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At least 793 records · Page 44Linked to original sources
PubMed2003

MDCT of renal and mesenteric vessels.

Computed tomography angiography (CTA) with multiple detector-row CT (MDCT) has evolved into an established technique for non-invasive imaging of renal and mesenteric vessels. With adequate selection of acquisition parameters (thin collimation) high spatial-resolution volumetric data sets for subsequent 2D and 3D reformation can be acquired. Contrast medium (CM) injection parameters need to be adjusted to the acquisition speed of the scanners. Whereas fast acquisitions allow a reduction of total CM volume in the setting of CTA, this is not the case when CTA is combined with a second-phase abdominal MDCT acquisition for parenchymal (e.g., hepatic) imaging. Renal CTA is an accurate and reliable test for visualizing vascular anatomy and renal artery stenosis, and therefore a viable alternative to MRA in the assessment of patients with renovascular hypertension and in potential living related renal donors. CTA, combined with abdominal/parenchymal MDCT is a first-line diagnostic test in patients with suspected abdominal vascular emergencies, such as acute mesenteric ischemia, and an excellent tool to assess a wide variety of vascular abnormalities of the abdominal viscera.

Acute Disease↗
PubMed2006

MR-based coronary artery blood velocity measurements in patients without coronary artery disease.

To evaluate the feasibility of MR-based coronary blood velocity measurements (MRvenc) in patients without coronary artery disease (CAD). Eighty-three patients with angiographically excluded CAD received MRvenc of the proximal segments of both coronary arteries (CAs). Using a retrospectively ECG-gated breath-hold phase-contrast FLASH sequence with high temporal resolution, flow data were technically acquirable in 137/166 (83%) CAs. Quantification and analysis of blood velocities in systole and diastole of both CAs were performed. Biphasic velocity profiles were found in 83/100 CAs. Median systolic and diastolic velocities differed significantly in LCA (19 cm/s, 24 cm/s; P<0.0001) and RCAs (14 cm/s, 16 cm/s; P<0.01). The diastolic/systolic velocity ratio was calculated in LCAs and RCAs with a median of 1.3 and 1.1, respectively. The velocity profiles of the remaining CAs were monophasic (17 CAs) or revealed severe alterations of the physiologic velocity profile with reduced flow undulations and steady velocities (37 CAs). Optimized clinical MRvenc is feasible to quantify blood velocities in the CAs. Potential indications are (1) non-invasive monitoring of patients after aortic valve reconstruction as well as (2) detection of asymptomatic CAD patients.

Adult↗
PubMed2006

An evaluation of accuracy and repeatability of a novel gait analysis device.

INTRODUCTION: Restoration of gait is a particularly important patient-based functional outcome following lower extremity trauma. A new portable device which measures gait parameters, the IDEEA, may be particularly useful in evaluating post-traumatic gait parameters in the office setting, but the accuracy and repeatability of this device relative to standard gait laboratory footswitches are unknown. MATERIAL AND METHODS: Twelve healthy subjects were tested simultaneously using the IDEEA device and standard gait laboratory footswitches, at slow, medium, and fast speeds. Parameters evaluated were single-limb support time (SLS), double-limb support time (DLS), swing phase duration (SPD), cycle duration, and cadence. RESULTS: The repeatability between right and left measurements tended to be better for the IDEEA, and was at least as good as the foot switches. The absolute differences of the timed gait parameters between the two devices were all in the range of 0.03 s, which is within the data sampling resolution of the gait laboratory foot switches (0.04 s). Furthermore, assuming a 1-s gait cycle, these differences account for only 3% of the gait cycle, which is also well within the clinical parameters for evaluating and differentiating between treatments. CONCLUSION: This device is accurate and repeatable, and may facilitate the evaluation of gait function in post-traumatic patients in settings outside of the traditional gait laboratory.

Adult↗
PubMed2016

Gene co-expression analysis identifies brain regions and cell types involved in migraine pathophysiology: a GWAS-based study using the Allen Human Brain Atlas.

Migraine is a common disabling neurovascular brain disorder typically characterised by attacks of severe headache and associated with autonomic and neurological symptoms. Migraine is caused by an interplay of genetic and environmental factors. Genome-wide association studies (GWAS) have identified over a dozen genetic loci associated with migraine. Here, we integrated migraine GWAS data with high-resolution spatial gene expression data of normal adult brains from the Allen Human Brain Atlas to identify specific brain regions and molecular pathways that are possibly involved in migraine pathophysiology. To this end, we used two complementary methods. In GWAS data from 23,285 migraine cases and 95,425 controls, we first studied modules of co-expressed genes that were calculated based on human brain expression data for enrichment of genes that showed association with migraine. Enrichment of a migraine GWAS signal was found for five modules that suggest involvement in migraine pathophysiology of: (i) neurotransmission, protein catabolism and mitochondria in the cortex; (ii) transcription regulation in the cortex and cerebellum; and (iii) oligodendrocytes and mitochondria in subcortical areas. Second, we used the high-confidence genes from the migraine GWAS as a basis to construct local migraine-related co-expression gene networks. Signatures of all brain regions and pathways that were prominent in the first method also surfaced in the second method, thus providing support that these brain regions and pathways are indeed involved in migraine pathophysiology.

Atlases as Topic↗
PubMed2001

Crystal structure of low-potential cytochrome c549 from Synechocystis sp. PCC 6803 at 1.21 A resolution.

The crystal structure of low-potential cytochrome c549, an extrinsic component of the photosystem II (PS II) from Synechocystis sp. PCC 6803, was obtained directly from single-wavelength 1.21 A resolution diffraction data. This is the first monodomain bis-histidinyl monoheme cytochrome c to be structurally characterized. The extended N-terminal region of c549 builds up a two-strand antiparallel beta-sheet in a hairpin motif, which extends through two molecules owing to crystal packing. Both peptide termini are involved in crystal contacts, which may explain their protrusion out of the globular fold. The C-terminus is preceded by a 9 A-long hydrophobic finger extending from a positively charged base and could be involved in PSII interactions, as well as a protruding negative patch built by a set of conserved acidic residues among c549 sequences.

Amino Acid Sequence↗
PubMed2006

Evaluating kriging as a tool to improve moderate resolution maps of forest biomass.

The USDA Forest Service, Forest Inventory and Analysis program (FIA) recently produced a nationwide map of forest biomass by modeling biomass collected on forest inventory plots as nonparametric functions of moderate resolution satellite data and other environmental variables using Cubist software. Efforts are underway to develop methods to enhance this initial map. We explored the possibility of modeling spatial structure to make such improvements. Spatial structure in the field biomass data as well as in residuals from the map was investigated across 18 ecological zones in the Interior Western U.S. Exploratory tools included directional graphs of summary statistics, three dimensional maps, Moran's I correlograms, and variograms. Where spatial pattern was present, field and residual biomass were kriged, and predictions made for an independent test set were evaluated for improvement over predictions in the initial biomass map. While kriging has some potential benefit when analyzing the field data and exploring spatial structure, kriging residuals resulted in little or no improvement in the initial biomass map developed using Cubist software. Stationarity assumptions, variogram behavior, and appropriate model fitting strategies are discussed.

Biomass↗
PubMed2005

Synthesis and in vitro cytotoxic activity of N-, F-, and S-ether derivatives of podophyllotoxin fatty acid adducts.

This paper represents the first synthesis, spectroscopic characterization, and antitumor evaluation of F-, N-, and S-containing C4alpha-FA derivatives of podophyllotoxin. In a synthetic strategy, a FA unit of 4-O-podophyllotoxinyl 12-hydroxyoctadec-Z-9-enoate 2, a derivative of podophyllotoxin, was functionalized at the C-12 position by incorporating the F atom and N-containing moieties. The FA olefin (Z, C-9/C-10) of 2 was hydrogenated to produce a derivative possessing a hydroxy function (C-12) on a saturated C18 FA chain. In another synthetic strategy, two S-ethers of podophyllotoxin (C4alpha) were synthesized from a terminal unsaturated FA analog, 4-O-podophyllotoxinyl undec-10-enoate. Syntheses were achieved through effective synthetic procedures; 1H NMR, 13C NMR, IR, and high-resolution mass data proved excellent tools to characterize these derivatives. In vitro antitumor activity was investigated against a panel of five human neoplastic cell lines, SK-MEL (malignant, melanoma), KB (epidermal carcinoma, oral), BT-549 (ductal carcinoma, breast), SK-OV-3 (ovary carcinoma), and HL-60 (human leukemia). Keeping in view the severe lack of tumor selectivity of podophyllotoxin over normal cells, we assayed new analogs against noncancerous mammalian VERO (African green monkey kidney fibroblast) cell lines to gauge their extent of toxicity. Several of these compounds showed excellent moderation of antitumor activity. In general, we found excellent growth inhibition against the human leukemia cell line (HL-60), particularly for the analogs containing S-ethers and carbamates. None of the compounds were toxic to normal cell lines.

Animals↗
PubMed1999

Preparation, separation, and confirmation of the eight geometrical cis/trans conjugated linoleic acid isomers 8,10- through 11,13-18:2.

Conjugated linoleic acid (CLA) mixtures were isomerized with p-toluenesulfinic acid or I2 catalyst. The resultant mixtures of the eight cis/trans geometric isomers of 8,10-, 9,11-, 10,12-, and 11,13-octadecadienoic (18:2) acid methyl esters were separated by silver ion-high-performance liquid chromatography (Ag+-HPLC) and gas chromatography (GC). Ag+-HPLC allowed the separation of all positional CLA isomers and geometric cis/trans CLA isomers except 10,12-18:2. However, one of the 8,10 isomers (8cis, 10trans-18:2) coeluted with the 9trans,11cis-18:2 isomer. There were differences in the elution order of the pairs of geometric CLA isomers resolved by Ag+-HPLC. For the 8,10 and 9,11 CLA isomers, cis,trans eluted before trans,cis, whereas the opposite elution pattern was observed for the 11,13-18:2 geometric isomers (trans,cis before cis,trans). All eight cis/trans CLA isomers were separated by GC on long polar capillary columns only when their relative concentrations were about equal. Large differences in the relative concentration of the CLA isomers found in natural products obscured the resolution and identification of a number of minor CLA isomers. In such cases, GC-mass spectrometry of the dimethyloxazoline derivatives was used to identify and confirm coeluting CLA isomers. For the same positional isomer, the cis,trans consistently eluted before the trans,cis CLA isomers by GC. High resolution mass spectrometry (MS) selected ion recording (SIR) of the molecular ions of the 18:1, 18:2, and 18:3 fatty acid methyl esters served as an independent and highly sensitive method to confirm CLA methyl ester peak assignments in GC chromatograms obtained from food samples by flame-ionization detection. The high-resolution MS data were used to correct for the nonselectivity of the flame-ionization detector.

Chromatography, Gas↗
PubMed1980

Intracellular oxygen measurements of mouse liver cells using quantitative fluorescence video microscopy.

Our currently developed fluorescence video microscope can measure fluorescence intensities with an error of +/- 1.5% of full scale in 65536 different positions of a microscope field. With a video frame freeze acquisition time of 33 ms, time-dependent changes of this order of time or slower can be followed. Using cells which have absorbed pyrene-1-butyrate to an intracellular concentration of 0.05 to 1 mM, the changes in fluorescence intensity with oxygen concentration are easily measured. The spatial resolution for data collection is 0.5 micron when a 54X objective is used. The individual Stern-Volmer quenching constants of each individual pixel were measured for agar slices and mouse liver cells treated with pyrenebutyric acid. The distribution of quenching constants for agar follows a normal curve about a mean value of 16 . 10(-4) torr-1. The data for mouse liver cells gave a non-normal distribution of quenching constants with a mean value of 18 . 10(-4) torr-1. The greater spread of the data from cells is interpreted as evidence for a real biological variation in the solubility coefficient of oxygen in different locations within the cell. In all the cells examined, this distribution has been observed to be non-random and appears to be associated with specific cell structures.

Animals↗
PubMed1992

Crystalline beta-cyclodextrin.12H2O reversibly dehydrates to beta-cyclodextrin.10.5 H2O under ambient conditions.

In contact with mother liquor, crystalline beta-cyclodextrin (beta-CD) hydrate has composition approximately beta-CD.12H2O. If crystals are dried at ambient conditions (18 degrees C, approximately 50% humidity), the unit cell volume diminishes approximately 30 to 50 A3. X-ray structure analysis of a dry crystal (0.89 A resolution, 4617 data, R = 0.059) showed the composition beta-CD.10.5 H2O, with approximately 5.5 water molecules in the beta-CD cavity (7 partially and 2 fully occupied sites) and approximately 5.0 between the beta-CD molecules. The positions of the beta-CD host and of most of the hydration waters are conserved during dehydration, but the occupancies of the waters in the beta-CD cavity diminish. Dry crystals put into solvent re-hydrate to the original form. The mechanism of de- and re-hydration is not evident.

Crystallization↗
PubMed1994

Predicted secondary structure of the 20 S proteasome and model structure of the putative peptide channel.

Secondary structure prediction has made great progress in recent years due to the incorporation of evolutionary information, and may be close to a point where (in combination with biochemical and low-resolution structural data) it can guide the modelling of tertiary structure in cases where no model building is possible by homology. Towards this goal it is important to gather information on the performance of prediction methods in advance of the publication of new structures. In anticipation of the soon-to-be-released structure of the 20 S proteasome from Thermoplasma acidophilum, we have applied several widely used secondary structure prediction methods to proteasome sequences and have attempted to model the putative channel in the outer proteasome rings (alpha-rings) based on the obtained predictions.

Amino Acid Sequence↗
PubMed1994

Lateral migration of blood cells and microspheres in two-dimensional Poiseuille flow: a laser-Doppler study.

The inertia-induced lateral migration of rigid microspheres, platelets and erythrocytes is studied experimentally. The concentration and velocity profiles of the particles have been determined with a laser-Doppler anemometer designed for high resolution measurements. Data are compared with empirical and analytical models on inertia-induced lateral migration of rigid spheres. Experiments done in rectangular flow channels of high aspect ratio reveal that at a sufficiently high particle Reynolds number, platelets exhibit tubular pinch effects comparable with those of rigid polystyrene microspheres. Erythrocytes also exhibit inertia-induced lateral migration at high particle Reynolds number and low medium viscosity. At a higher medium viscosity, erythrocytes show deformation-induced lateral migration towards the center of the flow channel.

Blood Flow Velocity↗
PubMed1984

The crystal structure of human deoxyhaemoglobin at 1.74 A resolution.

The structure of human deoxyhaemoglobin was refined at 1.74 A resolution using data collected on film at room temperature from a synchrotron X-ray source. The crystallographic R-factor is 16.0%. The estimated error in atomic positions is 0.1 A overall, 0.14 A for main-chain atoms of internal segments, and 0.05 A for the iron atoms. The effects of intermolecular contacts on the structure were investigated; such contacts cause only highly localized distortions, as judged from the degree of molecular asymmetry that they induce. The geometry of the iron-nitrogen complex closely resembles that of the deoxymyoglobin structure of Takano (1977) and of the 5-co-ordinated model compounds of Hoard (1975) and Jameson et al. (1980). The distance of the iron from the mean plane of N(porphyrin) is 0.40(5) A and 0.36(5) A, respectively, at the alpha and beta haems, in contrast to the corresponding distance of +0.12(8) A and -0.11(8) A in oxyhaemoglobin ( Shaanan , 1983); the Fe-N epsilon (F8) bond length is 2.12(4) A and the Fe-N(porphyrin) bond length is 2.06(2) A; the last is also in good agreement with extended X-ray fluorescence spectroscopy measurements on deoxyhaemoglobin ( Eisenberger et al., 1978; Perutz et al., 1982). The haems are domed toward the proximal side; the separation between the mean planes of N(porphyrin) and C(porphyrin) being 0.16(6) A and 0.10(6) A, respectively at the alpha and beta haems. At the alpha haems, the normals to the mean pyrrole planes are tilted uniformly toward the haem centre, by about three degrees relative to the haem normal, and there is a folding of about four degrees of the haem about an axis running between the methene carbons that are between the pyrrole rings bearing like-type side-chains. At the beta haems, there is no such folding, and only pyrroles II and IV (those eclipsed by His F8) are appreciably tilted, by about eight degrees. The independence of these parameters from restraints imposed on the model was verified by unrestrained refinement of the entire molecule starting from a structure with modified haem geometry.

Crystallography↗
PubMed1991

Crystallization and preliminary crystallographic analysis of a novel nuclease from Serratia marcescens.

Crystals have been obtained of the extracellular endonuclease from the bacterial pathogen Serratia marcescens. This magnesium-dependent enzyme is equally active against single and double-stranded DNA, as well as RNA, without any apparent base preference. The Serratia nuclease is not homologous with staphylococcal nuclease, the only other broad specificity endonuclease for which a structure exists, nor is it homologous with other nucleases that have been solved by X-ray diffraction. The structure of this enzyme should, therefore, provide new information about this class of enzyme. At present we have succeeded in obtaining large, high quality crystals using ammonium sulfate. They crystallize in the orthorhombic space group P2(1)2(1)2(1), with cell dimensions a = 106.7 A, b = 74.5 A, c = 68.9 A, and diffract to beyond 2 A. Low-resolution native data sets have been recorded and a search is under way for heavy-atom derivatives.

Endodeoxyribonucleases↗
PubMed1992

Modeling DNA structures: molecular mechanics and molecular dynamics.

Model building studies may be used to supplement structurally low resolution experimental data with detailed three-dimensional hypothetical atomic models. Because of the strong relation between structure and function in biological molecules such models may give a consistent, integral view of a wealth of experimental data. In most cases such models will predict the outcome of certain experiments. The outcome of these experiments will often either confirm the model may be used for further refinement or even demand a major revision of the model. Coordinates obtained from X-ray fiber diffraction data or in special cases single-crystal data may provide the elements for DNA or RNA model building. Local and nonlocal optimization may be used to refine these structures and to evaluate their statistical significance as estimated by a chosen force field. Appreciable progress using nonlocal optimization procedures can only be expected if the dimensionality of the problem can be reduced sufficiently to the relevant degrees of freedom. Taking advantage of structural symmetries may critically improve the convergence while refining the target molecule or its building blocks. Monte Carlo and molecular dynamics methods allow one to calculate averaged quantities. In addition, molecular dynamics provides time evolutions of certain averages. During the simulation of certain physical properties of molecules a huge amount of data will be generated. They will provide many answers, but these answers may not always apply to the original question. So what type of questions will be reliably answered by a force field? Relatively safe answers concern the local geometry of the molecules. If a conformation leads to strong distortions of bond distances or angles or to close van der Waals contacts, this conformation can safely be rejected. Optimizing such unfavorable structures energetically may lead to structures showing how to avoid such distortions. More difficult are energetical questions: which of two conformers is more stable, or what is the free energy of the substrate in the active site? One cannot always be sure that the force field provides the correct answer. Therefore, one should pose only those questions which can be checked experimentally. Because of the many possible answers, the experiment may benefit by starting with a choice proposed by the simulation. The application of this procedure to curved DNA and the DNA four-way junction was successful.

Base Sequence↗
PubMed1989

Purification, properties, and oxygen reactivity of p-hydroxybenzoate hydroxylase from Pseudomonas aeruginosa.

The monooxygenase, p-hydroxybenzoate hydroxylase (4-hydroxybenzoate, NADPH:oxygen oxidoreductase (3-hydroxylating), EC 1.14.13.2) has been isolated and purified from Pseudomonas aeruginosa. The reaction catalysed is linked to the pathways for degradation of aromatic compounds by microorganisms. The enzyme has been quantitatively characterized in this paper for use in the mechanistic analysis of the protein by site-directed mutagenesis. This can be achieved when the results presented are used in combination with the information on the sequence and structure of the gene for this protein and the high-resolution crystallographic data for the protein from P. fluorescens. The protein is a dimer of identical sub-units in solution, and has one FAD per polypeptide with a monomeric molecular weight of 45,000. A full steady-state kinetic analysis was carried out at the optimum pH (8.0). A Vmax of 3750 min-1 at 25 degrees C was calculated, and the enzyme has a concerted-substitution mechanism, involving the substrates, NADPH, oxygen, and p-hydroxybenzoate. Extensive analyses of the reactions of reduced enzyme with oxygen were carried out. The quality of the data obtained confirmed the mechanisms of these reactions as proposed earlier by the authors for the enzyme from P. fluorescens. It was found that the amino acid residue differences between enzyme from P. fluorescence and aeruginosa do marginally change some observed transient state kinetic parameters, even though the structure of the enzyme shows they have no direct role in catalysis. Thus, transient state kinetic analysis is an excellent tool to examine the role of amino acid residues in catalysis.

4-Hydroxybenzoate-3-Monooxygenase↗
PubMedDate not supplied

Electron microscopy of thin-sectioned three-dimensional crystals of SecA protein from Escherichia coli: structure in projection at 40 A resolution.

SecA is a single-chain, membrane-associated polypeptide (102 kDa) which functions as an essential component of the protein export machinery of Escherichia coli. SecA has been crystallized from ammonium sulfate as small, three-dimensional bipyramidal crystals (0.1 x 0.1 x 0.05 mm). These crystals did not demonstrate detectable diffraction of X-rays from rotating anode sources. For study by electron microscopy, individual crystals were cross-linked in glutaraldehyde and OsO4 solutions, dehydrated, embedded in epoxy resin, and sectioned normal to crystallographic axial directions inferred from the external morphology of the crystals. Fourier transformation of processed images of untilted thin sections stained with uranyl acetate and lead citrate show reflections extending to 31 A resolution. Diffraction data and reconstructed images of the projected density of the unit cell contents indicate that the bipyramidal SecA crystals belong to orthorhombic space group C222(1) with unit cell dimensions a = 414 A, b = 381 A, and c = 243 A. Filtered images and density maps of mutually orthogonal projections of the unit cell contents are consistent with a three-dimensional model in which the asymmetric unit contains eight SecA monomers. The large unit cell dimensions and packing of protein monomers suggest that SecA is crystallizing as an oligomer of either dimers or tetramers.

Adenosine Triphosphatases↗
PubMed2004

Crystallization and high-resolution X-ray diffraction data collection of an Asp49 PLA2 from Bothrops jararacussu venom both in the presence and absence of Ca2+ ions.

Snake venom PLA(2)s have been extensively studied due to their role in mediating and disrupting physiological processes such as coagulation, platelet aggregation and myotoxicity. The Ca(2+) ion bound to the putative calcium-binding loop is essential for hydrolytic activity. We report the crystallization in the presence and absence of Ca(2+) and X-ray diffraction data collection at 1.60 angstroms (with Ca(2+)) and 1.36 angstroms (without Ca(2+)) of an Asp49 PLA(2) from Bothrops jararacussu venom. The crystals belong to orthorhombic space group C222(1). Initial refinement and electron density analysis indicate significant conformational changes upon Ca(2+) binding.

Animals↗