Ashraf Al-Amoudi

Cryo-electron microscopy of vitreous sections

Since the beginning of the 1980s, cryo‐electron microscopy of a thin film of vitrified aqueous suspension has made it possible to observe biological particles in their native state, in the absence of the usual artefacts of dehydration and staining. Combined with 3‐d reconstruction, it has become an important tool for structural molecular biology. Larger objects such as cells and tissues cannot generally be squeezed in a thin enough film. Cryo‐electron microscopy of vitreous sections (CEMOVIS) provides then a solution. It requires vitrification of a sizable piece of biological material and cutting it into ultrathin sections, which are observed in the vitrified state. Each of these operations raises serious difficulties that have now been overcome. In general, the native state seen with CEMOVIS is very different from what has been seen before and it is seen in more detail. CEMOVIS will give its full potential when combined with computerized electron tomography for 3‐d reconstruction.

Cryo-Transmission Electron Microscopy of Frozen-Hydrated Sections of Escherichia coli and Pseudomonas aeruginosa

High-pressure freezing of Escherichia coli K-12 and Pseudomonas aeruginosa PAO1 in the presence of cryoprotectants provided consistent vitrification of cells so that frozen-hydrated sections could be cut, providing approximately 2-nm resolution of structure. The size and shape of the bacteria, as well as their surface and cytoplasmic constituents, were nicely preserved and compared well with other published high-resolution techniques. Cells possessed a rich cytoplasm containing a diffuse dispersion of ribosomes and genetic material. Close examination of cells revealed that the periplasmic space was compressed during cryosectioning, a finding which provided supporting evidence that this space is filled by a compressible gel. Since the outer membrane and peptidoglycan layer are bonded together via lipoproteins, the space between them (although still part of the periplasmic space) was not as compacted. Even when this cryosectioning compression was taken into account, there was still substantial variability in the width of the periplasmic space. It is possible that the protoplast has some capacity to float freely within the periplasm.

The molecular architecture of cadherins in native epidermal desmosomes

Desmosomes are cadherin-based adhesive intercellular junctions, which are present in tissues such as heart and skin. Despite considerable efforts, the molecular interfaces that mediate adhesion remain obscure. Here we apply cryo-electron tomography of vitreous sections from human epidermis to visualize the three-dimensional molecular architecture of desmosomal cadherins at close-to-native conditions. The three-dimensional reconstructions show a regular array of densities at ∼70 Å intervals along the midline, with a curved shape resembling the X-ray structure of C-cadherin, a representative ‘classical’ cadherin. Model-independent three-dimensional image processing of extracted sub-tomograms reveals the cadherin organization. After fitting the C-cadherin atomic structure into the averaged sub-tomograms, we see a periodic arrangement of a trans W-like and a cis V-like interaction corresponding to molecules from opposing membranes and the same cell membrane, respectively. The resulting model of cadherin organization explains existing two-dimensional data and yields insights into a possible mechanism of cadherin-based cell adhesion.

An oscillating cryo‐knife reduces cutting‐induced deformation of vitreous ultrathin sections

A new oscillating cryo‐knife for producing uncompressed vitreous sections is introduced. The knife is a modified cryo diamond knife that is driven by a piezo translator. Optimal setting for the oscillation was found to be in the inaudible frequency range of 20–25 kHz. Yeast cells and polystyrene spheres were used as model systems to describe compression in the vitreous sections. We found that compression could be reduced by a factor of about 2 when the knife was oscillating. When the oscillator was turned off, sections were compressed by 40–45%. However, only 15–25% compression was obtained when the knife was oscillating. In some cases completely uncompressed sections of yeast cells were produced. It was also found that the amount of compression depends on the specimen itself and on its embedding medium. With the results shown here, we demonstrate that the oscillating knife can produce high‐quality vitreous sections with minimum cutting artefacts.

How to “Read” a Vitreous Section

Publisher Summary Cryoelectron microscopy concerns the observation of hydrated specimen at a temperature so low that water does not evaporate significantly in the microscopes vacuum. This chapter addressed various scientists confronted with CEMOVIS data. It explains the ways to read micrographs, to interpret them, and to understand what they can and cannot provide. It is only recently that cryoelectron microscopy of vitreous sections (CEMOVIS) has been established as a practical method. CEMOVIS results in images that are much closer to the native state, and they provide higher resolution than those obtained from conventional sections. In the absence of any staining and with all the water present as immobilized liquid, CEMOVIS gives a faithful representation of the native state. What is seen on the image is the real distribution of the biological material within the thickness of the section. The global contrast between different regions of the micrograph is proportional to the density difference in the corresponding regions of the specimen.

Amorphous solid water produced by cryosectioning of crystalline ice at 113 K

Amorphous solid (vitreous) water can be obtained by a number of methods, including quick freezing of a very small volume of pure water, low pressure condensation of water vapour on a cold substrate or transformation of hexagonal ice (the ice which is naturally formed) under very high pressure at liquid nitrogen temperature. Larger volumes can be vitrified if cryoprotectant is added or when samples are frozen under high pressure. We show that a sample of 17.5% dextran solution or mouse brain tissue, respectively, frozen under high pressure (200 MPa) into cubic or hexagonal ice can be transformed into vitreous water by the very process of cryosectioning. The vitreous sections obtained by this procedure differ from cryosections obtained from vitreous samples by the irregular aspect of the sections and by small but significant differences in the electron diffraction patterns. For the growing community of cryo‐ultramicrotomists it is important to know that vitrification can occur at the knife edge. A vitreous sample is considered to show the best possible structural preservation. The sort of vitrification described here, however, can lead to bad structural preservation and is therefore considered to be a pitfall. Furthermore, we compare these sections with other forms of amorphous solid water and find it similar to high density amorphous water produced at very high pressures (about 1 GPa) from hexagonal ice and annealed close to its transformation temperature at 117 K.

The three-dimensional molecular structure of the desmosomal plaque

The cytoplasmic surface of intercellular junctions is a complex network of molecular interactions that link the extracellular region of the desmosomal cadherins with the cytoskeletal intermediate filaments. Although 3D structures of the major plaque components are known, the overall architecture remains unknown. We used cryoelectron tomography of vitreous sections from human epidermis to record 3D images of desmosomes in vivo and in situ at molecular resolution. Our results show that the architecture of the cytoplasmic surface of the desmosome is a 2D interconnected quasiperiodic lattice, with a similar spatial organization to the extracellular side. Subtomogram averaging of the plaque region reveals two distinct layers of the desmosomal plaque: a low-density layer closer to the membrane and a high-density layer further away from the membrane. When combined with a heuristic, allowing simultaneous constrained fitting of the high-resolution structures of the major plaque proteins (desmoplakin, plakophilin, and plakoglobin), it reveals their mutual molecular interactions and explains their stoichiometry. The arrangement suggests that alternate plakoglobin–desmoplakin complexes create a template on which desmosomal cadherins cluster before they stabilize extracellularly by binding at their N-terminal tips. Plakophilins are added as a molecular reinforcement to fill the gap between the formed plaque complexes and the plasma membrane.

Alignator: A GPU powered software package for robust fiducial-less alignment of cryo tilt-series

The robust alignment of tilt-series collected for cryo-electron tomography in the absence of fiducial markers, is a problem that, especially for tilt-series of vitreous sections, still represents a significant challenge. Here we present a complete software package that implements a cross-correlation-based procedure that tracks similar image features that are present in several micrographs and explores them implicitly as substitutes for fiducials like gold beads and quantum dots. The added value compared to previous approaches, is that the algorithm explores a huge number of random positions, which are tracked on several micrographs, while being able to identify trace failures, using a cross-validation procedure based on the 3D marker model of the tilt-series. Furthermore, this method allows the reliable identification of areas which behave as a rigid body during the tilt-series and hence addresses specific difficulties for the alignment of vitreous sections, by correcting practical caveats. The resulting alignments can attain sub-pixel precision at the local level and is able to yield a substantial number of usable tilt-series (around 60%). In principle, the algorithm has the potential to run in a fully automated fashion, and could be used to align any tilt-series directly from the microscope. Finally, we have significantly improved the user interface and implemented the source code on the graphics processing unit (GPU) to accelerate the computations.

A rapid microbiopsy system to improve the preservation of biological samples prior to high-pressure freezing

A microbiopsy system for fast excision and transfer of biological specimens from donor to high‐pressure freezer was developed. With a modified, commercially available, Promag 1.2 biopsy gun, tissue samples can be excised with a size small enough (0.6 mm × 1.2 mm × 0.3 mm) to be easily transferred into a newly designed specimen platelet. A self‐made transfer unit allows fast transfer of the specimen from the needle into the specimen platelet. The platelet is then fixed in a commercially available specimen holder of a high‐pressure freezing machine (EM PACT, Leica Microsystems, Vienna, Austria) and frozen therein. The time required by a well‐instructed (but not experienced) person to execute all steps is in the range of half a minute. This period is considered short enough to maintain the excised tissue pieces close to their native state. We show that a range of animal tissues (liver, brain, kidney and muscle) are well preserved. To prove the quality of freezing achieved with the system, we show vitrified ivy leaves high‐pressure frozen in the new specimen platelet.

Three-Dimensional Visualization of the Molecular Architecture of Cell–Cell Junctions In Situ by Cryo-Electron Tomography of Vitreous Sections

Cryo-electron tomography of vitreous sections is currently the only method for visualizing the eukaryotic ultrastructure at close to native state with molecular resolution. Here, we describe the detailed procedure of how to prepare suitable vitreous sections from mammalian skin for cryo-electron tomography, how to align the projection images of the tilt-series, and finally how to perform sub-tomogram averaging on macromolecular complexes with periodic arrangement such as desmosomes.