IVE (Image Visualization Environment): A Software Platform for All Three-Dimensional Microscopy Applications

Chen, Hans; Hughes, Diana D.; Chan, Tan-An; Sedat, John W.; Agard, David A.

doi:10.1006/jsbi.1996.0010

Cited by 141 publications

(118 citation statements)

References 5 publications

Supporting

Mentioning

117

Contrasting

Order By: Relevance

“…It reads several file formats (CCP4 29 or MRC, BRIX or DSN6, 30 CNS 31 or XPLOR, 32 SPIDER, 33 DelPhi 34 or GRASP 35 potential maps, PRIISM, 36 NetCDF, 37,38 and DOCK 23 scoring grids), displays isosurfaces, meshes, and translucent solids, and allows interactive adjustment of thresholds, transparency, and brightness. Volume data is often displayed with related molecular models.…”

Section: Volume Viewermentioning

confidence: 99%

UCSF Chimera—A visualization system for exploratory research and analysis

et al. 2004

View full text Add to dashboard Cite

Abstract:The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from

show abstract

Section: Volume Viewermentioning

confidence: 99%

UCSF Chimera—A visualization system for exploratory research and analysis

et al. 2004

View full text Add to dashboard Cite

show abstract

“…Alignment initially used cross-correlation and then used gold particles or other dense features as fiducials. Reconstructed 3D volumes were generated by back-projection or by an iterative alignment and reconstruction procedure using the Priism package (49). Images were analyzed using FFTRANS and Ximdisp programs from the MRC package (50).…”

Section: Methodsmentioning

confidence: 99%

Structural organization of a filamentous influenza A virus

Calder

Wasilewski²,

Berriman³

et al. 2010

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

212

280

View full text Add to dashboard Cite

Influenza is a lipid-enveloped, pleomorphic virus. We combine electron cryotomography and analysis of images of frozen-hydrated virions to determine the structural organization of filamentous influenza A virus. Influenza A/Udorn/72 virions are capsule-shaped or filamentous particles of highly uniform diameter. We show that the matrix layer adjacent to the membrane is an ordered helix of the M1 protein and its close interaction with the surrounding envelope determines virion morphology. The ribonucleoprotein particles (RNPs) that package the genome segments form a tapered assembly at one end of the virus interior. The neuraminidase, which is present in smaller numbers than the hemagglutinin, clusters in patches and are typically present at the end of the virion opposite to RNP attachment. Incubation of virus at low pH causes a loss of filamentous morphology, during which we observe a structural transition of the matrix layer from its helical, membrane-associated form to a multilayered coil structure inside the virus particle. The polar organization of the virus provides a model for assembly of the virion during budding at the host membrane. Images and tomograms of A/Aichi/68 X-31 virions show the generality of these conclusions to non-filamentous virions.electron cryomicroscopy | matrix protein | ribonucleoprotein particles hemagglutinin | neuramindase

show abstract

“…Filters used for YFP were exciter, 495/20 nm/nm; emitter: 535/30 nm/nm; and 86006bs beamspitter (Chroma Technology, Brattleboro, VT). The image stacks of nuclei with a Z step size of 0.15 m were subjected to constrained iterative (15 iterations) deconvolution (Chen et al, 1996) by using softWoRx software (Applied Precision) on an Octane Workstation (SGI, Mountain View, CA). The maximum projection or the middle optical section of the deconvolved sections were exported to TIF format and then processed by Adobe Photoshop 6.0 for the final images.…”

Section: Fluorescence Deconvolution Microscopymentioning

confidence: 99%

Tissue-specific Expression and Dynamic Organization of SR Splicing Factors inArabidopsis

Fang

Hearn

Spector

2004

MBoC

View full text Add to dashboard Cite

The organization of the pre-mRNA splicing machinery has been extensively studied in mammalian and yeast cells and far less is known in living plant cells and different cell types of an intact organism. Here, we report on the expression, organization, and dynamics of pre-mRNA splicing factors (SR33, SR1/atSRp34, and atSRp30) under control of their endogenous promoters in Arabidopsis. Distinct tissue-specific expression patterns were observed, and differences in the distribution of these proteins within nuclei of different cell types were identified. These factors localized in a cell type-dependent speckled pattern as well as being diffusely distributed throughout the nucleoplasm. Electron microscopic analysis has revealed that these speckles correspond to interchromatin granule clusters. Time-lapse microscopy revealed that speckles move within a constrained nuclear space, and their organization is altered during the cell cycle. Fluorescence recovery after photobleaching analysis revealed a rapid exchange rate of splicing factors in nuclear speckles. The dynamic organization of plant speckles is closely related to the transcriptional activity of the cells. The organization and dynamic behavior of speckles in Arabidopsis cell nuclei provides significant insight into understanding the functional compartmentalization of the nucleus and its relationship to chromatin organization within various cell types of a single organism. INTRODUCTIONPre-mRNA (pre-mRNA) splicing, a process of excision of introns and ligation of exons, is essential for generating mature transcripts and enhancing mRNA export from the nucleus to the cytoplasm. Splicing occurs within a large macromolecular complex called the spliceosome, which is composed of U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles and a large number of non-small nuclear ribonucleoprotein particle proteins (Zhou et al., 2002). The latter include members of the SR (Ser-Arg) family of pre-mRNA splicing factors characterized by one or two N-terminal RNA recognition motifs that interact with the pre-mRNAs and a C-terminal variable-length Arg/Ser(RS)-rich domain that influences its subcellular localization and splicing activity depending upon its phosphorylation levels (for review, see Graveley, 2000).In mammalian cells, pre-mRNA splicing factors are concentrated in 20 -50 distinct nuclear domains called speckles as well as being diffusely distributed throughout the nucleoplasm, and this distribution corresponds to interchromatin granule clusters (IGCs) and perichromatin fibrils (PFs). PFs often extend from the periphery of IGCs or are present in the nucleoplasm at some distance from an IGCs (for review, see Lamond and Spector, 2003). It has been proposed that IGCs are storage and/or modification/reassembly sites for premRNA splicing factors and that splicing factors are recruited from these compartments to the sites of active transcription (PFs) (Jiménez-García and Spector, 1993). Disassembly of IGCs by overexpression of an SR protein kinase Clk/STY disrupts the coo...

show abstract

IVE (Image Visualization Environment): A Software Platform for All Three-Dimensional Microscopy Applications

Cited by 141 publications

References 5 publications

UCSF Chimera—A visualization system for exploratory research and analysis

UCSF Chimera—A visualization system for exploratory research and analysis

Structural organization of a filamentous influenza A virus

Tissue-specific Expression and Dynamic Organization of SR Splicing Factors inArabidopsis

Contact Info

Product

Resources

About