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Bin Chen

Publications and source records attributed to Bin Chen.

At least 37 records · Page 2Linked to original sources
PubMed2006

Intramolecular triplet energy transfer in donor-acceptor molecules linked by a crown ether bridge.

Bichromophoric compounds BP-C-NP and BP-C-NBD were synthesized with benzophenone chromophore (BP) as the donor, and 2-naphthyl (NP) and norbornadiene group (NBD) as the acceptor, respectively. Their intramolecular triplet energy transfer was examined. The bridges linking the donor and acceptors in these molecules involve a crown ether moiety complexing a sodium ion. Phosphorescence quenching, flash photolysis and photosensitized isomerization experiments indicate that intramolecular triplet energy transfer occurs with rate constants of about 3.3 x 10(5) and 4.8 x 10(5) s(-1) and efficiencies of about 33 and 42 % for BP-C-NP and BP-C-NBD, respectively. Theoretical calculations indicate that these molecules adopt conformations below room temperature which allow their two-end chromophores conducive to through-space energy transfer.

Journal Article↗
PubMed2006

Chain conformation and solvent partitioning in reversed-phase liquid chromatography: Monte Carlo simulations for various water/methanol concentrations.

Many structural models for the stationary phase in reversed-phase liquid chromatography (RPLC) systems have been suggested from thermodynamic and spectroscopic measurements and theoretical considerations. To provide a molecular picture of chain conformation and solvent partitioning in a typical RPLC system, a particle-based Monte Carlo simulation study is undertaken for a dimethyl octadecyl (C(18)) bonded stationary phase on a model siliceous substrate in contact with mobile phases having different methanol/water concentrations. Following upon previous simulations for gas-liquid chromatography and liquid-liquid phase equilibria, the simulations are conducted using the configurational-bias Monte Carlo method in the Gibbs ensemble and the transferable potentials for phase equilibria force field. The simulations are performed for a chain surface density of 2.9 micromol/m(2), which is a typical bonded-phase coverage for mono-functional alkyl silanes. The solvent concentrations used here are pure water, approximately 33 and 67% mole fraction of methanol and pure methanol. The simulations show that the chain conformation depends only weakly on the solvent composition. Most chains are conformationally disordered and tilt away from the substrate normal. The interfacial width increases with increasing methanol content and, for mixtures, the solvent shows an enhancement of the methanol concentration in a 10 Angstrom region outside the Gibbs dividing surface. Residual surface silanol groups are found to provide hydrogen bonding sites that lead to the formation of substrate bound water and methanol clusters, including bridging clusters that penetrate from the solvent/chain interfacial region all the way to the silica surface.

Chromatography, Liquid↗
PubMed2006

Comparative genomics and evolution of the HSP90 family of genes across all kingdoms of organisms.

BACKGROUND: HSP90 proteins are essential molecular chaperones involved in signal transduction, cell cycle control, stress management, and folding, degradation, and transport of proteins. HSP90 proteins have been found in a variety of organisms suggesting that they are ancient and conserved. In this study we investigate the nuclear genomes of 32 species across all kingdoms of organisms, and all sequences available in GenBank, and address the diversity, evolution, gene structure, conservation and nomenclature of the HSP90 family of genes across all organisms. RESULTS: Twelve new genes and a new type HSP90C2 were identified. The chromosomal location, exon splicing, and prediction of whether they are functional copies were documented, as well as the amino acid length and molecular mass of their polypeptides. The conserved regions across all protein sequences, and signature sequences in each subfamily were determined, and a standardized nomenclature system for this gene family is presented. The proeukaryote HSP90 homologue, HTPG, exists in most Bacteria species but not in Archaea, and it evolved into three lineages (Groups A, B and C) via two gene duplication events. None of the organellar-localized HSP90s were derived from endosymbionts of early eukaryotes. Mitochondrial TRAP and endoplasmic reticulum HSP90B separately originated from the ancestors of HTPG Group A in Firmicutes-like organisms very early in the formation of the eukaryotic cell. TRAP is monophyletic and present in all Animalia and some Protista species, while HSP90B is paraphyletic and present in all eukaryotes with the exception of some Fungi species, which appear to have lost it. Both HSP90C (chloroplast HSP90C1 and location-undetermined SP90C2) and cytosolic HSP90A are monophyletic, and originated from HSP90B by independent gene duplications. HSP90C exists only in Plantae, and was duplicated into HSP90C1 and HSP90C2 isoforms in higher plants. HSP90A occurs across all eukaryotes, and duplicated into HSP90AA and HSP90AB in vertebrates. Diplomonadida was identified as the most basal organism in the eukaryote lineage. CONCLUSION: The present study presents the first comparative genomic study and evolutionary analysis of the HSP90 family of genes across all kingdoms of organisms. HSP90 family members underwent multiple duplications and also subsequent losses during their evolution. This study established an overall framework of information for the family of genes, which may facilitate and stimulate the study of this gene family across all organisms.

Alternative Splicing↗
PubMed2006

A novel method to design sparse linear arrays for ultrasonic phased array.

In ultrasonic phased array testing, a sparse array can increase the resolution by enlarging the aperture without adding system complexity. Designing a sparse array involves choosing the best or a better configuration from a large number of candidate arrays. We firstly designed sparse arrays by using a genetic algorithm, but found that the arrays have poor performance and poor consistency. So, a method based on the Minimum Redundancy Linear Array was then adopted. Some elements are determined by the minimum-redundancy array firstly in order to ensure spatial resolution and then a genetic algorithm is used to optimize the remaining elements. Sparse arrays designed by this method have much better performance and consistency compared to the arrays designed only by a genetic algorithm. Both simulation and experiment confirm the effectiveness.

Journal Article↗
PubMed2006

[Changes of nuclear factor-kappa gene binding expression in and apoptosis of spermatogenic epithelial cells in the restored testis after torsion: experiment with rats].

OBJECTIVE: To investigate the changes of nuclear factor-kappa gene binding (NF-kappaB) expression in and apoptosis of spermatogenic epithelial cells in the restored testis after torsion and analyze the relationship between them. METHODS: Sixteen male SD rats underwent torsion of the left testis clockwise at an angle of 720 degrees for 2 hours and then the testis was restored to the original position and fixed. Then the 16 rats were randomly divided into 2 equal group: Group I in which salicylazosulfapyridium (SASP) suspension was infused intra-gastrically 5 h after operation and then once a day for 4 times, and Group II in which normal saline (NS) was infused in the same manner. Eight rats (Group III) underwent sham operation and then infused with NS in the same manner as that of Group II. Three days after operation the rats were killed and the samples of the testes at the torsion side were taken out and the seminiferous tubules were isolated. Western blotting was used to detect the NF-kappaB expression in the cytoplasm and nucleus of spermatogenic epithelial cells. Immunohistochemistry was used to detect the in situ expression of NF-kappaB. The apoptosis of the spermatogenic epithelial cells was examined by TUNEL method. RESULTS: Western blotting showed that the NF-kappaB expression in the cytoplasm of spermatogenic epithelial cells of Group II was 9.4 +/- 2.68, somewhat lower, but not significantly, than those of Group I and III (12 +/- 2.2 and 11.1 +/- 3 respectively, both P > 0.05). The NF-kappaB expression in the nucleus of spermatogenic epithelial cells of Group II was 21.1 +/- 3.6, significantly higher than those of Group I and III (8.4 +/- 3.1 and 6.0 +/- 2.3 respectively, both P < 0.05). However, there were no significant differences in the NF-kappaB expression in the cytoplasm and nucleus of spermatogenic epithelial cells between Groups I and III. The NF-kappaB activity coefficient of spermatogenic epithelial cells of Group II was 2.32 +/- 0.4, significantly higher than those of Groups I and III (0.68 +/- 0.3 and 0.52 +/- 0.1 respectively, both P < 0.01). However, there was no significant difference in the NF-kappaB activity coefficient of spermatogenic epithelial cells between Groups I and III (P > 0.05). The NF-kappaB positive cell rate of Group II was 66.1% +/- 3.8%, significantly higher than those of Groups I and III (15.6% +/- 2.6% and 10.8% +/- 2.7%, both P < 0.01). The apoptotic cell rate of Group II was 37.2% +/- 3.3%, significantly higher than those of Groups I and III (7.7% +/- 2.0% and 5.9% +/- 1.7%, both P < 0.01). CONCLUSION: After the torsion of testis, NF-kappaB was activated and released from the nucleus into the cytoplasm, thus initiating the apoptosis of spermatogenic epithelial cells.

Animals↗
PubMed2006

Application of high-speed counter-current chromatography coupled with high-performance liquid chromatography-diode array detection for the preparative isolation and purification of hyperoside from Hypericum perforatum with online purity monitoring.

Following preparative isolation and purification by high-speed counter-current chromatography (HSCCC), the collected fractions were generally analyzed by high-performance liquid chromatography (HPLC) to determine the relative purities of each fraction. Our paper reports for the first time a preparative isolation-purity detection hyphenated system: online coupling of HSCCC with high-performance liquid chromatography-diode array detection (HSCCC-HPLC-DAD). The introduction of online purity analysis in HSCCC has dramatically improved the efficiency of this technique by overcoming the drawbacks of post analysis in HSCCC isolation. The effluent from the outlet of HSCCC was splitted into two parts: one was collected, while the other was introduced directly into an HPLC-DAD system for purity analysis through a switch valve. Therefore, the purities of the obtained fractions from HSCCC were monitored, and fractions with high purities were collected. This strategy has been successfully demonstrated with the preparative isolation and purification of hyperoside from Hypericum perforatum (St. Jone's Wort); a model of TBE-300A HSCCC was used to isolate and separate hyperoside from H. perforatum with a two-phase solvent system composed of ethyl acetate-ethanol-water at the volume ratio of 5:1:5 (v/v) using online detection technique. The isolation was done in less than 3.5 h, and a total of 83.0-mg hyperoside at over 99.0% purity was yielded from 300 mg of the partially purified extract. This new strategy possesses general utility in the preparation of bioactive compounds from traditional Chinese medicine (TCM).

Chromatography, High Pressure Liquid↗
PubMed2006

Relative pKa values from first-principles molecular dynamics: the case of histidine deprotonation.

Accurate calculation of pK(a) values and free energies for acid/base reactions in the condensed phase has been a long-standing goal of theoretical chemistry. We present a novel application of the Car-Parrinello molecular dynamics method to the problem of relative pK(a) determination. As a particular example, we focus on the second stage in the dissociation of histidine, a process that holds special importance for biology. Using constrained molecular dynamics, we have analyzed the structural, electronic, and dynamical transformations taking place along a preselected, intuitive reaction coordinate. By integrating the potentials of mean force for the deprotonation of histidine and for a reference reaction, autodissociation of water, we obtain a pK(a) value of 6.8, which appears to be in good agreement with the experimental estimate of 6.1. Detailed analysis was undertaken to determine the value of the constraint, which transformed the N*-H* from a covalent to a hydrogen bond. This helped to identify a number of properties that could be successfully used in monitoring the dissociation process. Additional analysis in terms of electron localization functions provided valuable insight into the nature of the deprotonation reaction.

Histidine↗
PubMed2006

Species-specific identification by inhibitor-controlled PCR of ruminant components contaminating industrial crude porcine heparin.

With the emergence of bovine spongiform encephalopathy, the source of pharmaceutical heparin is currently restricted to porcine intestinal mucosa. To control the species origin of industrial crude heparin, molecular biology methods relying on species-specific protein or DNA analysis should be developed to identify the ruminant components that might be contaminants in industrial crude porcine heparin (ICPH). Because heparin contained in ICPH is a strong PCR inhibitory substance, it is necessary to explore DNA extraction methods specific for ICPH and develop analysis methods that could monitor the presence of PCR inhibitory substances. In the present studies, DNA was extracted from ICPH by seven methods, and their abilities to remove the PCR inhibitory substances were compared using inhibitory-controlled PCR (IC-PCR). The results showed that, based on the optimization of the final concentration of the internal processing control (IPC), IC-PCR was a rapid, sensitive and efficient way to monitor the presence of PCR inhibitory substances contained in DNA extracted from ICPH, and only the agarose gel purification method could be used to completely eliminate the PCR inhibitory substances contained in ICPH.

Animals↗
PubMed2006

Pretreatment photosensitizer dosimetry reduces variation in tumor response.

PURPOSE: To compensate for photosensitizer uptake variation in photodynamic therapy (PDT), via control of delivered light dose through photodynamic dose calculation based on online dosimetry of photosensitizer in tissue before treatment. METHODS AND MATERIALS: Photosensitizer verteporfin was quantified via multiple fluorescence microprobe measurements immediately before treatment. To compensate individual PDT treatments, photodynamic doses were calculated on an individual animal basis, by matching the light delivered to provide an equal photosensitizer dose multiplied by light dose. This was completed for the lower quartile, median, and upper quartile of the photosensitizer distribution. PDT-induced tumor responses were evaluated by the tumor regrowth assay. RESULTS: Verteporfin uptake varied considerably among tumors and within a tumor. The coefficient of variation in the surviving fraction was found significantly decreased in groups compensated to the lower quartile (CL-PDT), the median (CM-PDT), and the upper quartile (CU-PDT) of photosensitizer distribution. The CL-PDT group was significantly less effective compared with NC-PDT (Noncompensated PDT), CM-PDT, and CU-PDT treatments. No significant difference in effectiveness was observed between NC-PDT, CM-PDT, and CU-PDT treatment groups. CONCLUSIONS: This research suggests that accurate quantification of tissue photosensitizer levels and subsequent adjustment of light dose will allow for reduced subject variation and improved treatment consistency.

Algorithms↗
PubMed2006

Unravelling the peculiar nucleation mechanisms for non-ideal binary mixtures with atomistic simulations.

Recent experiments reveal unusual nucleation behavior for seemingly simple mixtures that cannot be described by the classical theory. Molecular simulations using a combination of aggregation-volume-bias Monte Carlo, umbrella sampling, and histogram reweighting methods were carried out to study the nucleation events involved in the water/ethanol, water/n-nonane, and n-nonane/ethanol mixtures. These simulations reproduced their different nonideal behaviors observed by the experiments. Furthermore, the finding of their strikingly distinct mechanisms, as implied from the calculated free-energy maps, challenges the current theoretical description of this phenomenon.

Alkanes↗
PubMed2006

Structural correlations and motifs in liquid water at selected temperatures: ab initio and empirical model predictions.

To gain further insight into liquid water's structure and explore the role of different physical forces underlying the interaction between water molecules, the radial and angular structure of water is probed as a function of temperature for a carefully selected set of theoretical models. Simulations are performed with empirical rigid, empirical polarizable, empirical flexible with classical and quantum nuclei, and ab initio models with classical nuclei at 300 and 353 K and quantum nuclei at 300 K. The predicted radial distribution functions, spatial maps, and angular distributions of the neighboring water molecules are consistent with a model of liquid water in which water molecules are tetrahedrally coordinated. In addition, three-dimensional joint distribution functions are introduced and analyzed. By comparison of the functions obtained for hexagonal ice to those of liquid water, several thermally disordered, ice-like cluster structures are identified in the fluid.

Journal Article↗
PubMed2006

Microscopic structure and solvation in dry and wet octanol.

Octanol-water partition coefficients are extraordinarily successful for correlating and predicting numerous processes of pharmacological and environmental importance. The amphiphilic nature of the 1-octanol molecules allows the octanol phase to mimic the complexities of many different environments ranging from biomembranes to soil. However, the structural details of the octanol phase and whether its structure is altered upon water saturation are not yet fully understood. Configurational-bias Monte Carlo simulations in the Gibbs ensemble demonstrate that a diverse spectrum of hydrogen-bonded aggregates exists in dry and wet 1-octanol, and that water saturation substantially alters the 1-octanol environment from predominantly linear aggregates in dry octanol to larger cylindrical micelles with water cores in wet octanol. These simulation results are able to reconcile the conflicting views (chain-like or water-centered aggregates vs spherical micelles) of the 1-octanol structure inferred from thermodynamic arguments, spectroscopic measurements, and diffraction experiments. Calculated partition constants quantify the influence of water saturation on the solubility characteristics of the dry and wet octanol phases.

1-Octanol↗
PubMed2006

Structure and dynamics of the aqueous liquid-vapor interface: a comprehensive particle-based simulation study.

This research addresses a comprehensive particle-based simulation study of the structural, dynamic, and electronic properties of the liquid-vapor interface of water utilizing both ab initio (based on density functional theory) and empirical (fixed charge and polarizable) models. Numerous properties such as interfacial width, hydrogen bond populations, dipole moments, and correlation times will be characterized with identical schemes to draw useful conclusions on the strengths and weakness of the proposed models for interfacial water. Our findings indicate that all models considered in this study yield similar results for the radial distribution functions, hydrogen bond populations, and orientational relaxation times. Significant differences in the models appear when examining both the dipole moments and surface relaxation near the aqueous liquid-vapor interface. Here, the ab initio interaction potential predicts a significant decrease in the molecular dipole moment and expansion in the oxygen-oxygen distance as one approaches the interface in accordance with recent experiments. All classical polarizable interaction potentials show a less dramatic drop in the molecular dipole moment, and all empirical interaction potentials studied yield an oxygen-oxygen contraction as the interface is approached.

Computer Simulation↗