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PubMed2002

Land-cover change in upper Barataria Basin estuary, Louisiana, 1972-1992: increases in Wetland area.

The Barataria Basin, Louisiana, USA, is an extensive wetland and coastal estuary system of great economic and intrinsic value. Although high rates of wetland loss along the coastal margin of the Barataria Basin have been well documented, little information exists on whether freshwater wetlands in the upper basin have changed. Our objectives were to quantify land-cover change in the upper basin over 20 years from 1972-1992 and to determine land-cover transition rates among land-cover types. Using 80-m resolution Landsat MSS data from the North American Landscape Characterization (NALC) data archive, we classified images from three time steps (1972, 1985, 1992) into six land-cover types: agriculture, urban, bottomland hardwood forest, swamp forest, freshwater marsh, and open water. Significant changes in land cover occurred within the upper Barataria Basin over the study period. Urban land increased from 8% to 17% of the total upper basin area, primarily due to conversions from agricultural land, and to a lesser degree, bottomland forest. Swamp forest increased from 30% to 41%, associated with conversions from bottomland hardwood forest and freshwater marsh. Overall, bottomland forest decreased 38% and total wetland area increased 21%. Within the upper Barataria, increases in total wetland area may be due to land subsidence. Based on our results, if present trends in the reduction of bottomland forest land cover were to continue, the upper Barataria Basin may have no bottomland hardwood forests left by the year 2025, as it is subjected to multiple stressors both in the higher elevations (from urbanization) and lower elevations (most likely from land subsidence). These results suggest that changes in the upper freshwater portions of coastal estuaries can be large and quite different from patterns observed in the more saline coastal margins.

Agriculture↗
PubMed2004

Decision tree algorithm for detection of spatial processes in landscape transformation.

The conversion of landscapes by human activities results in widespread changes in landscape spatial structure. Regardless of the type of land conversion, there appears to be a limited number of common spatial configurations that result from such land transformation processes. Some of these configurations are considered optimal or more desirable than others. Based on pattern geometry, we define ten processes responsible for pattern change: aggregation, attrition, creation, deformation, dissection, enlargement, fragmentation, perforation, shift, and shrinkage. A novelty in this contribution is the inclusion of transformation processes causing expansion of the land cover of interest. Consequently, we propose a decision tree algorithm that enables detection of these processes, based on three parameters that have to be determined before and after the transformation of the landscape: area, perimeter length, and number of patches of the focal landscape class. As an example, the decision tree algorithm is applied to determine the transformation processes of three divergent land cover change scenarios: deciduous woodland degradation in Cadiz Township (Wisconsin, USA) 1831-1950, canopy gap formation in a terra firme rain forest at the Tiputini Biodiversity Station (Amazonian Ecuador) 1997-1998, and forest regrowth in Petersham Township (Massachusetts, USA) 1830-1985. The examples signal the importance of the temporal resolution of the data, since long-term pattern conversions can be subdivided in stadia in which particular pattern components are altered by specific transformation processes.

Algorithms↗
PubMed2003

Magnetic resonance imaging protocols for examination of the neurocranium at 3 T.

The increasing availability of high-field (3 T) MR scanners requires adapting and optimizing clinical imaging protocols to exploit the theoretically higher signal-to-noise ratio (SNR) of the higher field strength. Our aim was to establish reliable and stable protocols meeting the clinical demands for imaging the neurocranium at 3 T. Two hundred patients with a broad range of indications received an examination of the neurocranium with an appropriate assortment of imaging techniques at 3 T. Several imaging parameters were optimized. Keeping scan times comparable to those at 1.5 T we increased spatial resolution. Contrast-enhanced and non-enhanced T1-weighted imaging was best applying gradient-echo and inversion recovery (rather than spin-echo) techniques, respectively. For fluid-attenuated inversion recovery (FLAIR) imaging a TE of 120 ms yielded optimum contrast-to-noise ratio (CNR). High-resolution isotropic 3D data sets were acquired within reasonable scan times. Some artifacts were pronounced, but generally imaging profited from the higher SNR. We present a set of optimized examination protocols for neuroimaging at 3 T, which proved to be reliable in a clinical routine setting.

Adult↗
PubMed2006

X-ray structural studies of the fungal laccase from Cerrena maxima.

Laccases are members of the blue multi-copper oxidase family. These enzymes oxidize substrate molecules by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear centre. Dioxygen binds to the trinuclear centre and following the transfer of four electrons is reduced to two molecules of water. The X-ray structure of a laccase from Cerrena maxima has been elucidated at 1.9 A resolution using synchrotron data and the molecular replacement technique. The final refinement coefficients are Rcryst = 16.8% and Rfree = 23.0%, with root mean square deviations on bond lengths and bond angles of 0.015 A and 1.51 degrees , respectively. The type 1 copper centre has an isoleucine residue at the axial position and the "resting" state of the trinuclear centre comprises a single oxygen (OH) moiety asymmetrically disposed between the two type 3 copper ions and a water molecule attached to the type 2 ion. Several carbohydrate binding sites have been identified and the glycan chains appear to promote the formation of well-ordered crystals. Two tyrosine residues near the protein surface have been found in a nitrated state.

Binding Sites↗
PubMed2006

FlgM anti-sigma factors: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships.

FlgM proteins, also known as Anti-sigma-28 factor (sigma28), are negative regulators of flagellin synthesis. Recently, a three-dimensional structure of the Aquifex aeolicus sigma28/FlgM complex (PDB code: 1rp3) was determined by X-ray crystallography at 2.3 A resolution. Furthermore, experimental data on bacterial FlgM, including site-directed mutagenesis and structural characterization by NMR are also available. However, an interpretation of the sequence-structure-function relationships combining X-ray and NMR data with the evolutionary information extracted from the increasing number of FlgM-related sequences annotated in databases is not available. In the present study, we combined database sequence searches and sequence-analysis tools to update the multiple sequence alignment of a previously characterized cluster of orthologs (COG2747) and the PFAM classification of protein domains (PF04316) for the FlgM family. A phylogenetic analysis of 77 protein sequences revealed the presence of at least three major sequence clades within the FlgM family. Besides, we predicted functional residues using a SequenceSpace method. We also generated homology models for Bacillus subtilis and Salmonella typhimurium FlgM proteins, for which sequence-structure-function relationship data are available, and used the docking program ClusPro to hypothesize about the dimer association between FlgM proteins. In conclusion, the analysis presented in this work will be useful in designing new experiments to understand better protein-protein interactions between FglM, sigma factors, and putative molecules from the flagellar export apparatus. Electronic Supplementary Material is available in the online version of this article at http://link.springer.de/

Bacterial Proteins↗
PubMed2006

Preventing youth violence and delinquency through a universal school-based prevention approach.

Violence is an important public health problem among adolescents in the United States. Substance use and violence tend to co-occur among adolescents and appear to have similar etiologies. The present study examined the extent to which a comprehensive prevention approach targeting an array of individual-level risk and protective factors and previously found effective in preventing tobacco, alcohol, and illicit drug use is capable of decreasing violence and delinquency. Schools (N=41) were randomly assigned to intervention and control conditions. Participants in the 20 intervention schools received the Life Skills Training prevention program including material focusing on violence and the media, anger management, and conflict resolution skills. Survey data were collected from 4,858 sixth grade students prior to the intervention and three months later after the intervention. Findings showed significant reductions in violence and delinquency for intervention participants relative to controls. Stronger prevention effects were found for students who received at least half of the preventive intervention. These effects include less verbal and physical aggression, fighting, and delinquency. The results of this study indicate that a school-based prevention approach previously found to prevent tobacco, alcohol, and illicit drug use can also prevent violence and delinquency.

Adolescent↗
PubMed1985

Periodate oxidation products of hydroxylysine in the synthesis of 5-substituted prolines.

The amino acid hydroxylysine was subjected to oxidation by sodium metaperiodate under various conditions. It was found that in acid and high temperature, the initial oxidation product alpha-aminoglutaric gamma-semialdehyde was converted to glutamic acid with a yield of 60%. The use of alkaline conditions of oxidation favored the cyclization of alpha-aminoglutaric gamma-semialdehyde to form delta 1-pyrroline 5-carboxylic acid. Addition of NaCN to this intermediate generated new proline analogs, likely a mixture of cis- and trans-5-cyanoprolines, with a yield of 30%. Upon hydrolysis, the 5-cyanoprolines were converted to a probable mixture of cis- and trans-5-carboxyprolines. Infrared and high-resolution mass spectral data of the analogs and visual absorption spectra of the ninhydrin products were obtained to confirm the structures.

Hydrogen-Ion Concentration↗
PubMed1988

The effect of fast protein liquid chromatography (FPLC) cationic exchange purification on the crystallization of a monoclonal Fab fragment.

Fast protein liquid chromatography cationic exchange purification to homogeneity of a monoclonal Fab fragment has resulted in an improvement in the quality of crystals for X-ray diffraction studies. This improvement is displayed in a well-defined crystal morphology, reproducibility of crystal growth, and increased resolution of diffraction data.

Chromatography, Ion Exchange↗
PubMed1992

Purification, crystallization, and X-ray diffraction studies of lactotransferrin from buffalo colostrum.

Lactotransferrin is an iron-binding protein. It has been purified from buffalo colostrum. The purified lactotransferrin has been crystallized in 10% ethanol solution. The crystals are orthorhombic and the space group is P2(1)2(1)2(1) with unit cell dimensions a = 161.70 A, b = 155.75 A, c = 113.48 A. The asymmetric unit contains three molecules of the protein with a solvent content of about 59%. The crystals were stable in the X-ray beam and diffract beyond 3.5 A resolution. The native data have been collected and the structure determination is in progress.

Animals↗
PubMed1985

Interaction of Ca2+ with cardiolipin-containing liposomes and its inhibition by adriamycin.

The interaction of cardiolipin-containing, unilamellar liposomes with Ca2+ was assessed by flow dialysis in the presence of 2-100 microM 45Ca2+, using vesicles formed from phosphatidylcholine (PC) and from PC and cardiolipin in mole ratios from 16:1 to 1:1. Control (PC only) vesicles bound no detectable Ca2+. In contrast, Ca2+ binding to cardiolipin-containing vesicles was substantial and dependent on vesicle concentration. Scatchard plots for the binding were concave upward. Resolution of the data, assuming the presence of two independent classes of binding sites, indicated a high-affinity site with apparent KD = 5.57 +/- 0.48 microM (S.D.) and a second site with KD in the millimolar range. Interaction of cardiolipin-containing liposomes with Ca2+ was insensitive to monovalent cations (Na+, K+, Rb+), but was inhibited by ruthenium red much greater than La3+ greater than Mn2+ greater than Mg2+. Progressive increases in the PC: cardiolipin ratio markedly increased the apparent KD for Ca2+ at the high-affinity site. Stoichiometry of Ca2+ binding at the site passed through a maximum at a PC: cardiolipin ratio of 4:1. The potent antineoplastic agent adriamycin also inhibited the interaction of Ca2+ with cardiolipin-containing liposomes in a dose-dependent manner; effects were detected at 10 microM antibiotic. Unlike PC, adriamycin altered the stoichiometry of the high-affinity interaction but not the apparent KD. Adriamycin effects increased with pH in the range of the pKA of its amino group. These results suggest that inhibition by adriamycin may result from a mechanism other than simple competition for the charged head group of cardiolipin.

Binding Sites↗
PubMed1988

Spatial arrangement of DNA-dependent RNA polymerase of Escherichia coli and DNA in the specific complex. A neutron small angle scattering study.

In this paper we demonstrate that neutron small angle scattering is a suitable method to study the spatial arrangement of large specific protein-DNA complexes. We studied the complex of DNA-dependent RNA polymerase of Escherichia coli and a 130 base-pair DNA fragment containing the strong promoter A1 of bacteriophage T7. Contrast variation of the complex with deuterium allowed us to "visualize" either RNA polymerase, or DNA, or both components in situ. From the corresponding scattering curves information was derived about: (1) Conformational changes of RNA polymerase and DNA by complex formation: comparison of the scattering profiles of the isolated and complexed components showed that by specific complex formation the cross-section of RNA polymerase decreases, while the DNA fragment does not undergo a gross conformational change. (2) The spatial arrangement of RNA polymerase and DNA in the specific complex from the cross-sectional radii of gyration of the complex the normal distance dn between the centre of gravity of the RNA polymerase and the axis of the DNA fragment was derived as 5.0 (+/- 0.3) nm. On the basis of these and footprinting data a low resolution model of the RNA polymerase-promoter complex is proposed. The main feature of this model is the positioning of RNA polymerase to only one side of the DNA.

DNA, Bacterial↗
PubMed1991

Refined atomic structures of N9 subtype influenza virus neuraminidase and escape mutants.

The crystal structure of the N9 subtype neuraminidase of influenza virus was refined by simulated annealing and conventional techniques to an R-factor of 0.172 for data in the resolution range 6.0 to 2.2 A. The r.m.s. deviation from ideal values of bond lengths is 0.014 A. The structure is similar to that of N2 subtype neuraminidase both in secondary structure elements and in their connections. The three-dimensional structures of several escape mutants of neuraminidase, selected with antineuraminidase monoclonal antibodies, are also reported. In every case, structural changes associated with the point mutation are confined to the mutation site or to residues that are spatially immediately adjacent to it. The failure of antisera to cross-react between N2 and N9 subtypes may be correlated with the absence of conserved, contiguous surface structures of area 700 A2 or more.

Antigens, Bacterial↗
PubMed1989

Quantitative detection of rapid motions in spectrin by NMR.

Previous high resolution proton NMR data on human erythrocyte spectrin molecules has indicated the existence of regions exhibiting rapid internal motions within the intact molecules [L. W.-M. Fung, H.-Z. Lu, R. P. Hjelm, jr, M. E. Johnson, FEBS Lett., 197, 234 (1986)]. We have extended the studies by developing quantitative NMR methods to determine the fraction of spectrin protons exhibiting rapid internal motions, in both the isolated molecule and within the spectrin-actin network. Using both one-pulse and spin echo pulse sequences, we find that the fraction of the protons in rapid motion is about 15% of the total protons in the spectrin molecule at 37 degrees C in phosphate buffer with 150 mM NaCl at pH 7.4. Quantitative information on these rapid motions will be important in understanding the structural, mechanical and functional properties of spectrin molecules, as well as in understanding filamentous protein structures in general.

Erythrocyte Membrane↗
PubMed1990

Errors in three dimensions.

Now that some protein X-ray structures have been proved to contain major errors, the question of the precision of 3-dimensional structures is taken seriously by crystallographers and NMR spectroscopists. Errors which cannot be avoided during model building in electron density maps, should correct themselves during crystallographic refinement, and the precision of the refined model should reach 0.15 to 0.25 A depending on the resolution of the data. Independent estimates based on homologous protein structures confirm that better than 0.5 A precision is commonly achieved, at least for C alpha and main chain atoms. The precision of NMR structures is less easily evaluated, but it should be better than 2 A when a sufficient number of NOE distance constraints are available. One may deplore the fact that not all published structures meet these standards, but possible errors should not be an excuse for not depositing atomic co-ordinates in data banks.

Crystallography↗
PubMed1992

Detecting morphological convergence in true fungi, using 18S rRNA gene sequence data.

For the true fungi, phylogenetic relationships inferred from 18S ribosomal DNA sequence data agree with morphology when (1) the fungi exhibit diagnostic morphological characters, (2) the sequence-based phylogenetic groups are statistically supported, and (3) the ribosomal DNA evolves at roughly the same rate in the lineages being compared. 18S ribosomal RNA gene sequence data and biochemical data provide a congruent definition of true fungi. Sequence data support the traditional fungal subdivisions Ascomycotina and Basidiomycotina. In conflict with morphology, some zygomycetes group with chytrid water molds rather than with other terrestrial fungi, possibly owing to unequal rates of nucleotide substitutions among zygomycete lineages. Within the ascomycetes, the taxonomic consequence of simple or reduced morphology has been a proliferation of mutually incongruent classification systems. Sequence data provide plausible resolution of relationships for some cases where reduced morphology has created confusion. For example, phylogenetic trees from rDNA indicate that those morphologically simple ascomycetes classified as yeasts are polyphyletic and that forcible spore discharge was lost convergently from three lineages of ascomycetes producing flask-like fruiting bodies.

DNA, Fungal↗
PubMed1992

The selection of portal aperture using interactively displayed Beam's Eye Sections.

Portal apertures are often defined by wax-pencil lines drawn on simulator films. The simulator-film images suffer degradation due to X ray absorption and scatter in tissues proximal to and distal to the intended target volume. We describe a method for avoiding the degradation by using a 3-D dataset to produce high-contrast section images with a user-defined orientation. The calculation of these Beam's Eye Section (BES) images requires a set of medium-to high-resolution transverse section data (the 3-D dataset), as well as a medium- to high-performance computer workstation. These CT-like section images, providing more contrast and detail than a projection (that is, a simulator or Digitally Reconstructed Radiograph [DRR]) image, should allow for more accurate selection of portal apertures. The BES image plane is oriented perpendicular to the central axis of a user-selected beam. Once the user has created a beam, the system allows the user to step along that beam with a new BES image produced at each step. Contours manually drawn on these BES images are ultimately projected onto a DRR image. The outermost segments of these sometimes crisscrossing contours (the union of all projected areas) accurately defines the portal aperture needed to encompass the target at all levels.

Computer Simulation↗
PubMedDate not supplied

Computed tomography of the calvarium: a prospective study.

Retrospective analysis of high-resolution raw scanning data was prospectively applied in the evaluation of lesions of the scalp and the calvarium over a 12-month period. The spectrum of abnormalities identified and the impact of CT on both diagnosis and management of 25 patients are presented. Metastases and traumatic lesions were excluded. CT was useful in both diagnosis and subsequent patient management.

Adolescent↗