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Sequencing,annotation and comparative analysis of nine BACs of the giant panda(Ailuropoda melanoleuca)

science china(life sciences) 2010年第1期53卷 107-111页

作者： ZHENG Yang1,2,3,CAI Jing4,LI JianWen3,6,LI Bo3,LIN RunMao3,TIAN Feng3,WANG XiaoLing3 & WANG Jun3,5 1beijing Institute of Genomics,chinese academy of sciences(CAS),beijing 100029,china 2college of life science,graduate university of chinese academy of sciences,beijing 100049,china 3beijing Genomics Institute at Shenzhen,Shenzhen 518083,china 4CAS-Max Planck Junior Research Group on Evolutionary Genomics,State Key Laboratory of Genetic Resources and Evolution,Kunming Institute of Zoology,chinese academy of sciences(CAS),Kunming 650223,china 5Department of Biology,university of Copenhagen,Copenhagen DK-2200,Denmark 6School of Biological science and Engineering,South china university of Technology,Guangzhou 510006,china beijing Institute of Genomics Chinese Academy of Sciences (CAS) Beijing China college of life science Graduate University of Chinese Academy of Sciences Beijing China beijing Genomics Institute at Shenzhen Shenzhen China CAS-Max Planck Junior Research Group on Evolutionary Genomics State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences (CAS) Kunming China School of Biological science and Engineering South China University of Technology Guangzhou China Department of Biology University of Copenhagen Copenhagen Denmark

A 10-fold BAC library for the giant panda was constructed and nine BACs were selected to generate finish *** BACs could be used as a validation resource for the de novo assembly accuracy of the whole genome shotgun sequencing reads of the giant panda newly generated by Illumina GA sequencing *** Sanger sequencing,assembly,annotation and comparative analysis were carried out on the selected BACs of a joint length 878 *** search and de novo prediction methods were used to annotate genes and *** protein coding genes were predicted,seven of which could be functionally *** seven genes have an average gene size of about 41 kb,an average coding size of about 1.2 kb and an average exon number of 6 per ***,seven tRNA genes were *** 27 percent of the BAC sequence is composed of repeats.A phylogenetic tree was constructed using a neighbor-join algorithm across five species,including the giant panda,human,dog,cat and mouse,which reconfirms dog as the most closely related species to the giant *** results provide detailed sequence and structure information for new genes and repeats of the giant panda,which will be helpful for further studies about the giant panda.

关键词： giant panda BAC sequencing assembly annotation evolution

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Ovular development and perisperm formation in Phytolacca americana (Phytolaccaceae) and their systematic significance in Caryophyllales

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Journal of Systematics and Evolution 2010年第5期48卷 318-325页

作者： Hong-Chun ZHENG Sheng-Wen MA Tuan-Yao CHAI(college of life science,graduate university of chinese academy of sciences,beijing 100049,china) (college of life science Graduate University of Chinese Academy of Sciences Beijing 100049 China)

Phytolacca is the biggest and most original genus in Phytolaccaceae and an important genus in plant systematic *** microscopy results show that the Phytolacca americana *** arises from the caulis(floral receptacle).The perisperm and hypostase are simultaneously initiated from the top several layers of cells of chalaza after fertilization,and the perisperm is located between the nucellus and *** the early stages of development,the hypostase cells are thin-walled with dense cytoplasm,clear nuclei,and some reserve ***,at the heart-shaped embryo stage,the hypostase cells are dead and *** main functions of the hypostase may be to maintain cellular division and perisperm growth without delivering nutrient materials to the *** evolutionary picture of placentation in Caryophyllales is also presented.

关键词： hypostase nucellus ovule perisperm Phytolacca placentation.

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Observation results of relativistic electrons detected by Fengyun-1 satellite and analysis of relativistic electron enhancement (REE) events

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science china(Physics,Mechanics & Astronomy) 2008年第12期51卷 1947-1956页

作者： YANG XiaoChao1,2↑ & WANG ShiJin1 1 Center for Space science and Applied Research, chinese academy of sciences, beijing 100190, china 2 graduate university of chinese academy of sciences, beijing 100049, china Center for Space science and Applied Research Chinese Academy of Sciences Beijing China graduate university of chinese academy of sciences Beijing China

The space particle component detector on Fengyun-1 satellite which works at the sun-synchronous orbit of about 870 km altitude has detected relativistic electrons for a long time. In comparison with the SAMPEX satellite observations during 1999–2004, the relativistic electron data from Fengyun-1 satellite from June 1999 to 2005 are used to analyze the relativistic electron enhancement (REE) events at the low earth orbit, and the possible correlation among REE events at the low earth orbit, high-speed solar wind and geomagnetic storms is discussed. The statistical result presents that 45 REE events are found in total during this time period, and the strong REE events with the maximum daily average flux > 400 cm?2·srt-1·s?1 occur mostly during the transition period from solar maximum to solar minimum. Among these 45 REE events, four strong REE events last a longer time period from 26-to 51-day and correlate closely with high speed solar wind and strong geomagnetic storms. Meanwhile, several strong geomagnetic storms occur continuously before these REE events, and these continuous geomagnetic storms would be an important factor causing these long-lasting strong REE events. The correlation analysis for overall 45 events indicates that the strength of the REE events correlates with the solar wind speed and the strength of the geomagnetic storm, and the correlation for strong REE events is much stronger than that for weak REE events.

关键词： relativistic electron enhancement low earth orbit high-speed solar wind geomagnetic storm

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Strong decays of N~*(1535) in an extended chiral quark model

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science china(Physics,Mechanics & Astronomy) 2009年第10期52卷 1452-1457页

作者： AN ChunSheng1,2,3 & ZOU BingSong1,2,3 1 Institute of High Energy Physics,chinese academy of sciences,beijing 100049,china 2 Theoretical Physics Center for science Facilities,chinese academy of sciences,beijing 100049,china 3 graduate university of chinese academy of sciences,beijing 100049,china Institute of High Energy Physics Chinese Academy of Sciences Beijing China Theoretical Physics Center for science Facilities Chinese Academy of Sciences Beijing China graduate university of chinese academy of sciences Beijing China

The strong decays of the N*(1535) resonance are investigated in an extended chiral quark model by including the low-lying $ qqqq\bar q $ components in addition to the qqq component. The results show that these five-quark components in N*(1535) contribute significantly to the N*(1535) → Nπ and N*(1535) → Nη decays. The contributions to the Nη decay come from both the lowest energy and the next-tolowest energy five-quarks components, while the contributions to the Nπ decay come from only the latter one. Taking these contributions into account, the description for the strong decays of N*(1535) is improved, especially for the puzzling large ratio of the decays to Nη and Nπ.

关键词： N*(1535) strong decays five-quark components

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Applications of URANS on predicting unsteady turbulent separated flows

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Acta Mechanica Sinica 2009年第3期25卷 319-324页

作者： Jinglei Xu Huiyang Ma Department of Physics, graduate university of the chinese academy of sciences, 100049 beijing, china Department of Physics Graduate University of the Chinese Academy of Sciences Beijing China

Accurate prediction of unsteady separated turbulent flows remains one of the toughest tasks and a practi cal challenge for turbulence modeling. In this paper, a 2D flow past a circular cylinder at Reynolds number 3,900 is numerically investigated by using the technique of unsteady RANS （URANS）. Some typical linear and nonlinear eddy viscosity turbulence models （LEVM and NLEVM） and a quadratic explicit algebraic stress model （EASM） are evaluated. Numerical results have shown that a high-performance cubic NLEVM, such as CLS, are superior to the others in simulating turbulent separated flows with unsteady vortex shedding.

关键词： URANS Nonlinear eddy viscosity turbulencemodel ,Separated flows Circular cylinder

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The identity of some taxa of Schizophragma (Saxifragaceae)

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Journal of Systematics and Evolution 2009年第2期47卷 151-161页

作者： 1,2Wei LIU 1Xiang-Yun ZHU 1(Institute of Botany,chinese academy of sciences,beijing 100093,china) 2(graduate university of chinese academy of sciences,beijing 100049,china) Institute of Botany Chinese Academy of Sciences Beijing 100093 China graduate university of chinese academy of sciences Beijing 100049 China

After examining a large number of type and authoritative specimens of Schizophragma Siebold & Zucc.,*** *** and *** *** Rehder were reduced to synonyms of *** Rehder and *** *** *** was reduced to synonym of *** *** crassum *** *** was treated as the correct name of *** ***(Chun) *** name *** *** Rehder is *** taxonomic treat-ment is supported by leaf epidermal characters.

关键词： leaf epidermis new synonym reinstatement Schizophragma

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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 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 ～ 500 and ～50 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

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Structural Analysis and Identification of Cis-Elements of Rice osRACD Gene

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Acta Biochimica et Biophysica Sinica 2004年第3期36卷 191-198页

作者： Yun-Zhe XU, Rui-Lin YOU and Nai-Hu WU Institute of Genetics and Developmental Biology, chinese academy of sciences, beijing 100080, china 2college of life sciences, Peking university, beijing 100871, china Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100080 China college of life sciences Peking University Beijing 100871 China

The osRACD gene correlated with fertility transformation in the photoperiod sensitive genic male sterile rice (PGMR), Nongken 58S, encoded a rice (Oryza sativa L. ssp. japonica) small GTPase belonging to the Rac/Rho family. Inverse PCR was performed to amplify a fragment about 1.4 kb in 5' upstream region of the osRACD promoter. Deletion mutation and gel mobility shift assay characterized two fragments (–799 to –686 nt, and –686 to –431 nt) in the osRACD promoter that could be involved in its transcriptional regulation. When these two deletion fragments were used as probe respectively, a retarded band appeared in the nuclear extracts of fertile 58S rice under short day (58S-SD). Whereas no retarded band was shown in the nuclear extracts of sterile 58S rice under long day (58S-LD). Competition assay indicated that the factors in the retarded bands binding to these two fragments were the same trans-acting factor (termed rice factor, RF). The binding affinity of RF was affected by phosphorylation and was higher in SD-growth rice than that of LD-growth rice.

关键词： photoperiod-sensitive male genic sterile rice osRACD gene photoperiod fertility transformation cis-element

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Testing local realism in P → VV decays

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science china(Physics,Mechanics & Astronomy) 2010年第5期53卷 870-875页

作者： LI JunLi1 & QIAO CongFeng1,2 1Department of Physics,graduate university of chinese academy of sciences,beijing 100049,china 2Theoretical Physics Center for science Facilities(TPCSF),chinese academy of sciences,beijing 100049,china Department of Physics Graduate University of Chinese Academy of Sciences Beijing China Theoretical Physics Center for science Facilities (TPCSF) Chinese Academy of Sciences Beijing China

It was found that the vector meson pair from the pseudoscalar decays can form an entangled *** this work we give out detailed explanations on the polarization correlation of the two entangled vector *** is demonstrated that an experimental test of the Clauser-Horne inequality can be carried out through measuring the azimuthal distribution of four pseudoscalars in the cascade decay ηc→ VV →(PP)(PP),and the measurement of this process is feasible with the current running experiments in tau-charm ***,a brief discussion on the polarization correlation of the two vector mesons from B → VV decays is also presented.

关键词： nonlocality test high energy experiment meson decays

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Genetic structure and phylogeography of a relict tree fern,Sphaeropteris brunoniana (Cyatheaceae) from china and Laos inferred from cpDNA sequence variations:Implications for conservation

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Journal of Systematics and Evolution 2011年第1期49卷 72-79页

作者： 1,2 Zi-Juan WANG 1 Kai-Yun GUAN 1 (Kunming Institute of Botany, chinese academy of sciences, Kunming 650204, china) 2 (graduate university of chinese academy of sciences, beijing 100049, china) (Kunming Institute of Botany Chinese Academy of Sciences Kunming 650204 China) (graduate university of chinese academy of sciences Beijing 100049 China)

In this study, we analyzed the genetic structure and phylogeography of Sphaeropteris brunoniana from china and Laos. Combining cpDNA trnL-trnF and atpB-rbcL sequence variations, five haplotypes were identi- fied from the 10 investigated populations. Moderate haplotype diversity (h = 0.66580) and low nucleotide diver- sity (π = 0.23 × 10 ?3 ) were detected. The S. brunoniana in Yunnan region had much higher genetic diversity (h = 0.60195, π = 0.35 × 10 ?3 ) than that of Hainan–Laos (h = 0.00000, π = 0.00). A high level of genetic differentiation (94.74%) between the two regions was revealed by AMOVA. Nested clade analysis identified two major clusters of the five haplotypes, one clade in the Yunnan region and the other in Hainan–Laos. The analysis indicated that restricted gene flow with isolation by distance and allopatric fragmentation were likely the major processes that shaped the spatial distribution of the haplotypes. The isolated distribution of clades implied the emergence of independent refugia of this species in each region during Quaternary glaciations. The Yunnan populations frequently contained an ancestral haplotype, and most of them harbored other descendent haplotypes. Based on the distribution pattern of haplotypes and the nested clade analysis results, the Yunnan region potentially had several refugia of this species during glacial periods, whereas the Hainan populations were probable new colonizations.

关键词： atpB-rbcL Hainan–Laos phylogeography Sphaeropteris brunoniana trnL-trnF Yunnan.

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