What transmission electron microscopes can visualize now and in the future

Recognition of necroptosis: From molecular mechanisms to detection methods

Necroptosis is a crucial modality of programmed cell death characterized by distinct morphological and biochemical hallmarks, including cell membrane rupture, organelle swelling, cytoplasmic and nuclear disintegration, cellular contents leakage, and release of damage-associated molecular patterns (DAMPs), accompanied by the inflammatory responses. Studies have shown that necroptosis is involved in the etiology and evolution of a variety of pathologies including organ damage, inflammation disorders, and cancer. Despite its significance, the field of necroptosis research grapples with the challenge of non-standardized detection methodologies. In this review, we introduce the fundamental concepts and molecular mechanisms of necroptosis and critically appraise the principles, merits, and inherent limitations of current detection technologies. This endeavor seeks to establish a methodological framework for necroptosis detection, thereby propelling deeper insights into the research of cell necroptosis.

Exosomes derived from human umbilical cord mesenchymal stem cells alleviate acetaminophen-induced acute liver failure through activating ERK and IGF-1R/PI3K/AKT signaling pathway

This study aimed to investigate the therapeutic potential of human umbilical cord mesenchymal stem cells derived exosomes (hUCMSC-Exo) in acute liver failure (ALF) in mice as well as its underlying mechanism. We found that a single tail vein administration of hucMSC-Exo effectively enhanced the survival rate, inhibited apoptosis in hepatocytes, and improved liver function in APAP-induced mouse model of ALF. Furthermore, the deletion of glutathione (GSH) and superoxide dismutase (SOD), generation of malondialdehyde (MDA), and the over production of cytochrome P450 E1 (CYP2E1) and 4-hydroxynonenal (4-HNE) caused by APAP were also inhibited by hucMSC-Exo, indicating that hucMSC-Exo inhibited APAP-induced apoptosis of hepatocytes by reducing oxidative stress. Moreover, hucMSC-Exo significantly down-regulated the levels of inflammatory cytokines IL-6, IL-1β, and TNF-α in APAP-treated livers. Western blot showed that hucMSC-Exo significantly promoted the activation of ERK1/2 and IGF-1R/PI3K/AKT signaling pathways in APAP-injured LO2 cells, resulting in the inhibition of apoptosis of LO2 cells. Importantly, PI3K inhibitor LY294002 and ERK1/2 inhibitor PD98059 could reverse the function of hucMSC-Exo on APAP-injured LO2 cells in some extent. Our results suggest that hucMSC-Exo offer antioxidant hepatoprotection against APAP in vitro and in vivo by inhibitiing oxidative stress-induced apoptosis via upregulation of ERK1/2 and PI3K/AKT signaling pathways.

Synthesis, characterization and optical properties of nanosized lanthanum (III) complexes thin film with aryl-azo-pyrogallol derivatives

The present study is focused on the assembly of two new thin films based on the direct layer deposition of lanthanum ion from solution with two aryl-azo-pyrogallol ligands onto the surface of a glass substrate. Assembled lanthanum (III) complexes were characterized by different techniques including thermal gravimetric analysis, metal analysis by acid digestion and complexometric titration, Fourier transforms infrared, transmission electron microscopy, and X-ray diffraction. Two complexes were highly similar in their patterns and crystallinities with the characterized particle size range 23.16-23.31 nm. Energy gaps of the two complexes NS Na₃La(III)-(L1)₂ and NS Na₃La(III)-(L2)₂ were found to be 2.09 and 2.33 eV, respectively. Linear and calculated nonlinear optical properties have been studied for the two complexes. The nonlinear refractive index has been calculated and NS Na₃La(III)-(L2)₂ showed a high nonlinear behavior (n₂ = 8 × 10^-7 esu) and it could be a promising low-cost material in the optical nonlinear application.

Mineralized scale patterns on the cell periphery of the chrysophyte Mallomonas determined by comparative 3D Cryo-FIB SEM data processing

Unicellular protists can biomineralize spatially complex and functional shells. A typical cell of the photosynthetic synurophyte Mallomonas is covered by about 60-100 silica scales. Their geometric arrangement, the so-called scale case, mainly depends on the species and on the cell cycle. In this study, the scale case of the synurophyte Mallomonas was preserved in aqueous suspension using high-pressure freezing (HPF). From this specimen, a three-dimensional (3D) data set spanning a volume of about 25.6 μm × 19.2 μm × 4.2 μm with a voxel size of 12.5 nm × 12.5 nm × 25.0 nm was collected by Cryo-FIB SEM in 3 h and 24 min. SEM imaging using In-lens SE detection allowed to clearly differentiate between mineralized, curved scales of less than 0.2 μm thickness and organic cellular ultrastructure or vitrified ice. The three-dimensional spatial orientations and shapes of a minimum set of scales (N = 13) were identified by visual inspection, and manually segmented. Manual and automated segmentation approaches were comparatively applied to one arbitrarily selected reference scale using the differences in grey level between scales and other constituents. Computational automated routines and principal component analysis of the experimentally extracted data created a realistic mathematical model based on the Fibonacci pattern theory. A complete in silico scale case of Mallomonas was reconstructed showing an optimized scale coverage on the cell surface, similarly as it was observed experimentally. The minimum time requirements from harvesting the living cells to the final scale case determination by Cryo-FIB SEM and computational image processing are discussed.

Functional expression of the entire adhesiome of Salmonella enterica serotype Typhimurium

Adhesins are crucial virulence factors of pathogenic bacteria involved in colonization, transmission and pathogenesis. Many bacterial genomes contain the information for a surprisingly large number of diverse adhesive structures. One prominent example is the invasive and facultative intracellular pathogen Salmonella enterica with an adhesiome of up to 20 adhesins. Such large repertoire of adhesins contributes to colonization of a broad range of host species and may allow adaptation to various environments within the host, as well as in non-host environments. For S. enterica, only few members of the adhesiome are functionally expressed under laboratory conditions, and accordingly the structural and functional understanding of the majority of adhesins is sparse. We have devised a simple and versatile approach to functionally express all adhesins of S. enterica serotype Typhimurium, either within Salmonella or within heterologous hosts such as Escherichia coli. We demonstrate the surface expression of various so far cryptic adhesins and show ultrastructural features using atomic force microscopy and transmission electron microscopy. In summary, we report for the first time the expression of the entire adhesiome of S. enterica serotype Typhimurium.

Site-Specific Preparation of Intact Solid-Liquid Interfaces by Label-Free In Situ Localization and Cryo-Focused Ion Beam Lift-Out

Scanning transmission electron microscopy (STEM) allows atomic scale characterization of solid-solid interfaces, but has seen limited applications to solid-liquid interfaces due to the volatility of liquids in the microscope vacuum. Although cryo-electron microscopy is routinely used to characterize hydrated samples stabilized by rapid freezing, sample thinning is required to access the internal interfaces of thicker specimens. Here, we adapt cryo-focused ion beam (FIB) "lift-out," a technique recently developed for biological specimens, to prepare intact internal solid-liquid interfaces for high-resolution structural and chemical analysis by cryo-STEM. To guide the milling process we introduce a label-free in situ method of localizing subsurface structures in suitable materials by energy dispersive X-ray spectroscopy (EDX). Monte Carlo simulations are performed to evaluate the depth-probing capability of the technique, and show good qualitative agreement with experiment. We also detail procedures to produce homogeneously thin lamellae, which enable nanoscale structural, elemental, and chemical analysis of intact solid-liquid interfaces by analytical cryo-STEM. This work demonstrates the potential of cryo-FIB lift-out and cryo-STEM for understanding physical and chemical processes at solid-liquid interfaces.

Multimodal Imaging of Chemically Fixed Cells in Preparation for NanoSIMS

In this work, we have employed time-of-flight secondary ion mass spectrometry (ToF-SIMS) to image chemically fixed adrenal cells prepared for transmission electron microscopy (TEM) and subsequent high-spatial-resolution NanoSIMS imaging. The sample fixation methodology preserves cell morphology, allows analysis in the ultrahigh vacuum environment, and reduces topographic artifacts, thus making these samples particularly favorable for ToF-SIMS analysis. ToF-SIMS imaging enables us to determine the chemistry and preservation capabilities of the chemical fixation as well as to locate specific ion species from OsO4. The OsO4 species have been localized in lysosomes of cortical cells, a type of adrenal cell present in the culture. NanoSIMS imaging of the (190)Os(16)O(-) ion species in cortical cells reveals the same localization as a wide range of OsO4 ions shown with ToF-SIMS. Even though we did not use during NanoSIMS imaging the exact OsxOy(-) ion species discovered with ToF-SIMS, ToF-SIMS allowed us to define the specific subcellular features in a high spatial resolution imaging mode. This study demonstrates the possibility for application of ToF-SIMS as a screening tool to optimize high-resolution imaging with NanoSIMS, which could replace TEM for localization in ultrahigh resolution imaging analyses.

Cryo-planing of frozen-hydrated samples using cryo triple ion gun milling (CryoTIGM™)

Cryo-SEM is a high throughput technique for imaging biological ultrastructure in its most pristine state, i.e. without chemical fixation, embedding, or drying. Freeze fracture is routinely used to prepare internal surfaces for cryo-SEM imaging. However, the propagation of the fracture plane is highly dependent on sample properties, and the resulting surface frequently shows substantial topography, which can complicate image analysis and interpretation. We have developed a broad ion beam milling technique, called cryogenic triple ion gun milling (CryoTIGM™ ['krī-ə-,tīm]), for cryo-planing frozen-hydrated biological specimens. Comparing sample preparation by CryoTIGM™ and freeze fracture in three model systems, Baker's yeast, mouse liver tissue, and whole sea urchin embryos, we find that CryoTIGM™ yields very large (∼700,000 μm(2)) and smooth sections that present ultrastructural details at similar or better quality than freeze-fractured samples. A particular strength of CryoTIGM™ is the ability to section samples with hard-soft contrast such as brittle calcite (CaCO3) spicules in the sea urchin embryo.

Electron Microscopy: From 2D to 3D Images with Special Reference to Muscle

This is a brief and necessarily very sketchy presentation of the evolution in electron microscopy (EM) imaging that was driven by the necessity of extracting 3-D views from the essentially 2-D images produced by the electron beam. The lens design of standard transmission electron microscope has not been greatly altered since its inception. However, technical advances in specimen preparation, image collection and analysis gradually induced an astounding progression over a period of about 50 years. From the early images that redefined tissues, cell and cell organelles at the sub-micron level, to the current nano-resolution reconstructions of organelles and proteins the step is very large. The review is written by an investigator who has followed the field for many years, but often from the sidelines, and with great wonder. Her interest in muscle ultrastructure colors the writing. More specific detailed reviews are presented in this issue.

Nanodiamond landmarks for subcellular multimodal optical and electron imaging

There is a growing need for biolabels that can be used in both optical and electron microscopies, are non-cytotoxic, and do not photobleach. Such biolabels could enable targeted nanoscale imaging of sub-cellular structures, and help to establish correlations between conjugation-delivered biomolecules and function. Here we demonstrate a sub-cellular multi-modal imaging methodology that enables localization of inert particulate probes, consisting of nanodiamonds having fluorescent nitrogen-vacancy centers. These are functionalized to target specific structures, and are observable by both optical and electron microscopies. Nanodiamonds targeted to the nuclear pore complex are rapidly localized in electron-microscopy diffraction mode to enable "zooming-in" to regions of interest for detailed structural investigations. Optical microscopies reveal nanodiamonds for in-vitro tracking or uptake-confirmation. The approach is general, works down to the single nanodiamond level, and can leverage the unique capabilities of nanodiamonds, such as biocompatibility, sensitive magnetometry, and gene and drug delivery.

Cryogenic transmission electron microscopy: aqueous suspensions of nanoscale objects

Direct imaging of nanoscale objects suspended in liquid media can be accomplished using cryogenic transmission electron microscopy (cryo-TEM). Cryo-TEM has been used with particular success in microbiology and other biological fields. Samples are prepared by plunging a thin film of sample into an appropriate cryogen, which essentially produces a snapshot of the suspended objects in their liquid medium. With successful sample preparation, cryo-TEM images can facilitate elucidation of aggregation and self-assembly, as well as provide detailed information about cells and viruses. This work provides an explanation of sample preparation, detailed examples of the many artifacts found in cryo-TEM of aqueous samples, and other key considerations for successful cryo-TEM imaging.

Domain organization of membrane-bound factor VIII

Factor VIII (FVIII) is the blood coagulation protein which when defective or deficient causes for hemophilia A, a severe hereditary bleeding disorder. Activated FVIII (FVIIIa) is the cofactor to the serine protease factor IXa (FIXa) within the membrane-bound Tenase complex, responsible for amplifying its proteolytic activity more than 100,000 times, necessary for normal clot formation. FVIII is composed of two noncovalently linked peptide chains: a light chain (LC) holding the membrane interaction sites and a heavy chain (HC) holding the main FIXa interaction sites. The interplay between the light and heavy chains (HCs) in the membrane-bound state is critical for the biological efficiency of FVIII. Here, we present our cryo-electron microscopy (EM) and structure analysis studies of human FVIII-LC, when helically assembled onto negatively charged single lipid bilayer nanotubes. The resolved FVIII-LC membrane-bound structure supports aspects of our previously proposed FVIII structure from membrane-bound two-dimensional (2D) crystals, such as only the C2 domain interacts directly with the membrane. The LC is oriented differently in the FVIII membrane-bound helical and 2D crystal structures based on EM data, and the existing X-ray structures. This flexibility of the FVIII-LC domain organization in different states is discussed in the light of the FVIIIa-FIXa complex assembly and function.

Adding a new dimension to cardiac nano-architecture using electron microscopy: coupling membrane excitation to calcium signaling

Advances in microscopic imaging technologies and associated computational methods now allow descriptions of cellular anatomy to go beyond 2-dimensions, revealing new micro-domain dynamics at unprecedented resolutions. In cardiomyocytes, electron microscopy (EM) first described junctional membrane complexes between the sarcolemma and sarcoplasmic reticulum over a half-century ago. Since then, 3-dimensional EM technologies such as electron tomography have become successful in determining the realistic nano-geometry of membrane junctions (dyads and peripheral junctions) and associated structures such as transverse tubules (T-tubules, aka. T-system). Concomitantly, super-resolution light microscopy has gone beyond the diffraction-limit to determine the distribution of molecules, such as ryanodine receptors, with 10(-8) meter (10nm) order accuracy. This review provides the current structural perspective and functional interpretation of membrane junction complexes, which are the central machinery controlling cardiac excitation-contraction coupling via calcium signaling.

Förster resonance energy transfer (FRET) as a tool for dissecting the molecular mechanisms for maturation of the Shigella type III secretion needle tip complex

Förster resonance energy transfer (FRET) provides a powerful tool for monitoring intermolecular interactions and a sensitive technique for studying Å-level protein conformational changes. One system that has particularly benefited from the sensitivity and diversity of FRET measurements is the maturation of the Shigella type III secretion apparatus (T3SA) needle tip complex. The Shigella T3SA delivers effector proteins into intestinal cells to promote bacterial invasion and spread. The T3SA is comprised of a basal body that spans the bacterial envelope and a needle with an exposed tip complex that matures in response to environmental stimuli. FRET measurements demonstrated bile salt binding by the nascent needle tip protein IpaD and also mapped resulting structural changes which led to the recruitment of the translocator IpaB. At the needle tip IpaB acts as a sensor for host cell contact but prior to secretion, it is stored as a heterodimeric complex with the chaperone IpgC. FRET analyses showed that chaperone binding to IpaB’s N-terminal domain causes a conformational change in the latter. These FRET analyses, with other biophysical methods, have been central to understanding T3SA maturation and will be highlighted, focusing on the details of the FRET measurements and the relevance to this particular system.

Whole-cell imaging at nanometer resolutions using fast and slow focused helium ions

Observations of the interior structure of cells and subcellular organelles are important steps in unraveling organelle functions. Microscopy using helium ions can play a major role in both surface and subcellular imaging because it can provide subnanometer resolutions at the cell surface for slow helium ions, and fast helium ions can penetrate cells without a significant loss of resolution. Slow (e.g., 10-50 keV) helium ion beams can now be focused to subnanometer dimensions (∼0.25 nm), and keV helium ion microscopy can be used to image the surfaces of cells at high resolutions. Because of the ease of neutralizing the sample charge using a flood electron beam, surface charging effects are minimal and therefore cell surfaces can be imaged without the need for a conducting metallic coating. Fast (MeV) helium ions maintain a straight path as they pass through a cell. Along the ion trajectory, the helium ion undergoes multiple electron collisions, and for each collision a small amount of energy is lost to the scattered electron. By measuring the total energy loss of each MeV helium ion as it passes through the cell, we can construct an energy-loss image that is representative of the mass distribution of the cell. This work paves the way to use ions for whole-cell investigations at nanometer resolutions through structural, elemental (via nuclear elastic backscattering), and fluorescence (via ion induced fluorescence) imaging.

Imaging fluorescently labeled complexes by means of multidimensional correlative light and transmission electron microscopy: practical considerations

These days the common ground between structural biology and molecular biology continues to grow thanks to the biomolecular insights offered by correlative microscopy, even though the vision of combining insights from different imaging tools has been around for nearly four decades. The use of correlative imaging methods to dissect the cell's internal structure is progressing faster than ever as shown by the boom in the number of methodological approaches available for correlative microscopy studies, each designed to address a specific scientific question. In this chapter, we will present a relatively straightforward approach to combining information from fluorescence microscopy and electron microscopy at the supramolecular level. The method combines live-cell and/or confocal laser microscopy with classical sample preparation for transmission electron microscopy (TEM), thereby allowing the integration of dynamic details of subcellular processes with insights about the organelles and molecular machinery involved. We illustrate the applicability of this multidimensional correlative microscopy approach on cultured Caco-2 colorectal cancer cells exposed to fluorescently labeled cisplatin, and discuss how these methods can deepen our understanding of key cellular processes, such as drug uptake and cell fate.

Advances in the mass spectrometry of membrane proteins: from individual proteins to intact complexes

Rapid advances in structural genomics and in large-scale proteomic projects have yielded vast amounts of data on soluble proteins and their complexes. Despite these advances, progress in studying membrane proteins using mass spectrometry (MS) has been slow. This is due in part to the inherent solubility and dynamic properties of these proteins, but also to their low abundance and the absence of polar side chains in amino acid residues. Considerable progress in overcoming these challenges is, however, now being made for all levels of structural characterization. This progress includes MS studies of the primary structure of membrane proteins, wherein sophisticated enrichment and trapping procedures are allowing multiple posttranslational modifications to be defined through to the secondary structure level in which proteins and peptides have been probed using hydrogen exchange, covalent, or radiolytic labeling methods. Exciting possibilities now exist to go beyond primary and secondary structure to reveal the tertiary and quaternary interactions of soluble and membrane subunits within intact assemblies of more than 700 kDa.

Multifaceted nature of membrane microdomains in colorectal cancer

Membrane microdomains or lipid rafts are known to be highly dynamic and to act as selective signal transduction mediators that facilitate interactions between the cell’s external and internal environments. Lipid rafts play an important mediating role in the biology of cancer: they have been found in almost all existing experimental cancer models, including colorectal cancer (CRC), and play key regulatory roles in cell migration, metastasis, cell survival and tumor progression. This paper explores the current state of knowledge in this field by highlighting some of the pioneering and recent lipid raft studies performed on different CRC cell lines and human tissue samples. From this literature review, it becomes clear that membrane microdomains appear to be implicated in all key intracellular signaling pathways for lipid metabolism, drug resistance, cell adhesion, cell death, cell proliferation and many other processes in CRC. All signal transduction pathways seem to originate directly from those peculiar lipid islands, thereby orchestrating the colon cancer cells’ state and fate. As confirmed by recent animal and preclinical studies in different CRC models, continuing to unravel the structure and function of lipid rafts - including their associated complex signaling pathways - will likely bring us one step closer to better monitoring and treating of colon cancer patients.

Quantitative analysis of particle distributions by comparison with simulations

In characterization of metal nanoparticle doped spherical composites, the two-dimensional nature of transmission electron microscopy (TEM) images leads to ambiguities about the true location of the nanoparticles. Walking-in of simulated projections in comparison with actual TEM images leads to quantitative results such as location-dependent particle sizes and particle number density. This method takes advantage of the strength of fuzzy neural network computations via the human hunter-gatherer's visual system's evolved superiority while still allowing quantitative results by use of exact numerical simulations.

Electron cryomicroscopy of membrane proteins: specimen preparation for two-dimensional crystals and single particles

Membrane protein structure and function can be studied by two powerful and highly complementary electron cryomicroscopy (cryo-EM) methods: electron crystallography of two-dimensional (2D) crystals and single particle analysis of detergent-solubilized protein complexes. To obtain the highest-possible resolution data from membrane proteins, whether prepared as 2D crystals or single particles, cryo-EM samples must be vitrified with great care. Grid preparation for cryo-EM of 2D crystals is possible by back-injection, the carbon sandwich technique, drying in sugars before cooling in the electron microscope, or plunge-freezing. Specimen grids for single particle cryo-EM studies of membrane proteins are usually produced by plunge-freezing protein solutions, supported either by perforated or a continuous carbon film substrate. This review outlines the different techniques available and the suitability of each method for particular samples and studies. Experimental considerations in sample preparation and preservation include the protein itself and the presence of lipid or detergent. The appearance of cryo-EM samples in different conditions is also discussed.

Interpretation of very low resolution X-ray electron-density maps using core objects

A novel approach to obtaining structural information from macromolecular X-ray data extending to resolutions as low as 20 A is presented. Following a simple map-segmentation procedure, the approximate shapes of the domains forming the structure are identified. A pattern-recognition comparative analysis of these shapes and those derived from the structures of domains from the PDB results in candidate structural models that can be used for a fit into the density map. It is shown that the placed candidate models can be employed for subsequent phase extension to higher resolution.