人工栽培蛹虫草退化现象的分子分析

利用PCR-RFLP和RAPD方法对野生驯化蛹虫草及其退化菌种进行了基因水平的分析。PCR-RFLP实验,采用真菌通用引物ITS1和ITS4,扩增出5．8S和其两端的两个转录间隔区(ITS),选用5种识别四个碱基的内切酶(HaeⅢ、AfaI、TagI、AluI和XspI),其中只XspI酶切结果在两个菌种中存在差异,进一步测序表明,整个片段全长534bp,共有13个位点发生碱基突变,且都为c转换为t。RAPD实验,选用4组计80个随机引物进行PCR扩增,共筛选出9个对所有供试个体均存在明显差异的引物。结果表明了退化菌株较野生驯化菌株在DNA水平上发生了频率较高的突变,这些突变可能：直接与导致菌种退化的基因相关联。     

阴道分离因肯毛孢子菌的分子鉴定和种内分型

分别采用rRNA基因内转录间隔区(ITS)和基因间隔区(IGS1)测序,ITS和IGS1区PCR限制性片段长度多态性分析(PCR-RFLP)和基因组DNA的随机扩增多态性DNA(RAPD)等方法,对三株因肯毛孢子菌Trichosporon inkin进行分子特征及种内分型研究。结果显示,不同菌株的rRNA基因ITS区和IGS1区的序列相似性均高达100%,RFLP酶切图谱具有较理想的种内一致性,而不同菌株的RAPD图谱不尽相同。研究表明:rRNA基因IGS1区测序及RFLP酶切可考虑用于因肯毛孢子菌的菌种分子鉴定,而基因组DNA的RAPD则较适合于菌种的种内分型。     

捕食线虫真菌rDNA ITS区间RFLPs分析

利用PCR-RFLP方法对捕食线虫真菌进行了系统发育研究。以ITS1和ITS4为引物对3属14种16个菌株的核糖体DNA转录间区（ITS）进行了PCR扩增,4种内切酶（AluI、HaeIII、HpaII、TaqI）酶切,结果表明不同属的ITS区长度没有明显差异,其长度范围在585～695之间。酶切图谱种间差别明显,种内基本一致,同属菌株图谱没有特异性,暗示传统的分属可能过细,某些属的成立还有待商榷,PCR-RFLP对确定疑难种的地位有重要意义,但不适用于种下水平的系统学研究。     

应用PCR方法检测油菜菌核病菌对多菌灵的抗药性

通过保守的寡核苷酸引物B1/B3扩增出油菜菌核病菌MBCHR和MBCS菌株的部分β-微管蛋白基因,结果发现编码的198位氨基酸由Glu(GAG)突变为Ala(GCG),表现高水平抗药性。根据MBCHR菌株的突变设计2个快速检测方法:第一种方法是根据MBCHR菌株197和198位密码子(GACGAG→GACGCG)形成ThaI酶切位点(3’CGCG 5’),将B1/B3的扩增产物874bp片段酶切成193bp和681bp片段,而MBCS菌株的PCR产物不被酶切;第二种方法用198位突变密码子作为3’末端碱基设计2个等位基因特异性寡核苷酸引物(ASO)用于“nested”PCR或直接从基因组DNA扩增。通过PCR扩增和ThaI酶切能直接检测油菜菌核病菌的MBCHR和MBCS菌株,所得结果与传统菌落直径法相吻合。     

应用PCR方法检测油菜菌核病菌对多菌灵的抗药性*

通过保守的寡核苷酸引物B1/B3扩增出油菜菌核病菌MBCHR和MBCS菌株的部分β-微管蛋白基因,结果发现编码的198位氨基酸由Glu(GAG)突变为Ala(GCG),表现高水平抗药性。根据MBCHR菌株的突变设计2个快速检测方法:第一种方法是根据MBCHR菌株197和198位密码子(GACGAG→GACGCG)形成ThaI酶切位点(3’CGCG 5’),将B1/B3的扩增产物874bp片段酶切成193bp和681bp片段,而MBCS菌株的PCR产物不被酶切;第二种方法用198位突变密码子作为3’末端碱基设计2个等位基因特异性寡核苷酸引物(ASO)用于“nested”PCR或直接从基因组DNA扩增。通过PCR扩增和ThaI酶切能直接检测油菜菌核病菌的MBCHR和MBCS菌株,所得结果与传统菌落直径法相吻合。     

应用PCR方法检测油菜菌核病菌对多菌灵的抗药性

通过保守的寡核苷酸引物B1/B3扩增出油菜菌核病菌MBC^HR和MBC^S菌株的部分β-微管蛋白基因,结果发现编码的198位氨基酸由Clu(GAG)突变为Ala(GCG),表现高水平抗药性。根据MBC^HR菌株的突变设计2个快速检测方法：第一种方法是根据MBC^HR菌株197和198位密码子（GACGAG→GACGCG）形成HhaI酶切点（3'CGCG 5'）,将B1/B3的扩增产物874bp片段酶切成193bp和681bp片段,而MBC^S菌株的PCR产物不被酶切;第二种方法用198位突变密码子作为3'末端碱基设计2个等位基因特异性寡核苷酸引物（ASO）用一地“nested”PCR或直接从基因组DNA扩增。通过PCR扩增和ThaI酶切能直接检测油菜菌核病菌的MBC^HR和MBC^S菌株,所得结果与传统菌落直径法相吻合。     

用分子生物学技术对草菇进行菌株鉴别

利用AP-PCR和RAPD技术对三个草菇菌株进行鉴别,其结果与用草菇菌株V34基因文库中的中等重复序列为探针进行限制性内切酶长度多态性分析(RFLP),及对编码核糖体5.8SrRNA的DNA(rDNA)进行PCR扩增后的产物进行限制性内切酶长度多态性分析(PCR-RFLP)的结果相一致。这一结果显示出用这四种方法对草菇菌株进行鉴别具有相似的效果。同时用这四种方法构建的分子生物学标记显示出这三个菌株中的两个菌株在遗传上有着较大程度的相似性。     

分子标记对草原野生食用菌蒙古口蘑的鉴别分析

对采自内蒙古锡林郭勒草原的野生食用菌蒙古口蘑(Tricholoma mongolicum Imai.)等10个菌种进行了ITS和ISSR分子标记的鉴定,其中蒙古口蘑共计4个不同来源菌种,其它6个菌种为子实体与蒙古口蘑形态相近的常见草原菇类或市售食用菌,鉴定结果用RAPD进行辅助分析验证。从12条ISSR引物中筛选出2条可用引物,扩增总条带数为246条,多态性标记为215个,多态性频率为87.4%。经过NT-SYS软件聚类分析,发现在ISSR分析中结合ITS方法可以有效地将蒙古口蘑与其它菌种区分开,这与RAPD法的分析结果相一致,获得了可靠的野生食用菌分子标记方法。研究表明ISSR分子标记是蒙古口蘑等野生食用菌鉴定的理想手段之一。     

PCR-RFLP 方法测定 ras 癌基因点突变

曾使用 PCR-RFLP 方法分析过 c-Ha-ras 癌基因第12密码子的点突变.因N-ras 基因第12位密码子、K-ras 基因第12和13位密码子无已知的限制性内切酶的酶切位点,不能使用 PCR-RFLP 方法分析这些位点的突变.在 PCR 引物的3′端引入一个误配的碱基使之正好成为某限制性内切酶的酶切位点,这样便能使用PCR-RFLP 技术分析 c-Ha-ras 基因第61位、N-ras 基因第12位、K-ras 基因第12和13位密码子的点突变.     

海藻糖合酶产生菌筛选、鉴定及目的基因克隆

目的:为筛选出一株产海藻糖合酶的菌株,并以此菌的全DNA为模板,克隆出产海藻糖合酶的目的基因片段。方法:实验过程中采用了常规筛选菌种、快速提取细菌全基因、显微镜观察菌种、热启动PCR技术、电泳纯化回收基因片段、EcoRⅠ和HindⅢ双酶切鉴定目的基因片段等方法。结果:在电镜下可观察到有芽孢、杆菌;菌株16S rRNA基因扩增产物共计1490个碱基;PCR方法扩增出阳性克隆大约1700bp的基因片段。结论:通过生理、形态、结构特征分析及16S rRNA基因全序列比较得出结论:筛选到一株短小芽孢杆菌;PCR扩增出阳性克隆片段,全长1722bp,为实验所要的编码海藻糖合酶的基因片段。     

Analysis of the 5.8S rRNA gene and the internal transcribed spacers in Naegleria spp. and in N. fowleri

Internal transcribed spacers (ITS) and the 5.8S ribosomal gene of 21 Naegleria fowleri strains and eight other species including Naegleria gruberi were sequenced. The results showed that this region can help differentiate between and within species. The phylogeny of Naegleria spp. deduced from the ITS and the 5.8S gene produced four major lineages, fowleri-lovaniensis, galeacystis-italica-clarki-gruberi-australiensis, andersoni-jamiesoni, and pussardi, that fit perfectly with those inferred from the 18S rRNA gene analysis. The N. gruberi isolate, NG260, was closely related to Naegleria pussardi. The other N. gruberi isolates branched together with Naegleria australiensis in another lineage. The ITS and 5.8S results for N. fowleri were congruent with those previously deduced by RAPD analysis. The phylogenetic analysis inferred from ITS and RAPD data revealed two major groups. The French Cattenom and Chooz and South Pacific strains constituted the first group. The second group encompassed the strains corresponding to the Euro-American and Widespread RAPD variants and shared the same substitution in the 5.8S gene. In addition, it was possible to define species specific primers in ITS regions to rapidly identify N. fowleri.     

Molecular phylogeny in Indian Tinospora species by DNA based molecular markers

The phylogenetic relationships among the three species of Tinospora found in India are poorly understood. Morphology does not fully help to resolve the phylogeny and therefore a fast approach using molecular analysis was explored. Two molecular approaches viz Random Amplified Polymorphic DNA (RAPD) assay and restriction digestion of ITS1-5.8S-ITS2 rDNA (PCR-RFLP) were used to evaluate the genetic similarities between 40 different accessions belonging to three species. Of the 38 random primers used only six generated the polymorphism, while as three out of 11 restriction enzymes used gave polymorphic restriction patterns. The average proportion of polymorphic markers across primers was 95%, however restriction endonucleases showed 92% polymorphism. RAPD alone was found suitable for the species diversions. In contrast PCR- RFLP showed bias in detecting exact species variation. The correlation between the two markers was performed by Jaccard's coefficient of similarity. A significant (r= 0.574) but not very high correlation was obtained. Further to authenticate the results obtained by two markers, sequence analysis of ITS region of ribosomal DNA (ITS1 and ITS2, including 5.8S rDNA) was performed. Three independent clones of each species T. cordifolia, T. malabarica and T. crispa were sequenced. Phylogenetic relationship inferred from ITS sequences is in agreement with RAPD data.     

黑龙江省大豆菌核病菌核盘菌遗传多样性分析

了解黑龙江省不同地区侵染大豆核盘菌菌株分离物间的主要特性差异,利用PDA培养基对核盘菌进行分离和纯化,同时利用RAPD和rDNA-ITS标记方法对核盘菌进行遗传多样性分析,获得了50株纯化的核盘菌,用RAPD标记确定的遗传相似系数范围为0.54-0.98,平均相似系数为0.76,说明供试的核盘菌菌株的基因型具有一定的差异。对50个测定序列有差异的32个核盘菌ITS和5.8S rDNA片段的多序列对位分析,在ITS1区域的1-40bp种间变化较大,主要以碱基颠换和转换为进化形式。ITS2区域非常保守没有变异位点。黑龙江省核盘菌菌株在DNA水平上和ITS间隔区上具有较显著的遗传变异,显示出丰富的遗传多样性。     

The internal transcribed spacers and 5.8S rRNA gene show extensive diversity among isolates of the Cryptococcus neoformans species complex

Sequences of the internal transcribed spacer (ITS) region including the 5.8S rRNA gene delineated seven genotypes within the three varieties of Cryptococcus neoformans via specific combinations of eight nucleotide differences located at positions 10, 11, 15, 19, 108 (ITS1), 221 (5.8S), 298 and 346 (ITS2). The ITS types correlated to polymerase chain reaction fingerprint/random amplification of polymorphic DNA (RAPD) molecular types: with ITS type 1 (ATACTAGC)=C. neoformans var. grubii, molecular types VNI+VNII and the serotype A allele of the AD hybrid, VNIIIA; ITS type 2 (ATATAGGC)=the serotype D allele of the AD hybrid, VNIIIB, and C. neoformans var. neoformans, VNIV; and ITS type 3 (GCGCTGGC) and ITS type 7 (ACGCTGGC)=VGI=RAPD type III, ITS type 4 (ACACTGAC)=VGII=RAPD type II, ITS type 5: (ACACTGGG)=VGIII=RAPD type I, ITS type 6 (ACACTGGC)=VGIV=RAPD type IV, all corresponding to C. neoformans var. gattii. Cloned sequences from serotype AD revealed that the hybrid serotype is diploid at the ITS1-5.8S-ITS2 locus carrying the ITS type 1 (ATACTAGC) and the ITS type 2 (ATATAGGC) alleles. ITS sequencing is a useful technique for genotyping the three C. neoformans varieties and for subtyping within C. neoformans var. gattii.     

The genetic similarity of different generations of Neocallimastix frontalis SK

The genetic similarity of different generations of Neocallimastix frontalis SK was examined by random amplified polymorphic DNA (RAPD) profiling and internal transcribed spacer 1 (ITS1) sequence analysis. N. frontalis SK was subcultured every 2-4 days, and SK-1, SK-3M, and SK-1Y represented N. frontalis SK cultures after one subculture, 50 subcultures, and 150 subcultures. The DNA polymorphisms of the different N. frontalis SK generations were compared by RAPD profiling. The RAPD results gave the same patterns for SK-1, SK-3M and SK-1Y using 12 selected random primers. The partial 18S rDNA, 5.8S rDNA, and ITS1 regions of different generations of N. frontalis SK were amplified and sequenced. The results of alignment and pairwise similarity indicated that the analyzed rRNA sequences of SK-1, SK-3M and SK-1Y were totally identical. This study thus demonstrated genetically identical DNA polymorphisms by RAPD profiling and an unvaried ITS1 region for N. frontalis SK when the strain is subcultured frequently. This suggests that this strain is homokaryotic and grows via an asexual life cycle in vitro.     

IGS基因及RAPD标记分析在加特隐球酵母基因分类中的应用

根据ITS1-5.8S-ITS2区域的特异核酸序列变化,加特隐球酵母Cryptococcus gattii(≡新型隐球酵母加特变种Cryptococcu neoformans var.gattii)可分为6种基因型。本研究通过检测加特隐球酵母的IGS基因,发现其IGS序列有着更丰富的变异和信息位点。通过结合加特隐球酵母RAPD(随机扩增的多态性DNA)图谱比较研究,与IGS和ITS的序列分析结果大体一致,说明新近发现的加特隐球酵母ITS8型确实有别于以前报道过的其他加特隐球酵母ITS基因型。研究证明IGS1及IGS2基因片段分析可以作为加特隐球酵母基因分类鉴定中有效的辅助鉴别的分子生物学方法,联合多种基因分类鉴定的方法可以更有效地揭示新型隐球酵母加特变种种内不同基因亚型间的遗传进化关系。     

Plant growth promoting potential of the fungus <Emphasis Type="Italic">Discosia</Emphasis> sp. FIHB 571 from tea rhizosphere tested on chickpea,maize and pea

The ITS region sequence of a phosphate-solubilizing fungus isolated from the rhizosphere of tea growing in Kangra valley of Himachal Pradesh showed 96% identity with Discosia sp. strain HKUCC 6626 ITS 1, 5.8S rRNA gene and ITS 2 complete sequence, and 28S rRNA gene partial sequence. The fungus exhibited the multiple plant growth promoting attributes of solubilization of inorganic phosphate substrates, production of phytase and siderophores, and biosynthesis of indole acetic acid (IAA)-like auxins. The fungal inoculum significantly increased the root length, shoot length and dry matter in the test plants of maize, pea and chickpea over the uninoculated control under the controlled environment. The plant growth promoting attributes have not been previously studied for the fungus. The fungal strain with its multiple plant growth promoting activities appears attractive towards the development of microbial inoculants.     

CONSPECIFICITY AND INDO-PACIFIC DISTRIBUTION OF SYMBIODINIUM GENOTYPES (DINOPHYCEAE) FROM GIANT CLAMS

We previously reported the occurrence of genetically‐diverse symbiotic dinoflagellates (zooxanthellae) within and between 7 giant clam species (Tridacnidae) from the Philippines based on the algal isolates' allozyme and random amplified polymorphic DNA (RAPD) patterns. We also reported that these isolates all belong to clade A of the Symbiodinium phylogeny with identical 18S rDNA sequences. Here we extend the genetic characterization of Symbiodinium isolates from giant clams and propose that they are conspecific. We used the combined DNA sequences of the internal transcribed spacer (ITS)1, 5.8S rDNA, and ITS2 regions (rDNA‐ITS region) because the ITS1 and ITS2 regions evolve faster than 18S rDNA and have been shown to be useful in distinguishing strains of other dinoflagellates. DGGE of the most variable segment of the rDNA‐ITS region, ITS1, from clonal representatives of clades A, B, and C showed minimal intragenomic variation. The rDNA‐ITS region shows similar phylogenetic relationships between Symbiodinium isolates from symbiotic bivalves and some cnidarians as does 18S rDNA, and that there are not many different clade A species or strains among cultured zooxanthellae (CZ) from giant clams. The CZ from giant clams had virtually identical sequences, with only a single nucleotide difference in the ITS2 region separating two groups of isolates. These data suggest that there is one CZ species and perhaps two CZ strains, each CZ strain containing individuals that have diverse allozyme and RAPD genotypes. The CZ isolated from giant clams from different areas in the Philippines (21 isolates, 7 clam species), the Australian Great Barrier Reef (1 isolate, 1 clam species), Palau (8 isolates, 7 clam species), and Okinawa, Japan (1 isolate, 1 clam species) shared the same rDNA‐ITS sequences. Furthermore, analysis of fresh isolates from giant clams collected from these geographical areas shows that these bivalves also host indistinguishable clade C symbionts. These data demonstrate that conspecific Symbiodinium genotypes, particularly clade A symbionts, are distributed in giant clams throughout the Indo‐Pacific.     

Use of the 6-methylsalicylic-acid-synthase gene as a discriminating marker betweenaspergillus terreus andAspergillus flavipes

In nineteen pathogenic and saprophytic isolates denoted asAspergillus terreus the presence and restriction pattern of the genepksM (6-methylsalicylic acid synthase) was determined. Five patterns (A−E) were found and in three isolates the gene was missing. The RAPD (random amplified polymorphic DNA) patterns with three primers were analyzed. The strains withpksM pattern possibly derived from the most common pattern A by single mutation (patterns B−D) were also related by RAPD. Among them, three clades were found. The first one contained saprophytes from Asia, the other two clades contained both European and American pathogens and each of them one saprophyte. The sequences of rDNA region containing 5.8S rDNA and spacers ITS1 and ITS2 were established for representatives of each group and the strains missing thepksM gene. The isolates possessingpksM (although with different restriction patterns) grouped asA. terreus group, whereas the isolates lacking this gene were close toFennellia flavipes.     

New ITS genotype of Cryptococcus gattii isolated from an AIDS patient in Brazil

Based on combinations of nine variable nucleotides at nine different base positions in the ITS1-5.8S-ITS2 region, Cryptococcus gattii strains were classified into six genotypes. A new genotype of C. gattii , designated as ITS type 8, was isolated from an AIDS patient in Brazil. The ITS type 8 strain is closely related to the ITS type 4 strain, which has been frequently isolated in Brazil and the USA, but which shows ITS-signatured nucleotide difference at each nucleotide position. The ITS type 8 strain is also differentiated from all heretofore reported ITS types of C. gattii strains in the RAPD band patterns and IGS sequence information.