Imaging three-dimensional tissue architectures by focused ion beam scanning electron microscopy

The desmosome comes into focus

The desmosome is a cell-cell adhesive junction that provides integrity and mechanical resistance to tissues through its attachment to the intermediate filament cytoskeleton. Defects in desmosomes cause diseases impacting the heart, epidermis, and other epithelia. In this review, we provide a historical perspective on the discovery of the desmosome and how the evolution of cellular imaging technologies revealed insights into desmosome structure and function. We also discuss recent findings using contemporary imaging approaches that have informed the molecular order, three-dimensional architecture, and associations of desmosomes with organelles such as the endoplasmic reticulum. Finally, we provide an updated model of desmosome molecular organization and speculate upon novel functions of this cell junction as a signaling center for sensing mechanical and other forms of cell stress.

The importance of 3D fibre architecture in cancer and implications for biomaterial model design

The need for improved prediction of clinical response is driving the development of cancer models with enhanced physiological relevance. A new concept of 'precision biomaterials' is emerging, encompassing patient-mimetic biomaterial models that seek to accurately detect, treat and model cancer by faithfully recapitulating key microenvironmental characteristics. Despite recent advances allowing tissue-mimetic stiffness and molecular composition to be replicated in vitro, approaches for reproducing the 3D fibre architectures found in tumour extracellular matrix (ECM) remain relatively unexplored. Although the precise influences of patient-specific fibre architecture are unclear, we summarize the known roles of tumour fibre architecture, underlining their implications in cell-matrix interactions and ultimately clinical outcome. We then explore the challenges in reproducing tissue-specific 3D fibre architecture(s) in vitro, highlighting relevant biomaterial fabrication techniques and their benefits and limitations. Finally, we discuss imaging and image analysis techniques (focussing on collagen I-optimized approaches) that could hold the key to mapping tumour-specific ECM into high-fidelity biomaterial models. We anticipate that an interdisciplinary approach, combining materials science, cancer research and image analysis, will elucidate the role of 3D fibre architecture in tumour development, leading to the next generation of patient-mimetic models for mechanistic studies and drug discovery.

The application and development of electron microscopy for three-dimensional reconstruction in life science: a review

Imaging technologies have played a pivotal role in advancing biological research by enabling visualization of biological structures and processes. While traditional electron microscopy (EM) produces two-dimensional images, emerging techniques now allow high-resolution three-dimensional (3D) characterization of specimens in situ, meeting growing needs in molecular and cellular biology. Combining transmission electron microscopy (TEM) with serial sectioning inaugurated 3D imaging, attracting biologists seeking to explore cell ultrastructure and driving advancement of 3D EM reconstruction. By comprehensively and precisely rendering internal structure and distribution, 3D TEM reconstruction provides unparalleled ultrastructural insights into cells and molecules, holding tremendous value for elucidating structure-function relationships and broadly propelling structural biology. Here, we first introduce the principle of 3D reconstruction of cells and tissues by classical approaches in TEM and then discuss modern technologies utilizing TEM and on new SEM-based as well as cryo-electron microscope (cryo-EM) techniques. 3D reconstruction techniques from serial sections, electron tomography (ET), and the recent single-particle analysis (SPA) are examined; the focused ion beam scanning electron microscopy (FIB-SEM), the serial block-face scanning electron microscopy (SBF-SEM), and automatic tape-collecting lathe ultramicrotome (ATUM-SEM) for 3D reconstruction of large volumes are discussed. Finally, we review the challenges and development prospects of these technologies in life science. It aims to provide an informative reference for biological researchers.

Focused ion beam-scanning electron microscopy provides novel insights of drug delivery phenomena

Scanning electron microscopy (SEM) has long been a standard tool for morphological analyses, providing sub micrometer resolution of pharmaceutical formulations. However, analysis of internal morphologies of such formulations can often be biased due to the introduction of artifacts that originate from sample preparation. A recent advancement in SEM, is the focused ion beam scanning electron microscopy (FIB-SEM). This technique uses a focused ion beam (FIB) to remove material with nanometer precision, to provide virtually sample-independent access to sub-surface structures. The FIB can be combined with SEM imaging capabilities within the same instrumentation. As a powerful analytical tool, electron microscopy and FIB-milling are performed sequentially to produce high-resolution 3D models of structural peculiarities of diverse drug delivery systems or their behavior in a biological environment, i.e. intracellular or -tissue distribution. This review paper briefly describes the technical background of the method, outlines a wide array of potential uses within the drug delivery field, and focuses on intracellular transport where high-resolution images are an essential tool for mechanistical insights.

Efficient semi-supervised semantic segmentation of electron microscopy cancer images with sparse annotations

Electron microscopy (EM) enables imaging at a resolution of nanometers and can shed light on how cancer evolves to develop resistance to therapy. Acquiring these images has become a routine task.However, analyzing them is now a bottleneck, as manual structure identification is very time-consuming and can take up to several months for a single sample. Deep learning approaches offer a suitable solution to speed up the analysis. In this work, we present a study of several state-of-the-art deep learning models for the task of segmenting nuclei and nucleoli in volumes from tumor biopsies. We compared previous results obtained with the ResUNet architecture to the more recent UNet++, FracTALResNet, SenFormer, and CEECNet models. In addition, we explored the utilization of unlabeled images through semi-supervised learning with Cross Pseudo Supervision. We have trained and evaluated all of the models on sparse manual labels from three fully annotated in-house datasets that we have made available on demand, demonstrating improvements in terms of 3D Dice score. From the analysis of these results, we drew conclusions on the relative gains of using more complex models, and semi-supervised learning as well as the next steps for the mitigation of the manual segmentation bottleneck.

Studying zebrafish nervous system structure and function in health and disease with electron microscopy

Zebrafish (Danio rerio) is a well-established model for studying the nervous system. Findings in zebrafish often inform studies on human diseases of the nervous system and provide crucial insight into disease mechanisms. The functions of the nervous system often rely on communication between neurons. Signal transduction is achieved via release of signaling molecules in the form of neuropeptides or neurotransmitters at synapses. Snapshots of membrane dynamics of these processes are imaged by electron microscopy. Electron microscopy can reveal ultrastructure and thus synaptic processes. This is crucial both for mapping synaptic connections and for investigating synaptic functions. In addition, via volumetric electron microscopy, the overall architecture of the nervous system becomes accessible, where structure can inform function. Electron microscopy is thus of particular value for studying the nervous system. However, today a plethora of electron microscopy techniques and protocols exist. Which technique is most suitable highly depends on the research question and scope as well as on the type of tissue that is examined. This review gives an overview of the electron microcopy techniques used on the zebrafish nervous system. It aims to give researchers a guide on which techniques are suitable for their specific questions and capabilities as well as an overview of the capabilities of electron microscopy in neurobiological research in the zebrafish model.

Efficient semi-supervised semantic segmentation of electron microscopy cancer images with sparse annotations

Electron microscopy (EM) enables imaging at nanometer resolution and can shed light on how cancer evolves to develop resistance to therapy. Acquiring these images has become a routine task; however, analyzing them is now the bottleneck, as manual structure identification is very time-consuming and can take up to several months for a single sample. Deep learning approaches offer a suitable solution to speed up the analysis. In this work, we present a study of several state-of-the-art deep learning models for the task of segmenting nuclei and nucleoli in volumes from tumor biopsies. We compared previous results obtained with the ResUNet architecture to the more recent UNet++, FracTALResNet, SenFormer, and CEECNet models. In addition, we explored the utilization of unlabeled images through semi-supervised learning with Cross Pseudo Supervision. We have trained and evaluated all of the models on sparse manual labels from three fully annotated in-house datasets that we have made available on demand, demonstrating improvements in terms of 3D Dice score. From the analysis of these results, we drew conclusions on the relative gains of using more complex models, semi-supervised learning as well as next steps for the mitigation of the manual segmentation bottleneck.

CellRemorph: A Toolkit for Transforming, Selecting, and Slicing 3D Cell Structures on the Road to Morphologically Detailed Astrocyte Simulations

Understanding functions of astrocytes can be greatly enhanced by building and simulating computational models that capture their morphological details. Novel computational tools enable utilization of existing morphological data of astrocytes and building models that have appropriate level of details for specific simulation purposes. In addition to analyzing existing computational tools for constructing, transforming, and assessing astrocyte morphologies, we present here the CellRemorph toolkit implemented as an add-on for Blender, a 3D modeling platform increasingly recognized for its utility for manipulating 3D biological data. To our knowledge, CellRemorph is the first toolkit for transforming astrocyte morphologies from polygonal surface meshes into adjustable surface point clouds and vice versa, precisely selecting nanoprocesses, and slicing morphologies into segments with equal surface areas or volumes. CellRemorph is an open-source toolkit under the GNU General Public License and easily accessible via an intuitive graphical user interface. CellRemorph will be a valuable addition to other Blender add-ons, providing novel functionality that facilitates the creation of realistic astrocyte morphologies for different types of morphologically detailed simulations elucidating the role of astrocytes both in health and disease.

Methods to Evaluate Changes in Mitochondrial Structure and Function in Cancer

Mitochondria are regulators of key cellular processes, including energy production and redox homeostasis. Mitochondrial dysfunction is associated with various human diseases, including cancer. Importantly, both structural and functional changes can alter mitochondrial function. Morphologic and quantifiable changes in mitochondria can affect their function and contribute to disease. Structural mitochondrial changes include alterations in cristae morphology, mitochondrial DNA integrity and quantity, and dynamics, such as fission and fusion. Functional parameters related to mitochondrial biology include the production of reactive oxygen species, bioenergetic capacity, calcium retention, and membrane potential. Although these parameters can occur independently of one another, changes in mitochondrial structure and function are often interrelated. Thus, evaluating changes in both mitochondrial structure and function is crucial to understanding the molecular events involved in disease onset and progression. This review focuses on the relationship between alterations in mitochondrial structure and function and cancer, with a particular emphasis on gynecologic malignancies. Selecting methods with tractable parameters may be critical to identifying and targeting mitochondria-related therapeutic options. Methods to measure changes in mitochondrial structure and function, with the associated benefits and limitations, are summarized.

Uncovering the cytotoxic effects of air pollution with multi-modal imaging of in vitro respiratory models

Annually, an estimated seven million deaths are linked to exposure to airborne pollutants. Despite extensive epidemiological evidence supporting clear associations between poor air quality and a range of short- and long-term health effects, there are considerable gaps in our understanding of the specific mechanisms by which pollutant exposure induces adverse biological responses at the cellular and tissue levels. The development of more complex, predictive, in vitro respiratory models, including two- and three-dimensional cell cultures, spheroids, organoids and tissue cultures, along with more realistic aerosol exposure systems, offers new opportunities to investigate the cytotoxic effects of airborne particulates under controlled laboratory conditions. Parallel advances in high-resolution microscopy have resulted in a range of in vitro imaging tools capable of visualizing and analysing biological systems across unprecedented scales of length, time and complexity. This article considers state-of-the-art in vitro respiratory models and aerosol exposure systems and how they can be interrogated using high-resolution microscopy techniques to investigate cell-pollutant interactions, from the uptake and trafficking of particles to structural and functional modification of subcellular organelles and cells. These data can provide a mechanistic basis from which to advance our understanding of the health effects of airborne particulate pollution and develop improved mitigation measures.

Assessment of histological and immunohistochemical features of retinal tissues using a novel tissue submission procedure

We introduce a novel tissue submission procedure without additional equipment or storage facilities for assessing the histological and immunohistochemical features of retinal tissues. In total, 150 specimens were collected from patients who underwent vitrectomy or macular surgery from January to December 2020. Ninety-eight specimens were submitted using the new procedure, and 58 specimens were submitted as flat-mount slides to compare specimen adequacy. The tissues submitted using the new procedure were subjected to paraffin-embedding and sectioning for hematoxylin & eosin staining. Additional immunohistochemical analysis was performed to assess the cellular composition in retinal tissues with diverse etiologies. The new submission procedure had an adequacy ratio of 75.51%, which was comparable to that of the flat-mount method (p = 0.1397). The new method could produce high-quality images of histological features of tissues and facilitated immunohistochemical analysis to demonstrate cell origins. More glial cells (p = 0.000) and myofibroblasts (p = 0.012) were detected in the epiretinal membranes (ERMs) than in the internal limiting membranes (ILMs). Subgroup analysis revealed that secondary ERMs contained more macrophage-like cells (p = 0.001) and retinal pigment epithelial cells (p = 0.000) than did idiopathic ERMs. Our novel tissue submission procedure can be applied to routine clinical practice. Our study provides additional histological and immunohistochemical evidence of cellular components in retinal tissues based on a large number of human tissue samples. Moreover, tissues submitted using the new method can be permanently preserved, enabling future investigation for potential prognostic or therapeutic targets.

An Overview on Image-Based and Scanner-Based 3D Modeling Technologies

Advances in the scientific fields of photogrammetry and computer vision have led to the development of automated multi-image methods that solve the problem of 3D reconstruction. Simultaneously, 3D scanners have become a common source of data acquisition for 3D modeling of real objects/scenes/human bodies. This article presents a comprehensive overview of different 3D modeling technologies that may be used to generate 3D reconstructions of outer or inner surfaces of different kinds of targets. In this context, it covers the topics of 3D modeling using images via different methods, it provides a detailed classification of 3D scanners by additionally presenting the basic operating principles of each type of scanner, and it discusses the problem of generating 3D models from scans. Finally, it outlines some applications of 3D modeling, beyond well-established topographic ones.

Visualizing Dynamic Environmental Processes in Liquid at Nanoscale via Liquid-Phase Electron Microscopy

Visualizing the structure and processes in liquids at the nanoscale is essential for understanding the fundamental mechanisms and underlying processes of environmental research. Cutting-edge progress of in situ liquid-phase (scanning) transmission electron microscopy (LP-S/TEM) and inferred possible applications are highlighted as a more and more indispensable tool for visualization of dynamic environmental processes in this Perspective. Advancements in nanofabrication technology, high-speed imaging, comprehensive detectors, and spectroscopy analysis have made it increasingly convenient to use LP S/TEM, thus providing an approach for visualization of direct and insightful scientific information with the exciting possibility of solving an increasing number of tricky environmental problems. This includes evaluating the transformation fate and path of contamination, assessing toxicology of nanomaterials, simulating solid surface corrosion processes in the environment, and observing water pollution control processes. Distinct nanoscale or even atomic understanding of the reaction would provide dependable and precise identification and quantification of contaminants in dynamic processes, thus facilitating trouble-tracing of environmental problems with amplifying complexity.

Current methods to analyze lysosome morphology, positioning, motility and function

Since the discovery of lysosomes more than 70 years ago, much has been learned about the functions of these organelles. Lysosomes were regarded as exclusively degradative organelles, but more recent research has shown that they play essential roles in several other cellular functions, such as nutrient sensing, intracellular signalling and metabolism. Methodological advances played a key part in generating our current knowledge about the biology of this multifaceted organelle. In this review, we cover current methods used to analyze lysosome morphology, positioning, motility and function. We highlight the principles behind these methods, the methodological strategies and their advantages and limitations. To extract accurate information and avoid misinterpretations, we discuss the best strategies to identify lysosomes and assess their characteristics and functions. With this review, we aim to stimulate an increase in the quantity and quality of research on lysosomes and further ground-breaking discoveries on an organelle that continues to surprise and excite cell biologists.

Comparative Sample Preparation Using Focused Ion Beam and Ultramicrotomy of Human Dental Enamel and Dentine for Multimicroscopic Imaging at Micro- and Nanoscale

(1) Background: The aim of this study was to systematically compare TEM sections of mineralized human enamel and dentine prepared by focused ion beam (in situ lift-out) technique and ultramicrotomy through a combination of microscopic examination methods (scanning electron microscopy and transmission electron microscopy). In contrast with published studies, we compared the TEM preparation methods using the same specimen blocks as those for the ultramicrotomy and FIB technique. (2) Methods: A further evaluation of TEM sample preparation was obtained by confocal laser scanning microscopy and atomic force microscopy. In addition, ultramicrotome- and focused ion beam-induced artefacts are illustrated. (3) Results: The FIB technique exposed a major difference between non-decalcified enamel and dentine concerning the ultrastructural morphology compared to ultramicrotome-prepared sections. We found that ultramicrotomy was useful for cutting mineralized dentine, with the possibility of mechanical artefacts, but offers limited options for the preparation of mineralized enamel. FIB preparation produced high-quality TEM sections, showing the anisotropic ultrastructural morphology in detail, with minor structural artefacts. Our results show that the solution of artificial saliva and glutardialdehyde (2.5% by volume) is a very suitable fixative for human mineralized tissue. (4) Conclusions: The protocol that we developed has strong potential for the preparation of mineralized biomaterials for TEM imaging and analysis.

Correlative Organelle Microscopy: Fluorescence Guided Volume Electron Microscopy of Intracellular Processes

Intracellular processes depend on a strict spatial and temporal organization of proteins and organelles. Therefore, directly linking molecular to nanoscale ultrastructural information is crucial in understanding cellular physiology. Volume or three-dimensional (3D) correlative light and electron microscopy (volume-CLEM) holds unique potential to explore cellular physiology at high-resolution ultrastructural detail across cell volumes. However, the application of volume-CLEM is hampered by limitations in throughput and 3D correlation efficiency. In order to address these limitations, we describe a novel pipeline for volume-CLEM that provides high-precision (<100 nm) registration between 3D fluorescence microscopy (FM) and 3D electron microscopy (EM) datasets with significantly increased throughput. Using multi-modal fiducial nanoparticles that remain fluorescent in epoxy resins and a 3D confocal fluorescence microscope integrated into a Focused Ion Beam Scanning Electron Microscope (FIB.SEM), our approach uses FM to target extremely small volumes of even single organelles for imaging in volume EM and obviates the need for post-correlation of big 3D datasets. We extend our targeted volume-CLEM approach to include live-cell imaging, adding information on the motility of intracellular membranes selected for volume-CLEM. We demonstrate the power of our approach by targeted imaging of rare and transient contact sites between the endoplasmic reticulum (ER) and lysosomes within hours rather than days. Our data suggest that extensive ER-lysosome and mitochondria-lysosome interactions restrict lysosome motility, highlighting the unique capabilities of our integrated CLEM pipeline for linking molecular dynamic data to high-resolution ultrastructural detail in 3D.

Applications of scanning electron microscopy and focused ion beam milling in dental research

The abilities of scanning electron microscopy (SEM) and focused ion beam (FIB) milling for obtaining high-resolution images from top surfaces, cross-sectional surfaces, and even in three dimensions, are becoming increasingly important for imaging and analyzing tooth structures such as enamel and dentin. FIB was originally developed for material research in the semiconductor industry. However, use of SEM/FIB has been growing recently in dental research due to the versatility of dual platform instruments that can be used as a milling device to obtain low-artifact cross-sections of samples combined with high-resolution images. The advent of the SEM/FIB system and accessories may offer access to previously inaccessible length scales for characterizing tooth structures for dental research, opening exciting opportunities to address many central questions in dental research. New discoveries and fundamental breakthroughs in understanding are likely to follow. This review covers the applications, key findings, and future direction of SEM/FIB in dental research in morphology imaging, specimen preparation for transmission electron microscopy (TEM) analysis, and three-dimensional volume imaging using SEM/FIB tomography.

Field-Emission Scanning Electron Microscope as a Tool for Large-Area and Large-Volume Ultrastructural Studies

Simple Summary

Ultrastructural studies of cells and tissues are usually performed using transmission electron microscopy (TEM), which enables imaging at the highest possible resolution. The weak point of TEM is the limited ability to analyze the ultrastructure of large areas and volumes of biological samples. This limitation can be overcome by using modern field-emission scanning electron microscopy (FE-SEM) with high-sensitivity detection, which enables the creation of TEM-like images from the flat surfaces of resin-embedded biological specimens. Several FE-SEM-based techniques for two- and three-dimensional ultrastructural studies of cells, tissues, organs, and organisms have been developed in the 21st century. These techniques have created a new era in structural biology and have changed the role of the scanning electron microscope (SEM) in biological and medical laboratories. Since the premiere of the first commercially available SEM in 1965, these instruments were used almost exclusively to obtain topographical information over a large range of magnifications. Currently, FE-SEM offers many attractive possibilities in the studies of cell and tissue ultrastructure, and they are presented in this review.

Abstract

The development of field-emission scanning electron microscopes for high-resolution imaging at very low acceleration voltages and equipped with highly sensitive detectors of backscattered electrons (BSE) has enabled transmission electron microscopy (TEM)-like imaging of the cut surfaces of tissue blocks, which are impermeable to the electron beam, or tissue sections mounted on the solid substrates. This has resulted in the development of methods that simplify and accelerate ultrastructural studies of large areas and volumes of biological samples. This article provides an overview of these methods, including their advantages and disadvantages. The imaging of large sample areas can be performed using two methods based on the detection of transmitted electrons or BSE. Effective imaging using BSE requires special fixation and en bloc contrasting of samples. BSE imaging has resulted in the development of volume imaging techniques, including array tomography (AT) and serial block-face imaging (SBF-SEM). In AT, serial ultrathin sections are collected manually on a solid substrate such as a glass and silicon wafer or automatically on a tape using a special ultramicrotome. The imaging of serial sections is used to obtain three-dimensional (3D) information. SBF-SEM is based on removing the top layer of a resin-embedded sample using an ultramicrotome inside the SEM specimen chamber and then imaging the exposed surface with a BSE detector. The steps of cutting and imaging the resin block are repeated hundreds or thousands of times to obtain a z-stack for 3D analyses.

Hierarchical ultrastructure: An overview of what is known about tendons and future perspective for tendon engineering

Abnormal tendons are rarely ever repaired to the natural structure and morphology of normal tendons. To better guide the repair and regeneration of injured tendons through a tissue engineering method, it is necessary to have insights into the internal morphology, organization, and composition of natural tendons. This review summarized recent researches on the structure and function of the extracellular matrix (ECM) components of tendons and highlight the application of multiple detection methodologies concerning the structure of ECMs. In addition, we look forward to the future of multi-dimensional biomaterial design methods and the potential of structural repair for tendon ECM components. In addition, focus is placed on the macro to micro detection methods for tendons, and current techniques for evaluating the extracellular matrix of tendons at the micro level are introduced in detail. Finally, emphasis is given to future extracellular matrix detection methods, as well as to how future efforts could concentrate on fabricating the biomimetic tendons.

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Summarize recent research on the structure and function of the extracellular matrix (ECM) components of tendons.

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Comments on current research methods concerning the structure of ECMs.

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Perspective on the future of multi-dimensional detection techniques and structural repair of tendon ECM components.

Visualizing Trace Pollutants in Solids at Nanoscale via Electron Tomography

Visualizing trace pollutants such as toxic metals and viruses in environmental solids such as soils, sediments, aerosols, and suspended particles in water has long been the holy grail for scientists and engineers. In this Perspective, progress on the state-of-the-art electron tomography is highlighted as an increasingly indispensable tool for visualizing contaminant distribution and transformation in three-dimension (3D), including environmental pollutants at the water-minerals interfaces, toxicology assessment, environmental behavior of viruses in heterogeneous environmental media, etc. Adding a third dimension to the pollutant characterization will surely enrich our understanding on the complex and emerging environmental issues facing the global society, and provide vital support to the ongoing research and development of life-saving mitigation technologies from air filtration, to drinking water purification, to virus disinfection.

A structure-function based approach to floc hierarchy and evidence for the non-fractal nature of natural sediment flocs

Natural sediment flocs are fragile, highly irregular, loosely bound aggregates comprising minerogenic and organic material. They contribute a major component of suspended sediment load and are critical for the fate and flux of sediment, carbon and pollutants in aquatic environments. Understanding their behaviour is essential to the sustainable management of waterways, fisheries and marine industries. For several decades, modelling approaches have utilised fractal mathematics and observations of two dimensional (2D) floc size distributions to infer levels of aggregation and predict their behaviour. Whilst this is a computationally simple solution, it is highly unlikely to reflect the complexity of natural sediment flocs and current models predicting fine sediment hydrodynamics are not efficient. Here, we show how new observations of fragile floc structures in three dimensions (3D) demonstrate unequivocally that natural flocs are non-fractal. We propose that floc hierarchy is based on observations of 3D structure and function rather than 2D size distribution. In contrast to fractal theory, our data indicate that flocs possess characteristics of emergent systems including non-linearity and scale-dependent feedbacks. These concepts and new data to quantify floc structures offer the opportunity to explore new emergence-based floc frameworks which better represent natural floc behaviour and could advance our predictive capacity.

Reactive oxygen FIB spin milling enables correlative workflow for 3D super-resolution light microscopy and serial FIB/SEM of cultured cells

Correlative light and electron microscopy (CLEM) is a powerful tool for defining the ultrastructural context of molecularly-labeled biological specimens, particularly when superresolution fluorescence microscopy (SRM) is used for CLEM. Current CLEM, however, is limited by the stark differences in sample preparation requirements between the two modalities. For CLEM using SRM, the small region of interest (ROI) of either or both modalities also leads to low success rate and imaging throughput. To overcome these limitations, here we present a CLEM workflow based on a novel focused ion beam/scanning electron microscope (FIB/SEM) compatible with common SRM for imaging biological specimen with ultrahigh 3D resolution and improved imaging throughput. By using a reactive oxygen source in a plasma FIB (PFIB) and a rotating sample stage, the novel FIB/SEM was able to achieve several hundreds of micrometer large area 3D analysis of resin embedded cells through a process named oxygen serial spin mill (OSSM). Compared with current FIB mechanisms, OSSM offers gentle erosion, highly consistent slice thickness, reduced charging during SEM imaging, and improved SEM contrast without increasing the dose of post-staining and fixation. These characteristics of OSSM-SEM allowed us to pair it with interferometric photoactivated localization microscopy (iPALM), a recent SRM technique that affords 10–20 nm isotropic spatial resolution on hydrated samples, for 3D CLEM imaging. We demonstrate a CLEM workflow generalizable to using other SRM strategies using mitochondria in human osteosarcoma (U2OS) cells as a model system, where immunostained TOM20, a marker for the mitochondrial outer membrane, was used for iPALM. Owing to the large scan area of OSSM-SEM, it is now possible to select as many FOVs as needed for iPALM and conveniently re-locate them in EM, this improving the imaging throughput. The significantly reduced dose of post-fixation also helped to better preserve the sample ultrastructures as evidenced by the excellent 3D registration between OSSM-SEM and iPALM images and by the accurate localization of TOM20 (by iPALM) to the peripheries of mitochondria (by OSSM-SEM). These advantages make OSSM-SEM an ideal modality for CLEM applications. As OSSM-SEM is still in development, we also discuss some of the remaining issues and the implications to biological imaging with SEM alone or with CLEM.

Topographically guided hierarchical mineralization

Material platforms based on interaction between organic and inorganic phases offer enormous potential to develop materials that can recreate the structural and functional properties of biological systems. However, the capability of organic-mediated mineralizing strategies to guide mineralization with spatial control remains a major limitation. Here, we report on the integration of a protein-based mineralizing matrix with surface topographies to grow spatially guided mineralized structures. We reveal how well-defined geometrical spaces defined within the organic matrix by the surface topographies can trigger subtle changes in single nanocrystal co-alignment, which are then translated to drastic changes in mineralization at the microscale and macroscale. Furthermore, through systematic modifications of the surface topographies, we demonstrate the possibility of selectively guiding the growth of hierarchically mineralized structures. We foresee that the capacity to direct the anisotropic growth of such structures would have important implications in the design of biomineralizing synthetic materials to repair or regenerate hard tissues.

Plant multiscale networks: charting plant connectivity by multi-level analysis and imaging techniques

In multicellular and even single-celled organisms, individual components are interconnected at multiscale levels to produce enormously complex biological networks that help these systems maintain homeostasis for development and environmental adaptation. Systems biology studies initially adopted network analysis to explore how relationships between individual components give rise to complex biological processes. Network analysis has been applied to dissect the complex connectivity of mammalian brains across different scales in time and space in The Human Brain Project. In plant science, network analysis has similarly been applied to study the connectivity of plant components at the molecular, subcellular, cellular, organic, and organism levels. Analysis of these multiscale networks contributes to our understanding of how genotype determines phenotype. In this review, we summarized the theoretical framework of plant multiscale networks and introduced studies investigating plant networks by various experimental and computational modalities. We next discussed the currently available analytic methodologies and multi-level imaging techniques used to map multiscale networks in plants. Finally, we highlighted some of the technical challenges and key questions remaining to be addressed in this emerging field.

Protocol for preparation of heterogeneous biological samples for 3D electron microscopy: a case study for insects

Modern morphological and structural studies are coming to a new level by incorporating the latest methods of three-dimensional electron microscopy (3D-EM). One of the key problems for the wide usage of these methods is posed by difficulties with sample preparation, since the methods work poorly with heterogeneous (consisting of tissues different in structure and in chemical composition) samples and require expensive equipment and usually much time. We have developed a simple protocol allows preparing heterogeneous biological samples suitable for 3D-EM in a laboratory that has a standard supply of equipment and reagents for electron microscopy. This protocol, combined with focused ion-beam scanning electron microscopy, makes it possible to study 3D ultrastructure of complex biological samples, e.g., whole insect heads, over their entire volume at the cellular and subcellular levels. The protocol provides new opportunities for many areas of study, including connectomics.

ER-Mitochondria Contact Sites Reporters: Strengths and Weaknesses of the Available Approaches

Organelle intercommunication represents a wide area of interest. Over the last few decades, increasing evidence has highlighted the importance of organelle contact sites in many biological processes including Ca²⁺ signaling, lipid biosynthesis, apoptosis, and autophagy but also their involvement in pathological conditions. ER–mitochondria tethering is one of the most investigated inter-organelle communications and it is differently modulated in response to several cellular conditions including, but not limited to, starvation, Endoplasmic Reticulum (ER) stress, and mitochondrial shape modifications. Despite many studies aiming to understand their functions and how they are perturbed under different conditions, approaches to assess organelle proximity are still limited. Indeed, better visualization and characterization of contact sites remain a fascinating challenge. The aim of this review is to summarize strengths and weaknesses of the available methods to detect and quantify contact sites, with a main focus on ER–mitochondria tethering.

Composition, structure and function of the corneal stroma

No other tissue in the body depends more on the composition and organization of the extracellular matrix (ECM) for normal structure and function than the corneal stroma. The precise arrangement and orientation of collagen fibrils, lamellae and keratocytes that occurs during development and is needed in adults to maintain stromal function is dependent on the regulated interaction of multiple ECM components that contribute to attain the unique properties of the cornea: transparency, shape, mechanical strength, and avascularity. This review summarizes the contribution of different ECM components, their structure, regulation and function in modulating the properties of the corneal stroma. Fibril forming collagens (I, III, V), fibril associated collagens with interrupted triple helices (XII and XIV), network forming collagens (IV, VI and VIII) as well as small leucine-rich proteoglycans (SLRP) expressed in the stroma: decorin, biglycan, lumican, keratocan, and fibromodulin are some of the ECM components reviewed in this manuscript. There are spatial and temporal differences in the expression of these ECM components, as well as interactions among them that contribute to stromal function. Unique regions within the stroma like Bowman's layer and Descemet's layer are discussed. To define the complexity of corneal stroma composition and structure as well as the relationship to function is a daunting task. Our knowledge is expanding, and we expect that this review provides a comprehensive overview of current knowledge, definition of gaps and suggests future research directions.

3D characterisation using plasma FIB-SEM: A large-area tomography technique for complex surfaces like black silicon

This paper demonstrates an improved method to accurately extract the surface morphology of black silicon (BSi). The method is based on an automated Xe⁺ plasma focused ion beam (PFIB) and scanning electron microscope (SEM) tomography technique. A comprehensive new sample preparation method is described and shown to minimize the PFIB artifacts induced by both the top surface sample-PFIB interaction and the non-uniform material density. An optimized post-image processing procedure is also described that ensures the accuracy of the reconstructed 3D surface model. The application of these new methods is demonstrated by applying them to extract the surface topography of BSi formed by reactive ion etching (RIE) consisting of 2 µm tall needles. An area of 320 µm² is investigated with a controlled slice thickness of 10 nm. The reconstructed 3D model allows the extraction of critical roughness characteristics, such as height distribution, correlation length, and surface enhancement ratio. Furthermore, it is demonstrated that the particular surface studied contains regions in which under-etching has resulted in overhanging structures, which would not have been identified with other surface topography techniques. Such overhanging structures can be present in a broad range of BSi surfaces, including BSi surfaces formed by RIE and metal catalyst chemical etching (MCCE). Without proper measurement, the un-detected overhangs would result in the underestimation of many critical surface characteristics, such as absolute surface area, electrochemical reactivity and light-trapping.

Effect of three-dimensional porosity gradients of biomimetic coatings on their bonding strength and cell behavior

Surface modification techniques are often used to enhance the properties of Ti-based materials as hard-tissue replacements. While the microstructure of the coating and the quality of the interface between the substrate and coating are essential to evaluate the reliability and applicability of the surface modification. In this study, both a hydroxyapatite (HA) coating and a collagen-hydroxyapatite (Col-HA) composite coating were deposited onto a Ti-6Al-4V substrate using a biomimetic coating process. Importantly, a gradient cross-sectional structure with a porous coating toward the surface, while a dense layer adjacent to the interface between the coating and substrate was observed in three-dimensional (3D) from both the HA and Col-HA coatings via a dual-beam focused ion beam-scanning electron microscope (FIB-SEM). Moreover, the pore distributions within the entire coatings were reconstructed in 3D using Avizo, and the pores size distributions along the coating depth were calculated using RStudio. By evaluating the mechanical property and biocompatibility of these materials and closely observing the cross-sectional cell-coating-substrate interfaces using FIB-SEM, it was revealed that the porous surface created by both coatings well supports osteoblast cell adhesion while the dense inner layer facilitates a good bonding between the coating and the substrate. Although the mechanical property of the coating decreased with the addition of collagen, it is still strong enough for implant handling and the biocompatibility was promoted.

Morphometric Analysis of Paramylon Particles Produced by Euglena gracilis EOD-1 Using FIB/SEM Tomography

Euglena gracilis EOD-1, a microalgal strain, produces large quantities of paramylon, a class of polymers known as β-1,3-glucans and has been reported to function as a dietary fiber and to improve the metabolic syndrome including obesity. However, despite its importance, the morphometric analysis of paramylon has not been conducted so far. In this study, we attempted to observe the detailed three-dimensional structure of paramylon by focused ion beam/scanning electron microscopy (FIB/SEM). Paramylon samples were fixed and three-dimensional image reconstruction and segmentation of the image stack were created using computer software (Amira v6.0.1, FEI). The results indicated that the inside of paramylon particles (diameter: 5 µm, thickness: 3 µm) was comprised of a dense structure with no evidence of the presence of large pores and gaps, although a small 100 nm crack was observed. The specific surface area of paramylon particles measured by the Brunauer-Emmet-Teller (BET) method, was not as large as activated charcoal, but similar to those of plant starches, indicating that the cholesterol-lowering effect of paramylon cannot be simply attributed to its adsorption ability. The FIB/SEM method was found to be useful for elucidating the internal structure of small solid particles.

Cell-independent matrix configuration in early corneal development

Mechanisms controlling the spatial configuration of the remarkably ordered collagen-rich extracellular matrix of the transparent cornea remain incompletely understood. We previously described the assembly of the emerging corneal matrix in the mid and late stages of embryogenesis and concluded that collagen fibril organisation was driven by cell-directed mechanisms. Here, the early stages of corneal morphogenesis were examined by serial block face scanning electron microscopy of embryonic chick corneas starting at embryonic day three (E3), followed by a Fourier transform analysis of three-dimensional datasets and theoretical considerations of factors that influence matrix formation. Eyes developing normally and eyes that had the lens surgically removed at E3 were studied. Uniformly thin collagen fibrils are deposited by surface ectoderm-derived corneal epithelium in the primary stroma of the developing chick cornea and form an acellular matrix with a striking micro-lamellar orthogonal arrangement. Fourier transform analysis supported this observation and indicated that adjacent micro-lamellae display a clockwise rotation of fibril orientation, depth-wise below the epithelium. We present a model which attempts to explain how, in the absence of cells in the primary stroma, collagen organisation might be influenced by cell-independent, intrinsic mechanisms, such as fibril axial charge derived from associated proteoglycans. On a supra-lamellar scale, fine cords of non-collagenous filamentous matrix were detected over large tissue volumes. These extend into the developing cornea from the epithelial basal lamina and appear to associate with the neural crest cells that migrate inwardly to form, first the corneal endothelium and then keratocytes which synthesise the mature, secondary corneal stroma. In a small number of experimental specimens, matrix cords were present even when periocular neural crest cell migration and corneal morphogenesis had been perturbed following removal of the lens at E3.

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Highly-ordered connective tissue appears early in development of the avian cornea.

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Cell-independent mechanisms may contribute to the organisation of collagen fibrils into an orthogonal array.

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Matrix cords from epithelium into stroma contact invading neural crest cells.

Scleral structure and biomechanics

As the eye's main load-bearing connective tissue, the sclera is centrally important to vision. In addition to cooperatively maintaining refractive status with the cornea, the sclera must also provide stable mechanical support to vulnerable internal ocular structures such as the retina and optic nerve head. Moreover, it must achieve this under complex, dynamic loading conditions imposed by eye movements and fluid pressures. Recent years have seen significant advances in our knowledge of scleral biomechanics, its modulation with ageing and disease, and their relationship to the hierarchical structure of the collagen-rich scleral extracellular matrix (ECM) and its resident cells. This review focuses on notable recent structural and biomechanical studies, setting their findings in the context of the wider scleral literature. It reviews recent progress in the development of scattering and bioimaging methods to resolve scleral ECM structure at multiple scales. In vivo and ex vivo experimental methods to characterise scleral biomechanics are explored, along with computational techniques that combine structural and biomechanical data to simulate ocular behaviour and extract tissue material properties. Studies into alterations of scleral structure and biomechanics in myopia and glaucoma are presented, and their results reconciled with associated findings on changes in the ageing eye. Finally, new developments in scleral surgery and emerging minimally invasive therapies are highlighted that could offer new hope in the fight against escalating scleral-related vision disorder worldwide.

A molecular toolbox for interrogation of membrane contact sites

Membrane contact sites (MCSs) are specialized subcellular compartments formed by closely apposed membranes from two organelles. The intermembrane gap is separated by a distance ranging from 10 to 35 nm. MCSs are typically maintained through dynamic protein–protein and protein–lipid interactions. These intermembrane contact sites constitute important intracellular signalling hotspots to mediate a plethora of cellular processes, including calcium homeostasis, lipid metabolism, membrane biogenesis and organelle remodelling. In recent years, a series of genetically encoded probes and chemogenetic or optogenetic actuators have been invented to aid the visualization and interrogation of MCSs in both fixed and living cells. These molecular tools have greatly accelerated the pace of mechanistic dissection of membrane contact sites at the molecular level. In this review, we present an overview on the latest progress in this endeavour, and provide a general guide to the selection of methods and molecular tools for probing interorganellar membrane contact sites.

Morphometric analysis in mouse scleral fibroblasts using focused ion beam/scanning electron microscopy

The sclera as well as the cornea forms the principal part of the outer fibrous coat of the eye, with a primary function of protecting the intraocular contents and maintaining the shape of the globe. However, the exact morphometric arrangement of scleral fibroblasts remains unclarified. The aim of this study was to observe the three-dimensional structure of the mouse scleral fibroblasts by focused ion beam/scanning electron microscopy (FIB/SEM). Four eyes from C57BL/6J mice were fixed using a mixture of glutaraldehyde and formaldehyde. The sclera was cut out at the equatorial portion and the posterior pole, and postfixed with potassium ferrocyanide, osmium, thiocarbohydrazide, uranyl acetate and lead aspartate. Specimens were then dehydrated and embedded in an epoxy resin. Serial block face images were obtained using FIB/SEM. Three-dimensional image reconstruction and segmentation of the image stack were created using computer software (Amira v6.0.1, FEI). Scleral fibroblasts were arranged in collagenous layers. The cells frequently showed a cellular junction with the neighboring cells and formed cellular networks. Compared with equatorial fibroblasts, there was a more complicated cellular arrangement of the posterior scleral fibroblasts.

Gold-substituted Silver-intensified Peroxidase Immunolabeling for FIB-SEM Imaging

Modern electron microscopy offers a wide variety of tools to investigate the ultrastructural organization of cells and tissues and to accurately pinpoint intracellular localizations of macromolecules of interest. New volumetric electron microscopy techniques and new instrumentation provide unique opportunities for high-throughput analysis of comparatively large volumes of tissue and their complete reconstitution in three-dimensional (3D) electron microscopy. However, due to a variety of technical issues such as the limited penetration of label into the tissue, low antigen preservation, substantial electron density of secondary detection reagents, and many others, the adaptation of immuno-detection techniques for use with such 3D imaging methods as focused ion beam-scanning electron microscopy (FIB-SEM) has been challenging. Here, we describe a sample preparation method for 3D FIB-SEM, which results in an optimal preservation and staining of ultrastructural details at a resolution necessary for tracing immunolabeled neuronal structures and detailed reconstruction of synapses. This technique is applicable to neuronal and non-neuronal cells, tissues, and a wide variety of antigens.

Algal Viruses: The (Atomic) Shape of Things to Come

Visualization of algal viruses has been paramount to their study and understanding. The direct observation of the morphological dynamics of infection is a highly desired capability and the focus of instrument development across a variety of microscopy technologies. However, the high temporal (ms) and spatial resolution (nm) required, combined with the need to operate in physiologically relevant conditions presents a significant challenge. Here we present a short history of virus structure study and its relation to algal viruses and highlight current work, concentrating on electron microscopy and atomic force microscopy, towards the direct observation of individual algae⁻virus interactions. Finally, we make predictions towards future algal virus study direction with particular focus on the exciting opportunities offered by modern high-speed atomic force microscopy methods and instrumentation.

Cells Adhering to 3D Vertical Nanostructures: Cell Membrane Reshaping without Stable Internalization

The dynamic interface between the cellular membrane and 3D nanostructures determines biological processes and guides the design of novel biomedical devices. Despite the fact that recent advancements in the fabrication of artificial biointerfaces have yielded an enhanced understanding of this interface, there remain open questions on how the cellular membrane reacts and behaves in the presence of sharp objects on the nanoscale. Here we provide a multifaceted characterization of the cellular membrane's mechanical stability when closely interacting with high-aspect-ratio 3D vertical nanostructures, providing strong evidence that vertical nanostructures spontaneously penetrate the cellular membrane to form a steady intracellular coupling only in rare cases and under specific conditions. The cell membrane is able to conform tightly over the majority of structures with various shapes while maintaining its integrity.

The Three-Dimensional Microenvironment of the Mitral Valve: Insights into the Effects of Physiological Loads

INTRODUCTION

In the mitral valve (MV), numerous pathological factors, especially those resulting from changes in external loading, have been shown to affect MV structure and composition. Such changes are driven by the MV interstitial cell (MVIC) population via protein synthesis and enzymatic degradation of extracellular matrix (ECM) components.

METHODS

While cell phenotype, ECM composition and regulation, and tissue level changes in MVIC shape under stress have been studied, a detailed understanding of the three-dimensional (3D) microstructural mechanisms are lacking. As a first step in addressing this challenge, we applied focused ion beam scanning electron microscopy (FIB-SEM) to reveal novel details of the MV microenvironment in 3D.

RESULTS

We demonstrated that collagen is organized into large fibers consisting of an average of 605 ± 113 fibrils, with a mean diameter of 61.2 ± 9.8 nm. In contrast, elastin was organized into two distinct structural subtypes: (1) sheet-like lamellar elastin, and (2) circumferentially oriented elastin struts, based on both the aspect ratio and transmural tilt. MVICs were observed to have a large cytoplasmic volume, as evidenced by the large mean surface area to volume ratio 3.68 ± 0.35, which increased under physiological loading conditions to 4.98 ± 1.17.

CONCLUSIONS

Our findings suggest that each MVIC mechanically interacted only with the nearest 3-4 collagen fibers. This key observation suggests that in developing multiscale MV models, each MVIC can be considered a mechanically integral part of the local fiber ensemble and is unlikely to be influenced by more distant structures.

Protein disorder–order interplay to guide the growth of hierarchical mineralized structures

A major goal in materials science is to develop bioinspired functional materials based on the precise control of molecular building blocks across length scales. Here we report a protein-mediated mineralization process that takes advantage of disorder–order interplay using elastin-like recombinamers to program organic–inorganic interactions into hierarchically ordered mineralized structures. The materials comprise elongated apatite nanocrystals that are aligned and organized into microscopic prisms, which grow together into spherulite-like structures hundreds of micrometers in diameter that come together to fill macroscopic areas. The structures can be grown over large uneven surfaces and native tissues as acid-resistant membranes or coatings with tuneable hierarchy, stiffness, and hardness. Our study represents a potential strategy for complex materials design that may open opportunities for hard tissue repair and provide insights into the role of molecular disorder in human physiology and pathology.

There is evidence that disordered proteins play a role in the mineralization process. Here, the authors report on the development of elastin-like recombinant protein membranes using disordered-ordered interplay to investigate and guide mineralization.

Three-dimensional reconstruction of the intercalated disc including the intercellular junctions by applying volume scanning electron microscopy

The intercalated disc (ID) contains different kinds of intercellular junctions: gap junctions (GJs), desmosomes and areae compositae, essential for adhesion and communication between adjacent cardiomyocytes. The junctions can be identified based on their morphology when imaged using transmission electron microscopy (TEM), however, only with very limited information in the z-dimension. The application of volume EM techniques can give insight into the three-dimensional (3-D) organization of complex biological structures. In this study, we generated 3-D datasets using serial block-face scanning electron microscopy (SBF-SEM) and focused ion beam SEM (FIB-SEM), the latter resulting in datasets with 5 nm isotropic voxels. We visualized cardiomyocytes in murine ventricular heart tissue and, for the first time, we could three-dimensionally reconstruct the ID including desmosomes and GJs with 5 nm precision in a large volume. Results show in three dimensions a highly folded structure of the ID, with the presence of GJs and desmosomes in both plicae and interplicae regions. We observed close contact of GJs with mitochondria and a variable spatial distribution of the junctions. Based on measurements of the shape of the intercellular junctions in 3-D, it is seen that GJs and desmosomes vary in size, depending on the region within the ID. This demonstrates that volume EM is essential to visualize morphological changes and its potential to quantitatively determine structural changes between normal and pathological conditions, e.g., cardiomyopathies.

Three-Dimensional Analysis of Peeled Internal Limiting Membrane Using Focused Ion Beam/Scanning Electron Microscopy

Purpose

To reevaluate the effect of internal limiting membrane peeling during vitrectomy on the Müller cell damage, we examined the ultrastructure of the internal limiting membrane by using focused ion beam/scanning electron microscopy (FIB/SEM).

Methods

A total of 12 internal limiting membranes obtained during surgery in both the macular hole and the idiopathic epiretinal membrane groups were processed for observation by FIB/SEM. Three-dimensional structures of the internal limiting membrane were analyzed.

Results

The number of cell fragments in the macular hole group was 5.07 ± 1.03 per unit area of internal limiting membrane (100 μm²). The total volume of cell fragments was 3.54 ± 1.24 μm³/100 μm². In contrast, the number of cell fragments in the epiretinal membrane group was 12.85 ± 3.45/100 μm², and the total volume of cell fragments was 10.45 ± 2.77 μm³/100 μm². Data for both values were significantly higher than those observed in the macular hole group (P = 0.0024 and P = 0.0022, respectively, Mann-Whitney U test). No statistical difference was found for the mean volume of the cell fragment between the two groups.

Conclusions

All of the internal limiting membrane examined in this study showed cell fragments on the retinal surface of the internal limiting membrane. As compared with macular hole, epiretinal membrane exhibited a higher number and total volume of cell fragments, indicating that internal limiting membrane peeling for epiretinal membrane might have a higher risk of causing inner retinal damage.

Translational Relevance

FIB/SEM was a useful tool for three-dimensional quantitative analysis of the internal limiting membrane.

Unravelling the plant signalling machinery: an update on the cellular and genetic basis of plant signal transduction

Plant signalling is a set of phenomena that serves the transduction of external and internal signals into physiological responses such as modification of enzyme activity, cytoskeleton structure or gene expression. It operates at the level of cell compartments, whole cells, tissues, organs or even plant communities. To achieve this, plants have evolved a network of signalling proteins including plasma membrane receptors and ion transporters, cascades of kinases and other enzymes as well as several second messengers such as cytosolic calcium (Ca2+), reactive oxygen/nitrogen species (ROS/RNS), cyclic nucleotides (cAMP and cGMP) and others. Overall, these systems recognise and decode environmental signals and co-ordinate ontogeny programs. This paper summarises recent progress in the field of plant signalling, which was a major theme of the 4th International Symposium on Plant Signalling and Behaviour, 2016, in Saint Petersburg, Russia. Several novel hypotheses and concepts were proposed during this meeting. First, the concept of ROS-Ca2+ hubs has found further evidence and acceptance. This concept is based on reciprocal activation of NADPH oxidases by cytosolic Ca2+ on the one hand, and Ca2+-permeable channels that are activated by NADPH-produced ROS. ROS-Ca2+ hubs enhance the intensity and duration of originally weak Ca2+ and ROS signals. Hubs are directly involved in ROS- and Ca2+-mediated physiological reactions, such as stress response, growth, programmed cell death, autophagy and long-distance signalling. Second, recent findings have widened the list of cyclic nucleotide-regulated processes and strengthened the biochemical basis of cyclic nucleotide biochemistry by exploring cyclase activities of new receptors such as the Phytosulfokine Receptor 1, the pathogen peptide 1 receptor (atPepR1), the brassinosteroid BRI1 receptor and the cell wall-associated kinase like 10. cGMP and cAMP signalling has demonstrated strong link to Ca2+ signalling, via cyclic nucleotide-gated Ca2+-permeable ion channels (CNGCs), and to ROS and RNS via their nitrosylated forms. Third, a novel role for cytosolic K+ as a regulator of plant autophagy and programmed cell death has emerged. The cell death-associated proteases and endonucleases were demonstrated to be activated by a decrease of cytosolic K+ via ROS-induced stimulation of the plasma membrane K+ efflux channel GORK. Importantly, the origin of ROS for induction of autophagy and cell death varies in different tissues and comprises several pools, including NADPH oxidases, peroxidases, photosynthetic and respiratory electron-transporting chains and peroxisomal enzymes. The peroxisome pool is the 'latest' addition to established cellular ROS-producing machineries and is dependent on the state and abundance of catalase in this compartment. Finally, new aspects of phytohormone signalling, such as regulation of root hydraulic pressure by abscisic acid and rate of mitosis by cytokinins, as well as localising cytokinin receptors in endoplasmic reticulum, are reported. Other observations suggest that melatonin is a hormone-like substance in plants, because it targets Ca2+, ROS and RNS.

Imaging analysis of the interface between osteoblasts and microrough surfaces of laser-sintered titanium alloy constructs

Previous work using focused ion beam (FIB) analysis of osteoblasts on smooth and microrough Ti surfaces showed that the average cell aspect ratio and distance from the surface are greater on the rough surface. In order to better interrogate the relationship between individual cells and their substrate using multiple imaging modalities, we developed a method that tracks the same cell across confocal laser scanning microscopy (CLSM) to correlate surface microroughness with cell morphology and cytoskeleton; scanning electron microscopy (SEM) to provide higher resolution for observation of nanoroughness as well as chemical mapping via energy dispersive X-ray spectroscopy; and transmission electron microscopy (TEM) for high-resolution imaging. FIB was used to prepare thin sections of the cell-material interface for TEM, or for three-dimensional electron tomography. Cells were cultured on laser-sintered Ti-6Al-4V substrates with polished or etched surfaces. Direct cell to surface attachments were observed across surfaces, though bridging across macroscale surface features occurred on rough substrates. Our results show that surface roughness, cell cytoskeleton and gross morphology can be correlated with the cell-material cross-sectional interface at the single cell level across multiple high-resolution imaging modalities. This work provides a platform method for further investigating mechanisms of the cell-material interface.

Revealing the Cell-Material Interface with Nanometer Resolution by Focused Ion Beam/Scanning Electron Microscopy

The interface between cells and nonbiological surfaces regulates cell attachment, chronic tissue responses, and ultimately the success of medical implants or biosensors. Clinical and laboratory studies show that topological features of the surface profoundly influence cellular responses; for example, titanium surfaces with nano- and microtopographical structures enhance osteoblast attachment and host-implant integration as compared to a smooth surface. To understand how cells and tissues respond to different topographical features, it is of critical importance to directly visualize the cell-material interface at the relevant nanometer length scale. Here, we present a method for in situ examination of the cell-to-material interface at any desired location, based on focused ion beam milling and scanning electron microscopy imaging to resolve the cell membrane-to-material interface with 10 nm resolution. By examining how cell membranes interact with topographical features such as nanoscale protrusions or invaginations, we discovered that the cell membrane readily deforms inward and wraps around protruding structures, but hardly deforms outward to contour invaginating structures. This asymmetric membrane response (inward vs outward deformation) causes the cleft width between the cell membrane and the nanostructure surface to vary by more than an order of magnitude. Our results suggest that surface topology is a crucial consideration for the development of medical implants or biosensors whose performances are strongly influenced by the cell-to-material interface. We anticipate that the method can be used to explore the direct interaction of cells/tissue with medical devices such as metal implants in the future.

Pore shape and size dependence on cell growth into electrospun fiber scaffolds for tissue engineering: 2D and 3D analyses using SEM and FIB-SEM tomography

Electrospun nanofibers have ability to boost cell proliferation in tissue engineered scaffolds as their structure remind cells extra cellular matrix of the native tissue. The complex architecture and network of nanofibrous scaffolds requires advanced characterization methods to understand interrelationship between cells and nanofibers. In our study, we used complementary 2D and 3D analyses of electrospun polylactide-co-glycolide acid (PLGA) scaffolds in two configurations: aligned and randomly oriented nanofibers. Sizes of pores and fibers, pores shapes and porosity, before and after cell culture, were verified by imaging with scanning electron microscopy (SEM) and combination of focus ion beam (FIB) and SEM to obtain 3D reconstructions of samples. Using FIB-SEM tomography for 3D reconstructions and 2D analyses, a unique set of data allowing understanding cell proliferation mechanism into the electrospun scaffolds, was delivered. Critically, the proliferation of cells into nanofibers network depends mainly on the pore shape and pores interconnections, which allow deep integration between cells and nanofibers. The proliferation of cells inside the network of fibers is much limited for aligned fibers comparing to randomly oriented fibers. For random fibers cells have easier way to integrate inside the scaffold as the circularity of pores and their sizes are larger than for aligned scaffolds. The complex architecture of electrospun scaffolds requires appropriate, for tissue engineering needs, cell seeding and culture methods, to maximize tissue growth in vitro environment.

Quantifying the Structure and Composition of Flocculated Suspended Particulate Matter Using Focused Ion Beam Nanotomography

Suspended particulate matter (SPM) is present in the natural aquatic environment as loosely bound aggregates or "flocs" and is responsible for the transport and fate of sediment, carbon, nutrients, pollutants, pathogens and manufactured nanoparticles from catchment to coast. Accurate prediction of SPM hydrodynamics requires the quantification of 3D floc properties (size, shape, density and porosity) that span several spatial scales. Yet, current techniques (video camera systems, optical microscopy and transmission electron microscopy, TEM) can only provide 2D simplifications of size and shape with a spatial resolution gap between the "gross" (>100s μm) and nanoscale (<1 μm). Here, we translate 3D-microscopy techniques (focused ion beam nanotomography, FIB-nt) typically used in the biomedical sciences to the study of natural flocculated SPM filling both this spatial and dimensional gap. Fragile 3D floc samples were successfully captured and stabilized, identifying five basic organic and inorganic floc components and quantifying porosity and bacteria numbers. This provides new 3D floc geometric data sets at the nanoscale that will be critical in the development of cohesive sediment transport models. Detailed compositional and structural information could provide novel insights into the association of pathogens and pollutants with SPM and their impact on aquatic life.

Nanoscale Imaging of Collagen Gels with Focused Ion Beam Milling and Scanning Electron Microscopy

In vitro polymerized type I collagen hydrogels have been used extensively as a model system for three-dimensional (3D) cell and tissue culture, studies of fibrillogenesis, and investigation of multiscale force transmission within connective tissues. The nanoscale organization of collagen fibrils plays an essential role in the mechanics of these gels and emergent cellular behavior in culture, yet quantifying 3D structure with nanoscale resolution to fully characterize fibril organization remains a significant technical challenge. In this study, we demonstrate that a new imaging modality, focused ion beam scanning electron microscopy (FIB-SEM), can be used to generate 3D image datasets for visualizing and quantifying complex nanoscale organization and morphometry in collagen gels. We polymerized gels at a number of concentrations and conditions commonly used for in vitro models, stained and embedded the samples, and performed FIB-SEM imaging. The resulting image data had a voxel size of 25 nm, which is the highest resolution 3D data of a collagen fibril network ever obtained for collagen gels. This resolution was essential for discerning individual fibrils, fibril paths, and their branching and grouping. The resulting volumetric images revealed that polymerization conditions have a significant impact on the complex fibril morphology of the gels. We segmented the fibril network and demonstrated that individual collagen fibrils can be tracked in 3D space, providing quantitative analysis of network descriptors such as fibril diameter distribution, length, branch points, and fibril aggregations. FIB-SEM 3D reconstructions showed considerably less lateral grouping and overlap of fibrils than standard 2D SEM images, likely due to artifacts in SEM introduced by dehydration. This study demonstrates the utility of FIB-SEM for 3D imaging of collagen gels and quantitative analysis of 3D fibril networks. We anticipate that the method will see application in future studies of structure-function relationships in collagen gels as well as native collagenous tissues.

Ion-damage-free planarization or shallow angle sectioning of solar cells for mapping grain orientation and nanoscale photovoltaic properties

Ion beam milling is the most common modern method for preparing specific features for microscopic analysis, even though concomitant ion implantation and amorphization remain persistent challenges, particularly as they often modify materials properties of interest. Atomic force microscopy (AFM), on the other hand, can mechanically mill specific nanoscale regions in plan-view without chemical or high energy ion damage, due to its resolution, directionality, and fine load control. As an example, AFM-nanomilling (AFM-NM) is implemented for top-down planarization of polycrystalline CdTe thin film solar cells, with a resulting decrease in the root mean square (RMS) roughness by an order of magnitude, even better than for a low incidence FIB polished surface. Subsequent AFM-based property maps reveal a substantially stronger contrast, in this case of the short-circuit current or open circuit voltage during light exposure. Electron back scattering diffraction (EBSD) imaging also becomes possible upon AFM-NM, enabling direct correlations between the local materials properties and the polycrystalline microstructure. Smooth shallow-angle cross-sections are demonstrated as well, based on targeted oblique milling. As expected, this reveals a gradual decrease in the average short-circuit current and maximum power as the underlying CdS and electrode layers are approached, but a relatively consistent open-circuit voltage through the diminishing thickness of the CdTe absorber. AFM-based nanomilling is therefore a powerful tool for material characterization, uniquely providing ion-damage free, selective area, planar smoothing or low-angle sectioning of specimens while preserving their functionality. This enables novel, co-located advanced AFM measurements, EBSD analysis, and investigations by related techniques that are otherwise hindered by surface morphology or surface damage.