Identification of novel SINEs from Cyprinidae and their evolutionary significance

Short interspersed nuclear elements (SINEs) are widespread among eukaryotic genomes. They are repetitive DNA sequences that have been amplified by retrotransposition. In this study, a class of SINEs were isolated from the Opsariichthys bidens genome, and named Opsar. Sequence analysis confirmed that Opsar is a new class of typical SINEs derived from tRNA molecules. With the tRNA-derived region of Opsar and through BLASTN search, we further identified Zb-SINEs from the zebrafish genome, which includes two groups: Zb-SINE-A and Zb-SINE-B. The Zb-SINE-A group comprises subfamilies of -Al--A5, and the Zb-SINE-B group is a dimer of the tRNA(Ala)-derived region and shares a similar dimeric composition to Alu. Zb-SINEs are composed of three distinct regions: a 5 end tRNA-derived region, a tRNA-unrelated region and a 3 end AT-rich region. The flanking regions are AT rich. The average length of Zb-SINEs elements is about 340 6p. Zb-SINEs account for as much as 0.1% of the whole zebrafish genome. About 70% of the Zb-SINEs are on chromosomes 11, 18, and 19. These Zb-SINEs were characterized by PCR and dot hybridization. The distribution pattern of Zb-SINEs in genome strongly supports the master genes model. The tRNA-derived regions of Opsar and Zb-SINEs were compared with the tRNA(Ala) gene, and they showed 76% similarity, indicating that Opsar and Zb-SINEs originated from an inactive tRNA(Ala) sequence or a tRNA(Ala)-like sequence. In view of the evolutionary status of zebrafish in the Cyprinidae, we deduced that Zb-SINEs were a very old class of interspersed sequences.

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.

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.

Retroposon analysis of major cetacean lineages: The monophyly of toothed whales and the paraphyly of river dolphins

SINE (short interspersed element) insertion analysis elucidates contentious aspects in the phylogeny of toothed whales and dolphins (Odontoceti), especially river dolphins. Here, we characterize 25 informative SINEs inserted into unique genomic loci during evolution of odontocetes to construct a cladogram. and determine a total of 2.8 kb per taxon of the flanking sequences of these SINE loci to estimate divergence times among lineages. We demonstrate that: (i) Odontocetes are monophyletic; (ii) Ganges River dolphins, beaked whales, and ocean dolphins diverged (in this order) after sperm whales; (iii) three other river dolphin taxa, namely the Amazon, La Plata, and Yangtze river dolphins, form a monophyletic group with Yangtze River dolphins being the most basal; and (iv) the rapid radiation of extant cetacean lineages occurred some 28-33 million years B.P., in strong accord with the fossil record. The combination of SINE and flanking sequence analysis suggests a topology and set of divergence times for odontocete relationships, offering alternative explanations for several long-standing problems in cetacean evolution.

Nuclear potential and fusion cross sections for synthesizing super-heavy elements in di-nuclear systems

A double folding method with simplified Skyreme-type nucleon-nucleon interaction is used to calculate the nuclear interaction potential between two nuclei. The calculation is performed in tip-to-tip orientation of the two nuclei if they are deformed. Based on this methods, the potential energy surfaces, the fusion probabilities and the evaporation residue cross sections for some cold fusion reactions leading to super-heavy elements within di-nuclear system model are evaluated. It is indicated that after the improvement, the exponential decreasing systematics of the fusion probability with increasing charge number of projectile on the Pb based target become better and the evaporation residue cross sections are in better agreement with the experimental data.

Passive Q-switching of short-length Tm3+-doped silica fiber lasers by polycrystalline Cr2+:ZnSe microchips

We demonstrate passive Q-switching of short-length double-clad Tm3+-doped silica fiber lasers near 2 mu m pumped by a laser diode array (LDA) at 790 nm. Polycrystalline Cr2+:ZnSe microchips with thickness from 0.3 to 1 mm are adopted as the Q-switching elements. Pulse duration of 120 ns, pulse energy over 14 mu] and repetition rate of 53 kHz are obtained from a 5-cm long fiber laser. As high as 530 kHz repetition rate is achieved from a 50-cm long fiber laser at similar to 10-W pump power. The performance of the Q-switched fiber lasers as a function of fiber length is also analyzed. (c) 2008 Elsevier B.V. All rights reserved.

Identification of a putative oocyte-specific small nuclear ribonucleoprotein polypeptide C in gibel carp

Previous studies have demonstrated that germinal vesicle of amphibian oocyte contains small nuclear ribonucleoprotein polypeptide C (SNRPC). In this study, a putative member of SNRPC was identified from Carassius auratus gibelio oocyte cDNA library. Its full-length cDNA has an open reading frame of 201 nt for encoding a peptide of 66 an, a short 5'-UTR of 19 nt and a long 3'-UTR of 347 nt including a polyadenylation signal and poly- (A) tail, and the deduced amino acid sequence has 47% identity with the C-terminal of the zebrafish small nuclear ribonucleoprotein polypeptide C. Western blot analysis revealed its oocyte-specific expression. Immunofluorescence localization indicated that its gene product localized to numerous nucleoli within the oocytes and showed dynamic changes with the nucleoli during oocyte maturation. RT-PCR and Western blot analysis further revealed its constant presence in the oocytes and in the embryos until hatching. The data suggested that the newly identified CagOSNRPC might be a nucleolar protein. (c) 2006 Elsevier Inc. All rights reserved.

Tandem electroabsorption modulators integrated with DFB laser by ultra-low-pressure selective-area-growth MOCVD for 10 GHz optical short pulse generation

　

10 GHz optical short pulse generation using tandem electroabsorption modulators monolithically integrated with distributed feedback laser by ultra-low-pressure selective area growth

In this work, a novel light source of tandem InGaAsP/InGaAsP multiple quantum well electroabsoption modulator( EAM ) monolithically integrated with distributed feedback laser is fabricated by ultra-low-pressure ( 22 x 10(2) Pa ) selective area growth metal-organic chemical vapor diposition technique. Superior device performances have been obtained, such as low threshold current of 19 mA, output light power of 4.5 mW, and over 20 dB extinction ratio at 5 V applied voltage when coupled into a single mode fiber. Over 10 GHz 3dB bandwidth in EAM part is developed with a driving voltage of 2 V. Using this sinusoidal voltage driven integrated device, 10 GHz repetition rate pulse with an actual width of 13.7 ps without any compression elements is obtained due to the gate operation effect of tandem EAMs.

Tandem electroabsorption modulators integrated with DFB laser by ultra-low-pressure selective-area-growth MOCVD for 10 GHz optical short pulse generation - art. no. 60200O

A novel device of tandem multiple quantum wells (MQWs) electroabsorption modulators (EAMs) monolithically integrated with DFB laser is fabricated by ultra-low-pressure (22 mbar) selective area guowth (SAG) MOCVD technique. Experimental results exhibit superior device characteristics with low threshold of 19 mX output light power of 4.5 mW and over 20 dB extinction ratio when coupled into a single mode Fiber. Moreover, over 10 GHz modulation bandwidth is developed with a driving voltage of 2 V. Using I this sinusoidal voltage driven integrated device, 10GHz repetition rate pulse with a width of 13.7 ps without any compression elements is obtained.

Picosecond ultra-wideband short pulse radiated by antenna arrays

This report presents the experiments to study the characteristics of the picosecond ultra-wideband pulses coherent radiation. The testing involves bow-tie horn antennas for both the transninting and receiving antenna. Sixteen channels of electrical pulses with 290 ps duration and jitter < 30 ps have been used. The antenna arrays with various frames of 4 x 1, 4 x 2, 4 x 3, 4 x 4 are employed to radiate the pulses. The receiving antenna measures the electrical field in different distance front the transmitting antennas arrant The results show that if the pulses are in coherent condition, the peak power pulse of output by antennas array with N elements are N-2 of that of the single element antenna. (c) 2007 Wiley Periodicals, Inc.

Alpha decay half-lives of new superheavy elements through quasimolecular shapes

The lifetimes of alpha decays of the recently produced isotopes of the elements 112, 114, 116 and the element (294)118 and of some decay products have been calculated theoretically within the Wentzel-Kramers-Brillouin approximation. The alpha decay barriers have been determined in the quasimolecular shape path within a generalized liquid drop model including the proximity effects between nuclei in a neck, the mass and charge asymmetry and the precise nuclear radius. These calculations provide reasonable estimated for the observed alpha decay lifetimes. The calculated results have been compared with the results of the density-dependent M3Y effective interaction and the experimental data. It is indicated that the theoretical foundation of the generalized liquid drop model is as good as that of the microscopic DDM3Y model, at least in the sense of predicting the T-1/2 values as long as one uses a correct alpha decay energy. The half lives of these new nuclei are well tested from the consistence of the macroscopic, the microscopic and the experimental data.

The Main Path to C, N, O Elements in Big Bang Nucleosynthesis

The production of C, N, O elements in a standard big bang nucleosynthesis scenario is investigated. Using the up-to-date data of nuclear reactions in BBN, in particular the Li-8 (n, gamma) Li-9 which has been measured in China Institute of Atomic Energy, a full nucleosynthesis network calculation of BBN is carried out. Our calculation results show that the abundance of C-12 is increased for an order of magnitude after addition of the reaction chain Li-8(n, gamma) Li-9(alpha, n) B-12(beta) C-12, which was neglected in previous studies. We find that this sequence provides the main channel to convert the light elements into C, N, O in standard BBN.

Improvement of a Fission-Like Model for Nuclear alpha Decay

The alpha decay constant is the product of the penetrability P and assault frequency nu(0) in the fission-like model. An effective assault frequency P-nu replacing the previous assault frequency nu(0) is introduced for improvement of a fission-like model named the generalized liquid drop model (GLDM) to describe the nuclear alpha decay process more accurately. Two analytical formulae are proposed for the effective assault frequency due to experimental data within the GLDM. The improved model can be used to give accurate calculations for alpha decay half-lives.