Development of a model for microphysiological simulations: small nodes of ranvier from peripheral nerves of mice reconstructed by electron tomography

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.

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.

Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain

In order to combat molecular damage, most cellular proteins undergo rapid turnover. We have previously identified large nuclear protein assemblies that can persist for years in post-mitotic tissues and are subject to age-related decline. Here, we report that mitochondria can be long lived in the mouse brain and reveal that specific mitochondrial proteins have half-lives longer than the average proteome. These mitochondrial long-lived proteins (mitoLLPs) are core components of the electron transport chain (ETC) and display increased longevity in respiratory supercomplexes. We find that COX7C, a mitoLLP that forms a stable contact site between complexes I and IV, is required for complex IV and supercomplex assembly. Remarkably, even upon depletion of COX7C transcripts, ETC function is maintained for days, effectively uncoupling mitochondrial function from ongoing transcription of its mitoLLPs. Our results suggest that modulating protein longevity within the ETC is critical for mitochondrial proteome maintenance and the robustness of mitochondrial function.

Age Mosaicism across Multiple Scales in Adult Tissues

Most neurons are not replaced during an animal's lifetime. This nondividing state is characterized by extreme longevity and age-dependent decline of key regulatory proteins. To study the lifespans of cells and proteins in adult tissues, we combined isotope labeling of mice with a hybrid imaging method (MIMS-EM). Using ¹⁵N mapping, we show that liver and pancreas are composed of cells with vastly different ages, many as old as the animal. Strikingly, we also found that a subset of fibroblasts and endothelial cells, both known for their replicative potential, are characterized by the absence of cell division during adulthood. In addition, we show that the primary cilia of beta cells and neurons contains different structural regions with vastly different lifespans. Based on these results, we propose that age mosaicism across multiple scales is a fundamental principle of adult tissue, cell, and protein complex organization.

Location Specificity of Transcranial Electrical Stimulation on Neuronal Electrodynamics: A Mathematical Model of Ion Channel Gating Dynamics and Ionic Flux Due to Neurostimulation

Transcranial Electrical Stimulation (TES) continues to demonstrate success as a medical intervention for individuals with neurodegenerative diseases. Despite promising results from these neuromodulation modalities, the cellular level mechanisms by which this neurotherapy operates are not fully comprehended. In particular, the effects of TES on ion channel gating and ion transport are not known. Using the Poisson-Nernst-Planck model of electrodiffusion, coupled with a Hodgkin-Huxley based model of cellular ion transport, we present a model of TES that, for the first time, integrates electric potential energy, individualized ion species, voltage-gated ion channels, and transmembrane ionic flux during TES administration. Computational simulations are executed on a biologically-inspired domain with medically-based TES treatment parameters and quantify neuron-level electrical processes resulting from this form of neurostimulation. Results confirm prior findings that show that TES polarizes the cell membrane, however, these are extended as simulations in this paper show that polarization occurs in a location specific manner, where the type and degree of polarization depends on the position on the membrane within a node of Ranvier. In addition, results demonstrate that TES causes ion channel gating variables to change in a location specific fashion and, as a result, transmembrane current from distinct ion species depends on both time and membrane location. Another simulation finding is that intracellular calcium concentrations increase significantly due to a TES-induced calcium influx. As cytosolic calcium is critical in intracellular signaling pathways that govern proper neurotransmitter secretion as well as support cell viability, this alteration in calcium homeostasis suggests a possible mechanism by which TES operates at the neuronal level to achieve neurotherapeutic success.

Improved Simulation of Electrodiffusion in the Node of Ranvier by Mesh Adaptation

In neural structures with complex geometries, numerical resolution of the Poisson-Nernst-Planck (PNP) equations is necessary to accurately model electrodiffusion. This formalism allows one to describe ionic concentrations and the electric field (even away from the membrane) with arbitrary spatial and temporal resolution which is impossible to achieve with models relying on cable theory. However, solving the PNP equations on complex geometries involves handling intricate numerical difficulties related either to the spatial discretization, temporal discretization or the resolution of the linearized systems, often requiring large computational resources which have limited the use of this approach. In the present paper, we investigate the best ways to use the finite elements method (FEM) to solve the PNP equations on domains with discontinuous properties (such as occur at the membrane-cytoplasm interface). 1) Using a simple 2D geometry to allow comparison with analytical solution, we show that mesh adaptation is a very (if not the most) efficient way to obtain accurate solutions while limiting the computational efforts, 2) We use mesh adaptation in a 3D model of a node of Ranvier to reveal details of the solution which are nearly impossible to resolve with other modelling techniques. For instance, we exhibit a non linear distribution of the electric potential within the membrane due to the non uniform width of the myelin and investigate its impact on the spatial profile of the electric field in the Debye layer.

Minimizing the caliber of myelinated axons by means of nodal constrictions

In myelinated axons, most of the voltage-gated ion channels are concentrated at the nodes of Ranvier, which are short gaps in the myelin sheath. This arrangement leads to saltatory conduction and a larger conduction velocity than in nonmyelinated axons. Intriguingly, axons in the peripheral nervous system that exceed about 2 μm in diameter exhibit a characteristic narrowing of the axon at nodes that results in a local reduction of the axonal cross-sectional area. The extent of constriction increases with increasing internodal axonal caliber, reaching a threefold reduction in diameter for the largest axons. In this paper, we use computational modeling to investigate the effect of nodal constrictions on axonal conduction velocity. For a fixed number of ion channels, we find that there is an optimal extent of nodal constriction which minimizes the internodal axon caliber that is required to achieve a given target conduction velocity, and we show that this is sensitive to the precise geometry of the axon and myelin sheath in the flanking paranodal regions. Thus axonal constrictions at nodes of Ranvier appear to be a biological adaptation to minimize axonal volume, thereby maximizing the spatial and metabolic efficiency of these processes, which can be a significant evolutionary constraint. We show that the optimal nodal morphologies are relatively insensitive to changes in the number of nodal sodium channels.

Inner ear tissue preservation by rapid freezing: improving fixation by high-pressure freezing and hybrid methods

In the preservation of tissues in as ‘close to life’ state as possible, rapid freeze fixation has many benefits over conventional chemical fixation. One technique by which rapid freeze-fixation can be achieved, high pressure freezing (HPF), has been shown to enable ice crystal artefact-free freezing and tissue preservation to greater depths (more than 40 μm) than other quick-freezing methods. Despite increasingly becoming routine in electron microscopy, the use of HPF for the fixation of inner ear tissue has been limited. Assessment of the quality of preservation showed routine HPF techniques were suitable for preparation of inner ear tissues in a variety of species. Good preservation throughout the depth of sensory epithelia was achievable. Comparison to chemically fixed tissue indicated that fresh frozen preparations exhibited overall superior structural preservation of cells. However, HPF fixation caused characteristic artefacts in stereocilia that suggested poor quality freezing of the actin bundles. The hybrid technique of pre-fixation and high pressure freezing was shown to produce cellular preservation throughout the tissue, similar to that seen in HPF alone. Pre-fixation HPF produced consistent high quality preservation of stereociliary actin bundles. Optimising the preparation of samples with minimal artefact formation allows analysis of the links between ultrastructure and function in inner ear tissues.

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Routine high pressure freezing can preserve large depths of inner ear tissue.

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Stereocilial actin preserved by rapid freezing exhibits characteristic artefacts.

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Hybrid methods of fixation improved structural preservation of stereocilial actin.

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Improved fixation will reduce artefacts in ultrastructural studies of the inner ear.

Insights into cell entry and intracellular trafficking of peptide and protein drugs provided by electron microscopy

For widening the arsenal of protein and peptide therapeutics that act within cells, their cell-entry mechanisms, intracellular trafficking and distribution need to be characterized in detail. Immunofluorescence microscopy has been a prevalent tool for these studies. However, due to the limited resolution, it is often complemented with other methods. This article focuses on the perspectives of electron microscopy in tracking the intracellular delivery and trafficking of proteins, peptides and their carriers. This review introduces the electron microscopy techniques and labeling methods currently used for studying the cellular whereabouts of peptides and proteins with a focus on their intracellular trafficking. Since cell-penetrating peptides have widely been harnessed as carriers for proteins and peptides, and their usage is rapidly expanding, a particular emphasis has been placed on their applications and cell-entry mechanisms.

Dependence of paranodal junctional gap width on transverse bands

Mouse mutants with paranodal junctional (PNJ) defects display variable degrees of neurological impairment. In this study we compare control paranodes with those from three mouse mutants that differ with respect to a conspicuous PNJ component, the transverse bands (TBs). We hypothesize that TBs link the apposed junctional membranes together at a fixed distance and thereby determine the width of the junctional gap, which may in turn determine the extent to which nodal action currents can be short-circuited underneath the myelin sheath. Electron micrographs of aldehyde-fixed control PNJs, in which TBs are abundant, show a consistent junctional gap of ∼3.5 nm. In Caspr-null PNJs, which lack TBs entirely, the gap is wider (∼6-7 nm) and more variable. In CST-null PNJs, which have only occasional TBs, the mean PNJ gap width is comparable to that in Caspr-null mice. In the shaking mutant, in contrast, which has approximately 60% of the normal complement of TBs, mean PNJ gap width is not significantly different from that in controls. Correspondingly, shaking mice are much less impaired neurologically than either Caspr-null or CST-null mice. We conclude that in the absence or gross diminution of TBs, mean PNJ gap width increases significantly and suggest that this difference could underlie some of the neurological impairment seen in those mutants. Surprisingly, even in the absence of TBs, paranodes are to some extent maintained in their usual form, implying that in addition to TBs, other factors govern the formation and maintenance of overall paranodal structure.

Cardiac myocytes and local signaling in nano-domains

It is well known that calcium-induced calcium-release in cardiac myocytes takes place in spatially restricted regions known as dyads, where discrete patches of junctional sarcoplasmic reticulum tightly associate with the t-tubule membrane. The dimensions of a dyad are so small that it contains only a few Ca²⁺ ions at any given time. Ca²⁺ signaling in the dyad is therefore noisy, and dominated by the Brownian motion of Ca²⁺ ions in a potential field. Remarkably, from this complexity emerges the integrated behavior of the myocyte in which, under normal conditions, precise control of Ca²⁺ release and muscle contraction is maintained over the life of the cell. This is but one example of how signal processing within the cardiac myocyte and other cells often occurs in small "nano-domains" where proteins and protein complexes interact at spatial dimensions on the order of ∼1-10 nm and at time-scales on the order of nanoseconds to perform the functions of the cell. In this article, we will review several examples of local signaling in nano-domains, how it contributes to the integrative behavior of the cardiac myocyte, and present computational methods for modeling signal processing within these domains across differing spatio-temporal scales.

Systems biology in immunology: a computational modeling perspective

Systems biology is an emerging discipline that combines high-content, multiplexed measurements with informatic and computational modeling methods to better understand biological function at various scales. Here we present a detailed review of the methods used to create computational models and to conduct simulations of immune function. We provide descriptions of the key data-gathering techniques employed to generate the quantitative and qualitative data required for such modeling and simulation and summarize the progress to date in applying these tools and techniques to questions of immunological interest, including infectious disease. We include comments on what insights modeling can provide that complement information obtained from the more familiar experimental discovery methods used by most investigators and the reasons why quantitative methods are needed to eventually produce a better understanding of immune system operation in health and disease.

Modeling of intracellular transport and compartmentation

The complexity and internal organization of mammalian cells as well as the regulation of intracellular transport processes has increasingly moved into the focus of investigation during the past two decades. Advanced staining and microscopy techniques help to shed light onto spatial cellular compartmentation and regulation, increasing the demand for improved modeling techniques. In this chapter, we summarize recent developments in the field of quantitative simulation approaches and frameworks for the description of intracellular transport processes. Special focus is therefore laid on compartmented and spatiotemporally resolved simulation approaches. The processes considered include free and facilitated diffusion of molecules, active transport via the microtubule and actin filament network, vesicle distribution, membrane transport, cell cycle-dependent cell growth and morphology variation, and protein production. Commercially and freely available simulation packages are summarized as well as model data exchange and harmonization issues.

Towards quantitative 3D imaging of the osteocyte lacuno-canalicular network

Osteocytes are the most abundant cells in bone and the only cells embedded in the bone mineral matrix. They form an extended, three-dimensional (3D) network, whose processes interconnecting the cell bodies reside in thin canals, the canaliculi. Together with the osteocyte lacunae, the canaliculi form the lacuno-canalicular network (LCN). As the negative imprint of the cellular network within bone tissue, the LCN morphology is considered to play a central role for bone mechanosensation and mechanotransduction. However, the LCN has neither been visualized nor quantified in an adequate way up to now. On this account, this article summarizes the current state of knowledge of the LCN morphology and then reviews different imaging methods regarding the quantitative 3D assessment of bone tissue in general and of the LCN in particular. These imaging methods will provide new insights in the field of bone mechanosensation and mechanotransduction and thus, into processes of strain sensation and transduction, which are tightly associated with osteocyte viability and bone quality.

Imbalance of ionic conductances contributes to diverse symptoms of demyelination

Fast axonal conduction of action potentials in mammals relies on myelin insulation. Demyelination can cause slowed, blocked, desynchronized, or paradoxically excessive spiking that underlies the symptoms observed in demyelination diseases. The diversity and timing of such symptoms are poorly understood, often intermittent, and uncorrelated with disease progress. We modeled the effects of demyelination (and secondary remodeling) on intrinsic axonal excitability using Hodgkin-Huxley and reduced Morris-Lecar models. Simulations and analysis suggested a simple explanation for the breadth of symptoms and revealed that the ratio of sodium to leak conductance, g(Na)/g(L), acted as a four-way switch controlling excitability patterns that included spike failure, single spike transmission, afterdischarge, and spontaneous spiking. Failure occurred when this ratio fell below a threshold value. Afterdischarge occurred at g(Na)/g(L) just below the threshold for spontaneous spiking and required a slow inward current that allowed for two stable attractor states, one corresponding to quiescence and the other to repetitive spiking. A neuron prone to afterdischarge could function normally unless it was switched to its "pathological" attractor state; thus, although the underlying pathology may develop slowly by continuous changes in membrane conductances, a discontinuous change in axonal excitability can occur and lead to paroxysmal symptoms. We conclude that tonic and paroxysmal positive symptoms as well as negative symptoms may be a consequence of varying degrees of imbalance between g(Na) and g(L) after demyelination. The KCNK family of g(L) potassium channels may be an important target for new drugs to treat the symptoms of demyelination.

Mitochondrial configurations in peripheral nerve suggest differential ATP production

Physiological states of mitochondria often correlate with distinctive morphology. Electron microscopy and tomographic reconstruction were used to investigate the three-dimensional structure of axonal mitochondria and mitochondria in the surrounding Schwann cells of the peripheral nervous system (PNS), both in the vicinity of nodes of Ranvier and far from these nodes. Condensed mitochondria were found to be abundant in the axoplasm, but not in the Schwann cell. Uncharacteristic of the classical morphology of condensed mitochondria, the outer and inner boundary membranes are in close apposition and the crista junctions are narrow, consistent with their function as gates for the diffusion of macromolecules. There is also less cristae surface area and lower density of crista junctions in these mitochondria. The density of mitochondria was greater at the paranode-node-paranode (PNP) as was the crista junction opening, yet there were fewer cristae in these organelles compared to those in the internodal region. The greater density of condensed mitochondria in the PNS axoplasm and in particular at the PNP suggests a need for these organelles to operate at a high workload of ATP production.

The structural dynamics of macromolecular processes

Dynamic processes involving macromolecular complexes are essential to cell function. These processes take place over a wide variety of length scales from nanometers to micrometers, and over time scales from nanoseconds to minutes. As a result, information from a variety of different experimental and computational approaches is required. We review the relevant sources of information and introduce a framework for integrating the data to produce representations of dynamic processes.

Computational modeling of three-dimensional electrodiffusion in biological systems: application to the node of Ranvier

A computational model is presented for the simulation of three-dimensional electrodiffusion of ions. Finite volume techniques were used to solve the Poisson-Nernst-Planck equation, and a dual Delaunay-Voronoi mesh was constructed to evaluate fluxes of ions, as well as resulting electric potentials. The algorithm has been validated and applied to a generalized node of Ranvier, where numerical results for computed action potentials agree well with cable model predictions for large clusters of voltage-gated ion channels. At smaller channel clusters, however, the three-dimensional electrodiffusion predictions diverge from the cable model predictions and show a broadening of the action potential, indicating a significant effect due to each channel's own local electric field. The node of Ranvier complex is an elaborate organization of membrane-bound aqueous compartments, and the model presented here represents what we believe is a significant first step in simulating electrophysiological events with combined realistic structural and physiological data.

Shape-driven three-dimensional watersnake segmentation of biological membranes in electron tomography

Due to the significant complexity of membrane morphology and the generally poor image quality in electron tomographic volumes, current automatic methods for segmentation of membranes perform poorly. Users must resort to manual tracing of recognized patterns on 2-D slices of the volume, a method that suffers from subjectivity and is very labor intensive, preventing quantitative analyses of tomographic data that require comparative analyses of many volumes. To overcome these limitations, we develop an automatic 3-D segmentation method that fully exploits the prior knowledge about the shape of the membranes as well as the 3-D information provided by the tomograms, and systematically combines this knowledge with the image data to improve segmentation results. The method is based on the watersnake framework. By mathematically reformulating the traditional watershed segmentation as an energy minimization problem, the watersnake inherits the many strengths of the watershed method while overcoming the limitations of the traditional energy-based segmentation methods. In our previous work (H. Nguyen et al., 2003), the original watersnake model was successfully modified by incorporating smoothness into watershed segmentation. In this work, we further extend that model to incorporate into the energy function various constraints representing our prior knowledge about the global shape of the cellular features to be segmented. Segmentation can, therefore, be accomplished via minimization of the energy function subject to the shape prior constraints. Finally, the mathematical framework is further extended from 2-D to 3-D so that segmentation can be carried out in 3-D to take advantage of the additional information provided by the tomograms. We apply this method for the automatic extraction of biological membranes of varying complexities including those of bacterial walls and mitochondrial boundaries.

A formal ontology of subcellular neuroanatomy

The complexity of the nervous system requires high-resolution microscopy to resolve the detailed 3D structure of nerve cells and supracellular domains. The analysis of such imaging data to extract cellular surfaces and cell components often requires the combination of expert human knowledge with carefully engineered software tools. In an effort to make better tools to assist humans in this endeavor, create a more accessible and permanent record of their data, and to aid the process of constructing complex and detailed computational models, we have created a core of formalized knowledge about the structure of the nervous system and have integrated that core into several software applications. In this paper, we describe the structure and content of a formal ontology whose scope is the subcellular anatomy of the nervous system (SAO), covering nerve cells, their parts, and interactions between these parts. Many applications of this ontology to image annotation, content-based retrieval of structural data, and integration of shared data across scales and researchers are also described.

Electron tomographic analysis of cytoskeletal cross-bridges in the paranodal region of the node of Ranvier in peripheral nerves

The node of Ranvier is a site for ionic conductances along myelinated nerves and governs the saltatory transmission of action potentials. Defects in the cross-bridging and spacing of the cytoskeleton are a prominent pathological feature in diseases of the peripheral nerve. Electron tomography was used to examine cytoskeletal-cytoskeletal, membrane-cytoskeletal, and heterologous cell connections in the paranodal region of the node of Ranvier in peripheral nerves. Focal attachment of cytoskeletal filaments to each other and to the axolemma and paranodal membranes of the Schwann cell via narrow cross-bridges was visualized in both neuronal and glial cytoplasm. A subset of intermediate filaments associates with the cytoplasmic surfaces of supramolecular complexes of transmembrane structures that are presumed to include known and unknown junctional proteins. Mitochondria were linked to both microtubules and neurofilaments in the axoplasm and to neighboring smooth endoplasmic reticulum by narrow cross-bridges. Tubular cisternae in the glial cytoplasm were also linked to the paranodal glial cytoplasmic loop juxtanodal membrane by short cross-bridges. In the extracellular matrix between axon and Schwann cell, junctional bridges formed long cylinders linking the two membranes. Interactions between cytoskeleton, membranes, and extracellular matrix associations in the paranodal region are likely critical not only for scaffolding, but also for intracellular and extracellular communication.

The cell centered database project: an update on building community resources for managing and sharing 3D imaging data

Databases have become integral parts of data management, dissemination, and mining in biology. At the Second Annual Conference on Electron Tomography, held in Amsterdam in 2001, we proposed that electron tomography data should be shared in a manner analogous to structural data at the protein and sequence scales. At that time, we outlined our progress in creating a database to bring together cell level imaging data across scales, The Cell Centered Database (CCDB). The CCDB was formally launched in 2002 as an on-line repository of high-resolution 3D light and electron microscopic reconstructions of cells and subcellular structures. It contains 2D, 3D, and 4D structural and protein distribution information from confocal, multiphoton, and electron microscopy, including correlated light and electron microscopy. Many of the data sets are derived from electron tomography of cells and tissues. In the 5 years since its debut, we have moved the CCDB from a prototype to a stable resource and expanded the scope of the project to include data management and knowledge engineering. Here, we provide an update on the CCDB and how it is used by the scientific community. We also describe our work in developing additional knowledge tools, e.g., ontologies, for annotation and query of electron microscopic data.

Expedited approaches to whole cell electron tomography and organelle mark-up in situ in high-pressure frozen pancreatic islets

We have developed a simplified, efficient approach for the 3D reconstruction and analysis of mammalian cells in toto by electron microscope tomography (ET), to provide quantitative information regarding 'global' cellular organization at approximately 15-20 nm resolution. Two insulin-secreting beta cells-deemed 'functionally equivalent' by virtue of their location at the periphery of the same pancreatic islet-were reconstructed in their entirety in 3D after fast-freezing/freeze-substitution/plastic embedment in situ within a glucose-stimulated islet of Langerhans isolated intact from mouse pancreata. These cellular reconstructions have afforded several unique insights into fundamental structure-function relationships among key organelles involved in the biosynthesis and release of the crucial metabolic hormone, insulin, that could not be provided by other methods. The Golgi ribbon, mitochondria and insulin secretory granules in each cell were segmented for comparative analysis. We propose that relative differences between the two cells in terms of the number, dimensions and spatial distribution (and for mitochondria, also the extent of branching) of these organelles per cubic micron of cellular volume reflects differences in the two cells' individual capacity (and/or readiness) to respond to secretagogue stimulation, reflected by an apparent inverse relationship between the number/size of insulin secretory granules versus the number/size of mitochondria and the Golgi ribbon. We discuss the advantages of this approach for quantitative cellular ET of mammalian cells, briefly discuss its application relevant to other complementary techniques, and summarize future strategies for overcoming some of its current limitations.

The combination of chemical fixation procedures with high pressure freezing and freeze substitution preserves highly labile tissue ultrastructure for electron tomography applications

The emergence of electron tomography as a tool for three dimensional structure determination of cells and tissues has brought its own challenges for the preparation of thick sections. High pressure freezing in combination with freeze substitution provides the best method for obtaining the largest volume of well-preserved tissue. However, for deeply embedded, heterogeneous, labile tissues needing careful dissection, such as brain, the damage due to anoxia and excision before cryofixation is significant. We previously demonstrated that chemical fixation prior to high pressure freezing preserves fragile tissues and produces superior tomographic reconstructions compared to equivalent tissue preserved by chemical fixation alone. Here, we provide further characterization of the technique, comparing the ultrastructure of Flock House Virus infected DL1 insect cells that were (1) high pressure frozen without fixation, (2) high pressure frozen following fixation, and (3) conventionally prepared with aldehyde fixatives. Aldehyde fixation prior to freezing produces ultrastructural preservation superior to that obtained through chemical fixation alone that is close to that obtained when cells are fast frozen without fixation. We demonstrate using a variety of nervous system tissues, including neurons that were injected with a fluorescent dye and then photooxidized, that this technique provides excellent preservation compared to chemical fixation alone and can be extended to selectively stained material where cryofixation is impractical.

Serial sectioning and electron microscopy of large tissue volumes for 3D analysis and reconstruction: a case study of the calyx of Held

Serial section electron microscopy is typically applied to investigation of small tissue volumes encompassing subcellular structures. However, in neurobiology, the need to relate subcellular structure to organization of neural circuits can require investigation of large tissue volumes at ultrastructural resolution. Analysis of ultrastructure and three-dimensional reconstruction of even one to a few cells is time consuming, and still does not generate the necessary numbers of observations to form well-grounded insights into biological principles. We describe an assemblage of existing computer-based methods and strategies for graphical analysis of large photographic montages to accomplish the study of multiple neurons through large tissue volumes. Sample preparation, data collection and subsequent analyses can be completed within 3-4 months. These methods generate extremely large data sets that can be mined in future studies of nervous system organization.

Towards neural circuit reconstruction with volume electron microscopy techniques

Electron microscopy is the only currently available technique with a resolution adequate to identify and follow every axon and dendrite in dense neuropil. Reconstructions of large volumes of neural tissue, necessary to reconstruct even local neural circuits, have, however, been inhibited by the daunting task of serially sectioning and reconstructing thousands of sections. Recent technological developments have improved the quality of volume electron microscopy data and automated its acquisition. This opens up the prospect of reconstructing almost complete invertebrate and sizable fractions of vertebrate nervous systems. Such reconstructions of complete neural wiring diagrams could rekindle the tradition of relating neural function to the underlying neuroanatomical circuitry.

Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method

The signaling network underlying eukaryotic chemosensing is a complex combination of receptor-mediated transmembrane signals, lipid modifications, protein translocations, and differential activation/deactivation of membrane-bound and cytosolic components. As such, it provides particularly interesting challenges for a combined computational and experimental analysis. We developed a novel detailed molecular signaling model that, when used to simulate the response to the attractant cyclic adenosine monophosphate (cAMP), made nontrivial predictions about Dictyostelium chemosensing. These predictions, including the unexpected existence of spatially asymmetrical, multiphasic, cyclic adenosine monophosphate–induced PTEN translocation and phosphatidylinositol-(3,4,5)P₃ generation, were experimentally verified by quantitative single-cell microscopy leading us to propose significant modifications to the current standard model for chemoattractant-induced biochemical polarization in this organism. Key to this successful modeling effort was the use of “Simmune,” a new software package that supports the facile development and testing of detailed computational representations of cellular behavior. An intuitive interface allows user definition of complex signaling networks based on the definition of specific molecular binding site interactions and the subcellular localization of molecules. It automatically translates such inputs into spatially resolved simulations and dynamic graphical representations of the resulting signaling network that can be explored in a manner that closely parallels wet lab experimental procedures. These features of Simmune were critical to the model development and analysis presented here and are likely to be useful in the computational investigation of many aspects of cell biology.

Cells can orient their migration in response to small local differences in the concentration of extracellular chemicals (chemoattractants). Understanding this process (chemosensing) requires analyzing the time and position-dependent behavior of the signaling molecules within the responding cell, making it an especially interesting challenge for both experimental and computational investigation. Here, the authors report the development and testing of a new detailed molecular model of the chemosensing apparatus of the amoeba Dictyostelium discoidium reacting to the chemoattractant cyclic adenosine monophosphate. Computer simulations performed using this model predicted unexpected and previously unreported patterns of changes in the concentration and location of two important intracellular signaling molecules. These predictions were experimentally verified using microscopy, suggesting the need for modifications to the current “standard” model of eukaryotic chemosensing. The high degree of detail in their model was made possible by a new software suite called “Simmune,” which allows biologists to enter information about molecular interactions using a graphical interface. Without requiring the user to write any equations, the software automatically constructs the overall reaction network, simulates the model, and provides several ways to view the biochemistry of simulated cells. This new tool should help biologists to translate qualitative representations of cell biological processes into quantitative, predictive models.