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At least 1,351 records · Page 75Linked to original sources
PubMed1997

Utility of Butvar support film and methylamine tungstate stain in three-dimensional electron microscopy: agreement between stain and frozen-hydrated reconstructions.

A random conical tilt reconstruction of negatively stained Saccharomyces cerevisiae fatty acid synthase was used as a model to compute a three-dimensional reconstruction from untilted stain specimens of the molecules in multiple orientations using a three-dimensional projection alignment method. The resulting structure (24 A resolution) has a more uniform resolution than the initial structure and the handedness revealed in the random conical tilt method is preserved. In a similar approach, this model was used to compute a 21-A-resolution frozen-hydrated structure from untilted specimens of the molecules in multiple orientations. Even though the reconstructions are in close agreement, the stain structure appears to enhance the protein density associated with less robust features. These procedures significantly reduce the time and effort required to obtain a three-dimensional reconstruction from frozen-hydrated data with a resolution that is comparable to the best obtained by more laborious methods. The agreement between the stain and frozen-hydrated reconstructions affords convincing evidence concerning the validity of the structure and the information afforded by the two reconstructions significantly enhances the structural analysis of the molecule.

Coloring Agents↗
PubMed1998

Application of distance-dependent resolution compensation and post-reconstruction filtering for myocardial SPECT.

Compensation for distance-dependent resolution can be directly incorporated in maximum likelihood reconstruction. Our objective was to examine the effectiveness of this compensation using either the standard expectation maximization (EM) algorithm or an accelerated algorithm based on use of ordered subsets (OSEM). We also investigated the application of post-reconstruction filtering in combination with resolution compensation. Using the MCAT phantom, projections were simulated for 360 degrees data, including attenuation and distance-dependent resolution. Projection data were reconstructed using conventional EM and OSEM with subset size 2 and 4, with/without 3D compensation for detector response (CDR). Also post-reconstruction filtering (PRF) was performed using a 3D Butterworth filter of order 5 with various cutoff frequencies (0.2-1.2 cycles cm(-1)). Image quality and reconstruction accuracy were improved when CDR was included. Image noise was lower with CDR for a given iteration number. PRF with cutoff frequency greater than 0.6 cycles cm(-1) improved noise with no reduction in recovery coefficient for myocardium but the effect was less when CDR was incorporated in the reconstruction. CDR alone provided better results than use of PRF without CDR. Results suggest that using CDR without PRF, and stopping at a small number of iterations, may provide sufficiently good results for myocardial SPECT. Similar behaviour was demonstrated for OSEM.

Algorithms↗
PubMed2006

Navigator gated high temporal resolution tissue phase mapping of myocardial motion.

Data acquisition for phase contrast velocity mapping of myocardial motion is typically based on multiple breath-held 2D measurements with limited acquisition duration and consequently relatively poor temporal resolution. In order to overcome the limitations of breath-hold acquisitions, an improved navigator-guided technique was implemented based on 2 navigator signals within each cardiac cycle in combination with paired acceptance and rejection criteria of successive navigator signals. Respiratory gated phase contrast measurements with 3-directional velocity encoding were performed in 12 healthy volunteers in basal, midventricular, and apical locations of the left ventricle during free breathing with a temporal resolution of 13.8 ms. Results were compared to standard breath-hold measurements with a temporal resolution of 69 ms. Data from the high temporal resolution study revealed details in left ventricular motion patterns that were previously not seen in phase contrast measurements and are only known from echocardiography. The proposed navigator gated technique for high temporal resolution velocity mapping is, therefore, highly promising for the detection of local and global motion abnormalities in patients with disturbed left ventricular performance, such as diastolic dysfunction.

Adult↗
PubMed2006

Structural properties of prion protein protofibrils and fibrils: an experimental assessment of atomic models.

Decades after the prion protein was implicated in transmissible spongiform encephalopathies, the structure of its toxic isoform and its mechanism of toxicity remain unknown. By gathering available experimental data, albeit low resolution, a few pieces of the prion puzzle can be put in place. Currently, there are two fundamentally different models of a prion protofibril. One has its building blocks derived from a molecular dynamics simulation of the prion protein under amyloidogenic conditions, termed the spiral model. The other model was constructed by threading a portion of the prion sequence through a beta-helical structure from the Protein Data Bank. Here we compare and contrast these models with respect to all of the available experimental information, including electron micrographs, symmetries, secondary structure, oligomerization interfaces, enzymatic digestion, epitope exposure, and disaggregation profiles. Much of this information was not available when the two models were introduced. Overall, we find that the spiral model is consistent with all of the experimental results. In contrast, it is difficult to reconcile several of the experimental observables with the beta-helix model. While the experimental constraints are of low resolution, in bringing together the previously disconnected experiments, we have developed a clearer picture of prion aggregates. Both the improved characterization of prion aggregates and the existing atomic models can be used to devise further experiments to better elucidate the misfolding pathway and the structure of prion protofibrils.

Amyloid↗
PubMed1995

Cladistic analyses of combined traditional and molecular data sets reveal an algal lineage.

The chromophyte algae are a large and biologically diverse assemblage of brown seaweeds, diatoms, and other golden algae classified in 13 taxonomic classes. One subgroup (diatoms, pedinellids, pelagophytes, silicoflagellates, and certain enigmatic genera) is characterized by a highly reduced flagellar apparatus. The flagellar apparatus lacks microtubular and fibrous roots, and the flagellum basal body is attached directly to the nucleus. We hypothesize that the flagellar reduction is the result of a single evolutionary series of events. Cladistic analysis of ultrastructural and biochemical data reveals a monophyletic group that unites all taxa with a reduced flagellar apparatus, supporting our hypothesis. Phylogenetic analyses of 18S rRNA gene sequence data provide strong resolution within most of the major groups of chromophytes but only weakly resolve relationships among those groups. Some of the molecularly based most parsimonious trees, however, also unite the taxa with a reduced flagellar apparatus, although the diatoms are not included in this lineage. This grouping is further supported by a posteriori character weighting of the molecular data, suggesting that flagellar reduction occurred at least twice in parallel evolutionary series of events. To further test our hypothesis of a single evolutionary reduction in the flagellar apparatus, we combine the two data sets and subject the hybrid data matrix to parsimony analysis. The resulting trees unite the diatoms with the other reduced flagellar apparatus algae in a monophyletic group. This result supports our hypothesis of a single evolutionary reduction and indicates the existence of a previously unrecognized lineage of algae characterized by a highly reduced flagellar apparatus. Further, this study suggests that the traditional classification of the diatoms with the chrysophytes and xanthophytes in the division (= phylum) Chrysophyta, as presented in most textbooks, is unsatisfactory and that a significantly different classification should be employed.

Base Sequence↗
PubMed2005

X-ray crystallography and biological metal centers: is seeing believing?

Metalloenzyme crystal structures have a major impact on our understanding of biological metal centers. They are often the starting point for mechanistic and computational studies and inspire synthetic modeling chemistry. The strengths and limitations of X-ray crystallography in determining properties of biological metal centers and their corresponding ligand spheres are explored through examples, including ribonucleotide reductase R2 and particulate methane monooxygenase. Protein crystal structures locate metal ions within a protein fold and reveal the identities and coordination geometries of amino acid ligands. Data collection strategies that exploit the anomalous scattering effect of metal ions can establish metal ion identity. The quality of crystallographic data, particularly the resolution, determines the level of detail that can be extracted from a protein crystal structure. Complementary spectroscopic techniques can provide crucial information regarding the redox state of the metal center as well as the presence, type, and protonation state of exogenous ligands. The final result of the crystallographic characterization of a metalloenzyme is a model based on crystallographic data, supported by information from biophysical and modeling studies, influenced by sample handling, and interpreted carefully by the crystallographer.

Amino Acids↗
PubMed2004

Haplotype reconstruction from genotype data using Imperfect Phylogeny.

UNLABELLED: Critical to the understanding of the genetic basis for complex diseases is the modeling of human variation. Most of this variation can be characterized by single nucleotide polymorphisms (SNPs) which are mutations at a single nucleotide position. To characterize the genetic variation between different people, we must determine an individual's haplotype or which nucleotide base occurs at each position of these common SNPs for each chromosome. In this paper, we present results for a highly accurate method for haplotype resolution from genotype data. Our method leverages a new insight into the underlying structure of haplotypes that shows that SNPs are organized in highly correlated 'blocks'. In a few recent studies, considerable parts of the human genome were partitioned into blocks, such that the majority of the sequenced genotypes have one of about four common haplotypes in each block. Our method partitions the SNPs into blocks, and for each block, we predict the common haplotypes and each individual's haplotype. We evaluate our method over biological data. Our method predicts the common haplotypes perfectly and has a very low error rate (<2% over the data) when taking into account the predictions for the uncommon haplotypes. Our method is extremely efficient compared with previous methods such as PHASE and HAPLOTYPER. Its efficiency allows us to find the block partition of the haplotypes, to cope with missing data and to work with large datasets. AVAILABILITY: The algorithm is available via a Web server at http://www.calit2.net/compbio/hap/

Algorithms↗
PubMed1979

Acylglycines. the gas chromatograph/mass spectrometric identification and interpretation of their spectra.

The gas chromatographic retention time (methylene units) and mass spectra of a series of acylglycine compounds as their trimethylsilyl (TMS) derivatives are presented. A general scheme for the interpretation of these compounds is developed from the mass spectra of known compounds and is shown to be in agreement with data derived from other sources (e.g. stable isotope and high resolution mass spectra). These data should provide information for the identification of these compounds in physiological fluid of both normal and diseased patients. In addition, the general interpretation scheme should provide the investigator with an approach to the interpretation of the spectra of unknown acylglycines.

Chromatography, Gas↗
PubMed1992

Monovalent cation binding to cubic insulin crystals.

Two localized monovalent cation binding sites have been identified in cubic insulin from 2.8 A-resolution difference electron density maps comparing crystals in which the Na+ ions have been replaced by Tl+. One cation is buried in a closed cavity between insulin dimers and is stabilized by interaction with protein carbonyl dipoles in two juxtaposed alternate positions related by the crystal dyad. The second cation binding site, which also involves ligation with carbonyl dipoles, is competitively occupied by one position of two alternate His B10 side chain conformations. The cation occupancy in both sites depends on the net charge on the protein which was varied by equilibrating crystals in the pH range 7-10. Detailed structures of the cation binding sites were inferred from the refined 2-A resolution map of the sodium-insulin crystal at pH 9. At pH 9, the localized monovalent cations account for less than one of the three to four positive counterion charges necessary to neutralize the negative charge on each protein molecule. The majority of the monovalent counterions are too mobile to show up in the electron density maps calculated using data only at resolution higher than 10 A. Monovalent cations of ionic radius less than 1.5 A are required for crystal stability. Replacing Na+ with Cs+, Mg++, Ca++ or La+++ disrupts the lattice order, but crystals at pH 9 with 0.1 M Li+, K+, NH4+, Rb+ or Tl+ diffract to at least 2.8 A resolution.

Animals↗
PubMed2003

Granulysin crystal structure and a structure-derived lytic mechanism.

Our crystal structure of granulysin suggests a mechanism for lysis of bacterial membranes by granulysin, a 74-residue basic protein from human cytolytic T lymphocyte and natural killer cells. We determined the initial crystal structure of selenomethionyl granulysin by MAD phasing at 2A resolution. We present the structure model refined using native diffraction data to 0.96A resolution. The five-helical bundle of granulysin resembles other "saposin folds" (such as NK-lysin). Positive charges distribute in a ring around the granulysin molecule, and one face has net positive charge. Sulfate ions bind near the segment of the molecule identified as most membrane-lytic and of highest hydrophobic moment. The ion locations may indicate granulysin's orientation of initial approach towards the membrane. The crystal packing reveals one way to pack a sheet of granulysin molecules at the cell surface for a concerted lysis effort. The energy of binding granulysin charges to the bacterial membrane could drive the subsequent lytic processes. The loosely packed core facilitates a hinge or scissors motion towards exposure of hydrophobic surface that we propose tunnels the granulysin into the fracturing target membrane.

Anti-Infective Agents↗
PubMed2003

Crystallization and initial X-ray diffraction studies of higher plant photosystem I.

Complete photosystem I from a higher plant (pea; Pisum sativum) was isolated, purified and crystallized. The crystals diffract to 4 A resolution using synchrotron radiation and belong to the monoclinic crystal system, space group P2(1), with unit-cell parameters a = 181.90, b = 190.24, c = 219.66 A, beta = 90.484 degrees. Data sets from three crystals have been collected and were merged into a 4.4 A resolution data set, taking advantage of the high isomorphicity observed for these crystals. Analysis of the self-rotation Patterson function suggests the possible presence of two PSI complexes in the asymmetric unit.

Crystallization↗
PubMed2004

Crystallization and preliminary X-ray analysis of a novel Trichoderma reesei xylanase IV belonging to glycoside hydrolase family 5.

Xylanase IV (XYN IV) is a new recently characterized xylanase from Trichoderma reesei. It is able to degrade several different xylans, mainly producing xylose. XYN IV has been crystallized by the hanging-drop vapour-diffusion method, using PEG 6000 as a precipitant. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 86.3, b = 137.5, c = 196.1 A, alpha = beta = gamma = 90 degrees. Assuming a molecular weight of 50.3 kDa, the V(M) values indicate there to be four XYN IV monomers in an asymmetric unit and the solvent content of the crystals to be 57%. Based on dynamic light-scattering measurements, XYN IV is a dimer in solution. A native data set to 2.8 A resolution has been collected at a home laboratory and a data set to 2.2 A resolution has been collected using synchrotron radiation.

Crystallization↗
PubMed2005

A preliminary time-of-flight neutron diffraction study on amicyanin from Paracoccus denitrificans.

Crystals of the blue copper protein amicyanin suitable for neutron diffraction were grown by the sitting-drop method, followed by repeated macroseeding using solutions prepared with D(2)O. Although the crystal sizes were the same, crystals grown using solutions made up in H(2)O in the initial stages of macroseeding and solutions with D(2)O in later stages did not diffract neutrons well. However, when the protein was initially exchanged with buffered D(2)O and then crystallized and also macroseeded using solutions made up in D(2)O throughout, the crystals diffracted neutrons to high resolution. One of those crystals was used to collect a data set to a resolution of 1.9 A.

Crystallography↗
PubMed1999

Crystallization and preliminary X-ray crystallographic analysis of a Trichoderma reesei beta-mannanase from glycoside hydrolase family 5.

Crystals of the catalytic core domain of a Trichoderma reesei beta-mannanase belonging to glycoside hydrolase family 5 have been grown by the sitting-drop method at room temperature using ammonium sulfate as precipitant. The crystals grow as thin colourless plates and belong to space group P21, with unit-cell parameters a = 50.0, b = 54.3, c = 60.2 A, beta = 111.3 degrees, and have a single monomer of mannanase in the asymmetric unit. Native data to 2.0 A resolution have been collected at room temperature using synchrotron radiation. Data for a platinum derivative have been collected to 1.65 A at 110 K in a very short time at the CCLRC Daresbury synchrotron source, using a charge-coupled device (CCD) as detector.

Catalysis↗
PubMed2004

[A review on research of implement application for crop simulation model in regional scale by using remote sensing technology].

When applying crop simulation model developed from plot-scale level to regional scale, some challenges such as acquirement of some broader spatial data and regionalization of parameters will arise, while satellite can monitor crop growth status by remote sensing. Therefore, regional application of crop simulation model will be implement by remote sensing technique. In this paper, some research advances are reviewed, which include the methods of biophysical parameters retrieved from remote sensing data for crop model, the approach of biomass obtained by remote sensing data directly, and the means of matching temporal and spatial resolution between remote sensing data and crop model input. Three solutions (forcing, recalibration and validation) to the application of crop model in region scale by using remote sensing technique were emphasized, and the current problem and future research orientation in this filed were discussed in brief.

Computer Simulation↗
PubMed1998

Functional MRI for studying episodic memory in aging and Alzheimer's disease.

Anatomic and functional neuroimaging have a potential for clarifying the differential diagnosis of dementia and for evaluating new treatments for memory impairment. Our neuroimaging research examines the neural abnormalities underlying memory impairment in aging and Alzheimer's disease. We use data from high-resolution magnetic resonance imaging (MRI) to measure hippocampal volumes, and data from high-speed echo-planar imaging to evaluate cortical physiology. The results obtained with neuroimaging techniques are then related to the subject's performance on memory tasks (encoding and retrieval) performed inside the scanner during functional MRI.

Aging↗
PubMed2005

Pattern computation in neural communication systems.

Biological data suggests that activity patterns emerging in small- and large-scale neural systems may play an important role in performing the functions of the neural system, and in particular, neural computations. It is proposed in this paper that neural systems can be understood in terms of pattern computation and abstract communication systems theory. It is shown that analysing high-resolution surface EEG data, it is possible to determine abstract probabilistic rules that describe how emerging activity patterns follow earlier activity patterns. The results indicate the applicability of the proposed approach for understanding the working of complex neural systems.

Animals↗
PubMed1986

Spatial resolution analysis of computed tomographic images.

Methods are presented for the quantification of spatial resolution in x-ray computed tomographic (CT) images. Model-dependent methods are derived and compared with model independent methods for computation of the Modulation Transfer Function (MTF). These techniques are applied to phantom images of point, line, edge, and ring discontinuities. The model-dependent methods utilize multiparameter fits of a two-dimensional model function to the image data. Model predictions are compared with results obtained in a model-independent way by numerical transformation of the data. Results of resolution measurements of an Imatron C-100 CT scanner at UCSF and a second experimental scanner at the UCSF Physics Research Laboratory are presented.

Humans↗