Focused ion beams in biology

Coordination of force-generating actin-based modules stabilizes and remodels membranes in vivo

Membrane remodeling drives a broad spectrum of cellular functions, and it is regulated through mechanical forces exerted on the membrane by cytoplasmic complexes. Here, we investigate how actin filaments dynamically tune their structure to control the active transfer of membranes between cellular compartments with distinct compositions and biophysical properties. Using intravital subcellular microscopy in live rodents we show that a lattice composed of linear filaments stabilizes the granule membrane after fusion with the plasma membrane and a network of branched filaments linked to the membranes by Ezrin, a regulator of membrane tension, initiates and drives to completion the integration step. Our results highlight how the actin cytoskeleton tunes its structure to adapt to dynamic changes in the biophysical properties of membranes.

Sample preparation and data collection for serial block face scanning electron microscopy of mammalian cell monolayers

Volume electron microscopy encompasses a set of electron microscopy techniques that can be used to examine the ultrastructure of biological tissues and cells in three dimensions. Two block face techniques, focused ion beam scanning electron microscopy (FIB-SEM) and serial block face scanning electron microscopy (SBF-SEM) have often been used to study biological tissue samples. More recently, these techniques have been adapted to in vitro tissue culture samples. Here we describe step-by-step protocols for two sample embedding methods for in vitro tissue culture cells intended to be studied using SBF-SEM. The first focuses on cell pellet embedding and the second on en face embedding. En face embedding can be combined with light microscopy, and this CLEM workflow can be used to identify specific biological events by light microscopy, which can then be imaged using SBF-SEM. We systematically outline the steps necessary to fix, stain, embed and image adherent tissue culture cell monolayers by SBF-SEM. In addition to sample preparation, we discuss optimization of parameters for data collection. We highlight the challenges and key steps of sample preparation, and the consideration of imaging variables.

In vitro co-culture models for studying organoids-macrophages interaction: the golden technology of cancer immunotherapy

Macrophages, as the largest immune cell group in tumour tissues, play a crucial role in influencing various malignant behaviours of tumour cells and tumour immune evasion. As the research on macrophages and cancer immunotherapy develops, the importance of appropriate research models becomes increasingly evident. The development of organoids has bridged the gap between traditional two-dimensional (2D) cultures and animal experiments. Recent studies have demonstrated that organoids exhibit similar physiological characteristics to the source tissue and closely resemble the in vivo genome and molecular markers of the source tissue or organ. However, organoids still lack an immune component. Developing a co-culture model of organoids and macrophages is crucial for studying the interaction and mechanisms between tumour cells and macrophages. This paper presents an overview of the establishment of co-culture models, the current research status of organoid macrophage interactions, and the current status of immunotherapy. In addition, the application prospects and shortcomings of the model are explained. Ultimately, it is hoped that the co-culture model will offer a preclinical testing platform for maximising a precise cancer immunotherapy strategy.

Atomic-level imaging of beam-sensitive COFs and MOFs by low-dose electron microscopy

Electron microscopy, an important technique that allows for the precise determination of structural information with high spatiotemporal resolution, has become indispensable in unravelling the complex relationships between material structure and properties ranging from mesoscale morphology to atomic arrangement. However, beam-sensitive materials, particularly those comprising organic components such as metal-organic frameworks (MOFs) and covalent organic frameworks (COFs), would suffer catastrophic damage from the high energy electrons, hindering the determination of atomic structures. A low-dose approach has arisen as a possible solution to this problem based on the integration of advancements in several aspects: electron optical system, detector, image processing, and specimen preservation. This article summarizes the transmission electron microscopy characterization of MOFs and COFs, including local structures, host-guest interactions, and interfaces at the atomic level. Revolutions in advanced direct electron detectors, algorithms in image acquisition and processing, and emerging methodology for high quality low-dose imaging are also reviewed. Finally, perspectives on the future development of electron microscopy methodology with the support of computer science are presented.

Bridging structural and cell biology with cryo-electron microscopy

Most life scientists would agree that understanding how cellular processes work requires structural knowledge about the macromolecules involved. For example, deciphering the double-helical nature of DNA revealed essential aspects of how genetic information is stored, copied and repaired. Yet, being reductionist in nature, structural biology requires the purification of large amounts of macromolecules, often trimmed off larger functional units. The advent of cryogenic electron microscopy (cryo-EM) greatly facilitated the study of large, functional complexes and generally of samples that are hard to express, purify and/or crystallize. Nevertheless, cryo-EM still requires purification and thus visualization outside of the natural context in which macromolecules operate and coexist. Conversely, cell biologists have been imaging cells using a number of fast-evolving techniques that keep expanding their spatial and temporal reach, but always far from the resolution at which chemistry can be understood. Thus, structural and cell biology provide complementary, yet unconnected visions of the inner workings of cells. Here we discuss how the interplay between cryo-EM and cryo-electron tomography, as a connecting bridge to visualize macromolecules in situ, holds great promise to create comprehensive structural depictions of macromolecules as they interact in complex mixtures or, ultimately, inside the cell itself.

Dynamic changes in endoplasmic reticulum morphology and its contact with the plasma membrane in motor neurons in response to nerve injury

The endoplasmic reticulum (ER) extends throughout a cell and plays a critical role in maintaining cellular homeostasis. Changes in ER shape could provide a clue to explore the mechanisms that underlie the fate determination of neurons after axon injury because the ER drastically changes its morphology under neuronal stress to maintain cellular homeostasis and recover from damage. Because of their tiny structures and richness in the soma, the detailed morphology of the ER and its dynamics have not been well analysed. In this study, the focused ion beam/scanning electron microscopy (FIB/SEM) analysis was performed to explore the ultra-structures of the ER in the somata of motor neuron with axon regenerative injury models. In normal motor neurons, ER in the somata is abundantly localised near the perinucleus and represents lamella-like structures. After injury, analysis of the ER volume and ER branching points indicated a collapse of the normal distribution and a transformation from lamella-like structures to mesh-like structures. Furthermore, accompanied by ER accumulation near the plasma membrane (PM), the contact between the ER and PM (ER-PM contacts) significantly increased after injury. The accumulation of extended-synaptotagmin 1 (E-Syt1), a tethering protein of the ER and PM that regulates Ca2+-dependent lipid transfer, was also identified by immunohistochemistry and quantitative Real-time PCR after injury. These morphological alterations of ER and the increase in ER-PM contacts may be crucial events that occur in motor neurons as a resilient response for the survival after axonal injury.

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.

Exploration of fs-laser ablation parameter space for 2D/3D imaging of soft and hard materials by tri-beam microscopy

Tri-beam microscopes comprising a fs-laser beam, a Xe+ plasma focused ion beam (PFIB) and an electron beam all in one chamber open up exciting opportunities for site-specific correlative microscopy. They offer the possibility of rapid ablation and material removal by fs-laser, subsequent polishing by Xe-PFIB milling and electron imaging of the same area. While tri-beam systems are capable of probing large (mm) volumes providing high resolution microscopical characterisation of 2D and 3D images across exceptionally wide range of materials and biomaterials applications, presenting high quality/low damage surfaces to the electron beam can present a significant challenge, especially given the large parameter space for optimisation. Here the optimal conditions and artefacts associated with large scale volume milling, mini test piece manufacture, serial sectioning and surface polishing are investigated, both in terms of surface roughness and surface quality for metallic, ceramic, mixed complex phase, carbonaceous, and biological materials. This provides a good starting place for those wishing to examine large areas or volumes by tri-beam microscopy across a range of materials.

CDK2 inhibition disorders centrosome stoichiometry and alters cellular outcomes in aneuploid cancer cells

Cyclin-dependent Kinase 2 (CDK2) inhibition prevents supernumerary centrosome clustering. This causes multipolarity, anaphase catastrophe and apoptotic death of aneuploid cancers. This study elucidated how CDK2 antagonism affected centrosome stoichiometry. Focused ion beam scanning electron microscopy (FIB-SEM) and immunofluorescent imaging were used. Studies interrogated multipolar mitosis after pharmacologic or genetic repression of CDK2. CDK2/9 antagonism with CYC065 (Fadraciclib)-treatment disordered centrosome stoichiometry in aneuploid cancer cells, preventing centrosome clustering. This caused ring-like chromosomes or multipolar cancer cells to form before onset of cell death. Intriguingly, CDK2 inhibition caused a statistically significant increase in single centrioles rather than intact centrosomes with two centrioles in cancer cells having chromosome rings or multipolarity. Statistically significant alterations in centrosome stoichiometry were undetected in other mitotic cancer cells. To confirm this pharmacodynamic effect, CDK2 but not CDK9 siRNA-mediated knockdown augmented cancer cells with chromosome ring or multipolarity formation. Notably, engineered gain of CDK2, but not CDK9 expression, reversed emergence of cancer cells with chromosome rings or multipolarity, despite CYC065-treatment. In marked contrast, CDK2 inhibition of primary human alveolar epithelial cells did not confer statistically significant increases of cells with ring-like chromosomes or multipolarity. Hence, CDK2 antagonism caused differential effects in malignant versus normal alveolar epithelial cells. Translational relevance was confirmed by CYC065-treatment of syngeneic lung cancers in mice. Mitotic figures in tumors exhibited chromosome rings or multipolarity. Thus, CDK2 inhibition preferentially disorders centrosome stoichiometry in cancer cells. Engaging this disruption is a strategy to explore against aneuploid cancers in future clinical trials.

Revealing the 3D Structure of Block Copolymers with Electron Microscopy: Current Status and Future Directions

Block copolymers (BCPs) are considered model systems for understanding and utilizing self-assembly in soft matter. Their tunable nanometric structure and composition enable comprehensive studies of self-assembly processes as well as make them relevant materials in diverse applications. A key step in developing and controlling BCP nanostructures is a full understanding of their three-dimensional (3D) structure and how this structure is affected by the BCP chemistry, confinement, boundary conditions, and the self-assembly evolution and dynamics. Electron microscopy (EM) is a leading method in BCP 3D characterization owing to its high resolution in imaging nanosized structures. Here we discuss the two main 3D EM methods: namely, transmission EM tomography and slice and view scanning EM tomography. We present each method's principles, examine their strengths and weaknesses, and discuss ways researchers have devised to overcome some of the challenges in BCP 3D characterization with EM- from specimen preparation to imaging radiation-sensitive materials. Importantly, we review current and new cutting-edge EM methods such as direct electron detectors, energy dispersive X-ray spectroscopy of soft matter, high temporal rate imaging, and single-particle analysis that have great potential for expanding the BCP understanding through EM in the future.

Advances in lithographic techniques for precision nanostructure fabrication in biomedical applications

Nano-fabrication techniques have demonstrated their vital importance in technological innovation. However, low-throughput, high-cost and intrinsic resolution limits pose significant restrictions, it is, therefore, paramount to continue improving existing methods as well as developing new techniques to overcome these challenges. This is particularly applicable within the area of biomedical research, which focuses on sensing, increasingly at the point-of-care, as a way to improve patient outcomes. Within this context, this review focuses on the latest advances in the main emerging patterning methods including the two-photon, stereo, electrohydrodynamic, near-field electrospinning-assisted, magneto, magnetorheological drawing, nanoimprint, capillary force, nanosphere, edge, nano transfer printing and block copolymer lithographic technologies for micro- and nanofabrication. Emerging methods enabling structural and chemical nano fabrication are categorised along with prospective chemical and physical patterning techniques. Established lithographic techniques are briefly outlined and the novel lithographic technologies are compared to these, summarising the specific advantages and shortfalls alongside the current lateral resolution limits and the amenability to mass production, evaluated in terms of process scalability and cost. Particular attention is drawn to the potential breakthrough application areas, predominantly within biomedical studies, laying the platform for the tangible paths towards the adoption of alternative developing lithographic technologies or their combination with the established patterning techniques, which depends on the needs of the end-user including, for instance, tolerance of inherent limits, fidelity and reproducibility.

Spatial and Temporal Coordination of Force-generating Actin-based Modules Drives Membrane Remodeling In Vivo

Membrane remodeling drives a broad spectrum of cellular functions, and it is regulated through mechanical forces exerted on the membrane by cytoplasmic complexes. Here, we investigate how actin filaments dynamically tune their structure to control the active transfer of membranes between cellular compartments with distinct compositions and biophysical properties. Using intravital subcellular microscopy in live rodents we show that: a lattice composed of linear filaments stabilizes the granule membrane after fusion with the plasma membrane; and a network of branched filaments linked to the membranes by Ezrin, a regulator of membrane tension, initiates and drives to completion the integration step. Our results highlight how the actin cytoskeleton tunes its structure to adapt to dynamic changes in the biophysical properties of membranes.

Three-dimensional architecture of granulosa cell derived from oocyte cumulus complex, revealed by FIB-SEM

The oocyte cumulus complex is mainly composed of an oocyte, the perivitelline space, zona pellucida and numerous granulosa cells. The cumulus granulosa cells (cGCs) provide a particularly important microenvironment for oocyte development, regulating its growth, maturation and meiosis. In this study, we studied the internal structures and cell-to-cell connections of mouse cGCs using focused ion beam scanning electron microscopy (FIB-SEM). We reconstructed three-dimensional models to display characteristic connections between the oocyte and cGCs, and to illustrate various main organelles in cGCs together with their interaction relationship. A special form of cilium identified in granulosa cell was never reported in previous literature.

Virus structures revealed by advanced cryoelectron microscopy methods

Before the resolution revolution, cryoelectron microscopy (cryo-EM) single-particle analysis (SPA) already achieved resolutions beyond 4 Å for certain icosahedral viruses, enabling ab initio atomic model building of these viruses. As the only samples that achieved such high resolution at that time, cryo-EM method development was closely intertwined with the improvement of reconstructions of symmetrical viruses. Viral morphology exhibits significant diversity, ranging from small to large, uniform to non-uniform, and from containing single symmetry to multiple symmetries. Furthermore, viruses undergo conformational changes during their life cycle. Several methods, such as asymmetric reconstruction, Ewald sphere correction, cryoelectron tomography (cryo-ET), and sub-tomogram averaging (STA), have been developed and applied to determine virus structures in vivo and in vitro. This review outlines current advanced cryo-EM methods for high-resolution structure determination of viruses and summarizes accomplishments obtained with these approaches. Moreover, persisting challenges in comprehending virus structures are discussed and we propose potential solutions.

Minimal resin embedding of SBF-SEM samples reduces charging and facilitates finding a surface-linked region of interest

BACKGROUND

For decoding the mechanism of how cells and organs function information on their ultrastructure is essential. High-resolution 3D imaging has revolutionized morphology. Serial block face scanning electron microscopy (SBF-SEM) offers non-laborious, automated imaging in 3D of up to ~ 1 mm3 large biological objects at nanometer-scale resolution. For many samples there are obstacles. Quality imaging is often hampered by charging effects, which originate in the nonconductive resin used for embedding. Especially, if the imaged region of interest (ROI) includes the surface of the sample and neighbours the empty resin, which insulates the object. This extra resin also obscures the sample's morphology, thus making navigation to the ROI difficult.

RESULTS

Using the example of small arthropods and a fish roe we describe a workflow to prepare samples for SBF-SEM using the minimal resin (MR) embedding method. We show that for imaging of surface structures this simple approach conveniently tackles and solves both of the two major problems-charging and ROI localization-that complicate imaging of SBF-SEM samples embedded in an excess of overlying resin. As the surface ROI is not masked by the resin, samples can be precisely trimmed before they are placed into the imaging chamber. The initial approaching step is fast and easy. No extra trimming inside the microscope is necessary. Importantly, charging is absent or greatly reduced meaning that imaging can be accomplished under good vacuum conditions, typically at the optimal high vacuum. This leads to better resolution, better signal to noise ratio, and faster image acquisition.

CONCLUSIONS

In MR embedded samples charging is minimized and ROI easily targeted. MR embedding does not require any special equipment or skills. It saves effort, microscope time and eventually leads to high quality data. Studies on surface-linked ROIs, or any samples normally surrounded by the excess of resin, would benefit from adopting the technique.

Novel Focused Ion Beam Liftouts for Spatial Characterization of Spherical Biominerals With Transmission Electron Microscopy

Focused ion beam (FIB) is frequently used to prepare electron- and X-ray-beam-transparent thin sections of samples, called lamellae. Typically, lamellae are prepared from only a subregion of a sample. In this paper, we present a novel approach for FIB lamella preparation of microscopic samples, wherein the entire cross-section of the whole sample can be investigated. The approach was demonstrated using spherical, porous, and often hollow microprecipitates of biologically precipitated calcium carbonate. The microprecipitate morphology made these biogenic samples more fragile and challenging than materials commonly investigated using FIB lamellae. Our method enables the appropriate orientation of the lamellae required for further electron/X-ray analyses after attachment to the transmission electron microscopy (TEM) grid post and facilitates more secure adhesion onto the grid post. We present evidence of autofluorescence in bacterially precipitated vaterite using this lamella preparation method coupled with TEM selected area diffraction. This innovative approach allows studying biomineralization at the micro to nano scales, which can provide novel insights into bacterial responses to microenvironmental conditions.

Three-dimensional ultrastructure analysis of organelles in injured motor neuron

Morphological analysis of organelles is one of the important clues for understanding the cellular conditions and mechanisms occurring in cells. In particular, nanoscale information within crowded intracellular organelles of tissues provide more direct implications when compared to analyses of cells in culture or isolation. However, there are some difficulties in detecting individual shape using light microscopy, including super-resolution microscopy. Transmission electron microscopy (TEM), wherein the ultrastructure can be imaged at the membrane level, cannot determine the whole structure, and analyze it quantitatively. Volume EM, such as focused ion beam/scanning electron microscopy (FIB/SEM), can be a powerful tool to explore the details of three-dimensional ultrastructures even within a certain volume, and to measure several parameters from them. In this review, the advantages of FIB/SEM analysis in organelle studies are highlighted along with the introduction of mitochondrial analysis in injured motor neurons. This would aid in understanding the morphological details of mitochondria, especially those distributed in the cell bodies as well as in the axon initial segment (AIS) in mouse tissues. These regions have not been explored thus far due to the difficulties encountered in accessing their images by conditional microscopies. Some mechanisms of nerve regeneration have also been discussed with reference to the obtained findings. Finally, future perspectives on FIB/SEM are introduced. The combination of biochemical and genetic understanding of organelle structures and a nanoscale understanding of their three-dimensional distribution and morphology will help to match achievements in genomics and structural biology.

The 3D Controllable Fabrication of Nanomaterials with FIB-SEM Synchronization Technology

Nanomaterials with unique structures and functions have been widely used in the fields of microelectronics, biology, medicine, and aerospace, etc. With advantages of high resolution and multi functions (e.g., milling, deposition, and implantation), focused ion beam (FIB) technology has been widely developed due to urgent demands for the 3D fabrication of nanomaterials in recent years. In this paper, FIB technology is illustrated in detail, including ion optical systems, operating modes, and combining equipment with other systems. Together with the in situ and real-time monitoring of scanning electron microscopy (SEM) imaging, a FIB-SEM synchronization system achieved 3D controllable fabrication from conductive to semiconductive and insulative nanomaterials. The controllable FIB-SEM processing of conductive nanomaterials with a high precision is studied, especially for the FIB-induced deposition (FIBID) 3D nano-patterning and nano-origami. As for semiconductive nanomaterials, the realization of high resolution and controllability is focused on nano-origami and 3D milling with a high aspect ratio. The parameters of FIB-SEM and its working modes are analyzed and optimized to achieve the high aspect ratio fabrication and 3D reconstruction of insulative nanomaterials. Furthermore, the current challenges and future outlooks are prospected for the 3D controllable processing of flexible insulative materials with high resolution.

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.

Light and electron microscopy continuum-resolution imaging of 3D cell cultures

3D cell cultures, in particular organoids, are emerging models in the investigation of healthy or diseased tissues. Understanding the complex cellular sociology in organoids requires integration of imaging modalities across spatial and temporal scales. We present a multi-scale imaging approach that traverses millimeter-scale live-cell light microscopy to nanometer-scale volume electron microscopy by performing 3D cell cultures in a single carrier that is amenable to all imaging steps. This allows for following organoids' growth, probing their morphology with fluorescent markers, identifying areas of interest, and analyzing their 3D ultrastructure. We demonstrate this workflow on mouse and human 3D cultures and use automated image segmentation to annotate and quantitatively analyze subcellular structures in patient-derived colorectal cancer organoids. Our analyses identify local organization of diffraction-limited cell junctions in compact and polarized epithelia. The continuum-resolution imaging pipeline is thus suited to fostering basic and translational organoid research by simultaneously exploiting the advantages of light and electron microscopy.

A membrane reticulum, the centriculum, affects centrosome size and function in Caenorhabditis elegans

Centrosomes are cellular structures that nucleate microtubules. At their core is a pair of centrioles that recruit pericentriolar material (PCM). Although centrosomes are considered membraneless organelles, in many cell types, including human cells, centrosomes are surrounded by endoplasmic reticulum (ER)-derived membranes of unknown structure and function. Using volume electron microscopy (vEM), we show that centrosomes in the Caenorhabditis elegans (C. elegans) early embryo are surrounded by a three-dimensional (3D), ER-derived membrane reticulum that we call the centriculum, for centrosome-associated membrane reticulum. The centriculum is adjacent to the nuclear envelope in interphase and early mitosis and fuses with the fenestrated nuclear membrane at metaphase. Centriculum formation is dependent on the presence of an underlying centrosome and on microtubules. Conversely, increasing centriculum size by genetic means led to the expansion of the PCM, increased microtubule nucleation capacity, and altered spindle width. The effect of the centriculum on centrosome function suggests that in the C. elegans early embryo, the centrosome is not membraneless. Rather, it is encased in a membrane meshwork that affects its properties. We provide evidence that the centriculum serves as a microtubule "filter," preventing the elongation of a subset of microtubules past the centriculum. Finally, we propose that the fusion between the centriculum and the nuclear membrane contributes to nuclear envelope breakdown by coupling spindle elongation to nuclear membrane fenestration.

Positive-strand RNA viruses-a Keystone Symposia report

Positive-strand RNA viruses have been the cause of several recent outbreaks and epidemics, including the Zika virus epidemic in 2015, the SARS outbreak in 2003, and the ongoing SARS-CoV-2 pandemic. On June 18-22, 2022, researchers focusing on positive-strand RNA viruses met for the Keystone Symposium "Positive-Strand RNA Viruses" to share the latest research in molecular and cell biology, virology, immunology, vaccinology, and antiviral drug development. This report presents concise summaries of the scientific discussions at the symposium.

Liver inter-organelle membrane contact sites revealed by serial section electron tomography

Inter-organelle membrane contact sites (MCSs) are defined as areas of close proximity between the membranes of two organelles (10-80nm). They have been implicated in many physiological processes such as Ca++, lipids or small molecules transfer, organelles biogenesis or dynamic and have an important role in many cellular processes such as apoptosis, autophagy, and signaling. Since the distance and the extent of these contacts are in the nanometer range, high resolution techniques are ideal for imaging these structures. It is for this reason that transmission electron microscopy (TEM) has been considered the gold standard for MCSs visualization and the first technique that described them. However, often TEM analysis is limited to 2D lacking information on the 3D association between the organelles involved in MCSs. To fully describe the complex architecture of MSCs and to unveil their role in cellular physiology a 3D analysis is required. This chapter provides a method for the analysis of MCSs using serial section electron tomography (ssET), a technique able to reconstruct in 3D at nanometer resolution cellular and subcellular structures. By applying this procedure, it was possible to elucidate the role of the contacts between Endoplasmic Reticulum (ER) and other organelles in liver lipid metabolism.

Three-dimensional visualization of dentine occlusion based on FIB-SEM tomography

The occlusion of dentinal tubules has become a rapid and effective method for treating dentin hypersensitivity. Accurate evaluation of dentin occlusion is critical to illustrate the efficacy of oral care products and to optimize dental therapy in the clinics, which is limited by the conventional two-dimensional (2-D) characterization methods. Here, we demonstrate the visualization of the dentin occlusion via three-dimensional (3-D) characterization using a focused ion beam-scanning electron microscopy (FIB-SEM) tomography. Using the "Slice and View" approach, the material used for occluding dentin tubules is imaged with a very high-resolution voxel (10 nm × 10 nm × 20 nm) from 2-D SEM images and then reconstructed into a 3-D volume, which presents the mode of action of toothpaste for treating dentin hypersensitivity. Meanwhile, quantitative analysis of the depth of occlusion is successfully obtained. This work validates the feasibility of FIB-SEM tomography in the analysis of dentin occlusion within the complicated networks of dentine tubules at the nanoscale, and provides a novel approach to facilitate the research and development of oral care products.

Light and focused ion beam microscopy workflow for resin-embedded tissues

Although the automated image acquisition with the focused ion beam scanning electron microscope (FIB-SEM) provides volume reconstructions, volume analysis of large samples remains challenging. Here, we present a workflow that combines a modified sample protocol of the classical transmission electron microscope with FIB-SEM volume imaging. The proposed workflow enables efficient 3D structural surveys of rabbit ovaries collected at consecutive developmental stages. The precise trimming of the region of interest adds the time dimension to the volume, constructing a virtual 4D electron microscopy. We found filopodia-like processes emitted by oocyte cysts allowing contact between oocytes not previously observed.

Instance segmentation of mitochondria in electron microscopy images with a generalist deep learning model trained on a diverse dataset

Mitochondria are extremely pleomorphic organelles. Automatically annotating each one accurately and precisely in any 2D or volume electron microscopy (EM) image is an unsolved computational challenge. Current deep learning-based approaches train models on images that provide limited cellular contexts, precluding generality. To address this, we amassed a highly heterogeneous ∼1.5 × 10⁶ image 2D unlabeled cellular EM dataset and segmented ∼135,000 mitochondrial instances therein. MitoNet, a model trained on these resources, performs well on challenging benchmarks and on previously unseen volume EM datasets containing tens of thousands of mitochondria. We release a Python package and napari plugin, empanada, to rapidly run inference, visualize, and proofread instance segmentations. A record of this paper's transparent peer review process is included in the supplemental information.

EMPIAR: the Electron Microscopy Public Image Archive

Public archiving in structural biology is well established with the Protein Data Bank (PDB; wwPDB.org) catering for atomic models and the Electron Microscopy Data Bank (EMDB; emdb-empiar.org) for 3D reconstructions from cryo-EM experiments. Even before the recent rapid growth in cryo-EM, there was an expressed community need for a public archive of image data from cryo-EM experiments for validation, software development, testing and training. Concomitantly, the proliferation of 3D imaging techniques for cells, tissues and organisms using volume EM (vEM) and X-ray tomography (XT) led to calls from these communities to publicly archive such data as well. EMPIAR (empiar.org) was developed as a public archive for raw cryo-EM image data and for 3D reconstructions from vEM and XT experiments and now comprises over a thousand entries totalling over 2 petabytes of data. EMPIAR resources include a deposition system, entry pages, facilities to search, visualize and download datasets, and a REST API for programmatic access to entry metadata. The success of EMPIAR also poses significant challenges for the future in dealing with the very fast growth in the volume of data and in enhancing its reusability.

CLEMSite, a software for automated phenotypic screens using light microscopy and FIB-SEM

In recent years, Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) has emerged as a flexible method that enables semi-automated volume ultrastructural imaging. We present a toolset for adherent cells that enables tracking and finding cells, previously identified in light microscopy (LM), in the FIB-SEM, along with the automatic acquisition of high-resolution volume datasets. We detect the underlying grid pattern in both modalities (LM and EM), to identify common reference points. A combination of computer vision techniques enables complete automation of the workflow. This includes setting the coincidence point of both ion and electron beams, automated evaluation of the image quality and constantly tracking the sample position with the microscope's field of view reducing or even eliminating operator supervision. We show the ability to target the regions of interest in EM within 5 µm accuracy while iterating between different targets and implementing unattended data acquisition. Our results demonstrate that executing volume acquisition in multiple locations autonomously is possible in EM.

Nanoscale 3D Tomography by In-Flight Fluorescence Spectroscopy of Atoms Sputtered by a Focused Ion Beam

Nanoscale fabrication and characterization techniques critically underpin a vast range of fields, including nanoelectronics and nanobiotechnology. Focused ion beam (FIB) techniques are appealing due to their high spatial resolution and widespread use for processing of nanostructured materials. Here, we introduce FIB-induced fluorescence spectroscopy (FIB-FS) as a nanoscale technique for spectroscopic detection of atoms sputtered by an ion beam. We use semiconductor heterostructures to demonstrate nanoscale lateral and depth resolution and show that it is limited by ion-induced intermixing of nanostructured materials. Sensitivity is demonstrated qualitatively by depth profiling of 3.5, 5, and 8 nm quantum wells and quantitatively by detection of trace-level impurities present at parts-per-million levels. The utility of the FIB-FS technique is demonstrated by characterization of quantum wells and Li-ion batteries. Our work introduces FIB-FS as a high-resolution, high-sensitivity, 3D analysis and tomography technique that combines the versatility of FIB nanofabrication techniques with the power of diffraction-unlimited fluorescence spectroscopy.

How innovations in methodology offer new prospects for volume electron microscopy

Detailed knowledge of biological structure has been key in understanding biology at several levels of organisation, from organs to cells and proteins. Volume electron microscopy (volume EM) provides high resolution 3D structural information about tissues on the nanometre scale. However, the throughput rate of conventional electron microscopes has limited the volume size and number of samples that can be imaged. Recent improvements in methodology are currently driving a revolution in volume EM, making possible the structural imaging of whole organs and small organisms. In turn, these recent developments in image acquisition have created or stressed bottlenecks in other parts of the pipeline, like sample preparation, image analysis and data management. While the progress in image analysis is stunning due to the advent of automatic segmentation and server-based annotation tools, several challenges remain. Here we discuss recent trends in volume EM, emerging methods for increasing throughput and implications for sample preparation, image analysis and data management.

Unmasking the Resolution-Throughput Tradespace of Focused-Ion-Beam Machining

Focused-ion-beam machining is a powerful process to fabricate complex nanostructures, often through a sacrificial mask that enables milling beyond the resolution limit of the ion beam. However, current understanding of this super-resolution effect is empirical in the spatial domain and nonexistent in the temporal domain. This article reports the primary study of this fundamental tradespace of resolution and throughput. Chromia functions well as a masking material due to its smooth, uniform, and amorphous structure. An efficient method of in-line metrology enables characterization of ion-beam focus by scanning electron microscopy. Fabrication and characterization of complex test structures through chromia and into silica probe the response of the bilayer to a focused beam of gallium cations, demonstrating super-resolution factors of up to 6 ± 2 and improvements to volume throughput of at least factors of 42 ± 2, with uncertainties denoting 95% coverage intervals. Tractable theory models the essential aspects of the super-resolution effect for various nanostructures. Application of the new tradespace increases the volume throughput of machining Fresnel lenses by a factor of 75, enabling the introduction of projection standards for optical microscopy. These results enable paradigm shifts of sacrificial masking from empirical to engineering design and from prototyping to manufacturing.

A versatile enhanced freeze-substitution protocol for volume electron microscopy

Volume electron microscopy, a powerful approach to generate large three-dimensional cell and tissue volumes at electron microscopy resolutions, is rapidly becoming a routine tool for understanding fundamental and applied biological questions. One of the enabling factors for its adoption has been the development of conventional fixation protocols with improved heavy metal staining. However, freeze-substitution with organic solvent-based fixation and staining has not realized the same level of benefit. Here, we report a straightforward approach including osmium tetroxide, acetone and up to 3% water substitution fluid (compatible with traditional or fast freeze-substitution protocols), warm-up and transition from organic solvent to aqueous 2% osmium tetroxide. Once fully hydrated, samples were processed in aqueous based potassium ferrocyanide, thiocarbohydrazide, osmium tetroxide, uranyl acetate and lead acetate before resin infiltration and polymerization. We observed a consistent and substantial increase in heavy metal staining across diverse and difficult-to-fix test organisms and tissue types, including plant tissues (Hordeum vulgare), nematode (Caenorhabditis elegans) and yeast (Saccharomyces cerevisiae). Our approach opens new possibilities to combine the benefits of cryo-preservation with enhanced contrast for volume electron microscopy in diverse organisms.

Molecular organization of the early stages of nucleosome phase separation visualized by cryo-electron tomography

It has been proposed that the intrinsic property of nucleosome arrays to undergo liquid-liquid phase separation (LLPS) in vitro is responsible for chromatin domain organization in vivo. However, understanding nucleosomal LLPS has been hindered by the challenge to characterize the structure of the resulting heterogeneous condensates. We used cryo-electron tomography and deep-learning-based 3D reconstruction/segmentation to determine the molecular organization of condensates at various stages of LLPS. We show that nucleosomal LLPS involves a two-step process: a spinodal decomposition process yielding irregular condensates, followed by their unfavorable conversion into more compact, spherical nuclei that grow into larger spherical aggregates through accretion of spinodal materials or by fusion with other spherical condensates. Histone H1 catalyzes more than 10-fold the spinodal-to-spherical conversion. We propose that this transition involves exposure of nucleosome hydrophobic surfaces causing modified inter-nucleosome interactions. These results suggest a physical mechanism by which chromatin may transition from interphase to metaphase structures.

Volume electron microscopy

Life exists in three dimensions, but until the turn of the century most electron microscopy methods provided only 2D image data. Recently, electron microscopy techniques capable of delving deep into the structure of cells and tissues have emerged, collectively called volume electron microscopy (vEM). Developments in vEM have been dubbed a quiet revolution as the field evolved from established transmission and scanning electron microscopy techniques, so early publications largely focused on the bioscience applications rather than the underlying technological breakthroughs. However, with an explosion in the uptake of vEM across the biosciences and fast-paced advances in volume, resolution, throughput and ease of use, it is timely to introduce the field to new audiences. In this Primer, we introduce the different vEM imaging modalities, the specialized sample processing and image analysis pipelines that accompany each modality and the types of information revealed in the data. We showcase key applications in the biosciences where vEM has helped make breakthrough discoveries and consider limitations and future directions. We aim to show new users how vEM can support discovery science in their own research fields and inspire broader uptake of the technology, finally allowing its full adoption into mainstream biological imaging.

3D FIB-SEM structural insights into the architecture of sub-pellicular microtubules of Trypanosoma cruzi epimastigotes

BACKGROUND INFORMATION

Trypanosomatidae, which includes eukaryotic species agents of diseases like leishmaniasis, sleeping sickness, and Chagas disease, have special structures and organelles not found in mammalian cells. They present a layer of microtubules, known as subpellicular microtubules (SPMT), located underneath the plasma membrane and responsible for preserving cell morphology, cell polarity, the position of single copy organelles, and morphological changes that occur throughout the protozoan life cycle. Even though a lot of knowledge about the SPMT is available, we still do not know exactly how each microtubule in the system is organized in three dimensions. Here, we use focused ion beam scanning electron microscopy (FIB-SEM) to analyze the tridimensional organization of epimastigotes SPMT.

RESULTS

The high-resolution 3D analyses revealed that certain microtubules of the SPMT end more prematurely than the neighboring ones.

CONCLUSIONS

These microtubules could (1) be shorter or (2) have the same length as the neighboring ones, assuming that those end up earlier at their other end, might be treadmilling/catastrophe events that have not yet been described in trypanosomatids.

An Overview of Cryo-Scanning Electron Microscopy Techniques for Plant Imaging

Many research questions require the study of plant morphology, in particular cells and tissues, as close to their native context as possible and without physical deformations from some preparatory chemical reagents or sample drying. Cryo-scanning electron microscopy (cryoSEM) involves rapid freezing and maintenance of the sample at an ultra-low temperature for detailed surface imaging by a scanning electron beam. The data are useful for exploring tissue/cell morphogenesis, plus an additional cryofracture/cryoplaning/milling step gives information on air and water spaces as well as subcellular ultrastructure. This review gives an overview from sample preparation through to imaging and a detailed account of how this has been applied across diverse areas of plant research. Future directions and improvements to the technique are discussed.

Cryogenic Focused Ion Beam Enables Atomic-Resolution Imaging of Local Structures in Highly Sensitive Bulk Crystals and Devices

With the development of ultralow-dose (scanning) transmission electron microscopy ((S)TEM) techniques, atomic-resolution imaging of highly sensitive nanomaterials has recently become possible. However, applying these techniques to the study of sensitive bulk materials remains challenging due to the lack of suitable specimen preparation methods. We report that cryogenic focused ion beam (cryo-FIB) can provide a solution to this challenge. We successfully extracted thin specimens from metal-organic framework (MOF) crystals and a hybrid halide perovskite single-crystal film solar cell using cryo-FIB without damaging the inherent structures. The high quality of the specimens enabled the subsequent (S)TEM and electron diffraction studies to reveal complex unknown local structures at an atomic resolution. The obtained structural information allowed us to resolve planar defects in MOF HKUST-1, three-dimensionally reconstruct a concomitant phase in MOF UiO-66, and discover a new CH3NH3PbI3 structure and locate its distribution in a single-crystal film perovskite solar cell. This proof-of-concept study demonstrates that cryo-FIB has a unique ability to handle highly sensitive materials, which can substantially expand the range of applications for electron microscopy.

Super-resolution confocal cryo-CLEM with cryo-FIB milling for in situ imaging of Deinococcus radiodurans

Studying bacterial cell envelope architecture with electron microscopy is challenging due to the poor preservation of microbial ultrastructure with traditional methods. Here, we established and validated a super-resolution cryo-correlative light and electron microscopy (cryo-CLEM) method, and combined it with cryo-focused ion beam (cryo-FIB) milling and scanning electron microscopy (SEM) volume imaging to structurally characterize the bacterium Deinococcus radiodurans. Subsequent cryo-electron tomography (cryo-ET) revealed an unusual diderm cell envelope architecture with a thick layer of peptidoglycan (PG) between the inner and outer membranes, an additional periplasmic layer, and a proteinaceous surface S-layer. Cells grew in tetrads, and division septa were formed by invagination of the inner membrane (IM), followed by a thick layer of PG. Cytoskeletal filaments, FtsA and FtsZ, were observed at the leading edges of constricting septa. Numerous macromolecular complexes were found associated with the cytoplasmic side of the IM. Altogether, our study revealed several unique ultrastructural features of D. radiodurans cells, opening new lines of investigation into the physiology and evolution of the bacterium.

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User-friendly, commercially available method for correlative cryo-super resolution light microscopy (LM) and cryo-FIB-milling.

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Cryo-super resolution LM, cryo-FIB milling, cryo-SEM volume imaging, and cryo-electron tomography (cryo-ET) to study Deinococcus radiodurans.

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Unique D. radiodurans cell envelope is composed of two membranes, thick peptidoglycan, an additional layer, and an S-layer.

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Cytoskeletal filaments FtsA and FtsZ were observed at the leading edges of division septa.

Embedding of HIV Egress within Cortical F-Actin

F-Actin remodeling is important for the spread of HIV via cell-cell contacts; however, the mechanisms by which HIV corrupts the actin cytoskeleton are poorly understood. Through live cell imaging and focused ion beam scanning electron microscopy (FIB-SEM), we observed F-Actin structures that exhibit strong positive curvature to be enriched for HIV buds. Virion proteomics, gene silencing, and viral mutagenesis supported a Cdc42-IQGAP1-Arp2/3 pathway as the primary intersection of HIV budding, membrane curvature and F-Actin regulation. Whilst HIV egress activated the Cdc42-Arp2/3 filopodial pathway, this came at the expense of cell-free viral release. Importantly, release could be rescued by cell-cell contact, provided Cdc42 and IQGAP1 were present. From these observations, we conclude that a proportion out-going HIV has corrupted a central F-Actin node that enables initial coupling of HIV buds to cortical F-Actin to place HIV at the leading cell edge. Whilst this initially prevents particle release, the maturation of cell-cell contacts signals back to this F-Actin node to enable viral release & subsequent infection of the contacting cell.

Microscopes, tools, probes, and protocols: A guide in the route of correlative microscopy for biomedical investigation

In the last decades, the advancements of microscopes technology, together with the development of new imaging approaches, are trying to address some biological questions that have been unresolved in the past: the need to combine in the same analysis temporal, functional and morphological information on the biological sample has become pressing. For this reason, the use of correlative microscopy, in which two or more imaging techniques are combined in the same analysis, is getting increasingly widespread. In fact, correlative microscopy can overcome limitations of a single imaging method, giving access to a larger amount of information from the same specimen. However, correlative microscopy can be challenging, and appropriate protocols for sample preparation and imaging methods must be selected. Here we review the state of the art of correlating electron microscopy with different imaging methods, focusing on sample preparation, tools, and labeling methods, with the aim to provide a comprehensive guide for those scientists who are approaching the field of correlative methods.

Endocytosis mediated by an atypical CUBAM complex modulates slit diaphragm dynamics in nephrocytes

The vertebrate endocytic receptor CUBAM, consisting of three cubilin monomers complexed with a single amnionless molecule, plays a major role in protein reabsorption in the renal proximal tubule. Here, we show that Drosophila CUBAM is a tripartite complex composed of Amnionless and two cubilin paralogues, Cubilin and Cubilin2, and that it is required for nephrocyte slit diaphragm (SD) dynamics. Loss of CUBAM-mediated endocytosis induces dramatic morphological changes in nephrocytes and promotes enlarged ingressions of the external membrane and SD mislocalisation. These phenotypes result in part from an imbalance between endocytosis, which is strongly impaired in CUBAM mutants, and exocytosis in these highly active cells. Of note, rescuing receptor-mediated endocytosis by Megalin/LRP2 or Rab5 expression only partially restores SD positioning in CUBAM mutants, suggesting a specific requirement of CUBAM in SD degradation and/or recycling. This finding and the reported expression of CUBAM in podocytes suggest a possible unexpected conserved role for this endocytic receptor in vertebrate SD remodelling.

Summary: A genetic study revealing that endocytosis mediated by an atypical CUBAM endocytic receptor, composed of Amnionless and two Cubilin paralogues, regulates slit diaphragm remodelling in Drosophila nephrocytes.

Quality control methods in musculoskeletal tissue engineering: from imaging to biosensors

Tissue engineering is rapidly progressing toward clinical application. In the musculoskeletal field, there has been an increasing necessity for bone and cartilage replacement. Despite the promising translational potential of tissue engineering approaches, careful attention should be given to the quality of developed constructs to increase the real applicability to patients. After a general introduction to musculoskeletal tissue engineering, this narrative review aims to offer an overview of methods, starting from classical techniques, such as gene expression analysis and histology, to less common methods, such as Raman spectroscopy, microcomputed tomography, and biosensors, that can be employed to assess the quality of constructs in terms of viability, morphology, or matrix deposition. A particular emphasis is given to standards and good practices (GXP), which can be applicable in different sectors. Moreover, a classification of the methods into destructive, noninvasive, or conservative based on the possible further development of a preimplant quality monitoring system is proposed. Biosensors in musculoskeletal tissue engineering have not yet been used but have been proposed as a novel technology that can be exploited with numerous advantages, including minimal invasiveness, making them suitable for the development of preimplant quality control systems.

Niwaki Instead of Random Forests: Targeted Serial Sectioning Scanning Electron Microscopy With Reimaging Capabilities for Exploring Central Nervous System Cell Biology and Pathology

Ultrastructural analysis of discrete neurobiological structures by volume scanning electron microscopy (SEM) often constitutes a "needle-in-the-haystack" problem and therefore relies on sophisticated search strategies. The appropriate SEM approach for a given relocation task not only depends on the desired final image quality but also on the complexity and required accuracy of the screening process. Block-face SEM techniques like Focused Ion Beam or serial block-face SEM are "one-shot" imaging runs by nature and, thus, require precise relocation prior to acquisition. In contrast, "multi-shot" approaches conserve the sectioned tissue through the collection of serial sections onto solid support and allow reimaging. These tissue libraries generated by Array Tomography or Automated Tape Collecting Ultramicrotomy can be screened at low resolution to target high resolution SEM. This is particularly useful if a structure of interest is rare or has been predetermined by correlated light microscopy, which can assign molecular, dynamic and functional information to an ultrastructure. As such approaches require bridging mm to nm scales, they rely on tissue trimming at different stages of sample processing. Relocation is facilitated by endogenous or exogenous landmarks that are visible by several imaging modalities, combined with appropriate registration strategies that allow overlaying images of various sources. Here, we discuss the opportunities of using multi-shot serial sectioning SEM approaches, as well as suitable trimming and registration techniques, to slim down the high-resolution imaging volume to the actual structure of interest and hence facilitate ambitious targeted volume SEM projects.

Nanodissection of Selected Viral Particles by Scanning Transmission Electron Microscopy/Focused Ion Beam for Genetic Identification

This study presents the development of a new correlative workflow to bridge the gap between electron microscopy imaging and genetic analysis of viruses. The workflow enables the assignment of genetic information to a specific biological entity by harnessing the nanodissection capability of focused ion beam (FIB). This correlative workflow is based on scanning transmission electron microscopy (STEM) and FIB followed by a polymerase chain reaction (PCR). For this purpose, we studied the tomato brown rugose fruit virus (ToBRFV) and the adenovirus that have significant impacts on plant integrity and human health, respectively. STEM imaging was used for the identification and localization of virus particles on a transmission electron microscopy (TEM) grid followed by FIB milling of the desired region of interest. The final-milled product was subjected to genetic analysis by the PCR. The results prove that the FIB-milling process maintains the integrity of the genetic material as confirmed by the PCR. We demonstrate the identification of RNA and DNA viruses extracted from a few micrometers of an FIB-milled TEM grid. This workflow enables the genetic analysis of specifically imaged viral particles directly from heterogeneous clinical samples. In addition to viral diagnostics, the ability to isolate and to genetically identify specific submicrometer structures may prove valuable in additional fields, including subcellular organelle and granule research.