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At least 1,621 records · Page 90Linked to original sources
PubMed2000

New crystal forms and low resolution structure analysis of 20S proteasomes from bovine liver.

20S proteasomes from higher eukaryotes have immunological functions rather than those from archibacteria or yeast. To clarify the mechanism of the sorting and production of antigen-presenting peptides, it is important and worthwhile to determine the structure of mammalian proteasomes using a third generation synchrotron radiation source. Here we report new crystal forms of 20S proteasomes from bovine liver and preliminary structure analysis of them. The crystals belong to the same space group but have different cell dimensions. One crystal (form I) belongs to space group P2(1)2(1)2(1) with unit cell dimensions of a = 124.8, b =197.4, c =323.8 A, and diffracts to 3.0 A resolution. The other crystal (form II) belongs to the same space group with a =115.1, b =205.6, c =316. 0 A, and diffracts to 4.0 A resolution. The diffraction data for the form I crystal provided an interpretable electron density map for presenting the structural differences from yeast proteasomes.

Animals↗
PubMed1989

Crystal structure analysis of omega-amino acid:pyruvate aminotransferase with a newly developed Weissenberg camera and an imaging plate using synchrotron radiation.

The three-dimensional structure of omega-amino acid:pyruvate aminotransferase from Pseudomonas sp. F-126, an isologous alpha 4 tetramer containing pyridoxal 5'-phosphate (PLP) as a cofactor, has been determined at 2.0 A resolution. The diffraction data were collected with a newly developed Weissenberg camera with a Fuji Imaging Plate, using synchrotron radiation. The mean figure-of-merit was 0.57. The subunit is rich in secondary structure and comprises two domains. PLP is located in the large domain. The high homology in the secondary structure between this enzyme and aspartate aminotransferase strongly indicates that these two types of enzymes have evolved from a common ancestor.

Aspartate Aminotransferases↗
PubMed1994

Structure of azurin from Achromobacter xylosoxidans NCIB11015 at 2.5 A resolution.

The crystal structure of azurin from a denitrifying bacterium, Achromobacter xylosoxidans NCIB11015, has been refined at 2.5 A resolution using diffraction data obtained by means of synchrotron radiation at KEK. Crystals suitable for X-ray experiment were obtained by the macro-seeding method and an intensity data were obtained on imaging plates mounted on a Weissenberg camera (Rmerge = 0.09). The initial model was obtained by the molecular replacement method using the structure of azurin from Alcaligenes denitrificans NCTC8582 as a starting model. The structure was refined by molecular dynamics optimization and the restrained least-squares method to a crystallographic R-value of 0.205. However, the current model gave an electron-density of the side-chain regions of several residues close to the N-terminus quite different from those expected from the amino acid sequences reported. Very recently, two kinds of azurins (Az-I and Az-II) were isolated from this bacterium by a slightly modified purification method and have been characterized and found to have different CD spectra. On analysis of amino acid sequences around the N-terminus, the second azurin (Az-II) was proved to be a new type of azurin in this bacterium. It was consequently revealed that the current model corresponds to a new type of azurin because of the complete agreement between the electron-density and the amino acid sequence of the newly determined 20 residues from the N-terminus. Determination of the whole amino acid sequence of this azurin and further refinement are in progress.

Alcaligenes↗
PubMed2001

Evolution of proteasomal ATPases.

In eukaryotic cells, the majority of proteins are degraded via the ATP-dependent ubiquitin/26S proteasome pathway. The proteasome is the proteolytic component of the pathway. It is a very large complex with a mass of around 2.5 MDa, consisting of at least 62 proteins encoded by 31 genes. The eukaryotic proteasome has evolved from a simpler archaebacterial form, similar in structure but containing only three different peptides. One of these peptides is an ATPase belonging to the AAA (Triple-A) family of ATPASES: Gene duplication and diversification has resulted in six paralogous ATPases being present in the eukaryotic proteasome. While sequence analysis studies clearly show that the six eukaryotic proteasomal ATPases have evolved from the single archaebacterial proteasomal ATPase, the deep node structures of the phylogenetic constructions lack resolution. Incorporating physical data to provide support for alternative phylogenetic hypotheses, we have constructed a model of a possible evolutionary history of the proteasomal ATPASES:

Adenosine Triphosphatases↗
PubMed1992

Site-directed mutagenesis and X-ray crystallography of two phospholipase A2 mutants: Y52F and Y73F.

Tyr52 and Tyr73 are conserved amino acid residues throughout all vertebrate phospholipases A2. They are part of an extended hydrogen bonding system that links the N-terminal alpha-NH3(+)-group to the catalytic residues His48 and Asp99. These tyrosines were replaced by phenylalanines in a porcine pancreatic phospholipase A2 mutant, in which residues 62-66 had been deleted (delta 62-66PLA2). The mutations did not affect the catalytic properties of the enzyme, nor the folding kinetics. The stability against denaturation by guanidine hydrochloride was decreased, however. To analyse how the enzyme compensates for the loss of the tyrosine hydroxyl group, the X-ray structures of the delta Y52F and delta Y73F mutants were determined. After crystallographic refinement the final crystallographic R-factors were 18.1% for the delta Y52F mutant (data between 7 and 2.3 A resolution) and 19.1% for the delta Y73F mutant (data between 7 and 2.4 A resolution). No conformational changes occurred in the mutants compared with the delta 62-66PLA2, but an empty cavity formed at the site of the hydroxyl group of the former tyrosine. In both mutants the Asp99 side chain loses one of its hydrogen bonds and this might explain the observed destabilization.

Enzyme Stability↗
PubMed1999

Seasonal variations in leaf area index, leaf chlorophyll, and water content; scaling-up to estimate fAPAR and carbon balance in a multilayer, multispecies temperate forest.

Seasonal differences in phenology between coniferous and deciduous tree species need to be considered when developing models to estimate CO(2) exchange in temperate forest ecosystems. Because seasonal variations in CO(2) flux in temperate forests are closely correlated with plant phenology, we quantified the phenology of forest species in a multilayered forest with patches of Scots pine (Pinus sylvestris L.) and oak (Quercus robur L.) in Brasschaat, Belgium. A scaling-up modeling approach was developed to simulate reflectance at the leaf and canopy scales over a one-year cycle. Chlorophyll concentration, water content, specific leaf area and leaf area index of the forest species were measured throughout an entire year (1997). Scaling-up from the leaf to canopy was achieved by linking the PROSPECT and SAIL models. The result is the annual progression of the fraction of absorbed photosynthetically active radiation (fAPAR) in a 1 km(2) forest area, which can be directly related to high-resolution, remotely sensed data.

Journal Article↗
PubMed1996

Prevention of lidocaine aerosol-induced bronchoconstriction with intravenous lidocaine.

BACKGROUND: Lidocaine applied topically provokes bronchoconstriction in persons with hyperreactive airway disease. The authors questioned whether intravenous lidocaine would prevent lidocaine-aerosol induced bronchoconstriction. They compared the effects of lidocaine administered intravenously and by the aerosol route on baseline airway tone, and on the prevention of histamine-induced bronchoconstriction in five Basenji-Greyhound dogs. METHODS: Dogs were pretreated with either intravenous or aerosol lidocaine followed by histamine aerosol challenge. On separate days, dogs were pretreated with intravenous lidocaine, followed by aerosol lidocaine administration at similar doses. Airway caliber was assessed using high-resolution computed tomography. Data were analyzed by two-way analysis of variance. Serum lidocaine concentrations were obtained. RESULTS: Histamine alone decreased the airway area by 32 +/- 3%. Lidocaine administered intravenously or by the aerosol route significantly inhibited histamine-induced bronchoconstriction. There was no significant difference between the two routes in preventing histamine-induced bronchoconstriction. At the dose that inhibited histamine-induced bronchoconstriction, lidocaine administered by the aerosol route decreased baseline airway area by 27 +/- 3% (P < 0.01), whereas intravenous lidocaine had no effect. Intravenous lidocaine prevented lidocaine aerosol-induced bronchoconstriction, and the combination of intravenous and aerosol lidocaine significantly dilated the airways by 20 +/- 5% (P < 0.01 compared with control). CONCLUSIONS: An intravenous bolus of lidocaine prevents the initial bronchoconstriction induced by lidocaine when administered as an aerosol.

Aerosols↗
PubMed1996

How valid are clinical signs of dehydration in infants?

Our objective was to determine the ability of several clinical signs of dehydration to distinguish among degrees of dehydration in infants with acute diarrhea. The design was a prospective cohort study in a pediatric referral hospital in Cairo, Egypt. Infant boys, 3-18 months old, with a history of acute diarrhea (5 or more watery stools per day for no more than 7 days) were eligible, except those with frank protein-energy malnutrition, serious nongastrointestinal illness, or being exclusively breast-fed. Several clinical signs of dehydration were assessed upon study entry. Subjects were then rehydrated with an oral rehydration solution and fed a standardized diet until diarrhea ceased (no watery or loose stools for 16 h). The main outcome measure was percent body weight gain at rehydration and at resolution of illness. Data from 135 subjects were available for analysis. Average (SD) rehydration phase duration was 5.2 (2.1) h, and average (SD) duration of illness was 54.5 (38) h. Multiple regression analysis selected prolonged skinfold, altered neurologic status, sunken eyes, and dry oral mucosa as the clinical signs that correlated best with percent dehydration (R2 for model 0.244, p < 0.001). Mean weight gain for the two assessment systems was 3.6-3.9% for mild, 4.9-5.3% for moderate, and 9.5-9.8% for severe dehydration. The most valid clinical signs of dehydration include prolonged skinfold, altered neurologic status, sunken eyes, and dry oral mucosa. Children with clinical signs of mild or moderate dehydration have fluid deficits on the order of 3 or 5% body weight, respectively.

Acute Disease↗
PubMed1984

Emission tomography: a concise theoretical overview.

A concise theoretical overview of emission tomography is presented aiming at physical interpretation of the equations so that fundamental concepts, similarities and differences between SPECT and PET, become transparent. The framework is that of an indirect sensing problem and image reconstruction from projections. The projections are expressed in terms of: the activity distribution, the attenuation distribution, the interactions of the radiation with matter, and the measurement geometry. In discussing the attenuation problem, recourse is made to the projections obtained by a gamma-ray (or a hypothetical monoenergetic X-ray) transmission CT scanner. This expression would be the one to which the corresponding expressions for SPECT and PET would reduce to if the attenuation distributions were known. Although the attenuation problem is less severe in PET, its extent is demonstrated with results from computer simulations. Finally, under conditions of 'adequate sampling', equations are given relating administered activity to spatial resolution, time for data collection, noise/signal ratio and system sensitivity.

Humans↗
PubMed2004

Coronal ring involvement in patients treated for unilateral coronal craniosynostosis.

The etiopathology of the clinical entity normally referred to as unilateral coronal synostosis is commonly used to connote unilateral fusion of the frontoparietal suture. However, other sutures in the coronal ring may exhibit synostosis concomitant with or independent from frontoparietal synostosis and give rise to similar clinical phenotypes. This study retrospectively analyzes high-resolution computed tomographic data sets to determine patency of sutures within the coronal ring. Computed tomographic scan digital data from 33 infants who subsequently underwent surgical correction of unilateral coronal synostosis were assessed for sutural patency using Analyze imaging software. The frontosphenoidal suture was subdivided into intraorbital frontosphenoidal and extraorbital frontosphenoidal portions, and the patency of the frontoethmoidal suture was also assessed. Patients were sorted into two groups on the basis of the status of their frontosphenoidal sutures: group 1 had patent frontosphenoidal but synostotic frontoparietal sutures (n = 21) and group 2 had both frontosphenoidal and frontoparietal synostoses. Observer reproducibility was tested. The vertical and horizontal dimensions of the bony orbit and the endocranial base deflection angle were measured with the observer blinded with regard to sutural status group. Frontoethmoidal synostosis was not noted in any patients in either group. Two patients had no frontoparietal suture synostosis with isolated intraorbital frontosphenoidal and extraorbital frontosphenoidal suture closures. Suture diagnosis reproducibility was 99 percent. In group 1, the ipsilateral-to-contralateral vertical orbit dimension ratio averaged 1.11, whereas in group 2 it averaged 1.04 (p < 0.05). The ratio of horizontal orbit measurements was not significantly different between groups. In both groups, the endocranial base was deflected ipsilateral to the synostotic frontoparietal suture, with an average angle of 12 degrees in group 1 and 17 degrees in group 2 (p < 0.005). The extent of synostosis along the coronal sutural ring contributes to the dysmorphology of the orbit and the endocranial base deflection in patients whose clinical phenotypic diagnosis is unilateral coronal synostosis.

Child, Preschool↗
PubMed1997

Image reconstruction in optical tomography.

Optical tomography is a new medical imaging modality that is at the threshold of realization. A large amount of clinical work has shown the very real benefits that such a method could provide. At the same time a considerable effort has been put into theoretical studies of its probable success. At present there exist gaps between these two realms. In this paper we review some general approaches to inverse problems to set the context for optical tomography, defining both the terms forward problem and inverse problem. An essential requirement is to treat the problem in a nonlinear fashion, by using an iterative method. This in turn requires a convenient method of evaluating the forward problem, and its derivatives and variance. Photon transport models are described for obtaining analytical and numerical solutions for the most commonly used ones are reviewed. The inverse problem is approached by classical gradient-based solution methods. In order to develop practical implementations of these methods, we discuss the important topic of photon measurement density functions, which represent the derivative of the forward problem. We show some results that represent the most complex and realistic simulations of optical tomography yet developed. We suggest, in particular, that both time-resolved, and intensity-modulated systems can reconstruct variations in both optical absorption and scattering, but that unmodulated, non-time-resolved systems are prone to severe artefact. We believe that optical tomography reconstruction methods can now be reliably applied to a wide variety of real clinical data. The expected resolution of the method is poor, meaning that it is unlikely that the type of high-resolution images seen in computed tomography or medical resonance imaging can ever be obtained. Nevertheless we strongly expect the functional nature of these images to have a high degree of clinical significance.

Image Processing, Computer-Assisted↗
PubMed1978

A co-operative numerical analysis of Mycobacterium gastri, Mycobacterium kansasii and Mycobacterium marinum.

A co-operative taxonomic study has been performed on slowly growing photochromogenic mycobacteria (Runyon Group I) and closely related organisms. Phenetic data on 54 strains, studied in seven laboratories, were collected and analysed by numerical taxonomic methods. Immunological properties and phage susceptibility patterns were analysed independently to establish correlation with numerical classification. Mycobacterium gastri, M. kansasii and M. marinum appeared as distinct well-defined clusters and the serological and phage data supported the resolution of these three species. A table of definitive properties is presented. Two strains each of M. simiae and M. asiaticum formed a loose cluster which was clearly separated from the previously mentioned three species; the small number of strains examined precluded the establishment of a list of definitive properties of these two species. It is concluded that the Runyon Groups, which provided a practical though arbitrary basis for establishment of a series of co-operative studies, have served their purpose and should now be supplanted by classification and nomenclature based on species.

Bacteriophage Typing↗
PubMed2004

Reconstruction of thermally symmetrized quantum autocorrelation functions from imaginary-time data.

In this paper, I propose a technique for recovering quantum dynamical information from imaginary-time data via the resolution of a one-dimensional Hamburger moment problem. It is shown that the quantum autocorrelation functions are uniquely determined by and can be reconstructed from their sequence of derivatives at origin. A general class of reconstruction algorithms is then identified, according to Theorem 3. The technique is advocated as especially effective for a certain class of quantum problems in continuum space, for which only a few moments are necessary. For such problems, it is argued that the derivatives at origin can be evaluated by Monte Carlo simulations via estimators of finite variances in the limit of an infinite number of path variables. Finally, a maximum entropy inversion algorithm for the Hamburger moment problem is utilized to compute the quantum rate of reaction for a one-dimensional symmetric Eckart barrier.

Journal Article↗
PubMed2006

Large-scale flow effects, energy transfer, and self-similarity on turbulence.

The effect of large scales on the statistics and dynamics of turbulent fluctuations is studied using data from high resolution direct numerical simulations. Three different kinds of forcing, and spatial resolutions ranging from 256(3) to 1024(3), are being used. The study is carried out by investigating the nonlinear triadic interactions in Fourier space, transfer functions, structure functions, and probability density functions. Our results show that the large scale flow plays an important role in the development and the statistical properties of the small scale turbulence. The role of helicity is also investigated. We discuss the link between these findings and intermittency, deviations from universality, and possible origins of the bottleneck effect. Finally, we briefly describe the consequences of our results for the subgrid modeling of turbulent flows.

Journal Article↗
PubMed2000

Anomalously large oxygen-ordering contribution to the thermal expansion of untwinned YBa2Cu3O6.95 single crystals: A glasslike transition near room temperature

We present high-resolution thermal expansion data from 5-500 K of untwinned YBa2Cu3Ox (Y123) single crystals for x approximately 6.95 and x = 7.0. Large contributions to the thermal expansivities due to O ordering are found for x approximately 6.95, which disappear below a kinetic glasslike transition near 280 K. The kinetics at this glass transition is governed by an energy barrier of 0.98+/-0.07 eV, in very good agreement with other O-ordering studies. Using thermodynamic arguments, we show that O ordering in the Y123 system is particularly sensitive to uniaxial stress along the chain axis and that the lack of well-ordered chains in Nd123 and La123 is most likely a consequence of a chemical-pressure effect.

Journal Article↗
PubMed2005

Interoccurrence times in the Bak-Tang-Wiesenfeld sandpile model: a comparison with the observed statistics of solar flares.

A sequence of bursts observed in an intermittent time series may be caused by a single avalanche, even though these bursts appear as distinct events when noise and/or instrument resolution impose a detection threshold. In the Bak-Tang-Wiesenfeld sandpile, the statistics of quiet times between bursts switches from Poissonian to scale invariant on raising the threshold for detecting instantaneous activity, since each zero-threshold avalanche breaks into a hierarchy of correlated bursts. Calibrating the model with the time resolution of GOES data, qualitative agreement with the interoccurrence time statistics of solar flares at different intensity thresholds is found.

Journal Article↗
PubMed2000

Low-resolution direct phase determination in protein electron crystallography - breaking globular constraints.

Although the assumption of an overall globular scattering entity can be useful for determining crystallographic phases for a protein at low resolution, there is a point where this pseudoatomic model must be abandoned for further phase refinement. Using 6 A resolution electron diffraction data from aquaporin (AQP-CHIP) as an example, phases of the 16 most intense reflections from a previous direct solution (Dorset & Jap (1998). Acta Cryst. D54, 615-621) were modified with a Hadamard error-correcting code to produce potential maps very similar to the ones obtained using phases from the Fourier transform of averaged electron micrographs. The choice of the optimal phase set was made via the cross correlation of experimental with anticipated density histograms using the autocorrelation function of the latter histogram as the desired endpoint.

Aquaporin 1↗
PubMed1991

Molecular replacement solution of the structure of apolactoferrin, a protein displaying large-scale conformational change.

The crystal structure of an orthorhombic form of human apolactoferrin (ApoLf) has been determined from 2.8 A diffractometer data by molecular replacement methods. A variety of search models derived from the diferric lactoferrin structure (Fe2Lf) were used to obtain a consistent solution to the rotation function. An R-factor search gave the correct translational solution and the model was refined by rigid-body least-squares refinement (program CORELS). Only three of the four domains were located correctly by this procedure, however; the fourth was finally placed correctly by rotating it manually onto three strands of electron density which were recognized as part of its central beta-sheet. The final model, refined by restrained least-squares methods to an R factor of 0.214 for data in the resolution range 10.0 to 2.8 A, shows a large domain movement in the N-terminal half of the molecule (a 54 degree rotation of domain N2) and smaller domain movements elsewhere, when compared with Fe2Lf. A feature of the crystal structure is that although the ApoLf and Fe2Lf unit cells appear very similar, their crystal packing and molecular structures are quite different.

Apoproteins↗