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DNA barcoding provides distinction between Radix Astragali and its adulterants

Science china(Life sciences) 2010年第8期53卷 992-999页

作者： GUO HaiYan1,2, WANG WeiWei2, YANG Ning2, GUO BaoLin3, ZHANG Sun2, YANG RuiJing2, YUAN Ye2, YU JunLin4, HU SongNian2, SUN QiShi1 & YU Jun2 1School of Traditional chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, china 2key laboratory of genome sciences and information, beijing institute of genomics, chinese academy of sciences, beijing 101300, china 3chinese academy of Medical sciences, Peking Union Medical College institute of Medicinal Plant Development, beijing 100094, china 4Department of Chemistry, Tonghua Normal College, Tonghua 134002, china 1. School of Traditional chinese Materia Medica Shenyang Pharmaceutical University Shenyang 110016 China2. Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences Beijing 101300 China3. Peking Union Medical College Institute of Medicinal Plant Development Chinese Academy of Medical Sciences Beijing 100094 China4. Department of Chemistry Tonghua Normal College Tonghua 134002 China

Based on variable nuclear and/or organellar DNA sequences among vastly divergent species as well as morphologically indistinguishable species, DNA barcoding is widely applicable in species identification, biodiversity studies, forensic analyses, and authentication of medicinal plants. The roots of Astragalus membranaceus and A. membranaceus var. mongholica are commonly used as Radix Astragali in several Asian countries, including china, Japan, and Korea. However, in addition to the two species recorded in the chinese Pharmacopoeia, there are twenty-three species from different genera including Astragalus, Oxytropis, Hedysarum, and Glycyrrhiza, which have been used as adulterants not only in trading markets but also by the herbal medicine industry. Therefore, a simple, reliable, and accurate classification method is important for distinguishing authentic Radix Astragali from its adulterants. In this study, we acquired data for 37 samples from four related genera within the family Fabaceae. Then we compared four candidate DNA barcoding markers using ITS, matK, rbcL, and coxI sequences from nuclear, chloroplast, and mitochondrial genomes, all commonly used for plants to identify genetic variations among genera, intraspecies, and interspecies. We observed higher divergences among genera and interspecies for ITS, which have the average Kimura 2-parameter distances of 4.5% and 14.1%, respectively, whereas matK was found to have sufficient divergence at the intraspecific level. Moreover, two indels detected in the matK sequence are useful for PCR studies in distinguishing Radix Astragali from its adulterants. This study suggests that the combined barcoding regions of ITS and matK are superior barcodes for Radix Astragali and further studies should focus on evaluating the applicability and accuracy of such combined markers for a wide range of traditional chinese herbs.

关键词： Radix Astragali DNA barcode Astragalus adulterant identification

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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 School of the chinese academy of sciences, beijing 100039, 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

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Next-generation sequencing technology:A technology review and future perspective

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Science china(Life sciences) 2010年第1期53卷 44-57页

作者： ZHOU XiaoGuang1,REN LuFeng1,LI YunTao2,ZHANG Meng1,YU YuDe2 & YU Jun1 1 key laboratory of genome sciences and information,beijing institute of genomics,chinese academy of sciences,beijing 100029,china 2 institute of Semiconductors,chinese academy of sciences,beijing 100083,china key laboratory of genome sciences and information Beijing Institute of Genomics Chinese Academy of Sciences Beijing China institute of Semiconductor Chinese Academy of Sciences Beijing China

As one of the most powerful tools in biomedical research,DNA sequencing not only has been improving its productivity at an exponential growth rate but has also been evolving into a new layout of technological territories toward engineering and physical disciplines over the past three *** this technical review,we look into technical characteristics of the next-generation sequencers and provide insights into their future development and *** envisage that some of the emerging platforms are capable of supporting the USD1000 genome and USD100 genome goals if given a few years for technical *** also suggest that scientists from china should play an active role in this campaign that will have a profound impact on both scientific research and societal healthcare systems.

关键词： genomics DNA sequencing next generation sequencing technologies sequencer

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CMQV+:An authenticated key exchange protocol from CMQV

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Science china(information sciences) 2012年第7期55卷 1666-1674页

作者： LI Hui 1,2 & WU ChuanKun 1 1 State key laboratory of information Security,institute of Software,chinese academy of sciences,beijing 100190,china 2 Graduate University of chinese academy of sciences,beijing 100049,china 1. State key laboratory of information Security Institute of Software Chinese Academy of Sciences Beijing 100190 China2. Graduate University of Chinese Academy of Sciences Beijing 100049 China

Ustaoglu presents a secure and efficient key exchange protocol named CMQV,based on the design rationales of HMQV and *** with the latter two protocols,on one hand,CMQV achieves high performance of HMQV,and on the other,it is proven secure in eCK model as NAXOS ***,CMQV enjoys the security proof under gap Diffie-Hellman assumption as indicated by its *** this paper,we propose a variant of CMQV,called CMQV+,which is proven secure under a weaker assumption (*** Diffie-Hellman assumption) in eCK model with random oracles while maintaining the high-performance feature of CMQV as much as possible.

关键词： key exchange eCK model trapdoor-test technique provable security CDH assumption

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A two-round honest-verifier zero-knowledge protocol

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Science china(information sciences) 2010年第5期53卷 954-963页

作者： LIU HanWu 1,2 & LIN DongDai 1 1 The State key laboratory of information Security, institute of Software, chinese academy of sciences, beijing 100190, china 2 Graduate University of the chinese academy of sciences, beijing 100049, china 1. The State key laboratory of information Security Institute of Software Chinese Academy of Sciences Beijing 100190 China2. Graduate University of the Chinese Academy of Sciences Beijing 100049 China

Since the concept of zero-knowledge protocols was introduced, it has attracted a lot of attention and in turn showed significant effect on the development of cryptography, complexity theory and other areas. The round complexity of a zero-knowledge protocol is a very important efficiency consideration, and it is required to be as small as possible. Generally, it is desirable to have zero-knowledge protocols with constant numbers of rounds. Goldreich and Oren proved that only languages in BPP have one-round and two-round zero-knowledge protocols. Moreover, they also showed that only languages in BPP have one-round honest-verifier zero-knowledge protocols. The notion of honest-verifier zero-knowledge protocols is highly non-trivial and fascinating itself, and has many other uses. Thus, the problem as to whether there exist two-round honest-verifier zero-knowledge protocols becomes an important open problem. In this paper, we introduce a new simulation technique and present a two-round honest-verifier zero-knowledge protocol for any language in N P under a standard complexity assumption based on this technique.

关键词： proof system argument system zero-knowledge witness indistinguishability black-box one-way permutation commitment scheme zap

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A Scenario on the Stepwise Evolution of the Genetic Code

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genomics,Proteomics & Bioinformatics 2007年第Z1期 143-151页

作者： Jing-Fa Xiao and Jun Yu CAS key laboratory of genome sciences and information,beijing institute of genomics,chinese academy of sciences,beijing 100029,china.

It is believed that in the RNA world the operational (ribozymes) and the infor-mational (riboscripts) RNA molecules were created with only three (adenosine,uridine,and guanosine) and two (adenosine and uridine) nucleosides,respectively,so that the genetic code started uncomplicated. Ribozymes subsequently evolved to be able to cut and paste themselves and riboscripts were acceptive to rigor-ous editing (adenosine to inosine); the intensive diversification of RNA molecules shaped novel cellular machineries that are capable of polymerizing amino acids-a new type of cellular building materials for life. Initially,the genetic code,encoding seven amino acids,was created only to distinguish purine and pyrimidine; it was later expanded in a stepwise way to encode 12,15,and 20 amino acids through the relief of guanine from its roles as operational signals and through the recruitment of cytosine. Therefore,the maturation of the genetic code also coincided with (1) the departure of aminoacyl-tRNA synthetases (AARSs) from the primordial translation machinery,(2) the replacement of informational RNA by DNA,and (3) the co-evolution of AARSs and their cognate tRNAs. This model predicts gradual replacements of RNA-made molecular mechanisms,cellular processes by proteins,and informational exploitation by DNA.

关键词： genetic code codon aminoacyl-tRNA synthase GC content

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Overview of HBV whole genome data in public repositories and the chinese HBV reference sequences

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Progress in Natural Science:Materials International 2008年第1期18卷 13-20页

作者： Guanghua Wu a,b, Huiguo Ding c, Changqing Zeng b,* a Graduate School of chinese academy of sciences, beijing 100049, china b beijing institute of genomics, chinese academy of sciences, beijing 101300, china c beijing Youan Hospital, Capital Medical University, beijing 100069, china Graduate School of chinese academy of sciences Beijing 100049 China beijing institute of genomics Chinese Academy of Sciences Beijing 101300 China beijing Youan Hospital Capital Medical University Beijing 100069 China

The number of Hepatitis B virus (HBV) whole genomic sequences in public nucleotide databases (GenBank, EMBL, and DDBJ) had reached 866 by January 1, 2007. Coming from 46 countries and regions, these sequences were categorized as eight genotypes (A–H). With the statistical and phylogenetic analysis on all available complete genomic data of HBV, we here present an overview of HBV sequences in public databases. From all registered 229 HBV genomes in chinese regions as well as 59 sequencing data from our research group, we report the establishment of reference sequences of HBV strains prevailing in china. These analyses provide clues for the effects of HBV genotypes in host clinical progressions, geographic distribution of the infection, and the viral evolutionary history. Moreover, the viral sequence reference would be helpful in the identiffcation of various HBV mutations. Based on the analysis of various public databases, we suggest that the chinese HBV database with the clinical information should be constructed.

关键词： Public databases HBV genomic sequences Genotype Subtype chinese reference sequences

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The correspondence between the concepts in description logics for contexts and formal concept analysis

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Science china(information sciences) 2012年第5期55卷 1106-1122页

作者： MA Yue 1,2,SUI YueFei 1 & CAO CunGen 1 1 key laboratory of Intelligent information Processing,institute of Computing Technology,chinese academy of sciences,beijing 100190,china 2 Graduate University of chinese academy of sciences,beijing,china 1. key laboratory of Intelligent information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing 100190 China2. Graduate University of Chinese Academy of Sciences Beijing 100049 China

Formal concept analysis (FCA) and description logic (DL) are meant to be formalizations of concepts.A formal concept in the former consists of its intent and extent,where the intent is the set of all the attributes shared by each object in the extent of the concept,and the extent is the set of all the objects sharing each property in the intent of the concept.A concept in the latter formalization is simply a concept name,the interpretation of which is a subset of a *** consider the correspondence between concepts in both formalizations,a multi-valued formal context must be represented both as a knowledge base and as a model of the DL for contexts,where concepts are decomposed into tuple concepts C,interpreted as a set of tuples and value concepts V,interpreted as a set of attribute-value *** show that there is a difference between the interpretation of concepts R.V /R.C and the Galois connection between the extent/intent of formal concepts in *** to the Galois connection,there should be concepts of the form + R.V and + R.C inter-preted in FCA,and hence the logical language L for DL is extended to be L + together with + as a constructor so that + R.V and + R.C are well-defined ***,according to the interpretation in DL there should be pseudo concepts in FCA so that the interpretation of concepts R.V /R.C is the extent/intent of pseudo *** correspondence between formal concepts and concepts in L +,and between pseudo concepts and concepts in L are presented in this paper.

关键词： description logic formal concept analysis concept attribute/role

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Dynamic tree-based authenticated group key exchange protocol

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Science china(information sciences) 2010年第8期53卷 1591-1602页

作者： LI Hui 1,2 , WU ChuanKun 1 & TENG JiKai 1,2 1 State key laboratory of information Security, institute of Software, chinese academy of sciences, beijing 100190, china 2 Graduate University of chinese academy of sciences, beijing 100049, china 1. State key laboratory of information Security Institute of Software Chinese Academy of Sciences Beijing 100190 China2. Graduate University of Chinese Academy of Sciences Beijing 100049 China

Authenticated group key exchange protocols allow a group of users over a public network to establish a shared secret key for the subsequent cryptographic goals. In this paper, we extend BD-II scheme into a dynamic setting, and propose a tree-based authenticated key exchange protocol which is more suitable for dynamic groups in such as ad hoc networks. Our protocol is proven secure in random-oracle model. Additionally, we analyze the costs of our protocols in both communication and computation terms, and compare its performance with three well-known protocols.

关键词： tree-based group key exchange dynamic provable security

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Improved multi-pass fast correlation attacks with applications

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Science china(information sciences) 2011年第8期54卷 1635-1644页

作者： ZHANG Bin & FENG DengGuo State key laboratory of information Security,institute of Software,chinese academy of sciences,beijing 100190,china 1. State key laboratory of information Security Institute of Software Chinese Academy of Sciences Beijing 100190 China

In this paper we propose two new algorithms for multi-pass fast correlation attacks on stream *** first algorithm aims at fast symbol-wise decoding in the circumstances that the noise is not very high and we have little resource for *** second algorithm deals with the practical decoding problem in the high noise and limited keystream *** new algorithms are applicable to arbitrary form LFSR and compare favorably to the previously known algorithms in the scenarios under *** applications,we demonstrate new key recovery attacks on one-level Bluetooth E0 and LILI-128,*** 2 37 -bit keystream and 2 28-byte memory,our attack against one-level E0 needs 2 35.1 *** 2 24-bit keystream and 2 24.5 -byte memory,our attack on LILI-128 has time complexity 2 70.6 operations.

关键词： stream cipher fast correlation attacks linear feedback shift register (LFSR) Bluetooth E0 LILI-128

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