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PubMedDate not supplied

Phylogenetic relationships of Bacteria based on comparative sequence analysis of elongation factor Tu and ATP-synthase beta-subunit genes.

Comparative sequence analyses were performed on 14 genes encoding bacterial elongation factors EF-Tu and 7 genes encoding the beta-subunit of bacterial F1F0 type ATP-synthases. The corresponding predicted amino acid sequences were compared with published primary structures of homologous molecules. Phylogenetic trees were reconstructed from both data sets of aligned protein sequences and from an equivalent selection of 16S rRNA sequences by applying distance matrix and maximum parsimony methods. The EF-Tu data were in very good agreement with the rRNA data, although the resolution within the EF-Tu tree was reduced at certain phylogenetic levels. The resolution power of the ATPase beta-subunit sequence data were more reduced than those of the EF-Tu data. In comparison with the 16S rRNA tree there are minor differences in the order of adjacent branchings within the ATPase beta-subunit tree.

Amino Acid Sequence↗
PubMed2000

Statistical discrimination of natural modes of motion in rat exploratory behavior.

We analyze the locomotor behavior of the rat during exploration, and show that digitally collected data (time series of positions) provide a sufficient basis for establishing that the rat uses several distinct modes of motion (first, second, third, and sometimes fourth gear). The distinction between these modes is obtained by first segmenting the time series into sequences of data points occurring between arrests (as ascertained within the resolution of the data acquisition system). The statistical distribution of the maximal amount of motion occurring within each of these episodes is then analyzed and shown to be multi modal. This enables us to decompose motion into distinct modes. In one application of this decomposition we show that the ethological ad hoc notion of stopping behavior corresponds to progression without leaving first gear. We do so by showing that the spatial spread of such progressions is confined to a small 20-50 cm range in a 6.5 m diameter arena. This provides a justification for a construct of 'staying in place'. This construct is not defined in terms of position in objective space, but purely in terms of the rat's own behavior. We test the generality of our method by applying it to mouse exploratory behavior.

Animals↗
PubMed2000

Comparison of electron diffraction data from non-linear optically active organic DMABC crystals obtained at 100 and 300 kV

During the recent past, we have synthesized a new class of molecules with intramolecular two-dimensional charge transfer upon excitation. The present report presents such a molecule, 2,6-bis(4-dimethylamino-benzylidene)-cyclohexanone (DMABC), with an unusually high value of the second-order non-linear optical (NLO) coefficients. In order to optimize the macroscopic NLO properties of the compounds, it is necessary to relate their first hyperpolarizability tensors at a molecular level to those at a crystal bulk level. This requires a complete structure determination and refinement. However, the growth of sufficiently large single crystals, which are needed for structural analysis and refinement by X-ray methods, is a time consuming and sometimes impossible task. We have performed a complete structural analysis by electron diffraction combined with simulation methods and with maximum entropy and log likelihood statistics. In order to improve the quantitative analysis, a 300 kV data set using an on-line CCD camera was added and the best attainable R-values were compared with those from 100 kV data using film emulsions. Details regarding the maximum attainable resolution for both data sets are discussed as well as the problems which arise from the limited dynamic range in photographic emulsions as compared to a 14 bit CCD camera. Once the crystal structure was known, quantum-chemical methods were used to calculate non-linear optical susceptibility tensor components and these were related to the macroscopic coefficients of the crystalline quadratic non-linearity tensor. In the present work, both ab initio and semi-empirical quantum-chemical calculations were employed.

Journal Article↗
PubMed2003

Automated tracing of electron-density maps of proteins.

The tracing of experimental electron maps in the field of protein crystallography is not a rate-limiting step for structure elucidation, but does represent the process that requires the most expertise and user time. This paper presents a method for automatically tracing the electron-density maps of proteins which can reliably generate a C(alpha) trace for protein maps with data in the resolution range 1.5-4 A. The number of C(alpha) atoms placed and the precision of atom placement depends on the quality of the map, but even with poor maps (FOM approximately 0.5) the algorithm can provide a significant saving in time over conventional methods of interpretation. The interpretation of six experimental maps is presented at different resolutions and levels of phase error; these show that data with an FOM of 0.7 or better can be entirely traced with no user intervention.

Algorithms↗
PubMed1999

Structure of basic winged-bean lectin and a comparison with its saccharide-bound form.

The crystal structure of the saccharide-free form of the basic form of winged-bean agglutinin (WBAI) has been solved by the molecular-replacement method and refined at 2.3 A resolution. The final R factor is 19.7% for all data in the resolution range 8.0-2.3 A. The asymmetric unit contains two half-dimers, each located on a crystallographic twofold axis. The structure of the saccharide-free form is compared with that of the complex of WBAI with methyl-alpha-D-galactoside. The complex is composed of two dimers in the asymmetric unit. The intersubunit interactions in the dimer are nearly identical in the two structures. The binding site of the saccharide-free structure contains three ordered water molecules at positions similar to those of the hydroxyl groups of the carbohydrate which are hydrogen bonded to the protein. Superposition of the saccharide-binding sites of the two structures shows that the major changes involve expulsion of these ordered water molecules and a shift of about 0.6 A of the main-chain atoms of the variable loop.

Binding Sites↗
PubMed1987

The tertiary structure of azurin from Pseudomonas denitrificans as determined by Cu resonant diffraction using synchrotron radiation.

The structure of Pseudomonas denitrificans azurin has been solved at 3.0 A resolution by film data collection methods using synchrotron radiation. Bijvoet pairs of reflections were collected using 8.98 keV radiation where both delta f' and delta f", the real and imaginary corrections to azurin's Cu prosthetic group scattering, respectively, are large, and using 8.00 keV radiation where these corrections are smaller. The Cu atom was located by difference Patterson syntheses and used to phase the observed protein structure-factor moduli of selected reflections. An atomic model of the protein was built using a restricted data set and phases for all observed reflections to 3.0 A resolution were subsequently calculated from the initial model. The atomic model was subsequently rebuilt using all observed data. The results of this work are presented here and illustrate the utility of synchrotron radiation phasing techniques in solving the structures of metalloproteins without recourse to multiple isomorphous replacement.

Azurin↗
PubMed2000

The 2.0 A structure of bovine interferon-gamma; assessment of the structural differences between species.

The structure of bovine interferon-gamma (IFN-gamma) was determined by multiple isomorphous replacement at 2.0 A resolution. Bovine IFN-gamma crystallizes in two related crystal forms. Crystal form 1 diffracts to 2.9 A resolution and is reproducible and stable to derivatization. Crystal form 2 diffracts to 2.0 A resolution, but shows significant non-isomorphism from crystal to crystal. The previously determined structures of several different species of INF-gamma were either at too low a resolution [human, 1hig; Ealick et al. (1991), Science, 252, 698-702] or were too inaccurate [bovine, 1rfb; Samudzi & Rubin (1993), Acta Cryst. D49(6), 505-512; rabbit, 2rig; Samudzi et al. (1991), J. Biol. Chem. 266(32), 21791-21797] for the structure to be solved by molecular replacement. The structure was solved in crystal form 1 using two derivatives produced by chemically modifying two free cysteine residues that were introduced by site-directed mutagenesis (Ser30Cys, Asn59Cys). After model building and refinement, the final R value was 21.8% (R(free) = 30.9%) for all data in the resolution range 8.0-2.9 A. The crystal form 1 structure was then used as a molecular-replacement model for crystal form 2 data collected from a flash-cooled crystal. Subsequent model building and refinement, using all data in the resolution range 15.0-2.0 A, gave an R value of 19.7% and an R(free) of 27.5%. Pairwise comparison of C(alpha) positions of bovine IFN-gamma (BOV) and the previously determined 1rfb and 2rig structures indicated some significant differences in the models (r.m.s.d. values for BOV to 1rfb, 4.3 A; BOV to 2rig, 4.0 A). An assessment of the quality of the structures was made using the 3D-1D algorithm [Eisenberg et al. (1992), Faraday Discuss. 93, 25-34]. The resulting statistical scoring indicated that BOV was consistent with expected criteria for a 2.0 A structure, whereas both 1rfb and 2rig fell below acceptable criteria.

Amino Acid Sequence↗
PubMed2001

High-resolution analysis of tomato leaf elongation: the application of novel time-series analysis techniques.

This paper demonstrates the use of a novel suite of data-based, recursive modelling techniques for the investigation of biological and other time-series data, including high resolution leaf elongation. The Data-Based Mechanistic (DBM) modelling methodology rejects the common practice of empirical curve fitting for a more objective approach where the model structure is not assumed a priori, but instead is identified directly from the data series in a stochastic form. Further, this novel approach takes advantage of the latest techniques in optimal recursive estimation of non-stationary and non-linear time-series. Here, the utility and ease of use of these techniques is demonstrated in the examination of two time-series of leaf elongation in an expanding leaf of tomato (Lycopersicon esculentum L. cv. Ailsa Craig) growing in a root pressure vessel (RPV). Using this analysis, the component signals of the elongation series are extracted and considered in relation to physiological processes. It is hoped that this paper will encourage the wider use of these new techniques, as well as the associated Data-Based Mechanistic (DBM) modelling strategy, in analytical plant physiology.

Algorithms↗
PubMed2005

Estimation of the cortical connectivity by high-resolution EEG and structural equation modeling: simulations and application to finger tapping data.

Today, the concept of brain connectivity plays a central role in the neuroscience. While functional connectivity is defined as the temporal coherence between the activities of different brain areas, the effective connectivity is defined as the simplest brain circuit that would produce the same temporal relationship as observed experimentally between cortical sites. The most used method to estimate effective connectivity in neuroscience is the structural equation modeling (SEM), typically used on data related to the brain hemodynamic behavior. However, the use of hemodynamic measures limits the temporal resolution on which the brain process can be followed. The present research proposes the use of the SEM approach on the cortical waveforms estimated from the high-resolution EEG data, which exhibits a good spatial resolution and a higher temporal resolution than hemodynamic measures. We performed a simulation study, in which different main factors were systematically manipulated in the generation of test signals, and the errors in the estimated connectivity were evaluated by the analysis of variance (ANOVA). Such factors were the signal-to-noise ratio and the duration of the simulated cortical activity. Since SEM technique is based on the use of a model formulated on the basis of anatomical and physiological constraints, different experimental conditions were analyzed, in order to evaluate the effect of errors made in the a priori model formulation on its performances. The feasibility of the proposed approach has been shown in a human study using high-resolution EEG recordings related to finger tapping movements.

Algorithms↗
PubMed2000

Globbic approximation in low-resolution direct-methods phasing.

Probabilistic direct-methods phasing theory, originally based on a uniform atomic distribution hypothesis, is shown to be adaptable to a non-uniform bulk-solvent-compensated globbic approximation for protein crystals at low resolution. The effective number n(g) of non-H protein atoms per polyatomic glob increases with decreasing resolution; low-resolution phases depend on the positions of only N(g) = N(a)/n(g) globs rather than N(a) atoms. Test calculations were performed with measured structure-factor data and the refined structural parameters from a protein crystal with approximately 10 000 non-H protein atoms per molecule and approximately 60% solvent volume. Low-resolution data sets with d(min) ranging from 15 to 5 A gave n(g) = ad(min) + b, with a = 1.0 A(-1) and b = -1.9 for the test case. Results of tangent-formula phase-estimation trials emphasize that completeness of the low-resolution data is critically important for probabilistic phasing.

Crystallization↗
PubMed1994

Metal substitution in a blue-copper protein: the crystal structure of cadmium-azurin at 1.8 A resolution.

Crystals of cadmium-substituted azurin have been prepared by diffusing Cd(II) into crystals of apo-azurin grown previously and their structure has been determined at high resolution by X-ray crystallography. Data to 1.8 A resolution were collected by Weissenberg photography (with image plates) using synchrotron radiation. These data were combined with a 2.2 A diffractometer data set to give 90% coverage to 1.8 A. An initial model was derived from the isomorphous Cu(II)-azurin structure, and the cadmium and ligand positions added from 'omit' maps. Refinement was by restrained least squares (program PROLSQ), to a final R value of 0.168 for all data in the range 10.0-1.8 A (23 349 reflections). The final model of 1954 protein atoms, two Cd(II) ions (occupancy 0.75), four SO(4)(2-) ions and 239 water molecules has r.m.s. deviations of 0.015, 0.045 and 0.013 A from standard bond lengths, angle distances and planar groups. The protein structure is essentially the same as that of Cu(II)-azurin, with an r.m.s. deviation of 0.18 A for 97% of main-chain atoms after superposition of the two structures. The Cd atom is within 0.2 A of the equivalent copper position, displaced slightly away from the axial Met ligand towards the carbonyl O atom of Gly45. The latter has also moved slightly towards the metal, by a rotation of the peptide unit, to give a Cd-O bond of 2.76 A. The Cd-S(Cys) bond is lengthened to 2.39 A. The coordination geometry is slightly more tetrahedral than for Cu(II), and the cadmium-oxygen interaction is consistent with the presence of an oxygen ligand in the coordination sphere of stellacyanin.

Journal Article↗
PubMed2003

Mass spectrometric studies of cyclopentanol derivatives in the reductive coupling of alpha,beta-unsaturated ketones assisted by samarium diiodide.

The mass spectrometric fragmentations of a series of cyclopentanol derivatives in positive fast-atom bombardment (FAB(+)) mode were investigated. The corresponding pathways proposed were confirmed by MS/MS data obtained using linked scans at constant B/E, high-resolution accurate mass data, and comparisons with corresponding information for a specifically deuterated molecule.

Cyclopentanes↗
PubMed1994

The crystallization and preliminary X-ray analysis of allosteric chorismate mutase.

An allosteric chorismate mutase, the Thr226-->Ile mutant, from the yeast Saccharomyces cerevisiae has been crystallized in space group P6(1)(P6(5)) using the hanging drop vapour diffusion method at room temperature. The cell dimensions are a = b = 95.8 A, c = 157.9 A, alpha = beta = 90 degrees, gamma = 120 degrees. It contains a dimer in the crystallographic asymmetric unit. The crystal diffracts to 2.2 A resolution. A native data set has been collected to 82% completeness at this resolution.

Allosteric Regulation↗
PubMed2000

Potholes in the information highway: the use of health service utilization data by Alberta health care managers.

Reviews and consultations with regional health authority decision makers have indicated that both data quality and access can limit effective use of health services information when assessing outcomes, planning changes, testing solutions and making decisions. To further a more system-wide understanding of these data utilization issues, we asked senior managers, board members and information analysts in Alberta regional health authorities (n = 111) about the availability of, organizational supports for and barriers to the use of health service utilization data. Eighty percent of respondents stated that the lack of data impeded problem resolution, and 83 percent of managers stated that health service data alerted them to new problems. Examples of useful data related to good standardization and linkage of data sets, or to capacity for valid comparison and trending. Given the limitations highlighted in relation to meeting even the simplest needs of standardization, linkage, comparison and trending, Alberta health care managers indicate frustration in trying to use health service data as currently construed and distributed, particularly within their current frameworks and fast-paced timelines for decision making.

Administrative Personnel↗
PubMed2006

Spectroscopic characterization of the ground and low-lying electronic states of Ga2N via anion photoelectron spectroscopy.

Anion photoelectron spectra of Ga(2)N(-) were measured at photodetachment wavelengths of 416 nm(2.978 eV), 355 nm(3.493 eV), and 266 nm(4.661 eV). Both field-free time-of-flight and velocity-map imaging methods were used to collect the data. The field-free time-of-flight data provided better resolution of the features, while the velocity-map-imaging data provided more accurate anisotropy parameters for the peaks. Transitions from the ground electronic state of the anion to two electronic states of the neutral were observed and analyzed with the aid of electronic structure calculations and Franck-Condon simulations. The ground-state band was assigned to a transition between linear ground states of Ga(2)N(-)(X (1)Sigma(g) (+)) and Ga(2)N(X (2)Sigma(u) (+)), yielding the electron affinity of Ga(2)N, 2.506+/-0.008 eV. Vibrationally resolved features in the ground-state band were assigned to symmetric and antisymmetric stretch modes of Ga(2)N, with the latter allowed by vibronic coupling to an excited electronic state. The energy of the observed excited neutral state agrees with that calculated for the A (2)Pi(u) state, but the congested nature of this band in the photoelectron spectrum is more consistent with a transition to a bent neutral state.

Journal Article↗
PubMed2004

Desquamative interstitial pneumonia, respiratory bronchiolitis and their relationship to smoking.

AIMS: Respiratory bronchiolitis (RB) and desquamative interstitial pneumonia (DIP) are closely associated histological patterns of interstitial pneumonia, although there are no studies on the extent of individual histological parameters. Furthermore, the term smoking related-interstitial lung disease (SR-ILD) has been proposed as a term to encompass patients with both these histological patterns who give a history of smoking, though it is not well defined how this term relates to historical cases of DIP. The aim of this study was to compare histological parameters in cases of DIP and RB and then to review in detail clinical, imaging and histological data for DIP in relation to a history of smoking. METHODS AND RESULTS: Forty-nine cases were reviewed, 24 with RB and 25 with DIP; five cases of DIP were re-classified as RB on review due to bronchocentricity of the infiltrate. There was a significantly greater extent of interstitial fibrosis (P = 0.02), lymphoid follicles (P < 0.001) and eosinophilic infiltration (P < 0.0001) in patients with DIP compared with RB. In addition, the extents of these three parameters were significantly interrelated. Patients with DIP had a lower incidence of smoking (60%) when compared with patients with RB-ILD (93%) (P < 0.005). Further analysis of smokers versus never-smokers with DIP showed no difference in histological parameters, extent of haemosiderin deposition or the number of CD1a+ macrophages between the two groups, nor were there any differences in clinical data to suggest other aetiologies. Follow-up high-resolution computed tomography data from patients with DIP suggested that a pattern of fibrotic non-specific interstitial pneumonia (NSIP) may develop in the long term in both smokers and never-smokers. CONCLUSION: There are significant differences in the extent of interstitial fibrosis, lymphoid follicles and eosinophilic infiltration between DIP and RB, as well as a much lower incidence of smoking in patients with DIP. Whether the lower reported incidence of smoking in DIP reflects referral bias or conservatism in giving a history of smoking remains uncertain, as neither histological parameters nor clinical data indicate a difference between smokers and never-smokers with DIP. Nevertheless, some cases of DIP are likely to remain idiopathic and unrelated to RB, though still have a good prognosis. Furthermore, they may evolve into a pattern resembling fibrotic NSIP. Therefore, whilst SR-ILD is appropriate in the correct clinical setting, the distinction between the histological patterns of RB and DIP remains appropriate.

Adult↗
PubMed2006

Immunoglobulin G avidity in differentiation between early and late antibody responses to West Nile virus.

In 1999 West Nile virus (WNV) surfaced in the United States in the city of New York and spread over successive summers to most of the continental United States, Canada, and Mexico. Because WNV immunoglobulin M (IgM) antibodies have been shown to persist for up to 1 year, residents in areas of endemicity can have persistent WNV IgM antibodies that are unrelated to a current illness with which they present. We present data on the use of IgG avidity testing for the resolution of conflicting data arising from the testing of serum or plasma for antibodies to WNV. Thirteen seroconversion panels, each consisting of a minimum of four samples, were used. All samples were tested for the presence of WNV IgM and IgG antibodies, and the avidity index for the WNV IgG-positive samples was calculated. Panels that exhibited a rise in the WNV IgM level followed by a sequential rise in the WNV IgG level were designated "primary." Panels that exhibited a marked rise in the WNV IgG level followed by a sequential weak WNV IgM response and that had serological evidence of a prior flavivirus infection were designated "secondary." All samples from the "primary" panels exhibited low avidity indices (less than 40%) for the first 20 to 30 days after the recovery of the index sample (the sample found to be virus positive). All of the "secondary" samples had elevated WNV IgG levels with avidity indices of > or =55%, regardless of the number of days since the recovery of the index sample. These data demonstrate that it is possible to differentiate between recent and past exposure to WNV or another flavivirus through the measurement of WNV IgG avidity indices.

Antibodies, Viral↗
PubMed1994

Adeno-associated virus DNA replication in vitro: activation by a maltose binding protein/Rep 68 fusion protein.

The adeno-associated virus (AAV) nonstructural protein Rep 68 is required for viral DNA replication. An in vitro assay has been developed in which addition of Rep 68 to an extract from uninfected HeLa cells supports AAV DNA replication. In this paper, we report characterization of the replication process when a fusion of the maltose binding protein and Rep 68, expressed in Escherichia coli, was used in the assay. Replication was observed when the template was either linear double-stranded AAV DNA or a plasmid construct containing intact AAV DNA. When the recombinant plasmid construct was used as the template, there was replication of pBR322 DNA as well as the AAV DNA; however, linear pBR322 DNA was not replicated. When the plasmid construct was the template, replication appeared to initiate on the intact plasmid and led to separation of the AAV sequences from those of the vector, a process which has been termed rescue. There was no evidence that replication could initiate on the products of rescue. Rep 68 can make a site-specific nick 124 nucleotides from the 3' end of AAV DNA; the site of the nick has been called the terminal resolution site. Our data are most consistent with initiation occurring at the terminal resolution site and proceeding toward the 3' terminus. When the template was the plasmid construct, either elongation continued past the junction into pBR322 sequences or the newly synthesized sequence hairpinned, switched template strands, and replicated the AAV DNA. Replication was linear for 4 h, during which time 70% of the maximal synthesis took place. An additional finding was that the Rep fusion could resolve AAV dimer length duplex intermediates into monomer duplexes without DNA synthesis.

ATP-Binding Cassette Transporters↗