Use Of Atomic Force Microscopy Research Articles

Review – Interactions between diatoms and stainless steel: focus on biofouling and biocorrosion

There is a considerable body of information regarding bacterially enhanced corrosion, however, this review focuses on diatoms (unicellular algae) whose contribution to biocorrosion is less well studied. The reasons why diatoms have been neglected in studies of biocorrosion in natural waters are discussed and the question whether diatoms should be considered as inert with respect of electrochemical processes is considered. A particular focus is given to the case of stainless steels (SS), which are widely used in variety of applications in natural waters. Basic information on the cell biology of diatoms is included in the review, particularly with respect to their ability to ‘sense’ and adhere to surfaces. Investigations at the nanoscale are reviewed as these studies provide information about the behavior of cells at interfaces. Recent advances include the use of atomic force microscopy (AFM), although only a few studies have been applied to diatoms. Regarding the electrochemical behavior of SS, the mechanisms by which diatoms influence the potential ennoblement process is discussed. Such studies reveal the association of diatoms, in addition to bacteria, with biocorrosion processes.

Effect of particle size on iron nanoparticle oxidation state

Selecting catalyst particles is a very important part of carbon nanotube growth, although the properties of these nanoscale particles are unclear. In this article iron nanoparticles are analyzed through the use of atomic force microscopy and x-ray photoelectron spectroscopy in order to understand how the size affects the chemical composition of nanoparticles and thus their physical structure. Initially, atomic force microscopy was used to confirm the presence of iron particles, and to determine the average size of the particles. Next an analytical model was developed to estimate particle size as a function of deposition time using inputs from atomic force microscopy measurement. X-ray photoelectron spectroscopy analysis was then performed with a focus on the spectra relating to the 2p Fe electrons to study the chemical state of the particles as a function of time. It was shown that as the size of nanoparticles decreased, the oxidation state of the particles changed due to a high proportion of atoms on the surface.

Dimerization of Nitrosobenzene Derivatives on an Au(111) Surface

In this study, we have investigated the ability of C-nitrosobenzenes to dimerize on an Au(111) surface and form ordered self-assembled bilayers (SABs). Use of scanning tunneling microscopy (STM) revealed that nitrosobenzene derivatives are able to form both well-ordered monolayers (SAMs) and bilayers (SABs). High-resolution STM images showed that within SAM regions molecules are arranged into hexagonal structures. Moiré-type superstructure with a periodicity of 1.5 nm was observed, indicating a 3√3 × 3√3 molecular arrangement. Molecularly resolved STM images showed that within bilayers molecules are also arranged into hexagonally ordered structures at intermolecular spacing of ∼0.4 nm. Furthermore, it was observed that the second layer is better ordered than the first one, probably because of the softer background. Use of atomic force microscopy (AFM), through measured height differences between monolayers and bilayers, further confirmed the formation of SABs. The results of the present study demonstrate that nitrosobenzenes represent convenient molecular models that can be used for systematic design and study of bilayers on metal surfaces. Besides the previously known properties of C-nitroso compounds to form dimers in crystals, here we have found a new situation under which these molecules dimerize, which is, in principle, a 2D crystallization.

Immunochemical properties and pathological relevance of anti- 2-glycoprotein I antibodies of different avidity

Despite available treatment, there is still significant morbidity and mortality present among patients with the autoimmune thrombophilic condition termed 'antiphospholipid syndrome' (Espinosa, G. and Cervera, R. 2009. Morbidity and mortality in the antiphospholipid syndrome. Curr. Opin. Pulm. Med. 15:413.). High-avidity (HAv) anti-β(2)-glycoprotein I (anti-β(2)GPI) antibodies, shown to correlate with thrombotic events in patients, could represent the much needed improved prognostic marker. By studying their effect on crystalline annexin A5 shield on phospholipid surfaces (one of proposed pathogenic mechanisms), with the use of atomic force microscopy, the pathogenic potential of HAv anti-β(2)GPI antibodies was confirmed. Furthermore, by using surface plasmon resonance and enzyme-linked immunosorbent assays, unique binding characteristics of HAv antibodies in comparison with low avidity antibodies were established. HAv anti-β(2)GPI were confirmed to (i) recognize β(2)-glycoprotein I in a solution, (ii) interact predominantly monovalently (much lower dependency on the antigen density) and (iii) form more stable complexes with the antigen. Since enzyme-linked immunosorbent assays currently used in routine diagnostics detect anti-β(2)GPI antibodies of unknown avidity, our observations are potentially useful for the development of improved diagnostic tests capable of detecting clinically relevant antibodies.

Contribution of AFM Observations to the Understanding of Ni<sub>3</sub>Al Yield Stress Anomaly

We report in the present paper a practical situation where the use of atomic force microscopy allowed an irrefutable insight in material plasticity for discriminating between different modelling hypotheses concerning the yield stress anomaly of Ni3Al intermetallic compounds with the L12 ordered structure. The contribution of AFM to a better understanding of elementary rate controlling mechanisms as well as collective dislocation motions is highlighted.

Nanostructurization in X-ray amorphous organic substances of geological origin

The nanosized structures of natural X-ray amorphous organic substances were examined with the use of atomic-force microscopy. The supramolecular structure types and particle sizes of natural solid bitumens from asphaltites to high anthraxolites were determined. It was shown that the supramolecular structure is suitable as a diagnostic structural criterion for grouping and subgrouping natural solid bitumens. Specific features of the nanostructure of Baltic amber were determined.

Addressing new analytical challenges in protein formulation development

As the share of therapeutic proteins in the arsenal of modern medicine continue increasing, relatively little progress has been made in the development of analytical methods that would address specific needs encountered during the development of these new drugs. Consequently, the researchers resort to adaptation of existing instrumentation to meet the demands of rigorous bioprocess and formulation development. In this report, we present a number of such adaptations as well as new instruments that allow efficient and precise measurement of critical parameters throughout the development stage. The techniques include use of atomic force microscopy to visualize proteinacious sub-visible particles, use of extrinsic fluorescent dyes to visualize protein aggregates, particle tracking analysis, determination of the concentration of monoclonal antibodies by the analysis of second-derivative UV spectra, flow cytometry for the determination of subvisible particle counts, high-throughput fluorescence spectroscopy to study phase separation phenomena, an adaptation of a high-pressure liquid chromatography (HPLC) system for the measurement of solution viscosity and a variable-speed streamlined analytical ultracentrifugation method. An ex vivo model for understanding the factors that affect bioavailability after subcutaneous injections is also described. Most of these approaches allow not only a more precise insight into the nature of the formulated proteins, but also offer increased throughput while minimizing sample requirements.

Quantitative analysis of human keratinocyte cell elasticity using atomic force microscopy (AFM).

We present the use of atomic force microscopy (AFM) to visualize and quantify the dynamics of epithelial cell junction interactions under physiological and pathophysiological conditions at the nanoscale. Desmosomal junctions are critical cellular adhesion components within epithelial tissues and blistering skin diseases such as Pemphigus are the result in the disruption of these components. However, these structures are complex and mechanically inhomogeneous, making them difficult to study. The mechanisms of autoantibody mediated keratinocyte disassembly remain largely unknown. Here, we have used AFM technology to image and measure the mechanical properties of living skin epithelial cells in culture. We demonstrate that force measurement data can distinguish cells cultured with and without autoantibody treatment. Our demonstration of the use of AFM for in situ imaging and elasticity measurements at the local, or tissue level opens potential new avenues for the investigation of disease mechanisms and monitoring of therapeutic strategies in blistering skin diseases.

Characterizing a Detergent-Like Commonality Among Antimicrobial Peptides with Structural and Mechanistic Differences

Largely distributed among living organisms, antimicrobial peptides are a class of small (<100 amino acid residues) host defense peptides that induce selective membrane lytic activity against microbial pathogens. The permeabilizing behavior of these diverse peptides has been commonly applied to the formation of pores, categorized as the barrel-stave, toroidal, or carpet type. With the continuing discovery of new peptide species, many are uncharacterized and the exact mechanism is unknown. Through the use of atomic force microscopy, we have previously shown that the disruption of mica supported lipid bilayer patches by protegrin-1, an 18-residue, cationic, beta sheet antimicrobial peptide isolated from pig leukocytes, is concentration dependent. The intercalation of antimicrobial peptide into the bilayer results in structures beyond that of pore formation including the observance of worm-like micelles. This suggests that antimicrobial peptide acts to lower the interfacial energy of the bilayer in a way similar to detergents. We pose that antimicrobial peptides act universally within a detergent-like mechanism in which pore formation is a small part of a much more complex phase diagram that spans peptide-lipid aggregates beyond that of lamellar bilayers. Antimicrobial peptides with structural and mechanistic differences have been studied and current results with magainin-1 and aurein 1.1 for example exhibit a mechanistic commonality. Future aspirations of antimicrobial peptides as new sources of antibiotics may be realized as a universal mechanism can streamline the synthesis of de novo designed peptides.

Monoclonal Antibody Aggregation Intermediates Visualized by Atomic Force Microscopy

Ubiquitous but highly variable processes of therapeutic protein aggregation remain poorly characterized, especially in the context of common infusion reactions and clinical immunogenicity. Among the numerous challenges is the characterization of intermediate steps that lead to the appearance of precipitates. Although the biophysical methods for elucidation of secondary and tertiary structures as well as overall size distribution are typically well established in the development laboratories, the use of molecular scale imaging techniques is still relatively rare due to low throughput and technical complexity. In this work, we present the use of atomic force microscopy to examine morphology of monoclonal antibody aggregates. Despite varying in primary structure as a result of different complementarity defining regions, most antibodies studied exhibited a similar aggregation intermediate consisting of several monomers. However, the manner of subsequent condensation of these oligomers appeared to differ between the antibodies, suggesting stability-dependent mechanisms.

Atomic Force Microscope nanolithography on chromosomes to generate single-cell genetic probes

BackgroundChromosomal dissection provides a direct advance for isolating DNA from cytogenetically recognizable region to generate genetic probes for fluorescence in situ hybridization, a technique that became very common in cyto and molecular genetics research and diagnostics. Several reports describing microdissection methods (glass needle or a laser beam) to obtain specific probes from metaphase chromosomes are available. Several limitations are imposed by the traditional methods of dissection as the need for a large number of chromosomes for the production of a probe. In addition, the conventional methods are not suitable for single chromosome analysis, because of the relatively big size of the microneedles. Consequently new dissection techniques are essential for advanced research on chromosomes at the nanoscale level.ResultsWe report the use of Atomic Force Microscope (AFM) as a tool for nanomanipulation of single chromosomes to generate individual cell specific genetic probes. Besides new methods towards a better nanodissection, this work is focused on the combination of molecular and nanomanipulation techniques which enable both nanodissection and amplification of chromosomal and chromatidic DNA. Cross-sectional analysis of the dissected chromosomes reveals 20 nm and 40 nm deep cuts. Isolated single chromosomal regions can be directly amplified and labeled by the Degenerate Oligonucleotide-Primed Polymerase Chain Reaction (DOP-PCR) and subsequently hybridized to chromosomes and interphasic nuclei.ConclusionsAtomic force microscope can be easily used to visualize and to manipulate biological material with high resolution and accuracy. The fluorescence in situ hybridization (FISH) performed with the DOP-PCR products as test probes has been tested succesfully in avian microchromosomes and interphasic nuclei. Chromosome nanolithography, with a resolution beyond the resolution limit of light microscopy, could be useful to the construction of chromosome band libraries and to the molecular cytogenetic mapping related to the investigation of genetic diseases.

Efficacy of smear layer removal by cavity cleaning solutions: an atomic force microscopy study

PURPOSE: To evaluate the efficacy of smear layer removal by cavity cleaning agents by the use of atomic force microscopy (AFM). METHODS: Five intact human third molars were sectioned in the coronal portion to obtain dentin disks, which were ground with 600-grit abrasive paper for 10 s. Serial longitudinal sections were made perpendicular to each other to create four specimens, from each tooth. The specimens were divided into four treatment groups: GI, 2% chlorhexidine; GII, calcium hydroxide solution; GIII, 1.23% fluoride solution; and GIV, 37% phosphoric acid. The solutions were applied with a brush for 60 s, with the exception of the 37% phosphoric acid, which was applied for 15 s and rinsed with distilled water for 60 s. The specimens were examined by AFM. RESULTS: All of the specimens in GI and GII showed 100% of the dentin tubules obliterated by the smear layer. However, all of the specimens in GIII and GIV showed 0% of the dentin tubules obliterated by the smear layer. CONCLUSION: The 1.23% fluoride solution was effective in removing the smear layer and can be used as a cavity cleanser.

Use of Atomic Force Microscope for Selection of the Best Synthetic Reverse Osmosis Membranes for Water Desalination

Use of Atomic Force Microscope for Selection of the Best Synthetic Reverse Osmosis Membranes for Water Desalination

The use of atomic force microscopy to study the pathologic effects of anti-annexin autoantibodies

Patients with recurrent pregnancy loss and a history of thrombotic events have often been noted to have autoantibodies directed at annexin A5. However, the relationship of these autoantibodies to immunopathology is still unknown, although it has been proposed that they have a direct effect on the function of annexin A5. Annexin A5 may be a significant immunological target with pathologic implications. Essentially, annexin A5 is an anticoagulant protein that crystallizes over negatively charged phospholipid surfaces and thereby blocks them from availability for coagulation reactions. To address this issue, we have taken advantage of our expertise with atomic force microscopy and studied anti-annexin A5 autoantibodies isolated from patients and focused on the ability of these antibodies to influence annexin A5 crystallization on planar mica-supported phospholipid bilayers. We report herein that such antibodies from patients, but not controls, produced a significant disruption of incomplete annexin A5 crystalline shield on phospholipid bilayer. In addition, the IgG fraction isolated from such patients significantly decreased the velocity of annexin A5 crystallization. Atomic force microscopy is a powerful tool to study the pathologic mechanisms of autoantibodies and the data herein reflect the potential of anti-annexin A5 antibodies that produce pathology in a number of varied but overlapping clinical conditions, including autoimmune thrombosis and antiphospholipid syndrome.

The Use of Atomic Force Microscopy to Study Crack Tips in Glass

This article presents a review of the application of atomic force microscopy (AFM) to crack-tip corrosion during subcritical crack growth in glass. The two principal experimental techniques used in this type of study are (1) the direct observation of crack motion by scanning the tip of a crack during crack growth and (2) the examination of fracture surfaces once the specimen has been fractured in two. The first technique has been used to demonstrate and quantify water condensation at crack tips during subcritical crack growth and is particularly useful at low crack velocities. The second technique has been used to quantify the crack-tip corrosion process and the shape of the crack tip during crack growth. In this article, we discuss experimental results showing that the environment that develops at the tips of freshly fractured glass surfaces in soda lime glass can corrode the glass surfaces near the crack tip. Soda lime silicate glass contains mobile alkali ions that will exchange with hydronium ions in solution at the crack tip, forming a highly basic solution that is corrosive to glass. Experimental evidence for such corrosion has been obtained by the atomic force microscope, which demonstrates a displacement of the two fracture surfaces near the crack tip that can be as much as 20 nm, depending on how long the crack is held open at the fatigue limit. Despite the corrosion and displacement of the crack surfaces, the crack tip itself appears to remain sharp, suggesting that the fatigue limit in soda lime silicate glass is not due to crack-tip blunting. Most likely, the fatigue limit is a consequence of ion exchange at the crack tip, in which hydronium ions in the crack-tip solution exchange with sodium ions in the glass. As hydronium ions are larger than sodium ions, this exchange process leaves a compressive stress within the fresh fracture surface of the glass that resists crack motion and results in a stress-corrosion fatigue limit, as first proposed by Bunker and Michalske. In agreement with this mechanism, no fatigue limit is observed for silica glass, which also exhibits no ion exchange. As the crack-tip solution in silica glass is only mildly acidic, pH ≈ 5, corrosion does not occur at crack tips of this glass as supported by the observation that no crack-tip displacements are observed in silica glass by AFM. As the proposed ion exchange mechanism used to explain the stress corrosion limit in glass is at variance with the belief that the fatigue limit in glass is the result of crack-tip blunting, we discuss the possibility of plastic deformation at crack tips in glass and conclude that the available experimental data does not support such a model. At the present time, chemical reaction based crack growth theories are most consistent with the body of crack growth data that is available on glass and are probably the best explanation for the phenomenon.

Macro- and Microstructure of Erythrocyte Membranes Under Acute Massive Hemorrhage and Subsequent Blood Reinfusion

The authors studied changes in erythrocyte membrane nanostructure using a rodent model of hemorrhagic hypotension and resuscitation. Both macro- and microstructural elements were examined using atomic force microscopy. Membrane "roughness" was characterized using spatial Fourier transformation and was stratified according to the periodicity of the membrane. Acute hemorrhage resulted in an increase in the diameter and height of erythrocytes, which returned to baseline levels by the end of the hemorrhagic hypotensive period. The effect of hypotension on the erythrocyte surface was nonuniform. In those regions where damage was considerable, the rate of restoration of the membrane microstructure to baseline levels was prolonged. The less damaged surfaces were restored more rapidly to control values after reperfusion. More detailed use of atomic force microscopy in the definition of the erythrocyte membrane microstructure may further define the mechanisms of cellular functional restoration after hemorrhage.

Coaxial Core Shell Overgrowth of Zeolite L − Dependence on Original Crystal Growth Mechanism

In this study, the first reported core−shell material combining zeolite L (LTL) and barium-exchanged zeolite L (Ba-LTL) is described. The use of atomic force microscopy to probe the LTL surface growth mechanism was employed to understand the growth pattern of the resultant Ba-LTL coaxial overgrowth layer. Additionally, the dependence of the original crystal surface on the resulting habit of the Ba-LTL core−shell layer is explained. High-resolution scanning electron microscopy (HRSEM) was employed to observe the fine detail of the Ba-LTL layer, and cross-sectional polishing was used to view the boundary between the two crystalline materials.

Use of atomic force microscopy to detect wavelength dependent changes in wood veneers, and spin coated lignin and cellulose films exposed to solar radiation

We examined whether spin coated lignin and cellulose films could act as material models for wood exposed to solar radiation. Films and wood were exposed to sunlight under filters that transmitted different parts of solar radiation. Changes in surface roughness, hardness and polarity of the films were analysed with atomic force microscopy and compared with those occurring on wood. All properties changed after exposure and the magnitude depended on the wavelength and substrate. The roughness of wood and lignin films increased after exposure, whereas it decreased on cellulose. The surface hardness of all three substrates increased more after exposure to less energetic radiation. Lignin films became more hydrophilic, whereas polarity changes of wood and cellulose were wavelength dependent. We conclude that lignin and cellulose films can act as material models for wood exposed to solar radiation and discuss how they might be used to develop new photoprotective wood treatments.

Atomic force microscopy study of DNA conformation in the presence of drugs

Binding of ligands to DNA gives rise to several relevant biological and biomedical effects. Here, through the use of atomic force microscopy (AFM), we studied the consequences of drug binding on the morphology of single DNA molecules. In particular, we quantitatively analyzed the effects of three different DNA-binding molecules (doxorubicin, ethidium bromide, and netropsin) that exert various pharmacologic and therapeutic effects. The results of this study show the consequences of intercalation and groove molecular binding on DNA conformation. These single-molecule measurements demonstrate morphological features that reflect the specific modes of drug-DNA interaction. This experimental approach may have implications in the design of therapeutically effective agents.

Imaging the nanoscale organization of peptidoglycan in living Lactococcus lactis cells

The spatial organization of peptidoglycan, the major constituent of bacterial cell-walls, is an important, yet still unsolved issue in microbiology. In this paper, we show that the combined use of atomic force microscopy and cell wall mutants is a powerful platform for probing the nanoscale architecture of cell wall peptidoglycan in living Gram-positive bacteria. Using topographic imaging, we found that Lactococcus lactis wild-type cells display a smooth, featureless surface morphology, whereas mutant strains lacking cell wall exopolysaccharides feature 25-nm-wide periodic bands running parallel to the short axis of the cell. In addition, we used single-molecule recognition imaging to show that parallel bands are made of peptidoglycan. Our data, obtained for the first time on living ovococci, argue for an architectural feature of the cell wall in the plane perpendicular to the long axis of the cell. The non-invasive live cell experiments presented here open new avenues for understanding the architecture and assembly of peptidoglycan in Gram-positive bacteria.