改进的多片段重叠延伸PCR制作基因多位点突变

为在研究工作中提高制作目标基因多位点突变体的效率,对常规重叠延伸PCR进行适当改进:对于相距较近的两个突变位点,只需设计一对突变引物各自涵盖其中一个位点即可一次突变;对于相距较远的两个位点,可以采用三片段重叠延伸PCR的办法解决;两者结合则可一次性突变多个位点。以制作RBCT的6位点突变体PSM6为例,利用上述策略,设计两对突变引物;采用OE-PCR法,第一轮PCR扩增出三个片段,第二轮PCR同时利用三片段重叠延伸产物作为模板扩增出目标基因突变体,再按常规分子克隆方法将其连入质粒载体。经测序检测,发现得到了预期的目标基因多位点突变体。因此,采用灵活的引物设计策略,结合多片段重叠延伸PCR即可一次性制作基因的多位点突变体,此方案可解决研究工作中大多数多位点突变问题。     

山羊ZP3基因的cDNA克隆、序列分析及组织表达研究

对高繁金堂黑山羊和低繁藏山羊ZP3基因c DNA进行克隆、序列分析,并采用Real-time PCR技术对其在发情前期母羊卵巢组织的表达进行研究.结果表明:山羊ZP3基因编码区全长为1269bp,共编码422个氨基酸,两品种间有2处碱基差异,但未导致氨基酸的差异.山羊的ZP3基因在卵巢表达量高,与其他组织差异极显著(P<0.01),但两个品种间差异不显著(P>0.05).说明ZP3基因主要在卵巢中表达,但可能不是影响山羊多羔性状的主基因.     

山羊Apaf-3基因的cDNA克隆、序列分析及组织表达研究

对单胎藏山羊和多胎金堂黑山羊Apaf-3基因cDNA克隆、序列分析及组织表达特性研究.采集5只多胎金堂黑山羊和5只单胎藏山羊在发情期的卵巢、垂体等组织样,进行Apaf-3基因的cDNA克隆、序列分析,并采用定量PCR技术对其mRNA进行组织表达量研究.结果,克隆出山羊Apaf-3基因长度为1731bp编码区全长为1245bp,编码414个氨基酸.Apaf-3基因在两种山羊中序列相同,且在5种组织中的表达均无差异.同源性分析表明凋亡基因Apaf-3在动物的进化中保守性低,与山羊多羔性状的相关性需要进一步研究.     

牦牛Caspase-3克隆、序列分析与组织表达研究

半胱天冬酶3(Aspartate-specific cysteinyl proteinase 3,Caspase-3)是哺乳动物最重要的细胞凋亡执行者,为探究Caspase-3基因在牦牛繁殖活动中的调控作用奠定基础,试验对牦牛Caspase-3编码区进行克隆和生物信息学分析,并比较牦牛和黄牛下丘脑、垂体、卵巢、输卵管及子宫等组织的表达差异.结果表明:牦牛Caspase-3基因编码区全长834 bp,编码277个氨基酸,与黄牛Caspase-3基因相比同源性最高(99. 52%)且遗传距离最近,发生4个碱基突变;与鸡同源性最低(71. 32%)且遗传距离最远,保守且符合动物进化进程.q PCR结果显示Caspase-3在牦牛生殖轴中的表达量均高于黄牛,其中,在下丘脑、输卵管中达到P <0. 01水平,在子宫中达到P <0. 05水平.推测极端环境应激引起Caspase-3基因的高表达可能影响母牦牛的繁殖性能.     

一株鲤春病毒血症病毒SVCV-shlj4全基因组序列分析

为了分析中国北方地区现行的一株鲤春病毒血症病毒(Spring Virernia of Carp Virus,SVCV)SVCV-shlj4全基因组序列,根据GenBank收录的SVCV参考毒株(SVCV-A2,DQ491000.1)基因序列设计了3对重叠引物,对SVCV-shlj4毒株基因组编码区进行扩增,利用RACE试剂盒对该基因组5′和3′非编码区(Untranslated region, UTR)进行扩增,并利用DNAstar软件对测得的序列进行拼接,获得完整的SVCV-shlj4全基因组,结合Lasergene及MEGA 5.1生物信息学软件对该病毒基因组及其编码的核蛋白、糖蛋白和磷蛋白基因序列进行系统进化分析。结果表明:SVCV-shlj4毒株基因组全长为11 029 bp,共编码5种结构蛋白(3′端-5′端),分别为核蛋白(Nuclear protein,N)、磷蛋白(Phosphoprotein,P)、基质蛋白(Matrix protein,M)、糖蛋白(Glycoprotein,G)和RNA聚合酶(RNA polymerase,L);基因组序列系统进化分析显示,SVCV-shlj4毒株与中国株SVCV-A2的核苷酸序列一致性最高(99.0%),与欧洲株VR-1390核苷酸序列一致性最低(93.0%);编码M蛋白、G蛋白和P蛋白的基因序列进化分析结果显示,SVCV-shlj4毒株在进化上处于亚洲分支,属于Ⅰa基因型,Ⅰaii基因亚型;SVCV-shlj4毒株各基因变异位点分析显示,与中国株SVCV-A1相比,SVCV-shlj4毒株在N基因编码区第1357、1364和1376 nt位点分别缺失1个碱基,在G基因3′端非编码区4630 nt位点和4639 nt位点分别缺失两段基因序列(44 bp和31 bp),与欧洲株VR-1390相比,SVCV-shlj4毒株在G基因3′端非编码区(4637 nt位点)插入10 bp的基因片段,与中国株BJ0505-2相比,SVCV-shlj4毒株在L基因编码区(5822 nt位点)缺失18 bp碱基。本研究系统地分析了中国北方地区现行SVCV分离株的分子特征,为SVCV分子进化研究提供了数据支撑。     

卵胎生许氏平鲉Sox9基因的克隆、启动子分析、表达及其细胞定位研究

为研究卵胎生许氏平鲉Sebastes schlegeli性腺分化及性别决定分子机制,采用同源克隆和RACE技术从许氏平鲉(体质量758 g±15 g)性腺组织中获得了许氏平鲉Sox9基因全长cDNA,运用生物学软件对Sox9启动子转录因子结合位点进行预测,并利用实时定量PCR和原位杂交对Sox9基因的表达进行了研究。结果表明:许氏平鲉Sox9基因cDNA全长2039 bp,包括1461 bp的ORF,336 bp的5′UTR和242 bp的3′UTR,其编码产物(486 aa)含有高度保守的HMG结构域;许氏平鲉Sox9基因启动子区存在多个转录因子结合位点,包括AP-1、GATA-3、Oct-1、FOXD3,以及性别相关SRY、Sox5、Sox9等蛋白结合位点;实时定量PCR显示,许氏平鲉Sox9基因在仔鱼发育阶段(出生后1～35日龄)均有表达,在性腺分化的敏感时期(25日龄)表达量达到较高水平;在成体性腺中显示了性别两相性差异,即在精巢中的表达高于卵巢;原位杂交显示,许氏平鲉Sox9基因在精巢的生殖细胞、Sertoli细胞,以及卵巢的卵母细胞和滤泡细胞中均有表达。研究表明,Sox9基因在许氏平鲉性腺分化及性腺发育过程中可能发挥重要作用。     

苯并(a)芘诱导对双齿围沙蚕腺苷酸环化酶(AC)基因及酶活性表达的影响

为探讨双齿围沙蚕Perinereis aibuhitensis对外源污染物的毒性响应,分析了不同苯并(a)芘[B(a)P]浓度(0.5、5、10、15μg/L)胁迫下双齿围沙蚕(体质量为1.5～2.5 g)腺苷酸环化酶(adenylate cyclase,AC)的基因表达和酶活性变化特征,利用RACE方法获得了沙蚕AC基因cDNA全长,并利用实时荧光定量PCR技术分析了苯并(a)芘诱导下沙蚕AC基因的变化。结果表明:双齿围沙蚕AC基因cDNA全长为4900 bp,包括5′非翻译区127 bp,3′非翻译区1536 bp,开放阅读框3237 bp,编码1078个氨基酸;该序列包含两个保守环化酶催化结构域,与其他动物氨基酸序列一致性为34%～47%;不同浓度的苯并(a)芘诱导会引起沙蚕AC基因表达量上升,0.5、10μg/L苯并(a)芘浓度组AC表达量在诱导第7天时达到最大,而5、50μg/L苯并(a)芘浓度组在诱导第14天时达到最大;利用ELISA试剂盒分析苯并(a)芘诱导下双齿围沙蚕AC酶活性变化,结果显示,在第4天时0.5、5、50μg/L浓度组AC酶活性上升到最高,之后随时间的延长酶活性降低,而10μg/L浓度组AC酶活性略低于空白对照组且在第7天时达到最高值。研究表明,苯并(a)芘会在一定程度上诱导沙蚕AC的基因表达及酶活性变化。     

藏绵羊KAP3.2基因的cDNA克隆、序列分析及组织表达的研究

为研究藏绵羊角蛋白相关蛋白(KAP3.2)基因结构与功能,揭示该基因的组织特异性表达规律.以藏绵羊为研究对象,分别提取藏绵羊心、肝、脾、肾及皮肤组织中总RNA,并以此为模板,通过RT-PCR技术对藏绵羊KAP3.2基因的c DNA进行克隆、序列分析;利用Real-time PCR技术进行组织表达研究.结果表明:藏绵羊KAP3.2基因编码区全长297bp,编码98个氨基酸;藏绵羊与普通绵羊、山羊、藏羚羊、草原鼠、家鼠、人的相应核苷酸同源性分别为99%、97%、96%、79%、75%、73%;藏绵羊KAP3.2基因在皮肤中高表达,而在其它组织中相对表达量较低,说明该基因的表达具有组织特异性.     

向日葵ACC氧化酶基因(HaACO1)的克隆及表达分析

目的:克隆向日葵中的ACC氧化酶基因(HaACO1),并对其进行生物信息学分析及盐胁迫表达分析,为理解向日葵ACC氧化酶生理功能并加强对ACO基因的利用奠定基础。方法:以前期从盐胁迫的内葵杂4号根中获得的ACC氧化酶基因片段4-4-7TDF(KM823963)为基础,通过RT-PCR和5'/3'RACE技术克隆ACO基因的全长cDNA序列,利用生物信息学软件对获得的cDNA序列及编码的蛋白质序列进行分析。同时采用PCR方法克隆基因组DNA(genemic DNA,gDNA)序列,并对其进行结构分析。利用实时荧光定量PCR分析Na Cl胁迫下向日葵根、下胚轴、叶中HaACO1的表达量和不同NaCl浓度及不同胁迫时间下根中Ha ACO1的表达量。结果:Ha ACO1的cDNA序列全长为1 135bp,其开放阅读框为942bp,编码313个氨基酸。预测其分子质量和等电点分别为35.84k Da和5.13,基因登录号为KP966508。HaACO1与已报道的多种植物的ACO基因核苷酸序列及其推导的氨基酸序列有较高的相似性,分别为76%~83%和77%~88%。gDNA起始密码子至终止密码子序列长1 018bp,包含2个外显子和1个内含子,基因登录号为KP988289。实时荧光定量PCR分析表明向日葵HaACO1在不同器官及不同NaCl浓度、不同时间诱导下存在特异性表达差异。结论:获得的向日葵HaACO1是植物ACO家族成员之一,该基因应答盐胁迫具有独特的表达模式。     

铜绿假单胞菌mexA基因原核表达载体的构建

目的构建mexA基因的原核载体,为进一步表达MexA蛋白奠定基础。方法从临床分离多重耐药的铜绿假单胞菌抽提DNA,经PCR扩增出mexA1基因与PUC18克隆载体连接,PCR、酶切及测序鉴定,再以PUC/mexA1质粒为模板PCR扩增mexA目的基因,克隆至质粒pQE30中,构建表达质粒pQE30/mexA,构建的表达质粒pQE30/mexA转化大肠杆菌M15,培养后提取纯化重组质粒pQE30/mexA酶切鉴定。结果获得长约1.5 kbPCR mexA1产物,酶切结果显示所构建的重组质粒PUC/mexA1已成功地克隆了mexA1（1.5 kb）基因,序列分析结果与PAO1/mexA1序列相同,构建的表达质粒pQE30/mexA酶切鉴定,与插入pQE30的目的基因mexA（1.2 kb）片段相符。结论含mexA（1.2 kb）基因的原核表达载体构建成功,为进一步表达MexA蛋白奠定了基础。     

儿童感染的乙型肝炎病毒S基因的分子特征

目的初步调查儿童感染的乙型肝炎病毒表面抗原的基因特征。方法收集10名HBV感染的儿童血清标本,抽提血清中的HBV DNA,采用PCR扩增HBV S基因并测序,利用Genotyping软件对PCR产物序列进行分型,并分析HBV S基因的突变情况。结果 10份血清标本中,扩增出HBV S基因并成功测序6份,其余4份扩增阴性不满足测序要求。6份PCR产物所测序列标本经Genotyping比对后,均属于B型,与NCBI收录的参考序列AF100309同源性最高;5例是adw,1例是ayw。HBV S基因中编码＂a＂抗原决定簇的核苷酸序列突变点分别为G529A、T531C、C534A、T562A、T581A、A589C。编码＂a＂抗原决定簇的氨基酸序列突变点分别为I126T、P127T、S143T、G145A。核苷酸突变点G529A、T562A不引起编码＂a＂抗原决定簇的氨基酸序列突变,为无义突变。而其他4点突变均可引起编码＂a＂抗原决定簇相应氨基酸序列发生改变。结论所调查儿童主要感染B基因型HBV;其感染的HBV S抗原＂a＂决定簇的氨基酸序列出现I126T、P127T、S143T、G145A的突变,可能是逃避乙肝疫苗诱导的免疫保护的一种机制。     

Limitations of the use of group-specific primers in real-time PCR as appear from quantitative analyses of closely related ammonia-oxidising species

To study the ecology of ammonia-oxidising bacteria (AOB), quantitative techniques are essential. Real-time PCR assays based on the 16S rRNA or on the structural amoA gene are routinely used. The CTO primer set rooted on the 16S rRNA gene has a number of mismatches with some of the cultures of AOB. To examine if these mismatches have an effect on the outcome of real-time PCR assays, the assay was tested with DNA from a number of closely related isolates of AOB. Standard curves of known amounts of initial DNA were similar among most of the tested cultures of AOB, except for the standard curves of Nitrosomonas strain AL212 and Nitrosospira strain NpAV. Nitrosomonas strain AL212 had 3 mismatches with the CTO primer set. Adaptation of the CTO primer set in order to perfectly match the Nitrosomonas strain AL212 gave a standard curve similar to the majority of the AOB tested. As Nitrosospira strain NpAV has no mismatches with the original CTO primer set, there must be another reason for the less efficient amplification than the sequence itself. Application of an existing sigmoidal mathematical model gave no other results with respect to the standard curves of Nitrosomonas europaea and Nitrosomonas strain AL212, but also demonstrated that primer mismatches can seriously underestimate the initial target concentration. It was concluded that in general correct interpretation of real-time PCR results requires knowledge of the target community composition, in particular of the target sequences of the dominant community members.     

Evaluation of the noncovalent binding interactions between polycyclic aromatic hydrocarbon metabolites and human p53 cDNA

The binding of reactive polycyclic aromatic hydrocarbon (PAH) metabolites, formed enzymatically, to DNA is a crucial step in PAH carcinogenesis in vivo. We investigated the noncovalent binding interactions between 11 PAH metabolites and human p53 complementary DNA (p53 cDNA) using the fluorescence displacement method and molecular docking analysis. All of the examined metabolites predominantly interacted with p53 cDNA by intercalation instead of groove binding. The dissociation constants ranged from 0.02 to 12.34 μM. Of the metabolites tested, 1-hydroxypyrene and 3-hydroxybenzo[a]pyrene showed the strongest binding affinities to DNA, while 2-naphthol was the weakest DNA intercalator. The intercalation of the metabolites was stabilized by stacking the PAH phenyl rings with the DNA base pairs and the formation of hydrogen bonds between the oxide or hydroxyl groups on the metabolites, and DNA bases or backbones. The binding of the metabolites to DNA showed some sequence selectivity. The binding affinities and hydrogen bonds for 3-hydroxybenzo[a]pyrene, benzo[a]pyrene-4,5-dihydroepoxide (BPE) and benzo[a]pyrene-r-7,t-8-dihydrodiol-t-9,10-epoxide (BPDE) differed. It seems that the functional groups on the periphery of the PAH aromatic ring play crucial roles in regulating its binding affinity with DNA. Although it was difficult to determine the correlation between DNA noncovalent binding affinity and carcinogenicity for some of the PAH metabolites, the present study improved our understanding of the formation of PAH metabolite-DNA adducts.     

Bioaerosols in the Barcelona subway system

Subway systems worldwide transport more than 100 million people daily; therefore, air quality on station platforms and inside trains is an important urban air pollution issue. We examined the microbiological composition and abundance in space and time of bioaerosols collected in the Barcelona subway system during a cold period. Quantitative PCR was used to quantify total bacteria, Aspergillus fumigatus, influenza A and B, and rhinoviruses. Multitag 454 pyrosequencing of the 16S rRNA gene was used to assess bacterial community composition and biodiversity. The results showed low bioaerosol concentrations regarding the targeted microorganisms, although the bacterial bioburden was rather high (10⁴ bacteria/m³). Airborne bacterial communities presented a high degree of overlap among the different subway environments sampled (inside trains, platforms, and lobbies) and were dominated by a few widespread taxa, with Methylobacterium being the most abundant genus. Human‐related microbiota in sequence dataset and ascribed to potentially pathogenic bacteria were found in low proportion (maximum values below 2% of sequence readings) and evenly detected. Hence, no important biological exposure marker was detected in any of the sampled environments. Overall, we found that commuters are not the main source of bioaerosols in the Barcelona subway system.     

Degradation of plasmid and plant DNA in water microcosms monitored by natural transformation and real-time polymerase chain reaction (PCR)

Extracellular DNA exists in the environment and can be taken up by competent bacterial cells, leading to horizontal gene transfer. The persistence of extracellular plasmid and plant DNA in water microcosms was monitored in this study. Water samples were two groundwater (GW1 and GW2) and one river water (RW) samples. Three treatments included: (1) intact, (2) 0.22 microm filter-sterilized, and (3) autoclaved water. DNA from a plasmid (pNS1) and a transgenic Bt (Bacillus thuringiensis) corn line, both carrying a neomycin phosphotransferase gene (nptII gene) conferring kanamycin and neomycin resistance, was inoculated into the microcosms at 0.4 and 0.8 microg/ml, respectively. By monitoring its ability to transform a competent Pseudomonas stutzeri strain harboring plasmid pMR7 (P. stutzeri pMR7), plasmid DNA was degraded to undetectable levels in the intact and/or filter-sterilized water treatments within 48-96 h in GW1, GW2, and RW. Meanwhile, plasmid DNA persisted in the autoclaved treatment throughout the entire incubation period. For plant DNA, a highly sensitive real-time PCR method using SYBR Green I was developed to monitor the degradation dynamics of the nptII gene carried by the transgenic corn line in the microcosms. The results showed that the concentration of plant DNA was reduced by two orders of magnitude (from 0.8-0.008 microg/ml) within 96 h in the intact and filter-sterilized treatments of GW1, GW2, and RW, in contrast to its persistence in the autoclaved treatment. In addition, no kanamycin resistant (Km R) transformants were detected from in situ transformation of P. stutzeri pMR7 with plasmid pNS1 DNA.     

Use of eukaryotic mitochondrial DNA to differentiate human, bovine, porcine and ovine sources in fecally contaminated surface water

A molecular method based on the detection of mitochondrial DNA from various animal species was developed to track the origin of surface water pollutions, and to differentiate human and animal sources. Mitochondrial DNA sequences were used to design PCR primers specific for human, bovine, ovine and porcine DNA using single, multiplex and nested PCR protocols. The primers were tested with DNA extracted from untreated domestic sewage, agricultural soils run-off, swine farm effluents and water from two rivers with known pollution sources. At least one of the four species was detected in most of these samples. The limit of detection in wastewater was 10(3)-10(4) cells L(-1) with a multiplex PCR protocol. This is the first report of a method using eukaryotic genetic DNA to detect and differentiate animal DNA from fecal sources in water. This innovative method is simple and could be used to quickly differentiate sources of pollution in a watershed.     

一种具杀菌功能的haFGF融合基因在毕氏酵母中的表达

目的构建一种双功能活性多肽,实现其在酵母中的表达。方法通过体外DNA重组技术将cecropin AD连接在haFGF的5′端,构建成融合基因CADAF,将其克隆到分泌表达载体pPICZαA上,然后转化到毕氏酵母受体菌X-33中进行甲醇诱导表达。结果经SDS PAGE和Western blot分析,构建的CADAF基因在酵母中获得了表达,经抑菌实验及MTT实验结果表明,融合蛋白具有一定的抗菌功能和促细胞分裂活性。结论成功实现了haFGF与抗菌肽的在酵母中的融合表达,为多功能细胞生长因子在创伤治疗中的应用打下了基础。     

反枝苋花粉泛过敏原profilin基因的克隆表达、纯化及免疫学鉴定

目的克隆表达反枝苋花粉中泛变应原肌动蛋白抑制蛋白（profilin）,并鉴定其免疫学活性。方法利用RT-PCR结合RACE技术克隆反枝苋花粉泛变应原profilin的全长基因,并进行序列分析。设计带有酶切位点的特异性引物,采用RT-PCR获得整个反枝苋花粉profilin的开放阅读框,将其与pET28a载体连接并转化大肠杆菌BL21（DE3）进行诱导表达,Ni2＋亲和层析柱纯化重组蛋白,采用Western-blot检测其IgE结合活性。结果 cDNA核苷酸测序表明反枝苋花粉profilin的全长基因由675个碱基组成,开放阅读框为399 bp,编码131个氨基酸。重组反枝苋花粉profilin在大肠杆菌中可溶性表达,进一步经Western-blot检测具有良好的IgE结合活性。结论成功地克隆和表达了反枝苋花粉profilin,并具有良好的IgE应答免疫活性。     

Molecular Detection of Phytophthora colocasiae of Taro Leaf Blight Based on PCR

The present PCR assay was conducted to develop rapid and sensitive detection of Phytophthora colocasiae,in order to provide a robust and reliable tool for healthy seedling production of taro and limiting the transmission and spread of the causal organism of taro leaf blight in taro planting regions.The samples were used to extract total DNA and to be detected by PCR with P.colocasiae specific primer pairs PCSP-RL F/PCSP-RL R and PCSP-T F/PCSP-T R,respectively.Distinct fragments of about 200 bp and 240 bp were amplified by PCR using primers PCSP-RL F/PCSP-RL R and PCSP-T F/PCSP-T R,respectively.The analysis of the nucleotide sequence of the PCR products were found to be 99% identical to sequence of RAS-related protein (Ypt1) and phospho-ribosylanthranilate isomerase (TRP1) in P.colocasiae,respectively.It is concluded that rapid and sensitive developed PCR assay for detection of P.colocasiae could be used in routine diagnosis and aid in management practices to mitigate taro leaf blight.