Ulrike Ziese

Corneal collagen fibril structure in three dimensions: Structural insights into fibril assembly, mechanical properties, and tissue organization

The ability of the cornea to transmit light while being mechanically resilient is directly attributable to the formation of an extracellular matrix containing orthogonal sheets of collagen fibrils. The detailed structure of the fibrils and how this structure underpins the mechanical properties and organization of the cornea is understood poorly. In this study, we used automated electron tomography to study the three-dimensional organization of molecules in corneal collagen fibrils. The reconstructions show that the collagen molecules in the 36-nm diameter collagen fibrils are organized into microfibrils (≈4-nm diameter) that are tilted by ≈15° to the fibril long axis in a right-handed helix. An unexpected finding was that the microfibrils exhibit a constant-tilt angle independent of radial position within the fibril. This feature suggests that microfibrils in concentric layers are not always parallel to each other and cannot retain the same neighbors between layers. Analysis of the lateral structure shows that the microfibrils exhibit regions of order and disorder within the 67-nm axial repeat of collagen fibrils. Furthermore, the microfibrils are ordered at three specific regions of the axial repeat of collagen fibrils that correspond to the N- and C-telopeptides and the d-band of the gap zone. The reconstructions also show macromolecules binding to the fibril surface at sites that correspond precisely to where the microfibrils are most orderly.

Endosomal compartmentalization in three dimensions: implications for membrane fusion.

Endosomes are major sorting stations in the endocytic route that send proteins and lipids to multiple destinations in the cell, including the cell surface, Golgi complex, and lysosomes. They have an intricate architecture of internal membrane structures enclosed by an outer membrane. Recycling proteins remain on the outer membrane, whereas proteins that are destined for degradation in the lysosome are sorted to the interior. Recently, a retrograde pathway was discovered whereby molecules, like MHC class II of the immune system, return from the internal structures to the outer membrane, allowing their further transport to the cell surface for T cell activation. Whether this return involves back fusion of free vesicles with the outer membrane, or occurs via the continuity of the two membrane domains, is an unanswered question. By electron tomography of cryo-immobilized cells we now demonstrate that, in multivesicular endosomes of B-lymphocytes and dendritic cells, the inner membranes are free vesicles. Hence, protein transport from inner to outer membranes cannot occur laterally in the plane of the membrane, but requires fusion between the two membrane domains. This implies the existence of an intracellular machinery that mediates fusion between the exoplasmic leaflets of the membranes involved, which is opposite to regular intracellular fusion between cytoplasmic leaflets. In addition, our 3D reconstructions reveal the presence of clathrin-coated areas at the cytoplasmic face of the outer membrane, known to participate in protein sorting to the endosomal interior. Interestingly, profiles reminiscent of inward budding vesicles were often in close proximity to the coats.

Automated high-throughput electron tomography by pre-calibration of image shifts

Electron tomography is a versatile method for obtaining three‐dimensional (3D) images with transmission electron microscopy. The technique is suitable to investigate cell organelles and tissue sections (100–500 nm thick) with 4–20 nm resolution. 3D reconstructions are obtained by processing a series of images acquired with the samples tilted over different angles. While tilting the sample, image shifts and defocus changes of several µm can occur. The current generation of automated acquisition software detects and corrects for these changes with a procedure that incorporates switching the electron optical magnification. We developed a novel method for data collection based on the measurement of shifts prior to data acquisition, which results in a five‐fold increase in speed, enabling the acquisition of 151 images in less than 20 min. The method will enhance the quality of a tilt series by minimizing the amount of required focus‐change compensation by aligning the optical axis to the tilt axis of the specimen stage. The alignment is achieved by invoking an amount of image shift as deduced from the mathematical model describing the effect of specimen tilt. As examples for application in biological and materials sciences 3D reconstructions of a mitochondrion and a zeolite crystal are presented.

Three-dimensional localization of ultrasmall immuno-gold labels by HAADF-STEM tomography

The localization of scarce antigens in thin sections of biological material can be accomplished by pre-embedment labeling with ultrasmall immuno-gold labels. Moreover, with this method, labeling is not restricted to the section surface but occurs throughout the section volume. Thus, when combined with electron tomography, antigens can be localized in three dimensions in relation to the 3D (three-dimensional) ultrastructure of the cell. However, for visualization in a transmission electron microscope, these labels need to be enlarged by silver or gold enhancement. The increase in particle size reduces the resolution of the antigen detection and the large particles obscure ultrastructural details in the tomogram. In this paper we show for the first time that these problems can be avoided and that ultrasmall gold labels can be localized in three dimensions without the need for gold or silver enhancement by using HAADF-STEM (high angular annular dark-field-scanning transmission electron microscopy) tomography. This method allowed us to three-dimensionally localize Aurion ultrasmall goat anti-rabbit immuno-gold labels on sections of Epon-embedded, osmium-uranium-lead-stained biological material. Calculations show that a 3D reconstruction obtained from HAADF-STEM projection images can be spatially aligned to one obtained from transmission electron microscopy (TEM) projections with subpixel accuracy. We conclude that it is possible to combine the high-fidelity structural information of TEM tomograms with the ultrasmall label localization ability of HAADF-STEM tomograms.

Development and Application of 3-Dimensional Transmission ElectronMicroscopy (3D-TEM) for the Characterization of Metal-Zeolite CatalystSystems

With electron tomography (3D-TEM) a 3D-reconstruction is calculated from a series of TEM images taken at a tilt angle range (tilting range) of +70° to −70°. The reconstruction can be visualized with contour surfaces that give information about the surface of the sample as well as with slices through the reconstruction that give detailed information on the interior of the sample. Electron tomography gives much more information than Scanning Electron Microscopy (SEM), since SEM gives only information about the surface of a sample. As a case study, the imaging of silver clusters on zeolite NaY is given. The reconstruction shows silver particles at the external surface as well as a silver particle in a mesopore of the zeolite crystallite. It is concluded that 3D-TEM comprises a breakthrough in the characterization of nano-structured solid catalysts.

Three-dimensional reconstructions of extracellular matrix polymers using automated electron tomography.

The extracellular matrix is an intricate network of macromolecules which provides support for cells and a framework for tissues. The detailed structure and organisation of most matrix polymers is poorly understood. These polymers have a complex ultrastructure, and it has proved a major challenge both to define their structural organisation and to relate this to their biological function. However, new approaches using automated electron tomography are beginning to reveal important insights into the molecular assembly and structural organisation of two of the most abundant polymer systems in the extracellular matrix. We have generated three-dimensional reconstructions of collagen fibrils from bovine cornea and fibrillin microfibrils from ciliary zonules. Analysis of these data has provided new insights into the organisation and function of these large macromolecular assemblies.

Three-dimensional Architecture of Hair-bundle Linkages Revealed by Electron-microscopic Tomography

The senses of hearing and balance rest upon mechanoelectrical transduction by the hair bundles of hair cells in the inner ear. Located at the apical cellular surface, each hair bundle comprises several tens of stereocilia and a single kinocilium that are interconnected by extracellular proteinaceous links. Using electron-microscopic tomography of bullfrog saccular sensory epithelia, we examined the three-dimensional structures of basal links, kinociliary links, and tip links. We observed significant differences in the appearances and dimensions of these three structures and found two distinct populations of tip links suggestive of the involvement of different proteins, splice variants, or protein–protein interactions. We noted auxiliary links connecting the upper portions of tip links to the taller stereocilia. Tip links and auxiliary links show a tendency to adopt a globular conformation when disconnected from the membrane surface.

Electron tomography of molecular sieves

This chapter discusses electron tomography of molecular sieves. The chapter discusses prospects and limitations of different modes of electron microscopy. The use of three-dimensional transmission electron microscopy (TEM) is discussed—in particular, electron tomography (ET)—for the study of molecular sieves. The use of electron tomography in materials science is quite recent and exciting information on zeolites and mesoporous materials has already been obtained. ET can now be applied on a routine basis using an automated electron microscope in combination with image processing and visualization software. Three-dimensional information with nanometer resolution has been obtained for structural studies of molecular sieves. The application of electron tomography with zeolites has provided unique information on the nature of mesopores that have been obtained by secondary treatments or the use of carbon templates. Structural information obtained from ET should be complemented with other characterization techniques because of the intrinsically poor statistics of electron microscopy.

Quantitative morphological studies of mesoporous catalysts at nanometer scale resolution

We have combined electron tomography with posterior image processing for a quantitative morphological study of mesoporous catalysts at nanometer scale resolution. As a first example for the possibilities of the approach, mesopore size distributions of single crystallites of commercial USY and XVUSY zeolites were derived.

Robust Alignment of Transmission Electron Microscope Tilt Series

In this paper, we propose a novel method for automatic, feature-based alignment of transmission electron microscope images that is needed for computing 3D reconstructions in electron tomography. The proposed method, termed as trifocal alignment, is more accurate than the previous markerless methods. The key components of this work are: (1) a reliable multiresolution algorithm for matching feature points between images, (2) a robust, maximum-likelihood-based estimator for determining the trifocal constraint, needed for validating the correctness of the matches, (3) a robust, large scale optimisation framework to compute the alignment parameters from hundreds of thousands of feature point measurements from a couple of hundred images. The experiments show for the first time that by the proposed feature-based alignment approach the accuracy level of the fiducial marker alignment can be achieved