Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation

The chemokine receptor CCR5 is the receptor for several chemokines and major coreceptor for R5 human immunodeficiency virus type-1 strains entry into cell. Three-dimensional models of CCR5 were built by using homology modeling approach and 1 ns molecular dynamics (MD) simulation, because studies of site-directed mutagenesis and chimeric receptors have indicated that the N-terminus (Nt) and extracellular loops (ECLs) of CCR5 are important for ligands binding and viral fusion and entry, special attention was focused on disulfide bond function, conformational flexibility, hydrogen bonding, electrostatic interactions, and solvent-accessible surface area of Nt and ECLs of this protein part. We found that the extracellular segments of CCR5 formed a well-packet globular domain with complex interactions occurred between them in a majority of time of MID simulation, but Nt region could protrude from this domain sometimes. The disulfide bond Cys20-Cys269 is essential in controlling specific orientation of Nt region and maintaining conformational integrity of extracellular domain. RMS comparison analysis between conformers revealed the ECL1 of CCR5 stays relative rigid, whereas the ECL2 and Nt are rather flexible. Solvent-accessible surface area calculations indicated that the charged residues within Nt and ECL2 are often exposed to solvent. Integrating these results with available experimental data, a two-step gp120-CCR5 binding mechanism was proposed. The dynamic interaction of CCR5 extracellular domain with gp120 was emphasized. (C) 2004 Elsevier B.V. All rights reserved.

Transformation of accommodation space of the Cretaceous Qingshankou Formation, the Songliao Basin, NE China

Analysis of accommodation space variation during deposition of the Cretaceous Qingshankou Formation in the Songliao Basin, NE China, indicates that accommodation space changed both through time and across the basin as a seesaw movement. The mid-upper Qingshankou Formation is divided into three units. In each unit, changes of accommodation space differ in the southern and northern part of the basin. Increasing accommodation in the southern part is accompanied by a decrease in the northern part, and vice versa. Between the northern and southern basin, there was a neutral belt that is like a fulcrum, called the transformation belt here, where the accommodation did not change to any significant degree. We call this response 'accommodation transformation', whose characteristics are defined by tectonic subsidence analysis, palaeontological and sedimentary analyses. The accommodation increasing belt, decreasing belt, transformation belt and accommodation transformation boundary together constitute the accommodation transformation system. The recognition of accommodation transformation in the Songliao Basin provides a new insight into sequence stratigraphy and might be widely applicable.

Gene cloning and functional analysis of glycosaminoglycan-degrading enzyme chondroitin AC lyase from Flavobacterium columnare G(4)

The chondroitin AC lyase gene, cslA, was cloned for the first time from the fish bacterial pathogen F. columnare G(4). From the first transcription initiation site, the cslA extends 2620 nucleotides to the end of the 3' region. The open reading frame of cslA transcript has 2286 nucleotides encoding 762 amino acids with a 16 residues long signal peptide at the N-terminus. The gene, cslA was then successfully expressed in Escherichia coli and recombinant chondroitin AC lyase, rChonAC was purified, with its lytic activity analyzed. Zymography analysis copolymerized with chondroitin sulphate revealed the lytic activity of rChonAC and also the crude native ChonAC isolated from periplamic space of cultured F. columnare G(4). The low level of lytic activity observed in crude native ChonAC may be due possibly to the low level of expression of this gene in the cultured condition. The expression and the role of this virulence factor is of interest for further research on the pathogenesis of F. columnare.

Density matrix Loschmidt echo and quantum phase transitions

We introduce the concept of the Loschmidt echo (LE) to the space of the reduced density matrix of spin and fermionic systems to study the density matrix LEs (DMLEs) of the one-dimensional extended Hubbard model and the transverse field Ising model. Our results show that the DMLEs are remarkably influenced by the criticality of the system, and the method is a convenient way to study quantum phase transitions.

Effects of subretinal implant materials on the viability, apoptosis and barrier function of cultured RPE cells

Background: Subretinal microphotodiode array (MPDA) is a type of visual prosthesis used for the implantation in the subretinal space of patients with progressive photoreceptor cell loss. The present study aimed to evaluate the effect of materials for MPDA on the viability, apoptosis and barrier function of cultured pig retinal pigment epithelium (RPE) cells.Methods: Primary culture of pig RPE cells was performed and 24 pig eyes were used to start RPE culture. The third passage of the cultures was plated on different materials for MPDA and MPDAs. The tetrazolium dye-reduction assay (MTT) was used to determine RPE cell viability. Flow cytometry was measured to indicate the apoptosis rates of RPE cells on different materials. RPE cells were also cultured on microporous filters, and the transepithelial resistance and permeability of the experimental molecule were measured to determine the barrier function.Results: The data from all the methods indicated no significant difference between the materials groups and the control group, and the materials tested showed good biocompatibility.Conclusions: The materials for MPDA used in the present study had no direct toxicity to the RPE cells and did not release harmful soluble factors that affected the barrier function of RPE in vitro.

CALCULATION OF SPIN-REORIENTATION TEMPERATURE IN ND2FE14B

The spin-reorientation phenomenon in Nd2Fe14B has been investigated using an angular dependent free energy approach. A magnetic Hamiltonian which includes the crystal electric field term and the exchange term has been established using realistic band structure results. The temperature dependence of the molecular field is accounted for by introducing the Brillouin function and the magnetic Hamiltonian is diagonalized within the ground state multiplet of the Nd ion. The eigenstates are then used to form the partition function for the free energy. At each temperature, the direction of the molecular field is obtained by searching for the minimum in the angular parameter space of the free energy. Our calculations show that for Nd2Fe14B, the net magnetic anisotropy direction is canted away from the c axis at a temperature close to the experimentally reported spin-reorientation temperature of 150 K. The temperature dependence of the magnetic structure is found to be very sensitive to the size of the second order crystal field parameter B20.

Biomimetic (topological) pattern recognition - A new model of pattern recognition theory and its application

A new theoretical model of Pattern Recognition principles was proposed, which is based on "matter cognition" instead of "matter classification" in traditional statistical Pattern Recognition. This new model is closer to the function of human being, rather than traditional statistical Pattern Recognition using "optimal separating" as its main principle. So the new model of Pattern Recognition is called the Biomimetic Pattern Recognition (BPR)(1). Its mathematical basis is placed on topological analysis of the sample set in the high dimensional feature space. Therefore, it is also called the Topological Pattern Recognition (TPR). The fundamental idea of this model is based on the fact of the continuity in the feature space of any one of the certain kinds of samples. We experimented with the Biomimetic Pattern Recognition (BPR) by using artificial neural networks, which act through covering the high dimensional geometrical distribution of the sample set in the feature space. Onmidirectionally cognitive tests were done on various kinds of animal and vehicle models of rather similar shapes. For the total 8800 tests, the correct recognition rate is 99.87%. The rejection rate is 0.13% and on the condition of zero error rates, the correct rate of BPR was much better than that of RBF-SVM.

Retention modeling and simultaneous optimization of pH value and gradient steepness in RP-HPLC using feed-forward neural networks

A novel approach is proposed for the simultaneous optimization of mobile phase pH and gradient steepness in RP-HPLC using artificial neural networks. By presetting the initial and final concentration of the organic solvent, a limited number of experiments with different gradient time and pH value of mobile phase are arranged in the two-dimensional space of mobile phase parameters. The retention behavior of each solute is modeled using an individual artificial neural network. An "early stopping" strategy is adopted to ensure the predicting capability of neural networks. The trained neural networks can be used to predict the retention time of solutes under arbitrary mobile phase conditions in the optimization region. Finally, the optimal separation conditions can be found according to a global resolution function. The effectiveness of this method is validated by optimization of separation conditions for amino acids derivatised by a new fluorescent reagent.

Crystal structure and charge transfer energy of the vaterite-type orthoborate YBO3:Eu

Ligand-to-metal charge transfer energies of YBO3:Eu have been investigated from the chemical bond viewpoint. The chemical bond parameters, such as the covalency, the polarizability of the chemical bond volume, and the presented charge of the ligands in the chemical bond have been quantitatively determined based on the dielectric theory of complex crystal. We calculated the environmental factor (h(e)), which is the major factor influencing the charge transfer energy in the compounds. The calculated results show that the suitable group space of YBO3 is C2/c. The method provides us with a supplementary tool to judge the proper structure when the structure of the crystal has many uncertain space groups.

Effect of ancillary ligands on the properties of heteroleptic green iridium dendrimers functionalized with carbazole dendrons

A series of heteroleptic green iridium dendrimers functionalized with carbazole dendrons, such as G2(pic) and G2(acac), have been synthesized, in which picolinic acid and acetylacetone are used as the ancillary ligands, respectively. Compared with the corresponding homoleptic iridium dendrimer G2 (8%), these heteroleptic ones can be prepared under mild conditions with total yields as high as 55-67%. Both the dendrimer G2(pic) and G2(acac) display bright green emissions with photoluminescence quantum yields higher than 0.80 in toluene solution. As a result, a maximum external quantum efficiency of 7.1% (21.0 cd/A) for G2(pic) and 7.7% (25.8 cd/A) for G2(acac) has been realized based on non-doped device configuration. The state-of-art performance indicates that the heteroleptic dendrimers can be promising candidates used for non-doped electrophosphorescent devices, especially when the ease of synthesis in a large scale is considered.

Self-assembled monolayer of polyoxometalate on gold surfaces: Quartz crystal microbalance, electrochemistry, and in-situ scanning tunneling microscopy study

A new kind of inorganic self-assembled monolayer (SAM) was prepared by spontaneous adsorption of polyoxometalate anion, AsMo11VO404-, onto a gold surface from acidic aqueous solution. The adsorption process, structure, and electrochemical properties of the AsMo11VO404- SAM were investigated by quartz crystal microbalance (QCM), electrochemistry, and scanning tunneling microscopy (STM). The QCM data suggested that the self-assembling process could be described in terms of the Langmuir adsorption model, providing the value of the free energy of adsorption at -20 KJ mol(-1). The maximum surface coverage of the AsMo11VO404- SAM on gold surface was determined from the QCM data to be 1.7 x 10(-10) mol cm(-2), corresponding to a close-packed monolayer of AsMo11VO404- anion. The analysis of the voltammograms of the AsMo11VO404- SAM on gold electrode showed three pairs of reversible peaks with an equal surface coverage of 1.78 x 10(-10) mol cm(-2) for each of the peaks, and the value was agreed well with the QCM data. In-situ STM image demonstrated that the AsMo11VO404- SAM was very uniform and no aggregates or multilayer could be observed. Furthermore, the high-resolution STM images revealed that the AsMo11VO404- SAM on Au(lll) surface was composed of square unit cells with a lattice space of 10-11 Angstrom at +0.7 V (vs Ag\AgCl). The value was quite close to the diameter of AsMo11VO404- anion obtained from X-ray crystallographic study. The surface coverage of the AsMo11VO404- SAM on gold electrode estimated from the STM image was around 1.8 x 10(-10) mol cm(-2), which was consistent with the QCM and electrochemical results.

A preliminary genetic linkage map of the pacific abalone Haliotis discus hannai Ino

Preliminary genetic linkage maps were constructed for the Pacific abalone (Haliotis discus hannai Ino) using amplified fragment length polymorphism (AFLP), randomly amplified polymorphic DNA (RAPD), and microsatellite markers segregating in a F, family. Nine microsatellite loci, 41 RAPD, and 2688 AFLP markers were genotyped in the parents and 86 progeny of the mapping family. Among the 2738 markers, 384 (including 365 AFLP markers, 10 RAPD markers, and 9 microsatellite loci) were polymorphic and segregated in one or both parents: 241 in the female and 146 in the male. The majority of these markers, 232 in the female and 134 in the male, segregated according to the expected 1:1 Mendelian ratio (alpha = 0.05). Two genetic linkage maps were constructed using markers segregating in the female or the male parent. The female framework map consisted of 119 markers in 22 linkage groups, covering 1773.6 cM with an average intermarker space of 18.3 cM. The male framework map contained 94 markers in 19 linkage groups, spanning 1365.9 cM with an average intermarker space of 18.2 cM. The sex determination locus was mapped to the male map but not to the female map, suggesting a XY-male determination mechanism. Distorted markers showing excess of homozygotes were mapped in clusters, probably because of their linkage to a gene that is incompatible between two parental populations.

用改进的ART-2网络建立移动机器人环境模型的研究

本文应用自适应共振理论中ART-2神经网络进行移动机器人环境障碍模式识别。ART-2神经网络在处理单方向渐变的模式输入时具有模式漂移的特点，机器人在静态环境中运动依赖这种特点，但在动态环境中模式漂移的特点却会对机器人的安全造成威胁。为此，设计了一种改进的ART-2神经网络，使得移动机器人同时适应在静态和动态环境中安全运动。

Comparison of comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry and gas chromatography-mass spectrometry for the analysis of tobacco essential oils

A sample of tobacco essential oil was analyzed using gas chromatography-mass spectrometry (GUMS)and comprehensive two-dimensional gas chromatography coupled to a time-of-flight mass spectrometry (GC x GC/TOFMS), respectively. In the GUMS analysis, serially coupled columns were used. By comparing the GUMS results with GC x GC/TOFMS result,,, many more components in the essential oil could be found within the two-dimensional separation space of GC x GC. The quantitative determination of components in the essential oil was performed by GC x GC with flame ionization detection (FID), using a method of multiple internal standards calibration, (c) 2005 Elsevier B.V. All rights reserved.