Cryo-focused Ion Beam Research Articles

Recent Advances in Gas Injection System-Free Cryo-FIB Lift-Out Transfer for Cryo-Electron Tomography of Multicellular Organisms and Tissues

Abstract:Cryo-electron tomography (cryo-ET) enables visualization of protein complexes within their native cellular environment at molecular resolution. Most cells and all tissues, however, are too thick to be imaged directly by transmission electron microscopy (TEM). Overcoming this limitation requires the production of thin biological sections called lamellae. The procedure to obtain lamellae of cells, either seeded or grown directly on electron microscopy grids, requires cryo-focused ion beam (cryo-FIB) milling to thin the samples. This method faces an additional challenge when dealing with tissues and multicellular organisms, as these samples must be high-pressure frozen, which embeds the sample in a thick layer of ice. Nonetheless, lamellae can still be prepared from such samples by extracting a small volume and transferring it to a receiver grid for lamella preparation, a process called lift-out. Here, we describe the available workflows to produce lamellae by lift-out at cryogenic conditions and recent developments in gas injection system (GIS)-free approaches to the lift-out transfer. These advances expand the applications of cryo-ET, enabling the investigation of tissues and whole organisms in situ at molecular resolution.

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.

Preparation and Cryo-FIB micromachining of <em>Saccharomyces cerevisiae</em> for Cryo-Electron Tomography

Today, cryo-electron tomography (cryo-ET) is the only technique that can provide near-atomic resolution structural data on macromolecular complexes in situ. Owing to the strong interaction of an electron with the matter, high-resolution cryo-ET studies are limited to specimens with a thickness of less than 200 nm, which restricts the applicability of cryo-ET only to the peripheral regions of a cell. A complex workflow that comprises the preparation of thin cellular cross-sections by cryo-focused ion beam micromachining (cryo-FIBM) was introduced during the last decade to enable the acquisition of cryo-ET data from the interior of larger cells. We present a protocol for the preparation of cellular lamellae from a sample vitrified by plunge freezing utilizing Saccharomyces cerevisiae as a prototypical example of a eukaryotic cell with wide utilization in cellular and molecular biology research. We describe protocols for vitrification of S. cerevisiae into isolated patches of a few cells or a continuous monolayer of the cells on a TEM grid and provide a protocol for lamella preparation by cryo-FIB for these two samples.

Preparation and Cryo-FIB micromachining of Saccharomyces cerevisiae for Cryo-Electron Tomography.

Today, cryo-electron tomography (cryo-ET) is the only technique that can provide near-atomic resolution structural data on macromolecular complexes in situ. Owing to the strong interaction of an electron with the matter, high-resolution cryo-ET studies are limited to specimens with a thickness of less than 200 nm, which restricts the applicability of cryo-ET only to the peripheral regions of a cell. A complex workflow that comprises the preparation of thin cellular cross-sections by cryo-focused ion beam micromachining (cryo-FIBM) was introduced during the last decade to enable the acquisition of cryo-ET data from the interior of larger cells. We present a protocol for the preparation of cellular lamellae from a sample vitrified by plunge freezing utilizing Saccharomyces cerevisiae as a prototypical example of a eukaryotic cell with wide utilization in cellular and molecular biology research. We describe protocols for vitrification of S. cerevisiae into isolated patches of a few cells or a continuous monolayer of the cells on a TEM grid and provide a protocol for lamella preparation by cryo-FIB for these two samples.

In-cell structures of conserved supramolecular protein arrays at the mitochondria–cytoskeleton interface in mammalian sperm

Mitochondria-cytoskeleton interactions modulate cellular physiology by regulating mitochondrial transport, positioning, and immobilization. However, there is very little structural information defining mitochondria-cytoskeleton interfaces in any cell type. Here, we use cryofocused ion beam milling-enabled cryoelectron tomography to image mammalian sperm, where mitochondria wrap around the flagellar cytoskeleton. We find that mitochondria are tethered to their neighbors through intermitochondrial linkers and are anchored to the cytoskeleton through ordered arrays on the outer mitochondrial membrane. We use subtomogram averaging to resolve in-cell structures of these arrays from three mammalian species, revealing they are conserved across species despite variations in mitochondrial dimensions and cristae organization. We find that the arrays consist of boat-shaped particles anchored on a network of membrane pores whose arrangement and dimensions are consistent with voltage-dependent anion channels. Proteomics and in-cell cross-linking mass spectrometry suggest that the conserved arrays are composed of glycerol kinase-like proteins. Ordered supramolecular assemblies may serve to stabilize similar contact sites in other cell types in which mitochondria need to be immobilized in specific subcellular environments, such as in muscles and neurons.

Sample Preparation by 3D-Correlative Focused Ion Beam Milling for High-Resolution Cryo-Electron Tomography.

Cryo-electron tomography (cryo-ET) has become the method of choice for investigating cellular ultrastructure and molecular complexes in their native, frozen-hydrated state. However, cryo-ET requires that samples are thin enough to not scatter or block the incident electron beam. For thick cellular samples, this can be achieved by cryo-focused ion beam (FIB) milling. This protocol describes how to target specific cellular sites during FIB milling using a 3D-correlative approach, which combines three-dimensional fluorescence microscopy data with information from the FIB-scanning electron microscope. Using this technique, rare cellular events and structures can be targeted with high accuracy and visualized at molecular resolution using cryo-transmission electron microscopy (cryo-TEM).

New hardware for a streamlined cryo focused ion beam milling workflow

New hardware for a streamlined cryo focused ion beam milling workflow

Effects of Applied Interfacial Pressure on Li-Metal Cycling Performance and Morphology in 4 M LiFSI in DME.

Lithium-metal anodes can theoretically enable 10× higher gravimetric capacity than conventional graphite anodes. However, Li-metal anode cycling has proven difficult due to porous and dendritic morphologies, extensive parasitic solid electrolyte interphase reactions, and formation of dead Li. We systematically investigate the effects of applied interfacial pressure on Li-metal anode cycling performance and morphology in the recently developed and highly efficient 4 M lithium bis(fluorosulfonyl)imide in 1,2-dimethoxyethane electrolyte. We present cycling, morphology, and impedance data at a current density of 0.5 mA/cm2 and a capacity of 2 mAh/cm2 at applied interfacial pressures of 0, 0.01, 0.1, 1, and 10 MPa. Cryo-focused ion beam milling and cryo-scanning electron microscopy imaging in cross section reveal that increasing the applied pressure during Li deposition from 0 to 10 MPa leads to greater than a fivefold reduction in thickness (and therefore volume) of the deposited Li. This suggests that pressure during cycling can have a profound impact on the practical volumetric energy density for Li-metal anodes. A "goldilocks zone" of cell performance is observed at intermediate pressures of 0.1-1 MPa. Increasing pressure from 0 to 1 MPa generally improves cell-to-cell reproducibility, cycling stability, and Coulombic efficiency. However, the highest pressure (10 MPa) results in high cell overpotential and evidence of soft short circuits, which likely result from transport limitations associated with increased pressure causing local pore closure in the separator. All cells exhibit at least some signs of cycling instability after 50 cycles when cycled to 2 mAh/cm2 with thin 50 μm Li counter electrodes, though instability decreases with increasing pressure. In contrast, cells cycled to only 1 mAh/cm2 perform well for 50 cycles, indicating that capacity plays an important role in cycling stability.

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.

Abstract P-35: Cryo-Electron Tomography of Protein Conjugated Upconverting Nanophosphors

Background: Over the past decades, significant advances have been made in the field of creating nanobioreagents for solving modern medicine problems (Grebenik et al., JBO, 2013). However, the problem of their low accumulation rate in pathological tissue in vivo experiments still remains. First of all, it is associated with the adsorption of blood proteins on the surface of nanobioreagents and the protein layer formation, which significantly changes the surface properties, which leads to their rapid excretion by the reticuloendothelial system. In particular, it is possible to reduce the blood plasma proteins adsorption and increase the time spent in the circulatory system by forming a coating of proteins. Methods: In situ cryоelectron tomography (Cryo-ET) is the only method that allows the experimental observation of protein structures on the nanoparticle’s surface in their natural functional state. The basic principle of the method is to obtain a series of projections of a vitrified sample thin lamella at different tilt angles related to an incident electron beam. Their further processing leads to obtaining the volumetric information about the structure of the sample. The use of a cryo-focused ion beam (Cryo-FIB) in specimen thinning makes it possible to carry out experiments with thin sections of cellular structures and observe the penetration of nanoparticles into the intracellular environment. Results: Upconverting nanophosphors (AN) were used as a nanoplatform for creating a protein coating. To create a protein coating on the AN surface, they were functionalized using an amphiphilic polymer containing carboxyl groups. Then, conjugation with protein molecules from the class of immunoglobulins was carried out by the method of carbodiimide activation. At each stage of synthesis and modification, AN solutions with different size distribution were vitrified for subsequent tomography. After a series of experiments to study the morphology of nanoparticles, an experiment on their successful absorption by cells of the cancer line A549 was carried out. Conclusion: Within this work, a series of in situ Cryo-ET methods were proposed and applied for structural characterization and visualization of the processes of synthesis, modification, and engulfment of nanoparticles into cellular systems. For the first time in its native form, the engulfment of ANF into the internal environment of the A549 cancer line cells was demonstrated.

Abstract P-3: The Structure of Self-Assembled Surfactant Micellar Networks by in situ Cryo-Electron Tomography

Background: Surfactant molecules can form various self-assembled structures in aqueous solutions, including spherical and cylindrical micelles, lamellae, vesicles, etc. Elongated cylindrical (wormlike) micelles can entangle and form a dense network. The study of the un-perturbed native structure of wormlike micelles in such networks presents a great challenge, since the micelles are formed due to weak non-covalent interactions and may easily break when external conditions are changed. In this work in situ cryo-electron tomography (cryo-ET) was applied to reveal the relaxed structure of such entangled systems. Methods: To prepare samples for the cryo-ET study 1 µl of the aqueous surfactant-containing solution was applied to the glow discharged grid, blotted with filter paper for 10 sec, drained for 60 sec to allow for the relaxation of the system and plunge-frozen with Vitrobot Mark IV. The vitrified sample was transferred to Versa 3D cryo-focused ion beam / scanning electron microscope (cryo-FIB/SEM) to prepare thin (100-150 nm) sections of the sample. Cryo-ET study was conducted using Titan Krios. IMOD and Avizo software packages were used for data processing. Results: In this work, wormlike micelles formed by a mixture of an anionic and a cationic surfactant were investigated at the excess of the anionic surfactant. Cryo-ET study of the obtained lamellae demonstrated the formation of two different phases, consisting of straight rods oriented along the grid substrate (phase 1) and isotropic network formed by wormlike micelles (phase 2) above it. The topology of the second phase corresponded to the branched saturated network or entangled network depending on cation/anion ratio of the sample. However, the analysis of the thin samples obtained without cryo-FIB demonstrated only the presence of the metastable phase (phase 1), which could lead to false conclusions regarding the morphology of the micelles. Conclusion: Here we discuss the influence of different sample preparation approaches on the sample structure and demonstrate that the native un-perturbed conformation of charged cylindrical surfactant micelles in the dense network is that of a slightly bent rod or a wormlike chain with high persistence length.

A streamlined workflow for automated cryo focused ion beam milling

Cryo-electron tomography (cryo-ET) is an emerging technique to study the cellular architecture and the structure of proteins at high resolution in situ. Most biological specimens are too thick to be directly investigated and are therefore thinned by milling with a focused ion beam under cryogenic conditions (cryo-FIB). This procedure is prone to contaminations, which makes it a tedious process, often leading to suboptimal results. Here, we present new hardware that overcomes the current limitations. We developed a new glove box and a high vacuum cryo transfer system and installed a stage heater, a cryo-shield and a cryo-shutter in the FIB milling microscope. This reduces the ice contamination during the transfer and milling process and simplifies the handling of the sample. In addition, we tested a new software application that automates the key milling steps. Together, these improvements allow for high-quality, high-throughput cryo-FIB milling. This paves the way for new types of experiments, which have been previously considered infeasible.

Structure of the Yersinia injectisome in intracellular host cell phagosomes revealed by cryo FIB electron tomography

Many pathogenic bacteria use the type III secretion system (T3SS), or injectisome, to secrete toxins into host cells. These protruding systems are primary targets for drug and vaccine development. Upon contact between injectisomes and host membranes, toxin secretion is triggered. How this works structurally and functionally is yet unknown. Using cryo-focused ion beam milling and cryo-electron tomography, we visualized injectisomes of Yersinia enterocolitica inside the phagosomes of infected human myeloid cells in a close-to-native state. We observed that a minimum needle length is required for injectisomes to contact the host membrane and bending of host membranes by some injectisomes that contact the host. Through subtomogram averaging, the structure of the entire injectisome was determined, which revealed structural differences in the cytosolic sorting platform compared to other bacteria. These findings contribute to understanding how injectisomes secrete toxins into host cells and provides the indispensable native context. The application of these cryo-electron microscopy techniques paves the way for the study of the 3D structure of infection-relevant protein complexes in host-pathogen interactions.

Endocytosed nanogold fiducials for improved in-situ cryo–electron tomography tilt-series alignment

Cryo–electron tomography (CET) on cryo–focused ion beam (FIB)–milled lamellae is becoming a powerful technique for determining the structure of macromolecular complexes in their native cellular environment. Prior to tomogram reconstruction, CET tilt-series recorded on FIB lamellae need to be aligned. Traditionally, CET tilt-series alignment is performed with 5–20 nm gold fiducials, but it has thus far proven difficult to apply this to FIB lamellae of eukaryotic cells. In here, we describe a simple method to allow uptake of bovine serum albumin (BSA)-gold fiducials into mammalian cells via endocytosis, which can subsequently be used as fiducials for tilt-series alignment of cryo-FIB lamellae. We compare the alignment of tilt-series with BSA-gold fiducials to fiducial-less patch-tracking, and find better alignment results with BSA-gold. This technique can contribute to understand cells at a structural and ultrastructural level with both cryo- and room-temperature electron tomography. Furthermore, fluorescently labeled BSA-gold has the potential to be used as fiducials for correlative light and electron microscopy studies.

Cryo-correlative light and electron microscopy workflow for cryo-focused ion beam milled adherent cells.

In situ cryo-electron tomography of cryo-focused ion beam (cryo-FIB) milled cells enables the study of cellular organelles in unperturbed conditions and close to the molecular resolution. However, due to the crowdedness of the cellular environment, the identification of individual macromolecular complexes either on organelles or inside the cytosol in cryo-electron tomograms is challenging. Cryo-correlative light and electron microscopy (cryo-CLEM) employs a fluorescently labeled feature of interest imaged by cryo-light microscopy that is correlated to cryo-electron microscopy maps of cryo-FIB milled lamellae using correlation markers discernable by both imaging methods. Here, we provide a protocol for a post-correlation on-lamella cryo-CLEM approach for localization of fluorescently labeled organelles of interest in cryo-lamellae after cryo-FIB milling and tomography of adherent plunge frozen cells.

<i>In situ</i> Structure of Intestinal Apical Surface Reveals Nanosticks on Microvilli

Microvilli are actin bundle-supported membrane protrusions essential for absorption, secretion, and sensation. Microvilli defects cause gastrointestinal disorders; however, mechanisms controlling microvilli formation and organization remain unresolved. Here, we study microvilli by vitrifying the C. elegans larvae with high-pressure freezing, thinning them by cryo-focused ion beam milling, cryo-electron tomography, and sub-tomogram averaging. We uncover that hundreds of previously unrecognized stick-like structures, which we refer to as nanosticks, decorate the lateral surface of microvilli. Nanosticks are 37.5-nm long and 4.5-nm wide, and their formation requires the protocadherin family protein CDH-8. Loss of nanosticks slows down animal growth and increases the number of Y-shaped microvilli, the putative intermediate structures, when a microvillus splits from its tip and separates into two. We suggest that an existing microvillus may divide to form two nascent microvilli with uniformity and that nanosticks may space microvilli.

Cryo-Focused Ion Beam Lamella Preparation Protocol for in Situ Structural Biology.

The advances in electron cryo-microscopy have enabled high-resolution structural studies of vitrified macromolecular complexes in situ by cryo-electron tomography (cryo-ET). Since utilization of cryo-ET is generally limited to the specimens with thickness<500nm, a complex sample preparation protocol to study larger samples such as single eukaryotic cells by cryo-ET was developed and optimized over the last decade. The workflow is based on the preparation of a thin cellular lamella by cryo-focused ion beam milling (cryo-FIBM) from the vitrified cells. The sample preparation protocol is a multi-step process which includes utilization of several high-end instruments and comprises sample manipulation prone to sample deterioration. Here, we present a workflow for preparation of three different model specimens that was optimized to provide high-quality lamellae for cryo-ET or electron diffraction tomography with high reproducibility. Preparation of lamellae from large adherent mammalian cells, small suspension eukaryotic cell line, and protein crystals of intermediate size is described which represents examples of the most frequently studied samples used for cryo-FIBM in life sciences.

Practical Approaches for Cryo-FIB Milling and Applications for Cellular Cryo-Electron Tomography.

Cryo-electron tomography (cryo-ET) is a powerful technique to examine cellular structures as they exist in situ. However, direct imaging by TEM for cryo-ET is limited to specimens up to ∼400nm in thickness, narrowing its applicability to areas such as cellular projections or small bacteria and viruses. Cryo-focused ion beam (cryo-FIB) milling has emerged in recent years as a method to generate thin specimens from cellular samples in preparation for cryo-ET. In this technique, specimens are thinned with a beam of gallium ions to gradually ablate cellular material in order to leave a thin, electron-transparent section (a lamella) through the bulk material. The lamella can be used for high-resolution cryo-ET to visualize cells in 3D in a near-native state. This approach has proved to be robust and relatively simple for new users and exhibits minimal sectioning artifacts. In this chapter, we describe a general approach to cryo-FIB milling for users with prior cryo-EM experience, with extensive notes on operation and troubleshooting.

A mammalian system for high-resolution imaging of intact cells by cryo-electron tomography

Mammalian cells contain an elaborate network of organelles and molecular machines that orchestrate essential cellular processes. Visualization of this network at a molecular level is vital for understanding these cellular processes. Here we present a model system based on nerve growth factor (NGF)-differentiated PC12 cells (PC12+) and suitable for high resolution imaging of organelles and molecular machines in situ. We detail an optimized imaging pipeline that effectively combines correlative light and electron microscopy (CLEM), cryo-focused ion beam (cryo-FIB), cryo-electron tomography (cryo-ET), and sub-tomogram averaging to produce three-dimensional and molecular resolution snapshots of organelles and molecular machines in near-native cellular environments. Our studies demonstrate that cryo-ET imaging of PC12+ systems provides an accessible and highly efficient avenue for dissecting specific cellular processes in mammalian cells at high resolution.

3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy

Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications.