Enzymatic cyclization of a potent Bowman-Birk protease inhibitor, sunflower trypsin inhibitor-1, and solution structure of an acyclic precursor peptide

The most potent known naturally occurring Bowman-Birk inhibitor, sunflower trypsin inhibitor-1 (SFTI-1), is a bicyclic 14-amino acid peptide from sunflower seeds comprising one disulfide bond and a cyclic backbone. At present, little is known about the cyclization mechanism of SFTI-1. We show here that an acyclic permutant of SFTI-1 open at its scissile bond, SFTI-1[ 6,5], also functions as an inhibitor of trypsin and that it can be enzymatically backbone-cyclized by incubation with bovine beta-trypsin. The resulting ratio of cyclic SFTI-1 to SFTI1[6,5] is similar to9:1 regardless of whether trypsin is incubated with SFTI-1[ 6,5] or SFTI-1. Enzymatic resynthesis of the scissile bond to form cyclic SFTI-1 is a novel mechanism of cyclization of SFTI-1[ 6,5]. Such a reaction could potentially occur on a trypsin affinity column as used in the original isolation procedure of SFTI-1. We therefore extracted SFTI-1 from sunflower seeds without a trypsin purification step and confirmed that the backbone of SFTI-1 is indeed naturally cyclic. Structural studies on SFTI-1[ 6,5] revealed high heterogeneity, and multiple species of SFTI-1[ 6,5] were identified. The main species closely resembles the structure of cyclic SFTI-1 with the broken binding loop able to rotate between a cis/trans geometry of the I7-P8 bond with the cis conformer being similar to the canonical binding loop conformation. The non-reactive loop adopts a beta-hairpin structure as in cyclic wild-type SFTI-1. Another species exhibits an isoaspartate residue at position 14 and provides implications for possible in vivo cyclization mechanisms.

The preparation and characterization of tin(IV) complexes of 2-quinolinecarboxaldehyde Schiff bases of S-methyl- and S-benzyldithiocarbazates and the X-ray crystal and molecular structures of the 2-quinolinecarboxaldehyde Schiff base of S-benzyldithi

New tin(IV) complexes of empirical formula, Sn(NNS)I-3 (NNS = anionic forms of the 2-quinolinecarboxaldehyde Schiff bases of S-methyl- and S-benzyldithiocarbazate) have been prepared and characterized by a variety of physico-chemical techniques. In the solid state, the Schiff bases exist as the thione tautomer but in solution and in the presence of tin(IV) iodide they convert to the thiol tautomer and coordinate to the tin atom in their deprotonated thiolate forms. The structures of the free ligand, Hqaldsbz and its triiodotin(IV) complex, [Sn(qaldsbz)I-3] have been determined by X-ray diffraction. The complex, [Sn(qaldsbz)I-3] has a distorted octahedral structure with the Schiff base coordinated to the tin atom as a uninegatively charged tridentate chelating agent via the quinoline nitrogen atom, the azomethine nitrogen atom and the thiolate sulfur atom. The three iodo ligands are coordinated meridionally to the tin atom. The distortion from an ideal octahedral geometry of [Sn(qaldsbz)I-3] is attributed to the restricted bite size of the tridentate Schiff base ligand. (C) 2004 Elsevier Ltd. All rights reserved.

Stereocontrol in complexes of cyclam-like macrocycles - influences of chirality

Enforcement of chirality upon a macrocyclic tetramine ligand structure by the introduction of an asymmetric pendent arm which does not significantly modify the macrocycle conformation has no significant effect upon the geometry of the coordination sphere of a bound metal. Where substitution engendering chirality does cause a change in the ligand conformation, in particular for a ligand of restricted stereochemistry, these effects can be much greater. Thus, conversion of 3,7-diazacycloheptane to a macrocycle via attachment of chiral sidearms and ring closure through a template reaction leads to cyclam derivatives with unusual coordination properties. (C) 2004 Elsevier Ltd. All rights reserved.

Finite element analysis of fault bend influence on stick-slip instability along an intra-plate fault

Earthquakes have been recognized as resulting from stick-slip frictional instabilities along the faults between deformable rocks. A three-dimensional finite-element code for modeling the nonlinear frictional contact behaviors between deformable bodies with the node-to-point contact element strategy has been developed and applied here to investigate the fault geometry influence on the nucleation and development process of the stick-slip instability along an intra-plate fault through a typical fault bend model, which has a pre-cut fault that is artificially bent by an angle of 5.6degrees at the fault center. The numerical results demonstrate that the geometry of the fault significantly affects nucleation, termination and restart of the stick-slip instability along the intra-plate fault, and all these instability phenomena can be well simulated using the current finite-element algorithm.

Simulation of a complete reflected shock tunnel showing a vortex mechanism for flow contamination

Simulations of a complete reflected shock tunnel facility have been performed with the aim of providing a better understanding of the flow through these facilities. In particular, the analysis is focused on the premature contamination of the test flow with the driver gas. The axisymmetric simulations model the full geometry of the shock tunnel and incorporate an iris-based model of the primary diaphragm rupture mechanics, an ideal secondary diaphragm and account for turbulence in the shock tube boundary layer with the Baldwin-Lomax eddy viscosity model. Two operating conditions were examined: one resulting in an over-tailored mode of operation and the other resulting in approximately tailored operation. The accuracy of the simulations is assessed through comparison with experimental measurements of static pressure, pitot pressure and stagnation temperature. It is shown that the widely-accepted driver gas contamination mechanism in which driver gas 'jets' along the walls through action of the bifurcated foot of the reflected shock, does not directly transport the driver gas to the nozzle at these conditions. Instead, driver gas laden vortices are generated by the bifurcated reflected shock. These vortices prevent jetting of the driver gas along the walls and convect driver gas away from the shock tube wall and downstream into the nozzle. Additional vorticity generated by the interaction of the reflected shock and the contact surface enhances the process in the over-tailored case. However, the basic mechanism appears to operate in a similar way for both the over-tailored and the approximately tailored conditions.

Volcanic setting of the Bajo de la Alumbrera porphyry Cu-Au deposit, Farallon Negro Volcanics, Northwest Argentina

The late Miocene Farallon Negro volcanics, comprising basaltic to rhyodacitic volcano-sedimentary rocks, host the Bajo de la Alumbrera porphyry copper-gold deposit in northwest Argentina. Early studies of the geology of the district have underpinned the general model for porphyry ore deposits where hydrothermal alteration and mineralization develop in and around porphyritic intrusions emplaced at shallow depths (2.5-3.5 km) into stratovolcanic assemblages. The Farallon Negro succession is dominated by thick sequences of volcano-sedimentary breccias, with lavas forming a minor component volumetrically. These volcaniclastic rocks conformably overlie crystalline basement-derived sedimentary rocks deposited in a developing foreland basin southeast of the Puna-Altiplano plateau. Within the Farallon Negro volcanics, volcanogenic accumulations evolved from early mafic to intermediate and silicic compositions. The younger and more silicic rocks are demonstrably coeval and comagmatic with the earliest group of mineralized porphyritic intrusions at Bajo de la Alumbrera. Our analysis of the volcanic stratigraphy and facies architecture of the Farallon Negro volcanics indicates that volcanic eruptions evolved from effusive to mixed effusive and explosive styles, as magma compositions changed to more intermediate and silicic compositions. Air early phase of mafic to intermediate voleanism was characterized by small synsedimentary intrusions with peperitic contacts, and lesser lava units scattered widely throughout the district, and interbedded with thick and extensive successions of coarse-grained sedimentary breccias. These sedimentary breccias formed from numerous debris- and hyperconcentrated flow events. A later phase of silicic volcanism included both effusive eruptions, forming several areally restricted lavas, and explosive eruptions, producing more widely dispersed (up to 5 kin) tuff units, some tip to 30-m thickness in proximal sections. Four key features of the volcanic stratigraphy suggest that the Farallon Negro volcanics need not simply record the construction of a large steep-sided polygenetic stratovolcano: (1) sheetlike, laterally continuous debris-flow and other coarse-grained sedimentary deposits are dominant, particularly in the lower sections; (2) mafic-intermediate composition lavas are volumetrically minor; (3) peperites are present throughout the sequence; and (4) fine-grained lacustrine sandstone-siltstone sequences occur in areas previously thought to be proximal to the summit region of the stratovolcano. Instead, the nature, distribution, and geometry of volcanic and volcaniclastic facies suggest that volcanism occurred as a relatively low relief, multiple-vent volcanic complex at the eastern edge of a broad, > 200-km-wide late Miocene volcanic belt and oil ail active foreland sedimentary basin to the Puna-Altiplano. Volcanism that occurred synchronously with the earliest stages of porphyry-related mineralization at Bajo de la Alumbrera apparently developed in an alluvial to ring plain setting that was distal to larger volcanic edifices.

Model for gas-liquid flow through wet porous medium

A method involving bubbling of air through a fibrous filter immersed in water has recently been investigated (Agranovski et al. [1]). Experimental results showed that the removal efficiency for ultra-fine aerosols by such filters was greatly increased compared to dry filters. Nuclear Magnetic Resonance (NMR) imaging was used to examine the wet filter and to determine the nature of the gas flow inside the filter (Agranovski et al. [2]). It was found that tortuous preferential pathways (or flow tubes) develop within the filter through which the air flows and the distribution of air and water inside the porous medium has been investigated. The aim of this paper is to investigate the geometry of the pathways and to make estimates of the flow velocities and particle removal efficiency in such pathways. A mathematical model of the flow of air along the preferred pathways has been developed and verified experimentally. Even for the highest realistic gas velocity the flow field was essentially laminar (Re approximate to 250). We solved Laplace's equation for stream function to map trajectories of particles and gas molecules to investigate the possibility of their removal from the carrier.

Tris(ethylenediamine-N,N')zinc(II) dinitrate

The Zn-II atom in [Zn(C2H8N2)(3)](NO3)(2) has a distorted octahedral geometry of D-3 symmetry With three ethylenediamine bidentate Ligands completing the coordination.

Instabilities and drop formation in cylindrical liquid jets in reduced gravity

The effects of convective and absolute instabilities on the formation of drops formed from cylindrical liquid jets of glycerol/water issuing into still air were investigated. Medium-duration reduced gravity tests were conducted aboard NASA's KC-135 and compared to similar tests performed under normal gravity conditions to aid in understanding the drop formation process. In reduced gravity, the Rayleigh-Chandrasekhar Equation was found to accurately predict the transition between a region of absolute and convective instability as defined by a critical Weber number. Observations of the physics of the jet, its breakup, and subsequent drop dynamics under both gravity conditions and the effects of the two instabilities on these processes are presented. All the normal gravity liquid jets investigated, in regions of convective or absolute instability, were subject to significant stretching effects, which affected the subsequent drop and associated geometry and dynamics. These effects were not displayed in reduced gravity and, therefore, the liquid jets would form drops which took longer to form (reduction in drop frequency), larger in size, and more spherical (surface tension effects). Most observed changes, in regions of either absolute or convective instabilities, were due to a reduction in the buoyancy force and an increased importance of the surface tension force acting on the liquid contained in the jet or formed drop. Reduced gravity environments allow better investigations to be performed into the physics of liquid jets, subsequently formed drops, and the effects of instabilities on these systems. In reduced gravity, drops form up to three times more slowly and as a consequence are up to three times larger in volume in the theoretical absolute instability region than in the theoretical convective instability region. This difference was not seen in the corresponding normal gravity tests due to the masking effects of gravity. A drop is shown to be able to form and detach in a region of absolute instability, and spanning the critical Weber number (from a region of convective to absolute instability) resulted in a marked change in dynamics and geometry of the liquid jet and detaching drops. (C) 2002 American Institute of Physics.

Ground water model calibration using pilot points and regularization

Use of nonlinear parameter estimation techniques is now commonplace in ground water model calibration. However, there is still ample room for further development of these techniques in order to enable them to extract more information from calibration datasets, to more thoroughly explore the uncertainty associated with model predictions, and to make them easier to implement in various modeling contexts. This paper describes the use of pilot points as a methodology for spatial hydraulic property characterization. When used in conjunction with nonlinear parameter estimation software that incorporates advanced regularization functionality (such as PEST), use of pilot points can add a great deal of flexibility to the calibration process at the same time as it makes this process easier to implement. Pilot points can be used either as a substitute for zones of piecewise parameter uniformity, or in conjunction with such zones. In either case, they allow the disposition of areas of high and low hydraulic property value to be inferred through the calibration process, without the need for the modeler to guess the geometry of such areas prior to estimating the parameters that pertain to them. Pilot points and regularization can also be used as an adjunct to geostatistically based stochastic parameterization methods. Using the techniques described herein, a series of hydraulic property fields can be generated, all of which recognize the stochastic characterization of an area at the same time that they satisfy the constraints imposed on hydraulic property values by the need to ensure that model outputs match field measurements. Model predictions can then be made using all of these fields as a mechanism for exploring predictive uncertainty.

A time-harmonic target-field method for designing unshielded RF coils in MRI

Time-harmonic methods are required in the accurate design of RF coils as operating frequency increases. This paper presents such a method to find a current density solution on the coil that will induce some desired magnetic field upon an asymmetrically located target region within. This inverse method appropriately considers the geometry of the coil via a Fourier series expansion, and incorporates some new regularization penalty functions in the solution process. A new technique is introduced by which the complex, time-dependent current density solution is approximated by a static coil winding pattern. Several winding pattern solutions are given, with more complex winding patterns corresponding to more desirable induced magnetic fields.

Variability in Cobb angle measurements using reformatted computerized tomography scans

Study Design. Survey of intraobserver and interobserver measurement variability. Objective. To assess the use of reformatted computerized tomography (CT) images for manual measurement of coronal Cobb angles in idiopathic scoliosis. Summary of Background Data. Cobb angle measurements in idiopathic scoliosis are traditionally made from standing radiographs, whereas CT is often used for assessment of vertebral rotation. Correlating Cobb angles from standing radiographs with vertebral rotations from supine CT is problematic because the geometry of the spine changes significantly from standing to supine positions, and 2 different imaging methods are involved. Methods. We assessed the use of reformatted thoracolumbar CT images for Cobb angle measurement. Preoperative CT of 12 patients with idiopathic scoliosis were used to generate reformatted coronal images. Five observers measured coronal Cobb angles on 3 occasions from each of the images. Intraobserver and interobserver variability associated with Cobb measurement from reformatted CT scans was assessed and compared with previous studies of measurement variability using plain radiographs. Results. For major curves, 95% confidence intervals for intraobserver and interobserver variability were +/- 6.6 degrees and +/- 7.7 degrees, respectively. For minor curves, the intervals were +/- 7.5 degrees and +/- 8.2 degrees, respectively. Intraobserver and interobserver technical error of measurement was 2.4 degrees and 2.7 degrees, with reliability coefficients of 88% and 84%, respectively. There was no correlation between measurement variability and curve severity. Conclusions. Reformatted CT images may be used for manual measurement of coronal Cobb angles in idiopathic scoliosis with similar variability to manual measurement of plain radiographs.