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At least 217 records · Page 12Linked to original sources
PubMed1994

Crystal structure of toxin II from the scorpion Androctonus australis Hector refined at 1.3 A resolution.

The crystal structure of toxin II from the scorpion Androctonus australis Hector has been refined at 1.3 A resolution using restrained least-squares methods. The final R-factor is 0.148 for the 13,619 reflections between 7.0 A and 1.3 A resolution with F > 2.5 sigma (F) and the bond length standard deviation from ideality is 0.017 A. Although minor changes have been introduced relative to the model previously refined at 1.8 A resolution, the use of higher-resolution data has allowed the modelling of some discrete disorder. Thus, three residues (including a disulphide bridge) have been built with multiple conformations. Occupancies were refined for the 106 solvent molecules included in the model, nine of them with explicit multiple sites. There is well-defined electron density for some of the protein hydrogen atoms in the final difference Fourier map. A detailed description of the toxin structure is presented, along with a comparison with the high-resolution structure of the related variant-3 scorpion toxin.

Amino Acid Sequence↗
PubMed1986

Effect of elastic bend distortions on electron diffraction data from thin protein microcrystals.

The effect of small elastic bend distortions in thin protein crystals on electron diffraction intensities is investigated using a model calculation for rubredoxin. The calculation, based on analytical expression derived by Cowley, has been shown previously to give an almost quantitative description of kinematical diffraction from linear chain systems. It is therefore shown that, unless the selected area used in the electron diffraction experiment is very small (or alternatively the incident beam has a small coherence length), the high resolution data may not be useful for structure determination, since they do not represent the total contents of the unit cell.

Chemical Phenomena↗
PubMed2006

Tradeoffs of different types of species occurrence data for use in systematic conservation planning.

Data on the occurrence of species are widely used to inform the design of reserve networks. These data contain commission errors (when a species is mistakenly thought to be present) and omission errors (when a species is mistakenly thought to be absent), and the rates of the two types of error are inversely related. Point locality data can minimize commission errors, but those obtained from museum collections are generally sparse, suffer from substantial spatial bias and contain large omission errors. Geographic ranges generate large commission errors because they assume homogenous species distributions. Predicted distribution data make explicit inferences on species occurrence and their commission and omission errors depend on model structure, on the omission of variables that determine species distribution and on data resolution. Omission errors lead to identifying networks of areas for conservation action that are smaller than required and centred on known species occurrences, thus affecting the comprehensiveness, representativeness and efficiency of selected areas. Commission errors lead to selecting areas not relevant to conservation, thus affecting the representativeness and adequacy of reserve networks. Conservation plans should include an estimation of commission and omission errors in underlying species data and explicitly use this information to influence conservation planning outcomes.

Animals↗
PubMed2001

Studies on the hydrolyzing mechanism for cyclodextrins of Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII). X-ray structure of the mutant E354A complexed with beta-cyclodextrin, and kinetic analyses on cyclodextrins.

Crystals of the mutant E354A of Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII) complexed with beta-cyclodextrin were prepared by a soaking method, and the diffraction data were collected at 100 K, using Synchrotron radiation (SPring-8). The crystals belong to an orthorhombic system with the space group P2(1)2(1)2(1) and cell dimensions a = 111.1 A, b = 117.7 A, c = 113.3 A, which is almost isomorphous with crystals of the wild-type TVAII, and the structure was refined to an R-factor = 0.208 (R(free) = 0.252) using 3.0 A resolution data. The refined structure shows that the interactions between Phe286 and two C6 atoms of beta-cyclodextrin at the hydrolyzing site are important for TVAII to recognize cyclodextrins as substrates. This observation from the X-ray structure was supported by kinetic analyses of cyclodextrins using the wild-type TVAII, the mutant F286A and F286L. These studies also suggested that the TVAII-hydrolyzing mechanism for cyclodextrins is slightly different from that for starch.

Amino Acid Substitution↗
PubMed1989

Improvements in MR angiography using phase-corrected data sets.

The objective of this work is refinement of an MR angiography technique via postprocessing removal of phase errors which inhibit static signal subtraction. Projective views of the object are obtained using interleaved flow-compensated and noncompensated gradient waveforms. Complex subtraction of data sets is required since a projection dephase pulse is used for static signal suppression. This renders the difference image susceptible to systematic phase errors which are modeled as a smoothly varying multiplicative phase function. The error function is estimated by comparison of heavily spatial filtered renditions of the object acquired without projection dephasing in order to minimize influence of flow. The phase correction is then applied to high-resolution data sets collected with projection dephasing to enhance flow sensitivity. The technique is demonstrated by improvement of MR angiograms of rats acquired on a 2-T, 31-cm-bore system.

Animals↗
PubMed2001

Improvement of SAS triple invariant estimates for macromolecular direct-methods phasing.

Single-wavelength anomalous dispersion (SAS) data can in principle be phased by direct methods since a priori estimates of the three-phase structure invariants can be computed from these data. The mean phase error of the most reliable triple estimates for a small protein, however, is typically no better than 60 degrees, and does not bode well for applications to larger structures. A procedure is described that can substantially lower the error in these estimates and introduce a larger number of useful triple invariants into the phasing process. The mean phase error of the most reliable triples for a 2.5 A resolution data set from a Pt derivative of a 115-residue protein was reduced from 55 to 25 degrees by this method. It was also possible to identify a significant number of the poorest triple estimates, those with mean phase errors approaching 90 degrees, such that they could be reliably down-weighted or excluded from the phasing process.

Crystallography, X-Ray↗
PubMed1998

End-of-life confusion in patients with cancer.

PURPOSE/OBJECTIVES: To review the literature on confusion at the end of life, provide accurate definitional and defining characteristics of confusion, and outline nursing strategies for its resolution. DATA SOURCES: Published articles, computerized databases, book chapters, reference lists from chapters and journal articles. DATA SYNTHESIS: As a major component of symptom distress in terminal care, confusion has not been defined clearly and therefore has not benefited from rigorous assessment and study as have other end-of-life symptoms. CONCLUSIONS: Increased knowledge about confusion that occurs in patients with widely metastatic cancer will assist in accurate symptom identification, early recognition, and timely management to reduce cognitive symptom distress at the end of life. Improved symptom resolution also can benefit family coping during terminal care. IMPLICATIONS FOR NURSING PRACTICE: Oncology nurses can devise management protocols for confused patients that include screening criteria, pharmacologic interventions, environmental support, and prophylactic safety measures.

Confusion↗
PubMed2006

Molecular beacon-based temperature control and automated analyses for improved resolution of melting temperature analysis using SYBR I green chemistry.

BACKGROUND: Melting temperature analysis of products amplified with SYBR I Green chemistry is a cheap and effective method for identification of sequence differences. When used in conventional quantitative real-time PCR instruments (qPCR), this method is limited by temperature variations over the heating block and low numbers of fluorescence measurements during the dissociation step, which hamper the ability of most instruments to report accurate and precise melting temperatures. METHODS: We designed a molecular beacon-based temperature indicator probe (Tm-probe) to control for variations in temperatures over the heating block of the instrument. In addition, we wrote an automated curve-fit analysis algorithm of dissociation data to use multiple data points with a gaussian curve fit to extrapolate precise melting temperatures. RESULTS: Use of the Tm-probe in conjunction with the analysis algorithm and multiple dissociations improved SDs of melting temperatures over a 96-well plate from 0.19 to 0.06 degrees C. CONCLUSIONS: Melting temperature analyses with SYBR I Green chemistry on conventional qPCR instruments can be improved by the use of a Tm-probe in conjunction with curve-fit analysis of data. Resolution improvement up to 3-fold is possible and allows additional melting temperatures to be identified.

Algorithms↗
PubMed2005

The effect of delayed visual feedback on telerobotic surgery.

BACKGROUND: Telerobotic surgery is ideally suited for remote applications in which the instrument control console is stationed separately from the end-effectors at the patient's bedside. However, if the distance between the console and the patient is great enough, a lag effect or latency between end-effector manipulation and the depicted image leads to alterations in movement patterns. The purpose of this study was to determine the effect of visual delay on surgical task performance. METHODS: At an endoscopic skill station, an analogue delay device was interposed between the surgical field and monitor to delay the transmission of visual information, thus mimicking the distance effect of data transmission. Three surgeons with similar laparoscopic experience participated in the laparoscopic knot tying portion of the study, and seven residents participated in the accuracy and dexterity tasks. The time to complete a single throw was recorded in seconds after adding consecutively increasingly time delay in 50 ms increments. Similar time delay increments were added for the accuracy and dexterity tasks, which involved passing a needle through two adjacent circles and passing a small cylinder through a larger one to reproduce two-handed coordination and spatial resolution. Data were presented as the median time to complete each task. RESULTS: For all three tasks, an incremental increase in time delay was associated with a significant (p < 0.001) increase in the time to complete the task. For dexterity, a statistically significant (p <or= 0.05) delay was identified at 0.25 s of delay from control values without delay. A move-and-wait strategy was gradually adopted up to 0.4 s of visual delay. CONCLUSIONS: Compensation for visually delayed image perception occurs on several levels. Initial adaptations include slower end-effector manipulation; late adaptive changes include a move-and-wait strategy. Increased time to perform surgical maneuvers as well as diminished accuracy, diminished dexterity, and increasing fatigue represent additional performance encumbrances evoked by visual time delay. The nuances of both human and digital compensatory mechanisms for visual time delay must be defined and enhanced to maximize the potential for telerobotic surgical applications.

Adaptation, Physiological↗
PubMed2004

Using a GIS-based floating catchment method to assess areas with shortage of physicians.

This paper presents a geographic information system (GIS) based floating catchment method for identifying physician shortage areas. The traditional designation methods are primarily regional availability measures, which use administrative boundaries such as counties as the basic spatial units for calculating physician to population ratios and designate shortage based on those ratios. Such approaches have been criticized for their inability to account for either the spatial variations of population demand and physician supply within those boundaries or for population-physician interactions across them. The floating catchment method addresses the internal spatial distribution problem by deriving population data from a smaller unit, the census tract. The potential cross border patient-physician interaction is taken into consideration by using circles of reasonable radius around each census tract centroid as the basic spatial units, which can encompass areas on either side of an administrative border. By varying the radius of the catchment circle, this paper demonstrates that the physician to population ratio is scale dependent and that the greatest variability of the ratios and shortages occur at the most local scales (< 20 miles), which argues for using finer spatial resolution data in shortage designation practice.

Catchment Area, Health↗
PubMed2002

Experiments testing the abatement of radiation damage in D-xylose isomerase crystals with cryogenic helium.

Helium is a more efficient cryogen than nitrogen, and for macromolecular data collection at high-flux beamlines will deliver lower temperatures. An open-flow helium cryostat developed at the University of Toledo (the Pinkerton Device) has been used for macromolecular data collection. This device differs from standard commercial He cryostats by having a much narrower aperture providing a high velocity stream of He around the crystal that maximizes convective and conductive heat exchange between the crystal and the cryogen. This paper details a series of experiments conducted at the IMCA-CAT 17ID beamline using one crystal for each experimental condition to examine whether helium at 16 K provided better radiation-damage abatement compared with nitrogen at 100 K. These studies used matched high-quality crystals (0.94 A diffraction resolution) of D-xylose isomerase derived from the commercial material Gensweet SGI. Comparisons show that helium indeed abates the indicators of radiation damage, in this case resulting in longer crystal diffractive lifetimes. The overall trend suggests that crystals maintain order and that high-resolution data are less affected by increased radiation load when crystals are cooled with He rather than N(2). This is probably the result of a lower effective temperature at the crystal with concomitant reduction in free-radical diffusion. Other features, such as an apparent phase transition in macromolecular crystals at lower temperatures, require investigation to broaden the utility of He use.

Aldose-Ketose Isomerases↗
PubMed2004

Strategies and data analysis techniques for lipid and phospholipid chemistry elucidation by intact cell MALDI-FTMS.

Ions attributed to lipids and phospholipids are directly observed by desorption from whole bacteria using intact cell (IC) matrix-assisted laser desorption-ionization (MALDI) Fourier transform mass spectrometry (FTMS). Saccharomyces cerevisiae are grown in rich media broth, concentrated, and applied directly to the MALDI surface without lysis or chemical treatment. FTMS of MALDI ions gives excellent signal to noise ratios with typical resolving powers of 90,000 and mass precision better than 0.002 Da. Use of accurate mass measurements and a simple set of rules allow assignment of major peaks into one of twelve expected lipid classes. Subsequently, fractional mass versus whole number mass plots are employed to enhance visual interpretation of the high-resolution data and to facilitate detection of related ions such as those representing homologous series or different degrees of unsaturation. This approach, coupled with rules based on bacterial biochemistry, is used to classify ions with m/z up to about 1000. Major spectral peaks in the range m/z 200-1000 are assigned as lipids and phospholipids. In this study, it is assumed that biologically-derived ions with m/z values lower than 1000 are lipids. This is not unreasonable in view of the facts that molecular weights of lipids are almost always less than 1000 Da, that the copy numbers for lipids in a cell are higher than those for any single protein or other component, and that lipids are generally collections of distinct homologous partners, unlike proteins or other cell components. This paper presents a new rapid lipid-profiling method based on IC MALDI-FTMS.

Membrane Lipids↗
PubMed2000

Novel fold and capsid-binding properties of the lambda-phage display platform protein gpD.

The crystal structure of gpD, the capsid-stabilizing protein of bacteriophage lambda, was solved at 1.1 A resolution. Data were obtained from twinned crystals in space group P21 and refined with anisotropic temperature factors to an R-factor of 0.098 (Rfree = 0. 132). GpD (109 residues) has a novel fold with an unusually low content of regular secondary structure. Noncrystallographic trimers with substantial intersubunit interfaces were observed. The C-termini are well ordered and located on one side of the trimer, relatively far from its three-fold axis. The N-termini are disordered up to Ser 15, which is close to the three-fold axis and on the same side as the C-termini. A density map of the icosahedral viral capsid at 15 A resolution, obtained by cryo-electron microscopy and image reconstruction, reveals gpD trimers, seemingly indistinguishable from the ones seen in the crystals, at all three-fold sites. The map further reveals that the side of the trimer that binds to the capsid is the side on which both termini reside. Despite this orientation of the gpD trimer, fusion proteins connected by linker peptides to either terminus bind to the capsid, allowing protein and peptide display.

Amino Acid Sequence↗
PubMed1998

[Vascular applications of interventional MRI].

The flow sensitivity inherent to the MR experiment allows for the non-invasive assessment of both the arterial and venous vasculature in any desired plane with good spatial resolution. Data can be acquired in a three-dimensional form, permitting reformating in any plane. In addition, MRI is capable of providing quantitative blood flow information with the use of phase-contrast flow-mapping techniques. Ultrafast gradient echo and echoplanar data acquisition strategies even permit imaging in near-real time. The availability of open MRI configurations now permits one to take advantage of the unique imaging features inherent to MR imaging for the purpose of guidance and control of various intravascular procedures. With the recent development of the MR tracking and MR profiling techniques, permitting visualization of guide-wires and catheters relative to their surroundings in the MR environment in real time, one of the last obstacles to 'Interventional MR angiography' has in effect been overcome. In addition, MR catheters can be modified to acquire high-resolution MR images of the vascular wall, thereby opening vast possibilities regarding characterization of atherosclerotic plaques. This review introduces the underlying techniques for catheter and guide-wire visualization in the MR environment, describes preliminary interventions in animals and humans and discusses the potential of intravascular MRI.

Echo-Planar Imaging↗
PubMed2001

Structures and comparison of the Y98H (2.0 A) and Y98W (1.5 A) mutants of flavodoxin (Desulfovibrio vulgaris).

The structures for two mutants at the Tyr98 site of Desulfovibrio vulgaris flavodoxin have been determined. The first, a tyrosine-to-histidine (Y98H) variant, was determined at the moderately high resolution of 2.0 A, while the tyrosine-to-tryptophan variant (Y98W) yielded very high resolution data (beyond 1.5 A) allowing a detailed look at the water structure, alternate side-chain conformations and the planarity of the FMN. Both structures were solved by molecular replacement beginning with the native (P2A) coordinates as a starting point. The Y98H variant of D. vulgaris flavodoxin crystallizes in space group P2(1)2(1)2(1), with unit-cell parameters a = 41.96, b = 61.45, c = 57.04 A, while the Y98W mutant adopts space group P2(1), with a = 41.29, b = 55.82, c = 32.52 A, beta = 100.68 degrees. Refinement for both mutants utilized PROLSQ followed by, for the high-resolution Y98W structure, anisotropic refinement as implemented in SHELXL. Final R factors of 17% for the Y98H mutant and 9.8% for the Y98W mutant were obtained. For the high-resolution (1.5 A) Y98W mutant, 31,010 unique reflections were collected from a single crystal. The final model includes 273 solvent molecules, with eight side chains assuming multiple conformations. At this resolution, the detailed conformation of the FMN can be observed, with both a bow and twist being noted. A comparison is made between the two mutants and the different oxidation states of the native flavodoxin. Although both mutants show similar E(2) (oxidized/semiquinone) one-electron redox potentials to the native, the E(1) (semiquinone/hydroquinone) redox potential for the Y98H mutant is significantly different from that of the Y98W variant and the native protein. The surprising similarity in the folding of the polypeptide chain 60--64 between the two mutants and the reduced states of the native is discussed. The interaction between O61 and N5 in the flavin is discussed because of the new conformation of this loop.

Amino Acid Substitution↗
PubMed1995

Reconstruction of 12 MV bremsstrahlung spectra from measured transmission data by direct resolution of the numeric system AF = T.

An investigation of x-ray spectral reconstruction from transmission data by direct resolution of the matrix system A*F = T (using spectral algebra formalism) has been previously presented. The resolution has been done with simulated spectrum. In this paper, the method on a real case of a 12 MV photon beam was tested. A special study of the setup has been made to estimate and reduce the experimental errors that could alter the results. In order to convert F(E) (a fraction of the signal due to a photon of energy E) into photon fluence phi (E), the chamber energy response R(E) has been studied and an approximated analytical function for its representation was proposed. Spectra reconstructed from different transmission data using different attenuators, buildup caps, and ionization chambers have been compared to verify the uniqueness of the reconstructed spectra. To test the validity of the results, dosimetric values, such as Depth Dose Data have been calculated, from our spectrum, using a specific code developed by Kosunen et al. The results show a good agreement between the measured and calculated data.

Models, Structural↗
PubMed1994

Crystal structure of the ferredoxin I from Desulfovibrio africanus at 2.3 A resolution.

The crystal structure of the ferredoxin I from the sulfate-reducing bacterium Desulfovibrio africanus (DaFdI) has been solved and refined by X-ray diffraction. The crystals are orthorhombic with a = 96.6 A, b = 58.1 A, and c = 20.7 A, space group P2(1)2(1)2, and two ferredoxin molecules per asymmetric unit. The initial electron density map has been obtained by combining phasing by molecular replacement methods, anomalous scattering, and noncrystallographic averaging. The final crystallographic R factor is 0.182 with 10-2.3 A resolution data. In parallel, the amino acid sequence was redetermined. This showed that DaFdI contains 64 residues (instead of 61) including one free cysteine, one histidine, and one tryptophan in the C-terminal part of the molecule. The current molecular model includes the two molecules of the asymmetric unit, 67 water molecules, and one sulfate ion. The DaFdI overall folding very closely resembles that of ferredoxins of known structure. Comparisons with the single cluster ferredoxins from Desulfovibrio gigas and Bacillus thermoproteolyticus show that the presence or the absence of a disulfide bridge does not significantly affect the folding of the other half of the molecule, including the characteristic alpha-helix of the single cluster ferreddoxins. Like other ferredoxins or analogs, the [4Fe-4S] iron--sulfur cluster presents, at 2.3 A resolution, a cubane-like geometry. By contrast, its immediate environment is different as it includes, besides the four cysteic sulfur ligands, the sulfur atom of the free cysteine. This sulfur atom, which is buried within the protein, is in van der Waals contact with one labile sulfur of the cluster and one liganded cysteic sulfur. The association of a [4Fe-4S] cluster with one free cysteic sulfur is similar to that previously found in both X-ray structures of Azotobacter vinelandii and Peptococcus aerogenes [Stout, C. D. (1989) J. Mol. Biol. 205, 545-555; Backes, G., et al. (1991) J. Am. Chem. Soc. 113, 2055-2064]. Chemical sequence analysis suggests that this characteristic [4Fe-4S] cluster sulfur environment is widely distributed among ferredoxins.

Amino Acid Sequence↗
PubMed2002

Explosive events on the Sun.

I describe two of the most dynamic and highly energetic phenomena in the Solar System--the explosive flares that can occur when plasma is confined by magnetic fields and the large-scale ejections of material known as 'coronal mass ejections'. These explosive events are poorly understood and yet occur in a variety of contexts in the Universe, ranging from planetary magnetospheres to active galactic nuclei. Understanding why flares and coronal mass ejections occur is a major goal across a wide range of space physics and astrophysics. Although explosive events from the Sun have dramatic effects on Earth, flares in other stars, for example, can be vastly more energetic and have an even more profound effect on their environment. We are now in the unprecedented position of having access to a number of space observatories dedicated to the Sun: the Yohkoh spacecraft, the Solar and Heliospheric Observatory, the Transition Region and Coronal Explorer and the Ramaty High Energy Solar Spectroscopic Imager. These cover a wide wavelength range from white light to gamma rays with both spectroscopy and imaging, and allow huge progress to be made in understanding the processes involved in such large explosions. The high-resolution data show dramatic and complex explosions of material on all spatial scales on the Sun. They have revealed that the Sun is constantly changing everywhere on its surface--something that was never imagined before. One of the mechanisms that has been proposed to account for the large energy release is magnetic reconnection. Recent observations from space increasingly support this view. This article will discuss those observations that support this model and also those that suggest different processes. The current space missions have given us an excellent insight into the actual explosive processes in the Sun. However, they have provided us with only a tantalizing glimpse of what causes the elusive trigger. Future missions such as Solar-B (the follow-on to Yohkoh), the Solar Terrestrial Relations Observatory, the Solar Dynamics Observatory and the Solar Orbiter mission will allow us to probe the trigger in a way that was not dreamt of a decade ago, by providing stereo views, measurements from Sun-grazing orbit, and much higher spatial, temporal and spectral resolution. It is an exciting time for solar physics and everything that we learn about the Sun will improve our ability to understand other magnetic phenomena in the Universe.

Journal Article↗