Substitution Matrices of Residue Triplets Derived from Protein Blocks.

In protein sequence alignment, residue similarity is usually evaluated by substitution matrix, which scores all possible exchanges of one amino acid with another. Several matrices are widely used in sequence alignment, including PAM matrices derived from homologous sequence and BLOSUM matrices derived from aligned segments of BLOCKS. However, most matrices have not addressed the high-order residue-residue interactions that are vital to the bioproperties of protein.With consideration for the inherent correlation in residue triplet, we present a new scoring scheme for sequence alignment. Protein sequence is treated as overlapping and successive 3-residue segments. Two edge residues of a triplet are clustered into hydrophobic or polar categories, respectively. Protein sequence is then rewritten into triplet sequence with 2 · 20 · 2 = 80 alphabets. Using a traditional approach, we construct a new scoring scheme named TLESUMhp (TripLEt SUbstitution Matrices with hydropobic and polar information) for pairwise substitution of triplets, which characterizes the similarity of residue triplets. The applications of this matrix led to marked improvements in multiple sequence alignment and in searching structurally alike residue segments. The reason for the occurrence of the ‘‘twilight zone,’’ i.e., structure explosion of lowidentity sequences, is also discussed.

川西青杨组(Section Tacamahaca Spach)不同种的亲缘关系分析

青杨组（Section Tacamahaca Spach）杨树是我国重要的乡土经济树种，目前对其分子遗传变异和系统进化的研究还很少，尤其是在青杨组杨树遗传资源极为丰富的川西地区，杨树的分子进化及亲缘关系的研究极为缺乏，非常不利于该树种遗传资源的开发和利用。本研究从川西地区收集了青杨（Populus cathayana）、青海杨（P. prezewalskii）、滇杨（P. yunnanensis）、康定杨（P. kangdingensis）、西南杨（P. schneideri）、小叶杨（P.simonii）和三脉青杨（P. trinervis）这7 个青杨组树种的10 个群体，利用多种分子标记手段对其种间的亲缘关系进行比较，并结合形态和地史资料进行了全面的研究和评价，得到了如下的主要研究结果： 1. SSR 和ISSR 位点变异丰富。通过10 对引物对50 个杨树个体的DNA 样品进行了SSR 分析，所有位点展现了丰富的群体间和种间的多态性，多态位点率达到了100%，每位点的等位基因数变化范围为5 ~ 17，平均为11.9 个；通过11 条ISSR 随机引物对供试的混合DNA 样品进行分析，共检测到130 个标记，其中多态性标记为119 个，多态百分率为91.5%。研究认为，SSR 单个标记能展现高水平信息，而ISSR 单个引物能探测更多数量多态性。通过两个标记的遗传距离、聚类图和PCA 分析，表明：同一种内不同群体间的同源性最高；康定杨和西南杨有较近的亲缘关系；小叶杨和三脉青杨聚合在一起，显示了其相互较近的亲缘关系；滇杨与其它杨树种可能存在着较远的亲缘关系。 2. 采用4 对选择性引物对7 个青杨组杨树种10 个群体进行AFLP 分析，总共扩增出284 个位点，其中200 个位点显示出了多态性，多态位点百分比为70.4%，平均多态带为50 条。TE-AFLP 的分析总共扩增出192 个位点，其中139 个位点显示出了多态性，多态位点百分比为72.4%，平均多态带为34.7 条。比较的结果表明AFLP、TE-AFLP 的遗传信息含量比较接近，略小于ISSR，大约仅为SSR 的1/3；但这两个基于AFLP 的标记系统的信息探察能力也远大于ISSR 和SSR 标记系统。这两个分子标记的聚类结果，显示小叶杨、三脉青杨和滇杨三个种聚为一组，其中小叶杨与三脉青杨的亲缘关系更近；其它几个杨树种聚为一类，西南杨与青杨表现出较近的亲缘关系。 3. 所有7 对cpSSR 引物中，仅有4 个叶绿体位点在种间具有多态性，而在种内群体中并不具有多态性，共检测出13 个条带，组合成了4 种不同的单倍型；对于cpDNA的5 对引物，共检测出了73 条酶切片段，其中52 条是多态带，组合成了9 种不同的单倍型；而5 对mtDNA 通用引物未能检测出多态性的条带，表现出线粒体的保守性。叶绿体的聚类分析认为，小叶杨、三脉青杨和滇杨有较近的母性起源，且依次聚合；其余四种杨树聚为一类，并且康定杨与西南杨表现出最近的亲缘关系，并依次与青杨和青海杨聚合。 4. 根据本文的分子数据，结合形态和生境分布资料分析认为：青杨组杨树种内群体间的遗传变异程度是小于种间的遗传差异，显示了与传统分类一致的结果；三脉青杨和小叶杨有很近的亲缘关系，可能拥有相同的祖先类群；滇杨与小叶杨和三脉青杨之间具有一定的亲缘关系，特别是在其母性祖先的起源上有着一定的同源性；西南杨与青杨和康定杨均保持着较近的亲缘关系，且有可能是这两个种原始祖先杂交后所形成的。 Although western Sichuan is regarded as a natural distribution and variation center forthe Section Tacahamaca of the Populus species in China, little is currently known about themajority of poplar species occurring in this region. In the present study, molecular data wereutilized to determine the genetic relationships among Populus species in Section Tacamahacain western Sichuan including P. cathayana, P. prezewalskii, P. yunnanensis, P. kangdingensis,P. schneideri, P. simonii and P.trinervis. The results are as fellows: 1. The genetic variation at SSR and ISSR loci was abundant. All the 10 SSR loci werepolymorphic, and the number of alleles per locus varied from 5 to 17 with a mean valueequaling 11.9. Based on the 11 ISSR primers, 130 clear and reproducible DNA fragmentswere generated, of which 119 (91.5%) were polymorphic. Our results reveal that single SSRlocus can present more genetic information, while more polymorphic bands can be detectedby single ISSR primer. Moreover, the genetic distance, cluster and PCA analysisdemonstrated that: a close relationship among accessions of the same species and suggestedmonophyly in P. przewalskii and P. cathayana; P. schneideri is genetically highly similar to P.kangdingensis; P. trinervis and P. simonii have a close genetic affinity; P. yunnanensis isdistinct from the other species. 2. Genetic relationships of poplar species in Section Tacamahaca from western Sichuanwere evaluated by means of AFLP and TE-AFLP. For four AFLP primer combinations, atotal of 284 bands were obtained of which 200 (70.4%) were polymorphic with the average of50 polymorphic bands. For four TE-AFLP primer combinations, a total of 192 band wereobtained of which 139 (72.4%) were polymorphic with the average of 34.7 polymorphicbands. Our results indicate that the genetic information of AFLP is similar to that ofTE-AFLP, and little less than that of ISSR, but only about 1/3 of that of SSR. However, theability of information detection of the two AFLP-based markers is much higher than that ofISSR and SSR. In addition, the cluster analysis of AFLP, TE-AFLP and combined data revealthat: P. yunnanensis, P. trinervis and P. simonii clustered together, and P. trinervis and P.simonii showed more closed affinity; the other four poplar species clustered together, P.cathayana and P. schneideri showed more closed origin especially. 3. The cpSSR analysis for seven Populus species belonging to the Section Tacamahaca.Four out of the seven analyzed chloroplast loci were polymorphic, whereas none of the lociwere polymorphic across the accessions within a species. 13 bands and 4 different kinds ofhaplotypes were reduced. Based on 5 pairs of cpDNA primers, 73 fragments (52 polymorphic)and 9 kinds of haplotypes were produced. However, none of the polymorphic was detected bythe 5 mtDNA primer pairs, revealing conservation of mtDNA region. The cluster analysis ofcpDNA revealed that: similar maternal phylogeny among P. yunnanensis, P. trinervis and P.simonii; the other four species clustered together, P. schneideri and P. kangdingensis showedmore closed maternal lineage especially. 4. Our molecular data, morphological characters and nature habitat revealed that: sameto the traditional taxonomy assignment, genetic variation within a same Populus species islower than that among Populus species in Section Tacamahaca; P. yunnanensis may share itschloroplast ancestor with P. trinervis and P. simonii; moreover, sister genetic relationship of P.trinervis and P. simonii indicated their similar origin; P. schneideri clustered with P.kangdingensis and P. cathayana, respectively, and may have derived from an ancienthybridization event involving the ancestors of the two species.

香港地区湍蛙遗传多样性研究

依据线粒体上ND2和CO1两个变异较大的基因序列分析了香港地区香港湍蛙7种群、华南湍蛙1种群，以及大陆其他地区华南湍蛙7种群，戴云湍蛙1种群，武夷湍蛙1种群的系统发育关系，进而探讨香港湍蛙的遗传多样性、香港湍蛙特有性、如何确定香港湍蛙最佳保护单元以及这四种湍蛙的物种分类地位。 1． 香港湍蛙保护遗传学研究 香港湍蛙核苷酸传多样性较低，从其遗传多样性信息、单倍型网络分析、中性检验值以及岐点分布结果一致显示香港湍蛙很可能经历了瓶颈后的扩张，种群正在由一个较小的有效种群大小迅速增长, 有足够的时间通过变异用于积累单倍型的多态性, 而对于提高核苷酸多样化而言, 时间尚短（Nei M et al，1975，Avise J C，2000；李明等，2003）。 分子变异分析结果显示香港湍蛙种群间存在较多的基因交流，且系统发育树上各种群间交叉在一起，没有形成与地理单元相关的分支，而从其单倍型网络看，他们源于共同的祖先，是一个单系群，与地理单元间没有形成显著的遗传分化。因此应作为一个进化显著单元（ESU）。结合其与其他湍蛙发育关系及遗传距离以及野外采集信息认为香港湍蛙只在香港地区有分布，属于香港特有种。该物种内遗传多样性较低，又属于世界自然保护联盟红皮书中的近危种，同时也是《野生动物保护条例》中的受保护野生动物，且由于香港城市建设等使得其栖息环境受到威胁，因此在香港特别行政区应该受到重点保护。 从单倍型分布和核苷酸多样性可以看出大榄涌种群和城门种群具有较高的单倍型多样性和核苷酸多样性，应该作为保护的重点区域。 2. 华南湍蛙东、南沿海种群间系统关系 华南湍蛙分布广，各种群存在着丰富的遗传多样性信息且中部种群广西龙胜和湖南张家界种群核苷酸多样性明显高于其他边缘种群华南湍蛙。种群间几乎没有基因交流，且各种群间无共享单倍型，可见已形成了显著的遗传分化。各种群间遗传距离都较远，其中广东南昆山种群以及福建三港种群与其他种群距离最远，因此可以推测其他种群（广东深圳、香港大屿山、广西龙胜和防城以及湖南张家界种群）可能为独立进化的种群。但是否是一新种或一隐存种，还需要结合形态学进行更深入的研究。 本研究中无论从系统关系看还是从遗传距离看，大屿山种群与深圳种群最近，支持陈坚峰等将其定为华南湍蛙，即华南湍蛙新增一个分布点：香港大屿山。 系统树上广西防城种群（支B）与龙胜和湖南种群（支A）形成姐妹群。香港大屿山种群与深圳种群先形成姐妹群（支C），但却没有与其距离很近的广东南岭及南昆山种群（支D）形成姐妹群，可能粤北和粤中的环境及气候较复杂因此与粤南其他种群形成了明显的隔离。同时可以看出华南湍蛙种群遗传分化与地理距离没有显著的相关性。 3. 四种湍蛙间的系统关系 根据线粒体CO1基因建立四种湍蛙间的系统关系及其遗传距离，很清楚地看到，香港湍蛙与戴云湍蛙关系很近，而华南湍蛙则与武夷湍蛙较近。然而，戴云湍蛙同一个种群内部共有两个单倍型DY1和DY2，且两个单倍型间遗传距离大于DY1与香港湍蛙间遗传距离，更远远大于香港湍蛙种群内部的距离，即戴云湍蛙内部两个单倍型间遗传距离达到了种级水平，同样在系统发育树上这两个单倍型与香港湍蛙形成并系。但是，戴云湍蛙种内在形态上差异不显著。因此，其是否属于萌芽物种分化形成（budding speciation）或已经完全分化为两个不同的种值得进一步研究？ 与戴云湍蛙香港湍蛙关系类似，从系统树上看华南湍蛙不形成单系，而是分成两个大支，与武夷湍蛙形成并系，且福建和南昆山的华南湍蛙与武夷湍蛙遗传距离远大于武夷湍蛙种内福建种群与浙江种群的遗传距离，达到了种级分化水平。由此，可以推断武夷湍蛙是有效种。系统树上广东深圳、香港大屿山、广西防城和龙胜以及湖南张家界种群与华南湍蛙福建及南昆山各种群间遗传距离已超出了种内各种群间的遗传距离，但是至于这一支是否应为另外一个种，有必要扩大采样，并结合核基因及形态信息进行进一步研究。 MtDNA of ND2 and CO1 gene were used to investigate genetic diversity of Amolops in Hongkong .We collected seven populations of A. hongkongensis,，one population of A.ricketti from Hong Kong and other seven populations of A.ricketti from East and South of Chinese mainland. As well as one population of A. daiyunensis and one population of A.wuyiensis Phylogenetic relationship were analyzed of four species. Discussed whether A.hongkongensis is an endemic species and how can we make the conservation and management decisions. 1. Conservation Genetics of A. hongkongensis A. hongkongensis has a low nucleotide diversity, the results of genetic diversity, haplotype network, neutrality test and the mismatch distributions indicate that A. hongkongensis experienced a recent expansion after a bottle neck. They had enough time to accumulated haplotype diversity, but it’s too short to have a high nucleotide diversity（Nei M et al，1975，Avise J C，2000；Li et al，2003）. The result of AMOVA reveals that it has much gene exchange among the populations of A. hongkongensis. The clades of the phylogenetic tree were mixed together, no significant genetic differentiation among 8 populations and they share the same ancestor from the network analysis, these indicate that they are monophyly and should be protected as one ESU. Combined with the information of relationships of interspecies, genetic distance and distribution investigate, We conclude that A. hongkongensis is an endemic species of Hong Kong. Considering on the status of low genetic diversity in A.hongkongensis, and this species was listed in the IUCN red list as near threatened, as well as listed in the . Furthermore, it’s habitat loss and degradation more rapidly as the human activity got higher and higher. So it’s urgent to protect them in Hong Kong. Our results suggest that Tai Lam Wu and TAI MO Shan -Shing Mun populations have the higher priority to be protected because their higher genetic diversity. 2．Phylogenetic relationships among populations of Amolops ricketti from the Southern and eastern China A. ricketti has the considerable genetic diversity of mitochondrial haplotypes within and among populations, and Mitochondrial DNA diversity was higher in populations at the central area of the present distribution range of the frog，i. e. the Longsheng population and Zhangjiajie population, than at the edges of their distribution range. They have no share haplotype among populations, and have a significant genetic differentiation. Genetic distance is high among the populations, especially the distance of Nankun and Sangang group with others, which suggested that they evolved independently. May be there is a cryptic species or a new species, a further study is needed. The results of gene tree and the genetic distance clearly demonstrate that the population from LanTau island is A. ricketti, so we agree with Chen et al(2005) . That means A.ricketti have a new distribution site: LanTau island, HongKong. Phylogenetic relationships were analyzed through NJ and Mrbayes methods and got a consistent topological structure, the structure indicated that the ingroup were comprised four groups. Populations Longsheng and Zhangjiajie were first clustered as clade A; Populations Fangcheng was clustered together (clade B) as a sister group to clade A；Populations Shenzhen and Lantau island were sister groups and clustered as clade C；Then the clade D included populations Nankunshan and Nanling in Guangdong province and Sangang in Fujian province. 3. Phylogenetic Relationships among these four specises Phylogenetic relationships based on 1503bp CO1 gene and the genetic distance show that A. hongkongensis close to A. daiyunensis whereas A.ricketti near to A.wuyiensis. Nevertheless, there are two haplotypes in A.daiyunensis and the genetic distance between them higher than the distance between DY1 with A. hongkongensis. A. hongkongensis is nested in the paraphyletic ancestral species A. daiyunensis. Without significant difference in the morphological characters, So, we considered both A.daiyunensis and A.hongkongensis are valid species, may be this represents a case of ‘budding speciation’ like Batrachuperus pinchonii(Fu and Zeng,2008) in the population of A. daiyunensis. Just like two species above A. wuyiensis and A. ricketti are not monophyly, instead, A.wuyiensis is nested in the paraphyletic ancestral species A.ricketti. We need do more research to make sure whether they are new species.

小麦中微量元素锌铁硒的含量的分析

本研究应用微波消解ICP-AES 法对62 个小麦品种及3 个地区土壤的锌铁硒含量进行了分析测定，发现不同小麦品种中微量元素含量差异很大，姊妹系间也存在差异。含铁量最高与最低的小麦品种铁含量相差29.68mg/kg。含锌量最高与最低的小麦品种锌含量相差46.70 mg/kg。含硒量最高与最低的小麦品种硒含量相差0.056 mg/kg。对不同地点的小麦及土壤中锌铁硒含量进行方差分析，发现双流和西昌两地种植小麦的铁含量和硒含量均有显著差异，西昌和荣县种植的锌含量有显著差异。在3 个地点中双流种植小麦硒含量最高，西昌种植小麦的铁和锌含量最高。 通过对小麦微量元素含量与土壤中微量元素含量进行了相关性分析，结果表明：小麦中的锌铁含量与土壤中的锌铁含量呈显著正相关，土壤中铁与锌含量呈极显著正相关，小麦中铁与锌含量也呈极显著正相关。随着土壤微量元素锌铁的提高，小麦中的锌铁元素含量同时提高，而且小麦对两种元素的吸收互相促进。土壤中的硒含量与锌铁含量呈负相关。小麦中硒含量也与锌铁含量也呈负相关。说明锌和铁与硒互相拮抗。小麦硒含量与土壤硒含量呈正相关，但不显著。表明土壤硒含量可以影响小麦硒含量，但不是决定因素，小麦硒含量与小麦自身因素有关。 对姊妹系G290（高硒含量）和G289（低硒含量）进行抗重金属胁迫和抗旱性实验发现，高硒品种G290的抗逆性优于低硒品种G289。 利用RAPD 技术对7 个姊妹系进行遗传差异分析发现，高硒材料G290出现了特异条带，分别标为1、2、3、4，其他姊妹系品种中未发现特异条带，回收4 条特异条带并连接转化，得到目的片段1、2、3 的重组子，进行测序。NCBI 中结果显示没有找到植物中的同源序列，说明特异序列可能是未发现的基因片段，推测可能与小麦硒含量有关，有待进一步研究。 以上研究结果，对小麦营养研究及功能性小麦的筛选和栽培具有指导作用。 In this study, we determinated the contents of zinc, iron, selenium in 62 wheat cultivars and soil samples of three regions by method of microwave digestion/ ICPAES,found that there was great difference of zinc, iron, selenium contents in different wheat cultivars as well as different sister lines. Iron content difference was 29.68 mg/kg between the highest-iron-content cultivar and the lowest one, and zinc content difference was 46.70 mg/kg , selenium content difference was 0.056 mg/kg. Anova analysis was made on contents of zinc, iron, selenium in wheat and soil samples of different locations, significant differences of Fe and Se contents were found between wheat in Shuangliu and Xichang, significant difference of Zn content was found between wheat in Xichang and Rongxian. Se content in wheat of Shuangliu was highest, Fe and Zn contents in wheat of Xichang were highest. Relativity analysis was made on three trace elements in Wheat and in soil, the result showed that there was significant positive correlation of zinc, iron content between in Wheat and in soil, as well as between Fe and Zn both in wheat and in soil. With the improving of Zn, Fe contents in soil, contents of Zn and Fe in wheat increased and absorption of Zn and Fe in wheat will mutual promote. Negative correlation of Se and Zn contents was found in wheat and soil, but not significant, that meant the antagonism of Se and Zn. Positive correlation of Se content in wheat and soil was found. High selenium content G290 and low selenium content G289 in sister lines were selected for heavy metal stress and drought resistance experiments, the result showed that the resistance of high-selenium-content cultivar was better than low selenium one. Analysis on genetic difference was made by RAPD, and specific bands were selected, marked 1,2,3,4, no more specific bands were found in other sister lines.4 bands were recovered, ligated to T-vector and transformed E.coli. Three recombinant plasmids were obtained and sequenced. NCBI Blast showed there was no homology with other plants. It implied that these fragments probably be new genes and maybe were related to selenium in wheat. It needs further research. This paper would be useful for the study of wheat nutrition as well as selection and cultivation of functional wheat.

γ射线诱导人卵巢癌细胞G2-染色单体断裂与修复

应用早熟染色体凝集技术研究了γ-射线诱导人卵巢癌细胞G2-染色单体断裂畸变的剂量效应与畸变修复的时间效应。结果表明:G2-染色单体型断裂畸变(chromatid-type breaks)与辐射剂量呈线性关系;G2-等点染色单体型断裂畸变(iso-chromatid breaks)与辐射剂量呈线性平方关系。2Gyγ-射线诱导的G2染色单体断裂畸变随着孵育时间的延长发生了明显的连接即修复,对G2-染色单体型断裂畸变,有近65％的断裂在辐射后24h内得以修复;对G2-等点染色单体型断裂,在辐射后24h内只有20％左右得以修复,两类断裂畸变的修复主要发生在辐射后2h内,在辐射后12-24h内染色体断裂量趋于稳定,表明修复基本完成。

Radiosensitivity of hepatoma cell lines and human normal liver cell lines exposed in vitro to carbon ions and argon ions at the HIRFL

Human hepatoma (SMMC-7721) and normal liver (L02) cells were irradiated with c-rays, 12C6+ and 36Ar18+ ion beams at the Heavy Ion Research Facility in Lanzhou (HIRFL). By using the Calyculin-A induced premature chromosome condensation technique, chromatid-type breaks and isochromatid-type breaks were scored separately. Tumor cells irradiated with heavy ions produced a majority of isochromatid break, while chromatid breaks were dominant when cells were exposed to c-rays. The relative biological effectiveness (RBE) for irradiation-induced chromatid breaks were 3.6 for L02 and 3.5 for SMMC-7721 cell lines at the LET peak of 96 keVlm 1 12C6+ ions, and 2.9 for both of the two cell lines of 512 keVlm 1 36Ar18+ ions. It suggested that the RBE of isochromatid-type breaks was pretty high when high-LET radiations were induced. Thus we concluded that the high production of isochromatid-type breaks, induced by the densely ionizing track structure, could be regarded as a signature of high-LET radiation exposure.

Comparison of clonogenic assay with premature chromosome condensation assay in prediction of human cell radiosensitivity

Aim: To determine whether the number of non-rejoining G2-chromatid breaks can predict the radiosensitivity of human cell lines. Methods: Cell lines of human ovary carcinoma cells (HO8910), human hepatoma cells (HepG2) and liver cells (L02) were irradiated with a range of doses and assessed both of cell survival and non-rejoining G2-chromatid breaks at 24 h after irradiation. Cell survival was documented by a colony assay. Non-rejoining G2-chromatid breaks were measured by counting the number of non-rejoining G2 chromatid breaks at 24 h after irradiation, detected by the prematurely chromosome condensed (PCC) technique. Results: A linear-quadratic survival curve was observed in three cell lines, and HepG2 was the most sensitive to gamma-radiation. A dose-dependent linear increase was observed in radiation-induced non-rejoining G2-PCC breaks measured at 24 h after irradiation in all cell lines, and HepG2 was the most susceptible to induction of non-rejoining G2-PCC breaks. A close correlation was found between the clonogenic radiosensitivity and the radiation-induced non-rejoining G2-PCC breaks (r=0.923). Furthermore, survival-aberration correlations for two or more than two doses lever were also significant. Conclusion: The number of non-rejoining G2 PCC breaks holds considerable promise for predicting the radiosensitivity of normal and tumor cells when two or more than two doses lever is tested.

Radiobiological response of human hepatoma and normal liver cells exposed to carbon ions generated by Heavy Ion Research Facility in Lanzhou

Human hepatoma and normal liver cells were irradiated with C-12(6+), ion beams (LET= 96.05 keV/mu m) and gamma-rays at Heavy Ion Research Facility in Lanzhou (HIRFL). The chromatid breaks and break types were detected using the premature chromosome condensation technique. Our experimental results showed that chromatid breaks seem to have a good relation with C-12(6+) absorbed dose and C-12(6+) are more effective to induce chromatid breaks as compared to they-rays. For C-12(6+) ion irradiation the major break was isochromatid break, while chromatid breaks were dominant for gamma-ray irradiation. We also observed that the Relative Biology Effectiveness (RBE) of C-12(6+) ion is about 2.5 times higher than that of gamma-rays.

Importance of self-consistency in relativistic continuum random-phase approximation calculations

A fully consistent relativistic continuum random phase approximation (RCRPA) is constructed, where the contribution of the continuum spectrum to nuclear excitations is treated exactly by the single-particle Green's function technique. The full consistency of the calculations is achieved that the same effective Lagrangian is adopted for the ground state and the excited states. The negative energy states in the Dirac sea are also included in the single-particle Green's function in the no-sea approximation. The currents from the vector meson and photon exchanges and the Coulomb interaction in RCRPA are treated exactly. The spin-orbit interaction is included naturally in the relativistic frame. Numerical results of the RCRPA are checked with the constrained relativistic mean-field theory. We study the effects of the inconsistency, particularly the currents and Coulomb interaction in various collective multipole excitations.

eta production off the proton in a Regge-plus-chiral quark approach

A chiral constituent quark model approach, embodying s- and u-channel exchanges, complemented with a Reggeized treatment for the t channel is presented. A model is obtained allowing data for pi(-)p ->eta n and gamma p ->eta p to be described satisfactorily. For the latter reaction, recently released data by the CLAS and CBELSA/TAPS Collaborations in the system total energy range 1.6 less than or similar to W less than or similar to 2.8 GeV are well reproduced by the inclusion of Reggeized trajectories instead of simple. and. poles. The contribution from "missing" resonances, with masses below 2 GeV, is found to be negligible in the considered processes.

A novel structure analysis method for lanthanide complex - None paramagnetic shift tri-lanthanide mixture method

A new structure analysis method for lanthanide complexes was proposed, that is, none paramagnetic shift tri-lanthanide mixture method, It was found that the paramagnetic induced shift could be cancelled by mixing three kinds of paramagnetic lanthanide ions in appropriate proportion. As a result, the chelating sites would he seen simplely from the half widths and the relative distances between lanthanide ion and the ligand nucleus could be calculated from the relaxation time (T-1) or the half width. Care should be addressed that the analysis method is suitable for the systems in which intramolecular arrangements and intermolecular ligand exchanges are relatively fasten NMR time scale used.

The complete mitochondrial genome sequence of the cutlassfish Trichiurus japonicus (Perciformes: Trichiuridae) : Genome characterization and phylogenetic considerations

Mitochondrial genome sequence and structure analysis has become a powerful tool for studying molecular evolution and phylogenetic relationships. To understand the systematic status of Trichiurus japonicus in suborder Scombroidei, we determined the complete mitochondrial genome (mitogenome) sequence using the long-polymerase chain reaction (long-PCR) and shotgun sequencing method. The entire mitogenome is 16,796 by in length and has three unusual features, including (1) the absence of tRNA(Pro) gene, (2) the possibly nonfunctional light-strand replication origin (O-L) showing a shorter loop in secondary structure and no conserved motif (5'-GCCGG-3'), (3) two sets of the tandem repeats at the 5' and 3' ends of the control region. The three features seem common for Trichiurus mitogenomes, as we have confirmed them in other three T. japonicus individuals and in T nanhaiensis. Phylogenetic analysis does not support the monophyly of Trichiuridae, which is against the morphological result. T. japonicus is most closely related to those species of family Scombridae; they in turn have a sister relationship with Perciformes members including suborders Acanthuroidei, Caproidei, Notothenioidei, Zoarcoidei, Trachinoidei, and some species of Labroidei, based on the current dataset of complete mitogenome. T japonicus together with T. brevis, T lepturus and Aphanopus carbo form a clade distinct from Lepidopus caudatus in terms of the complete Cyt b sequences. T. japonicus mitogenome, as the first discovered complete mitogenome of Trichiuridae, should provide important information on both genomics and phylogenetics of Trichiuridae. (C) 2009 Elsevier B.V. All rights reserved.

Genetic mechanisms of multi-antimicrobial resistance in a pathogenic Edwardsiella tarda strain

TX01, a pathogenic Edwardsiella tarda strain isolated from diseased fish at an epidemic-inflicted fish farm in China, exhibits resistance to multiple classes of antimicrobial agents. The genes (kn(R). catA3, and tet(A), respectively) encoding resistance to kanamycin, chloramphenicol, and tetracycline were cloned and found to be 99-100% identical to the corresponding genes carried by known plasmids and transposons of human, animal, and environmental isolates. Further study demonstrated that TX01 harbors a plasmid, pETX, which proved to be (i) the carrier of the tet and cut operons; (ii) a mobile genetic element that is capable of transferring between bacteria of different genera. These results, which, to our knowledge, documented for the first time the co-existence of chloramphenicol and tetracycline resistance determinants on a conjugative plasmid in a pathogenic E tarda strain, indicated that gene acquisition via horizontal transferring of pETX-like mobile genetic entities may have played an important part in the dissemination of antimicrobial resistance and that there have existed for some time widespread genetic exchanges between bacteria of human, animal/fish, and environmental origins. (C) 2008 Elsevier B.V. All rights reserved.

Phylogenetic studies on two strains of Antarctic ice algae based on morphological and molecular characteristics

The taxonomic characterization of two strains of Antarctic ice algae, Chlamydomonas sp. ICE-L and Chlamydomonas sp. ICE-W, were analyzed on the basis of morphological and molecular traits. The results indicate that they are the same species and belong to Chlamydomonas (Chlorophyta). According to I SS rDNA and ITS-I sequences they are very close relatives of Chlamydomonas sp. Antarctic 2E9, if not identified as such. They belong to the 'monadina clade', Cd. monadina and Cm. subdivisa as the sister group, on the basis of 18S rDNA sequence. They occur in 'Chlamydomonas clade' according to rbcL sequencing and are close relatives of Cd. kuwadae. The ITS sequences of ICE-L and ICE-W are 1302 base pairs and 1300 base pairs in length, the longest Volvocales ITS sequences ever reported.

Characteristics of water exchange in the Luzon Strait during September 2006

The Luzon Strait is the only deep channel that connects the South China Sea (SCS) with the Pacific. The transport through the Luzon Strait is an important process influencing the circulation, heat and water budgets of the SCS. Early observations have suggested that water enters the SCS in winter but water inflow or outflow in summer is quite controversial. On the basis of hydrographic measurements from CTD along 120 degrees E in the Luzon Strait during the period from September 18 to 20 in 2006, the characteristics of temperature, salinity and density distributions are analyzed. The velocity and volume transport through the Luzon Strait are calculated using the method of dynamic calculation. The major observed results show that water exchanges are mainly from the Pacific to the South China Sea in the upper layer, and the flow is relatively weak and eastward in the deeper layer. The net volume transport of the Luzon Strait during the observation period is westward, amounts to about 3.25 Sv. This result is consistent with historical observations.