A PCR-based method to characterise and identify benzimidazole resistance in Helminthosporium solani

Control of Helminthosporium solani, the cause of silver scurf in potato tubers, has been impaired by selection of benzimidazole-resistant strains as a result of repeated use of the fungicide thiabendazole. Identification of thiabendazole-resistant strains of H. solani by conventional techniques takes several weeks. Primers designed from conserved regions of the fungal β-tubulin gene were used to PCR amplify and sequence a portion of the gene. A point mutation was detected at codon 198 in thiabendazole-resistant isolates causing a change in the amino acid sequence from glutamic acid to alanine or glutamine. Species-specific PCR primers designed to amplify this region were used in conjunction with a restriction endonuclease to cause cleavage in sensitive isolates only and thus provide a rapid diagnostic test to differentiate field isolates.     

香菇蛛网病病原菌树状枝葡霉生物学特性

香菇是我国产量最高的食用菌之一,因其独特浓郁的风味而广受赞誉。然而随着香菇栽培面积的不断扩大,其各种病害的发生也日趋频繁。近期在浙江省庆元县多个菇棚内发现一种新病害。为了明确致病菌,本研究通过对罹病香菇子实体进行组织分离和单孢分离获得纯化菌株QS02,随后结合形态学特征和分子生物学技术对其进行鉴定,并通过柯赫氏法则的验证,确定该病原菌为树状枝葡霉Cladobotryum dendroides。同时,本文还对该病原菌展开了生物学特性研究,结果表明:病原菌菌丝生长最适培养基为PDA培养基,最适温度为25℃,最适碳源为可溶性淀粉,最适氮源为牛肉膏,最适pH区间为5–6;光照对该菌菌丝生长有一定的抑制作用。这是由树状枝葡霉引起的香菇蛛网病在国内的首次报道。     

Identification and characterization of benzimidazole resistance in Monilinia fructicola from stone fruit orchards in California

Low and high levels of resistance to the benzimidazole fungicides benomyl and thiophanate-methyl were observed in field isolates of Monilinia fructicola, which is the causative agent of brown rot of stone fruit. Isolates that had low levels of resistance (hereafter referred to as LR isolates) and high levels of resistance (hereafter referred to as HR isolates) were also cold and heat sensitive, respectively. Results from microsatellite DNA fingerprints showed that genetic identities among the populations of sensitive (S), LR, and HR isolates were very high (>0.96). Analysis of DNA sequences of the beta-tubulin gene showed that the LR isolates had a point mutation at codon 6, causing a replacement of the amino acid histidine by tyrosine. Codon 198, which encodes a glutamic acid in S and LR isolates, was converted to a codon for alanine in HR isolates. Based on these point mutations in the beta-tubulin gene, allele-specific PCR assays were developed for rapid detection of benzimidazole-resistant isolates of M. fructicola from stone fruit.     

Conversion of barley SNPs into PCR-based markers using dCAPS method

Molecular genetic research relies heavily on the ability to detect polymorphisms in DNA. Single nucleotide polymorphisms (SNPs) are the most frequent form of DNA variation in the genome. In combination with a PCR assay, the corresponding SNP can be analyzed as a derived cleaved amplified polymorphic sequence (dCAPS) marker. The dCAPS method exploits the well-known specificity of a restriction endonuclease for its recognition site and can be used to virtually detect any SNP. Here, we describe the use of the dCAPS method for detecting single-nucleotide changes by means of a barley EST, CK569932, PCR-based marker.     

Detection of benzimidazole resistance in trichostrongylid nematodes

Benzimidazole anthelmintics (Box 1) have an important role in the control of economically-important nematode parasites of sheep and other ruminants. But effective control and management strategies using such compounds require a clear appraisal of the resistance or susceptibility of the target worms. Currently available tests for benzimidozole resistance in trichostrongylid nematodes tend to be costly, time-consuming and technically-demanding - as a result, attention is now turning to biochemical assays.     

Revealing constitutively expressed resistance genes in Agrostis species using PCR-based motif-directed RNA fingerprinting

Agrostis species are mainly used in athletic fields and golf courses. Their integrity is maintained by fungicides, which makes the development of disease-resistance varieties a high priority. However, there is a lack of knowledge about resistance (R) genes and their use for genetic improvement in Agrostis species. The objective of this study was to identify and clone constitutively expressed cDNAs encoding R gene-like (RGL) sequences from three Agrostis species (colonial bentgrass (A. capillaris L.), creeping bentgrass (A. stolonifera L.) and velvet bentgrass (A. canina L.)) by PCR-based motif-directed RNA fingerprinting towards relatively conserved nucleotide binding site (NBS) domains. Sixty-one constitutively expressed cDNA sequences were identified and characterized. Sequence analysis of ESTs and probable translation products revealed that RGLs are highly conserved among these three Agrostis species. Fifteen of them were shown to share conserved motifs found in other plant disease resistance genes such as MLA13, Xa1, YR6, YR23 and RPP5. The molecular evolutionary forces, analysed using the Ka/Ks ratio, reflected purifying selection both on NBS and leucine-rich repeat (LRR) intervening regions of discovered RGL sequences in these species. This study presents, for the first time, isolation and characterization of constitutively expressed RGL sequences from Agrostis species revealing the presence of TNL (TIR-NBS-LRR) type R genes in monocot plants. The characterized RGLs will further enhance knowledge on the molecular evolution of the R gene family in grasses.     

Modified jatrophane diterpenes as modulators of multidrug resistance from Euphorbia dendroides L

The new diterpenoids terracinolides J-L (1-3), 13alpha-OH terracinolide F (8), abeodendroidin F (11) and epiabeodendroidin F (12) have been identified from Euphorbia dendroides L. The new compounds and six co-occurring known terracinolides were tested as inhibitors of the drug-efflux activity of P-glycoprotein from cancer cells. The results were used to extend the structure-activity relationships established for this class of compounds highlighting the relevance of substitution at positions 2, 3, 6, and 15 and disclosing a remarkable tolerance toward connectivity changes in the terpenoid core.     

The molecular nature of benzimidazole resistance in helminths

The economic importance of benzimidazole (BZ) resistance has resulted in the isolation of resistant populations of helminths and their study (see pp 127-129 this issue). Recent research indicates that BZs act by binding to free beta-tubulin in the cell and inhibiting the formation of microtubules. The effects of BZs on other processes in the cell, such as transport and anaerobic metabolism, probably result from the inhibition of one or more of the functions of tubulin (see pp 112-115, this issue). In this article, Marleen Roos examines the evidence for changes in the beta-tubulin structure and the rate of its synthesis in BZ-resistant parasitic nematodes.     

Development of a PCR-based method for diagnostics of mycoses

Since the express-diagnostics of mycoses in immune-deficit patients still remains an acute problem, we developed an effective test system (Kan-Am) to detect DNA Candida albicans, which is a leader in the list of causative agents of candidosis. A comparison study of three PCR-systems used to detect a broad spectrum of fungoid pathogens was carried out, and a universal system (FungAm), which ensures the detection of DNAs of above 78 strains of 25 types of pathogenic fungi, was selected. The results of clinical testing of the species-specific and universal PCR-systems are well confirmed by the culture method, and they are indicative of the efficacy of applying them for the diagnostics of mycoses in neonatology. The use of the mentioned systems is a promising factor for the express-diagnostics of mycoses in immunodeficiency patients. The high sensitivity of the method makes it possible to detect 10 to 100 cells of a causative agent in 100 mcl of the examined biological material, which is compatible with the culture method. A kit of dry reagents (IonoMix) designed for an accelerated sample preparation and isolation, from them, of DNAs on the basis of Chelex-100 and of proteinase K was worked out; the kit is portable and meant for a long-term storing.     

Identification of plasmids by PCR-based replicon typing

The epidemiological importance of tracing plasmids conferring drug resistance prompted us to develop a PCR method based on replicons (inc/rep PCR) of the major plasmid incompatibility groups among Enterobacteriaceae. Eighteen pairs of primers were designed to perform 5 multiplex- and 3 simplex-PCRs, recognizing FIA, FIB, FIC, HI1, HI2, I1-Igamma, L/M, N, P, W, T, A/C, K, B/O, X, Y, F, and FIIA. The specificity of the method was tested on a collection of 61 reference plasmids and on 20 Salmonella enterica strains of different serotypes isolated in Italy. Results indicated that the inc/rep PCR method demonstrates high specificity and sensitivity in detecting replicons on reference plasmids and also revealed the presence of recurrent and common plasmids in epidemiologically unrelated Salmonella isolates of different serotypes. These results suggest that the method is potentially applicable to a large number of strains to trace the diffusion of specific multi-drug resistance plasmids in different environments.     

Identification of deoxynivalenol, 3-acetyldeoxynivalenol and zearalenone in the galactose oxidase-producing fungus Dactylium dendroides

The galactose oxidase-producing fungus Dactylium dendroides was re-identified as a Fusarium species. Fungi of this genus are well known for the production of mycotoxins. Verification of growth of this fungus on rice, corn and liquid medium described for the production of galactose oxidase is provided to determine whether the fungus could produce Fusarium toxins, namely, moniliformin, fusaric acid, fumonisin, zearalenone and the trichothecenes, deoxynivalenol, 3-acetyldeoxynivalenol, fusarenone, nivalenol, diacetoxyscirpenol, neosolaniol, and toxin T-2. Under the culture conditions used, deoxynivalenol, 3-acetyldeoxynivalenol and zearalenone were detected in the fungal culture medium. The finding is consistent with the hypothesis that the fungus is in fact a Fusarium species. This revised version was published online in July 2006 with corrections to the Cover Date.     

灵芝蛛网病病原菌及其生物学特性

为明确吉林省蛟河市灵芝Ganoderma lingzhi栽培主产区发生的疑似灵芝蛛网病的病原菌,作者通过罹病灵芝子实体病原物的分离纯化、致病性测定、形态学和分子生物学鉴定以及病原菌的生物学特性研究,证明引起吉林省蛟河市灵芝蛛网病的病原菌为嗜菌枝葡霉Cladobotryum mycophilum。该菌营养体最适生长条件为温度25℃、pH 5、蔗糖作碳源、酵母浸粉作氮源,光照对菌丝体生长有一定的抑制作用,完全黑暗最适宜生长。本文研究结果为进一步研究该病害的发生规律和防治措施提供了理论参考。     

Identification of differences in genome content among phlD-positive Pseudomonas fluorescens strains by using PCR-based subtractive hybridization

Certain 2,4-diacetylphloroglucinol-producing strains of Pseudomonas fluorescens colonize roots and suppress soilborne diseases more effectively than others from which they are otherwise phenotypically almost indistinguishable. We recovered DNA fragments present in the superior colonizer P. fluorescens Q8r1-96 but not in the less rhizosphere-competent strain Q2-87. Of the open reading frames in 32 independent Q8r1-96-specific clones, 1 was similar to colicin M from Escherichia coli, 3 resembled known regulatory proteins, and 28 had no significant match with sequences of known function. Seven clones hybridized preferentially to DNA from strains with superior rhizosphere competence, and sequences in two others were highly expressed in vitro and in the rhizosphere.     

Development of a PCR-based method for diagnosing Mycoplasma pneumoniae infections

The polymerase chain reaction was used to detect clinical samples of Mycoplasma pneumoniae. A 245-bp region of the cytoadhesin P1 gene was shown to be specifically amplified in Myc. pneumoniae , but not in other species of Mollicutes. Picogram amounts of Myc. pneumoniae DNA could be detected per ml blood serum by use of a simple and reliable protocol for sample preparation and a PCR reaction involving two rounds of amplification. Application of the PCR-based method for the detection of Myc. pneumoniae in serum samples and throat swabs from patients with atypical pneumonia showed that it could be used in clinical diagnosis.     

Role of a mutation in human cytomegalovirus gene UL104 in resistance to benzimidazole ribonucleosides

The benzimidazole D-ribonucleosides TCRB and BDCRB are potent and selective inhibitors of human cytomegalovirus (HCMV) replication. Two HCMV strains resistant to these compounds were selected and had resistance mutations in genes UL89 and UL56. Proteins encoded by these two genes are the two subunits of the HCMV "terminase" and are necessary for cleavage and packaging of viral genomic DNA, a process inhibited by TCRB and BDCRB. We now report that both strains also have a previously unidentified mutation in UL104, the HCMV portal protein. This mutation, which results in L21F substitution, was introduced into the genome of wild-type HCMV by utilizing a recently cloned genome of HCMV as a bacterial artificial chromosome. The virus with this mutation alone was not resistant to BDCRB, suggesting that this site is not involved in binding benzimidazole nucleosides. As in previous proposals for mutations in UL104 of murine cytomegalovirus and HCMV strains resistant to BAY 38-4766, we hypothesize that this mutation could compensate for conformational changes in mutant UL89 and UL56 proteins, since the HCMV terminase is likely to interact with the portal protein during cleavage and packaging of genomic DNA.