Scanning angle interference microscopy reveals cell dynamics at the nanoscale

Emerging questions in cell biology necessitate nanoscale imaging in live cells. Here we present scanning angle interference microscopy, which is capable of localizing fluorescent objects with nanoscale precision along the optical axis in motile cellular structures. We use this approach to resolve nanotopographical features of the cell membrane and cytoskeleton as well as the temporal evolution, three-dimensional architecture and nanoscale dynamics of focal adhesion complexes.     

Automated Correlation and Averaging of Three-Dimensional Reconstructions Obtained by Electron Tomography

We have developed a least-squares refinement procedure that in an automated way performs three-dimensional alignment and averaging of objects from multiple reconstructions. The computer implementation aligns the three-dimensional structures by a two-step procedure that maximizes the density overlap for all objects. First, an initial average density is built by successive incorporation of individual objects, after a global search for their optimal three-dimensional orientations. Second, the initial average is subsequently refined by excluding individual objects one at a time, realigning them with the reduced average containing all other objects and including them into the average again. The refinement is repeated until no further change of the average occurs. The resulting average model is therefore minimally biased by the order in which the individual reconstructions are incorporated into the average. The performance of the procedure was tested using a synthetic data set of randomly oriented objects with Poisson-distributed noise added. The program managed well to align and average the objects at the signal/noise ratio 1.0. The increase in signal/noise ratio was in all investigated cases almost equal to the expected square root of the number of objects. The program was also successfully tested on a set of authentic three-dimensional reconstructions from anin situspecimen containingEscherichia coli70S ribosomes, where the immediate environment of the reconstructed objects may also contain variable amounts of other structures.     

Cell interactions with three-dimensional matrices

Signaling and other cellular functions differ in three-dimensional compared with two-dimensional systems. Cell adhesion structures can evolve in vitro towards in-vivo-like adhesions with distinct biological activities. In this review, we examine recent advances in studies of interactions of fibroblasts with collagen gels and fibronectin-containing matrices that mimic in vivo three-dimensional microenvironments. These three-dimensional systems are illuminating mechanisms of cell-matrix interactions in living organisms.     

Electron tomography of ER, Golgi and related membrane systems

A primary goal of cell biology is to uncover the mechanisms of cellular processes. A detailed structural understanding of the organelles and subcellular structures involved in these processes has often formed the foundation for the elucidation of their function. Electron tomography is a powerful technique for characterizing subcellular architecture and structural details in three dimensions. Electron tomography of cryofixed, freeze-substituted, and plastic-embedded samples allows three-dimensional visualization and display of dynamic, pleiomorphic structures at a resolution of approximately 7 nm in cell volumes up to approximately 25 microm(3). In this review, we describe the electron tomography protocols that we have employed to determine the 3D architecture of complex cellular structures, thereby gaining insights into their functional organization. We stress the need for studying specimens preserved by cryofixation methods to obtain accurate information on the geometry and size of cellular structures. We also discuss some of the challenges associated with the staining of certain types of membranes. Finally, we provide examples of how tomographic data can be analyzed, dissected, and displayed using the tools built into the IMOD software package.     

Inferotemporal cortex subserves three-dimensional structure categorization

We perceive real-world objects as three-dimensional (3D), yet it is unknown which brain area underlies our ability to perceive objects in this way. The macaque inferotemporal (IT) cortex contains neurons that respond selectively to 3D structures defined by binocular disparity. To examine the causal role of IT in the categorization of 3D structures, we electrically stimulated clusters of IT neurons with a similar 3D-structure preference while monkeys performed a 3D-structure categorization task. Microstimulation of 3D-structure-selective IT clusters caused monkeys to choose the preferred structure of the 3D-structure-selective neurons considerably more often. Microstimulation in IT also accelerated the monkeys' choice for the preferred structure, while delaying choices corresponding to the nonpreferred structure of a given site. These findings reveal that 3D-structure-selective neurons in IT contribute to the categorization of 3D objects.     

Automated feature detection and imaging for high-resolution screening of zebrafish embryos

The development of automated microscopy platforms has enabled large-scale observation of biological processes, thereby complementing genome scale biochemical techniques. However, commercially available systems are restricted either by fixed-field-of-views, leading to potential omission of features of interest, or by low-resolution data of whole objects lacking cellular detail. This limits the efficiency of high-content screening assays, especially when large complex objects are used as in whole-organism screening. Here we demonstrate a toolset for automated intelligent high-content screening of whole zebrafish embryos at cellular resolution on a standard wide-field screening microscope. Using custom-developed algorithms, predefined regions of interest-such as the brain-are automatically detected. The regions of interest are subsequently imaged automatically at high magnification, enabling rapid capture of cellular resolution data. We utilize this approach for acquiring 3-D datasets of embryonic brains of transgenic zebrafish. Moreover, we report the development of a mold design for accurate orientation of zebrafish embryos for dorsal imaging, thereby facilitating standardized imaging of internal organs and cellular structures. The toolset is flexible and can be readily applied for the imaging of different specimens in various applications.     

Adhesion between cells and extracellular matrix with special reference to hepatic stellate cell adhesion to three-dimensional collagen fibers

Hepatic stellate cells are located in the perisinusoidal space (space of Disse), and extend their dendritic, thin membranous processes and fine fibrillar processes into this space. The stellate cells coexist with a three-dimensional extracellular matrix (ECM) in the perisinusoidal space. In turn the three-dimensional structure of the ECM regulates the proliferation, morphology, and functions of the stellate cell. In this review, the morphology of sites of adhesion between hepatic stellate cells and extracellular matrix is described. Hepatic stellate cells cultured in polystyrene dishes spread well, whereas the cells cultured on or in type I collagen gel become slender and elongate their long cellular processes which adhere directly to the collagen fibers. Cells in type I collagen gel form a large number of adhesive structures, each adhesive area forming a face but not a point. Adhesion molecules, integrins, for the ECM are localized on the cell surface. Elongation of the cellular processes occurs via integrin-binding to type I collagen fibers. The signal transduction mechanism, including protein and phosphatidylinositol phosphorylation, is critical to induce and sustain the cellular processes. Information on the three-dimensional structures of ECM is transmitted via three-dimensional adhesive structures containing the integrins.     

Three-dimensional multiple-wavelength fluorescence microscopy for the structural analysis of biological phenomena.

Cellular events are accomplished by the coordinated interactions of cellular components within the three-dimensional context of a cell. Simultaneous observation of multiple components in three dimensions can be essential for understanding such interactions. Toward this end, we have developed a computerized microscope workstation capable of recording three-dimensional images of multiple cellular components in fixed and living cells. All aspects of microscope control, data collection, image processing and analysis can be performed on the one workstation. In this report, we describe the components and capabilities of this integrated system. In addition, we discuss some general problems of multiple-wavelength, three-dimensional imaging and our application of this technology to the analysis of chromosome organization in Drosophila melanogaster. Three-dimensional imaging of fixed embryos stained by indirect immunofluorescence has revealed the structural organization of chromosomes, microtubules, and the nuclear lamins. Imaging of living embryos injected with fluorescently labelled proteins has confirmed and extended these results by allowing the study of these structures throughout the cell cycle. The combination of the molecular specificity of fluorescence microscopy and the three-dimensional structural information obtained by our workstation has provided novel insights into the dynamic aspects of chromosome behavior during the cell cycle. We believe this system has many important applications in the study of the molecular basis of cellular events.     

Ruby-Helix: an implementation of helical image processing based on object-oriented scripting language

Helical image analysis in combination with electron microscopy has been used to study three-dimensional structures of various biological filaments or tubes, such as microtubules, actin filaments, and bacterial flagella. A number of packages have been developed to carry out helical image analysis. Some biological specimens, however, have a symmetry break (seam) in their three-dimensional structure, even though their subunits are mostly arranged in a helical manner. We refer to these objects as "asymmetric helices". All the existing packages are designed for helically symmetric specimens, and do not allow analysis of asymmetric helical objects, such as microtubules with seams. Here, we describe Ruby-Helix, a new set of programs for the analysis of "helical" objects with or without a seam. Ruby-Helix is built on top of the Ruby programming language and is the first implementation of asymmetric helical reconstruction for practical image analysis. It also allows easier and semi-automated analysis, performing iterative unbending and accurate determination of the repeat length. As a result, Ruby-Helix enables us to analyze motor-microtubule complexes with higher throughput to higher resolution.     

Symmetry perception by poultry chicks and its implications for three-dimensional object recognition

Bilateral symmetry is visually salient to diverse animals including birds, but whereas experimental studies typically use bilaterally symmetrical two-dimensional patterns that are viewed approximately fronto-parallel; in nature, animals observe three-dimensional objects from all angles. Many animals and plant structures have a plane of bilateral symmetry. Here, we first (experiment I) give evidence that young poultry chicks readily generalize bilateral symmetry as a feature of two-dimensional patterns in fronto-parallel view. We then test the ability of chicks to recognize symmetry in images that would be produced by the transformed view produced by a 40° horizontal combined with a 20° vertical rotation of a pattern on a spherical surface. Experiment II gives evidence that chicks trained to distinguish symmetrical from asymmetrical patterns treat rotated views of symmetrical 'objects' as symmetrical. Experiment III gives evidence that chicks trained to discriminate rotated views of symmetrical 'objects' from asymmetrical patterns generalize to novel symmetrical objects either in fronto-parallel or rotated view. These findings emphasize the importance of bilateral symmetry for three-dimensional object recognition and raise questions about the underlying mechanisms of symmetry perception.     

DNA polymerase Family X: Function,structure, and cellular roles

The X family of DNA polymerases in eukaryotic cells consists of terminal transferase and DNA polymerases β, λ, and μ. These enzymes have similar structural portraits, yet different biochemical properties, especially in their interactions with DNA. None of these enzymes possesses a proofreading subdomain, and their intrinsic fidelity of DNA synthesis is much lower than that of a polymerase that functions in cellular DNA replication. In this review, we discuss the similarities and differences of three members of Family X: polymerases β, λ, and μ. We focus on biochemical mechanisms, structural variation, fidelity and lesion bypass mechanisms, and cellular roles. Remarkably, although these enzymes have similar three-dimensional structures, their biochemical properties and cellular functions differ in important ways that impact cellular function.     

Three-dimensional reconstruction of Paramecium primaurelia oral apparatus through confocal laser scanning optical microscopy

The oral apparatus of the ciliate protozoan Paramecium primaurelia, a single-celled eukaryotic organism, is a highly organized structure whose arrangement is of important taxonomic, phylogenetic and developmental significance. This paper analyses oral structures by means of a confocal laser scanning optical microscope (CLSM), which allows their three-dimensional visualization and measurement. The extraction of the intrinsic three-dimensional information related to the biological objects under investigation can in turn be related to their functional state, according to the classical paradigms of structure to function relationship identification. In our experiments, we acquired different data sets. These are optical slices of the biological sample under investigation, acquired in a confocal situation, through epi-illumination, in reflection. For comparison with conventional microscopy, two-dimensional images were acquired via a standard TV camera coupled to the microscope itself. The volumes obtained by piling up the slices were rendered through different techniques, some of them directly implemented on the workstation controlling the CLSM system, some of them on a SUN SPARCstation 1, where the original data were transferred via an Ethernet link. In this last instance, original software has been developed for the visualization and animation of the three-dimensional structures, under UNIX and X-Window, according to a ray-tracing algorithm.     

Organ printing: fiction or science

Aggregates of living cells (i.e. model tissue fragments) under appropriate conditions fuse like liquid drops. According to Steinberg's differential adhesion hypothesis (DAH), this may be understood by assuming that cells are motile and tissues made of such cells possess an effective surface tension. Here we show that based on these properties three-dimensional cellular structures of prescribed shape can be constructed by a novel method: cell aggregate printing. Spherical aggregates of similar size made of cells with known adhesive properties were prepared. Aggregates were embedded into biocompatible gels. When the cellular and gel properties, as well as the symmetry of the initial configuration were appropriately adjusted the contiguous aggregates fused into ring-like organ structures. To elucidate the driving force and optimal conditions for this pattern formation, Monte Carlo simulations based on a DAH motivated model were performed. The simulations reproduced the experimentally observed cellular arrangements and revealed that the control parameter of pattern evolution is the gel-tissue interfacial tension, an experimentally accessible parameter.     

Regulation of cytoskeletal structure in human mammary carcinoma cells MCF-7 by culture substrata

Three-dimensional cellular structures formed by MCF-7 human mammary carcinoma cells within collagen gels were isolated with collagenase and cultivated on plastic substratum to examine whether the cytoskeleton specific for cells forming cellular structures (S-type) changes to that specific for cells grown as monolayers (M-type). The cytoskeleton isolated as 0.05% Triton-insoluble fraction from the cellular structures after culture for 1 day on plastic was exclusively S-type. However, both types of cytoskeletons were observed in the cellular structures cultivated for 7 days on plastic as well as in the cells grown as monolayers for 2 days after dissociation of the cellular structures with trypsin. By use of an antibody raised against a 65-kD polypeptide that was specific for the M-type cytoskeleton, the presence of the polypeptide was found to be restricted to the cells grown out as monolayers from the edge of the cellular structures. In the cells grown for 2 days as monolayers, a mixture of cells both having and lacking the polypeptide was observed. After a 7-day culture of the dissociated cells as monolayers on plastic, however, most of the cells had M-type cytoskeletons. The present results show that the apparent change in the cytoskeleton of MCF-7 cells from S-type to M-type does not occur in cells involved in the three-dimensional cellular structures even in the absence of collagen gels, but that it occurs in cells which are grown as monolayers for at least 7 days on plastic substratum.     

Electron microscope tomography

Electron microscope tomography allows three-dimensional reconstruction of ultrastructural objects at the molecular level. The method is general and not limited to symmetric, or regularly ordered structures. Alone, or in combination with immunoelectron microscopy and electron spectroscopic imaging, electron microscope tomography is a powerful technique in cell and molecular biology.     

Striving for atomic resolution in biomolecular topography: The scanning force microscope (SFM)

The invention in 1986 of scanning force microscopy (SFM) provided a new and powerful tool for the investigation of biological structures. SFM yields a three-dimensional view at nanometer resolution of the surface topography associated with biological objects. The potential for imaging either macromolecules or biomolecules and cells under native (physiological) conditions is currently being exploited to obtain functional information at the molecular level. In addition, the forces involved in individual bimolecular interactions are being assessed under static and dynamic conditions. In this report we focus on the imaging capability of the SFM. The rather broad spectrum of applications represented is intended to orient the prospective user of biological SFM.     

Template matching as a tool for annotation of tomograms of stained biological structures

In recent years, electron tomography has improved our three-dimensional (3D) insight in the structural architecture of cells and organelles. For studies that involve the 3D imaging of stained sections, manual annotation of tomographic data has been an important method to help understand the overall 3D morphology of cellular compartments. Here, we postulate that template matching can provide a tool for more objective annotation and contouring of cellular structures. Also, this technique can extract information hitherto unharvested in tomographic studies. To evaluate the performance of template matching on tomograms of stained sections, we generated several templates representing a piece of microtubule or patches of membranes of different staining-thicknesses. These templates were matched to tomograms of stained electron microscopy sections. Both microtubules and ER-Golgi membranes could be detected using this method. By matching cuboids of different thicknesses, we were able to distinguish between coated and non-coated endosomal membrane-domains. Finally, heterogeneity in staining-thickness of endosomes could be observed. Template matching can be a useful addition to existing annotation-methods, and provide additional insights in cellular architecture.     

Improved method for visualizing cells revealed dynamic morphological changes of ventral neuroblasts during ventral cleft closure of Caenorhabditis elegans

The formation of intricate and functional biological structures depends on the dynamic changes of cellular morphology. Confocal laser scanning microscopy (CLSM) is a widely used method to reveal the three-dimensional (3-D) structure of cells during the development of Caenorhabditis elegans (C. elegans) and other model organisms. Improving the efficiency and image quality of CLSM would benefit studies using this method. We found that CED-10::GFP::CED-10, a green fluorescent protein (GFP) marker, is intensely expressed beneath the cell surface, facilitating visualization of cellular morphology in C. elegans embryos. By combining the unique properties of this marker, and with the help of direct 3-D rendering of images obtained by CLSM, we developed a simple but powerful method for investigating cellular morphology in developing embryos. Using this method we, for the first time, document the dynamic changes in the morphology of ventral neuroblasts in vivo during ventral cleft closure.     

Structural evidence for adaptive ligand binding of glycolipid transfer protein

Glycolipids participate in many important cellular processes and they are bound and transferred with high specificity by glycolipid transfer protein (GLTP). We have solved three different X-ray structures of bovine GLTP at 1.4 angstroms, 1.6 angstroms and 1.8 angstroms resolution, all with a bound fatty acid or glycolipid. The 1.4 angstroms structure resembles the recently characterized apo-form of the human GLTP but the other two structures represent an intermediate conformation of the apo-GLTPs and the human lactosylceramide-bound GLTP structure. These novel structures give insight into the mechanism of lipid binding and how GLTP may conformationally adapt to different lipids. Furthermore, based on the structural comparison of the GLTP structures and the three-dimensional models of the related Podospora anserina HET-C2 and Arabidopsis thaliana accelerated cell death protein, ACD11, we give structural explanations for their specific lipid binding properties.     

CORSEN,a new software dedicated to microscope-based 3D distance measurements: mRNA–mitochondria distance,from single-cell to population analyses

Recent improvements in microscopy technology allow detection of single molecules of RNA, but tools for large-scale automatic analyses of particle distributions are lacking. An increasing number of imaging studies emphasize the importance of mRNA localization in the definition of cell territory or the biogenesis of cell compartments. CORSEN is a new tool dedicated to three-dimensional (3D) distance measurements from imaging experiments especially developed to access the minimal distance between RNA molecules and cellular compartment markers. CORSEN includes a 3D segmentation algorithm allowing the extraction and the characterization of the cellular objects to be processed—surface determination, aggregate decomposition—for minimal distance calculations. CORSEN''s main contribution lies in exploratory statistical analysis, cell population characterization, and high-throughput assays that are made possible by the implementation of a batch process analysis. We highlighted CORSEN''s utility for the study of relative positions of mRNA molecules and mitochondria: CORSEN clearly discriminates mRNA localized to the vicinity of mitochondria from those that are translated on free cytoplasmic polysomes. Moreover, it quantifies the cell-to-cell variations of mRNA localization and emphasizes the necessity for statistical approaches. This method can be extended to assess the evolution of the distance between specific mRNAs and other cellular structures in different cellular contexts. CORSEN was designed for the biologist community with the concern to provide an easy-to-use and highly flexible tool that can be applied for diverse distance quantification issues.