Stability and molecular modeling of triplex DNA inhibiting DNA binding protein binding to the core promoter of hepatitis B virus.

Two three-dimensional structure models of the 21nt oligodeoxyribonucleotides, CPI (G3TG-2TGT2G5TG2TGT) and CP3 (TGTG2TGST2GTG2TG3), were constructed by InsightII (MSI) software in IRIS Indigo2 (SGI) workstation using the crystal structure of TAT tripler formation as the template. The initial structures subsequently were minimized by molecular mechanics. The final structures were believed as the dominant conformation. The results showed that the energy of CP1 is lower than that of CP3, and the former is more stable than the latter. Moreover, the results further proved that the 21nt oligodeoxyribo-nucleotide CP1 stably combines with the core promoter (Cp) fragment of hepatitis B virus (HBV) to form a tripler DNA, and CP1 specifically inhibits a specific cellular factor (DNA binding protein) binding to Cp fragment. These results indicated that specific repression of gene transcription of HBV DNA might be possible by tripler-formation DNA.

ANTHROPOGENIC ORGANIC CONTAMINANTS IN WATER AND SURFACE SEDIMENTS OF LARGE SHALLOW EUTROPHIC CHAOHU LAKE, CHINA

To characterize the contamination of anthropogenic organic contaminants in the aquatic environment of Chaohu Lake, China, 7 samples for both water and surface sediment were collected in the lake. Organic contaminants were extracted by solid phase extraction (SPE) and Soxhlet extraction from the water and surface sediment samples, respectively, and then analyzed by GC-MS. One hundred and twenty kinds of organic chemicals were detected in these samples including phenol, benzene series, benzaldehydes, ethanol, polycyclic aromatic hydrocarbons (PAHs), sulfur compounds, alcoholic halides, amines, ketones, esters, alkenes and alkanes. Among them, 13 kinds of chemicals were identified as priority pollutants listed by the U.S. Environmental Protection Agency (EPA), such as phthalate esters (PAEs) and PAHs. Besides, the concentrations of 19 of PAEs and PAHs including, priority pollutants identified were also determined. Bis(2-ethylhexyl)phthalate, the predominant component of the analyzed pollutants, was in the range from 72.34 ng g(-1) DW to 613.71 ng g(-1) DW, 14.80 ng L-1 to 47.05 ng L-1 in sediment and water, respectively. The results indicated that the northwest part of the lake was heavily polluted by domestic and industrial wastewater.

De novo RNA synthesis and homology modeling of the classical swine fever virus RNA polymerase

Classical swine fever virus (CSFV) non-structural protein 5B (NS5B) encodes an RNA-dependent RNA polymerase (RdRp), a key enzyme which initiates RNA replication by a de novo mechanism without a primer and is a potential target for anti-virus therapy. We expressed the NS5B protein in Escherichia coli. The rGTP can stimulate de novo initiation of RNA synthesis and mutation of the GDD motif to Gly-Asp-Asp (GAA) abolishes the RNA synthesis. To better understand the mechanism of viral RNA synthesis in CSFV, a three-dimensional model was built by homology modeling based on the alignment with several virus RdRps. The model contains 605 residues folded in the characteristic fingers, palm and thumb domains. The fingers domain contains an N-terminal region that plays an important role in conformational change. We propose that the experimentally observed promotion of polymerase efficiency by rGTP is probably due to the conformational changes of the polymerase caused by binding the rGTP. Mutation of the GDD to GAA interferes with the interaction between the residues at the polymerase active site and metal ions, and thus renders the polymerase inactive. (c) 2005 Elsevier B.V. All rights reserved.

Persistent organic pollutants in water and surface sediments of Taihu Lake, China and risk assessment

Organic pollutants, especially persistent organic pollutants were examined in the water and surface sediments of Taihu Lake, China. Both 12 water and 12 sediment samples were collected over the lake. C-18 solid-phase extraction technique was applied to extract organic pollutants in collected water samples. Soxhlet extraction procedure was used to extract organic pollutants in sediment samples. The analysis was performed by GC-MS controlled by a Hewlett Packard chemstation. Two hundred and seventy-three kinds of organic chemicals in water were examined, 200 more than that detected in 1985; 188 kinds of chemicals in sediments were detected as well. Among them 21 kinds of chemicals belong to priority pollutants as well as 17 kinds to be the endocrine disruptors. The concentrations of the pollutants were more than 2 times higher than that in 1985. The possible source and relation to anthropogenic activity were discussed. (C) 2002 Elsevier Science Ltd. All rights reserved.

Band-tail shape and transport near the metal-insulator transition in Si-doped

In the present work, an infrared light-emitting diode is used to photodope molecular-beam-epitaxy-grown Si: Al0.3Ga0.7As, a well-known persistent photoconductor, to vary the effective electron concentration of samples in situ. Using this technique, we examine the transport properties of two samples containing different nominal doping concentrations of Si [1 x 10(19) cm(-3) for sample 1 (S1) and 9 x 10(17) cm(-3) for sample 2 (S2)] and vary the effective electron density between 10(14) and 10(18) cm(-3). The metal-insulator transition for S1 is found to occur at a critical carrier concentration of 5.7 x 10(16) cm(-3) at 350 mK. The mobilities in both samples are found to be limited by ionized impurity scattering in the temperature range probed, and are adequately described by the Brooks-Herring screening theory for higher carrier densities. The shape of the band tail of the density of states in Al0.3Ga0.7As is found electrically through transport measurements. It is determined to have a power-law dependence, with an exponent of -1.25 for S1 and -1.38 for S2.

A Bragg-mirror-based semiconductor saturable absorption mirror at 800 nm with low temperature and surface state hybrid absorber

We present a novel 800-nm Bragg-mirror-based semiconductor saturable absorption mirror with low temperature and surface state hybrid absorber, with which we can realize the passive soliton mode locking of a Ti:sapphire laser pumped by 532-nm green laser which produces pulses as short as 37 fs. The reflection bandwidth of the mirror is 30 nm and the pulse frequency is 107 MHz. The average output power is 1.1 W at the pump power of 7.6 W.

Effects of shape and magnetic field on the optical properties of wurtzite quantum rods

The optical properties of quantum rods in the absence and presence of the magnetic field are studied in the framework of effective-mass envelope function theory. The two-dimensional (2D) and 1D transition dipoles of wurtzite quantum rods are investigated. It is found that the transition dipoles change from 2D to 1D as the aspect ratio of the ellipsoid increases, in agreement with the experimental results. The linear polarization factors of optical transitions of quantum rods with critical aspect ratio are zero at every orientation of the wave propagation. So quantum rods with critical aspect ratio have isotropic transition dipoles. Due to the 2D or 1D transition dipoles, the linear polarization factors of optical transitions of quantum rods change from negative or positive values to zero as the orientation of the wave propagation changes from the x axis of the crystal structure to the z axis, in agreement with the experimental results. Under magnetic field applied along the z axis of the crystal structure, the negative linear polarization factors in the 2D transition dipole case decrease as the magnetic field increases, while under magnetic field applied along the x axis, the negative linear polarization factors increase as the magnetic field increases. The antisymmetric Hamiltonian is very important to these effects of the magnetic field. It is found that quantum rods with a given radius at a given temperature have dark excitons in a range of aspect ratio. The dimensions along the x, y axes of the crystal structure play opposite roles to the dimension along the z axis on the dark exciton phenomenon. Dark excitons become bright under appropriate magnetic field.

Thermal quenching of luminescence from buried and surface InGaAs self-assembled quantum dots with high sheet density

Variable-temperature photoluminescence (PL) spectra of Si-doped self-assembled InGaAs quantum dots (QDs) with and without GaAs cap layers were measured. Narrow and strong emission peak at 1075 nm and broad and weak peak at 1310 nm were observed for the buried and surface QDs at low temperature, respectively. As large as 210 meV redshift of the PL peak of the surface QDs with respect to that of the buried QDs is mainly due to the change of the strain around QDs before and after growth of the GaAs cap layer. Using the developed localized-state luminescence model, we quantitatively calculate the temperature dependence of PL peaks and integrated intensities of the two samples. The results reveal that there exists a large difference in microscopic mechanisms of PL thermal quenching between two samples. (c) 2005 American Institute of Physics.

Effect of oxidation on the optical and surface properties of AlGaN

The chemical properties of AlxGa1-xN surfaces exposed to air for different time periods are investigated by atomic force microscopy (AFM), photoluminescence (PL) measurement and X-ray photoelectron spectroscopy (XPS). PL and AFM results show that AlxGa1-xN samples exhibit different surface characteristics for different air-exposure times and Al contents. The XPS spectra of the Al 2p and Ga 2p core levels indicate that the peaks shifted slightly, from an Al-N to an Al-O bond and from a Ga-N to a Ga-O bond. All of these results show that the epilayer surface contains a large amount of Ga and Al oxides. (c) 2006 Elsevier B.V. All rights reserved.

Effect on the optical properties and surface morphology of cubic GaN grown by metalorganic chemical vapor deposition using isoelectronic indium surfactant doping

The surfactant effect of isoelectronic indium doping during metalorganic chemical vapor deposition growth of cubic GaN on GaAs (1 0 0) substrates was studied. Its influence on the optical properties and surface morphology was investigated by using room-temperature photoluminescence (PL) and atomic force microscopy. It is shown that the sample with small amount of In-doping has a narrower PL linewidth, and a smoother surface than undoped cubic GaN layers. A slight red shift of the near-band-edge emission peak was observed. These results revealed that, for small TMIn flow rates, indium played the role of the surfactant doping and effectively improved the cubic GaN film quality; for large TMIn flow rates, the alloying formation of Ga1-xInxN might have occurred. (C) 2002 Elsevier Science B.V. All rights reserved.

The Deposition and Burning Characteristics During Slagging Co-Firing Coal and Wood: Modeling and Numerical Simulation

Numerical analysis was used to study the deposition and burning characteristics of combining co-combustion with slagging combustion technologies in this paper. The pyrolysis and burning kinetic models of different fuels were implanted into the WBSF-PCC2 (wall burning and slag flow in pulverized co-combustion) computation code, and then the slagging and co-combustion characteristicsespecially the wall burning mechanism of different solid fuels and their effects on the whole burning behavior in the cylindrical combustor at different mixing ratios under the condition of keeping the heat input samewere simulated numerically. The results showed that adding wood powder at 25% mass fraction can increase the temperature at the initial stage of combustion, which is helpful to utilize the front space of the combustor. Adding wood powder at a 25% mass fraction can increase the reaction rate at the initial combustion stage; also, the coal ignitability is improved, and the burnout efficiency is enhanced by about 5% of suspension and deposition particles, which is helpful for coal particles to burn entirely and for combustion devices to minimize their dimensions or sizes. The results also showed that adding wood powder at a proper ratio is helpful to keep the combustion stability, not only because of the enhancement for the burning characteristics, but also because the running slag layer structure can be changed more continuously, which is very important for avoiding the abnormal slag accumulation in the slagging combustor. The theoretic analysis in this paper proves that unification of co-combustion and slagging combustion technologies is feasible, though more comprehensive and rigorous research is needed.

PHOTOLUMINESCENCE AND SURFACE PHOTOVOLTAIC SPECTRA OF STRAINED INP ON GAAS

A high energy shift of the band-band recombination has been observed in the photoluminescence (PL) spectra of the strained InP epilayer on GaAs by metalorganic chemical vapor deposit. The strain determined by PL peak is in good agreement with calculated thermal strain. The surface photovoltalic spectra gives the information about energy gap, lattice mismatching, and composition of heteroepilayers, diffusion length, surface, and interface recombination velocity of minority carriers of heteroepitaxy layers.

800nm Semiconductor Absorber with Low Temperature Method and Surface State Method Combined Absorber for Kerr Lens Modelocking of Ti∶Al2O3 Laser

A novel 800nm Bragg mirror type of semiconductor saturable absorption mirror with low temperature method and surface state method combined absorber is presented.With which passive Kerr lens mode locking of Ti∶Al2O3 laser pumped by argon ion laser is realized,which produces pulses as short as 40fs.The spectrum bandwidth is 56nm,which means that it can support the modelocking of 20fs.The pulse frequency is 97.5MHz;average output power is 300mW at the pump power of 4.45W.