Sox genes evolution in closely related young tetraploid cyprinid fishes and their diploid relative

Previous study and analysis of cytochrome b suggested that polyploidization event in the genus Tor occurred about 10 Mya ago. In order to understand evolutionary fates of Sox gene in the early stage of genome duplication at the nucleotide level, PCR surveys for Sox genes in three closely related cyprinid fishes T douronensis (2n = 100), T qiaojiensis (2n = ?), T sinensis (2n = 100) and their relative T brevifilis (2n = 50) were performed. Totally, 52 distinct Sox genes were obtained in these four species, representing SoxB, SoxC, and SoxE group. As expected, isoforms of some Sox genes correspond with the ploidy of species, such as two copies of Sox9a exist in tetraploid species. Analysis indicated that duplicated Sox gene pairs caused by polyploidization evolved independently of each other within polyploid species. Results of substitution rate showed nearly equal rate of nonsynonymous substitution of duplicated Sox orthologs among different polyploid species and their diploid relative orthologs, suggesting at the early stage of genome duplicated Sox orthologs are under similar selective constraints in different polyploidy species and their diploid relative at the amino acid level. All PCR fragments of Sox genes obtained in this study are not accompanied by obvious increase in mutations and pseudogene formation which means that they are under strong purifying selection, suggesting that they are functional at the DNA level. Cenealogical analysis revealed that T qiaojiensis was tetraploid, and T douronensis, T qiaojiensis as well as T sinensis had an allotetraploid ancestor. (C) 2009 Elsevier B.V. All rights reserved.

Origin and evolution of the RIG-I like RNA helicase gene family

Background: The DExD/H domain containing RNA helicases such as retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 (MDA5) are key cytosolic pattern recognition receptors (PRRs) for detecting nucleotide pathogen associated molecular patterns (PAMPs) of invading viruses. The RIG-I and MDA5 proteins differentially recognise conserved PAMPs in double stranded or single stranded viral RNA molecules, leading to activation of the interferon system in vertebrates. They share three core protein domains including a RNA helicase domain near the C terminus (HELICc), one or more caspase activation and recruitment domains (CARDs) and an ATP dependent DExD/H domain. The RIG-I/MDA5 directed interferon response is negatively regulated by laboratory of genetics and physiology 2 (LGP2) and is believed to be controlled by the mitochondria antiviral signalling protein (MAVS), a CARD containing protein associated with mitochondria. Results: The DExD/H containing RNA helicases including RIG-I, MDA5 and LGP2 were analysed in silico in a wide spectrum of invertebrate and vertebrate genomes. The gene synteny of MDA5 and LGP2 is well conserved among vertebrates whilst conservation of the gene synteny of RIG-I is less apparent. Invertebrate homologues had a closer phylogenetic relationship with the vertebrate RIG-Is than the MDA5/LGP2 molecules, suggesting the RIG-I homologues may have emerged earlier in evolution, possibly prior to the appearance of vertebrates. Our data suggest that the RIG-I like helicases possibly originated from three distinct genes coding for the core domains including the HELICc, CARD and ATP dependent DExD/H domains through gene fusion and gene/domain duplication. Furthermore, presence of domains similar to a prokaryotic DNA restriction enzyme III domain (Res III), and a zinc finger domain of transcription factor (TF) IIS have been detected by bioinformatic analysis. Conclusion: The RIG-I/MDA5 viral surveillance system is conserved in vertebrates. The RIG-I like helicase family appears to have evolved from a common ancestor that originated from genes encoding different core functional domains. Diversification of core functional domains might be fundamental to their functional divergence in terms of recognition of different viral PAMPs.

Molecular evolution of connective tissue growth factor in Cyprinidae (Teleostei : Cypriniformes)

Connective tissue growth factor (CTGF) plays an important role in regulation of cell growth, differentiation, apoptosis and individual development in animals. The study of sequences variation and molecular evolution of CTGF gene across various species of the cyprinid could be helpful for understanding of speciation and gene divergence in this kind of fish. In this study, 19 novel sequences of CTGF gene were obtained from the representative species of the family Cyprinidae using PCR amplification, cloning and sequencing. Phylogenetic relationships of Cyprinidae were reconstructed by neighbor-joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian method. Oryzias latipes from the family Cyprinodontidae was assigned to be the outgroup taxon. Leuciscini and Barbini were clustered into the monophyletic lineages, respectively, with the high nodal supports. The estimation of the ratio of non-synonymous to synonymous substitution (dN/dS) for the various branches indicated that there stood the different evolution rates between the Leuciscini and the Barbini. With the ratio of dN/dS of the Leuciscini being lower than that of the Barbini, species within the Barbini were demonstrated to be subjected to the relatively less selection pressure and under the relaxable evolution background. A 6 by indel (insertion/deletion) was found at the 5' end of CTGF gene of Cyprinidae, and this 6 by deletion only appeared in the Leuciscini, which is a typical characteristic of the Leuciscini and provides evidence for the monophylogeny of the Leuciscini. For the amino acid sequences of CTGF protein, the most variations and indels were distributed in the signal region and IGFBP region of this protein, implying that these variations were correlated with the regulation of the CTGF gene expression and protein activity. (c) 2007 National Natural Science Foundation of China and Chinese Academy of Sciences. Published by Elsevier Limited and Science in China Press. All rights reserved.

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.

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.