A new look at Weibel-Palade body structure in endothelial cells using electron tomography

Multimers of von Willebrand Factor (vWF), a protein mediating blood clotting in response to vascular injury, are stored as tubular structures by endothelial cells in specific organelles, the Weibel–Palade Bodies (WPBs). To date very little is known about the 3D structure of WPBs in relation to the organization of the tubules. Therefore, we have initiated a thorough electron microscopic study in human umbilical vein endothelial cells (HUVECs) using electron tomography to gain further understanding of the ultrastructure of WPBs. We found that in addition to the well-documented cigar-shape, WPBs adopt irregular forms, which appeared to result from homotypic fusion. In transverse views of WPBs the tubular striations appear evenly spaced, which indicates a high level of organization that is likely to involve an underlying scaffold of structural proteins. Additionally, we found that the tubular striations twisted in an orderly fashion, suggesting that they are stored within the WPBs by a spring-loading mechanism. Altogether these data suggest that WPBs undergo a relatively complex maturation process involving homotypic fusion. Although the mechanism of assembly of vWF multimers into tubules is still unknown, the curled arrangement of the tubules within WPBs suggests a high degree of folding of the protein inside the organelle.     

Single-particle reconstruction using L(2)-gradient flow

In this paper, we present an iterative algorithm for reconstructing a three-dimensional density function from a set of two dimensional electron microscopy images. By minimizing an energy functional consisting of a fidelity term and a regularization term, an L²-gradient flow is derived. The flow is integrated by a finite element method in the spatial direction and an explicit Euler scheme in the temporal direction. Our method compares favorably with those of the weighted back projection, Fourier method, algebraic reconstruction technique and simultaneous iterative reconstruction technique.     

Stereology meets electron tomography: towards quantitative 3D electron microscopy

Stereological tools are the gold standard for accurate (i.e., unbiased) and precise quantification of any microscopic sample. The past decades have provided a broad spectrum of tools to estimate a variety of parameters such as volumes, surfaces, lengths, and numbers. Some of them require pairs of parallel sections that can be produced by either physical or optical sectioning, with optical sectioning being much more efficient when applicable. Unfortunately, transmission electron microscopy could not fully profit from these riches, mainly because of the large depth of field. Hence, optical sectioning was a long-time desire for electron microscopists. This desire was fulfilled with the development of electron tomography that yield stacks of slices from electron microscopic sections. Now, parallel optical slices of a previously unimagined small thickness (2-5 nm axial resolution) can be produced. These optical slices minimize problems related to overprojection effects, and allow for direct stereological analysis, e.g., volume estimation with the Cavalieri principle and number estimation with the optical disector method. Here, we demonstrate that the symbiosis of stereology and electron tomography is an easy and efficient way for quantitative analysis at the electron microscopic level. We call this approach quantitative 3D electron microscopy.     

Segmentation of electron tomographic data sets using fuzzy set theory principles

In electron tomography the reconstructed density function is typically corrupted by noise and artifacts. Under those conditions, separating the meaningful regions of the reconstructed density function is not trivial. Despite development efforts that specifically target electron tomography manual segmentation continues to be the preferred method. Based on previous good experiences using a segmentation based on fuzzy logic principles (fuzzy segmentation) where the reconstructed density functions also have low signal-to-noise ratio, we applied it to electron tomographic reconstructions. We demonstrate the usefulness of the fuzzy segmentation algorithm evaluating it within the limits of segmenting electron tomograms of selectively stained, plastic embedded spiny dendrites. The results produced by the fuzzy segmentation algorithm within the framework presented are encouraging.     

Rapid tilt-series acquisition for electron cryotomography

Using a new Titan Krios stage equipped with a single-axis holder, we developed two methods to accelerate the collection of tilt-series. We demonstrate a continuous-tilting method that can record a tilt-series in seconds, but with loss of details finer than ～4?nm. We also demonstrate a fast-incremental method that can record a tilt-series several-fold faster than current methods and with similar resolution. We characterize the utility of both methods in real biological electron cryotomography workflows. We identify opportunities for further improvements in hardware and software and speculate on the impact such advances could have on structural biology.     

Fluorescent labeling of resin-embedded sections for correlative electron microscopy using tomography-based contrast enhancement

Locating areas of interest by electron microscopy can be laborious. This is particularly true for electron tomography, where the use of thicker sections may obscure relevant details in the projection images. We evaluated the applicability of fluorescent probes to thin plastic sections, in combination with fluorescence microscopy, as an aid in selecting areas for subsequent electron microscopic analysis. We show that pre-embedding labeling of DNA and RNA with acridine orange yielded a predominant nuclear stain. The stain greatly reduced the time needed to scan sections for mitotic cells, or cells with characteristic nuclei such as neutrophils. Post-embedding labeling with SYTOX green yielded a nuclear stain comparable to acridine orange, and wheat germ agglutinin (WGA) conjugated to Alexa Fluor 488 labeled mucous granules and the Golgi area in intestinal goblet cells. The fluorescent labels were visualized directly on sections on electron microscope grids. It was therefore possible to establish a coordinate system based on the position of the grid bars, allowing for easy retrieval of selected areas. Because the fluorescent probes were incompatible with osmium tetroxide treatment, contrast in the sections was faint. We propose a simplified electron tomography procedure for the generation of 2D views with enhanced contrast and resolution.     

Performance and limitations of positron emission tomography (PET) scanners for imaging very low activity sources

Emerging applications for positron emission tomography (PET) may require the ability to image very low activity source distributions in the body. The performance of clinical PET scanners in the regime where activity in the field of view is <1 MBq has not previously been explored. In this study, we compared the counting rate performance of two clinical PET/CT scanners, the Siemens Biograph Reveal 16 scanner which is based on lutetium oxyorthosilicate (LSO) detectors and the GE Discovery-ST scanner which is based on bismuth germanate (BGO) detectors using a modified National Electrical Manufacturers Association (NEMA) NU 2-2007 protocol. Across the activity range studied (2–100 kBq/mL in a 5.5 mL line source in the NEMA scatter phantom), the BGO-based scanner significantly outperformed the LSO-based scanner. This was largely due to the effect of background counts emanating from naturally occurring but radioactive ¹⁷⁶Lu within the LSO detector material, which dominates the observed counting rate at the lowest activities. Increasing the lower energy threshold from 350 keV to 425 keV in an attempt to reduce this background did not significantly improve the measured NECR performance. The measured singles rate due to ¹⁷⁶Lu emissions within the scanner energy window was also found to be dependent on temperature, and to be affected by the operation of the CT component, making approaches to correct or compensate for the background more challenging. We conclude that for PET studies in a very low activity range, BGO-based scanners are likely to have better performance because of the lack of significant background.     

Reprint of "Three-dimensional elemental mapping of phosphorus by quantitative electron spectroscopic tomography (QuEST)" [J. Struct. Biol. 160 (2007) 35-48

We describe the development of quantitative electron spectroscopic tomography (QuEST), which provides 3-D distributions of elements on a nanometer scale. Specifically, it is shown that QuEST can be applied to map the distribution of phosphorus in unstained sections of embedded cells. A series of 2-D elemental maps is derived from images recorded in the energy filtering transmission electron microscope for a range of specimen tilt angles. A quantitative 3-D elemental distribution is then reconstructed from the elemental tilt series. To obtain accurate quantitative elemental distributions it is necessary to correct for plural inelastic scattering at the phosphorus L_2,3 edge, which is achieved by acquiring unfiltered and zero-loss images at each tilt angle. The data are acquired automatically using a cross correlation technique to correct for specimen drift and focus change between successive tilt angles. An algorithm based on the simultaneous iterative reconstruction technique (SIRT) is implemented to obtain quantitative information about the number of phosphorus atoms associated with each voxel in the reconstructed volume. We assess the accuracy of QuEST by determining the phosphorus content of ribosomes in a eukaryotic cell, and then apply it to estimate the density of nucleic acid in chromatin of the cell’s nucleus. From our experimental data, we estimate that the sensitivity for detecting phosphorus is 20 atoms in a 2.7 nm-sized voxel.     

Three-dimensional structure of the KdpFABC complex of Escherichia coli by electron tomography of two-dimensional crystals

The KdpFABC complex (Kdp) functions as a K⁺ pump in Escherichia coli and is a member of the family of P-type ATPases. Unlike other family members, Kdp has a unique oligomeric composition and is notable for segregating K⁺ transport and ATP hydrolysis onto separate subunits (KdpA and KdpB, respectively). We have produced two-dimensional crystals of the KdpFABC complex within reconstituted lipid bilayers and determined its three-dimensional structure from negatively stained samples using a combination of electron tomography and real-space averaging. The resulting map is at a resolution of 2.4 nm and reveals a dimer of Kdp molecules as the asymmetric unit; however, only the cytoplasmic domains are visible due to the lack of stain penetration within the lipid bilayer. The sizes of these cytoplasmic domains are consistent with Kdp and, using a pseudo-atomic model, we have described the subunit interactions that stabilize the Kdp dimer within the larger crystallographic array. These results illustrate the utility of electron tomography in structure determination of ordered assemblies, especially when disorder is severe enough to hamper conventional crystallographic analysis.     

Reprint of “Stereology meets electron tomography: towards quantitative 3D electron microscopy” [J. Struct. Biol. 159 (2007) 443–450]

Stereological tools are the gold standard for accurate (i.e., unbiased) and precise quantification of any microscopic sample. The past decades have provided a broad spectrum of tools to estimate a variety of parameters such as volumes, surfaces, lengths, and numbers. Some of them require pairs of parallel sections that can be produced by either physical or optical sectioning, with optical sectioning being much more efficient when applicable. Unfortunately, transmission electron microscopy could not fully profit from these riches, mainly because of the large depth of field. Hence, optical sectioning was a long-time desire for electron microscopists.This desire was fulfilled with the development of electron tomography that yield stacks of slices from electron microscopic sections. Now, parallel optical slices of a previously unimagined small thickness (2–5 nm axial resolution) can be produced. These optical slices minimize problems related to overprojection effects, and allow for direct stereological analysis, e.g., volume estimation with the Cavalieri principle and number estimation with the optical disector method.Here, we demonstrate that the symbiosis of stereology and electron tomography is an easy and efficient way for quantitative analysis at the electron microscopic level. We call this approach quantitative 3D electron microscopy.     

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.     

Performance of electron acceptors in catholyte of a two-chambered microbial fuel cell using anion exchange membrane

The performance of the cathodic electron acceptors (CEA) used in the two-chambered microbial fuel cell (MFC) was in the following order: potassium permanganate (1.11 V; 116.2 mW/m²) > potassium persulfate (1.10 V; 101.7 mW/m²) > potassium dichromate, K₂Cr₂O₇ (0.76 V; 45.9 mW/m²) > potassium ferricyanide (0.78 V; 40.6 mW/m²). Different operational parameters were considered to find out the performance of the MFC like initial pH in aqueous solutions, concentrations of the electron acceptors, phosphate buffer and aeration. Potassium persulfate was found to be more suitable out of the four electron acceptors which had a higher open circuit potential (OCP) but sustained the voltage for a much longer period than permanganate. Chemical oxygen demand (COD) reduction of 59% was achieved using 10 mM persulfate in a batch process. RALEX™ AEM-PES, an anion exchange membrane (AEM), performed better in terms of power density and OCP in comparison to Nafion®117 Cation Exchange Membrane (CEM).     

Investigation of the electron density of iridium(I) Vaska-type complexes using DFT calculations and structural results: Structure of trans-carbonyl-chloro-bis(tricyclohexylphosphine)-iridium(I)

[Ir(CO)Cl(PCy₃)₂] was obtained by the slow attack of 1,2-dichloromethane on (Bu₄N)[Ir₂(μ-Dcbp)(CO)₂(PCy₃)₂] (Dcbp = 3,5-dicarboxylatepyrazole). The Ir-CO, Ir-Cl and Ir-P bond distances are 1.778(10), 2.374(3) and 2.3486(8) Å, respectively. The Ir-P bond distances for a number of different Vaska complexes indicate the shortest bond distances for phoshines containing electron withdrawing groups. An excellent correlation between DFT (OLYP/ZORA/TZP) and experimental structures is obtained as reflected by the RMSD values (H excluded) of between 0.083 and 0.268 Å for the different complexes studied. The calculated Ir-P bond distances and ν(CO) stretching frequencies closely follow the trends obtained from the experimental results.     

Three-dimensional organization of pKi-67: a comparative fluorescence and electron tomography study using FluoroNanogold.

The monoclonal antibody (MAb) Ki-67 is routinely used in clinical studies to estimate the growth fraction of tumors. However, the role of pKi-67, the protein detected by the Ki-67 MAb, remains elusive, although some biochemical data strongly suggest that it might organize chromatin. To better understand the functional organization of pKi-67, we studied its three-dimensional distribution in interphase cells by confocal microscopy and electron tomography. FluoroNanogold, a single probe combining a dense marker with a fluorescent dye, was used to investigate pKi-67 organization at the optical and ultrastructural levels. Observation by confocal microscopy followed by 3D reconstruction showed that pKi-67 forms a shell around the nucleoli. Double labeling experiments revealed that pKi-67 co-localizes with perinucleolar heterochromatin. Electron microscopy studies confirmed this close association and demonstrated that pKi-67 is located neither in the fibrillar nor in the granular components of the nucleolus. Finally, spatial analyses by electron tomography showed that pKi-67 forms cords 250-300 nm in diameter, which are themselves composed of 30-50-nm-thick fibers. These detailed comparative in situ analyses strongly suggest the involvement of pKi-67 in the higher-order organization of perinucleolar chromatin.     

JUST (Java User Segmentation Tool) for semi-automatic segmentation of tomographic maps

We are presenting a program for interactive segmentation of tomographic maps, based on objective criteria so as to yield reproducible results. The strategy starts with the automatic segmentation of the entire volume with the watershed algorithm in 3D. The watershed regions are clustered successively by supervised classification, allowing the segmentation of known organelles, such as membranes, vesicles and microtubules. These organelles are processed with topological models and input parameters manually derived from the tomograms. After known organelles are extracted from the volume, all other watershed regions can be organized into homogeneous assemblies on the basis of their densities. To complete the process, all voxels in the volume are assigned either to the background or individual structures, which can then be extracted for visualization with any rendering technique. The user interface of the program is written in Java, and computational routines are written in C. For some operations, involving the visualization of the tomogram, we refer to existing software, either open or commercial. While the program runs, a history file is created, that allows all parameters and other data to be saved for the purposes of comparison or exchange. Initially, the program was developed for the segmentation of synapses, and organelles belonging to these structures have thus far been the principal targets modeled with JUST. Since each organelle is clustered independently from the rest of the volume, however, the program can accommodate new models of different organelles as well as tomograms of other types of preparations of tissue, such as citoskeletal components in vitreous ice.     

A procedure to deposit fiducial markers on vitreous cryo-sections for cellular tomography

We describe a novel approach for the accurate alignment of images in electron tomography of vitreous cryo-sections. Quantum dots, suspended in organic solvents at cryo-temperatures, are applied directly onto the sections and are subsequently used as fiducial markers to align the tilt series. Data collection can be performed from different regions of the vitreous sections, even when the sections touch the grid only at a few places. We present high-resolution tomograms of some organelles in cryo-sections of human skin cells using this method. The average error in image alignment was about 1nm and the resolution was estimated to be 5-7nm. Thus, the use of section-attached quantum dots as fiducial markers in electron tomography of vitreous cryo-sections facilitates high-resolution in situ 3D imaging of organelles and macromolecular complexes in their native hydrated state.     

流行性感冒裂解疫苗免疫原性试验及电镜观察

实验报告了以三硝基甲苯X-100(Triton X-100)为裂解剂对流行性感冒病毒裂解效果的电镜观察结果及裂解疫苗的免疫原性。通过对病毒纯化、裂解、再纯化制备的3批流行性感冒裂解疫苗样品的电镜观察,表明使用此裂解剂能使疫苗中的病毒裂解完全,无完整病毒颗粒,裂解效果好。安全试验和免疫试验结果表明疫苗的安全性好,免疫效果好。     

Reprint of "Fiducial-less alignment of cryo-sections" [J. Struct. Biol. 159 (2007) 413-423

Cryo-electron tomography of vitreous sections is currently the most promising technique for visualizing arbitrary regions of eukaryotic cells or tissue at molecular resolution. Despite significant progress in the sample preparation techniques over the past few years, the three dimensional reconstruction using electron tomography is not as simple as in plunge frozen samples for various reasons, but mainly due to the effects of irradiation on the sections and the resulting poor alignment. Here, we present a new algorithm, which can provide a useful three-dimensional marker model after investigation of hundreds to thousands of observations calculated using local cross-correlation throughout the tilt series. The observations are chosen according to their coherence to a particular model and assigned to virtual markers. Through this type of measurement a merit figure can be calculated, precisely estimating the quality of the reconstruction. The merit figures of this alignment method are comparable to those obtained with plunge frozen samples using fiducial gold markers. An additional advantage of the algorithm is the implicit detection of areas in the sections that behave as rigid bodies and can thus be properly reconstructed.     

Morphological and structural studies of early mineral formation in enamel of rat incisors by electron spectroscopic imaging (ESI) and electron spectroscopic diffraction (ESD)

Morphological and structural analysis of the earliest stage of crystal formation in enamel of rat incisors, by use of energy filtering transmission electron microscopy (EFTEM), has shown needlelike crystallites with a dotlike substructure. We conclude that these dots (nanometer-sized particles) have developed at nucleating, active sites along the non-collagenous matrix proteins in enamel. Calcium and phosphate groups are bound at such active sites and develop to nuclei, which grow to these stable dots (nanometer-sized particles). The dots coalesce rapidly in longitudinal direction, along the matrix proteins, with neighbouring dots to form parallel arranged needlelike crystallites. These needles grow and coalesce in lateral directions to ribbon-platelike crystallites. In enamel most of the organic substance becomes decomposed and transported to the ameloblasts. Consequently, the ribbon-platelike crystallites can coalesce to form much thicker (hydroxy)-apatite crystals than in dentine. Already in the earliest stage of crystal formation the mineral chains of dots (nanometer-sized particles) and the needlelike crystallites show a parallel orientation in the direction of the c-axis of hydroxyapatite. This is supported by the texture of the 002 reflections in the corresponding electron spectroscopic diffraction patterns (ESD), which appear as the first Bragg reflections.     

ATOM 1.0:基于GPU的电子断层重构软件

电子断层成像技术能够在纳米尺度下重构出不具有全同性的细胞或大分子的三维结构,正受到越来越广泛的重视。针对现有电子断层成像技术中重构软件的不足,特别是迭代重构算法速度慢的缺点,我们开发了一款基于Graphic Processor Unit(GPU)平台的电子断层重构软件——ATOM,实现了图像对位、重构参数计算、三维重构及数据可视化等电子断层重构的基本功能。其中,在二维对位方面,ATOM实现了迭代的无标记平移和旋转对位;在三维重构方面,实现了背投影和多种迭代重构算法,并实现了迭代重构在GPU平台上的并行加速,获得了良好的加速比,如SIRT算法得到了47倍加速比。ATOM是绿色开源软件,可以运行在支持Qt和CUDA的所有操作系统上。ATOM为图形界面软件,结合详尽的安装及使用文档,便于用户使用。