The complete mitochondrial genome of the Chinese hook snout carp Opsariichthys bidens (Actinopterygii : Cyprinifonnes) and an altemative pattem of mitogenomic evolution in vertebrate

The complete mitochondrial genome sequence of the Chinese hook snout carp, Opsariichthys bidens, was newly determined using the long and accurate polymerase chain reaction method. The 16,611-nucleotide mitogenome contains 13 protein-coding genes, two rRNA genes (12S, 16S) 22 tRNA genes, and a noncoding control region. We use these data and homologous sequence data from multiple other ostariophysan fishes in a phylogenetic evaluation to test hypothesis pertaining to codon usage pattern of O. bidens mitochondrial protein genes as well as to re-examine the ostariophysan phylogeny. The mitochondrial genome of O. bidens reveals an alternative pattern of vertebrate mitochondrial evolution. For the mitochondrial protein genes of O. bidens, the most frequently used codon generally ends with either A or C, with C preferred over A for most fourfold degenerate codon families; the relative synonymous codon usage of G-ending codons is greatly elevated in all categories. The codon usage pattern of O. bidens mitochondrial protein genes is remarkably different from the general pattern found previously in the relatively closely 9 related zebrafish and most other vertebrate mitochondria. Nucleotide bias at third codon positions is the main cause of codon bias in the mitochondrial protein genes of O. bidens, as it is biased particularly in favor of C over A. Bayesian analysis of 12 concatenated mitochondrial protein sequences for O. bidens and 46 other teleostean taxa supports the monophyly of Cypriniformes and Otophysi and results in a robust estimate of the otophysan phylogeny. (C) 2007 Published by Elsevier B.V.

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.

Cloning and analysis of 16 Rab genes from macronuclear DNA of Euplotes octocarinatus

Rab proteins belong to the largest family of the Ras superfamily of small GTPase that play an important role in intracellular vesicular traffic. So far, almost 60 members of Rab family have been identified in mammalian cells. To further study the diversity and function of Rab protein in evolution, unicellular protozoa ciliates, Euplotes octocarinatus, were used in this study, Rab genes were screened by PCR method from macronuclear DNA of E. octocarinatus. Sixteen Rab genes were obtained. They share 87.6 - 99.5% identities. Highly conserved GTP-binding domains were found. There are some hot regions that diverse sharply in these genes as well.

Identification of three duplicated Spin genes in medaka (Oryzias latipes)

Gene and genomic duplications are very important and frequent events in fish evolution, and the divergence of duplicated genes in sequences and functions is a focus of research on gene evolution. Here, we report the identification and characterization of three duplicated Spindlin (Spin) genes from medaka (Oryzias latipes): OlSpinA, OlSpinB, and OlSpinC. Molecular cloning, genomic DNA Blast analysis and phylogenetic relationship analysis demonstrated that the three duplicated OlSpin genes should belong to gene duplication. Furthermore, Western blot analysis revealed significant expression differences of the three OlSpins among different tissues and during embryogenesis in medaka, and suggested that sequence and functional divergence might have occurred in evolution among them. © 2005 Elsevier B.V. All rights reserved.

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.

Observation of intershell and hybridized energy states in InAs/GaAs quantum dots

We have investigated the evolution of exciton state filling as a function of excitation power density in InAs/GaAs quantum dots (QDs). In addition to the emission bands of exciton recombination corresponding to the atom-like S, P, and D, etc. shells of quantum dots, it was observed that some extra states, P-' (between the S and P shells) and D-' (between the P and D shells), appear in the spectra with increasing number of excitons occupying the QDs. The emergence of these intershell excitonic levels is an experimental demonstration of strong exciton-exciton exchange interaction and coupling as well as state mixing and hybridization of a multiexciton system in quantum dots.

Formation of GaAs/AlGaAs and InGaAs/GaAs nanorings by droplet molecular-beam epitaxy

GaAs/AlGaAs lattice-matched nanorings are formed on GaAs (100) substrates by droplet epitaxy. The crucial step in the formation of nanorings is annealing Ga droplets under As flux for proper time. The observed morphologic evolution of Ga droplets during annealing does not support the hypothesis that As atoms preferentially react with Ga around the periphery of the droplets, but somehow relates to a dewetting process similar to that of unstable films. Photoluminescene (PL) test results confirm the quantum-confinement effect of these GaAs nanorings. Using similar methods, we have fabricated InGaAs/GaAs lattice-mismatched rings. (c) 2005 American Institute of Physics.