Identification and viability assessment of dermatophytes infecting nail based on quantitative PCR of dermatophyte actin (ACT) mRNA]

The diagnosis and choice of treatment for dermatophytoses are usually based on the result of microscopic observation of hyphal elements and culture. However, false negative cultures have sometimes been encountered and appropriate timing of discontinuation of treatment has not been formulated. In this study, we attempted the identification and viability assessment of dermatophytes based on the quantitative measurement of dermatophyte actin (ACT) mRNA. An internal fragment of the ACT, 725 to 762 bp, was isolated by PCR from the genomic DNA of dermatophytes and sequenced. ACT intron-based primers were dermatophyte species-specific and primer pairs crossing the intron were dermatophyte genus-specific. The LightCycler (LC) instrument, employing the two-step RT-PCR/fluorescent hybridization system, was used to quantify the actin mRNA (ACT) of dermatophytes. A 669 bp ACT cDNA fragment was used as a quantification standard. Several mg of samples were collected from skin scales or nail plates before and after the treatment using oral terbinafine. The results indicated that quantification of ACT mRNA correlated with the results of culture and KOH examination and that copy numbers of dermatophyte ACT mRNA per mg sample decreased with progression of the therapy. This method comprises a sensitive (1 fg), specific, rapid (< 4 h) and quantitative assessment of the viability and identification of dermatophytes in skin tissue.     

Diagnosis of dermatophytoses: conventional methods and recent molecular biological methods]

Dermatophytoses such as tinea pedis and tinea unguium are very common diseases in the field of dermatology. The diagnosis of dermatophytoses is usually performed by direct microscopy and culture. The identification of species is based on morphological features of giant culture and slide culture. However, in some cases, it is difficult to identify the species clearly because the culture shows an atypical appearance or is false negative. Therefore, several molecular biological methods have been developed for precise identification of a species. The analysis of patterns of random amplification of polymorphic DNA (RAPD) and restriction fragment length polymorphisms (RFLP) of mitochondrial DNA is useful for identifying isolates which are not clearly identifiable by conventional biological techniques. The phylogenetic analysis of dermatophytes was made by using DNA direct sequencing of nuclear ribosomal internal transcribed spacer 1 (ITS1). Sequence analysis of chitin synthase 1 (CHS 1) is a rapid tool for species level identification. We attempted the identification and viability assessment of dermatophytes based on the quantitative measurement of dermatophyte actin (ACT) mRNA. An internal fragment of the ACT, 725 to 762 bp, was isolated by PCR from the genomic DNA of dermatophytes and sequenced. ACT intron based primers were dermatophyte species-specific and primer pairs crossing the intron were dermatophyte genus-specific. The results indicated that quantification of dermatophyte ACT mRNA correlated with the results of culture and KOH examination. It is important that the identification of dermatophyte be done by combining conventional methods with molecular biological methods. In some cases results of the two methods do not correspond, and is those the fungal species needs to be re-examined.     

Multiplex RT-nested PCR differentiation of gill-associated virus (Australia) from yellow head virus (Thailand) of Penaeus monodon

A multiplex RT-nested PCR has been developed to detect and differentiate the closely related prawn viruses, gill-associated virus (GAV) from Australia and yellow head virus (YHV) from Thailand. RT-PCR using primers to conserved sequences in the ORF1b gene amplified a 794 bp region of either GAV or YHV. Nested PCR using a conserved sense primer and either a GAV- or YHV-specific antisense primer to a divergent sequence differentially amplified a 277 bp region of the primary PCR amplicon. Multiplexing the YHV antisense primer with a GAV antisense primer to another divergent sequence allowed the viruses to be distinguished in a single nested PCR. Nested PCR enhanced detection sensitivity between 100- and 1000-fold and GAV or YHV RNA was detectable in approximately 10 fg lymphoid organ total RNA. The multiplex RT-nested PCR was also able to co-detect GAV and YHV RNA mixed over a wide range of concentrations to simulate potential dual-infection states. The robustness of the test was examined using RNA samples from Penaeus monodon prawns infected either chronically or acutely with GAV or YHV and collected at different locations in Eastern Australia and Thailand between 1994 and 1998. GAV- (406 bp) or YHV-specific (277 bp) amplicons were differentially generated in all cases, including five YHV RNA samples in which no primary RT-PCR amplicon was detected. Sequence analysis of GAV and YHV PCR amplicons identified minor variations in the regions targeted by the virus-specific antisense primers. However, none occurred at positions that critically affected the PCR.     

Chitin synthase (CHS) gene analysis of dermatophytes]

About 620-bp genomic DNA fragments of CHS1 genes were amplified from 13 species of dermatophytes by polymerase chain reaction (PCR) and sequenced. The phylogenetic analysis of CHS1 gene fragments of these dermatophyte species revealed that 3 genera of Epidermophyton, Microsporum and Trichophyton were genetically different from each other. The molecular analysis of CHS1 genes will provide useful information for the identification of dermatophytes. The species-specific primers were designed from the nucleotide sequences of CHS1 gene in 3 teleomorphs of T. mentagrophytes. Using these primers the PCR analysis identified the clinical isolates of T. mentagrophytes from rabbit as A. benhamiae. By PCR analysis with the dermatophyte specific primer pair, dermatophyte DNA could be diagnosed directly and rapidly in clinical skin samples. The full length of CHS1 and CHS2 genes of Arthroderma benhamiae (one of the teleomorphs of T. mentagrophytes) was sequenced by 5'-RACE and 3'-RACE methods using cDNA as a template. The full length cDNA sequences of CHS1 gene (3158bp) and CHS2 gene (3392bp) were proved to encode 890 and 419 amino acids, respectively. The amino acid sequences of A. benhamiae CHS1 and CHS2 in the conserved regions shared, respectively, about 70% and 80% sequence similarity with those of the other filamentous ascomycetes registered in the data base of the GeneBank. RT-PCR analysis suggested that chitin synthase inhibitors (nikkomycin Z and polyoxin D) might stimulate the expression of CHS1 mRNA in A. benhamiae, and not the expression of CHS2 mRNA.     

恶性疟原虫FCC—1／HN株环子孢子蛋白基因分枝杆菌——大肠杆穿梭表达重组质粒的构建及序列测定

本文对恶性疟原虫环子孢子蛋白(circumsporozoiteprotein,CSP)基因片段进行克隆和序列测定。根据恶性疟原虫837株基因编码序列设计合成一对引物,采用PCR技术从恶性疟原虫FCC-1/HN株基因组DNA中特异扩增CSP基因片段的Ⅰ区、中央重复区、重复区后可变区和Ⅱ区;经纯化的扩增产物用BamHⅠ和KpnⅠ双酶切后,定向克隆入大肠杆菌——分枝杆菌穿梭表达质粒,转化感受态大肠杆菌DH5α,重组克隆经抗性筛选和快速凝胶电泳鉴定,再经PCR和酶切鉴定,并对重组子进行序列测定。结果表明从恶性疟原虫FCC-1／HN株基因组DNA中可特异扩增出约1171bp的基因片段,阳性重组质粒经双酶切和PCR鉴定与预期的结果一致,序列测定表明所克隆的基因和编码环子孢子抗原的基因片段相符。     

rpoB作为蜡样芽胞杆菌群快速检测的标志基因的实验研究

目的探讨常规PCR和实时荧光定量PCR（Q-PCR）方法检测蜡样芽胞杆菌群rpoB基因的特异性和敏感性。方法提取蜡样芽胞杆菌群和其他各种对照细菌的基因组DNA,合成蜡样芽胞杆菌群rpoB基因扩增引物,采用常规PCR和SYBRgreen实时定量PCR两种方法扩增rpoB基因片段,并将PCR产物克隆到pMD18-T载体后进行DNA测序。结果常规PCR和Q-PCR均能扩增出蜡样芽胞杆菌群rpoB基因的174bpDNA片段,而各种对照菌株均未见扩增。序列比对发现蜡样芽胞杆菌群细菌在该片段中存在5处核苷酸的不同,差异率为2.88%。以炭疽芽胞杆菌基因组DNA系列稀释作为扩增模板显示常规PCR最小检出量为3.42pg,Q-PCR的敏感性达到171fg,3次重复实验显示Q-PCR检测rpoB基因的灵敏度为（3.32×101±7.45×100）拷贝。结论以rpoB基因为检测靶基因的Q-PCR方法具有高度的特异性和良好的敏感性,能实现对蜡样芽胞杆菌群快速而准确的检测。     

Molecular characterization of new clinical isolates of Candida albicans and C. dubliniensis in Japan: analysis reveals a new genotype of C. albicans with group I intron.

The genetic diversity of recent clinical isolates of Candida albicans in Japan was studied on the basis of amplified DNA band lengths determined with a specific PCR primer reported to have been designed to span a transposable intron region in the 25S rRNA gene. Our analyses of 301 clinical isolates of C. albicans showed that they could be classified into five genotypes: genotype A (172 isolates), genotype B (66 isolates), genotype C (56 isolates), genotype D (C. dubliniensis; 5 isolates), and a new genotype (designated genotype E; 2 isolates). The new genotype E was characterized to have a group I intron-like sequence, which is longer than hitherto reported ones and which has a nucleotide sequence length of 962 bp. Our analysis of the 962-bp sequence indicated that it is composed of an intron similar to that of C. dubliniensis of 621 bp with a 341-bp insertion. Analysis of the sequence of the internal transcribed spacer (ITS) region of the genotype E strain showed that its sequence is identical to those of strains of other genotypes, with only a few base substitution differences. Throughout the study, the possible horizontal transfer of the group I intron between C. dubliniensis and C. albicans was suggested. A high degree of correlation between the presence of a group I intron in C. albicans genotype E and susceptibility to the antifungal agent flucytosine was observed. The five isolates of C. dubliniensis examined in the present study showed genetic diversity when they were compared by randomly amplified polymorphic DNA fingerprinting pattern analysis, and this diversity was also confirmed by the analysis of ITS region sequences.     

Trf4 is a useful gene for discrimination of Candida tropicalis from other medically important Candida species.

Comparative studies of random amplified polymorphic DNA (RAPD) band patterns of Candida tropicalis with those of clinically important Candida species have shown the presence of specific RAPD bands for C. tropicalis. A band specific to C. tropicalis strains (ca. 400 bp) was extracted and sequenced. It was found to belong to a fragment of the Trf4 gene, which is essential for growth of these strains and has a characteristic sequence of C. tropicalis. A PCR primer was designed specifically for C. tropicalis which amplifies the 324 bp band. The PCR primer amplified DNA products for all C. tropicalis strains tested, but did not amplify any PCR bands from C. albicans, C. dubliniensis, C. glabrata, C. guilliermondii, C. kefer, C. krusei, C. parapsilosis, or C. zeylanoides. Usefulness of the PCR primer in differentiating from clinical isolates of other fungal species is discussed.     

地高辛标记的大鼠nNOS mRNA探针的制备和应用

目的　制备大鼠神经元型一氧化氮合酶 (neuronalnitricoxidesynthase,nNOS)地高辛 (digoxigenin)标记的RNA探针 ,探讨nNOS在脊髓中的表达定位。方法　采用RT PCR方法 ,从大鼠脑组织中扩增nNOS基因mRNA部分片段 ,并经序列测定。以dig nNOSmRNA为探针 ,采用原位杂交观察成年大鼠脊髓组织中nNOSmRNA表达。结果　RT PCR法扩增出一特异产物与预期长度 2 4 0bp相符 ,T载体克隆测序与nNOS基因 10 0 %同源。原位杂交结果显示阳性信号出现在成年大鼠脊髓组织中。结论　采用RT PCR和T载体技术获得了大鼠脑组织nNOS基因克隆 ,dig nNOSmRNA探针原位杂交显示正常SD大鼠腰段脊髓组织中表达nNOSmRNA。     

树鼩CD127全长编码序列的克隆及分子特征分析

目的 树鼩可作为多种人类疾病研究的良好模型,但其免疫系统各类细胞表面标志、功能以及在疾病发生、发展过程中的作用和意义尚无系统研究.研究以获得树鼩调节性T细胞(Tr)相关分子CD127为目的,以分析其分子特征.方法 提取树鼩外周血总RNA反转录,经巢式PCR扩增获得目的片段,进而以Discovery Studio等生物软件进行分析.结果 扩增得到全长为1 392 bp的树鼩CD127编码序列,确定了现有数据库中缺失的一处未知片段.树鼩CD127与人、黑猩猩亲缘关系较近,其氨基酸序列具有较高保守性,蛋白质三维结构整体与人相似,但N糖基化位点数目以及电荷分布存在差异.结论 所得序列能够编码具有正常功能的蛋白,全长序列为后续单克隆抗体制备奠定了基础,有助于鉴定树鼩Treg细胞以及相关疾病机理的研究.     

一个含有25bp内含子的阴道毛滴虫Rabl-like新基因

目的 克隆和鉴定一个新的阴道毛滴虫Rabl-like基因（TvRabl-like）及其内含子。方法 我们从一阴道毛滴虫cDNA表达文库中分离出一个cDNA克隆，它与各物种的Rab家族蛋白有较高的同源性，因此我们进一步用BLASTP、RPS-BLAST、ClustalW和MEGA3等分析软件对该cDNA克隆进行了序列分析和进化树分析；用PCR和RT-PCR等技术分别对该基因组和mRNA进行了扩增和测序分析。结果 序列分析结果表明该eDNA克隆长705bp，开放阅读框具603bp，推测肽链含有200个氨基酸。序列比较分析结果提示该cDNA克隆所推测的蛋白质是一个Rabl亚家族的亚型。进化树分析也表明它属于阴道毛滴虫Rabl亚家族。基因组PCR扩增和测序分析表明该基因包含一个25bp的内含子，该内含子具有阴道毛滴虫和其它真核生物较大内含子所具备的典型的5’GT-AG-3’和分支位点基序。RT-PCR产物及其测序分析表明在该基因的转录本中存在着未剪切和剪切后的mRNA，说明确实有内含子的存在。结论 TvRabl-like基因属于阴道毛滴虫Rabl亚家族，该基因含有一个25bp的内含子。该内含子是至今发现的最小的阴道毛滴虫基因内含子之一，很可能也是真核生物中最小的内含子。对诸类最低等真核生物内含子的研究将有助于我们理解真核生物内含子的起源和进化。     

Two-step polymerase chain reactions and restriction endonuclease analyses detect and differentiate ompA DNA of Chlamydia spp.

Specific and sensitive amplification of major outer membrane protein (MOMP) gene (ompA) DNA sequences of Chlamydia species with various MOMP genotypes was achieved by a two-step polymerase chain reaction (PCR). Degenerate, inosine-containing oligonucleotide primers homologous to the 5' and 3' ends of the translated regions of all chlamydial MOMP genes were used in a PCR to amplify a DNA fragment of approximately 1,120 bp. A portion of this DNA fragment was amplified in a second genus-specific reaction that yielded a DNA fragment of approximately 930 bp. A pair of degenerate oligonucleotide primers homologous to internal sequences of the primary DNA fragment was used in this PCR. This method detected three cognate chlamydial genomes in a background of 1 microgram of unrelated DNA. MOMP genes of 13 representative chlamydial MOMP genotypes of the species C. trachomatis, C. pneumoniae, and C. psittaci were amplified. In a secondary PCR, group-specific detection was achieved by the simultaneous use of one genus-specific primer and three primers derived from different fingerprint regions of three major groups of chlamydiae. This multiplex PCR differentiated the groups by the length of the amplified DNA fragments and detected the simultaneous presence of DNA sequences of the Chlamydia spp. with different MOMP genotypes. Further differentiation as ompA restriction fragment length polymorphism types among all chlamydial strains with the various MOMP genotypes analyzed here was achieved by restriction endonuclease analysis of the secondary PCR products. DNA sequences corresponding to the ompA restriction fragment length polymorphism type B577 of C. psittaci were detected in two of seven milk samples from cases of bovine mastitis.     

PCR identification of dermatophyte fungi Trichophyton rubrum, T. soudanense and T. gourvilii

Diagnosis of dermatophytosis employing conventional laboratory procedures has been complicated by the slow growth and varied morphological features shown by dermatophytes. After analysis of the nucleotide base sequences of a 1.2-kb fragment amplified from a dermatophyte fungus Trichophyton rubrum by arbitrarily primed PCR with random primer OPD18, a pair of primers (TRIF and TR1R) was designed and evaluated for specific identification of T. rubrum. The sensitivity of the primers TR1F and TR1R was high, as a specific PCR band of c. 600 bp was detected from as little as 7 pg of T. rubrum DNA. By examining 92 dermatophyte strains and clinical isolates, it was found that this pair of primers reacted in PCR with T. rubrum, T. soudanense and T. gourvilii through formation of the specific fragment of 600 bp, but not with any other of the dermatophyte species or varieties, fungi, yeasts or bacteria tested. As T rubrum is one of the most frequently isolated dermatophyte fungi, and T. soudanense and T. gourvilii are relatively uncommon in many parts of the world, these primers can be used for rapid, sensitive and specific identification and differentiation of T. rubrum from other fungi and micro-organisms.     

Erratum: A novel splice site mutation (3157+1G>T) in the dystrophin gene causing total exon skipping and DMD phenotype

Erratum: An error was printed in the original version of this article in the Comments section, paragraph 2, relating to the size of exon 22 and the RT‐PCR product size described as resulting from the mutation 3157+1G>T. The paragraph should read: “We report a case of a 5 year old DMD patient with a novel splice site mutation affecting the GT dinucleotide splice donor of exon 22. The RT‐PCR analysis with primer sets spanning dystrophin exons 17‐25 amplified no normal size fragment (1251 bp), but a product shorter by 146 bp (the length of exon 22). Direct sequencing of the faster migrating fragment revealed total skipping of exon 22.”     

粒细胞—巨噬细胞集落刺激因子与HBsAg融合蛋白基因的 …

目的 研究粒细胞－巨噬细胞集落刺激因子（ＧＭ－ＣＳＦ）的免疫活性。方法 用聚合酶链反应（ＰＣＲ）技术扩增出粒细胞－巨噬细胞集落刺激因子（ＧＭ－ＣＳＦ）３８４ｂｐ的基因片段及ＨＢｓＡｇ８４６ｂｐ基因片段，扩增产物经柱纯化后，由Ｔ４ＤＮＡ酶连结因子１２３０ｂｐ的片段，将此片段命名为ＬＧＨ，克隆到ｐＵＣ１９质粒中，利用菌落ＰＣＲ法快速筛选阳性克隆及限制酶切鉴定片段的大小。结果 该基因全长１２３０ｂｐ，经     

Use of denaturing gradient gel blots to screen for point mutations in the factor VIII gene

Denaturing gradient gel electrophoresis (DGGE) is commonly used to search for point mutations in DNA fragments amplified in vitro by the polymerase chain reaction (PCR). For the complete detection of mutations in large genes with many exons, the DGGE-PCR approach, or any other PCR-based method, requires many primer sets and amplification reactions to scan the entire protein-coding sequence. We previously demonstrated that DGGE analysis using DNA blots detects mutations in Drosophila genes and sequence polymorphisms in human genes without prior PCR amplification. To determine if human point mutations could be detected using denaturing gradient gels (DGG blots), genomic DNA samples from hemophilia A families were analyzed for mutations in the factor VIII (FVIII) gene. Restriction enzyme digested DNA samples were subjected to DGGE and transferred to nylon blots. Hybridization of the DGG blots with FVIII cDNA probes revealed mutant and polymorphic DNA sequence differences. Among 26 affected families that were not carriers of intron 22 inversion mutations, 18 family-specific DNA fragment polymorphisms and one multiexon deletion were mapped. DNA sequencing of eight patient-specific polymorphic DNA fragments revealed six single base change mutations, one 4 bp deletion, and one 13 bp duplication. Hum Mutat 12:393–402, 1998. © 1998 Wiley-Liss, Inc.     

Predictive modelling of fluorescent AFLP: a new approach to the molecular epidemiology of E. coli

Amplified fragment length polymorphism (AFLP) permits simultaneous sampling of multiple loci distributed throughout a genome, using restriction site/adaptor-specific primers under stringent conditions. Fluorescent detection instrumentation further refines this methodology, permitting internal size standards and accurate, reproducible sizing of amplified fragments. We have evaluated the potential of fluorescent AFLP (FAFLP) as a potentially definitive genotyping method for bacteria, by comparing MseI/EcoRI fragments derived experimentally from the Escherichia coli K12 MG1655 genome with those predicted by analysis of its published sequence. In silico, MseI/EcoRI digestion of this sequence produced 1200 fragments from 36 and 2151 base pairs (bp) in size. Fragment subsets which would be amplified by seven different selective (1-2 bases added to the 3' end of the core primer sequence) primer combinations were modelled. Depending on the primer pair, three to 54 fragments (range 70-400 bp) were predicted, while all seven primer pair combinations together generated 121 predicted fragments. When genomic DNA of strain MG1655 was subjected to experimental FAFLP with these seven primers, 111 correctly sized fragments were observed (+/- 1 bp) out of the 121 predicted (92% accuracy). Twenty-five unpredicted fragments were obtained; an average of four per primer pair. The size and number of fragments in FAFLP, and their gel distribution, were dictated by the choice of restriction endonucleases and the degree of primer selectivity. Our data show that FAFLP is accurate, discriminatory, reproducible and capable of standardisation. Under agreed conditions, this method shows considerable promise as a generally applicable standardised bacterial genotyping method. The fragments predicted in silico to result from amplification of MseI/EcoRI-digested DNA with the seven primer pairs described are here used to define a prototypic FAFLP analysis of E. coli.