Diversity, abundance and distribution of amoA-encoding archaea in deep-sea methane seep sediments of the Okhotsk Sea

The authors would like to thank Jin Sun, Jian Sun, Liangliang Kong, Nianshuang Wang, Chunhui Wang, Linbao Zhang and Ying Zhang for their assistance in the project. This work was supported by China Ocean Mineral Resources R&D Association grants DYXM-115-02-2-20 and DYXM-115-02-2-6, Hi-Tech Research and Development Program of China grant 2007AA091903, China National Natural Science Foundation grant 40576069, National Basic Research Program of China grant 2009CB219506 and the Fundamental Research Funds for the Central Universities of China grant 09CX05005A. M. G. K. was funded by incentive funds provided by the UofL-EVPR office and the US National Science Foundation (EF-0412129).

Cathodoluminescence study on in composition inhomogeneity of thick InGaN layer

We have investigated the optical properties of thick InGaN film grown on GaN by cathodeluminescence (CL) spectroscopy. It is found that there is obvious In composition variation in both growth and lateral direction of InGaN film. The depth distribution of In composition is closely related to the strain relaxation process of InGaN film. Accompanied with the relaxation of compressive strain, the In composition of InGaN layer increases and the CL peak energy shifts towards red. Moreover, a rather apparent In composition fluctuation is found in the relaxed upper part of InGaN layer as confirmed by CL imaging.

Design of Narrow-Gap TiO2: A Passivated Codoping Approach for Enhanced Photoelectrochemical Activity

To improve the photoelectrochemical activity of TiO2 for hydrogen production through water splitting, the band edges of TiO2 should be tailored to match with visible light absorption and the hydrogen or oxygen production levels. By analyzing the band structure of TiO2 and the chemical potentials of the dopants, we propose that the band edges of TiO2 can be modified by passivated codopants such as (Mo+C) to shift the valence band edge up significantly, while leaving the conduction band edge almost unchanged, thus satisfying the stringent requirements. The design principle for the band-edge modification should be applicable to other wide-band-gap semiconductors.

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.

Al composition variations in AlGaN films grown on low-temperature GaN buffer layer by metalorganic chemical vapor deposition

We have investigated the optical properties of AlGaN grown on sapphire. It is found that two main luminescence peaks occur in the cathodoluminescence (CL) spectra of AlGaN films, and their energy separation increases with the increase of Al source flux during the growth. Spatially resolved CL investigations have shown that the line splitting is a result of variation of AlN mole fraction within the layer. The Al composition varies in both lateral and vertical direction. It is suggested that the difference in the surface mobility of Al and Ga atoms, especially, its strong influence on the initial island coalescence process and the formation of island-like regions on the uneven film surface, is responsible for the Al composition inhomogeneity. (C) 2008 Elsevier B.V. All rights reserved.

Band crossing in isovalent semiconductor alloys with large size mismatch: First-principles calculations of the electronic structure of Bi and N incorporated GaAs

For large size- and chemical-mismatched isovalent semiconductor alloys, such as N and Bi substitution on As sites in GaAs, isovalent defect levels or defect bands are introduced. The evolution of the defect states as a function of the alloy concentration is usually described by the popular phenomenological band anticrossing (BAC) model. Using first-principles band-structure calculations we show that at the impurity limit the N-(Bi)-induced impurity level is above (below) the conduction- (valence-) band edge of GaAs. These trends reverse at high concentration, i.e., the conduction-band edge of GaAs1-xNx becomes an N-derived state and the valence-band edge of GaAs1-xBix becomes a Bi-derived state, as expected from their band characters. We show that this band crossing phenomenon cannot be described by the popular BAC model but can be naturally explained by a simple band broadening picture.

Investigation on the strain relaxation of InGaN layer and its effects on the InGaN structural and optical properties

The evolution of strain and structural properties of thick epitaxial InGaN layers grown on GaN with different thicknesses are investigated. It is found that, with increase in InGaN thickness, plastic relaxation via misfit dislocation generation becomes a more important strain relaxation mechanism. Accompanied with the relaxation of compressive strain, the In composition of InGaN layer increases and induces an apparent red-shift of the cathodoluminescence peak of the InGaN layer. On the other hand, the plastic relaxation process results in a high defect density, which degrades the structural and optical properties of InGaN layers. A transition layer region with both strain and In composition gradients is found to exist in the 450-nm-thick InGaN layer.

Short-range-order effects on intrinsic plasticity of metallic glasses

Through a systematical analysis of the elastic moduli for 137 metallic glasses (MGs) and 56 polycrystalline metals, we use a simple model developed by Knuyt et al. [J. Phys. F: Met. Phys. 16 (1986) p.1989; Phil. Mag. B 64 (1991) p.299] based on a Gaussian distribution for the first-neighbor distance to reveal the short-range-order (SRO) structural conditions for plasticity of MGs. It is found that the SRO structure with dense atomic packing, large packing dispersion and a significant anharmonicity of atomic interaction within an MG is favorable for its global plasticity. Although these conditions seem paradoxical, their perfect matching is believed to be a key for designing large plastic bulk MGs not only in compression but also in tension.

New Insights into the Evolution of Intronic Sequences of the beta-fibrinogen Gene and Their Application in Reconstructing Mustelid Phylogeny

Mustelidae is the largest and most diverse family in the order Carnivora. The phylogenetic relationships among the subfamilies have especially long been a focus of study. Herein we are among the first to employ two new introns (4 and 7) of the nuclear P-f

Characterization of TRPC2, an Essential Genetic Component of VNS Chemoreception, Provides Insights into the Evolution of Pheromonal Olfaction in Secondary-Adapted Marine Mammals

Pheromones are chemical cues released and sensed by individuals of the same species, which are of major importance in regulating reproductive and social behaviors of mammals. Generally, they are detected by the vomeronasal system (VNS). Here, we first investigated and compared an essential genetic component of vomeronasal chemoreception, that is, TRPC2 gene, of four marine mammals varying the degree of aquatic specialization and related terrestrial species in order to provide insights into the evolution of pheromonal olfaction in the mammalian transition from land to water. Our results based on sequence characterizations and evolutionary analyses, for the first time, show the evidence for the ancestral impairment of vomeronasal pheromone signal transduction pathway in fully aquatic cetaceans, supporting a reduced or absent dependence on olfaction as a result of the complete adaptation to the marine habitat, whereas the amphibious California sea lion was found to have a putatively functional TRPC2 gene, which is still under strong selective pressures, reflecting the reliance of terrestrial environment on chemical recognition among the semiadapted marine mammals. Interestingly, our study found that, unlike that of the California sea lion, TRPC2 genes of the harbor seal and the river otter, both of which are also semiaquatic, are pseudogenes. Our data suggest that other unknown selective pressures or sensory modalities might have promoted the independent absence of a functional VNS in these two species. In this respect, the evolution of pheromonal olfaction in marine mammals appears to be more complex and confusing than has been previously thought. Our study makes a useful contribution to the current understanding of the evolution of pheromone perception of mammals in response to selective pressures from an aquatic environment.

The role of MC1R gene in buffalo coat color

Melanocortin-1 receptor (MC1R) plays a major role in pigmentation in many species. To investigate if the MC1R gene is associated with coat color in water buffalo, the coding region of MC1R gene of 216 buffalo samples was sequenced, which included 49 black river buffalo (Murrah and Nili-Ravi), 136 swamp buffalo (Dehong, Diandongnan, Dechang, Guizhou, and Xilin) with white and gray body, and 31 hybrid offspring of river buffalo Nili-Ravi (or Murrah) and swamp buffalo. Among the three variation sites found, SNP684 was synonymous, while SNP310 and SNP384 were nonsynonymous, leading to p.S104G and p.I128M changes, respectively. Only Individuals carrying homozygote E-BR/E-BR were black. The genotype and phenotype analysis of the hybrid offspring of black river buffalo and gray swamp buffalo further revealed that the river buffalo type allele E-BR or the allele carrying the amino acid p.104S was important for the full function of MC1R. The in silico functional analysis showed that the amino acid substitutions p.G104S and p.M128I had significant impact on the function of MC1R. Above results indicate that the allele E-BR or the allele carrying the amino acid p.104S was associated with the black coat color in buffalo.

On the origin and evolution of new genes-a genomic and experimental perspective

The inherent interest on the origin of genetic novelties can be traced back to Darwin. But it was not until recently that we were allowed to investigate the fundamental process of origin of new genes by the studies on newly evolved Young genes. Two indisp

Sequencing, annotation and comparative analysis of nine BACs of giant panda (Ailuropoda melanoleuca)

A 10-fold BAC library for giant panda was constructed and nine BACs were selected to generate finish sequences. These BACs could be used as a validation resource for the de novo assembly accuracy of the whole genome shotgun sequencing reads of giant panda newly generated by the Illumina GA sequencing technology. Complete sanger sequencing, assembly, annotation and comparative analysis were carried out on the selected BACs of a joint length 878 kb. Homologue search and de novo prediction methods were used to annotate genes and repeats. Twelve protein coding genes were predicted, seven of which could be functionally annotated. The seven genes have an average gene size of about 41 kb, an average coding size of about 1.2 kb and an average exon number of 6 per gene. Besides, seven tRNA genes were found. About 27 percent of the BAC sequence is composed of repeats. A phylogenetic tree was constructed using neighbor-join algorithm across five species, including giant panda, human, dog, cat and mouse, which reconfirms dog as the most related species to giant panda. Our results provide detailed sequence and structure information for new genes and repeats of giant panda, which will be helpful for further studies on the giant panda.

Anti-HIV Activities of the Compounds Isolated from Polygonum cuspidatum and Polygonum multiflorum

The 70% EtOH extract of Polygonum cuspidatum showed inhibitory action against HIV-1-induced syncytium formation at non-cytotoxic concentrations in vitro with a 50% effective concentration (EC50) of 13.94 +/- 3.41 mu g/mL. Through bioactivity-guided fractionation, 20 phenolic compounds, including eight stilbenoids, were isolated from the roots of Polygonum cuspidatum, and their anti-HIV-1 activities were evaluated. Results showed that compounds 1, 13, 14, and 16 demonstrated fairly strong antiviral activity against HIV-1-induced cytopathic effects in C8166 lymphocytes at non-cytotoxic concentrations, with EC50 values of 4.37 +/- 1.96 mu g/mL, 19.97 +/- 5.09, 14.4 +/- 1.34 mu g/mL, and 11.29 +/- 6.26 mu g/mL and therapeutic index (TI) values of 8.12, > 10.02, > 13.89, and > 17.71, respectively. Other compounds showed either weak or no effects. Compound 6 also showed weak inhibition (153.42 +/- 19.25 mu g/mL); however, it possesses very good water solubility and showed almost no cytotoxicity (> 2000 mu g/mL), therefore achieving a fairly good TI (13.04). The activities of the two compounds (3 and 18) from Polygonum multiflorum were also assayed. The relationship between molecular structures and their bioactivities was also discussed.

Configural processing of different topologically structured figures: an ERP Study

According to Chen's theory, topological differences are perceived faster than feature differences in early visual perception. We hypothesized that topological perception is caused by the sensitivity in discriminating figures with and without "holes". An E