Identification of a Spindlin homolog in gibel carp (Carassius auratus gibelio)

Spindlin has been suggested to play an important role during the transition from oocyte maturation to embryo development in mouse, but its homolog similar to the mouse Spindlin in molecular and expression characterization has not been identified up to now in other vertebrates. In this study, a full length of cDNA sequence is cloned and sequenced from the gibel carp (Carassius auratus gibelio). It contains 1240 nucleotides with an open reading frame of 771 nt encoding 257 amino acids. Based on its amino acid sequence alignment and comparison analysis with the known Spin family proteins, the newly cloned Spin is named Carassius auratus gibelio Spindlin (CagSpin). Its product could be detected from mature eggs to blastula embryos, but its content decreased from the two-cell stage, and could not be detected after the gastrula stage. It suggests that the CagSpin should be a maternal protein that is expressed during oocyte maturation, and plays a crucial role in early cleavage of embryogenesis. CagSpin is the first homolog similar to mouse spindlin identified in fish, and also in other vertebrates. GST pull-down assay reveals the first biochemical evidence for the association of CagSpin and p-tubulin, the microtubule component. Therefore, CagSpin may play important functions by interacting with beta-tubulin and other spindle proteins during oocyte maturation and egg fertilization. (c) 2005 Elsevier Inc. All rights reserved.

Identification of three duplicated Spin genes in medaka (Oryzias latipes)

Gene and genomic duplications are very important and frequent events in fish evolution, and the divergence of duplicated genes in sequences and functions is a focus of research on gene evolution. Here, we report the identification and characterization of three duplicated Spindlin (Spin) genes from medaka (Oryzias latipes): OlSpinA, OlSpinB, and OlSpinC. Molecular cloning, genomic DNA Blast analysis and phylogenetic relationship analysis demonstrated that the three duplicated OlSpin genes should belong to gene duplication. Furthermore, Western blot analysis revealed significant expression differences of the three OlSpins among different tissues and during embryogenesis in medaka, and suggested that sequence and functional divergence might have occurred in evolution among them. © 2005 Elsevier B.V. All rights reserved.

Identification and characterization of Bacillus anthracis by multiplex PCR on DNA chip

Bacillus anthracis can be identified by detecting virulence factor genes located on two plasmids, pXO1 and pXO2. Combining multiplex PCR with arrayed anchored primer PCR and biotin-avidin alkaline phosphatase indicator system, we developed a qualitative DNA chip method for characterization of B. anthracis, and simultaneous confirmation of the species identity independent of plasmid contents. The assay amplifies pag gene (in pXO1), cap gene (in pXO2) and Ba813 gene (a B. anthracis specific chromosomal marker), and the results were indicated by an easy-to-read profile based on the color reaction of alkaline phosphatase. About 1 pg of specific DNA fragments on the chip wells could be detected after PCR. With the proposed method, the avirulent (pXO1(+)/2(-), pXO1(-)/2(+) and pXO1(-)/2(-)) strains of B. anthracis and distinguished 'anthrax-like' strains from other B. cereus group bacteria were unambiguously identified, while the genera other than Bacillus gave no positive signal. (C) 2004 Elsevier B.V. All rights reserved.

Vitellogenin in rare minnow (Gobiocypris rarus): identification and induction by waterborne diethylstilbestrol

Rare minnow (Gobiocypris rarus) is a tiny Chinese carp that has a short life cycle and is easily cultured in the laboratory. In this study, juvenile rare minnows were exposed to waterborne diethylstilbestrol (DES) at 0.05, 0.5 and 5 mug/l in laboratory aquaria. After exposure for 4, 8, 13 and 21 days, juvenile fish were collected and vitellogenin (Vtg) was measured in whole body homogenates. Native and SDS electrophoresis followed by Western blotting were performed for Vtg identification, and a non-competitive ELISA was developed. In the DES exposure groups (0.5 and 5 mug/l DES), Vtg appeared after 4 days, increased significantly after 8 days and reached a maximum on day 13. Further, a significant increase in the hepatosomatic index (HSI) was found in the 5 mug/l DES exposure group after 21 days. These results indicate that rare minnow provides a good model for assessing endocrine disruption by environmental estrogens. (C) 2004 Elsevier Inc. All rights reserved.

Identification of two novel interferon-stimulated genes from cultured CAB cells induced by UV-inactivated grass carp hemorrhage virus

Interferon (IFN) exerts its antiviral effect by inducing the expression of a number of IFN-stimulated genes (ISGs) to establish a host antiviral state. Earlier studies identified some important fish IFN system genes from IFN-induced CAB cells (crucian carp Carassius auratus L. embryonic blastulae cells) after treatment with UV-inactivated GCHV (grass carp hemorrhage virus). Herein, the cloning of 2 novel IFN-stimulated genes, termed Gig1 and Gig2, is described for the same cell system. The complete cDNA sequences of Gig1 and Gig2 contain 1244 bp encoding for a 194-amino-acid protein and 693 bp for a 158-amino-acid protein, respectively. A search of public databases revealed that these are 2 novel IFN-stimulated genes, since neither significant homologous genes nor conserved motifs were identified. Active GCHV, UV-inactivated GCHV and CAB IFN-containing supernatant (ICS) induced transcription of these genes and distinct kinetics were observed. An analysis of differences in expression between the 2 genes and the IFN signal factors CaSTAT1 and CaIRF7 indicated that GCHV infection activated different signal pathways for their up-regulation. Upon virus infection, the transcription of Gig1 but not of Gig2 is strongly suppressed by cycloheximide (CHX). In contrast, following treatment with CAB IFN-containing supernatant, CHX does not inhibit either gene transcription. The results suggest that GCHV infection can induce expression of both Gig1 and Gig2 via newly synthesized CAB IFN, most probably through the JAK-STAT signal pathway, and can also directly activate Gig2 transcription without ongoing protein synthesis.

Identification of a novel C1q family member in color crucian carp (Carassius auratus) ovary

Potential roles of Clq/tumor necrosis factor (TNF) superfamily proteins have been observed in vertebrate oogenesis and oocyte maturation, but no ovary-specific member has been identified so far. In this study, we have cloned and identified a novel member of Clq family with a Clq domain in the C-terminal from fully grown oocyte cDNA library of color crucian carp and demonstrated that the gene might be specifically expressed in ovary and therefore designated as Carassius auratus ovary-specific Clq-like factor, CaOClq-like factor. It encodes a 213 amino acid protein with a 17 amino acid signal peptide. There is only one protein band of about 24.5 kDa in the extracts from phase I to phase IV oocytes, but two positive protein bands are detected in the extracts of mature eggs and fertilized eggs. Furthermore, the mobility shift of the smaller target protein band cannot be eliminated by phosphatase treatment, but the larger protein band increases its mobility on the gel after phosphatase treatment, suggesting that the larger protein might be a phosphorylated form. Immunofluorescence localization indicates that the CaOClq-like proteins localize in cytoplasm, cytoplasm membrane and egg envelope of the oocytes at cortical granule stage and vitellogenesis stage, whereas they were compressed to cytoplasm margin in ovulated mature eggs and discharged into perivitelline space between cytoplasm membrane and egg envelope after egg fertilization. Further studies on distribution and translocation mechanism of the CaOClq-like factor will be benefit to elucidate the unique function in oogenesis, oocyte maturation and egg fertilization. (C) 2004 Elsevier Inc. All rights reserved.

Identification and expression analysis of two IFN-inducible genes in crucian carp (Carassius auratus L.)

Interferon (IFN) exerts its antiviral effects mainly through activation of a subset of IFN-stimulated genes (ISG), but relatively few of fish ISGs have been isolated and characterized so far. Here, we report two fish ISGs, termed CaIF158 and CaIF156, cloned from a subtractive cDNA library constructed with mRNAs obtained from crucian carp (Carassius auratus L.) blastulae embryonic (CAB) cells infected by UV-inactivated GCHV and mock-infected cells. Database search revealed that both ISGs had a high-level homology with all members of a well conserved gene family with multiple tetratricopeptide repeat (TPR) motifs, including human IF160, IF158, IF156, IFI54 and their homologues in some other mammalian species. The transcripts of CaIF158 and CaIF156 were undetectable in CAB cells but could be induced by active GCHV, UV-inactivated GCHV or CAB IFN. Analysis of expression difference between them and IFN signal factors, CaSTAT1 and CaIRF7, indicated that their transcriptions were mediated possibly through JAK-STAT signal pathway, which was further supported by the induction analysis in UV-inactivated GCHV infected, IFN-treated and untreated cells in the presence or absence of cycloheximide (CHX), a potent inhibitor of protein synthesis. In addition, a pufferfish (Fugu rubrides) DNA sequence representing putative FrIFI56 was also revealed when CalF158 and CalF156 were used to search the pufferfish genome database. Phylogenetic analysis showed that these fish ISGs form a unique clad independent of mammalian homologues, reflecting a distant evolutionary relationship from mammals. These studies identified the first teleost IFI56 and IFI58 orthologues. (C) 2003 Elsevier B.V All rights reserved.

Identification of antiviral-relevant genes in the cultured fish cells induced by UV-inactivated virus

UV-inactivated grass carp hemorrhage virus (GCHV) can induce high titer of interferon in cultured CAB (crucian carp (Carassius auratus L.) blastulae) cells, and thus defend host cells against the virus invasion. The mechanism is proposed that an antiviral state should be established in the host cells by activating expression of a set of antiviral-relevant genes. In this study, suppressive subtractive hybridization is applied to constructing a subtracted cDNA library with mRNAs isolated from UV-inactivated GCHV infected and mock-infected CAB cells. 272 differential cDNA fragments are identified by both PCR and dot blot from the subtractive cDNA library. Sequencing analysis reveals 69 genes, including 46 known gene homologues, and 23 unknown putative genes. The known genes include the genes involved in interferon signaling pathways, such as Stat1 and Jak1, the antiviral genes, such as Mx and Viperin, and a set of interferon-stimulated genes observed in mammalian cells. Most of the unknown putative genes contain AU-rich element in their sequences. Differential expressions of these genes are further confirmed by virtual Northern blot and RT-PCR. The data imply that UV-inactivated GCHV is not only able to induce production of interferon in the infected CAB cells, but also leads to the expression of a series of antiviral-relevant genes or immune-relevant genes, and therefore reveals that the signaling pathway of interferon system and antiviral mechanism in fish are similar to those in mammals.

A method for individual identification of echolocation signals in free-ranging finless porpoises carrying data loggers

Echolocation click events of a free-ranging juvenile and an adult finless porpoise (Neophocaena phocaenoides) were recorded with an acoustic data logger. Additionally, dive depth and swim speed of the juvenile were recorded with a behavior data logger. Echoes of echolocation signals from the water surface were clearly detected in shallow dives approximately less than 2 m. The delay time between a surface echo and a direct signal corresponded with the two-way transmission time for the animal's depth, indicating that the signals originated from the animal wearing the data loggers. The finless porpoises produced echolocation signals frequently and were thought to be able to detect their depth by listening to echoes from the water surface. (C) 2000 Acoustical Society of America. [S0001-4966(00)01609-X].

Peak identification for PCDD/Fs in environmental samples at different temperature programs

A method has been developed for peak recognition of 136 polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) at different temperature programs. Their retention behaviours are predicted on the basis of an identification database of retention values (A, B) of gas chromatography. By the retention times of C-13 labelled 2,3,7,8-substituted PCDD/F internal standards, the retentions of all PCDDs and PCDFs can be calculated. After comparison with the retentions of practical environmental samples, the predicted values have been proved to be very accurate. (C) 2000 Elsevier Science Ltd. All rights reserved.

Study on Closed-set Speaker Identification Based on Biomimetic Pattern Recognition

In this paper, a new classifier of speaker identification has been proposed, which is based on Biomimetic pattern recognition (BPR). Distinguished from traditional speaker recognition methods, such as DWT, HMM, GMM, SVM and so on, the proposed classifier is constructed by some finite sub-space which is reasonable covering of the points in high dimensional space according to distributing characteristic of speech feature points. It has been used in the system of speaker identification. Experiment results show that better effect could be obtained especially with lesser samples. Furthermore, the proposed classifier employs a much simpler modeling structure as compared to the GMM. In addition, the basic idea "cognition" of Biomimetic pattern recognition (BPR) results in no requirement of retraining the old system for enrolling new speakers.

Identification of vacancies in electron irradiated GaSb by coincidence Doppler broadening spectroscopy

In this paper we present the results of coincidence Doppler broadening (CDB) measurements and positron lifetime spectroscopy (PLS) on the semiconductor material GaSb. Gallium vacancy with positron lifetime of about 283 ps (V-Ga, (283 ps)) was identified in as-grown sample by CDB technique and PAS technique. For electron irradiated samples with dosages of 10(17) cm(-2) and 10(18) cm(-2), the PAS showed almost the same defectrelated positron lifetime of about 285 ps. CDB experiments indicated that defects in irradiated samples were related to Ga vacancies. (c) 2006 Published by Elsevier B.V.

Identification of induced reaction during XPS depth profile measurements of CeO2/Si films grown by ion beam epitaxy

An anomalous behavior was observed in X-ray photoelectron Spectroscopy (XPS) depth profile measurements conducted on CeO2/Si epilayers grown by ion beam epitaxy (IBE): the signals of Ce3+ and Ce4+ co-exist, and the ratio between them increases during the etching time and then tends to maintain a constant level before increasing again. The results of X-ray Diffraction (XRD), Auger Electron Spectroscopy (AES), and Rutherford Back-Scattering (RES) measurements proved that the reduction chemical reaction of CeO2 is induced by ion-etching. (C) 1998 Elsevier Science Ltd. All rights reserved.

Structural identification of a cubic phase in hexagonal GaN films grown on sapphire by gas-source molecular beam epitaxy

The structural characteristics of gallium nitride (GaN) films grown on sapphire(0001) substrates by gas source molecular beam epitaxy (GSMBE) have been investigated using high-resolution synchrotron irradiation X-ray diffraction and cathodoluminescence with a variable energy electron beam. Besides the well-known GaN hexagonal structure, a small portion of cubic phase GaN was observed. The X-ray measurements provide an essential means for the structural identification of the GaN layers. Arising from the variable penetration depth of the electron beam in the cathodoluminescence measurements, it was found that the fraction of the GaN cubic-phase typically increased as the probing depth was increased. The results suggest that the GaN cubic phase is mostly located near the interface between the substrate and GaN layer due to the initial nucleation.

Effects of Hydrogen Plasma Treatment on the Electrical and Optical Properties of ZnO Films: Identification of Hydrogen Donors in ZnO

Wurtzite ZnO has many potential applications in optoelectronic devices, and the hydrogenated ZnO exhibits excellent photoelectronic properties compared to undoped ZnO; however, the structure of H-related defects is still unclear. In this article, the effects of hydrogen-plasma treatment and subsequent annealing on the electrical and optical properties of ZnO films were investigated by a combination of Hall measurement, Raman scattering, and photoluminescence. It is found that two types of hydrogen-related defects, namely, the interstitial hydrogen located at the bond-centered (H-BC) and the hydrogen trapped at a O vacancy (H-O), are responsible for the n-type background conductivity of ZnO films. Besides introducing two hydrogen-related donor states, the incorporated hydrogen passivates defects at grain boundaries. With increasing annealing temperatures, the unstable H-BC atoms gradually diffuse out of the ZnO films and part of them are converted into H-O, which gives rise to two anomalous Raman peaks at 275 and 510 cm(-1). These results help to clarify the relationship between the hydrogen-related defects in ZnO described in various studies and the free carriers that are produced by the introduction of hydrogen.