Moisture content in Dall's porpoise (Phocoenoides dalli) tissues: a reference base for conversion factors between dry and wet weight trace element concentrations in cetaceans

Concentration of trace elements measured by dry weight basis has become more commonly used in recent studies on cetaceans than wet weight basis, which was used more in earlier studies. Because few authors present moisture content data in their papers, it is difficult to compare the concentrations of trace elements between various studies. Therefore, we felt that it would be useful if a reference conversion factor (CF) for tissue types could be found to convert between wet weight and dry weight data on trace element concentrations. We determined the moisture contents of 14 tissues of Dall's porpoise (Phocoenoides dalli), and then, calculated the CF values for those tissues. Because the moisture content of each tissue differs from other tissues, it is necessary to use a specific CIF for each tissue rather than a general CF for several tissues. We have also found that CIF values for Dall's porpoise tissues are similar to the same tissues in other cetaceans. Therefore CF values from Dall's porpoise can be reliably used to convert between wet and dry weight concentrations for other cetacean tissues as reference data. (C) 2002 Elsevier Science Ltd. All rights reserved.

Mitochondrial d-loop sequence variation and phylogeny of gobiobotine fishes

The mitochondrial DNA control region is amplified and sequenced from 8 genera and 10 species of gobiobotine fishes. The phylogenetic tree of Gobiobotinae and some representative species of other Cyprinid subfamilies obtained by the method of neighborhood joining, maximum likelihood and maximum parsimony with Danio rerio as an outgroup indicates that Gobiobotinae fishes are a monophyletic group which is close to Gobioninae subfamily. Gobiobotinae should be included into subfamily Gobioninae in terms of phylogenetic analysis. The research result supports that Gobiobotinae can be divided into genus Xenophysogobio and Gobiobotia. Xenophysogabio is the most primitive genera in the subfamily.

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.

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.

Improvement of the performance of GaN-based LEDs grown on sapphire substrates patterned by wet and ICP etching

Sapphire substrates patterned by a selective chemical wet and an inductively coupled plasma (ICP) etching technique was proposed to improve the performance of GaN-based light-emitting diodes (LEDs). GaN-based LEDs were fabricated on sapphire substrates through metal organic chemical vapor deposition (MOCVD). The LEDs fabricated on the patterned substrates exhibit improved device performance compared with the conventional LED fabricated on planar substrates when growth and device fabricating conditions were the same. The light output powers of the LEDs fabricated on wet-patterned and ICP-patterned substrates were about 37% and 17% higher than that of LEDs on planar substrates at an injection current of 20 mA, respectively. The enhancement is attributable to the combination of the improvement of GaN-based epilayers quality and the improvement of the light extraction efficiency. (c) 2008 Elsevier Ltd. All rights reserved.

Paired interference 3-dB coupler based on SOI rib waveguides with anisotropic chemical wet etching

A 3-dB paired interference (PI) optical coupler in silicon-on-insulator (SOI) based on rib waveguides with trapezoidal cross section was designed with simulation by a modified finite-difference beam propagation method (FD-BPM) and fabricated by potassium hydroxide (KOH) anisotropic chemical wet etching. Theoretically, tolerances of width, length, and port distance are more than 1, 100, and 1 mu m, respectively. Smooth interface was obtained with the propagation loss of 1.1 dB/cm at the wavelength of 1.55 mu m. The coupler has a good uniformity of 0.2 dB and low excess loss of less than 2 dB.

Characterization of Thick GaN Films Directly Grown on Wet-Etching Patterned Sapphire by HVPE

Thick GaN films of high quality are directly grown on wet-etching patterned sapphire in a vertical hydride vapour phase epitaxy reactor. The optical and structural properties of GaN films are studied using scanning electronic microscopy and cathodoluminescence. Test results show that initial growth of hydride vapour phase epitaxy GaN occurs not only on the mesas but also on the two asymmetric sidewalls of the V-shaped grooves without selectivity. After the two-step coalescence near the interface, the GaN films near the surface keep on growing along the direction perpendicular to the long sidewall. Based on Raman results, GaN of the coalescence region in the grooves has the maximum residual stress and poor crystalline quality over the whole GaN film, and the coalescence process can release the stress. Therefore, stress-free thick GaN films are prepared with smooth and crack-free surfaces by this particular growth mode on wet-etching patterned sapphire substrates.

Laterally confined modes in wet-etched, metal-coated, quantum-dot-inserted pillar microcavities

We report the fabrication and the measurement of microcavities whose optical eigenmodes were discrete and were well predicted by using the model of the photonic dot with perfectly reflected sidewalls. These microcavities were consisted of the semiconductor pillar fabricated by the simple wet-etched process and successive metal coating. Angle-resolved photoluminescence spectra demonstrate the characteristic emission of the corresponding eigenmodes, as its pattern revealed by varying both polar (0) and azimuthal (45) angles. It is shown that the metal-coated sidewalls can provide an efficient way to suppress the emission due to the leaking modes in these pillar microcavities.

Time dependence of wet oxidized AlGaAs/GaAs distributed Bragg reflectors

The time dependence of wet oxidized AlGaAs/GaAs in a distributed Bragg reflector (DBR) structure has been studied by mean of transmission electron microscopy and Raman spectroscopy. The wet oxidized AlGaAs transforms from an initial amorphous hydroxide phase to the polycrystalline gamma-Al2O3 phase with the extension of oxidation time. The thickness of oxide layers will contract due to the different volume per Al atom in AlGaAs and in the oxides. In the samples oxidized for 10 and 20 min, there are some fissures along the AlGaAs/GaAs interfaces. In the samples oxidized longer, although no such fissures are present along the interfaces, the whole oxidized DBR delaminates from the buffer. (c) 2005 American Vacuum Society.

Unveiling the morphology of buried In(Ga)As nanostructures by selective wet chemical etching: From quantum dots to quantum rings

The three-dimensional morphology of In(Ga)As nanostructures embedded in a GaAs matrix is investigated by combining atomic force microscopy and removal of the GaAs cap layer by selective wet etching. This method is used to investigate how the morphology of In(Ga)As quantum dots changes upon GaAs capping and subsequent in situ etching with AsBr3. A wave function calculation based on the experimentally determined morphologies suggests that quantum dots transform into quantum rings during in situ etching. (c) 2007 American Institute of Physics.

Phylogeny of SARS-CoV based on high-dimensional information geometry

We proposed a novel methodology, which firstly, extracting features from species' complete genome data, using k-tuple, followed by studying the evolutionary relationship between SARS-CoV and other coronavirus species using the method, called "High-dimensional information geometry". We also used the mothod, namely "caculating of Minimum Spanning Tree", to construct the Phyligenetic tree of the coronavirus. From construction of the unrooted phylogenetic tree, we found out that the evolution distance between SARS-CoV and other coronavirus species is comparatively far. The tree accurately rebuilt the three groups of other coronavirus. We also validated the assertion from other literatures that SARS-CoV is similar to the coronavirus species in Group I.

Interface of wet oxidized AlGaAs/GaAs distributed Bragg reflectors

The interface of wet oxidized Al0.97Ga0.03As/GaAs in a distributed Bragg reflector (DBR) structure has been studied by means of transmission electron microscopy and Raman spectroscopy. With the extension of oxidation time, the oxide/GaAs interfaces are not abrupt any more. There is an amorphous film near the oxide/GaAs interface, which is Ga2O3 related to the prolonged heating. In the samples oxidized for 10 and 20 min, there are some fissures along the oxidized AlGaAs/GaAs interfaces. In the samples oxidized or in situ annealed for long time, no such fissures are present due to the complete removal of the volatile products.

Measurement of threading dislocation densities in GaN by wet chemical etching

We demonstrate a technique based on wet chemical etching that enables quick and accurate evaluation of edge- and screw/mixed-type threading dislocations (TDs) in GaN. Large and small etch pits are formed by phosphoric acid on the etched surfaces. The large etch pits are attributed to screw/mixed TDs and the small ones to edge TDs, according to their locations on the surface and Burgers vectors of TDs. Additionally, the origin of small etch pits is confirmed by a transmission electron microscopy. The difference in the size of etch pits is discussed in view of their origin and merging. Overetching at elevated temperatures or for a long time may result in merging of individual etch pits and underestimating of the density of TDs. Wet chemical etching has also been proved efficient in revealing the distribution of TDs in epitaxial lateral overgrowth GaN.