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Identification of novel SINEs from Cyprinidae and their evolutionary significance

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Progress in Natural Science:Materials International 2007年第3期17卷 270-279页

作者： HAN Yawei, HE Slumping and CHEN Yiyu ( Institute of Hydrobiology, chinese academy of sciences, Wuhan 430072, china. graduate school, chinese academy of sciences, Beijing 100039, china) Institute of Hydrobiology Chinese Academy of Sciences Wuhan 430072 China

Short interspersed nuclear elements (SINEs) are widespread among eukaryotic genomes. They are repetitive DNA sequences that have been amplified by retrotransposition. In this study, a class of SINEs were isolated from the Opsariichthys bidens genome, and named Opsar. Sequence analysis confirmed that Opsar is a new class of typical SINEs derived from tRNA molecules. With the tRNA-derived region of Opsar and through BLASTN search, we further identified Zb-SINEs from the zebrafish genome, which includes two groups: Zb-SINE-A and Zb-SINE-B. The Zb-SINE-A. group comprises subfamilies of -Al--A5. and the Zb-SINE-B group is a dimer of the tRNA -derived region and shares a similar dimeric composition to Alu. Zb-SINEs are composed of three distinct regions: a 5. end tRNA-derived region, a tRNA-unrelated region and a 3’ end AT-rich region. The flanking regions are AT rich. The average length of Zb-SINEs elements is about 340 bp. Zb-SINEs account for as much as 0.1 % of the whole zebrafish genome. About 70% of the Zb-SINEs are on chromosomes 11, 18, and 19. These Zb-SINEs were characterized by PCR and dot hybridization. The distribution pattern of Zb-SINEs in genome strongly supports the master genes model. The tRNA-derived regions of Opsar and Zb-SINEs were compared with the tRNAAla gene, and they showed 76% similarity, indicating that Opsar and Zb-SINEs originated from an inactive tRNA sequence or a tRNA -like sequence. In view of the evolutionary status of zebrafish in the Cyprinidae, we deduced that Zb-SINEs were a very old class of interspersed sequences.

关键词： short interspersed nuclear elements (SINEs) master gene model Opsar Zb-SINEs and Cyprinidae.

The cDNA and Genomic DNA Organization of a Novel Toxin SHT-I from Spider Ornithoctonus huwena

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Acta Biochimica et Biophysica Sinica 2004年第10期36卷 656-660页

作者： Peng QIAO, Xiao-Pan ZUO, Zhi-Fang CHAI, and Yong-Hua JI* Institute of Physiology, Shanghai Institutes for Biological sciences, chinese academy of sciences, graduate school of the chinese academy of sciences, Shanghai 200031, china Institute of Physiology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Graduate School of the Chinese Academy of Sciences

In present study the full-length cDNA of a novel toxin from the venom gland of spider Ornithoctonus huwena, named as SHT-I, has been cloned using the strategy of rapid amplification of cDNA ends, and then the whole genomic sequence of SHT-I (Selenocosmia huwena toxin-I) was determined using sequence-specific primers synthesized based on the acquired 3’ and 5. ends of SHT-I cDNA sequence. It is unexpectedly found that intron was lacking in the genomic sequence of SHT-I. The result might evoke an interesting question whether the gene code of inhibitor cystine-knot peptides from spider venom is distinct from that of those known toxic peptides of scorpion and cone snail.

关键词： Ornithoctonus huwena spider cDNA genomic DNA peptide toxin ICK motif

Bio-regeneration of p-complexation desulfurization adsorbents

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Science china Chemistry 2005年第6期48卷 538-544页

作者： LI Wangliang1,2, XING Jianmin1, XIONG Xiaochao1,2, SHAN Guobin1,2 & LIU Huizhou1 1. Laboratory of Separation Science and Engineering, Institute of Process Engineering, chinese academy of sciences, Beijing 100080, china 2. graduate school of the chinese academy of sciences,Beijing 100039, china Laboratory of Separation Science and Engineering Institute of Process Engineering Chinese Academy of Sciences Beijing China graduate school of the chinese academy of sciences Beijing China

The coupling of adsorption desulfurization and biodesulfurization is a new approach to produce clean fuels. Sulfur compounds are firstly adsorbed on adsorbents, and then the ad-sorbents are regenerated by microbial conversion. p-Complexation adsorbent, Cu(I)-Y, was ob-tained by ion exchanging Y-type zeolite with Cu2+ and then by auto-reduction in helium at 45.℃ for 3 h. Dibenzothiophene (DBT) was used as a model compound. The effects of cell concentra-tion, volume of oil phase, the ratio of aqueous phase to adsorbent on DBT desorption by a bac-terium were studied. The amounts of DBT desorbed and 2-HBP produced can be apparently increased with addition of n-octane. BDS activity can be improved by increasing cell concentra-tion and the ratio of water-to-adsorbent. 89% of DBT desorbed from the adsorbents can be converted to 2-HBP within 6 h and almost 100% within 24 h, when the volume ratio of oil-to-water was 1/5.mL/mL, the cell concentration was 60 g·L?1, and the ratio of adsorbent-to-oil was 0.03 g·mL?1. The amount of 2-HBP produced was strongly dependent on the volume ratio of oil-to- water, cell concentration and amount of adsorbent. Adsorption capacity of the regenerated ad-sorbent is 95. that of the fresh one after being desorbed with Pseudomonas delafieldii R-8, washed with n-octane, dried at 100℃ for 24 h and auto-reduced in He.

关键词： adsorption desulfurization p-complexation adsorbents bio-regeneration Pseudomonas delafieldii desorption.

Functional Analysis of Multiple Transcription Factor Sites in a Regulatory Element of Human ε-Globin Gene

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Acta Biochimica et Biophysica Sinica 2004年第10期36卷 673-680页

作者： Chun-Hui HOU, Jian HUANG, and Ruo-Lan QIAN* 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 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

The developmental control of the human ε-globin gene expression is mediated by transcrip- tional regulatory elements in the 5. flanking DNA of this gene. A previously identified negative regulatory element (–3028 to –2902 bp, termed ε-NRAII) was analyzed and one putative NF-κB site and two GATA sites locate at –3004 bp, –2975.bp and –2948 bp were characterized. Electrophoresis mobility shift assay (EMSA) showed that the putative NF-κB site was specifically bound by nuclear proteins of K5.2 cells. Data obtained from transient transfection showed that the expression of reporter gene could be upregulated about 5.% or 100% respectively when ε-NRAII was inserted upstream of the SV40 promoter or ε-globin gene proximal promoter (–177 bp to +1 bp), suggesting that ε-NRAII might not be a classic silencer. Mutation in the putative NF-κB site or in the GATA site (at –2975.bp) slightly reduced the expression of reporter gene driven by SV40 promoter or ε-globin gene proximal promoter. However, the mutation of GATA site at –2948 bp remarkably reduced the reporter gene activity driven by SV40 promoter, but not by ε-globin gene proximal promoter. Further mutation analysis showed that the negative effect of mutation in GATA site at –2948 bp on SV40 promoter was not affected by the mutation of the putative NF-κB site, whereas it could be abolished by the mutation of GATA site at –2975.bp. Furthermore, the mutation of both GATA sites could synergistically reduce the reporter gene activity driven by ε-globin gene proximal promoter. Those results suggested that ε- NRAII might function differently on the SV40 promoter and ε-globin gene proximal promoter.

关键词： ε-globin gene regulatory element NF-κB GATA

Land cover changes based on plant successions: Deforestation, rehabilitation and degeneration of forest in the upper Dadu River watershed

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Science china Earth sciences 2005年第12期48卷 2214-2230页

作者： YAN Jianzhong1,2,3, ZHANG Yili1, BAI Wanqi1, LIU Yanhua4, BAO Weikai5. LIU Linshan1, 2 & ZHENG Du1 1. Institute of Geographic sciences and Natural Resources Research, chinese academy of sciences, Beijing 100101, china 2. graduate school of the chinese academy of sciences, Beijing 100039, china 3. College of Resources and Environment, Southwest Agricultural University, Chongqing 400716, china 4. The Ministry of Science and Technology, P. C. china, Beijing 100862, china 5. Chengdu Institute of Biology, chinese academy of sciences, Chengdu 610041, china Institute of Geographic sciences and Natural Resources Research Chinese Academy of Sciences Beijing China graduate school of the chinese academy of sciences Beijing China College of Resources and Environment Southwest Agricultural University Chongqing China The Ministry of Science and Technology P. C. China Beijing China Chengdu Institute of Biology Chinese Academy of Sciences Chengdu China

To link regional land use/cover changes with environmental effects, land cover changes are required to reflect vegetation successions, whereas the land cover classification systems commonly used nowadays cannot serve this purpose. In this paper, a new land cover classification system is established in which land covers are classified by the vegetation succes-sions, taking Zamtang County, Barkam County and Jinchuan County in the upper Dadu River watershed as a study area. Using multi-temporal remote sensing images, the land cover data of 1967, 1986 and 2000 are obtained by means of integration of unsupervised classification and visual interpretation methods. The database facilitates the study of land use/cover changes, en-vironmental effects and ecological construction. Land cover changes reflect the main ecological processes in the upper Dadu River watershed. The landscape composed mainly of grasslands, wildwoods and alpine scrubs in 1967 was changed to that of grasslands, secondary forests, al-pine scrubs, fragmentary wildwoods, artificial forests, secondary scrubs in 2000, meanwhile, the landscape got more fragmentized. The total area of the forests decreased by 9.43%. Study results have shown the process of restoration of logged areas in forest centers. From 1967 to 2000, only 6.86 percents of logged areas were converted to shrubs, meadows or crop-lands, and the rest were converted into artificial forests or secondary forests. So the ecological shelter functions will be restored, stage by stage. Firewood collection, charcoal production and overgrazing are the three major triggers for the extensive degradation of alpine oak forests, Sa-bina tibetica forests and meadows. The arid valley grasslands expanded too. The degradation of vegetation in the southern slopes impairs ecological shelter functions and affects livelihood of local residents, so it is essential to find effective measures for ecological restoration and recon-struction. Field investigations have found

关键词： land use/cover classification, upper Dadu River watershed, vegetation successions, GIS, RS.

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 graduate University of chinese academy of sciences, Beijing 100049, china National Astronomical Observatories Chinese Academy of Sciences graduate University of chinese academy of sciences

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

Origin of the Red Earth sequence on the northeastern Tibetan Plateau and its implications for regional aridity since the middle Miocene

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Science china Earth sciences 2006年第5期49卷 505-517页

作者： WANG Xianyan1,7, LU Huayu1,2, JI Junfeg3, WANG Xiaoyong1,7, ZHAO Jingbo4, HUANG Baochun5.& LI Zhen6 1. SKLLQG, Institute of Earth Environment, chinese academy of sciences, Xi’an 710075. china 2. Department of Urban and Resources sciences, Nanjing University, Nanjing 210093, china 3. Department of Earth sciences, Nanjing University, Nanjing 210093, china 4. Department of Geography, Shaanxi Normal University, Xi’an 710062, china 5. Institute of Geology and Geophysics, chinese academy of sciences, Beijing 100029, china 6 Department of Geography, Qinghai Normal University, Xining 810008, china 7. graduate school of the chinese academy of sciences, Beijing 100039, china SKLLQG Institute of Earth Environment Chinese Academy of Sciences Xi’an China graduate school of the chinese academy of sciences Beijing China Department of Urban and Resources sciences Nanjing University Nanjing China Department of Earth sciences Nanjing University Nanjing China Department of Geography Shaanxi Normal University Xi’an China Institute of Geology and Geophysics Chinese Academy of Sciences Beijing China Department of Geography Qinghai Normal University Xining China

The Red Earth deposit around Xining, northeastern Tibetan Plateau, has beenstudied in terms of soil micro-structure, grain-size distribution, major- and trace-elementchemistry and magne-tostratigraphy. Field investigations indicate that the Red Earth sequenceconsists of 25.visually definable yellow-brown and weakly-developed soils interbedded with reddishstrongly-developed soils, and has a similar structure to the aeolian Red Clay deposit on the chineseLoess Plateau. Grain-size analysis shows that the Red Earth deposit is very fine-grained with anegligible sand fraction ( > 63 μm). Thin-section observations under light microscopy show that thedeposit has a clayey texture and the coarse fraction ( > 10 μm) mainly consists of quartz,feldspar and micas. Pyroxene and hornblende were also observed. This mineralogical composition ofthe coarse fraction is similar to that of the Quaternary loess. In addition, all of the mineralgrains are semi angular semi-angular and are generally finer than 63 μm. There is a good agreementbetween the major and minor trace element chemistry of loess-soil units and the Red Earth *** REE distributions of the loess-soil and the Red Earth deposit are similar in shape, withenriched LREE and fairly flat HREE profiles and a clear negative Eu anomaly. The geochemicalcharacteristics of the Red Earth deposit are also identical to those of upper continental crust,thus indicating a wind-blown origin. Magnetostratigraphic investigation shows that onset of the RedEarth deposition predates 11.4 Ma BP (13.6 Ma at a nearby site). The distribution of the reportedMiocene aeolian loess at Qin''an of the Loess Plateau is still unknown. Our results indicate thatthis aeolian deposit had extended to the northeastern Tibetan Plateau by at least the middleMiocene. The similarity of the element geochemistry between the Red Earth deposit and the overlyingloess shows that they may have similar sources and dynamic transport system, and may indicate thatthe

关键词： Red Earth deposit, Northeastern Tibetan Plateau, aeolian deposit, aridity of Asia, the middle Miocene.

Models and methods for precise determination of ionospheric delay using GPS

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Progress in Natural Science:Materials International 2007年第2期17卷 187-196页

作者： YUAN Yunbin, HUO Xingliang and OU Jikun ( Institute of Geodesy and Geophysics, chinese academy of sciences, Wuhan 430077, china graduate University of chinese A-cademy of sciences, Beijing 100039, china) Institute of Geodesy and Geophysics Chinese Academy of Sciences Wuhan 430077 China. graduate University of chinese academy of sciences Beijing 100039 China

The basic principles and methods for precisely determining ionospheric delays in GPS observations are introduced and discussed. Various methods and models for fitting ionospheric delays based on GPS are compared and a... 详细信息

关键词： GPS ionospheric delay atmosphere modeling precise GPS positioning.

Relationships between tree-ring width index and NDVI of grassland in Delingha

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chinese Science Bulletin 2006年第9期51卷 1106-1114页

作者： HE Jicheng1,3 & SHAO Xuemei1,21. Institute of Geographical sciences and Natural Resources Research, chinese academy of sciences, Beijing 100101, china 2. Institute of Tibetan Plateau Research, chinese academy of sciences, Beijing 100085. china 3. {5. of chinese academy of sciences, Beijing 100039, china Institute of Geographical sciences and Natural Resources Research Chinese Academy of Sciences Beijing China graduate school of chinese academy of sciences Beijing China Institute of Tibetan Plateau Research Chinese Academy of Sciences Beijing China

Using five well-replicated Qilian juniper (Sabina przewalskii Kom.) tree-ring width index se- ries, monthly normalized difference vegetation index (NDVI) of grassland, and climatic data from 1982 to 2001, the relationships between tree-ring width index, NDVI of grassland, and climatic data were analyzed firstly. Then, the relationship between tree-ring width index and NDVI of grassland was explored. The re- sults showed that: (1) Temperature and precipitation in June influenced tree-ring width index and NDVI of grassland deeply in Delingha. (2) There were sig- nificant relationships between five tree-ring width index series (DLH1-DLH5. and monthly NDVI of grassland from June to September, with the most significant relationship being between tree-ring width index series and NDVI of grassland in August. (3) The PC1 (the first principal component derived from DLH1-DLH5.series) exhibited good agreement with monthly NDVI of grassland in the grass growth sea- son (from June to September) and the averaged NDVI in the growth season, which was attributed to their common responses to water-supply limit in Delingha. This study may allow an increase in studying the past dynamics of grassland in Delingha in that the variation of grassland NDVI during the last millennium has been reconstructed from PC1.

关键词：圆柏祁连山 NDVI 草原年轮宽度指数