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Plant protein kinase genes induced by drought, high salt and cold stresses

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Chinese science Bulletin 2000年第13期45卷 1153-1157页

作者： LIU Qiang , ZHANG Yong & Chen Shouyi1. Deparlmenl of biological science and {2., tsinghua university, Beijing 100084, china 2. department of biological science and biotechnology, slate key laboratory of biomembrane and membrane biotechnology, tsinghua university, Beijing 100084, china 3. Institute of Genetics, Chinese Academy of sciences, Beijing 100101, china department of biological {2. and biotechnology Tsinghua University Beijing China department of biological {2. and biotechnology State Key Laboratory of Biomembrane and Membrane Biotechnology Tsinghua University Beijing China Institute of Genetics Chinese Academy of Sciences Beijing China

Drought, high salt and cold are three different kinds of environment stresses that severely influence the growth, development and productivity of crops. They all decrease the water state of plant cells, and consequently result in the harm of plant from water deficit. Several genes encoding protein kinases and induced by drought, high salt and low temperature have been isolated from Arabidopsis. These protein kinases include receptor protein kinase (RPK), MAP kinases, ribosomal-protein kinases and transcription-regulation protein kinase. The expression features of these genes and the regulatory roles of these protein kinases in stress response and signal transduction are discussed.

关键词： protein kinase environment stress signal transduction gene expression.

Electrophysiological research of synapse formation from beginning to maturity

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Chinese science Bulletin 1998年第1期43卷 55-59页

作者： XIE Zuoping and ZHENG Yufang State key laboratory of {2. and {2. Biotechnique department of biological sciences and biotechnology, tsinghua university, Beijing 100084, china State key laboratory of {2. and {2. Biotechnique Tsinghua University Beijing China department of biological {2.s and biotechnology Tsinghua University Beijing China

The development of synapses is an important question in neurobiology. We employ patchclamp technique to record MEPCs and EPCs of myoballs in Xenopus cell culture. The rate of EPC/MEPC is related with synapses maturation. Accordingly, we define the mature synapses as those whose rate of presynaptic membrane’s EPC to MEPC is more than 8. The process of maturation needs about 2.5 h after neurites contact with myoballs. We divide the development of synapses into three stages: young, developing and mature. The neurotransmitters stack gradually and increase by hundreds of times along with young synapses growing into maturity. So the process of synapses maturation should include presynaptic membrane specialization, postsynaptic membrane specialization and neurotransmitters stack.

关键词： definition of mature synapse α latrotoxin (α LTX) neurotransmitter stack.

Structure and regulatory function of plant transcription factors

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Chinese science Bulletin 2001年第4期46卷 271-278页

作者： LIU Qiang, ZHANG Guiyou & CHEN Shouyidepartment of biological {2. and biotechnology, tsinghua Univorsity, Beijing 100084, china department of biological {2. and biotechnology, State laboratory of biomembrane and {12. biotechnology, tsinghua university, Beijing 100084, china Institute of Genetics, Chinese Academy of {2.s, Beijing 100101, china department of biological {2. and biotechnology Tsinghua University Beijing China department of biological {2. and biotechnology State Laboratory of Biomembrane and Membrane Biotechnology Tsinghua University Beijing China Institute of Genetics Chinese Academy of Sciences Beijing China

The expression of inducible genes in plants is regulated by specific transcription factors at the transcrip-tional level. A typical transcription factor usually contains a DNA-binding domain, a transcription regulation domain, a dimerization site and a nuclear localization domain. These functional domains define the characteristic, localization and regulatory role of a transcription factor. Transcription factors recognize and bind to specific cis-acting elements or interact with other proteins, and then activate or repress the transcription of target genes by their functional domains. In recent years, elucidation on the structure and function of transcription factors has become an important subject in plant molecular biology.

关键词： transcription factor DNA-binding domain cis-acting element.

A measurement error model for microarray data analysis

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Progress in Natural science:Materials International 2005年第7期15卷 614-620页

作者： ZHOU Yiming and CHENG Jing ( department of biological {2.s and biotechnology, tsinghua university, Beijing 100084, china State key laboratory of biomembrane and membrane biotechnology, tsinghua university, Beijing 100084, china National Engineering Research Center for Beijing Biochip Technology, 18 Life {2. Parkway, Beijing 102.06, china) department of biological {2.s and biotechnology Tsinghua University Beijing 100084 China. State key laboratory of {2. and {2. biotechnology Tsinghua University Beijing 100084 China. National Engineering Research Center for Beijing Biochip Technology 18 Life Science Parkway Beijing 102206 China

Microarray technology has been widely used to analyze the gene expression levels by detecting fluorescence intensity in a high throughput fashion. However, since the measurement error produced from various sources in microarray experiments is heterogeneous and too large to be ignored, we propose here a measurement error model for microarray data processing, by which the standard deviation of the measurement error is demonstrated to be linearly increased with fluorescence intensity. A robust algorithm, which estimates the parameters of the measurement error model from a single microarray without replicated spots, is provided. The model and algorithm for estimating of the parameters from a given data set are tested on both the real data set and the simulated data set, and the result has been proven satisfactory. And, combining the measurement error model with traditional Z-test method, a full statistical model has been developed It can significantly improve the statistical inference for identifying differentially expressed genes.

关键词： microarray measurement error model parameter estimation differentially expressed genes.

Effects of genistein, daidzein and glycitein on the osteogenic and adipogenic differentiation of bone marrow stromal cells and on the adipogenic trans-differentiation of osteoblasts

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Progress in Natural science:Materials International 2005年第11期15卷 993-999页

作者： LI Xianghui, ZHANG Jinchao, SUI Senfang and YANG Mengsu (State key laboratory of {2., {2. of biological sciences and biotechnology, tsinghua university, Beijing 100084, china {2. of Chemistry, College of Chemistry & Environmental science, Hebei university, Baoding 071002. china {2. of Biology and Chemistry, City university of Hong Kong, Hong Kong, china) State key laboratory of {2. Department of Biological Sciences and Biotechnology Tsinghua University Beijing 100084 China. department of Chemistry College of Chemistry & Environmental Science Hebei University Baoding 071002 China. department of Biology and Chemistry City University of Hong Kong Hong Kong China

The 3-(4,5-dimethylthiazol-2.yl)-2.5-diphenyl tetrazolium bromide (MTT), alkaline phosphatase (ALP) activity and oil red O assays were used to examine the effects of genistein, daidzein and glycitein on the osteogenic and adipogenic differentiation of primary mouse bone marrow stromal cells (MSCs) and the adipogenic trans-differentiation of primary mouse osteoblasts. The results indicated that daidzein, genistein and glycitein at concentrations from 1×10-8 mol/L to 1×10-5mol/L promoted the proliferation of MSCs and osteoblasts; genistein, daidzein and glycitein promoted osteogenic differentiation and inhibited adipogenic differentiation of MSCs, and inhibited adipocytic transdifferentiation of osteoblasts at appropriate concentrations as 17β-estradiol. It suggests that genistein, daidzein and glycitein regulate a dual differentiational process of MSCs into the osteogenic and adipogenic lineages, and trans-differentiational process of primary osteoblasts into the adipocyte lineages, causing a lineage shift toward osteoblast. Protective effects of them on bone may be mediated by a reversal of adipogenesis which may promote the proliferation, differentiation and mineralization of osteoblasts, and make adipocytes secrete less cytokines which may promote osteoclast formation and activation. In addition, the results also indicated that genistein, daidzein and glycitein may be helpful in preventing the development of steroid induced osteonecrosis.

关键词： genistein daidzein glycitein bone marrow stromal cells osteoblasts osteogenic differentiation adipogenic differentiation adipogenic trans-differentiation.

Cloning and characterization of cotton heteromeric acetyl-CoA carboxylase genes

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Progress in Natural science:Materials International 2007年第12期17卷 1412-1418页

作者： Qiao Zhixin and Liu Jinyuan(laboratory of Molecular Biology and Protein science laboratory of the Ministry of Education, department of biological sciences and biotechnology, tsinghua university, Beijing 100084, china) laboratory of Molecular Biology and Protein science laboratory of the Ministry of Education Department of Biological Sciences and Biotechnology Tsinghua University Beijing 100084 China

Heteromeric acetyl-coenzyme A (CoA) carboxylase (ACCase) catalyzes the formation of malonyl-CoA from acetyl-CoA. It plays an essential role in fatty acid synthesis in prokaryotes and most of plants. The heteromeric ACCase is composed of four subunits: biotin carboxylase (BC), biotin carboxyl carrier protein (BCCP), and α- and β-subunits of carboxyltransferase (α- and β-CT). In this study, we cloned five novel genes encoding the subunits of heteromeric ACCase (one BC, BCCP and β-CT, and two α-CTs) from cotton (Gossypium hirsutum cv. zhongmian 35) by RACE-PCR. The deduced amino acid sequence of these cDNAs shares high similarity with other reported heteromeric ACCase subunits. The phylogenetic analysis indicated that the different subunits of heteromeric ACCase were grouped in a similar pattern. Southern blot analysis revealed the milti-copy patterns of these heteromeric ACCase genes in cotton genome. Semi-quantitative RT-PCR demonstrated that heteromeric ACCase genes were constitutively expressed in all of the cotton tissues, but the transcripts accumulated at a relatively low level in roots. To our knowledge, this is the first report about characterization of the heteromeric ACCase genes in cotton.

关键词： heteromeric ACCase cotton gene cloning fatty acid synthesis.

Crystal Structure of the MH2.domain of Drosophila Mad

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science china(Life sciences) 2009年第6期52卷 539-544页

作者： WANG Chong,CHEN Lei,WANG Le & WU JiaWei MOE key laboratory of Bioinformatics,{2. of {2. sciences and biotechnology,tsinghua university,Beijing 100084,china 1. MOE key laboratory of Bioinformatics Department of Biological Sciences and Biotechnology Tsinghua University Beijing 100084 China

The decapentaplegic(Dpp),a member of the TGF-β superfamily,plays a pivotal role in the control of proliferation,global patterning and induction of specific cell fates during Drosophila *** against Dpp(Mad) is the founding member of the conserved Smad protein family which spe-cifically transduces the intracellular TGF-β signaling *** we report the 2.80 structure of the MH2.domain of Mad(Mad-MH2. that was readily superposed to the mammal Smad-MH2.*** unphosphorylated Mad-MH2.forms a symmetric homotrimer in crystals,consistent with the result of the size-exclusion chromatography that Mad-MH2.exhibited a propensity for concentration-dependent oligomerization prior to *** analysis revealed that the formation of homotrimeric Mad-MH2.is mainly mediated by contacts involving the extreme C-terminal SSVS motif,and is strengthened by phosphorylation of the last two Ser residues which was confirmed by the gel filtration analysis of the pseudophosphorylated Mad-MH2.DVD).Intriguingly,the homotrimer within an asymmetric unit only possesses two ordered C-terminal tails,reminiscent of the arrangement of the R-Smad/Smad4 complexes,indicating that the subunit with a flexible SSXS motif would be readily replaced by Co-Smad to form a functional heterotrimer.

关键词： TGF-β signaling Smad protein family MH2 domain crystal structure homotrimerization

Two forms of the membrane-bound state of the first C2.domain (C2.) of synaptotagminⅠand calcium-triggered membrane insertion

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Chinese science Bulletin 2003年第17期48卷 1822-1827页

作者： HE Yuhong, LI Xianghui, WANG Fu, XUE Yi & SUI Senfang department of biological {2.s & biotechnology, State key Labora-tory of biomembrane, tsinghua university, Beijing 100084, china department of biological {2.s and biotechnology State Key Laboratory of Biomembrane Tsinghua University Beijing 100084 China

The synaptic vesicle protein synaptotagminⅠ (sytⅠ) is a vesicle transmembrane protein present in synap-tic vesicles, which has been proposed as the Ca2. sensor that regulates secretion. The C2. domain is the membrane proximal part of its cytoplasmic domain. The interaction between C2. and lipid bilayer has been considered to be essential for triggering neurotransmitter release. In the pre-sent work, the measurements of membrane surface tension and surface concentration showed that the C2. domain of sytⅠexhibited two membrane-bound states: the surface adsorption state and the membrane insertion state. The sur-face absorption state formed in a Ca2.-independent manner with lower affinity, while the membrane insertion state formed with high affinity was only found in the presence of Ca2.. Both the Ca2.-independent and Ca2.-dependent sytⅠ- membrane interactions required anionic phospholipids, such as phosphatidylserine (PS). When expressed into rat pheo-chromocytoma (PC12. cells and human embryonic kidney (HEK-2.3) cells, as demonstrated by immunofluorescence staining and subcellular fractionation, most of the C2. was found at the plasma membrane, even when the cells were depleted of Ca2. by incubation with EGTA. These results suggested a new molecular mechanism of sytⅠas a Ca2. sensor in membrane fusion. Ca2.-independent surface ad-sorption might attach sytⅠto the release site during the docking or priming step. When intracellular Ca2. increased, sytⅠtriggered the neurotransmitter release following the Ca2.-dependent penetration into the target membrane.

关键词：突触小泡蛋白质膜贯通蛋白质钙离子薄膜插入 C2. 薄膜边界状态

Interaction of cellular-localized signature modules in response to prostate cancer

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Progress in Natural science:Materials International 2007年第11期17卷 1368-1375页

作者： Zhu Jing1, Guo Zheng1,2. Zhang Min2. Yang Da2. Wang Jing2.and Wang Chenguang2.1. School of Life science and Bioinformatics Centre, university of Electronic science and Technology of china, Chengdu 610054, china 2. department of Bioinformatics, Bio-Pharmaceutical key laboratory of Heilongjiang Province, Harbin Medical university, Harbin 150081, china) School of Life science and Bioinformatics Centre University of Electronic Science and Technology of China Chengdu 610054 China department of Bioinformatics Bio-Pharmaceutical Key Laboratory of Heilongjiang Province， Harbin Medical University， Harbin 150081 China

Rapid progress in high-throughput biotechnologies (e.g. microarrays) and exponential accumulation of gene functional knowledge makes it promising for systematic understanding of complex human diseases at the functional modules level. Current modular categorizations can be defined and selected more specifically and precisely in terms of both biological processes and cellular locations, aiming at uncovering the modular molecular networks highly relevant to cancers. Based on Gene Ontology, we identifed the functional modules enriched with differentially expressed genes and characterized by biological processes and specific cellular locations. Then, according to the ranking of the disease discriminating abilities of the pre-selected functional modules, we further defined and filtered signature modules which have higher relevance to the cancer under study. Applications of the proposed method to the analysis of a prostate cancer dataset revealed insightful biological modules.

关键词： microarray analysis Gene Ontology classification analysis cellular location functional module