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| 1 | 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 |
| 2 | 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 |
| 3 | 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 |
| 4 | 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 |
| 5 | 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 |
| 6 | 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 |
| 7 | 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 |
| 8 | 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 |
| 9 | 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 |
| 10 | Application of rapid rehabilitation surgery concept for gastrointestinal cancer surgery of nutrition management显示文摘 | Sun XuMin | | 0，，06： | 1 |
| 11 | Analysis of Large Slotted-Waveguide Antenna Arrays Using the Parallel DDA-FE-BI-MLFMA显示文摘An efficient analyzing approach is presented for large slotted-waveguide antenna arrays by using hybrid finite element-boundary integral-multilevel fast multipole algorithm(FE-BI-MLFMA)in this paper.A simple computation model for slotted-waveguide antenna is presented by using thin current probe excitation and perfectly matched layer(PML)absorber.Since each slotted-waveguide antenna can be considered as a single sub-domain,the domain decomposition algorithm(DDA)can be applied to FE-BI-MLFMA to greatly reduce the computation resources and achieve high efficiency.This DDA-FE-BI-MLMFA is parallelized to further strength its capability.The comparisons of the computed radiation patterns with measured data and results from the commercial software show that our method has good accuracy for slottedwaveguide array.Then the influence of mutual coupling between adjacent slotted-waveguides is studied.To demonstrate capability of the presented method,a carefully designed large X-band slotted-waveguide antenna array containing eighteen waveguides with Taylor amplitude and inverse phase excitation distribution are analyzed in the paper. | Xumin Sun Minglin Yang Hongwei Gao Xinqing Sheng | 2017 | Journal of Beijing Institute of Technology2017，26，1： | 0 |
| 12 | Transcriptome sequencing of essential marine brown and red algal species in China and its significance in algal biology and phylogeny显示文摘Most phaeophytes(brown algae) and rhodophytes(red algae) dwell exclusively in marine habitats and play important roles in marine ecology and biodiversity.Many of these brown and red algae are also important resources for industries such as food,medicine and materials due to their unique metabolisms and metabolites.However,many fundamental questions surrounding their origins,early diversification,taxonomy,and special metabolisms remain unsolved because of poor molecular bases in brown and red algal study.As part of the 1 000 Plant Project,the marine macroalgal transcriptomes of 19 Phaeophyceae species and 21 Rhodophyta species from China's coast were sequenced,covering a total of 2 phyla,3 classes,11 orders,and 19 families.An average of 2 Gb per sample and a total 87.3 Gb of RNA-seq raw data were generated.Approximately 15 000 to 25 000 unigenes for each brown algal sample and 5 000 to 10 000 unigenes for each red algal sample were annotated and analyzed.The annotation results showed obvious differences in gene expression and genome characteristics between red algae and brown algae;these differences could even be seen between multicellular and unicellular red algae.The results elucidate some fundamental questions about the phylogenetic taxonomy within phaeophytes and rhodophytes,and also reveal many novel metabolic pathways.These pathways include algal CO2 fixation and particular carbohydrate metabolisms,and related gene/gene family characteristics and evolution in brown and red algae.These findings build on known algal genetic information and significantly improve our understanding of algal biology,biodiversity,evolution,and potential utilization of these marine algae. | WU Shuangxiu SUN Jing CHI Shan WANG Liang WANG Xumin LIU Cui LI Xingang YIN Jinlong LIU Tao YU Jun | 2014 | Acta Oceanologica Sinica2014，33，2： | 0 |
| 13 | Comparative analysis on transcriptome sequencings of six Sargassum species in China显示文摘Species of Sargassum are distributed worldwide,and are of great ecological and economic importance in marine ecosystems and bioresources.In this study,transcriptome sequencings of six Sargassum species were performed for the first time using an Illumina platform.For each sample,a total of 2.1–2.5 Gb of nucleotides are collected and assembled into 69 871–116 790 scaffolds,with an average length of 410–550 bp and N50 length of 756–1 462 bp.A total of 20 512–28 684 unigenes of each sample were annotated and compared well with known gene sequences from nr database.Clusters of Orthologous Groups(COG),gene ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) analyses were also performed for further understanding of gene functions and regulation pathways.Gene expression levels were calculated based on RPKM values and compared among these species,especially for those genes related to carbohydrate metabolism.Cluster analyses indicated that the differences of global gene expression between S.fusiforme,which was nominated as Hizikia fusiformis before,and other five species were not significant.Further phylogenetic analysis of 108 orthologous genes confirmed that S.fusiforme had closer relationship with S.hemiphyllum rather than S.horneri.These transcriptome data provided valuable information for better understanding of genome and gene characteristics of Sargassum algae and benefiting comparative and phylogenetic studies of Phaeophyceae species in future studies. | WANG Guoliang SUN Jing LIU Guiming WANG Liang YU Jun LIU Tao CHI Shan LIU Cui GUO Haiyan WANG Xumin WU Shuangxiu | 2014 | Acta Oceanologica Sinica2014，33，2： | 0 |
| 14 | Comparative study of the pathogenicity of the mosquito origin strain and duck origin strain of Tembusu virus in ducklings and three-week-old mice显示文摘Dear Editor,Duck Tembusu virus(DTMUV)is the causative agent of a new,acute and severe infectious disease in ducks(Su et al.,2011).TMUV was first isolated from Culex tritaeniorhynchus in Malaysia in 1955(Platt et al.,1975),and this strain is regarded as a reference strain.In our previous study,an infectious clone for the mosquito-derived Tembusu virus prototypical strain MM_1775(GenBank:JX477685.2)was constructed,and the rMM_1775 virus was rescued successfully(Wang et al.,2021).And the TMUV strain rCQW1 was rescued by a reverse genetic system using the viral RNAs of CQW1(GenBank:KM233707.1)(Chen et al.,2018;Guo et al.,2020),which was isolated from ducks in 2013(Zhu et al.,2015). | Xiaoli Wang Yu He Jiaqi Guo Zhen Wu Andres Merits Mingshu Wang Renyong Jia Dekang Zhu Mafeng Liu Xinxin Zhao Qiao Yang Ying Wu Shaqiu Zhang Juan Huang Xumin Ou Qun Gao Di Sun Anchun Cheng Shun Chen | 2023 | Virologica Sinica2023，38，5： | 0 |
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