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At least 1,063 records · Page 59Linked to original sources
PubMed1988

New high-resolution 2-deoxyglucose method featuring double labeling and automated data collection.

A new approach to high-resolution 2-deoxy-D-glucose (2DG) emulsion-autoradiography which combines improved retention of 2DG labeling, staining with immunohistochemical and other specific markers, and automated data collection and analysis of local silver grain and stain densities is described. The Durham et al. (J. Neurosci. 1:519-526, '81) procedure for fixation of 2DG with periodate-lysine-paraformaldehyde (PLP, McLean and Nakane: J. Histochem. Cytochem. 22:1077-1083, '74) was adapted to increase retained label roughly tenfold. Phenobarbital anesthesia is induced 45 minutes after 2DG injection. Barbiturate anesthesia increases brain glycogen (Nelson et al.: J. Neurochem. 15:1271-1279, '68) and presumably increases the incorporation of intracellular 2DG from 2DG-6P into brain glycogen and other molecules (Nelson et al.: J. Neurochem. 43:949-956, '84; Pentreath et al.: Neuroscience 7:759-767, '82). Iodoacetate is added to cold fixative to prevent glycogen breakdown (Cammermeyer and Fenton: Histochemistry 76:339-356, '82). This high-resolution 2DG protocol is directly compatible with many other neuroanatomical techniques. We demonstrate 2DG emulsion autoradiography combined with cytochrome oxidase (CO) histochemistry, markers for axonal pathway tracing, plastic embedding for semithin sections, and immunohistochemical staining for glutamate decarboxylase (GAD). The method should be compatible with antibodies for other antigens and with other neuroanatomical stains. To collect the data directly from microscope slides, a computer-controlled microscope was integrated with image-processing software to eliminate the need for manual counting and scoring of autoradiograms. Regions of interest are scanned automatically at high resolution to map regional labeling and/or stain density. There is excellent correspondence between computer-enhanced two-dimensional maps of the data and the original autoradiograms. Automated counts for five specimens were compared to counts of labeled cells by trained observer. The correlation between the two sets of measurements is high (r = .93). Automated data collection has been generalized to measure regional stain densities on the autoradiographed sections for direct comparison with silver grain density. The method is extremely flexible, especially since new image-processing strategies can be developed in software to extract the desired information from materials labeled by other methods (e.g., HRP).(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2005

Structure of gramicidin D-RbCl complex at atomic resolution from low-temperature synchrotron data: interactions of double-stranded gramicidin channel contents and cations with channel wall.

Gramicidin D (gD) is a naturally occurring ionophoric antibiotic that forms membrane channels specific for monovalent cations. The crystal structure of the RbCl complex of gD has been determined at 1.14 A resolution from low-temperature (100 K) synchrotron-radiation data with a final R of 16%. The structure was refined with anisotropic temperature factors for all non-H atoms and with partial occupancies for many of them. The asymmetric unit in the crystal contains four crystallographically independent molecules that form two right-handed antiparallel double-stranded dimers. There are seven distinct rubidium-binding sites in each dimeric channel. The occupancy factors of Rb cations are between 0.11 and 0.35 and the total ion contents of the two crystallographically independent channels are 1.59 and 1.22 ions, respectively. Although each channel is 'chemically symmetrical', the side-chain conformations, the distributions of rubidium cations and their binding sites in the two independent channels are not. Cations are 'coordinated' by delocalized pi-electrons of three to five carbonyl groups that together with peptide backbone chains form the gramicidin channel walls. The water:cation ratio in the channel interior is four or five:one, and five or six waters separate Rb cations during their passage through the channel.

Binding Sites↗
PubMed2005

A web-based system for managing and co-ordinating multiple multisite studies.

Efficient and secure collection and management of information is essential in any modern biomedical study. Data management and coordination of multisite studies is a complex process. It involves development of systems for data collection, data cleaning with quality assurance checks, and specimen tracking, as well as development of procedures for conducting the study, training clinical sites, and communicating with sites to answer study questions and resolve and track data inquiries and resolutions. We developed a secure web-based system that is designed to automate evaluation of eligibility criteria and data collection, track specimens, serve as a resource for study-specific information, facilitate communication across sites in multisite studies, track data queries and resolutions, and allow administrative management of studies. The system combines a common framework across studies that defines the internal structure for all the web pages, with a study-specific one that defines the content of each page via a relational database. This combination creates a flexible and efficient environment enabling several multisite studies to be simultaneously or consecutively implemented and managed in a timely manner. We describe the development process, the system and its evaluation, current status, lessons learned, and future development plans.

Biomarkers, Tumor↗
PubMed2003

The effect of varying spectral resolution on the quality of high spectral and spatial resolution magnetic resonance images of the breast.

PURPOSE: To evaluate the effect of varying spectral resolution on image quality of high spectral and spatial resolution (HiSS) images. MATERIALS AND METHODS: Eight women with suspicious breast lesions and six healthy volunteers were scanned using echo-planar spectroscopic imaging (EPSI) at 1.5 Tesla with 0.75- to 1-mm in-plane resolution and 2.3- to 2.6-Hz spectral resolution. Time domain data were truncated to obtain proton spectra in each voxel with varying (2.6-83.3 Hz) resolution. Images with intensity proportional to water signal peak heights were synthesized. Changes in water signal line shape following contrast injection were analyzed. RESULTS: Fat suppression is optimized at approximately 10-Hz spectral resolution and is significantly improved by removal of wings of the fat resonance. This was accomplished by subtracting a Lorentzian fit to the fat resonance from the proton spectrum. The water resonance is often inhomogeneously broadened, and very high spectral resolution is necessary to resolve individual components. High spectral resolution is required for optimal contrast in anatomic features with very high T(2)* (e.g., within a lesion) and for detection of often subtle effects of contrast agents on water signal line shape. CONCLUSION: Despite a trade-off between the spectral resolution and signal-to-noise ratio, it is beneficial to acquire data at the highest spectral resolution currently attainable at 1.5 Tesla.

Breast↗
PubMed2001

Blood clot resolution in human cerebrospinal fluid: evidence of first-order kinetics.

OBJECTIVE: To determine the kinetics of blood clot resolution in human cerebrospinal fluid. METHODS: Computed tomographic scans of 17 adult patients with intraventricular hemorrhages were analyzed. Intraventricular clot volume was determined and analyzed over time to determine both a standardized percentage rate and an absolute rate of clot resolution. Results were analyzed by use of regression for cross sectional time-series data. To determine the kinetics of intraventricular clot resolution, the effect of the clot volume on the percentage rate of clot resolution, clot half-life, and absolute rate of clot resolution was analyzed. The potential effect of age, sex, type of hemorrhage, and treatment with external ventricular drainage on the percentage rate of clot resolution was assessed. RESULTS: The percentage rate of clot resolution was 10.8% per day (95% confidence interval, 9.05-12.61 %), and it was independent of initial clot volume, age, sex, type of underlying hemorrhage, and use of external ventricular drainage. The absolute rate of clot resolution varied directly with the maximal clot volume (R2 = 0.88; P < 0.001). The percentage clot resolution data are consistent with events during the first 24 to 48 hours that antagonize clot resolution. CONCLUSION: These findings demonstrate that intraventricular blood clot resolution in patients with intraventricular hemorrhage follows first-order kinetics. The thrombolytic enzyme system responsible for intraventricular clot resolution seems to be saturated at 24 to 48 hours after the initial hemorrhage.

Adult↗
PubMed2004

High-resolution serum proteomic features for ovarian cancer detection.

Serum proteomic pattern diagnostics is an emerging paradigm employing low-resolution mass spectrometry (MS) to generate a set of biomarker classifiers. In the present study, we utilized a well-controlled ovarian cancer serum study set to compare the sensitivity and specificity of serum proteomic diagnostic patterns acquired using a high-resolution versus a low-resolution MS platform. In blinded testing sets, the high-resolution mass spectral data contained multiple diagnostic signatures that were superior to the low-resolution spectra in terms of sensitivity and specificity (P<0.00001) throughout the range of modeling conditions. Four mass spectral feature set patterns acquired from data obtained exclusively with the high-resolution mass spectrometer were 100% specific and sensitive in their diagnosis of serum samples as being acquired from either unaffected patients or those suffering from ovarian cancer. Important to the future of proteomic pattern diagnostics is the ability to recognize inferior spectra statistically, so that those resulting from a specific process error are recognized prior to their potentially incorrect (and damaging) diagnosis. To meet this need, we have developed a series of quality-assurance and in-process control procedures to (a) globally evaluate sources of sample variability, (b) identify outlying mass spectra, and (c) develop quality-control release specifications. From these quality-assurance and control (QA/QC) specifications, we identified 32 mass spectra out of the total 248 that showed statistically significant differences from the norm. Hence, 216 of the initial 248 high-resolution mass spectra were determined to be of high quality and were remodeled by pattern-recognition analysis. Again, we obtained four mass spectral feature set patterns that also exhibited 100% sensitivity and specificity in blinded validation tests (68/68 cancer: including 18/18 stage I, and 43/43 healthy). We conclude that (a) the use of high-resolution MS yields superior classification patterns as compared with those obtained with lower resolution instrumentation; (b) although the process error that we discovered did not have a deleterious impact on the present results obtained from proteomic pattern analysis, the major source of spectral variability emanated from mass spectral acquisition, and not bias at the clinical collection site; (c) this variability can be reduced and monitored through the use of QA/QC statistical procedures; (d) multiple and distinct proteomic patterns, comprising low molecular weight biomarkers, detected by high-resolution MS achieve accuracies surpassing individual biomarkers, warranting validation in a large clinical study.

Biomarkers, Tumor↗
PubMed2003

Detection of vegetation degradation on Swedish mountainous heaths at an early stage by image interpretation.

Mountainous vegetation in general, and especially in subpolar regions, is sensitive, compared to vegetation in lowland areas, as mountainous vegetation has low resilience and low productivity. Mountainous areas have been perceived as being sensitive to mechanical damage. Quick methods with a high degree of accuracy are needed for the monitoring of mountainous areas and for planning the sustainable use of resources. The aim was i) to investigate if the dry dwarf shrub heath on hummocky moraine in the southern part of the mountains with a maritime climate and in open areas used for summer grazing, is susceptible to change; and ii) to test if high-resolution IKONOS-2 satellite data can, with a high degree of accuracy, be used for detection, and for quantification and mapping of erosion patches in montane vegetation. In which case, these data can substitute color infrared aerial photos for the early detection of changes. For the detection of changes, visual interpretations on high-quality printouts of IKONOS-2 satellite images from 2000 and of color infrared aerial photographs from 1975 were carried out and the results compared. Interpretations were verified in the field. The results show that for the period 1975-2000, erosion was in process on and around wind heaths, indicating that the wind heath and surrounding dry dwarf shrub heath in this landscape type of hummocky moraine are sensitive to mechanical damage by trampling and grazing, and thus susceptible to change. Most of the wind heaths and changes found were small (50-1000 m2). The results show that it is possible to detect, with good accuracy, detailed changes in the size and distribution of erosion patches and wind heaths by visual interpretation in single images of IKONOS-2 data. This implies that for monitoring these kinds of changes, these high-resolution (4 x 4 m pixel resolution) satellite data can substitute for color infrared aerial photographs.

Altitude↗
PubMed2004

Methods for generating high-resolution structural models from electron microscope tomography data.

Reconstructed volumes generated by tilt-image electron-microscope tomography offer the best spatial resolution currently available for studying cell structures in situ. Analysis is often accomplished by creating surface models that delineate grayscale contrast boundaries. Here, we introduce a specialized and convenient sequence of segmentation operations for making such models that greatly improves their reliability and spatial resolution as compared to current approaches, providing a basis for making accurate measurements. To assess the reliability of the surface models, we introduce a spatial uncertainty measurement based on grayscale gradient scale length. The model generation and measurement methods are validated by applying them to synthetic data, and their utility is demonstrated by using them to characterize macromolecular architecture of active zone material at the frog's neuromuscular junction.

Computer Simulation↗
PubMed1990

Structure of CaATPase: electron microscopy of frozen-hydrated crystals at 6 A resolution in projection.

Thin, three-dimensional crystals of CaATPase have been studied at high resolution by electron crystallography. These crystals were grown by adding purified CaATPase to appropriate concentrations of lipid, detergent and calcium. A thin film of crystals was then rapidly frozen and maintained in the frozen-hydrated state during electron microscopy. The resulting electron diffraction patterns extend to 4.1 A resolution and images contain phase data to 6 A resolution. By combining Fourier amplitudes from electron diffraction patterns with phases from images, a density map has been calculated in projection. Comparison of this map from unstained crystals with a previously determined map from negatively stained crystals reveals distinct contributions from intramembranous and extramembranous protein domains. On the basis of this distinction and of the packing of molecules in the crystal, we have proposed a specific arrangement for the ten alpha-helices that have been suggested as spanning the bilayer.

Animals↗
PubMed1998

Structure and interactions of fully hydrated dioleoylphosphatidylcholine bilayers.

This study focuses on dioleoylphosphatidylcholine (DOPC) bilayers near full hydration. Volumetric data and high-resolution synchrotron x-ray data are used in a method that compares DOPC with well determined gel phase dipalmitoylphosphatidylcholine (DPPC). The key structural quantity obtained is fully hydrated area/lipid A0 = 72.2 +/- 1.1 A2 at 30 degrees C, from which other quantities such as thickness of the bilayer are obtained. Data for samples over osmotic pressures from 0 to 56 atmospheres give an estimate for the area compressibility of KA = 188 dyn/cm. Obtaining the continuous scattering transform and electron density profiles requires correction for liquid crystal fluctuations. Quantitation of these fluctuations opens an experimental window on the fluctuation pressure, the primary repulsive interaction near full hydration. The fluctuation pressure decays exponentially with water spacing, in agreement with analytical results for soft confinement. However, the ratio of decay length lambda(fl) = 5.8 A to hydration pressure decay length lambda = 2.2 A is significantly larger than the value of 2 predicted by analytical theory and close to the ratio obtained in recent simulations. We also obtain the traditional osmotic pressure versus water spacing data. Our analysis of these data shows that estimates of the Hamaker parameter H and the bending modulus Kc are strongly coupled.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed1997

High resolution and high fields in biological solid state NMR.

2H solid state NMR spectra of a polypeptide in an oriented membrane environment is demonstrated to have an orientational resolution of 0.3 degree. Such data results in high resolution structural constraints. Similar spectra are demonstrated at 23.2 T using a resistive magnet at the National High Magnetic Field Laboratory.

Anti-Bacterial Agents↗
PubMed2001

A neutron Laue diffraction study of endothiapepsin: implications for the aspartic proteinase mechanism.

Current proposals for the catalytic mechanism of aspartic proteinases are largely based on X-ray structures of bound oligopeptide inhibitors possessing nonhydrolyzable analogues of the scissile peptide bond. However, the positions of protons on the catalytic aspartates and the ligand in these complexes have not been determined with certainty. Thus, our objective was to locate crucial protons at the active site of an inhibitor complex since this will have major implications for a detailed understanding of the mechanism of action. We have demonstrated that high-resolution neutron diffraction data can be collected from crystals of the fungal aspartic proteinase endothiapepsin bound to a transition state analogue (H261). The neutron structure of the complex has been refined at a resolution of 2.1 A to an R-factor of 23.5% and an R(free) of 27.4%. This work represents the largest protein structure studied to date by neutron crystallography at high resolution. The neutron data demonstrate that 49% of the main chain nitrogens have exchanged their hydrogen atoms with D2O in the mother liquor. The majority of residues resisting exchange are buried within core beta-sheet regions of the molecule. The neutron maps confirm that the protein has a number of buried ionized carboxylate groups which are likely to give the molecule a net negative charge even at very low pH, thereby accounting for its low pI. The functional groups at the catalytic center have clearly undergone H-D exchange despite being buried by the inhibitor occupying the active site cleft. Most importantly, the data provide convincing evidence that Asp 215 is protonated and that Asp 32 is the negatively charged residue in the transition state complex. This has an important bearing on mechanistic proposals for this class of proteinase.

Aspartic Acid↗
PubMed2000

Improved crystals of Thermus thermophilus prolyl-tRNA synthetase complexed with cognate tRNA obtained by crystallization from precipitate.

The complex between Thermus thermophilus prolyl-tRNA synthetase (ProRSTT) and its cognate tRNA has been crystallized using two different isoacceptors of tRNA(Pro). Similar bipyramidal crystals of the complexes of ProRSTT with the two different tRNA(Pro) isoacceptors grow within two weeks from 32% saturated ammonium sulfate solution. They belong to space group P4(3)2(1)2, with unit-cell parameters a = 143.1, b = 143.1, c = 228.6 A. The crystals diffract weakly to a maximum resolution of 3.1 A. Superior quality crystals were obtained by growing slowly from precipitate over 5-6 months. These are of the same space group but have slightly altered unit-cell parameters, a = 140.8, b = 140.8, c = 237.0 A. These crystals diffract more strongly to at least 2.8 A resolution and a complete data set to 2.85 A resolution has been collected from a single crystal. Comparison of the packing in the two crystal forms shows that domain flexibility contributes to the presence of different crystal contacts in the two forms.

Amino Acyl-tRNA Synthetases↗
PubMed2006

The purification, crystallization and preliminary structural characterization of PhzM, a phenazine-modifying methyltransferase from Pseudomonas aeruginosa.

Pyocyanin, phenazine-1-carboxylic acid and more than 70 related compounds collectively known as phenazines are produced by various species of Pseudomonas, including the fluorescent pseudomonad P. aeruginosa, a Gram-negative opportunistic pathogen in humans and animals. P. aeruginosa synthesizes a characteristic blue water-soluble compound called pyocyanin (1-hydroxy-5-methyl-phenazine). Two enzymes designated PhzM and PhzS are involved in the terminal steps of its synthesis and very little is known about these enzymes. In this study, PhzM, a dimeric S-adenosylmethionine-dependent methyltransferase, was purified and crystallized from PEG 3350/sodium cacodylate/sodium citrate pH 6.5. The crystals belong to space group P1, with unit-cell parameters a = 46.1, b = 61.8, c = 69.6 A, alpha = 96.3, beta = 106.6, gamma = 106.9 degrees . They contain one dimer in the asymmetric unit and diffract to a resolution of 1.8 A. Anomalous data to 2.3 A resolution have been collected from seleno-L-methionine-labelled PhzM.

Anti-Bacterial Agents↗
PubMed1977

Analog processing of vestibular nystagmus for on-line cross- correlation data analysis.

An analog processing circuit is described which allow accurate measurement of the phase relationships between input angular acceleration and resulting eye velocity. Vestibular nystagmic data are processed via analog technics to yield slowphase eye velocity. The turntable velocity input is cross-correlated with the eye velocity output, using a Nicolet MED-80 minicomputer system. The resulting correlograms are further processed to obtain precise phase information. Test data analysis shows a system resolution within 1 degree. Data from human and animal subjects are portrayed.

Acceleration↗
PubMed2006

Cytogenetic genotype-phenotype studies: improving genotyping, phenotyping and data storage.

High-resolution molecular cytogenetic techniques such as genomic array CGH and MLPA detect submicroscopic chromosome aberrations in patients with unexplained mental retardation. These techniques rapidly change the practice of cytogenetic testing. Additionally, these techniques may improve genotype-phenotype studies of patients with microscopically visible chromosome aberrations, such as Wolf-Hirschhorn syndrome, 18q deletion syndrome and 1p36 deletion syndrome. In order to make the most of high-resolution karyotyping, a similar accuracy of phenotyping is needed to allow researchers and clinicians to make optimal use of the recent advances. International agreements on phenotype nomenclature and the use of computerized 3D face surface models are examples of such improvements in the practice of phenotyping patients with chromosomal anomalies. The combination of high-resolution cytogenetic techniques, a comprehensive, systematic system for phenotyping and optimal data storage will facilitate advances in genotype-phenotype studies and a further deconstruction of chromosomal syndromes. As a result, critical regions or single genes can be determined to be responsible for specific features and malformations.

Chromosome Aberrations↗
PubMed2004

Pros and cons of cryocrystallography: should we also collect a room-temperature data set?

High-resolution protein structures are becoming more common owing to the availability of increasingly brilliant synchrotron X-ray sources. However, to withstand the increased X-ray dose the crystals must be held at cryogenic temperatures. To compare the benefit of increased resolution with the drawback of potential temperature-induced changes, three room-temperature and three cryogenic data sets for PAK pilin have been collected at resolutions between 1.8 and 0.78 A. The results show that although the high-resolution cryogenic structures are more precise and more detailed, they also show systematic deviations from the room-temperature structures. Small but significant differences are even observed in the structural core, whilst more extensive changes occur at the protein surface. These differences can affect biological interpretations, especially because many important biological processes take place at the protein surface. Accordingly, although high-quality cryogenic synchrotron data is extremely valuable to protein crystallography, room-temperature structures are still desirable, especially if the research question involves protein features that are sensitive to temperature-induced changes.

Crystallography↗
PubMed1999

Crystallization and preliminary X-ray studies on the molbindin ModG from Azotobacter vinelandii.

Crystals of the molbindin ModG (subunit Mr = 14359 Da), a cytoplasmic molybdate-binding protein from Azotobacter vinelandii, were grown by vapour diffusion. Both apo and tungstate-bound forms were crystallized and X-ray data were collected at 100 K. Apo-ModG crystallizes in space group P6322, with unit-cell dimensions a = b = 90.62, c = 79.46 A. Native data to a resolution of 2.5 A were collected from a single crystal, which showed a marked improvement in diffraction quality after annealing. Data from a single-site gold derivative were also collected at 2.7 A resolution. Crystals of the ligand-bound form of ModG belong to space group P321, with unit-cell parameters a = b = 50.57, c = 79.29 A. X-ray data to a resolution of 2.0 A were collected.

Azotobacter vinelandii↗