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

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 {3., 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 {3. 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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The protection effect of β-CD on DNA damage induced by ultrafine TiO_2

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science china Chemistry 2007年第2期50卷 272-275页

作者： ZHU RongRong,WANG ShiLong,SUN XiaoYu,ZHANG Rui & YAO SiDe school of life science and {3.,tongji university,shanghai 200092,china school of life science and {3. Tongji University Shanghai China

Under the photocatalysis of 3.5 nm ultraviolet radiation,ultrafine TiO2 caused the oxidative damage of Teasy plasmid DNA. The damage was determined by gel-electrophoresis. Then,a different dose of β-CD was added to the reaction,and the damage was restrained. The rate of damage restraining reached 97% when the mass of β-CD was 4 times as that of TiO2. Through UV scan and IR spectroscopy,it was found that the Ti-O of ultrafine TiO2 was bound with -OH of β-CD cavum and the -OH on the surface of ultrafine TiO2 disappeared,so the formation of ?OH was controlled. The ultrafine TiO2 has been widely used,but it was determined to be carcinogenic by some research. The protection effect of β-CD to DNA in the molecular level takes a new look on the surface modification of nano particles to decrease the toxic effect.

关键词： β-CD ultrafine TiO2 plasmid DNA oxide damage bond reaction damage restrain

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Impact and mechanism of TiO_2 nanoparticles on DNA synthesis in vitro

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science china Chemistry 2008年第4期51卷 367-372页

作者： LI ShiQiang, ZHU Hong, ZHU RongRong, SUN XiaoYu, YAO SiDe & WANG ShiLong school of life science and {3., tongji university, shanghai 200092, china school of life science and {3. Tongji University Shanghai China

The impact of TiO2 nanoparticles on DNA synthesis in vitro in the dark and the molecular mechanism of such impact were studied. The impact of TiO2 nanoparticles on DNA synthesis was investigated by adding TiO2 nanoparticles in different sizes and at various concentrations into the polymerase chain reaction (PCR) system. TiO2 nanoparticles were premixed with the DNA polymerase, the primer or the template, respectively and then the supernatant and the precipitation of each mixture were added into the PCR system separately to observe the impact on DNA synthesis. Sequentially the interaction be- tween TiO2 nanoparticles and the DNA polymerase, the primer or the template was further analyzed by using UV-visible spectroscopy and polyacrylamide gel electrophoresis (PAGE). The results suggest that TiO2 nanoparticles inhibit DNA synthesis in the PCR system in the dark more severely than mi- croscale TiO2 particles at the equivalent concentration and the inhibition effect of TiO2 nanoparticles is concentration dependent. The molecular mechanism of such inhibition is that in the dark, TiO2 nanoparticles interact with the DNA polymerase through physical adsorption while TiO2 nanoparticles do with the primer or the template in a chemical adsorption manner. The disfunction levels of the bio-molecules under the impact of TiO2 nanoparticles are in the following order: the primer > the tem- plate > the DNA polymerase.

关键词： TiO2 nanoparticles PCR DNA synthesis molecular mechanism

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Mechanisms of antiprostate cancer by gum mastic:NF-κB signal as target

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Acta Pharmacologica Sinica 2007年第3期28卷 446-452页

作者： Mei-lan HE~(2,4) Ang LI~2 Chun-su XU~2 Shun-li WANG~3.Meng-jie ZHANG~2 Hua GU~2 Yao-qin YANG~3.Hui-hong TAO~3.~2Institute of Cancer Research,life science and technology {3.,tongji university,shanghai 200092,china ~3.ellular Morphology Center,Medical {3.,tongji university,shanghai 200092,china Institute of Cancer Research Life Science and Technology SchoolTongji UniversityShanghai 200092China Cellular Morphology Center Medical SchoolTongji UniversityShanghai 200092China

Aim:To study the effect of gum mastic,a natural resin,on the proliferation ofandrogen-independent prostate cancer PC-3.cells,and further investigate themechanisms involved in this regulatory system,taking nuclear factor κB(NF-κB)signal as the ***:3.(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazoliumbromide(MTT)assay and a flow cytometer were used to detect the effect of gummastic on the proliferation of PC-3.***,reporter gene assay,RT-PCR,andWestern blotting were carried out to study the effects of gum mastic on the NF-κBprotein level and the NF-κB signal *** expression of genes involved inthe NF-κB signal pathway,including cyclin D1,inhibitors of κBs(IκBα),andphosphorylated Akt(p-AKT),were *** addition,transient transfectionassays with the 5×NF-κB consensus sequence promoter was also used to test theeffects of gum ***:Gum mastic inhibited PC-3.cell growth and blockedthe PC-3.cell cycle in the G1 *** mastic also suppressed NF-κB activity inthe PC-3.*** expression of cyclin D1,a crucial cell cycle regulator and anNF-κB downstream target gene,was reduced as ***,gum masticdecreased the p-AKT protein level and increased the IκBα protein ***:Gum mastic inhibited the proliferation and blocked the cell cycleprogression in PC-3.cells by suppressing NF-κB activity and the NF-κB signalpathway.

关键词： gum mastic prostate cancer NF-κB signal

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A simple solution route to control synthesis of Fe_3._4 nanomaterials at low temperature and their magnetic properties

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science china Chemistry 2009年第7期52卷 916-923页

作者： LIU Yi1,2, CHEN Yun1, ZENG YuPing2 & WANG ShiLong3.1 Department of Chemistry and Chemical Engineering, Zaozhuang university, Zaozhuang 277160, china 2 shanghai Institute of Ceramics, Chinese Academy of {3.s, shanghai 200050, china 3.school of life {3. and technology, tongji university, shanghai 200092, china Department of Chemistry and Chemical Engineering Zaozhuang University Zaozhuang China shanghai Institute of Ceramics Chinese Academy of Sciences Shanghai China school of life science and {3. Tongji University Shanghai China

A series of nanostructured iron compounds including cubic Fe3.4 and orthorhombic FeOOH were synthesized via a facile low temperature (in the range of 60-100℃) solution method. In the whole process, the interaction between FeCl2·4H2O and methenamine (C6H12N4) was carried out through a reflux device under different reaction conditions such as temperature, solvent, and duration. The samples were detected by XRD, TEM, SAED, physical property measurement system, and Mssbauer spectroscopy, separately. The experiments showed that magnetic mixture nanoparticles had flake and rod morphologies, and cubic Fe3.4 took on grain nanostructure. Magnetism measurements indicated that the saturated magnetization of the as-obtained magnetic mixture was lower than that of the cubic magnetite. Mssbauer spectroscopy testified the sample consisting of cubic magnetite rather than γ-Fe2O3. In addition, a possible growth mechanism of cubic magnetic nanoparticles under different conditions was discussed.

关键词： magnetic nanoparticles cubic Fe3.4 oxidation-coprecipitation method reflux magnetic properties at room temperature Mssbauer spectrum

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Protein Secondary Structure Prediction Using Dynamic Programming

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Acta Biochimica et Biophysica Sinica 2005年第3期37卷 167-172页

作者： Jing ZHAO Pei-Ming SONG Qing FANG Jian-Hua LUO school of life science & {3.,shanghai Jiaotong university,shanghai 200240,china shanghai Center for Bioinformation and {3.,shanghai 20023.,china Logistical Engineering university,Chongqing 400016,china school of life science & {3. Shanghai Jiaotong UniversityShanghai 200240 China shanghai Center for Bioinformation and technologyshanghai 20023. China Logistical Engineering universityChongqing 400016 China

In the present paper,we describe how a directed graph was constructed and then searched forthe optimum path using a dynamic programming approach,based on the secondary structure propensity ofthe protein short sequence derived from a training data *** protein secondary structure was thus pre-dicted in this *** average three-state accuracy of the algorithm used was 76.70%.

关键词： directed graph dynamic programming approach protein secondary structure

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Excavation and characterization of refuse in closed landfill

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Journal of Environmental sciences 2002年第3期14卷 303-308页

作者： ZHAO You cai (The State Key Laboratory of Pollution Control and Resource Reuse, school of Environmental science and Engineering, tongji university,{3., china. ) State Key Laboratory of Pollution Control and Resource Reuse School of Environmental Science and Engineering Tongji University Shanghai 200092 China

Refuse in landfills becomes stabilized as organic matter in refuse degrades and soluble inorganic substances dissolve during their long term stabilization process. In this paper, this process is also referred to as mineralization process and the resultant stabilized refuse referred to as aged refuse. Aged refuse contains a wide spectrum and huge quantity of microorganisms with strong decomposition capability for refractory organic matter present in some wastewater such as leachate. In this study, aged refuse excavated from 2 to 10 years old closed landfill compartments in shanghai Refuse Landfill is characterized in terms of particulate distribution by screening, total nitrogen, total phosphorus, biodegradable matter. The approaches for redevelopment of both land and aged refuse in the stabilized landfills are proposed.

关键词： landfill refuse mineralization

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Effect of Curing Regime on Bonding Strength of EVA Modified Mortar to Tile

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Journal of Wuhan university of technology(Materials science) 2010年第2期25卷 346-348页

作者：何代华 school of Materials science & Engineering University of Shanghai for Science Technology Key Laboratory of Advanced Civil Engineering Materials Ministry of Education Tongji University

Ethylene-Vinyl Acetate （EVA） redispersible powder and latex were used to modify mortar. Three kinds of curing regimes： standard curing, high temperature curing and freeze-thaw circle curing were adopted to cure the bonded samples. Bonding strength of EVA modified mortar was tested at 28 days. The development of bonding strengths under all three curing regimes were discussed and compared. The experimental results show that bonding strength increases with the increase of EVA content in mortar. The curing regime used within 28 days is critical according to the bonding strengths values under three curing regimes for different ages. The reasons of that the EVA can improve the bonding strength were analyzed.

关键词： EVA redispersible powder latex bonding strength curing regime

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Characteristics of fMRI BOLD signal and its neurophysiological mechanism

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Progress in Natural science:Materials International 2007年第6期17卷 630-638页

作者： Zhao Xiaohu1,2, Wu Yigen3.and Guo Shengli3.1. College of life sciences, Zhejiang university, Hangzhou 3.0058,{3. 2. Imaging Department of tongji Hospital of tongji university, shanghai 200065,{3. 3. College of Mathematics and Physics, Nanjing university of Information science and technology, Nanjing 210044,{3.) College of life sciences Zhejiang University Hangzhou 310058 China Imaging Department of tongji Hospital of tongji university Shanghai 200065 China College of Mathematics and Physics Nanjing University of Information Science and Technology Nanjing 210044 China

The functional magnetic resonance imaging (fMRI) based on blood oxygen level dependent (BOLD) contrast has emerged as one of the most potent noninvasive tools for mapping brain function and has been widely used to explore physiological, pathological changes and mental activity in the brain. Exploring the nature and property of BOLD signal has recently attracted more attentions. Despite that great progress has been made in investigation of the characteristics and neurophysiological basis, the exact nature of BOLD signal remains unclear. In this paper we discuss the characteristics of BOLD signals, the nonlinear BOLD response to external stimuli and the relation between BOLD signals and neural electrophysiological recordings. Furthermore, we develop our new opinions regarding nonlinear BOLD response and make some perspectives on future study.

关键词： functional magnetic resonance imaging blood oxygen level dependent nonlinear response neural electrophysiological activity.

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Effect of Polypropylene Fibers on the Long-term Tensile Strength of Concrete

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Journal of Wuhan university of technology(Materials science) 2007年第1期22卷 52-55页

作者：姚武 school of Materials science and Engineering Tongji University

The influence of low volume fraction of polypropylene（PP） fibers on the tensile properties of normal and high strength concretes was studied. The experimental results indicate that the addition of PP fibers in concrete leads to a reduction in tensile strength during the age of 28 d. Whereas, after 28 days, there is a notable effect in tensile strength due to PP fibers restraining the formation and growth of microcracks in concrete, which improves the continuity and integrality of concrete structure, Thus, a low volume fraction of PP fibers is beneficial to enhancing the long-term tensile strength of concrete materials and improving the durability of concrete structures.

关键词： polypropylene fiber concrete tensile strength microcrack

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