Substitution Matrices of Residue Triplets Derived from Protein Blocks.

In protein sequence alignment, residue similarity is usually evaluated by substitution matrix, which scores all possible exchanges of one amino acid with another. Several matrices are widely used in sequence alignment, including PAM matrices derived from homologous sequence and BLOSUM matrices derived from aligned segments of BLOCKS. However, most matrices have not addressed the high-order residue-residue interactions that are vital to the bioproperties of protein.With consideration for the inherent correlation in residue triplet, we present a new scoring scheme for sequence alignment. Protein sequence is treated as overlapping and successive 3-residue segments. Two edge residues of a triplet are clustered into hydrophobic or polar categories, respectively. Protein sequence is then rewritten into triplet sequence with 2 · 20 · 2 = 80 alphabets. Using a traditional approach, we construct a new scoring scheme named TLESUMhp (TripLEt SUbstitution Matrices with hydropobic and polar information) for pairwise substitution of triplets, which characterizes the similarity of residue triplets. The applications of this matrix led to marked improvements in multiple sequence alignment and in searching structurally alike residue segments. The reason for the occurrence of the ‘‘twilight zone,’’ i.e., structure explosion of lowidentity sequences, is also discussed.

飞行高度及设计长度对锥形流乘波体优化的影响 Altitude and Design Length Effects of Optimized Waverider Derived from Cone Flow

高超声速条件下,乘波体布局具有高升阻比特性,本文应用单纯形加速法,以最大升阻比为目标,开展了锥形流乘波体布局优化设计研究.特别是,研究了在高层大气飞行时雷诺数效应与气动特性的关系,从乘波体飞行高度与设计长度两方面探讨雷诺数对乘波体优化的影响,结果表明：给定设计马赫数和圆锥角情况下,对于最大升阻比优化乘波体,其雷诺数越小,摩擦阻力越大,而升阻比越低.

Waverider configurations derived from general conical flowfields

A method based on the computational fluid dynamics (CFD) is presented for a flexible waverider's design. The generating bodies of this method could be any cones. In addition, either the leading edge or the profile of the scramjet's inlet is used as the waverider's definition curve, parameterized by the quadric function, the sigmoid function or the B-spline function. Furthermore, several numerical examples are carried out to validate the method and the relevant codes. The CFD results of the configurations show that all the designs are successful. Moreover, primary suggestions are proposed for practical design by comparing the geometrical and aerodynamic performances of the cone-derived waveriders at Mach 6.

Formation and characterization of tin oxide aerogel derived from sol-gel process based on tetra(n-butoxy)tin(IV)

Transparent and translucent SnO2 aerogels with high specific surface area (>300m(2)/g) have been prepared by sol-gel process using tetra(n-butoxy)tin(IV) as a starting compound, and supercritical drying technique for solvent extraction. Light scattering measurements reveal that the polymeric cluster size distribution in sol system is gradually broadened during sol-gel transition. SEM images show that the aerogels are made up of the cottonlike oxide agglomerates with a large number of Pores. TEM images show that these aerogels seem to be self-similar at different magnifications. Their pore size distribution is pretty wide ranging, from mesopore to macropore especially for that of translucent aerogel. (C) 2004 Elsevier B.V. All rights reserved.

Effect of water content in sol on optical properties of hybrid sol-gel derived TiO2/SiO2/ormosil film

Sol-gel derived TiO2/SiO2/ormosil hybrid planar waveguides have been deposited on soda-lime glass slides and silicon substrates, films were heat treated at 150 degreesC for 2 h or dried at room temperature. Different amounts of water were added to sols to study their impacts on microstructures and optical properties of films. The samples were characterized by m-line spectroscopy, Fourier transform infrared spectroscopy (FT-IR), UV/VIS/NIR spectrophotometer (UV-vis), atomic force microscopy (AFM), thermal analysis instrument and scattering-detection method. The refractive index was found to have the largest value at the molar ratio H2O/OR = 1 in sol (OR means -OCH3, -OC2H5 and -OC4H9 in the sol), whereas the thickest film appears at H2O/OR = 1/2. The rms surface roughness of all the films is lower than 1.1 nm, and increases with the increase of water content in sol. Higher water content leads to higher attenuation of film. (C) 2004 Elsevier B.V. All rights reserved.

A novel algesic peptide derived from skin secretions of the frog Amolops loloensis

Several algesic agents including bradykinin and tachykinin have been identified from skin secretions of amphibians. They may act in defensive roles against aggressors. In this study, a novel peptide named Amolos with an amino acid sequence of FLPIVGAKL an

Identification of novel semenogelin I-derived antimicrobial peptide from liquefied human seminal plasma

Semenogelin I (SgI) is one of the most abundant proteins in human seminal plasma. SgI plays a key role in sperm coagulation and spermatozoon immobilization. in addition, SgI and/or its proteolytic fragments are involved in regulating spermatozoon motility

Novel cathelicidin-derived antimicrobial peptides from Equus asinus

In the present study, EA-CATH1 and EA-CATH2 were identified from a constructed lung cDNA library of donkey (Equus asinus) as members of cathelicidin-derived antimicrobial peptides, using a nested PCR-based cloning strategy. Composed of 25 and 26 residues, respectively, EA-CATH1 and EA-CATH2 are smaller than most other cathelicidins and have no sequence homology to other cathelicidins identified to date. Chemically synthesized EA-CATH1 exerted potent antimicrobial activity against most of the 32 strains of bacteria and fungi tested, especially the clinically isolated drug-resistant strains, and minimal inhibitory concentration values against Gram-positive bacteria were mostly in the range of 0.3-2.4 mu g center dot mL-1. EA-CATH1 showed an extraordinary serum stability and no haemolytic activity against human erythrocytes in a dose up to 20 mu g center dot mL-1. CD spectra showed that EA-CATH1 mainly adopts an alpha-helical conformation in a 50% trifluoroethanol/water solution, but a random coil in aqueous solution. Scanning electron microscope observations of Staphylococcus aureus (ATCC2592) treated with EA-CATH1 demonstrated that EA-CATH could cause rapid disruption of the bacterial membrane, and in turn lead to cell lysis. This might explain the much faster killing kinetics of EA-CATH1 than conventional antibiotics revealed by killing kinetics data. In the presence of CaCl2, EA-CATH1 exerted haemagglutination activity, which might potentiate an inhibition against the bacterial polyprotein interaction with the host erythrocyte surface, thereby possibly restricting bacterial colonization and spread.

In vitro construction of a recombinant human embryonic brain-derived neurotrophin-4 gene and pEGFP-N1 vector

BACKGROUND: Neurotrophin-4 (NT-4) can promote neuronal growth, development, differentiation, maturation, and survival. NT-4 can also improve recovery and regeneration of injured neurons, but cannot pass through the blood-brain barrier, which limits its ac