利用扩增片段长度多态性分析鉴别炭疽和蜡样芽孢杆菌

目的:利用扩增片段长度多态性(AFLP)分析建立鉴别炭疽芽孢杆菌和蜡样芽孢杆菌的分子生物学方法。方法:3株炭疽芽孢杆菌和3株蜡样芽孢杆菌基因组经限制性内切酶EcoRⅠ和MseⅠ酶切后与对应接头连接,通过预扩增和选择性扩增获得特异性DNA片段,将片段进行毛细管电泳,并利用GeneScan和BioNumerics软件对电泳数据进行分析。结果:选择性扩增最佳引物组合为EcoRⅠ-G/MseⅠ-A,其扩增片段在100~500 bp范围内的有效数量为40~50条;比较炭疽芽孢杆菌和蜡样芽孢杆菌的AFLP特征峰值图和DNA指纹图谱,确定了5个有明显差异的片段区。结论:利用AFLP分析可对芽孢杆菌属中相近的炭疽芽孢杆菌和蜡样芽孢杆菌进行鉴别,该方法可作为炭疽芽孢杆菌传统鉴定方法的补充。     

Genetic diversity in bambara groundnut (Vigna subterranea (L.) Verdc) landraces revealed by AFLP markers.

Bambara groundnut (Vigna subterranea (L.) Verdc), an African indigenous legume, is popular in most parts of Africa. The present study was undertaken to establish genetic relationships among 16 cultivated bambara groundnut landraces using fluorescence-based amplified fragment length polymorphism (AFLP) markers. Seven selective primer combinations generated 504 amplification products, ranging from 50 to 400 bp. Several landrace-specific products were identified that could be effectively used to produce landrace-specific markers for identification purposes. On average, each primer combination generated 72 amplified products that were detectable by an ABI Prism 310 DNA sequencer. The polymorphisms obtained ranged from 68.0 to 98.0%, with an average of 84.0%. The primer pairs M-ACA + P-GCC and M-ACA + P-GGA produced more polymorphic fragments than any other primer pairs and were better at differentiating landraces. The dendrogram generated by the UPGMA (unweighted pair-group method with arithmetic averaging) grouped 16 landraces into 3 clusters, mainly according to their place of collection or geographic origin. DipC1995 and Malawi5 were the most genetically related landraces. AFLP analysis provided sufficient polymorphism to determine the amount of genetic diversity and to establish genetic relationships in bambara groundnut landraces. The results will help in the formulation of marker-assisted breeding in bambara groundnut.     

Restriction fragment length polymorphism analysis of Cryptosporidium parvum isolates of bovine and human origin.

Cryptosporidium parvum oocysts isolated from different hosts and geographical areas were compared by restriction endonuclease analysis of repetitive DNA: Iowa (bovine), Florida (bovine), New York (bovine), Peru (human), Brazil (human), and Mexico (human). Southern blot hybridization analysis was performed using the restriction endonuclease enzyme Eco RI and the DNA probe pV47-2. The probe hybridized with 18 bands present in all the isolates. The Brazilian, Mexican, and Peruvian human isolates had an additional common band of 4.3 kbp that was absent in the bovine isolates. Two extra bands of 14 and 12 kbp were present in the Brazilian isolate whereas the Mexican isolate had an extra band of 14 kbp. When the Iowa and Peru C. parvum isolates were passed twice through calves, oocysts recovered from both passages showed identical banding patterns, suggesting that recombination of the repetitive sequences was not altered during sexual reproduction. The DNA digested with other restriction endonucleases were tested confirming differences between isolates. A genomic DNA library is currently being produced to better define isolate variation in C. parvum.     

Genomic typing of Escherichia coli O157:H7 by semi-automated fluorescent AFLP analysis

Escherichia coli serotype O157:H7 isolates were analyzed using a relatively new DNA fingerprinting method, amplified fragment length polymorphism (AFLP). Total genomic DNA was digested with two restriction endonucleases (EcoRI and MseI), and compatible oligonucleotide adapters were ligated to the ends of the resulting DNA fragments. Subsets of fragments from the total pool of cleaved DNA were then amplified by the polymerase chain reaction (PCR) using selective primers that extended beyond the adapter and restriction site sequences. One of the primers from each set was labeled with a fluorescent dye, which enabled amplified fragments to be detected and sized automatically on an automated DNA sequencer. Three AFLP primer sets generated a total of thirty-seven unique genotypes among the 48 E. coli O157:H7 isolates tested. Prior fingerprinting analysis of large restriction fragments from these same isolates by pulsed-field gel electrophoresis (PFGE) resulted in only 21 unique DNA profiles. Also, AFLP fingerprinting was successful for one DNA sample that was not typable by PFGE, presumably because of template degradation. AFLP analysis, therefore, provided greater genetic resolution and was less sensitive to DNA quality than PFGE. Consequently, this DNA typing technology should be very useful for genetic subtyping of bacterial pathogens in epidemiologic studies.     

新生隐球菌的AFLP分析

目的评估AFLP-DNA指纹技术在新生隐球菌分类中应用情况。方法新生隐球菌基因组DNA用双酶酶切,双链接头连于其酶切末端,用与接头和酶切位点互补的引物扩增DNA片段,其产物在高分辨的变性聚丙酰胺凝胶上电泳分离,然后进行银染。结果分析来自5种血清型和临床分离株的18株新生隐球菌,可见有30多条大小在30～500bp的DNA-AFLP指纹,相同的血清型有不同的指纹图谱,来自同一患者不同病期的两株分离株和来自同一患者患者的不同部位的两株分离株都显示出相同的带型。结论显示了AFLP的高分辨率,是适用于新生隐球菌流行病学调查的有力工具。     

Genomic Relatedness of Chlamydia Isolates Determined by Amplified Fragment Length Polymorphism Analysis

The genomic relatedness of 19 Chlamydia pneumoniae isolates (17 from respiratory origin and 2 from atherosclerotic origin), 21 Chlamydia trachomatis isolates (all serovars from the human biovar, an isolate from the mouse biovar, and a porcine isolate), 6 Chlamydia psittaci isolates (5 avian isolates and 1 feline isolate), and 1 Chlamydia pecorum isolate was studied by analyzing genomic amplified fragment length polymorphism (AFLP) fingerprints. The AFLP procedure was adapted from a previously developed method for characterization of clinical C. trachomatis isolates. The fingerprints of all C. pneumoniae isolates were nearly identical, clustering together at a Dice similarity of 92.6% (+/- 1.6% standard deviation). The fingerprints of the C. trachomatis isolates of human, mouse, and swine origin were clearly distinct from each other. The fingerprints of the isolates from the human biovar could be divided into at least 12 different types when the presence or absence of specific bands was taken into account. The C. psittaci fingerprints could be divided into a parakeet, a pigeon, and a feline type. The fingerprint of C. pecorum was clearly distinct from all others. Cluster analysis of selected isolates from all species revealed groups other than those based on sequence data from single genes (in particular, omp1 and rRNA genes) but was in agreement with available DNA-DNA hybridization data. In conclusion, cluster analysis of AFLP fingerprints of representatives of all species provided suggestions for a grouping of chlamydiae based on the analysis of the whole genome. Furthermore, genomic AFLP analysis showed that the genome of C. pneumoniae is highly conserved and that no differences exist between isolates of respiratory and atherosclerotic origins.     

A modified AFLP for Trypanosoma congolense isolate characterisation

The amplified fragment length polymorphism (AFLP) technique is a reliable and powerful DNA fingerprint tool for genetic characterisation and analysis. In this paper, we described a modified AFLP with high resolution for Trypanosoma congolense using one enzyme and agarose or Elchrom gel electrophoresis. Eleven allopatric and fourteen sympatric isolates of T. congolense savannah were used to assess the resolution of the method and its ability to characterise T. congolense isolates. Two enzymes (Eco RI or Bgl II) and corresponding non-selective and selective primers were used to identify the most appropriate combination. Patterns generated by Bgl II enzyme and a single selective primer A, C, G or T produced clear profiles. Each of the four selective primers produced different profiles for all the 25 T. congolense isolates. Due to the reduction in the number of bands, profiles could be analysed using agarose or Elchrom gels. Although comparison of a great number of samples could benefit from software help, this technique did not require flurochrome detection methods. The results of the present study demonstrated that this modified AFLP makes the characterisation of T. congolense easier while maintaining high resolution.     

Evaluation of Cryptosporidium parvum genotyping techniques.

We evaluated the specificity and sensitivity of 11 previously described species differentiation and genotyping PCR protocols for detection of Cryptosporidium parasites. Genomic DNA from three species of Cryptosporidium parasites (genotype 1 and genotype 2 of C. parvum, C. muris, and C. serpentis), two Eimeria species (E. neischulzi and E. papillata), and Giardia duodenalis were used to evaluate the specificity of primers. Furthermore, the sensitivity of the genotyping primers was tested by using genomic DNA isolated from known numbers of oocysts obtained from a genotype 2 C. parvum isolate. PCR amplification was repeated at least three times with all of the primer pairs. Of the 11 protocols studied, 10 amplified C. parvum genotypes 1 and 2, and the expected fragment sizes were obtained. Our results indicate that two species-differentiating protocols are not Cryptosporidium specific, as the primers used in these protocols also amplified the DNA of Eimeria species. The sensitivity studies revealed that two nested PCR-restriction fragment length polymorphism (RFLP) protocols based on the small-subunit rRNA and dihydrofolate reductase genes are more sensitive than single-round PCR or PCR-RFLP protocols.     

稻瘟病菌变异菌株的AFLP分析*

利用94对AFLP引物对3个起始菌株和9个致病性变异菌株进行分析,其中49对引物可以区别出不同菌株类型,辨别变异菌株与其起始菌株的关系,以及起始菌株间的亲缘关系。9个变异菌株中5个菌株的条带数减少1~3条,4个菌株条带数没有明显变化。结果还表明,致病性及其他特征变异似乎与条带数缺失多少相关联。     

杨树重要品种( 无性系) 的AFLP 指纹分析

品种的准确鉴定及其遗传相关性的了解对杨树育种和品种管理具有非常重要的意义。本试验采用AFLP对来自青杨组和黑杨组的21 个重要杨树品种( 无性系) 的鉴定与遗传相关性进行了研究。结果显示, 筛选的4对AFLP 引物总共产生了181 条多态性带,尤其是每对引物对每个品种都产生了独特的指纹图谱; 聚类分析和多维尺度分析将试验材料大体上分为五类, 结果不仅显示了组间不同品种的差异, 而且大体上区分了我国原生品种和外来品种。本研究表明, 所有品种都可被筛选的引物准确鉴定, 遗传相关性的推断结果与它们的系谱或分类基本一致。另外, 本研究还表明AFLP 技术完全可用于大规模地构建杨树树种DNA 指纹图谱、进行树种鉴定和遗传相关性的研究。     

稻瘟病菌变异菌株的AFLP分析

利用94对AFLP引物对3个起始菌株和9个致病性变异菌株进行分析,其中49对引物可以区别出不同菌株类型,辨别变异菌株与其起始菌株的关系,以及起始菌株间的亲缘关系。9个变异菌株中5个菌株的条带数减少1~3条,4个菌株条带数没有明显变化。结果还表明,致病性及其他特征变异似乎与条带数缺失多少相关联。     

Genetic variation among natural isolates of the ectomycorrhizal hypogenous fungus,Rhizopogon roseolus from Japanese pine forests inferred using AFLP markers

Genetic variation among 45 Rhizopogon roseolus isolates from 21 different regions of Japan were inferred using amplified fragment length polymorphism (AFLP) markers. Using three primer pair combinations, AFLP analysis reproducibly produced a total of 223 DNA fragments, 74.4% of which were polymorphic. Pairwise dissimilarity of AFLP patterns between isolates ranged from 0.043 to 0.228. Cluster analysis and principal coordinate analysis of AFLP data generally showed four major clusters from geographically distinct areas. The findings suggested that the Japanese populations of R. roseolus from different geographical regions can be distinguished based on AFLP characters.     

杨树重要品种(无性系)的AFLP指纹分析

品种的准确鉴定及其遗传相关性的了解对杨树育种和品种管理具有非常重要的意义。本试验采用AFLP对来自青杨组和黑杨组的21个重要杨树品种（无性系）的鉴定与遗传相关性进行了研究。结果显示,筛选的4对AFLP引物总共产生了181条多态性带,尤其是每对引物对每个品种都产生了独特的指纹图谱;聚类分析和多维尺度分析将试验材料大体上分为五类,结果不仅显示了组间不同品种的差异,而且大体上区分了我国原生品种和外来品种。本研究表明,所有品种都可被筛选的引物准确鉴定,遗传相关性的推断结果与它们的系谱或分类基本一致。另外,本研究还表明AFLP技术完全可用于大规模地构建杨树树种DNA指纹图谱、进行树种鉴定和遗传相关性的研究．     

Conversion of AFLP markers to sequence-specific markers for closely related lines in rice by use of the rice genome sequence

DNA polymorphism between two major japonica rice cultivars, Nipponbare and Koshihikari, was identified by AFLP. Eighty-four polymorphic AFLP markers were obtained by analysis with 360 combinations of primer pairs. Nucleotide sequences of 73 markers, 29 from Nipponbare and 44 from Koshihikari, were determined, and 46 AFLP markers could be assigned to rice chromosomes based on sequence homology to the rice genome sequence. Specific primers were designed for amplification of the regions covering the AFLP markers and the flanking sequences. Out of the 46 primer pairs, 44 amplified single DNA fragments, six of which showed different sizes between Nipponbare and Koshihikari, yielding codominant SCAR markers. Eight primer pairs amplified only Nipponbare sequences, providing dominant SCAR markers. DNA fragments amplified by 13 primer pairs showed polymorphism by CAPS, and polymorphism of those amplified by 13 other primer pairs were detected by PCR-RF-SSCP (PRS). Nucleotide sequences of the other four DNA fragments were determined in Koshihikari, but no difference was found between Koshihikari and Nipponbare. In total, 40 sequence-specific markers for the combination of Nipponbare and Koshihikari were produced. All the SNPs identified by AFLP were detectable by CAPS and PRS. The same method was applicable to a combination of Kokoromachi and Tohoku 168, and 23 polymorphic markers were identified using these two rice cultivars. The procedure of conversion of AFLP-markers to the sequence-specific markers used in this study enables efficient sequence-specific marker production for closely related cultivars.     

Characterization of Kenyan Isolates of Fusarium udum from Pigeonpea [Cajanus cajan (L.) Millsp.] by Cultural Characteristics, Aggressiveness and AFLP Analysis

Isolates of Fusarium udum from pigeonpea (Cajanus cajan) plants with wilt symptoms were collected from various districts in Kenya and were characterized using cultural characteristics, aggressiveness and amplified fragment length polymorphism (AFLP). The 56 isolates of F. udum showed a high level of variability in aerial mycelia growth, pigmentation and radial mycelia growth (colony diameter) on potato dextrose agar. The aggressiveness of 17 isolates of F. udum on seven pigeonpea varieties varied and five aggressive groups were observed in the present study. There were no relationships among cultural characteristics and aggressiveness. AFLP analysis of the 56 isolates was tested for genetic variability using seven primer combinations. A total of 326 fragments was generated of which 121 were polymorphic. Ten AFLP groups were identified among the Kenyan isolates and, although they were not genetically distinct, six AFLP subgroups were genetically distinct. AFLP had no relationship with cultural characteristics, aggressiveness and geographical origin of the isolates. This is the first report on the study of genetic variability of F. udum using DNA analysis.     

Evaluation of RAPD, ISSR and AFLP Markers for Characterization of the Loose Smut Fungus Ustilago tritici

Random Amplified Polymorphic DNA (RAPD), inter simple sequence repeat (ISSR) and Amplified Fragment Length Polymorphism (AFLP) profiling were evaluated for assessing the extent of genetic variation among the isolates of Ustilago tritici (Pers.) Rostr., which causes the loose smut disease of wheat.Thirty random decamer primers, six random primer pairs, four SSR primers such as (GACA)₄, (GATA)₄, (CAA)₅ and (GTG)₅ and nine combinations of AFLP selective primers were used to characterize nine isolates of the fungus. These isolates were collected from infected earheads of seven commercial wheat cultivars grown at eight different locations in Haryana, which is a major wheat growing state in the North-West Plain Zone of India. The RAPD and ISSR primers generated 21 0 scorable amplified fragments, all of which were monomorphic among the isolates.The AFLP primer combinations generated 239 fragments out of which 193 were polymorphic. All the isolates could be precisely differentiated from each other employing AFLP and grouped into two distinct clusters.The molecular classification partly corresponded with geographic distribution and host origin of the isolates. AFLP profiling was found superior to RAPD and ISSR and can be effectively utilized for further characterization of loose smut pathogen.     

Identification of a molecular marker for genotyping human lymphatic filarial nematode parasite Wuchereria bancrofti

In India, Mass Drug Administration is on going towards elimination of lymphatic filariasis in many areas, which might lead to intense selection pressure on the parasite populations and their genetic restructuring. This calls for molecular finger printing of Wuchereria bancrofti parasite populations at national level and monitoring genetic changes in the future. For this purpose a reliable, less expensive, rapid, and reproducible molecular tool is necessary, which is not available for W. bancrofti at this time. We identified robust molecular markers based on the comparison of random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) profiles and the genetic data generated from parasite populations collected from areas in Northern (Varanasi, Uttar Pradesh state), Southern (Kozhikode, Kerala State) and Central regions (Jagdalpur, Chattisgarh state) of India, where lymphatic filariasis is endemic for many decades. RAPD profiles for these parasite populations were generated using three different primers and the dendrograms constructed using the profiles were all different. In order to identify appropriate RAPD primer(s), we compared the results of RAPD with the fingerprint profile and genetic data obtained by the more reliable AFLP technique, using the parasite populations from the same areas. RAPD marker (OP8) primer produced phylogenetic data almost similar to that of AFLP analysis. The marker was able to reveal variations between the parasite populations collected from Varanasi, Kozhikode, and Jagdalpur. Most importantly, RAPD primer OP8 produced reproducible results, when tested in three different trials. In view of the limited availability of W. bancrofti parasite DNA, along with a lower cost and ease of performance, RAPD appears to be more suitable compared to AFLP at the present juncture, since complete genome information of this parasite is still not available. Thus, RAPD primer OP8 can be a very useful molecular maker for DNA finger printing of W. bancrofti populations at present.     

Use of an arbitrarily primed PCR product in the development of a Campylobacter jejuni-specific PCR.

Development of a PCR assay for Campylobacter jejuni is based on the isolation of species-specific DNA. An arbitrarily primed PCR incorporating 10-mer primers was used to generate fingerprints of C. jejuni M129 genomic DNA. Fingerprint products were then screened individually for their species specificity in dot blot hybridizations with 6 C. jejuni isolates, 4 Campylobacter species other than C. jejuni, and 27 enteric bacterial species other than Campylobacter spp. A 486-bp fingerprint product hybridized specifically to C. jejuni DNA under stringent conditions; no binding to Campylobacter DNA other than that of C. jejuni or to DNA from enteric bacteria was detected. The 486-bp fingerprint product was sequenced, and primers corresponding to three overlapping regions of the DNA probe were synthesized. Evaluation of the three primer pairs for specificity to C. jejuni DNA identified an oligonucleotide primer pair which amplified a 265-bp product from six C. jejuni isolates only. In sensitivity studies using a crude M129 lysate as the template, the C. jejuni-specific PCR amplified the 265-bp product in a lysate with as few as 100 bacteria.     

部分两用桃品种(系)指纹图谱的建立

以近亲个体'顺10-16'、'青北10-7'和'贺春'为材料建立了两用桃AFLP研究体系,从64对引物组合中筛选出了E-AAT/M-ACT、E-AAT/M-CTG、E-ACA/M-CTG和E-ACA/M-CTT等4个多态性好、分辨率高的引物组合;应用该体系对'锦春'等23个两用桃品种(系)进行AFLP分析,结果共扩增出127条带,其中多态性带62条,多态性百分率48.8%,以其中特异性较高的23个多态性条带构建了这23个两用桃品系的指纹图谱,为两用桃品种鉴定及保护奠定了基础.     

Cryptosporidium in farmed animals: the detection of a novel isolate in sheep.

We describe the discovery of polymorphisms in the Cryptosporidium oocyst wall protein (COWP) gene conferring a novel restriction fragment length polymorphism (RFLP) pattern in 26/60 (43%) isolates from a flock of sheep sampled following a waterborne outbreak of human cryptosporidiosis. The sheep isolates showed identical PCR-RFLP patterns to each other by COWP genotyping but different from those of most currently recognised genotypes, including the major Cryptosporidium parvum genotypes 1 and 2. Sequence analysis of the 550bp amplicon from the COWP gene was compared with a DNA coding region employed in previous studies and showed the novel isolate to differ from other Cryptosporidium species and C. parvum isolates by 7-21%. The sheep-derived isolates were compared at this and further three Cryptosporidium gene loci with isolates from other farmed animals. The loci employed were one in the thrombospondin related adhesive protein (TRAP-C2) gene and two in the 70kDa heat shock protein (HSP70) gene (CPHSP1 and 2). Other animal samples tested in our laboratory were from clinically ill animals and all contained C. parvum genotype 2. The sheep in which the novel isolate was identified were healthy and showed no symptoms of cryptosporidiosis, and the novel sheep isolate could represent a non-pathogenic strain. Our studies suggest that a previously undetected Cryptosporidium sub-type may exist in sheep populations, reflecting the increasingly recognised diversity within the parasite genus.