Three-Dimensional Electron Microscopy at Molecular Resolution

Cross-linking and mass spectrometry methodologies to facilitate structural biology: finding a path through the maze

Multiprotein complexes, rather than individual proteins, make up a large part of the biological macromolecular machinery of a cell. Understanding the structure and organization of these complexes is critical to understanding cellular function. Chemical cross-linking coupled with mass spectrometry is emerging as a complementary technique to traditional structural biology methods and can provide low-resolution structural information for a multitude of purposes, such as distance constraints in computational modeling of protein complexes. In this review, we discuss the experimental considerations for successful application of chemical cross-linking-mass spectrometry in biological studies and highlight three examples of such studies from the recent literature. These examples (as well as many others) illustrate the utility of a chemical cross-linking-mass spectrometry approach in facilitating structural analysis of large and challenging complexes.

Consensus among multiple approaches as a reliability measure for flexible fitting into cryo-EM data

Cryo-electron microscopy (cryo-EM) can provide low-resolution density maps of large macromolecular assemblies. As the number of structures deposited in the Protein Data Bank by fitting a high-resolution structure into a low-resolution cryo-EM map is increasing, there is a need to revise the protocols and improve the measures for fitting. A recent study suggested using a combination of multiple automated flexible fitting approaches to improve the interpretation of cryo-EM data. The current work further explores the use of multiple approaches by validating this "consensus" fitting approach and deriving a local reliability measure. Here four different flexible fitting approaches are applied for fitting an initial structure into a simulated density map of known target structure from a dataset of proteins. It is found that the models produced from different approaches often have a consensus in conformation and are also near to the target structure, whereas cases not showing consensus are away from the target. A high correlation is also observed between the RMSF profiles calculated with respect to the average and the target structures, which indicates that the relation between consensus and accuracy can also be extended to a per-residue level. Therefore, the RMSF among the fitted models is proposed as a local reliability measure, which can be used to assess the reliability of the fit at specific regions. Hence, we encourage the community to use consensus flexible fitting with different methods to report on local reliability of the resulting models and improve the interpretation of cryo-EM data.

Consensus among flexible fitting approaches improves the interpretation of cryo-EM data

Cryo-elecron microscopy (cryo-EM) can provide important structural information of large macromolecular assemblies in different conformational states. Recent years have seen an increase in structures deposited in the Protein Data Bank (PDB) by fitting a high-resolution structure into its low-resolution cryo-EM map. A commonly used protocol for accommodating the conformational changes between the X-ray structure and the cryo-EM map is rigid body fitting of individual domains. With the emergence of different flexible fitting approaches, there is a need to compare and revise these different protocols for the fitting. We have applied three diverse automated flexible fitting approaches on a protein dataset for which rigid domain fitting (RDF) models have been deposited in the PDB. In general, a consensus is observed in the conformations, which indicates a convergence from these theoretically different approaches to the most probable solution corresponding to the cryo-EM map. However, the result shows that the convergence might not be observed for proteins with complex conformational changes or with missing densities in cryo-EM map. In contrast, RDF structures deposited in the PDB can represent conformations that not only differ from the consensus obtained by flexible fitting but also from X-ray crystallography. Thus, this study emphasizes that a "consensus" achieved by the use of several automated flexible fitting approaches can provide a higher level of confidence in the modeled configurations. Following this protocol not only increases the confidence level of fitting, but also highlights protein regions with uncertain fitting. Hence, this protocol can lead to better interpretation of cryo-EM data.

Analytical capabilities of the ImageStream cytometer

Imaging cytometry has recently become an important achievement in development of flow cytometric technologies. The ImageStream cytometer combines the vast features of classical flow cytometry including an impartial analysis of great number of cells in short period of time which results in strong statistical data output, with essential features of fluorescence microscopy such us collecting of real multiparameter images of analyzed objects. In this chapter, we would like to introduce an overview of imaging cytometry platform and emphasize the potential advantages of using this system for several experimental purposes. Moreover, both well established as well as potential applications of imaging cytometry will be described. Eventually, we would like to illustrate the unique use of ImageStream cytometer for identification and characterization of subpopulations of stem/ progenitor cells present in different biological specimens.

EELS characterization of radiolytic products in frozen samples

Electron energy loss spectroscopy (EELS) was used to obtain information about the radiation chemistry of frozen aqueous specimens in the electron microscope by observing the hydrogen and oxygen K-edges. Measurements on frozen solutions of 30% hydrogen peroxide revealed the presence of molecular oxygen identified by a distinct 531-eV peak at the O K-edge even for electron doses below 100 e/nm². The molecular oxygen content of irradiated H₂O₂ solution was determined by least squares fitting of O K-edge reference spectra from water and gas-phase oxygen. It was found that the fraction of molecular oxygen to water oxygen was in the range 0.03-0.05. EELS from pure frozen water showed no features attributable to molecular oxygen or molecular hydrogen (K edge at ~13 eV) even at high electron doses above 10⁵ e/nm². Spectra from frozen sucrose and protein solutions and their mixtures, however, did show evolution of a molecular hydrogen peak at ~13 eV for doses above 10⁵ e/nm², consistent with previous measurements and indicative of hydrogen bubble formation. Molecular oxygen was not observed in any of the frozen solutions of organic compounds indicating that oxygen is not a major product of free radical decay, in contrast to molecular hydrogen formation.

Electron cryotomography

Electron cryotomography (ECT) is an emerging technology that allows thin samples such as macromolecular complexes and small bacterial cells to be imaged in 3-D in a nearly native state to "molecular" ( approximately 4 nm) resolution. As such, ECT is beginning to deliver long-awaited insight into the positions and structures of cytoskeletal fi laments, cell wall elements, motility machines, chemoreceptor arrays, internal compartments, and other ultrastructures. This article describes the technique and summarizes its contributions to bacterial cell biology. For comparable recent reviews, see (Subramaniam 2005; Jensen and Briegel 2007; Murphy and Jensen 2007; Li and Jensen 2009). For reviews on the history, technical details, and broader application of electron tomography in general, see for example (Subramaniam and Milne 2004; Lucić et al. 2005; Leis et al. 2008; Midgley and Dunin-Borkowski 2009).

Electron beam-induced radiation damage: the bubbling response in amorphous dried sodium phosphate buffer

Irradiation of an amorphous layer of dried sodium phosphate buffer (pH = 7.0) by transmission electron microscopy (100-120 kV) causes rapid formation of numerous small spherical bubbles [10-100 A (= 1-10 nm)] containing an unknown gas. Bubbling is detected even with the first low-dose exposure. In a thin layer (ca. 100-150 A), bubbling typically goes through nucleation, growth, possible fusion, and end-state, after which further changes are not apparent; co-irradiated adjacent areas having a slightly smaller thickness never develop bubbles. In moderately thicker regions (ca. over 200 A), there is no end-state. Instead, a complex sequence of microstructural changes is elicited during continued intermittent high-dose irradiation: nucleation, growth, early simple fusions, a second round of extensive multiple fusions, general reduction of matrix thickness (producing flattening and expansion of larger bubbles, occasional bubble fission, and formation of very large irregularly-shaped bubbles by a third round of compound fusion events), and slow shrinkage of all bubbles. The ongoing lighter appearance of bubble lumens, maintenance of their rounded shape, and extensive changes in size and form indicate that gas content continues throughout their surprisingly long lifetime; the thin dense boundary layer surrounding all bubbles is proposed to be the main mechanism for their long lifetime.

Correlative microscopy: a potent tool for the study of rare or unique cellular and tissue events

Biological studies have relied on two complementary microscope technologies - light (fluorescence) microscopy and electron microscopy. Light microscopy is used to study phenomena at a global scale to look for unique or rare events, and it also provides an opportunity for live imaging, whereas the forte of electron microscopy is the high resolution. Traditionally light and electron microscopy observations are carried out in different populations of cells/tissues and a 'correlative' inference is drawn. The advent of true correlative light-electron microscopy has allowed high-resolution imaging by electron microscopy of the same structure observed by light microscopy, and in advanced cases by video microscopy. Thus a rare event captured by low-resolution imaging of a population or transient events captured by live imaging can now also be studied at high resolution by electron microscopy. Here, the potential and difficulties of this approach, along with the most impressive breakthroughs obtained by these methods, are discussed.

Role of HAMP domains in chemotaxis signaling by bacterial chemoreceptors

Bacterial chemoreceptors undergo conformational changes in response to variations in the concentration of extracellular ligands. These changes in chemoreceptor structure initiate a series of signaling events that ultimately result in regulation of rotation of the flagellar motor. Here we have used cryo-electron tomography combined with 3D averaging to determine the in situ structure of chemoreceptor assemblies in Escherichia coli cells that have been engineered to overproduce the serine chemoreceptor Tsr. We demonstrate that chemoreceptors are organized as trimers of receptor dimers and display two distinct conformations that differ principally in arrangement of the HAMP domains within each trimer. Ligand binding and methylation alter the distribution of chemoreceptors between the two conformations, with serine binding favoring the "expanded" conformation and chemoreceptor methylation favoring the "compact" conformation. The distinct positions of chemoreceptor HAMP domains within the context of a trimeric unit are thus likely to represent important aspects of chemoreceptor structural changes relevant to chemotaxis signaling. Based on these results, we propose that the compact and expanded conformations represent the "kinase-on" and "kinase-off" states of chemoreceptor trimers, respectively.

Image processing for electron microscopy single-particle analysis using XMIPP

We describe a collection of standardized image processing protocols for electron microscopy single-particle analysis using the XMIPP software package. These protocols allow performing the entire processing workflow starting from digitized micrographs up to the final refinement and evaluation of 3D models. A particular emphasis has been placed on the treatment of structurally heterogeneous data through maximum-likelihood refinements and self-organizing maps as well as the generation of initial 3D models for such data sets through random conical tilt reconstruction methods. All protocols presented have been implemented as stand-alone, executable python scripts, for which a dedicated graphical user interface has been developed. Thereby, they may provide novice users with a convenient tool to quickly obtain useful results with minimum efforts in learning about the details of this comprehensive package. Examples of applications are presented for a negative stain random conical tilt data set on the hexameric helicase G40P and for a structurally heterogeneous data set on 70S Escherichia coli ribosomes embedded in vitrified ice.

Three-dimensional reconstruction of axonemal outer dynein arms in situ by electron tomography

We present here for the first time a 3D reconstruction of in situ axonemal outer dynein arms. This reconstruction has been obtained by electron tomography applied to a series of tilted images collected from metal replicas of rapidly frozen, cryofractured, and metal-replicated sperm axonemes of the cecidomid dipteran Monarthropalpus flavus. This peculiar axonemal model consists of several microtubular laminae that proved to be particularly suitable for this type of analysis. These laminae are sufficiently planar to allow the visualization of many dynein molecules within the same fracture face, allowing us to recover a significant number of equivalent objects and to improve the signal-to-noise ratio of the reconstruction by applying advanced averaging protocols. The 3D model we obtained showed the following interesting structural features: First, each dynein arm has two head domains that are almost parallel and are obliquely oriented with respect to the longitudinal axis of microtubules. The two heads are therefore positioned at different distances from the surface of the A-tubule. Second, each head domain consists of a series of globular subdomains that are positioned on the same plane. Third, a stalk domain originates as a conical region from the proximal head and ends with a small globular domain that contacts the B-tubule. Fourth, the stem region comprises several globular subdomains and presents two distinct points of anchorage to the surface of the A-tubule. Finally, and most importantly, contrary to what has been observed in isolated dynein molecules adsorbed to flat surfaces, the stalk and the stem domains are not in the same plane as the head.

Evaluation of denoising algorithms for biological electron tomography

Tomograms of biological specimens derived using transmission electron microscopy can be intrinsically noisy due to the use of low electron doses, the presence of a "missing wedge" in most data collection schemes, and inaccuracies arising during 3D volume reconstruction. Before tomograms can be interpreted reliably, for example, by 3D segmentation, it is essential that the data be suitably denoised using procedures that can be individually optimized for specific data sets. Here, we implement a systematic procedure to compare various nonlinear denoising techniques on tomograms recorded at room temperature and at cryogenic temperatures, and establish quantitative criteria to select a denoising approach that is most relevant for a given tomogram. We demonstrate that using an appropriate denoising algorithm facilitates robust segmentation of tomograms of HIV-infected macrophages and Bdellovibrio bacteria obtained from specimens at room and cryogenic temperatures, respectively. We validate this strategy of automated segmentation of optimally denoised tomograms by comparing its performance with manual extraction of key features from the same tomograms.

“Decoding the Dots”: The ImageStream system (ISS) as a novel and powerful tool for flow cytometric analysis

The aim of this article is to provide a brief review of the ImageStream system (ISS). The ISS technology was developed as a novel method for multiparameter cell analysis and subsequently as a supportive tool for flow cytometry (FC). ISS integrates the features of FC and fluorescent microscopy collecting images of acquired cells for offline digital image analysis. The article presents an overview of the main characteristics of ISS and a comparison between ISS, FC and the laser scanning cytometer (LSC). We reviewed ISS applications focusing on those involved in cellular phenotyping and provide our own experience with using ISS as a supportive tool to classical FC and demonstrate the compatibility between FC and ISS photometric analysis as well as the advantages of using ISS to confirm FC results.

Electron cryotomography

Electron cryotomography is an emerging technique that allows the structures of unique biological objects such as individual macromolecules, viruses, and even small whole cells to be reconstructed in their near-native states in three dimensions (3-D) to an approximate 5-nm resolution. The required instrumentation, sample preparation and limitations, data collection, typical results, and future prospects are summarized briefly.

Electron microscopy of integrins

Integrins are a family of heterodimeric, cell-surface receptors that mediate interactions between the cytoskeleton and the extracellular matrix. We have used electron microscopy and single-particle image analysis combined with molecular modeling to investigate the structures of the full-length integrin alpha(IIb)beta(3) and the ectodomain of alpha(V)beta(3) in a complex with fibronectin. The full-length integrin alpha(IIb)beta(3) is purified from human platelets by ion exchange and gel filtration chromatography in buffers containing the detergent octyl-beta-D-glucopyranoside, whereas the recombinant ectodomain of alpha(V)beta(3) is soluble in aqueous buffer. Transmission electron microscopy is performed either in negative stain, where the protein is embedded in a heavy metal such as uranyl acetate, or in the frozen-hydrated state, where the sample is flash-frozen such that the buffer is vitrified and native conditions are preserved. Individual integrin particles are selected from low-dose micrographs, either by manual identification or an automated method using a cross-correlation search of the micrograph against a set of reference images. Due to the small size of integrin heterodimers (approximately 250 kDa) and the low electron dose required to minimize beam damage, the signal-to-noise level of individual particles is quite low, both by negative-stain electron microscopy and electron cryomicroscopy. Consequently, it is necessary to average many particle images with equivalent views. The particle images are subjected to reference-free alignment and classification, in which the particles are aligned to a common view and further grouped by statistical methods into classes with common orientations. Assessment of the structure from a set of two-dimensional averaged projections is often difficult, and a further three-dimensional (3D) reconstruction analysis is performed to classify each particle as belonging to a specific projection from a single 3D model. The 3D reconstruction algorithm is an iterative projection-matching routine in which the classified particles are used to construct a new, 3D map for the next iteration. Docking of known high-resolution structures of individual subdomains within the molecular envelope of the 3D EM map is used to derive a pseudoatomic model of the integrin complex. This approach of 3D EM image analysis and pseudoatomic modeling is a powerful strategy for exploring the structural biology of transmembrane signaling by integrins because it is likely that multiple conformational states will be difficult to crystallize, whereas the different states should be amenable to electron cryomicroscopy.

3-D ultrastructure of O. tauri: electron cryotomography of an entire eukaryotic cell

The hallmark of eukaryotic cells is their segregation of key biological functions into discrete, membrane-bound organelles. Creating accurate models of their ultrastructural complexity has been difficult in part because of the limited resolution of light microscopy and the artifact-prone nature of conventional electron microscopy. Here we explored the potential of the emerging technology electron cryotomography to produce three-dimensional images of an entire eukaryotic cell in a near-native state. Ostreococcus tauri was chosen as the specimen because as a unicellular picoplankton with just one copy of each organelle, it is the smallest known eukaryote and was therefore likely to yield the highest resolution images. Whole cells were imaged at various stages of the cell cycle, yielding 3-D reconstructions of complete chloroplasts, mitochondria, endoplasmic reticula, Golgi bodies, peroxisomes, microtubules, and putative ribosome distributions in-situ. Surprisingly, the nucleus was seen to open long before mitosis, and while one microtubule (or two in some predivisional cells) was consistently present, no mitotic spindle was ever observed, prompting speculation that a single microtubule might be sufficient to segregate multiple chromosomes.

Computational resources for cryo-electron tomography in Bsoft

The Bsoft package [Heymann, J.B., Belnap, D.M., 2007. Bsoft: image processing and molecular modeling for electron microscopy. J. Struct. Biol. 157, 3-18] has been enhanced by adding utilities for processing electron tomographic (ET) data; in particular, cryo-ET data characterized by low contrast and high noise. To handle the high computational load efficiently, a workflow was developed, based on the database-like parameter handling in Bsoft, aimed at minimizing user interaction and facilitating automation. To the same end, scripting elements distribute the processing among multiple processors on the same or different computers. The resolution of a tomogram depends on the precision of projection alignment, which is usually based on pinpointing fiducial markers (electron-dense gold particles). Alignment requires accurate specification of the tilt axis, and our protocol includes a procedure for determining it to adequate accuracy. Refinement of projection alignment provides information that allows assessment of its precision, as well as projection quality control. We implemented a reciprocal space algorithm that affords an alternative to back-projection or real space algorithms for calculating tomograms. Resources are also included that allow resolution assessment by cross-validation (NLOO2D); denoising and interpretation; and the extraction, mutual alignment, and averaging of tomographic sub-volumes.

3D electron microscopy of biological nanomachines: principles and applications

Transmission electron microscopy is a powerful technique for studying the three-dimensional (3D) structure of a wide range of biological specimens. Knowledge of this structure is crucial for fully understanding complex relationships among macromolecular complexes and organelles in living cells. In this paper, we present the principles and main application domains of 3D transmission electron microscopy in structural biology. Moreover, we survey current developments needed in this field, and discuss the close relationship of 3D transmission electron microscopy with other experimental techniques aimed at obtaining structural and dynamical information from the scale of whole living cells to atomic structure of macromolecular complexes.

How electron cryotomography is opening a new window onto prokaryotic ultrastructure

Electron cryotomography is an emerging technology that enables thin samples, including small intact prokaryotic cells, to be imaged in three dimensions in a near-native 'frozen-hydrated' state to a resolution sufficient to recognize very large macromolecular complexes in situ. Following years of visionary technology development by a few key pioneers, several laboratories are now using the technique to produce biological results of major significance in the field of prokaryotic ultrastructure. Recent discoveries have included the surprising generality and complexity of the cytoskeleton, the connectivity of key membrane compartments, the location and architecture of large macromolecular machines such as the ribosome and flagellar motors, and the structure of some extraordinary external appendages. Through further technology development, identification of the most revealing model systems and sustained effort, electron cryotomography is poised to help resolve many fundamentally important questions about prokaryotic ultrastructure.

Annotating the human proteome: Beyond establishing a parts list

The completion of the human genome has shifted the attention from deciphering the sequence to the identification and characterisation of the functional components, including genes. Improved gene prediction algorithms, together with the existing transcript and protein information, have enabled the identification of most exons in a genome. Availability of the 'parts list' has fostered the development of experimental approaches to systematically interrogate gene function on the genome, transcriptome and proteome level. Studying gene function at the protein level is vital to the understanding of how cells perform their functions as variations in protein isoforms and protein quantity which may underlie a change in phenotype can often not be deduced from sequence or transcript level genomics experiments alone. Recent advancements in proteomics have afforded technologies capable of measuring protein expression, post-translational modifications of these proteins, their subcellular localisation and assembly into complexes and pathways. Although an enormous amount of data already exists on the function of many human proteins, much of it is scattered over multiple resources. Public domain databases are therefore required to manage and collate this information and present it to the user community in both a human and machine readable manner. Of special importance here is the integration of heterogeneous data to facilitate the creation of resources that go beyond a mere parts list.

Three-dimensional cryotransmission electron microscopy of cells and organelles

Cryoelectron microscopy of frozen-hydrated specimens is currently the only available technique for determining the "native" three-dimensional ultrastructure of individual examples of organelles and cells. Two techniques are available, stereo pair imaging and electron tomography, the latter providing full three-dimensional information about the specimen. A resolution of 4 to 10 nm can currently be obtained with cryotomography. We describe specimen preparation by means of plunge-freezing, which is straightforward and rapid compared with conventional EM techniques. We detail the considerations and preparation needed for successful cryotomography. Frozen-hydrated specimens are very radiation-sensitive and have low contrast because they lack heavy metal stains. The total electron dose that can be applied without damage to the specimen at a given resolution must be estimated, and this dose is fractionated among the images in the tilt series. The desired resolution determines the number and magnification of the images in the tilt series, as well as the objective lens defocus used for phase contrast imaging. The combination of the desired resolution and the maximum number of images into which a given dose can be fractionated sets an upper limit on specimen thickness. Because of these constraints, careful choice of imaging conditions, use of a sensitive CCD camera system, and microscope automation, are important requirements for conducting cryoelectron tomography.

Current and future issues in the manufacturing and development of monoclonal antibodies

Despite a slow beginning, monoclonal antibodies have had many successes over the past decade. It is important that these successes continue, bringing more products for more indications to market. Although manufacturing is not the most common cause of product failure, product quality issues can delay antibody development. Manufacturing has depended on the triad of process validation, process control and product testing. Applying product knowledge proactively to manufacturing (quality by design) may allow greater flexibility and maintain or improve product quality. An integrated approach to biological characterization is an important aspect of product knowledge. Greater product knowledge also facilitates development in other disciplines. Independent of manufacturing strategy, there are a number of regulatory hurdles in initial and ongoing antibody development. These are described to help prevent unnecessary delays.

Electron tomography of membrane-bound cellular organelles

Electron microscope tomography produces three-dimensional reconstructions and has been used to image organelles both isolated and in situ, providing new insight into their structure and function. It is analogous to the various tomographies used in medical imaging. Compared with light microscopy, electron tomography offers an improvement in resolution of 30- to 80-fold and currently ranges from 3 to 8 nm, thus filling the gap between high-resolution structure determinations of isolated macromolecules and larger-scale studies on cells and tissues by light microscopy. Here, we provide an introduction to electron tomography and applications of the method in characterizing organelle architecture that also show its power for suggesting functional significance. Further improvements in labeling modalities, imaging tools, specimen preparation, and reconstruction algorithms promise to increase the quality and breadth of reconstructions by electron tomography and eventually to allow the mapping of the cellular proteomes onto detailed three-dimensional models of cellular structure.

Site-specific 3D imaging of cells and tissues with a dual beam microscope

Current approaches to 3D imaging at subcellular resolution using confocal microscopy and electron tomography, while powerful, are limited to relatively thin and transparent specimens. Here we report on the use of a new generation of dual beam electron microscopes capable of site-specific imaging of the interior of cellular and tissue specimens at spatial resolutions about an order of magnitude better than those currently achieved with optical microscopy. The principle of imaging is based on using a focused ion beam to create a cut at a designated site in the specimen, followed by viewing the newly generated surface with a scanning electron beam. Iteration of these two steps several times thus results in the generation of a series of surface maps of the specimen at regularly spaced intervals, which can be converted into a three-dimensional map of the specimen. We have explored the potential of this sequential "slice-and-view" strategy for site-specific 3D imaging of frozen yeast cells and tumor tissue, and establish that this approach can identify the locations of intracellular features such as the 100 nm-wide yeast nuclear pore complex. We also show that 200 nm thick sections can be generated in situ by "milling" of resin-embedded specimens using the ion beam, providing a valuable alternative to manual sectioning of cells and tissues using an ultramicrotome. Our results demonstrate that dual beam imaging is a powerful new tool for cellular and subcellular imaging in 3D for both basic biomedical and clinical applications.

Automated Interpretation of Protein Subcellular Location Patterns

Proteomics is a major current focus of biomedical research, and location proteomics is the important branch of proteomics that systematically studies the subcellular distributions for all proteins expressed in a given cell type. Fluorescence microscopy of labeled proteins is currently the main methodology to obtain location information. Traditionally, microscope images are analyzed by visual inspection, which suffers from inefficiency and inconsistency. Automated and objective interpretation approaches are therefore needed for location proteomics. In this article, we briefly review recent advances in automated imaging interpretation tools, including supervised classification (which assigns location pattern labels to previously unseen images), unsupervised clustering (which groups proteins based on the similarity among their subcellular distributions), and additional statistical tools that can aid cell and molecular biologists who use microscopy in their work.

Unusual Axonemes of Hexapod Spermatozoa

Hexapod spermatozoa exhibit a great variation in their axoneme structure. The 9+2 pattern organization is present in a few basal taxa and in some derived groups. In most hexapods, a crown of nine accessory microtubules surrounds the 9+2 array, giving rise to the so-called 9+9+2 pattern. This general organization, however, displays a number of modifications in several taxa. In this review, the main variations concerning the number and localization of the accessory tubules, microtubular doublets, central microtubules, dynein arms, and axonemal length are summarized. We discuss the phylogenetic significance of all this structural information as well as the current hypotheses relating the sperm size and sperm polymorphism with reproductive success of some hexapod species. Also described are the biochemical data and the motility patterns which are currently known on some peculiar aberrant axonemes, in light of the contribution these models may give to the comprehension of the general functioning of the conventional 9+2 axoneme. Finally, we summarize methodological developments for the study of axoneme ultrastructure and the new opportunities for the molecular analysis of hexapod axonemes.

Electron Cryotomography of the E. coli Pyruvate and 2-Oxoglutarate Dehydrogenase Complexes

The E. coli pyruvate and 2-oxoglutarate dehydrogenases are two closely related, large complexes that exemplify a growing number of multiprotein "machines" whose domains have been studied extensively and modeled in atomic detail, but whose quaternary structures have remained unclear for lack of an effective imaging technology. Here, electron cryotomography was used to show that the E1 and E3 subunits of these complexes are flexibly tethered approximately 11 nm away from the E2 core. This result demonstrates unambiguously that electron cryotomography can reveal the relative positions of features as small as 80 kDa in individual complexes, elucidating quaternary structure and conformational flexibility.

Key Golgi factors for structural and functional maturation of bunyamwera virus

Several complex enveloped viruses assemble in the membranes of the secretory pathway, such as the Golgi apparatus. Among them, bunyaviruses form immature viral particles that change their structure in a trans-Golgi-dependent manner. To identify key Golgi factors for viral structural maturation, we have purified and characterized the three viral forms assembled in infected cells, two intracellular intermediates and the extracellular mature virion. The first viral form is a pleomorphic structure with fully endo-beta-N-acetylglucosaminidase H (Endo-H)-sensitive, nonsialylated glycoproteins. The second viral intermediate is a structure with hexagonal and pentagonal contours and partially Endo-H-resistant glycoproteins. Sialic acid is incorporated into the small glycoprotein of this second viral form. Growing the virus in glycosylation-deficient cells confirmed that acquisition of Endo-H resistance but not sialylation is critical for the trans-Golgi-dependent structural maturation and release of mature viruses. Conformational changes in viral glycoproteins triggered by changes in sugar composition would then induce the assembly of a compact viral particle of angular contours. These structures would be competent for the second maturation step, taking place during exit from cells, that originates fully infectious virions.

Microscopy and single molecule detection in photosynthesis

Progress in various fields of microscopy techniques brought up enormous possibilities to study the photosynthesis down to the level of individual pigment-protein complexes. The aim of this review is to present recent developments in the photosynthesis research obtained using such highly advanced techniques. Three areas of microscopy techniques covering optical microscopy, electron microscopy and scanning probe microscopy are reviewed. Whereas the electron microscopy and scanning probe microscopy are used in photosynthesis mainly for structural studies of photosynthetic pigment-protein complexes, the optical microscopy is used also for functional studies.

A “flip–flop” rotation stage for routine dual-axis electron cryotomography

Electron cryotomography can be used to solve the three-dimensional structures of individual large macromolecules, assemblies, and even small intact cells to medium (approximately 4-8 nm) resolution in a near-native state, but restrictions in the range of accessible views are a major limitation. Here we report on the design, characterization, and demonstration of a new "flip-flop" rotation stage that allows facile and routine collection of two orthogonal tilt-series of cryosamples. Single- and dual-axis tomograms of a variety of samples are compared to illustrate qualitatively the improvement produced by inclusion of the second tilt-series. Exact quantitative expressions are derived for the volume of the remaining "missing pyramid" in reciprocal space. When orthogonal tilt-series are recorded to +/-65 degrees in each direction, as this new cryostage permits, only 11% of reciprocal space is left unmeasured. The tomograms suggest that further improvement could be realized, however, through better software to align and merge dual-axis tilt-series of cryosamples.

An energy-based three-dimensional segmentation approach for the quantitative interpretation of electron tomograms

Electron tomography allows for the determination of the three-dimensional structures of cells and tissues at resolutions significantly higher than that which is possible with optical microscopy. Electron tomograms contain, in principle, vast amounts of information on the locations and architectures of large numbers of subcellular assemblies and organelles. The development of reliable quantitative approaches for the analysis of features in tomograms is an important problem, and a challenging prospect due to the low signal-to-noise ratios that are inherent to biological electron microscopic images. This is, in part, a consequence of the tremendous complexity of biological specimens. We report on a new method for the automated segmentation of HIV particles and selected cellular compartments in electron tomograms recorded from fixed, plastic-embedded sections derived from HIV-infected human macrophages. Individual features in the tomogram are segmented using a novel robust algorithm that finds their boundaries as global minimal surfaces in a metric space defined by image features. The optimization is carried out in a transformed spherical domain with the center an interior point of the particle of interest, providing a proper setting for the fast and accurate minimization of the segmentation energy. This method provides tools for the semi-automated detection and statistical evaluation of HIV particles at different stages of assembly in the cells and presents opportunities for correlation with biochemical markers of HIV infection. The segmentation algorithm developed here forms the basis of the automated analysis of electron tomograms and will be especially useful given the rapid increases in the rate of data acquisition. It could also enable studies of much larger data sets, such as those which might be obtained from the tomographic analysis of HIV-infected cells from studies of large populations.

A component-based software environment for visualizing large macromolecular assemblies

The interactive visualization of large biological assemblies poses a number of challenging problems, including the development of multiresolution representations and new interaction methods for navigating and analyzing these complex systems. An additional challenge is the development of flexible software environments that will facilitate the integration and interoperation of computational models and techniques from a wide variety of scientific disciplines. In this paper, we present a component-based software development strategy centered on the high-level, object-oriented, interpretive programming language: Python. We present several software components, discuss their integration, and describe some of their features that are relevant to the visualization of large molecular assemblies. Several examples are given to illustrate the interoperation of these software components and the integration of structural data from a variety of experimental sources. These examples illustrate how combining visual programming with component-based software development facilitates the rapid prototyping of novel visualization tools.

Miniaturization in functional genomics and proteomics

Proteins are the key components of the cellular machinery responsible for processing changes that are ordered by genomic information. Analysis of most human proteins and nucleic acids is important in order to decode the complex networks that are likely to underlie many common diseases. Significant improvements in current technology are also required to dissect the regulatory processes in high-throughtput and with low cost. Miniaturization of biological assays is an important prerequisite to achieve these goals in the near future.

Bridging the imaging gap: visualizing subcellular architecture with electron tomography

Transmission electron microscopy is a powerful tool that is used to explore the internal structure of tissues, cells, organelles and macromolecular complexes. By integrating data from a series of images in which the orientation of the specimen is progressively varied relative to the incident electron beam it is also possible to extend electron microscopic imaging into the third dimension. This approach, commonly referred to as electron tomography, has been greatly aided in recent years by advances in technology for imaging specimens at cryogenic temperatures, as well as by substantial progress in procedures for automated data collection and image processing. The intense pace of developments in this field is inspired, in a large part, by the hope that the quality of the data will ultimately be good enough to allow interpretation of tomograms of cells, organelles, bacteria and viruses in terms of the three-dimensional spatial arrangements of the constituent molecules.

High-throughput film-densitometry: an efficient approach to generate large data sets

A film-handling machine (robot) has been built which can, in conjunction with a commercially available film densitometer, exchange and digitize over 300 electron micrographs per day. Implementation of robotic film handling effectively eliminates the delay and tedium associated with digitizing images when data are initially recorded on photographic film. The modulation transfer function (MTF) of the commercially available densitometer is significantly worse than that of a high-end, scientific microdensitometer. Nevertheless, its signal-to-noise ratio (S/N) is quite excellent, allowing substantial restoration of the output to "near-to-perfect" performance. Due to the large area of the standard electron microscope film that can be digitized by the commercial densitometer (up to 10,000 x 13,680 pixels with an appropriately coded holder), automated film digitization offers a fast and inexpensive alternative to high-end CCD cameras as a means of acquiring large amounts of image data in electron microscopy.

Peach: A Simple Perl-Based System for Distributed Computation and Its Application to Cryo-EM Data Processing

A simple distributed processing system named "Peach" was developed to meet the rising computational demands of modern structural biology (and other) laboratories without additional expense by using existing hardware resources more efficiently. A central server distributes jobs to idle workstations in such a way that each computer is used maximally, but without disturbing intermittent interactive users. As compared to other distributed systems, Peach is simple, easy to install, easy to administer, easy to use, scalable, and robust. While it was designed to queue and distribute large numbers of small tasks to participating computers, it can also be used to send single jobs automatically to the fastest currently available computer and/or survey the activity of an entire laboratory's computers. Tests of robustness and scalability are reported, as are three specific electron cryomicroscopy applications where Peach enabled projects that would not otherwise have been feasible without an expensive, dedicated cluster.

Three-dimensional structure of HIV-1 virus-like particles by electron cryotomography

While the structures of nearly every HIV-1 protein are known in atomic detail from X-ray crystallography and NMR spectroscopy, many questions remain about how the individual proteins are arranged in the mature infectious viral particle. Here, we report the three-dimensional structures of individual HIV-1 virus-like particles (VLPs) as obtained by electron cryotomography. These reconstructions revealed that while the structures and positions of the conical cores within each VLP were unique, they exhibited several surprisingly consistent features, including similarities in the size and shape of the wide end of the capsid (the "base"), uniform positioning of the base and other regions of the capsid 11nm away from the envelope/MA layer, a cone angle that typically varied from 24 degrees to 18 degrees around the long axis of the cone, and an internal density (presumably part of the NC/RNA complex) cupped within the base. Multiple and nested capsids were observed. These results support the fullerene cone model for the viral capsid, indicate that viral maturation involves a free re-organization of the capsid shell rather than a continuous condensation, imply that capsid assembly is both concentration-driven and template-driven, suggest that specific interactions exist between the capsid and the adjacent envelope/MA and NC/RNA layers, and show that a particular capsid shape is favored strongly in-vivo.

Novel techniques in electron microscopy

Emerging techniques in electron microscopy promise to yield a wide range of new information about the nervous system. Aided by the development of detectors, electron optics, energy filters, computer automation and preparative methods, electron tomography now provides three-dimensional structures over a scale ranging from single receptor molecules to synapses and neurons. To relate structure to function, a variety of correlative methods are being developed, including protein tags observable both by light microscopy of living cells and, subsequently, by electron microscopy. It is also becoming possible to measure functionally important ions like Ca(2+) in cellular compartments at a scale of about 10 nm by exploiting new advances in electron energy loss and X-ray spectroscopic imaging.