Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei : Cypriniformes)

The mitochondrial 16S ribosomal RNA (rRNA) gene sequences from 93 cyprinid fishes were examined to reconstruct the phylogenetic relationships within the diverse and economically important subfamily Cyprininae. Within the subfamily a biased nucleotide composition (A > T, C > G) was observed in the loop regions of the gene, and in stem regions apparent selective pressures of base pairing showed a bias in favor of G over C and T over A. The bias may be associated with transition-transversion bias. Rates of nucleotide substitution were lower in stems than in loops. Analysis of compensatory substitutions across these taxa demonstrates 68% covariation in the gene and a logical weighting factor to account for dependence in mutations for phylogenetic inference should be 0.66. Comparisons of varied stem-loop weighting schemes indicate that the down-weightings for stem regions could improve the phylogenetic analysis and the degree of non-independence of stem substitutions was not as important as expected. Bayesian inference under four models of nucleotide substitution indicated that likelihood-based phylogenetic analyses were more effective in improving the phylogenetic performance than was weighted parsimony analysis. In Bayesian analyses, the resolution of phylogenies under the 16-state models for paired regions, incorporating GTR + G + I models for unpaired regions was better than those under other models. The subfamily Cyprininae was resolved as a monophyletic group, as well as tribe Labein and several genera. However, the monophyly of the currently recognized tribes, such as Schizothoracin, Barbin, Cyprinion + Onychostoma lineages, and some genera was rejected. Furthermore, comparisons of the parsimony and Bayesian analyses and results of variable length bootstrap analysis indicates that the mitochondrial 16S rRNA gene should contain important character variation to recover well-supported phylogeny of cyprinid taxa whose divergences occurred within the recent 8 MY, but could not provide resolution power for deep phylogenies spanning 10-19 MYA. (c) 2008 Published by Elsevier Inc.

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.

Cell responses of Dunaliella salina FACHB 435 (green alga) to microgravitational stimulation by clinorotation

Clinorotation experiments were established to simulate microgravity on ground. It was found that there were obvious changes of Dunaliella salina FACHB435 cells and their metabolic characteristics during clinorotation. The changes included the increases of glycerol content, the rate of H+ secretion and PM H+-ATPase activity, and the decrease of ratio of the plasma membrane (PM) phospholipid to PM protein. These results indicated that microgravity was a stress environment to Dunaliella salina. It is deduced that it would be possible to attribute the effect of microgravity on algal cells to the secondary activation of water stress.

Influence of Si doping on magnetic properties of (Ga,Mn)As

We have systematically investigated the magnetic properties of Si-doped (Ga,Mn)As films. When the Si content is low, both Curie temperature (T-C) and carrier density (p) decrease compared with undoped (Ga,Mn)As, whereas a monotonic increase of T-C and p is observed with further increase in the doping content of Si. We discuss the possible mechanism for the changes obtained by different Si doping contents and attribute the results to a competition between the existence of Si-Ga (Si substitutes for Ga site) that acts as a donor and Si-I (Si interstitials) which is in favor of the improvement of ferromagnetism. (C) 2008 Elsevier B.V. All rights reserved.

Neutron irradiation effect in two-dimensional electron gas of AlGaN/GaN heterostructures

AlGaN/GaN heterostructures have been irradiated by neutrons with different influences and characterized by means of temperature-dependent Hall measurements and Micro-Raman scattering techniques. It is found that the carrier mobility of two-dimensional electron gas (2DEG) is very sensitive to neutrons. At a low influence of 6.13 x 10(15) cm(-2), the carrier mobility drops sharply, while the sheet carrier density remains the same as that of an unirradiated sample. Moreover, even for a fluence of up to 3.66 x 10(16) cm(-2), the sheet carrier density shows only a slight drop. We attribute the degradation of the figure-of-merit (product of n(s) x mu) of 2DEG to the defects induced by neutron irradiation. Raman measurements show that neutron irradiation does not yield obvious change to the strain state of AlGaN/GaN heterostructures, which proves that degradation of sheet carrier density has no relation to strain relaxation in the present study. The increase of the product of n(s) x mu of 2DEG during rapid thermal annealing processes at relatively high temperature has been attributed to the activation of Ge-Ga transmuted from Ga and the recovery of displaced defects.

Room temperature photoluminescence of tensile-strained Ge/Si0.13Ge0.87 quantum wells grown on silicon-based germanium virtual substrate

We report a room temperature study of the direct band gap photoluminescence of tensile-strained Ge/Si0.13Ge0.87 multiple quantum wells grown on Si-based germanium virtual substrates by ultrahigh vacuum chemical vapor deposition. Blueshifts of the luminescence peak energy from the Ge quantum wells in comparison with the Ge virtual substrate are in good agreement with the theoretical prediction when we attribute the luminescence from the quantum well to the c Gamma 1-HH1 direct band transition. The reduction in direct band gap in the tensile strained Ge epilayer and the quantum confinement effect in the Ge/Si0.13Ge0.87 quantum wells are directly demonstrated by room temperature photoluminescence.

Effects of TMIn flow on the interface and optical properties of InGaN/GaN mutiple quantum wells

The effects of pre-TMIn flow prior to QW growth and TMIn flow rates during QW growth on the interface and optical properties of InGaN/GaN MQWs were investigated. Pre-depositing indium prior to QW growth and an appropriate TMIn flow rate can improve the interface abruptness and increase the EL intensity. InGaN/GaN MQWs with improved interface abruptness have increasing emission intensity and wavelength. We attribute the interface improvement and the increase of EL intensity to the improvement of the indium compositional profiles. (C) 2004 Elsevier B.V. All rights reserved.

Effect of SiO2 encapsulation on the nitrogen reorganization in a GaNAs/GaAs single quantum well

Effects of SiO2 encapsulation and rapid thermal annealing on the optical properties of a GaNAs/GaAs single quantum well (SQW) are studied by low-temperature photoluminescence (LTPL). After annealing at 800degreesC for 30s, a blueshift of the LTPL peak energy for the SiO2-capped region is 25meV and that for the bare region is 0.8meV. The results can attribute to the nitrogen reorganization in the GaNAs/GaAs SQW. It is also shown that the nitrogen reorganization can be obviously enhanced by SiO2 cap-layer. A simple model is used to describe the SiO2-enhanced blueshift of the LTPL peak energy. The estimated activation energy of the N atomic reorganization for the samples annealing with and without SiO2 cap-layer are 2.9eV and 3.1eV, respectively.

Observation of electric current induced by optically injected spin current

Linearly polarized light at normal incidence injects a spin current into a strip of two-dimensional electron gas with Rashba spin-orbit coupling. The authors report observation of an electric current when such light is shed on the vincinity of the junction in a crossbar-shaped InGaAs/InAlAs quantum well Rashba system. The polarization dependence of this electric current was experimentally observed to be the same as that of the spin current. The authors attribute the observed electric current to the scattering of the optically injected spin current at the crossing. (c) 2007 American Institute of Physics.

Application of rapid thermal annealing on 1.3-1.55 mu m GaInNAs(Sb) lasers grown by molecular beam epitaxy

Rapid thermal annealing (RTA) has been demonstrated as an effective way to improve the crystal quality of GaInNAs(Sb) quantum wells (QWs). However, few investigations have been made into its application in laser growth and fabrication. We have fabricated 1.3 mu m GaInNAs lasers, both as -grown and with post-growth RTA. Enhanced photoluminescence (PL) intensity and decreased threshold current are obtained with RTA, but the characteristic temperature T-o and slope efficiency deteriorate. Furthermore, T-o has an abnormal dependence on the cavity length. We attribute these problems to the deterioration of the wafer's surface. RTA with deposition Of SiO2 was performed to avoid this deterioration, T-o was improved over the samples that underwent RTA without SiO2. Post-growth and in situ annealing were also investigated in a 1.55 mu m GaInNAsSb system. Finally, continuous operation at room temperature of a GaAs-based dilute nitride laser with a wavelength over 1.55 mu m was realized by introducing an in situ annealing process. (c) 2007 Elsevier B.V. All rights reserved.

Intrasubband and intersubband transitions in GaAs/AlxGa1-xAs multiple quantum wells

Infrared absorption in GaAs/AlxGa1-xAs multiple quantum wells is investigated using a polarizer. Two main peaks, with wave numbers 723 and 1092 cm(-1), are observed. The peak with wave number 1092 cm(-1) corresponds to the 0 -> 1 intersubband transition, while the other one corresponds to the intrasubband transition. The polarized absorbance is one order of magnitude higher than the unpolarized one. The authors attribute the intrasubband transition to the plasma oscillation in the quantum wells.

Growth of low-density InAs/GaAs quantum dots on a substrate with an intentional temperature gradient by molecular beam epitaxy

InAs was deposited by molecular beam epitaxy (MBE) on a GaAs substrate with an intentional temperature gradient from centre to edge. Two-dimensional (2D) to three-dimensional (3D) morphology evolution was found along the direction in which the substrate temperature was decreasing. Quantum dots (QDs) with density as low as similar to 8 x 10(6) cm(-2) were formed in some regions. We attribute the morphological evolution to the temperature-dependent desorption of deposited indium and the intermixing between deposited indium and gallium from the buffer.

Role of different cap layers tuning the wavelength of self-assembled InAs/GaAs quantum dots

We have investigated the effect of different cap layers on the photoluminescence (PL) of self-assembled InAs/GaAs quantum dots (QDs). Based upon different cap layers, the wavelength of InAs QDs can be tuned to the range from 1.3 to 1.5 mum. An InAlAs and InGaAs combination layer can enlarge the energy separation between the ground and first excited radiative transition. GaAs/InAs short period superlattices (SLs) make the emission wavelength shift to 1.53 mum. The PL intensity of InAs QDs capped with GaAs/InAs SLs shows an anomalous increase with increasing temperature. We attribute this to the transfer of carriers between different QDs.

Time-resolved photoluminescence studies of AlInGaN alloys

We study the two samples of AIInGaN, i.e., 1-mum GaN grown at 1030degreesC on the buffer and followed by a 0.6-mum-thick epilayer of AIInGaN under the low pressure of 76 Torr and the AIInGaN layer deposited directly on the buffer layer without the high-temperature GaN layer, by temperature-dependent photoluminescence (PL) spectroscopy and picosecond time-resolved photoluminescence (TRPL) spectroscopy. The TRPL signals of both the samples were fitted well as a stretched exponential decay at all temperatures, indicating significant disorder in the material. We attribute the disorder to nanoscale quantum dots or discs of high indium concentration. Temperature dependence of dispersive exponent beta shows that the stretched exponential decay of the two samples comes from different mechanisms. The different depths of the localization potential account for the difference, which is illustrated by the results of temperature dependence of radiative recombination lifetime and PL peak energy.

Abnormal temperature dependence of photoluminescence from self-assembled InAs quantum dots covered by an InAlAs/InGaAs combination layer

In this report we have investigated the temperature dependence of photoluminescence (PL) from self-assembled InAs quantum dots (QDs) covered by an InAlAs/InGaAs combination layer. The ground state experiences an abnormal variation of PL linewidth from 15 K up to room temperature. Meanwhile, the PL integrated intensity ratio of the first excited state to the ground state for InAs QDs unexpectedly decreases with increasing temperature, which we attribute to the phonon bottleneck effect. We believe that these experimental results are closely related to the partially coupled quantum dots system and the large energy separation between the ground and the first excited states. (C) 2003 Elsevier Science Ltd. All rights reserved.