Efficient RNA interference in zebrafish embryos using siRNA synthesized with SP6 RNA polymerase

Double-stranded RNA (dsRNA) has been shown to be a useful tool for silencing genes in zebrafish (Danio rerio), while the blocking specificity of dsRNA is still of major concern for application. It was reported that siRNA (small interfering RNA) prepared by endoribonuclease digestion (esiRNA) could efficiently silence endogenous gene expression in mammalian embryos. To test whether esiRNA could work in zebrafish, we utilized Escherichia coli RNaseIII to digest dsRNA of zebrafish no tail (ntl), a mesoderm determinant in zebrafish and found that esi-ntl could lead to developmental defects, however, the effective dose was so close to the toxic dose that esi-ntl often led to non-specific developmental defects. Consequently, we utilized SP6 RNA polymerase to produce si-ntl, siRNA designed against ntl, by in vitro transcription. By injecting in vitro synthesized si-ntl into zebrafish zygotes, we obtained specific phenocopies of reported mutants of ntl. We achieved up to a 59%no tail phenotype when the injection concentration was as high as 4 mu g/mu L. Quantitative reverse transcription-polymerase chain reaction (RT-PCR) and whole-mount in situ hybridization analysis showed that si-ntl could largely and specifically reduce mRNA levels of the ntl gene. As a result, our data indicate that esiRNA is unable to cause specific developmental defects in zebrafish, while siRNA should be an alternative for downregulation of specific gene expression in zebrafish in cases where RNAi techniques are applied to zebrafish reverse genetics.

Quantitative structure-property relationships for octanol-air partition coefficients of polychlorinated naphthalenes, chlorobenzenes and p,p '-DDT

The octanol-air partition coefficient (K-OA) is a key descriptor of chemicals partitioning between the atmosphere and environmental organic phases. Quantitative structure-property relationships (QSPR) are necessary to model and predict KOA from molecular structures. Based on 12 quantum chemical descriptors computed by the PM3 Hamiltonian, using partial least squares (PLS) analysis, a QSPR model for logarithms of K-OA to base 10 (log K-OA) for polychlorinated naphthalenes (PCNs), chlorobenzenes and p,p'-DDT was obtained. The cross-validated Q(cum)(2) value of the model is 0.973, indicating a good predictive ability of the model. The main factors governing log K-OA of the PCNs, chlorobenzenes, and p,p'-DDT are, in order of decreasing importance, molecular size and molecular ability of donating/accepting electrons to participate in intermolecular interactions. The intermolecular dispersive interactions play a leading role in governing log K-OA. The more chlorines in PCN and chlorobenzene molecules, the greater the log K-OA values. Increasing E-LUMO (the energy of the lowest unoccupied molecular orbital) of the molecules leads to decreasing log K-OA values, implying possible intermolecular interactions between the molecules under study and octanol molecules. (C) 2002 Elsevier Science Ltd. All rights reserved.

Quantitative relationships between molecular structures, environmental temperatures and octanol-air partition coefficients of PCDD/Fs

A concise quantitative model that incorporates information on both environmental temperature M and molecular structures, for logarithm of octanol-air partition coefficient (K-OA) to base 10 (logK(OA)) of PCDDs, was developed. Partial least squares (PLS) analysis together with 14 quantum chemical descriptors were used to develop the quantitative relationships between structures, environmental temperatures and properties (QRSETP) model. It has been validated that the obtained QRSETP model can be used to predict logK(OA) of other PCDDs. Molecular size, environmental temperature (T), q(+) (the most positive net atomic charge on hydrogen or chlorine atoms in PCDD molecules) and E-LUMO (the energy of the lowest unoccupied molecular orbital) are main factors governing logK(OA) of PCDD/Fs under study. The intermolecular dispersive interactions and thus the size of the molecules play a leading role in governing logK(OA). The more chlorines in PCDD molecules, the greater the logK(OA) values. Increasing E-LUMO values of the molecules leads to decreasing logK(OA) values, implying possible intermolecular interactions between the molecules under study and octanol molecules. Greater q(+) values results in greater intermolecular electrostatic repulsive interactions between PCDD and octanol molecules and smaller logK(OA) values. (C) 2002 Elsevier Science B.V. All rights reserved.

Quantitative structure-property relationships for octanol-air partition coefficients of polychlorinated biphenyls

Based on nine quantum chemical descriptors computed by PM3 Hamiltonian, using partial least squares analysis, a significant quantitative structure-property relationship for the logarithm of octanol-air partition coefficients (log K-OA) of polychlorinated biphenyls (PCBs) was obtained. The cross-validated Q(cum)(2) value of the model is 0.962, indicating a good predictive ability. The intermolecular dispersive interactions and thus the size of the PCB molecules play a key role in governing log K-OA. The greater the size of PCB molecules, the greater the log K-OA values. Increasing E-LUMO (the energy of the lowest unoccupied molecular orbital) values of the PCBs leads to decreasing log K-OA values, indicating possible interactions between PCB and octanol molecules. Increasing Q(Cl)(+) (the most positive net atomic charges on a chlorine atom) and Q(C)(-) (the largest negative net atomic charge on a carbon atom) values of PCBs results in decreasing log K-OA values, implying possible intermolecular electrostatic interactions between octanol and PCB molecules. (C) 2002 Elsevier Science Ltd. All rights reserved.

Quantitative structure-property relationships (QSPRs) on direct photolysis of PCDDs

By the use of partial least squares (PLS) method and 27 quantum chemical descriptors computed by PM3 Hamiltonian, a statistically significant QSPR were obtained for direct photolysis quantum yields (Y) of selected Polychlorinated dibenzo-p-dioxins (PCDDs). The QSPR can be used for prediction. The direct photolysis quantum yields of the PCDDs are dependent on the number of chlorine atoms bonded with the parent structures, the character of the carbon-oxygen bonds, and molecular polarity. Increasing bulkness and polarity of PCDDs lead to decrease of log Y values. Increasing the frontier molecular orbital energies (E-lumo and E-homo) and heat of formation (HOF) values leads to increase of log Y values. (C) 2001 Elsevier Science Ltd. All rights reserved.

Quantitative structure-property relationship study on reductive dehalogenation of selected halogenated aliphatic hydrocarbons in sediment slurries

In this study, by the use of partial least squares (PLS) method and 26 quantum chemical descriptors computed by PM3 Hamiltonian, a quantitative structure-property relationship (QSPR) model was developed for reductive dehalogenation rate constants of 13 halogenated aliphatic compounds in sediment slurry under anaerobic conditions. The model can be used to explain the dehalogenation mechanism. Halogenated aliphatic compounds with great energy of the lowest unoccupied molecular orbital (E-lumo), total energy (TE), electronic energy (EE), the smallest bond order of the carbon-halogen bonds (BO) and the most positive net atomic charges on an atom of the molecule (q(+)) values tend to be reductively dehalogenated slow, whereas halogenated aliphatic compounds with high values of molecular weight (Mw), average molecular polarizability (a) and core-core repulsion energy (CCR) values tend to be reductively dehalogenated fastest. (C) 2001 Published by Elsevier Science Ltd.

The role of sense organs in the feeding behaviour of Chinese perch

Experiments were conducted to identify the rules of the individual sense organs in the feeding behaviour of Chinese perch Siniperca chuatsi by determining the consumption of natural food after selective removal or blocking of eyes, lateral lines and olfactory organs, and also by observing the behavioural response to visual, mechanical and chemical stimulation by artificial prey. Chinese perch were able to feed properly on live prey fish when either eyes or lateral lines were intact or functional, but could scarcely feed without these two senses. Chinese perch recognized its prey by vision through the perception of motion and shape, and showed a greater dependence on vision in predation when both visual and mechanical cues were available. Chemical stimulation by natural food could not elicit any feeding response in Chinese perch, and gustation was only important to the fish for the last stage of food discrimination in the oropharyngeal cavity. The sensory basis of Chinese perch in feeding is well adapted to its nocturnal stalking hunting strategy. and also explains its peculiar food habit of accepting live prey fish only and refusing dead prey fish or artificial diets. (C) 1998 The Fisheries Society of the British Isles.

First-principles LDA plus U and GGA plus U study of neptunium dioxide

We have performed a systematic first-principles investigation to calculate the electronic structures, mechanical properties, and phonon-dispersion curves of NpO2. The local-density approximation+U and the generalized gradient approximation+U formalisms have been used to account for the strong on-site Coulomb repulsion among the localized Np 5f electrons. By choosing the Hubbard U parameter around 4 eV, the orbital occupancy characters of Np 5f and O 2p are in good agreement with recent experiments [A. Seibert, T. Gouder, and F. Huber, J. Nucl. Mater. 389, 470 (2009)]. Comparing to our previous study of ThO2, we note that stronger covalency exists in NpO2 due to the more localization behavior of 5f electrons of Np in line with the localization-delocalization trend exhibited by the actinides series.

Donor-donor binding in In2O3: Engineering shallow donor levels

Using first-principles band structure methods, we investigate the interactions between different donors in In2O3. Through the formation energy and transition energy level calculations, we find that an oxygen-vacancy creates a deep donor level, while an indium-interstitial or a tin-dopant induces a shallow donor level. The coupling between these donor levels gives rise to even shallower donor levels and leads to a significant reduction in their formation energies. Based on the analysis of the PBE0-corrected band structure and the molecular-orbital bonding diagram, we demonstrate these effects of donor-donor binding. In addition, total energy calculations show that these defect pairs tend to be more stable with respect to the isolated defects due to their negative binding energies. Thus, we may design shallow donor levels to enhance the electrical conductivity via the donor donor binding.

Optical properties of UO2 and PuO2

We perform first-principles calculations of electronic structure and optical properties for UO2 and PuO2 based on the density functional theory using the generalized gradient approximation (GGA) + U scheme. The main features in orbital-resolved partial density of states for occupied f and p orbitals, unoccupied d orbitals, and related gaps are well reproduced compared to experimental observations. Based on the satisfactory ground-state electronic structure calculations, the dynamical dielectric function and related optical spectra, i.e., the reflectivity, adsorption coefficient, energy-loss, and refractive index spectrum, are obtained. These results are consistent with the available experiments.

Origins of magnetism in transition metal doped Cul

Cupric iodide is a p-type semiconductor and has a large band gap. Doping of Mn, Co, and Ni are found to make gamma-CuI ferromagnetic ground state, while Cr-doped and Fe-doped CuI systems are stabilized in antiferromagnetic configurations. The origins of the magnetic ordering are demonstrated successfully by the phenomenological band coupling model based on d-d level repulsions between the dopant ions. Furthermore, using a molecular-orbital bonding model, the electronic structures of the doped CuI are well understood. According to Heisenberg model, high-T-C may be expected for CuI:Mn and CuI:Ni if there are no native defects or other impurities.

Comment on

In a recent letter, Hsieh reported the growth of high-quality Ge epilayers with a SiGe buffer thickness of only 0.45 mu m, a surface root-mean-square roughness of less than 0.4 nm, and a threading dislocation of 7.6 x 10(6) cm(-2) on Si+ pre-ion-implantation Si substrate utilizing of strain relaxation enhancement by point defects and interface blocking of the dislocations. Our comment has focused on x-ray diffraction data shown in Fig. 3 of Ref. 1. We demonstrate that the strain in Ge epilayers is tensile, rather than compressive as misunderstood by the authors. (C) 2008 American Institute of Physics. [DOI: 10.1063/1.3003873]

First-principles study of the electronic structures and magnetic properties of 3d transition metal-doped anatase TiO2

We study the electronic structures and magnetic properties of the anatase TiO2 doped with 3d transition metals (V, Cr, Mn, Fe, Co, Ni), using first-principles total energy calculations based on density functional theory (DFT). Using a molecular-orbital bonding model, the electronic structures of the doped anatase TiO2 are well understood. A band coupling model based on d-d level repulsions between the dopant ions is proposed to understand the chemical trend of the magnetic ordering. Ferromagnetism is found to be stabilized in the V-, Cr-, and Co-doped samples if there are no other carrier native defects or dopants. The ferromagnetism in the Cr- and Co-doped samples may be weakened by the donor defects. In the Mn-, and Fe-doped samples, the ferromagnetism can be enhanced by the acceptor and donor defects, respectively.

High responsivity resonant-cavity-enhanced InGaAs/GaAs quantum-dot photodetector for wavelength of similar to 1 mu m at room temperature

The characteristics of a resonant cavity-enhanced InGaAs/GaAs quantum-dot n-i-n photodiode with only a bottom distributed Bragg reflector used as the cavity mirror, are reported. To suppress the dark current, an AlAs layer is inserted into the device structure as the blocking layer. It turns out that the structure still possesses the resonant coupling nature, and makes Rabi splitting discernible in the photoluminescence spectra. The measured responsivity spectrum of the photocurrent shows a peak at lambda = 1030 nm, and increases rapidly as the bias voltage increases. A peak responsivity of 0.75 A/W, or equivalently an external quantum efficiency of 90.3%, is obtained at V-bias = -1.4 V.

Electronic structure and optical property of semiconductor nanocrystallites

Semiconductor nanostructures show many special physical properties associated with quantum confinement effects, and have many applications in the opto-electronic and microelectronic fields. However, it is difficult to calculate their electronic states by the ordinary plane wave or linear combination of atomic orbital methods. In this paper, we review some of our works in this field, including semiconductor clusters, self-assembled quantum dots, and diluted magnetic semiconductor quantum dots. In semiconductor clusters we introduce energy bands and effective-mass Hamiltonian of wurtzite structure semiconductors, electronic structures and optical properties of spherical clusters, ellipsoidal clusters, and nanowires. In self-assembled quantum dots we introduce electronic structures and transport properties of quantum rings and quantum dots, and resonant tunneling of 3-dimensional quantum dots. In diluted magnetic semiconductor quantum dots we introduce magnetic-optical properties, and magnetic field tuning of the effective g factor in a diluted magnetic semiconductor quantum dot. (C) 2004 Elsevier B.V. All rights reserved.