells are important in the understanding of the onset and progression of disease states, for example cancer at the cellular level. Our study demonstrates the importance of the combined use of traditional and relatively novel microscopy techniques in understanding mechanical regulation by crucial cellular processes, such as the cell cycle.

Atomic force microscopy of biological samples

The ability to evaluate structural-functional relationships in real time has allowed scanning probe microscopy (SPM) to assume a prominent role in post genomic biological research. In this mini-review, we highlight the development of imaging and ancillary techniques that have allowed SPM to permeate many key areas of contemporary research. We begin by examining the invention of the scanning tunneling microscope (STM) by Binnig and Rohrer in 1982 and discuss how it served to team biologists with physicists to integrate high-resolution microscopy into biological science. We point to the problems of imaging nonconductive biological samples with the STM and relate how this led to the evolution of the atomic force microscope (AFM) developed by Binnig, Quate, and Gerber, in 1986. Commercialization in the late 1980s established SPM as a powerful research tool in the biological research community. Contact mode AFM imaging was soon complemented by the development of non-contact imaging modes. These non-contact modes eventually became the primary focus for further new applications including the development of fast scanning methods. The extreme sensitivity of the AFM cantilever was recognized and has been developed into applications for measuring forces required for indenting biological surfaces and breaking bonds between biomolecules. Further functional augmentation to the cantilever tip allowed development of new and emerging techniques including scanning ion-conductance microscopy (SICM), scanning electrochemical microscope (SECM), Kelvin force microscopy (KFM) and scanning near field ultrasonic holography (SNFUH).

How the atomic force microscope works?

This chapter aims at giving a quick but precise introduction of the atomic force microscope from the working principle point of view. It is intended to provide a useful starting point to those who first approach the instrument giving a general sketch of the working principles and technical implementations as well as last improvements. Subheading 1 is introductory: it gives an overview of what the instrument does and why it has been developed. Subheading 2 is focused on measurement ranges and on the comparison with scanning electron microscope (SEM) and transmission electron microscope (TEM) which have similar ranges and resolutions but different sample interactions and applications. Subheading 3 gives an overview of the working principles and the most diffused technical implementations on which most of the commercial microscopes rely, as we think it gives the useful base knowledge to understand possible applications, instrument capabilities, and results. In particular, technical improvements taking place over the past few years are highlighted. Despite of the simple and not very technical approach, it has a key importance in understanding concepts at the base of Chapter 3, which is, on the other side, useful for beginners and experienced users as well. Subheading 4 compares different instrument architectures and can, therefore, be useful for those who are going to choose an instrument having clear final applications. Latest solutions are once more highlighted. Subheading 5 gives an overview and some suggestions to start working, both in air and in liquid. Following the general philosophy of the book, it follows more an "how to do" concept than a general theoretical approach. Subheading 6 contains the future developments of the techniques.

Atomic force microscopy for biological imaging and mechanical testing across length scales

Atomic force microscopy (AFM) offers researchers a unique opportunity to visualize, manipulate, and quantitatively assess structural and mechanical aspects of native biological samples with nanometer resolution. An unparalleled advantage of AFM over other high-resolution microscopes is that biological specimens, ranging from tissues to cells to molecules, can be investigated in physiologically relevant aqueous environments. The AFM can be operated at 37°C, which makes it ideal for in situ cell or tissue studies. Combining an optical microscope with an AFM makes it possible to directly correlate structural/nanomechanical changes with optical/fluorescence images. This ability to simultaneously acquire structural and function information is unprecedented in biology. This article introduces the basics of AFM for imaging and investigating the properties of biological samples.

Molecular imaging of membrane proteins and microfilaments using atomic force microscopy

Atomic force microscopy (AFM) is an emerging technique for a variety of uses involving the analysis of cells. AFM is widely applied to obtain information about both cellular structural and subcellular events. In particular, a variety of investigations into membrane proteins and microfilaments were performed with AFM. Here, we introduce applications of AFM to molecular imaging of membrane proteins, and various approaches for observation and identification of intracellular microfilaments at the molecular level. These approaches can contribute to many applications of AFM in cell imaging.

Atomic force microscopy probing in the measurement of cell mechanics

Atomic force microscope (AFM) has been used incrementally over the last decade in cell biology. Beyond its usefulness in high resolution imaging, AFM also has unique capabilities for probing the viscoelastic properties of living cells in culture and, even more, mapping the spatial distribution of cell mechanical properties, providing thus an indirect indicator of the structure and function of the underlying cytoskeleton and cell organelles. AFM measurements have boosted our understanding of cell mechanics in normal and diseased states and provide future potential in the study of disease pathophysiology and in the establishment of novel diagnostic and treatment options.

Neuronal elasticity as measured by atomic force microscopy

A cell's form and function is determined to a great extent by its cellular membrane and the underlying cytoskeleton. Understanding changes in the cellular membrane and cytoskeleton can provide insight into aging and disease of the cell. The atomic force microscope (AFM) allows unparalled resolution for the imaging of these cellular components and the ability to probe their mechanical properties. This report describes our progress toward the use of AFM as a tool in neuroscience applications. Elasticity measurements are reported on living chick embryo dorsal root ganglion and sympathetic neurons in vitro. The neuronal cellular body and growth cones regions are examined for variations in cellular maturity. In addition, cellular changes due to exposure to various environmental conditions and neurotoxins are investigated. This report includes data obtained on different AFM systems, using various AFM techniques and thus also provides knowledge of AFM instruments and methodology.

Mitochondrial displacements in response to nanomechanical forces

Mechanical stress affects and regulates many aspects of the cell, including morphology, growth, differentiation, gene expression and apoptosis. In this study we show how mechanical stress perturbs the intracellular structures of the cell and induces mechanical responses. In order to correlate mechanical perturbations to cellular responses, we used a combined fluorescence-atomic force microscope (AFM) to produce well defined nanomechanical perturbations of 10 nN while simultaneously tracking the real-time motion of fluorescently labelled mitochondria in live cells. The spatial displacement of the organelles in response to applied loads demonstrates the highly dynamic mechanical response of mitochondria in fibroblast cells. The average displacement of all mitochondrial structures analysed showed an increase of approximately 40%, post-perturbation ( approximately 160 nm in comparison to basal displacements of approximately 110 nm). These results show that local forces can produce organelle displacements at locations far from the initial point of contact (up to approximately 40 microm). In order to examine the role of the cytoskeleton in force transmission and its effect on mitochondrial displacements, both the actin and microtubule cytoskeleton were disrupted using Cytochalasin D and Nocodazole, respectively. Our results show that there is no significant change in mitochondrial displacement following indentation after such treatments. These results demonstrate the role of the cytoskeleton in force transmission through the cell and on mitochondrial displacements. In addition, it is suggested that care must be taken when performing mechanical experiments on living cells with the AFM, as these local mechanical perturbations may have significant structural and even biochemical effects on the cell.

Past, present and future of atomic force microscopy in life sciences and medicine

To introduce this special issue of the Journal of Molecular Recognition dedicated to the applications of atomic force microscopy (AFM) in life sciences, this paper presents a short summary of the history of AFM in biology. Based on contributions from the first international conference of AFM in biological sciences and medicine (AFM BioMed Barcelona, 19-21 April 2007), we present and discuss recent progress made using AFM for studying cells and cellular interactions, probing single molecules, imaging biosurfaces at high resolution and investigating model membranes and their interactions. Future prospects in these different fields are also highlighted.

The NTA-His6 bond is strong enough for AFM single-molecular recognition studies

There is a need in current atomic force microscopy (AFM) molecular recognition studies for generic methods for the stable, functional attachment of proteins on tips and solid supports. In the last few years, the site-directed nitrilotriacetic acid (NTA)-polyhistidine (Hisn) system has been increasingly used towards this goal. Yet, a crucial question in this context is whether the NTA-Hisn bond is sufficiently strong for ensuring stable protein immobilization during force spectroscopy measurements. Here, we measured the forces between AFM tips modified with NTA-terminated alkanethiols and solid supports functionalized with His6-Gly-Cys peptides in the presence of Ni2+. The force histogram obtained at a loading rate of 6600 pN s(-1) showed three maxima at rupture forces of 153 +/- 57 pN, 316 +/- 50 pN and 468 +/- 44 pN, that we attribute primarily to monovalent and multivalent interactions between a single His6 moiety and one, two and three NTA groups, respectively. The measured forces are well above the 50-100 pN unbinding forces typically observed by AFM for receptor-ligand pairs. The plot of adhesion force versus log (loading rate) revealed a linear regime, from which we deduced a kinetic off-rate constant of dissociation, k(off) approximately 0.07 s(-1). This value is in the range of that estimated for the multivalent interaction involving two NTA, using fluorescence measurements, and may account for an increased binding stability of the NTA-His6 bond. We conclude that the NTA-His6 system is a powerful, well-suited platform for the stable, oriented immobilization of proteins in AFM single-molecule studies.

Site localization of membrane-bound proteins on whole cell level using atomic force microscopy

This study presents molecular recognition method, which is based on specific force measurements between modified AFM (atomic force microscopy) tip and mammalian cell. The presented method allows recognition of specific cell surface proteins and receptor sites by nanometer accuracy level. Here we demonstrate specific recognition of membrane-bound Osteopontin (OPN) sites on preosteogenic cell membrane. By merging specific force detection map of the proteins and topography image of the cell, we create a new image (recognition image), which demonstrates the exact locations of the proteins relative to the cell membrane. The recognition results indicate the strong affinity between the modified tip and the target molecules, therefore, it enables the use of an AFM as a remarkable nanoscale tracking tool on the whole cell level.

Interrogation of living cells using alternating current scanning electrochemical microscopy (AC-SECM)

In this paper we present the application of alternating current scanning electrochemical microscopy (AC-SECM) to the study of living cells. Commercial AFM instrumentation was modified to allow for performing robust AC-SECM measurements. Constant height AC imaging of the Cos-7 cells, performed directly in cell culture medium without the addition of a redox mediator, provided topographical information of the cell. Stationary tip measurements on the AC current were carried out to investigate the cellular activity of a single cell. The dependence of AC current magnitude on tip-to-sample separation distance was used to monitor real time changes in cell height of individual Cos-7 cells. Furthermore, AC-SECM was employed to observe changes in metabolic cellular activity stimulated by ethanol and phorbol-1,2-myristate-acetate-3. The effect of changing cellular activity on constant height AC-SECM imaging was also studied.

Nanomicrobiology

Recent advances in atomic force microscopy (AFM) are revolutionizing our views of microbial surfaces. While AFM imaging is very useful for visualizing the surface of hydrated cells and membranes on the nanoscale, force spectroscopy enables researchers to locally probe biomolecular forces and physical properties. These unique capabilities allow us to address a number of questions that were inaccessible before, such as how does the surface architecture of microbes change as they grow or interact with drugs, and what are the molecular forces driving their interaction with antibiotics and host cells? Here, we provide a flavor of recent achievements brought by AFM imaging and single molecule force spectroscopy in microbiology.

Elastic properties of the cell surface and trafficking of single AMPA receptors in living hippocampal neurons

Although various approaches are routinely used to study receptor trafficking, a technology that allows for visualizing trafficking of single receptors at the surface of living cells remains lacking. Here we used atomic force microscope to simultaneously probe the topography of living cells, record the elastic properties of their surface, and examine the distribution of transfected alpha-amino-3-hydroxy-5-methylisoxazole-4-proprionic acid (AMPA)-type glutamate receptors (AMPAR). On nonstimulated neurons, AMPARs were located in stiff nanodomains with high elasticity modulus relative to the remaining cell surface. Receptor stimulation with N-methyl-D-aspartate (NMDA) provoked a permanent disappearance of these stiff nanodomains followed by a decrease (53%) of the number of surface AMPARs. Blocking electrical activity before NMDA stimulation recruited the same number of AMPARs for internalization, preceded by the loss of the stiff nanodomains. However, in that case, the stiff nanodomains were recovered and AMPARs were reinserted into the membrane shortly after. Our results show that modulation of receptor distribution is accompanied by changes in the local elastic properties of cell membrane. We postulate, therefore, that the mechanical environment of a receptor might be critical to determine its specific distribution behavior in response to different stimuli.

Cellular chemomechanics at interfaces: sensing, integration and response

Living cells are complex entities whose remarkable, emergent capacity to sense, integrate, and respond to environmental cues relies on an intricate series of interactions among the cell's macromolecular components. Defects in mechanosensing, transduction,or responses underlie many diseases such as cancers, immune disorders, cardiac hypertrophy, genetic malformations, and neuropathies. Here, we highlight micro- and nanotechnology-based tools that have been used to study how chemical and mechanical cues modulate the responses of single cells in contact with the extracellular environment. Understanding the physical aspects of these complex processes at the micro- and nanometer scale could produce profound and fundamental new insights into how the processes of cell migration, metastasis, immune function and other areas which are regulated by mechanical forces.

Mechanical Stabilization Effect of Water on a Membrane-like System

The penetration resistance of a prototypical model-membrane system (HS-(CH2)11-OH self-assembled monolayer (SAM) on Au(111)) to the tip of an atomic force microscope (AFM) is investigated in the presence of different solvents. The compressibility (i.e., height vs tip load) of the HS-(CH2)11-OH SAM is studied differentially, with respect to a reference structure. The reference consists of hydrophobic alkylthiol molecules (HS-(CH2)17-CH3) embedded as nanosized patches into the hydrophilic SAM by nanografting, an AFM-assisted nanolithography technique. We find that the penetration resistance of the hydrophilic SAM depends on the nature of the solvent and is much higher in the presence of water than in 2-butanol. In contrast, no solvent-dependent effect is observed in the case of hydrophobic SAMs. We argue that the mechanical resistance of the hydroxyl-terminated SAM is a consequence of the structural order of the solvent-SAM interface, as suggested by our molecular dynamics simulations. The simulations show that in the presence of 2-butanol the polar head groups of the HS-(CH2)11-OH SAM, which bind only weakly to the solvent molecules, try to bind to each other, disrupting the local order at the interface. On the contrary, in the presence of water the polar head groups bind preferentially to the solvent that, in turn, mediates the release of the surface strain, leading to a more ordered interface. We suggest that the mechanical stabilization effect induced by water may be responsible for the stability of even more complex, real membrane systems.

A simple microindentation technique for mapping the microscale compliance of soft hydrated materials and tissues

Several recent studies have shown that cells respond to the elastic modulus and elasticity gradients on soft substrates. However, traditional macroscale methods for measuring elastic modulus cannot resolve elastic gradients or differences between the macroscale and microscale elastic modulus of layered tissues. Here, we present a technique for measurement of the microscale elastic modulus of soft, hydrated gels and tissues. This technique requires less equipment than equivalent atomic force microscopy (AFM) and can easily measure larger samples with high adhesiveness. We validate this technique by measuring the microscale modulus of a hydrogel with elasticity that does not depend on measurement scale. We show that the elastic modulus measured using microindentation correlates with measurements using AFM and the macroscale tensile modulus. We verified the ability of this technique to characterize a hydrogel with an elastic gradient of 2.2 kPa/mm across 19 mm and to measure the microscale elastic modulus of the endothelial side of human greater saphenous vein, which is an order of magnitude less than the whole vein macroscale modulus. This simple, inexpensive system allows the measurement of the spatial organization of microscale elastic properties of fully hydrated, soft gels and tissues as a routine laboratory technique.

Quantitative membrane electrostatics with the atomic force microscope

The atomic force microscope (AFM) is sensitive to electric double layer interactions in electrolyte solutions, but provides only a qualitative view of interfacial electrostatics. We have fully characterized silicon nitride probe tips and other experimental parameters to allow a quantitative electrostatic analysis by AFM, and we have tested the validity of a simple analytical force expression through numerical simulations. As a test sample, we have measured the effective surface charge density of supported zwitterionic dioleoylphosphatidylcholine membranes with a variable fraction of anionic dioleoylphosphatidylserine. The resulting surface charge density and surface potential values are in quantitative agreement with those predicted by the Gouy-Chapman-Stern model of membrane charge regulation, but only when the numerical analysis is employed. In addition, we demonstrate that the AFM can detect double layer forces at a separation of several screening lengths, and that the probe only perturbs the membrane surface potential by <2%. Finally, we demonstrate 50-nm resolution electrostatic mapping on heterogeneous model membranes with the AFM. This novel combination of capabilities demonstrates that the AFM is a unique and powerful probe of membrane electrostatics.