Showing papers in "Journal of Structural Biology in 2005"

TL;DR: A new method was developed to acquire images automatically at a series of specimen tilts, as required for tomographic reconstruction, using changes in specimen position at previous tilt angles to predict the position at the current tilt angle.

TL;DR: The primary automated data acquisition software system, Leginon, has been completely redesigned over the past two years and the system has demonstrated the capacity for high throughput data acquisition by acquiring images of more than 100,000 particles in a single session at the microscope.

TL;DR: A computationally efficient, two-dimensional, feature point tracking algorithm for the automated detection and quantitative analysis of particle trajectories as recorded by video imaging in cell biology.

TL;DR: The data suggests that the micelles of thioflavin T bind amyloid fibrils leading to enhancement of fluorescence emission, which suggests that positive charge on the thioFlavin T molecule has a role in its micelle formation that then bind the amyloids fibril.

TL;DR: The theoretical behaviour of the FSC in conjunction with the various factors which influence it are discussed: the number of "voxels" in a given Fourier shell, the symmetry of theructure, and the size of the structure within the reconstruction volume.

TL;DR: Thioflavin-T binds to amyloid fibrils such that their long axes are parallel, and it is proposed binding occurs in 'channels' that run along the length of the beta-sheet.

TL;DR: TOM software toolbox integrates established algorithms and new concepts tailored to the special needs of low dose ET, which provides a user-friendly unified platform for all processing steps: acquisition, alignment, reconstruction, and analysis.

TL;DR: The parameters influencing the quality of the sections are examined and a model taking into account the interplay between viscous flow and fracture is proposed, confirming that crevasses are formed on only one side of the section, and defining conditions by which they can be avoided.

TL;DR: A fourth low-dose state is created where the system can pre-select all the good holes in a grid square from a single CCD image taken at low magnification, making the system operative at much higher levels of automation.

TL;DR: 2D material property maps were generated from the mechanical-mineral correlation, showing that bands of high and low stiffness were found between the bone and tidemark, and between the ZCC and the unmineralized cartilage.

TL;DR: The results imply that the hydrophobic portion of amelogenin plays a role in an inhibition of crystal growth, whereas the C-terminal domain is essential for the alignment of crystals into parallel arrays.

TL;DR: A mechanical model of the normal cornea may be envisaged, whereby the fibril tension in the underlying "background" of isotropically arranged collagen helps to balance the intraocular pressure; while the extra preferentially aligned fibrils take up the additional tensile stress along the superior-inferior and nasal-temporal meridians exerted by the rectus muscles and the orbicularis.

TL;DR: High-energy synchrotron X-ray diffraction was used to study internal stresses in bone under in situ compressive loading of a 12-14 year old beagle fibula, and internal stresses rose proportionally with applied stress but at a higher rate, corresponding to stress concentration in the mineral of 2.8 times the stress applied.

TL;DR: It is shown that in both "centres of calcification" and fibres, organic compounds are associated with the mineral material at a deep structural level, and the hypothesis can be made that multiple and long recognized specificities of coral skeletons are linked to this biochemically driven crystallization process.

TL;DR: It is indicated that distinct actin conformations and/or structures are present in the nucleus and the cytoplasm of different cell types and that their distribution varies in response to external signals.

TL;DR: Two criteria based on a cross-validation approach, FSC(e/o) and NLOO, are mutually consistent when residual noise is the major resolution-limiting factor and provide a more reliable criterion, as expected, although it is computationally intensive.

TL;DR: The data suggest that PCD is a progressive and active process affecting all the anther tissues, first being triggered in the tapetum and then extended to other anther sporophytic tissues, leading to anther dehiscence.

TL;DR: A benchmark revealed that one of the most accurate models can usually be identified by the quality of its fit into the cryoEM density map, even for noisy maps at 15 angstroms resolution, which can be helpful in improving the accuracy of a comparative model.

TL;DR: Localised microcystins are localised in laboratory cultures of Microcystis PCC 7806 and PCC 7820 by immunogold labelling bycryosectioning and distribution of total gold label within each cell region or associated with inclusions indicated that most of the cells'microcystin pool was associated with the thylakoids.

TL;DR: Shell nacre (mother of pearl) of Pinctada margaritifera was analyzed by scanning electron microscopy and it is evidenced that tablets form a Voronoi tiling of the space: this suggests that their growth is controlled by an "aggregation-like" process of "crystallites" and not directly by the aragonite lattice growth.

TL;DR: An unprecedented view of the conversion of the PFO prepore to pore complex is provided and the change in inner-ring protein density is consistent with a mechanism in which the monomers within the prepore complex make a transition from a partially disordered state to a more ordered transmembrane beta-barrel in the porecomplex.

TL;DR: Atomic force microscopy is used to study the architecture of the photosynthetic apparatus and analyze the structure of single molecules in chromatophores of Phaeospirillum molischianum, finding the symmetry mismatch caused by octameric LH2 packing in a hexagonal lattice suggests lipophobic effects rather than specific inter-molecular interactions drive protein organization.

TL;DR: The reconstruction of freeze-fracture replicas with electron tomography has provided a novel experimental approach for the study of integral proteins inserted in phospholipid bilayer environments.

TL;DR: In this article, electron diffraction and X-ray diffraction data from filaments of Ure2p, of N-domains alone, of fragments thereof, and of an N-domain-containing fusion protein that demonstrate in each case the 4.7-A reflection that is typical for cross-β structure and highly indicative of amyloid.

TL;DR: Results show that an unmodified silicon nitride AFM tip is able to detect changes at the hair surface that can be related to the absence or presence of this layer due to treatment conditions and in particular that this monolayer has a lubricant effect.

TL;DR: Evidence for specific protein domain contact points between tropoelastin monomers during association by coacervation is provided and a specificity for particular lysines allowed for the construction of a model for the first close contacts between domains and the first detailed study of the cross-linking of tropoELastin.

TL;DR: A comparison of film and CCD detector in the acquisition of images in the low-to-medium resolution range using a 200 kV electron microscope equipped with field emission gun shows results that suggest the number of particle images needed for initial structure determination is reduced and the overall quality of the initial computed 3D models is improved.

TL;DR: A set of common conventions named the "3DEM Image Conventions" are proposed, designed as a standardized approach to image interpretation and presentation, which serve as a first step on which to build data-exchange solutions among existing software packages and as a vehicle for homogenous data representation in data archives, such as the EM Data Bank.

TL;DR: Investigation of the structural change of young healthy erythrocyte cytoskeletons upon extra Ca2+ binding to the cytoplasmic membrane in vitro shows that extra Ca 2+ binding increased the cytoskeleton rigidity and prevented spectrin aggregation during sample preparation.

TL;DR: The applicability of the spectral signal-to-noise ratio (SSNR) is extended to the evaluation of 3D volumes reconstructed with any reconstruction algorithm to measure the consistency between the data and a corresponding set of reprojections computed for the reconstructed 3D map.