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Cloning and expression of putative ethylene receptor genes in soybean plant

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Progress in Natural Science:Materials International 2007年第10期17卷 1152-1160页

作者： Xie Zongming1,2,3. Lei Gang1,2, Wuriyanghan Hada1,2, Tian Aiguo1, Zhang Jinsong1 and Chen Shouyi1(1. National Key Laboratory of Plant genomics, institute of Genetics and Developmental Biology, chinese {3. of sciences, Beijing 100101, china 2. Graduate School of chinese {3. of sciences, Beijing 10003., china 3. Xinjiang {3. of Agricultural and Reclamation Science, Shihezi 83.000, china) National Key Laboratory of Plant genomics Institute of Genetics and Developmental Biology Chinese Acad. of Sci. Beijing 100101 China Graduate School Chinese Acad. of Sci. Beijing 100039 China Xinjiang academy of Agricultural and Reclamation Science Shihezi 832000 China

Ethylene plays important roles in plant growth, development, and stress responses, and ethylene receptors have been identified and studied extensively in various plant species. Here we report the cloning of four ethylene receptor genes from soybean, i.e. GmETR1, GmERS1, GmETR2 and GmEIN4. Construction of the phylogenic tree showed that GmETR1 and GmERS1 belong to subfamily I whereas GmETR2 and GmEIN4 belong to subfamily II. The four ethylene receptor genes showed different tissue-specific expression patterns in roots, stems, leaves, cotyledons, flowers, pods and seeds of soybean. These genes were differentially regulated by various abiotic stresses and plant hormones. The possible roles of the four genes in soybean plant were also discussed.

关键词： abiotic stress expression analysis ethylene receptor plant hormone soybean.

Identification of human dopamine receptors agonists from chinese herbs

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Acta Pharmacologica Sinica 2007年第1期28卷 132-139页

作者： Yi-lin ZHANG~(1,2,3.4) Hai-qing ZHANG~(1,2,3.4) Xiao-yu LIU~3.Shi-neng HUA~3.Lu-bing ZHOU~3.Jun YU~2 Xue-hai TAN~(3.5)1 Graduate School of the chinese academy of sciences,Beijing 10003.,china 2 Beijing genomics {3.,chinese academy of sciences Beijing 1013.0,china 3.HD Biosciences Co Ltd,Shanghai 201203.china Graduate School of the chinese academy of sciences Beijing China Beijing genomics institute Chinese Academy of Sciences Beijing China HD Biosciences Co Ltd Shanghai China

Aim:To find human dopamine receptors,especially Dl-like receptor specific ago-nists from chinese herbs as potential antihypertension drug ***:TwoD l-like receptor cell lines carrying a μ-lactamase reporter gene,and a D2 receptorcell line coexpressing a promiscuous G protein G15 were constructed using HEK293.ells.A natural compound library made from fractionated samples of herbal ex-tracts was used for high-throughput screening（HTS）against one of the cell lines,HEK/D5R/*** interested hits were evaluated for their activities againstvarious dopamine ***:Fourteen hits were identified from primaryscreening,of which 2 of the better hit samples,HD0522 and HD0059,were selectedfor further material and activity analysis,and to obtain 2 compounds that ap-peared as 2 single peaks in HPLC,HD0522H01 and ***0059H01could activate D 1,D2,and D5 receptors,with EC50values of 2.28 μg/mL,0.85 μg/mL,and 1.41 μg/mL,***0522H01 could only activate DlR and D5Rwith EC50values of 2.95 μg/mL and 8.3. μg/***:We established cell-based assays for 3.different human dopamine receptors and identified specificagonists HD0522H01 and HD0059H01 through *** specific agonist to D1-like receptors,HD0522H01,may become a new natural product-based drug leadfor antihypertension treatment.

关键词： dopamine receptors natural products high throughput screening hypertension

Preparing a re-sequencing DNA library of 2 cancer candidate genes using the ligation-by-amplification protocol by two PCR reactions

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Science china(Life sciences) 2009年第5期52卷 483-491页

作者： SU YeYang1,2,3. LIN Lin1,2,3. TIAN Geng1,2,3. CHEN Chen2,3. LIU Tao2,3. XU Xingya3. QI XinPeng1,2,3. ZHANG XiuQing2,3. YANG HuanMing2,3.1 Graduate School of chinese academy of sciences, Beijing 100049,{3. 2 Beijing institute of genomics, chinese academy of sciences, Beijing 100029,{3. 3.Beijing genomics institute, Beijing 1013.0,{3. Graduate School of chinese academy of sciences Beijing China Beijing institute of genomics Chinese Academy of Sciences Beijing China Beijing genomics institute Beijing China

To meet the needs of large-scale genomic/genetic studies, the next-generation massively parallelized sequencing technologies provide high throughput, low cost and low labor-intensive sequencing service, with subsequent bioinformatic software and laboratory methods developed to expand their applications in various types of research. PCR-based genomic/genetic studies, which have significant usage in association studies like cancer research, haven't benefited much from those next-generation sequencing technologies, because the shortgun re-sequencing strategy used by such sequencing machines as the Illumina/Solexa Genome Analyzer may not be applied to direct re-sequencing of short-length target regions like those in PCR-based genomic/genetic studies. Although several methods have been proposed to solve this problem, including microarray-based genomic selections and selector-based technologies, they require advanced equipment and procedures which limit their applications in many laboratories. By contrast, we overcame such potential drawbacks by utilizing a ligation by amplification (LBA) protocol, a method using a pair of Universal Adapters to randomly ligate target regions in a two-step-PCR procedure, whose Long LBA products were easily fragmented and sequenced on the next-generation sequencing machine. In this concept-proven study, we chose the consensus coding sequences of two human cancer genes: BRCA1 and BRCA2 as target regions, specifically designed LBA primer pairs to amplify and randomly ligate them. 70 target sequences were successfully amplified and ligated into Long LBA products, which were then fragmented to construct DNA libraries for sequencing on both a conventional Sanger sequencer ABI 3.3.xl DNA Analyzer and the next-generation 'synthesis by sequencing technology' Illumina/Solexa Genome Analyzer. Bioinformatic analysis demonstrated the utility and efficiency (including the coverage and depth of each target sequence and the SNPs detection effectiveness) o

关键词： health genomics the next-generation sequencing techonology sequencing technology large-scale genomics PCR

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High Throughput SNP Genotyping with Two Mini-sequencing Assays

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Acta Biochimica et Biophysica Sinica 2004年第6期36卷 379-384页

作者： Chunqing LUO1,2#, Libin DENG1#, and Changqing ZENG1,2* The institute of Genetic and Developmental Biology, the chinese academy of sciences, Beijing 100101, china 2Beijing {3. institute, the chinese academy of sciences, Beijing 1013.0, china The institute of Genetic and Developmental Biology the Chinese Academy of SciencesBeijing 100101 China Beijing genomics institute the Chinese Academy of SciencesBeijing 101300 China

Two mini-sequencing methods, FP-TDI (template-directed dye-terminator incorporation with fluorescence-polarization) and MassArray (matrix assisted laser desorption ionization time of flight detection mass spectrometry), were optimized. A numeric standard was introduced to evaluate the SNP scoring quality of FP-TDI assay, thus made the optimization work easier. At the same time, using multi-PCR technology, 8-plex genotyping of MassArray assay was successfully carried out, some softwares were developed and the data process of MassArray was highly automated. Then these two methods were applied to high throughput SNP genotyping, the accuracy, efficiency and robustness were compared. The result shows FP-TDI is more sensitive to the concentration of SNPprimer and PCR product, as well as extension cycles, the SNPprimer length of FP-TDI should be 24–3. bp long, whereas MassArray assay prefers to be as short as only 16 *** 6440 SNP sites of human chromosome 3.were genotyped in a sample of 90 individuals, 4792 sites by FP-TDI assay and 1648 sites by MassArray assay, the success rates of FP-TDI and MassArray were 67.7% and 93.6% respectively. The throughput of MassArray was higher than FP-TDI, and the cost of MassArray was lower, MassArray was more suitable for high throughput SNP genotyping.

关键词： SNP genotyping FP-TDI MassArray high throughput

Exploring in vitro roles of siRNA in cardiovascular disease

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Acta Pharmacologica Sinica 2007年第1期28卷 1-9页

作者： Yu TANG~(2,3. Yu-zhi GE~3.James Q YIN~(2,4)2 institute of Biophysics,chinese academy of {3.,Beijing 100101,china 3.United Cardiovascular Department,Jiangxi Provincial People's Hospital,Nanchang 3.0046,china institute of Biophysics Chinese Academy of Sciences Beijing China United Cardiovascular Department Jiangxi Provincial People's Hospital Nanchang China

RNA interference(RNAi)is an adaptive defense mechanism through which double-stranded RNAs silence cognate genes in a sequence-specific *** has beenemployed widely as a powerful tool in functional genomics studies,target valida-tion and therapeutic product ***,the application of small-interfering RNA(siRNA)to the silencing of the disease-causing genes involvedin cardiovascular diseases has made great *** this overview,we attemptto provide a brief outline of the current understanding of the mechanism of RNAiand its potential application to the cardiovascular system,with particular empha-sis on its ability to identify the pathophysiological function of genes related toseveral important cardiovascular *** prospects of RNAi-basedtherapeutics,as well as the advantages and potential problems,are also discussed.

关键词： siRNA RNAigene silencing cardiovascular disease gene therapy

BUD2,encoding an S-adenosylmethionine decarboxylase,is required for Arabidopsis growth and development

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Cell Research 2006年第5期16卷 446-456页

作者： Chunmin Ge~(1,2,*) Xia Cui~(1,2,*) Yonghong Wang~1 Yuxin Hu~3.Zhiming Fu~1 Dongfen Zhang~(1,2) Zhukuan Cheng~1 Jiayang Li~1 ~1State Key Laboratory of Plant genomics and National Center for Plant Gene Research,institute of Genetics and Developmental Biology,chinese {3. of sciences,Beijing 100101,china ~2Graduate School,chinese {3. of sciences,Beijing 100101,china ~3.1} of Botany,chinese {3. of sciences,Beijing 100093.china State Key Laboratory of Plant genomics and National Center for Plant Gene Research Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing China Graduate School Chinese Academy of Sciences Beijing China institute of Botany Chinese Academy of Sciences Beijing China

Polyamines are implicated in regulating various developmental processes in plants,but their exact roles and how theygovern these processes still remain *** report here an Arabidopsis bushy and dwarf mutant,bud2,which resultsfrom the complete deletion of one member of the small gene family that encodes S-adenosylmethionine decarboxylases(SAMDCs) necessary for the formation of the indispensable intermediate in the polyamine biosynthetic ***2 plant has enlarged vascular systems in inflorescences,roots,and petioles,and an altered homeostasis *** double mutant of bud2 and samdcl,a knockdown mutant of another SAMDC member,is embryo lethal,demonstrat-ing that SAMDCs are essential for plant *** results suggest that polyamines are required for the normalgrowth and development of higher plants.

关键词： BUD2 polyamines embryogenesis plant architecture Arabidopsis

Progress in the detection of human genome structural variations

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Science china(Life sciences) 2009年第6期52卷 560-567页

作者： WU XueMei1,3.& XIAO HuaSheng1,2 1 Center of Functional genomics,Key Laboratory of System Biology,Shanghai institutes for Biological sciences,{3. academy of sciences,Shanghai 20003.,china 2 National Engineering Center for Biochip at Shanghai,Shanghai 201203.china 3.Graduate School of the chinese academy of sciences,Shanghai 20003.,china Center of Functional genomics Key Laboratory of System Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China Graduate School of the chinese academy of sciences Shanghai China National Engineering Center for Biochip at Shanghai Shanghai China

The emerging of high-throughput and high-resolution genomic technologies led to the detection of submicroscopic variants ranging from 1 kb to 3.Mb in the human *** variants include copy number variations(CNVs),inversions,insertions,deletions and other complex rearrangements of DNA *** paper briefly reviews the commonly used technologies to discover both genomic structural variants and their potential ***,we highlight the array-based,PCR-based and sequencing-based assays,including array-based comparative genomic hybridization(aCGH),representational oligonucleotide microarray analysis(ROMA),multiplex amplifiable probe hybridization(MAPH),multiplex ligation-dependent probe amplification(MLPA),paired-end mapping(PEM),and next-generation DNA sequencing ***,we discuss the limitations and challenges of current assays and give advices on how to make the database of genomic variations more reliable.

关键词： structural variation cytogenetic microarray PCR paired end mapping(PEM) next-generation sequencing

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LEAFY HEAD2,which encodes a putative RNA-binding protein,regulates shoot development of rice

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Cell Research 2006年第3期16卷 267-276页

作者： Guo Sheng Xiong~(1,3. Xing Ming Hu~2 Yong Qing Jiao~1 Yan Chun Yu~1 Cheng Cai Chu~1 Jia Yang Li~1 Qian Qian~2 Yong Hong Wang~11 State Key Laboratory of Plant genomics and National Center for Plant Gene Research,institute of Genetics and Developmental Biology,chinese {3. of sciences,Beijing 100101,china 2 State Key Laboratory of Rice Biology,china National Rice Research institute,chinese {3. of Agricultural sciences,Hangzhou 3.0006,china 3.Graduate University of chinese {3. of sciences,Beijing 100049,china State Key Laboratory of Plant genomics and National Center for Plant Gene Research Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing China Graduate University of chinese academy of sciences Beijing China State Key Laboratory of Rice Biology China National Rice Research Institute Chinese Academy of Agricultural Sciences Hangzhou China

During vegetative development,higher plants continuously form new leaves in regular spatial and temporal *** with abnormal leaf developmental patterns not only provide a great insight into understanding the regulatorymechanism of plant architecture,but also enrich the ways to its modification by which crop yield could be ***,we reported the characterization of the rice leafy-head2 (lhd2) mutant that exhibits shortened plastochron,dwarfism,reduced tiller number,and failure of phase transition from vegetative to reproductive *** and histologicalstudy revealed that the rapid emergence of leaves in lhd2 was resulted from the rapid initiation ofleafprimordia whereasthe reduced tiller number was a consequence of the suppression of the tiller bud *** molecular and geneticanalysis showed that LHD2 encodes a putative RNA binding protein with 67% similarity to maize *** ofgenome-scale expression profiles between wild-type and lhd2 plants suggested that LHD2 may regulate rice shoot devel-opment through KNOXand hormone-related *** similar phenotypes caused by LHD2 mutation and the conservedexpression pattern of LHD2 indicated a conserved mechanism in controlling the temporal leaf initiation in grass.

关键词： phyllotaxy plastochron LHD2 RNA-binding protein stem elongation plant architecture Oryza sativa L

miRNAs modulate the drug response of tumor cells

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Science china(Life sciences) 2009年第9期52卷 797-801页

作者： WU XueMei1,3.& XIAO HuaSheng1,2 1 Center of Functional genomics,Key Laboratory of System Biology,Shanghai institutes for Biological sciences,{3. academy of sciences,Shanghai 20003.,china 2 National Engineering Center for Biochip at Shanghai,Shanghai 201203.china 3.Graduate University of {3. academy of sciences,Shanghai 20003.,china Center of Functional genomics Key Laboratory of System Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China Graduate University of chinese academy of sciences Shanghai China National Engineering Center for Biochip at Shanghai Shanghai China

Chemotherapy is one of the major treatments of malignant carcinomas. However,its efficiency is affected by both intrinsic and acquired resistance to anticancer drugs. The cellular mechanisms of drug resistance include the overexpression of energy-dependent transporters that eject anticancer drugs from cells such as p-glycoprotein and multidrug resistance related protein (MRP),the mutation of drug targets,the activation of DNA repair pathways,the defects in cellular death pathways and so on. The genetic and epigenetic changes of these genes can lead to cancer drug resistance. Among these mechanisms,microRNAs (miRNAs) which are critical and essential for many important processes such as development,differentiation,and even carcinogenesis have been reported to regulate the chemosen-sitivity of tumor cells. In this paper we briefly review the relationship between miRNA and cancer drug resistance.

关键词： cancer drug resistance miRNAs

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