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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,{3. 2. graduate School of the chinese academy of sciences, beijing 100039, china 3. Genomics & Bioinformatics Institute, chinese academy of sciences, {13. 1013.0, 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

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, {3. 100080, china graduate School of chinese academy of sciences, beijing 100039, china) [a]chinese academy of sciences Institute of Automation Beijing China [b]graduate School of chinese academy of {3. Beijing 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.

SHRIMP zircon U-Pb geochronology of early Mesozoic felsic igneous rocks from the southern Lancangjiang and its tectonic implications

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Science china Earth sciences 2006年第10期49卷 1032-1042页

作者： PENG Touping1,2, WANG Yuejun1, FAN Weiming1, LIU Dunyi3. SHI Yuruo3.& MIAO Laicheng4 1. Key Laboratory of Isotope Geochronology and Geochemistry, Guangzhou Institute of Geochemistry, chinese academy of sciences, Guangzhou 510640,{3. 2. graduate University of chinese academy of sciences, beijing 100039,{3. 3. SHRIMP isotope Laboratory, chinese academy of Geological sciences, {13. 10003.,{3. 4. Institute of Geology and Geophysics, chinese academy of sciences, {13. 100029,{3. Key Laboratory of Isotope Geochronology and Geochemistry Guangzhou Institute of Geochemistry Chinese Academy of Sciences Guangzhou China graduate University of chinese academy of {3. Beijing China SHRIMP isotope Laboratory Chinese Academy of Geological Sciences Beijing China Institute of Geology and Geophysics Chinese Academy of Sciences Beijing China

The SHRIMP zircon U-Pb geochronology of three typical samples, including two monzo nitic granites from the Lincang batholith and a rhyolite from the Manghuai Formation are presented in the southern Lancangjiang, western Yunnan Province. The analyses of zircons for the biotite monzonitic granites from the northern (02DX-13.) and southern (20JH-10) Lincang batholith show the single and tight clusters on the concordia, and yield the weighted mean 206Pb/23.U ages of 229.4 ± 3.0 Ma and 23..4 ± 3.6 Ma, respectively, representing the crystallized ages of these granites. The zircons for the rhyolitic sample (02DX-95) from the Manghuai Formation give a weighted mean 206Pb/23.U age of 23..0 ± 5.0 Ma. These data suggest that the igneous rocks from the Lincang granitic batholith and Manghuai Formation have a similar crystallized age. In combination with other data, it is inferred that both were generated at a narrow age span (~23. Ma) and were originated from the postcollisional tectonic regime. An early Proterozoic 206Pb/23.U apparent age of 1977±44 Ma is additionally obtained from one zircon from the biotite monzonitic granite (southern Lincang batholith), indicative of devel- opment of the early Proterozoic Yangtze basement in the region. These precisely geochronological data provide important constraints on better understanding the Paleozoic tectonic evolution of the Tethys, western Yunnan Province.

关键词： SHRIMP zircon U-Pb dating, Middle Triassic, Lincang granitic batholith, Manghuai Formation rhyolite, southern Lancangjiang.

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. graduate School 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 {3. 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

Reconstruction of temperature series in china for the last 5000 years

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Progress in Natural Science:Materials International 2006年第8期16卷 838-845页

作者： GE Quansheng, WANG Shunbing and ZHENG Jingyun (Institute of Geographical sciences and Natural Resources Research, chinese academy of sciences, beijing 100101, china graduate School of the chinese academy of sciences, beijing 100039, china) [a]chinese academy of sciences Institute of Geographical Sciences and Natural Resources Research Beijing China [b]graduate School of the chinese academy of {3. Beijing China

A temperature series with a 100 year resolution for the last 5000 years in china has been reconstructed by using 3. longterm temperature proxy series selected from recent publications in the last 20 years. The proxy records include pollens, stalagmites, lake-sediments, peat, ice cores and historical documents. The result reveals that in the millennial scale temperature variation it was warm in 3.50-250 BC and it was cold in 250 BC-1950 AD. In the above two periods there were many stages of sub-scale temperature fluctuations. The result also shows an obvious temperature discrepancy on the century to multi-century scale between the Eastern Monsoon Region, the Qinghai-Tibet Region and the Northwestern Region in 2850 BC, 23.0 BC, 13.0 BC, 950-3.0 BC, 50-250 AD, and 550 AD. A comparison between the reconstructed series of this paper and some North Hemisphere temperature series indicates that in the longterm scale change, the temperature change in china is in phrase with that of the Northern Hemisphere during the last 5000 years, while on the century to multi-century scale there are differences at the beginning and end times, which may imply that temperature change does not occur simultaneously in different regions.

关键词： temperature series the last 5000 years china.

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 43.077,{3. 2. graduate School of the chinese academy of sciences, beijing 100039,{3. 3. Unite Center for Astro-geodymics Research, chinese academy of sciences, Shanghai 20003.,{3. 1. Institute of Geodesy and Geophysics Chinese Academy of Sciences 430077 Wuhan China 2. graduate School of the chinese academy of {3. 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

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 43.072,{3.. graduate School, chinese academy of sciences, beijing 100039,{3.) [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 3.0 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.

An improved method for evaluating the seasonal variability of total suspended sediment flux field in the Yellow and East china Seas

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International Journal of Sediment Research 2011年第1期26卷 1-14页

作者： PANG Chongguang~1,YU Wei~2,YANG Yang~3.and HAN Danxiu~4 Institute of Oceanology,chinese academy of sciences,Qingdao 266071,{3., 2 Institute of Oceanology,chinese academy of sciences,Qingdao 266071,{3.,graduate School of chinese academy of sciences,{12. {13.,{3. 3.Institute of Oceanology,chinese academy of sciences,Qingdao 266071,{3.,graduate School of chinese academy of sciences,{12. {13.,{3. 4 china University of Petroleum,{12. 102249,{3. [a] Doctor Researcher Institute of Oceanology chinese academy of sciences Qingdao 266071 china [b] Institute of Oceanology chinese academy of sciences Qingdao 266071 china graduate School of chinese academy of {3. beijing 100039 china [c] Institute of Oceanology chinese academy of sciences Qingdao 266071 china graduate School of chinese academy of {3. beijing 100039 china [d] china University of Petroleum beijing 102249 china

The suspended sediment flux field in the Yellow and East china Seas(YECS) displays its seasonal variability.A new method is introduced in this paper to obtain the flux field via retrieval of ocean color remote sensing data,statistical analysis of historical suspended sediment concentration data,and numerical simulation of three-dimensional(3.) flow *** components of the sediment flux field include(i) surface suspended sediment concentration inverted from ocean color remote sensing data;(ii) vertical distribution of suspended sediment concentration obtained by statistical analysis of historical observation data;and(iii) 3. flow field modeled by a numerical *** the improved method,the 3. suspended sediment flux field in the YECS has been *** comparison with the suspended sediment flux field solely based on the numerical simulation of a suspended sediment transport model,the suspended sediment flux field obtained by the improved method is found to be more *** 3. suspended sediment flux field from ocean colour remote sensing and in situ observation are more closer to the ***,by quantitatively analyzing the newly obtained suspended sediment flux field,the quantity of sediment erosion and deposition within the different regions can be *** sediment exchange between the Yellow Sea and the East china Sea can be *** mechanism of suspended sediment transport in the YECS can be better *** particular,it is suggested that the long-term transport of suspended sediment is controlled mainly by the circulation pattern,especially the current in winter.

关键词： Suspended sediment flux field Seasonal variability Yellow and East china Seas Regression equation Numerical simulation

Analysis of tandem repeats in the genome of chinese shrimp Fenneropenaeus chinensis

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chinese Science Bulletin 2005年第14期50卷 1462-1469页

作者： KONG Jie1 & GAO Huan2,3.1. Key Laboratory for Sustainable Utilization of Marine Fisheries Re- sources, Ministry of Agriculture, Yellow Sea Fisheris Research Insti- tute, chinese academy of Fishery sciences, Qingdao 266071,{3. 2. Institute of Oceanology, chinese academy of sciences, Qingdao 266071,{3. 3. The graduate School of the chinese academy of sciences,{12.,{3. Key Laboratory for Sustainable Utilization of Marine Fisheries Resources Ministry of Agriculture Yellow Sea Fisheris Research Institute Chinese Academy of Fishery Sciences Qingdao China Institute of Oceanology Chinese Academy of Sciences Qingdao China The graduate School of the chinese academy of {3. Beijing China

Through random sequencing, we found a total of 884000 base-pairs (bp) of random genomic sequences in the genome of chinese shrimp (Fenneropenaeus chinensis). Using bio-soft Tandem Repeat Finder (TRF) software, 2159 tandem repeats were found, in which there were 1714 mi- crosatellites and 445 minisatellites, accounting for 79.4% and 20.6% of repeat sequences, respectively. The cumulative length of repeat sequences was found to be 116685 bp, ac- counting for 13.2% of the total DNA sequence; the cumula- tive length of microsatellites occupied 9.78% of the total DNA sequence, and that of minisatellites occupied 3.42%. In decreasing order, the 20 most abundant repeat sequence classes were as follows: AT (557), AC (471), AG (274), AAT (92), A (56), AAG (28), ATC (27), ATAG (27), AGG (18), ACT (15), C (11), AAC (11), ACAT (11), CAGA (10), AGAA (9), AGGG (7), CAAA (7), CGCA (6), ATAA (6), AGAGAA (6). Dinucleotide repeats, not only in the aspect of the number, but also in cumulative length, were the preponderant repeat type. There were few classes and low copy numbers of repeat units of the pentanucleotide repeat type, which included only three classes: AGAGA, GAGGC and AAAGA. The classes and copy numbers of heptanucleotide, eleven-nucleotide and thirteen-nucleotide primer-number-composed repeats were distinctly less than that of repeat types beside them.

关键词：虾遗传特性遗传基因 DNA