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Discovery of immune related factors in Fenneropenaeus chinensis by annotation of ESTs

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Progress in Natural Science:Materials International 2004年第1期14卷 48-55页

作者： SHEN Yaoqing 1,2 , XIANG Jianhai 1*, WANG Bing 1,2 , LI Fuhua 1 and TONG Wei 3(1. Experimental Marine Biology Laboratory, Institute of Oceanology, chinese academy of sciences, Qingdao 266071,china 2. graduate {5. of the chinese academy of sciences, Beijing 10003., china 3. Genomics & Bioinformatics Institute, chinese academy of sciences, Beijing 101300, china) chinese Acad Sci Inst Oceanol Expt Marine Biol Lab Qingdao 266071 Peoples R China chinese Acad Sci Grad Sch Beijing 100039 Peoples R China chinese Acad Sci Geonom & Bioinformat Inst Beijing 101300 Peoples R China

A total of 10446 expressed sequence tags (ESTs) are obtained by a large scale sequencing of a cDNA library from cephalothorax of adult Fenneropenaeus chinensis . An EST analysis platform was built up based on local computers and bioinformatic techniques were used to annotate these ESTs in order to promptly find possible functional genes, especially for immune related factors. About 4% of the ESTs show similarity to the coding sequences of such factors, including lectin, serine protease, serpin, lysozyme, etc. These ESTs provide a partial profile of the immune system in F. chinensis and useful information for further study on these genes.

关键词： Fenneropenaeus chinensis bioinformatics ESTs immune factors

Rational redesign of inhibitors of furin/kexin processing proteases by electrostatic mutations

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Acta Pharmacologica Sinica 2004年第12期25卷 146-152页

作者： Xiao-hui CAI, Qing ZHANG, Da-fu DING2 Key Laboratory of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological sciences, chinese academy of sciences, graduate {5. of the chinese academy of sciences, Shanghai 200031, 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 Sciences Shanghai 200031 China

AIM: To model the three-dimensional structure and investigatethe interaction mechanism ofthe proprotein convertase furin/kexin and their inhibitors (eglin c mutants). METHODS: The three-dimensional complex structures of furin/ kexin with its inhibitors, eglin c mutants, were generated by modeller program using the newly published X-ray crystallographical structures of mouse furin and yeast kexin as templates. The electrostatic interaction energy of each complex was calculated and the results were compared with the experimentally determined inhibition con- stants to find the correlation between them. RESULTS: High quality models of furin/kexin-eglin c mutants were obtained and used for calculation of the electrostatic interaction energies between the proteases and their inhibitors. The calculated electrostaticenergies of interaction showeda linear correlation to the experimental inhibition constants. CONCLUSION: The modeled structures give good explanations of the specificity of eglin c mutants to furin/ kexin. The electrostatic interactions play important roles in inhibitory activity of eglin c mutants to furin/kexin. The results presented here provided quantitative structural and functional information concerning the role of the charge- charge interactions in the binding of furin/kexin and their inhibitors.

关键词： furin kexin eglin c drug design electrostatic mutation

Association between Alcohol, Smoking and HLA-DQA1*0201 Genotype in Psoriasis

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Acta Biochimica et Biophysica Sinica 2004年第9期36卷 597-602页

作者： Guang-Yong ZHENG1,2#, Sheng-Cai WEI3#, Tie-Liu SHI1, and Yi-Xue LI1* 1Bioinformatics Center, Shanghai Institutes for Biological sciences, chinese academy of sciences, graduate {5. of the chinese academy of sciences, Shanghai 200031, china Research Center for Proteome Analysis, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological sciences, chinese academy of sciences, graduate {5. of the chinese academy of sciences, Shanghai 200031, china 3Guangzhou Institute of Dermatology, Guangzhou 5.0095. china Bioinformatics Center Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Graduate School of the Chinese Academy of Sciences

Psoriasis is a chronic skin disease triggered by genetic, environment or other risk factors such as infection, drugs, stress, moisture, alcohol, and smoking. A major psoriasis susceptibility locus at 6p21.3 has been identified. Further studies found that HLA-DQA1*0201 allele was associated with psoriasis. However, there were few data exploring an association between the environmental factors and susceptibility genes. In this study, the samples of 189 patients with psoriasis and 333 healthy controls were collected with their consent and were carried on analysis through polymerase chain reaction sequence-specific primer (PCR- SSP) method. The proportion of male psoriasis patients engaging in the smoking and alcohol was much higher than that of the control group (P5.. The HLA-DQA1*0201 allele was present at significantly higher frequency in the patients with psoriasis (OR=4.25. P6.91, P<1.0×10–4).

关键词： psoriasis HLA-DQA1*0201 allele smoking alcohol association

Temperature variations in the past 6000 years inferred from δ^(18)O of peat cellulose from Hongyuan,china

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chinese Science Bulletin 2002年第18期47卷 1578-1584页

作者： XU Hai, HONG Yetang, LIN Qinghua, HONG Bing, JIANG Hongbo & ZHU YongxuanInstitute of Geochemistry, chinese academy of sciences, Guiyang 5.0002, china graduate {5. of chinese academy of sciences, Beijing 10003., china Institute of Geochemistry Chinese Academy of Sciences Guiyang China graduate school of chinese academy of sciences Beijing China

Trends of the temperature variations recorded in δ18O in Hongyuan peat cellulose are similar to those recorded in δ18O of Jinchuan peat cellulose and in δ18O of Dunde ice core. Climate events have been identified to be globally homogeneous. Two notable climate transition periods have been detected in the past 6000 years, namely 4000 aBP with climate shifting from cold to warm and 15.0 aBP with climate shifting from warm to relatively cold. Power spectrum analysis was performed to investigate the periodical signals in the δ18O time series. Typical periodicities of 12.0-1087 a, 75. a, 444 a, 325.a, 213 a, 12.-12. a, 88 a, 79 a were discovered, indicating an integrated influence on Hongyuan climate from solar, monsoon and ocean activities. Solar forcing has been addressed to be the main driving forcing of Hongyuan climate.

关键词： Hongyuan oxygen isotopic composition peat tempera-ture.

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 {5. of chinese academy of sciences, Beijing 100049, china 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

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

Ionization state of cosmic hydrogen by early stars and quasars

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Research in Astronomy and Astrophysics 2009年第6期9卷 665-681页

作者： Xiao-Chun Mao1,2 1 National Astronomical Observatories, chinese academy of sciences, Beijing 100012. china 2 {5. University of chinese academy of sciences, Beijing 100049, china National Astronomical Observatories Chinese Academy of Sciences Beijing 100012 China graduate University of chinese academy of sciences Beijing 100049 China

Cosmic hydrogen is reionized and maintained in its highly ionized state by the ultraviolet emission attributed to an early generation of stars and quasars. The Lyα opacity observed in absorption spectra of high-redshift quasars permits more stringent constraints on the ionization state of cosmic hydrogen. Based on density perturbation and structure formation theory, we develop an analytic model to trace the evolution of the ionization state in the post-overlap epoch of reionization, in which the bias factor is taken into account. For quasars, we represent an improved luminosity function by utilizing a hybrid approach for the halo formation rate that is in reasonable agreement with the published measurements at 2 ≤ z ≤ 6. Comparison with the classic Press-Schechter mass function of dark matter halos, we demonstrate that the biased mass distribution indeed enhances star formation efficiency in the overdense environment by more than 25.per cent following the overlap of ionized bubbles. In addition, an alternative way is introduced to derive robust estimates of the mean free path for ionizing photons. In our model, star-forming galaxies are likely to dominate the ionizing background radiation beyond z = 3, and quasars contribute equally above a redshift of z ～ 2.5. From 5.≤ z ≤ 6, the lack of evolution in photoionization rate can thus be explained by the relatively flat evolution in star formation efficiency, although the mean free path of ionizing photons increases rapidly. Moreover, in the redshift interval z ～ 2 - 6, the expected mean free path and Gunn-Peterson optical depth obviously evolve by a factor of ～ 5.0 and ～5. respectively. We find that the relative values of critical overdensities for hydrogen ionization and collapse could be 430% at z ≈2 and 2% at z ≈6, suggesting a rapid overlap process in the overdense regions around instant quasars following reionization. We further illustrate that the absolute estimates of the fraction of neutral hydrogen computed fr

关键词： cosmology theory -- formation galaxies -- quasars general -- diffuse radiation -- intergalactic medium

Wind vector retrieval using dual polarization imagery of ASAR

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Progress in Natural Science:Materials International 2006年第11期16卷 1183-1187页

作者： SONG Guiting~ 1,2 , HOU Yijun~1** and QI Peng~1(1. Institute of Oceanology, chinese academy of sciences, Qingdao 266071, china 2. graduate {5., chinese academy of sciences, Beijing 10003., china) [a]Institute of Oceanology Chinese Academy of Science Qingdao China [b]graduate school Chinese Academy of Sciences Beijing China

A new algorithm for retrieving wind vector using dual polarization imagery of advanced synthetic aperture radar (ASAR) is developed and tested. Based on the combination of co-polarization and cross-polarization, this new algorithm effectively eliminates the 180° ambiguity which occurs when using single imagery of the ASAR to retrieve wind vector. This algorithm also solves the problem that the retrieval results will break down on very small spatial scales. The results retrieved from dual polarization imagery of ASAR show that the wind speed and direction are in agreement with the data from Quikscat and buoy measurements. The root mean square errors of wind direction and speed between the retrieved results and data from Quikscat are 2.21° and 0.5. m/s, respectively. Comparisons between the new method and the traditional method show that the new methods fit the buoy data and Quikscat data a little better than the traditional method in this image.

关键词： wind vector retrieval ASAR dual polarization.

Spectral analysis of quasi-stationary sea surface topography from GRACE mission

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Science china Earth sciences 2005年第11期48卷 2040-2048页

作者： ZHANG Zizhan1,2 & LU Yang1,3 1. Institute of Geodesy and Geophysics, chinese academy of sciences, Wuhan 430077, china 2. graduate {5. of the chinese academy of sciences, Beijing 10003., china 3. Unite Center for Astro-geodymics Research, chinese academy of sciences, Shanghai 200030, china 1. Institute of Geodesy and Geophysics Chinese Academy of Sciences 430077 Wuhan China 2. graduate school of the chinese academy of sciences 100039 Beijing China 3. Unite Center for Astro-geodymics Research Chinese Academy of Sciences 200030 Shanghai China

During the last two decades satellite altimetry has offered an abundance of meas-urements of the sea surface resulting in the improvement of global mean sea surface height (MSSH) and marine geoid determination. On the other hand, with the launching of new genera-tion gravity satellites, some high accuracy long-wavelength gravity models are available. These breakthroughs give us a great opportunity for new estimation of quasi-stationary sea surface topography (QSST). In this paper, the new gravity model GGM01C derived from GRACE mission is briefly presented, and a new global high precision and high-resolution QSST is determined based on the GGM01C model and the global MSSH. The spectral features of the QSST esti-mated by GGM01C and EGM96 gravity model to degree/order 200 are discussed by spectral analysis. As a result, the QSST is mainly composed of long waves, medium waves partially and short waves scarcely, its power spectral structures are different between the zonal direction and the meridional direction, there are great differences between the two models, which maybe ex-plain why the ocean currents derived from the two gravity models by Tapley show different pat-terns.

关键词： quasi-stationary sea surface topography, mean sea surface height, GGM01, fast Fourier transform, spectral analysis

Molecular cloning of growth hormone receptor (GHR) from common carp(Cyprinus carpio L.)and identification of its two forms of mRNA transcripts

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Progress in Natural Science:Materials International 2006年第11期16卷 1156-1163页

作者： SUN Xiaofeng~ 1,2 , GUO Qionglin~1**, HU Wei~1, WANG Yaping~1 and ZHU Zuoyan~1(1. State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, chinese academy of sciences, Wuhan 430072, china 2. graduate {5. of chinese academy of sciences, Beijing 10003., china) [a]State key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences Wuhan China China [b]graduate school of chinese academy of sciences Beijing China

The cDNA of growth hormone receptor (GHR) was cloned from the liver of 2-year common carp (Cyprinus carpio L.) by reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA end (RACE). Its open reading frame (ORF) of 1806 nucleotides is translated into a putative peptide of 602 amino acids, including an extracellular ligand-binding domain of 244 amino acids (aa), a single transmembrane domain of 24 aa and an intracellular signal-transduction domain of 334 aa. Sequence analysis indicated that common carp GHR is highly homologous to goldfish (Carassius auratus) GHR at both gene and protein levels. Using a pair of gene-specific primers, a GHR fragment was amplified from the cDNA of 2-year common carp, a 224 bp product was identified in liver and a 321 bp product in other tissues. The sequencing of the products and the partial genomic DNA indicated that the difference in product size was the result of a 97 bp intron that alternatively spliced. In addition, the 321 bp fragment could be amplified from all the tissues of 4-month common carp including liver, demonstrating the occurrence of the alternative splicing of this intron during the development of common carp. Moreover, a semi-quantitative RT-PCR was performed to analyze the expression level of GHR in tissues of 2-year common carp and 4-month common carp. The result revealed that in the tissues of gill, thymus and brain, the expression level of GHR in 2-year common carp was significantly lower than that of 4-month common carp.

关键词： growth hormone receptor (GHR) molecular cloning transcript expression analysis common carp.