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PubMed1995

A biosensor concept based on imaging ellipsometry for visualization of biomolecular interactions.

A new type of optical biosensor system is proposed and its application to detection of antigen-antibody complexes on a silicon substrate is demonstrated. The biosensor system is utilizing specificities of biomolecular interactions in combination with protein patterned surfaces. Visualization of the thickness distributions of thin layers (protein patterns) on a surface is achieved by using imaging ellipsometry. This technique uses a CCD camera whereby an ellipsometric analysis of a large surface can be made. The biosensor system has the advantages of high spatial resolution, fast data acquisition, and simplicity in use.

Adsorption↗

PubMed1999

Transcription elongation: structural basis and mechanisms.

A ternary complex composed of RNA polymerase (RNAP), DNA template, and RNA transcript is the central intermediate in the transcription cycle responsible for the elongation of the RNA chain. Although the basic biochemistry of RNAP functioning is well understood, little is known about the underlying structural determinants. The absence of high- resolution structural data has hampered our understanding of RNAP mechanism. However, recent work suggests a structure-function model of the ternary elongation complex, if not at a defined structural level, then at least as a conceptual view, such that key components of RNAP are defined operationally on the basis of compelling biochemical, protein chemical, and genetic data. The model has important implications for mechanisms of transcription elongation and also for initiation and termination.

Bacterial Proteins↗

PubMed1999

Structure, dynamics and hydration of the nogalamycin-d(ATGCAT)2Complex determined by NMR and molecular dynamics simulations in solution.

The structure of the 1:1 nogalamycin:d(ATGCAT)2 complex has been determined in solution from high-resolution NMR data and restrained molecular dynamics (rMD) simulations using an explicit solvation model. The antibiotic intercalates at the 5'-TpG step with the nogalose lying along the minor groove towards the centre of the duplex. Many drug-DNA nuclear Overhauser enhancements (NOEs) in the minor groove are indicative of hydrophobic interactions over the TGCA sequence. Steric occlusion prevents a second nogalamycin molecule from binding at the symmetry-related 5'-CpA site, leading to the conclusion that the observed binding orientation in this complex is the preferred orientation free of the complication of end-effects (drug molecules occupy terminal intercalation sites in all X-ray structures) or steric interactions between drug molecules (other NMR structures have two drug molecules bound in close proximity), as previously suggested. Fluctuations in key structural parameters such as rise, helical twist, slide, shift, buckle and sugar pucker have been examined from an analysis of the final 500 ps of a 1 ns rMD simulation, and reveal that many sequence-dependent structural features previously identified by comparison of different X-ray structures lie within the range of dynamic fluctuations observed in the MD simulations. Water density calculations on MD simulation data reveal a time-averaged pattern of hydration in both the major and minor groove, in good agreement with the extensive hydration observed in two related X-ray structures in which nogalamycin is bound at terminal 5'-TpG sites. However, the pattern of hydration determined from the sign and magnitude of NOE and ROE cross-peaks to water identified in 2D NOESY and ROESY experiments identifies only a few "bound" water molecules with long residence times. These solvate the charged bicycloaminoglucose sugar ring, suggesting an important role for water molecules in mediating drug-DNA electrostatic interactions within the major groove. The high density of water molecules found in the minor groove in X-ray structures and MD simulations is found to be associated with only weakly bound solvent in solution.

Base Sequence↗

PubMed2001

The 1.2 A resolution structure of the Con A-dimannose complex.

The complex between concanavalin A (Con A) and alpha1-2 mannobiose (mannose alpha1-2 mannose) has been refined to 1.2 A resolution. This is the highest resolution structure reported for any sugar-lectin complex. As the native structure of Con A to 0.94 A resolution is already in the database, this gives us a unique opportunity to examine sugar-protein binding at high resolution. These data have allowed us to model a number of hydrogen atoms involved in the binding of the sugar to Con A, using the difference density map to place the hydrogen atoms. This map reveals the presence of the protonated form of Asp208 involved in binding. Asp208 is not protonated in the 0.94 A native structure. Our results clearly show that this residue is protonated and hydrogen bonds to the sugar. The structure accounts for the higher affinity of the alpha1-2 linked sugar when compared to other disaccharides. This structure identifies different interactions to those predicted by previous modelling studies. We believe that the additional data presented here will enable significant improvements to be made to the sugar-protein modelling algorithms.

Concanavalin A↗

PubMed1995

Mapping the spin-density and lineshape distribution of free radicals using 4D spectral-spatial EPR imaging.

The development and application of four-dimensional spectral-spatial electron paramagnetic resonance imaging (EPRI) techniques for unambiguous determination of spectral shape and spin distribution of paramagnetic samples are described. Strategies for optimizing acquisition and computation times, image resolution, and data presentation are described. The feasibility of studying small linewidth differences of approximately 0.1 G in samples of up to 25 mm in size was tested by computer simulations and by measurements on phantoms containing 0.5 mM nitroxide spin label. One thousand projections were used to reconstruct 32 x 32 x 32 x 32 pixel images. Similar 4D imaging experiments were performed on an isolated rat heart infused with a suspension of glucose char. The 4D image of the rat heart clearly showed the three-dimensional spatial structure of the heart and the spectral shape at each spatial point. Thus, we have demonstrated, for the first time, that 4D spectral-spatial EPRI could be performed on lossy biological samples or tissues at L-band frequencies, enabling the mapping of spectral information over the entire three-dimensional spatial structure of the object.

Animals↗

PubMed1997

The High-Resolution Infrared Spectrum of the nu1/2nu2 Fermi Dyad Bands of COF2

High-resolution FTIR data of carbonyl fluoride in the region of the C-O stretch nu1 fundamental have been analyzed. Satisfactory interpretation of the spectral data required a rigorous analysis that involved the inclusion of Fermi resonance with the 2nu2 state and Coriolis interaction with the 2nu3 + nu6 dark state. Deperturbed molecular constants for the three interacting states as well as perturbation parameters that fit the data within the limits of the experimental accuracy of approximately 0.00035 cm-1 have been obtained. Interesting evidence of "axis interchange" in the 2nu2 state has been observed. Copyright 1997 Academic Press. Copyright 1997Academic Press

Journal Article↗

PubMed2001

The X(1)(2)Pi(3/2) and X(2)(2)Pi(1/2) Potential Energy Surfaces of FO.

The X(1)(2)Pi(3/2) and X(2)(2)Pi(1/2) potential energy curves of the FO free radical have been determined from a fit to the available high-resolution spectroscopic data. The data set spans the vibrational states v = 0-7 and includes X(2)(2)Pi(1/2) <-- X(1)(2)Pi(3/2) fine-structure transitions. The determinable spectroscopic constants provide an excellent description of the equilibrium properties of both the X(1) and X(2) states in addition to the vibrational dependence of the spin-orbit coupling constant. The experimental properties of FO are used to evaluate the performance of different ab initio methods for describing the F-O bond. Copyright 2001 Academic Press.

Journal Article↗

PubMedDate not supplied

4-A projection map of bacteriophage T4 DNA helix-destabilizing protein (gp32*I) crystal by 400-kV electron cryomicroscopy.

Ice-embedded crystals of bacteriophage T4 DNA helix-destabilizing protein gp32*I were imaged by computer-controlled spot-scanning on a 400-kV electron cryomicroscope. gp32*I crystals generally have different steps of thickness within a crystal; each step can have different symmetry. Multivariate statistical analysis enabled us to unambiguously select spot-scan images that consist entirely of one motif which were processed subsequently by crystallographic Fourier-averaging techniques. The computed phases of the resulting reflections were evaluated for symmetry in projection, and some of those images were correlated with independent thickness measurements of freeze-dried samples of the same crystals. The structure factors with pgg symmetry from nine spot-scan images were merged, and the mean figure of merit of merged phases was better than 0.9 for data at resolution up to 4 A. A projection map was generated and showed multiple density peaks that corresponded to the high-resolution features of gp32*I.

Bacteriophage T4↗

PubMed1997

Crystallization and preliminary X-ray studies of two serine proteinase inhibitors, BGIA and BGIT, from the seeds of bitter gourd.

Two serine proteinase inhibitors from seeds of the bitter gourd, BGIA (bitter gourd inhibitor against acidic amino acid-specific proteinase of Streptomyces griseus) and BGIT (bitter gourd trypsin inhibitor), were crystallized for X-ray structure determination. Crystals of BGIA belong to the monoclinic space group C2 with cell dimensions of a = 54.0 A, b = 23.7 A, c = 47.9 A, and beta = 105.4 degrees, and diffracted X-ray up to 1.5 A resolution. Crystals of BGIT belong to the triclinic space group P1 with cell dimensions of a = 22.8 A, b = 23.5 A, c = 28.4 A, alpha = 93.1 degrees, beta = 99.6 degrees, and gamma = 101.0 degrees, giving X-ray diffraction of over 1.2 A resolution. Intensity data of BGIA and BGIT crystals were collected using synchrotron radiation up to 1.7 and 1.4 A, respectively.

Crystallization↗

PubMed2005

Inter-breath-hold registration for the production of high resolution cardiac MR volumes.

High resolution MRI images of the beating heart permit observation of detailed anatomical features and enable quantification of small changes in metrics of cardiac function. To obtain approximately isotropic sampling with an adequate spatial and temporal resolution, these images need to be acquired in multiple breath-holds. They are, therefore, often affected by through-plane discontinuities due to inconsistent breath-hold positions. This paper presents a method to correct for these discontinuities by performing breath-hold-by-breath-hold registration of high resolution 3D data to radial long axis images. The corrected images appear free of discontinuities, and it was found that they could be delineated more reproducibly than uncorrected images. This reduces the sample size required to detect systematic changes in blood pool volume by 57% at end systole and 78% at end diastole.

Algorithms↗

PubMed1996

On the relationship of thermodynamic parameters with the buried surface area in protein-ligand complex formation.

Prediction of thermodynamic parameters of protein-protein and antigen-antibody complex formation from high resolution structural parameters has recently received much attention, since an understanding of the contributions of different fundamental processes like hydrophobic interactions, hydrogen bonding, salt bridge formation, solvent reorganization etc. to the overall thermodynamic parameters and their relations with the structural parameters would lead to rational drug design. Using the results of the dissolution of hydrocarbons and other model compounds the changes in heat capacity (delta C(p)), enthalpy (delta H) and entropy (delta S) have been empirically correlated with the polar and apolar surface areas buried during the process of protein folding/unfolding and protein-ligand complex formation. In this regard, the polar and apolar surfaces removed from the solvent in a protein-ligand complex have been calculated from the experimentally observed values of changes in heat capacity (delta C(p)) and enthalpy (delta H) for protein-ligand complexes for which accurate thermodynamic and high resolution structural data are available, and the results have been compared with the x-ray crystallographic observations. Analyses of the available results show poor correlation between the thermodynamic and structural parameters. Probable reasons for this discrepancy are mostly related with the reorganization of water accompanying the reaction which is indeed proven by the analyses of the energetics of the binding of the wheat germ agglutinin to oligosaccharides.

Animals↗

PubMed2006

Mechanisms of valence selectivity in biological ion channels.

Transmembrane ion channels play a crucial role in the existence of all living organisms. They partition the exterior from the interior of the cell, maintain the proper ionic gradient across the cell membrane and facilitate signaling between cells. To perform these functions, ion channels must be highly selective, allowing some types of ions to pass while blocking the passage of others. Here we review a number of studies that have helped to elucidate the mechanisms by which ion channels discriminate between ions of differing charge, focusing on four channel families as examples: gramicidin, ClC chloride, voltage-gated calcium and potassium channels. The recent availability of high-resolution structural data has meant that the specific inter-atomic interactions responsible for valence selectivity can be pinpointed. Not surprisingly, electrostatic considerations have been shown to play an important role in ion specificity, although many details of the origins of this discrimination remain to be determined.

Calcium Channels↗

PubMed2001

Development of a reference material for routine performance monitoring of methods measuring polychlorinated dibenzo-p-dioxins, polychlorinated dibenzofurans and dioxin-like polychlorinated biphenyls.

Matrix-matched environmental certified reference materials (CRMs) are one of the most useful tools to validate analytical methods, assess analytical laboratory performance and to assist in the resolution of data conflicts between laboratories. This paper describes the development of a lake sediment as a CRM for polychorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs) and dioxin-like polychlorinated biphenyls (DLPCBs). The presence of DLPCBs in the environment is of increased concern and analytical methods are being developed internationally for monitoring DLPCBs in the environment. This paper also reports the results of an international interlaboratory study involving thirty-five laboratories from seventeen countries, conducted to characterize and validate levels of a sediment reference material for PCDDs, PCDFs and DLPCBs.

Benzofurans↗

PubMed2000

Virtual endoscopy of the inner ear and the auditory canal.

To assess the role of virtual endoscopy (VE) in the examination of intracisternal structures and of the inner ear, we studied the anatomy of the labyrinth and internal auditory canal using the original CT slices and VE on the unaffected side in three female and three male patients, age range 3-46 years, with contralateral retrocochlear hearing loss. We also examined seven patients with different pathological findings. VE was performed using an advanced postprocessing program with high-resolution 3D data sets of CT (1-1.5 mm thickness, pitch 1.25) and MRI-CISS-3D (constructive interference in steady state) images of the basal cisterns (1.5 T, slice thickness 0.7-1 mm). VE provides an endoscopic-like view from a given point within the basal cisterns of vessels and nerves (on MRI) or of the structures of the inner ear (on CT). The complex anatomy and pathological changes in the inner ear can be faithfully shown. The main advantage is not basic diagnostic information but demonstration of topographically complex situations, such as the canalicular system of the inner ear, for discussion, preoperative planning and teaching.

Adolescent↗

PubMed1999

Size distributions of chylomicrons from human lymph from dynamic light scattering measurements.

Chylomicrons, the vehicles for the transport of exogeneous triglycerides and cholesterol in the lymph and the blood, were characterized by their size from dynamic light scattering measurements. To achieve an appropriate resolution, correlation data were collected over several hours. Analysis was performed with an extended version of the regularization method CONTIN, and special attention was given to errors in the experimental baseline and to randomness of the residuals. The solutions selected by means of Fisher's F-test by CONTIN agreed with those obtained with the stability plot of Schnablegger and Glatter, when in the case of data of lower statistical accuracy the solution was taken from the lower part of the confidence interval of the F-test. The intensity-weighted size distributions indicated two classes of particle, their mean diameters being 100-140 nm and 330-350 nm. The ability to resolve two peaks of such a size ratio is demonstrated. The numbers of particles associated with the two peaks were estimated by means of the scattering properties of the particles, which showed that the overwhelming majority were small ones. This estimation also suggested that the mean size of the first peak of the number distribution is significantly smaller than the typical size of chylomicrons. This was consistent with the finding that the sample contained not only apolipoprotein B-48 but also a similar amount of apolipoprotein B-100, which is associated with lipoproteins of smaller size. The larger particles of the second peak are probably dietary triglyceride-rich chylomicrons.

Algorithms↗

PubMed2001

99mTc-ECD brain perfusion SPET: variability, asymmetry and effects of age and gender in healthy adults.

Reliable and high-resolution reference data for regional cerebral blood flow measured with single-photon emission tomography (SPET) are necessary for optimal clinical and research use. Therefore, a large dataset of normal technetium-99m labelled ethylene cysteine dimer (ECD) perfusion SPET in carefully screened healthy volunteers with an age range spanning six decades was created, with correction for non-uniform attenuation and scatter and based on an anatomically standardised analysis. Eighty-nine healthy volunteers, stratified for gender (46 females, 43 males; age 20-81 years), were included. Twelve volunteers underwent repeated 99mTc-ECD SPET after 2.5+/-2.3 weeks. An automated whole-brain volume of interest analysis with MANOVA as well as voxelwise analysis using SPM99 was conducted. Average intersubject variability was 4.8% while intrasubject reproducibility was 3.0%. An age-related decline in tracer uptake was found in the anterior cingulate gyrus, bilateral basal ganglia, left prefrontal, left lateral frontal and left superior temporal and insular cortex (all P=0.001-0.02). There was an overall increase in right/left asymmetry with age, which was most pronounced in the frontal and temporal neocortex. The most significant correlations between AI and age decade were found in the prefrontal (R=0.35, P=0.001) and superior temporal neocortex (R=0.43, P<0.001). Women had significantly higher uptake in the right parietal cortex (P<0.001), while men showed higher uptake in the cerebellum and the left anterior temporal and orbitofrontal cortex (all P<0.01). This normative dataset allows age- and gender-specific patient and group assessment of 99mTc-ECD perfusion SPET under a wide variety of clinical circumstances in relation to normal variations and highlights the importance of both age- and gender-specific normal datasets for optimal analysis sensitivity.

Adult↗

PubMedDate not supplied

Bowel endometriosis: CT-enteroclysis.

Although several radiological techniques have been used for the diagnosis of bowel endometriosis, no gold standard is currently established. We used multislice computerized tomography (CT) combined with the distention of the colon by rectal enteroclysis (MSCTe) for the diagnosis of bowel endometriosis. Following bowel preparation, pharmacological hypotonicity, retrograde colonic distention by water enteroclysis, and intravenous injection of iodinated contrast medium, a single volumetric acquisition of the abdomen is performed. MSCTe findings suggestive of bowel endometriosis are the presence of solid nodules with positive enhancement, contiguous or penetrating the colonic wall. When endometriotic lesions are detected, the degree of infiltration of the intestinal wall can be estimated; however, the depth infiltrated by nodules reaching the submucosa may be underestimated. MSCTe is well tolerated by the patients. The strength of MSCT consists in the high spatial resolution; volumetric data acquired by using thin slices provide isotropic voxels and multiplanar reconstructions have a quality comparable with that of the original axial scans. The potential of MSCTe for the diagnosis of bowel endometriosis relies on the fact that the serosal, muscular, and mucosal layers of the bowel wall can be evaluated.

Contrast Media↗

PubMed2026

Genomic Characterisation of Carbapenem-Resistant Klebsiella pneumoniae and Enterobacter hormaechei Clinical Isolates from Nigeria: Evidence of Resistance, Virulence, and Putative Plasmid-Mediated Gene Sharing.

The global proliferation of carbapenem-resistant Enterobacterales (CRE) constitutes one of the most urgent public health threats, yet high-resolution genomic data from sub-Saharan Africa remain critically scarce. We applied whole-genome sequencing (WGS) and comparative phylogenomics to characterise antimicrobial resistance determinants, virulence genes, and mobile genetic elements (MGEs) in three carbapenem-resistant clinical isolates originating from three tertiary hospitals (selected from a broader surveillance collection spanning four facilities) in Osun State, southwestern Nigeria. We purposively selected three isolates, two Klebsiella pneumoniae subsp. pneumoniae (K22, ST411; K31, ST17) and one Enterobacter hormaechei subsp. steigerwaltii (K32, ST45) from a broader surveillance collection of 27 carbapenem-non-susceptible Enterobacterales, to represent phenotypically and genotypically divergent lineages. Resistome analysis revealed extensive plasmid-associated β-lactam and aminoglycoside resistance in K31 (including blaCTX-M-15, blaOXA-1, and blaTEM-1). K32 harboured an intrinsic chromosomal blaACT-17 AmpC gene, while IS26 and ISEcp1 insertion sequences, consistent with transposon-mediated mobilisation, flanked its acquired aminoglycoside and sulfonamide resistance cassettes. K22 lacked detected acquired carbapenemase, ESBL, or plasmid-mediated AmpC genes, indicating that its carbapenem-resistant phenotype may involve non-carbapenemase mechanisms such as porin alteration or efflux-mediated reduced susceptibility; however, this mechanism requires confirmation by direct ompK35/ompK36 sequence analysis and/or phenotypic outer membrane protein profiling. Virulome profiling identified a broader repertoire of siderophore, adhesion, and biofilm genes in both K. pneumoniae isolates than in E. hormaechei. Phylogenomic analysis demonstrated that K22 and K31 cluster within the broader K. pneumoniae population framework but represent distinct high-risk lineages (ST411 and ST17) rather than a single clonal outbreak. Analysis also identified a shared plasmid backbone between K31 and K32, supporting interspecies horizontal gene transfer. These descriptive genomic findings identify clinically relevant resistance and virulence determinants in three purposively selected carbapenem-resistant Enterobacterales from Nigerian tertiary-care hospitals. The detection of shared resistance elements between K. pneumoniae and E. hormaechei suggests possible plasmid-mediated gene sharing. Still, larger WGS studies with long-read sequencing and patient-level epidemiological data are required to define transmission and dissemination patterns.

Nigeria↗