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Genomic research for important pathogenic bacteria in china

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Science china(Life sciences) 2009年第1期52卷 50-63页

作者： YANG RuiFu1,GUO XiaoKui2.YANG Jian3,JIANG YongQiang1,PANG Bo4,CHEN Chen5,YAO YuFeng2.QIN JinHong2.& LI QingTian2.1 Laboratory of Analytical Microbiology,State Key Laboratory of Pathogen and Biosecurity,Beijing Institute of Microbiology and Epidemiology,Beijing 100071,china 2.Department of Medical Microbiology and Parasitology,Institutes of Medical sciences,{2. Jiao Tong University School of Medicine,{2. 2.002.,china 3 State Key Laboratory for Molecular Virology and genetic engineering,Institute of Pathogen Biology,chinese academy of Medical sciences,Beijing 100176,china 4 State Key Laboratory for Infectious Disease Prevention and Control,Institute for Communicable Disease Control and Prevention,chinese center for Disease Control and Prevention,Beijing 102.06,china 5 Beijing Genomics Institute at Shenzhen,Shenzhen 518083,china 1. Laboratory of Analytical Microbiology State Key Laboratory of Pathogen and Biosecurity Beijing Institute of Microbiology and Epidemiology Beijing 100071 China 2. Department of Medical Microbiology and Parasitology Institutes of Medical Sciences Shanghai Jiao Tong University School of Medicine Shanghai 200025 China 3. State Key Laboratory for Molecular Virology and genetic engineering Institute of Pathogen Biology Chinese Academy of Medical Sciences Beijing 100176 China 4. State Key Laboratory for Infectious Disease Prevention and Control Institute for Communicable Disease Control and Prevention Chinese Center for Disease Control and Prevention Beijing 102206 China 5. Beijing Genomics Institute at Shenzhen Shenzhen 518083 China

Rapid accumulation of bacterial genomic data offered an unprecedented opportunity to understand bacterial biology from a holistic view of *** can thus closely look at the way in which a pathogen is evolved,and these data has been applied to molecular epidemiology and microbial forensics,and screening of novel diagnostic,vaccine and drug *** newly developed high-throughput low-cost sequencing technologies,such as 454,Solexa and SOLiD,will promote the acquisition and application of genomic data in new research areas that we dared not imagine previously,such as the metagenomics of human gastric-intestinal tract,for better and comprehensive understanding of human health and disease.

关键词： genome pathogenic bacteria sequencing application

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VERTICAL HEREDITY VS. HORIZONTAL gene TRANSFER: A CHALLENGE TO BACTERIAL CLASSIFICATION

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Journal of Systems Science & Complexity 2003年第3期16卷 307-314页

作者： HAO Bailin(Institute of Theoretical Physics, academy of chinese {2., Beijing 100080, china Senior International Fellow of the Santa Fe Institute T-Life research center, Fudan University,shanghai 2.0433, china)QI Ji(Institute of Theoretical Physics, Beijing 100080, china) Institute of Theoretical Physics Academy of Chinese Sciences 北京 100080 Institute of Theoretical Physics Chinese Academy of Sciences 北京 100080

The diversity and classification of microbes has been a long-standing *** phylogeny of the prokaryotes based on comparison of the 16S rRNA sequences of the small ribosomal subunit has led to a reasonable tree of life in the late 1970s. How-ever, the availability of more and more complete bacterial genomes has brought about complications instead of refinement of the tree. In particular, it turns out that different choice of genes may tell different history. This might be caused by possible horizontal gene transfer (HGT) among species. There is an urgent need to develop phylogenetic methods that make use of whole genome data. We describe a new approach in molecular phylogeny,namely, tree construction based on K-tuple frequency analysis of the genomic *** aside the technicalities, we emphasize the transition from randomness to determin-ism when the string length K increases and try to comment on the challenge mentioned in the title.

关键词： prokaryote phylogeny horizontal gene transfer fitness compositionaldistance

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Biomarkers of neurodegenerative disorders: How good are they?

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Cell research 2004年第5期14卷 347-358页

作者： Varun RACHAKONDA Department of Neurology Baylor College of Medicine Houston TX USA

Biomarkers are very important indicators of normal and abnormal biological processes. Specific changes in pathologies, biochemistries and genetics can give us comprehensive information regarding the nature of any particular disease. A good biomarker should be precise and reliable, distinguishable between normal and interested disease, and differential between different diseases. It is believed that biomarkers have great potential in predicting chances for diseases, aiding in early diagnosis, and setting standards for the development of new remedies to treat diseases. New technologies have enabled scientists to identify biomarkers of several different neurodegenerative diseases. The followings, for instance, are only a few of the many new biomarkers that have been recently identified: the phosphorylated tau protein and aggregated β-amyloid peptide for Alzheimer’s disease (AD), α-synuclein contained Lewy bodies and altered dopamine transporter (DAT) imaging for Parkinson’s disease (PD), SOD mutations for familial amyotrophic lateral sclerosis (ALS), and CAG repeats resulted from Huntington’s gene mutations in Huntington’s disease (HD). This article will focus on the most-recent findings of biomarkers belonging to the four mentioned neurodegenerative diseases.

关键词： Alzheimer’s disease Parkinson’s disease Amyotrophic Lateral Sclerosis Huntington’s disease biomarkers.

Studies of low-lying states of even-even Xe isotopes within the nucleon pair approximation

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Science china(Physics,Mechanics & Astronomy) 2011年第S1期54卷 103-108页

作者： ZHANG LiHua1, JIANG Hui1,2.& ZHAO YuMin1,3,4 1Institute of Nuclear, Particle, Astrophysics and Cosmology, Department of Physics, shanghai Jiao Tong University, shanghai 2.02.0,{2. 2.chool of Arts and sciences, shanghai Maritime University, shanghai 2.0135,{2. 3center of Theoretical Nuclear Physics, national Laboratory of Heavy Ion Accelerator, Lanzhou 730000,{2. 4CCAST, World Laboratory, P.O. Box 8730, Beijing 100080,{2. 1. Institute of Nuclear Particle Astrophysics and Cosmology Department of Physics Shanghai Jiao Tong University Shanghai 200240 China2. School of Arts and Sciences Shanghai Maritime University Shanghai 200135 China3. Center of Theoretical Nuclear Physics National Laboratory of Heavy Ion Accelerator Lanzhou 730000 China4. CCAST World Laboratory P.O. Box 8730 Beijing 100080 China

We study the relevance of nucleon pairs with higher spins, in addition to spin-zero and spin-two pairs (i.e., S D pairs), in low-lying states of even-even Xe nuclei. By including those higher-spin pairs in our configuration, we recalculate energy level schemes, elec trical quadrupole moments, magnetic moments and electric quadrupole transition rates, for low-lying states of even-even 12.-142.e nuclei. The agreement between our calculated results and the experimental data is substantially improved in comparison with previous studies.

关键词： nucleon pair approximation shell model configuration space low-lying states

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Large-scale genome sequencing based genotyping and genome-wide association studies in rice

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Large-scale genome sequencing based genotyping and genome-wi...

Construction of a small peptide library related to inhibitor OM99-2.and its structure-activity relationship to β-secretase

第十一届全国植物基因组学大会

作者： Bin Han national center for {2. research & Institute of Plant Physiology and Ecology,shanghai Institutes of Biological sciences,chinese academy of sciences Beijing Institute of Genomics,CAS

Rice(Oryza sativa L.) is the staple food for more than half of the world *** thousands of years of rice cultivation,china has accumulated an enormously diverse collection of landraces. This is an invaluable genetic re...

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Acta Pharmacologica Sinica 2006年第12期27卷 1586-1593页

作者： Bin HU Bing XIONG Bei-ying QIU Xin LI Hai-ping YU Kun XIAO Xin WANG Jia LI Jing-kang SHEN~2.State Key Laboratory of Drug research and national {2. for Drug Screening,shanghai Institute of Materia Medica,shanghai Institutes for Biological sciences,chinese academy of sciences,shanghai 2.12.3,china State Key Laboratory of Drug research and national {2. for Drug Screening Shanghai Institute of Materia Medica Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 201203 China

Aim:To develop probes for detecting the binding specificity between β-secretaseand substrate,and provide reliable biological activity data for further researchingencircling substrate-based ***:To prepare the inhibitors,thehydroxyethylene(HE)segment including P1and P1′ was synthesized after multi-step reactions;the combination of all segments was then completed through solidphase *** human β-secretase ectodomain(amino acid resi-dues 1-460)was expressed as a secreted protein with a C-terminal His tag in insectcells using baculovirus infection,and all compounds were evaluated in thisβ-secretase enzyme *** order to understand the interaction in detail,the theoretical methods,namely molecular dynamics(MD)simulation and mo-lecular mechanics-generalized-born surface area(MM-GBSA)analysis,were per-formed on the complex of β-secretase and OM99-2.to obtain the geometrical andenergetical ***:We designed and constructed a positional scan-ning combinatorial library including 16 compounds;all members of the librarywere synthesized based on HE dipeptide ***-activity relationshipstudies at the P4-P1and P1′-P4′ positions led to the discoveries of P and P’sidesbinding specificity and potent inhibitors 14,18,and *** binding free energyon the whole system and every residue were compared to the biological ***:The removal of P4′ yielded inhibitor 2.(A3*B2.with highpotency;further truncation of P3′ gave inhibitor 18(A3*B1)with equal activity,implying that the right side of the inhibitors play a less important role and could beeasily simplified,while change on the P side may cause substantial results.

关键词： β-secretase hydroxyethylene OM99-2 Alzheimer’s disease structure-activity relationship

Value-added cassava for bio-industrial development using biotechnological approaches

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Value-added cassava for bio-industrial development using bio...

Design,synthesis,antitumor evaluations and molecular modeling studies of novel 3,5-substituted indolin-2.one derivatives

2.11全国植物生物学研讨会

作者： Peng Zhang~(1,2. 1 SIBS-ETH shanghai center for Cassava Biotechnology,{2. Key Laboratory of Plant Molecular genetics,Institute of Plant Physiology and Ecology,shanghai Institutes for Biological sciences, chinese academy of sciences,300 Fenglin Road,shanghai 2.0032.china 2.shanghai Chenshan Plant Science research center,{12. academy of sciences,shanghai Chenshan Botanical Garden,3888 Chenhua Road,shanghai 2.1602.china

Cassava(Mantnot esculenta Crantz) accumulates a lot of starch in its storage roots that can be processed to food,feed,modified starches and *** high yield potential and robustness against unfavorable environmental conditions make cassava suitable crop for marginal lands,which will not highly compete with other food crops on arable *** are several key biological constraints in cassava for bio-industrial *** example,the post-harvest physiological deterioration (PPD) of cassava storage roots is the biggest disadvantage during starch and

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Acta Pharmacologica Sinica 2007年第1期28卷 140-152页

作者： Hai-hong LI~2.Xiu-hua ZHANG~3 Jin-zhi TAN~2.Li-li CHEN~2.Hong LIU~(2.5) Xiao-min LUO~(2.5) Xu SHEN~(2.4) Li-ping LIN~(3,5) Kai-xian CHEN~2.Jian DING~3 Hua-liang JIANG~(2.4)2.center for Drug Discovery and Design,State Key Laboratory of Drug research,{2. Institute of Materia Medica,{2. Institutes for Biological sciences,and Graduate School,chinese academy of sciences,{2. 2.12.3,china 3 Division of Anti-tumor Pharmacology,{2. Institute of Materia Medica,{2. Institutes for Biological sciences,chinese academy of sciences,{2. 2.12.3,china 4 School of Pharmacy,East china University of Science and Technology,{2. 2.02.7,china centerforDrugDiscoveryandDesign StateKeyLaboratoryofDrugResearchShanghaiInstituteofMateriaMedicaShanghaiInstitutesforBiologicalSciencesandGraduateSchoolChineseAcademyofSciencesShanghai201203China

Aim:To design and synthesize a novel class of antitumor agents,featuring the 3,5-substituted indolin-2.one ***:Based on enzyme binding fea-tures of（Z）-SU5402.introducing a β-pyrrole group at the 3-position of the indolin-2.one core,a series of novel 3,5-substituted indolin-2.ones were designed *** human carcinoma cell lines of A-43l,A-549,MDA-MB-468,and Autosomal Dominant Polycystic Kidney disease were chosen for the cellproliferation ***:Twenty new compounds（1a-t）with E configurationhave been designed,synthesized and *** structural features weredetermined by nuclear magnetic resonance（NMR）spectra,low-and high-resolu-tion mass spectra,and confirmed by X-ray *** the enzymeassay showed a weak inhibition effect against the epidermal growth factor receptor,vascular endothelial growth factor receptor,fibroblast growth factor receptor andplatelet-derived growth factor receptor tyrosine kinases,the cell-based antitumoractivity was *** 1 g and lh showed higher inhibitory activitytoward the A-549 and MDA-MB-468 cell lines with IC50of 0.065-9.4 μmol/***:This study provides a new template for further development ofpotent antitumor drugs.

关键词： protein-tyrosine kinase indolin-2.one antitumor drug screening assays drug design molecular models

Identification and classification of all potential hemolysin encoding genes and their products from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai

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Acta Pharmacologica Sinica 2005年第4期26卷 453-461页

作者： Yi-xuan ZHANG~(2.3,4,5) Yan GENG(2.3,4,5) Bo BI~(2.4) Jian-yong HE~4 Chun-fu WU~4 Xiao-kui GUO~3 Guo-ping ZHAO~(2.4,6,7) 2.research center of Biotechnology,{2. Institutes for Biological sciences,chinese academy of sciences,{2. 2.02.3,china 3 Department of Microbiology and Parasitology,{2. Second Medical University,{2. 2.002.,china 4 The School of Pharmaceutical Engineering,Shenyang Pharmaceutical University,Shenyang 110016,china 6 chinese national Human Genome center at {2.,ZhangJiang High Tech Park,{2. 2.12.3,china researchcenterofBiotechnology ShanghaiInstitutesforBiologicalSciencesChineseAcademyofSciencesShanghai200233

Aim:To identify and classify all potential hemolysin candidates of Leptospirainterrogans serogroup Icterohaemorrhagiae serovar ***:All of thepotential hemolysin encoding genes were characterized in *** geneswere cloned and expressed in Escherichia *** hemolytic activities of theexpressed proteins were assayed observing the hemolysis on sheep blood *** activities of the hemolysin candidates were measuredby thin-layer chromatography(TLC)and HPLC for *** and secretion of the hemolysins in L interrogans were studied byreverse transcription polymerase chain reaction,Western blot,and enzyme-linkedimmunosorbent *** and Conclusion:The hemolytic activities ofhemolysin candidates(LA032.,LA0378,LA102.,LA102.,LAI650,LA3050,LA3937,LA4004)from L interrogans strain Lai were *** were furtherdivided into two groups,sphingomyelinase hemolysins and non-sphingomyelinasehemolysins,based on their ability to hydrolyze *** of thesehemolysins were actually expressed in living L interrogans and some of themwere secreted into the *** study establishes an essential findcomplete basis for further studying the contribution of hemolysins to the patho-genesis of L interrogans.

关键词： hemolysin Leptospira interrogans sphingo myelinase