Mitochondrial cytochrome b sequence variations and phylogeny of the East Asian bagrid catfishes

The mitochondrial DNA cytochrome b gene was sequenced from 8 bagrid catfishes in China. Aligned with cytochrome b sequences from 9 bagrid catfishes in Japan, Korea and Russia retrieved from GenBank, and selected Silurus meridionalis, Liobagrus anguillicauda, Liobagrus reini and Phenacogrammus interruptus as outgroups, we constructed a matrix of 21 DNA sequences. The Kimura's two-parameter distances were calculated and molecule phylogenetic trees were constructed by using the maximum parsimony (MP) and neighbor-joining (NJ) methods. The results show that (i) there exist 3-bp deletions of mitochondrial cytochrome b gene compared with cypriniforms and characiforms; (ii) the molecular phylogenetic tree suggests that bagrid catfishes form a monophyletic group, and the genus Mystus is the earliest divergent in the East Asian bagrid catfishes, as well as the genus Pseudobagrus is a monophyletic group but the genus Pelteobagrus and Leiocassis are complicated; and 60 the evolution rate of the East Asian bagrids mitochondrial cytochrome b gene is about 0.18%-0.30% sequence divergence per million years.

Sequence variations in the mitochondrial DNA control region and their implications for the phylogeny of the Cypriniformes

The mitochondrial DNA control region of six cobitids and two catostomids was sequenced and compared with sequences of other cypriniforms to study their sequence variations. The extended termination associated sequence (ETAS) domain, central domain, and conserved sequence block (CSB) domain were partitioned and the ETAS sequence, CSB-D, CSB-E, ECSB-F, CSB1, CSB2, and CSB3 were identified. It is suggested that the "hairpin" TACAT-ATGTA is the key sequence of ETAS and GACATA is the symbol of CSB1. Phylogenetic analysis based on the CSB domain showed that all cyprinids evolved as one monophyletic group, while the non-cyprinid Cypriniformes could be another monophyly that is in accordance with the hypothesis proposed by Siebert. Further analysis of the phylogeny of the Cobitoidei was also conducted and it is tentatively suggested that their relationships are Catostomidae + (Gyrinocheilidae + (Botiinae + (Homalopteridae + (Cobitinae + Nemacheilinae)))).

Phylogeny of the specialized schizothoracine fishes (Teleostei : Cypriniformes : Cyprinidae)

Phylogeny of the specialized schizothoracine fishes (Teleostei: Cypriniformes: Cyprinidae). Zoological Studies 40(2). 147-157. To elucidate phylogenetic relationships within the specialized schizothoracine fishes, we used 41 variable osteological and external characters among this groups, three species of Schizothorax, and 1 fossil species. When the 3 species of Schizothorax were designated as an outgroup and all 41 characters were set as unordered with equal weighting, the data matrix yielded a single most-parsimonious tree with a tree length of 71 steps, a consistency index of 0.6761, and a retention index of 0.7416. Meanwhile, a bootstrap test was conducted to verify the reliability of the results. The matrix was also analyzed for different conditions: all characters were ordered and the fossil species was added as an outgroup. The phylogenetic analyses presented herein support the following hypotheses. 1) All species of the specialized schizo-thoracines fishes form a monophyletic group. 2) Monophyly of the genus Ptychobarbus is not supported by the bootstrap test or when these characters are ordered. 3) The genus Gymnodiptychus forms a monophyletic group. 4) All species of Ptychobarbus and Gymnodiptychus form a monophyletic group with Diptychus as its sister group.

Molecular phylogenetic systematics of twelve species of acipenseriformes based on mtDNA ND4L-ND4 gene sequence analysis

Acipenseriformes is an endangered primitive fish group, which occupies a special place in the history of ideas concerning fish evolution, even in vertebrate evolution. However, the classification and evolution of the fishes have been debated. The mitochondrial DNA (mtDNA) ND4L and partial ND4 genes were first sequenced in twelve species of the order Acipenseriformes, including endemic Chinese species. The following points were drawn from DNA sequences analysis: (i) the two species of Huso can be ascribed to Acipenser; (ii) A. dabryanus is the mostly closely related to A. sinensis, and most likely the landlocked form of A. sinensis; (iii) genus Acipenser in trans-Pacific region might have a common origin; (iv) mtDNA ND4L and ND4 genes are the ideal genetic markers for phylogenetic analysis of the order Acipenseriformes.

Phylogeny of the Amphiliidae (Teleostei : Siluriformes)

The freshwater African catfish family Amphiliidae had been reviewed based on the 73 osteological characters with Diplomystidae, dagger Hypsidoridae, Amblycipitidae, Sisoridae, and Bagridae as out-groups. Because the family position of Leptoglanis (Bagridae/Amphiliidae) is under debate, this genus has been taken as an out-group too. Results of the study indicate that: 1) the Amphiliidae is not a monophyletic group and must now be restricted to the genera Amphilius and Paramphilius; the two subfamilies Amphiliinae and Doumeinae are separated by the sisorids Euchiloglanis (with most of the glyptosternid fishes) and Glyptothorax (with most of the non-glyptosternid fishes); 2) no synapomorphies were found for the subfamily Amphiliinae. 3) The five genera of subfamily Doumeinae constitute a monophyletic group, Andersonia being the sister-group of the four other genera; subfamily Doumeinae + Leptoglanis form the family Doumeidae. The glyptosternids no longer belong to the Sisoridae (family restricted to the non-glyptosternids) and represent the new family Glyptosternidae. (C) 1999 Editions scientifiques et medicales Elsevier SAS.

Origin of antiferromagnetism in CoO: A density functional theory study

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Origin of insulating behavior of the p-type LaAlO3/SrTiO3 interface: Polarization-induced asymmetric distribution of oxygen vacancies

It is revealed from first-principles calculations that polarization-induced asymmetric distribution of oxygen vacancies plays an important role in the insulating behavior at p-type LaAlO3/SrTiO3 interface. The formation energy of the oxygen vacancy (V-O) is much smaller than that at the surface of the LaAlO3 overlayer, causing all the carriers to be compensated by the spontaneously formed V-O's at the interface. In contrast, at an n-type interface, the formation energy of V-O is much higher than that at the surface, and the V-O's formed at the surface enhance the carrier density at the interface. This explains the puzzling behavior of why the p-type interface is always insulating but the n-type interface can be conducting.

Interface as the origin of ferromagnetism in cobalt doped ZnO film grown on silicon substrate

We have investigated the magnetic properties of Co-doped zinc oxide (ZnO) film deposited on silicon substrate by magnetron sputtering. Co ions have a valence of 2+ and substitute for Zn sites in the lattice. By using a chemical etching method, an extrinsic ferromagnetism was demonstrated. The observed ferromagnetism is neither associated with magnetic precipitates nor with contamination, but originates from the silicon/silicon oxide interface. This interface ferromagnetism is characterized by being temperature independent and by having a parallel magnetic anisotropy. (C) 2008 American Institute of Physics. [DOI: 10.1063/1.2989128]

Investigation on the structural origin of n-type conductivity in InN films

This work presents a study of the correlation between the electrical properties and the structural defects in nominally undoped InN films. It is found that the density of edge-type threading dislocations (TDs) considerably affects the electron concentration and mobility in InN films. The Hall-effect measured electron concentration increases, while the Hall mobility decreases with the increase in the edge-type TD density. With the combination of secondary ion mass spectrometry and positron annihilation analysis, we suggest that donor-type point defects at the edge-type TD lines may serve as dominant donors in InN films and affect the carrier mobility.

Origin of the doping bottleneck in semiconductor quantum dots: A first-principles study

Doping difficulty in semiconductor nanocrystals has been observed and its origin is currently under debate. It is not clear whether this phenomenon is energetic or depends on the growth kinetics. Using first-principles method, we show that the transition energies and defect formation energies of the donor and acceptor defects always increase as the quantum dot sizes decrease. However, for isovalent impurities, the changes of the defect formation energies are rather small. The origin of the calculated trends is explained using simple band-energy-level models.

Possible origin of ferromagnetism in undoped anatase TiO2

Using first-principles electronic structure calculations we find that the titanium vacancy and divacancy may be responsible for the unexpected ferromagnetism in undoped anatase TiO2. An isolated titanium vacancy produces a magnetic moment of 3.5 mu(B), and an isolated titanium divacancy produces a magnetic moment of 2.0 mu(B). The origin of the collective magnetic moments is the holes introduced by the titanium vacancy or divacancy in the narrow nonbonding oxygen 2p(pi) band. At the center of the divacancy, an O-2 dimer forms during the relaxation, which lowers the total energy of the system and leads to the decrease in the total magnetic moment due to a hole compensation mechanism. For both the two native defects, the ferromagnetic state is more stable than the antiferromagnetic state.

Origin and Enhancement of Hole-Induced Ferromagnetism in First-Row d(0) Semiconductors

The origin of ferromagnetism in d(0) semiconductors is studied using first-principles methods with ZnO as a prototype material. We show that the presence of spontaneous magnetization in nitrides and oxides with sufficient holes is an intrinsic property of these first-row d(0) semiconductors and can be attributed to the localized nature of the 2p states of O and N. We find that acceptor doping, especially doping at the anion site, can enhance the ferromagnetism with much smaller threshold hole concentrations. The quantum confinement effect also reduces the critical hole concentration to induce ferromagnetism in ZnO nanowires. The characteristic nonmonotonic spin couplings in these systems are explained in terms of the band coupling model.

Experimental verification on the origin of plateau-like current-voltage characteristics of resonant tunneling diodes

Current-voltage (I-V) characteristics of GaAs-based resonant tunneling diodes have been investigated in the presence of a perpendicular magnetic field. Electron resonant tunneling is strongly suppressed by the applied magnetic field, leading to peak current decreasing with increasing magnetic field. The observed plateau-like structures appear in negative differential resistance region on the I-V curves and are magnetic-field dependent. The plateau-like structures are due to the coupling between the energy levels in the emitter well and in the main quantum well. (C) 2004 American Institute of Physics.

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.

Origin of the blueshift in the infrared absorbance of intersubband transitions in AlxGa1-x/GaN multiple quantum wells

A self-consistent calculation of the subband energy levels of n-doped quantum wells is studied. A comparison is made between theoretical results and experimental data. In order to account for the deviations between them, the ground-state electron-electron exchange interactions, the ground-state direct Coulomb interactions, the depolarization effect, and the exciton-like effect are considered in the simulations. The agreement between theory and experiment is greatly improved when all these aspects are taken into account. The ground-to-excited-state energy difference increases by 8 meV from its self-consistent value if one considers the depolarization effect and the exciton-like effect only. It appears that the electron-electron exchange interactions account for most of the observed residual blueshift for the infrared intersubband absorbance in AlxGa1-xN/GaN multiple quantum wells. It seems that electrons on the surface of the k-space Fermi gas make the main contribution to the electron-electron exchange interactions, while for electrons further inside the Fermi gas it is difficult to exchange their positions. (C) 2004 Elsevier B.V. All rights reserved.