Nanostructural analysis of starch components by atomic force microscopy

Morphological and structural features of starch from potato (Solanum tuberosa) and rice (Oryza sativa) have been examined using atomic force microscopy. Amylose from potato and rice was observed in aggregated structures, which are suggested to be a result of retrogradation during sample preparation. The degrees of polymerization of amylose from potato and rice starches were calculated from the mean contour lengths of the observed structures to be approximately 1440 and 1860, respectively. Potato amylopectin appeared as a highly branched and extended molecule. Our results show that atomic force microscopy provides a useful method for examining the fine structural features and estimating the dimensions of starch molecules.     

Scanning tunnelling and atomic force microscopy performed with the same probe in one unit

The technique demonstrated here provides features of both scanning tunnelling microscopy (STM) and atomic force microscopy (AFM). The metallic probe acts to record current variations and sense forces from the same sample area simultaneously. Thus, separate images may be recorded, in registry. The collected data allows real space correlations between some electrical properties and the geometric structure of a sample surface. The same tip is used since the geometry and condition of the tip can effect the data recordings. Platinum alloys, tungsten and graphite tips have been employed successfully. An AFM lever can respond to surface contact forces, within the elastic limits of the sample, while electric current is sensed by the tip of the lever. The usefulness of this experimental procedure is tested here by an application to semiconducting samples of Ag-doped CdTe in air and in paraffin oil media.     

C-banding visualized by atomic force microscopy

C-banding is a method used for studying chromosome rearrangements near centromeres and for investigating polymorphisms. In human chromosomes, the C-bands are located at the centromere of all the chromosomes and the distal long arm of the Y chromosome. In this study, we aimed to detect the structural changes in chromosomes during the stages of C-banding by atomic force microscopy. We observed crater-like structures in the chromosomes after 2xSSC (saline sodium citrate) treatment and measured the relative difference between the heights of chromatid and centromere of the chromosomes. Results showed that the relative difference was 3 nm in chromosomes 1, 9, 16, and Y, whereas in the other chromosomes this value was 11.6 nm. After Giemsa staining, the relative difference increased by a factor of 16 in chromosomes 1, 9, 16, and Y. The other chromosomes showed no such increase, which is in accordance with our suggestion that nonhiston proteins associated with DNA in constitutive heterochromatin can make the constitutive heterochromatin resistant to C-banding.     

Adhesion artefacts in atomic force microscopy imaging

Artefacts that affect contrast and arise from adhesion forces in atomic force microscopy images of aramid fibres (both fresh and plasma-treated) are investigated. It is demonstrated that these stem not only from variations in the chemical composition of the surface but also from certain topographical features (which may appear hidden or enhanced in the images), resulting in changes in the lateral forces that are detected by the cantilever and are comparable to the vertical forces. It is also shown that both types of contribution to the forces can be uncoupled to yield images free from these artefacts, thus allowing more accurate quantitative measurements. These artefactual effects are also generally applicable to many other materials.     

Determination of a translocation chromosome by atomic force microscopy

Atomic force microscopy (AFM) has been used to study the translocation involving chromosomes 11 and 13. An amniocentesis procedure was performed at 18 weeks of pregnancy on a familial balanced translocation carrier mother whose karyotype was 46,XX,t(11;13) (q23;q34). After harvesting the tissue cultures, light microscopy studies (LM) have indicated that the fetus had the same translocation. A 0.3 microm gap region on the derivative chromosome 13 was determined by AFM; it was equivalent to a mid-sized G-band. The enhanced resolution of AFM with respect to its line measure analysis and three-dimensional image capture capability has allowed an extension and reconsideration of conclusions about chromosomal aberrations based on the study of LM preparations. In this manner, chromosomal disorders will be studied at nanoscale to help in the planning of new therapy strategies.     

Numerical chromosomal abnormalities detected by atomic force microscopy.

The numerical abnormalities of human metaphase chromosomes, fixed according to standard procedures for optical microscopy but not treated for banding, were detected by atomic force microscopy (AFM). High-resolution AFM imaging of chromosomes in trisomy 13, 21, and Klinefelter syndrome can be compared directly with the traditional optical image. The unbanded metaphase chromosomes, including the extra ones in trisomic patients showed a structural pattern very similar to G-banding. Comparison of AFM images with light microscopic data allows the identification of specific chromosomes, and images of chromosomes showing numerical and structural abnormalities can then be analysed.     

Ultrastructure of Trypanosoma cruzi revisited by atomic force microscopy

Most advances in atomic force microscopy (AFM) have been accomplished in recent years. Previous attempts to use AFM to analyze the organization of pathogenic protozoa did not significantly contribute with new structural information. In this work, we introduce a new perspective to the study of the ultrastructure of the epimastigote form of Trypanosoma cruzi by AFM. Images were compared with those obtained using field emission scanning electron microscopy of critical point dried cells and transmission electron microscopy of negative stained detergent-extracted and air-dried cells. AFM images of epimastigote forms showed a flagellum furrow separating the axoneme from the paraflagellar rod (PFR) present from the emergence of the flagellar pocket to the tip of the flagellum. At high magnification, a row of periodically organized structures, which probably correspond to the link between the axoneme, the PFR and the flagellar membrane were seen along the furrow. In the origin of the flagellum, two basal bodies were identified. Beyond the basal bodies, small periodically arranged protrusions, positioned at 400 nm from the flagellar basis were seen. This structure was formed by nine substructures distributed around the flagellar circumference and may correspond to the flagellar necklace. Altogether, our results demonstrate the importance of the application of AFM in the structural characterization of the surface components and cytoskeleton on protozoan parasites.     

Effect of aging on the morphology of bitumen by atomic force microscopy

Effect of aging on the morphology of bitumen was investigated. Two bitumens were aged according to the thin film oven test (TFOT), pressure aging vessel (PAV) test and ultraviolet (UV) radiation, respectively. The morphology of the binders before and after aging was characterized by atomic force microscopy. The physical properties and chemical compositions of the binders were also measured. The results showed that aging affected the bitumen morphology significantly. Aging increased the overall surface stiffness of the bitumen and made the bitumen surface more solid-like. The extent of these changes was dependent on aging conditions. TFOT decreased the contrast between the dispersed domains and the matrix, which contributed to the single-phase trend of the binders. The effect of PAV aging on morphology of the binders was dependent on the base bitumen. In one case, it further accelerated the single-phase trend of bitumen in comparison with that after TFOT. In the other case, it caused the phase separation of bitumen. In both cases, PAV aging increased the surface roughness of the binders obviously. As a result of UV aging, the contrast between the matrix phase and dispersed phase was increased due to the difference in sensitivity to UV radiation of the bitumen molecules, which caused or further promoted the phase separation in the binders. Regardless of the aging procedure carried out, a strong correlation was observed between the changes in morphology and physical properties as well as chemical compositions of the binders before and after aging.     

The mechanism of G-banding detected by atomic force microscopy

The morphologic changes occurring in human chromosomes during G-banding by trypsin treatment on the same metaphase were followed with the aid of an atomic force microscope (AFM). It was found that trypsin treatment alone caused a pattern of collapse in the chromosomes that was clearly dependent on the duration of trypsinization. The progressive pattern of collapse first indicated the loss of internal differentiation between chromatids, then bands, and finally all internal structures, except for edges running around the chromosomes' perimeter. When stained with Giemsa, the collapsed chromosomes partly regained their original form, and transverse ridges appeared that correspond to G-positive band regions. However, the treatment of fixed chromosomes with trypsin for 42 s diminished the chromosomal edges, and the z-dimensions could not be measured even with the subsequent application of Giemsa.     

Imaging of silkworm meiotic chromosome by atomic force microscopy

Although structural information of mitotic chromosomes has been accumulated, little information is available for meiotic chromosome structures. Here, we applied atomic force microscopy (AFM) to investigate the ultrastructures of the silkworm, Bombyx mori, meiotic pachytene chromosome in its native state with nanometer scale resolution. Two levels of DNA folding were observed on the meiotic chromosome surface, 50-70 nm granules, which were considered to be 30 nm chromatin fibers, and spherical protrusions of 400-600 nm, which were considered to be chromomeres and arranged on the surface of the chromosome parallel to the chromosome longitudinal axis. These observations suggested that AFM study is an excellent approach for obtaining information concerning the silkworm pachytene chromosome higher order structure.     

Polysaccharide properties probed with atomic force microscopy

In recent years, polysaccharides have been extensively studied using atomic force microscopy (AFM). Owing to its high lateral and vertical resolutions and ability to measure interaction forces in liquids at pico‐ or nano‐Newton level, the AFM is an excellent tool for characterizing biopolymers. The first imaging studies showed the morphology of polysaccharides, but gradually more quantitative image analysis techniques were developed as the AFM grew easier to use in aqueous liquids and in non‐contact modes. Recently, AFM has been used to stretch polysaccharides and characterize their physicochemical properties by application of appropriate polymer stretching models, using a technique called single‐molecule force spectroscopy. From application of such models as the wormlike chain, freely jointed chain, extensible‐freely jointed chain, etc., properties such as the contour length, persistence length and segment elasticity or spring constant can be calculated for polysaccharides. The adhesion between polysaccharides and surfaces has been quantified with AFM, and this application is particularly useful for studying polysaccharides on microbial and other types of cells, because their adhesion is controlled by biopolymer characteristics. This review presents a synthesis of the theory and techniques currently in use to probe the physicochemical properties of polysaccharides with AFM.     

Investigation of nanoparticles by atomic and lateral force microscopy

Metallic nanoparticles have been produced on vitreous carbon substrates by means of thermal evaporation. From pictures of the particles, made by a high-resolution scanning electron microscope (HRSEM), a semispherical shape is suggested due to the total mass of deposited material. Atomic force microscopy (AFM) has been applied to this sample in order to get direct topographic information. The AFM has been operated with normal and super tips, the latter having a smaller cone angle and radius, thus following more precisely the contours of an object. Simultaneously lateral-force microscopic (LFM) images have been recorded. Major differences between the contents of HRSEM- and AFM-images are considered, emphasizing the important influence of the tips' geometry. Both the AFM and LFM line scans have been compared with and have qualitatively agreed with those calculated under simplifying assumptions.     

Effect of glutaraldehyde fixation on bacterial cells observed by atomic force microscopy

Atomic force microscopy (AFM) is a promising microscopy technique that can provide high-resolution images of bacterial cells without fixation. Three species of bacteria, Xanthomonas campestris, Pseudomonas syringae, and Bacillus subtilis, were used in this study. AFM images were obtained from unfixed and glutaraldehyde-fixed cells, and cell height was measured. The mean height of bacterial cells prepared by fixation was higher than that of those prepared by nonfixation. However, the height changes were different between Gram-negative and Gram-positive bacteria: the mean height of two fixed Gram-negative bacteria, X. campestris and P. syringae, increased by 112.31 and 84.08%, respectively, whereas Gram-positive bacterium, B. subtilis, increased only by 38.79%. The results above indicated that glutaraldehyde fixation could affect the measured height of cells imaged by AFM; further more, the effect of glutaraldehyde fixation on the measured height of Gram-negative bacterial cells imaged by AFM seemed much more than on that of Gram-positive bacterial cells.     

Combined atomic force microscopy and scanning tunneling microscopy imaging of cross-sectioned GaN light-emitting diodes

Cross-sectional scanning tunneling microscopy (STM) was combined with atomic force microscopy (AFM) over the same area to characterize a cross-sectioned GaN light emitting diode. Because GaN is typically grown on a non-native substrate and also forms a wurtzite crystal structure, a cryogenic cleaving technique was developed to generate smooth surfaces. The depletion region surrounding the p-n junction was clearly identified using STM. Furthermore, by imaging under multiple sample biases, distinctions between the n-doped and p-doped GaN could be made.     

Quantitative analysis of EcoR1 methylase-DNA complex by atomic force microscopy

The EcoR1 methylase specifically recognize 5'-GA* ATTC-3' in DNA duplex. We directly applied atomic force microscopy (AFM) to investigate linear pBR322-EcoR1 methylase complexes and quantitatively analyzed the bend angles of linear pBR322-EcoR1 methylase complexes and the bound protein widths. In this study, we made a novel observation that DNA-EcoR1 methylase complexes exhibited two populations of conformation at recognition site: DNA bent an acute angle at the recognition site in the presence of one EcoR1 methylase monomeric molecule, while DNA bent an unacute angle at the recognition site and the complementary site on duplex DNAs in the presence of EcoR1 methylase dimer. The data indicated that the unacute angle state was the result of unique interactions between EcoR1 methylase and the recognition site and the complementary site on duplex DNAs, and suggested that the acute angle conformation could be an intermediate in the formation of the unacute angle state. Our works provide a detail insight into the DNA structural variations involved in EcoR1 methylase-binding processes and demonstrate further the versatility of AFM as an imaging technique for studying the interaction between large DNA fragment and protein.     

Frictional effects in atomic force microscopy of Langmuir-Blodgett films

Frictional effects in atomic force microscopy (AFM) of Langmuir-Blodgett films of 1, 2-dipalmitoyl-snglycero-phosphoglycerol were examined. Height measurements of the Langmuir layers are strongly influenced by the orientation of the cantilevers used in AFM relative to the sample. A simple model is used to describe the frictional effects and to calculate the real height of the monolayers.     

Bitumen morphologies by phase-detection atomic force microscopy

Bitumen is a complex mixture of hydrocarbons for which microstructural knowledge is incomplete. In an effort to detail this microstructure, 13 bitumens were analysed by phase‐detection atomic force microscopy. Based on morphology, the bitumens could be classified into three distinct groups. One group showed fine domains down to 0.1 µm, another showed domains of about 1 µm, and a third group showed up to four different domains or phases of different sizes and shapes. No correlation was found between the atomic force microscopy morphology and the composition based on asphaltenes, polar aromatics, naphthene aromatics and saturates. A high correlation was found between the area of the ‘bee‐like’ structures and the vanadium and nickel content in bitumen, and between the atomic force microscopy groups and the average size of molecular planes made of fused aromatics. The morphology and the molecular arrangements in bitumen thus appear to be partly governed by the molecular planes and the polarity defined by metallic cations.     

Performance of a tilt-compensating tube scanner in atomic force microscopy

A tube scanner is constructed which avoids tilting of the sample surface when areas at some distance off the tube axis are scanned. Such tilt occurs with conventional piezo tubes, causes distorted vertical scaling, and limits the field of view to a few μm. These problems are partly overcome with a new design, which also uses a single tube, but with eight-segmented electrodes. It can be thought of being constructed of two four-segmented, conventional tubes, with the x- and y-sections in the two parts being connected crosswise. While no additional voltage supply is needed, the tube is forming an s-like shape, such that the bending of one half of the tube is compensated by a similar bending, but in the opposite direction, of the other half. Moreover, the displacement of the sample surface in z-direction can be compensated quantitatively by suitable compression or dilatation of the tube, which can always be calculated from the known lateral displacement of the axis. The performance of this scanner is demonstrated on steps of a calibration replica.     

Scanning electron microscopy studies of protein-functionalized atomic force microscopy cantilever tips

Protein-functionalized atomic force microscopy (AFM) tips have been used to investigate the interaction of individual ligand-receptor complexes. Herein we present results from scanning electron microscopy (SEM) studies of protein-functionalized AFM cantilever tips. The goals of this study were (1) to examine the surface morphology of protein-coated AFM tips and (2) to determine the stability of the coated tips. Based on SEM images, we found that bovine serum albumin (BSA) in solution spontaneously adsorbed onto the surface of silicon nitride cantilevers, forming a uniform protein layer over the surface. Additional protein layers deposited over the initial BSA-coated surface did not significantly alter the surface morphology. However, we found that avidin-functionalized tips were contaminated with debris after a series of force measurements with biotinylated agarose beads. The bound debris presumably originated from the transfer of material from the agarose bead. This observation is consistent with the observed deterioration of functional activity as measured in ligand-receptor binding force experiments.     

Bituminous emulsions and their characterization by atomic force microscopy

We present a new method for observing oil-in-water emulsions with a continuous water phase and a dispersed bitumen phase. The fine polydispersed bitumen micelles were adsorbed to an atomically smooth mica substrate and imaged in solution by atomic force microscopy in a liquid cell. The height of the adsorbed bitumen sheet in wet and dry states can be measured and the homogeneity of film formation by coalescence can be determined. Localization of surfactant onto and between bitumen micelles is also visualized.