药用美洲大蠊全基因组测序分析

以美洲大蠊Periplaneta americana为原料生产的康复新液等药品临床疗效显著,得到了广泛应用。本文以四川好医生攀西药业有限责任公司饲养的药用美洲大蠊为材料,首次采用Illumina Hi Seq 2000和Pac Bio SMRT测序平台开展了全基因组测序,并进行基因组组装、注释和分析。原始测序数据经过滤后得到1.4 Tb的二代测序数据和33.81 Gb的三代测序数据。组装结果表明,美洲大蠊基因组大小为3.26 Gb,这在已报道的昆虫基因组中仅次于东亚飞蝗Locusta migratoria。基因组重复序列含量为62.38%,杂合度为0.635%,表明其为复杂基因组。组装的Contig N50和scaffold N50长度分别为28.2 kb、315 kb,单拷贝基因完整性为88.1%,小片段文库测序数据平均比对率为99.8%,测序和组装质量满足后续分析要求。采用De novo预测、同源预测和基于转录本预测3种方法共注释到14 568个基因,其中92.4%的基因获得了功能注释。本研究首次完成了美洲大蠊的全基因组测序,也是大蠊属Periplaneta昆虫的第一个基因组,为美洲大蠊遗传进化分析和药用基因资源挖掘打下了重要基础。     

美洲大蠊变应原Pera2的生物信息学分析

目的:了解美洲大蠊变应原Per a 2的分子生物学特征。方法:从Genbank中获得Per a 2的核酸序列,用ExPaSy、EBI和NCBI网站的在线软件推导出编码氨基酸序列及其理化性质、空间结构、功能位点,并在Blastp比对后选择不同物种同源序列计算相似率、构建分子进化树。结果:Pera2由351个氨基酸细戍,分子量为38119Da、等电点为4.90、分子式为C1217H1825N285O297S18,为细胞外疏水性蛋白、属于肽酶a家族,信号肽位于1～20氨基酸处,三个跨膜螺旋区域依次位于1～19aa、51～78aa、282～300aa处;二级结构由α-螺旋(9.4%)、β延伸(28.49%)、随机线圈(62.11%)组成;美洲大蠊和德国小蠊相似率为55%、与马德拉蜚蠊相似率为51%,三者在Pera2与不同物种的同源序列构建的分子进化树中聚成一簇。结论:通过对Per a 2的生物信息学分析获得了该变应原分子特征,为进一步研究奠定基础。     

美洲大蠊变应原Per a 2的生物信息学分析

目的：了解美洲大蠊变应原Per a 2的分子生物学特征。方法：从Genbank中获得Per a 2的核酸序列,用ExPaSy、EBI和NCBI网站的在线软件推导出编码氨基酸序列及其理化性质、空间结构、功能位点,并在Blastp比对后选择不同物种同源序列计算井刖双率、构建分子进化树。结果：Per a 2由351个氨基酸细戍,分子量为38119Da、等电点为490、分子式为C1217H1825N285O297S18,为细胞外疏水性蛋白、属于肽酶a家族,信号肽位于1～20氨基酸处,三个跨膜螺旋区域依次位于1～19aa、51～78aa、282～300aa处;二级结构由α-螺旋（9．4％）、β延伸（28．49％）、随机线圈（62．11％）组成;美洲大蠊和德国小蠊相似率为55％、与马德拉蜚蠊相似率为51％,三者在Per a 2与不同物种的同源序列构建的分子进化树中聚成一簇。结论：通过对Per a 2的生物信息学分析获得了该变应原分子特征．为进一步研究奠定基础。     

美洲大蠊microRNA的初步研究

美洲大蠊Periplaneta americana是一种世界性的卫生害虫,但其提取物有较高的药用价值。本研究对饲养的雌雄美洲大蠊成虫进行microRNA测序,分别在雄性和雌性中得到12 155 616条和9 847 263条序列。序列长度主要为18～23 nt,且在22 nt和29 nt处有2个峰值。将所得序列与数据库(NCBI、Rfam)进行比对注释,最终在雄性成虫中鉴定到57种已知的microRNA和152种潜在的新microRNA,在雌性成虫中鉴定到53种已知的microRNA和94种潜在的新microRNA。差异表达分析发现只有一种microRNA:miR-750在雌雄之间差异表达,其在雌虫中表达量显著高于雄虫。本研究首次在基因组水平研究了美洲大蠊microRNA的组成并对其功能进行了预测,为其后续研究奠定了基础。     

药用美洲大蠊氨基酸和维生素含量分析

以人工饲养条件下不同发育阶段的美洲大蠊Periplaneta americana为材料,测定了其氨基酸和维生素的含量。结果表明,美洲大蠊各虫态均含有18种氨基酸,氨基酸总量为23. 27%～29. 44%,人体必需氨基酸含量占44. 04%～49. 55%,优于联合国粮农组织/世界卫生组织推荐的40%的标准,属于优质蛋白质资源。与成虫期相比,若虫期氨基酸含量较高,色氨酸、谷氨酸、丙氨酸、天门冬氨酸和甘氨酸较为丰富。所检测的5种维生素中,维生素E含量最高,刚蜕皮成虫及雌成虫含量均超过12 mg·kg^-1。美洲大蠊相关产品促睡眠、抗氧化功能可能与其富含色氨酸、谷氨酸和维生素E有关。     

美洲大蠊提取物促组织修复作用机制研究进展

基础研究和临床实验都已证实康复新液等美洲大蠊Periplaneta americana提取物对烧伤、外伤、溃疡和术后创面修复等具有良好的治疗效果。本文综述了美洲大蠊提取物促组织修复作用机制,主要包括降低炎症反应、提高免疫和抗氧化活性、调节细胞生长因子表达、调控创面愈合相关信号通路等,为阐明美洲大蠊促修复作用的分子机制及其开发利用提供了科学参考。     

基因组中重复序列的意义

从原核生物到真核生物,其基因组中的重复序列呈递增趋势.重复序列的作用也被各种实验所揭示.各种重复序列的类型与它在染色体上的分布密切相关.重复序列不是垃圾,而是影响着生命的进化、遗传、变异;同时它对基因表达、转录调控、染色体的构建以及生理代谢都起着不可或缺的作用.它们的功能及演化也正在被逐步阐明.     

美洲大蠊胸腺素THY3的表达模式分析

美洲大蠊Periplaneta americana胸腺素基因具有THY1、THY2和THY3三个不同剪接体,其中THY3结构域最多。本研究使用实时荧光定量PCR技术比较分析了THY3在美洲大蠊不同性别、不同发育阶段及不同组织中的表达差异,以及大肠杆菌Escherichia coli诱导对美洲大蠊血淋巴和脂肪体中THY3表达的影响。结果表明:THY3在成虫期的表达量显著高于其他虫期,雌虫表达量显著高于雄虫,脂肪体表达量显著高于血淋巴、头部、肌肉、体壁组织。雌性成虫体腔注射大肠杆菌3 h后血淋巴中THY3表达量显著增高,而在脂肪体中12 h后才检测到THY3表达明显上调,研究结果为进一步研究美洲大蠊胸腺素的功能打下了基础。     

Large-Scale Comparison Analysis of Genome Sequences

IIntMuctiona习nenC6allpoent13asenondynamiCpmpCgIsthemostWidely11。dllethed11。－quencecompgnsonatpresent．Wbenmpingon18I’ge一切degenomempence肛dyslswiththiskindofmethed,wefacetwomperdifficulties,the18ig6stompandtheIOllgmptationaltdrie．My。。dMill。［“spplyHi。比那’stecheniqJ‘、mpen。alipentpwhl。,wb。dgofl山mconsumeSpaceMypZ’Oportlonaltothesumd山eapuencelmphs．AnewpIOgTgnSIM”,utilizingthealgorithm,hasbeenueding。eequ。ceallpoent．How。,themptationaltimebySIMisstilltoolO…     

Novel Repetitive Structures, Deviant Protein-Encoding Sequences andUnidentified ORFs in the Mitochondrial Genome of the BrachiopodLingula anatina

Complete sequence determination of the brachiopod Lingula anatina mtDNA (28,818 bp) revealed an organization that is remarkably atypical for an animal mt-genome. In addition to the usual set of 37 animal mitochondrial genes, which make up only 57% (16,555 bp) of the entire sequence, the genome contains lengthy unassigned sequences. All the genes are encoded in the same DNA strand, generally in a compact way, whereas the overall gene order is highly divergent in comparison with known animal mtDNA. Individual genes are generally longer and deviate considerably in sequence from their homologues in other animals. The genome contains two major repeat regions, in which 11 units of unassigned sequences and six genes (atp8, trnM, trnQ, trnV, and part of cox2 and nad2) are found in repetition, in the form of nested direct repeats of unparalleled complexity. One of the repeat regions contains unassigned repeat units dispersed among several unique sequences, novel repetitive structure for animal mtDNAs. Each of those unique sequences contains an open reading frame for a polypeptide between 80 and 357 amino acids long, potentially encoding a functional molecule, but none of them has been identified with known proteins. In both repeat regions, tRNA genes or tRNA gene-like sequences flank major repeated units, supporting the view that those structures play a role in the mitochondrial gene rearrangements. Although the intricate repeated organization of this genome can be explained by recurrent tandem duplications and subsequent deletions mediated by replication errors, other mechanisms, such as nonhomologous recombinations, appear to explain certain structures more easily.     

SARS冠状病毒全基因组序列初步分析

对已经完成全序列测定的12个SARS病毒基因组进行了多序列比对,发现序列主体部分29708 b具有99．82％的相同碱基,除2个序列各有5个和6个碱基的缺失外,其余部分共有42个位点核苷酸碱基的差异,其中28个位点的碱基差异可引起氨基酸残基改变。利用蛋白质二级结构和跨膜螺旋预测以及蛋白质定位等生物信息学工具,分析了这些产生氨基酸改变部位的蛋白质构像,推测了可能产生的结构和功能改变,为进一步生物学实验提供参考。所有分析结果同时在北京大学生物信息中心抗SARS网站(antisars.cbi.pku．edu．cn)上发布。     

Initial Analysis of Complete Genome Sequences of SARS Coronavirus

TheoutbreakoftheSevereAcuteRespiratorySyndrome (SARS)startingfromsouthernChinaearlythisyearhasasignificantinfluenceonpublichealth .TheidentificationofSARS CoVasthemajorcausativefactoroftheSARSdiseaseandthegenomicse quencingofthevirusmakesitpossibleforbioinformaticsstudy .Atotalof16SARS CoVgenomesequencesareavailablefromthenucleicaciddatabaseGenBank EMBL DDBJby 2 0May 2 0 0 3.SARS CoVZJ0 1(AY2 970 2 8 1)wasshowninGenBankaftertheanalysiswasperformed .12completegenomeswereretri…     

The First Complete Chloroplast Genome Sequences in Actinidiaceae: Genome Structure and Comparative Analysis

Actinidia chinensis is an important economic plant belonging to the basal lineage of the asterids. Availability of a complete Actinidia chloroplast genome sequence is crucial to understanding phylogenetic relationships among major lineages of angiosperms and facilitates kiwifruit genetic improvement. We report here the complete nucleotide sequences of the chloroplast genomes for Actinidia chinensis and A. chinensis var deliciosa obtained through de novo assembly of Illumina paired-end reads produced by total DNA sequencing. The total genome size ranges from 155,446 to 157,557 bp, with an inverted repeat (IR) of 24,013 to 24,391 bp, a large single copy region (LSC) of 87,984 to 88,337 bp and a small single copy region (SSC) of 20,332 to 20,336 bp. The genome encodes 113 different genes, including 79 unique protein-coding genes, 30 tRNA genes and 4 ribosomal RNA genes, with 16 duplicated in the inverted repeats, and a tRNA gene (trnfM-CAU) duplicated once in the LSC region. Comparisons of IR boundaries among four asterid species showed that IR/LSC borders were extended into the 5’ portion of the psbA gene and IR contraction occurred in Actinidia. The clap gene has been lost from the chloroplast genome in Actinidia, and may have been transferred to the nucleus during chloroplast evolution. Twenty-seven polymorphic simple sequence repeat (SSR) loci were identified in the Actinidia chloroplast genome. Maximum parsimony analyses of a 72-gene, 16 taxa angiosperm dataset strongly support the placement of Actinidiaceae in Ericales within the basal asterids.     

Comparative Analysis of Genome Sequences Covering the Seven Cronobacter Species

Background

Species of Cronobacter are widespread in the environment and are occasional food-borne pathogens associated with serious neonatal diseases, including bacteraemia, meningitis, and necrotising enterocolitis. The genus is composed of seven species: C. sakazakii, C. malonaticus, C. turicensis, C. dublinensis, C. muytjensii, C. universalis, and C. condimenti. Clinical cases are associated with three species, C. malonaticus, C. turicensis and, in particular, with C. sakazakii multilocus sequence type 4. Thus, it is plausible that virulence determinants have evolved in certain lineages.

Methodology/Principal Findings

We generated high quality sequence drafts for eleven Cronobacter genomes representing the seven Cronobacter species, including an ST4 strain of C. sakazakii. Comparative analysis of these genomes together with the two publicly available genomes revealed Cronobacter has over 6,000 genes in one or more strains and over 2,000 genes shared by all Cronobacter. Considerable variation in the presence of traits such as type six secretion systems, metal resistance (tellurite, copper and silver), and adhesins were found. C. sakazakii is unique in the Cronobacter genus in encoding genes enabling the utilization of exogenous sialic acid which may have clinical significance. The C. sakazakii ST4 strain 701 contained additional genes as compared to other C. sakazakii but none of them were known specific virulence-related genes.

Conclusions/Significance

Genome comparison revealed that pair-wise DNA sequence identity varies between 89 and 97% in the seven Cronobacter species, and also suggested various degrees of divergence. Sets of universal core genes and accessory genes unique to each strain were identified. These gene sequences can be used for designing genus/species specific detection assays. Genes encoding adhesins, T6SS, and metal resistance genes as well as prophages are found in only subsets of genomes and have contributed considerably to the variation of genomic content. Differences in gene content likely contribute to differences in the clinical and environmental distribution of species and sequence types.     

三核苷酸双链重复序列扩展合成特性及其机理

简单重复序列在各种生物基因组中广泛存在,同分子进化、遗传多样性、分子标记和某些遗传性疾病等密切相关．本文以全部32种18 bp三核苷酸双链重复序列作为研究对象,对它们在聚合酶作用下的扩展合成进行了系统研究．探讨了反应温度、序列本身等对扩展效率和产物长度的影响．结果显示,几乎所有的序列都能扩展变长．但序列对其扩展效率有很大影响：GC含量较多的短链,尤其是一条链中同时有G和C的短链扩展效率较高;全由AC和GT组成的双链也较易扩展．短链的最适扩展温度与短链GC组成呈一定的正相关关系．琼脂糖凝胶电泳和聚丙烯酰胺凝胶电泳分析发现,大部分产物单一性良好,且产物分子质量的大小随反应时间线性增加;随着反应温度升高,产物差异性增大．最后分析了双链重复序列的“复制滑移”扩展机理,有望为进一步研究重复序列的分子进化和基因检测中的非特异性扩增等奠定基础．