Four-dimensional imaging for cryo-electron microscopy experiments using molecular simulations and manifold learning

Elucidating protein conformational changes is essential because conformational changes are closely related to the functions of proteins. Cryo-electron microscopy (cryo-EM) experiment can be used to reconstruct protein conformational changes via a method that involves using the experimental data (two-dimensional protein images). In this study, a reconstruction method, referred to as the "four-dimensional imaging," was proposed. In our four-dimensional imaging technique, the protein conformational change was obtained using the two-dimensional protein images (the three-dimensional electron density maps used in previously proposed techniques were not used). The protein conformation for each two-dimensional protein image was obtained using our original protocol with molecular dynamics simulations. Using a manifold-learning technique and two-dimensional protein images, the protein conformations were arranged according to the conformational change of the protein. By arranging the protein conformations according to the arrangement of the protein images, four-dimensional imaging is constructed. A simulation for a cryo-EM experiment demonstrated the validity of our four-dimensional imaging technique.

Speckle variance optical coherence tomography of blood flow in the beating mouse embryonic heart

Efficient separation of blood and cardiac wall in the beating embryonic heart is essential and critical for experiment-based computational modelling and analysis of early-stage cardiac biomechanics. Although speckle variance optical coherence tomography (SV-OCT) relying on calculation of intensity variance over consecutively acquired frames is a powerful approach for segmentation of fluid flow from static tissue, application of this method in the beating embryonic heart remains challenging because moving structures generate SV signal indistinguishable from the blood. Here, we demonstrate a modified four-dimensional SV-OCT approach that effectively separates the blood flow from the dynamic heart wall in the beating mouse embryonic heart. The method takes advantage of the periodic motion of the cardiac wall and is based on calculation of the SV signal over the frames corresponding to the same phase of the heartbeat cycle. Through comparison with Doppler OCT imaging, we validate this speckle-based approach and show advantages in its insensitiveness to the flow direction and velocity as well as reduced influence from the heart wall movement. This approach has a potential in variety of applications relying on visualization and segmentation of blood flow in periodically moving structures, such as mechanical simulation studies and finite element modelling. Picture: Four-dimensional speckle variance OCT imaging shows the blood flow inside the beating heart of an E8.5 mouse embryo.

A comparison of different approaches for imaging cracks in composites by X-ray microtomography

X-ray computed tomography (CT) has emerged as a key imaging tool in the characterization of materials, allowing three-dimensional visualization of an object non-destructively as well as enabling the monitoring of damage accumulation over time through time-lapse imaging. However, small defects and cracks can be difficult to detect, particularly in composite materials where low-contrast, plate-like geometries of large area can compromise detectability. Here, we investigate a number of strategies aimed at increasing the capability of X-ray CT to detect composite damage such as transverse ply cracking and delamination, looking specifically at a woven glass fibre-reinforced three-dimensional composite. High-resolution region of interest (ROI) scanning, in situ loading, phase contrast and contrast agents are examined systematically as strategies for improving the defect detectability. Spatial resolution, contrast, signal-to-noise ratio, full width at half maximum, user friendliness and measurement time are all considered. Taken together, the results suggest that high-resolution ROI scanning combined with the increased contrast resulting from staining give the highest defect detectability. This article is part of the themed issue 'Multiscale modelling of the structural integrity of composite materials'.

The quest for four-dimensional imaging in plant cell biology: it's just a matter of time

BACKGROUND

Analysis of plant cell dynamics over time, or four-dimensional imaging (4-DI), represents a major goal of plant science. The ability to resolve structures in the third dimension within the cell or tissue during developmental events or in response to environmental or experimental stresses (i.e. 4-DI) is critical to our understanding of gene expression, post-expression modulations of macromolecules and sub-cellular system interactions.

SCOPE

Microscopy-based technologies have been profoundly integral to this type of investigation, and new and refined microscopy technologies now allow for the visualization of cell dynamics with unprecedented resolution, contrast and experimental versatility. However, certain realities of light and electron microscopy, choice of specimen and specimen preparation techniques limit the scope of readily attaining 4-DI. Today, the plant microscopist must use a combinatorial strategy whereby multiple microscopy-based investigations are used. Modern fluorescence, confocal laser scanning, transmission electron and scanning electron microscopy provide effective conduits for synthesizing data detailing live cell dynamics and highly resolved snapshots of specific cell structures that will ultimately lead to 4-DI. This review provides a synopsis of such technologies available.

Multimodality optical imaging of embryonic heart microstructure

Study of developmental heart defects requires the visualization of the microstructure and function of the embryonic myocardium, ideally with minimal alterations to the specimen. We demonstrate multiple endogenous contrast optical techniques for imaging the Xenopus laevis tadpole heart. Each technique provides distinct and complementary imaging capabilities, including: 1. 3-D coherence microscopy with subcellular (1 to 2 microm) resolution in fixed embryos, 2. real-time reflectance confocal microscopy with large penetration depth in vivo, and 3. ultra-high speed (up to 900 frames per second) that enables real-time 4-D high resolution imaging in vivo. These imaging modalities can provide a comprehensive picture of the morphologic and dynamic phenotype of the embryonic heart. The potential of endogenous-contrast optical microscopy is demonstrated for investigation of the teratogenic effects of ethanol. Microstructural abnormalities associated with high levels of ethanol exposure are observed, including compromised heart looping and loss of ventricular trabecular mass.