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At least 1,783 records · Page 99Linked to original sources
PubMed2005

Correlation of high-resolution ultrasonographic findings with the clinical symptoms and electrodiagnostic data in carpal tunnel syndrome.

There are several different imaging methods that are helpful in the diagnosis of carpal tunnel syndrome, including traditional radiography, computed tomography (CT), and magnetic resonance imaging (MRI). CT and MRI offer the advantage of providing direct visualization of the structural abnormality of the carpal tunnel and median nerve, but both of these modalities are expensive and time-consuming. Recently, high-resolution ultrasonography has been reported to be effective in the study of the musculoskeletal system. The authors designed a case-control study to assess the diagnostic value of high-resolution ultrasonography. Forty-eight patients, for a total of 96 hands, whose diagnosis was confirmed by self-administered questionnaire and electrodiagnostic tests, underwent high-resolution ultrasonographic studies. The authors compared the sonographic findings with the electromyographic data and the patients' severity scores on the self-questionnaires. Proximal swelling of the median nerve at the entrance to the carpal tunnel was found to correlate with the nerve conduction data. Also, compression of the median nerve under the transverse carpal ligament was found to correlate with the subjective symptoms. Although ultrasonography is not an ideal method of diagnosis for carpal tunnel syndrome, it may be helpful for estimating the symptom severity and nerve conduction deficit.

Adult↗
PubMed2006

Modeling human mortality using mixtures of bathtub shaped failure distributions.

Aging and mortality is usually modeled by the Gompertz-Makeham distribution, where the mortality rate accelerates with age in adult humans. The resulting parameters are interpreted as the frailty and decrease in vitality with age. This fits well to life data from 'westernized' societies, where the data are accurate, of high resolution, and show the effects of high quality post-natal care. We show, however, that when the data are of lower resolution, and contain considerable structure in the infant mortality, the fit can be poor. Moreover, the Gompertz-Makeham distribution is consistent with neither the force of natural selection, nor the recently identified 'late life mortality deceleration'. Although actuarial models such as the Heligman-Pollard distribution can, in theory, achieve an improved fit, the lack of a closed form for the survival function makes fitting extremely arduous, and the biological interpretation can be lacking. We show, that a mixture, assigning mortality to exogenous or endogenous causes, using the reduced additive and flexible Weibull distributions, models well human mortality over the entire life span. The components of the mixture are asymptotically consistent with the reliability and biological theories of aging. The relative simplicity of the mixture distribution makes feasible a technique where the curvature functions of the corresponding survival and hazard rate functions are used to identify the beginning and the end of various life phases, such as infant mortality, the end of the force of natural selection, and late life mortality deceleration. We illustrate our results with a comparative analysis of Canadian and Indonesian mortality data.

Adolescent↗
PubMed1999

Anomalous signal of solvent bromides used for phasing of lysozyme.

The anomalous signal of bromide ions, present in the crystal structure of tetragonal hen egg-white lysozyme through the substitution of NaCl by NaBr in the crystallization medium, was used for phasing of X-ray data collected to 1.7 A resolution with a wavelength near the absorption edge of bromine. Phasing of a single wavelength data set, based purely on anomalous deltaf " contribution, led to easily interpretable electron density, equivalent to the complete multiwavelength anonalous dispersion phasing based on four-wavelength data. The classic small-structure direct methods program SHELXS run against all anomalous differences gave a successful solution of six highest peaks corresponding to six bromide ions in the structure with data limited up to a resolution of 3.5 A. Interpretable maps were obtained at a resolution up to 3.0 A using programs MLPHARE and DM. Bromide ions occupy well ordered positions at the protein surface. Phasing based on the single wavelength signal of anomalous scatterers introduced into the ordered solvent shell can be proposed as a tool for solving structures of well diffracting crystals.

Algorithms↗
PubMed2005

Detection and characterization of merohedral twinning in crystals of oxalyl-coenzyme A decarboxylase from Oxalobacter formigenes.

Oxalyl-coenzyme A decarboxylase is a thiamin diphosphate dependent enzyme active in the catabolism of the highly toxic compound oxalate. The enzyme from Oxalobacter formigenes has been expressed as a recombinant protein in Escherichia coli, purified to homogeneity and crystallized. Two crystal forms were obtained, one showing poor diffraction and the other merohedral twinning. Crystals in the former category belong to the tetragonal space group P4(2)2(1)2. Data to 4.1 A resolution were collected from these crystals and an incomplete low resolution structure was initially determined by molecular replacement. Crystals in the latter category were obtained by co-crystallizing the protein with coenzyme A, thiamin diphosphate and Mg(2+)-ions. Data to 1.73 A were collected from one of these crystals with apparent point group 622. The crystal was found to be heavily twinned, and a twin ratio of 0.43 was estimated consistently by different established methods. The true space group P3(1)21 was deduced, and a molecular replacement solution was obtained using the low resolution structure as template when searching in detwinned data.

Carboxy-Lyases↗
PubMed1998

1.2 A refinement of the Kunitz-type domain from the alpha3 chain of human type VI collagen.

The recombinant Kunitz-type domain (C5) of human collagen alpha3(VI) chain was previously described at 1.6 A resolution at room temperature. By changing the crystallization conditions and using synchrotron radiation, we are able to record diffraction data to 1.2 A resolution for crystals of the same space group at 291 K. The protein-water-ion model has been refined anisotropically against these new data using the program SHELXL93; the results converged to an R factor of 15.0%, with all data between 7 and 1.2 A. The final electron-density map reveals a clear chain tracing with a few disordered residues and five residues out of 58 that present alternate conformations. The Cys14-Cys38 bond presents the less frequently observed left-hand conformation (chi1 = -60 degrees). The solvent molecules and a phosphate ion are well ordered with an average B of 38 A2. The high-resolution structure reveals the N and C termini which were missing from the 1.6 A structure.

Amino Acid Sequence↗
PubMed1994

Five viral peptide-HLA-A2 co-crystals. Simultaneous space group determination and X-ray data collection.

We prepared and crystallized five complexes of the human histocompatibility molecule HLA-A2 with peptides derived from human immunodeficiency virus type 1, human T lymphotropic virus type 1, influenza A virus and hepatitis B virus proteins. Each HLA-A2 complex was refolded in vitro from insoluble proteins produced in bacteria; to crystallize, two of the complexes required seeding with microcrystals of another complex. Maintained at -160 degrees C, single co-crystals of each of the five peptide-HLA-A2 complexes yielded complete X-ray diffraction data sets to a resolution of approximately 2.5 A. After a sufficient number of diffraction peaks were acquired during data collection, the direct analysis of integrated intensities established the point group of the co-crystal, thus allowing an efficient data collection strategy to be designed. The subsequent examination of systematic absences revealed that the five peptide-HLA-A2 co-crystals formed in space groups P1, P2(1), or P2(1)2(1)2(1). Molecular replacement structure solutions yielded unambiguous protein electron density maps, thus confirming the space group determinations. The system of obtaining HLA-A2 co-crystal structures described here is applicable to other crystallographic problems where structures of several related molecules from uncharacterized single crystals are required.

Amino Acid Sequence↗
PubMed1994

New crystal forms and preliminary X-ray diffraction studies of mitochondrial cytochrome bc1 complex from bovine heart.

Two new crystal forms of the cytochrome bc1 complex (ubiquinol:ferricytochrome c oxidoreductase, EC. 1.10.2.2) from bovine heart mitochondria were obtained by the batch method with polyethylene glycol 4000 as the precipitant, when buffer was exchanged from Tris-HCl to potassium phosphate. The first crystal form belongs to the hexagonal space group P61 or P6(5) with unit-cell constants of a = b = 131 A and c = 720 A. The reproducibility of crystallization and the quality of this crystal form were improved by an addition of ZnCl2 to the protein solution. The second crystal form, obtained from the enzyme preparation purified by crystallization, belongs to the tetragonal space group P4(1) or P4(3) with unit-cell constants of a = b = 190 A and c = 445 A. Both crystals diffracted X-rays to 6.5 A resolution and gave sharper diffraction spots than the previous monoclinic form. X-ray intensity data to 8.0 A resolution for the hexagonal crystal and to 7.0 A resolution for the tetragonal one were collected with synchrotron radiation.

Animals↗
PubMed1989

Scapharca hemoglobins, type cases of a novel mode of chain assembly and heme-heme communication. Amino acid sequence and subunit interactions of the tetrameric component.

The sequences of the A and B chains of the Scapharca inaequivalvis tetrameric hemoglobin (HbII) are reported. They are homologous to the corresponding chains of other Arcid hemoglobins. Moreover, a comparison of the present data with the sequence of the S. inaequivalvis dimeric hemoglobin (HbI), for which high-resolution X-ray data are available, allows the identification of the residues that direct the assembly of the two components and of those that may be involved in the interdimeric contacts.

Allosteric Regulation↗
PubMed2003

The supramolecular organization of collagen VI microfibrils.

Collagen VI has a ubiquitous distribution throughout connective tissues, and has key roles in linking cells and matrix macromolecules. We have generated three-dimensional reconstructions of collagen VI microfibrils using automated electron tomography (AET) in order to obtain new insights into the organisation of collagen VI in assembled microfibrils. Analysis of the reconstruction data has allowed the resolution of the double-beaded structure into smaller subunits. Volume calculations from the tomography data indicate that ten and six A-domains could be packed into the N and C-terminal regions from each monomer, respectively. A putative location for the globular N-terminal regions of the alpha3 chain, important for microfibril assembly and function, has been identified. Some surfaces of the alpha3 chain N-terminal domains appear to be exposed on the surface of a microfibril, where they may provide an interactive surface for molecules. Analysis of the interbead region provides evidence for complex triple helical supercoiling in microfibrils. Frequently, two strands were visualised emerging from the beaded region and merging into a single interbead region. Measurements taken from the AET data show that there is a decrease in periodicity from dimer/tetramer to microfibrils. Molecular combing reverses this effect by mechanically increasing periodicity to give measurements similar to the component dimers/tetramers. Together, these data have provided important new insights into the organisation and function of these large macromolecular assemblies.

Animals↗
PubMed1990

X-ray analysis of new crystal forms of the sweet protein thaumatin.

Thaumatin is a plant protein that in the mature form contains 8 disulfide bonds and 207 amino acids. Several forms of this protein occur naturally and each elicits an intense sweetness sensation when tasted in microgram quantities. The two major forms of thaumatin are easily separable by ion exchange chromatography. Crystals of the two proteins (designated here A and B) have been grown by vapor equilibration from solutions containing polyethylene glycol and examined by X-ray diffraction. The thaumatin A crystals are of space group P2(1)2(1)2(1) with a = 44.3 A, b = 63.7 A and c = 72.7 A. The crystals of thaumatin B are of space group C2 with a = 117.7 A, b = 44.9 A, and c = 38.0 A and beta = 94.0 degrees. Both crystals diffract to well beyond 2.3 A and appear suitable for high resolution structure analysis. Four heavy atom derivatives of thaumatin B have been generated and diffraction data to 4 A resolution have been collected. This work is designed to provide a basis for studying the 3-dimensional structure of more than 100 genetically generated thaumatin derivatives, several of which show enhanced stability and improved taste characteristics.

Crystallization↗
PubMed2005

Conserved solvent and side-chain interactions in the 1.35 Angstrom structure of the Kelch domain of Keap1.

The Kelch repeat is a common sequence motif in eukaryotic genomes and is approximately 50 amino acids in length. The structure of the Kelch domain of the human Keap1 protein has previously been determined at 1.85 Angstrom, showing that each Kelch repeat forms one blade of a six-bladed beta-propeller. Here, use of 1.35 Angstrom SAD data for de novo structure determination of the Kelch domain and for refinement at atomic resolution is described. The high quality and resolution of the diffraction data and phase information allows a detailed analysis of the role of solvent in the structure of the Kelch repeat. Ten structurally conserved water molecules are identified in each blade of the Kelch beta-propeller. These appear to play distinct structural roles that include lining the central channel of the propeller, interacting with residues in loops between strands of the blade and making contacts with conserved residues in the Kelch repeat. Furthermore, we identify a conserved C-H...pi hydrogen bond between two key residues in the consensus Kelch repeat. This analysis extends our understanding of the structural roles of conserved residues in the Kelch repeat and highlights the potential role of solvent in maintaining the fold of this common eukaryotic structural motif.

Amino Acid Motifs↗
PubMed1998

The refined structure of dUTPase from Escherichia coli.

Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase, E.C. 3.6. 1.23) catalyzes the hydrolysis of dUTP to dUMP and pyrophosphate and is involved in nucleotide metabolism and DNA synthesis. A crystal of the recombinant E. coli enzyme, precipitated from polyethylene glycol mixtures in the presence of succinate at pH 4.2, was used to collect synchrotron diffraction data to 1.9 A resolution, in space group R3, a = b = 86.62, c = 62.23 A. Mercury and platinum derivative data were collected at wavelengths to optimize the anomalous contribution. The resulting 2.2 A MIRAS phases differed from the final set by 40 degrees on average and produced an excellent map which was easy to interpret. The model contains 132 water molecules and refined to an R value of 13.7%. 136 residues have clear electron density out of 152 expected from the gene sequence. The 16 C-terminal residues are presumably disordered in the crystal lattice. The monomer is a 'jelly-roll' type, containing mostly beta-sheet and only one short helix. The molecule is a tight trimer. A long C-terminal arm extends from one subunit and encompasses the next one within the trimer contributing to its beta-sheet. Conserved sequence motifs common among dUTPases, previously suggested to compose the active site and confirmed in a recent study of the dUDP complex, are located at subunit-subunit interfaces along the threefold axis, in parts of the beta-sheet and in loop regions. A similar molecular architecture has recently been found in two other trimeric dUTPases.

Amino Acid Sequence↗
PubMed2005

[Studies on the resources survey methods of Panax notogingseng based on remote sensing].

OBJECTIVE: To explore the survey methods for the cultivated medicinal plant resources such as Panax notogingseng based on remote sensing. METHOD: Through the preliminary study by remote sensing technique and field survey in the study area, the optimal methods in the procedure were chosen for the survey. RESULT: In this study,a set of survey method for P. notogingseng based on remote sensing technique was founded, which included the remotely sensed data-source selecting, the remote sensing image processing, interpretation and validation etc. CONCLUSION: With different resolution remotely-sensing data at the study area, the area, the natural storage and the yield of P. notoginseng were calculated. For Maguan county, with SPOT5 (5 m), the relative right rate of judgement, the relative precision of area and the relative precision of yield with statistics was 92.7%, 94.4% and 78.2% separately, and with TM (30 m), the relative right rate of judgement, the relative precision of area was only 71.4% and 58.8%, though, for Qiubei county, with TM (30 m), the relative precision of area with statistics could reach 74.7%, which showed that choosing appropriate remotely-sensing data and processing methods for different area, the remote sensing technique is feasible for resource survey of cultivated medicinal plants such as P. notoginseng.

China↗
PubMed2002

Method for efficient fast spin echo Dixon imaging.

In order to satisfy the Carr-Purcell-Meiboom-Gill (CPMG) condition, echo shift as dictated in fast-spin-echo (FSE)-based Dixon imaging was previously achieved by applying a time shift to the readout gradient and the data acquisition window. Accordingly, interecho spacing is increased, which entails increased image blurring and, in multislice imaging, a significant reduction in the slice coverage for a given imaging time. In this work, a new method is developed by which the echo shift is induced by "sandwiching" in time the readout gradient with a pair of small gradients of equal area and of opposite polarity. While data with non-zero phase shifts between water and fat signals are collected as fractional echoes, no increase in echo spacing is necessary with the modified acquisition strategy, and increased time efficiency is therefore achieved. In order to generate separate water-only and fat-only images in data processing, a set of low-resolution images are first reconstructed from the central symmetric portion (either 128 x 128 or 64 x 64) of the acquired multipoint Dixon data. High-resolution images using all the acquired data, including some partial Fourier-reconstructed images, are then phase demodulated using the phase errors determined from the low-resolution images. The feasibility of the technique is demonstrated using a water and fat phantom as well as in clinical patient imaging.

Adipose Tissue↗
PubMed1987

Three dimensional structure of bacterial pili.

Crystallographic and associated biochemical and structural studies are in progress on the fiber-forming pilin proteins of the gonococcal pilus. Preparative scale purification procedures have been developed for the gonococcal pilin protein, which appear generally applicable to bacterial pilins. For three gonococcal pilin protein strains, we have obtained both reassembled pilus fibers and three-dimensional crystals. One needle-shaped crystal form of gonococcal C30 pilin diffracts beyond 3 A resolution using synchrotron x-ray radiation. A diffraction data set to 3.5 A resolution has been collected on these needle-shaped crystals (lattice spacings a = 125.4(3) b = 120.4(3), c = 26.61(4) A) in which the packing arrangement of the pilin subunits appears to resemble that seen in the pilus fibers using electron microscopy. X-ray diffraction data confirm our proposed model for the overall polypeptide fold of a pilin subunit, which is an antiparallel 4-alpha helix bundle similar to tobacco mosaic virus coat protein and myohemerythrin.

Bacterial Outer Membrane Proteins↗
PubMed1996

Crystallization and preliminary structural studies of lactose-specific enzyme IIA from Lactococcus lactis.

Lactose-specific enzyme IIA of the phosphoenol:pyruvate-dependent sugar phosphotransferase system from Lactococcus lactis has been crystallized in phosphate buffer. The crystals belong to space group P4(1)2(1)2 or its enantiomorph P4(3)2(1)2 with unit-cell axes a = b = 90.9 and c = 82.4 A. The packing parameter (Matthews parameter) V(m) of 2.48 A(3) Da(-1) is consistent with one trimer per asymmetric unit and non-crystallographic threefold symmetry has been confirmed by calculating a self-rotation function. The crystals diffract X-rays to at least 2.3 A resolution, are stable in an X-ray beam and are therefore appropriate for structure determination. Native data to 2.3 A resolution have been collected using a MAR image-plate system at a synchrotron source. One isomorphous heavy-atom derivative has been identified and the presence of an isomorphous signal in the data has been confirmed by Patterson methods.

Journal Article↗
PubMed2002

Patchwork peptide sequencing: extraction of sequence information from accurate mass data of peptide tandem mass spectra recorded at high resolution.

The accurate mass values of all immonium, y(1), y(2), a(2), and b(2) ions of tryptic peptides composed of the 20 standard amino acids were calculated. The differences between adjacent masses in this data set are greater than 10 mDa for more than 80% of the values. Using this mass list, the majority of low mass ions in quadrupole-time of flight tandem mass spectra of peptides from tryptic digests and from an elastase digest could be assigned. Besides the a(2)/b(2) ions, which carry residues 1-2 from the N-terminus, a variety of internal dipeptide b ions were regularly observed. In case internal proline was present, corresponding dipeptide b ions carrying proline at the N-terminal position occurred. By assigning the dipeptide b ions on the basis of their accurate mass, bidirectional or unidirectional sequence information was obtained, which is localized to the peptide N-terminus (a(2)/b(2) ions) or not localized (internal b ions). Identification of the y(1) and y(2) ions by their accurate mass provides unidirectional sequence information localized to the peptide C-terminus. It is shown that this patchwork-type sequence information extractable from accurate mass data of low-mass ions is highly efficient for protein identification.

Amino Acid Sequence↗
PubMed1994

Postmortem anatomy from cryosectioned whole human brain.

A system of histologic and digital processing protocols are presented for the acquisition of high-resolution digital imagery from postmortem cryosectioned whole human brain and head for computer-based 3-dimensional (3D) representation and visualization. We designed and evaluated several protocols for optimal preparation of frozen specimens including fixation, decalcification, cryoprotection, freezing and sectioning procedures. High-resolution (1024(2) pixel) serial images were captured directly from the cryoplaned blockface using an integrated color digital camera and fiber optic illumination system mounted over a modified cryomacrotome. Specimens frozen and sectioned with the cranium intact preserved brain spatial relationships and anatomic bony landmarks. Color preservation was superior in unfixed tissue heads were incompatible with decalcification and cryoprotection procedures and section collection from such specimens was complicated by bone fragmentation. Collection of 1024(2) images from whole brain resulted in a spatial resolution of 200 microns/pixel in a 1-3 Gbyte data space. Even higher 3D spatial resolution was possible by primary image capture of selected regions such as hippocampus or brain stem. Discrete registration errors were corrected using image processing strategies such as cross-correlative and other algorithmic approaches. Data sets were amenable to resampling in multiple planes as well as scaling and transpositioning into standard coordinate systems. These methods enable quantitative measurements for comparison between subjects and to published atlas data. These techniques allow visualization and measurement at resolutions far higher than those available through other imaging technologies and provide greatly enhanced contrast for delineation of neuroanatomic structures, pathways, and subregions.

Brain↗