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| 1 | The Epitope Study on the SARS-CoV Nucleocapsid Protein显示文摘The nucleocapsid protein (N protein) has been found to be an antigenic protein in a number of coronaviruses. Whether the N protein in severe acute respiratory syndrome-associated coronavirus (SARS-CoV) is antigenic remains to be elucidated. Using Western blot and Enzyme-linked Immunosorbent Assay (ELISA),the recombinant N proteins and the synthesized peptides derived from the N protein were screened in sera from SARS patients. All patient sera in this study displayed strong positive immunoreactivities against the recombinant N proteins,whereas normal sera gave negative immunoresponses to these proteins, indicating that the N protein of SARS-CoV is an antigenic protein. Furthermore, the epitope sites in the N protein were determined by competition experiments, in which the recombinant proteins or the synthesized peptides competed against the SARS-CoV proteins to bind to the antibodies raised in SARS sera. One epitope site located at the C-terminus was confirmed as the most antigenic region in this protein. A detailed screening of peptide with ELISA demonstrated that the amino sequence from Codons 371 to 407 was the epitope site at the C-terminus of the N protein. Understanding of the epitope sites could be very significant for developing an effective diagnostic approach to SARS. | Shuting Li, Liang Lin, Hao Wang, Jianning Yin, Yan Ren, Zhe Zhao, Jie Wen, Cuiqi Zhou, Xumin Zhang, Xiaolei Li, Jingqiang Wang, Zhengfeng Zhou, Jinxiu Liu, Jianmin Shao, Tingting Lei, Jianqiu Fang, Ningzhi Xu, and Siqi LiuBeijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China & Beijing Proteomics Institute, Beijing 101300, China | 2003 | Genomics, Proteomics & Bioinformatics2003，1，3： | 9 |
| 2 | Characteristics of distribution of Mycobacterium tuberculosis lineages in China显示文摘The genotyping methods of Mycobacterium tuberculosis would dramatically improve our understanding of the molecular epidemiology of tuberculosis. 3,929 isolates, from a National Survey of Drug-Resistant Tuberculosis in 2007 in China, were successfully genotyped by large sequence polymorphisms and 15 loci variable number tandem repeats. We found that 2,905(2,905/3,929, 73.9%) cases belonged to Lineage 2, dominated in the east and central regions, 975 cases(975/3,929, 24.8%) were Lineage 4, highly prevailed in the west regions, and 36 and 13 cases were Lineage 3 and Lineage 1, respectively. We also explored the associations between lineages(Lineage 2 vs. Lineage 4) and clinical characteristics by logistic regression. For Lineage 2, the risk factors were Han-ethnicity population and fever. However, for Lineage 4, they were occupation(farmer), and degree of education(non-literate). Fully understanding of the distribution of Mycobacterium tuberculosis lineage and its risk factors would play a critical role in tuberculosis prevention, control, and treatment. | Haixia Chen Li He Chao Cai Jingyi Liu Junnan Jia Liang Ma Hairong Huang Lixia Wang Xumin Ni Jimin Gao Weimin Li | 2018 | Science China(Life Sciences)2018，61，6： | 7 |
| 3 | Full-duplex light communication with a monolithic multicomponent system显示文摘A monolithic multicomponent system is proposed and implemented on a III-nitride-on-silicon platform,whereby two multiple-quantum-well diodes(MQW-diodes)are interconnected by a suspended waveguide.Both MQW-diodes have an identical low-In-content InGaN/Al0.10Ga0.90N MQW structure and are produced by the same fabrication process flow.When appropriately biased,both MQW-diodes operate under a simultaneous emission-detection mode and function as a transmitter and a receiver at the same time,forming an in-plane full-duplex light communication system.Real-time full-duplex audio communication is experimentally demonstrated using the monolithic multicomponent system in combination with an external circuit. | Yongjin Wang Xin Wang Bingcheng Zhu Zheng Shi Jialei Yuan Xumin Gao Yuhuai Liu Xiaojuan Sun Dabing Li Hiroshi Amano | 2018 | Light(Science & Applications)2018，7，1： | 5 |
| 4 | A complete genome assembly of Glaciecola mesophila sp. nov. sequenced by using BIGIS-4 sequencer system显示文摘Using a pyrosequencing-based custom-made sequencer BIGIS-4, we sequenced a Gram-negative bacterium Glaciecola mesophila sp. nov. (Gmn) isolated from marine invertebrate specimens. We generated 152043 sequencing reads with a mean high-quality length of 406 bp, and assembled them using the BIGIS-4 post-processing module. No systematic low-quality data was detected beyond expected homopolymer-derived errors. The assembled Gmn genome is 5144318 bp in length and harbors 4303 annotated genes. A large number of metabolic genes correspond to various nutrients from surface marine invertebrates. Its abundant cold-tolerant and cellular signaling and related genes reveal a fundamental adaptation to low-temperature marine environment. | YUAN LiNa REN LuFeng LI YunTao HAN WeiJing YU Yong CHU YaNan LIU GuiMing YU Dan TENG MingJing WANG Liang WANG XuMin ZHOU XiaoGuang YU YuDe YU Jun | 2011 | Science China(Life Sciences)2011，54，9： | 4 |
| 5 | Comparative analysis of four essential Gracilariaceae species in China based on whole transcriptomic sequencing显示文摘Three Gracilaria species,G.chouae,G.blodgettii,G.vermiculophylla and a close relative species,Gracilariopsis lemaneiformis which is now nominated as Gracilaria lemaneiformis,are the typically indigenous species which are important resources for the production of special proteins,phycobilisomes,special carbohydrates,and agar in China.In this study,de novo transcriptome sequencing on these four species using the next generation sequencing technology was performed for the first time.Functional annotations on assembled sequencing reads showed that the transcriptomic profiles were quite different between G.lemaneiformis and other three Gracilaria species.Comparative analysis of differential gene expression related to carbohydrate and phycobiliprotein metabolisms also showed that the expression profiles of these essential genes were different in four species.The genes encoding allophycocyanin,phycocyanin and phycoerythrin were further examined in four species and their deduced amino acid sequences were used for phylogenetic analysis to confirm that G.lemaneiformis had close relationship to genus Gracilaria,as well as that within genus Gracilaria,G.chouae had closer relationship to G.vermiculophylla rather than to G.blodgettii.The de novo transcriptome study on four species provided a valuable genomic resource for further understanding and analysis on biological and evolutionary study among marine algae. | XU Jiayue SUN Jing YIN Jinlong WANG Liang WANG Xumin LIU Tao CHI Shan LIU Cui REN Lufeng WU Shuangxiu YU Jun | 2014 | Acta Oceanologica Sinica2014，33，2： | 3 |
| 6 | Phylogenetic analyses of the genes involved in carotenoid biosynthesis in algae显示文摘Carotenoids play a crucial role in absorbing light energy for photosynthesis,as well as in protecting chlorophyll from photodamage.In contrast to the Streptophyta,few studies have examined carotenoid biosynthetic pathways in algae,owing to a shortage of datasets.As part of the 1000 Plants Project,we sequenced and assembled the transcriptomes of 41 marine macroalgal species,including 22 rhodophytes and 19 phaeophytes,and then combined the datasets with publicly available data from Gen Bank(National Center for Biotechnology Information) and the U.S.Department of Energy Joint Genome Institute.As a result,we identified 68 and 79 fulllength homologs in the Rhodophyta and Phaeophyceae,respectively,of seven inferred carotenoid biosynthetic genes,including the genes for phytoene synthase(PSY),phytoene desaturase(PDS),ζ-carotene desaturase(ZDS),ζ-carotene isomerase(Z-ISO),prolycopene isomerase(crt ISO),lycopene β-cyclase(LCYB),and lycopene ε-cyclase(LCYE).We found that the evolutionary history of the algal carotenoid biosynthetic pathway was more complex than that of the same pathway in the Streptophyta and,more specifically,that the evolutionary history involved endosymbiotic gene transfer,gene duplication,and gene loss.Almost all of the eukaryotic algae that we examined had inherited the seven carotenoid biosynthesis genes via endosymbiotic gene transfer.Moreover,PSY,crt ISO,and the ancestral lycopene cyclase gene(LCY) underwent duplication events that resulted in multiple gene copies,and the duplication and subsequent divergence of LCYB and LCYE specialized and complicated the cyclization of lycopene.Our findings also verify that the loss of LCYE in both the microphytic rhodophytes and phaeophytes explains the differences in their carotenoid patterns,when compared to the macrophytic rhodophytes.These analyses provide a molecular basis for further biochemical and physiological validation in additional algal species and should help elucidate the origin and evolution of carotenoid biosynthetic pathways. | WANG Shanshan ZHANG Lei CHI Shan WANG Guoliang WANG Xumin LIU Tao TANG Xuexi | 2018 | Acta Oceanologica Sinica2018，37，4： | 3 |
| 7 | Transcriptome-wide evolutionary analysis on essential brown algae(Phaeophyceae)in China显示文摘Brown algae(Chromista,Ochrophyta,Phaeophyceae) are a large group of multicellular algae that play important roles in the ocean's ecosystem and biodiversity.However,poor molecular bases for studying their phylogenetic evolutions and novel metabolic characteristics have hampered progress in the field.In this study,we sequenced the de novo transcriptome of 18 major species of brown algae in China,covering six orders and seven families,using the high-throughput sequencing platform Illumina HiSeq 2000.From the transcriptome data of these 18 species and publicly available genome data of Ectocarpus siliculosus and Phaeodactylum tricornutum,we identified 108 nuclear-generated orthologous genes and clarified the phylogenetic relationships among these brown algae based on a multigene method.These brown algae could be separated into two clades: Clade Ishigeales-Dictyotales and Clade Ectocarpales-Laminariales-Desmarestiale-Fucales.The former was at the base of the phylogenetic tree,indicating its early divergence,while the latter was divided into two branches,with Order Fucales diverging from Orders Ectocarpales,Laminariales,and Desmarestiale.In our analysis of taxonomy-contentious species,Sargassum fusiforme and Saccharina sculpera were found to be closely related to genera Sargassum and Saccharina,respectively,while Petalonia fascia showed possible relation to genus Scytosiphon.The study provided molecular evidence for the phylogenetic taxonomy of brown algae. | SUN Jing WANG Liang WU Shuangxiu WANG Xumin XIAO Jingfa CHI Shan LIU Cui REN Lufeng ZHAO Yuhui LIU Tao YU Jun | 2014 | Acta Oceanologica Sinica2014，33，2： | 2 |
| 8 | Hyperbolic polynomial uniform B-spline curves and surfaces with shape parameter显示文摘 | Liu Xumin Xu Weixiang Guan Yong Shang Yuanyuan | 2009 | Graphical Models2009，，1： | 2 |
| 9 | Transcriptome characterization of Ishige okamurae(Phaeophyceae)shows strong environmental acclimation显示文摘Ishige okamurae,with leathery branched narrow fronds consisting of cylindrical hairs,is the typical species of the genus Ishige,which is considered as one of the most basal genera in the phylogeny of the Phaeophyceae.Apart from great public interest from the evolutionary respect,more attention has been brought on the abundant bioactive compounds in I.okamurae for therapeutic or economic considerations,such as diphlorethohydroxycarmalol and ishigoside.Yet little is known about related key genes or metabolic pathways involved in I.okamurae,which calls upon us to carry out global analyses of transcriptome by next generation sequencing.Altogether,we obtained 78 583 assembled scaffolds with N50 of 1 709 nucleotides,and 25 357 unigenes with significant BLAST matches(E-value cutoff of 10-5).In terms of characterization of the transcriptome of I.okamurae,we focused on anti-stress metabolic pathways and synthetic routes of bioactive compounds in an attempt to obtain a better understanding of the interactive organism-environment regulatory networks.Pathway-based analysis helped us to deepen our comprehension of the interaction between I.okamurae and its surroundings,with MAPK signal pathway as an example.Furthermore,we discovered a wide range of novel putative functional proteins that could be of wide application,such as Rab family,using sequence-based transcriptome.In conclusion,transcriptome characterization of I.okamurae(Phaeophyceae) shows strong environmental acclimation. | QU Jieqiong WANG Xumin CHI Shan WU Shuangxiu SUN Jing LIU Cui CHEN Shengping YU Jun LIU Tao | 2014 | Acta Oceanologica Sinica2014，33，2： | 1 |
| 10 | Analysis of Saccharina japonica transcriptome using the high-throughput DNA sequencing technique and its vanadium-dependent haloperoxidase gene显示文摘Saccharina is one of the most important cold-water living marine brown algal genera.In this study we analyzed the transcriptome of S.japonica,which belongs to the 1 000 Plants(OneKP) Project,by using a nextgeneration high-throughput DNA sequencing technique.About 5.16 GB of raw data were generated,and 65 536 scaffolds with an average length of 454 bp were assembled with SOAP de novo assembly method.In total,19 040 unigenes were identified by BLAST;25 734 scaffolds were clustered into 37 Gene ontology functional groups;6 760 scaffolds were classified into 25 COG categories,as well as 2 665 scaffolds that were assigned to 306 KEGG pathways.Majority of the unigenes exhibited more similarities to algae including brown algae and diatom than other cyanobacteria,marine diatom,and plant.Saccharina japonica has the outstanding capability to accumulate halogen such as Br and I via halogenation processes from seawater.We acquired 42 different vanadium-dependent haloperoxidases(vHPO) in S.japonica transcriptome data,including 5 segments of vanadium-dependent iodoperoxidase(vIPO) and 37 segments of vanadium-dependent bromoperoxidase(vBPO).Complicated analyses of identified fulllength S.japonica vBPO1 and S.japonica vBPO2 revealed the importance of vBPO among species of brown algae and the strong relationship between marine algal vBPOs and vIPOs.This study will enhance our understanding of the biological characteristics and economic values of S.japonica species. | LIANG Xiayuan WANG Xumin CHI Shan WU Shuangxiu SUN Jing LIU Cui CHEN Shengping YU Jun LIU Tao | 2014 | Acta Oceanologica Sinica2014，33，2： | 1 |
| 11 | De novo sequencing and comparative analysis of three red algal species of Family Solieriaceae to discover putative genes associated with carrageenan biosysthesis显示文摘Betaphycus gelatinus,Kappaphycus alvarezii and Eucheuma denticulatum of Family Solieriaceae,Order Gigartinales,Class Rhodophyceae are three important carrageenan-producing red algal species,which produce different types of carrageenans,beta(β)-carrageenan,kappa(κ)-carrageenan and iota(ι)-carrageenan.So far the carrageenan biosynthesis pathway is not fully understood and few information is about the Solieriaceae genome and transcriptome sequence.Here,we performed the de novo transcriptome sequencing,assembly,functional annotation and comparative analysis of these three commercial-valuable species using an Illumina short-sequencing platform Hiseq 2000 and bioinformatic software.Furthermore,we compared the different expression of some unigenes involved in some pathways relevant to carrageenan biosynthesis.We finally found 861 different expressed KEGG orthologs which contained a glycolysis/gluconeogenesis pathway(21 orthologs),carbon fixation in photosynthetic organisms(16 orthologs),galactose metabolism(5 orthologs),and fructose and mannose metabolism(9 orthologs) which are parts of the carbohydrate metabolism.We also found 8 different expressed KEGG orthologs for sulfur metabolism which might be importantly related to biosynthesis of different types of carrageenans.The results presented in this study provided valuable resources for functional genomics annotation and investigation of mechanisms underlying the biosynthesis of carrageenan in Family Solieriaceae. | SONG Lipu WU Shuangxiu SUN Jing WANG Liang LIU Tao CHI Shan LIU Cui LI Xingang YIN Jinlong WANG Xumin YU Jun | 2014 | Acta Oceanologica Sinica2014，33，2： | 1 |
| 12 | Origin and evolution of alginate-c5-mannuronan-epimerase gene based on transcriptomic analysis of brown algae显示文摘The coding product of alginate-c5-mannuronan-epimerase gene(algG gene) can catalyze the conversion of mannuronate to guluronate and determine the M/G ratio of alginate.Most of the current knowledge about genes involved in the alginate biosynthesis comes from bacterial systems.In this article,based on some algal and bacterial algG genes registered on GenBank and EMBL databases,we predicted 94 algG genes open reading frame(ORF) sequences of brown algae from the 1 000 Plant Transcriptome Sequencing Project(OneKP).By method of transcriptomic sequence analysis,gene structure and gene localization analysis,multiple sequence alignment and phylogenetic tree construction,we studied the algal algG gene family characteristics,the structure modeling and conserved motifs of AlgG protein,the origin of alginate biosynthesis and the variation incidents that might have happened during evolution in algae.Although there are different members in the algal algG gene family,almost all of them harbor the conserved epimerase region.Based on the phylogenetic analysis of algG genes,we proposed that brown algae acquired the alginate biosynthesis pathway from an ancient bacterium by horizontal gene transfer(HGT).Afterwards,followed by duplications,chromosome disorder,mutation or recombination during evolution,brown algal algG genes were divided into different types. | WANG Ren WANG Xumin ZHANG Yalan YU Jun LIU Tao CHEN Shengping CHI Shan | 2014 | Acta Oceanologica Sinica2014，33，2： | 1 |
| 13 | Phylogenomic analysis of transcriptomic sequences of mitochondria and chloroplasts for marine red algae(Rhodophyta)in China显示文摘The chloroplast and mitochondrion of red algae(Phylum Rhodophyta) may have originated from different endosymbiosis.In this study,we carried out phylogenomic analysis to distinguish their evolutionary lineages by using red algal RNA-seq datasets of the 1 000 Plants(1KP) Project and publicly available complete genomes of mitochondria and chloroplasts of Rhodophyta.We have found that red algae were divided into three clades of orders,Florideophyceae,Bangiophyceae and Cyanidiophyceae.Taxonomy resolution for Class Florideophyceae showed that Order Gigartinales was close to Order Halymeniales,while Order Gracilariales was in a clade of Order Ceramials.We confirmed Prionitis divaricata(Family Halymeniaceae) was closely related to the clade of Order Gracilariales,rather than to genus Grateloupia of Order Halymeniales as reported before.Furthermore,we found both mitochondrial and chloroplastic genes in Rhodophyta under negative selection(Ka/Ks < 1),suggesting that red algae,as one primitive group of eukaryotic algae,might share joint evolutionary history with these two organelles for a long time,although we identified some differences in their phylogenetic trees.Our analysis provided the basic phylogenetic relationships of red algae,and demonstrated their potential ability to study endosymbiotic events. | JIA Shangang WANG Xumin QIAN Hao LI Tianyong SUN Jing WANG Liang YU Jun LI Xingang YIN Jinlong LIU Tao WU Shuangxiu | 2014 | Acta Oceanologica Sinica2014，33，2： | 1 |
| 14 | Phylogenomic analysis of transcriptomic sequences of mitochondria and chloroplasts of essential brown algae(Phaeophyceae)in China显示文摘The chloroplast and mitochondrion of brown algae(Class Phaeophyceae of Phylum Ochrophyta) may have originated from different endosymbiosis.In this study,we carried out phylogenomic analysis to distinguish their evolutionary lineages by using algal RNA-seq datasets of the 1 000 Plants(1KP) Project and publicly available complete genomes of mitochondria and chloroplasts of Kingdom Chromista.We have found that there is a split between Class Phaeophyceae of Phylum Ochrophyta and the others(Phylum Cryptophyta and Haptophyta) in Kingdom Chromista,and identified more diversity in chloroplast genes than mitochondrial ones in their phylogenetic trees.Taxonomy resolution for Class Phaeophyceae showed that it was divided into Laminariales-Ectocarpales clade and Fucales clade,and phylogenetic positions of Kjellmaniella crassifolia,Hizikia fusifrome and Ishige okamurai were confirmed.Our analysis provided the basic phylogenetic relationships of Chromista algae,and demonstrated their potential ability to study endosymbiotic events. | JIA Shangang WANG Xumin LI Tianyong QIAN Hao SUN Jing WANG Liang YU Jun REN Lufeng YIN Jinlong LIU Tao WU Shuangxiu | 2014 | Acta Oceanologica Sinica2014，33，2： | 1 |
| 15 | Endogenous viral elements in algal genomes显示文摘Endogenous viral elements(EVEs) are host-genomic fragments originated from viral genomes.They have been found universally in animal and plant genomes.Here we carried out a systematic screening and analysis of EVEs in algal genomes and found that EVEs commonly exist in algal genomes.We classified the EVE fragments into three categories according to the length of EVE fragments.Due to the probability of sequence similarity by chance,we ignored the potential function of medium-length EVE fragments.However,longlength EVE fragments probably had capability to encode protein domains or even entire proteins,and some short-length EVE fragments had high similarity with host's siRNA sequences and possibly served functions of small RNAs.Therefore,short and long EVE fragments might provide regulomic and proteomic novelty to the host's metabolism and adaptation.We also found several EVE fragments shared by more than 3 algal genomes.By phylogenetic analysis of the shared EVEs and their corresponding species,we found that the integration of viral fragments into host genomes was an ancient event,possibly before the divergence of Chlorophytes and Ochrophytes.Our findings show that there is a frequent genetic flow from viruses to algal genomes.Moreover,study on algal EVEs shed light on the virus-host interaction in large timescale and could also help us understand the balance of marine ecosystems. | WANG Liang WU Shuangxiu LIU Tao SUN Jing CHI Shan LIU Cui LI Xingang YIN Jinlong WANG Xumin YU Jun | 2014 | Acta Oceanologica Sinica2014，33，2： | 1 |
| 16 | The discovery of archaea origin phosphomannomutase in algae based on the algal transcriptome显示文摘Phosphomannomutase(PMM;EC 5.4.2.8) is an enzyme that catalyzes the interconversion reaction between mannose-6-phosphate and mannose-1-phosphate.However,its systematic molecular and functional investigations in algae have not hitherto been reported.In this work,with the accomplishment of the 1 000 Plant Project(OneKP) in which more than 218 species of Chromista,including 19 marine phaeophytes,22 marine rhodophytes,171 chlorophytes,5 cryptophytes,4 haptophytes,and 5 glaucophytes were sequenced,we used a gene analysis method to analyze the PMM gene sequences in algae and confirm the existence of the PMM gene in the transcriptomic sequencing data of Rhodophyta and Ochrophyta.Our results showed that only one type of PMM with four conserved motifs exists in Chromista which is similar to human PMM.Moreover,the phylogenetic tree revealed that algae PMM possibly originated from archaea. | FENG Yanjing CHI Shan LIU Cui CHEN Shengping YU Jun WANG Xumin LIU Tao | 2014 | Acta Oceanologica Sinica2014，33，2： | 1 |
| 17 | Hyperbolic polynomial uniform B-spline curves and surfaces with shape parameter显示文摘 | Liu Xumin Xu Weixiang Guan Yong Shang Yuanyuan | 2010 | Graphical Models2010，72，1： | 1 |
| 18 | Deploying and managing Web services: Issues, solutions, and directions显示文摘 | Yu Qi Liu Xumin Athman Bouguettaya | 2008 | The International Journal on Very Large Data Bases2008，17，3： | 1 |
| 19 | Constrained co-clustering with non-negative matrix faetorisation 显示文摘 | Salunke A Liu Xumin Rege M | 2012 | Journal of Business Intelligence and Data Mining2012，7，12： | 1 |
| 20 | Hyerbolic polynomial uniform B-spline curves and surfaces with shape parameters 显示文摘 | Liu Xumin Xu Weixiang Guan Yong | 2010 | Graphical Models2010，72，1： | 1 |
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