Cellular Electron Cryotomography: Toward Structural Biology In Situ

Using in vivo intact structure for system-wide quantitative analysis of changes in proteins

Mass spectrometry-based methods can provide a global expression profile and structural readout of proteins in complex systems. Preserving the in vivo conformation of proteins in their innate state is challenging during proteomic experiments. Here, we introduce a whole animal in vivo protein footprinting method using perfusion of reagents to add dimethyl labels to exposed lysine residues on intact proteins which provides information about protein conformation. When this approach is used to measure dynamic structural changes during Alzheimer's disease (AD) progression in a mouse model, we detect 433 proteins that undergo structural changes attributed to AD, independent of aging, across 7 tissues. We identify structural changes of co-expressed proteins and link the communities of these proteins to their biological functions. Our findings show that structural alterations of proteins precede changes in expression, thereby demonstrating the value of in vivo protein conformation measurement. Our method represents a strategy for untangling mechanisms of proteostasis dysfunction caused by protein misfolding. In vivo whole-animal footprinting should have broad applicability for discovering conformational changes in systemic diseases and for the design of therapeutic interventions.

CryoDRGN-ET: deep reconstructing generative networks for visualizing dynamic biomolecules inside cells

Advances in cryo-electron tomography (cryo-ET) have produced new opportunities to visualize the structures of dynamic macromolecules in native cellular environments. While cryo-ET can reveal structures at molecular resolution, image processing algorithms remain a bottleneck in resolving the heterogeneity of biomolecular structures in situ. Here, we introduce cryoDRGN-ET for heterogeneous reconstruction of cryo-ET subtomograms. CryoDRGN-ET learns a deep generative model of three-dimensional density maps directly from subtomogram tilt-series images and can capture states diverse in both composition and conformation. We validate this approach by recovering the known translational states in Mycoplasma pneumoniae ribosomes in situ. We then perform cryo-ET on cryogenic focused ion beam-milled Saccharomyces cerevisiae cells. CryoDRGN-ET reveals the structural landscape of S. cerevisiae ribosomes during translation and captures continuous motions of fatty acid synthase complexes inside cells. This method is openly available in the cryoDRGN software.

Linking Mitochondrial Dysfunction, Neurotransmitter, and Neural Network Abnormalities and Mania: Elucidating Neurobiological Mechanisms of the Therapeutic Effect of the Ketogenic Diet in Bipolar Disorder

There is growing interest in the ketogenic diet as a treatment for bipolar disorder (BD), and there are promising anecdotal and small case study reports of efficacy. However, the neurobiological mechanisms by which diet-induced ketosis might ameliorate BD symptoms remain to be determined, particularly in manic and hypomanic states-defining features of BD. Identifying these mechanisms will provide new markers to guide personalized interventions and provide targets for novel treatment developments for individuals with BD. In this critical review, we describe recent findings highlighting 2 types of neurobiological abnormalities in BD: 1) mitochondrial dysfunction and 2) neurotransmitter and neural network functional abnormalities. We link these abnormalities to mania/hypomania and depression in BD and then describe the biological underpinnings by which the ketogenic diet may have a beneficial effect in individuals with BD. We end the review by describing approaches that can be employed in future studies to elucidate the neurobiology that underlies the therapeutic effect of the ketogenic diet in BD. Doing this may provide marker predictors to identify individuals who will respond well to the ketogenic diet, as well as offer neural targets for novel treatment developments for BD.

Optimize Electron Beam Energy toward In Situ Imaging of Thick Frozen Bio-Samples with Nanometer Resolution Using MeV-STEM

To optimize electron energy for in situ imaging of large biological samples up to 10 μm in thickness with nanoscale resolutions, we implemented an analytical model based on elastic and inelastic characteristic angles. This model has been benchmarked by Monte Carlo simulations and can be used to predict the transverse beam size broadening as a function of electron energy while the probe beam traverses through the sample. As a result, the optimal choice of the electron beam energy can be realized. In addition, the impact of the dose-limited resolution was analysed. While the sample thickness is less than 10 μm, there exists an optimal electron beam energy below 10 MeV regarding a specific sample thickness. However, for samples thicker than 10 μm, the optimal beam energy is 10 MeV or higher depending on the sample thickness, and the ultimate resolution could become worse with the increase in the sample thickness. Moreover, a MeV-STEM column based on a two-stage lens system can be applied to reduce the beam size from one micron at aperture to one nanometre at the sample with the energy tuning range from 3 to 10 MeV. In conjunction with the state-of-the-art ultralow emittance electron source that we recently implemented, the maximum size of an electron beam when it traverses through an up to 10 μm thick bio-sample can be kept less than 10 nm. This is a critical step toward the in situ imaging of large, thick biological samples with nanometer resolution.

Distinct life cycle stages of an ectosymbiotic DPANN archaeon

DPANN archaea are a diverse group of microorganisms that are thought to rely on an ectosymbiotic lifestyle; however, the cell biology of these cell-cell interactions remains largely unknown. We applied live-cell imaging and cryo-electron tomography to the DPANN archaeon Nanobdella aerobiophila and its host, revealing two distinct life cycle stages. Free cells possess archaella and are motile. Ectobiotic cells are intimately linked with the host through an elaborate attachment organelle. Our data suggest that free cells may actively seek a new host, while the ectobiotic state is adapted to mediate intricate interaction with the host.

Sample Preparation for Electron Cryo-Microscopy of Macromolecular Machines

High-resolution structure determination by electron cryo-microscopy underwent a step change in recent years. This now allows study of challenging samples which previously were inaccessible for structure determination, including membrane proteins. These developments shift the focus in the field to the next bottlenecks which are high-quality sample preparations. While the amounts of sample required for cryo-EM are relatively small, sample quality is the key challenge. Sample quality is influenced by the stability of complexes which depends on buffer composition, inherent flexibility of the sample, and the method of solubilization from the membrane for membrane proteins. It further depends on the choice of sample support, grid pre-treatment and cryo-grid freezing protocol. Here, we discuss various widely applicable approaches to improve sample quality for structural analysis by cryo-EM.

Handling Difficult Cryo-ET Samples: A Study with Primary Neurons from Drosophila melanogaster

Cellular neurobiology has benefited from recent advances in the field of cryo-electron tomography (cryo-ET). Numerous structural and ultrastructural insights have been obtained from plunge-frozen primary neurons cultured on electron microscopy grids. With most primary neurons having been derived from rodent sources, we sought to expand the breadth of sample availability by using primary neurons derived from 3rd instar Drosophila melanogaster larval brains. Ultrastructural abnormalities were encountered while establishing this model system for cryo-ET, which were exemplified by excessive membrane blebbing and cellular fragmentation. To optimize neuronal samples, we integrated substrate selection, micropatterning, montage data collection, and chemical fixation. Efforts to address difficulties in establishing Drosophila neurons for future cryo-ET studies in cellular neurobiology also provided insights that future practitioners can use when attempting to establish other cell-based model systems.

Preparing Arabidopsis thaliana root protoplasts for cryo electron tomography

The use of protoplasts in plant biology has become a convenient tool for the application of transient gene expression. This model system has allowed the study of plant responses to biotic and abiotic stresses, protein location and trafficking, cell wall dynamics, and single-cell transcriptomics, among others. Although well-established protocols for isolating protoplasts from different plant tissues are available, they have never been used for studying plant cells using cryo electron microscopy (cryo-EM) and cryo electron tomography (cryo-ET). Here we describe a workflow to prepare root protoplasts from Arabidopsis thaliana plants for cryo-ET. The process includes protoplast isolation and vitrification on EM grids, and cryo-focused ion beam milling (cryo-FIB), with the aim of tilt series acquisition. The whole workflow, from growing the plants to the acquisition of the tilt series, may take a few months. Our protocol provides a novel application to use plant protoplasts as a tool for cryo-ET.

Big data in contemporary electron microscopy: challenges and opportunities in data transfer, compute and management

The second decade of the twenty-first century witnessed a new challenge in the handling of microscopy data. Big data, data deluge, large data, data compliance, data analytics, data integrity, data interoperability, data retention and data lifecycle are terms that have introduced themselves to the electron microscopy sciences. This is largely attributed to the booming development of new microscopy hardware tools. As a result, large digital image files with an average size of one terabyte within one single acquisition session is not uncommon nowadays, especially in the field of cryogenic electron microscopy. This brings along numerous challenges in data transfer, compute and management. In this review, we will discuss in detail the current state of international knowledge on big data in contemporary electron microscopy and how big data can be transferred, computed and managed efficiently and sustainably. Workflows, solutions, approaches and suggestions will be provided, with the example of the latest experiences in Australia. Finally, important principles such as data integrity, data lifetime and the FAIR and CARE principles will be considered.

Handling difficult cryo-ET samples: A study with primary neurons from Drosophila melanogaster

Cellular neurobiology has benefited from recent advances in the field of cryo-electron tomography (cryo-ET). Numerous structural and ultrastructural insights have been obtained from plunge-frozen primary neurons cultured on electron microscopy grids. With most primary neurons been derived from rodent sources, we sought to expand the breadth of sample availability by using primary neurons derived from 3rd instar Drosophila melanogaster larval brains. Ultrastructural abnormalities were encountered while establishing this model system for cryo-ET, which were exemplified by excessive membrane blebbing and cellular fragmentation. To optimize neuronal samples, we integrated substrate selection, micropatterning, montage data collection, and chemical fixation. Efforts to address difficulties in establishing Drosophila neurons for future cryo-ET studies in cellular neurobiology also provided insights that future practitioners can use when attempting to establish other cell-based model systems.

Munc13- and SNAP25-dependent molecular bridges play a key role in synaptic vesicle priming

Synaptic vesicle tethering, priming, and neurotransmitter release require a coordinated action of multiple protein complexes. While physiological experiments, interaction data, and structural studies of purified systems were essential for our understanding of the function of the individual complexes involved, they cannot resolve how the actions of individual complexes integrate. We used cryo-electron tomography to simultaneously image multiple presynaptic protein complexes and lipids at molecular resolution in their native composition, conformation, and environment. Our detailed morphological characterization suggests that sequential synaptic vesicle states precede neurotransmitter release, where Munc13-comprising bridges localize vesicles <10 nanometers and soluble N-ethylmaleimide-sensitive factor attachment protein 25-comprising bridges <5 nanometers from the plasma membrane, the latter constituting a molecularly primed state. Munc13 activation supports the transition to the primed state via vesicle bridges to plasma membrane (tethers), while protein kinase C promotes the same transition by reducing vesicle interlinking. These findings exemplify a cellular function performed by an extended assembly comprising multiple molecularly diverse complexes.

In vivo Protein Footprinting Reveals the Dynamic Conformational Changes of Proteome of Multiple Tissues in Progressing Alzheimer's Disease

Numerous studies have investigated changes in protein expression at the system level using proteomic mass spectrometry, but only recently have studies explored the structure of proteins at the proteome level. We developed covalent protein painting (CPP), a protein footprinting method that quantitatively labels exposed lysine, and have now extended the method to whole intact animals to measure surface accessibility as a surrogate of in vivo protein conformations. We investigated how protein structure and protein expression change as Alzheimer's disease (AD) progresses by conducting in vivo whole animal labeling of AD mice. This allowed us to analyze broadly protein accessibility in various organs over the course of AD. We observed that structural changes of proteins related to 'energy generation,' 'carbon metabolism,' and 'metal ion homeostasis' preceded expression changes in the brain. We found that proteins in certain pathways undergoing structural changes were significantly co-regulated in the brain, kidney, muscle, and spleen.

Computational Methods Toward Unbiased Pattern Mining and Structure Determination in Cryo-Electron Tomography Data

Cryo-electron tomography can uniquely probe the native cellular environment for macromolecular structures. Tomograms feature complex data with densities of diverse, densely crowded macromolecular complexes, low signal-to-noise, and artifacts such as the missing wedge effect. Post-processing of this data generally involves isolating regions or particles of interest from tomograms, organizing them into related groups, and rendering final structures through subtomogram averaging. Template-matching and reference-based structure determination are popular analysis methods but are vulnerable to biases and can often require significant user input. Most importantly, these approaches cannot identify novel complexes that reside within the imaged cellular environment. To reliably extract and resolve structures of interest, efficient and unbiased approaches are therefore of great value. This review highlights notable computational software and discusses how they contribute to making automated structural pattern discovery a possibility. Perspectives emphasizing the importance of features for user-friendliness and accessibility are also presented.

Bacterial Type II Secretion System and Its Mitochondrial Counterpart

Over the billions of years that bacteria have been around, they have evolved several sophisticated protein secretion nanomachines to deliver toxins, hydrolytic enzymes, and effector proteins into their environments. Of these, the type II secretion system (T2SS) is used by Gram-negative bacteria to export a wide range of folded proteins from the periplasm across the outer membrane.

Structure and Function of the Dot/Icm T4SS

The Legionella pneumophila Dot/Icm type IV secretion system (T4SS) delivers effector proteins into host cells during infection. Despite its significance as a potential drug target, our current understanding of its atomic structure is limited to isolated subcomplexes. In this study, we used subtomogram averaging and integrative modeling to construct a nearly-complete model of the Dot/Icm T4SS accounting for seventeen protein components. We locate and provide insights into the structure and function of six new components including DotI, DotJ, DotU, IcmF, IcmT, and IcmX. We find that the cytosolic N-terminal domain of IcmF, a key protein forming a central hollow cylinder, interacts with DotU, providing insight into previously uncharacterized density. Furthermore, our model, in combination with analyses of compositional heterogeneity, explains how the cytoplasmic ATPase DotO is connected to the periplasmic complex via interactions with membrane-bound DotI/DotJ proteins. Coupled with in situ infection data, our model offers new insights into the T4SS-mediated secretion mechanism.

Genetic and biochemical strategies for regulation of L-ascorbic acid biosynthesis in plants through the L-galactose pathway

Vitamin C (L-ascorbic acid, AsA) is an essential compound with pleiotropic functions in many organisms. Since its isolation in the last century, AsA has attracted the attention of the scientific community, allowing the discovery of the L-galactose pathway, which is the main pathway for AsA biosynthesis in plants. Thus, the aim of this review is to analyze the genetic and biochemical strategies employed by plant cells for regulating AsA biosynthesis through the L-galactose pathway. In this pathway, participates eight enzymes encoded by the genes PMI, PMM, GMP, GME, GGP, GPP, GDH, and GLDH. All these genes and their encoded enzymes have been well characterized, demonstrating their participation in AsA biosynthesis. Also, have described some genetic and biochemical strategies that allow its regulation. The genetic strategy includes regulation at transcriptional and post-transcriptional levels. In the first one, it was demonstrated that the expression levels of the genes correlate directly with AsA content in the tissues/organs of the plants. Also, it was proved that these genes are light-induced because they have light-responsive promoter motifs (e.g., ATC, I-box, GT1 motif, etc.). In addition, were identified some transcription factors that function as activators (e.g., SlICE1, AtERF98, SlHZ24, etc.) or inactivators (e.g., SlL1L4, ABI4, SlNYYA10) regulate the transcription of these genes. In the second one, it was proved that some genes have alternative splicing events and could be a mechanism to control AsA biosynthesis. Also, it was demonstrated that a conserved cis-acting upstream open reading frame (5'-uORF) located in the 5'-untranslated region of the GGP gene induces its post-transcriptional repression. Among the biochemical strategies discovered is the control of the enzyme levels (usually by decreasing their quantities), control of the enzyme catalytic activity (by increasing or decreasing its activity), feedback inhibition of some enzymes (GME and GGP), subcellular compartmentation of AsA, the metabolon assembly of the enzymes, and control of AsA biosynthesis by electron flow. Together, the construction of this basic knowledge has been establishing the foundations for generating genetically improved varieties of fruits and vegetables enriched with AsA, commonly used in animal and human feed.

In Situ Structure Determination of Bacterial Surface Nanomachines Using Cryo-Electron Tomography

Bacterial surface nanomachines are often refractory to structural determination in their intact form due to their extensive association with the cell envelope preventing them from being properly purified for traditional structural biology methods. Cryo-electron tomography (cryo-ET) is an emerging branch of cryo-electron microscopy that can visualize supramolecular complexes directly inside frozen-hydrated cells in 3D at nanometer resolution, therefore posing a unique capability to study the intact structures of bacterial surface nanomachines in situ and reveal their molecular association with other cellular components. Furthermore, the resolution of cryo-ET is continually improving alongside methodological advancement. Here, using the type IV pilus machine in Myxococcus xanthus as an example, we describe a step-by-step workflow for in situ structure determination including sample preparation and screening, microscope and camera tuning, tilt series acquisition, data processing and tomogram reconstruction, subtomogram averaging, and structural analysis.

Integrated multimodality microscope for accurate and efficient target-guided cryo-lamellae preparation

Cryo-electron tomography (cryo-ET) is a revolutionary technique for resolving the structure of subcellular organelles and macromolecular complexes in their cellular context. However, the application of the cryo-ET is hampered by the sample preparation step. Performing cryo-focused ion beam milling at an arbitrary position on the sample is inefficient, and the target of interest is not guaranteed to be preserved when thinning the cell from several micrometers to less than 300 nm thick. Here, we report a cryogenic correlated light, ion and electron microscopy (cryo-CLIEM) technique that is capable of preparing cryo-lamellae under the guidance of three-dimensional confocal imaging. Moreover, we demonstrate a workflow to preselect and preserve nanoscale target regions inside the finished cryo-lamellae. By successfully preparing cryo-lamellae that contain a single centriole or contact sites between subcellular organelles, we show that this approach is generally applicable, and shall help in innovating more applications of cryo-ET.

Self-supervised learning for macromolecular structure classification based on cryo-electron tomograms

Macromolecular structure classification from cryo-electron tomography (cryo-ET) data is important for understanding macro-molecular dynamics. It has a wide range of applications and is essential in enhancing our knowledge of the sub-cellular environment. However, a major limitation has been insufficient labelled cryo-ET data. In this work, we use Contrastive Self-supervised Learning (CSSL) to improve the previous approaches for macromolecular structure classification from cryo-ET data with limited labels. We first pretrain an encoder with unlabelled data using CSSL and then fine-tune the pretrained weights on the downstream classification task. To this end, we design a cryo-ET domain-specific data-augmentation pipeline. The benefit of augmenting cryo-ET datasets is most prominent when the original dataset is limited in size. Overall, extensive experiments performed on real and simulated cryo-ET data in the semi-supervised learning setting demonstrate the effectiveness of our approach in macromolecular labeling and classification.

Computational methods for ultrastructural analysis of synaptic complexes

Electron microscopy (EM) provided fundamental insights about the ultrastructure of neuronal synapses. The large amount of information present in the contemporary EM datasets precludes a thorough assessment by visual inspection alone, thus requiring computational methods for the analysis of the data. Here, I review image processing software methods ranging from membrane tracing in large volume datasets to high resolution structures of synaptic complexes. Particular attention is payed to molecular level analysis provided by recent cryo-electron microscopy and tomography methods.

Quantitative Frameworks for Multivalent Macromolecular Interactions in Biological Linear Lattice Systems

Multivalent macromolecular interactions underlie dynamic regulation of diverse biological processes in ever-changing cellular states. These interactions often involve binding of multiple proteins to a linear lattice including intrinsically disordered proteins and the chromosomal DNA with many repeating recognition motifs. Quantitative understanding of such multivalent interactions on a linear lattice is crucial for exploring their unique regulatory potentials in the cellular processes. In this review, the distinctive molecular features of the linear lattice system are first discussed with a particular focus on the overlapping nature of potential protein binding sites within a lattice. Then, we introduce two general quantitative frameworks, combinatorial and conditional probability models, dealing with the overlap problem and relating the binding parameters to the experimentally measurable properties of the linear lattice-protein interactions. To this end, we present two specific examples where the quantitative models have been applied and further extended to provide biological insights into specific cellular processes. In the first case, the conditional probability model was extended to highlight the significant impact of nonspecific binding of transcription factors to the chromosomal DNA on gene-specific transcriptional activities. The second case presents the recently developed combinatorial models to unravel the complex organization of target protein binding sites within an intrinsically disordered region (IDR) of a nucleoporin. In particular, these models have suggested a unique function of IDRs as a molecular switch coupling distinct cellular processes. The quantitative models reviewed here are envisioned to further advance for dissection and functional studies of more complex systems including phase-separated biomolecular condensates.

Zooming in on host-symbiont interactions: advances in cryo-EM sample processing methods and future application to symbiotic tissues

Animals, plants, and fungi live in a microbe-dominated world. Investigating the interactions and processes at the host-microbe interface offers insight to how bacteria influence the development, health, and disease of the host. Optimization of existing imaging technologies and development of novel instrumentation will provide the tools needed to fully understand the dynamic relationship that occurs at the host-microbe interface throughout the lifetime of the host. In this review, we describe the current methods used in cryo-electron microscopy (cryo-EM) including cryo-fixation, sample processing, FIB-SEM, and cryotomography. Further, we highlight the new advances associated with these methods that open the cryo-EM discipline to large, complex multicellular samples, like symbiotic tissues. We describe the advantages and challenges associated with correlative imaging techniques and sample thinning methods like lift-out. By highlighting recent pioneering studies in the large-volume or symbiotic sample workflows, we provide insight into how symbiotic model systems will benefit from cryo-EM methods to provide artefact-free, near-native, macromolecular-scale resolution imaging at the host-microbe interface throughout the development and maintenance of symbiosis. Cryo-EM methods have brought a deep fundamental understanding of prokaryotic biology since its conception. We propose the application of existing and novel cryo-EM techniques to symbiotic systems is the logical next step that will bring an even greater understanding how microbes interact with their host tissues.

Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere

The tree of life (TOL) is a powerful framework to depict the evolutionary history of cellular organisms through time, from our microbial origins to the diversification of multicellular eukaryotes that shape the visible biosphere today. During the past decades, our perception of the TOL has fundamentally changed, in part, due to profound methodological advances, which allowed a more objective approach to studying organismal and viral diversity and led to the discovery of major new branches in the TOL as well as viral lineages. Phylogenetic and comparative genomics analyses of these data have, among others, revolutionized our understanding of the deep roots and diversity of microbial life, the origin of the eukaryotic cell, eukaryotic diversity, as well as the origin, and diversification of viruses. In this review, we provide an overview of some of the recent discoveries on the evolutionary history of cellular organisms and their viruses and discuss a variety of complementary techniques that we consider crucial for making further progress in our understanding of the TOL and its interconnection with the virosphere.

High-Throughput Native Mass Spectrometry Screening in Drug Discovery

The design of new therapeutic molecules can be significantly informed by studying protein-ligand interactions using biophysical approaches directly after purification of the protein-ligand complex. Well-established techniques utilized in drug discovery include isothermal titration calorimetry, surface plasmon resonance, nuclear magnetic resonance spectroscopy, and structure-based drug discovery which mainly rely on protein crystallography and, more recently, cryo-electron microscopy. Protein-ligand complexes are dynamic, heterogeneous, and challenging systems that are best studied with several complementary techniques. Native mass spectrometry (MS) is a versatile method used to study proteins and their non-covalently driven assemblies in a native-like folded state, providing information on binding thermodynamics and stoichiometry as well as insights on ternary and quaternary protein structure. Here, we discuss the basic principles of native mass spectrometry, the field's recent progress, how native MS is integrated into a drug discovery pipeline, and its future developments in drug discovery.

Electron microscopy for imaging organelles in plants and algae

Recent developments in both instrumentation and image analysis algorithms have allowed three-dimensional electron microscopy (3D-EM) to increase automated image collections through large tissue volumes using serial block-face scanning EM (SEM) and to achieve near-atomic resolution of macromolecular complexes using cryo-electron tomography (cryo-ET) and sub-tomogram averaging. In this review, we discuss applications of cryo-ET to cell biology research on plant and algal systems and the special opportunities they offer for understanding the organization of eukaryotic organelles with unprecedently resolution. However, one of the most challenging aspects for cryo-ET is sample preparation, especially for multicellular organisms. We also discuss correlative light and electron microscopy (CLEM) approaches that have been developed for ET at both room and cryogenic temperatures.

Structural Biology Illuminates Molecular Determinants of Broad Ebolavirus Neutralization by Human Antibodies for Pan-Ebolavirus Therapeutic Development

Monoclonal antibodies (mAbs) have proven effective for the treatment of ebolavirus infection in humans, with two mAb-based drugs Inmazeb™ and Ebanga™ receiving FDA approval in 2020. While these drugs represent a major advance in the field of filoviral therapeutics, they are composed of antibodies with single-species specificity for Zaire ebolavirus. The Ebolavirus genus includes five additional species, two of which, Bundibugyo ebolavirus and Sudan ebolavirus, have caused severe disease and significant outbreaks in the past. There are several recently identified broadly neutralizing ebolavirus antibodies, including some in the clinical development pipeline, that have demonstrated broad protection in preclinical studies. In this review, we describe how structural biology has illuminated the molecular basis of broad ebolavirus neutralization, including details of common antigenic sites of vulnerability on the glycoprotein surface. We begin with a discussion outlining the history of monoclonal antibody therapeutics for ebolaviruses, with an emphasis on how structural biology has contributed to these efforts. Next, we highlight key structural studies that have advanced our understanding of ebolavirus glycoprotein structures and mechanisms of antibody-mediated neutralization. Finally, we offer examples of how structural biology has contributed to advances in anti-viral medicines and discuss what opportunities the future holds, including rationally designed next-generation therapeutics with increased potency, breadth, and specificity against ebolaviruses.

High-resolution mapping of metal ions reveals principles of surface layer assembly in Caulobacter crescentus cells

Surface layers (S-layers) are proteinaceous crystalline coats that constitute the outermost component of most prokaryotic cell envelopes. In this study, we have investigated the role of metal ions in the formation of the Caulobacter crescentus S-layer using high-resolution structural and cell biology techniques, as well as molecular simulations. Utilizing optical microscopy of fluorescently tagged S-layers, we show that calcium ions facilitate S-layer lattice formation and cell-surface binding. We report all-atom molecular dynamics simulations of the S-layer lattice, revealing the importance of bound metal ions. Finally, using electron cryomicroscopy and long-wavelength X-ray diffraction experiments, we mapped the positions of metal ions in the S-layer at near-atomic resolution, supporting our insights from the cellular and simulations data. Our findings contribute to the understanding of how C. crescentus cells form a regularly arranged S-layer on their surface, with implications on fundamental S-layer biology and the synthetic biology of self-assembling biomaterials.

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Live imaging shows Ca²⁺-dependent expansion of the C. crescentus S-layer

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Molecular simulations reveal Ca²⁺-binding properties of the S-layer

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Ca²⁺ ion mapping in three-dimensional crystals using in-vacuum X-ray anomalous diffraction

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Ca²⁺ replacement by Ho³⁺ allows cryo-EM mapping of heavy metals

In Situ Visualization of the pKM101-Encoded Type IV Secretion System Reveals a Highly Symmetric ATPase Energy Center

Bacterial conjugation systems are members of the type IV secretion system (T4SS) superfamily. T4SSs can be classified as “minimized” or “expanded” based on whether they are composed of a core set of signature subunits or additional system-specific components. Prototypical minimized systems mediating Agrobacterium tumefaciens transfer DNA (T-DNA) and pKM101 and R388 plasmid transfer are built from subunits generically named VirB1 to VirB11 and VirD4. We visualized the pKM101-encoded T4SS in its native cellular context by in situ cryo-electron tomography (CryoET). The T4SS_pKM101 is composed of an outer membrane core complex (OMCC) connected by a thin stalk to an inner membrane complex (IMC). The OMCC exhibits 14-fold symmetry and resembles that of the T4SS_R388 analyzed previously by single-particle electron microscopy. The IMC is highly symmetrical and exhibits 6-fold symmetry. It is dominated by a hexameric collar in the periplasm and a cytoplasmic complex composed of a hexamer of dimers of the VirB4-like TraB ATPase. The IMC closely resembles equivalent regions of three expanded T4SSs previously visualized by in situ CryoET but differs strikingly from the IMC of the purified T4SS_R388, whose cytoplasmic complex instead presents as two side-by-side VirB4 hexamers. Analyses of mutant machines lacking each of the three ATPases required for T4SS_pKM101 function supplied evidence that TraB_B4 as well as VirB11-like TraG contribute to distinct stages of machine assembly. We propose that the VirB4-like ATPases, configured as hexamers of dimers at the T4SS entrance, orchestrate IMC assembly and recruitment of the spatially dynamic VirB11 and VirD4 ATPases to activate the T4SS for substrate transfer.

From cells to atoms: Cryo-EM as an essential tool to investigate pathogen biology, host-pathogen interaction, and drug discovery

Electron cryo-microscopy (cryo-EM) has lately emerged as a powerful method in structural biology and cell biology. While cryo-EM single-particle analysis (SPA) is now routinely delivering structures of purified proteins and protein complexes at near-atomic resolution, the use of electron cryo-tomography (cryo-ET), together with subtomogram averaging, is allowing visualization of macromolecular complexes in their native cellular environment, at unprecedented resolution. The unique ability of cryo-EM to provide information at many spatial resolution scales from ångströms to microns makes it an invaluable tool that bridges the classic "resolution-gap" between structural biology and cell biology domains. Like in many other fields of biology, in recent years, cryo-EM has revolutionized our understanding of pathogen biology, host-pathogen interaction and has made significant strides toward structure-based drug discovery. In a very recent example, during the ongoing coronavirus disease (COVID-19) pandemic, the structure of the stabilized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein was deciphered by SPA. This led to the development of multiple vaccines. Alongside, cryo-ET provided key insights into the structure of the native virion, mechanism of its entry, replication, and budding; demonstrating the unrivaled power of cryo-EM in investigating pathogen biology, host-pathogen interaction, and drug discovery. In this review, we showcase a few examples of how different imaging modalities within cryo-EM have enabled the study of microbiology and host-pathogen interaction.

Integrating on-grid immunogold labeling and cryo-electron tomography to reveal photosystem II structure and spatial distribution in thylakoid membranes

A long-standing challenge in cell biology is elucidating the structure and spatial distribution of individual membrane-bound proteins, protein complexes and their interactions in their native environment. Here, we describe a workflow that combines on-grid immunogold labeling, followed by cryo-electron tomography (cryoET) imaging and structural analyses to identify and characterize the structure of photosystem II (PSII) complexes. Using an antibody specific to a core subunit of PSII, the D1 protein (uniquely found in the water splitting complex in all oxygenic photoautotrophs), we identified PSII complexes in biophysically active thylakoid membranes isolated from a model marine diatom Phaeodactylum tricornutum. Subsequent cryoET analyses of these protein complexes resolved two PSII structures: supercomplexes and dimeric cores. Our integrative approach establishes the structural signature of multimeric membrane protein complexes in their native environment and provides a pathway to elucidate their high-resolution structures.

UNSUPERVISED DOMAIN ALIGNMENT BASED OPEN SET STRUCTURAL RECOGNITION OF MACROMOLECULES CAPTURED BY CRYO-ELECTRON TOMOGRAPHY

Cellular cryo-Electron Tomography (cryo-ET) provides three-dimensional views of structural and spatial information of various macromolecules in cells in a near-native state. Subtomogram classification is a key step for recognizing and differentiating these macromolecular structures. In recent years, deep learning methods have been developed for high-throughput subtomogram classification tasks; however, conventional supervised deep learning methods cannot recognize macromolecular structural classes that do not exist in the training data. This imposes a major weakness since most native macromolecular structures in cells are unknown and consequently, cannot be included in the training data. Therefore, open set learning which can recognize unknown macromolecular structures is necessary for boosting the power of automatic subtomogram classification. In this paper, we propose a method called Margin-based Loss for Unsupervised Domain Alignment (MLUDA) for open set recognition problems where only a few categories of interest are shared between cross-domain data. Through extensive experiments, we demonstrate that MLUDA performs well at cross-domain open-set classification on both public datasets and medical imaging datasets. So our method is of practical importance.

Structure and dynamics of photoreceptor sensory cilia

The rod and cone photoreceptor cells of the vertebrate retina have highly specialized structures that enable them to carry out their function of light detection over a broad range of illumination intensities with optimized spatial and temporal resolution. Most prominent are their unusually large sensory cilia, consisting of outer segments packed with photosensitive disc membranes, a connecting cilium with many features reminiscent of the primary cilium transition zone, and a pair of centrioles forming a basal body which serves as the platform upon which the ciliary axoneme is assembled. These structures form a highway through which an enormous flux of material moves on a daily basis to sustain the continual turnover of outer segment discs and the energetic demands of phototransduction. After decades of study, the details of the fine structure and distribution of molecular components of these structures are still incompletely understood, but recent advances in cellular imaging techniques and animal models of inherited ciliary defects are yielding important new insights. This knowledge informs our understanding both of the mechanisms of trafficking and assembly and of the pathophysiological mechanisms of human blinding ciliopathies.

An Overview of Microcrystal Electron Diffraction (MicroED)

The bedrock of drug discovery and a key tool for understanding cellular function and drug mechanisms of action is the structure determination of chemical compounds, peptides, and proteins. The development of new structure characterization tools, particularly those that fill critical gaps in existing methods, presents important steps forward for structural biology and drug discovery. The emergence of microcrystal electron diffraction (MicroED) expands the application of cryo-electron microscopy to include samples ranging from small molecules and membrane proteins to even large protein complexes using crystals that are one-billionth the size of those required for X-ray crystallography. This review outlines the conception, achievements, and exciting future trajectories for MicroED, an important addition to the existing biophysical toolkit.

Locating macromolecular assemblies in cells by 2D template matching with cisTEM

For a more complete understanding of molecular mechanisms, it is important to study macromolecules and their assemblies in the broader context of the cell. This context can be visualized at nanometer resolution in three dimensions (3D) using electron cryo-tomography, which requires tilt series to be recorded and computationally aligned, currently limiting throughput. Additionally, the high-resolution signal preserved in the raw tomograms is currently limited by a number of technical difficulties, leading to an increased false-positive detection rate when using 3D template matching to find molecular complexes in tomograms. We have recently described a 2D template matching approach that addresses these issues by including high-resolution signal preserved in single-tilt images. A current limitation of this approach is the high computational cost that limits throughput. We describe here a GPU-accelerated implementation of 2D template matching in the image processing software cisTEM that allows for easy scaling and improves the accessibility of this approach. We apply 2D template matching to identify ribosomes in images of frozen-hydrated Mycoplasma pneumoniae cells with high precision and sensitivity, demonstrating that this is a versatile tool for in situ visual proteomics and in situ structure determination. We benchmark the results with 3D template matching of tomograms acquired on identical sample locations and identify strengths and weaknesses of both techniques, which offer complementary information about target localization and identity.

Challenges in solving structures from radiation-damaged tomograms of protein nanocrystals assessed by simulation

Structure-determination methods are needed to resolve the atomic details that underlie protein function. X-ray crystallography has provided most of our knowledge of protein structure, but is constrained by the need for large, well ordered crystals and the loss of phase information. The rapidly developing methods of serial femtosecond crystallography, micro-electron diffraction and single-particle reconstruction circumvent the first of these limitations by enabling data collection from nanocrystals or purified proteins. However, the first two methods also suffer from the phase problem, while many proteins fall below the molecular-weight threshold required for single-particle reconstruction. Cryo-electron tomography of protein nanocrystals has the potential to overcome these obstacles of mainstream structure-determination methods. Here, a data-processing scheme is presented that combines routines from X-ray crystallography and new algorithms that have been developed to solve structures from tomograms of nanocrystals. This pipeline handles image-processing challenges specific to tomographic sampling of periodic specimens and is validated using simulated crystals. The tolerance of this workflow to the effects of radiation damage is also assessed. The simulations indicate a trade-off between a wider tilt range to facilitate merging data from multiple tomograms and a smaller tilt increment to improve phase accuracy. Since phase errors, but not merging errors, can be overcome with additional data sets, these results recommend distributing the dose over a wide angular range rather than using a finer sampling interval to solve the protein structure.

The Structure, Composition, and Role of Periplasmic Stator Scaffolds in Polar Bacterial Flagellar Motors

In the bacterial flagellar motor, the cell-wall-anchored stator uses an electrochemical gradient across the cytoplasmic membrane to generate a turning force that is applied to the rotor connected to the flagellar filament. Existing theoretical concepts for the stator function are based on the assumption that it anchors around the rotor perimeter by binding to peptidoglycan (P). The existence of another anchoring region on the motor itself has been speculated upon, but is yet to be supported by binding studies. Due to the recent advances in electron cryotomography, evidence has emerged that polar flagellar motors contain substantial proteinaceous periplasmic structures next to the stator, without which the stator does not assemble and the motor does not function. These structures have a morphology of disks, as is the case with Vibrio spp., or a round cage, as is the case with Helicobacter pylori. It is now recognized that such additional periplasmic components are a common feature of polar flagellar motors, which sustain higher torque and greater swimming speeds compared to peritrichous bacteria such as Escherichia coli and Salmonella enterica. This review summarizes the data available on the structure, composition, and role of the periplasmic scaffold in polar bacterial flagellar motors and discusses the new paradigm for how such motors assemble and function.

Assessment of scoring functions to rank the quality of 3D subtomogram clusters from cryo-electron tomography

Cryo-electron tomography provides the opportunity for unsupervised discovery of endogenous complexes in situ. This process usually requires particle picking, clustering and alignment of subtomograms to produce an average structure of the complex. When applied to heterogeneous samples, template-free clustering and alignment of subtomograms can potentially lead to the discovery of structures for unknown endogenous complexes. However, such methods require scoring functions to measure and accurately rank the quality of aligned subtomogram clusters, which can be compromised by contaminations from misclassified complexes and alignment errors. Here, we provide the first study to assess the effectiveness of more than 15 scoring functions for evaluating the quality of subtomogram clusters, which differ in the amount of structural misalignments and contaminations due to misclassified complexes. We assessed both experimental and simulated subtomograms as ground truth data sets. Our analysis showed that the robustness of scoring functions varies largely. Most scores were sensitive to the signal-to-noise ratio of subtomograms and often required Gaussian filtering as preprocessing for improved performance. Two scoring functions, Spectral SNR-based Fourier Shell Correlation and Pearson Correlation in the Fourier domain with missing wedge correction, showed a robust ranking of subtomogram clusters without any preprocessing and irrespective of SNR levels of subtomograms. Of these two scoring functions, Spectral SNR-based Fourier Shell Correlation was fastest to compute and is a better choice for handling large numbers of subtomograms. Our results provide a guidance for choosing an accurate scoring function for template-free approaches to detect complexes from heterogeneous samples.

Integrative approaches in cryogenic electron microscopy: Recent advances in structural biology and future perspectives

Cellular factories engage numerous highly complex "molecular machines" to perform pivotal biological functions. 3D structural visualization is an effective way to understand the functional mechanisms of these biomacromolecules. The "resolution revolution" has established cryogenic electron microscopy (cryo-EM) as a preferred structural biology tool. In parallel with the advances in cryo-EM methodologies aiming at atomic resolution, several innovative approaches have started emerging where other techniques are sensibly integrated with cryo-EM to obtain additional insights into the biological processes. For example, combining the time-resolved technique with high-resolution cryo-EM enables discerning structures of short-lived intermediates in the functional pathway of a biomolecule. Likewise, integrating mass spectrometry (MS) techniques with cryo-EM allows deciphering structural organizations of large molecular assemblies. Here, we discuss how the data generated upon combining either time resolve or MS techniques with cryo-EM supplement structural elucidations with in-depth understanding of the function of cellular macromolecules when they participate in fundamental biological processes.

One-Shot Learning With Attention-Guided Segmentation in Cryo-Electron Tomography

Cryo-electron Tomography (cryo-ET) generates 3D visualization of cellular organization that allows biologists to analyze cellular structures in a near-native state with nano resolution. Recently, deep learning methods have demonstrated promising performance in classification and segmentation of macromolecule structures captured by cryo-ET, but training individual deep learning models requires large amounts of manually labeled and segmented data from previously observed classes. To perform classification and segmentation in the wild (i.e., with limited training data and with unseen classes), novel deep learning model needs to be developed to classify and segment unseen macromolecules captured by cryo-ET. In this paper, we develop a one-shot learning framework, called cryo-ET one-shot network (COS-Net), for simultaneous classification of macromolecular structure and generation of the voxel-level 3D segmentation, using only one training sample per class. Our experimental results on 22 macromolecule classes demonstrated that our COS-Net could efficiently classify macromolecular structures with small amounts of samples and produce accurate 3D segmentation at the same time.

Structure and regulation of phospholipase Cβ and ε at the membrane

Phospholipase C (PLC) β and ε enzymes hydrolyze phosphatidylinositol (PI) lipids in response to direct interactions with heterotrimeric G protein subunits and small GTPases, which are activated downstream of G protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs). PI hydrolysis generates second messengers that increase the intracellular Ca²⁺ concentration and activate protein kinase C (PKC), thereby regulating numerous physiological processes. PLCβ and PLCε share a highly conserved core required for lipase activity, but use different strategies and structural elements to autoinhibit basal activity, bind membranes, and engage G protein activators. In this review, we discuss recent structural insights into these enzymes and the implications for how they engage membranes alone or in complex with their G protein regulators.

Endogenous membrane stress induces T6SS activity in Pseudomonas aeruginosa

The type 6 secretion system (T6SS) is a dynamic organelle encoded by many gram-negative bacteria that can be used to kill competing bacterial prey species in densely occupied niches. Some predatory species, such as Vibrio cholerae, use their T6SS in an untargeted fashion while in contrast, Pseudomonas aeruginosa assembles and fires its T6SS apparatus only after detecting initial attacks by other bacterial prey cells; this targeted attack strategy has been termed the T6SS tit-for-tat response. Molecules that interact with the P. aeruginosa outer membrane such as polymyxin B can also trigger assembly of T6SS organelles via a signal transduction pathway that involves protein phosphorylation. Recent work suggests that a phospholipase T6SS effector (TseL) of V. cholerae can induce T6SS dynamic activity in P. aeruginosa when delivered to or expressed in the periplasmic space of this organism. Here, we report that inhibiting expression of essential genes involved in outer membrane biogenesis can also trigger T6SS activation in P. aeruginosa Specifically, we developed a CRISPR interference (CRISPRi) system to knock down expression of bamA, tolB, and lptD and found that these knockdowns activated T6SS activity. This increase in T6SS activity was dependent on the same signal transduction pathway that was previously shown to be required for the tit-for-tat response. We conclude that outer membrane perturbation can be sensed by P. aeruginosa to activate the T6SS even when the disruption is generated by aberrant cell envelope biogenesis.

Antibacterial activity of geraniin from sugar maple leaves: an ultrastructural study with the phytopathogen Xanthomonas campestris pv. vitians

Effect of geraniin extracted from sugar maple (Acer saccharum) leaves on the viability of the phytopathogen Xanthomonas campestris pv. vitians was evaluated with the SYTOX Green nucleic acid stain, penetrating only compromised membranes, and plate counts. In parallel, structural changes of treated bacteria were examined in transmission electron microscopy (TEM). Based on SYTOX Green and plate counts, geraniin at the minimum bactericidal concentration (3.125 mg/ml) increased mortality after 45 min by 37% and 62%, respectively, when compared with controls. According to observations in TEM, geraniin caused morphological alterations of these rod-shaped bacteria, including degradation of their envelopes, as also suggested by the incorporation of SYTOX. These alterations were often accompanied by cytoplasm leakage and the formation of more pronounced whitish areas in the cytoplasm similar to vacuolization. Moreover, multi-membranous and/or -wall systems were at times formed in the treated bacteria. The presence of some extracellular electron-dense material was frequently noted around the treated bacteria. The matrix surrounding control bacteria tended to disappear after geraniin treatment. This study highlights for the first time the effect of geraniin on bacterial ultrastructure, thus contributing to a better understanding of the mechanism by which this molecule exerts antibacterial activity.

John PC, Bomble YJ. Advances in integrative structural biology: Towards understanding protein complexes in their cellular context

Microorganisms rely on protein interactions to transmit signals, react to stimuli, and grow. One of the best ways to understand these protein interactions is through structural characterization. However, in the past, structural knowledge was limited to stable, high-affinity complexes that could be crystallized. Recent developments in structural biology have revolutionized how protein interactions are characterized. The combination of multiple techniques, known as integrative structural biology, has provided insight into how large protein complexes interact in their native environment. In this mini-review, we describe the past, present, and potential future of integrative structural biology as a tool for characterizing protein interactions in their cellular context.

Platelet Imaging

The knowledge gained through imaging platelets has formed the backbone of our understanding of their biology in health and disease. Early investigators relied on conventional light microscopy with limited resolution and were primarily able to identify the presence and basic morphology of platelets. The advent of high resolution technologies, in particular, electron microscopy, accelerated our understanding of the dynamics of platelet ultrastructure dramatically. Further refinements and improvements in our ability to localize and reliably identify platelet structures have included the use of immune-labeling techniques, correlative-fluorescence light and electron microscopy, and super-resolution microscopies. More recently, the expanded development and application of intravital microscopy in animal models has enhanced our knowledge of platelet functions and thrombus formation in vivo, as these experimental systems most closely replicate native biological environments. Emerging improvements in our ability to characterize platelets at the ultrastructural and organelle levels include the use of platelet cryogenic electron tomography with quantitative, unbiased imaging analysis, and the ability to genetically label platelet features with electron dense markers for analysis by electron microscopy.

In situ structure of virus capsids within cell nuclei by correlative light and cryo-electron tomography

Cryo electron microscopy (cryo-EM), a key method for structure determination involves imaging purified material embedded in vitreous ice. Images are then computationally processed to obtain three-dimensional structures approaching atomic resolution. There is increasing interest in extending structural studies by cryo-EM into the cell, where biological structures and processes may be imaged in context. The limited penetrating power of electrons prevents imaging of thick specimens (> 500 nm) however. Cryo-sectioning methods employed to overcome this are technically challenging, subject to artefacts or involve specialised and costly equipment. Here we describe the first structure of herpesvirus capsids determined by sub-tomogram averaging from nuclei of eukaryotic cells, achieved by cryo-electron tomography (cryo-ET) of re-vitrified cell sections prepared using the Tokuyasu method. Our reconstructions confirm that the capsid associated tegument complex is present on capsids prior to nuclear egress. We demonstrate that this method is suited to both 3D structure determination and correlative light/electron microscopy, thus expanding the scope of cryogenic cellular imaging.

Spark-based parallel calculation of 3D fourier shell correlation for macromolecule structure local resolution estimation

Background

Resolution estimation is the main evaluation criteria for the reconstruction of macromolecular 3D structure in the field of cryoelectron microscopy (cryo-EM). At present, there are many methods to evaluate the 3D resolution for reconstructed macromolecular structures from Single Particle Analysis (SPA) in cryo-EM and subtomogram averaging (SA) in electron cryotomography (cryo-ET). As global methods, they measure the resolution of the structure as a whole, but they are inaccurate in detecting subtle local changes of reconstruction. In order to detect the subtle changes of reconstruction of SPA and SA, a few local resolution methods are proposed. The mainstream local resolution evaluation methods are based on local Fourier shell correlation (FSC), which is computationally intensive. However, the existing resolution evaluation methods are based on multi-threading implementation on a single computer with very poor scalability.

Results

This paper proposes a new fine-grained 3D array partition method by key-value format in Spark. Our method first converts 3D images to key-value data (K-V). Then the K-V data is used for 3D array partitioning and data exchange in parallel. So Spark-based distributed parallel computing framework can solve the above scalability problem. In this distributed computing framework, all 3D local FSC tasks are simultaneously calculated across multiple nodes in a computer cluster. Through the calculation of experimental data, 3D local resolution evaluation algorithm based on Spark fine-grained 3D array partition has a magnitude change in computing speed compared with the mainstream FSC algorithm under the condition that the accuracy remains unchanged, and has better fault tolerance and scalability.

Conclusions

In this paper, we proposed a K-V format based fine-grained 3D array partition method in Spark to parallel calculating 3D FSC for getting a 3D local resolution density map. 3D local resolution density map evaluates the three-dimensional density maps reconstructed from single particle analysis and subtomogram averaging. Our proposed method can significantly increase the speed of the 3D local resolution evaluation, which is important for the efficient detection of subtle variations among reconstructed macromolecular structures.

Exploring the bacterial nano-universe

Since the days of the first acknowledged microscopist, Antonie van Leeuwenhoek, the 'animalcules', that is, bacteria and other microbes have been subject to increasingly detailed visualization. With the currently most sophisticated molecular imaging method; cryo electron tomography (Cryo-ET), we are reaching the milestone of being able to image an entire organism in a single dataset at nanometer resolution. Cryo-ET will enable the next revolution in our understanding of bacterial cells, their ultra-structure and intricate molecular nanomachines. Here, we highlight recent research discoveries based on constantly progressing technology developments. We discuss advantages and challenges of using Cryo-ET to visualize spatial structure of microorganisms and macromolecular complexes in their native environment.

Use of electron microscopy to study platelets and thrombi

Electron microscopy has been a valuable tool for the study of platelet biology and thrombosis for more than 70 years. Early studies using conventional transmission and scanning electron microscopy (EM) provided a foundation for our initial understanding of platelet structure and how it changes upon platelet activation. EM approaches have since been utilized to study platelets and thrombi in the context of basic, translational and clinical research, and they are instrumental in the diagnosis of multiple platelet function disorders. In this brief review, we provide a sampling of the many contributions EM based studies have made to the field, including both historical highlights and contemporary applications. We will also discuss exciting new imaging modalities based on EM and their utility for the study of platelets, hemostasis and thrombosis into the future.