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.

Genomic organization, nucleotide sequence analysis of the core histone genes cluster in Chlamys farreri and molecular evolution assessment of the H2A and H2B

This work represents the nucleotide sequence of the core histone gene cluster from scallop Chlamys farreri. The tandemly repeated unit of 5671 bp containing a copy of the four core histone genes H4, H2B, H2A and H3 was amplified and identified by the techniques of homology cloning and genomic DNA walking. All the histone genes in the cluster had the structures in their 3' flanking region which related to the evolution of histone gene expression patterns throughout the cell cycle, including two different termination signals, the hairpin structure and at least one AATAAA polyadenylation signal. In their 5' region, the transcription initiation sites with a conserved sequence of 5'-PyATTCPu-3' known as the CAP site were present in all genes except to H2B, generally 37-45 bp upstream of the start code. Canonical TATA and CAAT boxes were identified only in certain histone genes. In the case of the promoters of H2B and H2A genes, there was a 5'-GATCC-3' element, which had been found to be essential to start transcription at the appropriate site. After this element, in the promoter of H2B, there was another sequence, 5'-GGATCGAAACGTTC-3', which was similar to the consensus sequence of 5'-GGAATAAACGTATTC-3' corresponding to the H2B-specific promoter element. The presence of enhancer sequences (5'-TGATATATG-3') was identified from the H4 and H3 genes, matching perfectly with the consensus sequence defined for histone genes. There were several slightly more complex repetitive DNA in the intergene regions. The presence of the series of conserved sequences and reiterated sequences was consistent with the view that mollusc histone gene cluster arose by duplicating of an ancestral precursor histone gene, the birth-and-death evolution model with strong purifying selection enabled the histone cluster less variation and more conserved function. Meanwhile, the H2A and the H2B were demonstrated to be potential good marks for phylogenetic analysis. All the results will be contributed to the characterization of repeating histone gene families in molluscs.

Chromosomal in situ hybridization of Cyprinus carpio genomic DNA repetitive sequence CR1

Common carp Cyprinus carpio genomic DNA repetitive sequence CR1 has been DIG-labeled and hybridized in situ against chromosomes of red common carp (Cyprinus carpio L. Xingguo red var.). It is found that the repetitive sequence CR1 is mainly localized at the centromeric regions of chromosomes of the red common carp, The application of the chromosomal in situ hybridization technique on fish and the relationship between CR1 repetitive sequence distribution and its function have been discussed.

麂属动物以及六带犰狳DNA重复序列家族的克隆、序列分析和染色体定位

1．黑麂和费氏麂卫星DNA的克隆、序列分析和染色体定位 麂属动物在很短的时间内经历了快速的物种辐射，并且种间染色体数目存在巨大差异，是研究动物核型进化和物种起源的理想模型。近二十年来的分子细胞遗传学研究已基本上证实染色体串联融合(端粒－着丝粒融合)是麂属动物核型演化的主要染色体重排方式。尽管染色体串联融合的分子机制仍不清楚，但研究提示着丝粒区域的卫星DNA可能介导染色体的非同源重组。因此，着丝粒卫星DNA的克隆、分析序列以及染色体定位研究不仅有助于阐明麂属染色体核型演化规律，还可能揭示染色体串联融合的分子机制。迄今为止，上述研究工作已经在赤麂、小麂和小麂台湾亚种开展过。但是，尚无有关黑麂、费氏麂和贡山麂卫星 DNA 克隆、序列分析以及染色体定位研究的报道。 在本研究中，我成功地克隆了黑麂的卫星DNA I、II和IV，分别命名为BMC5、BM700和BM1.1k，并且从费氏麂中克隆了卫星DNA II，命名为FM700。对这些卫星DNA克隆进行序列分析，并将这些克隆探针分别与黑麂、费氏麂、贡山麂和小麂的染色体杂交。研究结果表明： 1)黑麂的卫星DNA I(BMC5)与小麂卫星DNA I(C5)序列高度相似，并且在小麂、黑麂、费氏麂和贡山麂染色体上的大部分串联融合位点处均有分布，因此卫星DNA I可能代表着染色体发生串联融合后保存下来，来源于麂属动物祖先染色体着丝粒的一种卫星DNA。卫星DNA I在这四种麂属动物染色体上的分布也表明黑麂、费氏麂和贡山麂与赤麂的核型演化过程相似，很可能从一个2n ＝ 70的共同祖先通过一系列的串联易位进化而来。 2) 将卫星DNA II（BM700和FM700）克隆探针分别杂交到黑麂和费氏麂的染色体上，只检测到几对间隔分布的信号。这提示在核型进化过程中不同卫星DNA间可能发生了广泛的重组，从而导致卫星DNA II大量丢失。大部分重组断裂位点可能位于卫星DNA I 与卫星DNA II之间，或者在卫星DNA II 区域内。 2．六带犰狳重复序列家族的克隆、序列分析和染色体定位 六带犰狳属于犰狳科、贫齿目，是六带犰狳属中唯一的一个代表物种。系统发育研究认为贫齿目与非洲兽总目是有胎盘哺乳动物中最原始的两个类群。C显带结果揭示六带犰狳30%的基因组是由组成性异染色质构成的，并且C带分布的位置也较复杂，提示在六带犰狳基因组中存在多种重复序列元件。 为了研究六带犰狳异染色质的组成，我从六带犰狳的基因组中克隆了七种位点特异性的重复序列。根据测序结果以及它们在染色体上的分布，将这些重复序列分为五个重复序列家族。其中AMD-EcoRI 837与AMD-BglII 811的序列相似，都是由大小约116 bp的单位组成，分布在大多数染色体的着丝粒区域，同时在一些染色体臂也有分布。AMD-EcoRI 832，AMD-EcoRI 836和AMD-EcoRI 934是特定染色体的重复序列，并且都分布于着丝粒区域。另外，AMD-BglII 634，AMD-EcoRI 731两个克隆都属于长散在分布重复序列(L1)，倾向于分布在G带阳性、富含AT碱基的区域，并且这两种重复序列在染色体上的定位与C带阳性的非着丝粒的异染色质区域很相似。本研究提供了六带犰狳异染色质区域的部分基因组信息，并且这些重复序列家族也可以用于研究六带犰狳及其近缘物种的系统发育关系。

Reduction Approaches for Vibration Control of Repetitive Structures

The reduction approaches are presented for vibration control of symmetric, cyclic periodic and linking structures. The condensation of generalized coordinates, the locations of sensors and actuators, and the relation between system inputs and control forces are assumed to be set in a symmetric way so that the control system posses the same repetition as the structure considered. By employing proper transformations of condensed generalized coordinates and the system inputs, the vibration control of an entire system can be implemented by carrying out the control of a number of sub-structures, and thus the dimension of the control problem can be significantly reduced.

Molecular Dynamics Simulation of Peeling a DNA Molecule on Substrate

Molecular dynamics (MD) simulations are performed to study adhesion and peeling of a short fragment of single strand DNA (ssDNA) molecule from a graphite surface. The critical peel-off force is found to depend on both the peeling angle and the elasticity of ssDNA. For the short ssDNA strand under investigation, we show that the simulation results can be explained by a continuum model of an adhesive elastic band on substrate. The analysis suggests that it is often the peak value, rather than the mean value, of adhesion energy which determines the peeling of a nanoscale material.

Static shape control of repetitive structures integrated with piezoelectric actuators

In this paper, several simplification methods are presented for shape control of repetitive structures such as symmetrical, rotational periodic, linear periodic, chain and axisymmetrical structures. Some special features in the differential equations governing these repetitive structures are examined by considering the whole structures. Based on the special properties of the governing equations, several methods are presented for simplifying their solution process. Finally, the static shape control of a cantilever symmetrical plate with piezoelectric actuator patches is demonstrated using the present simplification method. The result shows that present methods can effectively be used to find the optimal control voltage for shape control.

Investigation on Depth of Heat Affected Zone of Discharge Spot by High Repetitive Rate YAG Laser-Induced Discharge Texturing

It is known that the press formability and the elongation of laser textured sheet are improved, and the service life of textured roll is longer than that of the un-textured roll due to hardening of the treated surface. One of the goals to develop high repetitive rate YAG laser-induced discharge texturing (LIDT) is to get deeper hardening zone. By observing and measuring cross-section of LIDT spots in different discharge conditions, it is found that the single-crater, which is formed by the discharge conditions of anode, which is covered by an oil film and with rectangular current waveform, has the most depth of heat affected zone (HAZ) comparing with other crater shapes when discharge energy is the same. The depth of HAZ is mainly depends on pulse duration when the discharge spot is single-crater. The results are analyzed.

Metric representation of DNA sequences

A metric representation of DNA sequences is borrowed from symbolic dynamics. In view of this method, the pattern seen in the chaos game representation of DNA sequences is explained as the suppression of certain nucleotide strings in the DNA sequences. Frequencies of short nucleotide strings and suppression of the shortest ones in the DNA sequences can be determined by using the metric representation.

Recurrence plot analysis of DNA sequences

Recurrence plot technique of DNA sequences is established on metric representation and employed to analyze correlation structure of nucleotide strings. It is found that, in the transference of nucleotide strings, a human DNA fragment has a major correlation distance, but a yeast chromosome's correlation distance has a constant increasing. (C) 2004 Elsevier B.V All rights reserved.