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A feature ensemble technology to identify molecular mechanisms for distinction between multiple subtypes of lymphoma

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Progress in Natural Science:Materials International 2008年第12期18卷 1491-1500页

作者： Yueying Yang~(a,1) Haiyun Wang~(a,b,1) Xia Li~(a,b,c) Xue Xiao~c Su Fei~a Chuanxing Li~a Hongzhi Wang~d Shaoqi Rao~(a,c,e) Yadong Wang~d a College of Bioinformatics Science and Technology,Bio-pharmaceutical key laboratory of Heilongjiang Province and State,Harbin Medical University,Harbin 150081,china b College of Life Science and Technology,Tongji University,Shanghai 200092,china c The Biomedical engineering Institute,Capital Medieal University,beijing 100054,china d Department of Computer Science,Harbin Institute of Technology,Harbin 150080,china e Department of molecular Cardiology,Cheveland Clinic Foundation,Cleveland,OH 44195,USA College of Bioinformatics Science and Technology Bio-pharmaceutical Key Laboratory of Heilongjiang Province and State Harbin Medical University Harbin 150081 China College of Life Science and Technology Tongji University Shanghai 200092 China The Biomedical engineering Institute Capital Medical University Beijing 100054 China Department of Computer Science Harbin Institute of Technology Harbin 150080 China Department of molecular Cardiology Cleveland Clinic Foundation Cleveland OH 44195 USA

Due to complexities and genetic heterogeneities of biological phenotypes,robust computational approaches are desirable to achieve high generalization performance with multiple classifiers,perturbations of the data structures,and biological *** purpose of this study is to extend our developed ensemble decision approach to distinguish multiple heterogeneous phenotypes and to elucidate the underlying molecular bridges that intertwine the *** work identifies the significant molecular mechanisms (disease-relevant genes and functions) that underpin the complex molecular mechanisms for distinction between multiple phenotypes. Feature genes and hierarchical gene cores identified by our method have achieved high accuracy in the classification of multiple pheno- *** results show that the proposed analysis strategy is feasible and powerful in the classification of biological subtypes and in the explanation of the molecular connections between clinical *** interpretations with gene Ontology revealed concerted genetic pathways for some lymphoma subtypes.

关键词： Ensemble decision approach molecular mechanisms Lymphoma Microarray

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Cloning and expression of low-molecular-weight glutenin genes from Chinese elite wheat cultivar "xiaoyan 54

Cloning and expression of low-molecular-weight glutenin gene...

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2003年全国作物遗传育种学术研讨会

作者： WANG Xin-Yu WAN Yong-Fang LIU Zhi-Jie WANG Dao-Wen (1. The key laboratory of Crop genetics & Breeding, Ministry of Agriculture, Institute of Crop Breeding and Cultivation, Chinese Academy of Agricultural Sciences, beijing 100081,china 2. The State key laboratory of Plant Cell & Chromosome engineering, Institute of genetics and Developmental biology, Chinese Academy of Sciences, beijing 100101,china)

The low-molecular-weight glutenin subunits (LMW-GS) account for 40%wheat gluten protein content by mass, and these proteins are considered to significantly affect dough-quality characteristics. Five n

关键词： low-molecular-weight glutenin subunit (LMW-GS) low-molecular-weight glutenin subunit genes low-molecular-weight M type gene (LMW-m) low-molecular-weight I type gene (LMW-I)

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The Zinc finger protein,Zfrlp,is conjugation specific expressed and required for sexual development in Tetrahymena thermophila

The Zinc finger protein,Zfrlp,is conjugation specific expres...

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“细胞活动生命活力”——中国细胞生物学学会全体会员代表大会暨第十二次学术大会

作者： Xu Jing,Liang Aihua,Wang Wei key laboratory of Chemical biology and molecular engineering of Ministry of Education,Institute of Biotechnology,Shanxi University, Taiyuan,030006,china

Conjugation in Tetrahymena thermophila involves a developmental program which is characterized by three prezygotic nuclear divisions,pronuclear exchange and fusion,postzygotic and exconjugant stage. Conjugation junction structure appeared with conjugation development initiation and disappeared during exconjugant *** structural and functional proteins are involved in the junction structure establishment and *** and RT-PCR showed a zinc finger protein encoding gene, ZFR1,is conjugation specific expressed and significantly upregulated at 2hr during conjugation stage. Immunofluorescence staining of HA-Zfrlp showed Zfrlp specifically localized in conjugation junction region.N-terminal Zinc domain and C-terminal hydrophobic domain of Zfrlp is required for Zfrlp conjugation junction specific *** development of somatic ZFR1 knockout cell is aborted at 8-10 hr pronuclear exchange and fusion ***,Zfrlp maintain conjugation junction stability during prezygotic nuclear division *** results argue that zinc protein Zfrlp is required for conjugation structure integrity and is essential for development of sexual life cycle in Tetrahymena cell.

关键词： ZFR1 Conjugation junction Localization Tetrahymena thermophila

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Cloning,Sequencing and Expression Analysis of the First Cellulase gene Encoding Cellobiohydrolase 1 from a Cold-adaptive Penicillium chrysogenum FS010

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Acta Biochimica et Biophysica Sinica 2007年第2期39卷 101-107页

作者： Yunhua HOU~(1,2) Tianhong WANG~1 Hao LONG~1 and Huiynan ZHU~(1,2) ~1State key laboratory of Microbial Technology,Shandong University,Jinan 250100,china ~2Department of Food and Biologic engineering,Shandong Institute of Light Industry,Jinan 250323,china State key laboratory of Microbial Technology Shandong University Jinan 250100 China Department of Food and Biologic engineering Shandong Institute of Light Industry Jinan 250323 China

A cellobiohydrolase 1 gene (cbhl) was cloned from Penicillium chrysogenum FS010 by amodified thermal asymmetric interlaced polymerase chain reaction (TAIL-PCR).DNA sequencing showsthat cbhl has an open reading frame of 1590 bp, encoding a putative protein of 529 amino acid *** amino acid sequence revealed that CBHI has a modular structure with a predicted molecular massof 56 kDa and consists of a fungal type carbohydrate binding module separated from a catalytic domain bya threonine rich linker *** putative gene product is homologous to fungal cellobiohydrolases inFamily 7 of the glycosyl hydrolases.A novel cbhl promoter (1.3 kb) was also cloned and sequenced,whichcontains seven putative binding sites (5'-SYGGRG-3') for the carbon catabolite repressor *** ofvarious carbon sources to the cbhl transcription of *** was examined by Northern analysis,suggesting that the expression of cbhl is regulated at transcriptional *** cbhl gene in cold-adaptivefungus *** was expressed as an active enzyme in Saccharomyces cerevisiae *** recombinantCBHI accumulated intracellularly and could not be secreted into the medium.

关键词： Penicillum chrysogenum cellobiohydrolase TAIL-PCR promoter of cbh1

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Codon Optimizing of Porcine Growth Hormone for high Efficient Expression and Purification

Codon Optimizing of Porcine Growth Hormone for high Efficien...

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2008年全国生物化学与分子生物学学术大会

作者： Zhen-xing Zhang Bao-feng Chai (key laboratory of Chemical biology and molecular engineering of Ministry of Education,Institute of Biotechnology Shanxi University,Taiyuan 030006,china)

Growth of animal is largely regulated by growth hormone (GH).The porcine growth hormone is a peptide hormone with about 190 *** activities resulting from GH involve binding to its receptor to regulate growth,developme...

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生长抑制因子(GIF)与G蛋白Rab3a直接相互作用

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生物化学与生物物理进展 2001年第6期28卷 880-884页

作者：康巧华陈巧林任宏伟茹炳根北京大学生命科学学院蛋白质工程与植物基因工程国家重点实验室北京100871 扬州大学畜牧兽医学院扬州225009

生长抑制因子 (growthinhibitoryfactor,GIF) ,又称金属硫蛋白 3,为 6 8个氨基酸组成的脑特异性金属硫蛋白 ,具有广泛的生理功能 ;GIF可能与阿尔茨海默氏症 (Alzheimer s)病理相关 ,在Alzheimer s脑提取物存在下 ,还对神经细胞具有特异... 详细信息

生长抑制因子 (growthinhibitoryfactor,GIF) ,又称金属硫蛋白 3,为 6 8个氨基酸组成的脑特异性金属硫蛋白 ,具有广泛的生理功能 ;GIF可能与阿尔茨海默氏症 (Alzheimer s)病理相关 ,在Alzheimer s脑提取物存在下 ,还对神经细胞具有特异的生长抑制活性 .然而 ,对其发挥生长抑制作用的分子机制并不清楚 .运用酵母双杂交系统从人脑cDNA文库中筛选与GIF相互作用因子 ,从 4 1× 10 6个人脑cDNA文库转化子中 ,首次筛选到Ras家族G蛋白Rab3aC端 ,包含 87个氨基酸的片段能与GIF相互作用 ;用PCR自人胎盘总cDNA中获得包含完整Rab3a编码序列的cDNA ;通过酵母双杂交实验表明 ,全长Rab3a蛋白亦能与GIF相互作用 .免疫共沉淀和蛋白质印迹实验进一步验证了GIF与Rab3a在哺乳动物细胞中可以相互作用 ;而且 ,Rab3a是以GTP结合形式(GTP Rab3a)

关键词：生长抑制因子阿尔茨海默氏症酵母双杂交系统 Rab3a 免疫共沉淀 G蛋白相互作用 GIF

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Quantitative detection of ING1 mRNA under different gene regulation based on molecular beacon

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Chinese Science Bulletin 2006年第17期51卷 2059-2064页

作者： LIU Bin1,2,3,4, WANG Kemin1,2,3,4, XIAO Zhiqiang5,6, WANG Wei1,3,4, TAN Weihong1,2,3,4, SUN Yi5,6, TANG Hongxing1,3,4 & YANG Xiaohai1,3,41. State key laboratory of Chemo/Biosensing and Chemometrics, Hu- nan University, Changsha 410082, china 2. Life Science and Biotechnology Institute, Hunan University, Chang- sha 410082, china 3. Chemistry and Chemical Engineer College, Hunan University, Changsha 410082, china 4. Hunan engineering Research Center for Bio-Nanotechnology, Hunan University, Changsha 410082, china 5. Medical Experiment Research Center, Xiangya Hospital, Central South University, Changsha 410008, china 6. key laboratory of Cancer Proteomics of Chinese Ministry of Health, Changsha 410008, china State key laboratory of Chemo/Biosensing and Chemometrics Hunan University Changsha China Life Science and Biotechnology Institute Hunan University Changsha China Chemistry and Chemical Engineer College Hunan University Changsha China Hunan engineering Research Center for Bio-Nanotechnology Hunan University Changsha China Medical Experiment Research Center Xiangya Hospital Central South University Changsha China key laboratory of Cancer Proteomics of Chinese Ministry of Health Changsha China

The effects of drug treatment, gene transfection, and p53 RNA interference (RNAi) on level of ING1 mRNA in tumor cells were quantitatively detected with the help of ING1 molecular beacon (MB)/cRNA standard curve based on MB detection technology. Results showed that the level of ING1 mRNA could be upregulated by 5-FU treatment or ING1 transfection in low expression cell line of MCF-7 and be inhibited by silencing p53 with RNAi technology in normal expression cell line of CNE2. The level of ING1 varied from 7.7×10?16 to 53.4× 10?16 mol/μg total RNA of tumor cells. The results not only provided evidence for the regulation effects of gene expression but also were applied to investigat- ing the interaction of multigenes on signal transduc- tion pathway.

关键词： ING1 RT-PCR 定量分析分子信号 mRNA

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A novel model-free approach for reconstruction of time-delayed gene regulatory networks

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中国科学：生命科学英文版 2006年第2期49卷 190-200页

作者： JIANG Wei1,2, LI Xia1,2,3,4, GUO Zheng1,2,3, LI Chuanxing1, WANG Lihong1 & RAO Shaoqi1,5 1. Department of Bioinformatics, Harbin Medical University, Harbin 150086, china 2. Department of Computer Science, Harbin Institute of Technology, Harbin 150080, china 3. School of Life Science and Technology, Tongji University, Shanghai 200092, china 4. Biomedical engineering Institute, Capital University of Medical Sciences, beijing 100054, china 5. Departments of Cardiovascular Medicine and molecular Cardiology, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA Department of Bioinformatics Harbin Medical University Harbin China Department of Computer Science Harbin Institute of Technology Harbin China School of Life Science and Technology Tongji University Shanghai China Departments of Cardiovascular Medicine and molecular Cardiology Cleveland Clinic Foundation Cleveland USA

Reconstruction of genetic networks is one of the key scientific challenges in functional genomics. This paper describes a novel approach for addressing the regulatory dependencies be-tween genes whose activities can be delayed by multiple units of time. The aim of the proposed ap-proach termed TdGRN (time-delayed gene regulatory networking) is to reversely engineer the dy-namic mechanisms of gene regulations, which is realized by identifying the time-delayed gene regu-lations through supervised decision-tree analysis of the newly designed time-delayed gene expres-sion matrix, derived from the original time-series microarray data. A permutation technique is used to determine the statistical classification threshold of a tree, from which a gene regulatory rule(s) is ex-tracted. The proposed TdGRN is a model-free approach that attempts to learn the underlying regula-tory rules without relying on any model assumptions. Compared with model-based approaches, it has several significant advantages: it requires neither any arbitrary threshold for discretization of gene transcriptional values nor the definition of the number of regulators (k). We have applied this novel method to the publicly available data for budding yeast cell cycling. The numerical results demonstrate that most of the identified time-delayed gene regulations have current biological knowledge supports.

关键词： gene regulatory networks, time delayed, decision tree.

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Highly Efficient G-quadruplex Recognition by a Novel Phenanthroline Compound

Highly Efficient G-quadruplex Recognition by a Novel Phenant...

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第六届全国化学生物学学术会议

作者： Lihua Wang Chunying Wei~* (key laboratory of Chemical biology and molecular engineering of Ministry of Education,Institute of molecular Science,Shanxi University,Taiyuan 030006)

＜正＞Phenanthroiine derivatives are of great interest as anticancer drugs for telomerase inhibition resulting from binding to G4 motifs in human *** this paper,A compound N,N’-bis（phenyl-4-ethoxy-piperidine）-1,10-...

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Genome-wide Analysis of Smad Targets Reveals the Role of BMP Signaling in Embryonic Stem Cell Fate Determination

Genome-wide Analysis of Smad Targets Reveals the Role of BMP...

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第十一次中国生物物理学术大会暨第九届全国会员代表大会

作者： Teng Fei 1# ,Kai Xia 2# ,Zhang Chen 2 ,Hua Chen 1 ,Zhongwei Li 1 ,Jianping Zhang 1 ,Bing Zhou 2 ,Huasheng Xiao 3 ,Jing-Dong J.Han 2* ,Ye-Guang Chen 1* 1The State key laboratory of Biomembrane and Membrane Biotechnology, Department of Biological Sciences and Biotechnology,Tsinghua University,beijing 100084,china 2CAS key laboratory of molecular Developmental biology and Center for molecular Systems biology,Institute of genetics and Developmental biology,the Chinese Academy of Sciences,beijing 100101,china 3National engineering Center for Biochip at Shanghai,Zhangjiang Hi-Tech Park, Shanghai,201203,china

＜正＞Embryonic stem（ES）cells are under precise control of both intrinsic self-renewal gene regulatory network and extrinsic growth factor-triggered signaling *** external

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