Nanoscale imaging of untreated mammalian cells in a medium with low radiation damage using scanning electron-assisted dielectric microscopy

Direct observation of the effects of chemical fixation in MNT-1 cells: A SE-ADM and Raman study

Aldehydes fixation was accidentally discovered in the early 20th century and soon became a widely adopted practice in the histological field, due to an excellent staining enhancement in tissues imaging. However, the fixation process itself entails cell proteins denaturation and crosslinking. The possible presence of artifacts, that depends on the specific system under observation, must therefore be considered to avoid data misinterpretation. This contribution takes advantage of scanning electron assisted-dielectric microscopy (SE-ADM) and Raman 2D imaging to reveal the possible presence and the nature of artifacts in unstained, and paraformldehyde, PFA, fixed MNT-1 cells. The high resolution of the innovative SE-ADM technique allowed the identification of globular protein clusters in the cell cytoplasm, formed after protein denaturation and crosslinking. Concurrently, SE-ADM images showed a preferential melanosome adsorption on the cluster's outer surface. The micron-sized aggregates were discernible in Raman 2D images, as the melanosomes signal, extracted through 2D principal component analysis, unequivocally mapped their location and distribution within the cells, appearing randomly distributed in the cytoplasm. Protein clusters were not observed in living MNT-1 cells. In this case, mature melanosomes accumulate preferentially at the cell periphery and are more closely packed than in fixed cells. Our results show that, although PFA does not affect the melanin structure, it disrupts melanosome distribution within the cells. Proteins secondary structure, conversely, is partially lost, as shown by the Raman signals related to α-helix, β-sheets, and specific amino acids that significantly decrease after the PFA treatment.

A Novel Approach for Identifying Nanoplastics by Assessing Deformation Behavior with Scanning Electron Microscopy

As plastic production continues to increase globally, plastic waste accumulates and degrades into smaller plastic particles. Through chemical and biological processes, nanoscale plastic particles (nanoplastics) are formed and are expected to exist in quantities of several orders of magnitude greater than those found for microplastics. Due to their small size and low mass, nanoplastics remain challenging to detect in the environment using most standard analytical methods. The goal of this research is to adapt existing tools to address the analytical challenges posed by the identification of nanoplastics. Given the unique and well-documented properties of anthropogenic plastics, we hypothesized that nanoplastics could be differentiated by polymer type using spatiotemporal deformation data collected through irradiation with scanning electron microscopy (SEM). We selected polyvinyl chloride (PVC), polyethylene terephthalate (PET), and high-density polyethylene (HDPE) to capture a range of thermodynamic properties and molecular structures encompassed by commercially available plastics. Pristine samples of each polymer type were chosen and individually milled to generate micro and nanoscale particles for SEM analysis. To test the hypothesis that polymers could be differentiated from other constituents in complex samples, the polymers were compared against proxy materials common in environmental media, i.e., algae, kaolinite clay, and nanocellulose. Samples for SEM analysis were prepared uncoated to enable observation of polymer deformation under set electron beam parameters. For each sample type, particles approximately 1 µm in diameter were chosen, and videos of particle deformation were recorded and studied. Blinded samples were also prepared with mixtures of the aforementioned materials to test the viability of this method for identifying near-nanoscale plastic particles in environmental media. Based on the evidence collected, deformation patterns between plastic particles and particles present in common environmental media show significant differences. A computer vision algorithm was also developed and tested against manual measurements to improve the usefulness and efficiency of this method further.

Development of General-purpose Dielectric Constant Imaging Unit for SEM and Direct Observation of Samples in Aqueous Solution

Electron microscopes can observe samples with a spatial resolution of 10 nm or higher; however, they cannot observe samples in solutions due to the vacuum conditions inside the sample chamber. Recently, we developed a scanning electron-assisted dielectric microscope (SE-ADM), based on scanning electron microscope, which enables the observation of various specimens in solution. Until now, the SE-ADM system used a custom-made SE-ADM stage with a built-in amplifier and could not be linked to the scanning electron microscopy (SEM) operation system. Therefore, it was necessary to manually acquire images from the SE-ADM system after setting the EB focus, astigmatism, and observation field-of-view from the SEM operating console. In this study, we developed a general-purpose dielectric constant imaging unit attached to commercially available SEMs. The new SE-ADM unit can be directly attached to the standard stage of an SEM, and the dielectric signal detected from this unit can be input to the external input terminal of the SEM, enabling simultaneous observation yielding SEM and SE-ADM images. Furthermore, 4.5 nm spatial resolution was achieved using a 10 nm thick silicon nitride film in the sample holder in the observation of aggregated PM2.5. We carried out the observation of cultured cells, PM2.5, and clay samples in solution.

Structural analysis of melanosomes in living mammalian cells using scanning electron-assisted dielectric microscopy with deep neural network

Melanins are the main pigments found in mammals. Their synthesis and transfer to keratinocytes have been widely investigated for many years. However, analysis has been mainly carried out using fixed rather than live cells. In this study, we have analysed the melanosomes in living mammalian cells using newly developed scanning electron-assisted dielectric microscopy (SE-ADM). The melanosomes in human melanoma MNT-1 cells were observed as clear black particles in SE-ADM. The main structure of melanosomes was toroidal while that of normal melanocytes was ellipsoidal. In tyrosinase knockout MNT-1 cells, not only the black particles in the SE-ADM images but also the Raman shift of melanin peaks completely disappeared suggesting that the black particles were really melanosomes. We developed a deep neural network (DNN) system to automatically detect melanosomes in cells and analysed their diameter and roundness. In terms of melanosome morphology, the diameter of melanosomes in melanoma cells did not change while that in normal melanocytes increased during culture. The established DNN analysis system with SE-ADM can be used for other particles, e.g. exosomes, lysosomes, and other biological particles.

Matrix Vesicle-Mediated Mineralization and Potential Applications

Hard tissues, including the bones and teeth, are a fundamental part of the body, and their formation and homeostasis are critically regulated by matrix vesicle-mediated mineralization. Matrix vesicles have been studied for 50 y since they were first observed using electron microscopy. However, research progress has been hampered by various technical barriers. Recently, there have been great advancements in our understanding of the intracellular biosynthesis of matrix vesicles. Mitochondria and lysosomes are now considered key players in matrix vesicle formation. The involvement of mitophagy, mitochondrial-derived vesicles, and mitochondria-lysosome interaction have been suggested as potential detailed mechanisms of the intracellular pathway of matrix vesicles. Their main secretion pathway may be exocytosis, in addition to the traditionally understood mechanism of budding from the outer plasma membrane. This basic knowledge of matrix vesicles should be strengthened by novel nano-level microscopic technologies, together with basic cell biologies, such as autophagy and interorganelle interactions. In the field of tissue regeneration, extracellular vesicles such as exosomes are gaining interest as promising tools in cell-free bone and periodontal regenerative therapy. Matrix vesicles, which are recognized as a special type of extracellular vesicles, could be another potential alternative. In this review, we outline the recent significant progress in the process of matrix vesicle-mediated mineralization and the potential clinical applications of matrix vesicles for tissue regeneration.

Giant Carbon Nano-Test Tubes as Versatile Imaging Vessels for High-Resolution and In Situ Observation of Proteins

Cryogenic electron microscopy is one of the fastest and most robust methods for capturing high-resolution images of proteins, but stringent sample preparation, imaging conditions, and in situ radiation damage inflicted during data acquisition directly affect the resolution and ability to capture dynamic details, thereby limiting its broader utilization and adoption for protein studies. We addressed these drawbacks by introducing synthesized giant carbon nano-test tubes (GCNTTs) as radiation-insulating materials that lessen the irradiation impact on the protein during data acquisition, physical molecular concentrators that localize the proteins within a nanoscale field of view, and vessels that create a microenvironment for solution-phase imaging. High-resolution electron microscopy images of single and aggregated hemoglobin molecules within GCNTTs in both solid and solution states were acquired. Subsequent scanning transmission electron microscopy, small-angle neutron scattering, and fluorescence studies demonstrated that the GCNTT vessel protected the hemoglobin molecules from electron irradiation-, light-, or heat-induced denaturation. To demonstrate the robustness of GCNTT as an imaging platform that could potentially augment the study of proteins, we demonstrated the robustness of the GCNTT technique to image an alternative protein, d-fructose dehydrogenase, after cyclic voltammetry experiments to review encapsulation and binding insights. Given the simplicity of the material synthesis, sample preparation, and imaging technique, GCNTT is a promising imaging companion for high-resolution, single, and dynamic protein studies under electron microscopy.

Understanding Complex Electron Radiolysis in Saline Solution by Big Data Analysis

In this article, we developed a new method to analyze the complex chemical reactions induced by electron beam radiolysis based on big data analysis. At first, we built an element transport network to show the chemical reactions. Furthermore, the linearity between the species was quantified by Pearson correlation coefficient analysis. Based on the analysis, the mechanism of the high linearity between the special species pairs was interpreted by the element transport roadmap and chemical equations. The time variation of the pH of the solution and bubble formation in the solution were analyzed by simulation and data analysis. The simulation indicates that O₂ and H₂ can easily oversaturate and form bubbles. Finally, the radiolysis of high-energy electrons in pure water was analyzed as a reference for the radiolysis of high-energy electrons in saline solution. This work provides a new method for investigating a high-energy electron radiolysis process and for simplifying a complex chemical reaction based on quantitative analysis of the species variation in the reaction.

Raman scattering enhancement of dielectric microspheres on silicon nitride film

Circulating light in the total internal reflection within dielectric spheres or disks is called the whispering gallery mode (WGM), which by itself is highly sensitive to its surface and capable of detecting viruses and single atomic ions. The detection site of the sensors using WGM is created by the evanescent light from the circulating light inside spheres. Here we report anomalous Raman scattering enhancement in dielectric microspheres on a silicon nitride (SiN) film. This Raman enhancement occurs at the periphery of the spheres, and a similar ring of light was also observed under a fluorescence microscope. This is caused by the light circulating around the dielectric spheres as in the WGM. We observed anomalously enhanced Raman spectrum at the periphery of 3 μm diameter polystyrene (PS) microspheres on a SiN film using confocal laser Raman microscopy. The wavelength intensity of this enhanced Raman spectrum was accompanied by periodic changes due to interference. These features may lead to the development of high-sensitive sensors and optical devices.

Opalescence Arising from Network Assembly in Antibody Solution

Opalescence of therapeutic antibody solutions is one of the concerns in drug formulation. However, the mechanistic insights into the opalescence of antibody solutions remain unclear. Here, we investigated the assembly states of antibody molecules as a function of antibody concentration. The solutions of bovine gamma globulin and human immunoglobulin G at around 100 mg/mL showed the formation of submicron-scale network assemblies. The network assembly resulted in the appearance of opalescence with a transparent blue color without the precipitates of antibodies. Furthermore, the addition of trehalose and arginine, previously known to act as protein stabilizers and protein aggregation suppressors, was able to suppress the opalescence arising from the network assembly. These results will provide an important information for evaluating and improving protein formulations.

Recovery of Au from dilute aqua regia solutions via adsorption on the lyophilized cells of a unicellular red alga Galdieria sulphuraria: A mechanism study

The high electrical conductivity, chemical stability, and low toxicity of elemental Au make it a highly valuable resource. However, wastewater produced during the mining, utilization, and disposal of Au inevitably contains small amounts (10-40 mg L^-1) of Au, thus posing environmental risks. It is too acidic to be treated with inexpensive and eco-friendly bioadsorbents previously studied for the remediation of less acidic effluents. Herein, lyophilized Galdieria sulphuraria cells are shown to directly adsorb Au from simulated Au-containing wastewater with a total acid concentration of 4 M, achieving an adsorption capacity of 35 ± 2.5 mg g^-1 Au after 30-min exposure and a selectivity that exceeds that of an ion-exchange resin and is comparable to that of activated carbon. Additionally, Au adsorbed on these cells is more easily eluted than that adsorbed on the ion-exchange resin or activated carbon. Detailed characterizations reveal that Au accumulates on the surface of lyophilized cells, where it is mainly present as AuCl₄^- and not as Au⁰, in contrast to a previously proposed adsorption mechanism. Thus, our work provides valuable insights into the mechanism of Au adsorption on biomaterials and paves the way to the cheap and eco-friendly recovery of Au from acidic wastewater.

Development of multi-frequency impedance scanning electron microscopy

Nanometre-scale observation of specimens in water is indispensable in many scientific fields like biology, chemistry, material science and nanotechnology. Scanning electron microscopy (SEM) allows high-resolution images of biological samples to be obtained under high vacuum conditions but requires specific sample-preparation protocols. Therefore, there is a need for convenient and minimally invasive methods of observing samples in solution. We have developed a new type of impedance microscopy, namely multi-frequency impedance SEM (IP-SEM), which allows nanoscale imaging of various specimens in water while minimising radiation damage. By varying the frequency of the input voltage signal of the sine wave, the present system can detect dielectric properties of the sample’s composition at nanometre resolution. It also enables examination of unstained biological specimens and material samples in water. Furthermore, it can be used for diverse samples in liquids across a broad range of scientific subjects such as nanoparticles, nanotubes and organic and catalytic materials.

Arginine and its Derivatives Suppress the Opalescence of an Antibody Solution

Opalescence is a problem concerned with the stability of an antibody solution. It occurs when a high concentration of a protein is present. Arginine (Arg) is a versatile aggregation suppressor of proteins, which is among the candidates that suppress opalescence in antibody solutions. Here, we investigated the effect of various types of small molecular additives on opalescence to reveal the mechanism of Arg in preventing opalescence in antibody solution. As expected, Arg suppressed the opalescence of the immunoglobulin G (IgG) solution. Arg also concentration dependently inhibited the formation of microstructures in IgG molecules. Interestingly, the intrinsic fluorescence spectra of highly concentrated IgG solutions differed from those having low concentrations, even though IgG retained a distinct tertiary structure. Arginine ethylester was more effective in suppressing the opalescence of IgG solutions than Arg, whereas lysine and γ-guanidinobutyric acid were less effective. These results indicated that positively charged groups of both α-amine and guanidinium actively influence Arg as an additive for suppressing opalescence. Diols, which are the suppressors of the liquid-liquid phase separation of proteins were also effective in suppressing the opalescence. These results therefore provide insight into the control of opalescence of antibody solutions at high concentrations using solution additives.

Nano-Microscopy of Therapeutic Antibody Aggregates in Solution

Scanning electron-assisted dielectric microscopy (SE-ADM) is a new microscope technology developed to observe the fine structure of biological samples in aqueous solution. One main advantage of SE-ADM is that it does not require sample pretreatment, including dehydration, drying, and staining, which is indispensable in conventional scanning electron microscopy (SEM) and can cause sample deformation. In addition, the sample is not directly irradiated with an electron beam in SE-ADM, further avoiding damage. The resolution of SE-ADM is higher than that of an optical microscope, which is typically used for observing biological samples in a solution, allowing for the observation of the detailed structure of samples. Considering these advantages, we applied SE-ADM to observe aggregates of therapeutic immunoglobulin G (IgG) of various sizes and shapes in an aqueous solution. In this chapter, we outline the step-by-step procedure for observing aggregates of monoclonal antibodies using SE-ADM and the subsequent analysis of the particle distribution and calculation of the fractal dimension using SE-ADM image data. The proposed method for particle analysis is highly reliable with respect to size measurement and can determine the diameter of a sample with an accuracy of ±20%, a precision of ±10%, and a lower limit of quantification of ≤50 nm. Further, by calculating the fractal dimension of the image, it is possible to classify the shape of the aggregates and determine the mechanism of aggregation.

Scanning Electron-Assisted Dielectric Microscopy Reveals Autophagosome Formation by LC3 and ATG12 in Cultured Mammalian Cells

Autophagy is an intracellular self-devouring system that plays a central role in cellular recycling. The formation of functional autophagosomes depends on several autophagy-related proteins, including the microtubule-associated proteins 1A/1B light chain 3 (LC3) and the conserved autophagy-related gene 12 (Atg12). We have recently developed a novel scanning electron-assisted dielectric microscope (SE-ADM) for nanoscale observations of intact cells. Here, we used the SE-ADM system to observe LC3- and Atg12-containing autophagosomes in cells labelled in the culture medium with antibodies conjugated to colloidal gold particles. We observed that, during autophagosome formation, Atg12 localized along the actin meshwork structure, whereas LC3 formed arcuate or circular alignments. Our system also showed a difference in the distribution of LC3 and Atg12; Atg12 was broadly distributed while LC3 was more localized. The difference in the spatial distribution demonstrated by our system explains the difference in the size of fluorescent spots due to the fluorescently labelled antibodies observed using optical microscopy. The direct SE-ADM observation of cells should thus be effective in analyses of autophagosome formation.

Nanoscale observation of PM2.5 incorporated into mammalian cells using scanning electron-assisted dielectric microscope

PM2.5 has been correlated with risk factors for various diseases and infections. It promotes tissue injury by direct effects of particle components. However, effects of PM2.5 on cells have not been fully investigated. Recently, we developed a novel imaging technology, scanning electron-assisted dielectric-impedance microscopy (SE-ADM), which enables observation of various biological specimens in aqueous solution. In this study, we successfully observed PM2.5 incorporated into living mammalian cells in culture media. Our system directly revealed the process of PM2.5 aggregation in the cells at a nanometre resolution. Further, we found that the PM2.5 aggregates in the intact cells were surrounded by intracellular membrane-like structures of low-density in the SE-ADM images. Moreover, the PM2.5 aggregates were shown by confocal Raman microscopy to be located inside the cells rather than on the cell surface. We expect our method to be applicable to the observation of various nanoparticles inside cells in culture media.

Direct observation of unstained biological samples in water using newly developed impedance scanning electron microscopy

Nanometre-scale observation of specimens in water is indispensable in several scientific fields, such as biology, chemistry, materials science and nanotechnology. Scanning electron microscopy (SEM) obtains high-resolution images of biological samples under high vacuum conditions but requires specific sample-preparation protocols. Observations of unstained biological samples in water require more convenient and less invasive methods. Herein, we have developed a new type of impedance microscopy, namely impedance SEM (IP-SEM), which allows the imaging and sub-micrometer scale examination of various specimens in water. By varying the frequency of the input signal, the proposed system can detect the impedance properties of the sample’s composition at sub-micrometer scale resolution. Besides examining various unstained biological specimens and material samples in water. Furthermore, the proposed system can be used for diverse liquid samples across a broad range of scientific fields, such as nanoparticles, nanotubes and organic and catalytic materials.

Osteoblastic lysosome plays a central role in mineralization

Mineralization is the most fundamental process in vertebrates. It is predominantly mediated by osteoblasts, which secrete mineral precursors, most likely through matrix vesicles (MVs). These vesicular structures are calcium and phosphate rich and contain organic material such as acidic proteins. However, it remains largely unknown how intracellular MVs are transported and secreted. Here, we use scanning electron-assisted dielectric microscopy and super-resolution microscopy for assessing live osteoblasts in mineralizing conditions at a nanolevel resolution. We found that the calcium-containing vesicles were multivesicular bodies containing MVs. They were transported via lysosome and secreted by exocytosis. Thus, we present proof that the lysosome transports amorphous calcium phosphate within mineralizing osteoblasts.

In-Solution Microscopic Imaging of Fractal Aggregates of a Stressed Therapeutic Antibody

Aggregates of therapeutic proteins that can contaminate drug products during manufacture is a growing concern for the pharmaceutical industry because the aggregates are potentially immunogenic. Electron microscopy is a typical, indispensable method for imaging nanometer- to micrometer-sized structures. Nevertheless, it is not ideal because it must be performed with ex situ monitoring under high-vacuum conditions, where the samples could be altered by staining and drying. Here, we introduce a scanning electron-assisted dielectric microscopy (SE-ADM) technique for in-solution imaging of monoclonal immunoglobulin G (IgG) aggregates without staining and drying. Remarkably, SE-ADM allowed assessment of the size and morphology of the IgG aggregates in solution by completely excluding drying-induced artifacts. SE-ADM was also beneficial to study IgG aggregation caused by temporary acid exposure followed by neutralization, pH-shift stress. A box-counting analysis of the SE-ADM images provided fractal dimensions of the larger aggregates, which complemented the fractal dimensions of the smaller aggregates measured by light scattering. The scale-free or self-similarity nature of the fractal aggregates indicated that a common mechanism for antibody aggregation existed between the smaller and larger aggregates. Consequently, SE-ADM is a useful method for characterizing protein aggregates to bridge the gaps that occur among conventional analytical methods, such as those related to in situ/ ex situ techniques or size/morphology assessments.

Nanoscale imaging of the adhesion core including integrin β1 on intact living cells using scanning electron-assisted dielectric-impedance microscopy

The integrins are a superfamily of transmembrane proteins composed of α and β subunit dimers involved in cell-cell and cell-extracellular matrix interactions. The largest integrin subgroup is integrin β1, which contributes to several malignant phenotypes. Recently, we have developed a novel imaging technology named scanning electron-assisted dielectric-impedance microscopy (SE-ADM), which visualizes untreated living mammalian cells in aqueous conditions with high contrast. Using the SE-ADM system, we observed 60-nm gold colloids with antibodies directly binding to the focal adhesion core containing integrin β1 on mammalian cancer cells without staining and fixation. The adhesion core contains three or four high-density regions of integrin β1 and connects to the actin filament. An adhesion core with high-density integrin β1 is suggested to contain 10-20 integrin dimers. Our SE-ADM system can also visualize various other membrane proteins in living cells in medium without staining and fixation.

Applying Pattern Recognition to High-Resolution Images to Determine Cellular Signaling Status

Two frequently used tools to acquire high- resolution images of cells are scanning electron microscopy (SEM) and atomic force microscopy (AFM). The former provides a nanometer resolution view of cellular features rapidly and with high throughput, while the latter enables visualizing hydrated and living cells. In current practice, these images are viewed by eye to determine cellular status, e.g., activated versus resting. Automatic and quantitative data analysis is lacking. This paper develops an algorithm of pattern recognition that works very effectively for AFM and SEM images. Using rat basophilic leukemia cells, our approach creates a support vector machine to automatically classify resting and activated cells. Ten-fold cross-validation with cells that are known to be activated or resting gives a good estimate of the generalized classification results. The pattern recognition of AFM images achieves 100% accuracy, while SEM reaches 95.4% for our images as well as images published in prior literature. This outcome suggests that our methodology could become an important and frequently used tool for researchers utilizing AFM and SEM for structural characterization as well as determining cellular signaling status and function.

Nanoscale observation of the natural structure of milk-fat globules and casein micelles in the liquid condition using a scanning electron assisted dielectric microscopy

Recently, aqueous nanoparticles have been used in drug-delivery systems for new type medicines. In particular, milk-casein micelles have been used as drug nanocarriers for targeting cancer cells. Therefore, nanostructure observation of particles and micelles in their native liquid condition is indispensable for analysing their function and mechanisms. However, traditional optical and scanning electron microscopy have difficulty observing the nanostructures of aqueous micelles. Recently, we developed a novel imaging technique called scanning electron-assisted dielectric microscopy (SE-ADM) that enables observation of various biological specimens in water with very little radiation damage and high-contrast imaging without staining or fixation at an 8-nm spatial resolution. In this study, for the first time, we show that the SE-ADM system is capable of high-resolution observation of whole-milk specimens in their natural state. Moreover, we successfully observe the casein micelles and milk-fat globules in an intact liquid condition. Our SE-ADM system can be applied to various biological particles and micelles in a native liquid state.

High-resolution imaging of living mammalian cells bound by nanobeads-connected antibodies in a medium using scanning electron-assisted dielectric microscopy

Nanometre-scale-resolution imaging technologies for liquid-phase specimens are indispensable tools in various scientific fields. In biology, observing untreated living cells in a medium is essential for analysing cellular functions. However, nanoparticles that bind living cells in a medium are hard to detect directly using traditional optical or electron microscopy. Therefore, we previously developed a novel scanning electron-assisted dielectric microscope (SE-ADM) capable of nanoscale observations. This method enables observation of intact cells in aqueous conditions. Here, we use this SE-ADM system to clearly observe antibody-binding nanobeads in liquid-phase. We also report the successful direct detection of streptavidin-conjugated nanobeads binding to untreated cells in a medium via a biotin-conjugated anti-CD44 antibody. Our system is capable of obtaining clear images of cellular organelles and beads on the cells at the same time. The direct observation of living cells with nanoparticles in a medium allowed by our system may contribute the development of carriers for drug delivery systems (DDS).