Axial Resolution Enhancement by 4Pi Confocal Fluorescence Microscopy with Two-Photon Excitation

Confocal fluorescence microscopy and two-photon microscopy have become important techniques for the three-dimensional imaging of intact cells. Their lateral resolution is about 200–300 nm for visible light, whereas their axial resolution is significantly worse. By superimposing the spherical wave fronts from two opposing objective lenses in a coherent fashion in 4Pi microscopy, the axial resolution is greatly improved to ～100 nm. In combination with specific tagging of proteins or other cellular structures, 4Pi microscopy enables a multitude of molecular interactions in cell biology to be studied. Here, we discuss the choice of appropriate fluorescent tags for dual-color 4Pi microscopy and present applications of this technique in cellular biophysics. We employ two-color fluorescence detection of actin and tubulin networks stained with fluorescent organic dyes; mitochondrial networks are imaged using the photoactivatable fluorescent protein EosFP. A further example concerns the interaction of nanoparticles with mammalian cells.     

Conserved Fiber-Penton Base Interaction Revealed by Nearly Atomic Resolution Cryo-Electron Microscopy of the Structure of Adenovirus Provides Insight into Receptor Interaction

Adenovirus (Ad) cell attachment is initiated by the attachment of the fiber protein to a primary receptor (usually CAR or CD46). This event is followed by the engagement of the penton base protein with a secondary receptor (integrin) via its loop region, which contains an Arg-Gly-Asp (RGD) motif, to trigger virus internalization. To understand the well-orchestrated adenovirus cell attachment process that involves the fiber and the penton base, we reconstructed the structure of an Ad5F35 capsid, comprising an adenovirus type 5 (Ad5) capsid pseudotyped with an Ad35 fiber, at a resolution of approximately 4.2 Å. The fiber-penton base interaction in the cryo-electron microscopic (cryo-EM) structure of Ad5F35 is similar to that in the cryo-EM structure of Ad5, indicating that the fiber-penton base interaction of adenovirus is conserved. Our structure also confirms that the C-terminal segment of the fiber tail domain constitutes the bottom trunk of the fiber shaft. Based on the conserved fiber-penton base interaction, we have proposed a model for the interaction of Ad5F35 with its primary and secondary receptors. This model could provide insight for designing adenovirus gene delivery vectors.     

Confocal Microscopy of Microtubule Cytoskeleton in the Pollen Protoplast of Narcissus

Pollen protoplasts were isolated from the mature pollen grains of Narcissus cyclamineus using cellulase Onozuka'R-10 and pectinase in Bs medium. The microtubule cytoskeleton in the pollen protoplasts was studied using immunofluorescence and confocal microscopy. In the cortical region there was a very complex microtubule network. The network contained numerous whirl-like arrays. The microtubule bundles in the whirl-like arrays were connected with each other by smaller bundles indicating that the arrangement of the whirl-like bundles were quite well organized and not at random. From the cortex to the centre of the protoplast another microtubule network having a structure different from the one in the cortical region was present. This network was much loosely packed than the cortical network. The arrangement of the microtubule bundles near the vegetative nucleus was again different. Numerous granules appeared outside the nuclear membrane. From these granules microtubule bundles radiated towards the cytoplasm. The arrangement of the microtubule network around the generative cell showed no specialized features. But inside the cell three types of microtubule arrays were present. 1. parallel arrays, 2. network, and 3. a mixture of the two. In the bursted pollen protoplast (as a result of osmotic shock treatment )some microtubule bundles could still be found attached to the ghost. The microtubule bundles associated with the ghost were much fragmented. But some still retained their branches and junctions. In the dry cleaved samples,a number of organelles still remained attached to the membrane and they included : microtubules, microfilaments, coated vesicles, endoplasmic reticulum and numerous honey-comb-like apparatus. The honey-comb-like apparatus was named as coated pits by Traas (1984). But we feel that it is more appropriate to call this organelle the honey-comb apparatus and we also believe that this organelle may be involved in microtubule and/or microfilament organization.     

Correlation of 4Pi and Electron Microscopy to Study Transport Through Single Golgi Stacks in Living Cells with Super Resolution

Two problems have hampered the use of light microscopy for structural studies of cellular organelles for a long time: the limited resolution and the difficulty of obtaining true structural boundaries from complex intensity curves. The advent of modern high-resolution light microscopy techniques and their combination with objective image segmentation now provide us with the means to bridge the gap between light and electron microscopy in cell biology applications. In this study, we provide the first comparative correlative analysis of three-dimensional structures obtained by 4Pi microscopy and segmented by a zero-crossing procedure with those of transmission electron microscopy (TEM). The distribution within the cisternae of isolated Golgi stacks of the cargo protein procollagen 3 was mapped by both 4Pi microscopy and TEM for a detailed comparative analysis of their imaging capabilities. A high correlation was seen for the structures, indicating the particular accuracy of the 4Pi microscopy. Furthermore, for the first time, transport of a cargo molecule (vesicular stomatitis virus G protein-pEGFP) through individual Golgi stacks (labeled by galactosyl transferase-venusYFP) was visualized by 4Pi microscopy. Following the procedures validated by the correlative analysis, our transport experiments show that (i) VSVG-pEGFP rapidly enter/exit individual Golgi stacks, (ii) VSVG-pEGFP never fills the GalT-venusYFP compartments completely and (iii) the GalT-venusYFP compartment volume increases upon VSVG-pEGFP arrival. This morphological evidence supports some previous TEM-based observations of intra-Golgi transport of VSVG-pEGFP and provides new insights toward a better understanding of protein progression across Golgi stacks. Our study thus demonstrates the general applicability of super-resolution fluorescence microscopy, coupled with the zero-crossing segmentation procedure, for structural studies of suborganelle protein distributions under living cell conditions.     

三维肺部图像中疑似肺结节结构的自动提取

本文提出了一种肺部CT图像三维数据中自动提取疑似结节区域的方法。首先结合阈值分割、种子填充等方法,在三维体数据上分割出肺实质。进而利用改进的模糊C均值聚类,提取出结节及具有结节特征的血管、支气管等感兴趣区域。该工作对感兴趣区域的特征提取有重要意义,是早期肺癌计算机辅助诊断重要的一步。     

Under-exploration of Three-Dimensional Images Leads to Search Errors for Small Salient Targets

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Visualization by Immune Electron Microscopy of a 27-nm Particle Associated with Acute Infectious Nonbacterial Gastroenteritis

A 27-nm particle was observed by immune electron microscopy in an infectious stool filtrate derived from an outbreak in Norwalk, Ohio, of acute infectious nonbacterial gastroenteritis. Both experimentally and naturally infected individuals developed serological evidence of infection; this along with other evidence suggested that the particle was the etiological agent of Norwalk gastroenteritis.     

Micron-scale Resolution Optical Tomography of Entire Mouse Brains with Confocal Light Sheet Microscopy

Understanding the architecture of mammalian brain at single-cell resolution is one of the key issues of neuroscience. However, mapping neuronal soma and projections throughout the whole brain is still challenging for imaging and data management technologies. Indeed, macroscopic volumes need to be reconstructed with high resolution and contrast in a reasonable time, producing datasets in the TeraByte range. We recently demonstrated an optical method (confocal light sheet microscopy, CLSM) capable of obtaining micron-scale reconstruction of entire mouse brains labeled with enhanced green fluorescent protein (EGFP). Combining light sheet illumination and confocal detection, CLSM allows deep imaging inside macroscopic cleared specimens with high contrast and speed. Here we describe the complete experimental pipeline to obtain comprehensive and human-readable images of entire mouse brains labeled with fluorescent proteins. The clearing and the mounting procedures are described, together with the steps to perform an optical tomography on its whole volume by acquiring many parallel adjacent stacks. We showed the usage of open-source custom-made software tools enabling stitching of the multiple stacks and multi-resolution data navigation. Finally, we illustrated some example of brain maps: the cerebellum from an L7-GFP transgenic mouse, in which all Purkinje cells are selectively labeled, and the whole brain from a thy1-GFP-M mouse, characterized by a random sparse neuronal labeling.     

Cell-by-Cell Alignment of Repeated Specular Microscopy Images from the Same Eye

Purpose

Modern specular microscopes (SM) robustly depict the same central area of the corneal endothelium at different time points through a built-in fixation light. However, repeated image acquisitions slightly shift and rotate because of minute changes in head position in the chin and forehead rest. This prevents the manual retrieval of individual corneal endothelial cells (CECs) in repeated measurements because SM images usually lack obvious landmarks. We devised and validated an image registration algorithm that aligns SM images from the same eye to make corresponding CECs coincide.

Methods

We retrospectively selected 27 image pairs for the presence of significant image overlap. Each image pair had been recorded on the same day and of the same eye. We applied our registration method in each image pair. Two observers independently validated, by means of alternation flicker, that the image pairs had been correctly aligned. We also repeatedly applied our registration method on unrelated image pairs by randomly drawing images and making certain that the images did not originate from the same eye. This was done to assess the specifity of our method.

Results

All automated registrations of the same-day and same-eye image pairs were accurate. However, one single image incorrectly failed to trigger the non-match diagnosis twice in 81 registration attempts between unrelated images. As it turned out, this particular image depicted only 73 CECs. The average number of CECs was 253 (range 73–393).

Conclusion

Repeated non-contact SM images can be automatedly aligned so that the corresponding CECs coincide. Any successful alignment can be considered as proof of the retrieval of identical CECs as soon as at least 100 CEC centroids have been identified. We believe our method is the first to robustly confirm endothelial stability in individual eyes.     

Use of Peroxidatic-Enzyme Staining to Enhance Resolution of Cultured Mammalian Cells Under Phase Microscopy

Staining of glutaraldehyde-fixed mammalian cells with peroxidatic enzymes (horseradish peroxidase or horse heart cytochrome c) greatly enhances resolution of their structure under phase microscopy. The topography of cell processes and regions of intercellular contact and overlapping is resolved precisely, even in dense cultures mounted in media which ordinarily do not permit clear demonstration of these areas. The technique is therefore a useful aid to the study of cultured cells with phase optics. Labeling depends on introducing free aldehydes into cells through the use of bi functional fixatives such as glutaraldehyde. Acetone or formaldehyde fixation prevents staining, and labeling intensity is greatly diminished by pretreatment with spermine, a polyamine that reacts with glutaraldehyde. Electron microscopy reveals that peroxidase tags membranes preferentially; some areas are labeled smoothly, others in a punctate manner. Ribosomes are sharply contrasted, but nuclei remain unstained. Cytochrome c labels condensed nuclear chromatin intensely, and also stains ribosomes and portions of the cyto plamic ground substance; membranes are mostly unmarked.     

Self-Organization of the Escherichia coli Chemotaxis Network Imaged with Super-Resolution Light Microscopy

The Escherichia coli chemotaxis network is a model system for biological signal processing. In E. coli, transmembrane receptors responsible for signal transduction assemble into large clusters containing several thousand proteins. These sensory clusters have been observed at cell poles and future division sites. Despite extensive study, it remains unclear how chemotaxis clusters form, what controls cluster size and density, and how the cellular location of clusters is robustly maintained in growing and dividing cells. Here, we use photoactivated localization microscopy (PALM) to map the cellular locations of three proteins central to bacterial chemotaxis (the Tar receptor, CheY, and CheW) with a precision of 15 nm. We find that cluster sizes are approximately exponentially distributed, with no characteristic cluster size. One-third of Tar receptors are part of smaller lateral clusters and not of the large polar clusters. Analysis of the relative cellular locations of 1.1 million individual proteins (from 326 cells) suggests that clusters form via stochastic self-assembly. The super-resolution PALM maps of E. coli receptors support the notion that stochastic self-assembly can create and maintain approximately periodic structures in biological membranes, without direct cytoskeletal involvement or active transport.     

Visualizing Taste Papillae In Vivo with Scanning Electron Microscopy of a High Resolution Cast

A method using polyvinylsiloxane (PVS), a high-resolution dentalimpression material, to obtain negative images of lingual surfacesis described. Epoxy-resin tongue replicas made from these impressionswere examined with scanning electron microscopy (SEM). Thismethod has been developed to visualize structural details ofthe tongue surface of living human beings and laboratory animals.The utility of the method is demonstrated with hamster tongues,which have well-defined fungiform papillae with single tastepores, and human tongues, which have more variable surface structures.Replicas made from PVS impressions of tongues of living hamsterswere compared with the same tongues after fixation. The replicascontained much of the detail present in fixed tongues. WithSEM, it was possible to identify individual fungiform papillae,which contained depressions with the size and the location ofhamster taste pores. Individual papillae could also be recognizedin human-tongue replicas, but taste pores could not be identifiedwith certainty. These replicas provide permanent, three-dimensionalrecords of tongue topography that could be used to documentchanges due to trauma, disease and aging.     

Interaction of CDK5RAP2 with EB1 to Track Growing Microtubule Tips and to Regulate Microtubule Dynamics

Mutations in cdk5rap2 are linked to autosomal recessive primary microcephaly, and attention has been paid to its function at centrosomes. In this report, we demonstrate that CDK5RAP2 localizes to microtubules and concentrates at the distal tips in addition to centrosomal localization. CDK5RAP2 interacts directly with EB1, a prototypic member of microtubule plus-end tracking proteins, and contains the basic and Ser-rich motif responsible for EB1 binding. The EB1-binding motif is conserved in the CDK5RAP2 sequences of chimpanzee, bovine, and dog but not in those of rat and mouse, suggesting a function gained during the evolution of mammals. The mutation of the Ile/Leu-Pro dipeptide within the motif abolishes EB1 interaction and plus-end attachment. In agreement with the mutational analysis, suppression of EB1 expression inhibits microtubule tip-tracking of CDK5RAP2. We have also found that the CDK5RAP2–EB1 complex regulates microtubule dynamics and stability. CDK5RAP2 depletion by RNA interference impacts the dynamic behaviors of microtubules. The CDK5RAP2–EB1 complex induces microtubule bundling and acetylation when expressed in cell cultures and stimulates microtubule assembly and bundle formation in vitro. Collectively, these results show that CDK5RAP2 targets growing microtubule tips in association with EB1 to regulate microtubule dynamics.     

Intracellular Transport Dynamics of Endosomes Containing DNA Polyplexes along the Microtubule Network

We have explored the transport of DNA polyplexes enclosed in endosomes within the cellular environment by multiple particle tracking (MPT). The polyplex-loaded endosomes demonstrate enhanced diffusion at short timescales (t < 7 s) with their mean-square displacement (MSD) 〈Δx(t)²〉 scaling as t^1.25. For longer time intervals they exhibit subdiffusive transport and have an MSD scaling as t^0.7. This crossover from an enhanced diffusion to a subdiffusive regime can be explained by considering the action of motor proteins that actively transport these endosomes along the cellular microtubule network and the thermal bending modes of the microtubule network itself.     

Three-Dimensional Structure of the Photosystem II Core Dimer of Higher Plants Determined by Electron Microscopy

Here we report the first three-dimensional structure of a higher plant photosystem II core dimer determined by electron crystallography at a resolution sufficient to assign the organization of its transmembrane helices. The locations of 34 transmembrane helices in each half of the dimer have been deduced, 22 of which are assigned to the major subunits D1 (5), D2 (5), CP47 (6), and CP43 (6). CP47 and CP43, located on opposite sides of the D1/D2 heterodimer, are structurally similar to each other, consisting of 3 pairs of transmembrane helices arranged in a ring. Both CP47 and CP43 have densities protruding from the lumenal surface, which are assigned to the loops joining helices 5 and 6 of each protein. The remaining 12 helices within each half of the dimer are attributed to low-molecular-weight proteins having single transmembrane helices. Comparison of the subunit organization of the higher plant photosystem II core dimer reported here with that of its thermophilic cyanobacterial counterpart recently determined by X-ray crystallography shows significant similarities, indicative of a common evolutionary origin. Some differences are, however, observed, and these may relate to variations between the two classes of organisms in antenna linkage or thermostability.     

Rapid Reconstruction of 3D Neuronal Morphology from Light Microscopy Images with Augmented Rayburst Sampling

Digital reconstruction of three-dimensional (3D) neuronal morphology from light microscopy images provides a powerful technique for analysis of neural circuits. It is time-consuming to manually perform this process. Thus, efficient computer-assisted approaches are preferable. In this paper, we present an innovative method for the tracing and reconstruction of 3D neuronal morphology from light microscopy images. The method uses a prediction and refinement strategy that is based on exploration of local neuron structural features. We extended the rayburst sampling algorithm to a marching fashion, which starts from a single or a few seed points and marches recursively forward along neurite branches to trace and reconstruct the whole tree-like structure. A local radius-related but size-independent hemispherical sampling was used to predict the neurite centerline and detect branches. Iterative rayburst sampling was performed in the orthogonal plane, to refine the centerline location and to estimate the local radius. We implemented the method in a cooperative 3D interactive visualization-assisted system named flNeuronTool. The source code in C++ and the binaries are freely available at http://sourceforge.net/projects/flneurontool/. We validated and evaluated the proposed method using synthetic data and real datasets from the Digital Reconstruction of Axonal and Dendritic Morphology (DIADEM) challenge. Then, flNeuronTool was applied to mouse brain images acquired with the Micro-Optical Sectioning Tomography (MOST) system, to reconstruct single neurons and local neural circuits. The results showed that the system achieves a reasonable balance between fast speed and acceptable accuracy, which is promising for interactive applications in neuronal image analysis.     

Bright Field Microscopy as an Alternative to Whole Cell Fluorescence in Automated Analysis of Macrophage Images

Background

Fluorescence microscopy is the standard tool for detection and analysis of cellular phenomena. This technique, however, has a number of drawbacks such as the limited number of available fluorescent channels in microscopes, overlapping excitation and emission spectra of the stains, and phototoxicity.

Methodology

We here present and validate a method to automatically detect cell population outlines directly from bright field images. By imaging samples with several focus levels forming a bright field -stack, and by measuring the intensity variations of this stack over the -dimension, we construct a new two dimensional projection image of increased contrast. With additional information for locations of each cell, such as stained nuclei, this bright field projection image can be used instead of whole cell fluorescence to locate borders of individual cells, separating touching cells, and enabling single cell analysis. Using the popular CellProfiler freeware cell image analysis software mainly targeted for fluorescence microscopy, we validate our method by automatically segmenting low contrast and rather complex shaped murine macrophage cells.

Significance

The proposed approach frees up a fluorescence channel, which can be used for subcellular studies. It also facilitates cell shape measurement in experiments where whole cell fluorescent staining is either not available, or is dependent on a particular experimental condition. We show that whole cell area detection results using our projected bright field images match closely to the standard approach where cell areas are localized using fluorescence, and conclude that the high contrast bright field projection image can directly replace one fluorescent channel in whole cell quantification. Matlab code for calculating the projections can be downloaded from the supplementary site: http://sites.google.com/site/brightfieldorstaining