Applications of a bilateral denoising filter in biological electron microscopy

Jiang, Wen; Baker, Matthew L.; Qiu, Wu; Bajaj, Chandrajit L.; Chiu, Wah

doi:10.1016/j.jsb.2003.09.028

Cited by 114 publications

(105 citation statements)

References 23 publications

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“…For interactive exploration of the three-dimensional volumes, we routinely used the Volume Rover package , usually followed by one round of bilateral filtering (Jiang et al 2003) or denoising by nonlinear anisotropic diffusion (Frangakis and Hegerl PLT Dehydration during progressive lowering of temperature, CP conventional preparation with dehydration on ice, TX extraction with Triton X-100 followed by fixation and dehydration during progressive lowering of temperature 2001). In some cases, features were extracted by the boundary segmentation approach Bajaj and Yu 2005) or the watershed immersion algorithm (Volkmann 2002).…”

Section: Three-dimensional Tomographic Analysis Of Hair-bundle Linksmentioning

confidence: 99%

“…Although it is unclear whether the auxiliary link and main tip link are made of the same proteins, both structures occupy comparable volumes and curl up when detached. The divergence of an auxiliary link from the main tip link may underlie the forking of tip links (Furness and Hackney 1985;Kachar et al 2000), for both filaments in the main link connect to the membrane surface. In our projection images, as well as in published micrographs (Zhao et al 1996;Siemens et al 2004), the sides of stereocilia often display globular extracellular densities that may reflect detached auxiliary links.…”

Section: Organization Of Tip Linksmentioning

confidence: 99%

“…If exposed to lanthanoid ions or Ca 2+ chelators, tip links disappear concomitantly with the loss of responsiveness; as they regenerate over several hours, transduction recovers (Zhao et al 1996). When analyzed by high-resolution scanning electron microscopy, each tip link appears to comprise two filaments arranged in a right-handed, coiled-coil configuration (Kachar et al 2000). Fourier analysis of projection images suggests instead a double-or triple-helical structure (Tsuprun and Santi 2000;Tsuprun et al 2004).…”

Section: Introductionmentioning

confidence: 99%

“…Fourier analysis of projection images suggests instead a double-or triple-helical structure (Tsuprun and Santi 2000;Tsuprun et al 2004). A tip link may branch 10-50 nm below its upper insertion and may contact the membrane at two or three sites at its lower end (Furness and Hackney 1985;Kachar et al 2000). The tip link may consist of glycosylated protein, for polycationic compounds label it (Neugebauer and Thurm 1987;Tsuprun and Santi 2000), and in avian preparations, it is severed by proteases only after deglycosylation (Kachar et al 2000).…”

Section: Introductionmentioning

confidence: 99%

“…A tip link may branch 10-50 nm below its upper insertion and may contact the membrane at two or three sites at its lower end (Furness and Hackney 1985;Kachar et al 2000). The tip link may consist of glycosylated protein, for polycationic compounds label it (Neugebauer and Thurm 1987;Tsuprun and Santi 2000), and in avian preparations, it is severed by proteases only after deglycosylation (Kachar et al 2000). Genetic and immunological evidence localizes cadherin 23 to the tip link Sollner et al 2004), where it evidently constitutes the structure's upper two thirds (Kazmierczak et al 2007).…”

Section: Introductionmentioning

confidence: 99%

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

Auer

Koster

Ziese

et al. 2008

JARO

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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.

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Section: Three-dimensional Tomographic Analysis Of Hair-bundle Linksmentioning

confidence: 99%

Section: Organization Of Tip Linksmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

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

Auer

Koster

Ziese

et al. 2008

JARO

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Macromolecular structure modeling from 3D EM using VolRover 2.0

2012

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We report several tools for 3DEM structure identification and model-based refinement developed by our research group and implemented in our in-house software package, VolRover. For viral density maps with icosahedral symmetry, we segment the capsid, polymeric and monomeric subunits using segmentation techniques based on symmetry detection and fast marching. For large biomolecules without symmetry information, we use a multi-seeded fast-marching method to segment meaningful substructures. In either case, we subject the resulting segmented subunit to secondary structure detection when the EM resolution is sufficiently high, and rigid-body fitting when the corresponding crystal structure is available. Secondary structure elements are identified by our volume- and boundary-based skeletonization methods as well as a new method, currently in development, based on solving the grassfire flow equation. For rigid-body fitting, we use a translational fast Fourier based scheme. We apply our segmentation, secondary structure elements identification, and rigid-body fitting techniques to the PSB 2011 cryo-EM modeling challenge data, and compare our results to those submitted from other research groups. The comparisons show that our software is capable of segmenting relatively accurate subunits from a viral or protein assembly, and that the high segmentation quality leads in turn to high-quality results of secondary structure elements identification and rigid-body fitting.

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Geometric modeling of subcellular structures, organelles, and multiprotein complexes

Feng

Xia

Tong

et al. 2012

Numer Methods Biomed Eng

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SUMMARY Recently, the structure, function, stability, and dynamics of subcellular structures, organelles, and multi-protein complexes have emerged as a leading interest in structural biology. Geometric modeling not only provides visualizations of shapes for large biomolecular complexes but also fills the gap between structural information and theoretical modeling, and enables the understanding of function, stability, and dynamics. This paper introduces a suite of computational tools for volumetric data processing, information extraction, surface mesh rendering, geometric measurement, and curvature estimation of biomolecular complexes. Particular emphasis is given to the modeling of cryo-electron microscopy data. Lagrangian-triangle meshes are employed for the surface presentation. On the basis of this representation, algorithms are developed for surface area and surface-enclosed volume calculation, and curvature estimation. Methods for volumetric meshing have also been presented. Because the technological development in computer science and mathematics has led to multiple choices at each stage of the geometric modeling, we discuss the rationales in the design and selection of various algorithms. Analytical models are designed to test the computational accuracy and convergence of proposed algorithms. Finally, we select a set of six cryo-electron microscopy data representing typical subcellular complexes to demonstrate the efficacy of the proposed algorithms in handling biomolecular surfaces and explore their capability of geometric characterization of binding targets. This paper offers a comprehensive protocol for the geometric modeling of subcellular structures, organelles, and multiprotein complexes.

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Applications of a bilateral denoising filter in biological electron microscopy

Cited by 114 publications

References 23 publications

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

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

Macromolecular structure modeling from 3D EM using VolRover 2.0

Geometric modeling of subcellular structures, organelles, and multiprotein complexes

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