Evolution of conserved secondary structures and their function in transcriptional regulation networks

Background: Many conserved secondary structures have been identified within conserved elements in the human genome, but only a small fraction of them are known to be functional RNAs. The evolutionary variations of these conserved secondary structures in h

Evolution of structures and specific recognitions in aminoacyl-tRNA synthetases

The aminoacyl-tRNA synthetases (AARS) are very important during the protein biosynthesis, which can make the gene sequence be accurately translated into the protein sequence by the specific recognition between AARS and tRNA/amino acids. However, the recog

Gene structures and promoter characteristics of interferon regulatory factor 1 (IRF-1), IRF-2 and IRF-7 from snakehead Channa argus

Three interferon regulatory factor (IRF) genes, CaIRF-1, CaIRF-2 and CaIRF-7, and their promoters of snakehead (Channa argus) were cloned and characterized. The CaIRF-1 gene consists of ten exons, spans 4.3 kb and encodes a putative peptide of 299 aa. The CaIRF-2 gene consists of nine exons, spans 8 kb and encodes a putative peptide of 328 aa. The gene organizations of CaIRF-1 and CaIRF-2 are very similar to that of human IRF-1 and IRF-2 except more compact. Comparison of exon-intron organization of the two genes indicated a common evolutionary structure, notably within the exons encoding the DNA binding domain (DBD) of the two factors. The CaIRF-7 gene spans 4.1 kb and encodes a putative peptide of 437 aa. However, the gene organization of CaIRF-7 consisting of ten exons is different to human IRF-7a gene which has an intron in 5' UTR. Three CaIRFs share homology in N-terminal encompassing the DBD that contains a characteristic repeat of tryptophan residues. The promoters of CaIRF-1 and CaIRF-2 genes contain the conserved sites for NF-kappa B and Sp1. The gamma-IFN activation sites (GAS) were found in the promoters of CaIRF-1 and CaIRF-7. The promoter of CaIRF-7 contains conserved interferon stimulating response element (ISRE) which is characteristic of IFN-induced gene promoter, and suggests that there also exist intracellular amplifier circuit in fish IFN signal pathway. Moreover, the element GAAANN oriented in both directions is repeated in CaIRF promoter regions, which confers to further inducibility by IFN. The constitutive expression of CaIRF genes were found to increase obviously in response to induction by the known IFN-inducer poly I:C. (c) 2008 Published by Elsevier Ltd.

Important aspects when modelling the interaction between surface structures and tunnelling in sand

Tunnelling in urban areas continues to increase and has highlighted the need for a better understanding of the impact of tunnel excavations on existing buildings. This paper considers the influence of surface structures on ground displacements caused by tunnelling in sand through finite element modelling and centrifuge testing. First, the importance of modelling assumptions is evaluated by comparing centrifuge modelling results to finite element modelling results for various soil constitutive models: both a Young's modulus that linearly increases with depth and a power law relation between the soil stiffness and stresses are considered. Second, the most effective soil constitutive model was used to perform a sensitivity study on the effect of different factors governing the structural response. In particular, the effect of the building stiffness and weight on the modification of soil displacements is investigated by introducing a simple surface structure. The use of a no-tension interface between the building and the soil was found to be essential to investigate the effect of weight on gap formation between the soil and the structure, as observed during the experimental tests. Results show the importance of considering the relation between the building weight and the relative stiffness between the building and the soil when assessing the structural response. © 2014 Korean Geotechnical Society.

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.

Electronic structures and mechanical properties of uranium monocarbide from first-principles LDA plus U and GGA plus U calculations

The electronic structure, elastic constants, Poisson's ratio, and phonon dispersion curves of UC have been systematically investigated from the first-principles calculations by the projector-augmented-wave (PAW) method. In order to describe precisely the strong on-site Coulomb repulsion among the localized U 5f electrons, we adopt the local density approximation (LDA) + U and generalized gradient approximation (GGA) + U formalisms for the exchange correlation term. We systematically study how the electronic properties and elastic constants of UC are affected by the different choice of U as well as the exchange-correlation potential. We show that by choosing an appropriate Hubbard U parameter within the GGA + U approach, most of our calculated results are in good agreement with the experimental data. Therefore. the results obtained by the GGA + U with effective Hubbard parameter U chosen around 3 eV for UC are considered to be reasonable. (C) 2009 Elsevier B.V. All rights reserved.

Controlled growth of III-V compound semiconductor nano-structures and their application in quantum-devices

This paper reviews our work on controlled growth of self-assembled semiconductor nanostructures, and their application in light-emission devices. High-power, long-life quantum dots (QD) lasers emitting at similar to 1 mu m, red-emitting QD lasers, and long-wavelength QD lasers on GaAs substrates have successfully been achieved by optimizing the growth conditions of QDs.

Semiconductor nanometer structures and devices

Self-assembled quantum dots and wires were obtained in the InxGa1-xAs/GaAs and InAs/In0.52Al0.48As/lnP systems, respectively, using molecular beam epitaxy (MBE). Uniformity in the distribution, density, and spatial ordering of the nanostructures can be controlled to some extent by adjusting and optimizing the MBE growth parameters. Laser devices and superluminescent diodes were fabricated with InAs/GaAs self-assembled quantum dots as the active region.

Columnar structures and stress relaxation in thick GaN films grown on sapphire by HVPE

Thick GaN films with high quality are directly grown on sapphire in a home-built vertical hydride vapour phase epitaxy (HVPE) reactor. The optical and structural properties of large scale columnar do-mains near the interface are studied using cathodoluminescence and micro-Raman scattering. These columnar do-mains Show a strong emission intensity due to extremely high free carrier concentration up to 2 x 10(19) cm(-3), which are related with impurities trapped in structural defects. The compressive stress in GaN Elm clearly decreases with increasing distance from interface. The quasi-continuous columnar domains play an important role in the stress relaxation for the upper high quality layer.

Electroluminescence from Au/(SiO2/Si/SiO2) nanometer double barrier/p-Si structures and its mechanism

SiO2/Si/SiO2 nanometer double barriers (SSSNDB) with Si layers of twenty-seven different thicknesses in a range of 1-5 nm with an interval of 0.2 nm have been deposited on p-Si substrates using two-target alternative magnetron sputtering. Electroluminescence (EL) from the semitransparent Au film/SSSNDB/p-Si diodes and from a control diode without any Si layer have been observed under forward bias. Each EL spectrum of all these diodes can be fitted by two Gaussian bands with peak energies of 1.82 and 2.25 eV, and full widths at half maximum of 0.38 and 0.69 eV, respectively. It is found that the current, EL peak wavelength and intensities of the two Gaussian bands of the Au/SSSNDB/p-Si structure oscillate synchronously with increasing Si layer thickness with a period corresponding to half a de Broglie wavelength of the carriers. The experimental results strongly indicate that the EL originates mainly from two types of luminescence centres with energies of 1.82 and 2.25 eV in the SiO2 barriers, rather than from the nanometer Si well in the SSSNDB. The EL mechanism is discussed in detail.

High energy ion implantation enhanced intermixed quantum well structures and their absorption characteristics in passive optical waveguides

We have shown that high energy ion implantation enhanced intermixing (HE-IIEI) technology for quantum well (QW) structures is a powerful technique which can be used to blue shift the band gap energy of a QW structure and therefore decrease its band gap absorption. Room temperature (RT) photoluminescence (PL) and guided-wave transmission measurements have been employed to investigate the amount of blue shift of the band gap energy of an intermixed QW structure and the reduction of band gap absorption, Record large blue shifts in PL peaks of 132 nm for a 4-QW InGaAs/InGaAsP/InP structure have been demonstrated in the intermixed regions of the QW wafers, on whose non-intermixed regions, a shift as small as 5 nm is observed. This feature makes this technology very attractive for selective intermixing in selected areas of an MQW structure. The dramatical reduction in band gap absorption for the InP based MQW structure has been investigated experimentally. It is found that the intensity attenuation for the blue shifted structure is decreased by 242.8 dB/cm for the TE mode and 119 dB/cm for the TM mode with respect to the control samples. Electro-absorption characteristics have also been clearly observed in the intermixed structure. Current-Voltage characteristics were employed to investigate the degradation of the p-n junction in the intermixed region. We have achieved a successful fabrication and operation of Y-junction optical switches (JOS) based on MQW semiconductor optical amplifiers using HE-IIEI technology to fabricate the low loss passive waveguide. (C) 1997 Published by Elsevier Science B.V.

Controlled growth of III-V compound semiconductor nano-structures and their application in quantum-devices

Various techniques on the growth of self-assembled compound semiconductor nano-structures (quantum dots, QDs) have been tried to enhance the controlling on size, density, emitting wavelength, uniformity in size and ordering in location of the QDs. Optimized growth conditions have been used in the application of the QD materials in opto-electronic devices. High-power long-lifetime quantum-dot laser-diodes (QD-LDs) emitting near 1 mu m, QD-LDs emitting in red-light range, 1.3 mu m QD-LDs on GaAs substrate and quantum-dot super-luminescent diodes (QD-SLDs) have successfully been achieved.