Cryo-FIB preparation of whole cells and tissue for cryo-TEM: use of high-pressure frozen specimens in tubes and planchets

Advances, challenges, and applications of cryo-electron tomography workflows for three-dimensional cellular imaging of infectious pathogens

Cryo-electron tomography (cryo-ET) has become a powerful tool for visualising cellular structures at sub-nanometer resolution in their near-native state, offering unique insights into the molecular architecture of diverse biological systems, including infectious agents and their interactions with host cells. This paper reviews key methodologies and recent advancements in cryo-ET, with a particular focus on sample preparation of protozoan parasites and host cells. Topics covered include photopatterning for cell positioning on EM grids, vitrification techniques, whole-cell imaging, and cryo-FIB milling followed by cryo-ET. The manuscript also addresses how these approaches are providing valuable structural information on pathogens and pathogen-host interactions, which are critical for understanding mechanisms of pathogenesis and the development of therapeutic strategies. Additionally, we examine the principles and practical considerations of the multistep workflow, highlighting innovations such as integrated fluorescence microscopy (iFLM) within cryo-FIB SEM systems for improved target identification and lamella positioning. Challenges such as ion beam damage, sample thickness constraints, and the need for greater workflow automation are also discussed as areas for future improvement. As cryo-ET continues to evolve and deliver transformative insights into the molecular architecture of life, it inspires great hope for the development of future therapies against infectious diseases. LAY DESCRIPTION: Cryo-electron tomography (cryo-ET) is a special type of microscopy that allows researchers to look at the inside of cells in 3D, almost as if a hologram of the cell in its natural state was generated. This technique reveals molecular structures inside cells, allowing scientists to better understand how molecules and cellular components work together. To obtain such detailed images, biological samples need to be thin and frozen very quickly so that they remain undamaged and close to their natural state. One recent breakthrough involves using a tool called cryo-focused ion beam scanning electron microscopy (cryo-FIB SEM), which allows a thin slice of a frozen sample to be collected and then analysed using cryo-ET. In addition, photopatterning of support surfaces are being used to place cells in a strategic position for cryo-FIB SEM, and improved plunge freezing and high-pressure freezing methods have been developed to better preserve samples. Together, these techniques make it easier to reproducibly prepare high-quality samples for cryo-ET. These innovations allow capturing clearer and detailed images of cells, tissues, and even entire small organisms. Cryo-ET has led to important discoveries in biology, such as how proteins and other molecules interact within cells at the sub-nanometre scale. This technique holds great promise for revealing how life works at a molecular level, understanding diseases, and discovering new drugs.

Soft X-ray spectromicroscopy of human fibroblasts with impaired sialin function

Salla disease (SD) is a lysosomal storage disease where free sialic acid (SA) accumulates in lysosomes due to the impaired function of a membrane protein, sialin. Synchrotron radiation-based scanning transmission soft X-ray spectromicroscopy (STXM) was used to analyze both SD patients' fibroblasts and normal human dermal fibroblasts (NHDF) from healthy controls. Both cell lines were also cultured with N-acetyl-d-mannosamine monohydrate (ManNAc) to see if it increased SA concentration in the cells. The STXM technique was chosen to simultaneously observe the morphological and chemical changes in cells. It was observed that free SA did not remain in the lysosomes during the sample processing, leaving empty vacuoles to the fibroblasts. The total cytosol and entire cell spectra, however, showed systematic differences between the SD and NHDF samples, indicating changes in the relative macromolecular concentrations of the cells. The NHDF cell lines contained a higher relative protein concentration compared to the SD cell lines, and the addition of ManNAc increased the relative protein concentration in both cell lines. In this study, two sample preparation methods were compared, resin-embedded thin sections and cells grown directly on sample analysis grids. While the samples grown on the grids exhibited clean, well-resolved spectra not masked by embedding resin, the low penetration depth of soft X-rays hindered the analysis to only the thin region of the microfilaments away from the thick nucleus.

CryoFIB milling large tissue samples for cryo-electron tomography

Cryo-electron tomography (cryoET) is a powerful tool for exploring the molecular structure of large organisms. However, technical challenges still limit cryoET applications on large samples. In particular, localization and cutting out objects of interest from a large tissue sample are still difficult steps. In this study, we report a sample thinning strategy and workflow for tissue samples based on cryo-focused ion beam (cryoFIB) milling. This workflow provides a full solution for isolating objects of interest by starting from a millimeter-sized tissue sample and ending with hundred-nanometer-thin lamellae. The workflow involves sample fixation, pre-sectioning, a two-step milling strategy, and localization of the object of interest using cellular secondary electron imaging (CSEI). The milling strategy consists of two steps, a coarse milling step to improve the milling efficiency, followed by a fine milling step. The two-step milling creates a furrow-ridge structure with an additional conductive Pt layer to reduce the beam-induced charging issue. CSEI is highlighted in the workflow, which provides on-the-fly localization during cryoFIB milling. Tests of the complete workflow were conducted to demonstrate the high efficiency and high feasibility of the proposed method.

Cryo-electron tomography on focused ion beam lamellae transforms structural cell biology

Cryogenic electron microscopy and data processing enable the determination of structures of isolated macromolecules to near-atomic resolution. However, these data do not provide structural information in the cellular environment where macromolecules perform their native functions, and vital molecular interactions can be lost during the isolation process. Cryogenic focused ion beam (FIB) fabrication generates thin lamellae of cellular samples and tissues, enabling structural studies on the near-native cellular interior and its surroundings by cryogenic electron tomography (cryo-ET). Cellular cryo-ET benefits from the technological developments in electron microscopes, detectors and data processing, and more in situ structures are being obtained and at increasingly higher resolution. In this Review, we discuss recent studies employing cryo-ET on FIB-generated lamellae and the technological developments in ultrarapid sample freezing, FIB fabrication of lamellae, tomography, data processing and correlative light and electron microscopy that have enabled these studies. Finally, we explore the future of cryo-ET in terms of both methods development and biological application.

Electron microscopy of cellular ultrastructure in three dimensions

Electron microscopy in three dimensions (3D) of cells and tissues can be essential for understanding the ultrastructural aspects of biological processes. The quest for 3D information reveals challenges at many stages of the workflow, from sample preparation, to imaging, data analysis and segmentation. Here, we outline several available methods, including volume SEM imaging, cryo-TEM and cryo-STEM tomography, each one occupying a different domain in the basic tradeoff between field-of-view and resolution. We discuss the considerations for choosing a suitable method depending on research needs and highlight recent developments that are essential for making 3D volume imaging of cells and tissues a standard tool for cellular and structural biologists.

Neurons: The Interplay between Cytoskeleton, Ion Channels/Transporters and Mitochondria

Neurons are permanent cells whose key feature is information transmission via chemical and electrical signals. Therefore, a finely tuned homeostasis is necessary to maintain function and preserve neuronal lifelong survival. The cytoskeleton, and in particular microtubules, are far from being inert actors in the maintenance of this complex cellular equilibrium, and they participate in the mobilization of molecular cargos and organelles, thus influencing neuronal migration, neuritis growth and synaptic transmission. Notably, alterations of cytoskeletal dynamics have been linked to alterations of neuronal excitability. In this review, we discuss the characteristics of the neuronal cytoskeleton and provide insights into alterations of this component leading to human diseases, addressing how these might affect excitability/synaptic activity, as well as neuronal functioning. We also provide an overview of the microscopic approaches to visualize and assess the cytoskeleton, with a specific focus on mitochondrial trafficking.

Electron microscopy of cardiac 3D nanodynamics: form, function, future

The 3D nanostructure of the heart, its dynamic deformation during cycles of contraction and relaxation, and the effects of this deformation on cell function remain largely uncharted territory. Over the past decade, the first inroads have been made towards 3D reconstruction of heart cells, with a native resolution of around 1 nm³, and of individual molecules relevant to heart function at a near-atomic scale. These advances have provided access to a new generation of data and have driven the development of increasingly smart, artificial intelligence-based, deep-learning image-analysis algorithms. By high-pressure freezing of cardiomyocytes with millisecond accuracy after initiation of an action potential, pseudodynamic snapshots of contraction-induced deformation of intracellular organelles can now be captured. In combination with functional studies, such as fluorescence imaging, exciting insights into cardiac autoregulatory processes at nano-to-micro scales are starting to emerge. In this Review, we discuss the progress in this fascinating new field to highlight the fundamental scientific insight that has emerged, based on technological breakthroughs in biological sample preparation, 3D imaging and data analysis; to illustrate the potential clinical relevance of understanding 3D cardiac nanodynamics; and to predict further progress that we can reasonably expect to see over the next 10 years.

Fine Cryo-SEM Observation of the Microstructure of Emulsions Frozen Via High-Pressure Freezing

An emulsion, a type of soft matter, is complexed with at least two materials in the liquid state (e.g., water and oil). Emulsions are classified into two types: water-in-oil (W/O) and oil-in-water (O/W), depending on the strength of the emulsifier. The properties and behavior of emulsions are directly correlated with the size, number, localization, and structure of the dispersed phases in the continuous phase. Therefore, an understanding of the microstructure comprising liquid-state emulsions is essential for producing and evaluating these emulsions. Generally, it is impossible for conventional electron microscopy to examine liquid specimens, such as emulsion. Recent advances in cryo-scanning electron microscopy (cryo-SEM) could allow us to visualize the microstructure of the emulsions in a frozen state. Immersion freezing in slush nitrogen has often been used for preparing the frozen samples of soft matters. This preparation could generate ice crystals, and they would deform the microstructure of specimens. High-pressure freezing contributes to the inhibition of ice-crystal formation and is commonly used for preparing frozen biological samples with high moisture content. In this study, we compared the microstructures of immersion-frozen and high-pressure frozen emulsions (O/W and W/O types, respectively). The cryo-SEM observations suggested that high-pressure freezing is more suitable for preserving the microstructure of emulsions than immersion freezing.

VHUT-cryo-FIB, a method to fabricate frozen hydrated lamellae from tissue specimens for in situ cryo-electron tomography

Cryo-electron tomography (cryo-ET) provides a promising approach to study intact structures of macromolecules in situ, but the efficient preparation of high-quality cryosections represents a bottleneck. Although cryo-focused ion beam (cryo-FIB) milling has emerged for large and flat cryo-lamella preparation, its application to tissue specimens remains challenging. Here, we report an integrated workflow, VHUT-cryo-FIB, for efficiently preparing frozen hydrated tissue lamella that can be readily used in subsequent cryo-ET studies. The workflow includes vibratome slicing, high-pressure freezing, ultramicrotome cryo-trimming and cryo-FIB milling. Two strategies were developed for loading cryo-lamella via a side-entry cryo-holder or an FEI AutoGrid. The workflow was validated by using various tissue specimens, including rat skeletal muscle, rat liver and spinach leaf specimens, and in situ structures of ribosomes were obtained at nanometer resolution from the spinach and liver samples.

Recent Advances in Single-Particle Electron Microscopic Analysis of Autophagy Degradation Machinery

Macroautophagy (also known as autophagy) is a major pathway for selective degradation of misfolded/aggregated proteins and damaged organelles and non-selective degradation of cytoplasmic constituents for the generation of power during nutrient deprivation. The multi-step degradation process, from sequestering cytoplasmic cargo into the double-membrane vesicle termed autophagosome to the delivery of the autophagosome to the lysosome or lytic vacuole for breakdown, is mediated by the core autophagy machinery composed of multiple Atg proteins, as well as the divergent sequence family of selective autophagy receptors. Single-particle electron microscopy (EM) is a molecular imaging approach that has become an increasingly important tool in the structural characterization of proteins and macromolecular complexes. This article summarizes the contributions single-particle EM have made in advancing our understanding of the core autophagy machinery and selective autophagy receptors. We also discuss current technical challenges and roadblocks, as well as look into the future of single-particle EM in autophagy research.

Cryo-FIB-lift-out: practically impossible to practical reality

In this paper, we explore the development of the Cryo-Lift-Out (cryo-LO) technique as preparation tool for cryogenic transmission electron microscopy (cryo-TEM). What started in early work defying what was considered 'practically impossible' has developed into state-of-the-art practical reality. This paper presents the key hardware, basic principles and key considerations for the practical usage of cryogenic Lift-Out for those new to the field. Detailed protocols and in-depth description of considerations and points for further development are presented. The authors have attempted to formalise everything known about the technique gathered together from their expertise gained in the development of this approach. LAY DESCRIPTION: A major challenge in electron microscopy is the production of suitable samples from hydrated biological and soft-matter materials for subnanometre resolution imaging in a cryo-Transmission Electron Microscope (TEM). A well-known solution for room temperature materials is called (in situ) Lift-Out. It uses a fine needle that picks up a tiny section called a lamella. Lamellae are made by a Focused Ion Beam (FIB). In this paper, we seek to set out the beginnings of Lift-Out sample preparation conducted under cryogenic conditions and the development of this approach as applied to frozen, hydrated biological and soft-matter samples. We discuss the required basic hardware and provide a thorough description of developed protocols. We aim at those new to the field of cryo-Lift-Out to fully educate them in the finer points of hardware setup and practical considerations when attempting to perform cryo-Lift-Out and to demonstrate what has been achieved thus far. We also discuss areas of further improvement and talking points for the future direction of this promising sample preparation technique.

An introduction to cryo-FIB-SEM cross-sectioning of frozen, hydrated Life Science samples

The introduction of cryo‐techniques to the focused ion‐beam scanning electron microscope (FIB‐SEM) has brought new opportunities to study frozen, hydrated samples from the field of Life Sciences. Cryo‐techniques have long been employed in electron microscopy. Thin electron transparent sections are produced by cryo‐ultramicrotomy for observation in a cryo‐transmission electron microscope (TEM). Cryo‐TEM is presently reaching the imaging of macromolecular structures. In parallel, cryo‐fractured surfaces from bulk materials have been investigated by cryo‐SEM.

Both cryo‐TEM and cryo‐SEM have provided a wealth of information, despite being 2D techniques. Cryo‐TEM tomography does provide 3D information, but the thickness of the volume has a maximum of 200–300 nm, which limits the 3D information within the context of specific structures. FIB‐milling enables imaging additional planes by creating cross‐sections (e.g. cross‐sectioning or site‐specific X‐sectioning) perpendicular to the cryo‐fracture surface, thus adding a third imaging dimension to the cryo‐SEM. This paper discusses how to produce suitable cryo‐FIB‐SEM cross‐section results from frozen, hydrated Life Science samples with emphasis on ‘common knowledge’ and reoccurring observations.

Lay Description

Life Sciences studies life down to the smallest details. Visualising the smallest details requires electron microscopy, which utilises high‐vacuum chambers. One method to maintain the integrity of Life Sciences samples under vacuum conditions is freezing. Frozen samples can remain in a suspended state. As a result, research can be carried out without having to change the chemistry or internal physical structure of the samples.

Two types of electron microscopes equipped with cryo‐sample handling facilities are used to investigate samples: The scanning electron microscope (SEM) which investigates surfaces and the transmission electron microscope (TEM) which investigates thin electron transparent sections (called lamellae). A third method of investigation combines a SEM with a focused ion beam (FIB) to form a cryo‐FIB‐SEM, which is the basis of this paper. The electron beam images the cryo‐sample surface while the ion beam mills into the surface to expose the interior of the sample. The latter is called cross‐sectioning and the result provides a way of investigating the 3rd dimension of the sample. This paper looks at the making of cross‐sections in this manner originating from knowledge and experience gained with this technique over many years. This information is meant for newcomers, and experienced researchers in cryo‐microscopy alike.