Application of atomic force microscopy to microbial surfaces: from reconstituted cell surface layers to living cells.

The application of atomic force microscopy (AFM) to probe the ultrastructure and physical properties of microbial cell surfaces is reviewed. The unique capabilities of AFM can be summarized as follows: imaging surface topography with (sub)nanometer lateral resolution; examining biological specimens under physiological conditions; measuring local properties and interaction forces. AFM is being used increasingly for: (i) visualizing the surface ultrastructure of microbial cell surface layers, including bacterial S-layers, purple membranes, porin OmpF crystals and fungal rodlet layers; (ii) monitoring conformational changes of individual membrane proteins; (iii) examining the morphology of bacterial biofilms, (iv) revealing the nanoscale structure of living microbial cells, including fungi, yeasts and bacteria, (v) mapping interaction forces at microbial surfaces, such as van der Waals and electrostatic forces, solvation forces, and steric/bridging forces; and (vi) probing the local mechanical properties of cell surface layers and of single cells.     

Probing bacterial interactions: integrated approaches combining atomic force microscopy, electron microscopy and biophysical techniques

Recent developments in the application of Atomic Force Microscopy (AFM) and other biophysical techniques for the study of bacterial interactions and adhesion are discussed in the light of established biological and microscopic approaches. Whereas molecular-biological techniques combined with electron microscopy allow the identification and localization of surface constituents mediating bacterial interactions, with AFM it has become possible to actually measure the forces involved in bacterial interactions. Combined with the flexibility of AFM in probing various types of physical interactions, such as electrostatic interactions, specific ligand-receptor interactions and the elastic forces of deformation and extension of bacterial surface polymers and cell wall, this provides prospects for the elucidation of the biophysical mechanism of bacterial interaction. However, because of the biochemical and a biophysical complexity of the bacterial cell wall, integrated approaches combining AFM with electron microscopy and biophysical techniques are needed to elucidate the mechanism by which a bacterium interacts with a host or material surface. The literature on electron microscopy of the bacterial cell wall is reviewed, with particular emphasis on the staining of specific classes of cell-wall constituents. The application of AFM in the analysis of bacterial surfaces is discussed, including AFM operating modes, sample preparation methods and results obtained on various strains. For various bacterial strains, the integration of EM and AFM data is discussed. Various biophysical aspects of the analysis of bacterial surface structure and interactions are discussed, including the theory of colloidal interactions and Bell's theory of cell-to-cell adhesion. An overview is given of biophysical techniques used in the analysis of the properties of bacterial surfaces and bacterial surface constituents and their integration with AFM. Finally, we discuss recent progress in the understanding of the role of bacterial interactions in medicine within the framework of the techniques and concepts discussed in the paper.     

Atomic force microscopy: a powerful tool for studying bacterial swarming motility

Swarming motility is a fascinating phenomenon by which some bacteria use flagella to move over solid surfaces. Understanding the molecular mechanisms underlying swarming motility requires studying the factors that induce and control flagella expression in swarming cells. Traditionally, flagella are observed by optical or electron microscopy, but none of these techniques combine versatility and easiness, with quantitative and high-resolution information. We report an atomic force microscopy (AFM)-based approach for the fast imaging of bacterial phenotypes (cell shape, flagella expression) in swarming motility studies. Cells from the gram-positive bacterium Bacillus thuringiensis sv. israelensis were inoculated on energy-rich media containing increasing agar concentrations. Following swarming assays (2 days), the cell morphology and the amount of flagella were directly observed by AFM imaging in air. Consistent with the macroscopic swarming behavior, cells harvested from the rim of colonies spreading on soft agar were hyperflagellated, elongated and arranged in chains. Increasing the agar concentration led to much lower amounts of flagella and to shorter rod-shaped cells, a finding consistent with the slower swarming motility of the cells. Cells taken from colony centers on soft and hard agar surfaces were generally non-flagellated, rod-shaped, rarely arranged in chains, and exhibited lysis and sporulation. This study shows that AFM imaging can readily discriminate between swarming and non-swarming cells, and quantify their morphological details, thus offering an important tool to study the dynamics of bacterial populations.     

Increased imaging speed and force sensitivity for bio-applications with small cantilevers using a conventional AFM setup

In this study, we demonstrate the increased performance in speed and sensitivity achieved by the use of small AFM cantilevers on a standard AFM system. For this, small rectangular silicon oxynitride cantilevers were utilized to arrive at faster atomic force microscopy (AFM) imaging times and more sensitive molecular recognition force spectroscopy (MRFS) experiments. The cantilevers we used had lengths between 13 and 46μm, a width of about 11μm, and a thickness between 150 and 600nm. They were coated with chromium and gold on the backside for a better laser reflection. We characterized these small cantilevers through their frequency spectrum and with electron microscopy. Due to their small size and high resonance frequency we were able to increase the imaging speed by a factor of 10 without any loss in resolution for images from several μm scansize down to the nanometer scale. This was shown on bacterial surface layers (s-layer) with tapping mode under aqueous, near physiological conditions and on nuclear membranes in contact mode in ambient environment. In addition, we showed that single molecular forces can be measured with an up to 5 times higher force sensitivity in comparison to conventional cantilevers with similar spring constants.     

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.     

Investigation into layers formed by selective transfer CMP mechanisms with atomic force microscope

To understand mechanisms of chemical mechanical planarization (CMP), an atomic force microscope (AFM) was used to characterize polished layer surfaces formed by selective transfer after a set of polishing experiments. It is know that in the process of friction of two materials and in the presence of own lubricants, wear phenomenon itself manifests as a transfer of material from an element of a friction couple on the other, this phenomenon being characteristic to the selective transfer process. A selective transfer can be safely achieved in a friction couple, if there is a favorable energy, and in the presence of relative movement, if in the friction area is a material made by copper and the lubricant is adequate (glycerin or special lubricant). The forming selective layer on the contact surfaces makes that the friction force to be very low because of the structure formed by selective transfer. To optimize the CMP process, one needs to obtain information on the interaction between the slurry abrasive particles (with the size range of about 30–70 nm) and the polished surface. To study such interactions, we used AFM. Surface analysis of selective layer using the AFM revealed detailed surface characteristics obtained by CMP. Studying the selective layer CMP, of which the predominated one is copper (in proportion of over 85%), we found that the AFM scanning removes the surface oxide layer in different rates depending on the depth of removal and the pH of the solution. Oxide removal happens considerably faster than the copper CMP removal from the selective layer. This is in agreement with generally accepted models of copper CMP. It was found that removal mechanisms depend on the slurry chemistry, potential per cent of oxidizer, and the applied load. This presentation discusses these findings. Both load force and the friction forces acting between the AFM tip and surface during the polishing process were measured. One big advantage of using the AFM tip (of radius about 50 nm) as abrasive silica particle is that we can measure forces acting between the particle-tip and the surface being polished. Here, we report measurement of the friction force while scratching and polishing. The correlation between those forces and removal rate is discussed.     

MFM and AFM study of thin cobalt films modified by fluorosilane

Polycrystalline cobalt films 100 nm thick were thermally evaporated on oxidized Si(100) substrates. Then 1H, 1H, 2H, 2H perfluorodecyltrichlorosilane (FDTS) films of various thicknesses, in the range of about 2 nm to 30 nm, were grown on cobalt surfaces by vapor phase deposition (VPD). The cobalt films modified by FDTS were investigated using magnetic force microscopy (MFM) and atomic force microscopy (AFM). MFM observation showed that the magnetic structure of the cobalt films modified by FDTS is composed of domains with a considerable component of magnetization perpendicular to the film surface. This in turn indicates that the cobalt films on oxidized Si(100) substrates crystallize in the hexagonal close-packed (HCP) phase and exhibit a texture with the hexagonal axis perpendicular to the film surface. The magnetic domains formed a maze structure. The domain width increased from typically 80–120 nm to 400–500 nm with increasing the thickness of FDTS films from about 2 nm to 30 nm. AFM imaging of the surfaces of FDTS films revealed the presence of an agglomerate morphology. The agglomerates varied in size from typically 30–70 nm to 150–300 nm as the film thickness was increased from about 2 nm to 30 nm.     

Scanning tunnelling microscopy imaging and modification of hydrogen-passivated Ge(100) surfaces

Scanning tunnelling microscopy (STM) study and modification of hydrogen (H)-passivated Ge(100) surfaces have been investigated. Thermal oxidation procedures were used to minimise surface roughness. Ge samples were passivated in HF solution after thermal oxidation. STM and atomic force microscope (AFM) imaging showed that, using HF etching after thermal oxidation, we can obtain a natural H-passivatedtopographically and chemically flat Ge(100) surface. The root-mean-square (rms) roughness ofa H-passivatedGe(100) surface measured both by STM and AFM is less than 2 ?. Electric properties of H-passivatedGe(100) surfaces were studied by scanning tunnelling spectroscopy (STS) in nitrogen ambient. STS showed that the H-passivated Ge surfaces were not pinned. Modification on H-passivated Ge(100) surfaces was carried out using STM by applying an electric voltage between the sample and tip in air. Modified features were characterised by STM and AFM imaging. On the H-passivated Ge(100) surfaces, stable, low-voltage, nanometer-scale modified features can be produced.     

Towards a nanoscale view of lactic acid bacteria

Probiotic bacteria have a strong potential in biomedicine owing to their ability to induce various beneficial health effects. Bacterial cell surface constituents play a key role in establishing tight interactions between probiotics and their host. Yet, little is known about the spatial organization and biophysical properties of the individual molecules. In this paper, we discuss how we have been using atomic force microscopy imaging and force spectroscopy to probe the nanoscale surface properties of gram-positive lactic acid bacteria, with an emphasis on probiotic strains. Topographic imaging has enabled us to visualize bacterial cell surface structures (peptidoglycan, teichoic acids, pili, polysaccharides) under physiological conditions and with unprecedented resolution. In parallel, single-molecule force spectroscopy has been used to localize and force probe single cell surface constituents, providing novel insights into their spatial distribution and molecular elasticity.     

AFM imaging of fenestrated liver sinusoidal endothelial cells

Each microscope with its dedicated sample preparation technique provides the investigator with a specific set of data giving an instrument-determined (or restricted) insight into the structure and function of a tissue, a cell or parts thereof. Stepwise improvements in existing techniques, both instrumental and preparative, can sometimes cross barriers in resolution and image quality. Of course, investigators get really excited when completely new principles of microscopy and imaging are offered in promising new instruments, such as the AFM. The present paper summarizes a first phase of studies on the thin endothelial cells of the liver. It describes the preparation-dependent differences in AFM imaging of these cells after isolation. Special point of interest concerned the dynamics of the fenestrae, thought to filter lipid-carrying particles during their transport from the blood to the liver cells. It also describes the attempts to image the details of these cells when alive in cell cultures. It explains what physical conditions, mainly contributed to the scanning stylus, are thought to play a part in the limitations in imaging these cells. The AFM also offers promising specifications to those interested in cell surface details, such as membrane-associated structures, receptors, coated pits, cellular junctions and molecular aggregations or domains. The AFM also offers nano-manipulation possibilities, strengths and elasticity measurements, force interactions, affinity measurements, stiffness and other physical aspects of membranes and cytoskeleton. The potential for molecular approaches is there. New developments in cantilever construction and computer software promise to bring real time video imaging to the AFM. Home made accessories for the first generation of AFM are now commodities in commercial instruments and make the life of the AFM microscopist easier. Also, the combination of different microscopies, such as AFM and TEM, or AFM and SEM find their way to the market allowing comfortable correlative microscopy.     

Measurements of metal-polymer adhesion properties with dynamic force spectroscopy

We investigate nanoscale interface properties using dynamic mode atomic force microscopy (AFM) operated in the frequency modulation mode in ultrahigh vacuum. The AFM tip was was functionalised by a thin layer of aluminium and the polymer was treated by plasma-etching. In the spectroscopy mode we could measure the adhesion properties between the metal and the polymer surfaces. We found that plasma-etching of the polymer resulted in strongly enhanced force interactions, indicating a chemical activation of the polymer surface. Values for the adhesion force and work of adhesion were measured on the nanometer scale and are compared to conventional macroscopic adhesion failure tests.     

Atomic force microscopy studies of chemical–mechanical processes on silicon(100) surfaces

Atomic force microscopy (AFM) is used to examine chemical–mechanical processes on Si(100) surfaces. The AFM tip serves as a single asperity contact to exert tribological forces as well as an imaging tool. By scanning in chemically aggressive solutions, material removal can be observed directly. In the silicon system, high-force scans are used to remove oxide and initiate etching in selected locations, followed by low-force scans to image the resulting surfaces. Material removal rates were measured as a function of applied load, number of scans, solution composition, and time. In basic solution, places where the underlying silicon is exposed etch rapidly, producing structures 100 nm or less in size. Although the surface roughness initially increases during etching, the final surfaces are smooth. The oxide is extremely sensitive to applied stress: even very light scanning accelerates oxide dissolution. Once the oxide is removed, chemical etching proceeds through the underlying silicon with or without AFM scanning; but the silicon etches more rapidly if AFM scanning is continued, due to true chemical–mechanical (tribochemical) effects.     

Probing into adsorption behavior of human plasma fibrinogen on self-assembled monolayers with different chemical properties by scanning probe microscopy

The adsorption behaviors of fibrinogen on the self-assembled monolayers (SAMs) with different chemical properties were investigated using an atomic force microscopy (AFM). AFM images indicated that the adsorption amounts of fibrinogen molecules increased with an increase of the surface hydrophobicity. High-resolution AFM imaging revealed that the fibrinogen conformations adsorbed on the SAM surface changed with dependent on the surface chemistry. The adsorption models of fibrinogen molecules adsorbed on SAM surfaces with different chemical properties were proposed based on the high-resolution AFM images.     

Atomic force microscopy: determination of unbinding force, off rate and energy barrier for protein-ligand interaction

Recently, atomic force microscopy (AFM) based force measurements have been applied biophysically and clinically to the field of molecular recognition as well as to the evaluation of dynamic parameters for various interactions between proteins and ligands in their native environment. The aim of this review is to describe the use of the AFM to measure the forces that control biological interaction, focusing especially on protein-ligand and protein-protein interaction modes. We first considered the measurements of specific and non-specific unbinding forces which together control protein-ligand interactions. As such, we will look at the theoretical background of AFM force measurement curves for evaluating the unbinding forces of protein-ligand complexes. Three AFM model dynamic parameters developed recently for use in protein-ligand interactions are reviewed: (i) unbinding forces, (ii) off rates, and (iii) binding energies. By reviewing the several techniques developed for measuring forces between biological structures and intermolecular forces in the literature, we show that use of an AFM for these applications provides an excellent tool in terms of spatial resolution and lateral resolution, especially for protein-protein and protein-ligand interactions.     

Instrumentation of STM and AFM combined with transmission electron microscope

A scanning tunneling microscope (STM) combined with a transmission electron microscope (TEM) is a powerful tool for direct investigation of structures, electronic properties, and interactions at the atomic scale. Here, we report on two different designs of such TEM-STM as well as an extension with an atomic force microscope (TEM-AFM). In the first TEM-STM design, a stepper motor, combined with a one-dimensional inertial slider, was used to perform the coarse approach. The advantage of this design was the strong pulling force that enabled notched metallic wires to be broken inside the TEM, which lead to clean sample surfaces. A second design, with a three-dimensional inertial slider, allowed lateral motion inside the TEM, which simplified the adjustment of tip location on the sample. By replacing the STM tip with a standard AFM-cantilever chip, a new combination was demonstrated: TEM-AFM. Here the force was simply measured by direct TEM imaging of the motion of the AFM tip. Some experimental results are included to illustrate the capabilities of TEM-STM and TEM-AFM.     

Tribological behavior of micro/nano-patterned surfaces in contact with AFM colloidal probe

In effort to investigate the influence of the micro/nano-patterning or surface texturing on the nanotribological properties of patterned surfaces, the patterned polydimethylsiloxane (PDMS) surfaces with pillars were fabricated by replica molding technique. The surface morphologies of patterned PDMS surfaces with varying pillar sizes and spacing between pillars were characterized by atomic force microscope (AFM) and scanning electron microscope (SEM). The AFM/FFM was used to acquire the friction force images of micro/nano-patterned surfaces using a colloidal probe. A difference in friction force produced a contrast on the friction force images when the colloidal probe slid over different regions of the patterned polymer surfaces. The average friction force of patterned surface was related to the spacing between the pillars and their size. It decreased with the decreasing of spacing between the pillars and the increasing of pillar size. A reduction in friction force was attributed to the reduced area of contact between patterned surface and colloidal probe. Additionally, the average friction force increased with increasing applied load and sliding velocity.     

Staleya guttiformis attachment on poly(tert-butylmethacrylate) polymeric surfaces

The attachment behaviour of Staleya guttiformis DSM 11458^T on poly(tert-butyl methacrylate) (P(tBMA)) polymeric surfaces has been studied. The electrostatic charge of the S. guttiformis cell surface (measured as zeta potential via microelectrophoresis) was −43.18 mV. S. guttiformis cells appeared weakly hydrophilic as the water contact angle measured on lawns of bacterial cells was found to be 55 ± 4.9°. It was found that while attaching on P(tBMA) surfaces, S. guttiformis cells produced extracellular polymeric substances (EPS) as observed from atomic force microscopy (AFM) and scanning electron microscopy (SEM) analysis. The AFM high resolution imaging revealed the nano-topography of the ‘free’ (the EPS that is produced by the bacterial cells, but no longer directly attached to the cells) EPS associated on the cell surface and also found on P(tBMA) surface. The ‘free’ EPS exhibited granular structure with lateral dimensions of 30–50 nm and a vertical nano-roughness of 7–10 nm. Another type of the EPS secreted by S. guttiformis cells appeared as a hydogel substance, presumably polysaccharide that formed a biopolymer network that facilitated bacterial attachment.     

Modifying protein adsorption by layers of glutathione pre-adsorbed on Au(111)

Molecular interaction with metal surfaces raises fundamental questions regarding their binding tendency, their dispersion on the surface, as well as their conformation which may change their biological properties; addressing these questions, and being able to tune protein interactions, is of primary importance for the control of biointerfaces. In this study, one tripeptide, GSH (glu-cys-gly), was used to condition gold surfaces and thus influence the adsorption of bovine serum albumin (BSA). Depending on the pH value of the GSH solution, cationic, zwitterionic or anionic forms of the tripeptide could be stabilised on the surface, before interacting with BSA solutions. The amount of proteins was observed to depend both on the chemical state of the adsorbed underlying peptide and on the solvent of the protein solution, indicating an important role of electrostatic interactions upon protein adsorption. Moreover, atomic force microscopy (AFM), and synchrotron IR microscopy revealed a heterogeneous distribution of proteins on the GSH layer.     

Forced Air Plasma Treatment (FAPT) of Hybrid Wood Plastic Composite (WPC)–Fiber Reinforced Plastic (FRP) Surfaces

Forced atmospheric (air) plasma treatment (FAPT) was applied to wood plastic composite (WPC) and continuous glass fiber reinforced plastic (FRP) surfaces to improve their adhesive bonding properties. The FRP was composed of oriented continuous E-glass fibers in a polypropylene matrix, while the WPC was fabricated using wood flour, polypropylene and additives. The FAPT was applied using two levels of discharge length projected from the discharge head (2.5″ and 1″) to ionize the air, oxidize the surfaces and improve wettability. The treatment was performed by passing the electrode over either surface, five or ten times. Surface characterization consisted of thermodynamic (surface energy determination), chemical (X-ray photoelectron spectroscopy), mechanical (shear strength) and microscopic (atomic force microscopy (AFM)) analysis. The results indicate that the acid–base component of the surface energy for both WPC and FRP after FAPT correlates with an increase in wettability. X-ray photoelectron spectroscopy was performed on wood regions and non-wood regions of the WPC surfaces; the oxygen concentration increased to a larger extent in the non-wood regions. Bonding shear strength measurements indicated increases of 50% after FAPT on WPC surfaces (2.5″ discharge length, 1 pass) and up to 200% for the hybrid WPC–FRP. Atomic force microscopy measurements using a silicon tip probe showed increases in adhesive force interactions up to 56% on WPC surfaces post-FAPT.     

Quantitative atomic force microscopy with carbon monoxide terminated tips

Noncontact atomic force microscopy (AFM) has recently progressed tremendously in achieving atomic resolution imaging through the use of small oscillation amplitudes and well-defined modification of the tip apex. In particular, it has been shown that picking up simple inorganic molecules (such as CO) by the AFM tip leads to a well-defined tip apex and to enhanced image resolution. Here, we use the same approach to study the three-dimensional intermolecular interaction potential between two molecules and focus on the implications of using molecule-modified AFM tips for microscopy and force spectroscopy experiments. The flexibility of the CO at the tip apex complicates the measurement of the intermolecular interaction energy between two CO molecules. Our work establishes the physical limits of measuring intermolecular interactions with scanning probes.