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Phylogeny of fireflies (Coleoptera: Lampyridae) inferred from mitochondrial 16S ribosomal DNA, with references to morphological and ethological traits

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Progress in Natural Science:Materials International 2006年第8期16卷 817-826页

作者： LI Xueyan, YANG Shuang, XIE Meng and LIANG Xingcai (laboratory of Entomology, kunming institute of zoology, chinese academy of sciences, kunming 650223. china Key laboratory of cellular and molecular evolution, kunming institute of zoology, chinese academy of sciences, kunming 650223. china Graduate School of the chinese academy of sciences, Beijing 100039, china) [a]laboratory of Entomology Kunming Institute of Zoology Chinese Academy of Sciences Kunming China [b]Graduate School of the chinese academy of sciences Beijing China [c]Key laboratory of cellular and molecular evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China

We sequenced partial mitochondrial 16S ribosomal DNA (16S rDNA) of 18 firefly species from Southwest of china. Combined with homologous sequences previously reported, phylogenetic trees including Japanese, Korean and chinese species were reconstructed by neighbor-joining, maximum parsimony and Bayesian methods. All reconstructions agree on most nodes of the trees. Monophyly of Lampyridae is not supported because Rhagophthalmus ohbai in Rhagophthalmidae is included within it. Lamprigera, a genus placed unreliably in Lampyrinae, shows a close relationship to Amydetinae. Monophyly of Luciolinae is not supported because Pristolycus sagulatus (Lampyrinae) is included within it. In the Luciolinae, monophyly of Curtos and Hotaria is well established, respectively, but both morphological and molecular data continue to indicate that Luciola is not monophyletic and its subdivision is indeed necessary. Within the Lampyrinae, both Pyrocoelia and Diaphanes are not monophyletic, but monophyly of Pyrocoelia + Diaphanes is well supported. Phylogeny of Diaphanes is discussed for the first time. Generic placement of a newly discovered species (Diaphanes pectinealis Li et Liang) sharing some characters of Pyrocoelia and Diaphanes challenges the delimitation of these two similar genera. With references to the firefly mating systems, we suggest that more emphases should be placed on those sexually selected characters such as antennal structure in taxonomy of Lampyridae.

关键词： Lampyridae mitochondrial 16S rDNA morphological and ethological traits phylogeny.

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Dynamics of RNA with A6 bulge loop

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chinese Science Bulletin 2002年第12期47卷 1003-1006页

作者： LIANG Chongrong & LIU CiquanKey laboratory of cellular & molecular evolution, kunming institute of zoology, chinese academy of sciences, kunming 650223. china Biology Department, Jinan University, Guangzhou 510630, china Key laboratory of cellular & molecular evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China Biology Department Jinan University Guangzhou China

In order to understand the behavior of RNAs with large bulges in solution, molecular dynamics was performed on the RNA molecule in water with A6 bulge. The result of simulation showed that nonstacked conformation is the main conformation in large bulges, and the backbone of large bulge is of great conformational flexibility, but bulges-induced bends are relatively rigid. The fluctuation in bulge has little influence on the bend angle of RNAs.

关键词： RNA large bulge conformation bend angle.

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Melanocortin-1 receptor gene variants in four chinese ethnic populations

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Cell Research 2001年第1期11卷 81-84页

作者： SHI PENG, XUE MEI LU, HUAI RONG LUO, JIN-GONG XIANG-YU, YA PING ZHANG (laboratory of cellular and molecular evolution, kunming institute of zoology, the chinese academy of sciences, kunming 650223. china) 1laboratory of cellular and molecular evolution Kunming Institute of Zoology the Chinese Academy of Sciences Kunming 650223 China 1laboratory of cellular and molecular evolution Kunming Institute of Zoology the Chinese Academy of Sciences Kunming 650223 China 1laboratory of cellular and molecular evolution Kunming Institute of Zoology the Chinese Academy of Sciences Kunming 650223 China 1laboratory of cellular and molecular evolution Kunming Institute of Zoology the Chinese Academy of Sciences Kunming 650223 China 1laboratory of cellular and molecular evolution Kunming Institute of Zoology the Chinese Academy of Sciences Kunming 650223 China

There is strong relationship between melanocortin-1 receptor (MCIR) gene variants and human hair color and skin type. Based on a sequencing study of MC1R gene in 50 individuals from the Uygur, Tibetan, Wa and Dai ethnic populations, we discuss the occurrence of 7 mc1r variants consisting of 5 nonsynonymous sites (Val60Leu, Arg67Gln, Val92Met, Arg163Gln and Ala299Val) and 2 synonymous sites (C414T and A942G), among which C414T and Ala299Val were reported for the first time. Confirmation and analysis were the made of 122 individuals at three common point mutations (Val92Met, Arg163Gln, A942G) using PCR-SSCP. The frequency of Arg163Gln variant varies in the four ethnic populations, with percentage of 40%, 85.0%, 66. 2% and 72.7%, respectively, while those of Val92Met and A942G are roughly similar in these four populations. The different environments, migration and admixture of various ethnic groups in china might have impact on the observed frequency of Arg163Gln.

关键词： MC1R gene ethnic populations nonsynonymous site synonymous site.

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Fractals of Protein Backbone Structures

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生物数学学报 1997年第S1期12卷 385-392页

作者： Huang Jingfei Liu Ciquan(laboratory of cellular and molecular evolution,kunming institute of zoology,The chinese academy of sciences,kunming,Yunnan 650223.

Ths paper，based on the principles of geometric self-similarity of fractal theory and some research results of rotein chemistry，improved the method of comput－ing protein fractal dimensions，and computed fractal dimensions of some protein back bone，secondary and assumed folding *** relationship between protein back-bone strucrural fractal dimensions and its spatial structures was *** results indicated that protein backbone fractal dimensions not only have a close relation with protein secondary structure，but also with its *** addition，the folding of protein Polypeptide chains in 3-D space may be similar to the other macromolecular chain be haviour described by the self-avoiding walks（SAW）model．

关键词： Fractal dimension protein backbone structure secondary structure folding

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Characterization of Giardia cell nucleus:Its implication on the nature and origin of the primitive cell nucleus

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Cell Research 1995年第1期5卷 115-124页

作者： LI JINGYAN (Department of evolutionary Cell Biology, laboratory of cellular and molecular evolution, kunming institute of zoology, chinese academy of sciences, kunming 650223. china.) Department of evolutionary Cell Biology Laboratory of Cellular and Molecular Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China.Received 20October1994 Revised 8June1995 Accepted 18June1995

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A possible mode of the specific recognition of nucleic acids by proteins

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chinese Science Bulletin 2001年第11期46卷 930-934页

作者： LI Xuqing & LIU CiquanDepartment of Computer Science, kunming University of Science and Technology, kunming 650041, china laboratory of cellular and molecular evolution, kunming institute of zoology, chinese academy of sciences, kunming 650223. china Yunnan Observatory, chinese academy of sciences, kunming 650011, china 4. Modern Biological Center, Yunnan University, kunming 650091, china Department of Computer Science Kunming University of Science and Technology Kunming China Yunnan Observatory Chinese Academy of Sciences Kunming China laboratory of cellular and molecular evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China Modern Biological Center Yunnan University Kunming China

Seven sets of protein target sites, which occur in several gene promoters, have been analyzed. The results suggest that there is a possible mode of specific recognition of double-helical nucleic acids by proteins. This recognition mode is related to a special topological property of double-helical DNA, which is termed base spatial pattern (BSP) of DNA segment. BSP is the spatial topological property determined only by the spatial arrangement of the bases on double-helical DNA segment.

关键词： protein nucleic acids recognition base spatial pattern (BSP) target sites.

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Genomic organization and sequence analysis of the vomeronasal receptor V2R genes in mouse genome

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chinese Science Bulletin 2007年第3期52卷 336-342页

作者： YANG Hui1,2 & Zhang YaPing1,3 1 laboratory of cellular and molecular evolution, kunming institute of zoology, chinese academy of sciences, kunming 650223. china 2 Graduate University of the chinese academy of sciences, Beijing 100049, china 3 laboratory for Conservation and Utilization of Bio-resources, Yunnan University, kunming 650091, china laboratory of cellular and molecular evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming 650223 China

Two multigene superfamilies, named V1R and V2R, encoding seven-transmembrane-domain G-protein coupled receptors (GPCRs) have been identified as pheromone receptors in mammals. Three V2R gene families have been described in mouse and rat. Here we screened the updated mouse genome se- quence database and finally retrieved 63 putative functional V2R genes including three newly identified genes which formed a new additional family. We described the genomic organization of these genes and also characterized the conservation of mouse V2R protein sequences. These genomic and se- quence information we described are useful as part of the evidence to speculate the functional domain of V2Rs and should give aid to the functionality study in the future.

关键词：大白鼠基因组犁鼻受体2 多基因超家族序列分析

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Perspectives on the origin of microfilaments, microtubules, the relevant chaperonin system and cytoskeletal motors- a commentary on the spiro chaete origin of flagella

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Cell Research 2003年第4期13卷 219-227页

作者： JING YAN LI, CHUAN FEN WUlaboratory of cellular and molecular evolution, kunming institute of zoology, chinese academy of sciences, kunming, Yunnan 650223. china Department of molecular Genetics, M. D. Anderson Cancer Center, The University of Texas, Houston, TX 77030, USA 1laboratory of cellular and molecular evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming Yunnan 650223 China 1laboratory of cellular and molecular evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming Yunnan 650223 China

The origin of cytoskeleton and the origin of relevant intracellular transportation system are big problems for understanding the emergence of eukaryotic cells. The present article summarized relevant information of evidences and molecular traces on the origin of actin, tubulin, the chaperonin system for folding them, myosins, kinesins, axonemal dyneins and cytoplasmic dyneins. On this basis the authors proposed a series of works, which should be done in the future, and indicated the ways for reaching the targets. These targets are mainly: 1) the reconstruction of evolutionary path from MreB protein of archaeal ancestor of eukaryotic cells to typical actin; 2) the finding of the MreB or MreB-related proteins in crenarchaea and using them to examine J. A. Lake’s hypothesis on the origin of eukaryote from 'eocytes' (crenarchaea); 3) the examinations of the existence and distribution of cytoskeleton made of MreB-related protein within coccoid archaea, especially in amoeboid archaeon Thermoplasm acidophilum;

关键词： origin actin tubulin motor proteins Bagella and cilia spirochaete hypothesis.

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Pitfalls in the analysis of ancient human mtDNA

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chinese Science Bulletin 2003年第8期48卷 826-830页

作者： YAO Yonggang1,3 & ZHANG Yaping1,2 1. laboratory of molecular evolution and Genome Diversity, kunming institute of zoology, chinese academy of sciences, kunming 650223. china 2. laboratory for Conservation and Utilization of Bio-resource, Yunnan University, kunming 650091, china 3. Graduate School of the chinese academy of sciences, Beijing 100039, china Correspondence should be addressed to Zhang Yaping (e-mail: zhang- yp1@***) laboratory of molecular evolution and Genome Diversity Kunning Institute of Zoology Chinese Academy of Sciences China Graduate School of the chinese academy of sciences China laboratory for Conservation and Utilization of Bio-resource Yunnan University China

The retrieval of DNA from ancient human specimens is not always successful owing to DNA deteriora-tion and contamination although it is vital to provide new insights into the genetic structure of ancient people and to reconstruct the past history. Normally, only short DNA fragments can be retrieved from the ancient specimens. How to identify the authenticity of DNA obtained and to uncover the information it contained are difficult. We employed the ancient mtDNAs reported from Central Asia (including Xin-jiang, china) as an example to discern potentially extraneous DNA contamination based on the updated mtDNA phylog-eny derived from mtDNA control region, coding region, as well as complete sequence information. Our results demon-strated that many mtDNAs reported are more or less prob-lematic. Starting from a reliable mtDNA phylogeney and combining the available modern data into analysis, one can ascertain the authenticity of the ancient DNA, distinguish the potential errors in a data set, and efficiently decipher the meager information it harbored. The reappraisal of the mtDNAs with the age of more than 2000 years from Central Asia gave support to the suggestion of extensively (pre)historical gene admixture in this region.

关键词：古代人类遗传构造 DNA 脱氧核糖核酸

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不具有3-碱基周期性的编码序列初探

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生物化学与生物物理进展 2002年第2期29卷 267-272页

作者：张静石秀凡云南大学应用统计中心昆明650091 中国科学院昆明动物研究所昆明650223

对 12 0个较短编码序列 (<12 0 0bp)的Fourier频谱进行分析表明 ,3 碱基周期性在短编码序列中并不是绝对存在的 .统计分析提示 ,编码序列有无 3 碱基周期性与序列的碱基组成和分布、所编码蛋白质氨基酸的选用和顺序以及同义密码子的使... 详细信息

对 12 0个较短编码序列 (<12 0 0bp)的Fourier频谱进行分析表明 ,3 碱基周期性在短编码序列中并不是绝对存在的 .统计分析提示 ,编码序列有无 3 碱基周期性与序列的碱基组成和分布、所编码蛋白质氨基酸的选用和顺序以及同义密码子的使用都有一定的关系 .一般地 ,非周期 3序列中A +U含量高于G +C含量 ,周期 3序列的情况则相反 ;非周期 3序列中碱基在密码子三个位点上的分布比周期 3序列中的分布均匀 ;非周期 3序列密码子和氨基酸的使用偏向没有周期 3序列的大 .在利用Fourier分析方法预测DNA序列中的基因和外显子时。

关键词：编码序列 Fourier分析 3-碱基周期性非3-碱基周期性

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