Robustness and Coherence of a Three-Protein Circadian Oscillator: Landscape and Flux Perspectives

Three-protein circadian oscillations in cyanobacteria sustain for weeks. To understand how cellular oscillations function robustly in stochastic fluctuating environments, we used a stochastic model to uncover two natures of circadian oscillation: the potential landscape related to steady-state probability distribution of protein concentrations; and the corresponding flux related to speed of concentration changes which drive the oscillations. The barrier height of escaping from the oscillation attractor on the landscape provides a quantitative measure of the robustness and coherence for oscillations against intrinsic and external fluctuations. The difference between the locations of the zero total driving force and the extremal of the potential provides a possible experimental probe and quantification of the force from curl flux. These results, correlated with experiments, can help in the design of robust oscillatory networks.

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Effect of doped dye on the charge-carrier transport and electroluminescent performance in molecularly doped polymer light-emitting diodes

The effects of the concentration of 10-(2-benzothiazolyl)-2,3,6,7-tetrahydro-1,1,7,7-tetramethyl-1H, 5H, 11H-(1)-benzopyropyrano(6, 78-i,j)quinolizin-11-one (C545T) as dopant in polyfluorene (PFO) on the charge-carrier transport and electroluminescence (EL) performance were investigated by steady-state and transient EL measurements. A fully green emission from C545T was observed and the EL performance depends strongly on the C545T concentration. The mobility in the C545T-doped PFO film was determined by transient EL. The dopant concentration dependence of the current-voltage relationship indicated clearly the carrier trapping by the C545T molecules. The mobility in C545T:PFO changed significantly with the C545T concentration, and showed a nontrivial dependence on the doping level. The behavior may be understood in terms of the formation of an additional energy disorder due to potential fluctuation caused by the Coulomb interaction of the randomly distributed doping molecules.

Effects of doped dye on the charge carrier injection, transport, and electroluminescent performance in polymeric light-emitting diodes

The effects of doped fluorescent dye 4-(dicyanomethylene)-2-i-propyl-6-(1, 1, 7, 7-tetramethyljulolidyl-9-enyl)-4H-pyran (DCJTI) on the charge carrier injection, transport and electroluminescence (EL) performance in polyfluorene (PFO)-based polymer light-emitting diodes (PLEDs) were investigated by steady-state current-voltage (I-V) characteristics and transient EL measurements. A red EL from DCJTI was observed and the EL performance depended strongly on the DCJTI concentration. The analysis of the steady-state I-V characteristics at different DCJTI concentrations found that three regions was shown in the I-V characteristics, and each region was controlled by different processes depending on the applied electric field. The effect of the dopant concentration on the potential-barrier height of the interface is estimated using the Fowler-Nordheim model. The dopant concentration dependence of the current-voltage relationship indicated clearly the carrier trapping by the DCJTI molecules. The mobility in DCJTI: PFO changed significantly with the DCJTI concentration, and showed a nontrivial dependence on the doping level. The behavior may be understood in terms of the formation of an additional energy disorder due to potential fluctuation caused by the Coulomb interaction of the randomly distributed doping molecules.

Potential energy landscape and robustness of a gene regulatory network: Toggle switch

Finding a multidimensional potential landscape is the key for addressing important global issues, such as the robustness of cellular networks. We have uncovered the underlying potential energy landscape of a simple gene regulatory network: a toggle switch. This was realized by explicitly constructing the steady state probability of the gene switch in the protein concentration space in the presence of the intrinsic statistical fluctuations due to the small number of proteins in the cell. We explored the global phase space for the system. We found that the protein synthesis rate and the unbinding rate of proteins to the gene were small relative to the protein degradation rate; the gene switch is monostable with only one stable basin of attraction. When both the protein synthesis rate and the unbinding rate of proteins to the gene are large compared with the protein degradation rate, two global basins of attraction emerge for a toggle switch. These basins correspond to the biologically stable functional states. The potential energy barrier between the two basins determines the time scale of conversion from one to the other. We found as the protein synthesis rate and protein unbinding rate to the gene relative to the protein degradation rate became larger, the potential energy barrier became larger. This also corresponded to systems with less noise or the fluctuations on the protein numbers.

Quantifying robustness and dissipation cost of yeast cell cycle network: The funneled energy landscape perspectives

We study the origin of robustness of yeast cell cycle cellular network through uncovering its underlying energy landscape. This is realized from the information of the steady-state probabilities by solving a discrete set of kinetic master equations for the network. We discovered that the potential landscape of yeast cell cycle network is funneled toward the global minimum, G1 state. The ratio of the energy gap between G1 and average versus roughness of the landscape termed as robustness ratio ( RR) becomes a quantitative measure of the robustness and stability for the network. The funneled landscape is quite robust against random perturbations from the inherent wiring or connections of the network. There exists a global phase transition between the more sensitive response or less self-degradation phase leading to underlying funneled global landscape with large RR, and insensitive response or more self-degradation phase leading to shallower underlying landscape of the network with small RR. Furthermore, we show that the more robust landscape also leads to less dissipation cost of the network. Least dissipation and robust landscape might be a realization of Darwinian principle of natural selection at cellular network level. It may provide an optimal criterion for network wiring connections and design.

Daunomycin binding to detergent micelles: A model system for evaluating the hydrophobic contribution to drug-DNA interactions

The interaction of daunomycin with sodium dodecyl sulfate and Triton X-100 micelles was investigated as a model for the hydrophobic contribution to the free energy of DNA intercalation reactions. Measurements of visible absorbance, fluorescence lifetime, steady-state fluorescence emission intensity, and fluorescence anisotropy indicate that the anthraquinone ring partitions into the hydrophobic micelle interior. Fluorescence quenching experiments using both steady-state and lifetime measurements demonstrate reduced accessibility of daunomycin in sodium dodecyl sulfate micelles to the anionic quencher iodide and to the neutral quencher acrylamide. Quenching of daunomycin fluorescence by iodide in Triton X-100 micelles was similar to that seen with free daunomycin. Studies of the energetics of the interaction of daunomycin with micelles by fluorescence and absorbance titration methods and by isothermal titration calorimetry in the presence of excess micelles revealed that association with sodium dodecyl sulfate and Triton X-100 micelles is driven by a large negative enthalpy. Association of the drug with both types of micelles also has a favorable entropic contribution, which is larger in magnitude for Triton X-100 micelles than for sodium dodecyl sulfate micelles.

Room temperature ionic liquid doped DNA network immobilized horseradish peroxidase biosensor for amperometric determination of hydrogen peroxide

A novel electrochemical H2O2 biosensor was constructed by embedding horseradish peroxide (HRP) in a 1-butyl-3-methylimidazolium tetrafluoroborate doped DNA network casting on a gold electrode. The HRP entrapped in the composite system displayed good electrocatalytic response to the reduction of H2O2. The composite system could provide both a biocompatible microenvironment for enzymes to keep their good bioactivity and an effective pathway of electron transfer between the redox center of enzymes, H2O2 and the electrode surface. Voltammetric and time-based amperometric techniques were applied to characterize the properties of the biosensor. The effects of pH and potential on the amperometric response to H2O2 were studied. The biosensor can achieve 95% of the steady-state current within 2 s response to H2O2. The detection limit of the biosensor was 3.5 mu M, and linear range was from 0.01 to 7.4 mM. Moreover, the biosensor exhibited good sensitivity and stability. The film can also be readily used as an immobilization matrix to entrap other enzymes to prepare other similar biosensors.

Dissolution, characterization and photo functionalization of carbon nanotubes

A simple method to disperse carbon nanotubes (CNTs) has been achieved, which gives two photofunctionalized CNTs, hydrazine nanotubes (h-CNTs) and 1,3,4-oxadiazole nanotubes (o-CNTs). Results from FTIR, H-1 NMR spectroscopy and TEM observations showed that the functionalization was successful. The modified nanombes can dissolve in most of the nonpolar organic solvents and no precipitate was observed in the solution of the nanombes even after 2 months. The functionalized nanotubes showed photo-electronic properties, which is due to the attachment of the function groups to them as proved by steady-state fluorescence spectroscopy. Both h-CNTs and o-CNTs showed good thermal stability below 300 C and might be used as functional materials.

Facilitated ion-transfer of sodium cation by (anthraquinone-1-yloxy) methane-15-crown-5 across the water/1,2-dichloroethane microinterface

The transfer of sodium cation facilitated by (anthraquinone-1-yloxy) methane-15-crown-5(L) has been investigated at the water/1,2-dichloroethane microinterface supported at the tip of a micropipette. The diffusion coefficient of (anthraquinone-1-yloxy) methane-15-crown-5 obtained was (3.42 +/- 0.20) x 10(-6) cm(2) s(-1). The steady-state voltammograms were observed for forward and backward scans due to sodium ion transfer facilitated by L with 1:1 stoichiometry. The mechanism corresponded to an interfacial complexation (TIC) and interfacial dissociation (TID) process. The association constant was calculated to be log beta(o) = 11.08 +/- 0.03 in the DCE phase. The association constant of other alkali metals (Li+, K+, Rb+) were also obtained.

A novel hydrogen peroxide sensor based on horseradish peroxidase immobilized in DNA films on a gold electrode

A novel third-generation hydrogen peroxide (H2O2) biosensor was developed by immobilizing horseradish peroxidase (HRP) on a biocompatible gold electrode modified with a well-ordered, self-assembled DNA film. Cysteamine was first self-assembled on a gold electrode to provide an interface for the assembly of DNA molecules. Then DNA was chemisorbed onto the self-assembled monolayers (SAMs) of cysteamine to form a network by controlling DNA concentration. The DNA-network film obtained provided a biocompatible microenvironment for enzyme molecules, greatly amplified the coverage of HRP molecules on the electrode surface, and most importantly could act as a charge carrier which facilitated the electron transfer between HRP and the electrode. Finally, HRP was adsorbed on the DNA-network film. The process of the biosensor construction was followed by atomic force microscopy (AFM). Voltammetric and time-based amperometric techniques were employed to characterize the properties of the biosensor derived. The enzyme electrode achieved 95% of the steady-state current within 2 s and had a 0.5 mu mol l(-1) detection limit of H2O2. Furthermore, the biosensor showed high sensitivity, good reproducibility, and excellent long-term stability.

Synthesis and catalytic kinetics of tellurium-modified hyaluronic acid with glutathione peroxidase activity

A novel mimic TeHA was synthesized by modifying hyaluronic acid (HA) with tellurium, whose function is similar to that of glutathione peroxidase (GPX). The structure of TeHA was characterized by means of infrared spectroscopy and nuclear magnetic resonance spectroscopy, showing that the target Te is located at -CH2OH of the N-acetyl-D-glucosamine of HA. The activity of TeHA is 163.6 U/mu mol according to Wilson's method. In contrast to other mimics, TeHA displays a high activity. Moreover, TeHA can use many hydroperoxides as substrates, such as H2O2, cumenyl hydroperoxide, and tert-butyl hydroperoxide, and cumenyl hydroperoxide is the optimal substrate. A ping-pong mechanism was deduced for the reduction reactions catalyzed by TeHA according to the steady-state kinetic studies.

Dependence of performance of organic light-emitting devices on sheet resistance of indium-tin-oxide anodes

The dependence of the performance of organic light-emitting devices(OLEDs) on the sheet resistance of indium-tin-oxide(ITO) anodes was investigated by measuring the steady state current density brightness voltage characteristics and the electroluminescent spectra. The device with a higher sheet resistance anode shows a lower current density, a lower brightness level, and a higher operation voltage. The electroluminescence(EL) efficiencies of the devices with the same structure but different ITO anodes show more complicated differences. Furthermore, the shift of the light-emitting zone toward the anode was found when an anode with a higher sheet resistance was used. These performance differences are discussed and attributed to the reduction of hole injection and the increase in voltage drop over ITO anode with the increase in sheet resistance.

Synthesis and kinetics of a novel mimic with glutathione peroxidase activity - Tellurium-containing hyaluronic acid (TeHA)

A novel mimic was synthesized by modifying hyaluronic acid (HA) with tellurium, whose function is similar to that of glutathione peroxidase (GPX). The structure of TeHA was characterized by means of IR and NMR, the target-Te was located at -CH2OH of the N-acetyl-D-glucosamine of HA. The H2O2 reducing activity of TeHA, by glutathione (GSH), was 163.6 U/mu mol according to Wilson's method. In contrast to other mimics, TeHA displayed the highest activity. Moreover, TeHA accepted many hydroperoxides as its substrates, such as H2O2, cumenyl hydroperoxide (CuOOH) and tert-butyl hydroperoxide (t-BuOOH), and CuOOH was the optimal substrate of TeHA. A ping-pong mechanism was observed in the steady-state kinetic studies of the reactions catalyzed by TeHA.

Systematic study of the transfer of amino acids across the water/1,2-dichloroethane interface facilitated by dibenzo-18-crown-6

Facilitated ion transfer reactions of 20 amino acids with di.benzo-18-crown-6 (DB18C6) at the water/1,2-dichloroethane (W/DCE) interfaces supported at the tips of micro- and nano-pipets were investigated systematically using cyclic voltammetry. It was found that there were only 10 amino acids, that is, Leu, Val, Ile, Phe, Trp, Met, Ala, Gly, Cys, Gln (in brief), whose protonated forms as cations can give well-defined facilitated ion transfer voltammograms within the potential window, and the reaction pathway was proven to be consistent with the transfer by interfacial complexation/dissociation (TIC/TID) mechanisms. The association constants of DB 18C6 with different amino acids in the DCE (beta(0)), and the kinetic parameters of reaction were evaluated based on the steady-state voltammetry of micro- or nano-pipets, respectively The experimental results demonstrated that the selectivity of complexation of protonated amino acid by DB18C6 compared with that of alkali metal cations was low, which can be attributed to the vicinal effect arising from steric hindrance introduced by their side group and the steric bulk effect by lipophilic stabilization.