苛求芽孢杆菌基因组DNA提取方法的比较

目的:比较不同方法提取苛求芽孢杆菌基因组DNA的差异。方法:用经典CTAB提取法、改进CTAB法(溶菌酶处理结合CTAB提取法)、UniQ柱吸附提取法制备苛求芽孢杆菌基因组DNA,比较产物完整性和用于PCR扩增的有效性。结果:三种方法制备基因组DNA纯度接近,但改进CTAB法产率最高,UniQ法产率最低。经典CTAB法和UniQ法提取基因组DNA易降解。三种方法所得基因组DNA用于PCR扩增效率接近。结论:溶菌酶裂解结合CTAB提取更适合制备苛求芽孢杆菌基因组DNA。     

黑翅土白蚁基因组DNA提取方法的优化

目的 为快速地提取到质量较好的黑翅土白蚁基因组DNA进行白蚁种群多样性的研究,对基因组DNA提取方法进行了比较与改进.方法 先初步采取CTAB法与蛋白酶K法对黑翅土白蚁基因组DNA的提取方法进行比较,再利用正交设计法对蛋白酶K法中裂解液、蛋白酶、RNA酶及作用时间4个因素进行优化.结果 蛋白酶K法获得的基因组DNA的质量与产量稍优于CTAB法;较佳的提取步骤组合为:裂解液150 μL,蛋白酶K 6μL,作用时间1h,RNA酶可不添加.结论 采用优化后的方法获得的基因组DNA为模板进行PCR扩增,得到了清晰、稳定的扩增谱带,完全可用于相关后续实验.     

RAPD分析用白花丹参叶片DNA的提取方法

本研究采用改良CTAB法和SDS法提取新鲜白花丹参叶片的基因组DNA,初步筛选RAPD扩增引物。结果表明改良CTAB法提取的DNA较SDS法质量好,随机引物p2扩增条带相对较为清晰。再利用p2随机引物对2种方法提取的DNA进行RAPD检测比较,结果显示仅改良CTAB法能扩增出有效条带,说明改良CTAB法更适合用于白花丹参基因组DNA的RAPD检测分析。本文将为白花丹参叶片DNA的提取提供方法学参考。     

适合于胞质基因组扩增的红麻成熟叶片DNA提取改良方法

为了从成熟红麻叶片中提取高质量、高产量的基因组DNA,针对红麻成熟叶片中多糖、多酚含量较高的特性,利用改良CTAB法及改良SDS法分别提取红麻品种福红952成熟叶基因组DNA,并通过琼脂糖凝胶电泳和紫外分光光度计测定进行DNA质量检测。结果表明:改良CTAB法提取的基因组DNA电泳时点样孔干净,条带整齐无拖带,OD260/OD280为1.9左右,产率可达1.84μg/g,其质量、产量都高于改良SDS法,所提取的DNA可用于红麻RAPD分子标记、线粒体DNA、叶绿体DNA通用引物PCR扩增。改良CTAB法是提取成熟红麻叶片DNA的有效方法,并且可用于红麻分子标记及胞质基因组学研究。     

小鼠胚胎胃肠道细菌基因组DNA提取方法比较

目的:筛选能均衡地提取小鼠胚胎胃肠道微生物区系各种细菌总DNA的方法.方法:分别采用反复冻融法、CTAB -SDS法、柱式基因组DNA提取试剂盒法提取小鼠胚胎胃肠道细菌基因组DNA,对其进行琼脂糖凝胶电泳、紫外分光光度计测定、PCR扩增等质量检测.结果:CTAB -SDS方法提取的基因组DNA纯度较高,OD260/OD280平均值最高,为1.845,电泳条带清晰,能满足下游的PCR扩增等分子操作.结论:确定CTAB -SDS方法为提取小鼠胚胎胃肠道细菌基因组DNA的最佳方法,为研究不同种动物胚胎的肠道菌群的结构和多样性奠定了基础.     

短序十大功劳基因组总DNA提取方法研究

以短序大功劳嫩叶为材料,采用CTAB法、CTAB改良法1、CTAB改良法2、SDS法和试剂盒法五种方法提取短序十大功劳基因组总DNA,用分光光度计和琼脂糖凝胶电泳方法检测所得总DNA的纯度和得率,用ISSR-PCR扩增的方法检测所得总DNA的质量。结果表明,五种方法均能从短序大功劳叶片中提取到基因组DNA,但不同方法提取得的基因组DNA的纯度、浓度和得率存在明显的差异。CTAB改良法2和试剂盒法提取的DNA纯度高,可直接用于下游分子生物学实验,CTAB法、CTAB改良法1和SDS法提取的总DNA质量较差,不利于下游的分子生物学实验;五种方法提取的总DNA的得率在10.836~451.709μg/g之间,呈CTAB法>SDS法>CTAB改良法1>CTAB改良法2>试剂盒法的现象。此实验获得的结果可以为短序十大功劳分子生物学研究提供基础。     

三种提取冬虫夏草菌丝体基因组DNA方法的比较

采用改良氯化苄法、CTAB法、蛋白酶K裂解法这三种方法,对冬虫夏草菌丝体基因组DNA进行提取,将提取的基因组DNA经过紫外分光光度计检测纯度和计算浓度、琼脂糖凝胶电泳分析及PCR扩增,结果表明,3种方法均能提取到符合分子生物学的DNA,其中蛋白酶K裂解法纯度最高,含蛋白质少,改良氯化苄法、CTAB法次之。而浓度则是改良氯化苄法最高,CTAB法、蛋白酶K裂解法次之。3种方法所提取的DNA均能扩增出理想条带。     

金藻基因组DNA的提取与PCR扩增

以金藻门群体和单细胞藻类的典型代表--球形棕囊藻和绿色巴夫藻为研究对象,对金藻基因组DNA的提取方法进行了深入研究,并以psbA基因的PCR扩增结果对4种DNA提取方法进行了检测.结果显示,PVP法和高盐法安全、快速、经济,获得的基因组DNA产量高,但DNA杂质含量也较高.CTAB法虽然也具有安全、快速等优势,但提取的DNA产量较低.玻璃粉法提取的DNA质量好,产量也较高,但操作略为烦琐,经济费用高.结论:就球形棕囊藻而言,玻璃粉法是4种方法中最好的DNA提取方法.就绿色巴夫藻而言,4种方法都行,但是从经济和方便考虑,以高盐法为最好.     

降香黄檀基因组DNA的提取方法研究

目的：建立适合降香黄檀基因组DNA的提取方法。方法：采用常规SDS法、常规CTAB法和改良CTAB法等3种方法提取降香黄檀叶片基因组DNA,经电泳、吸光度、酶切检测比较提取结果;对采用改良CTAB法提取的基因组DNA进行ISSR-PCR检测。结果：改良CTAB法通过增加洗涤样品步骤,有效去除了多糖和多酚类物质,提取的DNA质量好,无降解现象,无蛋白质、盐离子及RNA污染。结论：改良CTAB法是一种高效的提取方法,使用该方法所得DNA的质量完全能够满足相应的分子操作需要。     

利用改良CTAB法快速小量提取微胚乳玉米基因组DNA

为了能快速小量提取微胚乳玉米基因组DNA,以微胚乳玉米幼叶为试材,采用改良CTAB法和传统CTAB法提取微胚乳玉米基因组DNA,并对所提取的DNA通过紫外分光光度计、琼脂糖凝胶电泳和PCR扩增等方法进行检测。两种方法所得基因组DNA的OD260/OD280在1.8~1.9之间,电泳条带清晰,无蛋白质和RNA污染,DNA无明显降解,其浓度和纯度都适合基因工程实验操作的条件。改良CTAB法与传统CTAB法相比更简便快捷,可实现大批量的不同样本基因组DNA的同时提取,提供了一种简便、快捷、有效和实用的微量提取微胚乳玉米基因组DNA方法,可满足以PCR为基础的分子生物学研究。     

Molecular diversity and growth features of Flavobacterium columnare strains isolated in Finland

Columnaris disease caused by Flavobacterium columnare is a problem in fish farming worldwide. During the last 15 yr, outbreaks have started to emerge in Finland. Flavobacterium columnare Type Strain NCIMB 2248T and 30 Finnish F. columnare isolates were studied using analysis of 16S rDNA by restriction-fragment length polymorphism (16S RFLP), length heterogeneity analysis of polymerase chain reaction (LH-PCR) products, automated ribosomal intergenic spacer analysis (ARISA), and 16S rDNA sequence analysis. All isolates fell into RFLP Genomovar I and had the same length in the LH-PCR analysis. Based on ARISA, 8 genetically different strains were selected for further analyses. The growth of these strains under different temperatures, NaCl concentrations, and pH values was tested. The Finnish F. columnare strains did not grow at NaCl concentrations >0.1% or at pH values < or = 6.5, and they were susceptible to several antimicrobial agents, but not to Polymyxin B or neomycin. These findings may aid in development of methods for disease management at fish farms.     

Transmission and detection of Flavobacterium columnare in channel catfish Ictalurus punctatus

A specific and rapid PCR detection method for Flavobacterium columnare based on the 16S-23S rDNA intergenic spacer region (ISR) of the ribosomal RNA operon has been developed. The ISR of 30 F. columnare strains and other Flavobacterium species was amplified using universal primers and sequenced. Once F. columnare specific sequences within the ISR were recognized, specific PCR primers were designed against them (FCISRFL and FCISRR1). The primers were sensitive and able to detect as low as 7 colony forming units from pure culture by PCR. The new PCR detection method was applied to experimentally infected channel catfish. Two different experiments in which channel catfish fingerlings were infected by intramuscular injection or by immersion bath showed the advantage of the PCR method over standard culture techniques. F. columnare was detected by PCR in both tank water and catfish tissue samples with a higher frequency and in less time than standard microbiological methods. Furthermore, PCR detection confirmed that F. columnare can be transmitted horizontally indirectly through the water column without fish-to-fish contact. The newly developed PCR detection method for F. columnare was more sensitive and rapid than standard culture on bacteriological media for detection of F. columnare in channel catfish tissues and in tank water.     

Sensitive and rapid detection of Flavobacterium columnare in channel catfish Ictalurus punctatus by a loop-mediated isothermal amplification method

AIMS: To evaluate the loop-mediated isothermal amplification method (LAMP) for rapid detection of Flavobacterium columnare and determine the suitability of LAMP for rapid diagnosis of columnaris infection in channel catfish, Ictalurus punctatus. METHODS AND RESULTS: A set of four primers, two outer and two inner, were designed specifically to recognize 16S ribosomal RNA gene of this pathogen. Bacterial genomic DNA templates were prepared by hot lysis in a lysis buffer. Amplification of the specific gene segments was carried out at 65 degrees C for 1 h. The amplified gene products were analysed by agarose gel electrophoresis and detected by staining gels with ethidium bromide. A PCR assay was also included in this study. Our results demonstrate that the ladder-like pattern of bands from 204 bp specific to the Fl. columnare 16S ribosomal RNA gene was amplified. The detection limit of the LAMP assay was comparable to that of PCR in prepared genomic DNA reactions. In addition, this optimized LAMP assay was able to detect the Fl. columnare 16S ribosomal RNA gene in experimentally infected channel catfish. CONCLUSIONS: The LAMP assay for Fl. columnare detection in channel catfish was established. SIGNIFICANCE AND IMPACT OF THE STUDY: Because LAMP assay is a rapid, sensitive, specific, simple and cost-effective assay for Fl. columnare detection in channel catfish, it is useful for rapid diagnosis of Fl. columnare in fish hatcheries and the field.     

Diagnosis of flavobacteriosis by direct amplification of rRNA genes

A broad-range bacterial PCR method with universal 16S rDNA targeting primers and bacterial cultivation was used to identify the putative pathogen in flavobacterial outbreaks. Restriction fragment length polymorphism (PCR-RFLP) analysis and sequencing of the partial 16S rDNA PCR products of 10 skin samples and 10 representative isolates derived from the same fish specimens revealed differences between direct molecular and cultivation-based analysis. Flavobacterium columnare-like sequences dominated in the direct molecular analysis in most cases, whereas most of the isolates belonged to a phylogenetically heterogeneous group of flavobacteria clustering with F. hibernum. F. columnare was isolated in only 1 outbreak. The possible explanations for the different results may be attributable to difficulties in the plate cultivation procedure of external flavobacterial samples. During plate cultivation, the dominating Flavobacterium species can be masked by saprophytic species of the same genus or other genera, or the growth of flavobacteria can be completely inhibited by antagonistic bacteria such as Pseudomonas. Direct analysis of the prevailing 16S rDNA sequences avoids the problems with cultivation and may thus be preferable for the diagnosis of flavobacterial diseases. When isolating flavobacteria from external samples, serial dilution of the sample before plating can improve the results.     

刺参基因组DNA提取的探讨

以刺参为试验材料,分别以CTAB法、SDS法、Segama试剂盒法对刺参的触手、管足、体壁、纵肌、肠和呼吸树组织进行基因组DNA的提取,均得到了高质量的基因组DNA。Segama试剂盒提取DNA条带较其他两种方法清晰,杂质少且无降解,效果最佳。对比6种不同的刺参组织,其中纵肌组织3种方法均获得高质量基因组DNA,为提取基因组DNA的首选组织。开发了利用刺参触手和管足活体取样提取基因组DNA的方法,得到了高质量的基因组DNA,这为刺参无损伤取样提供了数据支持,使得将来刺参家系建立过程中保证亲体的健康存活及减少试验样品取样所带来的损伤成为可能。     

我国淡水鱼类柱形病病原菌柱状黄杆菌的遗传多样性

为认识我国淡水鱼类烂鳃病的病原以及柱形病在我国的发生情况,实验从发生烂鳃病的病鱼中分离细菌性病原,经过生理生化特性分析以及是否在含托普霉素的Shieh培养基中生长并形成黄色假根状菌落,是否产生降解明胶和硫酸软骨素的酶类等特性的鉴定,并结合16SrDNA序列分析,证实柱状黄杆菌(Flavobacterium columnare)是所分离的烂鳃病的病原。同时,研究也证实20世纪曾经命名为烂鳃(Gill-rot)病病原的鱼害黏球菌(Myxococcus piscicola Lu,Nie & Ko,1975)是柱状黄杆菌的同物异名。利用分离到的16株柱状黄杆菌的16SrDNA序列,以及已经发表的柱状黄杆菌的相关序列,构建了系统发育树,发现柱状黄杆菌的菌株聚成3枝,与柱状黄杆菌的三种基因组型(Genomovar)相对应。其中当时命名为鱼害黏球菌的强毒株G4与分别分离自日本和美国的两株聚为一枝。另外两枝包括的菌株较多,它们中的一些菌株来源于相同的鱼类宿主,如鲤形目的种类;但是,这两枝也包括一些特有的株,如从欧洲和美国的鲑形目鱼类上分离的柱状黄杆菌聚为一枝,这一枝还包括我国曾经命名为鱼害黏球菌的G18弱毒株。从我国隶属于鲈形目的鳜鱼和鲟形目的中华鲟上分离到的柱状黄杆菌则聚为另外一枝。作者认为对不同基因组型菌株的致病性和致病机理的研究将可能从根本上认识鱼类柱形病的流行规律。       

Molecular typing of isolates of the fish pathogen, Flavobacterium columnare, by single-strand conformation polymorphism analysis

Flavobacterium columnare intraspecies diversity was revealed by analyzing the 16S rRNA gene and the 16S-23S internal spacer region (ISR). Standard restriction fragment length polymorphism (RFLP) of these sequences was compared with single-strand conformation polymorphism (SSCP). Diversity indexes showed that both 16S-SSCP and ISR-SSCP improved resolution (D>or=0.9) when compared with standard RFLP. ISR-SSCP offered a simpler banding pattern than 16S-SSCP while providing high discrimination between isolates. SSCP analysis of rRNA genes proved to be a simple, rapid, and cost-effective method for routine fingerprinting of F. columnare.     

一种褐飞虱病原真菌的分子生物学鉴定

从田间褐飞虱Nilaparvata lugens( St(a)l)罹病虫体分离得到一株绿僵菌,以该菌为供试菌体,采用氯化苄法、CTAB法以及裂解液法分别提取了该菌的基因组DNA;以ITS1和ITS4为绿僵菌通用引物,对供试菌株的rDNA ITS序列进行PCR扩增、琼脂糖凝胶电泳检测和序列分析,并在核酸序列数据库中进行同...