An overview of the biophysical applications of atomic force microscopy

Atomic force microscopy imaging of plant cell walls

Plant cell walls are highly dynamic, complex structures composed of multiple biopolymers that form a scaffold surrounding the plant cell. A nanoscale understanding of their architecture, mechanical properties, and formation/degradation dynamics is crucial for revealing structure-function relationships, mechanisms of shape formation, and cell development. Although imaging techniques have been extensively used in recent decades to reveal the structural organization and chemical compositions of cell walls, observing the detailed native architecture and identifying the physicochemical properties of plant cell walls remains challenging. Atomic force microscopy (AFM) is a powerful tool for simultaneously characterizing the morphology, nanomechanical properties, single-molecule interactions, and surface potentials of living biological systems. However, studies employing AFM to investigate plant cell walls have been relatively scarce. In this review, we discuss the latest advancements in AFM for in situ imaging of the multidimensional structure of the cell wall, measuring the mechanical properties of plant tissues or single cells, specific single-molecule recognition of cell wall-related enzymes-polysaccharides, and detecting the Kelvin potential of plant cell walls. We emphasize the fundamental challenges of AFM in characterizing plant cell walls and review potential applications for state-of-the-art AFM-based infrared/Raman spectroscopy toward answering open questions in plant biology.

Colloidal adsorption in planar polymeric brushes

The design of nano-functionalised membranes or channels, able to effectively adsorb pollutants in aqueous solutions, is a topic that is gaining a great deal of attention in the materials science community. With this work we explore, through a combination of scaling theories and molecular dynamics simulations, the adsorption of spherical non-deformable colloidal nanoparticles within planar polymeric brushes. Our strategy is twofold: first, we generalise the Alexander-de Gennes theory for planar homopolymeric brushes to the case of diblock copolymer brushes, then we map the adsorbing homopolymeric brushes onto a diblock copolymer system, where the adsorbed colloids and all interacting monomers are considered monomers in bad solvent and we apply the generalised scaling theory to this effective diblock copolymer. This allows the prediction of the average conformation of the grafted substrate, i.e. its average height, as a function of the amount of loaded particles, as well as the introduction of a continuous mapping between a homopolymeric brush, the fraction of loaded particles and the average height of the adsorbing substrate.

Differences in erythrocytes size and shape in prediabetes and diabetes assessed by two microscopy techniques and its association with dietary patterns. Pilot study

Hemorheology and microcirculation alterations are caused by erythrocyte size and shape (ESS) modifications. People´s diets can alter erythrocyte functions and membrane fluidity by changing cell membrane components. The aim was to identify differences in ESS obtained by scanning electron (SEM) and atomic force microscopy (AFM) in people with prediabetes and type 2 diabetes (T2DM) and assess their relationship with dietary patterns. The study population included 31 participants (14 healthy, 11 with prediabetes, and 6 with T2DM). Dietary intake was assessed by a food frequency questionnaire, and dietary patterns were obtained using principal component analysis. ESS (diameter, height, axial ratio, thickness, and concave depth) were obtained by SEM and AFM. Differences in ESS between groups were observed with SEM (height) and AFM (height, axial ratio, and concave depth). T2DM presented smaller erythrocytes, more elongated and more altered forms. Two dietary patterns were identified: (1) Unhealthy: more refined cereals, high-fat dairy, fast food, sugary beverages, and fewer fruits, fish, seafood, low-fat dairy, and water. (2) Prudent: higher consumption of refined cereals, vegetables, poultry, low-fat dairy and nuts, and lower tortillas, eggs, high-fat dairy, and legumes. Tertile 3 of the Unhealthy dietary pattern had 80% of healthy participants. A difference in diameter and height (0.44 and 0.32 μm, respectively) obtained by SEM was observed when comparing tertile 2 (smaller erythrocytes) versus tertile 3 in the Unhealthy dietary pattern. SEM and AFM are excellent tools to assess ESS. Unhealthy dietary patterns might be associated with altered ESS. HIGHLIGHTS: SEM and AFM are excellent tools to assess erythrocyte size and shape modifications. Two dietary patterns were identified: healthy and prudent. Smaller erythrocytes were observed in the second tertile of the unhealthy pattern.

Single-particle virology

The development of advanced experimental methodologies, such as optical tweezers, scanning-probe and super-resolved optical microscopies, has led to the evolution of single-molecule biophysics, a field of science that allows direct access to the mechanistic detail of biomolecular structure and function. The extension of single-molecule methods to the investigation of particles such as viruses permits unprecedented insights into the behavior of supramolecular assemblies. Here we address the scope of viral exploration at the level of individual particles. In an era of increased awareness towards virology, single-particle approaches are expected to facilitate the in-depth understanding, and hence combating, of viral diseases.

Nanoscale Characteristics of Ocular Lipid Thin Films Using Kelvin Probe Force Microscopy

Purpose

To describe the use of Kelvin probe force microscopy (KPFM) to investigate the electrical surface potential of human meibum and to demonstrate successful use of this instrument on both human meibum and a meibum model system (six-lipid stock [6LS]) to elucidate nanoscale surface chemistry and self-assembly characteristics.

Materials and Methods

6LS and meibum were analyzed in this study. Mica-supported thin films were created using the Langmuir-Blodgett trough. Topography and electrical surface potential were quantified using simultaneous atomic force microscopy/KPFM imaging.

Results

Both lipid mixtures formed thin film patches on the surface of the mica substrate, with large aggregates resting atop. The 6LS had aggregate heights ranging from 41 to 153 nm. The range in surface potential was 33.0 to 125.9 mV. The meibum thin films at P = 5 mN/m had aggregates of 170 to 459 nm in height and surface potential ranging from 15.9 to 76.1 mV, while thin films at P = 10 mN/m showed an aggregate size range of 147 to 407 nm and a surface potential range of 11.5 to 255.1 mV.

Conclusions

This study showed imaging of the differences in electrical surface potential of meibum via KPFM and showed similarities in nanoscale topography. 6LS was also successfully analyzed, showing the capabilities of this method for use in both in vitro and ex vivo ocular research.

Translational Relevance

This study describes the use of KPFM for the study of ocular surface lipids for the first time and outlines possibilities for future studies to be carried out using this concept.

Single-Molecule Biophysical Techniques to Study Actomyosin Force Transduction

Inside the cellular environment, molecular motors can work in concert to conduct a variety of important physiological functions and processes that are vital for the survival of a cell. However, in order to decipher the mechanism of how these molecular motors work, single-molecule microscopy techniques have been popular methods to understand the molecular basis of the emerging ensemble behavior of these motor proteins.In this chapter, we discuss various single-molecule biophysical imaging techniques that have been used to expose the mechanics and kinetics of myosins. The chapter should be taken as a general overview and introductory guide to the many existing techniques; however, since other chapters will discuss some of these techniques more thoroughly, the readership should refer to those chapters for further details and discussions. In particular, we will focus on scattering-based single-molecule microscopy methods, some of which have become more popular in the recent years and around which the work in our laboratories has been centered.

Microscopic Techniques for the Analysis of Micro and Nanostructures of Biopolymers and Their Derivatives

Natural biopolymers, a class of materials extracted from renewable sources, is garnering interest due to growing concerns over environmental safety; biopolymers have the advantage of biocompatibility and biodegradability, an imperative requirement. The synthesis of nanoparticles and nanofibers from biopolymers provides a green platform relative to the conventional methods that use hazardous chemicals. However, it is challenging to characterize these nanoparticles and fibers due to the variation in size, shape, and morphology. In order to evaluate these properties, microscopic techniques such as optical microscopy, atomic force microscopy (AFM), and transmission electron microscopy (TEM) are essential. With the advent of new biopolymer systems, it is necessary to obtain insights into the fundamental structures of these systems to determine their structural, physical, and morphological properties, which play a vital role in defining their performance and applications. Microscopic techniques perform a decisive role in revealing intricate details, which assists in the appraisal of microstructure, surface morphology, chemical composition, and interfacial properties. This review highlights the significance of various microscopic techniques incorporating the literature details that help characterize biopolymers and their derivatives.

Nanoparticles decorated carbon nanotubes as novel matrix: A comparative study of influences of immobilization on the catalytic properties of Lensculinarisβ-galactosidase (Lcβ-gal)

In the present study, Multiwalled carbon nanotubes (MWCNT) decorated with two different nanoparticles namely tungsten disulfide (WS₂) and tin oxide (SnO₂), nanocomposites (NCs) were synthesized via hydrothermal method. Spectroscopic studies showed that both synthesized NCs possess nearly same functional groups but MWCNT-SnO₂ NCs are rich in O-functional group. Microscopic studies revealed that both NCs have different morphological microstructure. Lens culinaris β-galactosidase (Lcβ-gal) was immobilized using glutaraldehyde cross-linker resulted in immobilization efficiency of 91.5% and 88% with MWCNT-WS₂ and MWCNT-SnO₂ NCs, respectively. Remarkable increase in rate of hydrolysis of whey lactose has been observed with both NCs i.e. Lcβ-gal immobilized MWCNT-WS₂ hydrolyzes the 97% whey lactose in 1.5 h while MWCNT-SnO₂ showed maximum 92% of whey hydrolysis in 2 h at optimum conditions. Both nanobiocatalyst could serve as a promising candidates for dairy industries and would offer a potential platform for enzyme based biosensor fabrication.

Deciphering multivalent glycocluster-lectin interactions through AFM characterization of the self-assembled nanostructures

Pseudomonas aeruginosa is a human opportunistic pathogen responsible for lung infections in cystic fibrosis patients. The emergence of resistant strains and its ability to form a biofilm seem to give a selective advantage to the bacterium and thus new therapeutic approaches are needed. To infect the lung, the bacterium uses several virulence factors, like LecA lectins. These proteins are involved in bacterial adhesion due to their specific interaction with carbohydrates of the host epithelial cells. The tetrameric LecA lectin specifically binds galactose residues. A new therapeutic approach is based on the development of highly affine synthetic glycoclusters able to selectively link with LecA to interfere with the natural carbohydrate-LecA interaction. In this study, we combined atomic force microscopy imaging and molecular dynamics simulations to visualize and understand the arrangements formed by LecA and five different glycoclusters. Our glycoclusters are small scaffolds characterized by a core and four branches, which terminate in a galactose residue. Depending on the nature of the core and the branches, the glycocluster-lectin interaction can be modulated and the affinity increased. We show that glycocluster-LecA arrangements highly depend on the glycocluster architecture: the core influences the rigidity of the geometry and the directionality of the branches, whereas the nature of the branch determines the compactness of the structure and the ease of binding.

Biophysical Techniques to Analyze Elastic Tissue Extracellular Matrix Proteins Interacting with ADAMTS Proteins

Multidomain matrix-associated zinc extracellular proteases ADAMTS and ADAMTS-like proteins have important biological activities in cells and tissues. Beyond their traditional role in procollagen and von Willebrand factor processing and proteoglycan cleavage, ADAMTS/ADAMTSL likely participate in or at least have some role in ECM assembly as some of these proteins bind ECM proteins including fibrillins, fibronectin, and LTBPs. In this chapter, we present four biophysical techniques largely used for the characterization, multimerization, and interaction of proteins: surface plasmon resonance spectroscopy, dynamic light scattering, atomic force microscopy, and circular dichroism spectroscopy.

Reconstruction of low-resolution molecular structures from simulated atomic force microscopy images

BACKGROUND

Atomic Force Microscopy (AFM) is an experimental technique to study structure-function relationship of biomolecules. AFM provides images of biomolecules at nanometer resolution. High-speed AFM experiments produce a series of images following dynamics of biomolecules. To further understand biomolecular functions, information on three-dimensional (3D) structures is beneficial.

METHOD

We aim to recover 3D information from an AFM image by computational modeling. The AFM image includes only low-resolution representation of a molecule; therefore we represent the structures by a coarse grained model (Gaussian mixture model). Using Monte-Carlo sampling, candidate models are generated to increase similarity between AFM images simulated from the models and target AFM image.

RESULTS

The algorithm was tested on two proteins to model their conformational transitions. Using a simulated AFM image as reference, the algorithm can produce a low-resolution 3D model of the target molecule. Effect of molecular orientations captured in AFM images on the 3D modeling performance was also examined and it is shown that similar accuracy can be obtained for many orientations.

CONCLUSIONS

The proposed algorithm can generate 3D low-resolution protein models, from which conformational transitions observed in AFM images can be interpreted in more detail.

GENERAL SIGNIFICANCE

High-speed AFM experiments allow us to directly observe biomolecules in action, which provides insights on biomolecular function through dynamics. However, as only partial structural information can be obtained from AFM data, this new AFM based hybrid modeling method would be useful to retrieve 3D information of the entire biomolecule.

Single-molecule force spectroscopy to decipher the early signalling step in membrane-bound penicillin receptors embedded into a lipid bilayer

Understanding the molecular mechanism by which the signal of the presence of an antibiotic is transduced from outside to inside the bacterial cell is of fundamental interest for the β-lactam antibiotic resistance problem, but remains difficult to accomplish. No approach has ever addressed entire penicillin receptors in a membrane environment. Here we describe a method to investigate the purified Bacillus licheniformis BlaR1 receptor -a membrane-bound penicillin receptor involved in β-lactam resistance- embedded into a lipid bilayer in absence or presence of penicillin. By selecting a mutated receptor blocked in its signal transduction pathway just after its activation by penicillin, we revealed the very first step of receptor signalling by unfolding the receptor from its C-terminal end by AFM-based single-molecule force spectroscopy. We showed that the presence of the antibiotic entails significant conformational changes within the receptor. Our approach opens an avenue to study signal-transduction pathways mediated by membrane-bound proteins in a membrane environment.

Toward Precision Measurement and Manipulation of Single-Molecule Reactions by a Confined Space

All chemical reactions can be divided into a series of single molecule reactions (SMRs), the elementary steps that involve only isomerization of, dissociation from, and addition to an individual molecule. Analyzing SMRs is of paramount importance to identify the intrinsic molecular mechanism of a complex chemical reaction, which is otherwise implausible to reveal in an ensemble fashion, owing to the significant static and dynamic heterogeneity of real-world chemical systems. The single-molecule measurement and manipulation methods developed recently are playing an increasingly irreplaceable role to detect and recognize short-lived intermediates, visualize their transient existence, and determinate the kinetics and dynamics of single bond breaking and formation. Notably, none of the above SMRs characterizations can be realized without the aid of a confined space. Therefore, this Review aims to highlight the recent progress in the development of confined space enabled single-molecule sensing, imaging, and tuning methods to study chemical reactions. Future prospects of SMRs research are also included, including a push toward the physical limit on transduction of information to signals and vice versa, transmission and recording of signals, computational modeling and simulation, and rational design of a confined space for precise SMRs.

Cryopreserved Cells Regeneration Monitored by Atomic Force Microscopy and Correlated With State of Cytoskeleton and Nuclear Membrane

Atomic force microscopy (AFM) helps to describe and explain the mechanobiological properties of living cells on the nanoscale level under physiological conditions. The stiffness of cells is an important parameter reflecting cell physiology. Here, we have provided the first study of the stiffness of cryopreserved cells during post-thawing regeneration using AFM combined with confocal fluorescence microscopy. We demonstrated that the nonfrozen cell stiffness decreased proportionally to the cryoprotectant concentration in the medium. AFM allowed us to map cell surface reconstitution in real time after a freeze/thaw cycle and to monitor the regeneration processes at different depths of the cell and even different parts of the cell surface (nucleus and edge). Fluorescence microscopy showed that the cytoskeleton in fibroblasts, though damaged by the freeze/thaw cycle, is reconstructed after long-term plating. Confocal microscopy confirmed that structural changes affect the nuclear envelopes in cryopreserved cells. AFM nanoindentation analysis could be used as a noninvasive method to identify cells that have regenerated their surface mechanical properties with the proper dynamics and to a sufficient degree. This identification can be important particularly in the field of in vitro fertilization and in future cell-based regeneration strategies.

Methods for Lipid Droplet Biophysical Characterization in Flaviviridae Infections

Lipid droplets (LDs) are intracellular organelles for neutral lipid storage, originated from the endoplasmic reticulum. They play an essential role in lipid metabolism and cellular homeostasis. In fact, LDs are complex organelles, involved in many more cellular processes than those initially proposed. They have been extensively studied in the context of LD-associated pathologies. In particular, LDs have emerged as critical for virus replication and assembly. Viruses from the Flaviviridae family, namely dengue virus (DENV), hepatitis C virus (HCV), West Nile virus (WNV), and Zika virus (ZIKV), interact with LDs to usurp the host lipid metabolism for their own viral replication and pathogenesis. In general, during Flaviviridae infections it is observed an increasing number of host intracellular LDs. Several viral proteins interact with LDs during different steps of the viral life cycle. The HCV core protein and DENV capsid protein, extensively interact with LDs to regulate their replication and assembly. Detailed studies of LDs in viral infections may contribute for the development of possible inhibitors of key steps of viral replication. Here, we reviewed different techniques that can be used to characterize LDs isolated from infected or non-infected cells. Microscopy studies have been commonly used to observe LDs accumulation and localization in infected cell cultures. Fluorescent dyes, which may affect LDs directly, are widely used to probe LDs but there are also approaches that do not require the use of fluorescence, namely stimulated Raman scattering, electron and atomic force microscopy-based approaches. These three are powerful techniques to characterize LDs morphology. Raman scattering microscopy allows studying LDs in a single cell. Electron and atomic force microscopies enable a better characterization of LDs in terms of structure and interaction with other organelles. Other biophysical techniques, such as dynamic light scattering and zeta potential are also excellent to characterize LDs in terms of size in a simple and fast way and test possible LDs interaction with viral proteins. These methodologies are reviewed in detail, in the context of viral studies.

Effects of Various Processing Methods on the Ultrastructure of Tendon Collagen Fibrils from Qinchuan Beef Cattle Observed with Atomic Force Microscopy

Atomic force microscopy was utilized to study the effects of ultrasound oscillation, microwave heating, water bath cooking, and acid-base soaking on the ultrastructure of collagen fibrils of Qinchuan beef cattle tendons. D-spacing length and roughness of collagen fibrils always showed a 1.02% increment in the group which was processed for 20 min rather than for 10 min under different ultrasound frequencies. Microwave heating had a slight impact on D-spacing length and roughness at lower power (140–560 W), and collagen fibrils always showed a 1.02% increment for 20 min. Then, visible changes were noted with increasing power and time. D-spacing length reduced by 1.01% at 50°C for treatment periods of 10 min, 20 min, and 30 min, and there was no obvious change at 60°C; the periodic structure disappeared after cooking for 20 min, when fibrils had become gelatinized at 70°C. Collagen fibrils became disorganized at pH 3, following acid-base soaking. The present study indicated that acid-base soaking had an outstanding effect on the ultrastructure of collagen fibrils, especially in an acidic environment in consideration of the special structure of collagen.

Imaging in Biologically-Relevant Environments with AFM Using Stiff qPlus Sensors

High-resolution imaging of soft biological samples with atomic force microscopy (AFM) is challenging because they must be imaged with small forces to prevent deformation. Typically, AFM of those samples is performed with soft silicon cantilevers (k ≈ 0.1-10 N/m) and optical detection in a liquid environment. We set up a new microscope that uses a stiff qPlus sensor (k ≥ 1 kN/m). Several complex biologically-relevant solutions are non-transparent, and even change their optical properties over time, such as the cell culture medium we used. While this would be problematic for AFM setups with optical detection, it is no problem for our qPlus setup which uses electrical detection. The high stiffness of the qPlus sensor allows us to use small amplitudes in frequency-modulation mode and obtain high Q factors even in liquid. The samples are immersed in solution in a liquid cell and long tips are used, with only the tip apex submerged. We discuss the noise terms and compare the minimal detectable signal to that of soft cantilevers. Atomic resolution of muscovite mica was achieved in various liquids: H₂O, Tris buffer and a cell culture medium. We show images of lipid membranes in which the individual head groups are resolved.

Mechanotransduction in tumor progression: The dark side of the force

Broders-Bondon et al. review the pathological mechanical properties of tumor tissues and how abnormal mechanical signals result in oncogenic biochemical signals during tumor progression.

Cancer has been characterized as a genetic disease, associated with mutations that cause pathological alterations of the cell cycle, adhesion, or invasive motility. Recently, the importance of the anomalous mechanical properties of tumor tissues, which activate tumorigenic biochemical pathways, has become apparent. This mechanical induction in tumors appears to consist of the destabilization of adult tissue homeostasis as a result of the reactivation of embryonic developmental mechanosensitive pathways in response to pathological mechanical strains. These strains occur in many forms, for example, hypervascularization in late tumors leads to high static hydrodynamic pressure that can promote malignant progression through hypoxia or anomalous interstitial liquid and blood flow. The high stiffness of tumors directly induces the mechanical activation of biochemical pathways enhancing the cell cycle, epithelial–mesenchymal transition, and cell motility. Furthermore, increases in solid-stress pressure associated with cell hyperproliferation activate tumorigenic pathways in the healthy epithelial cells compressed by the neighboring tumor. The underlying molecular mechanisms of the translation of a mechanical signal into a tumor inducing biochemical signal are based on mechanically induced protein conformational changes that activate classical tumorigenic signaling pathways. Understanding these mechanisms will be important for the development of innovative treatments to target such mechanical anomalies in cancer.

Atomic Force Microscopy: An Introduction

Imaging of nano-sized particles and sample features is crucial in a variety of research fields. For instance in biological sciences, where it is paramount to investigate structures at the single particle level. Often two-dimensional images are not sufficient and further information such as topography and mechanical properties are required. Furthermore, to increase the biological relevance, it is desired to perform the imaging in close to physiological environments. Atomic force microscopy (AFM) meets these demands in an all-in-one instrument. It provides high-resolution images including surface height information leading to three-dimensional information on sample morphology. AFM can be operated both in air and in buffer solutions. Moreover, it has the capacity to determine protein and membrane material properties via the force spectroscopy mode. Here we discuss the principles of AFM operation and provide examples of how biomolecules can be studied. By including new approaches such as high-speed AFM (HS-AFM) we show how AFM can be used to study a variety of static and dynamic single biomolecules and biomolecular assemblies.

Morphological changes in erythrocytes of people with type 2 diabetes mellitus evaluated with atomic force microscopy: A brief review

Prevalence of type 2 diabetes mellitus (T2DM) has been increasing worldwide. Cardiovascular diseases are one of the main causes of death among people with T2DM. Morphological changes in erythrocytes have been associated with higher risk of cardiovascular diseases. Atomic force microscopy (AFM) is a new technique that allows non-invasive imaging of cells and the evaluation of changes in mechanical properties.

AIM

To evaluate by AFM the erythrocytes morphological changes of people with T2DM METHODS: Search was conducted from in PubMed, ScienceDirect, Scielo, and Lilacs. Erythrocyte, type 2 Diabetes Mellitus and, Microscopy, Atomic Force were the keywords used for the search. Papers included were cross-sectional studies performed in humans.

RESULTS

Five of seven articles fulfilled the inclusion criteria. Compared with healthy cells, the erythrocytes from individuals affected by T2DM had morphological changes such as a decreased concave depth, diameter, height and a deformation index, while axial ratio, stiffness, adhesive force, aggregation, and rigidity index were increased. The results regarding the erythrocyte roughness were inconclusive.

CONCLUSIONS

The AFM is an excellent instrument to study the altered erythrocytes of subjects affected by T2DM. Morphology changes in erythrocytes could lead to cardiovascular events, which are major complications in people living with this disease.

Electron Paramagnetic Resonance of a Single NV Nanodiamond Attached to an Individual Biomolecule

Electron paramagnetic resonance (EPR), an established and powerful methodology for studying atomic-scale biomolecular structure and dynamics, typically requires in excess of 10(12) labeled biomolecules. Single-molecule measurements provide improved insights into heterogeneous behaviors that can be masked in ensemble measurements and are often essential for illuminating the molecular mechanisms behind the function of a biomolecule. Here, we report EPR measurements of a single labeled biomolecule. We selectively label an individual double-stranded DNA molecule with a single nanodiamond containing nitrogen-vacancy centers, and optically detect the paramagnetic resonance of nitrogen-vacancy spins in the nanodiamond probe. Analysis of the spectrum reveals that the nanodiamond probe has complete rotational freedom and that the characteristic timescale for reorientation of the nanodiamond probe is slow compared with the transverse spin relaxation time. This demonstration of EPR spectroscopy of a single nanodiamond-labeled DNA provides the foundation for the development of single-molecule magnetic resonance studies of complex biomolecular systems.

Genetically-Tunable Mechanical Properties of Bacterial Functional Amyloid Nanofibers

Bacterial biofilms are highly ordered, complex, dynamic material systems including cells, carbohydrates, and proteins. They are known to be resistant against chemical, physical, and biological disturbances. These superior properties make them promising candidates for next generation biomaterials. Here we investigated the morphological and mechanical properties (in terms of Young's modulus) of genetically-engineered bacterial amyloid nanofibers of Escherichia coli (E. coli) by imaging and force spectroscopy conducted via atomic force microscopy (AFM). In particular, we tuned the expression and biochemical properties of the major and minor biofilm proteins of E. coli (CsgA and CsgB, respectively). Using appropriate mutants, amyloid nanofibers constituting biofilm backbones are formed with different combinations of CsgA and CsgB, as well as the optional addition of tagging sequences. AFM imaging and force spectroscopy are used to probe the morphology and measure the Young's moduli of biofilm protein nanofibers as a function of protein composition. The obtained results reveal that genetically-controlled secretion of biofilm protein components may lead to the rational tuning of Young's moduli of biofilms as promising candidates at the bionano interface.

Atomic Force Microscopy: A Powerful Tool to Address Scaffold Design in Tissue Engineering

Functional polymers currently represent a basic component of a large range of biological and biomedical applications including molecular release, tissue engineering, bio-sensing and medical imaging. Advancements in these fields are driven by the use of a wide set of biodegradable polymers with controlled physical and bio-interactive properties. In this context, microscopy techniques such as Atomic Force Microscopy (AFM) are emerging as fundamental tools to deeply investigate morphology and structural properties at micro and sub-micrometric scale, in order to evaluate the in time relationship between physicochemical properties of biomaterials and biological response. In particular, AFM is not only a mere tool for screening surface topography, but may offer a significant contribution to understand surface and interface properties, thus concurring to the optimization of biomaterials performance, processes, physical and chemical properties at the micro and nanoscale. This is possible by capitalizing the recent discoveries in nanotechnologies applied to soft matter such as atomic force spectroscopy to measure surface forces through force curves. By tip-sample local interactions, several information can be collected such as elasticity, viscoelasticity, surface charge densities and wettability. This paper overviews recent developments in AFM technology and imaging techniques by remarking differences in operational modes, the implementation of advanced tools and their current application in biomaterials science, in terms of characterization of polymeric devices in different forms (i.e., fibres, films or particles).

Stiffness of Intact Endothelial Cells From Fresh Aortic Bifurcations of Atherosclerotic Rabbits-Atomic Force Microscopic Study

Stiffness of intact endothelial cells (ECs) in the abdominal aorta (AA) and in the medial and lateral wall of the common iliac artery (CIA(Medial) and CIA(Lateral), respectively), which were freshly obtained from cholesterol-fed rabbits, were measured with an atomic force microscopic indentation method. In the areas away from atherosclerotic plaques (Off-plaque), ECs were significantly stiffer in CIA(Medial) than in the other two locations; this result was similar to that from normal diet-fed animals. On the other hand, there were no significant differences in the stiffness of ECs located on atherosclerotic plaques (On-plaque) among the three sites; the stiffness was equal to those in "Off-plaque" wall of CIA(Lateral) and AA. Moreover, the stiffness of ECs covering plaques decreased with the progression of atherosclerosis. The precise quantification of the stiffness of vascular ECs would provide a better understanding of cellular remodeling and adaptation in atherosclerosis. J. Cell. Physiol. 232: 7-13, 2017. © 2016 Wiley Periodicals, Inc.

Elasto-mechanical properties of living cells

The possibility to directly measure the elasticity of living cell has emerged only in the last few decades. In the present study the elastic properties of two cell lines were followed. Both types are widely used as cell barrier models (e.g. blood-brain barrier). During time resolved measurement of the living cell elasticity a continuous quasi-periodic oscillation of the elastic modulus was observed. Fast Fourier transformation of the signals revealed that a very limited number of three to five Fourier terms fitted the signal in the case of human cerebral endothelial cells. In the case of canine kidney epithelial cells more than 8 Fourier terms did not result a good fit. Calculating the correlation between nucleus and periphery of the signals revealed a higher correlation factor for the endothelial cells compared to the epithelial cells.

Pollen from Arabidopsis thaliana and other Brassicaceae are functionally omniaperturate

PREMISE OF THE STUDY

Most pollen walls are interrupted by apertures, thin areas providing access to stigmatic fluids and exit points for pollen tubes. Unexpectedly, pollen tubes of Arabidopsis thaliana are not obligated to pass through apertures and can instead take the shortest route into the stigma, passing directly through a nonaperturate wall.

METHODS

We used stains and confocal microscopy to follow early pollen tube formation in A. thaliana and 200+ other species. We germinated pollen in vitro and in situ (at control and high humidities) and also used atomic force microscopy to assay material properties of nonaperture and aperture walls.

KEY RESULTS

Pollen tubes of A. thaliana breached nonaperture walls despite these being an order of magnitude stiffer than aperture walls. Breakout was associated with localized swelling of the pectin-rich (alcian blue positive) intine. The precision of pollen tube exit at the pollen-stigma interface was lost at high humidity. Pollen from ∼4% of the species surveyed exhibited breakout germination behavior; all nine breakout species identified so far are in the Brassicaceae family (∼25% of the Brassicaceae sampled) and are scattered across seven tribes.

CONCLUSIONS

The polarity of pollen germination in A. thaliana is externally induced, not linked to aperture location. The biomechanical force for breaking nonaperture walls is found in localized swelling of intine pectins. As such, the pollen from A. thaliana, and likely many Brassicaceae family members, are functionally omniaperturate. This new mechanism for germination between extant apertures raises questions about exine porosity and the diversity of mechanisms across taxa.

Surface imaging beyond the diffraction limit with optically trapped spheres

Optical traps play an increasing role in the bionanosciences because of their ability to apply forces flexibly on tiny structures in fluid environments. Combined with particle-tracking techniques, they allow the sensing of miniscule forces exerted on these structures. Similar to atomic force microscopy (AFM), but much more sensitive, an optically trapped probe can be scanned across a structured surface to measure the height profile from the displacements of the probe. Here we demonstrate that, by the combination of a time-shared twin-optical trap and nanometre-precise three-dimensional interferometric particle tracking, both reliable height profiling and surface imaging are possible with a spatial resolution below the diffraction limit. The technique exploits the high-energy thermal position fluctuations of the trapped probe, and leads to a sampling of the surface 5,000 times softer than in AFM. The measured height and force profiles from test structures and Helicobacter cells illustrate the potential to uncover specific properties of hard and soft surfaces.

Taking nanomedicine teaching into practice with atomic force microscopy and force spectroscopy

Atomic force microscopy (AFM) is a useful and powerful tool to study molecular interactions applied to nanomedicine. The aim of the present study was to implement a hands-on atomic AFM course for graduated biosciences and medical students. The course comprises two distinct practical sessions, where students get in touch with the use of an atomic force microscope by performing AFM scanning images of human blood cells and force spectroscopy measurements of the fibrinogen-platelet interaction. Since the beginning of this course, in 2008, the overall rating by the students was 4.7 (out of 5), meaning a good to excellent evaluation. Students were very enthusiastic and produced high-quality AFM images and force spectroscopy data. The implementation of the hands-on AFM course was a success, giving to the students the opportunity of contact with a technique that has a wide variety of applications on the nanomedicine field. In the near future, nanomedicine will have remarkable implications in medicine regarding the definition, diagnosis, and treatment of different diseases. AFM enables students to observe single molecule interactions, enabling the understanding of molecular mechanisms of different physiological and pathological processes at the nanoscale level. Therefore, the introduction of nanomedicine courses in bioscience and medical school curricula is essential.

Generating and characterizing the mechanical properties of cell-derived matrices using atomic force microscopy

Mechanical interaction between cells and their surrounding extracellular matrix (ECM) controls key processes such as proliferation, differentiation and motility. For many years, two-dimensional (2D) models were used to better understand the interactions between cells and their surrounding ECM. More recently, variation of the mechanical properties of tissues has been reported to play a major role in physiological and pathological scenarios such as cancer progression. The 3D architecture of the ECM finely tunes cellular behavior to perform physiologically relevant tasks. Technical limitations prevented scientists from obtaining accurate assessment of the mechanical properties of physiologically realistic matrices. There is therefore a need for combining the production of high-quality cell-derived 3D matrices (CDMs) and the characterization of their topographical and mechanical properties. Here, we describe methods that allow to accurately measure the young modulus of matrices produced by various cellular types. In the first part, we will describe and review several protocols for generating CDMs matrices from endothelial, epithelial, fibroblastic, muscle and mesenchymal stem cells. We will discuss tools allowing the characterization of the topographical details as well as of the protein content of such CDMs. In a second part, we will report the methodologies that can be used, based on atomic force microscopy, to accurately evaluate the stiffness properties of the CDMs through the quantification of their young modulus. Altogether, such methodologies allow characterizing the stiffness and topography of matrices deposited by the cells, which is key for the understanding of cellular behavior in physiological conditions.

Magnetic Force Microscopy in Liquids

In this work, the use of magnetic force microscopy (MFM) to acquire images of magnetic nanostructures in liquid environments is presented. Optimization of the MFM signal acquisition in liquid media is performed and it is applied to characterize the magnetic signal of magnetite nanoparticles. The ability for detecting magnetic nanostructures along with the well-known capabilities of atomic force microscopy in liquids suggests potential applications in fields such as nanomedicine, nanobiotechnology, or nanocatalysis.

Quantitative characterization of adhesion and stiffness of corneal lens of Drosophila melanogaster using atomic force microscopy

Atomic force Microscopy (AFM) has become a versatile tool in biology due to its advantage of high-resolution imaging of biological samples close to their native condition. Apart from imaging, AFM can also measure the local mechanical properties of the surfaces. In this study, we explore the possibility of using AFM to quantify the rough eye phenotype of Drosophila melanogaster through mechanical properties. We have measured adhesion force, stiffness and elastic modulus of the corneal lens using AFM. Various parameters affecting these measurements like cantilever stiffness and tip geometry are systematically studied and the measurement procedures are standardized. Results show that the mean adhesion force of the ommatidial surface varies from 36 nN to 16 nN based on the location. The mean stiffness is 483 ± 5 N/m, and the elastic modulus is 3.4 ± 0.05 GPa (95% confidence level) at the center of ommatidia. These properties are found to be different in corneal lens of eye expressing human mutant tau gene (mutant). The adhesion force, stiffness and elastic modulus are decreased in the mutant. We conclude that the measurement of surface and mechanical properties of D. melanogaster using AFM can be used for quantitative evaluation of 'rough eye' surface.

Atomic force microscopy and Langmuir-Blodgett monolayer technique to assess contact lens deposits and human meibum extracts

PURPOSE

The purpose of this exploratory study was to investigate the differences in meibomian gland secretions, contact lens (CL) lipid extracts, and CL surface topography between participants with and without meibomian gland dysfunction (MGD).

METHODS

Meibum study: Meibum was collected from all participants and studied via Langmuir-Blodgett (LB) deposition with subsequent Atomic Force Microscopy (AFM) visualization and surface roughness analysis. CL Study: Participants with and without MGD wore both etafilcon A and balafilcon A CLs in two different phases. CL lipid deposits were extracted and analyzed using pressure-area isotherms with the LB trough and CL surface topographies and roughness values were visualized using AFM.

RESULTS

Meibum study: Non-MGD participant meibum samples showed larger, circular aggregates with lower surface roughness, whereas meibum samples from participants with MGD showed more lipid aggregates, greater size variability and higher surface roughness. CL Study: Worn CLs from participants with MGD had a few large tear film deposits with lower surface roughness, whereas non-MGD participant-worn lenses had many small lens deposits with higher surface roughness. Balafilcon A pore depths were shallower in MGD participant worn lenses when compared to non-MGD participant lenses. Isotherms of CL lipid extracts from MGD and non-MGD participants showed a seamless rise in surface pressure as area decreased; however, extracts from the two different lens materials produced different isotherms.

CONCLUSIONS

MGD and non-MGD participant-worn CL deposition were found to differ in type, amount, and pattern of lens deposits. Lipids from MGD participants deposited irregularly whereas lipids from non-MGD participants showed more uniformity.

Tattoo ink nanoparticles in skin tissue and fibroblasts

Tattooing has long been practised in various societies all around the world and is becoming increasingly common and widespread in the West. Tattoo ink suspensions unquestionably contain pigments composed of nanoparticles, i.e., particles of sub-100 nm dimensions. It is widely acknowledged that nanoparticles have higher levels of chemical activity than their larger particle equivalents. However, assessment of the toxicity of tattoo inks has been the subject of little research and ink manufacturers are not obliged to disclose the exact composition of their products. This study examines tattoo ink particles in two fundamental skin components at the nanometre level. We use atomic force microscopy and light microscopy to examine cryosections of tattooed skin, exploring the collagen fibril networks in the dermis that contain ink nanoparticles. Further, we culture fibroblasts in diluted tattoo ink to explore both the immediate impact of ink pigment on cell viability and also to observe the interaction between particles and the cells.

A nano-scale probing system with a gold nano-dot array for measurement of a single biomolecular interaction force

A new nano-scale probing system was proposed and developed to measure and analyze the interaction force between biomolecules at the single molecular level.

Material properties of viral nanocages explored by atomic force microscopy

Single-particle nanoindentation by atomic force microscopy (AFM) is an emergent technique to characterize the material properties of nano-sized proteinaceous systems. AFM uses a very small tip attached to a cantilever to scan the surface of the substrate. As a result of the sensitive feedback loop of AFM, the force applied by the tip on the substrate during scanning can be controlled and monitored. By accurately controlling this scanning force, topographical maps of fragile substrates can be acquired to study the morphology of the substrate. In addition, mechanical properties of the substrate like stiffness and breaking point can be determined by using the force spectroscopy capability of AFM. Here we discuss basics of AFM operation and how this technique is used to determine the structure and mechanical properties of protein nanocages, in particular viral particles. Knowledge of morphology as well as mechanical properties is essential for understanding viral life cycles, including genome packaging, capsid maturation, and uncoating, but also contributes to the development of diagnostics, vaccines, imaging modalities, and targeted therapeutic devices based on viruslike particles.

Single virus detection by means of atomic force microscopy in combination with advanced image analysis

In the present contribution virions of five different virus species, namely Varicella-zoster virus, Porcine teschovirus, Tobacco mosaic virus, Coliphage M13 and Enterobacteria phage PsP3, are investigated using atomic force microscopy (AFM). From the resulting height images quantitative features like maximal height, area and volume of the viruses could be extracted and compared to reference values. Subsequently, these features were accompanied by image moments, which quantify the morphology of the virions. Both types of features could be utilized for an automatic discrimination of the five virus species. The accuracy of this classification model was 96.8%. Thus, a virus detection on a single-particle level using AFM images is possible. Due to the application of advanced image analysis the morphology could be quantified and used for further analysis. Here, an automatic recognition by means of a classification model could be achieved in a reliable and objective manner.

Investigating biomolecular recognition at the cell surface using atomic force microscopy

Probing the interaction forces that drive biomolecular recognition on cell surfaces is essential for understanding diverse biological processes. Force spectroscopy has been a widely used dynamic analytical technique, allowing measurement of such interactions at the molecular and cellular level. The capabilities of working under near physiological environments, combined with excellent force and lateral resolution make atomic force microscopy (AFM)-based force spectroscopy a powerful approach to measure biomolecular interaction forces not only on non-biological substrates, but also on soft, dynamic cell surfaces. Over the last few years, AFM-based force spectroscopy has provided biophysical insight into how biomolecules on cell surfaces interact with each other and induce relevant biological processes. In this review, we focus on describing the technique of force spectroscopy using the AFM, specifically in the context of probing cell surfaces. We summarize recent progress in understanding the recognition and interactions between macromolecules that may be found at cell surfaces from a force spectroscopy perspective. We further discuss the challenges and future prospects of the application of this versatile technique.

Atomic force microscopic investigation of respiratory syncytial virus infection in HEp-2 cells

Respiratory syncytial virus (RSV) primarily causes bronchiolitis and pneumonia in infants. In spite of intense research, no safe and effective vaccine has been developed yet. For understanding its pathogenesis and development of anti-RSV drugs/therapeutics, it is indispensable to study the RSV-host interaction. Although, there are limited studies using electron microscopy to elucidate the infection process of RSV, to our knowledge, no study has reported the morphological impact of RSV infection using atomic force microscopy. We report the cytoplasmic and nuclear changes in human epidermoid cell line type 2 using atomic force microscopy. Human epidermoid cell line type 2 cells, grown on cover slips, were infected with RSV and fixed after various time periods, processed and observed for morphological changes using atomic force microscopy. RSV infected cells showed loss of membrane integrity, with degeneration in the cellular content and cytoskeleton. Nuclear membrane was disintegrated and nuclear volume was decreased. The chromatin of the RSV infected cells was condensed, progressing towards degeneration via pyknosis and apoptosis. Membrane protrusions of ~150-200 nm diameter were observed on RSV infected cells after 6 h, suggestive of prospective RSV budding sites. To our knowledge, this is the first study of RSV infection process using atomic force microscopy. Such morphological studies could help explore viral infection process aiding the development of anti-RSV therapies.

Characterizing ultrathin and thick organic layers by surface plasmon resonance three-wavelength and waveguide mode analysis

A three-wavelength angular-scanning surface plasmon resonance based analysis has been utilized for characterizing optical properties of organic nanometer-thick layers with a wide range of thicknesses. The thickness and refractive index were determined for sample layers with thicknesses ranging from subnanometer to hundreds of nanometers. The analysis approach allows for simultaneous determination of both the refractive index and thickness without prior knowledge of either the refractive index or the thickness of the sample layers and without the help of other instruments, as opposed to current methods and approaches for characterizing optical properties of organic nanometer-thick layers. The applicability of the three-wavelength angular-scanning surface plasmon resonance approach for characterizing thin and thick organic layers was demonstrated by ex situ deposited mono- and multilayers of stearic acid and hydrogenated soy phosphatidylcholine and in situ layer-by-layer deposition of two different polyelectrolyte multilayer systems. In addition to the three-wavelength angular-scanning surface plasmon resonance approach, another surface plasmon resonance optical phenomenon, i.e., the surface plasmon resonance waveguide mode, was utilized to characterize organic sample layers whose thicknesses border the micrometer scale. This was demonstrated by characterizing both in situ layer-by-layer deposited polyelectrolyte multilayer systems and an ex situ deposited spin-coated polymer layer.