The Local Maximum Clustering Method and Its Application in Microarray Gene Expression Data Analysis

Wu, Xiongwu; Chen, Yidong; Brooks, Bernard R.; Su, Yan

doi:10.1155/s1110865704309145

Cited by 25 publications

(14 citation statements)

References 14 publications

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“…From the tomographic volumes described above, 1,200 subvolumes (50 ϫ 50 ϫ 150 in pixels; 7.5 Å/pixel) were extracted from the ordered regions of the Caulobacter tomograms to create a stack of subvolumes. The subvolumes were classified by using the local-maximum clustering method (25), and the major clusters were averaged to create an initial template for further alignment and averaging. The subvolumes were aligned against the initial template by using the grid-threading Monte Carlo searching algorithm (26).…”

Section: Methodsmentioning

confidence: 99%

Chemoreceptors in Caulobacter crescentus : Trimers of Receptor Dimers in a Partially Ordered Hexagonally Packed Array

Khursigara

Subramaniam

2008

J Bacteriol

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Chemoreceptor arrays are macromolecular complexes that form extended assemblies primarily at the poles of bacterial cells and mediate chemotaxis signal transduction, ultimately controlling cellular motility. We have used cryo-electron tomography to determine the spatial distribution and molecular architecture of signaling molecules that comprise chemoreceptor arrays in wild-type Caulobacter crescentus cells. We demonstrate that chemoreceptors are organized as trimers of receptor dimers, forming partially ordered hexagonally packed arrays of signaling complexes in the cytoplasmic membrane. This novel organization at the threshold between order and disorder suggests how chemoreceptors and associated molecules are arranged in signaling assemblies to respond dynamically in the activation and adaptation steps of bacterial chemotaxis.Two key multiprotein complexes are essential for mediating bacterial chemotaxis: the chemosensory apparatus, which receives and transmits environmental cues, and the motility system that mediates cellular movement (23). Methyl-accepting chemotaxis proteins (MCPs), or chemoreceptors, form the basis of the signaling apparatus and direct cell movement by regulating the histidine autokinase CheA, which ultimately modulates the direction of flagellum rotation. Chemoreceptors and CheA form a ternary complex with the adaptor protein CheW, which together provide a signaling scaffold that plays a crucial role in signal processing in bacterial chemotaxis (12,13,27). In the dimorphic gram-negative Caulobacter crescentus, the chemosensory apparatus and sole flagellum are localized to a single pole of the highly motile swarmer cell type (2, 7), while both complexes are completely absent from nonmotile stalked cells (1,10,19).We previously identified chemoreceptor arrays at the polar region of intact wild-type Escherichia coli and Bdellovibrio bacteriovorus cells by using low-dose cryo-electron microscopy (5, 27). In these organisms, arrays were characterized in an edge-on orientation by striations orthogonal to the cytoplasmic membrane that corresponded to chemoreceptors, and by a line of density near the cell poles, which was designated as the signaling scaffold composed of CheA and CheW. The presence of both chemoreceptors and CheA within the arrays was confirmed by immuno-electron microscopy (27). Here, we extend these studies to another gram-negative bacterium and describe the partially ordered hexagonal arrangement of chemotaxis signaling complexes at the flagellated pole in Caulobacter swarmer cells. MATERIALS AND METHODSBacterial strains and culture conditions. C. crescentus strain CB15N was cultured in peptone-yeast extract (PYE) medium (0.2% Bacto peptone, 0.1% yeast extract, 0.03% MgSO 4 ⅐ 7H 2 O, and 0.007% CaCl 2 ⅐ 2H 2 O) (8) at 30°C and 250 rpm. Specimen preparation, data collection, and image analysis. Chemoreceptor arrays were observed in over 65 individual Caulobacter swarmer cells that were separated from the stalked cell population by using a modified synchronization protocol. Brief...

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Section: Methodsmentioning

confidence: 99%

Chemoreceptors in Caulobacter crescentus : Trimers of Receptor Dimers in a Partially Ordered Hexagonally Packed Array

Khursigara

Subramaniam

2008

J Bacteriol

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“…It is mainly composed of four steps: 1) calculate the filter response using Eq. (5) with γ = 2 and a set of σ ∈ [ σ min , σ max ]; 2) exploit the distance map to constrain the maximal scale and obtain

R (x, y) = \arg \max_{σ \in [σ_{m i n}, σ_{M A X}]} \nabla^{2} L (x, y; σ)

, where σ MAX = max{ σ min , min{ σ max , 2 × D ( x, y )}} and D ( x, y ) represents distance map; 3) seek local maxima of R ( x, y ) as seeds; 4) use a local-maximum clustering algorithm [88] to remove false seeds caused by minor peaks in the distance map. Instead of using local-maxima clustering, Chang et al [69] have exploited the response strength and the blue ratio intensity to constrain the LoG based nucleus marker selection on H&E stained histopathology images.…”

Section: Nucleus and Cell Detection Methodsmentioning

confidence: 99%

“…η ( L v , L u ) = 1 if L v ≠ L u , otherwise 0. σ is a fixed parameter. After foreground segmentation, nuclei are initially segmented with LoG detection followed by size-constrained clustering [88]. Finally, graph cut with α -expansion [277] and graph coloring [233] are used to refine the initial segmented contours.…”

Section: Nucleus and Cell Segmentation Methodsmentioning

confidence: 99%

Robust Nucleus/Cell Detection and Segmentation in Digital Pathology and Microscopy Images: A Comprehensive Review

Xing

Yang

2016

IEEE Rev. Biomed. Eng.

425

220

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Digital pathology and microscopy image analysis is widely used for comprehensive studies of cell morphology or tissue structure. Manual assessment is labor intensive and prone to inter-observer variations. Computer-aided methods, which can significantly improve the objectivity and reproducibility, have attracted a great deal of interest in recent literatures. Among the pipeline of building a computer-aided diagnosis system, nucleus or cell detection and segmentation play a very important role to describe the molecular morphological information. In the past few decades, many efforts have been devoted to automated nucleus/cell detection and segmentation. In this review, we provide a comprehensive summary of the recent state-of-the-art nucleus/cell segmentation approaches on different types of microscopy images including bright-field, phase-contrast, differential interference contrast (DIC), fluorescence, and electron microscopies. In addition, we discuss the challenges for the current methods and the potential future work of nucleus/cell detection and segmentation.

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“…30 The distances between conformations are calculated as the sum of the difference square of the backbone dihedral angles. Figure 10 shows the representative structures of these six major clusters.…”

Section: Folding Of a Pentamer Peptidementioning

confidence: 99%

Force-momentum-based self-guided Langevin dynamics: A rapid sampling method that approaches the canonical ensemble

Brooks²

2011

The Journal of Chemical Physics

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The self-guided Langevin dynamics (SGLD) is a method to accelerate conformational searching. This method is unique in the way that it selectively enhances and suppresses molecular motions based on their frequency to accelerate conformational searching without modifying energy surfaces or raising temperatures. It has been applied to studies of many long time scale events, such as protein folding. Recent progress in the understanding of the conformational distribution in SGLD simulations makes SGLD also an accurate method for quantitative studies. The SGLD partition function provides a way to convert the SGLD conformational distribution to the canonical ensemble distribution and to calculate ensemble average properties through reweighting. Based on the SGLD partition function, this work presents a force-momentum-based self-guided Langevin dynamics (SGLDfp) simulation method to directly sample the canonical ensemble. This method includes interaction forces in its guiding force to compensate the perturbation caused by the momentum-based guiding force so that it can approximately sample the canonical ensemble. Using several example systems, we demonstrate that SGLDfp simulations can approximately maintain the canonical ensemble distribution and significantly accelerate conformational searching. With optimal parameters, SGLDfp and SGLD simulations can cross energy barriers of more than 15 kT and 20 kT, respectively, at similar rates for LD simulations to cross energy barriers of 10 kT. The SGLDfp method is size extensive and works well for large systems. For studies where preserving accessible conformational space is critical, such as free energy calculations and protein folding studies, SGLDfp is an efficient approach to search and sample the conformational space.

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The Local Maximum Clustering Method and Its Application in Microarray Gene Expression Data Analysis

Cited by 25 publications

References 14 publications

Chemoreceptors in Caulobacter crescentus : Trimers of Receptor Dimers in a Partially Ordered Hexagonally Packed Array

Chemoreceptors in Caulobacter crescentus : Trimers of Receptor Dimers in a Partially Ordered Hexagonally Packed Array

Robust Nucleus/Cell Detection and Segmentation in Digital Pathology and Microscopy Images: A Comprehensive Review

Force-momentum-based self-guided Langevin dynamics: A rapid sampling method that approaches the canonical ensemble

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