Three-dimensional bright-field scanning transmission electron microscopy elucidate novel nanostructure in microbial biofilms

Characterization and morphological methods for oral biofilm visualization: where are we nowadays?

The oral microbiome represents an essential component of the oral ecosystem whose symbiotic relationship contributes to health maintenance. The biofilm represents a state of living of microorganisms surrounding themselves with a complex and tridimensional organized polymeric support and defense matrix. The substrates where the oral biofilm adhere can suffer from damages due to the microbial community metabolisms. Therefore, microbial biofilm represents the main etiological factor of the two pathologies of dental interest with the highest incidence, such as carious pathology and periodontal pathology. The study, analysis, and understanding of the characteristics of the biofilm, starting from the macroscopic structure up to the microscopic architecture, appear essential. This review examined the morphological methods used through the years to identify species, adhesion mechanisms that contribute to biofilm formation and stability, and how the action of microbicidal molecules is effective against pathological biofilm. Microscopy is the primary technique for the morphological characterization of biofilm. Light microscopy, which includes the stereomicroscope and confocal laser microscopy (CLSM), allows the visualization of microbial communities in their natural state, providing valuable information on the spatial arrangement of different microorganisms within the biofilm and revealing microbial diversity in the biofilm matrix. The stereomicroscope provides a three-dimensional view of the sample, allowing detailed observation of the structure, thickness, morphology, and distribution of the various species in the biofilm while CLSM provides information on its three-dimensional architecture, microbial composition, and dynamic development. Electron microscopy, scanning (SEM) or transmission (TEM), allows the high-resolution investigation of the architecture of the biofilm, analyzing the bacterial population, the extracellular polymeric matrix (EPS), and the mechanisms of the physical and chemical forces that contribute to the adhesion of the biofilm to the substrates, on a nanometric scale. More advanced microscopic methodologies, such as scanning transmission electron microscopy (STEM), high-resolution transmission electron microscopy (HR-TEM), and correlative microscopy, have enabled the evaluation of antibacterial treatments, due to the potential to reveal the efficacy of different molecules in breaking down the biofilm. In conclusion, evidence based on scientific literature shows that established microscopic methods represent the most common tools used to characterize biofilm and its morphology in oral microbiology. Further protocols and studies on the application of advanced microscopic techniques are needed to obtain precise details on the microbiological and pathological aspects of oral biofilm.

Identification of NpdA as the protein forming the surface layer in Paracidovorax citrulli and evidence of its occurrence as a surface layer protein in diverse genera of the Betaproteobacteria and Gammaproteobacteria

The phytopathogen Paracidovorax citrulli possesses an ortholog of a newly identified surface layer protein (SLP) termed NpdA but has not been reported to produce a surface layer (S-layer). This study had two objectives. First, to determine if P. citrulli formed an NpdA-based S-layer and, if so, assess the effects of S-layer formation on virulence, production of nanostructures termed nanopods, and other phenotypes. Second, to establish the distribution of npdA orthologs throughout the Pseudomonadota and examine selected candidate cultures for physical evidence of S-layer formation. Formation of an NpdA-based S-layer by P. citrulli AAC00-1 was confirmed by gene deletion mutagenesis (ΔnpdA), proteomics, and cryo-electron microscopy. There were no significant differences between the wild-type and mutant in virulence assays with detached watermelon fruit. Nanopods contiguous with S-layers of multiple biofilm cells were visualized by transmission electron microscopy. Orthologs of npdA were identified in 62 Betaproteobacteria species and 49 Gammaproteobacteria species. In phylogenetic analyses, NpdA orthologs largely segregated into distinct groups. Cryo-electron microscopy imaging revealed an NpdA-like S-layer in all but one of the 16 additional cultures examined. We conclude that NpdA represents a new family of SLP, forming an S-layer in P. citrulli and other Pseudomonadota. While the S-layer did not contribute to virulence in watermelon fruit, a potential role of the P. citrulli S-layer in another dimension of pathogenesis cannot be ruled out. Lastly, formation of cell-bridging nanopods in biofilms is a new property of S-layers; it remains to be determined if nanopods can mediate intercellular movement of materials.

Transmission Electron Microscopy as a Powerful Tool to Investigate the Interaction of Nanoparticles with Subcellular Structures

Nanomedical research necessarily involves the study of the interactions between nanoparticulates and the biological environment. Transmission electron microscopy has proven to be a powerful tool in providing information about nanoparticle uptake, biodistribution and relationships with cell and tissue components, thanks to its high resolution. This article aims to overview the transmission electron microscopy techniques used to explore the impact of nanoconstructs on biological systems, highlighting the functional value of ultrastructural morphology, histochemistry and microanalysis as well as their fundamental contribution to the advancement of nanomedicine.

From Diospyros kaki L. (Persimmon) Phytochemical Profile and Health Impact to New Product Perspectives and Waste Valorization

Persimmon (Diospyros kaki L.) fruit's phytochemical profile includes carotenoids, proanthocyanidins, and gallic acid among other phenolic compounds and vitamins. A huge antioxidant potential is present given this richness in antioxidant compounds. These bioactive compounds impact on health benefits. The intersection of nutrition and sustainability, the key idea behind the EAT-Lancet Commission, which could improve human health and decrease the global impact of food-related health conditions such as cancer, heart disease, diabetes, and obesity, bring the discussion regarding persimmon beyond the health effects from its consumption, but also on the valorization of a very perishable food that spoils quickly. A broad option of edible products with better storage stability or solutions that apply persimmon and its byproducts in the reinvention of old products or even creating new products, or with new and better packaging for the preservation of food products with postharvest technologies to preserve and extend the shelf-life of persimmon food products. Facing a global food crisis and the climate emergency, new and better day-to-day solutions are needed right now. Therefore, the use of persimmon waste has also been discussed as a good solution to produce biofuel, eco-friendly alternative reductants for fabric dyes, green plant growth regulator, biodegradable and edible films for vegetable packaging, antimicrobial activity against foodborne methicillin-resistant Staphylococcus aureus found in retail pork, anti-Helicobacter pylori agents from pedicel extracts, and persimmon pectin-based emulsifiers to prevent lipid peroxidation, among other solutions presented in the revised literature. It has become clear that the uses for persimmon go far beyond the kitchen table and the health impact consumption demonstrated over the years. The desired sustainable transition is already in progress, however, mechanistic studies and clinical trials are essential and scaling-up is fundamental to the future.

Electrochemical and Structural Analysis in All-Solid-State Lithium Batteries by Analytical Electron Microscopy: Progress and Perspectives

Advanced scanning transmission electron microscopy (STEM) and its associated instruments have made significant contributions to the characterization of all-solid-state (ASS) Li batteries, as these tools provide localized information on the structure, morphology, chemistry, and electronic state of electrodes, electrolytes, and their interfaces at the nano- and atomic scale. Furthermore, the rapid development of in situ techniques has enabled a deep understanding of interfacial dynamic behavior and heterogeneous characteristics during the cycling process. However, due to the beam-sensitive nature of light elements in the interphases, e.g., Li and O, thorough and reliable studies of the interfacial structure and chemistry at an ultrahigh spatial resolution without beam damage is still a formidable challenge. Herein, the following points are discussed: (1) the recent contributions of advanced STEM to the study of ASS Li batteries; (2) current challenges associated with using this method; and (3) potential opportunities for combining cryo-electron microscopy and the STEM phase contrast imaging techniques.

Visualizing the macroscale spatial distributions of biofilms in complex flow channels using industrial computed tomography

The presence of biofilms in enclosed pipelines can lead to numerous deleterious issues. To date, it has been difficult to use optical imaging techniques to monitor the macroscale spatial distributions of biofilms. To address this concern, a combination of industrial computed tomography (ICT) and a contrast agent was explored to noninvasively visualize biofilms in three types of drip irrigation emitters. The results showed that ICT successfully observed and quantified the macroscale spatial distributions of biofilms. The complex hydrodynamic characteristics in the emitter channels affected the local distributions of biofilms. Biofilms were mainly attached to the lateral and medial faces and biomass decreased along the flow directions. Based on the distributions of biofilms, some emitter structural design defects were further diagnosed. Applying ICT in combination with the contrast agent could potentially provide a visual and effective way to reveal the formation mechanisms of biofilms and to optimize flow channel structures to avoid biofilm accumulations.

Unveiling the potentials of biocompatible silver nanoparticles on human lung carcinoma A549 cells and Helicobacter pylori

Silver nanoparticles (AgNPs) are gaining importance in health and environment. This study synthesized AgNPs using the bark extract of a plant, Toxicodendron vernicifluum (Tv) as confirmed by a absorption peak at 420 nm corresponding to the Plasmon resonance of AgNPs. The AgNPs were spherical, oval-shaped with size range of 2–40 nm as evident by field emission transmission electron microscopy (FE-TEM) and particle size analysis (PSA). The particles formed were crystalline by the presence of (111), (220) and (200) planes, as revealed by X ray diffraction (XRD) and energy dispersive spectroscopy (EDS). The presence of amine, amide, phenolic, and alcoholic aromatics derived from Tv extract was found to be capping and or reducing agents as evident by Fourier-transform infrared spectroscopy (FTIR) spectra. The Tv-AgNPs were observed to be biocompatible to chick embryonic and NIH3T3 cells at various concentrations. Interestingly, Tv-AgNPs at the concentration of 320 µg. mL⁻¹ induced 82.5% of cell death in human lung cancer, A549 cells and further 95% of cell death with annexin V FITC/PI based apoptosis. The Tv-AgNPs selectively targeted and damaged the cancer cells through ROS generation. The Tv-AgNPs displayed minimal inhibitory concentration (MIC) of 8.12 µg.mL⁻¹ and 18.14 µg.mL⁻¹ against STEC and H. pylori respectively. This multi-potent property of Tv-AgNPs was due to shape and size specific property that facilitated easy penetration into the bacterial and cancer cells for targeted therapy.

Extensive membrane systems at the host-arbuscular mycorrhizal fungus interface

During arbuscular mycorrhizal (AM) symbiosis, cells within the root cortex develop a matrix-filled apoplastic compartment in which differentiated AM fungal hyphae called arbuscules reside. Development of the compartment occurs rapidly, coincident with intracellular penetration and rapid branching of the fungal hypha, and it requires much of the plant cell's secretory machinery to generate the periarbuscular membrane that delimits the compartment. Despite recent advances, our understanding of the development of the periarbuscular membrane and the transfer of molecules across the symbiotic interface is limited. Here, using electron microscopy and tomography, we reveal that the periarbuscular matrix contains two types of membrane-bound compartments. We propose that one of these arises as a consequence of biogenesis of the periarbuscular membrane and may facilitate movement of molecules between symbiotic partners. Additionally, we show that the arbuscule contains massive arrays of membrane tubules located between the protoplast and the cell wall. We speculate that these tubules may provide the absorptive capacity needed for nutrient assimilation and possibly water absorption to enable rapid hyphal expansion.

Quantitative Cryo-Scanning Transmission Electron Microscopy of Biological Materials

Electron tomography provides a detailed view into the 3D structure of biological cells and tissues. Physical fixation by vitrification of the aqueous medium provides the most faithful preservation of biological specimens in the native, fully hydrated state. Cryo-microscopy is challenging, however, because of the sensitivity to electron irradiation and due to the weak electron scattering of organic material. Tomography is even more challenging because of the dependence on multiple exposures of the same area. Tomographic imaging is typically performed in wide-field transmission electron microscopy (TEM) mode with phase contrast generated by defocus. Scanning transmission electron microscopy (STEM) is an alternative mode based on detection of scattering from a focused probe beam, without imaging optics following the specimen. While careful configuration of the illumination and detectors is required to generate useful contrast, STEM circumvents the major restrictions of phase contrast TEM to very thin specimens and provides a signal that is more simply interpreted in terms of local composition and density. STEM has gained popularity in recent years for materials science. The extension of STEM to cryomicroscopy and tomography of cells and macromolecules is summarized herein.

Fungal enzyme-mediated synthesis of chitosan nanoparticles and its biocompatibility, antioxidant and bactericidal properties

This paper reports the synthesis of chitosan nanoparticles (T-CSNPs) using the fungal enzyme of Trichoderma harzianum and its biocompatibility, antioxidant and bactericidal properties. The T-CSNPs synthesis was confirmed by absorbance at 280 nm using UV-Vis spectrophotometer. T-CSNPs were of spherical shape, as evident by field emission transmission electron microscopic (FETEM) analysis, and the average size of T-CSNPs was 90.8 nm, as calculated using particle size analyzer (PSA). The functional groups showed modifications of chitosan in T-CSNPs as evident by fourier-transform infrared spectroscopic (FTIR) analysis. T-CSNPs were found soluble at the wide range of pH, showing 100% solubility at pH 1-3 and 72% at pH 10. The T-CSNPs exhibited antioxidant property in a dose-dependent manner with pronounced activity at 100 mg·mL^-1. The T-CSNPs also showed bactericidal activity against Staphylococcus aureus and Salmonella enterica Typhimurium by causing detrimental effects on bacterial cells. The T-CSNPs (50 μg·mL^-1) did not display any cytotoxic effect on murine fibroblast NIH-3T3 cells, as evident by cell viability and acridine orange/ethidium bromide staining assays, which confirmed biocompatibility of the nanoparticles. This work suggested further investigations on the utilization of the mycosynthesized nanochitosan in biomedical applications.

Single-Cell Analysis Using Hyperspectral Imaging Modalities

Almost a decade ago, hyperspectral imaging (HSI) was employed by the NASA in satellite imaging applications such as remote sensing technology. This technology has since been extensively used in the exploration of minerals, agricultural purposes, water resources, and urban development needs. Due to recent advancements in optical re-construction and imaging, HSI can now be applied down to micro- and nanometer scales possibly allowing for exquisite control and analysis of single cell to complex biological systems. This short review provides a description of the working principle of the HSI technology and how HSI can be used to assist, substitute, and validate traditional imaging technologies. This is followed by a description of the use of HSI for biological analysis and medical diagnostics with emphasis on single-cell analysis using HSI.

Comparison of 3D cellular imaging techniques based on scanned electron probes: Serial block face SEM vs. Axial bright-field STEM tomography

Microscopies based on focused electron probes allow the cell biologist to image the 3D ultrastructure of eukaryotic cells and tissues extending over large volumes, thus providing new insight into the relationship between cellular architecture and function of organelles. Here we compare two such techniques: electron tomography in conjunction with axial bright-field scanning transmission electron microscopy (BF-STEM), and serial block face scanning electron microscopy (SBF-SEM). The advantages and limitations of each technique are illustrated by their application to determining the 3D ultrastructure of human blood platelets, by considering specimen geometry, specimen preparation, beam damage and image processing methods. Many features of the complex membranes composing the platelet organelles can be determined from both approaches, although STEM tomography offers a higher ∼3 nm isotropic pixel size, compared with ∼5 nm for SBF-SEM in the plane of the block face and ∼30 nm in the perpendicular direction. In this regard, we demonstrate that STEM tomography is advantageous for visualizing the platelet canalicular system, which consists of an interconnected network of narrow (∼50-100 nm) membranous cisternae. In contrast, SBF-SEM enables visualization of complete platelets, each of which extends ∼2 µm in minimum dimension, whereas BF-STEM tomography can typically only visualize approximately half of the platelet volume due to a rapid non-linear loss of signal in specimens of thickness greater than ∼1.5 µm. We also show that the limitations of each approach can be ameliorated by combining 3D and 2D measurements using a stereological approach.

The cellular basis of platelet secretion: Emerging structure/function relationships

Platelet activation has long been known to be accompanied by secretion from at least three types of compartments. These include dense granules, the major source of small molecules; α-granules, the major protein storage organelle; and lysosomes, the site of acid hydrolase storage. Despite ~60 years of research, there are still many unanswered questions about the cell biology of platelet secretion: for example, how are these secretory organelles organized to support cargo release and what are the key routes of cargo release, granule to plasma membrane or granule to canalicular system. Moreover, in recent years, increasing evidence points to the platelet being organized for secretion of the contents from other organelles, namely the dense tubular system (endoplasmic reticulum) and the Golgi apparatus. Conceivably, protein secretion is a widespread property of the platelet and its organelles. In this review, we concentrate on the cell biology of the α-granule and its structure/function relationships. We both review the literature and discuss the wide array of 3-dimensional, high-resolution structural approaches that have emerged in the last few years. These have begun to reveal new and unanticipated outcomes and some of these are discussed. We are hopeful that the next several years will bring rapid advances to this field that will resolve past controversies and be clinically relevant.