SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs)

SNPNB is a user-friendly and platform-independent application for analyzing Single Nucleotide Polymorphism NeighBoring sequence context and nucleotide bias patterns, and subsequently evaluating the effective SNP size for the bias patterns observed from the whole data. It was implemented by Java and Perl. SNPNB can efficiently handle genome-wide or chromosome-wide SNP data analysis in a PC or a workstation. It provides visualizations of the bias patterns for SNPs or each type of SNPs.

Tentative study of the coding sequences without 3-base periodicity

Fourier spectra of 120 short coding sequences (<1 200 bp) show that not all coding sequences are characterized by 3-base periodicity. Statistical analysis suggests that whether a coding sequence has 3-base periodicity may be related to the composition and distribution of bases, the usage and the order of the amino acids of the encoded protein as well as the synonymous codon usage. Generally, the content of A+U is higher than that of G+C in non-period-3 sequences, inversely in period-3 sequences. In the three codon positions, the base distribution in the non-periodic-3 sequences is more uniform than in the periodic-3 sequences. The usage biases of the amino acids and the codons in non-period-3 sequences are weaker than that in period-3 sequences. All of these phenomena should be considered sufficiently in predicting the genes and exons of DNA sequences by Fourier analysis method.

Genome-wide identification and characterization of cytochrome P450 monooxygenase genes in the ciliate Tetrahymena thermophila

Background: Cytochrome P450 monooxygenases play key roles in the metabolism of a wide variety of substrates and they are closely associated with endocellular physiological processes or detoxification metabolism under environmental exposure. To date, however, none has been systematically characterized in the phylum Ciliophora. T. thermophila possess many advantages as a eukaryotic model organism and it exhibits rapid and sensitive responses to xenobiotics, making it an ideal model system to study the evolutionary and functional diversity of the P450 monooxygenase gene family. Results: A total of 44 putative functional cytochrome P450 genes were identified and could be classified into 13 families and 21 sub-families according to standard nomenclature. The characteristics of both the conserved intron-exon organization and scaffold localization of tandem repeats within each P450 family clade suggested that the enlargement of T. thermophila P450 families probably resulted from recent separate small duplication events. Gene expression patterns of all T. thermophila P450s during three important cell physiological stages (vegetative growth, starvation and conjugation) were analyzed based on EST and microarray data, and three main categories of expression patterns were postulated. Evolutionary analysis including codon usage preference, sit-especific selection and gene-expression evolution patterns were investigated and the results indicated remarkable divergences among the T. thermophila P450 genes. Conclusion: The characterization, expression and evolutionary analysis of T. thermophila P450 monooxygenase genes in the current study provides useful information for understanding the characteristics and diversities of the P450 genes in the Ciliophora, and provides the baseline for functional analyses of individual P450 isoforms in this model ciliate species.

Mitochondrial 16S rRNA sequence variations and phylogeny of the Chinese sisorid catfishes

Partial sequences of mitochondrial 16S rRNA gene were obtained by PCR amplification for comparisons among nine species of glyptosternoid fishes and six species of non-glyptosternoids representing 10 sisorid genera. There are compositional biases in the A-rich impaired regions and G-rich paired regions. A-G transitions are primarily responsible for the Ts/Tv bias in impaired regions. The overall substitution rate in impaired regions is almost two times higher than that in the paired regions. Saturation plots at comparable levels of sequence divergence demonstrate no saturation effects. Phylogenetic analyses using both maximum likelihood and Bayesian methods support the monophyly of Sisoridae. Chinese sisorid catfishes are composed of two major lineages, one represented by (Gagata (Bagarius, Glyptothorax)) and the other by "glyptosternoids + Pseudecheneis". The glyptosternoids may not be a monophyletic group. A previous hypothesis referring to Pseudecheneis as the sister group of monophyletic glyptosternoids, based on morphological evidence, is not supported by the molecular data. Pseudecheneis is shown to be a sister taxon of Glaridoglanis. Pareuchiloglanis might be paraphyletic with Pseudexostoma and Euchiloglanis. Our results also support the hypothesis that Pareuchiloglanis anteanalis might be considered as the synonyms of Pareuchiloglanis sinensis, and genus Euchiloglanis might have only one valid species, Euchiloglanis davidi.

Electrical control of dynamic spin splitting induced by exchange interaction as revealed by time-resolved Kerr rotation in a degenerate spin-polarized electron gas

Manipulation of the spin degree of freedom has been demonstrated in a spin-polarized electron plasma in a heterostructure by using exchange-interaction-induced dynamic spin splitting rather than the Rashba and Dresselhaus types, as revealed by time-resolved Kerr rotation. The measured spin splitting increases from 0.256 meV to 0.559 meV as the bias varies from -0.3 V to -0.6 V. Both the sign switch of the Kerr signal and the phase reversal of Larmor precessions have been observed with biases, which all fit into the framework of exchange-interaction-induced spin splitting. The electrical control of it may provide a new effective scheme for manipulating spin-selected transport in spin FET-like devices. Copyright (C) EPLA, 2008.

Confined LO-phonon-assisted magnetotunneling in a parabolic quantum well with double barriers

The confined longitudinal-optical phonon-assisted tunneling through a parabolic quantum well with double barriers in a magnetic field perpendicular to the interfaces is studied theoretically based on a dielectric continuum model. The numerical results show that the applied magnetic field sharpens and heightens the phonon-assisted tunneling peaks in agreement with experimental observation. Furthermore, the phonon-assisted magnetotunneling peaks shift towards the higher biases as the magnetic field increases. In contrast to the results for a rectangular quantum well, the ratio of peak to valley of the phonon-assisted tunneling is larger for the wider well case. It also indicates that the phonon-assisted tunneling current peaks can be easily observed for a wider parabolic quantum well. (C) 2008 Published by Elsevier B.V.

Photovoltaic effect in a photon storage cell

The response of photonic memory effect in I-V characteristics of a specially designed photonic memory cell was reported. When the cell is biased in a storage mode, the optical excitation with the photon's energy larger than the energy gap gives rise to a step-like jump in the current. A set-up was used to measure the transient photocurrent at the biases where the step-like jump showed up. It is proved that the falling transient edge of the photocurrent, as the photoexcitation turns off, mainly maps the decaying of electrons and holes, which were previously stored in the cell during the illumination. Its time constant is a measure of photonic memory time.

Proof of solid state cathodoluminescence by using brightness waveform

Three different inorganic-organic hetero-junctions (A : ITO/SiO2/Alq(3)/Al, B: ITO/Alq3/SiO2/Al and C: ITO/SiO2/Alq(3)/ SiO2/Al) were fabricated. The emission can be observed only under positive bias in devices A and B, but under both biases in device C according to their brightness waveforms. With increasing voltage, the increase in blue emission in devices B and C is faster than that in green emission. This is because that the recombination of hot electrons and holes, i.e., electron-hole pairs, produced blue emission in devices B and C, and the recombination of electrons injected from Al with the accumulated holes, which are excited by hot electrons, produced green emission in device A. Hence, the emissions of the devices are attributed to not only the recombination of electrons and accumulated holes, but also the cathodoluminescence-like (CL-like) emission.

Electrical properties and electroluminescence of 4H-SiC p-n junction diodes

Homoepitaxial growth of 4H-SiC on off-oriented Si-face(0001) substrates was performed by using the step-controlled epitaxy technique in a newly developed low-pressure hot-wall CVD (LP-HWCVD) system with a horizontal air-cooled quartz tube at around 1500 degreesC and 1.33 x 10(4) Pa by employing SiH4 + C2H4 + H-2. In-situ doping during growth was carried out by adding NH3 gas into the precursor gases. It was shown that the maximum Hall mobility of the undoped 4H-SiC epilayers at room temperature is about 430 cm(2) (.) V-1 (.) s(-1) with a carrier concentration of similar to 10(16) cm(-3) and the highest carrier concentration of the N-doped 4H-SiC epilayer obtained at NH3 flow rate of 3 sccm is about 2.7 x 10(21) cm(-3) with a mobility of 0.75 cm(2) (.) V-1 (.) s(-1). SiC p-n junctions were obtained by epitaxially growing N-doped 4H-SiC epilayers on Al-doped 4H-SiC substrates. The C - V characteristics of the diodes were linear in the 1/C-3 - V coordinates indicating that the obtained p-n junctions were graded with a built-in voltage of 2.7 eV. The room temperature electroluminescence spectra of 4H-SiC p-n junctions are studied as a function of forward current. The D-A pair recombination due to nitrogen donors and the unintentional, deep boron center is dominant at low forward bias, while the D-A pair recombination due to nitrogen donors and aluminum acceptors are dominant at higher forward biases. The p-n junctions could operate at temperature of up to 400 degreesC, which provides a potential for high-temperature applications.

Violet electroluminescence of AlInGaN-InGaN multiquantum-well light-emitting diodes: Quantum-confined stark effect and heating effect

Electroluminescence (EL) from AlInGaN-InGaN multiquantum-well violet light-emitting diodes is investigated as a function of forward bias. Two distinct regimes have been identified: 1) quantum-confined Stark effect at low and moderately high forward biases; 2) heating effect at high biases. In the different regimes, the low-temperature EL spectra exhibit different spectral features which are discussed in detail.

Broad-band semiconductor optical amplifiers

Broad-band semiconductor optical amplifiers (SOAs) with different thicknesses and thin bulk tensile-strained active layers were fabricated and studied. Amplified spontaneous emission (ASE) spectra and gain spectra of SOAs were measured and analyzed at different CW biases. A maximal 3 dB ASE bandwidth of 136 nm ranging from 1480 to 1616 nm, and a 3 dB optical amplifier gain bandwidth of about 90 nm ranging from 1510 to 1600 nm, were obtained for the very thin bulk active SOA. Other SOAs characteristics such as saturation output power and polarization sensitivity were measured and compared. (c) 2006 Elsevier B.V. All rights reserved.

Visible blind p(+)-pi-n(-)-n(+) ultraviolet photodetectors based on 4H-SiC homoepilayers

p(+)-pi-n(-)-n(+) ultraviolet photodetectors based on 4H-SiC homoepilayers have been presented. The growth of the 4H-SiC homoepilayers was carried out in a LPCVD system. The size of the active area of the photodetectors was 300 x 300 mu m(2). The dark and illuminated I-V characteristics had been measured at reverse biases form 0 to 20 V at room temperature, and the illuminated current was at least two orders of magnitude than that of dark current below 13 V bias. The peak value zones of the photoresponse were located at 280-310 nm at different reverse biases, and the peak value located at 300 nm was 100 times greater than the cut-off response value in 380 nm at a bias of 10V, which showed the device had good visible blind performance. A small red-shift about 5 nm on the peak responsivity occurred when reverse bias increased from 5 to 15 V. (c) 2006 Elsevier Ltd. All rights reserved.

Resonant tunneling of holes in GaMnAs-related double- barrier structures

Using the multiband quantum transmitting boundary method (MQTBM), hole resonant tunneling through AlGaAs/GaMnAs junctions is investigated theoretically. Because of band-edge splitting in the DMS layer, the current for holes with different spins are tuned in resonance at different biases. The bound levels of the "light" hole in the quantum well region turned out to be dominant in the tunneling channel for both "heavy" and "light" holes. The resonant tunneling structure can be used as a spin filter for holes for adjusting the Fermi energy and the thickness of the junctions.