SEARCH · Search PubMed

Results for “data resolution”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 271 records · Page 15Linked to original sources

PubMed2000

Fourier Transform Spectroscopy of the O(2) Herzberg Bands. III. Absorption Cross Sections of the Collision-Induced Bands and of the Herzberg Continuum.

Absorption spectra of molecular oxygen were measured in the laboratory under temperature and pressure conditions prevailing in the Earth's atmosphere. Spectra of pure O(2), O(2) + N(2), and O(2) + Ar were recorded in the 41 700 to 33 000 cm(-1) region (240-300 nm) at a maximal optical path difference of 0.45 cm using a Fourier transform spectrometer and a multiple reflection gas cell. The different components of the spectra, namely the discrete bands of the three Herzberg systems, the Herzberg continuum, and the collision-induced diffuse Wulf bands, were separated. The contribution of the Herzberg bands was first subtracted using the line parameters determined previously [A. Jenouvrier, M.-F. Mérienne, B. Coquart, M. Carleer, S. Fally, A. C. Vandaele, C. Hermans, and R. Colin, J. Mol. Spectrosc. 198, 136-162 (1999)] from high-resolution data. Spectra recorded at various pressures then made it possible to determine by linear regression the intensity of the Wulf bands and the Herzberg continuum. The characteristics of the Wulf bands have been investigated in details: vibrational analysis, pressure effect, foreign gas effect, and a simulated spectrum are reported. The Herzberg continuum cross section is determined below the dissociation limit. A comparison with literature data is given. The new O(2) absorption cross sections and O(2)-O(2) collision-induced absorption cross sections are useful in connection with atmospheric measurements of ozone and other trace gases in the UV spectral region. Copyright 2000 Academic Press.

Journal Article↗

PubMed2001

Improvement of the Spectroscopic Constants of the PF(A(3)Pi) State and Assignment of the PF(A-X) Transition Dipole Function.

High-resolution laser-excitation spectra were acquired for the v'=3-7 levels of the PF(A(3)Pi(0,1,2)<--X(3)Sigma(-)) transition from PF(X(3)Sigma(-)) molecules generated in a discharge flow reactor. These results were combined with lower resolution excitation spectra for the v'=8-11 levels and with existing high-resolution data in the literature for v'=0 and 1 to assign improved spectroscopic constants for PF(A(3)Pi(0,1,2)). The abnormal vibrational energy level spacings for all spin components of the PF(A(3)Pi) state are evidence for a homogeneous interaction with another (3)Pi state. The Lambda-doublet separation in the PF((3)Pi(0)) substate increases with vibrational level, which is taken as evidence for interaction with the PF(b(1)Sigma(+)) state. Laser-induced fluorescence spectra from individual v'=0-5 levels were used to obtain vibrational band intensities of the A-X transition. The strong dependence of the transition dipole on the r-centroid is consistent with the reduction in the radiative lifetimes with increasing v' level. The similarity between the isovalent PF(A(3)Pi) and SO(A(3)Pi) states is noted and the bond dissociation energy of PF(X(3)Sigma(-)) is discussed. Copyright 2001 Academic Press.

Journal Article↗

PubMedDate not supplied

Crystallization and preliminary X-ray diffraction studies of glycine methyltransferase from rat liver.

Glycine methyltransferase from rat liver is a tetrameric enzyme with 292 amino acid residues in each identical subunit and catalyzes the AdoMet-dependent methylation of glycine to form sarcosine. The enzyme was crystallized by the hanging drop vapor diffusion method, using polyethylene glycol 4000 as a precipitant. The crystal belongs to the orthorhombic space group P2(1)2(1)2, with unit cell dimensions of a = 86.4, b = 175.7, c = 45.5 A and with two subunits in the asymmetric unit. The crystals diffract beyond 2.4 A resolution, and a set of 2.4 A resolution data were measured.

Animals↗

PubMedDate not supplied

Preservation of 2-D crystals of tubulin for electron crystallography.

Zinc-induced sheets of tubulin are two-dimensional crystalline polymers that constitute an ideal sample for high resolution studies of tubulin by electron crystallography. We show that these 2-dimensional tubulin crystals can be stabilized by taxol against low-temperature depolymerization and degradation with time, easing the way for the preparation of electron microscopy samples. The preservation of the crystals to high resolution has been tested with different embedding media. While glucose-embedded samples diffract poorly, samples embedded in tannin consistently diffract to a resolution of at least 3.5 A. Even better results are obtained by embedding with a combination of tannin and glucose, which improves the flatness of the crystals and allows the collection of isotropic high-resolution data from tilted specimens.

Animals↗

PubMedDate not supplied

Situs: A package for docking crystal structures into low-resolution maps from electron microscopy.

Three-dimensional image reconstructions of large-scale protein aggregates are routinely determined by electron microscopy (EM). We combine low-resolution EM data with high-resolution structures of proteins determined by x-ray crystallography. A set of visualization and analysis procedures, termed the Situs package, has been developed to provide an efficient and robust method for the localization of protein subunits in low-resolution data. Topology-representing neural networks are employed to vector-quantize and to correlate features within the structural data sets. Microtubules decorated with kinesin-related ncd motors are used as model aggregates to demonstrate the utility of this package of routines. The precision of the docking has allowed for the extraction of unique conformations of the macromolecules and is limited only by the reliability of the underlying structural data.

Animals↗

PubMed1999

EMAN: semiautomated software for high-resolution single-particle reconstructions.

We present EMAN (Electron Micrograph ANalysis), a software package for performing semiautomated single-particle reconstructions from transmission electron micrographs. The goal of this project is to provide software capable of performing single-particle reconstructions beyond 10 A as such high-resolution data become available. A complete single-particle reconstruction algorithm is implemented. Options are available to generate an initial model for particles with no symmetry, a single axis of rotational symmetry, or icosahedral symmetry. Model refinement is an iterative process, which utilizes classification by model-based projection matching. CTF (contrast transfer function) parameters are determined using a new paradigm in which data from multiple micrographs are fit simultaneously. Amplitude and phase CTF correction is then performed automatically as part of the refinement loop. A graphical user interface is provided, so even those with little image processing experience will be able to begin performing reconstructions. Advanced users can directly use the lower level shell commands and even expand the package utilizing EMAN's extensive image-processing library. The package was written from scratch in C++ and is provided free of charge on our Web site. We present an overview of the package as well as several conformance tests with simulated data.

Algorithms↗

PubMed2002

The 11S regulators of 20S proteasome activity.

Although substantial progress has been made in understanding the biochemical properties of 11S regulators since their discovery in 1992, we still only have a rudimentary understanding of their biological role. As discussed above, we have proposed a model in which the alpha/beta complex promotes the production of antigenic peptides by opening the exit port of the 20S proteasome (Whitby et al. 2000). There are other possibilities, however, that are not exclusive of the exit port hypothesis. For example the alpha/beta complex may promote assembly of immunoproteasome as suggested by Preckel et al. 1999, or it may function as a docking module and conduit for the delivery of peptides to the ER lumen (Realini et al. 1994b). There are also unanswered structural and mechanistic questions. Higher resolution data are needed to discern important structural details of the PA26/20S proteasome complex. The models for binding and activation that are suggested from the structural data have to be tested by mutagenesis and biochemical analysis. What is the role of homolog-specific inserts? Will cognate regulator/proteasome complexes show conformational changes that are not apparent in the currently available crystal structures, including perhaps signs of allosteric communication between the regulator and the proteasome active sites?

Adenosine Triphosphatases↗

PubMed1991

The neural basis of the behaviorally relevant N1 component of the somatosensory-evoked potential in SI cortex of awake monkeys: evidence that backward cortical projections signal conscious touch sensation.

Studies of touch intensity discrimination in monkeys have identified a component of the somatosensory-evoked cortical potential, N1, generated within 50 ms of the stimulus, that predicts their behavioral performance. This study employed multiple-electrode arrays with relatively high spatial resolution (0.1 or 0.2 mm spacing) to record laminar profiles of somatosensory-evoked potentials (SEPs), multiple unit activity (MUA) and current source-densities (CSDs) at several sites across the postcentral gyri of two awake monkeys. This high resolution laminar analysis strongly supports our earlier hypothesis based upon low resolution data that N1 is generated by synaptic excitation targeted specifically at the most superficial cortical layers I/II: (1) The excitatory nature of N1 was indicated by elevated MUA which was maximal in layer III and extended down to subcortical white matter where fiber activity exceeded prestimulus levels; (2) In addition to CSD analysis, the observation that N1 was maximally negative within 0.10 mm of the border between layers I and II verified the superficial site of N1 synaptic excitation regardless of conductivity boundaries near the pial surface. A review of the anatomical literature finds that the most likely inputs responsible for N1 activation are the "backward" cortico-cortical projections from secondary somatosensory areas to SI which in area 1 are the major source of sensory-related input that specifically terminates in layers I/II. We suggest, therefore, that backward projections are involved in the conscious process of touch sensation as it is signaled by N1.

Animals↗

PubMed1990

Fractal descriptions for spatial statistics.

Measures of spatial statistics have been available for estimating means, calculating or assessing differences, estimating nearest neighbor distances, and such, but have not provided a general approach to describing variances. Because measures of heterogeneity depend upon choosing a particular element size in the domain, estimates of apparent heterogeneity are larger with high-resolution observations than with low-resolution data. Many descriptors might be used to describe the relationships between apparent heterogeneity and the size of the observed spatial elements, but we have found that fractal relationships provide concise and precise descriptions of many types of data over large ranges of element sizes. Perhaps more importantly, the fractal approaches give additional insight, such as measures of spatial correlation, and often suggest ways of approaching the underlying basis of the heterogeneity.

Animals↗

PubMed2005

Stochastic modelling of apoptosis kinetics.

Robust quantitative estimation of average whole cell mitochondrial dysfunction is a useful tool for assessing sensitivity to apoptotic stimuli induced either by novel agents, or following manipulation of apoptotic threshold by pharmacological or functional genomics approaches. We have mathematically modelled the kinetics of whole cell mitochondrial membrane potential depolarisation within a population of cells as a Bernouli transition. An exponential distribution enables the median latency preceding mitochondrial membrane potential dissipation to be derived. The kinetic model can be fitted to in vitro single cell resolution data derived from kinetic flow cytometric studies by non-linear regression. We propose that kinetic determination of cumulative frequency distributions provides a useful approach for estimating apoptosis sensitivity across cell populations over short time-frames.

Apoptosis↗

PubMed1988

Phosphorimeters for analysis of decay profiles and real time monitoring of exponential decay and oxygen concentrations.

A phosphorimeter which can be assembled at low cost from mainly commercially available components and which has better time resolution, data acquisition rate, sensitivity, and flexibility than commercially available instruments is described. As a phosphorescence analyzer the instrument can measure phosphorescence lifetimes ranging from approximately 30 microseconds to seconds from samples with variable intensity, excitation, and emission spectra and which may follow complex decay behavior. Configured as a phosphorescence monitor it is designed for fast, repetitive calculation of phosphorescence lifetime, assuming single-exponential decay, and can be used to calculate oxygen concentration in biological samples in real time.

Luminescent Measurements↗

PubMed1988

Opto-electronic analyses of masticatory mandibular movements and velocities in the rat.

High-speed, high-resolution data (frontal plane) were collected from 6 Sprague-Dawley rats by opto-electronic mandibular tracking (OMT), followed by microcomputer analysis of individual chew cycles. Mastication comprised rapidly alternating, unilateral cycles with variable degrees of lateral translation. There was no evidence of bilateral mastication (simultaneous chewing on both left and right sides). Analysis revealed significant (p less than or equal to 0.01) differences between whole-cycle, slow-open (SO) phase, fast-open (FO) phase, fast-close (FC) phase, and slow-close (SC) phase duration, height, width, and velocity during mastication of standardized foods (pellets and slurry). Regression analysis between millimetres of vertical/horizontal movement (Y) and vertical/horizontal velocity (X) revealed differences during these mastications. Whole-cycle and SO-phase regression equations had the greatest disparity between pellet and slurry chewing for both vertical and horizontal movements. Correlation coefficient analysis between movement and velocity data indicated that (1) vertical correlations were smaller than horizontal ones, (2) slurry correlations were greater than pellet ones except for whole cycles, (3) FO phase had the largest movement/velocity correlation during both pellet and slurry mastication, and, that (4) SC phase had the smallest movement/velocity correlation. Vertical and horizontal movements during pellet FC phase were significantly (p less than or equal to 0.01) greater than slurry ones; both vertical and horizontal movements during pellet SC phase were significantly (p less than or equal to 0.01) less than slurry ones. This phase-isostasy was also detected during vertical movements in SO and FO phases.(ABSTRACT TRUNCATED AT 250 WORDS)

Animal Feed↗

PubMed1996

Measuring bonds between surface-associated molecules.

Adhesive interactions play an essential role in immune function. Much information on these phenomena was recently obtained by applying sophisticated methods such as the surface forces apparatus, atomic force microscopy, lipid vesicle-based technology or flow chambers. In the present review it is shown that the use of hydrodynamic flow allows quantitative study of the formation and dissociation of individual molecular bonds between receptor-bearing cells or particles and ligand-derivatized surfaces. In addition, it should be possible to determine particle-surface interaction forces with subpiconewton sensitivity and nanometer resolution. Data analysis shows that the classical concepts of bond strength, or association and dissociation rates must be reexamined in order to achieve a correct understanding of the behavior of individual molecules.

Cell Adhesion Molecules↗

PubMed1987

Determination of the quaternary structure of protocatechuate 3,4-dioxygenase from Pseudomonas aeruginosa.

A 2.5 A resolution data set has been collected for crystals of protocatechuate 3,4-dioxygenase from Pseudomonas aeruginosa. Analysis of the data using the rotation function shows that the alpha 2 beta 2 tetramers associate to form a particle with cubic 23 (T) point group symmetry. Prior to this analysis it was believed that eight tetramers associated to form the holoenzyme. The symmetry of the crystalline holoenzyme also addresses questions concerning its iron content and substrate stoichiometry.

Crystallization↗

PubMed1989

Structure of the complex of Streptomyces griseus proteinase B and polypeptide chymotrypsin inhibitor-1 from Russet Burbank potato tubers at 2.1 A resolution.

A low molecular weight protein inhibitor of serine proteinases from Russet Burbank potato tubers, polypeptide chymotrypsin inhibitor-1 (PCI-1), has been crystallized in complex with Streptomyces griseus proteinase B (SGPB). The three-dimensional structure of the complex has been solved at 2.1 A resolution by the molecular replacement method and has been refined to a final R-factor (= sigma[[Fo[-[Fc[[/sigma[Fo[) of 0.142 (8.0 to 2.1 A resolution data). The reactive site bond of PCI-1 (Leu38I to Asn39I) is intact in the complex, and there is no significant distortion of the peptide from planarity. The distance between the active site serine O gamma of SGPB and the carbonyl carbon of the scissile bond of PCI-1 is 2.8 A (1 A = 0.1 nm). The inhibitor has little secondary structure, having a three-stranded antiparallel beta-sheet on the side opposite the reactive site and four beta-turns. PCI-1 has four disulphide bridges; these presumably take the place of extensive secondary structure in keeping the reactive site conformationally constrained. The pairing of the cystine residues, which had not been characterized chemically, is as follows: Cys3I to Cys40I, Cys6I to Cys24I, Cys7I to Cys36I, and Cys13I to Cys49I. The molecular structure of SGPB in the PCI-1 complex agrees closely with the structure of SGPB complexed with the third domain of the turkey ovomucoid inhibitor (OMTKY3). A least-squares overlap of all atoms in SGPB gives a root-mean-square difference of 0.37 A. One of the loops of SGPB (Ser35 to Gly40) differs in conformation in the two complexes by more than 2.0 A root-mean-square for the main-chain atoms. Thr39 displays the largest differences with the carbonyl carbon atom deviating by 3.6 A. This conformational alternative is a result of the differences in the molecular structures of the P'4 residues following the reactive site bonds of the two inhibitors. This displacement avoids a close contact (1.3 A) between the carbonyl oxygen of Ser38 of SGPB and Pro42I C beta of PCI-1. The solvent structure of the PCI-1-SGPB complex includes 179 waters, two sulphate or phosphate ions, and one calcium or potassium ion, which appears to play a role in crystal formation. The molecular structure of PCI-1 determined here has allowed the proposal of a model for the structure of a two-domain inhibitor from potatoes and tomatoes, inhibitor II.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗

PubMed1991

Crystallization and preliminary X-ray crystallographic analysis of verotoxin-1 B-subunit.

The B-subunit of verotoxin-1, which is believed to form a pentamer (monomer Mr = 7691), has been crystallized by vapor diffusion over a wide range of conditions. The best crystals, obtained with polyethylene glycol 8000 as the precipitant, belong to the orthorhombic space group P2(1)2(1)2(1), with cell dimensions a = 59.2 A, b = 102.7 A, c = 56.3 A. The cell dimensions are consistent with one B-subunit pentamer per asymmetric unit, and the crystals diffract to at least 2.0 A resolution. Data collected using synchrotron radiation at a wavelength of 2.070 A may allow the structure to be solved using the anomalous signal from three sulfur atoms in the monomer, combined with averaging over the non-crystallographic symmetry.

Bacterial Toxins↗

PubMed1991

Three-dimensional structure of the complexes between bovine chymotrypsinogen A and two recombinant variants of human pancreatic secretory trypsin inhibitor (Kazal-type).

Variants of the human pancreatic secretory trypsin inhibitor (PSTI) have been created during a protein design project to generate a high-affinity inhibitor with respect to some serine proteases other than trypsin. Two modified versions of human PSTI with high affinity for chymotrypsin were crystallized as a complex with chymotrypsinogen. Both crystallize isomorphously in space group P4(1)2(1)2 with lattice constants a = 84.4 A, c = 86.7 A and diffract to 2.3 A resolution. The structure was solved by molecular replacement. The final R-value after refinement with 8.0 to 2.3 A resolution data was 19.5% for both complexes after inclusion of about 50 bound water molecules. The overall three-dimensional structure of PSTI is similar to the structure of porcine PSTI in the trypsinogen complex (1TGS). Small differences in the relative orientation of the binding loop and the core of the inhibitors indicate flexible adaptation to the proteases. The chymotrypsinogen part of the complex is similar to chymotrypsin. After refolding induced by binding of the inhibitor the root-mean-square difference of the active site residues A186 to A195 and A217 to A222 compared to chymotrypsin was 0.26 A.

Amino Acid Sequence↗

PubMed1991

Molecular size and symmetry of Pseudomonas aeruginosa catabolic ornithine carbamoyltransferase. An X-ray crystallography analysis.

The catabolic ornithine carbamoyltransferase (EC 2.1.3.3) from Pseudomonas aeruginosa, that shows allosteric behaviour, and a mutant version of this enzyme has been crystallized in several different crystal forms. All of these have been characterized by X-ray diffraction methods. A 4.5 A resolution data set has been collected on a triclinic crystal. Analysis of the data using the self-rotation function shows that 12 monomers associate to form a particle with cubic 23 point group symmetry.

Macromolecular Substances↗