Single nuclear pores visualized by confocal microscopy and image processing.

How nuclear pore complexes, mediating the transport of nucleic acids, proteins, and metabolites between cell nucleus and cytoplasm, are arranged in the nuclear envelope is essentially unknown. Here we describe a method combining high-resolution confocal imaging with image processing and pattern recognition to visualize single nuclear pore complexes (120 nm diameter), determine their relative positions with nanometer accuracy, and analyze their distribution in situ. The method was tested by means of a model system in which the very same sample areas could be imaged by confocal and electron microscopy. It was thus found that single fluorescent beads of 105 nm nominal diameter could be localized with a lateral accuracy of <20 nm and an axial accuracy of approximately 20 nm. The method was applied to digitonin-permeabilized 3T3 cells, whose nuclear pore complexes were fluorescently labeled with the anti-nucleoporin antibody mAb414. Stacks of optical sections were generated by confocal imaging at high resolution. Herein the nuclear pore complexes appeared as bright diffraction-limited spots whose centers were localized by fitting them by three-dimensional gaussians. The nearest-neighbor distribution function and the pair correlation function were calculated and found to agree well with those of randomly distributed hard cylinders of 138 +/- 17 nm diameter, but not with those of randomly distributed points or nonrandomly distributed cylinders. This was supported by a cluster analysis. Implications for the direct observation of the transport of single particles and molecules through individual nuclear pore complexes are discussed.     

Three-dimensional structure of living chloroplasts as visualized by confocal scanning laser microscopy

Summary The newly developed confocal scanning laser microscope, together with image processing by computer, has been used to obtain three-dimensional information on the organization of grana in chloroplasts in living plant tissue. Chloroplasts are ideally suited for such studies because their pigments show bright autofluorescence. The high-resolution stereo images bridge a gap between classic light microscopy and electron microscopy. Our preliminary observations on several plant species resemble most the early observations of Strugger (1951: Die Strukturordnung im Chloroplasten. Ber Deutsch Bot Ges 64: 69–83) and suggest that the 3-D technique might well be suitable to solve discrepancies in the interpretation of classical light microscopic and electron microscopic observations.Abbreviations 3-D three dimensional - CSLM confocal scanning laser microscopy - DCMU 3-(3,4-dichlorophenyl)-1,1-dimethyl urea - DNA deoxyribonucleic acid     

Living sieve cells of conifers as visualized by confocal,laser-scanning fluorescence microscopy

Summary Confocal laser scanning microscopy (CLSM) and fluorochromes were used to visualize the assimilate-conducting sieve cells of conifers in vivo. When still nucleate, the cytoplasm of these cells shows streaming and occupies the cell periphery including the pitlike, thin wall regions where sieve areas would develop. During differentiation the nuclear fluorescence and the central vacuoles disappear. At maturity and after ER-specific staining the sieve areas are the most conspicuous character of sieve cells. Those linking two sieve cells are covered on either side with prominent amounts of ER, while those leading to a Strasburger (=albuminous) cell show fluorescence on the sieve-cell side only. Within the sieve-area wall fluorescence appears also in the common median cavity which is part of the symplastic path between sieve cells. Electron microscopy (EM) depicts the ER as complexes of densely convoluted tubules of smooth ER, equally on either side of a sieve area, provided that the fixation of this sensitive tissue is appropriate. Purposeful wounding causes a swelling and vesiculation of the ER-tubules which is visible in both CLSM and EM. Electron micrographs of ER-complexes at sieve areas -in this paper demonstrated in vivo -have often been argued to be artefacts, since they should raise flow resistance considerably and are not consistent with the Münch hypothesis on phloem transport. The implications of this location for phloem transport are discussed.Abbreviations CLSM confocal laser scanning microscopy - DiOC 3,3-dioxacarbocyanine iodide - EM electron microscopy - ER endoplasmic reticulum - FDA fluorescein diacetate     

Hepatitis C virus budding at lipid droplet-associated ER membrane visualized by 3D electron microscopy

The mechanisms underlying hepatitis C virus (HCV) morphogenesis remain elusive, but lipid droplets have recently been shown to be important organelles for virus production. We investigated the interaction between HCV-like particles and lipid droplets by three-dimensional reconstructions of serial ultrathin electron microscopy sections of cells producing the HCV core protein. The budding of HCV-like particles was mostly initiated at membranes close to the lipid droplets rather than at membranes directly apposed to the lipid droplets. This may have important implications for our understanding of the complex relationship between HCV and lipids and may make easier to dissect out the HCV life cycle.     

Effects of low-protein diet on Schistosoma mansoni morphology visualized by morphometry and confocal laser scanning microscopy

Previous studies have shown that protein deficiencies can hamper both the course of experimental schistosomiasis and normal development of adult worms. To further investigate this relationship, we compared adult male and female Schistosoma mansoni from malnourished and well-fed mice through morphometric and confocal laser scanning microscopy analysis. Swiss mice were fed protein-deficient diets (8%) and infected subcutaneously with approximately 80 S. mansoni cercariae (BH strain, Brazil). Control mice were fed a standard rodent diet (23% protein). The nutritional status was evaluated by body weight gain and albumin values. Mice were sacrificed 63 days post-infection. Recovered worms were stained with hydrochloric carmine and preserved as whole-mounts for bright-field examination and confocal microscopy. The body weight gain and serum albumin concentrations were significantly lower (P < 0.05) in malnourished mice than in controls. In general, all morphometric values of specimens grown in malnourished mice were lower than those of control mice. Schistosome worms grown in malnourished mice had statistically significant differences (P < 0.05) in the reproductive system and tegument than those grown in mice fed standard diets. In female worms, vitelline glands showed few remaining follicles and ovaries lacked mature oocytes. In male parasites, tubercles were fewer in number on the dorsal surface and testicular lobes presented fewer differentiated germinal cells. In summary, we describe novel data supporting the view that low-protein diets may influence the development of adult worms.     

Unsupervised noise removal algorithms for three-dimensional confocal fluorescence microscopy

Algorithms are presented for effective suppression of the quantum noise artifact that is inherent to three-dimensional confocal fluorescence microscopy images of extended spatial objects such as neurons. The specific advances embodied in these algorithms are as follows: (i) they incorporate an automatic and pattern-constrained three-dimensional segmentation of the image field, and use it to limit any smoothing to the interiors of specified image regions and hence avoid the blurring that is inevitably associated with conventional noise removal algorithms; (ii) they are ‘unsupervised’ in the sense that they automatically estimate and adapt to the unknown spatially and temporally varying noise level in the microscopy data. Fast computation is achieved by parallel computation methods, rather than by algorithmic or modelling compromises.The quantum noise artifact is modelled using a mixture of spatially non-homogeneous Poisson point processes. The intensity of each component process is constrained to lie in specific intervals. A set of segmentation and edge-site variables are used to determine the intensity of the mixture process. Using this model, the noise-removal process is formulated as the joint optimal estimation of the segmentation labels, edge-sites and intensity of the mixture Poisson point process, subject to a combination of stochastic priors and syntactic pattern constraints. The computations proceed iteratively, starting from a set of approximate user-supplied, or default initial guesses of the underlying random process parameters. An Expectation Maximization algorithm is used to obtain a more precise characterization of these parameters, that are then input to a joint estimation algorithm.Stereoscopic renderings of processed three-dimensional images of murine hippocampal neurons are presented to demonstrate the effectiveness of the method. The processed images exhibit increased contrast and significant smoothing and reduction of the background intensity while avoiding any blurring of the foreground neuronal structures.     

The potential of 3D-FISH and super-resolution structured illumination microscopy for studies of 3D nuclear architecture: 3D structured illumination microscopy of defined chromosomal structures visualized by 3D (immuno)-FISH opens new perspectives for studies of nuclear architecture

Three-dimensional structured illumination microscopy (3D-SIM) has opened up new possibilities to study nuclear architecture at the ultrastructural level down to the ~100 nm range. We present first results and assess the potential using 3D-SIM in combination with 3D fluorescence in situ hybridization (3D-FISH) for the topographical analysis of defined nuclear targets. Our study also deals with the concern that artifacts produced by FISH may counteract the gain in resolution. We address the topography of DAPI-stained DNA in nuclei before and after 3D-FISH, nuclear pores and the lamina, chromosome territories, chromatin domains, and individual gene loci. We also look at the replication patterns of chromocenters and the topographical relationship of Xist-RNA within the inactive X-territory. These examples demonstrate that an appropriately adapted 3D-FISH/3D-SIM approach preserves key characteristics of the nuclear ultrastructure and that the gain in information obtained by 3D-SIM yields new insights into the functional nuclear organization.     

F-actin in mitotic spindles of synchronized suspension culture cells of tobacco visualized by confocal laser scanning microscopy

TRITC-labelled phalloidin was used to visualize F-actin distribution during mitosis in Nicotiana tabacum BY-2 suspension cells. Aphidicolin was used to synchronize cell suspensions, which enabled sufficient numbers of mitotic cells to be obtained. F-actin was present in the spindle, and its orientation seemed to correlate with the known microtubular arrays. The use of confocal microscopy greatly reduced background fluorescence, and therefore fine actin filaments could be observed in spindles previously thought to be devoid of actin.     

Equilibration and exchange of fluorescently labeled molecules in skinned skeletal muscle fibers visualized by confocal microscopy.

Confocal laser fluorescence microscopy was used to study in real time under nearly physiological conditions the equilibration and exchange characteristics of several different fluorescently labeled molecules into chemically skinned, unfixed skeletal muscle fibers of rabbit psoas. The time required for equilibration was found to vary widely from a few minutes up to several days. Specific interactions of molecules with myofibrillar structures seem to slow down equilibration significantly. Time for equilibration, therefore, cannot simply be predicted from diffusion parameters in solution. Specific interactions resulted in characteristic labeling patterns for molecules like creatine kinase (muscle type), pyruvate kinase, actin-binding IgG, and others. For the very slowly equilibrating Rh-NEM-S1, changes in affinity upon binding to actin in the absence of calcium and subsequent slow cooperative activation, beginning at the free end of the filament at the H-zone, were observed. In the presence of calcium, however, binding of Rh-NEM-S1 was homogeneous along the whole actin filament from the very beginning of equilibration. The dissociation properties of the dynamic interactions were analyzed using a chase protocol. Even molecules that bind with rather high affinity and that can be removed only by applying extreme experimental conditions like Rh-phalloidine or Rh-troponin could be displaced easily by unlabeled homologous molecules.     

The three-dimensional micro- and nanostructure of the aortic medial lamellar unit measured using 3D confocal and electron microscopy imaging.

Changes in arterial wall composition and function underlie all forms of vascular disease. The fundamental structural and functional unit of the aortic wall is the medial lamellar unit (MLU). While the basic composition and organization of the MLU is known, three-dimensional (3D) microstructural details are tenuous, due (in part) to lack of three-dimensional data at micro- and nano-scales. We applied novel electron and confocal microscopy techniques to obtain 3D volumetric information of aortic medial microstructure at micro- and nano-scales with all constituents present. For the rat abdominal aorta, we show that medial elastin has three primary forms: with approximately 71% of total elastin as thick, continuous lamellar sheets, 27% as thin, protruding interlamellar elastin fibers (IEFs), and 2% as thick radial struts. Elastin pores are not simply holes in lamellar sheets, but are indented and gusseted openings in lamellae. Smooth muscle cells (SMCs) weave throughout the interlamellar elastin framework, with cytoplasmic extensions abutting IEFs, resulting in approximately 20 degrees radial tilt (relative to the lumen surface) of elliptical SMC nuclei. Collagen fibers are organized as large, parallel bundles tightly enveloping SMC nuclei. Quantification of the orientation of collagen bundles, SMC nuclei, and IEFs reveal that all three primary medial constituents have predominantly circumferential orientation, correlating with reported circumferentially dominant values of physiological stress, collagen fiber recruitment, and tissue stiffness. This high resolution three-dimensional view of the aortic media reveals MLU microstructure details that suggest a highly complex and integrated mural organization that correlates with aortic mechanical properties.     

Localization of telomeres in plant interphase nuclei by in situ hybridization and 3D confocal microscopy

We investigated the three-dimensional (3D) arrangement of telomeres in structurally well preserved, interphase nuclei of Pisum stativum and Vicia faba root tips using in situ hybridization of a probe to telomeric sequences. The probe was labelled with either digoxygenin or biotin and hybridized sequences were detected by immunofluorescence. Three-dimensional data sets were collected by confocal optical microscopy or using a cooled CCD camera. Twelve stacks of optical sections of P. sativum nuclei and nine of V. faba nuclei were studied in detail. Projections through the stacks of optical sections revealed that, in both species, most of the telomeres were adjacent to the nuclear envelope except for a small number next to the nucleolar periphery. In V. faba nuclei, the telomeres were clearly clustered at one pole while in P. sativum there was only a slight tendency for clustering. In V. faba, clusters were found at opposite poles in pairs of sister nuclei rather than at adjacent poles as would be expected if the arrangement at telophase were maintained into interphase.by D. Bazett-Jones     

Robust pore size analysis of filamentous networks from three-dimensional confocal microscopy

We describe a robust method for determining morphological properties of filamentous biopolymer networks, such as collagen or other connective tissue matrices, from confocal microscopy image stacks. Morphological properties including pore size distributions and percolation thresholds are important for transport processes, e.g., particle diffusion or cell migration through the extracellular matrix. The method is applied to fluorescently labeled fiber networks prepared from rat-tail tendon and calf-skin collagen, at concentrations of 1.2, 1.6, and 2.4 mg/ml. The collagen fibers form an entangled and branched network. The medial axes, or skeletons, representing the collagen fibers are extracted from the image stack by threshold intensity segmentation and distance-ordered homotopic thinning. The size of the fluid pores as defined by the radii of largest spheres that fit into the cavities between the collagen fibers is derived from Euclidean distance maps and maximal covering radius transforms of the fluid phase. The size of the largest sphere that can traverse the fluid phase between the collagen fibers across the entire probe, called the percolation threshold, was computed for both horizontal and vertical directions. We demonstrate that by representing the fibers as the medial axis the derived morphological network properties are both robust against changes of the value of the segmentation threshold intensity and robust to problems associated with the point-spread function of the imaging system. We also provide empirical support for a recent claim that the percolation threshold of a fiber network is close to the fiber diameter for which the Euler index of the networks becomes zero.     

Birefringent objects visualized by circular polarization microscopy

In the standard polarizing microscope, birefringent material appears bright only if its optic axis is oblique to the axes of the polarizer and analyzer filters; consequently, an object may be visualized as several disconnected bright regions. This confusing appearance is avoided if the crossed plane polarizers of the conventional microscope are replaced by circular polarizers of opposite handedness. All orientations of the optic axis in the focal plane then become equivalent; objects generally appear uniformly bright. Ordinary microscopes are easily modified to use this technic with readily available components.     

Qualitative and quantitative analysis of monocyte transendothelial migration by confocal microscopy and three-dimensional image reconstruction

A novel method for qualitative and quantitative analysis of monocyte transendothelial migration is described. By labeling monocytes and endothelial cells with different fluorophores, and utilizing confocal microscopy and three-dimensional image reconstruction, transmigrating monocytes were resolved and quantified within a subendothelial collagen gel. Comparison of monocyte migration across endothelial monolayers derived from human brain microvessels versus umbilical veins revealed diapedesis across brain endothelium to be significantly delayed. Inclusion of astrocytes within the subendothelial collagen gel resulted in the formation of an array of astrocytic processes that simulated the glia limitans surrounding brain microvessels in situ, thus yielding a more physiologic paradigm of the blood-brain barrier. By virtue of its unique capacity to provide information on the total number of migrating cells, this analytic approach overcomes significant caveats associated with sampling only aspects of the migration process. The potential adaptability of this method to computer-assisted analysis further enhances its prospective use in high-throughput screening.     

Modulation of hexokinase association with mitochondria analyzed with quantitative three-dimensional confocal microscopy

Hexokinase isozyme I is proposed to be associated with mitochondria in vivo. Moreover, it has been suggested that this association is modulated in coordination with changes in cell metabolic state. To test these hypotheses, we analyzed the subcellular distribution of hexokinase relative to mitochondria in paraformaldehyde-fixed astrocytes using immunocytochemistry and quantitative three-dimensional confocal microscopy. Analysis of the extent of colocalization between hexokinase and mitochondria revealed that approximately 70% of cellular hexokinase is associated with mitochondria under basal metabolic conditions. In contrast to the immunocytochemical studies, between 15 to 40% of cellular hexokinase was found to be associated with mitochondria after fractionation of astrocyte cultures depending on the exact fractionation conditions. The discrepancy between fractionation studies and those based on imaging of distributions in fixed cells indicates the usefulness of using techniques that can evaluate the distributions of "cytosolic" enzymes in cells whose subcellular ultrastructure is not severely disrupted. To determine if hexokinase distribution is modulated in concert with changes in cell metabolism, the localization of hexokinase with mitochondria was evaluated after inhibition of glucose metabolism with 2-deoxyglucose. After incubation with 2-deoxyglucose there was an approximate 35% decrease in the amount of hexokinase associated with mitochondria. These findings support the hypothesis that hexokinase is bound to mitochondria in rat brain astrocytes in vivo, and that this association is sensitive to cell metabolic state.     

DNA-fluorescence of mammalian intra-nucleolar chromatin detected by confocal laser scanning microscopy (CLSM)

The complex spatial DNA distribution in the mammalian interphase nucleus was investigated in Feulgen stained thick sections through mouse trophoblast giant nuclei after Lowicryl embedding. DNA-fluorescence was visualized using confocal laser scanning microscopy. Our results show that the spatial arrangement of major interphase chromatin areas can be precisely documented, including the distribution of small intra-nucleolar chromatin zones.     

The internal ribosome entry site (IRES) of hepatitis C virus visualized by electron microscopy

Translation of hepatitis C virus (HCV) RNA is initiated via the internal ribosome entry site (IRES), located within the 5' untranslated region. Although the secondary structure of this element has been predicted, little information on the tertiary structure is available. Here we report the first structural characterization of the HCV IRES using electron microscopy. In vitro transcribed RNA appeared as particles with characteristic morphology and gold labeling using a specific oligonucleotide confirmed them to be HCV IRES. Dimerization of the IRES by hybridization with tandem repeat oligonucleotides allowed the identification of domain III and an assignment of domains II and IV to distinct regions within the molecule. Using immunogold labeling, the pyrimidine tract binding protein (PTB) was shown to bind to domain III. Structure-function relationships based on the flexible hinge between domains II and III are suggested. Finally, the architecture of the HCV IRES was seen to be markedly different from that of a picornavirus, foot-and-mouth disease virus (FMDV).     

Subnuclear localization,rates and effectiveness of UVC-induced unscheduled DNA synthesis visualized by fluorescence widefield,confocal and super-resolution microscopy

Unscheduled DNA synthesis (UDS) is the final stage of the process of repair of DNA lesions induced by UVC. We detected UDS using a DNA precursor, 5-ethynyl-2′-deoxyuridine (EdU). Using wide-field, confocal and super-resolution fluorescence microscopy and normal human fibroblasts, derived from healthy subjects, we demonstrate that the sub-nuclear pattern of UDS detected via incorporation of EdU is different from that when BrdU is used as DNA precursor. EdU incorporation occurs evenly throughout chromatin, as opposed to just a few small and large repair foci detected by BrdU. We attribute this difference to the fact that BrdU antibody is of much larger size than EdU, and its accessibility to the incorporated precursor requires the presence of denatured sections of DNA. It appears that under the standard conditions of immunocytochemical detection of BrdU only fragments of DNA of various length are being denatured. We argue that, compared with BrdU, the UDS pattern visualized by EdU constitutes a more faithful representation of sub-nuclear distribution of the final stage of nucleotide excision repair induced by UVC. Using the optimized integrated EdU detection procedure we also measured the relative amount of the DNA precursor incorporated by cells during UDS following exposure to various doses of UVC. Also described is the high degree of heterogeneity in terms of the UVC-induced EdU incorporation per cell, presumably reflecting various DNA repair efficiencies or differences in the level of endogenous dT competing with EdU within a population of normal human fibroblasts.     

Synaptosomal cytoskeleton visualized by whole mount electron microscopy

Organization of synaptosomal cytoskeleton was reproducibly visualized by the technique of whole mount electron microscopy. Synaptosomes from rat cerebrums were immobilized on the formvar membrane of the electron microscopic grid, partly solubilized by detergents of various kinds, and treated with chemicals to reveal cytoskeletons and their characteristics. Synaptosomal cytoskeletons consisted of three types: (1) pre-synaptic fiber network structure whose composite fiber was 15–20 nm in diameter and formed 60–100 nm circular rings. The rings had small particles inside and were organized into three-dimensional networks. The pre-synaptic network was different from the Triton-unextractable structure of mitochondria. (2) Post-synaptic fiber aggregate was constructed of 10-nm filaments that were typically visualized as deoxycholate- or N-lauroyl sarcosinate-unextractable cytoskeletons. The aggregate was a major structure in the Triton-unextractable cytoskeleton of synaptic plasma membrane (more than 95%). (3) Fiber connecting individual clusters of synaptosomal cytoskeletons which was probably an artifactual product formed during and after synaptosomal isolation. Existence of actin was indicated both in pre- and post-synaptic cytoplasm.