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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 {2., chinese academy of sciences, {5. 100039, china) [a]Institute of Hydrobiology Chinese Academy of Sciences Wuhan China [b]Graduate school Chinese Academy of Sciences Beijing 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.

Growth characteristics and response to climate change of Larix Miller tree-ring in china

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Science china Earth sciences 2010年第6期53卷 871-879页

作者： SUN Yu1,4, WANG LiLi1,2.3, CHEN Jin5. DUAN JianPing1,4, SHAO XueMei1,2.& CHEN KeLong6 1 Institute of Geographic sciences and Natural Resources Research, chinese academy of sciences, {2. 100101,{5. 2.Institute of Tibetan Plateau Research, chinese academy of sciences, {2. 100085.{5. 3 Institute of Desert and Meteorology,{5. Meteorological Administration, Urumqi 830002.{5. 4 Graduate University of chinese academy of sciences, {2. 100049,{5. 5.Institute of Vertebrate Paleontology and Paleoanthropology, chinese academy of sciences, {2. 100044,{5. 6 school of Life and Geography sciences, Qinghai Normal University, Xining 810008,{5. 1. Institute of Geographic sciences and Natural Resources Research Chinese Academy of Sciences Beijing 100101 China4. Graduate University of Chinese Academy of Sciences Beijing 100049 China2. Institute of Tibetan Plateau Research Chinese Academy of Sciences Beijing 100085 China3. Institute of Desert and Meteorology China Meteorological Administration Urumqi 830002 China5. Institute of Vertebrate Paleontology and Paleoanthropology Chinese Academy of Sciences Beijing 100044 China6. School of Life and Geography Sciences Qinghai Normal University Xining 810008 China

As one of the earliest species used in dendrochronological studies, Larix responds sensitively to climate change. In this study, nine larch species and one variety from eleven sites were collected to study the growth characteristics of tree-ring width using dendrochronological methods. Ten residual tree-ring chronologies were developed to analyze their relationships with regional standardized anomaly series by Pearson’s correlation analysis. The results suggest that most of the chronologies had significantly positive correlations with the mean temperature and mean maximum temperature in May. The spring temperature evidently limited the radial growth of the larch species without precipitation control. The largest mean tree-ring width was found in Himalayan Larch in Jilong, whereas Master Larch in Si’er reflected the smallest mean value. Both species presented little climate information in this study. chinese, Potanin, and Tibetan larches are significantly correlated with climate change, implying a huge potential for climate history reconstruction. The elevation of the sampling sites appears to be an important condition for tree-ring growth of larches responding to climate factors.

关键词： Larix Miller tree-ring climate change mean temperature in May

Biomass estimation and uncertainty analysis based on CBERS-02.CCD camera data and field measurement

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Science china(Technological sciences) 2005年第S2期48卷 116-128页

作者： CHEN Liangfu1,2. GAO Yanhua1,3, CHENG Yu1,3, WEI Zheng1,3, XIAO Qing1,4, LIU Qinhuo1, YU Tao1, LIU Qijing5. GU Xingfa1 & TIAN Guoliang1 1. State Key Laboratory of Remote Sensing Science, Institute of Remote Sensing Applications, chinese academy of sciences, beijing 100101,{2. 2. Geography and Environment College, Jiangxi Normal University, Nanchang 33002.,{2. 3. Graduate University of chinese academy of sciences, beijing 100039,{2. 4. beijing Research Institute of Uranium Geology, beijing 100875.{2. 5. Institute of Geographic sciences and Natural Resources Research, chinese academy of sciences, beijing 100101,{2. 1. State Key Laboratory of Remote Sensing Science Institute of Remote Sensing Applications Chinese Academy of Sciences 100101 Beijing China 2. Geography and Environment College Jiangxi Normal University 330027 Nanchang China 3. Graduate University of chinese academy of sciences 100039 Beijing China 4. beijing Research Institute of Uranium Geology 100875 Beijing China 5. Institute of Geographic sciences and Natural Resources Research Chinese Academy of Sciences 100101 Beijing China

The study site is located in Qianyanzhou experimental station and the surrounding area. Based on CBERS-02.satellite data and field measurement, we not only discussed the relationship between NDVI and biomass of two species of coniferous plantations, namely, Pinus massoniana Lamb and Pinus elliottii Engelm, but also introduced the biomass models based on NDVI. The comparison between measured biomass in Qianyanzhou and biomass derived from CBERS-02.CCD data showed that it is feasible to estimate biomass based on NDVI. But its limitations cannot be ignored. This kind of model depends on the dominant vegetation species. There are some effect factors in estimating biomass based on NDVI. This paper analyzes these factors based on fine-resolution CBERS-02.CCD data and some conclusions are drawn: In Qianyanzhou, the area with good vegetation coverage, the nonlinearity of NDVI has little influence on scaling-up of NDVI. As a result of surface heterogeneity, scaling-up can cause NDVI within each pixel to change. Because scaling-up can cause pixel attribute to change, the applicability of biomass model is one of the sources of error in estimating biomass.

关键词： NDVI biomass scaling effect scaling-up.

Topography and functional information of plasma membrane

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Science china(Life sciences) 2008年第2期51卷 95-103页

作者： SUN DeLan1, CHEN JianMin1, SONG YanMei1, ZHU ChuanFeng2. PAN GeBo2.& WAN LiJun2.1 Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, chinese academy of sciences, beijing 100093,{2. 2.Institute of Chemistry, chinese academy of sciences, beijing 100080,{2. 1. Key Laboratory of Photosynthesis and Environmental Molecular Physiology Institute of Botany Chinese Academy of Sciences Beijing 100093 China 2. Institute of Chemistry Chinese Academy of Sciences Beijing 100080 China

By using atomic force microscope (AFM), the topography and function of the plasmalemma surface of the isolated protoplasts from winter wheat mesophyll cells were observed, and compared with dead protoplasts induced by dehydrating stress. The observational results revealed that the plasma membrane of living protoplasts was in a state of polarization. Lipid layers of different cells and membrane areas exhibited distinct active states. The surfaces of plasma membranes were unequal, and were characterized of regionalisation. In addition, lattice structures were visualized in some regions of the membrane surface. These typical structures were assumed to be lipid molecular complexes, which were measured to be 15.8±0.09 nm in diameter and 1.9±0.3 nm in height. Both two-dimensional and three-dimensional imaging showed that the plasmalemma surfaces of winter wheat protoplasts were covered with numerous protruding particles. In order to determine the chemical nature of the protruding particles, living protoplasts were treated by proteolytic enzyme. Under the effect of enzyme, large particles became relatively looser, resulting that their width was increased and their height decreased. The results demonstrated that these particles were likely to be of protein nature. These protein particles at plasmalemma surface were different in size and unequal in distribution. The diameter of large protein particles ranged from 2.0 to 440 nm, with a central micropore, and the apparent height of them was found to vary from 12.to 40 nm. The diameter of mid-sized protein particles was between 40―60 nm, and a range of 1.8―5.nm was given for the apparent height of them. As for small protein particles, obtained values were 12.40 nm for their diameter and 0.7―2.2.nm for height. Some invaginated pits were also observed at the plasma membrane. They were formed by the endocytosis of protoplast. Distribution density of them at plasmalemma was about 16 pits per 15.μm2. According to their size, we clas

关键词： atomic force microscope winter wheat protoplast plasma membrane surface membrane protein invaginated pits

Cloning and characterization of interferon stimulated genes Viperin and ISG15.and their promoters from snakehead Channa argus

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Progress in Natural Science:Materials International 2007年第12期17卷 1425-1435页

作者： Jia Weizhang1,2. Zhou Xiuxia1,2. Huang Rong1,2.and Guo Qionglin1(1. Institute of Hydrobiololgy, chinese academy of sciences, Wuhan 430072.{5. 2. Graduate University of chinese academy of sciences, beijing 100039,{5.) Institute of Hydrobiololgy Chinese Academy of Sciences Wuhan 430072 China Graduate University of chinese academy of sciences Beijing 100039 China

By suppression subtractive hybridization, rapid amplification of cDNA ends and gene walking methods, interferon stimulated genes (ISGs), Viperin and ISG15. and their promoters have been cloned and characterized from snakehead Channa argus. The Viperin cDNA was found to be 1474 nt and contain an open reading frame (ORF) of 105. nt that translates into a putative peptide of 35.0}amino acid (aa). The putative peptide of Viperin shows high identity to that in teleosts and mammals except for the N-terminal 70 aa. The ISG15.cDNA was found to be 75. nt and contain an ORF of 468 nt that translates into a putative peptide of 15. aa. The putative peptide of ISG15.is composed of two tandem repeats of ubiquitin-like (UBL) domains, and a canonical conjugation motif (LRGG) at C-terminal. Viperin and ISG15.promoter regions were characterized by the presence of interferon stimulating response elements (ISRE) and γ-IFN activation sites (GAS). ISRE is a feature of IFN-induced gene promoter and partially overlaps interferon regulatory factor (IRF) 1 and IRF2.recognition sites. GAS is responsible for the γ-IFN mediated transcription. One conserved site for NF-κB was found in the promoter region of Viperin. This is the first report of conservative binding motif for NF-κB in accordance with the consensus sequence (GGGRNNYYCC) among teleost ISG promoters. Moreover, there were also TATA, CAAT and Sp1 transcription factor sites in Viperin and ISG15.promoters. In 5. untranslated region (UTR), snakehead ISG15.gene contains a single intron, which differs from Viperin gene. The transcripts of Vipeirn and ISG15.mRNA were mainly expressed in head kidney, posterior kidney, spleen and gill. The expression levels in liver were found to increase obviously in response to induction by IFN-inducer poly I∶C.

关键词： interferon interferon stimulated gene (ISG) Viperin ISG15 snakehead (Channa argus).

Numerical simulation of Meiyu front and the diagnosis of moist vorticity vector

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Progress in Natural Science:Materials International 2007年第11期17卷 1341-1347页

作者： Ping Fan1,2.and Luo Zhexian2.1. Institute of Atmospheric Physics, chinese academy of sciences, beijing 10002.,{2. 2. Nanjing University of Information sciences & Technology, Nanjing 2.0044,{2.) Institute of Atmospheric Physics Chinese Academy of Sciences Beijing 100029 China Nanjing University of Information sciences & Technology Nanjing 210044 China

Moist vorticity vector is introduced to study the development and evolution of mesoscale convective vortex (MCV) in the Meiyu front precipitation with the Advanced Regional Predication System (ARPS). In this study, the heavy rainfall is simulated to investigate the genesis, development and dissipation of middle scale convective vortex, which occurred from 0000 UTC 3 July to 12.0 UTC 5.July over the Jianghuai River valley. Moist vorticity vector (MVV) has zonal, radial and vertical components in its 3D spatial distribution. The simulation shows that the vertical component of moist vorticity vector well demonstrates the spatial distribution characteristics of middle scale convective vortex, especially in the process of Meiyu front precipitation. Diagnosis upon zonal, radial averaged and mass-integrated quantities of MVV shows that its vertical component and the surface precipitating ratio are in phase with a correlation coefficient of 0.68, indicating that the vertical component of MVV is closely associated with the Meiyu front precipitation. In addition, the tendency of the vertical component of MVV is mainly determined by the interaction between the vorticity and the zonal and radial gradient of condensational or depositional heating.

关键词： moist vorticity vector mesoscale convective vortex Meiyu front precipitation

Modeling the climate effects of different subregional uplifts within the Himalaya-Tibetan Plateau on Asian summer monsoon evolution

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chinese Science Bulletin 2012年第35期57卷 4617-4626页

作者： ZHANG Ran 1,JIANG DaBang 1,2.3,LIU XiaoDong 4 & TIAN ZhiPing 2.5.1 Climate Change Research Center,chinese academy of {2.,{5. 10002.,china 2.Nansen-Zhu International Research Centre,Institute of Atmospheric Physics,chinese academy of {2.,{5. 10002.,china 3 Key Laboratory of Regional Climate-Environment Research for Temperate East Asia,chinese academy of {2.,{5. 10002.,china 4 State Key Laboratory of Loess and Quaternary Geology,Institute of Earth Environment,chinese academy of {2.,Xi’an 710075.china 5.Graduate University of{25.,{5. 100049,china 1. Climate Change Research Center Chinese Academy of Sciences Beijing 100029 China 2. Nansen-Zhu International Research Centre Institute of Atmospheric Physics Chinese Academy of Sciences Beijing 100029 China 3. Key Laboratory of Regional Climate-Environment Research for Temperate East Asia Chinese Academy of Sciences Beijing 100029 China 4. State Key Laboratory of Loess and Quaternary Geology Institute of Earth Environment Chinese Academy of Sciences Xi’an 710075 China 5. Graduate University of chinese academy of sciences Beijing 100049 China

Considering the different uplifting time of different subregions of the Himalaya-Tibetan Plateau(TP),a series of numerical simulations have been conducted with the Community Atmosphere Model(CAM4) developed at the National Center for Atmospheric Research to explore the effects of the phased tectonic uplift of the Himalaya-TP on the evolution of Asian summer *** results show that the uplifts of the Himalaya and northern TP significantly affect the evolutions of South Asian summer monsoon and northern East Asian summer monsoon *** is,the tectonic uplift of the Himalaya intensifies the South Asian summer monsoon circulation and increases the precipitation in South Asia,whereas the uplift of the northern TP intensifies the northern East Asian summer monsoon circulation and increases the precipitation in northern East *** with previous simulations,current comparative analyses of modeling results for different subregional uplifts within the Himalaya-TP help deepen our understanding of the evolutionary history of Asian monsoons.

关键词：青藏高原隆升喜马拉雅亚洲季风高原气候夏季季风次区域隆起演化建模

A one-dimensional heat transfer model of the Antarctic Ice Sheet and modeling of snow temperatures at Dome A, the summit of Antarctic Plateau

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Science china Earth sciences 2010年第5期53卷 763-772页

作者： CHEN BaiLian1,3, ZHANG RenHe2. SUN ShuFen1, BIAN LinGen2. XIAO CunDe4,2.& ZHANG TingJun5.1 Institute of Atmospheric Physics, chinese academy of sciences, beijing 10002.,{2. 2.chinese academy of Meteorological sciences, beijing 100081,{2. 3 Graduate University of chinese academy of sciences, beijing 100049,{2. 4 Cold and Arid Regions Environmental and Engineering Research Institute, chinese academy of sciences, Lanzhou 730000,{2. 5.The National Snow and Ice Data Center, University of Colorado, Boulder, CO 80309-0449, USA 1. Institute of Atmospheric Physics Chinese Academy of Sciences Beijing 100029 China3. Graduate University of Chinese Academy of Sciences Beijing 100049 China2. Chinese Academy of Meteorological Sciences Beijing 100081 China4. Cold and Arid Regions Environmental and Engineering Research Institute Chinese Academy of Sciences Lanzhou 730000 China5. The National Snow and Ice Data Center University of Colorado Boulder CO 80309-0449 USA

A vertical one-dimensional numerical model for heat transferring within the near-surface snow layer of the Antarctic Ice Sheet was developed based on simplified parameterizations of associated physical processes for the atmosphere, radiation, and snow/ice systems. Using the meteorological data of an automatic weather station (AWS) at Dome A (80°2.′S, 70°2.′E), we applied the model to simulate the seasonal temperature variation within a depth of 2. m. Comparison of modeled results with observed snow temperatures at 4 measurement depths (0.1, 1, 3, 10 m) shows good agreement and consistent seasonal variations. The model results reveal the vertical temperature structure within the near-surface snow layer and its seasonal variance with more details than those by limited measurements. Analyses on the model outputs of the surface energy fluxes show that: 1) the surface energy balance at Dome A is characterized by the compensation between negative net radiation and the positive sensible fluxes, and 2. the sensible heat is on average transported from the atmosphere to the snow, and has an evident increase in spring. The results are considered well representative for the highest interior Antarctic Plateau.

关键词： Antarctic Ice Sheet near-surface layer energy transfer numerical model

The impact of vegetation restoration on erosion-induced sediment yield in the middle Yellow River and management prospect

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Science china Earth sciences 2005年第6期48卷 724-741页

作者： CHEN Hao1, ZHOU Jinxing2. CAI Qiangguo1, YUE Zhongqi3, LU Zhongchen4, LIANG Guanglin1& HUANG Jianguo5.1. Key Laboratory of Water Cycle and Related Land Surface Processes, Institute of Geographic sciences and Natural Resources Re-search, chinese academy of sciences, {2. 100101, china 2. Institute of Forestry, chinese academy of Forestry sciences, {2. 100091, china 3. Department of Civil Engineering, University of Hong Kong, Hong Kong, china 4. Eco-environmental Research Center, chinese academy of sciences, {2. 100085. china 5. College of Resources and Environment, Southwest Agricultural University, Chongqing 400716, china Correspondence should be addressed to Chen Hao 1. Key Laboratory of Water Cycle and Related Land Surface Processes Institute of Geographic Sciences and Natural Resources Research Chinese Academy of Sciences 100101 Beijing China 2. Institute of Forestry Chinese Academy of Forestry Sciences 100091 Beijing China 3. Department of Civil Engineering University of Hong Kong Hong Kong China 4. Eco-environmental Research Center Chinese Academy of Sciences 100085 Beijing China 5. College of Resources and Environment Southwest Agricultural University 400716 Chongqing China

According to the characteristics of water and erosion environments of different natural zones on the Loess Plateau, this paper studies changes of vegetation types, distribution boundaries of forest and grass as well as restoration capacity of vegetation in different natural zones in the middle Yellow River. The annual precipitation of 5.0 mm is the critical annual pre-cipitation for forest and grass distribution in the middle Yellow River. Among the zonal and azonal environmental factors affecting watershed sediment yield, the intermediate diameter D5. (mm) of suspended load and forest coverage (V, %) play the leading role. Of them the effect weight of forest coverage (V, %) on catchments sediment yield is only 3.4% less than the role of the intermediate diameter (D5., mm), they are almost the same. To effectively control soil erosion in semiarid, especially in hilly-gullied areas and make sediment transport modulus reduce to less than 6000 t/km2. it is rather difficult by merely relying on natural restoration of forest. In the process of cultivated land conversion into forest land and grassland, measures suiting local conditions should be adopted in tree species selection and artificial afforestation (grass planting) based on management with biological measures for slopeland and engineering measures for hilly-gullied areas, so that watershed forest coverage in key counties can reach at least over 30%.Compared with the standard period of precipitation prior to the 1960s, with the decrease of an-nual precipitation at various periods, plant productivities decline to different degrees under natural conditions. The main reason accountable for the low survival rate of new seedlings and grass over years is due to precipitation decrease. In light with regression models of annual pre-cipitation and natural vegetation productivities, it is possible to obtain estimated values of wa-tershed natural vegetation productivity and eco-water consumption needed for the restoration to

关键词： vegetation restoration, eco-water requirement, watershed sediment yield, the middle Yellow River.