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Comparative Analysis of Two-component Signal Transduction System in Two Streptomycete Genomes

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Acta Biochimica et Biophysica Sinica 2007年第5期39卷 317-325页

作者： WU WEI~(1,3#), Weihua WANG~(2#), Zhiwei CAO~(3#), Hong YU~3, Xiaojing WANG~1, Jing ZHAO~3, Hao TAN~3, Hao XU~3, Weihong JIANG~(2*), and Yixue LI~(1,3*) 1 Bioinformation Center, Key Lab of Systems Biology, shanghai Institutes for Biological sciences, chinese academy of sciences, graduate school of the chinese academy of sciences, shanghai 200031, china.2 Laboratory of Molecular Microbiology, Institute of Plant Physiology and Ecology, shanghai Institutes for Biological sciences, chinese academy of sciences, graduate school of the chinese academy of sciences, shanghai 200032, china.3 shanghai Center for Bioinformation Technology, shanghai 200235, china Bioinformation Center Key Lab of Systems Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Graduate School of the Chinese Academy of SciencesShanghai 200031 China shanghai Center for Bioinformation Technologyshanghai 200235 China Laboratory of Molecular Microbiology Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Graduate School of the Chinese Academy of SciencesShanghai 200032 China

Species of the genus Streptomyces are major bacteria responsible for producing most natural antibiotics. Streptomyces coelicolor A3(2) and Streptomyces avermitilis were sequenced in 2002 and 2003, respectively. Two-component signal transduction systems (TCSs), consisting of a histidine sensor kinase (SK) and a cognate response regulator (RR), form the most common mechanism of transmembrane signal transduction in prokaryotes. TCSs in S. coelicolor A3(2) have been analyzed in detail. Here, we identify and classify the SK and RR of S. avermitilis and compare the TCSs with those of S. coelicolor A3(2) by computational approaches. Phylogenetic analysis of the cognate SK-RR pairs of the two species indicated that the cognate SK-RR pairs fall into four classes according to the distribution of their orthologs in other organisms. In addition to the cognate SK-RR pairs, some potential partners of non-cognate SK-RR were found, including those of unpaired SK and orphan RR and the cross-talk between different components in either strain. Our study provides new clues for further exploration of the molecular regulation mechanism of streptomycetes with industrial importance.

关键词： Streptomyces two-component system cross-talk phylogenetic analysis

Identification and Categorization of Horizontally Transferred Genes in Prokaryotic Genomes

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Acta Biochimica et Biophysica Sinica 2005年第8期37卷 561-566页

作者： Shuo-Yong SHI~1 Xiao-Hui CAI~1 and Da-fu DING~(1,2*) Key Laboratory of Proteomics.Institute of Biochemistry and Cell Biology.shanghai Institutes for Biological sciences,chinese academy of sciences,graduate school of the chinese academy of sciences.shanghai 200031,china.~2 school of Life Science & Technology.shanghai Jiaotong University.shanghai 200030.china Key Laboratory of Proteomics Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Graduate School of the Chinese Academy of SciencesShanghai 200031 China school of Life Science & Technology Shanghai Jiaotong UniversityShanghai 200030 China

Horizontal gene transfer(HGT),a process through which genomes acquire genetic materialsfrom distantly related organisms,is believed to be one of the major forces in prokaryotic genome ***,systematic investigation is still scarce to clarify two basic issues about HGT:(1) what types ofgenes are transferred:and(2)what influence HGT events over the organization and evolution of ***-scale investigations of these two issues will advance the systematical understanding ofHGT in the context of prokaryotic genome *** investigated 82 genomes,we constructed anHGT database across broad evolutionary *** identified four function categories containing a highproportion of horizontally transferred genes:cell envelope,energy metabolism,regulatory functions,andtransport/binding *** biased function distribution indicates that HGT is not completely random;instead,it is under high selective pressure,required by function restraints in ***,wemapped the transferred genes onto the connectivity structure map of organism-specific pathways listed inKyoto Encyclopedia of Genes and Genomes(KEGG).Our results suggest that recruitment of transferredgenes into pathways is also selectively constrained because of the tuned interaction between original *** organization structures still conserve well through evolution even with the recruitment ofhorizontally transferred ***,in pathways whose organization were significantly affected byHGT events,the operon-like arrangement of transferred genes was found to be *** resultssuggest that operon plays an essential and directional role in the integration of alien genes into pathways.

关键词： genome evolution horizontal gene transfer function and pathway analysis

Magnesium lithospermate B ameliorates renal cortical microperfusion in rats

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Acta Pharmacologica Sinica 2006年第2期27卷 217-222页

作者： Chun-guang CHEN~(2,3) Yi-ping WANG~(2,4) ~2State Key Laboratory of Drug Research.shanghai Institute of Materia Medica,shanghai Institutes for Biological sciences graduate school of the chinese academy of sciences,chinese academy of sciences,shanghai 201203,china State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Shanghai Institutes for Biological Sciences Shanghai China graduate school of the chinese academy of sciences Chinese Academy of Sciences Shanghai China

Aim:To investigate the effects of magnesium lithospermate B（MLB）isolatedfrom Salviae miltiorrhizae on renal microcirculation,and renal and systemic he-modynamics in Sprague-Dawley ***:MLB（10,30,and 60 mg/kg）wasinjected intravenously and renal blood flow（RBF）,renal cortical microperfusion（RCM）,and systemic hemodynamic function parameters including heart rate（HR）,mean arterial pressure（MAP）,left ventricular systolic pressure（LVSP）,left ven-tricular end-diastolic pressure（LVEDP）,and maximal velocity of pressure increase(dp/dtmax)were measured for 45 min after ***:IntravenousMLB at doses of 10,30,and 60 mg/kg increased RCM significantly,but had noobvious effects on RBF or systemic *** effect of MLB on RCMreached its peak 15 rain after injection and returned to baseline after 45 *** to60 mg/kg MLB increased RCM by 62.4%±20.2%（changes from baseline,P4%±9.1%vs baseline）did not obviously ***:These results indicate thatMLB ameliorates renal microcirculation in a dose-dependent manner,which maybe related to the renoprotective effects of MLB.

关键词： magnesium lithospermate B hemodynamics renal blood flow renal cortical microperfusion

C/EBPαp30 plays transcriptional regulatory roles distinct from C/EBPαp42

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Cell Research 2007年第4期17卷 374-383页

作者： Chunxi Wang~1 Xiaotao Chen~1 Yanping Wang~1 Jialei Gong~1 Gengxi Hu ~1State Key Laboratory of Molecular Biology institute of Biochemistry and Cell Biology,shanghai Institutes for Biological sciences,chinese academy of sciences,graduate school of the chinese academy of sciences,shanghai 200031,china State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Graduate School of the Chinese Academy of Sciences Shanghai China

CCAAT/enhancer binding protein α(C/EBPα)is a transcriptional regulatory factor that inhibits cell proliferation,andalternative translational initiation produces two polypeptides,C/EBPcαp30 and C/EBPα*** expression profiling,it was revealed that C/EBPαp30 specifically inhibited a unique set of genes,including MPP11,p84N5 and SMYD2,which were not affected by C/EBPαp42 in both QSG-7701 hepatocyte cell line and QGY-7703 hepatoma ***-quantitative RT-PCR analysis independently confirmed these *** immunoprecipitation assay showed thatC/EBPαp30 bound to the promoters of these genes more strongly than C/EBPα*** clinical hepatoma samples inwhich C/EBPα was downregulated,all three genes specifically inhibited by C/EBPαp30 were ***,repression of MPP11,p84N5 and SMYD2 genes might not be directly involved in C/EBPαp30-mediated growth *** data suggest that C/EBPαp30 regulates a unique set of target genes and is more than a dominant-negativeregulator of C/EBPαp42.

关键词： C/EBPα expression pattern p84N5 MPP11 SMYD2

A Test on Different Types of the Time Curve of Hardness Ratio of Gamma-Ray Bursts based on the Curvature Effect

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chinese Journal of Astronomy and Astrophysics 2008年第4期8卷 451-464页

作者： Lan-Wei Jia National Astronomical Observatories/Yunnan Observatory,chinese academy of sciences,Kunming 650011,china.graduate school of chinese academy of sciences,Beijing 100049,china National Astronomical Observatories/ Yunnan Observatory Chinese Academy of Sciences Kunming 650011 China graduate school of chinese academy of sciences Beijing 100049 China

We analyzed a sample of 66 gamma-ray bursts （GRBs） and statistically confirmed the prediction on the time curve of the hardness ratio of GRBs made by Qin et al. based on the curvature effect. In their analysis, GRB pulses are divided into three types according to the shape of their raw hardness ratio （RHR） time curves, defined as to include the background counts to the signal counts, so as to make use of counts within small time intervals. Of the three types, very hard sources exhibit a perfect pulse-like profile （type 1）, hard bursts possess a pulse-like profile with a dip in the decay phase （type 2）, and soft bursts show no pulse-like profile but have only a dipped profile （type 3）. In terms of the conventional hardness ratio, type 3 sources are indeed generally softer than those of type 1 and type 2, in agreement with the prediction. We found that the minimum value of RHR is sensitive in distinguishing the different types. We propose that GRB pulses can be classified according to the minimum value of RHR and that the different type sources may be connected with different strengths of the shock or/and the magnetic field.

关键词： gamma-rays burst -- gamma-rays observations - methods statistical

Cytotoxicity of carbon nanotubes

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Science china.Chemistry 2008年第11期51卷 1021-1029页

作者： ZHU Ying1,2 & LI WenXin1 1 Laboratory of Nano-biology and Medicine, shanghai Institute of Applied Physics, chinese academy of sciences, shanghai 201800, china.2 graduate school of chinese academy of sciences, Beijing 100049, china Laboratory of Nano-biology and Medicine Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai China graduate school of chinese academy of sciences Beijing China

With large-scale production and application at large scale, carbon nanotubes (CNTs) may cause ad-verse response to the environment and human health. Thus, study on bio-effects and safety of CNTs has attracted great attention from scientists and governments worldwide. This report briefly summa-rizes the main results from the in vitro toxicity study of CNTs. The emphasis is placed on the descrip-tion of a variety of factors affecting CNTs cytotoxicity, including species of CNTs, impurities contained, lengths of CNTs, aspect ratios, chemical modification, and assaying methods of cytotoxicity. However, experimental information obtained thus far on CNTs' cytotoxicity is lacking in comparability, and some-times there is controversy about it. In order to assess more accurately the potential risks of CNTs to human health, we suggest that care should be taken for issues such as chemical modification and quantitative characterization of CNTs in cytotoxicity assessment. More importantly, studies on physical and chemical mechanisms of CNTs' cytotoxicity should be strengthened; assaying methods and evaluating criteria characterized by nanotoxicology should be gradually established.

关键词： carbon nanotubes (CNTs) cell bio-security

Infrared Galaxies in the Nearby Universe

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chinese Journal of Astronomy and Astrophysics 2008年第6期8卷 643-652页

作者： Jian-Ling Wang 1 National Astronomical Observatories,chinese academy of sciences,Beijing 100012,china.2 graduate school of chinese academy of sciences,Beijing 100049,china National Astronomical Observatories Chinese Academy of Sciences Beijing 100012 China graduate school of chinese academy of sciences Beijing 100049 China

We used the Sloan Digital Sky Survey （SDSS） Data Release 5 （DR5） to study the morphological properties of 1137 nearby infrared （IR） galaxies, most of which are brighter than 15.9 mag in r-band. This sample was drawn from a cross-correlation of the Infra-Red Astronomical Satellite （IRAS） point source catalog redshift survey with DR5 at z ≤ 0.08. Based on this IR galaxy sample, we constructed five volume-limited sub-samples with IR luminosity ranging from 10^9.5 L⊙ to 10^12L⊙. By deriving the IR luminosity functions （LF） for different morphological types, we found that normal spiral galaxies are the dominant population below LIR ~ 8 ~ 10^10 L⊙; while the fraction of barred spiral galaxies increases with increasing IR luminosity and becomes dominant in spiral galaxies beyond LIR ≈ 5 × 10^10L⊙. As the IR luminosity decreases, the IR galaxies become more compact and have lower stellar masses. The analysis also shows that normal spiral galaxies give the dominant contribution to the total comoving IR energy density in the nearby universe, while, in contrast, the contribution from peculiar galaxies is only 39%.

关键词： galaxies evolution galaxies interactions galaxies starburst infrared galaxies galaxies luminosity function

Effects of cosmological constant on motion of UHECR particles

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Science china.Physics,Mechanics & Astronomy) 2005年第1期48卷 44-56页

作者： CHEN Shaoxia & CHANG Zhe Institute of High Energy Physics, chinese academy of sciences, Beijing 100039, china.graduate school of chinese academy of sciences, Beijing 100039, china Institute of High Energy Physics Chinese Academy of Sciences Beijing 100039 China graduate school Chinese Academy of Sciences Beijing 100039 China

Recent astronomical observations manifest that about two-thirds of the whole energy in the Universe is contributed by a small positive cosmological constant A (> 0). Then, an asymptotically de Sitter spacetime is premised naturally. However, physics in the de Sitter spacetime is very different from that in the Minkowski spacetime. As the first step, a covariant formalism of the kinematics in the de Sitter spacetime is presented here. By solving exactly the equations of motion for a field, we obtain the dispersion relation of a free particle. It is noticed that the dispersion relation is dependent on the degree of freedom of angular momentum of the particle. We show the threshold anomaly of the ultra high energy cosmic ray disappears naturally in the framework of the de Sitter kinematics.

关键词： ultrahigh energy cosmic ray, cosmological constant, curved spacetime.

Recent advances in the data analysis method of functional magnetic resonance imaging and its applications in neuroimaging

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Progress in Natural Science:Materials International 2006年第8期16卷 785-795页

作者： TIAN Jie, YANG Lei and HU Jin (Institute of Automation, chinese academy of sciences, Beijing 100080, china.graduate school of chinese academy of sciences, Beijing 100039, china. Institute of Automation Chinese Academy of Sciences Beijing 100080 China graduate school of chinese academy of sciences Beijing 100039 China

Functional magnetic resonance imaging (fMRI) has opened a new area to explore the human brain. The fMRI can reveal the deep insights of spatial and temporal changes underlying a broad range of brain function, such as motor, vision, memory and emotion, all of which are helpful in the clinical investigation. In this paper, we introduce some recent-developed algorithms for fMRI signal detection such as model-driven method (general linear model, deconvolution model, non-linear model, etc. ) and data-driven method (principle component analysis, independent component analysis, self-organization mapping, clustered constrained non-negative matrix factorization, etc. ). We also propose several important applications of neuroimaging and point out their shortcomings and future perspectives.

关键词： fMR1 data analysis neuroimaging.