Evolutionary implications of multiple SINE insertions in an intronic region from diverse mammals

An analysis of the nuclear beta-fibrinogen intron 7 locus from 30 taxa representing 12 placental orders of mammals reveals the enriched occurrences of short interspersed clement (SINE) insertion events. Mammalian-wide interspersed repeats (MIRs) are present at orthologous sites of all examined species except those in the order Rodentia. The higher substitution rate in mouse and a rare MIR deletion from rat account for the absence of MIR in the rodents. A minimum of five lineage-specific SINE sequences are also found to have independently inserted into this intron in Carnivora, Artiodactyla and Lagomorpha. In the case of Carnivora, the unique amplification pattern of order-specific CAN SINE provides important evidence for the "pan-carnivore" hypothesis of this repeat element and reveals that the CAN SINE family may still be active today. Particularly interesting is the finding that all identified lineage-specific SINE elements show a strong tendency to insert within or in very close proximity to the preexisting MIRs for their efficient integrations, suggesting that the MIR clement is a hot spot for successive insertions of other SINEs. The unexpected MIR excision as a result of a random deletion in the rat intron locus and the non-random site targeting detected by this study indicate that SINEs actually have a greater insertional flexibility and regional specificity than had previously been recognized. Implications for SINE sequence evolution upon and following integration, as well as the fascinating interactions between retroposons and the host genomes are discussed.

Molecular cloning of TRAF2 binding protein gene and its promoter region from the grass carp Ctenopharyngodon idellus

A tumor necrosis factor receptor-associated factor 2 binding protein (T2BP) gene was isolated from the grass carp (Ctenopharyngodon idellus) by utilizing suppression subtractive hybridization (SSH) and rapid amplification of cDNA ends (RACE). The grass carp T2BP (GT2BP) gene contains an open reading frame of 579 nucleotide(s) (nt), encoding 193 amino acids, with 23 nt 5'-untranslated region and a long 3'-untranslated region of 434 nt including poly (A), 1 AUUUA motif and 4 AUUUUA motifs. No signal peptide has been detected in the predicted GT2BP, but a characteristic forkhead associated domain is present. The GT2BP mRNA shares 83% identity with the zebrafish DNA sequence, and they both have no introns in the genomic DNA. The putative transcription factor binding sites of GT2BP include two C/EBP alpha binding sites, and one c-Jun binding, one AP-1 binding, and one nuclear factor kappa B (NF kappa B) binding sites. Southern blot analysis revealed that the GT2BP was a single-copy gene. Individual difference was observed in GT2BP expression in examined organs of healthy grass carp. However, the expression of GT2BP in all examined organs in a fish with the highest copepod infection level and the significantly higher expression level in spleen and liver in infected fish may indicate its up-regulation with the parasite infection. (c) 2005 Elsevier B.V. All rights reserved.

Molecular cloning of the viperin gene and its promoter region from the mandarin fish Siniperca chuatsi

A viperin gene has been cloned from the mandarin fish (Siniperca chuatsi). From the first transcription initiation site, the mandarin fish viperin gene extends 3163 nucleotides to the end of the 3' untranslated region, and it contains six exons and five introns. The open reading frame of the viperin transcript has 1062 nucleotides which encode a 354 amino acid peptide. The amino acid sequence of mandarin fish viperin shows high identities with its homologues in teleosts and mammals except for the first 70 amino acids. A characteristic feature in the viperin promoter region was the presence of five putative ICSBP (IRF8) binding sites and one IRFI binding site. The viperin gene expressed mainly in lymphoid tissues before stimulation, but its expression can be examined in almost all the organs investigated after stimulation with virus or Poly I:C. The expression pattern and promoter sequence may be considered as the indirect evidence that the transcription of viperin is regulated by interferons or interferon induced genes. (C) 2004 Elsevier B.V. All rights reserved.

Characteristics of rDNA intergenic spacer region from a waterbloom cyanobacteria species Oscillatoria sp.

Sequence of rDNA intergenic spacer region (ISR) from a waterbloom cyanobacterial species Oscillatoria sp, was determined and analyzed. The results of sequence comparison showed that the spacer had a high level sequence divergence, suggesting the sequence may be a target sequence for developing cyanobacteria genus- and species-specific oligonucleotide probes. In addition, a 20bp sequence of rDNA ISR was found highly conserved in all species of cyanobacteria, which was not found in other eubacteria. This conserved sequence within a variable region indicates that it might be a functional oligonucleotide in the processing of the rRNA precursor.

Stimulated emission in the blue wavelength region from a copolymer containing PPV segment

The lasing properties of a soluble conjugated polymer, Poly[1,8-octanedioxy-2,6-dimethoxy-1,4-phenylene-1,2-ethenylene-1,2-phenylene-1,2-ethenylene-3,5-dimethoxy-1,4-phenylene] (CNMBC-Ph) in chloroform solution were investigated. The third harmonic radiation of a Nd:YAG laser was used as the pump light. The stimulated emission with a linewidth of 15 nm was observed in the blue wavelength region with the peak at 450 nm. The threshold pulse peak power was about 2.8 MW/cm(2). The energy conversion yield of the laser was estimated to be about 3.4%. The maximum peak power of the laser output pulse reached 40 kW. (C) 2000 Published by Elsevier Science S.A. All rights reserved.

Stimulated emission in blue wavelength region from a copolymer

A dye laser based on the soluble conjugated polymer, Poly[1,8-octanedioxy-2,6-dimethoxy-1,4-phenylene-1,2-ethenylene-1, 4-phenylene-1,2-ethenylene-3,5-dimethoxy-1,4-phenylene], has been fabricated. The laser was pumped by light pulses from the third harmonic radiation of an Nd:YAG laser. The lasing was observed in the blue wavelength region with the peak at 450 nm. The threshold energy is about 19 mu J. The energy conversion yield of the laser is about 3.4%. The maximum peak power of the laser output pulse arrives at about 20 kW.

Ultrabroad infrared luminescences from Bi-doped alkaline earth metal germanate glasses

We report on ultrabroad infrared (IR) luminescences covering the 1000-1700-nm wavelength region, from Bi-doped 75GeO(2) 20RO-5Al(2)O(3) 1B(2)O(3) (R = Sr, Ca, and Mg) glasses. The full width at half-maximum of the IR luminescences excited at 980 nm increases (315 -> 440 -> 510 nm) with the change of alkaline earth metal (Mg2+ -> Ca2+ -> Sr2+). The fluorescence lifetime of the glass samples is 1725, 157, and 264 mu s when R is Sr, Ca, and Mg, respectively. These materials may be promising candidates for broad-band fiber amplifiers and tunable laser resources.

Effect of various alkaline-earth metal oxides on the broadband infrared luminescence from bismuth-doped silicate glasses

We report on the effect of various alkaline-earth metal oxides on the broadband infrared luminescence covering 1000-1600 nm wavelength region from bismuth-doped silicate glasses. The full width at half maximum (FWHM) of the infrared luminescence and the fluorescent lifetime is more than 200 nm and 400 mu s, respectively. The fluorescent intensity decreases with increasing basicity of host glasses. Besides the broadband infrared luminescence, luminescence centered at 640 nm was also observed, which should be ascribed to Bi2+ rather than to the familiar Bi3+. We suggest that the infrared luminescence should be assigned to the X-2 (2)Pi (3/2) -> X-1 (2)Pi(1/2) transition of BiO molecules dispersed in the host glasses. (c) 2006 Elsevier Ltd. All rights reserved.

Broadband infrared luminescence from Li2O-Al2O3-ZnO-SiO2 glasses doped with Bi2O3

The broadband emission in the 1.2 similar to 1.6 mu m region from Li2O-Al2O3-ZnO-SiO2 ( LAZS) glass codoped with 0.01mol.% Cr2O3 and 1.0mol.% Bi2O3 when pumped by the 808nm laser at room temperature is not initiated from Cr4+ ions, but from bismuth, which is remarkably different from the results reported by Batchelor et al. The broad similar to 1300nm emission from Bi2O3-containing LAZS glasses possesses a FWHM ( Full Width at Half Maximum) more than 250nm and a fluorescent lifetime longer than 500 mu s when excited by the 808nm laser. These glasses might have the potential applications in the broadly tunable lasers and the broadband fiber amplifiers. (c) 2005 Optical Society of America.

Phylogenetic relationships among six species of Epistylis inferred from 18S-ITS1 sequences

Phylogenetic relationships among six species of Epistylis (i.e. E. plicatilis, E. urceolata, E. chrysemydis, E. hentscheli, E. wenrichi, and E, galea) were investigated using sequences of the first internal transcribed spacer region (ITS-1) of ribosomal DNA (rDNA). Amplified rDNA fragment sequences consisted of 215 or 217 bases of the flanking 18S and 5.8S regions, and the entire ITS-1 region (from 145 to 155 bases). There were more than 33 variable bases between E. galea and the other five species in both the 18S region and the ITS-1 region. The affiliation of them was assessed using Neighbor-joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) analyses. In all the NJ, MP and ML analyses E. galea, whose macronucleic position and shape are distinctly different from those of the other five species, was probably diverged from the ancestor of Epistylis earlier than the other five species. The topology in which E. plicatilis and E, hentscheli formed a strongly supported sister clade to E. urceolata, E. chrysemydis, and E. wenrichi was consistent with variations in the thickness of the peristomial lip. We concluded that the macronucleus and peristomial lip might be the important phylogenetic characteristics within the genus Epistylis.

White electroluminescence from a poly(N-vinylcarbazole) layer doped with CdSe/CdS core-shell quantum dots

Hybrid organic/inorganic white light-emitting diodes (LEDs) were fabricated of semiconductor polymer poly(N-vinylcarbazole) (PVK) doped with CdSe/CdS core-shell semiconductor quantum dots (QDs). The device, with a structure of indium-tin-oxide (ITO)vertical bar 3,4-polyethylene-dioxythiophene- polystyrene sulfonate (PEDOT:PSS)vertical bar PVK:CdSe/CdS vertical bar Al, emitted a pure white light spanning the whole visible region from 400 to 800 nm. The Commission Internationale del'Eclairage coordinates (CIE) remained at x = 0.33, y = 0.34 at wide applied voltages. The maximum brightness and electroluminescence (EL) efficiency reached 180 cd m(-2) at 19 V and 0.21 cd A(-1) at current density of 2 mA cm(-2), respectively. The realization of the pure white light emission is attributed to the incomplete energy and charge transfer from PVK to CdSe/CdS core-shell QDs.

Effects of wall temperature on boundary layer stability over a blunt cone at Mach 7.99

Effects of wall temperature on stabilities of hypersonic boundary layer over a 7-degree half-cone-angle blunt cone are studied by using both direct numerical simulation (DNS) and linear stability theory (LST) analysis. Four isothermal wall cases with Tw/T0= 0.5, 0.7, 0.8 and 0.9, as well as an adiabatic wall case are considered. Results of both DNS and LST indicate that wall temperature has significant effects on the growth of disturbance waves. Cooling the surface accelerates unstable Mack II mode waves and decelerates the first mode (Tollmien–Schlichting mode) waves. LST results show that growth rate of the most unstable Mack II mode waves for the cases of cold wall Tw/T0=0.5 and 0.7 are about 45% and 25% larger than that for the adiabatic wall, respectively. Numerical results show that surface cooling modifies the profiles of rdut/dyn and temperature in the boundary layers, and thus changes the stability haracteristic of the boundary layers, and then effects on the growth of unstable waves. The results of DNS indicate that the disturbances with the frequency range from about 119.4 to 179.1 kHz, including the most unstable Mack modes, produce strong mode competition in the downstream region from about 11 to 100 nose radii. And adiabatic wall enhances the amplitudes of disturbance according to the results of DNS, although the LST indicates that the growth rate of the disturbance of cold wall is larger. That because the growth of the disturbance does not only depend on the development of the second unstable mode.

Ultrabroadband infrared luminescence and optical amplification in bismuth-doped germanosilicate glass

This letter reports the ultrabroadband infrared luminescence from 1000- to 1700-nm wavelength range and demonstrate optical amplification at the second optical communication window in a novel bismuth-doped germanosilicate glass. The full-width at half-maximum of the luminescence is about 300 mn and the optical gain is larger than 1.37 within the wavelength region from 1272 to 1348 nm with pump power 0.97 W. This material could be useful to fabricate ultrabroadband optical fiber amplifiers.

Molecular basis of albinism in the rhesus monkey

Sequence analysis of the tyrosinase (TYR) coding region from one albino rhesus monkey (Macaca mulatta) family revealed that the two monkeys with phenotype similar to human TYR-negative oculocutaneous albinism (OCA) were homozygous for a missense mutation (S184TER) in exon 1 at codon 184. The offspring of one of the albino monkey (''Kangkang'') are all heterozygous for the S184TER mutation, but the S184TER mutation was not observed in 93 control individuals. We conclude that the point mutation is responsible and sufficient to generate the albino rhesus monkey phenotype. The rough age of the S184TER nonsense mutation may be about 0.8 million years using a rate of 0.16% per million years. (C) 2000 Elsevier Science B.V. All rights reserved.

Mitochondrial diversity and phylogeographic structure of Chinese domestic goats

China has numerous native domestic goat breeds, but so far there has been no extensive study on genetic diversity, population demographic history, and origin of Chinese goats. Here, we examined the genetic diversity and phylogeographic structure of Chinese domestic goats by determining a 481-bp fragment of the first hypervariable region of mitochondrial DNA (mtDNA) control region from 368 individuals representing 18 indigenous breeds. Phylogenetic analyses revealed that there were four mtDNA lineages (A-D) identified in Chinese goats, in which lineage A was predominant, lineage B was moderate, and lineages C and D were at low frequency. These results further support the multiple maternal origins of domestic goats. The pattern of genetic variation in goat mtDNA sequences indicated that the two larger lineages A and B had undergone population expansion events. In a combined analysis of previously reported sequences and our sequences belonging to lineage B, we detected two subclades, in which one was unique to eastern Asia and another was shared between eastern and southern Asia. A larger genetic variation in eastern Asia than southern Asia and the pattern of phylogeographic variation in lineage B suggest that at least one subclade of lineage B originated from eastern Asia. There was no significant geographical structuring in Chinese goat populations, which suggested that there existed strong gene flow among goat populations caused by extensive transportation of goats in history. (c) 2005 Elsevier Inc. All rights reserved.