Analysis of mitochondrial DNA variants in Japanese patients with schizophrenia

To test the hypothesis that mitochondrial DNA (mtDNA) variants contribute to the susceptibility to schizophrenia, we sequenced the entire mtDNAs from 93 Japanese schizophrenic patients. Three non-synonymous homoplasmic variants in subunit six of the ATP s

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.

The evolution of YidC/Oxa/Alb3 family in the three domains of life: a phylogenomic analysis

Background: YidC/Oxa/Alb3 family includes a group of conserved translocases that are essential for protein insertion into inner membranes of bacteria and mitochondria, and thylakoid membranes of chloroplasts. Because mitochondria and chloroplasts are of b

Cardioviral RNA structure logo analysis: entropy, correlations, and prediction

In recent years, there has been an increased number of sequenced RNAs leading to the development of new RNA databases. Thus, predicting RNA structure from multiple alignments is an important issue to understand its function. Since RNA secondary structures are often conserved in evolution, developing methods to identify covariate sites in an alignment can be essential for discovering structural elements. Structure Logo is a technique established on the basis of entropy and mutual information measured to analyze RNA sequences from an alignment. We proposed an efficient Structure Logo approach to analyze conservations and correlations in a set of Cardioviral RNA sequences. The entropy and mutual information content were measured to examine the conservations and correlations, respectively. The conserved secondary structure motifs were predicted on the basis of the conservation and correlation analyses. Our predictive motifs were similar to the ones observed in the viral RNA structure database, and the correlations between bases also corresponded to the secondary structure in the database.

Combined effects of polyfluorinated and perfluorinated compounds on primary cultured hepatocytes from rare minnow (Gobiocypris rarus) using toxicogenomic analysis

Polyfluorinated and perfluorinated compounds (PFCs) are used in numerous commercial products and have been ubiquitously detected in the environment as well as in the blood of humans and wildlife. To assess the combined effects caused by PFCs in mixtures, gene expression profiles were generated using a custom cDNA microarray to detect changes in primary cultured hepatocytes of rare minnows exposed to six individual PFCs (perfluorooctanoic acid, perfluorononanoic acid, perfluorodecanoic acid, perfluorododecanoic acid, perfluorooctane sulfonate, and 8:2 fluorotelomer alcohol) and four formulations of the PFCs mixtures. Mixtures as well as individual compounds consistently regulated a particular gene set, which suggests that these conserved genes may play a central role in the toxicity mediated by PFCs. Specifically, a number of genes regulated by the mixtures were identified in this study, which were not affected by exposure to any single component. These genes are implicated in multiple biological functions and processes, including fatty acid metabolism and transport, xenobiotic metabolism, immune responses, and oxidative stress. More than 80% of the altered genes in the PFOA- and PFOS-dominant mixture groups were of the same gene set, while the gene expression profiles from single PFOA and PFOS exposures were not as similar. This work contributes to the development of toxicogenomic approaches in combined toxicity assessment and allows for comprehensive insights into the combined action of PFCs mixtures in multiple environmental matrices. (C) 2009 Elsevier B.V. All rights reserved.

NK-lysin of channel catfish: Gene triplication, sequence variation, and expression analysis

Antimicrobial peptides (AMPs) are important components of the host innate immune response against microbial invasion. In addition to the previously known four classes of antimicrobial peptides, a fifth class of antimicrobial peptides has been recently identified to include NK-lysins that have a globular three-dimensional structure and are larger with 74-78 amino acid residues. NK-lysin has been shown to harbor antimicrobial activities against a wide spectrum of microorganisms including bacteria, fungi, protozoa, and parasites. To date, NK-lysin genes have been reported from only a limited number of organisms. We previously identified a NK-lysin cDNA in channel catfish. Here we report the identification of two noveltypes of NK-lysin transcripts in channel catfish. Altogether, three distinct NK-lysin transcripts exist in channel catfish. In this work, their encoding genes were identified, sequenced, and characterized. We provide strong evidence that the catfish NK-lysin gene is tripled in the same genomic neighborhood. All three catfish NK-lysin genes are present in the same genomic region and are tightly linked on the same chromosome, as the same BAC clones harbor all three copies of the NK-lysin genes. All three NK-lysin genes are expressed, but exhibit distinct expression profiles in various tissues. In spite of the existence of a single copy of NK-lysin gene in the human genome, and only a single hit from the pufferfish,genome, there are two tripled clusters of NK-lysin genes on chromosome 17 of zebrafish in addition to one more copy on its chromosome 5. The similarity in the genomic arrangement of the tripled NK-lysin genes in channel catfish and zebrafish suggest similar evolution of NK-lysin genes. (c) 2005 Elsevier Ltd. All rights reserved.

Cloning and expression analysis in mature individuals of two chicken type-II GnRH (cGnRH-II) genes in common carp (Cyprinus carpio)

Gonadotropin-releasing hormone (GnRH) is a conservative neurodecapeptide family, which plays a crucial role in regulating the gonad development and in controlling the final sexual maturation in vertebrate. Two differing cGnRH-II cDNAs of common carp, namely cGnRH-II cDNA1 and cDNA2, were firstly cloned from the brain by rapid amplification of cDNA end (RACE) and reverse transcription- polymerase chain reaction (RT-PCR). The length of cGnRH-II cDNA1 and cDNA2 was 622 and 578 base pairs (bp), respectively. The cGnRH-II precursors encoded by two cDNAs consisted of 86 amino acids, including a signal peptide, cGnRH-II decapeptide and a GnRH-associated peptide (GAP) linked by a Gly-Lys-Arg proteolytic site. The results of intron trapping and Southern blot showed that two differing cGnRH-II genes in common carp genome were further identified, and that two genes might exist as a single copy. The multi-gene coding of common carp cGnRH-II gene offered novel evidence for gene duplication hypothesis. Using semi-quantitative RT-PCR, expression and relative expression levels of cGnRH-II genes were detected in five dissected brain regions, pituitary and gonad of common carp. With the exception of no mRNA2 in ovary, two cGnRH-II genes could be expressed in all the detected tissues. However, expression levels showed an apparent difference in different brain regions, pituitary and gonad. According to the expression characterization of cGnRH-II genes in brain areas, it was presumed that cGnRH-II might mainly work as the neurotransmitter and neuromodulator and also operate in the regulation for the GnRH releasing. Then, the expression of cGnRH-II genes in pituitary and gonad suggested that cGnRH-II might act as the autocrine or paracrine regulator.

Differential screening and characterization analysis of the egg envelope glycoprotein ZP3 cDNAs between gynogenetic and gonochoristic crucian carp

Gynogenetic silver crucian carp, Carassius auratus gibelio, is an intriguing model. system. In the present work, a systemic study has been initiated by introducing suppression subtractive hybridization technique into this model system to identify the differentially expressed genes in oocytes between gynogenetic silver crucian carp and its closely related gonochoristic color crucian carp. Five differential cDNA fragments were identified from the preliminary screening, and two of them are ZP3 homologues. Moreover, the full length ZP3 cDNAs were cloned from their oocyte cDNA libraries. The length of ZP3 cDNAs were 1378 bp for gyno-carp and 1367 bp for gono-carp, and they can be translated into proteins with 435 amino acids. Obvious differences are not only in the composition of amino acids, but also in the number of potential O-linked oligosaccharide sites. In addition, gyno-carp ZP3 amino acid sequence has an unexpected higher identity value with common carp (83.5%) than that with the closely related gono-carp (74.7%). The unique homology may be originated from the ancient hybridization. Northern blot analysis confirmed that expression of the ZP3 gene occurred exclusively in the oocytes. Because O-linked oligosaccharides on ZP3 have been demonstrated to play very important roles in fertilization, it is suggested that the extra O-linked glycosylation sites may be related to the unique sperm-egg recognition mechanism in gynogenesis.

Analysis of organchlorine compounds in water by solid phase microextraction and gas chromatography

In this work, both,solid phase microextraction (SPME) and solid phase extraction(SPE) were used to enrich organochlorine compounds in water samples and analyzed by gas chromatography with electron capture detector. The operating conditions of SPME have been studied and different kinds of solid phase were compared. Linear alkybenzene sulfonate(LAS) was added to the samples to investigate its effect on the analysis. The results indicated that polyacrylate was better than other commercial solid phases in extraction of moderated polar organic compounds and the sensitivity of SPME was higher than SPE. LAS affect much in liquid-liquid extraction and headspace SPME; but it has little effect on SPE and direct-SPME method. The applications showed that SPME was a fast and effective method in sample preparation.

Analysis of lateral current spreading in solar cell devices by spatially-resolved electroluminescence

Spatially-resolved electroluminescence (EL) images from solar cells contain information of local current distribution. By theoretical analysis of the EL intensity distribution, the current density distribution under a certain current bias and the sheet resistance can be obtained quantitatively. Two-dimensional numerical simulation of the current density distribution is employed to a GaInP cell, which agrees very well with the experimental results. A reciprocity theorem for current spreading is found and used to interpret the EL images from the viewpoint of current extraction. The optimization of front electrodes is discussed based on the results. (C) 2010 American Institute of Physics. [doi:10.1063/1.3431390]

Mode Analysis and Design of a Low-Loss Photonic Crystal 60 degrees Waveguide Bend

The guided modes of a two-dimensional photonic crystal straight waveguide and a waveguide bend are studied in order to find the high transmission mechanism for the waveguide bend. We find that high transmission occurs when the mode patterns and wave numbers match, while the single-mode condition in the waveguide bend is not necessarily required. According to the mechanism, a simply modified bend structure with broad high transmission band is proposed. The bandwidth is significantly increased from 19 to 116 nm with transmission above 90%, and covers the entire C band of optical communication.

Finite element beam propagation method for analysis of plasmonic waveguide

The basic idea of the finite element beam propagation method (FE-BPM) is described. It is applied to calculate the fundamental mode of a channel plasmonic polariton (CPP) waveguide to confirm its validity. Both the field distribution and the effective index of the, fundamental mode are given by the method. The convergence speed shows the advantage and stability of this method. Then a plasmonic waveguide with a dielectric strip deposited on a metal substrate is investigated, and the group velocity is negative for the fundamental mode of this kind of waveguide. The numerical result shows that the power flow direction is reverse to that of phase velocity.

Numerical analysis for four-wave mixing based wavelength conversion of differential phase-shift keying signals

We numerically investigate the main constrains for high efficiency wavelength conversion of differential phase-shift keying (DPSK) signals based on four-wave mixing (FWM) in highly nonlinear fiber (HNLF). Using multi-tone pump phase modulation techniques, high efficiency wavelength conversion of DPSK signals is achieved with the stimulated Brillouin scattering (SBS) effects effectively suppressed. Our analysis shows that there is a compromise between conversion efficiency and converted idler degradation. By optimizing the pump phase modulation configuration, the converted DPSK idler's degradation can be dramatically decreased through balancing SBS suppression and pump phase modulation degradation. Our simulation results also show that these multi-tone pump phase modulation techniques are more appropriate for the future high bit rate systems.

Development of Swept Frequency Method for Measuring Frequency Response of Photodetectors Based on Harmonic Analysis

We develop a swept frequency method for measuring the frequency response of photodetectors; (PDs) based on harmonic analysis. In this technique, a lightwave from a laser source is modulated by a radio-frequency (RF) signal via a Mach-Zehnder LiNbO3 modulator, and detected by a PD under test. The measured second-order harmonic of the RF signal contains information of the frequency responses and nonlinearities of the RF source, modulator, and PD. The frequency response of the PD alone is obtained by deducting the known frequency responses and nonlinearities of the RF source and modulator. Compared with the conventional swept frequency method, the measurement frequency range can be doubled using the proposed method. Experiment results show a good agreement between the measured results and those obtained using other techniques.

Mode Analysis for Equilateral-Triangle-Resonator Microlasers with Metal Confinement Layers

Mode characteristics are analyzed for electrically injected equilateral-triangle-resonator (ETR) semiconductor microlasers, which are laterally confined by insulating barrier SiO2 and electrode metals Ti-Au. For the ETR without metal layers, the totally confined mode field patterns are derived based on the reflection phase shifts, and the Q-factors are calculated from the far-field emission of the analytical near field distribution, which are agreement very well with the numerical results of the finite-difference time-domain (FDTD) simulation. The polarization dependence reflections for light rays incident on semiconductor-SiO2 -Ti-Au multi-layer structures are accounted in considering the confinement of TE and TM modes in the ETR with the metal layers. The reflectivity will greatly reduce with a Ti layer between SiO2 and Au for light rays with incident angle less than 30 especially for the TE mode, even the thickness of the Ti layer is only 10 nm. If the ETR is laterally confined by SiO2-Au layers without the Ti layer, the Fabry-Perot type modes with an incident angle of zero on one side of the ETR can also have high Q-factor. The FDTD simulation for the ETR confined by metal layers verifies the above analysis based on multi-layer reflections. The output spectra with mode intervals of whispering-gallery modes and Fabry-Perot type modes are observed from different ETR lasers with side length of 10 m, respectively.