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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 Sciences and biotechnology, Tsinghua University, beijing 100084,{2. state key laboratory of biomembrane and membrane biotechnology, Tsinghua University, beijing 100084,{2. National Engineering Research Center for beijing Biochip Technology, 18 Life Science Parkway, beijing 102.06,{2.) Department of Biological Sciences and biotechnology Tsinghua University Beijing 100084 China state key {2. of {2. and membrane 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.

PTEN,a general negative regulator of cyclin D expression

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Cell Research 2007年第4期17卷 291-292页

作者： Eirong Diao~1 Ye-Guang Chen ~1state key {2. of {2. and membrane biotechnology,Department of Biological Sciences and biotechnology Tsing-hua Universiry,beijing 100084,china Department of Biological Sciences and biotechnology State Key Laboratory of Biomembrane and Membrane Biotechnology Tsinghua University Beijing China

The tumor-suppressor phosphatase with tensin homol-ogy(PTEN)is frequently mutated in many malignanciesand is one of the most well studied tumor suppressor genes[1,2..PTEN,a lipid and protein dual phosphatase,plays avital role in embryonic development,cell growth,apoptosisand cell *** well-known function of PTEN isphosphatidylinositol-3(PI)-phosphatase,which functionsas a negative regulator of the PIkinase(PI3K)*** well established that PTEN regulates the G1-S transitionby modulating the expression of cyclin D1 and *** passage of any cell through cell cycles is subtlymodulated by a series of proteins,among which the mainplayers in animal cells include cyclins,CDKs(cyclin-de-pendent kinases,positive regulators)and CDK inhibitors(negative regulators such as p2.and *** Dsare key regulators during the G1 phase and there are threetypes of cyclin Ds,D1,D2.and D3 in mammalian cells[3].Although the phenotypic analyses of single cyclin Dknockout mice revealed that each of the D type cyclinsis sufficient to drive normal development of the majority

关键词： PTEN,a general negative regulator of cyclin D expression

Density functional theory study of the reaction paths of reactions of CH3C（O）O2.radicals with HO2.in the gas phase

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Progress in Natural Science:Materials International 2006年第12期16卷 1269-1274页

作者： ZHOU Yuzhi~ 1,2., ZHANG Shaowen~1 and LI Qianshu~1**(1. state key {2. of Explosion Science and Technology, {2. institute of Technology, {2. 100081, china 2. {2. institute of Education, {2. 100044, china) state key {2. of Explosion Science and Technology Beijing Institute of Technology Beijing 100081 China beijing institute of Education Beijing 100044 China

A DFT study on the reactions between CH_3C（O）O_2.nd HO_2.adicals has been carried out. It is suggested that both the triplet and singlet potential surfaces involve a complex mechanism with the formation of loosely bound intermediate complexes of reactants and products. The reaction prefers to occur on the triplet surface to produce peracetic acid (CH_3C（O）O_2.) and triplet O_2.olecule. The CH_3C（O）O_2. can further convert into CH_3C（O）O and HO radicals.

关键词： acetyl peroxy radicals HO2.radicals reaction mechanism DFT.

Propagation characteristics of converted refracted wave and its application in static correction of converted wave

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Science china Earth Sciences 2008年第S2期51卷 226-232页

作者： LIU Yang1,2.& WEI XiuCheng3 1 state key {2. of Petroleum Resource and Prospecting,china University of Petroleum,beijing 102.49,china 2.CNPC Geophysical Exploration key {2.,china University of Petroleum,beijing 102.49,china 3 Exploration and Production Research institute,SINOPEC,beijing 100083,china state key {2. of Petroleum Resource and Prospecting China University of Petroleum Beijing China CNPC Geophysical Exploration key laboratory China University of Petroleum Beijing China Exploration and Production Research institute SINOPEC Beijing China

Three-component seismic exploration through P-wave source and three-component geophone is an effective technique used in complicated reservoir exploration. In three-component seismic exploration data processing,one of the difficulties is static correction of converted wave. This paper analyzes propagation characteristics of non-converted and converted refracted waves,and discovers a favor-able condition for the formation of converted refracted wave,i.e. the velocity of overlaying medium S wave is much lower than that of underlying medium S wave. In addition,the paper proposes the static correction method of converted wave based on PPS converted refracted wave,and processes the real three-component seismic data with better results of static correction of converted wave.

关键词： PPS converted refracted wave converted wave static correction

GM-CSF-induced Ca_(2.) -activated non-voltage-dependent inwardly rectifying K_+ channel in murine peritoneal exudate macrophages

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Chinese Science Bulletin 1997年第11期42卷 947-952页

作者： ZHANG Xiaofeng, FENG Meifu, WU Caihong and ZHOU Pei’aistate key {2. of {2. and membrane biotechnology, Chinese Academy of Sciences, beijing 100080, china 1 . In-stitute of zoology, Chinese Academy of Sciences, beijing 100080, china 2.College of Life Sciences, Peking University, beijing 100871, china state key {2. of {2. and membrane biotechnology Chinese Academy of Sciences Beijing China institute of zoology Chinese Academy of Sciences Beijing China College of Life Sciences Peking University Beijing China

GRANULOCYTE-MACROPHAGE colony-stimulating factor(GM-CSF),a member in the family ofglycoprotein cytokines,can not only act to stimulate proliferation of immature progenitors,butalso enhance differentiated functions of mature effector *** has two kinds of biologicaleffects on mature effector cells,*** effect and indirect *** latter is also

关键词： K+ channel patch clamp GM-CSF macrophage.

Inhibition of the activating signals in NK92.cells by recombinant GST-sHLAG1α chain

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Cell Research 2004年第2期14卷 155-160页

作者： Ai Yu YAO~(1,2., Hai Yang TANG~1, Yun WANG~1, Mei Fu FENG~(1,*), Rou Li ZHOU~(2.*) ~1state key {2. of {2. and membrane biotechnology, institute of zoology, Chinese Academy of Science, beijing 100080, china ~2.epartment of Cell Biology and Medical Genetics, School of Basic Medical Sciences, Health Science Center, Peking University, beijing 100083, china. state key {2. of {2. and membrane biotechnology Institute of Zoology Chinese Academy of Science Beijing China Department of Cell Biology and Medical Genetics School of Basic Medical Sciences Health Science Center Peking University Beijing China

The soluble HLA-G1 (sHLA-G1) isoform was found to be secreted by trophoblast cells at the matemo-fetal interface, which suggests that it may act as an immunomodulator during pregnancy. In this paper, we reported that GST-sHLA-G1α chain could bind to its receptor ILT-2.on NK92.cells and then the latter recruited Src homology 2.domaincontaining tyrosine phosphatase-1 (SHP-1), which consequently dephosphorylated some important protein tyrosine kinases and blocked the activation of downstream molecules such as MEK and ERK so that the cytotoxicity of natural killer (NK) cells was inhibited. These results indicated that GST-sHLA-G1α chain might be exploited in new immunotherapy strategies aiming at inducing immunotolerance during allograft, xenograft and autoimmune situations. In addition, we found that modification of O-linked β-N-acetylglucosamine (O-GlcNAc) was involved in NK cells’ activating and inhibitory signals. This may provide a novel molecular target for inducing immunotolerance but needs furthe

关键词： NK92 GST-sHLA-G1α chain signal transduction SHP-1 O-G1cNAc.

Cloning and sequence characteristics of the genomic gene of a rice metallothionein

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Chinese Science Bulletin 2000年第2期45卷 153-156页

作者： YU Lihua, LIU Jinyuan, Masaaki Umeda, Hirofumi Uchimiya & ZHAO Nanming Department of Biological Sciences and biotechnology, state {2. {2. of biomembrane and membrane biotechnology, beijing 100084, china institute of Molecular and Cellular Bioscie Department of Biological Sciences and biotechnology State Key Laboratory of Biomembrane and Membrane Biotechnology Beijing China institute of Molecular and Cellular Biosciences The University of Tokyo Tokyo Japan

Northern blot analysis showed that a metallothionein gene, ricMT is expressed strongly in the stem of rice with an expression level that could be more than 100-fold stronger than in leaf blades. The results suggest that the 5’ upstream region flanking the coding sequence of the ricMT may contain a fairly strong promoter To elucidatr its regulation and promoter structure, the genomic clones of ricMT were screened out from a rice genomic library and a fragment of about 4084 bp was sequenced. The fragment included a 5’ upstream region of ca. 2.70 bp, a transcription region of ca. 690 bp and a 3’ downstream region of ca. 42. bp. Computer analysis of the sequence homology showed that the 5’ upstream region included a putative TATA box, a putative CAAT box, and a typical metal-responsive element TGCGCGCG. The results will promote further understanding of the mechanisms of gene regulation and metal response of plant metallothionein proteins.

关键词： rice metallothionein genomic gene regulatory sequence.

Effective solutions to a global 3D visual system in networking environments

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Science china Earth Sciences 2005年第11期48卷 2032-2039页

作者： ZHANG Liqiang1,2. ZHANG Yan3, YANG Chongjun2. LIU Suhong1, REN Yingchao2. RUI Xiaoping2.& LIU Donglin2.1. state key {2. of Remote Sensing Sciences, School of Geography and Remote Sensing, {2. Normal University, {2. 100875, china 2. state key {2. of Remote Sensing Sciences, institute of Remote Sensing Applications, Chinese Academy of Sciences, {2. 101001, china 3. institute of Geographical Sciences and Natural Resources Research, Chinese Academy of Sciences, {2. 101001, china state key {2. of Remote Sensing Sciences School of Geography and Remote Sensing Beijing Normal University Beijing China Chinese Academy of Sciences State Key Laboratory of Remote Sensing SciencesInstitute of Remote Sensing Applications China institute of Geographical Sciences and Natural Resources Research Chinese Academy of Sciences China

The development of Web-based global 3D visual system has made progresses. However, there exist few mature and effective ways for managing, transmitting and visualizing massive spatial data. Based on the related work, the paper illustrates the ellipsoidal quadtree technique for rapid access multi-scale and multiple level geographical data, integrates the streaming with level-of-detail rendering method for transmitting the data on the network, and im-plements large-scale terrain surface simplification using M-band wavelet transforms and mul-tiresolution triangulations. We fulfil a web-based global terrain visual system using COM com-ponents on the basis of the above techniques. The system has a good prospect in the military simulation and city plans.

关键词： massive spatial data, streaming transmission, system architecture, M-band wavelet

The role of Smad signaling in vascular and hematopoietic development revealed by studies using genetic mouse models

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Science china(Life Sciences) 2010年第4期53卷 485-489页

作者： LAN Yu & YANG Xiao state key {2. of Proteomics, Genetic {2. of Development and Diseases, institute of biotechnology, beijing 100071, china state key {2. of Proteomics Genetic Laboratory of Development and Diseases Institute of Biotechnology Beijing China

Smads are intracellular mediators of transforming growth factor β (TGF-β) superfamily signaling. In this review, we focus on the genetic mouse models for Smad pathways, which have provided functional evidence regarding the complex circuitry in angiogenesis and hematopoiesis during development. In the early stages of vascular development, TGF-β signaling is a contri buting factor in angiogenesis and vascular maturation. Whereas in the later embryogenesis, selected molecules of Smad pathways, such as TGF-β type II receptor (TbRII), ALK5, and Smad5, seem to be dispensable for vessel morphogenesis and integrity. TGF-β signaling is not required in the induction of hematopoietic precursors from mesoderm, but inhibits the subsequent expansion of committed hematopoietic precursors. By contrast, bone morphogenetic protein 4 (BMP4) has long been acknowledged pivotal in mesoderm induction and hematopoietic commitment during development. However, recent genetic evidence shows the BMP4-ALK3 axis is not crucial for the formation of hematopoietic cells from FLK1+ mesoderm. Because of the highly redundant mechanisms within the Smad pathways, the precise role of the Smad signaling involved in vascular and hematopoietic development remains nebulous. The generation of novel cell lineage restricted Cre transgenes would shed new light on the future relevant investigations.

关键词： Smad transforming growth factor β (TGF-β) bone morphogenetic protein (BMP) angiogenesis hematopoiesis knockout development