应用生物信息学方法筛选幽门螺杆菌疫苗候选抗原

目的：应用生物信息学分析方法筛选幽门螺杆菌新的疫苗候选抗原。方法：从TIGRCMR下载幽门螺杆菌26695和J99株全基因组序列,应用生物信息学SignalP、PredTMBB、LipoP、TMHMM、Phobius、PSORT-B和SubLoc等分析软件,筛选幽门螺杆菌新的外膜蛋白和分泌蛋白疫苗候选抗原。结果：从幽门螺杆菌26695株筛选得到54个编码β-桶型跨膜蛋白、脂蛋白或分泌表达蛋白的疫苗候选蛋白抗原,从幽门螺杆菌J99株得到61个呈现上述表达方式的疫苗候选蛋白抗原;且这2株细菌的疫苗候选蛋白呈现良好的交集状况,即有43个候选疫苗蛋白是相同的。结论：用生物信息学分析方法可以从全基因组范围内快速筛选到保守的分泌或表面暴露的疫苗候选抗原,为疫苗抗原的快速筛选与鉴定奠定了基础。     

一株新的多重耐药福氏志贺菌噬菌体生物学特性及基因组分析北大核心CSCD

抗生素的大量使用和滥用造成细菌耐药性问题愈发严峻,噬菌体疗法作为一种精准治疗多重耐药病原菌的有效方法开始被人们日益重视。采用双层琼脂平板法从活性污泥中分离出多重耐药福氏志贺菌(Shigella flexneri)噬菌体P003,鉴定为肌尾噬菌体科(Myoviridae)。通过生物学特性测定表明P003的最佳感染复数为10,潜伏期约10 min;在4-70℃、pH 3.0-10.0的条件下保持活性。全基因组测序表明,噬菌体基因组长约68 721 bp,GC含量46.14%,预测编码99个开放阅读框(open reading frame,ORF),未发现已知耐药基因和毒力基因。全基因组多序列线性与进化树分析结果表明,P003与大肠杆菌噬菌体有较近的亲缘关系,但不能侵染大肠杆菌。从活性污泥原位分离到一株新的多重耐药福氏志贺菌噬菌体P003,为利用噬菌体疗法防治多重耐药病原菌S.flexneri感染提供了新的菌种资源。     

水稻黑条矮缩病毒基因组片段S9的cDNA克隆和全序列分析

应用RT PCR技术克隆了 3个中国水稻黑条矮缩病毒 (riceblack streakeddwarfvirus,RBSDV)分离株基因组片段S9,并测定了它们的全序列。结果表明 :RBSDV浙江分离株 (RBSDV Zj)基因组片段S9全长 190 0nt(EMBL登录号为AJ2 97430 ) ,RBSDV河北分离株 (RBSDV Heb)基因组片段S9全长 1898nt(EMBL登录号为AJ2 9742 9) ,湖北分离株S9全长 190 0nt(EMBL登录号为AJ2 9170 6 )。 3个分离株S9均含有两个开放阅读框(ORF) ,分别编码约 40kD和 2 4kD的多肽。3个中国分离株之间的核苷酸同源性高达 98.5 %～ 98.8% ,与日本分离株S9的核苷酸同源性均为 89.9%～ 90 .2 % ,而与意大利MRDVS8同源性仅为 85 .3%～ 86 .4%。我们发现ORF2十分保守 ,4个RBSDV分离株S9的ORF2同源性高达为 97.6 %～ 10 0 % ,与意大利MRDVS8的ORF2同源性也高达 94.3%。     

桃拉综合征病毒中国株ZHZC3全基因测序及分子结构预测

设计8对引物分片段扩增桃拉综合征病毒中国分离株ZHZC3全基因组,病毒两末端序列采用末端快速扩增方法(RACE)获取.扩增产物克隆到pMD18-T载体并测序,用DNAstar软件拼接全序列及同源性比较.结果显示ZHZC3全序列除去3' poly (A)尾,由10202个碱基组成,有两个开放阅读框,分别编码2107和1011个氨基酸的聚蛋白.与美国参考株HI94相比,在编码区没有核苷酸的缺失和插入,但在5' UTR缺失3个A,两者整体核酸同源性达97.9%.ORF1 中ZHZC3与HI94及巴西株(BLZ01)的核酸同源性分别为97.6%、97.7%,在ORF2中ZHZC3与HI94、BLZ01的核酸同源性则分别为98.3、97%.与国外株ORF2的部分序列比较发现ZHZC3和中国台湾株均与美国株HI94同源性最高.克隆分析6株TSV中国大陆株主要结构蛋白CP2基因,发现其编码的氨基酸存在三个高变区,中国大陆株更有其独特的氨基酸变异模式,312 (S), 449 (A), 451 (Q) 和468 (H).表明该病毒的整体变异性不高,但中国的流行株已形成其自己的遗传演变特征.在此基础上,利用生物学软件对CP2蛋白功能域和三维结构进行了预测,为进一步分析CP2蛋白结构与功能关系奠定了基础.ZHZC3株是第一个测定全序列的TSV中国株.     

洋葱伯克霍尔德氏菌L68双加氧酶区基因克隆及序列分析

克隆洋葱伯克霍尔德氏菌L68双加氧酶区基因并对其进行序列分析。采用邻苯二酚喷洒方法从洋葱伯克霍尔德氏菌L68的基因文库中筛选到了1株含有双加氧酶区基因的重组子,其重组质粒命名为pB2k。重组质粒pB2k含有8030bp的L68基因片断,经BLAST比对,该片断含有11个与已报道的ORF相近的ORF。在该片断的5’端,ORF1和ORF2分别编码两个转移酶基因,tomA1t、omA2t、omA3和tomA4编码酚羟化酶组份,tomA5编码氧化还原酶,phnT编码铁氧还蛋白,phnE编码邻苯二酚2,3-双加氧酶,ORF3编码未知功能蛋白,phnG编码部分2-羟粘糠酸半醛脱氢酶。     

猪圆环病毒Ⅱ型SC株ORF3基因克隆及其编码蛋白的生物信息学分析

本研究根据GenBank登录的猪圆环病毒基因组序列(DQ180392.1)来设计引物,用PCR法扩增出PCV-2四川株(PCV-2SC)ORF3基因,并克隆到PMD19-T载体进行测序,同时利用在线生物信息学软件及数据库对ORF3基因及其编码蛋白进行生物信息学分析。研究结果表明,成功构建了命名为P-S-PCV-2SCORF3的重组质粒;测序结果得知PCV-2SCORF3基因全长315bp,共编码104个氨基酸;BLAST比对发现该基因与GenBank中国内外参考毒株核苷酸同源性在98%~100%之间。利用在线生物信息学软件对PCV-2SCORF3编码蛋白结构特征进行分析,发现该蛋白含有12个潜在的磷酸化位点,ORF3成熟蛋白有4个主要的抗原位点;亚细胞定位分析结果表明,编码蛋白主要存在于线粒体中和细胞核中并各占43.5%和34.8%,这证实了PCV-2SCORF3编码蛋白属于胞质蛋白,抗原区位集中于胞膜,有向胞核移动的趋势,功能强大,可能与细胞凋亡有关。疏水性分析发现,该编码蛋白具有一定的疏水性,与该蛋白的表面抗原决定族和膜蛋白中穿越膜的肽片段及该蛋白的高级结构的形成有关,预示其高疏水性区又与膜蛋白的跨膜区有着明显相关性。本研究成功进行了PCV-2SCORF3基因的克隆和生物信息学分析,为今后研究此基因的生物学功能以及研究该病毒疫苗的方法奠定理论基础。     

弗氏2a志贺氏菌2457T株yciD基因缺失突变株的构建

目的:构建弗氏2a志贺氏菌2457T株yciD基因缺失突变体,以研究yciD基因的功能。方法:根据弗氏2a志贺氏菌2457T株基因组全序列,采用Red重组系统对yciD基因进行缺失,并经PCR和SDS-PAGE证实;对野生株和突变株的生长状态及生化反应进行比较研究。结果:构建了弗氏2a志贺氏菌2457T株的yciD基因缺失突变株2457TΔyciD,该突变株外膜蛋白样品中缺失了一条相对分子质量与从yciD基因推导的蛋白相当(约22000)的蛋白带。该突变株比野生株生长快,利用葡萄糖和甘露醇的能力也比野生株大为增强。结论:获得了弗氏2a志贺氏菌2457T株的yciD基因缺失突变株。     

桃拉综合征病毒中国株ZHZC3全基因测序及分子结构预测

设计8对引物分片段扩增桃拉综合征病毒中国分离株ZHZC3全基因组,病毒两末端序列采用末端快速扩增方法(RACE)获取。扩增产物克隆到pMD18-T载体并测序,用DNAstar软件拼接全序列及同源性比较。结果显示ZHZC3全序列除去3′poly(A)尾,由10202个碱基组成,有两个开放阅读框,分别编码2107和1011个氨基酸的聚蛋白。与美国参考株HI94相比,在编码区没有核苷酸的缺失和插入,但在5′UTR缺失3个A,两者整体核酸同源性达97.9%。ORF1中ZHZC3与HI94及巴西株(BLZ01)的核酸同源性分别为97.6%、97.7%,在ORF2中ZHZC3与HI94、BLZ01的核酸同源性则分别为98.3、97%。与国外株ORF2的部分序列比较发现:ZHZC3和中国台湾株均与美国株HI94同源性最高。克隆分析6株TSV中国大陆株主要结构蛋白CP2基因,发现其编码的氨基酸存在三个高变区,中国大陆株更有其独特的氨基酸变异模式,312(S),449(A),451(Q)和468(H)。表明该病毒的整体变异性不高,但中国的流行株已形成其自己的遗传演变特征。在此基础上,利用生物学软件对CP2蛋白功能域和三维结构进行了预测,为进一步分析CP2蛋白结构与功能关系奠定了基础。ZHZC3株是第一个测定全序列的TSV中国株。     

狂犬病疫苗株病毒aG株全基因序列测定及特征分析

对我国狂犬病疫苗生产株aG株进行全基因序列测定分析,为完善aG株毒种的质量控制提供数据支持。将aG株病毒全基因组RNA分成8段进行RT-PCR分段扩增,其中基因组5′末端采取5′RACE方法,将PCR扩增产物分别克隆入pGEM-T载体中,测定序列并拼接获得病毒全基因序列;用DNAStar软件包中的相应软件对基因全序列进行分析,并与国内外主要狂犬病疫苗生产株进行基因同源性分析和主要抗原位点比较。aG株病毒基因组序列全长11 925bp(GenBank登录号为JN234411),属基因Ⅰ型狂犬病病毒;各疫苗株生物信息学分析表明,各株病毒存在同源性差异。本研究获得了aG株病毒全基因组序列,对aG株基因特征进行了分析并将其与国内外疫苗株进行了比较,为完善其质量控制提供了参考和数据支持。     

金黄色葡萄球菌基因组表达文库的构建及免疫学初步筛选

为从基因组水平筛选金黄色葡萄球菌疫苗抗原,建立金黄色葡萄球菌基因组表达文库,用患者恢复期血清对表达文库进行血清学筛选,并对获得的阳性克隆进行序列测定及同源性分析。结果显示,构建的金黄色葡萄球菌基因组表达文库共有5×10~4个克隆,片段插入正确率为91.67%。对文库进行初步筛选,共获得6个阳性克隆,经测序鉴定和同源性分析发现6个克隆涉及金黄色葡萄球菌基因组6个开放阅读框(ORF)。结果表明,本研究建立的疫苗抗原筛选方法可用于金黄色葡萄球菌疫苗抗原的系统筛选。     

Curcuminoids as inhibitors of thioredoxin reductase: A receptor based pharmacophore study with distance mapping of the active site

Curcumin is the yellow pigment of turmeric that interacts irreversibly forming an adduct with thioredoxin reductase (TrxR), an enzyme responsible for redox control of cell and defence against oxidative stress. Docking at both the active sites of TrxR was performed to compare the potency of three naturally occurring curcuminoids, namely curcumin, demethoxy curcumin and bis-demethoxy curcumin. Results show that active sites of TrxR occur at the junction of E and F chains. Volume and area of both cavities is predicted. It has been concluded by distance mapping of the most active conformations that Se atom of catalytic residue SeCYS498, is at a distance of 3.56 from C13 of demethoxy curcumin at the E chain active site, whereas C13 carbon atom forms adduct with Se atom of SeCys 498. We report that at least one methoxy group in curcuminoids is necessary for interation with catalytic residues of thioredoxin. Pharmacophore of both active sites of the TrxR receptor for curcumin and demethoxy curcumin molecules has been drawn and proposed for design and synthesis of most probable potent antiproliferative synthetic drugs.     

A Unique Protease Cleavage Site Predicted in the Spike Protein of the Novel Pneumonia Coronavirus (2019-nCoV) Potentially Related to Viral Transmissibility

正Dear Editor,In December 2019, a novel human coronavirus caused an epidemic of severe pneumonia(Coronavirus Disease 2019,COVID-19) in Wuhan, Hubei, China(Wu et al. 2020; Zhu et al. 2020). So far, this virus has spread to all areas of China and even to other countries. The epidemic has caused 67,102 confirmed infections with 1526 fatal cases     

Comparative morphology of the carpel in the Liliaceae: Hewardieae, Petrosavieae, and Tricyrteae

The young pistils in the melanthioid tribes, Hewardieae, Petrosavieae and Tricyrteae, are uniformly tricarpellate and syncarpous. They lack raphide idioblasts. All are multiovulate, with bitegmic ovules. The Petrosavieae are marked by the presence of septal glands and incomplete syncarpy. Tepals and stamens adhere to the ovary in the Hewardieae and the Petrosavieae but not in the Tricyrteae. Two vascular bundles occur in the stamens of the Hewartlieae and Tricyrtis latifolia. Ventral bundles in the upper part of the ovary of the Hewardieae are continuous with compound septal bundles and placental bundles in the lower part. Putative ventral bundles occur in the alternate position in the Tricyrteae and putative placental bundles in the opposite. position in the Petrosavieae. The dichtomously branched stigma in each carpel of the Tricyrteae is supplied by a bifurcated dorsal bundle.     

Entwicklungsgeschichte und Ultrastruktur von Pollenkitt und Exine bei nahe verwandten entomophilen und anemophilen Angiospermensippen derAlismataceae,Liliaceae, Juncaceae,Cyperaceae, Poaceae undAraceae

Some closely related members of the monocotyledonous familiesAlismataceae, Liliaceae, Juncaceae, Cyperaceae, Poaceae andAraceae with variable modes of pollination (insect- and wind-pollination) were studied in relation to the ultrastructure of pollenkitt and exine (amount, consistency and distribution of pollenkitt on the surface of pollen grains). The character syndromes of pollen cementing in entomophilous, anemophilous and intermediate (ambophilous or amphiphilous) monocotyledons are the same in principal as in dicotyledons. Comparing present with former results one can summarize: 1) The pollenkitt is always produced in the same manner by the anther tapetum in all angiosperm sub-classes. 2) The variable stickiness of entomophilous and anemophilous pollen always depends on the particular distribution and consistency of the pollenkitt, but not its amount on the pollen surface. 3) The mostly dry and powdery pollen of anemophilous plants always contains a variable amount of inactive pollenkitt in its exine cavities. 4) A step-by step change of the pollen cementing syndrome can be observed from entomophily towards anemophily. 5) From the omnipresence of pollenkitt in all wind-pollinated angiosperms studied one can conclude that the ancestors of anemophilous angiosperms probably have been zoophilous (i.e. entomophilous) throughout.

     

Identification and Characterization of the First Equine Parainfluenza Virus 5

正Dear Editor,Parainfluenza virus 5 (PIV5), known as canine parainfluenza virus in the veterinary field, is a negative-sense,nonsegmented, single-stranded RNA virus belonging to the Paramyxoviridae family (Chen 2018). The virus was first reported in primary monkey kidney cells in 1954 (Hsiung1972), then it has been frequently discovered in various     

Pathogenic Characterization and Full Length Genome Sequence of a Reassortant Infectious Bursal Disease Virus Newly Isolated in Pakistan

<正>Dear Editor,Infectious bursal disease (IBD) is one of the most important diseases of the poultry. The IBD virus (IBDV), a nonenveloped virus belonging to the Birnaviridae family with a genome consisting of two segments of double-stranded RNA (segments A and B), targets B lymphocytes of bursa of Fabricious leading to immunosuppression. In Pakistan,poultry farming is the second biggest industry and IBD is the second biggest disease threating the poultry sector.However, there is limited genome information of IBDV