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A PCA-based method for ancestral informative markers selection in structured populations

science china({2. sciences) 2009年第10期52卷 972-976页

作者： ZHANG Feng1,3, ZHANG Lei1,3 & DENG Hong-Wen1,2.3 1 Key Laboratory of Biomedical Information Engineering of Ministry of Education, institute of molecular Genetics, School of {2. science and Technology, Xi’an Jiaotong University, Xi’an 710049, china 2.institute of Bioscience and Biotechnology, School of science, beijing Jiaotong University, beijing 100044, china 3 Departments of Orthopedic Surgery and Basic Medical science, School of {12., University of Missouri-Kansas City, Kansas City, MO 64108, USA 1. Key Laboratory of Biomedical Information Engineering of Ministry of Education Institute of Molecular Genetics School of Life Science and Technology Xi’an Jiaotong University Xi’an 710049 China 3. Departments of Orthopedic Surgery and Basic Medical science School of Medicine University of Missouri-Kansas City Kansas City MO 64108 USA 2. institute of Bioscience and Biotechnology School of Science Beijing Jiaotong University Beijing 100044 China

Identification of population structure can help trace population histories and identify disease genes. Structured association (SA) is a commonly used approach for population structure identification and association mapping. A major issue with SA is that its performance greatly depends on the informa-tiveness and the numbers of ancestral informative markers (AIMs). Present major AIM selection meth-ods mostly require prior individual ancestry information, which is usually not available or uncertain in practice. To address this potential weakness, we herein develop a novel approach for AIM selection based on principle component analysis (PCA), which does not require prior ancestry information of study subjects. Our simulation and real genetic data analysis results suggest that, with equivalent AIMs, PCA-based selected AIMs can significantly increase the accuracy of inferred individual ancestries compared with traditionally randomly selected AIMs. Our method can easily be applied to whole genome data to select a set of highly informative AIMs in population structure, which can then be used to identify potential population structure and correct possible statistical biases caused by population stratification.

关键词： population structure principle component analysis ancestral informative markers

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Reconstruction of the most recent common ancestor sequences of SARS-Cov S gene and detection of adaptive evolution in the spike protein

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Chinese science Bulletin 2004年第12期49卷 1311-1313页

作者： ZHANG Yuan1, ZHENG Nan2.3, HAO Pei4,5 & ZHONG Yang6 1. Laboratory of Systematic and Evolutionary Botany, institute of Bot- any, Chinese Academy of sciences, {2. 100093, china 2. college of life sciences, {2. Normal University, {2. 100875, china 3. institute of Viral Disease Control and Prevention, Chinese CDC, {2. 100052. china 4. Bioinformation Center, Shanghai institutes for Biological sciences, Chinese Academy of sciences, Shanghai 2.0031, china 5. Shanghai Center for Bioinformation Technology, Shanghai 2.02.5, china 6. School of life sciences, Fudan University, Shanghai 2.0433, china 1. Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences 100093 Beijing China 2. college of life {2.s Beijing Normal University 100875 Beijing China 3. institute of Viral Disease Control and Prevention Chinese CDC 100052 Beijing China 4. Bioinformation Center Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 200031 Shanghai China 5. Shanghai Center for Bioinformation Technology 200235 Shanghai China 6. School of life sciences Fudan University 200433 Shanghai China

The genome oiganization and expression strategy of severe acute respiratory syndrome coronavirus (SARS-CoV) have been described extensively. As a structural glycoprotein on the virion surface, the spike protein is responsible for binding to host cellular receptors and for the fusion between the viral envelope and the cellular membrane. It also induces neutralizing antibodies in the host and mediates cellular immunity. Previous studies suggested that amino acid replacements in the spike protein coulddramatically alter the pathogenesis and virulence of some coronaviruses. It is therefore reasonable to test the hypothesis that radical amino acid replacements in the spike protein, favored by environmental selective pressure during the process of SARS-CoV interspecific transmission, might make this pathogen adapt to a new host, In this study, we investigated a total of 108 complete sequences of the SARS-CoV S gene from Gen-Bank (until March 2., 2.04). After omission of those records containing frame-shift mutations or low quality sequences, e.g. ZJ01, and selection of one sequence for identical records, an alignment of 42.sequences was obtained using the program Clustal-X. Then, we reconstructed the most recent common ancestor (MRCA) sequences of theSARS-CoV S gene and detected the adaptive evolution in the spike protein.

关键词： SARS冠状病毒自适应进化基因表达糖蛋白分子免疫学波峰病毒

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Single-molecule studies of DNA by molecular combing

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Progress in Natural science:Materials International 2007年第5期17卷 493-499页

作者： Liu Yuying, Wang Pengye and Dou Shuoxing (college of science, {2. Agricultural University, beijing 100083, {2. Laboratory of Soft Matter Physics, beijing National Laboratory for Condensed Matter Physics, institute of Physics, Chinese Academy of sciences, beijing 100080, {2.) [a]college of science China Agricultural University Beijing China [b]Laboratory of Soft Matter Physics Beijing National Laboratory for Condensed Matter PhysicsInstitute of Physics Chinese Academy of Sciences Beijing China

molecular combing is a powerful method for aligning a large array of DMA molecules onto a surface. It is a process whereby DNA molecules are stretched and aligned on a glass surface by the force via fluid flow. The ability to comb up to several hundred DNAs on a single cover slip allows for a statistically significant number of measurements to be made. These features make molecular combing an attractive tool for genomic studies, such as DNA replication, DNA transcription, DNA-protein interaction and so on. In this review article, we discuss the molecular combing principle, method and its applications.

关键词： DNA molecule molecular combing DNA-protein interaction.

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molecular dynamics simulation of kink in 〈100〉 edge dislocation in body centred cubic iron

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Chinese science Bulletin 2007年第16期52卷 2291-2296页

作者： CHEN LiQun1,2.WANG ChongYu2.3,4 & YU Tao2.1 college of sciences,Central South University of Forestry & Technology,Changsha 410004,{2. 2.Central Iron and Steel Research institute,beijing 100081,{2. 3 Department of Physics,Tsinghua University,beijing 100084,{2. 4 International Center for Materials Physics,Chinese Academy of sciences,Shenyang 110016,{2. college of sciences Central South University of Forestry and Technology Changsha 410004 China

Using the molecular dynamics method,we have constructed two kink models corresponding to the 〈100〉{010} and 〈100〉{011} edge dislocations (EDs) in body centred cubic (bcc) Fe. It is found that the geometric structure of a kink depends on the type of edge dislocation and the structural energies of the atoms sites in the dislocation core region. The formation energies,migration energies and widths of the kinks in different types of EDs are calculated. The results show that formation and migration of the kink in the 〈100〉{010} edge dislocation are difficult. The 〈100〉{011} edge dislocation moves primarily through kink nucleation,rather than kink migration.

关键词：分子动力学边缘位移铁纽结结构

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Chlorophyll in desiccated seeds of a euhalophyte, Suaeda physophora, and its significancy in plant adaptation to salinity during germination

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science china({2. sciences) 2008年第5期51卷 410-417页

作者： LI Yang1, ZHANG ShiRong1, SONG Jie2. WU ChenXi1, TIAN ChangYan3 & FENG Gu1 1 college of Resource and Environmental science, {2. Agricultural University, beijing 100094, {2. 2.college of life science, Shandong Normal University, Ji’nan 2.0014, {2. 3 Xinjiang institute of Ecology and Geography, Chinese Academy of sciences, Urumqi 830000, {2. 1. college of Resource and Environmental science China Agricultural University Beijing 100094 China 2. college of life {2. Shandong Normal University Ji’an 250014 China 3. Xinjiang institute of Ecology and Geography Chinese Academy of Sciences Urumqi 830000 China

The seed cotyledons of a euhalophyte, Suaeda physophora, were found to be dark green. The pigment extracted from the cotyledons was proved to be chlorophyll for the absorption spectra curve of extracts the same as that for leaves. Photosynthetic oxygen-exchanging could be detected after the seeds were moistened for 6 h. Microstructure of organelles in cotyledons of ungerminated seeds was detected by transmission electron microscopy. Histochemical pigmentation was used to investigate the degree of damage on the membrane of radicles. A xerophyte, Haloxylon persicum, whose cotyledons of desiccated seeds also contain chlorophyll was used as a comparative species. The results showed that S. physophora maintained the ultra-structure of chloroplasts, the integrity of plasma membranes of radicles kept much better than that of H. persicum, which showed the great adaptability to salinity of the euhalophyte even at the seed-germination stage. Seeds were incubated in 0 and 700 mmol/L NaCl for 10 days in darkness at 2. ℃ , then ungerminated seeds in NaCl solution were transferred to deionised water and reincubated for another 8 days and was recorded the germination recovery. Dry seeds moistened with deionised water germinated gradually in the dark and germination was maximal after 3 or 4 d. Seeds at 700 mmol/L NaCl for 10 d and transferred back to deionised water germinated abruptly, most seeds germinated in one day and photosynthesis was also detected. It is concluded that recovery germination of S. physophora ensured the seeds could germinate rapidly after salinity declines, for example under the mild but transitory favorable edaphic condition in early spring. Photosynthesis function in seeds might also promoted radicle growth and seedling establishment.

关键词： euhalophyte Suaeda physophora cotyledons of dessicated seed chlorophyll germination

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Development of rabbit monoclonal and polyclonal antibodies for detection of site-specific histone modifications and their application in analyzing overall modification levels

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Cell Research 2006年第5期16卷 519-527页

作者： Lan Guo~(1,2.*) Benliang Yin~(1,*) Junli Zhou~(1,3) Xueyong Li~3 Xing Wang Deng~(1,2.3) ~1National institute of Biological science,Zhongguancun {2. science Park,beijing 102.06,china ~2.6}-Yale Joint Center of Plant molecular Genetics and Agrobiotechnology,college of {2. sciences,peking University,{12.,china ~3Department of molecular,Cellular,and Developmental Biology,Yale University,New Haven,Connecticut 0652.-8104,USA 2.0}-Yale Joint Center of Plant molecular Genetics and Agrobiotechnology College of Life Sciences Peking University Beijing 100871 China 1National institute of Biological science Zhongguancun Life Science Park Beijing 102206 China 3Department of molecular Cellular and Developmental Biology Yale University New Haven Connecticut 06520-8104 USA 3Department of molecular Cellular and Developmental Biology Yale University New Haven Connecticut 06520-8104 USA 3Department of molecular Cellular and Developmental Biology Yale University New Haven Connecticut 06520-8104 USA

In addition to DNA sequence information,site-specific histone modifications are another important determinant ofgene expression in a eukaryotic *** selected four modification sites in common histones that are known tosignificantly impact chromatin function and generated monoclonal or polyclonal antibodies that recognize each of thosesite-specific *** used these antibodies to demonstrate that the site-specific histone modification levelsremain relatively constant in different organs of the same *** also compared the levels of selected histonemodifications among several representative organisms and found that site-specific modifications are highly variable amongdifferent organisms,providing new insight into the evolutionary divergence of specific histone modifications.

关键词： histone modification site-specific antibody chromatin

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Recombinant expression of rt-PA gene (encoding Reteplase) in gametophytes of the seaweed Laminaria japonica (Laminariales,Phaeophyta)

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science china({2. sciences) 2008年第12期51卷 1116-1120页

作者： ZHANG YiChen1,2. JIANG Peng1, GAO JiangTao1,3, LIAO JianMin4, SUN ShiJing4, SHEN ZiLong4 & QIN Song1, 1 institute of Oceanology, Chinese Academy of sciences, Qingdao 2.6071, {2. 2.college of Chemistry and life science, Tianjin Normal University, Tianjin 300387, {2. 3 Graduate University of Chinese Academy of sciences, beijing 100049, {2. 4 Biotechnology Center, {2. Pharmaceutical University, Nanjing 2.0009, {2. institute of Oceanology Chinese Academy of Sciences Qingdao 266071 China college of Chemistry and life {2. Tianjin Normal University Tianjin 300387 China Graduate University of Chinese Academy of sciences Beijing 100049 China Biotechnology Center China Pharmaceutical University Nanjing 210009 China

The life cycle of seaweed Laminaria japonica involves a generation alternation between diploid sporophyte and haploid gametophte. The expression of foreign genes in sporophte has been proved. In this research, the recombinant expression in gametophyte was investigated by particle bombardment with the rt-PA gene encoding the recombinant human tissue-type plasminogen activator (Reteplase), which is a thrombolytic agent for acute myocardial infarction (AMI). Transgenic gametophytes were selected by their resistance to herbicide phosphiothricin (PPT), and proliferated in an established bubble column photo-bioreactor. According to the results from quantitative ELISA, Southern blotting, and fibrin agarose plate assay (FAPA) for bioactivity, it was showed that the rt-PA gene had been inte-grated into the genome of gametophytes of L. japonica, and the expression product showed the ex-pected bioactivity, implying the proper post-transcript modification in haploid gametophyte.

关键词： Laminaria japonica gametophyte genetic engineering Reteplase rt-PA bioreactor

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molecular pharmacognosy

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science china({2. sciences) 2010年第6期53卷 643-652页

作者： HUANG LuQi1,XIAO PeiGen2.GUO LanPing1 & GAO WenYuan3 1institute of Chinese Materia Medica,china Academy of Chinese Medical {2.s,beijing 100700,china 2.0} of Medicinal Plant Development,Chinese Academy of Medical {2.s,peking Union Medical college,beijing 100094,china 3School of Pharmaceutical {2. and Technology,Tianjin University,Tianjin 300072.china 1. institute of Chinese Materia Medica China Academy of Chinese Medical Sciences Beijing 100700 China2. Institute of Medicinal Plant Development Chinese Academy of Medical Sciences Peking Union Medical College Beijing 100094 China3. School of Pharmaceutical Science and Technology Tianjin University Tianjin 300072 China

This article analyzes the background and significance of molecular pharmacognosy,including the molecular identification of medicinal raw materials,phylogenetic evolution of medicinal plants and animals,evaluation and preservation of germplasm resources for medicinal plants and animals,etiology of endangerment and protection of endangered medicinal plants and animals,biosynthesis and bioregulation of active components in medicinal plants,and characteristics and the molecular bases of top-geoherbs.

关键词： molecular pharmacognosy pharmacognosy borderline subject

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Chemokine RANTES is upregulated in monocytes from patients with hyperhomocysteinemia

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Acta Pharmacologica Sinica 2005年第11期26卷 1317-1321页

作者： Wei SUN~(2.5), Guang WANG~(3,5), Zhen-min ZHANG~4, Xiao-kun ZENG~2. Xian WANG~(2.4,6) ~2.institute of Vascular medicine ~3 Department of Gerontology, {2. University Third Hospital ~4 Department of Physiology and Pathophysiology, Key Laboratory of molecular Cardiovascular science, Ministry of Education, Basic Medical college, {2. University, beijing 100083, china instituteofVascularmedicine KeyLaboratoryofMolecularCardiovascularScienceMinistryofEducationBasicMedicalCol

Aim: To investigate the changes in plasma level of the chemokine RANTES (regulated upon activation, normal T cells expressed and secreted) and the responsiveness of lipopolysaccharide (LPS)-induced RANTES secretion from monocytes in patients with hyperhomocysteinemia (HHcy). Methods: The plasma levels of homocysteine (Hcy), folate, and RANTES were measured in 38 control patients with normal Hcy levels and 40 patients with HHcy and the mRNA synthesis of RANTES in isolated human monocytes was determined by RNase protection assays. Results: The plasma level of RANTES was elevated in HHcy patients compared with controls (median 5.3 vs 3.5 ng/mL, P<0.01). LPS-induced RANTES production from monocytes of HHcy patients was also increased significantly. In addition, Hcy directly increased the mRNA level of RANTES in isolated normal human monocytes in a time- and dose-dependent manner. Conclusion: Upregulated RANTES from monocytes in HHcy patients may be involved in the atherogenesis of HHcy-induced atherosclerosis.

关键词： homocysteine monocytes RANTES folic acid atherosclerosis humans

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The cessation and detoxification effect of tea filters on cigarette smoke

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science china({2. sciences) 2010年第5期53卷 533-541页

作者： YAN JingQi1,2.DI XiaoJing1,4,LIU CaiYi3,ZHANG HuiMin3,HUANG XiouQin3,ZHANG JunJing1,2.ZHAO Yan5,ZHANG LongZe1,CHANG YanZhong4,LIANG YongLin2.,TAO Ran3 & ZHAO BaoLu1,2. State Key Laboratory of Brain and Cognitive science,institute of Biophysics,Chinese Academy of sciences,beijing 100101,china 2.Key Laboratory of Mental Health,institute of Psychology,Chinese Academy of sciences,beijing 100101,china 3 Addiction Branch,beijing Military Region General Hospital,beijing 100700,china 4 institute of molecular Neurobiology,Hebei Normal University,Shijiazhuang 050016,china 5 Department of Food sciences and Technology,Harbin institute of Technology at Weihai,Weihai 2.42.9,china 1. State Key Laboratory of Brain and Cognitive science Institute of Biophysics Chinese Academy of Sciences Beijing 100101 China2. Key Laboratory of Mental Health Institute of Psychology Chinese Academy of Sciences Beijing 100101 China4. Institute of Molecular Neurobiology Hebei Normal University Shijiazhuang 050016 China3. Addiction Branch Beijing Military Region General Hospital Beijing 100700 China5. Department of Food Sciences and Technology Harbin Institute of Technology at Weihai Weihai 264209 China

To treat tobacco addiction,a tea filter was developed and studied for smoking *** work reports the smoking cessation effect of tea when it was used as a component of cigarette *** one trial it was found that after using the tea filters for 2.months,the volunteer smokers decreased their cigarette consumption by 56.5%,and 31.7% of them stopped *** work identified a new method and material,tea filter and theanine,which inhibit tobacco and nicotine addiction and provide an effective strategy for treating tobacco addiction.

关键词： cigarette smoking addiction cigarette cessation tea filter theanine nicotine dependence nicotine acetylcholine receptor(nAChR) dopamine public health free radical

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