Funneled landscape leads to robustness of cellular networks: MAPK signal transduction

We uncover the underlying potential energy landscape for a cellular network. We find that the potential energy landscape of the mitogen-activated protein-kinase signal transduction network is funneled toward the global minimum. The funneled landscape is quite robust against random perturbations. This naturally explains robustness from a physical point of view. The ratio of slope versus roughness of the landscape becomes a quantitative measure of robustness of the network. Funneled landscape is a realization of the Darwinian principle of natural selection at the cellular network level. It provides an optimal criterion for network connections and design. Our approach is general and can be applied to other cellular networks.

Characterization of triterpenoidic saponin mixture in crude extracts from leaves of Acanthopanax senticosus Harms by saponin structural correlation and mass spectrometry

Eighteen triterpenoidic saponins in crude extracts from leaves of Acanthopanax senticous Harms have been investigated by electrospray ionization multi-stage tandem mass spectrometry and high-resolution mass spectrometry. In ESI-MS spectra, predominant [M + Na](+) ions in the positive ion mode have been observed for molecular mass information. Meanwhile, specific structural correlations between these ions are firstly found. The 18 peaks (ions) can be classified into three groups (group D, E, and F with mass increase) with each group including six peaks. There is a mass difference of 132 Da between group D and E for each corresponding peak in turn (for example peak 1 to peak 7), indicating one more pentose residue was attached to saponins in group E than those corresponding in group D. The mass difference of 146 Da between group E and F implies one more deoxy-hexose attached to saponins in group F than those corresponding in group E. The structural correlations of the corresponding ions are confirmed by tandem mass spectrometry and high-re solution mass spectrometry. These structural features can not only facilitate the rapid characterization of the native known saponins in crude plant extracts, thus avoiding tedious derivation and separation of saponins, but also help find novel compounds of the same type in a specific medicinal plant.

Determination of ethenzamide and acetoaminophen in quaternary powdered samples by near infrared spectroscopy and searching combination moving window partial least squares algorithm: effects of spectral resolution and signal-to-noise ratio

The present study reports an application of the searching combination moving window partial least squares (SCMWPLS) algorithm to the determination of ethenzamide and acetoaminophen in quaternary powdered samples by near infrared (NIR) spectroscopy. Another purpose of the study was to examine the instrumentation effects of spectral resolution and signal-to-noise ratio of the Buchi NIRLab N-200 FT-NIR spectrometer equipped with an InGaAs detector. The informative spectral intervals of NIR spectra of a series of quaternary powdered mixture samples were first located for ethenzamide and acetoaminophen by use of moving window partial least squares regression (MWPLSR). Then, these located spectral intervals were further optimised by SCMWPLS for subsequent partial least squares (PLS) model development. The improved results are attributed to both the less complex PLS models and to higher accuracy of predicted concentrations of ethenzamide and acetoaminophen in the optimised informative spectral intervals that are featured by NIR bands. At the same time, SCMWPLS is also demonstrated as a viable route for wavelength selection.

Discrete wavelets transform for signal denoising in capillary electrophoresis with electrochemiluminescence detection

Discrete wavelets transform (DWT). was applied to noise on removal capillary electrophoresis-electrochemiluminescence (CE-ECL) electropherograms. Several typical wavelet transforms, including Haar, Daublets, Coiflets, and Symmlets, were evaluated. Four types of determining threshold methods, fixed form threshold, rigorous Stein's unbiased estimate of risk (rigorous SURE), heuristic SURE and minimax, combined with hard and soft thresholding methods were compared. The denoising study on synthetic signals showed that wave Symmlet 4 with a level decomposition of 5 and the thresholding method of heuristic SURE-hard provide the optimum denoising strategy. Using this strategy, the noise on CE-ECL electropherograms could be removed adequately. Compared with the Savitzky-Golay and Fourier transform denoising methods, DWT is an efficient method for noise removal with a better preservation of the shape of peaks.

Correlation analysis of the structures and stability constants of gadolinium(III) complexes

To simplify the abstraction of descriptors, for the correlation analysis of the stability constants of gadolinium(III) complexes and their ligand structures, aiming at gadolinium(III) complexes, we only considered the ligands and ignored the common parts of the structures, i.e., the metal ions. Quantum-chemical descriptors and topological indices were calculated to describe the structures of the ligands. Multiple regression analysis and neural networks were applied to construct the models between the ligands and the stability constants of gadolinium(III) complexes and satisfactory results were obtained.

New technique for capillary electrophoresis directly coupled with end-column electrochemiluminescence detection

capillary electrophoresis (CE) is characterized. A 300 mum diameter Pt working electrode was used to directly couple with a 75 mum inner diameter separation capillary without an electric field decoupler. The hydrodynamic cyclic voltammogram (CV) of Ru(bpy)(3)(2+) showed that electrophoretic current did not affect the ECL reaction. The presence of high-voltage (HV) field only resulted in the shift of the ECL detection potential. The distance of capillary to electrode was an important parameter for optimizing detection performance as it determined the characteristics of mass transport toward the electrode and the actual concentration of Ru(bpy)(3)(2+) in the detection region. The optimum distance of capillary to electrode was decided by the inner diameter of the capillary, too. For a 75 mum capillary, the working electrode should be placed away from the capillary outlet at a distance within the range of 20-260 mum. The effects of pH value of ECL solution and molecular structure of analytes on peak height and theoretical plate numbers were discussed. Using the 75 mum capillary, under the optimum conditions, the method provided a linear range for tripropylamine (TPA) between 1 x 10(-10) and 1 X 10(-5) mol/L with correlation coefficient of 0.998. The detection limit (signal-to-noise ratio S/N = 3) was 5.0 x 10(-11) mol/L. The relative standard deviation in peak height for eight consecutive injections was 5.6%. By this new technique lidocaine spiked in a urine sample was determined. The method exhibited the linear range for lidocaine from 5.0 x 10(-8) to 1.0 X 10(-5) mol/L with correlation efficient of 0.998. The limit of detection (S/N = 3) was 2.0 x 10(-1) mol/L.

Capillary electrophoresis with solid-state electrochemiluminescence detector

We report capillary electrophoresis coupling to a solid-state electrochemiluminescence (ECL) detector for the first time. The solid-state ECL detector was fabricated by immobilizing the ECL reagent tris(2,2'-bipyridyf)ruthenium (TBR) in poly-(p-styrenesulfonate)-silica-poly(vinyl alcohol) grafting 4-vinylpyridine copolymer films. The excellent stability of the solid-state ECL detector in the phosphate solution satisfied application in CE. The CE with solid-state ECL detector system was characterized using tripropylamine (TPA) and proline. The influences of detection potential, the concentration of TBR in the film, and pH value of ECL buffer were investigated. The linear range for TPA and proline was 0.005-10 muM and 5-10 mM with correlation coefficients of 0.997 and 0.998, respectively. The detection limit (signal-to-noise ratio S/N = 3) was estimated to be 0.002 and 2.0 muM for TPA and proline, respectively. The relative standard deviations for 1.0 pm TPA and 1.0 mm proline were 8.7% and 7.5% with theoretical plate numbers of 70 000 and 16 000, respectively. Compared with the CE-ECL of TBR in aqueous solution, the CE coupling with solid-state ECL detector system gave the same sensitivity of analysis.

Correlation analysis of the structures and pK(a) values of carboxylic acids

The quantum-chemical descriptors were used for QSPR study of the structures of carboxylic acids and their pK(a) values. The algorithm of "Leaps and Bounds" regression was performed for selection of the variables. The CoMFA method was carried out for 3D-QSPR. As the introduction of the charge of oxygen atom(Q(2)), the results obtained by CoMFA were improved greatly.

Application of 2D Raman correlation spectroscopy to studing the effect of rare-earth Eu3+ on hemoglobin

The effect of rare-earth ion Eu3+ on hemoglobin (Hb) was studied by using two-dimensional Raman correlation spectroscopy. The results show that with the variation of Eu3+ concentrations as perturbation, the oxidation state of Hb and its spin state are both sensitive to the perturbation. Eu3+ added to Hb affects the oxidation and spin state synchronously. The four structure-sensitive bands of Hb are more accessible to the Eu3+ than other bands.

Electrochemiluminescence of the Ru(bpy)(3)(2+)/S(2)O(8)(2-)system in purely aqueous solution at carbon paste electrode

The electrochemiluminescence (ECL) of the Ru(bgy)(3)(2-)/S2O82- system in purely aqueous solution at a carbon paste electrode can be clearly seen with the naked eye for Ru(bpy)(3)(2+) concentrations higher than 1 mmol L-1. The log-log plot of the emmitted light intensity vs. Ru(bpy)(3)(2+) concentration is linear over the region 10(-3)-10(-7) mol L-1 with a correlation coefficient of 0.997. The ECL intensity increases linearly with the S2O82- concentration from 10(-6) mol L-1 up to 0.3 mmol L-1 and drops off sharply at concentrations higher than 1 mmol L-1. In addition, a weak ECL signal was obtained when the potential was biased more negative than -0.6 V even in the absence of S2O82-.

Correlation analysis of the structures and gas-liquid chromatographic retention indices of amines

Quantitative structure-retention relationship(QSRR) was studied for amines to gas-liquid chromatography on three stationary phases of different polarities with the topological indices A(m) (A(m1), A(m2), A(m3)) and gravitational index GI. The algorithm of "Leaps and Bounds" was performed for selection of the variables. And the multi-regression and the quasi-Newton neural networks were employed for the calculation with better results.

Amplification of antigen-antibody interactions based on biotin labeled protein-streptavidin network complex using impedance spectroscopy

Antibody was covalently immobilized by amine coupling method to gold surfaces modified with a self-assembled monolayer of thioctic acid. The electrochemical measurements of cyclic voltammetry and impedance spectroscopy showed that the hexacyanoferrate redox reactions on the gold surface were blocked due to the procedures of self-assembly of thioctic acid and antibody immobilization. The binding of a specific antigen to antibody recognition layer could be detected by measurements of the impedance change. A new amplification strategy was introduced for improving the sensitivity of impedance measurements using biotin labeled protein- streptavidin network complex. This amplification strategy is based on the construction of a molecular complex between streptavidin and biotin labeled protein. This complex can be formed in a cross-linking network of molecules so that the amplification of response signal will be realized due to the big molecular size of complex. The results show that this amplification strategy causes dramatic improvement of the detection sensitivity of hIgG and has good correlation for detection of hIgG in the range of 2-10 mug/ml. (C) 2001 Elsevier Science B.V. All rights reserved.

Chemiluminescent determination of luminol and hydrogen peroxide using hematin immobilized in the bulk of a carbon paste electrode

A new method for immobilization of a chemiluminescent reagent is presented. It is based on immobilizing hematin, a catalyst for luminol reaction, in the bulk of a carbon paste electrode. Bulk-immobilization allows renewal of the surface by simple polishing or cutting to expose anew and fully active surface in the case of fouling or deactivation by other means. By using a hematin-modified carbon paste electrode, the applied potential shifted negatively compared with that of unmodified carbon paste electrode or a glassy carbon electrode. The shift in potential changed the reaction processes and effectively stabilized the chemiluminescent signal during successive measurements. Under this condition, the signal was stable during 3 hours of continuous operation. The log-log plots of the emitted light intensity vs. luminol concentration and hydrogen peroxide concentration were linear over the region 10(-8)-10(-3) mol L-1 with a correlation coefficient of 0.999 and 3.9 x 10(-6)-10(-3) mol L-1 with a correlation coefficient of 0.994, respectively. Application of this method for other chemiluminescent and bioluminescent systems is suggested.

Chemical bond analysis of the correlation between crystal structure and nonlinear optical properties of complex crystals

Second order nonlinear optical (NLO) properties of single crystals with complex structures are studied, from the chemical bond viewpoint. Contributions of each type of constituent chemical bond to the total linearity and nonlinearity are calculated from the actual crystal structure, using the chemical bond theory of complex crystals and the modified bond charge model. We have quantitatively proposed certain relationships between the crystal structure and its NLO properties. Several relations have been established from the calculation. Our method makes it possible for us to identify, predict and modify new NLO materials according to our needs. (C) 1999 Elsevier Science B.V. All rights reserved.

Correlation between chain conformations and optical anisotropy of thin films of an organo-soluble polyimide

An organo-soluble polyimide was successfully synthesized by two step polycondensation accompanied with chemical imidization. Optical anisotropy of thin films was detected by a prism-coupler technique. The results showed that the optical anisotropic properties of thin films prepared from solutions in different solvents depend on the solution properties. It is concluded that the more expanded the chain conformation in solution, the larger the negative birefringence of thin films. (C) 1997 Elsevier Science Ltd.