Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation

Background: Short and long interspersed elements (SINEs and LINEs, respectively), two types of retroposons, are active in shaping the architecture of genomes and powerful tools for studies of phylogeny and population biology. Here we developed special protocol to apply biotin-streptavidin bead system into isolation of interspersed repeated sequences rapidly and efficiently, in which SINEs and LINEs were captured directly from digested genomic DNA by hybridization to bead-probe complex in solution instead of traditional strategy including genomic library construction and screening. Results: A new couple of SINEs and LINEs that shared an almost identical 3'tail was isolated and characterized in silver carp and bighead carp of two closely related species. These SINEs (34 members), designated HAmo SINE family, were little divergent in sequence and flanked by obvious TSD indicated that HAmo SINE was very young family. The copy numbers of this family was estimated to 2 x 10(5) and 1.7 x 10(5) per haploid genome by Real-Time qPCR, respectively. The LINEs, identified as the homologs of LINE2 in other fishes, had a conserved primary sequence and secondary structures of the 3'tail region that was almost identical to that of HAmo SINE. These evidences suggest that HAmo SINEs are active and amplified recently utilizing the enzymatic machinery for retroposition of HAmoL2 through the recognition of higher-order structures of the conserved 42-tail region. We analyzed the possible structures of HAmo SINE that lead to successful amplification in genome and then deduced that HAmo SINE, SmaI SINE and FokI SINE that were similar in sequence each other, were probably generated independently and created by LINE family within the same lineage of a LINE phylogeny in the genomes of different hosts. Conclusion: The presented results show the advantage of the novel method for retroposons isolation and a pair of young SINE family and its partner LINE family in two carp fishes, which strengthened the hypotheses containing the slippage model for initiation of reverse transcription, retropositional parasitism of SINEs on LINEs, the formation of the stem loop structure in 3'tail region of some SINEs and LINEs and the mechanism of template switching in generating new SINE family.

Effects of brominated flame retardants and brominated dioxins on steroidogenesis in H295R human adrenocortical carcinoma cell line

Brominated flame retardants (BFRs) and brominated dioxins are emerging persistent organic pollutants that are ubiquitous in the environment and can be accumulated by wildlife and humans. These chemicals can disturb endocrine function. Recent studies have demonstrated that one of the mechanisms of endocrine disruption by chemicals is modulation of steroidogenic gene expression or enzyme activities. In this study, an in vitro assay based on the H295R human adrenocortical carcinoma cell line, which possesses most key genes or enzymes involved in steroidogenesis, was used to examine the effects of five bromophenols, two polybrominated biphenyls (PBBs 77 and 169), 2,3,7,8-tetrabromodibenzo-p-dioxin, and 2,3,7,8-tetrabromodibenzofuran on the expression of 10 key steroidogenic genes. The H295R cells were exposed to various BFR concentrations for 48 h, and the expression of specific genescytochrome P450 (CYP11A, CYP11B2, CYP17, CYP19, and CYP21), 3 beta-hydroxysteroid dehydrogenase (3PHSD2), 17 beta-hydroxysteroid dehydrogenase (17 beta HSD1 and 17 beta HSD4), steroidogenic acute regulatory protein (StAR), and 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR)-was quantitatively measured using real-time polymerase chain reaction. Cell viability was not affected at the doses tested. Most of the genes were either up- or down-regulated, to some extent, by BFR exposure. Among the genes tested, 3PHSD2 was the most markedly up-regulated, with a range of magnitude from 1.6- to 20-fold. The results demonstrate that bromophenol, bromobiphenyls, and bromodibenzo-p-dioxin/furan are able to modulate steroidogenic gene expression, which may lead to endocrine disruption.

Electron microscopic examination of the viromatrix of Rana grylio virus in a fish cell line

Rana grylio virus (RGV), a Ranavirus belonging to the family Iridoviridae, assembles in the viromatrix which is a factory for viral genome replication and particle assembly. Ultrastructural studies of the viromatrix will clarify the pathway of assembly. The viromatrix and quantitative changes in RGV infected epithelipma papulosum cyprini (EPC) cells, one of fish cell lines, were studied by electron microscopy. It was shown that viromatrices were adjacent to the nucleus, and the electron density was lower than that of the surrounding cytoplasm. The viromatrix contained virus particles with different forms, electron-dense materials and amorphous structures which included tubules and membranous materials. Tubules were often observed in direct continuity with empty capsids. Several bundles of intermediate filaments were seen alongside the viromatrix and crystalline aggregates. Large clusters of mitochondria occurred in proximity to viromatrix. A total of 990 cells profiles were examined. The results showed that 394 cells contained viromatrix: 89.3% contained one, and 10.7% contained two to four viromatrices. The number of viromatrices increased gradually and reached a peak at 16 h p.i. The viromatrix area at 24 h p.i. increased up to 7.4 +/- 0.69 mu m(2) which was three-times lower than that at 6 h p.i. The number of empty capsids within viromatrix was generally more than that of "full" particles at different time points, and there was a strong positive correlation between them. (c) 2005 Elsevier B.V. All rights reserved.

Inductive expression and characterization analysis of Paralichthys olivaceus pigment epithelium-derived factor in a virally infected cell line

Pigment epithelium-derived factor (PEDF) is acknowledged to be a non-inhibitory member of the serine protease inhibitor (serpin) superfamily, with antiangiogenesis, and neuroprotective and immumoregulatory function, mainly in the tissues of nervous system. Here, A PEDF gene homolog, Paralichthys olivaceus PEDF (PoPEDF), was isolated from flounder embryonic cells (FEC) treated with UV-inactivated Grass carp hemorrhage virus (GCHV) and subsequently identified as a differentially expressed gene. The full length of PoPEDF cDNA is 1803 bp with an open reading frame of 1212 bp encoding a 403-amino-acid protein. This deduced protein contains an N-terminal signal peptide, a glycosylation site, a consensus serpin motif, and a 34-mer and a 44-mer fragment, all of which are very conserved in the PEDF family. PoPEDF gene exhibits a conserved exon-intron arrangement with 8 exons and 7 introns. This conserved evolutionary relationship was further confirmed by a phylogenetic analysis, where fish PEDFs and mammalian members formed a well-supported clade. Constitutive expression of PoPEDF was widely detected in many tissues. In response to UV-inactivated GCHV or poly(I:C), PEDF mRNA was upregulated in FEC cells with time. This is the first report on the transcriptional induction of PEDF in virally infected cells. (C) 2005 Elsevier Inc. All rights reserved.

High efficiency operation of butt joint line-defect-waveguide microlaser in two-dimensional photonic crystal slab

Butt joint line-defect-waveguide microlasers are demonstrated on photonic crystal slabs with airholes in a triangular lattice. Such microlaser is designed to increase the output power from the waveguide edge directly. The output power is remarkably enhanced to 214 times higher by introducing chirped structure in the output waveguide. The lasing mode operates in the linear dispersion region of the output waveguide so that the absorption loss due to the band-edge effect is reduced. The laser resonance is illustrated theoretically using the finite difference time domain method. A practical high power efficiency of 20% is obtained in this microlaser. (C) 2008 American Institute of Physics.

Line defect splitters for self-collimated beams in photonic crystals

A one-to-two splitter for self-collimated beams in photonic crystal (PC) is designed by inserting one row of line defects. Finite-difference time-domain (FDTD) method is used to simulate the light propagation process. Our systematical studies show that the splitting ratio is a function of the airholes size of the line defect radius, and stays fairly constant as a function of frequency. Furthermore, it is shown the numerical results can be analyzed by coupled-mode theory. (C) 2005 Elsevier B.V. All rights reserved.

Experimental investigation of slow light phenomenon in photonic crystal waveguide line defect laser

The guide mode whose frequency locates in the band edge in photonic crystal single line defect waveguide has very low group velocity. So the confinement and gain of electromagnetic field in the band edge are strongly enhanced. Photonic crystal waveguide laser is fabricated and the slow light phenomenon is investigated. The laser is pumped by pulsed pumping light at 980nm whose duty ratio is 0.05%. The active layer in photonic crystal slab is InGaAsP multiple quantum well. Light is transimited by a photonic crystal chirp waveguide in one facet of the laser. Then the output light is coupled to a fiber and the character of laser is analysis by an optical spectrometer. It is found that single mode and multimode happens with different power of pumping light. Meanwhile the plane wave expansion and finite-difference time-domain methods are used to simulate the phenomenon of slow light. And the result of the experiment is compared with the theory which proves the slow light results in lasing oscillation.

Study on charge equilibration time of highly charged ions in carbon foils

Charge state distribution of 0.8MeV/u uranium ions after transmission through a thin carbon foil has been studied. It is observed that the charge state distribution is equilibrated after the uranium ions have passed through a 15 mu g/cm(2) carbon foil. The equilibrated average charge state is 33.72 and the charge equilibration time of uranium ions in carbon foil is less than 5.4fs.

Restoration of the signals from multi-hit three-layer delay-line anode position-sensitive detector

Multi-hit 3-layer delay-line anode (Hexanode) has an increased ability to detect multi-hit events in a collision experiment. Coupled with a pair of micro-channel plates, it can provide position information of the particles even if the particles arrive at the same time or within small time dwell. But it suffers from some ambiguous outputs and signal losses due to timing order and triggering thresholds etc. We have developed a signal reconstruction program to correct those events. After the program correction, the dead time only exists when 2 paxticles arrive at the same time and the same position within a much smaller range. With the combination of Hexanode and the program, the experimental efficiencies will be greatly improved in near threshold double ionization on He collisions.

A high performance Time-of-Flight detector applied to isochronous mass measurement at CSRe

A high performance Time-of-Flight detector has been designed and constructed for isochronous mass spectrometry at the experimental Cooler Storage Ring (CSRe) The detector has been successfully used in an experiment to measure the masses of the N approximate to Z approximate to 33 nuclides near the proton drip-line Of particular interest is the mass of As-65 A maximum detection efficiency of 70% and a time resolution of 118 +/- 8 Ps (FWHM) have been achieved in the experiment The dependence of detection efficiency and signal average pulse height (APH) on atomic number Z has been studied The potential of APH for Z identification has been discussed (C) 2010 Elsevier B V All rights reserved

On-line voltammetric monitoring of dissolved Cu and Ni in the Gulf of Cadiz, south-west Spain

Geochemical processes in estuarine and coastal waters often occur on temporally and spatially small scales, resulting in variability of metal speciation and dissolved concentrations. Thus, surveys, which are aimed to improve our understanding of metal behaviour in such systems, benefit from high-resolution, interactive sampling campaigns. The present paper discusses a high-resolution approach to coastal monitoring, with the application of an automated voltammetric metal analyser for on-line measurements of dissolved trace metals in the Gulf of Cadiz, south-west Spain. This coastal sea receives metal-rich inputs from a metalliferous mining area, mainly via the Huelva estuary. On-line measurements of dissolved Cu, Zn, Ni and Co were carried out on-board ship during an eight-day sampling campaign in the study area in June 1997. A pumping system operated continuously underway and provided sampled water from a depth of ca. 4 m. Total dissolved metal concentrations measured on-line in the Gulf of Cadiz ranged between <5 nM Cu (<3 nM Ni) ca. 50 km off-shore and 60–90 nM Cu (5–13 nM Ni) in the vicinity of the Huelva estuary. The survey revealed steep gradients and strong tidal variability in the dissolved metal plume extending from the Huelva estuary into the Gulf of Cadiz. Further on-line measurements were carried out with the automatic metal monitor from the bank of the Odiel estuary over a full tidal cycle, at dissolved metal concentrations in the μM range. The application confirmed the suitability of the automated metal monitor for coastal sampling, and demonstrated its adaptability to a wide range of environmental conditions in the dynamic waters of estuaries and coastal seas. The near-real time acquisition of dissolved metal concentrations at high resolution enabled an interactive sampling campaign and therefore the close investigation of tidal variability in the development of the Huelva estuary metal plume.

The research of cellulose derivatives as chiral stationary phases and high performance liquid chromatography with polarimeter as on-line detector

Three cellulose derivatives were synthesized and used as chiral stationary phases based on silica gel. The effects of adsorbances on the column numbers and stabilities have been investigated. These stationary phases exhibited high chiral recognition for various racemates. At the same time, the on-line curves of polarimeter were obtained by high performance liquid chromatography with polarimeter as on-line detector.

On-line concentration of proteins in pressurized capillary electrochromatography coupled with electrospray ionization-mass spectrometry

Pressurized capillary electrochromatography (pCEC) and electrospray ionization-mass spectrometry (ESI-MS) have been hyphenated for protein analysis. Taken cytochrome c, lysozyme, and insulin as samples, the limits of detection (LODs) for absolute concentrations are 10(-11) mol (signal-to-noise ratio S/N = 3) with relative standard deviations (RSDs) of retention time and peak area, respectively, of less than 1.7% and 4.8%. In order to improve the detection sensitivity, on-line concentration by field-enhanced sample-stacking effect and chromatographic zone-sharpening effect has been developed, and parameters affecting separation and detection, such as pH and electrolyte concentration in the mobile phase, separation voltage, as well as enrichment voltage and time, have been studied systematically. Under the optimized conditions, the LODs of the three proteins could be decreased up to 100-fold. In addition, the feasibility of such techniques has been further demonstrated by the analysis of modified insulins at a concentration of 20 mu g/mL.

On-line concentration of peptides and proteins with the hyphenation of polymer monolithic immobilized metal affinity chromatography and capillary electrophoresis

An iminodiacetic acid (IDA)-type adsorbent is prepared at the one end of a capillary by covalently bonding IDA to the monolithic rods of macroporous poly(glycidyl methacrylate-co-ethylene dimethacrylate). Cu(II) is later introduced to the support via the interaction with IDA. By this means, polymer monolithic immobilized metal affinity chromatography (IMAC) materials are prepared. With such a column, IMAC for on-line concentration and capillary electrophoresis (CE) for the subsequent analysis are hyphenated for the analysis of peptides and proteins. The reproducibility of such a column has been proved good with relative standard deviations (RSDs) of dead time of less than 5% for injection-to-injection and 12% for column-to-column (n = 3). Through application on the analysis of standard peptides and real protein samples, such a technique has shown promising in proteome study.