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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. {2. of molecular evolution and Genome Diversity, kunming institute of Zoology, chinese academy of sciences, kunming 6502.3, china 2. {2. 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 {2. 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 2.00 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

molecular evolution of stress-response gene Leptin in high-altitude {2. snub-nosed monkeys (Rhinopithecus genus)

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chinese Science Bulletin 2010年第36期55卷 4132-4135页

作者： WANG XiaoPing1,2. JIN Wei1,2. YU Li1,2.& zhang yaping1,2.1 laboratory for Conservation and Utilization of Bio-resource, Yunnan University, {2. 650091, china 2.State Key laboratory of Genetic Resources and evolution, {2. institute of Zoology, chinese academy of sciences, kunming 6502.3, china laboratory for Conservation and Utilization of Bio-resource Yunnan University Kunming 650091 China State Key laboratory of Genetic Resources and evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China

chinese snub-nosed monkeys (genus Rhinopithecus, subfamily Colobinae), including R. bieti, R. brelichi and R. roxellana, are well-known as the non-human primates with the highest known altitudinal distribution. They represent an interesting model organism of adaptation to the extreme environmental stresses. However, no study at the molecular level has yet been reported for the high-altitude adaptation in chinese snub-nosed monkeys. Leptin, as an adipocyte-derived hormone, is believed to play an important role in energy homeostasis in adaptation to high altitude environments. In the present study, we sequenced and compared leptin sequences of the chinese snub-nosed monkeys (R. bieti and R. roxellana) with their lowland close relative R. avunculus and other Colobines. Unexpectedly, no amino acid changes were observed in the 7 Colobinae species examined, including the 2.chinese snub-nosed monkeys, indicating no difference in the evolutionary pattern of the Leptin gene between high-altitude monkeys and their lowland counterparts. In contrast to a previous finding of adaptive evolution of Leptin gene in plateau pikas, our study suggests that this gene may not have an important role in high-altitude adaptation of chinese snub-nosed monkeys. Other nuclear genes associated with energy metabolism, or mitochondrial genes, are most likely to be involved the molecular mechanism underlying adaptation of these monkeys to cold and hypoxia associated with the highland environment.

关键词： Leptin基因金丝猴属瘦素基因压力反应分子进化高空鼻极端环境

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 {2. and molecular evolution, kunming institute of Zoology, the chinese academy of sciences, kunming 6502.3, china) 1laboratory of cellular and {2. evolution Kunming Institute of Zoology the Chinese Academy of Sciences Kunming 650223 China 1laboratory of cellular and {2. evolution Kunming Institute of Zoology the Chinese Academy of Sciences Kunming 650223 China 1laboratory of cellular and {2. evolution Kunming Institute of Zoology the Chinese Academy of Sciences Kunming 650223 China 1laboratory of cellular and {2. evolution Kunming Institute of Zoology the Chinese Academy of Sciences Kunming 650223 China 1laboratory of cellular and {2. 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, Val92.et, Arg163Gln and Ala2.9Val) and 2.synonymous sites (C414T and A942.), among which C414T and Ala2.9Val were reported for the first time. Confirmation and analysis were the made of 12. individuals at three common point mutations (Val92.et, Arg163Gln, A942.) 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 Val92.et and A942. 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.

evolution of cd59 gene in mammals

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Science china(Life sciences) 2007年第6期50卷 773-779页

作者： GONG YuanYing1,2. PENG MinSheng1,2. ZHOU WeiPing1,3,4 & zhang yaping1,4 1 State Key {2. of Genetic Resources and evolution, kunming institute of Zoology, chinese academy of sciences, kunming 6502.3, china 2.Graduate University of the chinese academy of sciences, Beijing 100049, china 3 molecular and Cell Biology, University of Science and Technology of china, Hefei 2.002., china 4 {2. for Conservation and Utilization of Bio-resources, Yunnan University, kunming 650091, china State Key laboratory of Genetic Resources evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China Graduate University of the chinese academy of sciences Beijing 100049 China molecular Cell Biology University of Science Technology of china Hefei 230026 China laboratory for Conservation Utilization of Bio-resources Yunnan University Kunming 650091 China

The CD59-coding sequences were obtained from 5 mammals by PCR and BLAST, and combined with the available sequences in GenBank, the nucleotide substitution rates of mammalian cd59 were calcu- lated. Results of synonymous and nonsynonymous substitution rates revealed that cd59 experienced negative selection in mammals overall. Four sites experiencing positive selection were found by using "site-specific" model in PAML software. These sites were distributed on the molecular surface, of which 2.sites located in the key functional domain. Furthermore, "branch-site-specific" model detected 1 positive site in cd59a and cd59b lineages which underwent accelerated evolution caused by positive selection after gene duplication in mouse.

关键词： cd59, evolution, positive selection

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不具有3-碱基周期性的编码序列初探

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

酵母内含子在基因序列中的分布对基因转录效率的影响

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生物化学与生物物理进展 2003年第6期30卷 945-949页

作者：张静石秀凡杨恒芬云南大学应用统计中心中国科学院昆明动物研究所

对酵母中高效转录和低效转录基因内含子序列寡核苷酸使用情况的对照分析 ,显示两类内含子的序列结构有差异 ,并且高效转录基因内含子序列含有较多潜在的转录因子结合位点 ,由此推测内含子可能参与基因转录的调控 .这个结论有待更多的数... 详细信息

对酵母中高效转录和低效转录基因内含子序列寡核苷酸使用情况的对照分析 ,显示两类内含子的序列结构有差异 ,并且高效转录基因内含子序列含有较多潜在的转录因子结合位点 ,由此推测内含子可能参与基因转录的调控 .这个结论有待更多的数据证实 .对内含子和外显子在两组基因序列中的分布 (长度、位置等 )进行详细比较分析后显示 ,高效转录基因内含子和低效转录基因内含子的长度有比较明显的界限 .两组基因中外显子长度的均值虽然有些差异 ,却没有明显的界限 .基因序列长度与外显子长度的情况相似 .虽然内含子的相对位置在两类基因中都很靠近 5′端 ,但是从实际位置看 ,高效转录基因中比较多的内含子很靠近基因的 5′端 ,有些则位于 5′ UTR区域 .这些结果提示 ,基因的转录效率与内含子的长度有关 ,与外显子及基因序列的长度无关 ,内含子的位置也可能影响转录效率 ,内含子对基因转录的调控可能与基因上游的转录调控有关联。

关键词：酵母基因转录频率内含子长度内含子位置基因序列基因转录

evolutionary implications of Avian Infectious Bronchitis Virus(AIBV)analysis

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Cell Research 2006年第3期16卷 323-327页

作者： Peng Shi~(1,2. Li Yu~2.Yun-xin Fu~3 Jing-Fei Huang~1 Ke-Qin zhang~2.Ya-ping zhang~(1,2.1 {2. of cellular and molecular evolution,and molecular Biology of Domestic Animals,kunming lnstitute of Zoology,chinese academy of sciences,kunming {12.,china 2.{2. for Conservation and Utilization of Bio-resource,Yunnan University,kunming 650091,china 3 Human Genetics Center,University of Texas at Houston,Houston,Texas 77030,USA laboratory of cellular and {2. evolution and Molecular Biology of Domestic Animals Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China.

For developing efficient vaccines,it is essential to identify which amino acid changes are most important to the sur-vival of the *** investigate the amino acid substitution features in the Avian Infectious Bronchitis Virus (AIBV)antigenic domain of a vaccine serotype (DE072. and a virulent viral strain (GA98) to better understand adaptive evo-lution of *** addition,the SARS Coronavirus (SARS-CoV) was also analyzed in the same *** is interestingto find that extreme comparability exists between AIBV and SARS in amino acid substitution *** suggests thatamino acid changes that result in overall shift of residue charge and polarity should be paid special attention to duringthe development of vaccines.

关键词： Avian Infectious Bronchitis Virus SARS Coronavirus positive selection adaptive evolution vaccine development

Dramatic divergences in size between two vomeronasal pheromone receptor gene families in mice and rats

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Dramatic divergences in size between two vomeronasal pheromo...

Membrane tension evolution and mechanical regulation of melittin-induced membrane poration

中国遗传学会七届一次青年研讨会暨上海高校模式生物E——研究院第一届模式生物学术研讨会

作者： hui yang, Peng Shi, Jianzhi {2., Ya-ping {2. (laboratory of molecular Biology of Domestic Animals, and cellular and molecular evolution, kunming institute of Zoology, kunming,{12., Department of Ecology and evolutionary Biology, University of Michigan, USA, The Graduate School of chinese academy of sciences, Beijing,{12. )

Mammalians can detect pheromonal signals via the vomeronasal organ (VNO) primarily to discriminate individuals in the same species and elicit certain social or reproductive behaviors. Two superfamilies, V1r and V2., encode the pheromone receptors. In this study, we provide a global draft of V2. repertoires in mice and rats through a computational approach. A total of 182.and 141 V2. genes are identified including 46 and 44 putatively functional genes in mouse and rat, respectively. These genes can be phylogenetically divided into two families with a species-specific pattern. Genomic distribution and evolutionary analysis reveal that V2. evolvement in rodents was a complicated process which involved tandem duplication, unequal crossover and selective pressure variation. Diverging time estimation indicates that a great part of V2. genes are products of recent expansion within 10 MYA in mice and 10-2. MYA in rats, which supports the observation that genes from each species clustered and it is mainly the result of postspeciation duplications. Unlike to V1rs, the number of putative functional V2. members in mice and rats is much smaller. As comparisons of gene structure and binding ligands of both Vlr and V2. are taken into account, we hypothesize that the identified -50 V2. genes can function well if they recognize ligands sharing a common structural motif. Our results also suggest function divergence between the two vomeronasal pheromone receptors.

关键词：

来源： cnki会议评论

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chinese Physics B 2024年第10期33卷 465-475页

作者： Wanting zhang Rong Xu Wendong Ma Zhao Lin Kai yang Bing Yuan Center for Soft Condensed Matter Physics and Interdisciplinary Research&School of Physical Science and Technology Soochow UniversitySuzhou 215006China Songshan Lake Materials laboratory Dongguan 523808China Biomedicine Discovery institute Infection&Immunity ProgramMonash UniversityMelbourneAustralia Beijing National laboratory for Condensed Matter Physics Institute of PhysicsChinese Academy of SciencesBeijing 100190China

Membrane tension plays a crucial role in various fundamental cellular processes,with one notable example being the T cell-mediated elimination of tumor cells through perforin-induced membrane perforation by amplifying cellular ***,the mechanisms governing the regulation of bio{2. activities at the cell interface by membrane tension remain *** this study,we investigated the correlation between membrane tension and poration activity of melittin,a prototypical pore-forming peptide,using dynamic giant unilamellar vesicle leakage assays combined with flickering tension analysis,{2. dynamics simulations,and live cell *** results demonstrate that an increase in membrane tension enhances the activity of melittin,particularly near its critical pore-forming ***,peptide actions such as binding,insertion,and aggregation in the membrane further influence the evolution of membrane *** cell experiments reveal that artificially enhancing membrane tension effectively enhances melittin’s ability to induce pore formation and disrupt membranes,resulting in up to a ten-fold increase in A549 cell mortality when exposed to a concentration of 2.0-μg·mL^(-1)*** findings elucidate the relationship between membrane tension and the mechanism of action as well as pore-forming efficiency of melittin,while providing a practical mechanical approach for regulating functional activity of molecules at the cell-membrane interface.

关键词： membrane tension mechanical regulation membrane poration giant unilamellar vesicle leakage assay