Mesophasic organization of GABAA receptors in hippocampal inhibitory synapses

New insights into the molecular architecture of neurons by cryo-electron tomography

Cryo-electron tomography (cryo-ET) visualizes natively preserved cellular ultrastructure at molecular resolution. Recent developments in sample preparation workflows and image processing tools enable growing applications of cryo-ET in cellular neurobiology. As such, cryo-ET is beginning to unravel the in situ macromolecular organization of neurons using samples of increasing complexity. Here, we highlight advances in cryo-ET technology and review its recent use to study neuronal architecture and its alterations under disease conditions.

Resolving native GABAA receptor structures from the human brain

Type A GABA (γ-aminobutyric acid) receptors (GABAA receptors) mediate most fast inhibitory signalling in the brain and are targets for drugs that treat epilepsy, anxiety, depression and insomnia and for anaesthetics1,2. These receptors comprise a complex array of 19 related subunits, which form pentameric ligand-gated ion channels. The composition and structure of native GABAA receptors in the human brain have been inferred from subunit localization in tissue1,3, functional measurements and structural analysis from recombinant expression4-7 and in mice8. However, the arrangements of subunits that co-assemble physiologically in native human GABAA receptors remain unknown. Here we isolated α1 subunit-containing GABAA receptors from human patients with epilepsy. Using cryo-electron microscopy, we defined a set of 12 native subunit assemblies and their 3D structures. We address inconsistencies between previous native and recombinant approaches, and reveal details of previously undefined subunit interfaces. Drug-like densities in a subset of these interfaces led us to uncover unexpected activity on the GABAA receptor of antiepileptic drugs and resulted in localization of one of these drugs to the benzodiazepine-binding site. Proteomics and further structural analysis suggest interactions with the auxiliary subunits neuroligin 2 and GARLH4, which localize and modulate GABAA receptors at inhibitory synapses. This work provides a structural foundation for understanding GABAA receptor signalling and targeted pharmacology in the human brain.

Tuning synapse strength by nanocolumn plasticity

The precise organization of the complex set of synaptic proteins at the nanometer scale is crucial for synaptic transmission. At the heart of this nanoscale architecture lies the nanocolumn. This aligns presynaptic neurotransmitter release with a high local density of postsynaptic receptor channels, thereby optimizing synaptic strength. Although synapses exhibit diverse protein compositions and nanoscale organizations, the role of structural diversity in the notable differences observed in synaptic physiology remains poorly understood. In this review we examine the current literature on the molecular mechanisms underlying the formation and maintenance of nanocolumns, as well as their role in modulating various aspects of synaptic transmission. We also discuss how the reorganization of nanocolumns contributes to functional dynamics in both synaptic plasticity and pathology.

Overcoming the preferred-orientation problem in cryo-EM with self-supervised deep learning

While advances in single-particle cryo-EM have enabled the structural determination of macromolecular complexes at atomic resolution, particle orientation bias (the 'preferred' orientation problem) remains a complication for most specimens. Existing solutions have relied on biochemical and physical strategies applied to the specimen and are often complex and challenging. Here, we develop spIsoNet, an end-to-end self-supervised deep learning-based software to address map anisotropy and particle misalignment caused by the preferred-orientation problem. Using preferred-orientation views to recover molecular information in under-sampled views, spIsoNet improves both angular isotropy and particle alignment accuracy during 3D reconstruction. We demonstrate spIsoNet's ability to generate near-isotropic reconstructions from representative biological systems with limited views, including ribosomes, β-galactosidases and a previously intractable hemagglutinin trimer dataset. spIsoNet can also be generalized to improve map isotropy and particle alignment of preferentially oriented molecules in subtomogram averaging. Therefore, without additional specimen-preparation procedures, spIsoNet provides a general computational solution to the preferred-orientation problem.

Understanding GABAergic synapse diversity and its implications for GABAergic pharmacotherapy

Despite the substantial contribution of disruptions in GABAergic inhibitory neurotransmission to the etiology of psychiatric, neurodevelopmental, and neurodegenerative disorders, surprisingly few drugs targeting the GABAergic system are currently available, partly due to insufficient understanding of circuit-specific GABAergic synapse biology. In addition to GABA receptors, GABAergic synapses contain an elaborate organizational protein machinery that regulates the properties of synaptic transmission. Until recently, this machinery remained largely unexplored, but key methodological advances have now led to the identification of a wealth of new GABAergic organizer proteins. Notably, many of these proteins appear to function only at specific subsets of GABAergic synapses, creating a diversity of organizer complexes that may serve as circuit-specific targets for pharmacotherapies. The present review aims to summarize the methodological developments that underlie this newfound knowledge and provide a current overview of synapse-specific GABAergic organizer complexes, as well as outlining future avenues and challenges in translating this knowledge into clinical applications.

From Blur to Brilliance: The Ascendance of Advanced Microscopy in Neuronal Cell Biology

The intricate network of the brain's neurons and synapses poses unparalleled challenges for research, distinct from other biological studies. This is particularly true when dissecting how neurons and their functional units work at a cell biological level. While traditional microscopy has been foundational, it was unable to reveal the deeper complexities of neural interactions. However, an imaging renaissance has transformed our capabilities. Advancements in light and electron microscopy, combined with correlative imaging, now achieve unprecedented resolutions, uncovering the most nuanced neural structures. Maximizing these tools requires more than just technical proficiency. It is crucial to align research aims, allocate resources wisely, and analyze data effectively. At the heart of this evolution is interdisciplinary collaboration, where various experts come together to translate detailed imagery into significant biological insights. This review navigates the latest developments in microscopy, underscoring both the promise of and prerequisites for bending this powerful tool set to understanding neuronal cell biology.

Nanoscale architecture of synaptic vesicles and scaffolding complexes revealed by cryo-electron tomography

The spatial distribution of proteins and their arrangement within the cellular ultrastructure regulates the opening of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors in response to glutamate release at the synapse. Fluorescence microscopy imaging revealed that the postsynaptic density (PSD) and scaffolding proteins in the presynaptic active zone (AZ) align across the synapse to form a trans-synaptic "nanocolumn," but the relation to synaptic vesicle release sites is uncertain. Here, we employ focused-ion beam (FIB) milling and cryoelectron tomography to image synapses under near-native conditions. Improved image contrast, enabled by FIB milling, allows simultaneous visualization of supramolecular nanoclusters within the AZ and PSD and synaptic vesicles. Surprisingly, membrane-proximal synaptic vesicles, which fuse to release glutamate, are not preferentially aligned with AZ or PSD nanoclusters. These synaptic vesicles are linked to the membrane by peripheral protein densities, often consistent in size and shape with Munc13, as well as globular densities bridging the synaptic vesicle and plasma membrane, consistent with prefusion complexes of SNAREs, synaptotagmins, and complexin. Monte Carlo simulations of synaptic transmission events using biorealistic models guided by our tomograms predict that clustering AMPARs within PSD nanoclusters increases the variability of the postsynaptic response but not its average amplitude. Together, our data support a model in which synaptic strength is tuned at the level of single vesicles by the spatial relationship between scaffolding nanoclusters and single synaptic vesicle fusion sites.

Demixing is a default process for biological condensates formed via phase separation

Excitatory and inhibitory synapses do not overlap even when formed on one submicron-sized dendritic protrusion. How excitatory and inhibitory postsynaptic cytomatrices or densities (e/iPSDs) are segregated is not understood. Broadly, why membraneless organelles are naturally segregated in cellular subcompartments is unclear. Using biochemical reconstitutions in vitro and in cells, we demonstrate that ePSDs and iPSDs spontaneously segregate into distinct condensed molecular assemblies through phase separation. Tagging iPSD scaffold gephyrin with a PSD-95 intrabody (dissociation constant ~4 nM) leads to mistargeting of gephyrin to ePSD condensates. Unexpectedly, formation of iPSD condensates forces the intrabody-tagged gephyrin out of ePSD condensates. Thus, instead of diffusion-governed spontaneous mixing, demixing is a default process for biomolecules in condensates. Phase separation can generate biomolecular compartmentalization specificities that cannot occur in dilute solutions.

Overcoming the preferred orientation problem in cryoEM with self-supervised deep-learning

While advances in single-particle cryoEM have enabled the structural determination of macromolecular complexes at atomic resolution, particle orientation bias (the so-called "preferred" orientation problem) remains a complication for most specimens. Existing solutions have relied on biochemical and physical strategies applied to the specimen and are often complex and challenging. Here, we develop spIsoNet, an end-to-end self-supervised deep-learning-based software to address the preferred orientation problem. Using preferred-orientation views to recover molecular information in under-sampled views, spIsoNet improves both angular isotropy and particle alignment accuracy during 3D reconstruction. We demonstrate spIsoNet's capability of generating near-isotropic reconstructions from representative biological systems with limited views, including ribosomes, β-galactosidases, and a previously intractable hemagglutinin trimer dataset. spIsoNet can also be generalized to improve map isotropy and particle alignment of preferentially oriented molecules in subtomogram averaging. Therefore, without additional specimen-preparation procedures, spIsoNet provides a general computational solution to the preferred orientation problem.

Shank3 Deficiency Results in a Reduction in GABAergic Postsynaptic Puncta in the Olfactory Brain Areas

Dysfunctional sensory systems, including altered olfactory function, have recently been reported in patients with autism spectrum disorder (ASD). Disturbances in olfactory processing can potentially result from gamma-aminobutyric acid (GABA)ergic synaptic abnormalities. The specific molecular mechanism by which GABAergic transmission affects the olfactory system in ASD remains unclear. Therefore, the present study aimed to evaluate selected components of the GABAergic system in olfactory brain regions and primary olfactory neurons isolated from Shank3-deficient (-/-) mice, which are known for their autism-like behavioral phenotype. Shank3 deficiency led to a significant reduction in GEPHYRIN/GABAAR colocalization in the piriform cortex and in primary neurons isolated from the olfactory bulb, while no change of cell morphology was observed. Gene expression analysis revealed a significant reduction in the mRNA levels of GABA transporter 1 in the olfactory bulb and Collybistin in the frontal cortex of the Shank3-/- mice compared to WT mice. A similar trend of reduction was observed in the expression of Somatostatin in the frontal cortex of Shank3-/- mice. The analysis of the expression of other GABAergic neurotransmission markers did not yield statistically significant results. Overall, it appears that Shank3 deficiency leads to changes in GABAergic synapses in the brain regions that are important for olfactory information processing, which may represent basis for understanding functional impairments in autism.

Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries

Most membrane proteins are modified by covalent addition of complex sugars through N- and O-glycosylation. Unlike proteins, glycans do not typically adopt specific secondary structures and remain very mobile, shielding potentially large fractions of protein surface. High glycan conformational freedom hinders complete structural elucidation of glycoproteins. Computer simulations may be used to model glycosylated proteins but require hundreds of thousands of computing hours on supercomputers, thus limiting routine use. Here, we describe GlycoSHIELD, a reductionist method that can be implemented on personal computers to graft realistic ensembles of glycan conformers onto static protein structures in minutes. Using molecular dynamics simulation, small-angle X-ray scattering, cryoelectron microscopy, and mass spectrometry, we show that this open-access toolkit provides enhanced models of glycoprotein structures. Focusing on N-cadherin, human coronavirus spike proteins, and gamma-aminobutyric acid receptors, we show that GlycoSHIELD can shed light on the impact of glycans on the conformation and activity of complex glycoproteins.

Engineered Multifunctional Zinc-Organic Framework-Based Aggregation-Induced Emission Nanozyme for Accelerating Spinal Cord Injury Recovery

Functional recovery following a spinal cord injury (SCI) is challenging. Traditional drug therapies focus on the suppression of immune responses; however, strategies for alleviating oxidative stress are lacking. Herein, we developed the zinc-organic framework (Zn@MOF)-based aggregation-induced emission-active nanozymes for accelerating recovery following SCI. A multifunctional Zn@MOF was modified with the aggregation-induced emission-active molecule 2-(4-azidobutyl)-6-(phenyl(4-(1,2,2-triphenylvinyl)phenyl)amino)-1H-phenalene-1,3-dione via a bioorthogonal reaction, and the resulting nanozymes were denoted as Zn@MOF-TPD. These nanozymes gradually released gallic acid and zinc ions (Zn2+) at the SCI site. The released gallic acid, a scavenger of reactive oxygen species (ROS), promoted antioxidation and alleviated inflammation, re-establishing the balance between ROS production and the antioxidant defense system. The released Zn2+ ions inhibited the activity of matrix metalloproteinase 9 (MMP-9) to facilitate the regeneration of neurons via the ROS-mediated NF-κB pathway following secondary SCI. In addition, Zn@MOF-TPD protected neurons and myelin sheaths against trauma, inhibited glial scar formation, and promoted the proliferation and differentiation of neural stem cells, thereby facilitating the repair of neurons and injured spinal cord tissue and promoting functional recovery in rats with contusive SCI. Altogether, this study suggests that Zn@MOF-TPD nanozymes possess a potential for alleviating oxidative stress-mediated pathophysiological damage and promoting motor recovery following SCI.

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.

Structural insights into gating mechanism and allosteric regulation of NMDA receptors

N-methyl-d-aspartate receptors (NMDARs) belong to the ionotropic glutamate receptors (iGluRs) superfamily and act as coincidence detectors that are crucial to neuronal development and synaptic plasticity. They typically assemble as heterotetramers of two obligatory GluN1 subunits and two alternative GluN2 (from 2A to 2D) and/or GluN3 (3A and 3B) subunits. These alternative subunits mainly determine the diverse biophysical and pharmacological properties of different NMDAR subtypes. Over the past decade, the unprecedented advances in structure elucidation of these tetrameric NMDARs have provided atomic insights into channel gating, allosteric modulation and the action of therapeutic drugs. A wealth of structural and functional information would accelerate the artificial intelligence-based drug design to exploit more NMDAR subtype-specific molecules for the treatment of neurological and psychiatric disorders.

An intelligent workflow for sub-nanoscale 3D reconstruction of intact synapses from serial section electron tomography

BACKGROUND

As an extension of electron tomography (ET), serial section electron tomography (serial section ET) aims to align the tomographic images of multiple thick tissue sections together, to break through the volume limitation of the single section and preserve the sub-nanoscale voxel size. It could be applied to reconstruct the intact synapse, which expands about one micrometer and contains nanoscale vesicles. However, there are several drawbacks of the existing serial section ET methods. First, locating and imaging regions of interest (ROIs) in serial sections during the shooting process is time-consuming. Second, the alignment of ET volumes is difficult due to the missing information caused by section cutting and imaging. Here we report a workflow to simplify the acquisition of ROIs in serial sections, automatically align the volume of serial section ET, and semi-automatically reconstruct the target synaptic structure.

RESULTS

We propose an intelligent workflow to reconstruct the intact synapse with sub-nanometer voxel size. Our workflow includes rapid localization of ROIs in serial sections, automatic alignment, restoration, assembly of serial ET volumes, and semi-automatic target structure segmentation. For the localization and acquisition of ROIs in serial sections, we use affine transformations to calculate their approximate position based on their relative location in orderly placed sections. For the alignment of consecutive ET volumes with significantly distinct appearances, we use multi-scale image feature matching and the elastic with belief propagation (BP-Elastic) algorithm to align them from coarse to fine. For the restoration of the missing information in ET, we first estimate the number of lost images based on the pixel changes of adjacent volumes after alignment. Then, we present a missing information generation network that is appropriate for small-sample of ET volume using pre-training interpolation network and distillation learning. And we use it to generate the missing information to achieve the whole volume reconstruction. For the reconstruction of synaptic ultrastructures, we use a 3D neural network to obtain them quickly. In summary, our workflow can quickly locate and acquire ROIs in serial sections, automatically align, restore, assemble serial sections, and obtain the complete segmentation result of the target structure with minimal manual manipulation. Multiple intact synapses in wild-type rat were reconstructed at a voxel size of 0.664 nm/voxel to demonstrate the effectiveness of our workflow.

CONCLUSIONS

Our workflow contributes to obtaining intact synaptic structures at the sub-nanometer scale through serial section ET, which contains rapid ROI locating, automatic alignment, volume reconstruction, and semi-automatic synapse reconstruction. We have open-sourced the relevant code in our workflow, so it is easy to apply it to other labs and obtain complete 3D ultrastructures which size is similar to intact synapses with sub-nanometer voxel size.

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.

Bringing synapses into focus: Recent advances in synaptic imaging and mass-spectrometry for studying synaptopathy

Synapses are integral for healthy brain function and are becoming increasingly recognized as key structures in the early stages of brain disease. Understanding the pathological processes driving synaptic dysfunction will unlock new therapeutic opportunities for some of the most devastating diseases of our time. To achieve this we need a solid repertoire of imaging and molecular tools to interrogate synaptic biology at greater resolution. Synapses have historically been examined in small numbers, using highly technical imaging modalities, or in bulk, using crude molecular approaches. However, recent advances in imaging techniques are allowing us to analyze large numbers of synapses, at single-synapse resolution. Furthermore, multiplexing is now achievable with some of these approaches, meaning we can examine multiple proteins at individual synapses in intact tissue. New molecular techniques now allow accurate quantification of proteins from isolated synapses. The development of increasingly sensitive mass-spectrometry equipment means we can now scan the synaptic molecular landscape almost in totality and see how this changes in disease. As we embrace these new technical developments, synapses will be viewed with clearer focus, and the field of synaptopathy will become richer with insightful and high-quality data. Here, we will discuss some of the ways in which synaptic interrogation is being facilitated by methodological advances, focusing on imaging, and mass spectrometry.

Understanding small-scale COVID-19 transmission dynamics with the Granger causality test

Mobility patterns have been broadly studied and deeply altered due to the coronavirus disease (COVID-19). In this paper, we study small-scale COVID-19 transmission dynamics in the city of Valencia and the potential role of subway stations and healthcare facilities in this transmission. A total of 2,398 adult patients were included in the analysis. We study the temporal evolution of the pandemic during the first six months at a small-area level. Two Voronoi segmentations of the city (based on the location of subway stations and healthcare facilities) have been considered, and we have applied the Granger causality test at the Voronoi cell level, considering both divisions of the study area. Considering the output of this approach, the so-called 'donor stations' are subway stations that have sent more connections than they have received and are mainly located in interchanger stations. The transmission in primary healthcare facilities showed a heterogeneous pattern. Given that subway interchange stations receive many cases from other regions of the city, implementing isolation measures in these areas might be beneficial for the reduction of transmission.

Quantifying postsynaptic receptor dynamics: insights into synaptic function

The molecular composition of presynaptic and postsynaptic neuronal terminals is dynamic, and yet long-term stabilizations in postsynaptic responses are necessary for synaptic development and long-term plasticity. The need to reconcile these concepts is further complicated by learning- and memory-related plastic changes in the molecular make-up of synapses. Advances in single-particle tracking mean that we can now quantify the number and diffusive properties of specific synaptic molecules, while statistical thermodynamics provides a framework to analyse these molecular fluctuations. In this Review, we discuss the use of these approaches to gain quantitative descriptions of the processes underlying the turnover, long-term stability and plasticity of postsynaptic receptors and show how these can help us to understand the balance between local molecular turnover and synaptic structural identity and integrity.

Structural investigation of eukaryotic cells: From the periphery to the interior by cryo-electron tomography

Cryo-electron tomography (cryo-ET) combines a close-to-life preservation of the cell with high-resolution three-dimensional (3D) imaging. This allows to study the molecular architecture of the cellular landscape and provides unprecedented views on biological processes and structures. In this review we mainly focus on the application of cryo-ET to visualize and structurally characterize eukaryotic cells - from the periphery to the cellular interior. We discuss strategies that can be employed to investigate the structure of challenging targets in their cellular environment as well as the application of complimentary approaches in conjunction with cryo-ET.

Structural and functional imaging of brains

Analyzing the complex structures and functions of brain is the key issue to understanding the physiological and pathological processes. Although neuronal morphology and local distribution of neurons/blood vessels in the brain have been known, the subcellular structures of cells remain challenging, especially in the live brain. In addition, the complicated brain functions involve numerous functional molecules, but the concentrations, distributions and interactions of these molecules in the brain are still poorly understood. In this review, frontier techniques available for multiscale structure imaging from organelles to the whole brain are first overviewed, including magnetic resonance imaging (MRI), computed tomography (CT), positron emission tomography (PET), serial-section electron microscopy (ssEM), light microscopy (LM) and synchrotron-based X-ray microscopy (XRM). Specially, XRM for three-dimensional (3D) imaging of large-scale brain tissue with high resolution and fast imaging speed is highlighted. Additionally, the development of elegant methods for acquisition of brain functions from electrical/chemical signals in the brain is outlined. In particular, the new electrophysiology technologies for neural recordings at the single-neuron level and in the brain are also summarized. We also focus on the construction of electrochemical probes based on dual-recognition strategy and surface/interface chemistry for determination of chemical species in the brain with high selectivity and long-term stability, as well as electrochemophysiological microarray for simultaneously recording of electrochemical and electrophysiological signals in the brain. Moreover, the recent development of brain MRI probes with high contrast-to-noise ratio (CNR) and sensitivity based on hyperpolarized techniques and multi-nuclear chemistry is introduced. Furthermore, multiple optical probes and instruments, especially the optophysiological Raman probes and fiber Raman photometry, for imaging and biosensing in live brain are emphasized. Finally, a brief perspective on existing challenges and further research development is provided.

Cryomicroscopy in situ: what is the smallest molecule that can be directly identified without labels in a cell?

Electron cryomicroscopy (cryoEM) has made great strides in the last decade, such that the atomic structure of most biological macromolecules can, at least in principle, be determined. Major technological advances - in electron imaging hardware, data analysis software, and cryogenic specimen preparation technology - continue at pace and contribute to the exponential growth in the number of atomic structures determined by cryoEM. It is now conceivable that within the next decade we will have structures for hundreds of thousands of unique protein and nucleic acid molecular complexes. But the answers to many important questions in biology would become obvious if we could identify these structures precisely inside cells with quantifiable error. In the context of an abundance of known structures, it is appropriate to consider the current state of electron cryomicroscopy for frozen specimens prepared directly from cells, and try to answer to the question of the title, both now and in the foreseeable future.

Bridging length scales from molecules to the whole organism by cryoCLEM and cryoET

Resolving atomic structures of isolated proteins has uncovered mechanisms and fundamental processes in biology. However, many functions can only be tested in the context of intact cells and tissues that are many orders of magnitude larger than the macromolecules on which they depend. Therefore, methods that interrogate macromolecular structure in situ provide a means of directly relating structure to function across length scales. Here, we developed several workflows using cryogenic correlated light and electron microscopy (cryoCLEM) and electron tomography (cryoET) that can bridge this gap to reveal the molecular infrastructure that underlies higher order functions within cells and tissues. We also describe experimental design considerations, including cryoCLEM labelling, sample preparation, and quality control, for determining the in situ molecular architectures within native, hydrated cells and tissues.

Isotropic reconstruction for electron tomography with deep learning

Cryogenic electron tomography (cryoET) allows visualization of cellular structures in situ. However, anisotropic resolution arising from the intrinsic "missing-wedge" problem has presented major challenges in visualization and interpretation of tomograms. Here, we have developed IsoNet, a deep learning-based software package that iteratively reconstructs the missing-wedge information and increases signal-to-noise ratio, using the knowledge learned from raw tomograms. Without the need for sub-tomogram averaging, IsoNet generates tomograms with significantly reduced resolution anisotropy. Applications of IsoNet to three representative types of cryoET data demonstrate greatly improved structural interpretability: resolving lattice defects in immature HIV particles, establishing architecture of the paraflagellar rod in Eukaryotic flagella, and identifying heptagon-containing clathrin cages inside a neuronal synapse of cultured cells. Therefore, by overcoming two fundamental limitations of cryoET, IsoNet enables functional interpretation of cellular tomograms without sub-tomogram averaging. Its application to high-resolution cellular tomograms should also help identify differently oriented complexes of the same kind for sub-tomogram averaging.

The Mechanical Microenvironment Regulates Axon Diameters Visualized by Cryo-Electron Tomography

Axonal varicosities or swellings are enlarged structures along axon shafts and profoundly affect action potential propagation and synaptic transmission. These structures, which are defined by morphology, are highly heterogeneous and often investigated concerning their roles in neuropathology, but why they are present in the normal brain remains unknown. Combining confocal microscopy and cryo-electron tomography (Cryo-ET) with in vivo and in vitro systems, we report that non-uniform mechanical interactions with the microenvironment can lead to 10-fold diameter differences within an axon of the central nervous system (CNS). In the brains of adult Thy1-YFP transgenic mice, individual axons in the cortex displayed significantly higher diameter variation than those in the corpus callosum. When being cultured on lacey carbon film-coated electron microscopy (EM) grids, CNS axons formed varicosities exclusively in holes and without microtubule (MT) breakage, and they contained mitochondria, multivesicular bodies (MVBs), and/or vesicles, similar to the axonal varicosities induced by mild fluid puffing. Moreover, enlarged axon branch points often contain MT free ends leading to the minor branch. When the axons were fasciculated by mimicking in vivo axonal bundles, their varicosity levels reduced. Taken together, our results have revealed the extrinsic regulation of the three-dimensional ultrastructures of central axons by the mechanical microenvironment under physiological conditions.

Nano-organization of spontaneous GABAergic transmission directs its autonomous function in neuronal signaling

Earlier studies delineated the precise arrangement of proteins that drive neurotransmitter release and postsynaptic signaling at excitatory synapses. However, spatial organization of neurotransmission at inhibitory synapses remains unclear. Here, we took advantage of the molecularly specific interaction of antimalarial artemisinins and the inhibitory synapse scaffold protein, gephyrin, to probe the functional organization of gamma-aminobutyric acid A receptor (GABA_AR)-mediated neurotransmission in central synapses. Short-term application of artemisinins severely contracts the size and density of gephyrin and GABAaR γ2 subunit clusters. This size contraction elicits a neuronal activity-independent increase in Bdnf expression due to a specific reduction in GABAergic spontaneous, but not evoked, neurotransmission. The same functional effect could be mimicked by disruption of microtubules that link gephyrin to the neuronal cytoskeleton. These results suggest that the GABAergic postsynaptic apparatus possesses a concentric center-surround organization, where the periphery of gephyrin clusters selectively maintains spontaneous GABAergic neurotransmission facilitating its autonomous function regulating Bdnf expression.

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.

A Versatile Synthetic Affinity Probe Reveals Inhibitory Synapse Ultrastructure and Brain Connectivity**

Visualization of inhibitory synapses requires protocol tailoring for different sample types and imaging techniques, and usually relies on genetic manipulation or the use of antibodies that underperform in tissue immunofluorescence. Starting from an endogenous ligand of gephyrin, a universal marker of the inhibitory synapse, we developed a short peptidic binder and dimerized it, significantly increasing affinity and selectivity. We further tailored fluorophores to the binder, yielding “Sylite”—a probe with outstanding signal‐to‐background ratio that outperforms antibodies in tissue staining with rapid and efficient penetration, mitigation of staining artifacts, and simplified handling. In super‐resolution microscopy Sylite precisely localizes the inhibitory synapse and enables nanoscale measurements. Sylite profiles inhibitory inputs and synapse sizes of excitatory and inhibitory neurons in the midbrain and combined with complimentary tracing techniques reveals the synaptic connectivity.

From Chaos to Ordering: New Studies in the Shannon Entropy of 2D Patterns

Properties of the Voronoi tessellations arising from random 2D distribution points are reported. We applied an iterative procedure to the Voronoi diagrams generated by a set of points randomly placed on the plane. The procedure implied dividing the edges of Voronoi cells into equal or random parts. The dividing points were then used to construct the following Voronoi diagram. Repeating this procedure led to a surprising effect of the positional ordering of Voronoi cells, reminiscent of the formation of lamellae and spherulites in linear semi-crystalline polymers and metallic glasses. Thus, we can conclude that by applying even a simple set of rules to a random set of seeds, we can introduce order into an initially disordered system. At the same time, the Shannon (Voronoi) entropy showed a tendency to attain values that are typical for completely random patterns; thus, the Shannon (Voronoi) entropy does not distinguish the short-range ordering. The Shannon entropy and the continuous measure of symmetry of the patterns demonstrated the distinct asymptotic behavior, while approaching the close saturation values with the increase in the number of iteration steps. The Shannon entropy grew with the number of iterations, whereas the continuous measure of symmetry of the same patterns demonstrated the opposite asymptotic behavior. The Shannon (Voronoi) entropy is not an unambiguous measure of order in the 2D patterns. The more symmetrical patterns may demonstrate the higher values of the Shannon entropy.

Inhibitory postsynaptic density from the lens of phase separation

To faithfully transmit and decode signals released from presynaptic termini, postsynaptic compartments of neuronal synapses deploy hundreds of various proteins. In addition to distinct sets of proteins, excitatory and inhibitory postsynaptic apparatuses display very different organization features and regulatory properties. Decades of extensive studies have generated a wealth of knowledge on the molecular composition, assembly architecture and activity-dependent regulatory mechanisms of excitatory postsynaptic compartments. In comparison, our understanding of the inhibitory postsynaptic apparatus trails behind. Recent studies have demonstrated that phase separation is a new paradigm underlying the formation and plasticity of both excitatory and inhibitory postsynaptic molecular assemblies. In this review, we discuss molecular composition, organizational and regulatory features of inhibitory postsynaptic densities through the lens of the phase separation concept and in comparison with the excitatory postsynaptic densities.

Cytology, transcriptomics, and mass spectrometry imaging reveal changes in late-maturation elm (Ulmus pumila) seeds

During seed maturation, the seed deposits storage compounds (starches, oils, and proteins), synthesizes defense compounds, produces a seed coat, initiates embryo dormancy, and becomes desiccated. During the late-maturation stage, seed storage compound contents and compositions change dramatically. Although maturation has been extensively studied in model species and crops, it remains less well characterized in woody perennial plants. In this study, we conducted morphological and cytological observations, transcriptome profiling, and chemical constituent analysis of elm (Ulmus pumila L.) seeds during the late-maturation stage. Light and electron microscopy revealed that closely packed yet discrete lipid bodies frequently surrounded the densely stained protein bodies, and the protein bodies became irregular or even partially disintegrated at the end of seed development. RNA-seq detected substantial transcriptome changes during the late-maturation stage, and pathway enrichment analysis showed that the differentially expressed genes were associated with phenylpropanoid biosynthesis, starch and sucrose metabolism, plant-pathogen interactions, and hormone signal transduction. Furthermore, we used mass spectrometry imaging to detect the relative intensity and spatial distribution of fatty acids, phospholipids, and waxes in elm seeds. Our findings provide a framework for understanding the changes in cytological features and chemical composition during the final stage of elm seed development, and a detailed reference for seed development in woody plants.

Neurons as a model system for cryo-electron tomography

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Cryo-ET imaging of neurons is a versatile system for cell biology in situ.

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Structural and spatial localization analysis yields new insights into synaptic transmission.

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The synapse provides a rich environment for the development of image processing tools.

Cryo-electron tomography (Cryo-ET) provides unique opportunities to image cellular components at high resolution in their native state and environment. While many different cell types were investigated by cryo-ET, here we review application to neurons. We show that neurons are a versatile system that can be used to investigate general cellular components such as the cytoskeleton and membrane-bound organelles, in addition to neuron-specific processes such as synaptic transmission. Furthermore, the synapse provides a rich environment for the development of cryo-ET image processing tools suitable to elucidate the functional and spatial organization of compositionally and morphologically heterogeneous macromolecular complexes involved in biochemical signaling cascades, within their native, crowded cellular environments.

Identification of a stereotypic molecular arrangement of endogenous glycine receptors at spinal cord synapses

Precise quantitative information about the molecular architecture of synapses is essential to understanding the functional specificity and downstream signaling processes at specific populations of synapses. Glycine receptors (GlyRs) are the primary fast inhibitory neurotransmitter receptors in the spinal cord and brainstem. These inhibitory glycinergic networks crucially regulate motor and sensory processes. Thus far, the nanoscale organization of GlyRs underlying the different network specificities has not been defined. Here, we have quantitatively characterized the molecular arrangement and ultra-structure of glycinergic synapses in spinal cord tissue using quantitative super-resolution correlative light and electron microscopy. We show that endogenous GlyRs exhibit equal receptor-scaffold occupancy and constant packing densities of about 2000 GlyRs µm^-2 at synapses across the spinal cord and throughout adulthood, even though ventral horn synapses have twice the total copy numbers, larger postsynaptic domains, and more convoluted morphologies than dorsal horn synapses. We demonstrate that this stereotypic molecular arrangement is maintained at glycinergic synapses in the oscillator mouse model of the neuromotor disease hyperekplexia despite a decrease in synapse size, indicating that the molecular organization of GlyRs is preserved in this hypomorph. We thus conclude that the morphology and size of inhibitory postsynaptic specializations rather than differences in GlyR packing determine the postsynaptic strength of glycinergic neurotransmission in motor and sensory spinal cord networks.

Informational Measure of Symmetry vs. Voronoi Entropy and Continuous Measure of Entropy of the Penrose Tiling. Part II of the “Voronoi Entropy vs. Continuous Measure of Symmetry of the Penrose Tiling”

The notion of the informational measure of symmetry is introduced according to: Hsym(G)=−∑i=1kP(Gi)lnP(Gi), where P(Gi) is the probability of appearance of the symmetry operation Gi within the given 2D pattern. Hsym(G) is interpreted as an averaged uncertainty in the presence of symmetry elements from the group G in the given pattern. The informational measure of symmetry of the “ideal” pattern built of identical equilateral triangles is established as Hsym(D3)= 1.792. The informational measure of symmetry of the random, completely disordered pattern is zero, Hsym=0. The informational measure of symmetry is calculated for the patterns generated by the P3 Penrose tessellation. The informational measure of symmetry does not correlate with either the Voronoi entropy of the studied patterns nor with the continuous measure of symmetry of the patterns. Quantification of the “ordering” in 2D patterns performed solely with the Voronoi entropy is misleading and erroneous.

Electron cryo-tomography reveals the subcellular architecture of growing axons in human brain organoids

During brain development, axons must extend over great distances in a relatively short amount of time. How the subcellular architecture of the growing axon sustains the requirements for such rapid build-up of cellular constituents has remained elusive. Human axons have been particularly poorly accessible to imaging at high resolution in a near-native context. Here, we present a method that combines cryo-correlative light microscopy and electron tomography with human cerebral organoid technology to visualize growing axon tracts. Our data reveal a wealth of structural details on the arrangement of macromolecules, cytoskeletal components, and organelles in elongating axon shafts. In particular, the intricate shape of the endoplasmic reticulum is consistent with its role in fulfilling the high demand for lipid biosynthesis to support growth. Furthermore, the scarcity of ribosomes within the growing shaft suggests limited translational competence during expansion of this compartment. These findings establish our approach as a powerful resource for investigating the ultrastructure of defined neuronal compartments.

Neuronal excitation/inhibition imbalance: core element of a translational perspective on Alzheimer pathophysiology

Our incomplete understanding of the link between Alzheimer's Disease pathology and symptomatology is a crucial obstacle for therapeutic success. Recently, translational studies have begun to connect the dots between protein alterations and deposition, brain network dysfunction and cognitive deficits. Disturbance of neuronal activity, and in particular an imbalance in underlying excitation/inhibition (E/I), appears early in AD, and can be regarded as forming a central link between structural brain pathology and cognitive dysfunction. While there are emerging (non-)pharmacological options to influence this imbalance, the complexity of human brain dynamics has hindered identification of an optimal approach. We suggest that focusing on the integration of neurophysiological aspects of AD at the micro-, meso- and macroscale, with the support of computational network modeling, can unite fundamental and clinical knowledge, provide a general framework, and suggest rational therapeutic targets.

Clustering acetylcholine receptors in neuromuscular junction by phase-separated Rapsn condensates

In this issue of Neuron, Xing et al. (2021) demonstrate that the multidomain scaffold protein Rapsn can form dense molecular condensates in vitro and in vivo via phase separation. The formation of Rapsn condensates is essential for clustering acetylcholine receptors on muscle membranes and for forming neuromuscular junctions.

Protein-Lipid Interplay at the Neuromuscular Junction

Many new structures of membrane proteins have been determined over the last decade, yet the nature of protein–lipid interplay has received scant attention. The postsynaptic membrane of the neuromuscular junction and Torpedo electrocytes has a regular architecture, opening an opportunity to illuminate how proteins and lipids act together in a native membrane setting. Cryo electron microscopy (Cryo-EM) images show that cholesterol segregates preferentially around the constituent ion channel, the nicotinic acetylcholine receptor, interacting with specific sites in both leaflets of the bilayer. In addition to maintaining the transmembrane α-helical architecture, cholesterol forms microdomains – bridges of rigid sterol groups that link one channel to the next. This article discusses the whole protein–lipid organization of the cholinergic postsynaptic membrane, its physiological implications and how the observed details relate to our current concept of the membrane structure. I suggest that cooperative interactions, facilitated by the regular protein–lipid arrangement, help to spread channel activation into regions distant from the sites of neurotransmitter release, thereby enhancing the postsynaptic response.

Elephants in the Dark: Insights and Incongruities in Pentameric Ligand-gated Ion Channel Models

The superfamily of pentameric ligand-gated ion channels (pLGICs) comprises key players in electrochemical signal transduction across evolution, including historic model systems for receptor allostery and targets for drug development. Accordingly, structural studies of these channels have steadily increased, and now approach 250 depositions in the protein data bank. This review contextualizes currently available structures in the pLGIC family, focusing on morphology, ligand binding, and gating in three model subfamilies: the prokaryotic channel GLIC, the cation-selective nicotinic acetylcholine receptor, and the anion-selective glycine receptor. Common themes include the challenging process of capturing and annotating channels in distinct functional states; partially conserved gating mechanisms, including remodeling at the extracellular/transmembrane-domain interface; and diversity beyond the protein level, arising from posttranslational modifications, ligands, lipids, and signaling partners. Interpreting pLGIC structures can be compared to describing an elephant in the dark, relying on touch alone to comprehend the many parts of a monumental beast: each structure represents a snapshot in time under specific experimental conditions, which must be integrated with further structure, function, and simulations data to build a comprehensive model, and understand how one channel may fundamentally differ from another.

Differential regulation of glycinergic and GABAergic nanocolumns at mixed inhibitory synapses

Super‐resolution imaging has revealed that key synaptic proteins are dynamically organized within sub‐synaptic domains (SSDs). To examine how different inhibitory receptors are regulated, we carried out dual‐color direct stochastic optical reconstruction microscopy (dSTORM) of GlyRs and GABA_ARs at mixed inhibitory synapses in spinal cord neurons. We show that endogenous GlyRs and GABA_ARs as well as their common scaffold protein gephyrin form SSDs that align with pre‐synaptic RIM1/2, thus creating trans‐synaptic nanocolumns. Strikingly, GlyRs and GABA_ARs occupy different sub‐synaptic spaces, exhibiting only a partial overlap at mixed inhibitory synapses. When network activity is increased by 4‐aminopyridine treatment, the GABA_AR copy numbers and the number of GABA_AR SSDs are reduced, while GlyRs remain largely unchanged. This differential regulation is likely the result of changes in gephyrin phosphorylation that preferentially occurs outside of SSDs. The activity‐dependent regulation of GABA_ARs versus GlyRs suggests that different signaling pathways control the receptors' sub‐synaptic clustering. Taken together, our data reinforce the notion that the precise sub‐synaptic organization of GlyRs, GABA_ARs, and gephyrin has functional consequences for the plasticity of mixed inhibitory synapses.

Presynaptic bouton compartmentalization and postsynaptic density-mediated glutamate receptor clustering via phase separation

Neuronal synapses encompass three compartments: presynaptic axon terminal, synaptic cleft, and postsynaptic dendrite. Each compartment contains densely packed molecular machineries that are involved in synaptic transmission. In recent years, emerging evidence indicates that the assembly of these membraneless substructures or assemblies that are not enclosed by membranes are driven by liquid-liquid phase separation. We review here recent studies that suggest the phase separation-mediated organization of these synaptic compartments. We discuss how synaptic function may be linked to its organization as biomolecular condensates. We conclude with a discussion of areas of future interest in the field for better understanding of the structural architecture of neuronal synapses and its contribution to synaptic functions.

Expanding GABAAR pharmacology via receptor-associated proteins

Drugs directly targeting γ-aminobutyric acid type A receptors (GABA_ARs), the major mediators of fast synaptic inhibition, contribute significantly to today's neuropharmacology. Emerging evidence establishes intracellularly GABA_AR-associated proteins as the central players in determining cellular and subcellular GABAergic input sites, thereby providing pharmacological opportunities to affect distinct receptor populations and address discrete neuronal dysfunctions. Here, we report on recently studied GABA_AR-associated proteins and highlight challenges and newly available methods for their functional and physical mapping. We anticipate these efforts to contribute to decipher the complexity of GABAergic signalling in the brain and eventually enable therapeutic avenues for, so far, untreatable neuronal disorders and diseases.

Trans-synaptic assemblies link synaptic vesicles and neuroreceptors

Synaptic transmission is characterized by fast, tightly coupled processes and complex signaling pathways that require a precise protein organization, such as the previously reported nanodomain colocalization of pre- and postsynaptic proteins. Here, we used cryo-electron tomography to visualize synaptic complexes together with their native environment comprising interacting proteins and lipids on a 2- to 4-nm scale. Using template-free detection and classification, we showed that tripartite trans-synaptic assemblies (subcolumns) link synaptic vesicles to postsynaptic receptors and established that a particular displacement between directly interacting complexes characterizes subcolumns. Furthermore, we obtained de novo average structures of ionotropic glutamate receptors in their physiological composition, embedded in plasma membrane. These data support the hypothesis that synaptic function is carried by precisely organized trans-synaptic units. It provides a framework for further exploration of synaptic and other large molecular assemblies that link different cells or cellular regions and may require weak or transient interactions to exert their function.

Interferon-γ induces tumor resistance to anti-PD-1 immunotherapy by promoting YAP phase separation

Interferon-γ (IFN-γ)-mediated adaptive resistance is one major barrier to improving immunotherapy in solid tumors. However, the mechanisms are not completely understood. Here, we report that IFN-γ promotes nuclear translocation and phase separation of YAP after anti-PD-1 therapy in tumor cells. Hydrophobic interactions of the YAP coiled-coil domain mediate droplet initiation, and weak interactions of the intrinsically disordered region in the C terminus promote droplet formation. YAP partitions with the transcription factor TEAD4, the histone acetyltransferase EP300, and Mediator1 and forms transcriptional hubs for maximizing target gene transcriptions, independent of the canonical STAT1-IRF1 transcription program. Disruption of YAP phase separation reduced tumor growth, enhanced immune response, and sensitized tumor cells to anti-PD-1 therapy. YAP activity is negatively correlated with patient outcome. Our study indicates that YAP mediates the IFN-γ pro-tumor effect through its nuclear phase separation and suggests that YAP can be used as a predictive biomarker and target of anti-PD-1 combination therapy.

Comparative 2D and 3D Ultrastructural Analyses of Dendritic Spines from CA1 Pyramidal Neurons in the Mouse Hippocampus

Three-dimensional (3D) reconstruction from electron microscopy (EM) datasets is a widely used tool that has improved our knowledge of synapse ultrastructure and organization in the brain. Rearrangements of synapse structure following maturation and in synaptic plasticity have been broadly described and, in many cases, the defective architecture of the synapse has been associated to functional impairments. It is therefore important, when studying brain connectivity, to map these rearrangements with the highest accuracy possible, considering the affordability of the different EM approaches to provide solid and reliable data about the structure of such a small complex. The aim of this work is to compare quantitative data from two dimensional (2D) and 3D EM of mouse hippocampal CA1 (apical dendrites), to define whether the results from the two approaches are consistent. We examined asymmetric excitatory synapses focusing on post synaptic density and dendritic spine area and volume as well as spine density, and we compared the results obtained with the two methods. The consistency between the 2D and 3D results questions the need—for many applications—of using volumetric datasets (costly and time consuming in terms of both acquisition and analysis), with respect to the more accessible measurements from 2D EM projections.