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分子生物学技术在海洋微生物多样性研究中的应用 被引量:18
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作者 柳承璋 宋林生 吴青 《海洋科学》 CAS CSCD 北大核心 2002年第8期27-30,57,共5页
关键词 分子生物学技术 海洋微生物 多样性 应用
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淡水枝角水蚤(Daphnia pulex)微小RNA(miRNA)的生物信息学发掘与分析 被引量:6
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作者 柳承璋 李富花 相建海 《海洋与湖沼》 CAS CSCD 北大核心 2013年第4期837-845,共9页
微小RNA(microRNA或miRNA),是广泛存在于多细胞生物及其病毒的一类由22个左右核苷酸组成的内源性非编码RNA,具有转录后水平上的基因表达调控功能。本文在淡水枝角水蚤的全基因组序列的基础上,通过生物信息学方法对淡水枝角水蚤(Daphnia ... 微小RNA(microRNA或miRNA),是广泛存在于多细胞生物及其病毒的一类由22个左右核苷酸组成的内源性非编码RNA,具有转录后水平上的基因表达调控功能。本文在淡水枝角水蚤的全基因组序列的基础上,通过生物信息学方法对淡水枝角水蚤(Daphnia pulex)miRNA进行了发掘,得到miRNA前体(pre-miRNA)252个、可编码262个功能miRNA;发现了6个miRNA簇。8号染色体miRNA的出现频率显著高于其他染色体,而4号染色体miRNA频率明显显著较低。通过与几种两侧对称动物的聚类分析将pre-miRNA归为191个miRNA家族,其中105个家族为淡水枝角水蚤所特有,15个家族为节肢动物门特有。在几种两侧对称动物中,淡水枝角水蚤的miRNA与果蝇最为相似。 展开更多
关键词 淡水枝角水蚤 甲壳动物 microRNA MIRNA 微小RNA 生物信息学
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凡纳滨对虾C-型凝集素LvLec2对不同刺激的免疫应答 被引量:9
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作者 罗展 张继泉 +2 位作者 李富花 柳承璋 相建海 《海洋科学》 CAS CSCD 北大核心 2010年第11期103-110,共8页
克隆获得了与中国明对虾(Fenneropenaeus chinensis)C-type lectin 3同源的C-型凝集素LvLec2基因序列,并通过Real-time PCR研究了其在脂多糖(lipopolysaccharide,简称LPS)、灭活溶壁微球菌(Micrococcus lysodeikticus)和白斑综合症病毒(... 克隆获得了与中国明对虾(Fenneropenaeus chinensis)C-type lectin 3同源的C-型凝集素LvLec2基因序列,并通过Real-time PCR研究了其在脂多糖(lipopolysaccharide,简称LPS)、灭活溶壁微球菌(Micrococcus lysodeikticus)和白斑综合症病毒(white spot syndrome virus,简称WSSV)刺激后的转录表达变化。结果表明,LvLec2编码157个氨基酸,含有1个糖识别结构域(carbohydrate recognition domain,简称CRD),其CRD结构域中具有决定糖结合特异性的基序"EPS"(Glu118-Pro119-Ser120)序列。系统进化树分析表明LvLec2与已发表的凡纳滨对虾(Litopenaeus vannamei)C-型凝集素亲缘较远。LPS、灭活溶壁微球菌和WSSV刺激后,LvLec2基因在肝胰脏中的转录表达有明显的变化但表达模式不同。LvLec2可能作为模式识别受体参与了对虾对病原的识别或防御。 展开更多
关键词 凡纳滨对虾(Litopenaeus vannamei) C-型凝集素 基因克隆 不同刺激 免疫应答
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东海二甲基硫丙酸的分布及其制约因素的初步研究 被引量:12
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作者 焦念志 柳承璋 陈念红 《海洋与湖沼》 CAS CSCD 北大核心 1999年第5期525-531,共7页
于1994年4月对东海水域二甲基硫面酸(DMSP)浓度进行观测,结合对叶绿素和营养盐的监测结果,分析研究了DMSP分布及其调控因素。结果表明,DMSP浓度范围为0.17-5.66nmol/L,最高浓度出现于410站(125.0°E,29.3°N)。垂... 于1994年4月对东海水域二甲基硫面酸(DMSP)浓度进行观测,结合对叶绿素和营养盐的监测结果,分析研究了DMSP分布及其调控因素。结果表明,DMSP浓度范围为0.17-5.66nmol/L,最高浓度出现于410站(125.0°E,29.3°N)。垂直分布浓度最大层出现在表层20m以内。DMSP分布与叶绿素a的分布基本一致,与硝酸氮(NO3-N)的关系在NO3-N浓度小于0.5μmol/L时是正相关,而在NO3-N浓度高于10μmol/L时呈负相关。 展开更多
关键词 二甲基硫丙酸 叶绿素α 硝酸氮 东海
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凡纳滨对虾大量EST的生物信息学分析 被引量:1
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作者 孙政 柳承璋 +3 位作者 李富花 张晓军 张俊彬 相建海 《海洋学报》 CAS CSCD 北大核心 2013年第5期128-136,共9页
凡纳滨对虾是我国乃至世界最重要的对虾养殖种。EST(expressed sequence tags)测序是对没有基因组背景的生物进行功能基因分析最为有效的方法之一。为了研究凡纳滨对虾重要功能基因、以及为筛选分子标记奠定基础,本文集成了一套快速高效... 凡纳滨对虾是我国乃至世界最重要的对虾养殖种。EST(expressed sequence tags)测序是对没有基因组背景的生物进行功能基因分析最为有效的方法之一。为了研究凡纳滨对虾重要功能基因、以及为筛选分子标记奠定基础,本文集成了一套快速高效的EST信息深度挖掘的方法,并对公共数据库中161 241条凡纳滨对虾EST序列进行分析,获得了20 410条unigenes,包括14 236条contigs和6 174条singlets。通过与NR数据库比对发现有注释的基因7 984条,并对其余12 426条未知基因中的4 702条进行了功能域注释。对有NR注释的基因的GO分类分析获得其中2 715条基因的生物学过程、细胞定位和分子功能分类信息。此外,通过与模式生物通路图进行比对和定位,将3738条基因定位到270个KEGG通路图中,发现凡纳滨对虾的9条unigenes与果蝇丝裂原活化蛋白激酶(MAPK)通路的5个关键基因对应,提示凡纳滨对虾很可能存在类似的重要信号转导通路。另外,通过对6种组织,包括肝胰腺、淋巴器官、血细胞、鳃、眼柄和神经的EST进行比较分析,筛选获得了组织特异性转录本共7 000余条,并对这些特异性转录本进行了功能分类。本研究不仅开发了公共基因资源发掘的方法,也为对虾功能基因的研究利用提供了重要参考数据。 展开更多
关键词 凡纳滨对虾 EST 基因组织特异性表达
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基于中国明对虾不同组织EST数据的基因表达差异分析
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作者 隗健凯 柳承璋 +4 位作者 张晓军 王兵 董波 李富花 相建海 《水产学报》 CAS CSCD 北大核心 2013年第5期661-671,共11页
对前期获得的中国明对虾头胸部、血液、眼柄、卵巢4种组织的EST测序数据进行了生物信息学挖掘和分析。4种组织的原始EST序列分别为10 446条、2 690条、1 067条和1 282条,通过聚类拼接得到unigene 3 454条、1 053条、406条和544条,对其... 对前期获得的中国明对虾头胸部、血液、眼柄、卵巢4种组织的EST测序数据进行了生物信息学挖掘和分析。4种组织的原始EST序列分别为10 446条、2 690条、1 067条和1 282条,通过聚类拼接得到unigene 3 454条、1 053条、406条和544条,对其进行了NR、GO、KEGG等数据库的功能注释,并在此基础上进行了组织差异分析。通过同源比对的方法找出了各组织特异的转录本,并根据注释信息将其进行了GO功能分类。结果显示,血液组在细胞杀伤、迁移和节律等功能分类上特异性富集;眼柄组在色素生成、信号传递和生物学调控等功能分类上特异性富集;卵巢组在营养贮存运输、繁殖和定位等功能分类上特异性富集。拼接时聚类到一起的EST数目在一定程度上可以代表基因的表达量,据此对各组织的高表达基因进行了分析。结果显示,peritrophin、elongation factor 1-alpha、thrombospondin和arginine kinase 4个基因在组织中分布较为广泛且表达量高,提示其可能参与对虾多种重要的生物学过程。而在血液组中注释到的高表达基因还包括penaeidin、cytochrome c oxidase和14-3-3 like protein基因,在眼柄组中注释到的高表达基因还包括arrestin和rhodopsin基因。此外,为了解各组织共有基因的差异表达情况,对peritrophin和peroxiredoxin进行了分析,发现了peritrophin基因的多形式和高表达现象。 展开更多
关键词 中国明对虾 表达序列标签(EST) 组织差异 组织高表达基因
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EST-derived SNP discovery and selective pressure analysis in Pacific white shrimp(Litopenaeus vannamei) 被引量:3
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作者 柳承璋 王霞 +1 位作者 相建海 李富花 《Chinese Journal of Oceanology and Limnology》 SCIE CAS CSCD 2012年第5期713-723,共11页
Pacific white shrimp has become a major aquaculture and fishery species worldwide.Although a large scale EST resource has been publicly available since 2008,the data have not yet been widely used for SNP discovery or ... Pacific white shrimp has become a major aquaculture and fishery species worldwide.Although a large scale EST resource has been publicly available since 2008,the data have not yet been widely used for SNP discovery or transcriptome-wide assessment of selective pressure.In this study,a set of 155 411 expressed sequence tags(ESTs) from the NCBI database were computationally analyzed and 17 225 single nucleotide polymorphisms(SNPs) were predicted,including 9 546 transitions,5 124 transversions and 2 481 indels.Among the 7 298 SNP substitutions located in functionally annotated contigs,58.4%(4 262) are non-synonymous SNPs capable of introducing amino acid mutations.Two hundred and fifty nonsynonymous SNPs in genes associated with economic traits have been identified as candidates for markers in selective breeding.Diversity estimates among the synonymous nucleotides were on average 3.49 times greater than those in non-synonymous,suggesting negative selection.Distribution of non-synonymous to synonymous substitutions(Ka/Ks) ratio ranges from 0 to 4.01,(average 0.42,median 0.26),suggesting that the majority of the affected genes are under purifying selection.Enrichment analysis identified multiple gene ontology categories under positive or negative selection.Categories involved in innate immune response and male gamete generation are rich in positively selected genes,which is similar to reports in Drosophila and primates.This work is the first transcriptome-wide assessment of selective pressure in a Penaeid shrimp species.The functionally annotated SNPs provide a valuable resource of potential molecular markers for selective breeding. 展开更多
关键词 Litopenaeus vannamei single nucleotide polymorphism (SNP) expressed sequence tag (EST) shrimp population genetics adaptive evolution Darwinian selection
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DISTRIBUTION OF β-GLUCOSIDASE ACTIVITIES IN THE SOUTH CHINA SEA
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作者 柳承璋 焦念志 《Chinese Journal of Oceanology and Limnology》 SCIE CAS CSCD 2002年第S1期15-21,共7页
Distribution of extracellular β-glucosidase activity (β-GlcA), bacteria abundance andTOC were investigated during tbe SCSMEX98 cruise in May and June 1998 in the South China Sea. Re-sults showed that β-GlcA varied ... Distribution of extracellular β-glucosidase activity (β-GlcA), bacteria abundance andTOC were investigated during tbe SCSMEX98 cruise in May and June 1998 in the South China Sea. Re-sults showed that β-GlcA varied significantly in both vertical and horizontal distribution. Hydrolysis rateranged from under detectable limit to 29% /h. In most cases, β-GlcA was highest in surface water; some-times there was a second-highest value at the bottom of the euphotic zone. Temperature controlled experi-ments showed that low temperature could significantly decrease β-GlcA; but that the low β-GlcA in 展开更多
关键词 EXTRACELLULAR ENZYME ACTIVITY (EEA) Β-GLUCOSIDASE ACTIVITY (β-GlcA) the South China Sea
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DISTRIBUTION AND SEA-AIR FLUX OF BIOGENIC CLIMATIC GAS-DIMETHYLSULPHIDE(DMS)IN JIAOZHOU BAY
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作者 柳承璋 焦念志 《Chinese Journal of Oceanology and Limnology》 SCIE CAS CSCD 2002年第S1期102-110,共9页
Concentrations of dimethylsulfide (DMS) and dimethylsulfoniopropionate (DMSP) were measured from Nov. 1995 to Sep. 1997 in seawater of Jiaozhou Bay, other ecological factors such as water temperature, salinity, Chl a ... Concentrations of dimethylsulfide (DMS) and dimethylsulfoniopropionate (DMSP) were measured from Nov. 1995 to Sep. 1997 in seawater of Jiaozhou Bay, other ecological factors such as water temperature, salinity, Chl a and zooplankton were also investigated. Distribution of DMS showed remarkable variation spatially and temporally, ranging from 0.3 to 52.3 nmol/L. Seasonally, DMS concentration was high in late spring and low in autumn and winter. There was similar but weaker seasonal variation of DMSP. Generally, DMS concentration inside the bay was higher than that outside the bay; highest concentration often occurred nearshore. In some summer and autumn cruises DMS surface water was significantly higher than that in bottom water. Analysis indicated that salinity and zooplankton had significant influence on total DMS level in seawater. The estimation of sea-air flux of DMS showed significant seasonal variation, was the highest in spring [2441 μgS/(m2·d)] and lowest in winter [272 (m2 · d) ], with an annual average of 924 μgS/(m2 ·d) . 展开更多
关键词 dimdelsuffide sea-air flux BAY
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Identification of a novel C-type lectin from the shrimp Litopenaeus vannamei and its role in defense against pathogens infection 被引量:1
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作者 罗展 张继泉 +3 位作者 李富花 张晓军 柳承璋 相建海 《Chinese Journal of Oceanology and Limnology》 SCIE CAS CSCD 2011年第5期942-951,共10页
Acting as one of the pattern recognition receptors (PRRs), C-type lectin is believed to mediate pathogen recognition and plays an important role in the clearance of pathogens as part of the innate immune system. In ... Acting as one of the pattern recognition receptors (PRRs), C-type lectin is believed to mediate pathogen recognition and plays an important role in the clearance of pathogens as part of the innate immune system. In this work, a novel C-type lectin gene (named LvLecl) was cloned from the shrimp Litopenaeus vannamei, The ORF of LvLecl is 510 bp, encoding 169 amino acids. The deduced amino acid sequence contains a putative signal peptide of 19 amino acids at the N-terminal and a carbohydrate recognition domain (CRD) at the C-terminal. LvLecl was mainly expressed in the hepatopancreas. Real-time PCR analysis indicated that the level of LvLecl transcripts significantly changed in the hepatopancreas after the shrimp were artificially challenged with LPS, Micrococcus lysodeikticus and white spot syndrome virus (WSSV). RNAi-based silencing of LvLecl resulted in increases in mortality when the shrimp were challenged with WSSV, and the median lethal time was reduced compared with controls. Although there was no characteristic "EPN" (Glu-Pro-Ser) or "QPD" (Gin-Pro-Asp) motif, the recombinant LvLecl, expressed in Escherichia coli BL21 (DE3), could also agglutinate M. lysodeikticus and Vibrio anguillarum. The agglutinating activities were calcium-dependent and could be inhibited by D-mannose, D-glucose, D-galactose and N-Acetyl-D-mannose. These results suggest that LvLecl might be involved in the immune response against WSSV and bacterial infections and contribute to non-self recognition as a pattern recognition receptor in the innate immune system of the shrimp L. vannamei. 展开更多
关键词 Litopenaeus vannamei innate immune pattern recognition receptor C-type lectin RNAinterference (RNAi) recombinant expression
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BAC end sequencing of Pacific white shrimp Litopenaeus vannamei: a glimpse into the genome of Penaeid shrimp 被引量:1
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作者 赵翠 张晓军 +4 位作者 柳承璋 郇聘 李富花 相建海 黄超 《Chinese Journal of Oceanology and Limnology》 SCIE CAS CSCD 2012年第3期456-470,共15页
Little is known about the genome of Pacific white shrimp (Litopenaeus vannamei). To address this, we conducted BAC (bacterial artificial chromosome) end sequencing of L. vannamei. We selected and sequenced 7 812 BAC c... Little is known about the genome of Pacific white shrimp (Litopenaeus vannamei). To address this, we conducted BAC (bacterial artificial chromosome) end sequencing of L. vannamei. We selected and sequenced 7 812 BAC clones from the BAC library LvHE from the two ends of the inserts by Sanger sequencing. After trimming and quality filtering, 11 279 BAC end sequences (BESs) including 4 609 paired- ends BESs were obtained. The total length of the BESs was 4 340 753 bp, representing 0.18% of the L. vannamei haploid genome. The lengths of the BESs ranged from 100 bp to 660 bp with an average length of 385 bp. Analysis of the BESs indicated that the L. vannamei genome is AT-rich and that the primary repeats patterns were simple sequence repeats (SSRs) and low complexity sequences. Dinucleotide and hexanucleotide repeats were the most common SSR types in the BESs. The most abundant transposable element was gypsy, which may contribute to the generation of the large genome size of L. vannamei. We successfully annotated 4 519 BESs by BLAST searching, including genes involved in immunity and sex determination. Our results provide an important resource for functional gene studies, map construction and integration, and complete genome assembly for this species. 展开更多
关键词 Litopenaeus vannamei BES repetitive sequences SSR genome survey
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