Sox genes in grass carp (Ctenopharyngodon idella) with their implications for genome duplication and evolution

The Sox gene family is found in a broad range of animal taxa and encodes important gene regulatory proteins involved in a variety of developmental processes. We have obtained clones representing the HMG boxes of twelve Sox genes from grass carp (Ctenopharyngodon idella), one of the four major domestic carps in China. The cloned Sox genes belong to group B1, B2 and C. Our analyses show that whereas the human genome contains a single copy of Sox4, Sox11 and Sox14, each of these genes has two co-orthologs in grass carp, and the duplication of Sox4 and Sox11 occurred before the divergence of grass carp and zebrafish, which support the "fish-specific whole-genome duplication" theory. An estimation for the origin of grass carp based on the molecular clock using Sox1, Sox3 and Sox11 genes as markers indicates that grass carp (subfamily Leuciscinae) and zebrafish (subfamily Danioninae) diverged approximately 60 million years ago. The potential uses of Sox genes as markers in revealing the evolutionary history of grass carp are discussed.

Identification of one intron loss and phylogenetic evolution of Dfak gene in the Drosophila melanogaster species group

Intron loss and its evolutionary significance have been noted in Drosophila. The current study provides another example of intron loss within a single-copy Dfak gene in Drosophila. By using polymerase chain reaction (PCR), we amplified about 1.3 kb fragment spanning intron 5-10, located in the position of Tyr kinase (TyK) domain of Dfak gene from Drosophila melanogaster species group, and observed size difference among the amplified DNA fragments from different species. Further sequencing analysis revealed that D. melanogaster and D. simulans deleted an about 60 bp of DNA fragment relative to other 7 Drosophila species, such as D. elegans, D. ficusphila, D. biarmipes, D. takahashii, D. jambulina, D. prostipennis and D. pseudoobscura, and the deleted fragment located precisely in the position of one intron. The data suggested that intron loss might have occurred in the Dfak gene evolutionary process of D. melanogaster and D. simulans of Drosophila melanogaster species group. In addition, the constructed phylogenetic tree based on the Dfak TyK domains clearly revealed the evolutionary relationships between subgroups of Drosophila melanogaster species group, and the intron loss identified from D. melanogaster and D. simulans provides a unique diagnostic tool for taxonomic classification of the melanogaster subgroup from other group of genus Drosophila.

Structural evolution of mechanically alloyed nanocrystalline FeAl intermetallics

Nanostructured FeAl intermetallics were prepared directly by mechanical alloying (MA) in a high-energy planetary ball-mill. The phase transformations and structural changes occurring in the studied material during mechanical alloying were investigated by X-ray diffraction (XRD). Transmission electron microscopy (TEM) was employed to examine the morphology of the powders. Thermal behavior of the milled powders was examined by differential scanning calorimetry (DSC). Disordered Fe(Al) solid solution was formed at the early stage. After 30 h of milling, Fe(Al) solid solution transformed into an ordered FeAl phase. The average crystallite size reduction down to about 12 nm was accompanied by the introduction of the average lattice strain up to 1.7%. The TEM picture showed that the size of milled powders was less than 30 nm. (c) 2007 Elsevier B.V. All rights reserved.

Evolution of structural defects in SiOx films fabricated by electron cyclotron resonance plasma chemical vapour deposition upon annealing treatment

We study the structural defects in the SiOx film prepared by electron cyclotron resonance plasma chemical vapour deposition and annealing recovery evolution. The photoluminescence property is observed in the as-deposited and annealed samples. [-SiO3](2-) defects are the luminescence centres of the ultraviolet photoluminescence (PL) from the Fourier transform infrared spectroscopy and PL measurements. [-SiO3](2-) is observed by positron annihilation spectroscopy, and this defect can make the S parameters increase. After 1000 degrees C annealing, [-SiO3](2-) defects still exist in the films.

Evolution of Ge and SiGe quantum dots under excimer laser annealing

We present different relaxation mechanisms of Ge and SiGe quantum dots under excimer laser annealing. Investigation of the coarsening and relaxation of the dots shows that the strain in Ge dots on Ge films is relaxed by dislocation since there is no interface between the Ge dots and the Ge layer, while the SiGe dots on Si0.77Ge0.23 film relax by lattice distortion to coherent clots, which results from the obvious interface between the SiGe clots and the Si0.77Ge0.23 film. The results are suggested and sustained by Vanderbilt and Wickham's theory, and also demonstrate that no bulk diffusion oGeurs during the excimer laser annealing.

Evolution of surface morphology and photoluminescence characteristics of 1.3-mu m In0.5Ga0.5As/GaAs quantum dots grown by molecular beam epitaxy

Evolution of surface morphology and optical characteristics of 1.3-mu m In0.5Ga0.5As/GaAs quantum dots (QDs) grown by molecular beam epitaxy (MBE) are investigated by atomic force microscopy (AFM) and photoluminescence (PL). After deposition of 16 monolayers (ML) of In0.5Ga0.5As, QDs are formed and elongated along the [110] direction when using sub-ML depositions, while large size InGaAs QDs with better uniformity are formed when using ML or super-ML depositions. It is also found that the larger size QDs show enhanced PL efficiency without optical nonlinearity, which is in contrast to the elongated QDs.

Entanglement evolution of a spin-chain bath coupled to a quantum spin

For an electron spin in coupling with an interacting spin chain via hyperfine-type interaction, we investigate the dynamical evolutions of the pairwise entanglement of the spin chain, and a correlation function joined the electron spin with a pair of chain spins in correspondence to the electron-spin coherence evolution. Both quantities manifest a periodic and a decaying evolution. The entanglement of the spin bath is significant in distinguishing the zero-coherence status exhibited in periodic and decoherence evolutions of the electron spin. The periodical concurrence evolution of the spin bath characterizes the whole system in a coherence-preserving phase, particularly for the case that the associated periodic coherence evolution is predominated by zero value in the infinite chain-length limit, which was often regarded as the realization of decoherence.

Decay lifetime and evolution of semiconductor quantum dots in photonic crystals

Spontaneous emission from GaAs/AlGaAs quantum dots (QDs) embedded in photonic crystals with a narrow photonic band gap is studied theoretically. The results show that the decay lifetime is very sensitive to the sizes of QDs, and both inhibited and accelerated emission can occur, which had been indicated in a previous experiment. The Weisskopf-Wigner approximation, good for atoms and molecules, may be incorrect for QDs. A damped Rabi oscillation of the excited state with the transition frequency outside the photonic band gap may appear, which is impossible for atoms and molecules. (c) 2008 Elsevier Ltd. All rights reserved.

Defect evolution and accompanied change of electrical properties during the GaN growth by metalorganic chemical vapor deposition

The defect evolution and its correlation with electrical properties of GaN films grown by metalorganic chemical vapor deposition are investigated. It is found that the dislocation density decreases gradually during the growth process, and the dislocation reduction rate in the island coalescence process is especially rapid. The changes in electron mobility of GaN with the increase of growth time are mainly dependent on the dislocations acting as scattering centers. Furthermore, the variation of carrier concentration in GaN may be related with the point defects and their clusters. The quality of GaN could be improved by suitably increasing the film thickness. (C) 2009 Elsevier B.V. All rights reserved.

Origin and evolution of photoluminescence from Si nanocrystals embedded in a SiO2 matrix

A detailed analysis of the photoluminescence (PL) from Si nanocrystals (NCs) embedded in a silicon-rich SiO2 matrix is reported. The PL spectra consist of three Gaussian bands (peaks A,B, and C), originated from the quantum confinement effect of Si NCs, the interface state effect between a Si NC and a SiO2 matrix, and the localized state transitions of amorphous Si clusters, respectively. The size and the surface chemistry of Si NCs are two major factors affecting the transition of the dominant PL origin from the quantum confinement effect to the interface state recombination. The larger the size of Si NCs and the higher the interface state density (in particular, Si = O bonds), the more beneficial for the interface state recombination process to surpass the quantum confinement process, in good agreement with Qin's prediction in Qin and Li [Phys. Rev. B 68, 85309 (2003)]. The realistic model of Si NCs embedded in a SiO2 matrix provides a firm theoretical support to explain the transition trend.

Experimental study of mode field evolution of dual-core photonic crystal fiber

The accurate mode field profile of high negative dispersion dual-core photonic crystal fiber (DCPCF) is measured. The mode field evolution of DCPCF with wavelength is studied experimentally for the first time. The measurement result shows that no individual inner core mode or outer core mode exists, but two modes coexist simultaneously, and either one of them is dominant. The mode field evolution versus wavelength indicates that the wavelength range where the modes coupling takes place between inner core and outer core is broader than that of theoretical design.

Influence of AlN thickness on strain evolution of GaN layer grown on high-temperature AlN interlayer

The strain evolution of a GaN layer grown on a high- temperature AlN interlayer with varying AlN thickness by metalorganic chemical vapour deposition is investigated. In the growth process, the growth strain changes from compression to tension in the top GaN layer, and the thickness at which the compressive- to- tensile strain transition takes place is strongly influenced by the thickness of the AlN interlayer. It is confirmed from the x- ray diffraction results that the AlN interlayer has a remarkable effect on introducing relative compressive strain to the top GaN layer. The strain transition process during the growth of the top GaN layer can be explained by the threading dislocation inclination in the top GaN layer. Adjusting the AlN interlayer thickness could change the density of the threading dislocations in the top GaN layer and then change the stress evolution during the top GaN layer's growth.

Stress evolution influenced by oxide charges on GaN metal-organic chemical vapor deposition on silicon-on-insulator substrate

GaN epilayers have been deposited on silicon-on-insulator (SOI) and bulk silicon substrates. The stress transition thickness and the initial compressive stress of a GaN epilayer on the SOI substrate are larger than those on the bulk silicon substrate, as shown in in situ stress measurement results. It is mainly due to the difference of the three-dimensional island density and the threading dislocation density in the GaN layer. It can increase the compressive stress in the initial stage of growth of the GaN layer, and helps to offset the tensile stress generated by the lattice mismatch.

Evolution of InAs nanostructures grown by droplet epitaxy

The authors report the growth evolution of InAs dot and ring nanostructures with the indium deposition amount on GaAs (001) by droplet molecular beam epitaxy. There is a critical flux for the indium to form InAs dots even when there is no droplet. When the flux exceeds a critical value, In droplets form, which act as nucleation centers for the formation of InAs rings. (C) 2007 American Institute of Physics.

The wave function evolution of an exciton in a bilayer system: Turning on a static in-plane electric field

The time evolution of the ground state wave function of an exciton in an ideal bilayer system is investigated within the framework of the effective-mass approximation. All of the moduli squared of the ground state wave functions evolve with time as cosine functions after an in-plane electric field is applied to the bilayer system. The variation amplitude and period of the modulus squared of the ground state wave function increase with the in-plane electric field F-r for a fixed in-plane relative coordinate r and fixed separation d between the electron and hole layers. Moreover, the variation amplitude and period of the modulus squared of the ground state wave function increase with the separation d for a fixed r and fixed in-plane electric field. Additionally, the modulus squared of the ground state wave function decreases as r increases at a given time t for fixed values of d and F-r. (c) 2007 American Institute of Physics.