Fast tomographic reconstruction on multicore computers

Agulleiro, J.I.; Fernández, José‐Jesús

doi:10.1093/bioinformatics/btq692

Cited by 249 publications

(188 citation statements)

References 8 publications

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“…An input/output library for the MRC file format maintains the header information generated during collection throughout the processing. The main executable encompasses the following: drift correction of dose-fractionated data using dosefgpu_driftcorr (29) and the assembly of corrected sums into tilt series, automatic fiducial seed model generation by RAPTOR software (44), alignment and contrast transfer function correction of tilt series by IMOD software (45,46), and reconstruction of tilt series into tomograms by TOMO3D software (47). The flowchart is shown in SI Appendix, Fig.…”

Section: Methodsmentioning

confidence: 99%

Visualization of the type III secretion sorting platform of Shigella flexneri

Hu¹,

Morado²,

Margolin³

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

204

300

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Bacterial type III secretion machines are widely used to inject virulence proteins into eukaryotic host cells. These secretion machines are evolutionarily related to bacterial flagella and consist of a large cytoplasmic complex, a transmembrane basal body, and an extracellular needle. The cytoplasmic complex forms a sorting platform essential for effector selection and needle assembly, but it remains largely uncharacterized. Here we use high-throughput cryoelectron tomography (cryo-ET) to visualize intact machines in a virulent Shigella flexneri strain genetically modified to produce minicells capable of interaction with host cells. A high-resolution in situ structure of the intact machine determined by subtomogram averaging reveals the cytoplasmic sorting platform, which consists of a central hub and six spokes, with a pod-like structure at the terminus of each spoke. Molecular modeling of wild-type and mutant machines allowed us to propose a model of the sorting platform in which the hub consists mainly of a hexamer of the Spa47 ATPase, whereas the MxiN protein comprises the spokes and the Spa33 protein forms the pods. Multiple contacts among those components are essential to align the Spa47 ATPase with the central channel of the MxiA protein export gate to form a unique nanomachine. The molecular architecture of the Shigella type III secretion machine and its sorting platform provide the structural foundation for further dissecting the mechanisms underlying type III secretion and pathogenesis and also highlight the major structural distinctions from bacterial flagella.nanomachine | injectisome | pathogen-host interaction | cryo-electron tomography | protein secretion

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Section: Methodsmentioning

confidence: 99%

Visualization of the type III secretion sorting platform of Shigella flexneri

Hu¹,

Morado²,

Margolin³

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

204

300

View full text Add to dashboard Cite

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“…The final aligned tilt series were normalized and reconstructed using the simultaneous iterative reconstruction technique implemented in Tomo3D (33). Individual virus particles were extracted from tomograms using IMOD.…”

Section: Methodsmentioning

confidence: 99%

The Role of Capsid Maturation on Adenovirus Priming for Sequential Uncoating

Pérez-Berná

Ortega-Esteban

Menéndez-Conejero

et al. 2012

Journal of Biological Chemistry

132

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“…The acquired images were rescaled by a four-fold binning factor to yield a pixel size at the specimen level in the range 1.56-2.33 nm. Standard electron tomography processing then followed (Fernandez, 2012), using patch-tracking-based alignment with IMOD (Kremer et al, 1996) and Weighted-BackProjection reconstruction with Tomo3D software (Agulleiro and Fernandez, 2011). The resulting tomogram was subjected to noise reduction using slight Gaussian filtering (Martinez-Sanchez et al, 2011).…”

Section: Electron Tomographymentioning

confidence: 99%

3D electron tomography of brain tissue unveils distinct Golgi structures that sequester cytoplasmic contents in neurons

Fernández-Fernández

Ruiz-Garcia

Martin-Solana

et al. 2016

Journal of Cell Science

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Macroautophagy is morphologically characterized by autophagosome formation. Autophagosomes are double-membraned vesicles that sequester cytoplasmic components for further degradation in the lysosome. Basal autophagy is paramount for intracellular quality control in post-mitotic cells but, surprisingly, the number of autophagosomes in post-mitotic neurons is very low, suggesting that alternative degradative structures could exist in neurons. To explore this possibility, we have examined neuronal subcellular architecture by performing three-dimensional (3D) electron tomography analysis of mouse brain tissue that had been preserved through high-pressure freezing. Here, we report that sequestration of neuronal cytoplasmic contents occurs at the Golgi complex in distinct and dynamic structures that coexist with autophagosomes in the brain. These structures are composed of several concentric double-membraned layers that appear to be formed simultaneously by the direct bending and sealing of discrete Golgi stacks. These structures are labelled for proteolytic enzymes, and lysosomes and late endosomes are found in contact with them, leading to the possibility that the sequestered material could be degraded inside them. Our findings highlight the key role that 3D electron tomography, together with tissue rapid-freezing techniques, will have in gaining new knowledge about subcellular architecture.

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Fast tomographic reconstruction on multicore computers

Cited by 249 publications

References 8 publications

Visualization of the type III secretion sorting platform of Shigella flexneri

Visualization of the type III secretion sorting platform of Shigella flexneri

The Role of Capsid Maturation on Adenovirus Priming for Sequential Uncoating

3D electron tomography of brain tissue unveils distinct Golgi structures that sequester cytoplasmic contents in neurons

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