Molecular characterization of a weak fibrinogen-clotting enzyme from Trimeresurus jerdonii venom

A fibrinogen-clotting enzyme designed as jerdonobin-II was isolated from the venom of Trimeresurus jerdonii. It differed in molecular weight and N-terminal sequence with the previously isolated jerdonobin, a thrombin-like enzyme from the same venom. The enzyme consists of a single polypeptide chain with molecular weights of 30,000 and 32,000 under non-reducing and reducing conditions, respectively. Jerdonobin-II showed weak fibrinogen clotting activity and its activity unit on fibrinogen was calculated to be less than one unit using human thrombin as standard. The precursor protein sequence of jerodonobin-II was deduced from cloned cDNA sequence. The sequence shows high similarity (identity = 89%) to TSV-PA, a specific plasminogen activator from venom of T stejnegeri. Despite of the sequence similarity, jerdonobin-II was found devoid of plasminogen activating effect. Sequence alignment analysis suggested that the replacement of Lys(239) in TSV-PA to Gln(239) in jerdonobin-II might play an important role on their plasminogen activating activity difference. (C) 2005 Elsevier Ltd. All rights reserved.

Electroluminescence behavior of ZnO/Si heterojunctions: Energy band alignment and interfacial microstructure

n-ZnO/p-Si heterojunction light-emitting diodes (LEDs) show weak defect-related electroluminescence (EL). In order to analyze the origin of the weak EL, the energy band alignment and interfacial microstructure of ZnO/Si heterojunction are investigated by x-ray photoelectron spectroscopy. The valence band offset (VBO) is determined to be 3.15 +/- 0.15 eV and conduction band offset is -0.90 +/- 0.15 eV, showing a type-II band alignment. The higher VBO means a high potential barrier for holes injected from Si into ZnO, and hence, charge carrier recombination takes place mainly on the Si side rather than the ZnO layer. It is also found that a 2.1 nm thick SiOx interfacial layer is formed at the ZnO/Si interface. The unavoidable SiOx interfacial layer provides to a large number of nonradiative centers at the ZnO/Si interface and gives rise to poor crystallinity in the ZnO films. The weak EL from the n-ZnO/p-Si LEDs can be ascribed to the high ZnO/Si VBO and existence of the SiOx interfacial layer.

Weak Zone Related Seismic Cycles in Progressive Failure Leading to Collapse in Brittle Crust

Until quite recently our understanding of the basic mechanical process responsible for earthquakes and faulting was not well known. It can be argued that this was partly a consequence of the complex nature of fracture in crust and in part because evidence of brittle phenomena in the natural laboratory of the earth is often obliterated or obscured by other geological processes. While it is well understood that the spatial and temporal complexity of earthquakes and the fault structures emerge from geometrical and material built-in heterogeneities, one important open question is how the shearing becomes localized into a band of intense fractures. Here the authors address these questions through a numerical approach of a tectonic plate by considering rockmass heterogeneity both in microscopic scale and in mesoscopic scale. Numerical simulations of the progressive failure leading to collapse under long-range slow driving forces in the far-field show earthquake-like rupture behavior. $En Echelon$ crack-arrays are reproduced in the numerical simulation. It is demonstrated that the underlying fracturing induced acoustic emissions (or seismic events) display self-organized criticality------from disorder to order. The seismic cycles and the geometric structures of the fracture faces, which are found greatly depending on the material heterogeneity (especially on the macroscopic scale), agree with that observed experimentally in real brittle materials. It is concluded that in order to predict a main shock, one must have extremely detailed knowledge on very minor features of the earth's crust far from the place where the earthquake originated. If correct, the model proposed here seemingly provides an explanation as to why earthquakes to date are not predicted so successfully. The reason is not that the authors do not understand earthquake mechanisms very well but that they still know little about our earth's crust.

An experimental study of the influence of weak convection on perikinetic coagulation

A remarkably increased coagulation rate for 2-mu m PS spheres was previously reported for a perikinetic coagulation experiment performed under microgravity conditions (1998, R. Folkersma, A. J. G. van Diemen, and H. N. Stein, J. Colloid Interface Sci. 206, 482); from this experiment, it was assumed that the leading factor slowing the coagulation process under normal gravitation was free convection due to gravity (1998, R. Folkersma, and H. N. Stein, J. Colloid Interface Sci. 206, 494). To test the influence of free convection as a single-effect factor on the coagulation process, a ground-based experiment was constructed. The coagulation rate of 2-mu m PS spheres dispersed in water was determined by measuring the turbidity of the dispersion solution while convection-driven flows in the solution were checked with a visual magnification system. We found that it was possible to cease free convection-driven particle flows on the ground, as long as the experiments were carefully operated. The strength of convection was controlled by changing the temperature gradient applied to the sample cell. By monitoring both the coagulation rate and convection-driven flows simultaneously, our experiments showed that weak free convection (maximum speed <150 mu m/s) actually has negligible effects on the coagulation rate.

Effect of weak Brownian motion on gravitational coagulation

The effect of a small amount of Brownian diffusion on gravitational coagulation is numerically calculated by incorporating gravitational and interparticle forces (both attractive and repulsive), as well as hydrodynamic interactions. It is found that weak Brownian diffusion, the effect of which is nonlinearly coupled with gravity, can act to decrease the coagulation rate.

Clemaps: Multiple Alignment Of Protein Structures Based On Conformational Letters

CLEMAPS is a tool for multiple alignment of protein structures. It distinguishes itself from other existing algorithms for multiple structure alignment by the use of conformational letters, which are discretized states of 3D segmental structural states. A letter corresponds to a cluster of combinations of three angles formed by C-alpha pseudobonds of four contiguous residues. A substitution matrix called CLESUM is available to measure the similarity between any two such letters. The input 3D structures are first converted to sequences of conformational letters. Each string of a fixed length is then taken as the center seed to search other sequences for neighbors of the seed, which are strings similar to the seed. A seed and its neighbors form a center-star, which corresponds to a fragment set of local structural similarity shared by many proteins. The detection of center-stars using CLESUM is extremely efficient. Local similarity is a necessary, but insufficient, condition for structural alignment. Once center-stars are found, the spatial consistency between any two stars are examined to find consistent star duads using atomic coordinates. Consistent duads are later joined to create a core for multiple alignment, which is further polished to produce the final alignment. The utility of CLEMAPS is tested on various protein structure ensembles.

A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features

As a basic tool of modern biology, sequence alignment can provide us useful information in fold, function, and active site of protein. For many cases, the increased quality of sequence alignment means a better performance. The motivation of present work is to increase ability of the existing scoring scheme/algorithm by considering residue–residue correlations better. Based on a coarse-grained approach, the hydrophobic force between each pair of residues is written out from protein sequence. It results in the construction of an intramolecular hydrophobic force network that describes the whole residue–residue interactions of each protein molecule, and characterizes protein's biological properties in the hydrophobic aspect. A former work has suggested that such network can characterize the top weighted feature regarding hydrophobicity. Moreover, for each homologous protein of a family, the corresponding network shares some common and representative family characters that eventually govern the conservation of biological properties during protein evolution. In present work, we score such family representative characters of a protein by the deviation of its intramolecular hydrophobic force network from that of background. Such score can assist the existing scoring schemes/algorithms, and boost up the ability of multiple sequences alignment, e.g. achieving a prominent increase (50%) in searching the structurally alike residue segments at a low identity level. As the theoretical basis is different, the present scheme can assist most existing algorithms, and improve their efficiency remarkably.

Alignment of nanoparticles formed on the surface of 6H-SiC crystals irradiated by two collinear femtosecond laser beams

Nanoripples with periods of 150 and 80 nm are formed on the surface of 6H-SiC crystals irradiated by the p-polarized 800 nm and the s-polarized 400 nm femtosecond lasers, respectively. When both of the two collinear laser beams focus simultaneously on the sample surface, nanoparticles are formed on the whole ablation area, and they array in parallel lines. We propose and confirm that the second harmonics in the sample surface excited by the incident lasers plays an important role in the formation of nanostructures.

Quantum interference in laser-induced nonsequential double ionization in diatomic molecules: Role of alignment and orbital symmetry

We address the influence of the orbital symmetry and the molecular alignment with respect to the laser-field polarization on laser-induced nonsequential double ionization of diatomic molecules, in the length and velocity gauges. We work within the strong-field approximation and assume that the second electron is dislodged by electron-impact ionization, and also consider the classical limit of this model. We show that the electron-momentum distributions exhibit interference maxima and minima due to electron emission at spatially separated centers. The interference patterns survive integration over the transverse momenta for a small range of alignment angles, and are sharpest for parallel-aligned molecules. Due to the contributions of the transverse-momentum components, these patterns become less defined as the alignment angle increases, until they disappear for perpendicular alignment. This behavior influences the shapes and the peaks of the electron-momentum distributions.

Laser beam automatic alignment in multipass amplifier

A laser beam automatic alignment system is applied in a multipass amplifier of the SG-III prototype laser. Considering the requirements of the SG-III prototype facility, by combining the general techniques of the laser beam automatic alignment system, according to the image relayed of the pinholes in the spatial filter, and utilizing the optical position and the spatial distribution of the four pinholes of the main spatial filter in the multipass amplifier of the SG-III prototype, a reasonable and optimized scheme for automatic aligning multipass beam paths is presented. It is demonstrated on the multipass amplifier experimental system. (C) 2004 Society of Photo-Optical Instrumentation Engineers.

Split-aperture laser pulse compressor design tolerant to alignment and line-density differences

We introduce a four-pass laser pulse compressor design based on two grating apertures with two gratings per aperture that is tolerant to some alignment errors and, importantly, to grating-to-grating period variations. Each half-beam samples each grating in a diamond-shaped compressor that is symmetric about a central bisecting plane. For any given grating, the two half-beams impinge on opposite sides of its surface normal. It is shown that the two split beams have no pointing difference from paired gratings with different periods. Furthermore, no phase shift between half-beams is incurred as long as the planes containing a grating line and the surface normal for each grating of the pair are parallel. For grating pairs satisfying this condition, gratings surfaces need not be on the same plane, as changes in the gap between the two can compensate to bring the beams back in phase. © 2008 Optical Society of America.