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The combined use of fluorescence microscopy with atomic force microscopy (AFM) has been introduced to analyze the replication-banding patterns of human chromosomes. Human lymphocytes synchronized with excess thymidine are treated with 5-ethynyl-2'-deoxyuridine (EdU) during the late S phase. EdU-labeled DNA is detected in metaphase chromosomes using Alexa Fluor 488(®) azide, through the 1,3-dipolar cycloaddition reaction of organic azides with the terminal acetylene group of EdU. Chromosomes with EdU incorporated during the late S phase show a banding pattern similar to the G-banding pattern of normal human chromosomes. The comparison between the fluorescence and AFM image of the same chromosome indicates the presence of ridges and grooves in the chromatid arms, which correspond to G-positive and G-negative bands, respectively. This technique of EdU-labeled replication bands combined with AFM is useful to analyze the structure of chromosomes in relation to the banding pattern.

The atomic force microscope (AFM) has been widely used for surface fabrication and manipulation. However, nanomanipulation using a conventional AFM is inefficient because of the sequential nature of the scan-manipulation scan cycle, which makes it difficult for the operator to observe the region of interest and perform the manipulation simultaneously. In this paper, a nanomanipulation technique using a high-speed atomic force microscope (HS-AFM) is described. During manipulation using the AFM probe, the operation is periodically interrupted for a fraction of a second for high-speed imaging that allows the topographical image of the manipulated surface to be periodically updated. With the use of high-speed imaging, the interrupting time for imaging can be greatly reduced, and as a result, the operator almost does not notice the blink time of the interruption for imaging during the manipulation. This creates a more intuitive interface with greater feedback and finesse to the operator. Nanofabrication under real-time monitoring was performed to demonstrate the utility of this arrangement for real-time nanomanipulation of sample surfaces under ambient conditions. Furthermore, the HS-AFM is coupled with a haptic device for the human interface, enabling the operator to move the HS-AFM probe to any position on the surface while feeling the response from the surface during the manipulation., (Copyright © 2013 Elsevier B.V. All rights reserved.)

We introduce a compact nanomanipulator that can be operated inside the sample chamber of a scanning electron microscope (SEM) for biological sample manipulation. The design of the nanomanipulator is based on that of an atomic force microscope (AFM). A self-sensitive cantilever is used to realize the compact body and thus it is possible to put a pair of the standalone AFM units on the sample stage in the SEM chamber. Using this system, we accomplished nanodissection of biological samples as well as AFM imaging under SEM observation. We then fabricated the surface of a rat renal glomerulus by scan-scratching and succeeded in making a small hole on the wall of a blood capillary. As a result, it was possible to observe the internal structure of the capillary, which had been hidden beneath the surface wall. Furthermore, using two AFM units on the sample stage of the SEM, we successfully dissected the lens fiber cells taken from a rat eye in a multi-probe operation using the two cantilevers. This system is expected to become a very useful tool for micro- and nanometer-scale anatomy and engineering applications.

Methods for atomic force microscopy (AFM) imaging of human metaphase chromosomes were -introduced in the present study. Chromosomes from the lymphocytes were fixed and prepared onto glass slides as the chromosome spread, and observed in phosphate-buffered saline by dynamic mode AFM. On the contrary, chromosomes from the human cell line BALL-1 were isolated using the hexylene glycol method, absorbed onto a silane-coated glass slide, and observed in a hexylene glycol buffer solution by dynamic mode AFM. AFM provides three-dimensional topographic images of both fixed and unfixed human chromosomes with height information. The ultrastructural image of a pair of chromatids was also obtained by AFM in a liquid condition. The combined use of the AFM and light microscopy of cytochemically and/or immunocytochemically stained chromosomes is also expected to be useful for studies on the localization of chemical components in relation to the higher-order structure of the chromosomes.

The relationship between the higher-order structure of human metaphase chromosomes and the distribution of topoisomerase IIα was analyzed by a comparison of atomic force microscope (AFM) and fluorescence microscope images of the same chromosome. AFM imaging of chromosomes in liquid revealed the presence of alternating ridges and grooves on the surfaces of the sister chromatids. In contrast, the fluorescence image of the chromosomes stained with the anti-topoisomerase IIα antibody showed that the fluorescence intensity of topoisomerase IIα was not uniform and that there were alternating strong and weak spots along the chromosome axes. A comparison of the AFM image with a fluorescence microscope image of the same chromosome further demonstrated that ridges and grooves corresponded to strong and weak fluorescence intensities of topoisomerase IIα, respectively. These findings suggest that the distribution of topoisomerase IIα has a close connection with the higher-order structure of human metaphase chromosomes.

We developed a novel nano manipulator based on an atomic force microscope (AFM) that can be operated inside the sample chamber of a scanning electron microscope (SEM). This AFM manipulator is also coupled with a haptic device, and the nanometer-scale movement of the AFM cantilever can be scaled up to the millimeter-scale movement of the pen handle of the haptic device. Using this AFM manipulation system, we were able to observe the AFM cantilever and samples under the SEM and obtain topographical images of the AFM under the SEM. These AFM images contained quantitative height information of the sample that is difficult to obtain from SEM images. Our system was also useful for positioning the cantilever for accurate AFM manipulation because the manipulation scene could be directly observed in real time by SEM. Coupling of the AFM manipulator with the haptic device was also useful for manipulation in the SEM since the operator can move the AFM probe freely at any position on the sample surface while feeling the interaction force between the probe and the sample surface. We tested two types of cutting methods: simple cutting and vibration cutting. Our results showed that vibration cutting with probe oscillation is very useful for the dissection of biological samples which were dried for SEM observation. Thus, cultivated HeLa cells were successfully micro-dissected by vibration cutting, and the dissection process could be observed in real time in the SEM. This AFM manipulation system is expected to serve as a powerful tool for dissecting various biological samples at the micro and nanometer-scale under SEM observation.

The present study introduces the principle of atomic force microscopy (AFM) and reviews our results of human metaphase chromosomes obtained by AFM. AFM imaging of the chromosomes revealed that the chromatid arm was not uniform in structure but had ridges and grooves along its length, which was most prominent in the late metaphase. The arrangement of these ridges and grooves was roughly symmetrical with the counterpart of the paired sister chromatids. AFM imaging of banded chromosomes also showed that the ridges and grooves were related to the G/Q-positive and G/Q-negative bands, respectively. At high magnification, the chromatid was seen to be produced by the compaction of highly twisted chromatin fiber loops, and its compaction tended to be stronger in the ridged regions of the chromosomes than in the grooved regions. Our AFM studies also showed the presence of catenation of chromatin fibers between the ridged portions of the chromatid in the late metaphase. Thus, AFM is useful for obtaining the three-dimensional surface topography not only in ambient conditions but also in physiological liquid conditions, and is expected to be an attractive tool for investigating the structure of chromosomes.

The present study introduces a method for obtaining three-dimensional images of native (i.e., unfixed) chromosomes by atomic force microscopy (AFM) in a liquid. Human metaphase chromosomes were isolated from a human lymphoblast-like cell line, K562, by the hexylene glycol procedure according to Wray and Stubble- field (1970), adsorbed on a silane-coated glass slide, and observed in a dynamic force mode (i.e., intermittent contact mode) of AFM in a hexylene buffer solution. In adequate operating conditions, the shape of chromosomes with paired chromatids was clearly and three-dimensionally observed by AFM. At high magnification, globular or fibrous structures about 50 nm thick could be found on the surface of each chromaid, implying that chromatin fibers were strongly wound or twisted in the chromatid. Thus, AFM imaging enabled the direct visualization of native chromosomes in a liquid at high resolution--which is comparable with that of scanning electron microscopy--and can serve to analyze the mechanism of chromosome condensation and separation in relation to the structure of chromosomes.

Human metaphase chromosomes were observed using an intermittent contact mode of atomic force microscopy (AFM) in a phosphate-buffered saline solution to clarify their conformation close to that in the physiological state. In the AFM images in liquid, symmetric alternating ridges and grooves were evident on their surface of the paired sister chromatids. The number of the ridges and grooves were rather specific to the type of the chromosome. The structural changes of chromosomes caused by trypsin treatment were also directly observable using AFM in liquid. These results suggest that the intermittent contact mode AFM is useful not only for analyzing the structure of chromosomes in a liquid condition but also for studying the effect of chemical treatments on chromosomes in relation to their structural changes., (Copyright 2004 S. Karger AG, Basel)

The present study applied scanning near field optical/atomic force microscopy (SNOM/AFM) to the observation of human chromosomes immunostained with an anti-BrdU antibody after incorporation of BrdU into DNA. Human lymphocytes were cultured in BrdU for 72 h and their chromosomes were prepared with a standard method for light microscopy. After additional fixation with 15% formalin in phosphate buffered saline, the specimens were denatured with 2N HCI with 0.1% Triton-X 100, immunostained with the anti-BrdU antibody, and observed both by fluorescence microscopy and by SNOM/AFM. The preparation technique used in the present study enabled the differential staining of sister chromatids in each chromosome, and sister chromatid exchanges (SCEs) were recognized in some chromosomes of the metaphase spread. Observations of the specimens by SNOM/AFM further provided the simultaneous collection of topographical and fluorescent images of the same portions of BrdU-incorporated chromosomes. The resolution of the fluorescence images by SNOM/AFM was greater than that obtained by fluorescence microscopy. Superimposition of topographical and fluorescent images of the chromosomes is useful for the precise analysis of the fine structure of chromosomes in relation to the SCEs. The application of SNOM/AFM to the BrdU-incorporated chromosomes is thus useful for the analysis of the fine structure of chromosomes in relation to their function.

Studies on the structure of the human chromosome were reviewed from the histological perspective and discussed in connection with our recent findings obtained mainly by atomic force microscopy (AFM). In this paper, we introduce several hitherto known models of the high-order structure of the metaphase chromosome and discuss the actual structure of chromosomes in relation to such structures as spiral chromatids, chromosome bands, and chromosome scaffolds. In chromosomes treated with Ohnuki's hypotonic solution, the chromosome arms were elongated and showed a characteristic spiral pattern of chromatid fibers. On the other hand, alternating transverse ridges and grooves were clearly observed on the surface of chromosomes treated with 0.025% trypsin for G-banding, and these ridges and grooves corresponded to the dark and pale bands of G-banded chromosomes. Similar findings were also found in chromosomes treated with quinacrine mastards for Q-banding. Fibers bridging the gap between the sister chromatids were often observed in G/Q-banded chromosomes; these fibers tended to be restricted within the G/Q-positive portions, suggesting the presence of chromatin fibers bridging these regions. Based on these findings in conjunction with previous studies, we outlined the high-order structure of the human chromosome. Recent advances in nanotechnology have provided new AFM techniques for the imaging and handling of materials at nano-scale resolution. Application of these techniques to chromosome research is expected to provide valuable information on the chromosome structure in relation to its function.

Topographic and fluorescent images of whole barley chromosomes stained with YOYO-1 were observed simultaneously by scanning near-field optical/ atomic force microscopy (SNOM/AFM). The chromosome was relatively smooth and flat in the topographic images and no significant difference in height was present between regions of high fluorescent and low fluorescent intensity in the chromosomes. The telomeric region, labeled by fluorescence in situ hybridization (FISH) method, was also observed by SNOM/AFM at high resolution, and fluorescent signals of the telomeric region were clearly defined on the topographic image of chromatin fibers on the chromosome at the nano-meter scale level. Although the telomeric signals were usually visualized as a single fluorescent region at the end of sister chromatids by conventional light microscopy, they were observed separately as two fluorescent regions, less than 100-200 nm distance, using the SNOM/AFM. The SNOM/AFM offers great potential in identifying particular single gene location on chromosomes in the near future.

The present study was performed to introduce a novel chromosome dissection method employing atomic force microscopy (AFM) in a dynamic force mode for the chemical or molecular biological analysis of tiny chromosomal fragments. After AFM observation of human chromosomes prepared for light microscopy, a region of interest was dissected by increasing the loading force in a series of single-line scans of the target portion by controlling it with the amplitude reference of the tip in a dynamic force mode. The marker gene of the nucleolar organizing region (NOR) was amplified by our designed primers for 5.8S ribosomal DNA. After the dissection, topographic profiles in the section were then obtained with a carbon nanotube (CNT) probe in ambient condition. These results are discussed in relation to a fundamental technology for chromosomal analysis.

Purpose: We attempted to analyze the three-dimensional ultrastructure of human corneal and scleral collagen fibrils with an atomic force microscope (AFM)., Methods: A normal eye removed from a 66-year-old male patient during therapy was used in this study. Suspended corneal and scleral collagen fibrils were individually attached to glass slides by centrifugation. These collagen fibrils were air-dried and observed with a noncontact-mode AFM in air., Results: AFM imaging provided information on the surface topography of both corneal and scleral collagen fibrils. The corneal collagen fibrils had a height of 11.9 +/- 1.0 nm (mean +/- SD) and scleral fibrils a height of 82.5 +/- 35.6 nm. A periodic banding pattern of grooves and ridges was clearly found on both types of fibrils; the D-periodicity and the groove depth were 65.7 +/- 0.8 nm and 1.46 +/- 0.50 nm in the corneal fibrils, and 67.3 +/- 1.1 nm and 6.16 +/- 1.23 nm in the scleral fibrils., Conclusions: Surface topographic images of human corneal and scleral collagen fibrils were clearly obtained with the AFM. This technique provides quantitative information on the surface morphology of the collagen fibrils at high resolution.

The structure of G-bands in human metaphase chromosomes was analyzed by comparison between light microscopic and atomic force microscopic (AFM) images of the same chromosomes. G-bands of the chromosomes were made by trypsin treatment followed by staining with a Giemsa solution. The banded chromosomes examined by light microscopy were dried either in air or in a critical point-drier, and observed by non-contact mode AFM. Air-dried chromosomes after G-band staining showed alternating ridges and grooves on their surface, which corresponded to light-microscopically determined G-positive and G-negative bands, respectively. At high magnification, the G-positive ridges were composed of densely packed chromatin fibers, while the fibers were loose in the G-negative grooves. Fibers bridging the gap between sister chromatids of a mitotic pair were often found, especially in the G-positive portions. These findings suggest that the G-banding pattern reflects the high-order structure of human metaphase chromosomes.

The atomic force microscope (AFM), invented in 1986, is a new instrument which provides three-dimensional surface images of samples by scanning a sharp probing tip over the sample surface. Unlike electron microscopes (EM), the AFM has the advantage to obtain high-resolution pictures not only in a vacuous but also in a non-vacuous (i.e., air or liquid) environment. This paper reviews our recent studies on the AFM application to the biomedical fields. AFM is useful for observing biological structures such as DNA, collagen molecules, collagen fibrils and chromosomes. AFM images of living cultured cells in liquid can be used for investigating the movement of cellular processes in relation to subcellular cytoskeletal elements. Recently, numerous AFM-related microscopes, or scanning probe microscopes (SPM), have been invented in parallel with the development of the AFM itself. These microscopes allow the simultaneous collection of topographical and other (e.g., viscoelastic, near-field optical) images of samples in the same portions. Thus, the combination of AFM and the other SPM has great potential for providing valuable new findings on structure and function of cells and tissues.

Atomic force microscopy (AFM) was performed for the analysis of the fine structure of rice starch granules in the nanometre scale which were prepared by a physical destruction method. The present study directly demonstrated that fine particles of approximately 30 nm in diameter were present inside each granule and occasionally formed straight chain arrangements. We considered that these fine particles correspond to the individual single cluster in the cluster model which has been proposed in previous studies on the starch granule structure.

Using the force modulation mode in atomic force microscopy, we have succeeded in capturing time-lapse viscoelastic images of living mouse fibroblasts (NIH3T3) for several hours in a physiological condition without damaging the fibroblasts. Elongation of the lamellipodia and swelling of blebs were observed in time-lapse topographic images, which were taken every 10 min. The corresponding viscoelastic responses at a frequency of 600 Hz were visualized as consecutive images. The stiffer part of the cell body was fairly stable and did not show morphological changes for over 1 h. This is probably due to excess condensation of the actin network, hardening the cell cortex, and lowering the cytoskeletal activity. The nuclear portion of the cell body seems to be slightly less viscous than the peripheral region.

We examined the interior structure of exocytotic apertures in synaptic vesicles of neuroblastoma x glioma hybrid cells using atomic force microscopy. The atomic force microscopy detected apertures of 50-100nm in diameter at various depths within the varicosities of these cells. We were also able to image a regular radial pattern on the wall and lump-like structures at the bottom of these apertures. In contrast, scanning electron microscopy could only detect the apertures but not the fine details of their interior. The cells examined here exhibited the same electrophysiological properties and expression of synaptophysin and syntaxin 1 as presynaptic terminals, as studied by various electrophysiological and imaging techniques. Our results indicate that atomic force microscopy allows three-dimensional viewing of the fine structures located inside exocytotic apertures in nerve cells.

The present study was performed to analyse the structure of non-digested and digested collagen type I molecules by atomic force microscopy (AFM). Collagen type I molecules from the bovine skin were diluted with 0.05 N acetic acid, spread on a mica plate, air-dried and observed by non-contact mode AFM in air. Collagen molecules digested with Clostridium histolyticum collagenase were also examined by AFM. Intact collagen type I molecules were observed as twisted threads ranging mainly between 280 and 310 nm in length. The surface of the molecules was uneven and both ends usually slightly bulged like a globule. Depressions on the molecules were found throughout the length, and were most prominent approximately 70 nm from one end of the molecules. The collagenase-treated collagen molecules were degraded into fragments with various lengths, which corresponded to the data from sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis. The end of these fragments often appeared like a tuft, suggesting that the triple-helix unraveled at these regions.

The present paper describes the applicability of atomic force microscopy (AFM) to the observation of living cultured cells of an epithelial nature (human esophageal squamous cell carcinoma cells, or C7 subclone of KESC2 cells) in a culture medium. For this purpose, we made a fluid chamber system which allows a constant-speed perfusion of fluid at a regulated temperature in the chamber. Using this system, AFM images of living cells were successfully obtained for over one hour at time intervals of 2-4 min during continuous perfusion of the fresh culture medium. A series of these AFM images proved useful for examining the movements of cellular processes in relation to subcellular cytoskeletal elements. Time-lapse movie records produced by sequential AFM images further verify the reality of the cellular dynamics.

A new stable substrate applicable to the observation of DNA molecules by atomic force microscopy (AFM) was fabricated from a ultrasmooth sapphire (alpha-Al2O3 single crystal) plate. The atomically ultrasmooth sapphire as obtained by high-temperature annealing has hydrophobic surfaces and could not be used for the AFM observation of DNA. However, sapphire treated with Na3PO4 aqueous solution exhibited a hydrophilic character while maintaining a smooth surface structure. The surface of the wet-treated sapphire was found by x-ray photoelectron spectroscopy and AFM to be approximately 0.3 nm. The hydrophilic surface character of the ultrasmooth sapphire plate made it easy for DNA molecules to adhere to the plate. Circular molecules of the plasmid DNA could be imaged by AFM on the hydrophilic ultrasmooth sapphire plate.

This review briefly introduces the principles of the atomic force microscope (AFM) and shows our own results of AFM application to biological samples. The AFM, invented in 1986, is an instrument that traces the surface topography of the sample with a sharp probe while monitoring the interaction forces working between the probe and sample surface. Thus, the AFM provides three-dimensional surface images of the sample with high resolution. The advantage of the AFM for biologists is that AFM can visualize non-conductive materials in a non-vacuous (i.e., air or liquid) environment. AFM images of the plasmid DNA are comparable to those by transmission electron microscopy using a rotary shadowing technique, and have the advantage of examining directly the molecule without staining nor coating. The surface structure of human metaphase chromosomes and mouse collagen fibrils demonstrated in air by the non-contact mode AFM is comparable to that obtained by scanning electron microscopy. Quantitative information on the heights of structures is further obtainable from the AFM images. Embedment-free thin tissue-sections are useful for observing intracellular structures by AFM. The present review also shows AFM images of living cultured cells which have been collected in a contact mode in liquid. This technique afforded us three-dimensional observation of the cellular movement with high resolution. Although there are some innate limitations for AFM imaging, the AFM has great potential for providing valuable new information in histology and cytology.

We have developed scanning near-field optical/atomic force microscopy (SNOM/AFM). The SNOM/AFM uses a bent optical fiber simultaneously as a dynamic force AFM cantilever and a SNOM probe. Resonant frequency of the optical fiber cantilever is 15-40 kHz. Optical resolution of the SNOM/AFM images shows less than 50 nm. The SNOM/AFM system contains photon counting system and polychrometer/intensified coupled charge devise (ICCD) system to observe fluorescence image and spectrograph of micro areas, respectively. Cultured cells were stained with fluorescein isothiocyanate (FITC)-labeled anti-keratin antibody or FITC-labeled phalloidin after treatment with Triton X-100. Fluorescence and topographic images were obtained in air and water. The fluorescence images showed clear images of keratin and actin filaments. The SNOM/AFM is perfect to observe biomaterials in liquid with a liquid chamber while the topographic Images showed subcellular structures which correspond to keratin and actin filaments.

The atomic force microscope (AFM) was applied for the first time to embedment-free biological sections. Aldehyde-fixed tissues (kidney, liver etc.) of mice were postfixed with osmium tetroxide and cut into 500-700 nm thick sections after embedding of the tissue block in polyethylene glycol (PEG); the sections mounted on glass slides were deembedded and critical point-dried. The AFM images were collected in air from those tissue sections in a dynamic force mode. Solid-height-mode images, which were comparable to transmission electron microscope (TEM) images, seemed to provide us more useful information than the solid-mode images which resembled scanning electron microscope (SEM) images. Internal structures including chromatin fibers in the nuclei and cytoplasmic organelles were clearly recognizable by AFM. Minute surface structures including the end-feet of renal podocytes were demonstrated. We confirm that a vertical resolution of 0.1 nm and a lateral resolution of 5-10 nm are attainable with the dynamic force mode of AFM using thin sections of tissues. The present paper proposes the usefulness of AFM for observation of biological materials without metal coating in a non-vacuous environment.