Mode-coupling analysis of three-dimensional microdisk resonators by the finite-difference time-domain technique

Quality factor enhancement due to mode coupling is observed in a three-dimensional microdisk resonator. The microdisk, which is vertically sandwiched between air and a substrate, with a radius of 1 mu m, a thickness of 0.2 mu m, and a refractive index of 3.4, is considered in a finite-difference time-domain (FDTD) numerical simulation. The mode quality factor of the fundamental mode HE71 decreases with an increase of the refractive index of the substrate, n(sub), from 2.0 to 3.17. However, the mode quality factor of the first-order mode HE72 reaches a peak value at n(sub) = 2.7 because of the mode coupling between the fundamental and the first-order modes. The variation of mode field distributions due to the mode coupling is also observed. This mechanism may be used to realize high-quality-factor modes in microdisks with high-refractive-index substrates. (c) 2006 Optical Society of America.

Analysis of mode characteristics for deformed square resonators by FDTD technique

The mode frequencies and quality factors (Q-factors) in two-dimensional (2-D) deformed square resonators are analyzed by finite-difference time-domain (FDTD) technique. The results show that the deformed square cavities with circular and cut corners have larger Q-factors than the perfect ones at certain conditions. For a square cavity with side length of 2 mu m and refractive index of 3.2, the mode Q-factor can increase 13 times as the perfect corners are replaced by a quarter of circle with radius of 0.3 pm. Furthermore the blue shift with the increasing deformations is found as a result of the reduction in effective resonator area. In square cavities with periodic roughness at sidewalls which maintains the symmetry of the square, the Q-factors of the whisperin gallery (WG)-like modes are still one order of magnitude larger that those of non-WG-like modes. However, the Q-tactors of these two types of modes are of the same order in the square cavity with random roughness. We also find that the rectangular and rhombic deformation largely reduce the Q-factors with the increasing offset and cause the splitting of the doubly degenerate modes due to the breaking of certain symmetry properties.

Influence of output waveguide on mode quality factor in semiconductor microlasers with an equilateral triangle resonator

Semiconductor microlasers with an equilateral triangle resonator (ETR) and an output waveguide are proposed and analyzed by the finite-difference time-domain technique and the Pade approximation. The numerical results show that microlasers with an output waveguide still have a high-quality factor (Q factor) and are suitable to realize directional emission. For the ETR with a 0.46-mum-width opening in one of the vertices connected to the output waveguide, we have the Q factor of 1.5x10(3) and 2.5x10(2) for the TM fundamental mode at the wavelength of 1.55 mum, as the side length of the ETR is 5 and 3 mum. The simulated intensity distributions are presented for the fundamental mode in the ETR with a side length of 3 mum and an opening of 0.23 mum. (C) 2000 American Institute of Physics. [S0003-6951(00)01749-6].

Dynamic dc voltage band observed within each current branch in the transition from static to dynamic electric-field domain formation in a doped GaAs/AlAs superlattice

A dynamic dc voltage band was found emerging from each sawtooth-like branch of the current-voltage characteristics of a doped GaAs/AlAs superlattice in the transition process from static to dynamic electric-field domain formation caused by increasing the sample temperature. As the temperature increases, these dynamic dc voltage bands expand within each sawtooth-like branch, squeeze out the static regions, and join up together to turn the whole plateau into dynamic electric-field domain formation. These results are well explained by a general analysis of stability of the sequential tunneling current in superlattices. (C) 1999 American Institute of Physics. [S0003-6951(99)04443-5].

Investigation of vertical radiation loss for whispering-gallery modes in 3-D microresonators by FDTD simulation

The vertical radiation loss of three-dimensional (3-D) microresonators is investigated by 3-D finite-difference time-domain (FDTD) simulation. The simulation shows that the vertical radiation causes an important loss in the microresonators with weak waveguiding, and result in decrease of the quality factors (Q-factors) of whispering-gallery (WG) modes. Through the simulation, we find that TM-like modes have much weaker vertical radiation loss than TE-like modes. High Q-factor TM-like modes are observed in the 3-D microresonators with weak vertical waveguiding, but the Q-factors of TE-like modes decrease greatly.

High-quality-factor EH modes in microcylinder resonators predicted by 3D FDTD simulation

The mode characteristis of a microcylinders with center layer thickness 0.2 mu m and radius 1 mu m are investigated by the three-dimensional (31)) finite-difference time-domain (FDTD) technique and the Pade approximation. The mode quality factor (Q-factor) of the EH71 mode obtained by 3D FDTD increase with the increase of the refractive index of the cladding layer n(2) as n(2) smaller than 3.17, and can be as large as 2.4 x 10(4) as the vertical refractive index distribution is 3.17/3.4/3.17, which is much larger than that of the HE71 mode with the same vertical refractive index distribution.

Modulation of Photonic Bandgap and Localized States by Dielectric Constant Contrast and Filling Factor in Photonic Crystals

The band structure of 2D photonic crystals (PCs) and localized states resulting from defects are analyzed by finite-difference time-domain (FDTD) technique and Pade approximation. The effect of dielectric constant contrast and filling factor on photonic bandgap (PBG) for perfect PCs and localized states in PCs with point defects are investigated. The resonant frequencies and quality factors are calculated for PCs with different defects. The numerical results show that it is possible to modulate the location, width and number of PBGs and frequencies of the localized states only by changing the dielectric constant contrast and filling factor.

APPLICATION OF FACTOR-ANALYSIS TO CORRECTION OF SPECTRAL OVERLAP INTERFERENCE IN INDUCTIVELY COUPLED PLASMA ATOMIC EMISSION-SPECTROMETRY

Correction of spectral overlap interference in inductively coupled plasma atomic emission spectrometry by factor analysis is attempted. For the spectral overlap of two known lines, a data matrix can be composed from one or two pure spectra and a spectrum of the mixture. The data matrix is decomposed into a spectra matrix and a concentration matrix by target transformation factor analysis. The component concentration of interest in a binary mixture is obtained from the concentration matrix and interference from the other component is eliminated. This method is applied to correcting spectral interference of yttrium on the determination of copper and aluminium: satisfactory results are obtained. This method may also be applied to correcting spectral overlap interference for more than two lines. Like other methods of correcting spectral interferences, factor analysis can only be used for additive spectral overlap. Results obtained from measurements on copper/yttrium mixtures with different white noise added show that random errors in measurement data do not significantly affect the results of the correction method.

Comparative expression analysis of transcription factor genes in the endostyle of invertebrate chordates

The endostyle of invertebrate chordates is a pharyngeal organ that is thought to be homologous with the follicular thyroid of vertebrates. Although thyroid-like features such as iodine-concentrating and peroxidase activities are located in the dorsolateral part of both ascidian and amphioxus endostyles, the structural organization and numbers of functional units are different. To estimate phylogenetic relationships of each functional zone with special reference to the evolution of the thyroid, we have investigated, in ascidian and amphioxus, the expression patterns of thyroid-related transcription factors such as TTF-2/MoxE4 and Pax2/5/8, as well as the forkhead transcription factors FoxQ1 and FoxA. Comparative gene expression analyses depicted an overall similarity between ascidians and amphioxus endostyles, while differences in expression patterns of these genes might be specifically related to the addition or elimination of a pair of glandular zones. Expressions of Ci-FoxE and BbFoxE4 suggest that the ancestral FoxE class might have been recruited for the formation of thyroid-like region in a possible common ancestor of chordates. Furthermore, coexpression of FoxE4, Pax2/5/8, and TPO in the dorsolateral part of both ascidian and amphioxus endostyles suggests that genetic basis of the thyroid function was already in place before the vertebrate lineage. (c) 2005 Wiley-Liss, Inc.

First molluscan TNFR homologue in Zhikong scallop: Molecular characterization and expression analysis

Tumor necrosis factor receptors (TNFRs) are a superfamily of proteins characterized by the unique cysteine-rich domain (CRD) and their important roles in diverse physiological and pathological events such as inflammation, apoptosis, autoimmunity and organogenesis. The first member of the molluscan TNFR family, designated as CfTNFR, was identified from Zhikong scallop Chlamys farreri by expressed sequence tag (EST) and rapid amplification of cDNA ends (RACE) approaches. The full-length cDNA of CfTNFR was of 1334 bp, consisting of a 5' UTR of 17 bp, a 3'UTR of 69 by with a poly (A) tail, and an open reading frame (ORE) of 1248 by encoding a polypeptide of 415 amino acids with a theoretical isoelectric point of 8.33 and predicted molecular weight of 47.07 kDa. There were a signal peptide, a CRD, a transmembrane region and a death domain in the deduced amino acid sequence of CfTNFR, suggesting that it was a typical type 1 membrane protein. The high identities (22-40%) of CfTNFR with other TNFR superfamily members indicated that CfTNFR should be a member of TNFR superfamily, and moreover, it should be the first death domain-containing TNFR found in invertebrates. Phylogenetic analysis revealed that CfTNFR was closely related to TNFR-like proteins from Strongylocentrotus purpuratus, Drosophila melanogaster and Ciona intestinalis, and they formed a separate branch apart from vertebrate TNFRs. The spatial expression of CfTNFR transcripts in healthy and bacteria challenged scallops was examined by quantitative real-time PCR. CfTNFR transcripts could be detected in all tested tissues, including haemocytes, gonad, gill, mantle and hepatopancreas, and significantly up-regulated in the tissues of gonad, gill, mantle and hepatopancreas after Listonella anguillarum challenge, indicating that CfTNFR was constitutive and inducible acute-phase protein involved in immune defence. The present results suggested the existence of the TNFR-like molecules and TNF-TNFR system in low invertebrates, and provided new insights into the role of CfTNFR in scallop innate immune responses to invading microorganisms. (C) 2009 Elsevier Ltd. All rights reserved.

Characterization of an ETS transcription factor in the sea scallop Chlamys farreri

We have cloned and characterized a cDNA encoding a putative ETS transcription factor, designated Cf-ets. The Cf-ets encodes a 406 amino acid protein containing a conserved ETS domain and a Pointed domain. Phylogenetic analysis revealed that Cf-ets belongs to the ESE group of ETS transcription factor family. Real-time PCR analysis of Cf-ets expression in adult sea scallop tissues revealed that Cf-ets was expressed mainly in gill and hemocytes, in a constitutive manner. Cf-ets mRNA level in hemocytes increased drastically after microbial challenge indicated its indispensable role in the anti-infection process. Simultaneously, the circulating hemocyte number decreased. In mammals, most ETS transcription factors play indispensable roles in blood cell differentiation and linage commitment during hematopoisis. Cf-ets is therefore likely to be a potential biomarker for hematopoiesis studies in scallops. (C) 2009 Elsevier Ltd. All rights reserved.

Identification and expression of TRAF6 (TNF receptor-associated factor 6) gene in Zhikong Scallop Chlamys farreri

Tumor necrosis factor receptor-associated factor 6 (TRAF6), a key signaling adaptor molecule common to the TNFR superfamily and IL-IR/TLR family, is important not only for a diverse array of physiological processes functions of the TNFR superfamily, but also is involved in adaptive immunity and innate immunity. In this report, the first bivalve TRAF6 (named as CfTRAF6) gene is identified and characterized from Zhikong scallop Chlamys farreri. The full-length cDNA of CfTRAF6 is of 2510 bp, consisting of a 5'-terminal untranslated region (UTR) of 337 bp, a 3'-terminal UTR of 208 bp with a canonical polyadenylation signal sequence AATAAA and a poly (A) tail, and an open reading frame (ORF) encoding a polypeptide of 655 amino acids. The predicted amino acid sequence of CfTRAF6 comprises characteristic motifs of the TRAF proteins, including a Zinc finger of RING-type, two Zinc fingers of TRAF-type, a coiled-coil region, and a MATH (the meprin and TRAF homology) domain. The overall amino acid sequence identity between CfTRAF6 and other TRAF6s is 28-68%. Phylogenetic analyses of CfTRAF6 sequence with TRAF sequences from other organisms indicate that CfTRAF6 is a true TRAF6 orthologue. The mRNA expression of CfTRAF6 in various tissues is measured by Real-time RT-PCR. The mRNA transcripts are constitutively expressed in tissues of haemocyte, muscle, mantle, heart, gonad and gill, but the highest expression is observed in the gonad. The temporal expressions of CfTRAF6 mRNA in the mixed primary cultured haemocytes are recorded after treatment with 20 mu g mL(-1) and 0.5 mu g mL(-1) peptido-glycan (PGN). The expression level of CfTRAF mRNA is down-regulated from 1.5 h to 3 h after the treatment with 0.5 mu g mL(-1) PGN, and then recovers to the original level. While the expression of CfTRAF6 is obviously decreased after treatment with 20 mu g mL(-1) PGN, and reach the lowest point (only about 1/9 times to control) at 3 h. The result Suggests that CfTRAF6 can be greatly regulated by PGN and it may be involved in signal transduction and immune response of scallop. (C) 2008 Published by Elsevier Ltd.

Expression pattern of dmrt4 from olive flounder (Paralichthys olivaceus) in adult gonads and during embryogenesis

The dmrt (doublesex and mab-3 related transcription factor) gene family comprises several transcription factors that share a conserved DM domain. Dmrt1 is considered to be involved in sexual development, but the precise function of other family members is unclear. In this study, we isolated genomic DNA and cDNA sequences of dmrt4, a member of the dmrt gene family, from olive flounder, Paralichthys olivaceus, through genome walking and real-time reverse transcriptase (RT)-PCR. Sequence analysis indicated that its genomic DNA contains two exons and one intron. A transcriptional factor binding sites prediction program identified a sexual development-related protein, Sox9 (Sry-like HMG box containing 9) in its 5' promoter. Protein alignment and phylogenetic analysis suggested that flounder Dmrt4 is closely related to tilapia Dmo (DM domain gene in ovary). The expression of dmrt4 in adult flounder was sexually dimorphic, as shown by real-time RT-PCR analysis, with strong expression in the testis but very weak expression in the ovary. Its expression was also strong in the brain and gill, but there was only weak or no expression at all in some of the other tissues tested of both sexes. During embryogenesis, its expression was detected in most developmental stages, although the level of expression was distinctive of the various stages. Whole mount in situ hybridization revealed that the dmrt4 was expressed in the otic placodes, forebrain, telencephalon and olfactory placodes of embryos at different developmental stages. These results will improve our understanding of the possible role of flounder dmrt4 in the development of the gonads, nervous system and sense organs.

Cloning and expression of tumor necrosis factor (TNF alpha) cDNA from red seabream Pagrus major

A fragment of TNFalpha cDNA sequence from red seabream was cloned by homology cloning approach with two degenerated primers which were designed based on the conserved regions of other animals' TNF sequences. The sequence was elongated by 3' and 5' RACE to get the full length CDS sequence. This sequence contained 1264 nucleotides that included a 5' UTR of 85 bp, a 3' UTR of 514 bp and an open reading frame (ORF) of 666 bp which could encode 222 amino acids propeptide. In 3' UTR, there were several mRNA instability motifs and three endotoxin-responsive sequences, but the sequence lacked the polyadenylation signal. The deduced peptide had a clear transmembrane domain, a TNFalpha family signature and a TNF2 family profile. The cell attachment sequence and the glycosaminoglycan attachment sites were also found in the sequence. The red seabream TNF sequence shared relatively high similarity with both mammalian TNFalpha and TNFbeta by multiple sequence alignments. Phylogenetic analysis showed that the piscine TNFalpha were located independently in a different branch compared with mammalian TNFalpha and TNFbeta. Based on the primary and secondary structure analysis and gene expression study, we could concluded that the red seabream TNF should be a TNFalpha, not TNFbeta. RT-PCR was used to study TNFa transcript expression. 24 h after the red seabream was challenged by Vibrio anguillarum, the RS TNFalpha transcript expression were detected in blood, brain, gill, heart, head kidney, kidney, Ever, muscle and spleen. Results showed that TNFalpha mRNA was constitutively expressed in parts of the tissues both in stimulated and unstimulated fish and the expression could be enhanced after the pathogen infection.