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High Resolution (high + resolution)
Kinds of High Resolution Terms modified by High Resolution Selected AbstractsApplication of mass spectrometry in the analysis of polybrominated diphenyl ethersMASS SPECTROMETRY REVIEWS, Issue 5 2010Dongli Wang Abstract This review summarized the applications of mass spectrometric techniques for the analysis of the important flame retardants polybrominated diphenyl ethers (PBDEs) to understand the environmental sources, fate and toxicity of PBDEs that were briefly discussed to give a general idea for the need of analytical methodologies. Specific performance of various mass spectrometers hyphenated with, for example, gas chromatograph, liquid chromatograph, and inductively coupled plasma (GC/MS, LC/MS, and ICP/MS, respectively) for the analysis of PBDEs was compared with an objective to present the information on the evolution of MS techniques for determining PBDEs in environmental and human samples. GC/electron capture negative ionization quadrupole MS (GC/NCI qMS), GC/high resolution MS (GC/HRMS) and GC ion trap MS (GC/ITMS) are most commonly used MS techniques for the determination of PBDEs. New analytical technologies such as fast tandem GC/MS and LC/MS become available to improve analyses of higher PBDEs. The development and application of the tandem MS techniques have helped to understand environmental fate and transformations of PBDEs of which abiotic and biotic degradation of decaBDE is thought to be one major source of Br1-9BDEs present in the environment in addition to direct loading from commercial mixtures. MS-based proteomics will offer an insight into the molecular mechanisms of toxicity and potential developmental and neurotoxicity of PBDEs. © 2009 Wiley Periodicals, Inc., Mass Spec Rev 29:737,775, 2010 [source] Fabrication of Active Horseradish Peroxidase Micropatterns with a High Resolution by Scanning Electrochemical MicroscopyELECTROANALYSIS, Issue 16 2007Xuemei Li Abstract We used a new reactive species OH, to fabricate active horseradish peroxidase (HRP) micropatterns with a high resolution by scanning electrochemical microscopy (SECM) coupled with a carbon fiber disk electrode as the SECM tip. In this method, except for active HRP micropatterns predesigned other regions on a HRP-immobilized substrate were deactivated by OH, generated at the tip held at ,1.7,V in 1.0,mol/L KCl containing 2.0×10,3 mol/L benzoquinone (BQ) (pH,8.0). The feedback mode of SECM with a tip potential of ,0.2,V was used to characterize the active HRP micropatterns in 1.0,mol/L KCl containing 2.0×10,3 mol/L BQ and 2.0×10,3 mol/L H2O2. [source] NMR Characterization of Complex p- Oligophenyl Scaffolds by Means of Aliasing Techniques to Obtain Resolution-Enhanced Two-Dimensional SpectraHELVETICA CHIMICA ACTA, Issue 9 2004Damien Jeannerat The usefulness of computer-assisted aliasing to secure maximal resolution of signal clusters in 1H- and 13C-NMR spectra (which is essential for structure determination by HMBC 2D NMR spectroscopy) in minimal acquisition time is exemplified by the complete characterization of the two complementary p -octiphenyls 1 and 2 with complex substitution patterns. The need for digital resolution near 1,Hz/pt to dissect the extensive signal clusters in the NMR spectra of these refined oligomers excluded structure determination under routine conditions. High resolution was secured by exploiting the low signal density in the 13C dimension of HMBC spectra by using computer-assisted aliasing to maximize signal density. Based on the observed shifts in DEPT and 1H-decoupled 13C-NMR spectra of 1 and 2, computer-assisted aliasing allowed to reduce the number of required time increments by a factor of 20 to 30 compared to full-width spectra with identical resolution. Without signal-to-noise constraints, this computer-assisted aliasing reduced the acquisition time for high-resolution NMR spectra needed for complete characterization of refined oligomers 1 and 2 by the same factor (e.g., from over a day to about an hour). With resolved signal clusters in fully aliased HSQC and HMBC spectra, unproblematic structure determination of 1 and 2 is demonstrated by unambiguous assignment of all C- and H-atoms. These findings demonstrate that computer-assisted aliasing of the underexploited 13C dimension makes extensive molecular complexity accessible by conventional multidimensional heteronuclear NMR experiments without extraordinary efforts. [source] High resolution in heteronuclear 1H,13C NMR experiments by optimizing spectral aliasing with one-dimensional carbon dataMAGNETIC RESONANCE IN CHEMISTRY, Issue 1 2003Damien Jeannerat Abstract In the chemistry literature it is common to provide NMR data on both proton and carbon spectra based on one-dimensional experiments, but often only proton spectra are assigned. The absence of a complete attribution of the carbons is in good part due to the difficulty in reaching the necessary resolution in the carbon dimension of two-dimensional experiments. It has already been shown that high-resolution heteronuclear spectra can be acquired within nearly the same acquisition time using a violation of the Nyquist condition. For a spectral width reduction by a given factor k, the resolution increases by the same factor as long as it is not limited by relaxation. The price to pay for such an improvement is a k -fold ambiguity in the chemical shift of the signal along the folded or aliased dimension. The computer algorithm presented in this paper takes advantage of the peak list stemming from one-dimensional spectra in order to calculate spectral widths for which the ambiguities in the aliased dimension of heteronuclear experiments are eliminated or at least minimized. The resolution improvement factor is only limited by the natural lineshape and reaches a typical value higher than 100. The program may be set to run automatically on spectrometers equipped with automatic sample changers. Applications to short-range HSQC experiments and long-range HMBC spectra of steroids, carbohydrates, a peptide and a mixture of isomers are shown as examples. Copyright © 2002 John Wiley & Sons, Ltd. [source] High resolution in z -direction: The simulation of disc-bulge-halo galaxies using the particle-mesh code SUPERBOXASTRONOMISCHE NACHRICHTEN, Issue 9-10 2008R. Bien Abstract SUPERBOX is known as a very efficient particle-mesh code with highly-resolving sub-grids. Nevertheless, the height of a typical galactic disc is small compared to the size of the whole system. Consequently, the numerical resolution in z direction, i. e. vertically with respect to the plane of the disc, remains poor. Here, we present a new version of SUPERBOX that allows for a considerably higher resolution along z. The improved code is applied to investigate disc heating by the in-fall of a galaxy satellite. We describe the improvement and communicate our results. As an important application we discuss the disruption of a dwarf galaxy within a disc-bulge-halo galaxy that consists of some 106 particles. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Synthesis of chiral vicinal diols and analysis of them by capillary zone electrophoresisCHIRALITY, Issue 2 2008Peng Liu Abstract This paper describes an improved access to 1,4-bis (9- O -quininyl) phthalazine [(QN)2PHAL], a very useful chiral ligand for catalytic asymmetric dihydroxylation (AD), by using CaH2 as acid-binding reagent in a high yield under mild conditions. The application of (QN)2PHAL to the AD reactions of eight olefins exhibited excellent enantioselectivity and activity with corresponding chiral vicinal diols. Furthermore, a capillary zone electrophoresis method was developed to separate the aforementioned chiral vicinal diols by using of neutral ,-cyclodextrin (,-CD) as chiral selector and borate as running buffer. High resolution was achieved under the optimal conditions of ,-CD 2.2% (w/v), pH 10, 200 mM borate buffer at 15 kV, and 20°C within 15 min. The relative standard deviations of the corrected peak areas and migration time were less than 3.9% and 1.3%, respectively. In addition, the developed method was successfully applied to the determination of the purity and the enantiomeric excesses value (%ee) of the AD reaction products. Chirality, 2008. © 2007 Wiley-Liss, Inc. [source] A robust cross-linked polyacrylamide coating for microchip electrophoresis of dsDNA fragmentsELECTROPHORESIS, Issue 19 2006Joann J. Lu Abstract Surface derivatization plays an important role in microchip electrophoresis. It not only enhances the resolution, but also improves the reproducibility. So far, the most popularly used derivatization method for glass microchannels is to covalently attach a layer of linear polyacrylamide,(LPA) to the channel surfaces. However, LPA coating has two problems: incomplete coverage and limited lifetime. To address these issues, we have recently developed a cross-linked polyacrylamide,(CPA) derivatization protocol and demonstrated it for high-resolution protein separations by CIEF, CGE, and CZE. In this report, we used this protocol to coat microchip channels and exhibited the reliability and robustness of CPA coating for microchip electrophoresis of DNA molecules. dsDNA fragments were used as our test samples. High resolutions were obtained for fragments ranging from 100,bp to 10,kpb. After more than 800,runs, the CPA-coated microchannels still performed well and comparable resolutions were maintained throughout these runs. [source] Using pulsed gradient spin echo NMR for chemical mixture analysis: How to obtain optimum resultsCONCEPTS IN MAGNETIC RESONANCE, Issue 4 2002Brian Antalek Abstract Pulsed gradient spin echo NMR is a powerful technique for measuring diffusion coefficients. When coupled with appropriate data processing schemes, the technique becomes an exceptionally valuable tool for mixture analysis, the separation of which is based on the molecular size. Extremely fine differentiation may be possible in the diffusion dimension but only with high-quality data. For fully resolved resonances, components with diffusion coefficients that differ by less than 2% may be distinguished in mixtures. For highly overlapped resonances, the resolved spectra of pure components with diffusion coefficients that differ by less than 30% may be obtained. In order to achieve the best possible data quality one must be aware of the primary sources of artifacts and incorporate the necessary means to alleviate them. The origin of these artifacts are described, along with the methods necessary to observe them. Practical solutions are presented. Examples are shown that demonstrate the effects of the artifacts on the acquired data set. Many mixture analysis problems may be addressed with conventional high resolution pulsed field gradient probe technology delivering less than 0.5 T m,1 (50 G cm,1). © 2002 Wiley Periodicals, Inc. Concepts Magn Reson 14: 225,258, 2002. [source] What drives cell morphogenesis: A look inside the vertebrate photoreceptorDEVELOPMENTAL DYNAMICS, Issue 9 2009Breandán Kennedy Abstract Vision mediating photoreceptor cells are specialized light-sensitive neurons in the outer layer of the vertebrate retina. The human retina contains approximately 130 million of such photoreceptors, which enable images of the external environment to be captured at high resolution and high sensitivity. Rod and cone photoreceptor subtypes are further specialized for sensing light in low and high illumination, respectively. To enable visual function, these photoreceptors have developed elaborate morphological domains for the detection of light (outer segments), for changing cell shape (inner segments), and for communication with neighboring retinal neurons (synaptic terminals). Furthermore, rod and cone subtypes feature unique morphological variations of these specialized characteristics. Here, we review the major aspects of vertebrate photoreceptor morphology and key genetic mechanisms that drive their formation. These mechanisms are necessary for cell differentiation as well as function. Their defects lead to cell death. Developmental Dynamics 238:2115,2138, 2009. © 2009 Wiley-Liss, Inc. [source] MR imaging methods for assessing fetal brain developmentDEVELOPMENTAL NEUROBIOLOGY, Issue 6 2008Mary Rutherford Abstract Fetal magnetic resonance imaging provides an ideal tool for investigating growth and development of the brain in vivo. Current imaging methods have been hampered by fetal motion but recent advances in image acquisition can produce high signal to noise, high resolution 3-dimensional datasets suitable for objective quantification by state of the art post acquisition computer programs. Continuing development of imaging techniques will allow a unique insight into the developing brain, more specifically process of cell migration, axonal pathway formation, and cortical maturation. Accurate quantification of these developmental processes in the normal fetus will allow us to identify subtle deviations from normal during the second and third trimester of pregnancy either in the compromised fetus or in infants born prematurely. © 2008 Wiley Periodicals, Inc. Develop Neurobiol, 2008 [source] Empirical prediction of debris-flow mobility and deposition on fansEARTH SURFACE PROCESSES AND LANDFORMS, Issue 2 2010Christian Scheidl Abstract A new method to predict the runout of debris flows is presented. A data base of documented sediment-transporting events in torrent catchments of Austria, Switzerland and northern Italy has been compiled, using common classification techniques. With this data we test an empirical approach between planimetric deposition area and event volume, and compare it with results from other studies. We introduce a new empirical relation to determine the mobility coefficient as a function of geomorphologic catchment parameters. The mobility coefficient is thought to reflect some of the flow properties during the depositional part of the debris-flow event. The empirical equations are implemented in a geographical information system (GIS) based simulation program and combined with a simple flow routing algorithm, to determine the potential runout area covered by debris-flow deposits. For a given volume and starting point of the deposits, a Monte-Carlo technique is used to produce flow paths that simulate the spreading effect of a debris flow. The runout zone is delineated by confining the simulated potential spreading area in the down slope direction with the empirically determined planimetric deposition area. The debris-flow volume is then distributed over the predicted area according to the calculated outflow probability of each cell. The simulation uses the ARC-Objects environment of ESRI© and is adapted to run with high resolution (2·5,m × 2·5,m) digital elevation models, generated for example from LiDAR data. The simulation program called TopRunDF is tested with debris-flow events of 1987 and 2005 in Switzerland. Copyright © 2009 John Wiley & Sons, Ltd. [source] Macro,micro analysis method for wave propagation in stochastic mediaEARTHQUAKE ENGINEERING AND STRUCTURAL DYNAMICS, Issue 4 2006T. Ichimura Abstract This paper presents a new analysis method, called macro,micro analysis method (MMAM) for numerical simulation of wave propagation in stochastic media, which could be used to predict distribution of earthquake strong motion with high accuracy and spatial resolution. This MMAM takes advantage of the bounding medium theory (BMT) and the singular perturbation expansion (SPE). BMT can resolve uncertainty of soil and crust structures by obtaining optimistic and pessimistic estimates of expected strong motion distribution. SPE leads to efficient multi-scale analysis for reducing a huge amount of computation. The MMAM solution is given as the sum of waves of low resolution covering a whole city and waves of high resolution for each city portion. This paper presents BMT and SPE along with the formulation of MMAM for wave propagation in three-dimensional elastic media. Application examples are presented to verify the validity of the MMAM and demonstrate potential usefulness of this approach. In a companion paper (Earthquake Engng. Struct. Dyn., this issue) application examples of earthquake strong motion prediction are also presented. Copyright © 2005 John Wiley & Sons, Ltd. [source] Fabrication of Active Horseradish Peroxidase Micropatterns with a High Resolution by Scanning Electrochemical MicroscopyELECTROANALYSIS, Issue 16 2007Xuemei Li Abstract We used a new reactive species OH, to fabricate active horseradish peroxidase (HRP) micropatterns with a high resolution by scanning electrochemical microscopy (SECM) coupled with a carbon fiber disk electrode as the SECM tip. In this method, except for active HRP micropatterns predesigned other regions on a HRP-immobilized substrate were deactivated by OH, generated at the tip held at ,1.7,V in 1.0,mol/L KCl containing 2.0×10,3 mol/L benzoquinone (BQ) (pH,8.0). The feedback mode of SECM with a tip potential of ,0.2,V was used to characterize the active HRP micropatterns in 1.0,mol/L KCl containing 2.0×10,3 mol/L BQ and 2.0×10,3 mol/L H2O2. [source] Cationic and anionic lipid-based nanoparticles in CEC for protein separationELECTROPHORESIS, Issue 11 2010Christian Nilsson Abstract The development of new separation techniques is an important task in protein science. Herein, we describe how anionic and cationic lipid-based liquid crystalline nanoparticles can be used for protein separation. The potential of the suggested separation methods is demonstrated on green fluorescent protein (GFP) samples for future use on more complex samples. Three different CEC-LIF approaches for protein separation are described. (i) GFP and GFP N212Y, which are equally charged, were separated with high resolution by using anionic nanoparticles suspended in the electrolyte and adsorbed to the capillary wall. (ii) High efficiency (800,000 plates/m) and peak capacity were demonstrated separating GFP samples from Escherichia coli with cationic nanoparticles suspended in the electrolyte and adsorbed to the capillary wall. (iii) Three single amino-acid-substituted GFP variants were separated with high resolution using an approach based on a physical attached double-layer coating of cationic and anionic nanoparticles combined with anionic lipid nanoparticles suspended in the electrolyte. The soft and porous lipid-based nanoparticles were synthesized by a one-step procedure based on the self-assembly of lipids, and were biocompatible with a large surface-to-volume ratio. The methodology is still under development and the optimization of the nanoparticle chemistry and separation conditions can further improve the separation system. In contrast to conventional LC, a new interaction phase is introduced for every analysis, which minimizes carry-over and time-consuming column regeneration. [source] Two-dimensional protein separation in microfluidic devicesELECTROPHORESIS, Issue 5 2009Hong Chen Abstract Proteomics is emerging as an important tool in modern drug discoveries and medical diagnostics. One of the techniques used in proteomics studies is 2-DE. The process of the conventional 2-DE is time-consuming and it has substandard reproducibility. Many efforts have been made to address the limitations, with an aim for fast separation and high resolution. In this paper, we reviewed the work on achieving 2-DE in microfluidic devices, including individual dimension in one channel, two dimensions in two intersected channels, and 2-D separation in a large number of channels. We also discussed the need for integrating microvalves within 2-DE devices to prevent different separation media from contaminating with each other. Although more efforts are required to match the performance of conventional 2-DE in a slab gel, microfluidics-based 2-D separation has a potential to become an alternative in the future. [source] Sodium dodecyl sulfate-capillary gel electrophoresis of polyethylene glycolylated interferon alphaELECTROPHORESIS, Issue 3 2004Dong H. Na Abstract Sodium dodecyl sulfate-capillary gel electrophoresis (SDS-CGE) using a hydrophilic replaceable polymer network matrix was applied to characterize the polyethylene glycol(PEG)ylated interferon alpha (PEG-IFN). The SDS-CGE method resulted in a clearer resolution in both the PEG-IFN species and the native IFN species. The distribution profile of PEGylation determined by SDS-CGE was consistent with that obtained by SDS-polyacrylamide gel electrophoresis (PAGE) with Coomassie blue or barium iodide staining. The result was also compared using matrix-assisted laser desorption/ionization-time of flight-mass spectrometry. SDS-CGE was also useful for monitoring the PEGylation reaction to optimize the reaction conditions, such as reaction molar ratio. This study shows the potential of SDS-CGE as a new method for characterizing the PEGylated proteins with advantages of speed, minimal sample consumption and high resolution. [source] Enantioseparation of warfarin and its metabolites by capillary zone electrophoresisELECTROPHORESIS, Issue 15 2003Qingyu Zhou Abstract A capillary zone electrophoresis (CZE) method with direct ultraviolet (UV)-absorbance detection is presented for the simultaneous enantiomeric separation of warfarin and its main metabolites, including warfarin alcohols, 4'-, 6-, and 7-hydroxywarfarin, using highly sulfated ,-cyclodextrin (HS-,-CD) as the chiral selector. This chiral separation method was optimized in terms of the electrophoretic parameters, which included the concentration of HS-,-CD used, the type and composition of organic modifier added to the background electrolyte (BGE) buffer, and the BGE buffer pH. Chiral separation of warfarin and its major metabolites was achieved with high resolution, selectivity, efficiency, repeatability, and reproducibility. This optimized chiral analysis of warfarin along with its metabolites was completed within a satisfactory electrophoresis time of 20 min. [source] Direct chiral resolution of tartaric acid by ion-pair capillary electrophoresis using an aqueous background electrolyte with (1R,2R)-(,)-1,2-diaminocyclohexane as a chiral counterionELECTROPHORESIS, Issue 15 2003Shuji Kodama Abstract Chiral resolution of native DL -tartaric acid was achieved by ion-pair capillary electrophoresis (CE) using an aqueous-ethanol background electrolyte with (1R,2R)-(,)-1,2-diaminocyclohexane (R -DACH) as a chiral counterion. Factors affecting chiral resolution and migration time of tartaric acid were studied. By increasing the viscosity of the background electrolyte and the ion-pair formation, using organic solvents with a lower relative dielectric constant, resulted in a longer migration time. The optimum conditions for both high resolution and short migration time of tartaric acid were found to be a mixture of 65% v/v ethanol and 35% v/v aqueous solution containing 30 mMR -DACH and 75 mM phosphoric acid (pH 5.1) with an applied voltage of ,30 kV at 25°C, using direct detection at 200 nm. By using this system, the resolution (Rs) of racemic tartaric acid was approximately 1. The electrophoretic patterns of tartaric and malic acids suggest that two carboxyl groups and two hydroxyl groups of tartaric acid are associated with the enantioseparation of tartaric acid by the proposed CE method. [source] Plasticity and Grain Boundary Diffusion at Small Grain Sizes,ADVANCED ENGINEERING MATERIALS, Issue 8 2010Gerhard Wilde Bulk nanostructured,or ultrafine-grained materials are often fabricated by severe plastic deformation to break down the grain size by dislocation accumulation. Underlying the often spectacular property enhancement that forms the basis for a wide range of potential applications is a modification of the volume fraction of the grain boundaries. Yet, along with the property enhancements, several important questions arise concerning the accommodation of external stresses if dislocation-based processes are not longer dominant at small grain sizes. One question concerns so-called "non-equilibrium" grain boundaries that have been postulated to form during severe deformation and that might be of importance not only for the property enhancement known already today, but also for spectacular applications in the context of, e.g., gas permeation or fast matter transport for self-repairing structures. This contribution addresses the underlying issues by combining quantitative microstructure analysis at high resolution with grain boundary diffusion measurements. [source] Microstructural Characterization of Lamellar Features in TiAl by FIB Imaging,ADVANCED ENGINEERING MATERIALS, Issue 6 2010Dennis Peter A novel experimental procedure is introduced to determine phase fractions and the distribution of individual phases of TiAl-based two-phase alloys using the focused ion beam (FIB) technique. Two , -titanium aluminide alloys with a fine-grained duplex and a nearly lamellar microstructure are examined. The special FIB-based preparation procedure results in high contrast ion beam-induced images for all investigated alloys and allows to quantify the phase contents easily by automated microstructural analysis. Fine two-phase structures, e.g. lamellar colonies in , -TiAl, can be imaged in high resolution with respect to different phases. To validate the FIB-derived data, we compare them to results obtained with another method to determine phase fractions, electron back-scatter diffraction (EBSD). This direct comparison shows that the FIB-based technique generally provides slightly higher ,2 -fractions, and thus helps to overcome the limited lateral resolution near grain boundaries and interfaces associated with the conventional EBSD approach. Our study demonstrates that the FIB-based technique is a simple, fast, and more exact way to determine high resolution microstructural characteristics with respect to different phase constitutions in two-phase TiAl alloys and other such materials with fine, lamellar microstructures. [source] Sensitivity of multi-coil frequency domain electromagnetic induction sensors to map soil magnetic susceptibilityEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 4 2010D. Simpson Magnetic susceptibility is an important indicator of anthropogenic disturbance in the natural soil. This property is often mapped with magnetic gradiometers in archaeological prospection studies. It is also detected with frequency domain electromagnetic induction (FDEM) sensors, which have the advantage that they can simultaneously measure the electrical conductivity. The detection level of FDEM sensors for magnetic structures is very dependent on the coil configuration. Apart from theoretical modelling studies, a thorough investigation with field models has not been conducted until now. Therefore, the goal of this study was to test multiple coil configurations on a test field with naturally enhanced magnetic susceptibility in the topsoil and with different types of structures mimicking real archaeological features. Two FDEM sensors were used with coil separations between 0.5 and 2 m and with three coil orientations. First, a vertical sounding was conducted over the undisturbed soil to test the validity of a theoretical layered model, which can be used to infer the depth sensitivity of the coil configurations. The modelled sounding values corresponded well with the measured data, which means that the theoretical models are applicable to layered soils. Second, magnetic structures were buried in the site and the resulting anomalies measured to a very high resolution. The results showed remarkable differences in amplitude and complexity between the responses of the coil configurations. The 2-m horizontal coplanar and 1.1-m perpendicular coil configurations produced the clearest anomalies and resembled best a gradiometer measurement. [source] Fabrication of Al2O3/SiC Composite Microcomponents using Non-aqueous Suspension,ADVANCED ENGINEERING MATERIALS, Issue 1-2 2009Hany Hassanin This paper introduces a new process for fabrication of high resolution Al2O3/SiC composite microcomponents using softlithography and non-aqueous ceramic suspension. Polysilazane is used to provide both binding force and SiC composition. The shape retention and dimensions of the microcomponents were analyzed using a scanning electron microscope. Surface roughness, shrinkage, and density of the resultant sintered components were also discussed. [source] Structure of the HIV-1 Rev response element alone and in complex with regulator of virion (Rev) studied by atomic force microscopyFEBS JOURNAL, Issue 15 2009Jesper Pallesen The interaction of multiple HIV-1 regulator of virion (Rev) proteins with the viral RNA target, the Rev response element (RRE), is critical for nuclear export of incompletely spliced and unspliced viral RNA, and for the onset of the late phase in the viral replication cycle. The heterogeneity of the Rev,RRE complex has made it difficult to study using conventional structural methods. In the present study, atomic force microscopy is applied to directly visualize the tertiary structure of the RRE RNA alone and in complex with Rev proteins. The appearance of the RRE is compatible with the earlier proposed RRE secondary structure in dimensions and overall shape, including a stalk and a head interpreted as stem I, and stem-loops II,V in the secondary structure model, respectively. Atomic force microscopy imaging of the Rev,RRE complex revealed an increased height of the structure both in the stalk and head regions, which is in accordance with a binding model in which Rev binding to a high affinity site in stem IIB triggers oligomerization of Rev proteins through cooperative binding along stem I in RRE. The present study demonstrates that atomic force microscopy comprises a useful technique to study complex biological structures of nucleic acids at high resolution. [source] TICL , a web tool for network-based interpretation of compound lists inferred by high-throughput metabolomicsFEBS JOURNAL, Issue 7 2009Alexey V. Antonov High-throughput metabolomics is a dynamically developing technology that enables the mass separation of complex mixtures at very high resolution. Metabolic profiling has begun to be widely used in clinical research to study the molecular mechanisms of complex cell disorders. Similar to transcriptomics, which is capable of detecting genes at differential states, metabolomics is able to deliver a list of compounds differentially present between explored cell physiological conditions. The bioinformatics challenge lies in a statistically valid interpretation of the functional context for identified sets of metabolites. Here, we present TICL, a web tool for the automatic interpretation of lists of compounds. The major advance of TICL is that it not only provides a model of possible compound transformations related to the input list, but also implements a robust statistical framework to estimate the significance of the inferred model. The TICL web tool is freely accessible at http://mips.helmholtz-muenchen.de/proj/cmp. [source] The role of group bulkiness in the catalytic activity of psychrophile cold-active protein tyrosine phosphataseFEBS JOURNAL, Issue 17 2008Hiroki Tsuruta The cold-active protein tyrosine phosphatase found in psychrophilic Shewanella species exhibits high catalytic efficiency at low temperatures as well as low thermostability, both of which are characteristics shared by many cold-active enzymes. The structure of cold-active protein tyrosine phosphatase is notable for the presence of three hydrophobic sites (termed the CA, Zn-1 and Zn-2 sites) behind the loop structures comprising the catalytic region. To identify the structural components responsible for specific enzyme characteristics, we determined the structure of wild-type cold-active protein tyrosine phosphatase at high resolution (1.1 Ĺ) and measured the catalytic efficiencies of enzymes containing mutations in the three hydrophobic sites. The bulkiness of the amino acid side chains in the core region of the Zn-1 site strongly affects the thermostability and the catalytic efficiency at low temperatures. The mutant enzyme I115M possessed a higher kcat at low temperatures. Elucidation of the crystal structure of I115M at a resolution of 1.5 Ĺ revealed that the loop structures involved in retaining the nucleophilic group and the acid catalyst are more flexible than in the wild-type enzyme. [source] Structural evidence for a constant c11 ring stoichiometry in the sodium F-ATP synthaseFEBS JOURNAL, Issue 21 2005Thomas Meier The Na+ -dependent F-ATP synthases of Ilyobacter tartaricus and Propionigenium modestum contain membrane-embedded ring-shaped c subunit assemblies with a stoichiometry of 11. Subunit c from either organism was overexpressed in Escherichia coli using a plasmid containing the corresponding gene, extracted from the membrane using detergent and then purified. Subsequent analyses by SDS/PAGE revealed that only a minor portion of the c subunits had assembled into stable rings, while the majority migrated as monomers. The population of rings consisted mainly of c11, but more slowly migrating assemblies were also found, which might reflect other c ring stoichiometries. We show that they consisted of higher aggregates of homogeneous c11 rings and/or assemblies of c11 rings and single c monomers. Atomic force microscopy topographs of c rings reconstituted into lipid bilayers showed that the c ring assemblies had identical diameters and that stoichiometries throughout all rings resolved at high resolution. This finding did not depend on whether the rings were assembled into crystalline or densely packed assemblies. Most of these rings represented completely assembled undecameric complexes. Occasionally, rings lacking a few subunits or hosting additional subunits in their cavity were observed. The latter rings may represent the aggregates between c11 and c1, as observed by SDS/PAGE. Our results are congruent with a stable c11 ring stoichiometry that seems to not be influenced by the expression level of subunit c in the bacteria. [source] Functional properties of the protein disulfide oxidoreductase from the archaeon Pyrococcus furiosusFEBS JOURNAL, Issue 16 2004A member of a novel protein family related to protein disulfide-isomerase Protein disulfide oxidoreductases are ubiquitous redox enzymes that catalyse dithiol,disulfide exchange reactions with a CXXC sequence motif at their active site. A disulfide oxidoreductase, a highly thermostable protein, was isolated from Pyrococcus furiosus (PfPDO), which is characterized by two redox sites (CXXC) and an unusual molecular mass. Its 3D structure at high resolution suggests that it may be related to the multidomain protein disulfide-isomerase (PDI), which is currently known only in eukaryotes. This work focuses on the functional characterization of PfPDO as well as its relation to the eukaryotic PDIs. Assays of oxidative, reductive, and isomerase activities of PfPDO were performed, which revealed that the archaeal protein not only has oxidative and reductive activity, but also isomerase activity. On the basis of structural data, two single mutants (C35S and C146S) and a double mutant (C35S/C146S) of PfPDO were constructed and analyzed to elucidate the specific roles of the two redox sites. The results indicate that the CPYC site in the C-terminal half of the protein is fundamental to reductive/oxidative activity, whereas isomerase activity requires both active sites. In comparison with PDI, the ATPase activity was tested for PfPDO, which was found to be cation-dependent with a basic pH optimum and an optimum temperature of 90 °C. These results and an investigation on genomic sequence databases indicate that PfPDO may be an ancestor of the eukaryotic PDI and belongs to a novel protein disulfide oxidoreductase family. [source] High resolution X-ray analysis of two mutants of a curaremimetic snake toxinFEBS JOURNAL, Issue 5 2000Jean-François Gaucher A previous mutational analysis of erabutoxin a (Ea), a curaremimetic toxin from sea snake venom, showed that the substitutions S8G and S8T caused, respectively, 176-fold and 780-fold affinity decreases for the nicotinic acetylcholine receptor (AchR). In view of the fact that the side-chain of Ser8 is buried in the wild-type toxin, we wondered whether these affinity changes reflect a direct binding contribution of S8 to the receptor and/or conformational changes that could have occurred in Ea as a result of the introduced mutations. To approach this question, we solved X-ray structures of the two mutants S8G and S8T at high resolution (0.18 nm and 0.17 nm, with R factors of 18.0% and 17.9%, respectively). The data show that none of the mutations significantly modified the toxin structure. Even within the site where the toxin binds to the receptor the backbone conformation remained unchanged. Therefore, the low affinities of the mutants S8T and S8G cannot be explained by a large conformational change of the toxin structure. Although we cannot exclude the possibility that undetectable structural changes have occurred in the toxin mutants, our data support the view that, although buried between loop I and II, S8 is part of the functional epitope of the toxin. [source] Pattern Formation of Silver Nanoparticles in 1-, 2-, and 3D Microstructures Fabricated by a Photo- and Thermal Reduction MethodADVANCED FUNCTIONAL MATERIALS, Issue 14 2010Jong-Jin Park Abstract One-, two-, and three-dimensional microstructures with dispersed silver nanoparticles are fabricated by a combination of photopatterning and thermal treatment from a silver salt containing photosensitive epoxy resin. Ultraviolet photo-irradiation and subsequent thermal treatment are combined to control the rate of silver salt reduction, the size and the arrangement of nanoparticles, as well as the reticulation of the epoxy resin. This approach allows the creation of high resolution 1-, 2-, and 3D patterns containing silver nanoparticles, with a homogeneous distribution of nanoparticles regardless of the irradiated area. [source] Molecular typing of meningococci: recommendations for target choice and nomenclatureFEMS MICROBIOLOGY REVIEWS, Issue 1 2007Keith A. Jolley Abstract The diversity and dynamics of Neisseria meningitidis populations generate a requirement for high resolution, comprehensive, and portable typing schemes for meningococcal disease surveillance. Molecular approaches, specifically DNA amplification and sequencing, are the methods of choice for various reasons, including: their generic nature and portability, comprehensive coverage, and ready implementation to culture negative clinical specimens. The following target genes are recommended: (1) the variable regions of the antigen-encoding genes porA and fetA and, if additional resolution is required, the porB gene for rapid investigation of disease outbreaks and investigating the distribution of antigenic variants; (2) the seven multilocus sequence typing loci,these data are essential for the most effective national, and international management of meningococcal disease, as well as being invaluable in studies of meningococcal population biology and evolution. These targets have been employed extensively in reference laboratories throughout the world and validated protocols have been published. It is further recommended that a modified nomenclature be adopted of the form: serogroup: PorA type: FetA type: sequence type (clonal complex), thus: B: P1.19,15: F5-1: ST-33 (cc32). [source] | |||||||||||||||||||||||||||||||||||||||||||||||||