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PubMed2003

Statistical analysis of crystallographic data obtained from squid ganglion DFPase at 0.85 A resolution.

The X-ray crystal structure of squid-type diisopropylfluorophosphatase (DFPase) has been refined to a resolution of 0.85 A and a crystallographic R value of 9.4%. Crystal annealing improved both the mosaicity and resolution of the crystals considerably. The overall structure of this protein represents a six-bladed beta-propeller with two calcium ions bound in a central water-filled tunnel. 496 water, two glycerol and two MES buffer molecules and 18 PEG fragments of different lengths could be refined in the solvent region. 45 of the 314 residues have been refined with alternative orientations. H atoms have been omitted from disordered residues. For the residues of the inner beta-strands, H atoms are visible in a normal F(o) - F(c) difference map of a hydrogen-deficient structure model. The 208 most reliable residues, without disorder or reduced occupancy in their side chains, were finally refined without restraints. A subsequent full-matrix refinement cycle for the positional parameters yielded estimated standard deviations (e.s.d.s) by matrix inversion. The thus calculated bond lengths and bond angles and their e.s.d.s were used to obtain averaged bond lengths and bond angles, which were compared with the restraints applied in the preceding refinement cycles. The lengths and angles of the hydrogen bonds inside the antiparallel beta-sheets of the DFPase structure were compared with data averaged over 11 high-resolution protein structures. Torsion angles were averaged according to angle types used as restraints in X-PLOR and CNS and subsequently compared with values obtained from 46 high-resolution structures. Side-chain torsion angles were also classified into rotamer types according to the Penultimate Rotamer Library. Moreover, precise dimensions for both Ca(2+)-coordination polyhedra could be obtained and the coordination of one Ca(2+) ion by an imidazole N atom was confirmed. This statistical analysis thus provides a first step towards a set of restraints that are founded completely on macromolecular data; however, 10-20 additional protein data sets of comparable accuracy and size will be required to obtain a larger statistical base, especially for side-chain analysis.

Amino Acids↗
PubMed2005

Modelling malaria risk in East Africa at high-spatial resolution.

OBJECTIVES: Malaria risk maps have re-emerged as an important tool for appropriately targeting the limited resources available for malaria control. In Sub-Saharan Africa empirically derived maps using standardized criteria are few and this paper considers the development of a model of malaria risk for East Africa. METHODS: Statistical techniques were applied to high spatial resolution remotely sensed, human settlement and land-use data to predict the intensity of malaria transmission as defined according to the childhood parasite ratio (PR) in East Africa. Discriminant analysis was used to train environmental and human settlement predictor variables to distinguish between four classes of PR risk shown to relate to disease outcomes in the region. RESULTS: Independent empirical estimates of the PR were identified from Kenya, Tanzania and Uganda (n = 330). Surrogate markers of climate recorded on-board earth orbiting satellites, population settlement, elevation and water bodies all contributed significantly to the predictive models of malaria transmission intensity in the sub-region. The accuracy of the model was increased by stratifying East Africa into two ecological zones. In addition, the inclusion of urbanization as a predictor of malaria prevalence, whilst reducing formal accuracy statistics, nevertheless improved the consistency of the predictive map with expert opinion malaria maps. The overall accuracy achieved with ecological zone and urban stratification was 62% with surrogates of precipitation and temperature being among the most discriminating predictors of the PR. CONCLUSIONS: It is possible to achieve a high degree of predictive accuracy for Plasmodium falciparum parasite prevalence in East Africa using high-spatial resolution environmental data. However, discrepancies were evident from mapped outputs from the models which were largely due to poor coverage of malaria training data and the comparable spatial resolution of predictor data. These deficiencies will only be addressed by more random, intensive small areas studies of empirical estimates of PR.

Animals↗
PubMed1995

Crystal structure of human pepsin and its complex with pepstatin.

The three-dimensional crystal structure of human pepsin and that of its complex with pepstatin have been solved by X-ray crystallographic methods. The native pepsin structure has been refined with data collected to 2.2 A resolution to an R-factor of 19.7%. The pepsin:pepstatin structure has been refined with data to 2.0 A resolution to an R-factor of 18.5%. The hydrogen bonding interactions and the conformation adopted by pepstatin are very similar to those found in complexes of pepstatin with other aspartic proteinases. The enzyme undergoes a conformational change upon inhibitor binding to enclose the inhibitor more tightly. The analysis of the binding sites indicates that they form an extended tube without distinct binding pockets. By comparing the residues on the binding surface with those of the other human aspartic proteinases, it has been possible to rationalize some of the experimental data concerning the different specificities. At the S1 site, valine at position 120 in renin instead of isoleucine, as in the other enzymes, allows for binding of larger hydrophobic residues. The possibility of multiple conformations for the P2 residue makes the analysis of the S2 site difficult. However, it is possible to see that the specific interactions that renin makes with histidine at P2 would not be possible in the case of the other enzymes. At the S3 site, the smaller volume that is accessible in pepsin compared to the other enzymes is consistent with its preference for smaller residues at the P3 position.

Amino Acid Sequence↗
PubMed1993

X-ray structure of monoclinic turkey egg lysozyme at 1.3 A resolution.

Monoclinic crystals of turkey egg lysozyme (TEL, E.C. 3.2.1.17) were obtained from 2.2 M ammonium sulfate solution at pH 4.2. They belong to space group P2(1) with unit-cell dimensions a = 38.07, b = 33.20, c = 46.12 A and beta = 110.1 degrees, and contain one molecule in the asymmetric unit (V(m) = 1.91 A(3) Da(-1)). The three-dimensional structure of TEL was solved by the method of multiple isomorphous replacement with anomalous scattering. Area detector data to 1.5 A resolution from native and heavy-atom derivatives were used for the structure determination. The structure was refined by the simulated-annealing method with diffraction data of 10-1.30 A resolution. The conventional R factor was 0.189. The root-mean-square deviations from ideal bond distances and angles were 0.016 A and 2.9 degrees, respectively. The backbone structure of TEL is very similar to that of hen egg lysozyme (HEL) and the difference in seven amino-acid residues does not affect the basic folding of the polypeptide chain. Except for the region from Gly101 to Gly104, the geometry of the active-site cleft is conserved between TEL and HEL. The Gly101 residue is located at the end of the sugar-binding site and the structural change in this region between TEL and HEL is considered to be responsible for the difference in their enzymatic properties.

Journal Article↗
PubMed1984

Dual-mode computer processing for high resolution DNA thermal denaturation experiments.

Two modes of data processing are appropriate in conducting high resolution thermal denaturation experiments (thermal increments of 0.05 degrees or closer). In the first mode, a general purpose microcomputer provides on-line services important to the control and monitoring of the initial experiment, including control of the spectrophotometer and heater, the recording of data, and the display of current hyperchromicities and approximate first derivatives. A subsequent microcomputer program then reads the recorded data files and carries out accurate calculations of derivative denaturation profiles and the estimate of the statistical error of the first derivative at each point. The data collection program handles three samples at a time and was designed to provide optimal results in thermal denaturation experiments with a single-beam spectrophotometer.

Computers↗
PubMed1992

Processing images of helical structures: a new twist.

Helical macromolecular assemblies are particularly difficult to study by X-ray diffraction but are quite well suited to analysis by electron microscopy. Most of our information about helical macromolecular assemblies has come from the electron microscope but has been limited to about 25 A resolution. With the use of low-dose electron cryomicroscopy, one can obtain structural data to near atomic resolution on two-dimensional crystals, but the problem is to extract the information from the noise. In this paper we present methods to extract signal from low-dose electron cryomicrographs of helically symmetric structures. We apply these methods to extract 10 A data from the bacterial flagellar filament.

Algorithms↗
PubMed1986

Persistent ventricular adaptations in postoperative coarctation of the aorta.

To evaluate ventricular performance and myocardial contractility after surgical correction of congenital coarctation of the aorta, we studied 25 patients (16 men and 9 women, mean age 26.1 years [range 19 to 34]), an average of 10.6 years (range 2 to 25) after repair. Radionuclide ventriculography at rest and exercise and digitized, quantitative two-dimensional echocardiography were performed. Data from derived, high resolution time-activity curves by radionuclide ventriculography, combined with noninvasive hemodynamic/ventricular volume data, were compared with values in an age- and sex-matched normal population. Despite essentially identical baseline and exercise hemodynamics, postoperative coarctation subjects demonstrated enhanced ventricular contraction, as determined by the peak ejection rate at rest (-3.79 versus -3.20 stroke volume/s, p less than 0.01) and exercise (-3.00 versus -2.90 stroke volume/s, p = NS), and overall ejection fraction at rest (56.4 versus 48.0%, p less than 0.01) and exercise (70.8 versus 59.3%, p less than 0.01). An intrinsic activation-contraction delay was observed, as illustrated by a prolonged time to peak ejection rate at rest (27.7 versus 21.5% of the RR interval, p less than 0.01) and exercise (28.4 versus 21.2% of the RR interval, p less than 0.01), and total systolic time at rest (50.2 versus 43.4% of the RR interval, p less than 0.01) and exercise (56.8 versus 50.4% of the RR interval, p less than 0.01). Although left ventricular meridinal wall stress was statistically indistinguishable (62 versus 74 mm Hg/mm2, p = NS), intrinsic myocardial contractility, as assessed by the peak systolic pressure/volume ratio, was increased in the postoperative coarctation group (1.88 versus 2.87 mm Hg/ml, p less than 0.01).(ABSTRACT TRUNCATED AT 250 WORDS)

Adaptation, Physiological↗
PubMed1991

Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal structure of mandelate racemase at 2.5-A resolution: identification of the active site and possible catalytic residues.

The crystal structure of mandelate racemase (MR) has been solved at 3.0-A resolution by multiple isomorphous replacement and subsequently refined against X-ray diffraction data to 2.5-A resolution by use of both molecular dynamics refinement (XPLOR) and restrained least-squares refinement (PROLSQ). The current crystallographic R-factor for this structure is 18.3%. MR is composed of two major structural domains and a third, smaller, C-terminal domain. The N-terminal domain has an alpha + beta topology consisting of a three-stranded antiparallel beta-sheet followed by an antiparallel four alpha-helix bundle. The central domain is a singly wound parallel alpha/beta-barrel composed of eight central strands of beta-sheet and seven alpha-helices. The C-terminal domain consists of an irregular L-shaped loop with several short sections of antiparallel beta-sheet and two short alpha-helices. This C-terminal domain partially covers the junction between the major domains and occupies a region of the central domain that is filled by an eight alpha-helix in all other known parallel alpha/beta-barrels except for the barrel domain in muconate lactonizing enzyme (MLE) [Goldman, A., Ollis, D. L., & Steitz, T. A. (1987) J. Mol. Biol. 194, 143] whose overall polypeptide fold and amino acid sequence are strikingly similar to those of MR [Neidhart, D. J., Kenyon, G. L., Gerlt, J. A., & Petsko, G. A. (1990) Nature 347, 692]. In addition, the crystal structure reveals that, like MLE, MR is tightly packed as an octamer of identical subunits. The active site of MR is located between the two major domains, at the C-terminal ends of the beta-strands in the alpha/beta-barrel domain. The catalytically essential divalent metal ion is ligated by three side-chain carboxyl groups contributed by residues of the central beta-sheet. A model of a productive substrate complex of MR has been constructed on the basis of difference Fourier analysis at 3.5-A resolution of a complex between MR and (R,S)-p-iodomandelate, permitting identification of residues that may participate in substrate binding and catalysis. The ionizable groups of both Lys 166 and His 297 are positioned to interact with the chiral center of substrate, suggesting that both of these residues may function as acid/base catalysts.(ABSTRACT TRUNCATED AT 400 WORDS)

Binding Sites↗
PubMed2000

Upgrading the twin variables algorithm for large structures.

Phase extension from lower to higher resolution by using an upgraded TWIN variables algorithm [Hountas & Tsoucaris (1995). Acta Cryst. A51, 754-763] in protein molecules with close to 1,000 non-H atoms is presented. Three points of this procedure are of particular interest. (i) The use of a set of auxiliary variables providing a satisfactory fit for many kinds of constraints: the new algorithm works efficiently despite the extreme 'dilution' of very limited initial phase information into a much larger set of auxiliary variables. (ii) The extension of this auxiliary variables set beyond the resolution of the observed data, which enhances the phase extension in a so-called 'super-resolution' sphere. (iii) The use of the crystallographic symmetry as a new figure of merit and as a reliable test for the correctness of the phase-extension process allows an efficient screening.

Algorithms↗
PubMed1998

Crystallization and preliminary structural studies of Scilla campanulata lectin complexed with alpha1-6 mannobiose.

Recent work has shown that Scilla campanulata agglutinin from bluebell bulbs has a strong affinity for alpha(1,3)- and alpha(1,6)-linked mannosyl residues and possesses moderate antiretroviral activity. This lectin has been crystallized by the hanging-drop method of vapour diffusion complexed with the disaccharide mannose-alpha1,6-D-mannose. The crystals are in the space group P21212 with unit-cell dimensions a = 70.63, b = 92.79 and c = 47.25 A, and with a dimer in the asymmetric unit. The crystals diffract X-rays to beyond 1.5 A resolution at 277 K and are stable in an X-ray beam. Data to 1.6 A resolution have been collected using a MAR image-plate system at a synchrotron source and the structure of the complex has been solved by the molecular replacement method.

Crystallization↗
PubMed2006

High-resolution recombination patterns in a region of human chromosome 21 measured by sperm typing.

For decades, classical crossover studies and linkage disequilibrium (LD) analysis of genomic regions suggested that human meiotic crossovers may not be randomly distributed along chromosomes but are focused instead in "hot spots." Recent sperm typing studies provided data at very high resolution and accuracy that defined the physical limits of a number of hot spots. The data were also used to test whether patterns of LD can predict hot spot locations. These sperm typing studies focused on several small regions of the genome already known or suspected of containing a hot spot based on the presence of LD breakdown or previous experimental evidence of hot spot activity. Comparable data on target regions not specifically chosen using these two criteria is lacking but is needed to make an unbiased test of whether LD data alone can accurately predict active hot spots. We used sperm typing to estimate recombination in 17 almost contiguous ~5 kb intervals spanning 103 kb of human Chromosome 21. We found two intervals that contained new hot spots. The comparison of our data with recombination rates predicted by statistical analyses of LD showed that, overall, the two datasets corresponded well, except for one predicted hot spot that showed little crossing over. This study doubles the experimental data on recombination in men at the highest resolution and accuracy and supports the emerging genome-wide picture that recombination is localized in small regions separated by cold areas. Detailed study of one of the new hot spots revealed a sperm donor with a decrease in recombination intensity at the canonical recombination site but an increase in crossover activity nearby. This unique finding suggests that the position and intensity of hot spots may evolve by means of a concerted mechanism that maintains the overall recombination intensity in the region.

Chromosome Mapping↗
PubMed2004

[Potentialities of high-resolution computed tomography in diagnosis of pulmonary lesions after bone marrow transplantation in blood diseases].

AIM: To study characteristics of a skialogical picture of pulmonary parenchyma and roentgenomorphological signs of inflammatory changes before and after bone marrow transplantation (BMT); relationship between the data of high-resolution computed tomography (HRCT) and clinical data. MATERIAL AND METHODS: HRCT (computer tomograph of the third generation "Somatom CR-3") was made in fever, changes in physical examination in patients (n = 28) after BMT from November 2001 to January 2003. BMT was made in myelomic disease, lymphogranulomatosis, acute leukemia, chronic myeloid leukemia, lymphosarcoma, autoimmune hemolytic anemia. RESULTS: Twenty four patients were examined before BMT. Of them, 18 patients had roentgenomorphological changes of the parenchyma, primarily, diffuse. Three patients were examined during conditioning, two cases had signs of toxic pulmonitis. One day after allo-BMT all the patients exhibited lowering of densitometric values of pulmonary tissue by 70 HU vs the baseline. Infectious affection of the lungs was diagnosed in 13 cases during day 0-100. From day 100 after allo-BMT 7 recipients were observed. In 6 cases the changes resulted from transplant against host reaction. Infectious affection of pulmonary tissue was observed in 1 case. Characteristic x-ray picture of pulmonary stroma in secondary disease was determined. CONCLUSION: For early diagnosis of pneumonia in myelotoxic agranulocytosis it is necessary to make examination by HRCT before BMT. HRCT of the chest is indicated in even minor changes in the clinical picture. It is necessary to perform a control over water-electrolyte balance and active respiratory exercise in the course of conditioning. Viral pneumonias show the picture of metainflammatory changes for a long time. Fungal pneumonias tend to recurrence at "previous site". HRCT examination of the pulmonary tissue provides more information about pulmonary tissue in patients with secondary disease.

Adolescent↗
PubMed2004

Visual field of high-pass resolution perimetry in normal subjects.

PURPOSE: To investigate the properties of the visual field of high-pass resolution perimetry in normal subjects. METHODS: Four centers collected normative data for high-pass resolution perimetry. In two of the centers the subjects were stratified by age. One eye was tested per subject using high-pass resolution perimetry (Ophthimus). We tested 640 normal subjects and describe their visual field results by test location. We also analyzed the data by concentric zone, age, and by testing center. RESULTS: The individual test location averages confirmed a reduction in resolution with eccentricity. Resolution thresholds increased with age by 0.025 dB per year (P < 0.001). The mean ring size increased by about 1 dB from age 20 to 70. Among centers there were significant differences in the means and the change in threshold with age (P = 0.009). CONCLUSION: The normal visual field of high-pass resolution perimetry is characterized by an increase in threshold with eccentricity. We found significant differences among the centers that were likely due to multiple factors including differences in subject selection criteria. Whether such differences occur with other perimetric techniques is unknown.

Adult↗
PubMed1984

Structure of bovine pancreatic trypsin inhibitor. Results of joint neutron and X-ray refinement of crystal form II.

The structure of form II crystals of bovine pancreatic trypsin inhibitor has been investigated by joint refinement of X-ray and neutron data. Crystallographic R factors for the final model were 0.200 for the X-ray data extending to 1 A resolution and 0.197 for the 1.8 A neutron data. This model was strongly restrained, with 0.020 A root-mean-square (r.m.s.) departure of bond lengths from their ideal values and 0.019 A r.m.s. departure of planar groups from planarity. The resulting structure was very similar to that of crystal form I (r.m.s. deviation for main chain atoms was 0.40 A); nevertheless larger deviations were observed in particular regions of the chain. Twenty out of 63 ordered water molecules occupy similar positions (deviation less than 1 A) in both models. Eleven amide hydrogens were found to be protected from exchange after three months of soaking the crystals in deuterated mother liquor at pH 8.2. Their locations were in excellent agreement with the results obtained by two-dimensional nuclear magnetic resonance, but the rates of exchange are much lower in the crystalline state.

Amino Acid Sequence↗
PubMed2002

Estimating the effective degrees of freedom in univariate multiple regression analysis.

The general linear model provides the most widely applied statistical framework for analyzing functional MRI (fMRI) data. With the increasing temporal resolution of recent scanning protocols, and more elaborate data preprocessing schemes, data independency is no longer a valid assumption. In this paper, we revise the statistical background of the general linear model in the presence of temporal autocorrelations. First, when detecting the activation signal, we explicitly account for the temporal autocorrelation structure, which yields a generalized F-test and the associated corrected (or effective) degrees of freedom (DOF). The proposed approach is data driven and thus independent of any specific preprocessing method. Then, for event-related protocols, we propose a new model for the temporal autocorrelations ("damped oscillator" model) and compare this model to another, previously used in the field (first-order autoregressive model, or AR(1) model). In the case of long fMRI time series, an efficient approximation for the number of effective DOF is provided for both models. Finally, the validity of our approach is assessed using simulated and real fMRI data and is compared with more conventional methods.

Analysis of Variance↗
PubMed1999

Crystallization and preliminary X-ray diffraction studies of blasticidin S deaminase from Aspergillus terreus.

Blasticidin S deaminase from Aspergillus terreus was crystallized with polyethylene glycol 8000. Two types of crystals were grown under the same crystallization conditions. One type grew as thin plates, while the other had a rhombic shape. The rhombic shaped crystal was suitable for high-resolution crystal structure analysis. Precession photographs and diffraction data showed that the crystal belonged to orthorhombic space group P212121, with unit-cell dimensions a = 70.33, b = 146.56 and c = 56.48 A. The calculated Vm value was acceptable when a tetramer of the enzyme was contained in an asymmetric unit. Preliminary diffraction data were collected to a resolution of 2.0 A with good statistics.

Aminohydrolases↗
PubMed2006

Use of point-of-sale data to track usage patterns of residential pesticides: methodology development.

BACKGROUND: Residential-use pesticides have been shown to be a major source of pesticide exposure to people in the United States. However, little is understood about the exposures to household pesticides and the resultant health effects. One reason that little is known about home-use pesticide exposure is the lack of comprehensive data on exposures to pesticides in the home. One method to help ascertain the amount of pesticides present in the home is use of point-of-sale data collected from marketing companies that track product sales to obtain the volume of pesticides sold for home-use. This provides a measure of volume of home-use pesticide. METHODS: We have constructed a searchable database containing sales data for home-use permethrin-containing pesticides sold by retail stores in the United States from January 1997 through December 2002 in an attempt to develop a tracking method for pesticide. This pilot project was conducted to determine if point-of-sale data would be effective in helping track the purchase of home-use permethrin containing pesticides and if it would stand as a good model for tracking sales of other home-use pesticides. RESULTS: There are several limitations associated with this tracking method, including the availability of sales data, market coverage, and geographic resolution. As a result, a fraction of sales data potentially available for reporting is represented in this database. However, the database is sensitive to the number and type of merchants reporting permethrin sales. Further, analysis of the sale of individual products included in the database indicates that year to year variability has a greater impact on reported permethrin sales than the amount sold by each type of merchant. CONCLUSION: We conclude that, while nothing could completely replace a detailed exposure assessment to estimate exposures to home-use pesticides, a point-of-sale database is a useful tool in tracking the purchase of these types of pesticides to 1) detect anomalous trends in regional and seasonal pesticide sales warranting further investigation into the potential causes of the trends; 2) determine the most commonly purchased application types; and 3) compare relative trends in sales between indoor and outdoor use products as well as compare trends in sales between different active ingredients.

Commerce↗
PubMed2003

Occurrence and distribution of Anopheles (Diptera: Culicidae) larval habitats on land cover change sites in urban Kisumu and urban Malindi, Kenya.

A multitemporal, land use land cover (LULC) classification dataset incorporating distributions of mosquito larval habitats was produced in ERDAS Imagine using the combined images from the Multispectral Thermal Imager (MTI) at 5 m spatial resolution from 2001 with Thematic Mapper-classification data at 28.5 m spatial resolution from 1987 and 1989 for Kisumu and Malindi, Kenya. Total LULC change for Kisumu over 14 yr was 30.2%. Total LULC change for Malindi over 12 yr was 30.6%. Of those areas in which change was detected, the LULC change for Kisumu was 72.5% for nonurban to urban, 21.7% urban to nonurban, 0.4% urban to water, 4.5% water to urban, and 0.9% water to nonurban. The proportion of LULC change for Malindi was 93.5% for nonurban to urban, 5.9% urban to nonurban, 0.2% urban to water, 0.3% nonurban to water, and 0.1% water to urban. A grid (270 m x 270 m cells) was overlaid over the maps stratifying grid cells based on drainage and planning. Of 84 aquatic habitats in Kisumu, 32.1% were located in LULC change sites and 67.9% were located in LULC nonchange sites. Of 170 aquatic habitats in Malindi, 26.5% were located in LULC change sites and 73.5% were located in LULC nonchange sites. The most abundant LULC change per strata with anopheline habitats was unplanned and poorly drained. Ditches and puddles in Kisumu and car tracks in Malindi displayed the highest number of anopheline larval habitats for all LULC change sites. The proportion of site positive aquatic habitats for anopheline larvae was higher in LULC change sites than for LULC nonchange sites for Kisumu. This evidence suggests LULC change can influence anopheline larval habitat distribution.

Animals↗