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At least 1,207 records · Page 67Linked to original sources
PubMed1998

Microfabricated device coupled with an electrospray ionization quadrupole time-of-flight mass spectrometer: protein identifications based on enhanced-resolution mass spectrometry and tandem mass spectrometry data.

We describe the coupling of a microfabricated fluidic device to an electrospray ionization (ESI) quadrupole time-of-flight mass spectrometer (QqTOFMS) for the identification of protein samples. The microfabricated devices consisted of three reservoirs connected via channels to a main capillary, which in turn was linked via a microspray interface to the QqTOFMS. Here we present preliminary results obtained using this system. Standardized solutions of myoglobin tryptic digest were analyzed indicating a limit of detection at the low to sub fmol/microL. The combination of the microfabricated device for rapid sample delivery and the rapid acquisition capability, enhanced resolution and mass accuracy of the QqTOF offers unique possibilities for the rapid identification of proteins by database searching. This platform can generate MS data suitable for protein database searching by the peptide-mass fingerprinting approach and MS/MS data suitable for protein database searching. Here the results of the two database-searching approaches are compared and the possibilities of combining the two approaches for rapid identification of protein are discussed. Also, we present a comparison of the results obtained using the three-position microfabricated device coupled to the ESI-QqTOFMS and to an ESI-ion trap MS. Finally the combination of C-terminal 18O labeling of peptides and the microfabricated system for automated combined peptide-mass fingerprinting and sequence-tag database searching is discussed.

Databases, Factual↗
PubMed2000

Population bottlenecks and Pleistocene human evolution.

We review the anatomical and archaeological evidence for an early population bottleneck in humans and bracket the time when it could have occurred. We outline the subsequent demographic changes that the archaeological evidence of range expansions and contractions address, and we examine how inbreeding effective population size provides an alternative view of past population size change. This addresses the question of other, more recent, population size bottlenecks, and we review nonrecombining and recombining genetic systems that may reflect them. We examine how these genetic data constrain the possibility of significant population size bottlenecks (i.e., of sufficiently small size and/or long duration to minimize genetic variation in autosomal and haploid systems) at several different critical times in human history. Different constraints appear in nonrecombining and recombining systems, and among the autosomal loci most are incompatible with any Pleistocene population size expansions. Microsatellite data seem to show Pleistocene population size expansions, but in aggregate they are difficult to interpret because different microsatellite studies do not show the same expansion. The archaeological data are only compatible with a few of these analyses, most prominently with data from Alu elements, and we use these facts to question whether the view of the past from analysis of inbreeding effective population size is valid. Finally, we examine the issue of whether inbreeding effective population size provides any reasonable measure of the actual past size of the human species. We contend that if the evidence of a population size bottleneck early in the evolution of our lineage is accepted, most genetic data either lack the resolution to address subsequent changes in the human population or do not meet the assumptions required to do so validly. It is our conclusion that, at the moment, genetic data cannot disprove a simple model of exponential population growth following a bottleneck 2 MYA at the origin of our lineage and extending through the Pleistocene. Archaeological and paleontological data indicate that this model is too oversimplified to be an accurate reflection of detailed population history, and therefore we find that genetic data lack the resolution to validly reflect many details of Pleistocene human population change. However, there is one detail that these data are sufficient to address. Both genetic and anthropological data are incompatible with the hypothesis of a recent population size bottleneck. Such an event would be expected to leave a significant mark across numerous genetic loci and observable anatomical traits, but while some subsets of data are compatible with a recent population size bottleneck, there is no consistently expressed effect that can be found across the range where it should appear, and this absence disproves the hypothesis.

Animals↗
PubMed2002

Visualization of excitation energy transfer processes in plants and algae.

Development of the time-resolved fluorescence spectroscopy in the pico-second time range and its application to the energy transfer processes in many photosynthetic organisms is reviewed here. This method enabled visualization of energy transfer processes by three-dimensional expression of fluorescence spectra and discrimination of kinetic components and spectral components. The second generation of the ultrafast fluorescence spectroscopy is the femto-second (fs) fluorescence up-conversion, and this has enabled analyses of the transfer processes from carotenoids to chlorophylls with a resolution of less than 100 fs. For future progress, a further development of the spectroscopy is indispensable as well as structural data at atomic resolution.

Journal Article↗
PubMed1997

Geographic structure of mitochondrial and nuclear gene polymorphisms in Australian green turtle populations and male-biased gene flow.

The genetic structure of green turtle (Chelonia mydas) rookeries located around the Australian coast was assessed by (1) comparing the structure found within and among geographic regions, (2) comparing microsatellite loci vs. restriction fragment length polymorphism analyses of anonymous single copy nuclear DNA (ascnDNA) loci, and (3) comparing the structure found at nuclear DNA markers to that of previously analyzed mitochondrial (mtDNA) control region sequences. Significant genetic structure was observed over all regions at both sets of nuclear markers, though the microsatellite data provided greater resolution in identifying significant genetic differences in pairwise tests between regions. Inferences about population structure and migration rates from the microsatellite data varied depending on whether statistics were based on the stepwise mutation or infinite allele model, with the latter being more congruent with geography. Estimated rates of gene flow were generally higher than expected for nuclear DNA (nDNA) in comparison to mtDNA, and this difference was most pronounced in comparisons between the northern and southern Great Barrier Reef (GBR). The genetic data combined with results from physical tagging studies indicate that the lack of nuclear gene divergence through the GBR is likely due to the migration of sGBR turtles through the courtship area of the nGBR population, rather than male-biased dispersal. This example highlights the value of combining comparative studies of molecular variation with ecological data to infer population processes.

Alleles↗
PubMed1997

Issues in establishing an aerosol radiological baseline for the waste isolation pilot plant near Carlsbad, New Mexico.

The Department of Energy has constructed a deep geologic repository for defense transuranic waste disposal. The Waste Isolation Pilot Plant, located in Southeastern New Mexico, is slated to receive transuranic waste by truck delivery beginning in 1998. The Environmental Evaluation Group (EEG) provides an independent evaluation of the impact on the health and environment in New Mexico of the WIPP project. Since 1985, the EEG has operated a network of air monitoring sites around WIPP and in nearby communities. The radionuclide concentration data from these air samples have been assembled into a useful baseline data base after resolution of a number of methodological and quality assurance issues. Investigation thresholds for the principal radionuclides have been calculated from combined data collected from several sites. These action levels will provide a critical quantitative basis for decisions of whether future airborne radionuclide measurements are attributable to accidental releases.

Air Pollutants, Radioactive↗
PubMed2001

Non-covalent interactions in the crystallization of the enantiomers of 1,7-dioxaspiro.

The enantiomers of racemic olive fly sex pheromone 1,7-dioxaspiro[5.5]undecane (1) have been isolated by crystallization with enantiospecific cyclodextrin hosts: (S)-(1) crystallizes with heptakis(2,3,6-tri-O-methyl)-beta-cyclodextrin (TMbetaCD) and (R)-(1) with hexakis(2,3,6-tri-O-methyl)-alpha-cyclodextrin (TMalphaCD). The crystal structure of TMbetaCD/(S)-(1) from synchrotron radiation data at 100 K, determined for the first time, proves that TMbetaCD crystallizes with only the (S)-enantiomer from the racemic mixture. Comparison with the 100 K structure of TMalphaCD/(R)-(1) redetermined with synchrotron data has provided insight into the interactions between each of the hosts with the corresponding enantiomeric guests. Owing to the high resolution of the data and the unusually high quality of the crystals, localization of the H atoms has been achieved, a rare accomplishment for cyclodextrin X-ray structures. This made possible, apart from the geometry of the complexes, the detailed description of a five-membered-ring water cluster with very well ordered hydrogen bonding. The enantiospecificity exhibited by the described systems reveals the subtle differences of the weak intermolecular forces involved in the selective binding of the two optical antipodes by the two hosts. The binding geometry in the two complexes is different, but it is effected in both by numerous host-guest C-H.O interactions, resulting from induced fit of the hosts toward each of the enantiomeric guests. In TMalphaCD/(R)-(1) two of these H.O host-guest distances, directed toward the acetal O atoms defining the chirality of the guest, are much shorter than the rest and also shorter than all the H.O distances in TMbetaCD/(S)-(1). Moreover, (R)-(1) interacts not only with the enclosing host, but with other hosts in the crystal lattice, in contrast to (S)-(1) in the TMbetaCD/(S)-(1) complex which is isolated inside channels formed by the host molecules. The above differences are reflected in the much higher binding constant of TMalphaCD/(R)-(1) compared with that of TMbetaCD/(S)-(1) ( approximately 6800 and approximately 935 M(-1), respectively), determined by NMR in aqueous solution, and the ability of TMalphaCD to selectively precipitate (R)-(1) from racemic (1) in much higher yield than TMbetaCD precipitates (S)-(1).

Animals↗
PubMed2001

Structure determination of the [Fe(teec)(6)](BF(4))(2) metal complex from laboratory and synchrotron X-ray powder diffraction data with grid-search techniques.

The structure of the coordination compound [Fe(teec)(6)](BF(4))(2), hexa[1-(2-chloroethyl)tetrazole]iron(II) di(borotetrafluoride), has been determined using the grid-search techniques of the program suite MRIA. A Guinier-camera data set was used to determine the unit cell, the space group and to position the initial model. A high-resolution synchrotron powder data set was used to position a more detailed model using torsion-angle variation and to refine the structure leading to Rp = 0.0689, Rw = 0.0805 and GoF = 1.38. The crystal structure at room temperature shows the existence of two symmetry-equivalent iron(II) ions in the high-spin state.

Journal Article↗
PubMed1996

Use of non-crystallographic symmetry in protein structure refinement.

Several methods to assess the (dis)similarity of protein structures objectively are described, some of which, when applied to non-crystallographically related protein models, are able to discriminate between significant differences and 'random noise'. Some of these methods have been used to investigate a sample of several hundred protein structures which have been solved by means of X-ray crystallography in order to investigate the extent to which non-crystallographically related protein models differ from one another. It is shown that the extent of such differences is largely dependent on the resolution of the data used for the determination and refinement of the structure and, measured by some statistics, even varies essentially linearly with the resolution. The implications of these findings for the strategies used to refine structures with non-crystallographic symmetry, in particular at low resolution, are discussed. Finally, two examples are given of recent structure determinations from this laboratory in which the presence (and employment) of non-crystallographic symmetry was crucial to the solution and refinement of the structure.

Journal Article↗
PubMed1999

Rapid velocity-encoded cine imaging with turbo-BRISK.

Velocity-encoded cine (VEC) imaging is potentially an important clinical diagnostic technique for cardiovascular diseases. Advances in gradient technology combined with segmentation approaches have made possible breathhold VEC imaging, allowing data to be obtained free of respiratory artifacts. However, when using conventional segmentation approaches, spatial and temporal resolutions are typically compromised to accommodate short breathhold times. Here we apply a sparse sampling technique, turbo-BRISK (i.e., segmented block regional interpolation scheme for k-space) to VEC imaging, allowing increased spatial and temporal resolution to be obtained in a short breathhold period. BRISK is a sparse sampling technique with interpolation used to generate unsampled data. BRISK was implemented to reduce the scan time by 70% compared with a conventional scan. Further, turbo-BRISK scans, using segmentation factors up to 5, reduce the scan time by up to 94%. Phantom and in vivo results are presented that demonstrate the accuracy of turbo-BRISK VEC imaging. In vitro validation is performed using conventional magnetic resonance VEC. Pulsatile centerline flow velocity measurements obtained with turbo-BRISK acquisitions were correlated with conventional magnetic resonance imaging measurements and achieved r values of 0.99 +/- 0.004 (mean +/- SD) with stroke volumes agreeing to within 4%. A potential limitation of BRISK is reduced accuracy for rapidly varying velocity profiles. We present low- and high-resolution data sets to illustrate the resolution dependence of this phenomenon and demonstrate that at conventional resolutions, turbo-BRISK can accurately represent rapid velocity changes. In vivo results indicate that centerline velocity waveforms in the descending aorta correlate well with conventional measurements with an average r value of 0.98 +/- 0.01.

Blood Flow Velocity↗
PubMed1997

Human plasminogen binding protein tetranectin: crystallization and preliminary X-ray analysis of the C-type lectin CRD and the full-length protein.

The recombinant human plasminogen binding protein tetranectin (TN) and the C-type lectin CRD of this protein (TN3) have been crystallized. TN3 crystallizes in the tetragonal space group P4(2)2(1)2 with cell dimensions a = b = 64.0, c = 75.7 A and with one molecule per asymmetric unit. The crystals diffract X-rays to at least 2.0 A resolution. A complete diffraction data set has been collected to 2.7 A resolution. The crystals of TN, obtained by the vapour-diffusion reverse salting-in method at 280 K, are rhombohedral, space group R3, with the hexagonal axes a = b = 89.1, c = 75.8 A, and diffract to at least 2.5 A. A full data set has been collected to 3.0 A. The asymmetric unit contains one monomer of TN. Molecular replacement solutions for TN3 and TN have been obtained using the structure of the C-type lectin CRD of rat mannose-binding protein as search model. The rhombohedral space group indicates that trimers of TN are formed in accordance with the observation of trimerization in solution.

Journal Article↗
PubMed2003

Enantioselectivity of alcohol-modified polymeric surfactants in micellar electrokinetic chromatography.

A novel method of modifying sodium undecanoyl-L-leucinate (SUL) micelles employed in chiral separation of analytes in micellar electrokinetic chromatography (MEKC) to enhance selectivity toward specific analytes is discussed. The current study aimed at modifying the SUL micelles by introducing different alcohols into the mono-SUL micelles. The micellar solutions were then polymerized in the presence of alcohols followed by postpolymerization extraction of the alcohols to yield alcohol-free polymeric surfactants (poly-L-SUL). The effects of hexanol (C(6)OH) and undecylenyl alcohol (C(11)OH) on micellar properties of this surfactant were investigated by use of surface tensiometry, fluorescence spectroscopy, pulsed field gradient-nuclear magnetic resonance (PFG-NMR), and MEKC. The surface tension and PFG-NMR studies indicated an increase in the critical micelle concentration (cmc) and micellar size upon increasing the alcohol concentration. Fluorescence measurements suggested that alcohols induce closely packed micellar structures. Coumarinic and benzoin derivatives, as well as (+/-)-1, 1'-binaphthyl-2,2'-dihydrogen phosphate (BNP) were used as test analytes for MEKC experiments. Examination of MEKC data showed remarkable resolutions and capacity factors of coumarinic derivatives obtained with modified poly-L-SUL as compared to the unmodified poly-L-SUL. Evaluation of fluorescence, PFG-NMR, and MEKC data suggest a strong correlation between the polarity and hydrodynamic radii of alcohol-modified micelles and the resolution of the test analytes.

Alcohols↗
PubMed1996

Crystallographic investigations of subtilisin BPN' mutants engineered for studying thermal stability.

Subtilisin BPN' (BPN) is an industrially important serine protease that has been extensively investigated in many laboratories. In an effort to improve the thermal stability of the enzyme, researchers at Procter & Gamble have used site-directed mutagenesis techniques to produce several variants of BPN in which residues at the surface of the enzyme have been substituted. We initiated crystallographic studies to determine the structural consequences of these amino acid substitutions. In the course of this work we obtained excellent crystals that correspond to the C2 crystal form of native BPN that has been previously reported. Since the structure reported in that work was of only medium resolution, high-resolution X-ray data for this crystal form of native BPN have been collected and the refinement of the structure has been extended using these new data. Isomorphous crystals of two variants, Q19E and Q271E, have also been grown, high-resolution X-ray data have been collected for these crystals, and the experimental results are described. The structures of the native enzyme and the Q271E variant have been refined and are described.

Binding Sites↗
PubMed2005

Sea surface temperature 1871-2099 in 38 cells in the Caribbean region.

Sea surface temperature (SST) data with monthly resolution are provided for 38 cells in the Caribbean Sea and Bahamas region, plus Bermuda. These series are derived from the HadISST1 data set for historical time (1871-1999) and from the HadCM3 coupled climate model for predicted SST (1950-2099). Statistical scaling of the forecast data sets are performed to produce confluent SST series according to a now established method. These SST series are available for download. High water temperatures in 1998 killed enormous amounts of corals in tropical seas, though in the Caribbean region the effects at that time appeared less marked than in the Indo-Pacific. However, SSTs are rising in accordance with world-wide trends and it has been predicted that temperature will become increasingly important in this region in the near future. Patterns of SST rise within the Caribbean region are shown, and the importance of sub-regional patterns within this biologically highly interconnected area are noted.

Caribbean Region↗
PubMed1995

Risk assessment of environmentally influenced airway diseases based on time-series analysis.

Threshold values are of prime importance in providing a sound basis for public health decisions. A key issue is determining threshold or maximum exposure values for pollutants and assessing their potential health risks. Environmental epidemiology could be instrumental in assessing these levels, especially since the assessment of ambient exposures involves relatively low concentrations of pollutants. This paper presents a statistical method that allows the determination of threshold values as well as the assessment of the associated risk using a retrospective, longitudinal study design with a prospective follow-up. Morbidity data were analyzed using the Fourier method, a time-series analysis that is based on the assumption of a high temporal resolution of the data. This method eliminates time-dependent responses like temporal inhomogeneity and pseudocorrelation. The frequency of calls for respiratory distress conditions to the regional Mobile Medical Emergency Service (MMES) in the city of Leipzig were investigated. The entire population of Leipzig served as a pool for data collection. In addition to the collection of morbidity data, air pollution measurements were taken every 30 min for the entire study period using sulfur dioxide as the regional indicator variable. This approach allowed the calculation of a dose-response curve for respiratory diseases and air pollution indices in children and adults. Significantly higher morbidities were observed above a 24-hr mean value of 0.6 mg SO2/m3 air for children and 0.8 mg SO2/m3 for adults.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed1978

Performance characteristics of a gamma camera over a wide range of energies.

The problem of choosing which collimator to use for imaging a new isotope has been approached by collecting resolution and sensitivity data for a selected group of isotopes. These have been chosen to be readily available and to have generally a single gamma-ray only. Resolution and sensitivity plots for a low energy collimator and a high energy collimator are presented and their use with several isotopes of interest is discussed. The interpretation of recommedations in the literature on the choice of collimators for newly introduced isotopes would be considerably simpler if data in this format were commonly available.

Humans↗
PubMed1973

Structure of liver alcohol dehydrogenase at 2.9-angstrom resolution.

The conformation of the polypeptide chain in horse liver alcohol dehydrogenase (EC 1.1.1.1), as well as the binding sites for some inhibitor molecules, have been determined from x-ray crystallographic data to a resolution of 2.9 A. Each subunit of the dimeric molecule is organized into two parts unequal in size and separated by a wide and deep active-site cleft. The adenosine moiety of the coenzyme is bound within the smaller region. Interactions between these coenzyme-binding substructures define the subunit contact area of the molecule. The "catalytic" zinc atoms are bound at the bottom of the clefts about 20 A from the surface of the molecule. The coenzyme binding region has a main-chain conformation very similar to a corresponding region in lactate and malate dehydrogenase. It is suggested that this substructure is a general one for binding of nucleotides and, in particular, the coenzyme NAD(+).

Alcohol Oxidoreductases↗
PubMed1998

Refinement of triclinic hen egg-white lysozyme at atomic resolution.

X-ray diffraction data have been collected at both low (120 K) and room temperature from triclinic crystals of hen egg-white lysozyme to 0.925 and 0.950 A resolution, respectively, using synchrotron radiation. Data from one crystal were sufficient for the low-temperature study, whereas three crystals were required at room temperature. Refinement was carried out using the programs PROLSQ, ARP and SHELXL to give final conventional R factors of 8.98 and 10.48% for data with F > 4sigma(F) for the low- and room-temperature structures, respectively. The estimated r.m.s. coordinate error is 0.032 A for protein atoms, 0.050 A for all atoms in the low-temperature study, and 0.038 A for protein atoms and 0.049 A for all atoms in the room-temperature case, as estimated from inversion of the blocked least-squares matrix. The low-temperature study revealed that the side chains of 24 amino acids had multiple conformations. A total of 250 waters, six nitrate ions and three acetate ions, two of which were modelled with alternate orientations were located in the electron-density maps. Three sections of the main chain were modelled in alternate conformations. The room-temperature study produced a model with multiple conformations for eight side chains and a total of 139 water molecules, six nitrate but no acetate ions. The occupancies of the water molecules were refined in both structures and this step was shown to be meaningful when assessed by use of the free R factor. A detailed description and comparison of the structures is made with reference to the previously reported structure refined at 2.0 A resolution.

Animals↗
PubMed1997

Image processing for improved eye-tracking accuracy.

Video cameras provide a simple, noninvasive method for monitoring a subject's eye movements. An important concept is that of the resolution of the system, which is the smallest eye movement that can be reliably detected. While hardware systems are available that estimate direction of gaze in real-time from a video image of the pupil, such systems must limit image processing to attain real-time performance and are limited to a resolution of about 10 arc minutes. Two ways to improve resolution are discussed. The first is to improve the image processing algorithms that are used to derive an estimate. Off-line analysis of the data can improve resolution by at least one order of magnitude for images of the pupil. A second avenue by which to improve resolution is to increase the optical gain of the imaging setup (i.e., the amount of image motion produced by a given eye rotation). Ophthalmoscopic imaging of retinal blood vessels provides increased optical gain and improved immunity to small head movements but requires a highly sensitive camera. The large number of images involved in a typical experiment imposes great demands on the storage, handling, and processing of data. A major bottleneck had been the real-time digitization and storage of large amounts of video imagery, but recent developments in video compression hardware have made this problem tractable at a reasonable cost. Images of both the retina and the pupil can be analyzed successfully using a basic toolbox of image-processing routines (filtering, correlation, thresholding, etc.), which are, for the most part, well suited to implementation on vectorizing supercomputers.

Algorithms↗