Atomic force microscopy imaging and 3-D reconstructions of serial thin sections of a single cell and its interior structures

Atomic Force Microscopy to Study Cell Wall Mechanics in Plants

Atomic force microscopy (AFM) is an indentation technique used to reconstruct the topography of various materials and organisms. AFM can also measure the mechanical properties of the sample. In plants, AFM is applied to image cell wall structural details and measure the elastic properties in the outer cell walls. Here, I describe the use of high-resolution AFM to measure the elasticity of resin-embedded ultrathin sections of leaf epidermal cell walls. This approach allows to access the fine details within the wall matrix and eliminate the influence of the topography or the turgor on mechanical measurements. In this chapter, the sample preparation, AFM image acquisition, and processing of force curves are described. Altogether, these methods allow to measure the wall stiffness and compare different cell wall regions.

Visualization of internal in situ cell structure by atomic force microscopy

Light and electron microscopy have been used to study cell structure for many years, but atomic force microscopy is a more recent technique used to analyze cells, mainly due to the absence of techniques to prepare the samples. Isolated molecules or organelles, whole cells, and to a lesser extent in situ cell structure have been observed by different atomic force microscopy imaging modes. Here, we review efforts intended to analyze in situ the cell structures using approaches involving imaging of the surface of semithin sections of samples embedded in resin and sections prepared with an ultramicrotome. The results of such studies are discussed in relation to their implications to analyze the fine structure of organelles at the nanoscale in situ at enhanced resolution compared to light microscopy.

A Cryosectioning Technique for the Observation of Intracellular Structures and Immunocytochemistry of Tissues in Atomic Force Microscopy (AFM)

The use of cryosectioning facilitates the morphological analysis and immunocytochemistry of cells in tissues in atomic force microscopy (AFM). The cantilever can access all parts of a tissue sample in cryosections after the embedding medium (sucrose) has been replaced with phosphate-buffered saline (PBS), and this approach has enabled the production of a type of high-resolution image. The images resembled those obtained from freeze-etching replica electron microscopy (EM) rather than from thin-section EM. The AFM images showed disks stacked and enveloped by the cell membrane in rod photoreceptor outer segments (ROS) at EM resolution. In addition, ciliary necklaces on the surface of connecting cilium, three-dimensional architecture of synaptic ribbons, and the surface of the post-synaptic membrane facing the active site were revealed, which were not apparent using thin-section EM. AFM could depict the molecular binding of anti-opsin antibodies conjugated to a secondary fluorescent antibody bound to the disk membrane. The specific localization of the anti-opsin binding sites was verified through correlation with immunofluorescence signals in AFM combined with confocal fluorescence microscope. To prove reproducibility in other tissues besides retina, cryosectioning-AFM was also applied to elucidate molecular organization of sarcomere in a rabbit psoas muscle.

An atomic-force basis for the bacteriolytic effects of granulysin

While granulysin has been suggested to play an important role in adaptive immune responses against bacterial infections by killing pathogens, and molecular force for protein-protein interaction or protein-bacteria interaction may designate the specific functions of a protein, the molecular-force basis underlying the bacteriolytic effects of granulysin at single-molecule level remains unknown. Here, we produced and purified bactericidal domain of macaque granulysin (GNL). Our bacterial lysis assays suggested that GNL could efficiently kill bacteria such as Listeria monocytogenes. Furthermore, we found that the interaction force between GNL and L. monocytogenes measured by an atomic force microscopy (AFM) was about 22.5 pN. Importantly, our AFM-based single molecular analysis suggested that granulysin might lyse the bacteria not only through electrostatic interactions but also by hydrogen bonding and van der Waals interaction. Thus, this work provides a previous unknown mechanism for bacteriolytic effects of granulysin.

Elasticity of Human Embryonic Stem Cells as Determined by Atomic Force Microscopy

The expansive growth and differentiation potential of human embryonic stem cells (hESCs) make them a promising source of cells for regenerative medicine. However, this promise is off set by the propensity for spontaneous or uncontrolled differentiation to result in heterogeneous cell populations. Cell elasticity has recently been shown to characterize particular cell phenotypes, with undifferentiated and differentiated cells sometimes showing significant differences in their elasticities. In this study, we determined the Young’s modulus of hESCs by atomic force microscopy using a pyramidal tip. Using this method we are able to take point measurements of elasticity at multiple locations on a single cell, allowing local variations due to cell structure to be identified. We found considerable differences in the elasticity of the analyzed hESCs, reflected by a broad range of Young’s modulus (0.05-10 kPa). This surprisingly high variation suggests that elasticity could serve as the basis of a simple and efficient large scale purification/separation technique to discriminate subpopulations of hESCs.

Atomic force microscopy of isolated mitochondria

This chapter describes methods for isolating and imaging metabolically and toxicologically challenged mitochondria with atomic force microscopy. Mitochondria were isolated from rat dorsal root ganglia or brain and exposed to glucose or dinitrobenzene (DNB) to simulate the cellular environment of a diabetic animal that has been exposed to excess glucose or to DNB. It is one of only a few articles to present images of membrane structures, such as voltage-dependent, anion-selective channel pores, on intact organelles. The purpose of the chapter is not to report on the metabolic or toxic effects, but to communicate in more detail than a typical journal paper allows the methods used to image isolated organelles. We also provide a series images revealing the outer membrane and outer membrane pores. An image of an isolated nucleus as well as a set of notes written to avoid common pitfalls in isolation, labeling, and imaging is also included.

Tissue section AFM: In situ ultrastructural imaging of native biomolecules

Conventional approaches for ultrastructural high-resolution imaging of biological specimens induce profound changes in bio-molecular structures. By combining tissue cryo-sectioning with non-destructive atomic force microscopy (AFM) imaging we have developed a methodology that may be applied by the non-specialist to both preserve and visualize bio-molecular structures (in particular extracellular matrix assemblies) in situ. This tissue section AFM technique is capable of: i) resolving nm–µm scale features of intra- and extracellular structures in tissue cryo-sections; ii) imaging the same tissue region before and after experimental interventions; iii) combining ultrastructural imaging with complimentary microscopical and micromechanical methods. Here, we employ this technique to: i) visualize the macro-molecular structures of unstained and unfixed fibrillar collagens (in skin, cartilage and intervertebral disc), elastic fibres (in aorta and lung), desmosomes (in nasal epithelium) and mitochondria (in heart); ii) quantify the ultrastructural effects of sequential collagenase digestion on a single elastic fibre; iii) correlate optical (auto fluorescent) with ultrastructural (AFM) images of aortic elastic lamellae.

NSOM- and AFM-based nanotechnology elucidates nano-structural and atomic-force features of a Y. pestis V immunogen-containing particle vaccine capable of eliciting robust response

It is postulated that unique nanoscale proteomic features of immunogen on vaccine particles may determine immunogen-packing density, stability, specificity, and pH-sensitivity on the vaccine particle surface and thus impact the vaccine-elicited immune responses. To test this presumption, we employed near-filed scanning optical microscopy (NSOM)- and atomic force microscopy (AFM)-based nanotechnology to study nano-structural and single-molecule force bases of Yersinia pestis (Y. pestis) V immunogen fused with protein anchor (V-PA) loaded on gram positive enhancer matrix (GEM) vaccine particles. Surprisingly, the single-molecule sensitive NSOM revealed that approximately 90% of V-PA immunogen molecules were packed as high-density nanoclusters on GEM particle. AFM-based single-molecule force analyses indicated a highly stable and specific binding between V-PA and GEM at the physiological pH. In contrast, this specific binding was mostly abrogated at the acidic pH equivalent to the biochemical pH in phagolysosomes of antigen-presenting-cells in which immunogen protein is processed for antigen presentation. Intranasal mucosal vaccination of mice with such immunogen loaded on vaccine particles elicited robust antigen-specific immune response. This study indicated that high-density, high-stability, specific, and immunological pH-responsive loading of immunogen nanoclusters on vaccine particles could readily be presented to the immune system for induction of strong antigen-specific immune responses.

Atomic force microscope (AFM) combined with the ultramicrotome: a novel device for the serial section tomography and AFM/TEM complementary structural analysis of biological and polymer samples

A new device (NTEGRA Tomo) that is based on the integration of the scanning probe microscope (SPM) (NT-MDT NTEGRA SPM) and the Ultramicrotome (Leica UC6NT) is presented. This integration enables the direct monitoring of a block face surface immediately following each sectioning cycle of ultramicrotome sectioning procedure. Consequently, this device can be applied for a serial section tomography of the wide range of biological and polymer materials. The automation of the sectioning/scanning cycle allows one to acquire up to 10 consecutive sectioned layer images per hour. It also permits to build a 3-D nanotomography image reconstructed from several tens of layer images within one measurement session. The thickness of the layers can be varied from 20 to 2000 nm, and can be controlled directly by its interference colour in water. Additionally, the NTEGRA Tomo with its nanometer resolution is a valid instrument narrowing and highlighting an area of special interest within volume of the sample. For embedded biological objects the ultimate resolution of SPM mostly depends on the quality of macromolecular preservation of the biomaterial during sample preparation procedure. For most polymer materials it is comparable to transmission electron microscopy (TEM). The NTEGRA Tomo can routinely collect complementary AFM and TEM images. The block face of biological or polymer sample is investigated by AFM, whereas the last ultrathin section is analyzed with TEM after a staining procedure. Using the combination of both of these ultrastructural methods for the analysis of the same particular organelle or polymer constituent leads to a breakthrough in AFM/TEM image interpretation. Finally, new complementary aspects of the object's ultrastructure can be revealed.

Chondrocytes interconnecting tracks and cytoplasmic projections observed within the superficial zone of normal human articular cartilage--a transmission electron microscopy, atomic force microscopy, and two-photon excitation microscopy studies

The morphology of the normal human and rat articular cartilage was assessed using transmission electron microscopy (TEM), atomic force microscopy (AFM), and two-photon excitation (2PE) microscopy. Spurr-embedded sections from fixed human cartilage were simultaneously evaluated using TEM and AFM. The presences of tracks among the chondrocytes from the superficial zone of the cartilage were observed. In order to ratify the presence of interconnecting tracks among superficial zone chondrocytes, whole fixed human and rat cartilage, as well as fresh whole rat cartilage, were examined under the 2PE. In all cases, these tracks were observed. In addition, porous matrix, well-defined lacunae, and cytoplasmic projections anchored to the extracellular matrix (ECM) were also detected. We conclude that normal human and rat flattened superficial chondrocytes might be interconnected by tracks running through the ECM. In addition, cytoplasmic projections were observed anchored to the ECM. All these structures may possibly be related to cell/cell and ECM/chondrocytes signaling. Our findings provide new information that possibly will be of relevant importance for a more profound study of normal cartilage physiology and eventually, the pathogenesis of osteoarthritis.

Profiling TRA-1-81 antigen distribution on a human embryonic stem cell

Human embryonic stem (hES) cells hold great promise in regenerative medicine. Although hES cells have unlimited self-renewal potential, they tend to differentiate spontaneously in culture. TRA-1-81 is a biomarker of undifferentiated hES cells. Quantitative characterization of TRA-1-81 expression level in a single cell helps capture the "turn-on" signal and understand the mechanism of early differentiation. Here, we report on our examination of TRA-1-81 distribution and association on a hES cell membrane using an atomic force microscope (AFM). Our results suggest that aggregated distribution of TRA-1-81 antigen is characteristic for undifferentiated hES cells. We also evaluated the TRA-1-81 expression level at approximately 17,800 epitopes and approximately 700 epitopes per cell on an undifferentiated cell and a spontaneously differentiated cell, respectively. The method in this study can be adapted in examining other surface proteins on various cell types, thus providing a general tool for investigating protein distribution and association at the single cell level.

The investigation of Protein A and Salmonella antibody adsorption onto biosensor surfaces by atomic force microscopy

The investigation of Protein A and antibody adsorption on surfaces in a biological environment is an important and fundamental step for increasing biosensor sensitivity and specificity. The atomic force microscope (AFM) is a powerful tool that is frequently used to characterize surfaces coated with a variety of molecules. We used AFM in conjunction with scanning electron microscopy to characterize the attachment of protein A and its subsequent binding to the antibody and Salmonella bacteria using a gold quartz crystal. The rms roughness of the base gold surface was determined to be approximately 1.30 nm. The average step height change between the solid gold and protein A layer was approximately 3.0 +/- 1.0 nm, while the average step height of the protein A with attached antibody was approximately 6.0 +/- 1.0 nm. We found that the antibodies did not completely cover the protein A layer, instead the attachment follows an island model. Salt crystals and water trapped under the protein A layer were also observed. The uneven adsorption of antibodies onto the biosensor surface might have led to a decrease in the sensitivity of the biosensor. The presence of salt crystals and water under the protein A layer may deteriorate the sensor specificity. In this report, we have discussed the application and characterization of protein A bound to antibodies which can be used to detect bacterial and viral pathogens.

Optimization of specimen preparation of thin cell section for AFM observation

High resolution imaging of intracellular structures of ultrathin cell section samples is critical to the performance of precise manipulation by atomic force microscopy (AFM). Here, we test the effect of multiple factors during section sample preparation on the quality of the AFM image. These factors include the embedding materials, the annealing process of the specimen block, section thickness, and section side. We found that neither the embedding materials nor the temperature and speed of the annealing process has any effect on AFM image resolution. However, the section thickness and section side significantly affect the surface topography and AFM image resolution. By systematically testing the image quality of both sides of cell sections over a wide range of thickness (40-1000 nm), we found that the best resolution was obtained with upper-side sections approximately 50-100 nm thick. With these samples, we could observe precise structure details of the cell, including its membrane, nucleoli, and other organelles. Similar results were obtained for other cell types, including Tca8113, C6, and ECV-304. In brief, by optimizing the condition of ultrathin cell section preparation, we were able to obtain high resolution intracellular AFM images, which provide an essential basis for further AFM manipulation.

NSOM/QD-based nanoscale immunofluorescence imaging of antigen-specific T-cell receptor responses during an in vivo clonal Vγ2Vδ2 T-cell expansion

Nanoscale imaging of an in vivo antigen-specific T-cell immune response has not been reported. Here, the combined near-field scanning optical microscopy- and fluorescent quantum dot-based nanotechnology was used to perform immunofluorescence imaging of antigen-specific T-cell receptor (TCR) response in an in vivo model of clonal T-cell expansion. The near-field scanning optical microscopy/quantum dot system provided a best-optical-resolution (<50 nm) nano-scale imaging of Vgamma2Vdelta2 TCR on the membrane of nonstimulated Vgamma2Vdelta2 T cells. Before Ag-induced clonal expansion, these nonstimulating Vgamma2Vdelta2 TCRs appeared to be distributed differently from their alphabeta TCR counterparts on the cell surface. Surprisingly, Vgamma2Vdelta2 TCR nanoclusters not only were formed but also sustained on the membrane during an in vivo clonal expansion of Vgamma2Vdelta2 T cells after phosphoantigen treatment or phosphoantigen plus mycobacterial infection. The TCR nanoclusters could array to form nanodomains or microdomains on the membrane of clonally expanded Vgamma2Vdelta2 T cells. Interestingly, expanded Vgamma2Vdelta2 T cells bearing TCR nanoclusters or nanodomains were able to rerecognize phosphoantigen and to exert better effector function. These studies provided nanoscale insight into the in vivo T-cell immune response.

Atomic force microscopic investigation on the potential early intermediate stages of fibrillogenesis of fibronectin within fibrils

To date, a large number of literature have focused on the mechanisms of fibronectin (FN) fibril initiation and elongation, discovering many binding sites on FN molecules that are required for FN fibril growth. However, it is still poorly understood how FN fibrils widen while elongating. Here, single molecules and polymers, FN fibrillogenesis, and FN fibril bundles around cells have all been investigated visually using atomic force microscopy. We found that the formation of ring-shaped and beaded-filament-like FN aggregates may be two early intermediate stages of FN fibrillogenesis within the fibrils away from cells, perhaps involving in the FN fibril widening/bundling.

Long polymeric tips of atomic force microscopy for large biological samples

We show a new atomic force microscopy technique for obtaining high-resolution topographic images of large bio-samples. To obtain high-resolution topographic images for the samples, we fabricated a long polymeric tip with a small protrusion using two-photon adsorbed photo-polymerization techniques. The obtained tip length was over 50 microm, and the tip was used directly to visualize COS-1 and 293 cells. Compared with commercial tips, the long tip made it easier to obtain topographic images of the large cells. In the magnified topographic images, the sub-100-nm resolution was confirmed with the long tips. This long probe tip is expected to broaden large sample-related studies and applications in the future.

Nanotomography in the chemical, biological and materials sciences

Nanotomography is a technique of growing importance in the investigation of the shape, size, distribution and elemental composition of a wide variety of materials that are of central interest to investigators in the physical and biological sciences. Nanospatial factors often hold the key to a deeper understanding of the properties of matter at the nanoscale level. With recent advances in tomography, it is possible to achieve experimental resolution in the nanometre range, and to determine with elemental specificity the three-dimensional distribution of materials. This critical review deals principally with electron tomography, but it also outlines the power and future potential of transmission X-ray tomography, and alludes to other related techniques.

High-resolution solid modeling of biological samples imaged with 3D fluorescence microscopy

Optical-sectioning, digital fluorescence microscopy provides images representing temporally- and spatially-resolved molecular-scale details of the substructures of living cells. To render such images into solid models for further computational analyses, we have developed an integrated system of image acquisition, processing, and rendering, which includes a new empirical technique to correct for axial distortions inherent in fluorescence microscopy due to refractive index mismatches between microscope objective immersion medium, coverslip glass, and water. This system takes advantage of the capabilities of ultra-high numerical aperture objectives (e.g. total internal reflection fluorescence microscopy) and enables faithful three-dimensional rendering of living cells into solid models amenable to further computational analysis. An example of solid modeling of bovine aortic endothelial cells and their nuclei is presented. Since many cellular level events are temporally and spatially confined, such integrated image acquisition, processing, rendering, and computational analysis, will enable, in silico, the generation of new computational models for cell mechanics and signaling.

Membrane deformation of unfixed erythrocytes in air with time lapse investigated by tapping mode atomic force microscopy

Estimation of the time of death is one of the most important problems for forensic medicine and law. Physical and chemical postmortem changes are evaluated together while estimating the time of death. The pattern analysis of antemortem and postmortem bloodstains is one of the important parameters for forensic science, and cellular changes of blood cells can be useful for the quantitative assessment of the time of death. In this study, by successively investigating erythrocytes exposed in air on mica for 5 days using tapping mode atomic force microscopy (TM-AFM), we observed deformation of whole cell and membrane surface of unfixed erythrocytes with time lapse. We found that the time-dependent cellular changes occurred after exposure of erythrocytes in air for several days. At 0.5 days of exposure, fissures and cell shrinkage were observed. At 2.5 days of exposure, the emergence of nanometer-scale protuberances were observed and these protuberances increased in number with increasing time. The changes of cell shape and cell membrane surface ultrastructure can be used to estimate the time of death. Futhermore, smear-induced abnormal erythrocytes and immunostained erythrocytes were observed here. The need for more precise research is indicated, such as the correlation of membrane changes to intervals of less than 0.5 day of air exposure, and use of various substrates in addition to mica, including glass, metals, fabrics, among others, on which the bloodstains appear in crime scenes. The results of this research demonstrate the efficacy of AFM as a potentially powerful analytical tool in forensic science.