Abstract：
:AVS (Application Visualization System) is commercially available software for analyzing and viewing data. AVS is primarily used in the physical sciences and engineering, and here we describe the application of AVS for examining three-dimensional density maps generated by electron microscopy and image processing. For this purpose, AVS can be applied with relative ease, even though the software is indeed quite sophisticated. The primary advantage is that visualization applications can be generated by combining software components, called modules, into executable flow networks. Simple networks are described for generating ribbon diagrams of macromolecules, surface-shaded views, and contour maps. Easy to use dials, bar sliders, and buttons provide tremendous versatility for real-time manipulation of isosurface values, depth cueing, view orientation, size, and animation. In addition, AVS supplies a framework for building new modules in C or FORTRAN. Modules for excavation and cropping provide tools that are particularly useful for extracting segments of a map and for examining maps of supramolecular complexes such as viruses. We describe a number of modules we have designed for analysis of three-dimensional data sets, as well as modules for importing image data from other software packages into AVS. We also describe xformat, a stand-alone file conversion utility designed to allow import of a variety of image and map file formats into AVS.
journal_name
J Struct Bioljournal_title
Journal of structural biologyauthors
Sheehan B,Fuller SD,Pique ME,Yeager Mdoi
10.1006/jsbi.1996.0017subject
Has Abstractpub_date
1996-01-01 00:00:00pages
99-106issue
1eissn
1047-8477issn
1095-8657pii
S1047-8477(96)90017-9journal_volume
116pub_type
杂志文章abstract：:Two-dimensional crystallization on lipid monolayers is a versatile tool to obtain structural information of proteins by electron microscopy. An inherent problem with this approach is to prepare samples in a way that preserves the crystalline order of the protein array and produces specimens that are sufficiently flat ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2007.06.002
更新日期：2007-12-01 00:00:00
abstract：:Citropin 1.1 is a basic, highly hydrophobic, 16-amino acid peptide (GLFDVIKKVASVIGGL-NH(2)), displaying wide-spectrum antimicrobial activities. In this paper we describe the synthesis and antimicrobial properties of citropin 1.1 and its 18 analogs constituting mostly truncated fragments of citropin 1.1. Moreover, we e...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2009.07.012
更新日期：2009-11-01 00:00:00
abstract：:Single crystals of UDP-N-acetylglucosamine enolpyruvyltransferase of Enterobacter cloacae have been grown by vapor diffusion using phosphate buffer as the precipitant. The crystals belong to the monoclinic space group C2 with a = 86.9 A, b = 155.9 A, c = 83.8 A, beta = 91.6 degrees. Assuming two monomers per asymmetri...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1996.0071
更新日期：1996-07-01 00:00:00
abstract：:We have developed a simplified, efficient approach for the 3D reconstruction and analysis of mammalian cells in toto by electron microscope tomography (ET), to provide quantitative information regarding 'global' cellular organization at approximately 15-20 nm resolution. Two insulin-secreting beta cells-deemed 'functi...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2007.09.015
更新日期：2008-03-01 00:00:00
abstract：:Uptake and metabolism of silicon by diatoms are studied by the combined use of solid-state 29Si NMR spectroscopy and confocal laser fluorescence microscopy especially with respect to the presence and nature of an intracellular silicon-storage pool. Cells of the marine diatom Thalassiosira pseudonana were synchronized ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2007.09.010
更新日期：2008-01-01 00:00:00
abstract：:The repetitive Gly-X-Y sequence is the telltale sign of triple helical domains in collagens and collagen-like proteins. Most collagen sequences contain sporadic interruptions of this pattern, which may have functional roles in molecular flexibility, assembly or molecular recognition. However, the structural signatures...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2014.03.022
更新日期：2014-06-01 00:00:00
abstract：:Antifreeze proteins have the ability to bind to ice with high affinity and inhibit further crystal growth. The insect antifreeze protein from spruce budworm exhibits very high thermal hysteresis activity and is implicated in the protection of overwintering larvae from freezing. This protein has been crystallized in 20...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1999.4087
更新日期：1999-06-01 00:00:00
abstract：:Using a combination of atomic force, scanning and transmission electron microscopy, we found that avian erythrocytes infected with the avian malaria parasite Plasmodium gallinaceum develop approximately 60 nm wide and approximately 430 nm long furrow-like structures on the surface. Furrows begin to appear during the e...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2008.03.005
更新日期：2008-06-01 00:00:00
abstract：:High-resolution light-microscopy and high-throughput screening are two essential methodologies for characterizing cellular phenotypes. Optimally combining these methodologies in cell-based screening to test detailed molecular and cellular responses to multiple perturbations constitutes a major challenge. Here we descr...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2006.12.013
更新日期：2007-05-01 00:00:00
abstract：:The collagen which forms the egg case of the dogfish, Scyliorhinus canicula, is assembled in a three-dimensional network that results in a very resistant capsule. The capsule presumably accomplishes both a protective and a filtering role for the embryo contained within it. In the present work we have obtained electron...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1998.3994
更新日期：1998-01-01 00:00:00
abstract：:Charge contrast imaging (CCI) is a dynamic phenomenon recently reported in insulating and semiconducting materials imaged with low vacuum or variable pressure scanning electron microscopes (SEM). Data presented in this paper illustrates that CCI can also be applied to biominerals and biological soft-tissues and that u...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2006.04.004
更新日期：2006-09-01 00:00:00
abstract：:Gap junctions containing extensive, highly ordered crystalline arrays of hexagonally packed connexons have been isolated from the hepatopancreas of the arthropod, Homarus americanus (American lobster). The structure of such junctions has been studied to a resolution of approximately 25 A in three dimensions by electro...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/1047-8477(91)90075-8
更新日期：1991-06-01 00:00:00
abstract：:In Streptomycetes, tetracycline repressor family of transcription regulators (TetR-FTRs) controls various biological processes including antibiotic biosynthesis, cellular morphology and innate resistance. Here, we focus on understanding the structural basis of transcription regulation by CprB, a member of TetR-FTRs fr...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2017.03.006
更新日期：2017-05-01 00:00:00
abstract：:The concept of presenting antigens in a repetitive array to obtain high titers of specific antibodies is increasingly applied by using surface-engineered viruses or bacterial envelopes as novel vaccines. A case for this concept was made 25 years ago, when producing high-titer antisera against ordered arrays of gp23, t...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2003.08.004
更新日期：2003-09-01 00:00:00
abstract：:A novel preparation of spontaneously contracting heart cells embedded in a collagen strand provides an ideal experimental system for correlative structure-function experiments that utilize the techniques of electron microscopy, quantitative electron probe x-ray microanalysis (EPXMA) and imaging. Heart cells grown with...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/1047-8477(91)90061-z
更新日期：1991-02-01 00:00:00
abstract：:The first step to understanding brain function is to determine the brain's network structure. We report a three-dimensional analysis of the brain network of the fruit fly Drosophila melanogaster by synchrotron-radiation tomographic microscopy. A skeletonized wire model of the left half of the brain network was built b...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2013.08.012
更新日期：2013-11-01 00:00:00
abstract：:In recent years, cryo-electron microscopy (cryo-EM) has established itself as a key method in structural biology, permitting the structural characterization of large biomolecular complexes in various functional states. The data obtained through single-particle cryo-EM has recently seen a leap in resolution thanks to l...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2010.09.024
更新日期：2011-03-01 00:00:00
abstract：:A topological localization of epitopes on the surface of the Aa6 subunit of Androctonus australis hemocyanin has been carried out. First, immunocomplex strings composed of native hemocyanin and monoclonal antibodies were examined in the electron microscope and submitted to an image processing by correspondence analysi...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/1047-8477(90)90087-s
更新日期：1990-03-01 00:00:00
abstract：:The emergence of electron tomography as a tool for three dimensional structure determination of cells and tissues has brought its own challenges for the preparation of thick sections. High pressure freezing in combination with freeze substitution provides the best method for obtaining the largest volume of well-preser...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2007.09.002
更新日期：2008-03-01 00:00:00
abstract：:Three questions central to understanding the initiation of DNA replication in eukaryotes are: (1) Does DNA synthesis begin at a defined place? (2) What determines replication initiation sites? (3) What regulates an origin to fire only once per cell cycle? A key player in this is the origin recognition complex (ORC), r...
journal_title：Journal of structural biology
pub_type： 杂志文章,评审
doi：10.1016/s1047-8477(02)00538-5
更新日期：2002-10-01 00:00:00
abstract：:DNA regions close to the origin of replication were visualized by the green fluorescent protein (GFP)-Lac repressor/lac operator system. The number of oriC-GFP fluorescent spots per cell and per nucleoid in batch-cultured cells corresponded to the theoretical DNA replication pattern. A similar pattern was observed in ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2005.06.004
更新日期：2005-09-01 00:00:00
abstract：:Tobacco mosaic virus (TMV) is a plant virus with a highly ordered organisation and has been described in three different structural states: As stacked disks without RNA (X-ray crystallography), as a helical form with RNA (X-ray fibre diffraction) and as a second distinct helical form with RNA (cryo-EM). Here we presen...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2010.06.011
更新日期：2010-09-01 00:00:00
abstract：:Enhanced Green Fluorescent Protein (EGFP) is a variant of wild-type Green Fluorescent Protein from the jellyfish Aequorea victoria, whose mutations S65T and F64L increase brightness and folding efficiency. EGFP is extensively used in cell biology and biochemistry as a colocalization or expression reporter. Surprisingl...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2011.02.004
更新日期：2011-05-01 00:00:00
abstract：:Traditional single particle reconstruction methods use either the Fourier or the delta function basis to represent the particle density map. This paper proposes a more flexible algorithm that adaptively chooses the basis based on the data. Because the basis adapts to the data, the reconstruction resolution and signal-...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2012.04.012
更新日期：2012-07-01 00:00:00
abstract：:Immunoelectron microscopy of serial sections of leaf cells of wheat doubly infected by wheat streak mosaic virus and Agropyron mosaic virus or wheat spindle streak mosaic virus showed that structural proteins or virions associated only with homologous cylindrical inclusions (CI) or with self in aggregates. CI protein ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1993.1021
更新日期：1993-05-01 00:00:00
abstract：:Microbial type III polyketide synthases (PKSs) have revealed remarkable mechanistic as well as functional versatility. Recently, a type III PKS homolog from Azotobacter has been implicated in the biosynthesis of resorcinolic lipids, thus adding a new functional significance to this class of proteins. Here, we report t...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2008.02.009
更新日期：2008-06-01 00:00:00
abstract：:Here we introduce plusTipTracker, a Matlab-based open source software package that combines automated tracking, data analysis, and visualization tools for movies of fluorescently-labeled microtubule (MT) plus end binding proteins (+TIPs). Although +TIPs mark only phases of MT growth, the plusTipTracker software allows...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2011.07.009
更新日期：2011-11-01 00:00:00
abstract：:This study demonstrates the effects of progesterone on eggshell quality and ultrastructure by injecting progesterone into laying hens 2 and 5 h post-oviposition, respectively. Progesterone injected 2 h post-oviposition (P4-2 h) improved eggshell quality with a significant decrease (P < 0.01) in the thickness of the ma...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2019.107430
更新日期：2020-02-01 00:00:00
abstract：:The structures of the compact and swollen southern bean mosaic virus (SBMV) particles have been compared by X-ray diffraction and proton magnetic resonance (PMR). Small-angle X-ray scattering showed that removal of divalent cations at alkaline pH causes the particle diameter to increase from 289Å in the native SBMV by...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2017.06.003
更新日期：2017-12-01 00:00:00
abstract：:The Contrast Transfer Function (CTF) of an image, which modulates images taken from a Transmission Electron Microscope (TEM), is usually determined from the radial average of the power spectrum of the image (Frank, J., Three-dimensional Electron Microscopy of Macromolecular Assemblies, Oxford University Press, Oxford,...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2008.06.012
更新日期：2008-10-01 00:00:00
