Zeyun Yu

Three-dimensional electron microscopy reveals new details of membrane systems for Ca2+ signaling in the heart.

In the current study, the three-dimensional (3D) topologies of dyadic clefts and associated membrane organelles were mapped in mouse ventricular myocardium using electron tomography. The morphological details and the distribution of membrane systems, including transverse tubules (T-tubules), junctional sarcoplasmic reticulum (SR) and vicinal mitochondria, were determined and presumed to be crucial for controlling cardiac Ca2+ dynamics. The geometric complexity of T-tubules that varied in diameter with frequent branching was clarified. Dyadic clefts were intricately shaped and remarkably small (average 4.39×105 nm3, median 2.81×105 nm3). Although a dyadic cleft of average size could hold maximum 43 ryanodine receptor (RyR) tetramers, more than one-third of clefts were smaller than the size that is able to package as many as 15 RyR tetramers. The dyadic clefts were also adjacent to one another (average end-to-end distance to the nearest dyadic cleft, 19.9 nm) and were distributed irregularly along T-tubule branches. Electron-dense structures that linked membrane organelles were frequently observed between mitochondrial outer membranes and SR or T-tubules. We, thus, propose that the topology of dyadic clefts and the neighboring cellular micro-architecture are the major determinants of the local control of Ca2+ in the heart, including the establishment of the quantal nature of SR Ca2+ releases (e.g. Ca2+ sparks).

New algorithms in 3D image analysis and their application to the measurement of a spatialized pore size distribution in soils

We introduce a skeletization method based on the Voronoi diagram to determine local pole sizes in any porous medium. Using the skeleton of the pore space in a 3D image of the porous medium, a pole size value is assigned to each voxel and a reconstructed image of a spatialized local pore size distribution is created. The reconstructed image provides a means for calculating the global volume versus size pore distribution. It is also used to carry out fluid invasion simulation which take into account the connectivity of and constrictions in the pore network. As an example we simulate mercury intrusion in a 3D soil image

A fast and adaptive method for image contrast enhancement

In this paper we describe a fast approach for image contrast enhancement, based on localized contrast manipulation. Our approach is not only last and easy to implement, but also has several other promising properties (adaptive, multiscale, weighted localization, etc.). We will also discuss in this paper an anisotropic version of our approach. Several examples of medical images, including brain MR images, chest CT images and mammography images, will be provided to demonstrate the performance of our approach.

Feature-preserving adaptive mesh generation for molecular shape modeling and simulation

We describe a chain of algorithms for molecular surface and volumetric mesh generation. We take as inputs the centers and radii of all atoms of a molecule and the toolchain outputs both triangular and tetrahedral meshes that can be used for molecular shape modeling and simulation. Experiments on a number of molecules are demonstrated, showing that our methods possess several desirable properties: feature-preservation, local adaptivity, high quality, and smoothness (for surface meshes). We also demonstrate an example of molecular simulation using the finite element method and the meshes generated by our method. The approaches presented and their implementations are also applicable to other types of inputs such as 3D scalar volumes and triangular surface meshes with low quality, and hence can be used for generation/improvement of meshes in a broad range of applications.

Computational Approaches for Automatic Structural Analysis of Large Biomolecular Complexes

We present computational solutions to two problemsof macromolecular structure interpretation from reconstructedthree-dimensional electron microscopy (3D-EM) maps of largebio-molecular complexes at intermediate resolution (5A-15A). Thetwo problems addressed are: (a) 3D structural alignment (matching)between identified and segmented 3D maps of structure units(e.g. trimeric configuration of proteins), and (b) the secondarystructure identification of a segmented protein 3D map (i.e.locations of a-helices, b -sheets). For problem (a), we presentan efficient algorithm to correlate spatially (and structurally)two 3D maps of structure units. Besides providing a similarityscore between structure units, the algorithm yields an effectivetechnique for resolution refinement of repeated structure units,by 3D alignment and averaging. For problem (b), we present anefficient algorithm to compute eigenvalues and link eigenvectorsof a Gaussian convoluted structure tensor derived from theprotein 3D Map, thereby identifying and locating secondarystructural motifs of proteins. The efficiency and performanceof our approach is demonstrated on several experimentallyreconstructed 3D maps of virus capsid shells from single-particlecryo-EM, as well as computationally simulated protein structuredensity 3D maps generated from protein model entries in theProtein Data Bank.

Modelling cardiac calcium sparks in a three‐dimensional reconstruction of a calcium release unit

•  We have developed a detailed computational model of a cardiac Ca2+ spark based on a three dimensional reconstruction of electron tomograms. •  Our model predicts near total junctional Ca2+ depletion after the spark, while regional Ca2+ reserve is preserved. The local Ca2+ gradient inferred by these findings reconciles previous model predictions with experimental measurements. •  Differences in local distribution of calsequestrin have a profound impact on spark termination time, as reported by Fluo5, solely based on its Ca2+ buffering capacity. •  The SERCA pump can prolong spark release time by pumping Ca2+ back into the junctional SR during the spark.

Automatic ultrastructure segmentation of reconstructed CryoEM maps of icosahedral viruses

We present an automatic algorithm to segment all the local and global asymmetric units of a three-dimensional density map of icosahedral viruses. This approach is readily applicable to the structural analysis of a broad range of virus structures that are reconstructed using cryo-electron microscopy (cryo-EM) technique. Our algorithm includes three major steps operating on the three dimensional density map: the detection of critical points of the volumetric density function, the detection of global and local symmetry axes, and, finally, the boundary segmentation of all the asymmetric units. We demonstrate the efficacy of our algorithm and report our results on several experimental volumetric datasets, consisting of both reconstructed cryo-EM molecular density maps taken from the European Bioinformatics Institute archive, as well our own synthetically generated (blurred) maps calculated from X-ray resolution molecular structural data taken from the Protein Data Bank.

Nanoscale Distribution of Ryanodine Receptors and Caveolin-3 in Mouse Ventricular Myocytes: Dilation of T-Tubules near Junctions

We conducted super-resolution light microscopy (LM) imaging of the distribution of ryanodine receptors (RyRs) and caveolin-3 (CAV3) in mouse ventricular myocytes. Quantitative analysis of data at the surface sarcolemma showed that 4.8% of RyR labeling colocalized with CAV3 whereas 3.5% of CAV3 was in areas with RyR labeling. These values increased to 9.2 and 9.0%, respectively, in the interior of myocytes where CAV3 was widely expressed in the t-system but reduced in regions associated with junctional couplings. Electron microscopic (EM) tomography independently showed only few couplings with caveolae and little evidence for caveolar shapes on the t-system. Unexpectedly, both super-resolution LM and three-dimensional EM data (including serial block-face scanning EM) revealed significant increases in local t-system diameters in many regions associated with junctions. We suggest that this regional specialization helps reduce ionic accumulation and depletion in t-system lumen during excitation-contraction coupling to ensure effective local Ca²⁺ release. Our data demonstrate that super-resolution LM and volume EM techniques complementarily enhance information on subcellular structure at the nanoscale.

A segmentation-free approach for skeletonization of gray-scale images via anisotropic vector diffusion

In this paper we describe a method for skeletonization of gray-scale images without segmentation. Our method is based on anisotropic vector diffusion. The skeleton strength map, calculated from the diffused vector field, provides us a measure of how possible each pixel could be on the skeletons. The final skeletons are traced from the skeleton strength map, which mimics the behavior of edge detection from the edge strength map of the original image. A couple of real or synthesized images will be shown to demonstrate the performance of our algorithm.

Image segmentation using gradient vector diffusion and region merging

The Active Contour (or Snake) Model is recognized as one of the efficient tools for 2D/3D image segmentation. However traditional snake models prove to be limited in several aspects. The present paper describes a set of diffusion equations applied to image gradient vectors, yielding a vector field over the image domain. The obtained vector field provides the Snake Model with an external force as well as an automatic way to generate the initial contours. Finally a region merging technique is employed to further improve the segmentation results.