The mitochondrial genome organization of the rice frog, Fejervarya limnocharis (Amphibia : Anura): a new gene order in the vertebrate mtDNA

The mitochondrial DNA of the rice frog, Fejervarya limnocharis (Amphibia, Anura), was obtained using long-and-accurate polymerase chain reaction (LA-PCR) combining with subcloning method. The complete nucleotide sequence (17,717 bp) of mitochondrial genome was determined subsequently. This mitochondrial genome is characterized by four distinctive features: the translocation of ND5 gene, a cluster of rearranged tRNA genes (tRNA(Thr), tRNA(Pro), tRNA(Leu) ((CUN))) a tandem duplication of tRNA(Mer) gene, and eight large 89-bp tandem repeats in the control region, as well as three short noncoding regions containing two repeated motifs existing in the gene cluster of ND5/tRNA(Thr)/tRNA(Pro)/tRNA(Leu)/tRNA(Phe). The tandem duplication of gene regions followed by deletions of supernumerary genes can be invoked to explain the shuffling of tRNAM(Met) and a cluster of tRNA and ND5 genes, as observed in this study. Both ND5 gene translocation and tandem duplication of tRNA(Met) were first observed in the vertebrate mitochondrial genomes. (c) 2004 Elsevier B.V. All rights reserved.

Phylogenetic relationships within mammalian order Carnivora indicated by sequences of two nuclear DNA genes

Phylogenetic relationships among 37 living species of order Carnivora spanning a relatively broad range of divergence times and taxonomic levels were examined using nuclear sequence data from exon1 of the IRBP gene (approximate to1.3 kb) and first intron

Parallel and Convergent Evolution of the Dim-Light Vision Gene RH1 in Bats (Order: Chiroptera)

Rhodopsin, encoded by the gene Rhodopsin (RH1), is extremely sensitive to light, and is responsible for dim-light vision. Bats are nocturnal mammals that inhabit poor light environments. Megabats (Old-World fruit bats) generally have well-developed eyes, while microbats (insectivorous bats) have developed echolocation and in general their eyes were degraded, however, dramatic differences in the eyes, and their reliance on vision, exist in this group. In this study, we examined the rod opsin gene (RH1), and compared its evolution to that of two cone opsin genes (SWS1 and M/LWS). While phylogenetic reconstruction with the cone opsin genes SWS1 and M/LWS generated a species tree in accord with expectations, the RH1 gene tree united Pteropodidae (Old-World fruit bats) and Yangochiroptera, with very high bootstrap values, suggesting the possibility of convergent evolution. The hypothesis of convergent evolution was further supported when nonsynonymous sites or amino acid sequences were used to construct phylogenies. Reconstructed RH1 sequences at internal nodes of the bat species phylogeny showed that: (1) Old-World fruit bats share an amino acid change (S270G) with the tomb bat; (2) Miniopterus share two amino acid changes (V104I, M183L) with Rhinolophoidea; (3) the amino acid replacement I123V occurred independently on four branches, and the replacements L99M, L266V and I286V occurred each on two branches. The multiple parallel amino acid replacements that occurred in the evolution of bat RH1 suggest the possibility of multiple convergences of their ecological specialization (i.e., various photic environments) during adaptation for the nocturnal lifestyle, and suggest that further attention is needed on the study of the ecology and behavior of bats.

Phylogenetic relationships of Danio within the order cypriniformes: A framework for comparative and evolutionary studies of a model species

The evolutionary relationships of species of Danio and the monophyly and phylogenetic placement of the genus within the family Cyprinidae and subfamily Rasborinae provide fundamentally important phyloinformatics necessary for direct evaluations of an array of pertinent questions in modern comparative biology. Although the genus Danio is not one of the most diverse within the family, Danio rerio is one of the most important model species in biology. Many investigations have used this species or presumed close relatives to address specific questions that have lasting impact on the hypothesis and theory of development in vertebrates. Largely lacking from this approach has been a holistic picture of the exact phylogenetic or evolutionary relationships of this species and its close relatives. One thing that has been learned over the previous century is that many organismal attributes (e.g., developmental pathways, ecologies, behaviors, speciation) are historically constrained and their origins and functions are best explained via a phylogenetic approach. Herein, we provide a molecular evaluation of the phylogenetic placement of the model species Danio rerio within the genus Danio and among hypothesized closely related species and genera. Our analysis is derived from data using two nuclear genes (RAG1, rhodopsin) and five mitochondrial genes (ND4, ND4L, ND5, COI, cyt b) evaluated using parsimony, maximum likelihood, and Bayesian analyses. The family Cyprinidae is resolved as monophyletic but the subfamily Rasborinae (priority over Danioinae) is an unnatural assemblage. Danio is identified as a monophyletic group sister to a clade inclusive of the genera Chela, Microrasbora, Devario, and Inlecypris, not Devario nor Esomus as hypothesized in previous studies. Danio rerio is sister to D. kyathit among the species of Danio evaluated in this analysis. Microrasbora and Rasbora are non-monophyletic assemblages; however, Boraras is monophyletic.

Degree of fourth-order coherence by double Hanbury Brown-Twiss detections

Photon quantum statistics of light can be shown by the high-order coherence. The fourth-order coherences of various quantum states including Pock states, coherent states, thermal states and squeezed vacuum states are investigated based on a double Banbury Brown Twiss (HBT) scheme. The analytical results are obtained by taking the overall efficiency and background into account.

Interaction between the intrinsic second- and third-order optical fields in an Al0.53Ga0.47N/GaN heterostructure

We present an experimental demonstration of the interaction between the intrinsic second- and third-order optical fields in an Al0.53Ga0.47N/GaN heterostructure. The sample was deposited by metal-organic chemical vapor deposition on (0001) sapphire. The nonlinear optical coefficients of the sample, which were measured with a Mach-Zehnder interferometer system, quadratically increase with the applied modulating voltage, indicating the existence of the third-order optical field. The third-order signal was then detected by the Z-scan method and we calculated the built-in dc field on the AlGaN/GaN interface to confirm the strong interaction between the intrinsic second- and third-order optical fields. (c) 2008 American Institute of Physics.

Third-order optical nonlinearities of lead-free (Na1-xKx)(0.5)Bi0.5TiO3 thin films

(Na1-xKx)(0.5)Bi0.5TiO3 (NKBT) (x = 0.1, 0.2, and 0.3) thin films with good surface morphology and rhombohedral perovskite structure were fabricated on quartz substrates by a sol-gel process. The fundamental optical constants (the band gaps, linear refractive indices and absorption coefficients) of the films were obtained through optical transmittance measurements. The nonlinear optical properties were investigated by Z-scan technique performed at 532 nm with a picosecond laser. A two-photon absorption effect closely related with potassium-doping content was found in thin films, and the nonlinear refractive index n(2) increases evidently with potassium-doping. The real part of the third-order nonlinear susceptibility chi((3)) is much larger than its imaginary part, indicating that the third-order optical nonlinear response of the NKBT films is dominated by the optical nonlinear refractive behavior. These results show that NKBT thin films have potential applications in nonlinear optics. (C) 2007 Elsevier B.V. All rights reserved.

Optical response of high-order band gap photonic crystal applying in-plane in one-dimensional integration

A new broadband filter, based on the high-order band gap in one-dimensional photonic crystal (PCs) of the form Si vertical bar air vertical bar Si vertical bar air vertical bar Si vertical bar air vertical bar Si vertical bar air vertical bar Si vertical bar air vertical bar Si, has been designed by the plane wave expansion method (PWEM) and transfer matrix method (TMM) and fabricated by lithography. The optical response of this filter to normal-incident and oblique-incident light proves that utilizing the high-order band gaps of PCs is an efficient method to lower the difficulties of fabricating PCs, increase the etching depth of semiconductor materials, and reduce the coupling loss at the interface between optical fibers and PC device. (c) 2007 Elsevier B.V. All rights reserved.

Two-dimensional simulation of high-order laterally-coupled GaAs-AlGaAs DFB laser diodes

Laterally-coupled distributed feedback (LC-DFB) laser diodes made without an epitaxial re-growth process have the advantage of a simple fabrication process. In this paper, two-dimensional optical field distribution of the fundamental quasi TE (transverse electric) mode is calculated by means of a semivectorial finite-difference method (SV-FDM). The dependence of the effective coupling coefficient (kappa(eff)) on the dutycycle of first-, second- and third-order LC-DFB LDs is investigated using modified coupled wave equations.

Effect of metal contact's reflection on the effective coupling coefficient of second-order DFB laser diodes

For a second-order DFB-LD, the presence of a metal contact layer can reduce I-st-order radiation. Part of the reflected power is redistributed into guided modes and results in a variation of the effective coupling coefficient kappa(eff). In this paper, we study the effect of the Au top contact's reflection on the kappa(eff) of 2(nd)-order DFB lasers. (C) 2004 Wiley Periodicals, Inc.

The diphasic nc-Si/a-Si : H thin film with improved medium-range order

A series of silicon film samples were prepared by plasma enhanced chemical vapor deposition (PECVD) near the threshold from amorphous to nanocrystalline state by adjusting the plasma parameters and properly increasing the reactions between the hydrogen plasma and the growing surface. The microstucture of the films was studied by micro-Raman and Fourier transform infrared (FTIR) spectroscopy. The influences of the hydrogen dilution ratio of silane (R-H = [H-2]/[SiH4]) and the substrate temperature (T-s) on the microstructural and photoelectronic properties of silicon films were investigated in detail. With the increase of RH from 10 to 100, a notable improvement in the medium-range order (MRO) of the films was observed, and then the phase transition from amorphous to nanocrystalline phase occurred, which lead to the formation of diatomic hydrogen complex, H-2* and their congeries. With the increase of T-s from 150 to 275 degreesC, both the short-range order and the medium range order of the silicon films are obviously improved. The photoconductivity spectra and the light induced changes of the films show that the diphasic nc-Si/a-Si:H films with fine medium-range order present a broader light spectral response range in the longer wavelength and a lower degradation upon illumination than conventional a-Si:H films. (C) 2004 Elsevier B.V. All rights reserved.

Mode coupling between first- and second-order whispering-gallery modes in coupled microdisks

The mode characteristics for two coupled microdisks are investigated by the finite-difference time-domain technique. In the two coupled micodisks, mode coupling between the same order whispering-gallery modes (WGMs) results in coupled WGMs with split mode wavelengths. The numerical results show that the split mode wavelengths of the coupled first- and second-order WGMs can have a crossing point in some cases, which can induce anticrossing mode coupling between them and greatly reduce the mode Q factor of the coupled first-order WGMs. The time variation of mode field pattern shows the transformation between the coupled first- and second-order WGMs. (C) 2007 Optical Society of America

First and second order Raman scattering spectroscopy of nonpolar a-plane GaN

Nonpolar a-plane [(1120)] GaN samples have been grown on r-plane [(1102)] sapphire substrates by low-pressure metal-organic chemical-vapor deposition. The room-temperature first and second order Raman scattering spectra of nonpolar a-plane GaN have been measured in surface and edge backscattering geometries. All of the phonon modes that the selection rules allow have been observed in the first order Raman spectra. The frequencies and linewidths of the active modes have been analyzed. The second order phonon modes are composed of acoustic overtones, acoustic-optical and optical-optical combination bands, and optical overtones. The corresponding assignments of second order phonon modes have been made. (c) 2007 American Institute of Physics.

A direct digital frequency synthesizer with fourth-order phase domain Delta Sigma noise shaper and 12-bit current-steering DAC

This paper presents a direct digital frequency synthesizer (DDFS) with a 16-bit accumulator, a fourth-order phase domain single-stage Delta Sigma interpolator, and a 300-MS/s 12-bit current-steering DAC based on the Q(2) Random Walk switching scheme. The Delta Sigma interpolator is used to reduce the phase truncation error and the ROM size. The implemented fourth-order single-stage Delta Sigma noise shaper reduces the effective phase bits by four and reduces the ROM size by 16 times. The DDFS prototype is fabricated in a 0.35-mu m CMOS technology with active area of 1.11 mm(2) including a 12-bit DAC. The measured DDFS spurious-free dynamic range (SFDR) is greater than 78 dB using a reduced ROM with 8-bit phase, 12-bit amplitude resolution and a size of 0.09 mm(2). The total power consumption of the DDFS is 200)mW with a 3.3-V power supply.

A novel line-order of InAs quantum dots on GaAs

A novel line-order of InAs quantum dots (QDs) along the [1, 1, 0] direction on GaAs substrate has been prepared by self-organized growth. After 2.5 monolayer InAs deposition, QDs in the first layer of multi-layer samples started to gather in a line. Owing to the action of strong stress between layers, almost all the dots of the fourth layer gathered in lines. The dots lining up tightly are actually one-dimensional superlattice of QDs, of which the density of electronic states is different from that of isolated QDs or quantum wires. The photoluminescence spectra of our multi-layer QD sample exhibited a feature of very broad band so that it is suitable for the active medium of super luminescent diode. The reason of dots lining up is attributed to the hill-and-valley structure of the buffer, anisotropy and different diffusion rates in the different directions on the buffer and strong stress between QD layers. (C) 2002 Published by Elsevier Science B. V.