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PubMed1997

Determining variations in colonic circulation during aortic surgery.

The aim of this study was to compare transanal Doppler examination, intraoperative angiography via the inferior mesenteric artery, and the inferior mesenteric artery stump pressure measurement during abdominal aortic surgery to assess the collateral circulation to the inferior mesenteric artery bed. Transanal Doppler examination revealed that the collateral circulation depended on the superior mesenteric artery in 25 patients (superior mesenteric artery-dominant group), the inferior mesenteric artery in two patients (inferior mesenteric artery-dominant group), and the internal iliac artery in one patient (internal iliac artery-dominant group). The mean (+/-S.D.) inferior mesenteric artery stump pressure index was 0.65 (+/-0.12) in the superior mesenteric artery-dominant group, which was significantly different from 0.43 (+/-0.00) in the inferior mesenteric artery- and internal iliac artery-dominant groups. The Intraoperative angiography showed the meandering mesenteric artery clearly in the superior mesenteric artery-dominant group. The Transanal Doppler examination as well as inferior mesenteric artery stump pressure measurement were useful methods to assess a dominant artery to the inferior mesenteric artery bed and colonic viability.

Aged↗

PubMed1998

Crystal structure of p14TCL1, an oncogene product involved in T-cell prolymphocytic leukemia, reveals a novel beta-barrel topology.

BACKGROUND: Chromosome rearrangements are frequently involved in the generation of hematopoietic tumors. One type of T-cell leukemia, T-cell prolymphocytic leukemia, is consistently associated with chromosome rearrangements characterized by the juxtaposition of the TCRA locus on chromosome 14q11 and either the TCL1 gene on 14q32.1 or the MTCP1 gene on Xq28. The TCL1 gene is preferentially expressed in cells of early lymphoid lineage; its product is a 14 kDa protein (p14TCL1), expressed in the cytoplasm. p14TCL1 has strong sequence similarity with one product of the MTCP1 gene, p13MTCP1 (41% identical and 61% similar). The functions of the TCL1 and MTCP1 genes are not known yet. They have no sequence similarity to any other published sequence, including those of well-documented oncogene families responsible for leukemia. In order to gain a more fundamental insight into the role of this particular class of oncogenes, we have determined the three-dimensional structure of p14TCL1. RESULTS: The crystal structure of p14TCL1 has been determined at 2.5 A resolution. The structure was solved by molecular replacement using the solution structure of p13MTCP1, revealing p14TCL1 to be an all-beta protein consisting of an eight-stranded antiparallel beta barrel with a novel topology. The barrel consists of two four-stranded beta-meander motifs, related by a twofold axis and connected by a long loop. This internal pseudo-twofold symmetry was not expected on basis of the sequence alone, but structure-based sequence analysis of the two motifs shows that they are related. The structures of p13MTCP1 and p14TCL1 are very similar, diverging only in regions that are either flexible and/or involved in crystal packing. p14TCL1 forms a tight crystallographic dimer, probably corresponding to the 28 kDa species identified in solution by gel filtration experiments. CONCLUSIONS: Structural similarities between p14TCL1 and p13MTCP1 suggest that their (unknown) function may be analogous. This is confirmed by the fact that these proteins are implicated in analogous diseases. Their structure does not show similarity to other oncoproteins of known structure, confirming their classification as a novel class of oncoproteins.

Amino Acid Sequence↗

PubMed2002

Clinical evaluation of safety and human tolerance of electrical sensation induced by electric fields with non-invasive electrodes.

This paper reports the first clinical safety study of human tolerance of electrical sensation using non-invasive, flexible surface-type electrodes and exponentially decaying electric pulses. The study evaluated the effect of electric fields in the absence of a drug and an anesthetic, and was performed in light of potential applications in the field of erectile dysfunction (ED). Twenty impotent patients who had previously received injection or intraurethral therapies were enrolled in the study. Voltage escalations from 50 to 80 V (in 10-V increments) with a single pulse of 3-ms duration were performed with meander-type electrodes placed on the shaft and part of the glans of the penis. The electric fields-induced sensation was assessed via a pain scale from 0 to 10. All 20 patients, who were free to withdraw from the study at any point, completed the voltage escalation study. No clinical safety concerns were apparent and no skin irritation was observed after electric treatment. Our initial study indicates that the pulses in the tested voltage range were well tolerated by most patients. In previous animal experiments under analogous experimental conditions, the application of 50 V has been found effective for transdermal drug delivery into the penis.

Adaptation, Physiological↗

PubMed1990

Cortical connections of MT in four species of primates: areal, modular, and retinotopic patterns.

Cortical connections were investigated by restricting injections of WGA-HRP to different parts of the middle temporal visual area, MT, in squirrel monkeys, owl monkeys, marmosets, and galagos. Cortex was flattened and sectioned tangentially to facilitate an analysis of the areal patterns of connections. In the experimental cases, brain sections reacted for cytochrome oxidase (CO) or stained for myelin were used to delimit visual areas of occipital and temporal cortex and visuomotor areas of the frontal lobe. Major findings are as follows: (1) The architectonic analysis suggests that in addition to the commonly recognized visual fields, area 17 (V-I), area 18 (V-II), and MT, all three New World monkeys and prosimian galagos have visual areas DL, DI, DM, MST, and FST. (2) Measurements of the size of these areas indicate that about a third of the neocortex in these primates is occupied by the eight visual areas, but they occupy a somewhat larger proportion of neocortex in the diurnal marmosets and squirrel monkeys than the nocturnal owl monkeys and galagos. The diurnal primates also have proportionally more neocortex devoted to areas 17, 18, and DL and less to MT. These differences are compatible with the view that diurnal primates are more specialized for detailed object and color vision. (3) In all four primates, restricted locations in MT receive major inputs from short meandering rows of neurons in area 17 and several bands of neurons in area 18. (4) Major feedforward projections of MT are to two visual areas adjoining the rostral half of MT, areas MST and FST. Other ipsilateral connections are with DL, DI, and in some cases DM, parts of inferotemporal (IT) cortex, and posterior parietal cortex. (5) In squirrel monkeys, where injection sites varied from caudal to rostral MT, caudal parts of MT representing central vision connect more densely to DL and IT than other parts. Both DL and IT cortex emphasize central vision. (6) In the frontal lobe, MT has dense connections with the frontal ventral area (FV), but not with the frontal eye field (FEF). (7) Callosal connections of MT are most dense with matched locations in MT of the other hemisphere, rather than with the outer boundary of MT representing the vertical meridian. Targets of sparser callosal connections include FST, MST, and DL.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

PubMed1995

The peptide-binding domain of the chaperone protein Hsc70 has an unusual secondary structure topology.

Modern NMR methods were used to determine the secondary structure topology of the 18 kDa peptide binding domain of the chaperone protein Hsc70 in solution. This report constitutes the first experimental conformational information on this important domain of the class of Hsp70 proteins. The domain consists of two four-stranded antiparallel beta-sheets and a single alpha-helix. The topology does not resemble at all the topology observed in the human leukocyte antigen (HLA) proteins of the major histocompatibility complex. This is significant because such resemblance was predicted on the basis of limited amino acid homology, secondary structure prediction, and related function. Moreover, the exact meander-type beta-sheet topology identified in Hsc70 has to our best knowledge not been observed in any other known protein structure.

Amino Acid Sequence↗

PubMed2002

Robustness of the long-range structure in denatured staphylococcal nuclease to changes in amino acid sequence.

A nativelike low-resolution structure has been shown to persist in the Delta 131 Delta denatured fragment of staphylococcal nuclease, even in the presence of 8 M urea. In this report, the physical-chemical basis of this structure is addressed by monitoring changes in structure reflected in residual dipolar couplings and diffusion coefficients as a function of changes in amino acid sequence. Ten large hydrophobic residues, previously shown to play dominant roles in the stability of the native state, are replaced with polar residues of similar shape. Modest increases in the Stokes radius determined by NMR methods result from replacement of five isoleucine/valine residues with threonine, one leucine with glutamine, and oxidation of four methionines to the sulfoxides. Yet in the presence of all ten hydrophobic to polar substitutions and 8 M urea, the NMR signature of a native-like topology is still largely intact. In addition, removal of 30 residues from either the N-terminus (which deletes a three-strand beta meander) or C-terminus (a long extended segment and the final alpha helix) produces only very small changes in long-range structure. These data indicate that both the general shape of the denatured state and the angular relationships of individual bond angles to the axes describing the spatial distribution of the protein chain are insensitive to large changes in the amino acid sequence, a finding consistent with the conclusion that the long-range structure of denatured proteins is encoded primarily by local steric interactions between side chains and the polypeptide backbone.

Binding Sites↗

PubMed2004

Selection of human cytochrome P450 1A2 mutants with enhanced catalytic activity for heterocyclic amine N-hydroxylation.

Cytochrome P450 (P450) 1A2 is the major enzyme involved in the metabolism of 2-amino-3,5-dimethylimidazo[4,5-f]quinoline (MeIQ) and other heterocyclic arylamines and their bioactivation to mutagens. Random mutant libraries of human P450 1A2, in which mutations were made throughout the entire open reading frame, were screened with Escherichia coli DJ3109pNM12, a strain designed to bioactivate MeIQ and detect mutagenicity of the products. Mutant clones with enhanced activity were confirmed using quantitative measurement of MeIQ N-hydroxylation. Three consecutive rounds of random mutagenesis and screening were performed and yielded a highly improved P450 1A2 mutant, SF513 (E225N/Q258H/G437D), with >10-fold increased MeIQ activation based on the E. coli genotoxicity assay and 12-fold enhanced catalytic efficiency (k(cat)/K(m)) in steady-state N-hydroxylation assays done with isolated membrane fractions. SF513 displayed selectively enhanced activity for MeIQ compared to other heterocyclic arylamines. The enhanced catalytic activity was not attributed to changes in any of several individual steps examined, including substrate binding, total NADPH oxidation, or H(2)O(2) formation. Homology modeling based on an X-ray structure of rabbit P450 2C5 suggested that the E225N and Q258H mutations are located in the F-helix and G-helix, respectively, and that the G437D mutation is in the "meander" region, apparently rather distant from the substrate. In summary, the approach generated a mutant enzyme with selectively elevated activity for a single substrate, even to the extent of a difference of a single methyl group, and several mutations had interacting roles in the development of the selected mutant protein.

Amino Acid Sequence↗

PubMed2001

Geostatistical assessment and validation of uncertainty for three-dimensional dioxin data from sediments in an estuarine river.

Contaminated sediment management is an urgent environmental and regulatory issue worldwide. Because remediation is expensive, sound quantitative assessments of uncertainty aboutthe spatial distribution of contaminants are critical, butthey are hampered bythe physical complexity of sediment environments. This paper describes the use of geostatistical modeling approaches to quantify uncertainty of 2,3,7,8-tetrachlorodibenzo-p-dioxin concentrations in Passaic River (New Jersey) sediments and to incorporate this information in decision-making processes, such as delineation of contaminated areas and additional sampling needs. First, coordinate transformation and analysis of three-dimensional semivariograms were used to describe and modelthe directional variability accounting forthe meandering course of the river. Then, indicator kriging was employed to provide models of local uncertainty at unsampled locations without requiring a prior transform (e.g. log-normal) of concentrations. Cross-validation results show that the use of probability thresholds leads to more efficient delineation of contaminated areas than a classification based on the exceedence of regulatory thresholds by concentration estimates. Depending on whether additional sampling aims at reducing prediction errors or misclassification rates, the variance of local probability distributions or a measure of the expected closeness to the regulatory threshold can be used to locate candidate locations.

Decision Making↗

PubMed2000

From simple trans-[a2Pt(2-hydroxypyrimidine)2]2+ (a = NH3, CH3NH2) complexes to structures of higher complexity. Molecular recognition of 2-aminopyrimidine by hydrogen bond formation and reactivity toward additional metal ions.

The new complexes trans-[a2Pt(Hpymo-N1)2]X2 (a = NH3, X = NO3 (1a); a = CH3NH2, X = NO3 (1b); a = CH3NH2, X = ClO4 (1c); Hpymo = 2-hydroxypyrimidine) have been prepared by reaction of trans-[a2Pt(H2O)2]-X2 with 2-hydroxypyrimidine at 80 degrees C in water. Complex 1c cocrystallizes in water with 2-aminopyrimidine (ampym) through formation of complementary pairs of hydrogen bonds to give the supramolecular hexagon [trans-[(CH3NH2)2Pt(pymo-N1)(Hpymo-N1)].Hampym[2(ClO4)4 (2). Molecular recognition of ampym by 1c is responsible for a conformational change of the two hydroxypyrimidine ligands in 1c from anti (1c) to syn and in addition for a proton transfer from a Hpymo residue to ampym against 1.5 units of pKa gradient. 1H NMR concentration-dependent studies as well as NOE experiments in dmso-d6 and dmf-d7 show that 2 dissociates in solution. Compound 1a reacts in NH3:H2O (1:3) with AgI to give the polymeric species [trans-[(NH3)2Pt(mu-pymo-N1,N3)2Ag(H2O)]-NO3]n (3). In contrast to 2, in the polymeric structure the trans-[NH3)2Pt(pymo)2] entities adopt an anti conformation. Nevertheless, the [(H2O)Ag(pymo)2] residues present a syn conformation that leads to a meander-like global structure. Compounds 1b, 1c, 2, and 3 have been studied by X-ray crystallography: (1b) triclinic space group, P1, a = 9.300(2) A, b = 10.483(2) A, c = 11.050(2) A, alpha = 68.21(3) degrees, beta = 75.47(3) degrees, gamma = 73.83(3) degrees, Z = 2, R1 = 0.025, and wR2 = 0.062; (1c) triclinic space group, P1, a = 5.692(1) A, b = 7.758(2) A, c = 11.236(2) A, alpha = 93.12(3) degrees, beta = 92.86(3) degrees, gamma = 102.58(3) degrees, Z = 2, R1 = 0.048, and wR2 = 0.119; (2) triclinic space group, P1, a = 8.355(2) A, b = 11.221(2) A, c = 13.004(3) A, alpha = 86.76(3) degrees, beta = 78.62(3) degrees, gamma = 77.96(3) degrees, Z = 2, R1 = 0.033, and wR2 = 0.080; (3) monoclinic space group, C2/c, a = 5.345(1) A, b = 23.998(5) A, c = 12.474(2) A, beta = 102.27(3) degrees, Z = 8, R1 = 0.041, and wR2 = 0.093.

Journal Article↗

PubMed2006

Negative-tension instability of scroll waves and winfree turbulence in the oregonator model.

Excitable media support self-organized scroll waves which can be unstable and give rise to three-dimensional wave chaos. Winfree turbulence of scroll waves results from the negative-tension instability of scroll waves; it plays an important role in the cardiac tissue where it may lead to ventricular fibrillation. By numerical simulations of the Oregonator model, we show that this instability and, thus, the Winfree turbulence may also be observed in the Belousov-Zhabotinsky reaction. The region in the parameter space, where the instability takes place, is determined, and a relationship between the negative-tension instability and the meandering behavior of spiral waves is found. The application of global periodic forcing to control such turbulence in the Oregonator model is discussed.

Journal Article↗

PubMed1998

Three-dimensional microanatomy of perineuronal proteoglycan nets enveloping motor neurons in the rat spinal cord.

Spinal motor neurons possess reticular coats of extracellular matrix proteoglycans on their somata and proximal dendrites. In order to define the anatomical background of the network, spatial relationships of the perineuronal proteoglycans with synaptic boutons and astrocyte processes were analyzed in rat motor neurons by TEM after histochemical detection of the substances with cationic iron colloid, and by SEM after exposure of the cytoarchitecture with NaOH maceration. Narrow intercellular channels filled with proteoglycan were found to extend along the surface of the neurons to form a homogeneous network of a mesh size of about 1 microm. The system of perineuronal channels consisted of two parts: a primary intervaricose net which meandered among synaptic boutons on the surface of the motor neuron, and secondary subvaricose nets which irrigated interfaces between larger boutons and the neuron. No elements in the perineuronal cytoarchitecture coincided with the meshwork of proteoglycan, indicating the involvement of postsynaptic factors in the distribution of the substance. Thin astrocyte processes surrounding the neurons formed a distinct network with heterogeneous meshes corresponding to boutons of various sizes. The perineuronal glial nets extended their surface area in contact with the intervaricose nets of proteoglycan by complex cellular interdigitations. The subvaricose nets of proteoglycan compartmentalized multiple synapses on large boutons, suggesting an involvement in the division of the synapses during development.

Animals↗

PubMed2000

Chromosome no. 1 of Crepis capillaris shows defined 3D-shapes in mitotic prophase.

The shape of mitotic prophase chromosomes has been studied in root tip nuclei by confocal microscopy and 3D-image analysis. Crepis capillaris chromosome no. 1 was used as a test object. Chromosome conformation was studied in early, mid- and in late prophase. In mid- and late prophase, individual chromosomes could be distinguished on the basis of their length. Early prophase chromosomes could not be distinguished as individuals. The central axes of prophase chromosomes were traced with an automated computer procedure and then represented as a string of 3D coordinates. This representation facilitated measurement along the chromosome axis of shape parameters such as curvature (amount of bending), torsion (helical winding) and torsion sign (helical handedness). Stretches of early prophase chromosomes showed full helical turns, which could be left- or right-handed. In the later prophase stages curvature and torsion were statistically analysed. Our data on 40 midprophase chromosomes no. 1 show that they are still highly curved, but full helical turns were no longer found. Instead, an overall meandering pattern was observed. In late prophase, one central loop persisted, flanked by two preferential regions of high curvature.

Algorithms↗

PubMed2001

On the connection between the T-system and the subsynaptic folds in the motor end plate of amphibians.

Using lanthanum as an extracellular marker, the transition between the subsynaptic folds of the motor end plate and the T-system of frog muscle fibres is portrayed for the first time. On the lower segment of the subsynaptic folds of frogs, there are numerous caveolae which can connect with one another to form meandering, branching tubes. The T-system is in contact with these tubes (which run through the sarcoplasm) beneath the motor end plate. In those segments of the end plate with massed sarcoplasm and a cell nucleus, these tubes form networks in close proximity to the cellular organelles. The morphological findings obtained here are compared with findings from mammals. The physiological significance of the transition between the subsynaptic fold and the T-system is discussed.

Animals↗

PubMed1990

Atomic structure of the actin:DNase I complex.

The atomic models of the complex between rabbit skeletal muscle actin and bovine pancreatic deoxyribonuclease I both in the ATP and ADP forms have been determined by X-ray analysis at an effective resolution of 2.8 A and 3A, respectively. The two structures are very similar. The actin molecule consists of two domains which can be further subdivided into two subdomains. ADP or ATP is located in the cleft between the domains with a calcium ion bound to the beta- or beta- and gamma-phosphates, respectively. The motif of a five-stranded beta sheet consisting of a beta meander and a right handed beta alpha beta unit appears in each domain suggesting that gene duplication might have occurred. These sheets have the same topology as that found in hexokinase.

Actins↗

PubMed2006

A magnetic torsional wave near the Galactic Centre traced by a 'double helix' nebula.

The magnetic field in the central few hundred parsecs of the Milky Way has a dipolar geometry and is substantially stronger than elsewhere in the Galaxy, with estimates ranging up to a milligauss (refs 1-6). Characterization of the magnetic field at the Galactic Centre is important because it can affect the orbits of molecular clouds by exerting a drag on them, inhibit star formation, and could guide a wind of hot gas or cosmic rays away from the central region. Here we report observations of an infrared nebula having the morphology of an intertwined double helix about 100 parsecs from the Galaxy's dynamical centre, with its axis oriented perpendicular to the Galactic plane. The observed segment is about 25 parsecs in length, and contains about 1.25 full turns of each of the two continuous, helically wound strands. We interpret this feature as a torsional Alfvén wave propagating vertically away from the Galactic disk, driven by rotation of the magnetized circumnuclear gas disk. The direct connection between the circumnuclear disk and the double helix is ambiguous, but the images show a possible meandering channel that warrants further investigation.

Journal Article↗

PubMed2004

Anabaena circadian clock proteins KaiA and KaiB reveal a potential common binding site to their partner KaiC.

The cyanobacterial clock proteins KaiA and KaiB are proposed as regulators of the circadian rhythm in cyanobacteria. Mutations in both proteins have been reported to alter or abolish circadian rhythmicity. Here, we present molecular models of both KaiA and KaiB from the cyanobacteria Anabaena sp PCC7120 deduced by crystal structure analysis, and we discuss how clock-changing or abolishing mutations may cause their resulting circadian phenotype. The overall fold of the KaiA monomer is that of a four-helix bundle. KaiB, on the other hand, adopts an alpha-beta meander motif. Both proteins purify and crystallize as dimers. While the folds of the two proteins are clearly different, their size and some surface features of the physiologically relevant dimers are very similar. Notably, the functionally relevant residues Arg 69 of KaiA and Arg 23 of KaiB align well in space. The apparent structural similarities suggest that KaiA and KaiB may compete for a potential common binding site on KaiC.

Amino Acid Sequence↗

PubMedDate not supplied

An impact-effect mathematical model incorporating the influence of exposures to fluctuating concentrations in a dispersing plume of pollutant in the atmosphere.

The statistical properties of the impact or toxic load (pollutant concentration raised to an exponent and multiplied by exposure duration), obtained from fluctuating concentrations in a plume dispersing in the atmosphere, are investigated both analytically and experimentally. A general expression for the kth order moment of the impact is derived in terms of the k-time point joint moment of the nth power of the fluctuating plume concentration field. Special cases of this general relationship are treated explicitly: (i) a simple model for the ensemble-mean impact (or equivalently, the ensemble-mean impact ratio) is derived on the basic hypothesis that the higher moments of concentration can be adequately modelled using an exponential probability density function (PDF), and this hypothesis is shown to give results that agree remarkably well with an extensive new set of concentration fluctuation measurements; and (ii) a model for the integral time scale of the process obtained by raising the concentration to the nth power is formulated using Gifford's meandering plume model, and the latter is subsequently used to derive a simple expression for estimating the impact variance for all exposure times, given the mean and mean-square concentrations and the plume concentration integral time scale only. The results of this model for impact variance are favorably compared with some data from full-scale field experiments. The impact PDF is found to be reasonably well-characterized by a clipped-normal PDF for exposure times, t(e), of practical interest (e.g., t(e) approximately >5 s). The implications of these results, for determining the fraction of an exposed population that will experience a specified level of effect from a random impact arising from exposure to a fluctuating plume of pollutant, are discussed briefly.

Air Pollutants↗

PubMed2004

Sequential DNA hybridisation assays by fast micromixing.

The prospects of performing DNA hybridisation assays in a novel sequential scheme are explored in this article. It is based on recording the kinetics of hybridisation on a microfluidic device measuring only 10 by 5 mm. It contains a split channel system for fast mixing and a subsequent meandering channel to observe the evolution of the mixture by optical means. The problems of diffusion limitations in the laminar flow regime are overcome by reducing the average diffusion distance to a few micrometers only. DNA oligomers (20-mers) of different sequences were injected on the chip for mixing. The detection of hybridisation was based on the fluorescence of DNA-intercalating dyes. Two modes of operation were investigated. First, the samples were injected into the micromixing device at a high flow rate of 40 microl min(-1). When the sample passed through the actual micromixing unit, the flow rate was reduced to allow for measurement of fluorescence levels at various steady-state reaction times in the range of 2-15 s, as defined by the channel geometry. Using this continuous flow approach, photobleaching of fluorophores could be avoided. In a buffer containing 0.2 M NaCl, 2 base-pair mismatches could routinely be detected within 5-20 s. Single base-pair mismatches were successfully identified under low salt conditions. In the second mode, the flow was completely stopped and the evolution of the total fluorescence signal influenced by the hybridisation of oligomers and photobleaching was observed. Whereas the sequence-dependent effects remained unchanged, the assay times between the mixing of two oligomers and clear identification of their hybridisation properties could be reduced down to a maximum of 5-7 s, in some cases even below 1 s.

DNA↗