DNA microarray to detect and identify trichothecene- and moniliformin-producing Fusarium species

AIMS: To develop a DNA microarray for easy and fast detection of trichothecene- and moniliformin-producing Fusarium species. METHOD AND RESULTS: A DNA microarray was developed for detection and identification of 14 trichothecene- and moniliformin-producing species of the fungal genus Fusarium. The array could also differentiate between four species groups. Capture probes were designed based on recent phylogenetic analyses of translation elongation factor-1 alpha (TEF-1alpha) sequences. Particular emphasis was put on designing capture probes corresponding to groups or species with particular mycotoxigenic synthetic abilities. A consensus PCR amplification of a part of the TEF-1alpha is followed by hybridization to the Fusarium chip and the results are visualized by a colorimetric Silverquant detection method. We validated the Fusarium chip against five naturally infected cereal samples for which we also have morphological and chemical data. The limit of detection was estimated to be less than 16 copies of genomic DNA in spiked commercial wheat flour. CONCLUSIONS: The current Fusarium chip proved to be a highly sensitive and fast microarray for detection and identification of Fusarium species. We postulate that the method also has potential for (semi-)quantification. SIGNIFICANCE AND IMPACT OF THE STUDY: The Fusarium chip may prove to be a very valuable tool for screening of cereal samples in the food and feed production chain, and may facilitate detection of new or introduced Fusarium spp.     

Rapid PCR-based procedure to identify lactic acid bacteria: application to six common Lactobacillus species

The goal of this study was to develop a method allowing rapid identification of the lactic acid bacteria strains in use in the laboratory (Lactobacillus plantarum NCIMB8826; L. fermentum KLD; L. reuteri 100-23; L. salivarius UCC43321; L. paracasei LbTGS1.4; L. casei ATCC393), based on PCR amplification of 16S RNA coding sequences. First, specific forward oligonucleotides were designed in the variable regions of 16S RNA coding sequences of six Lactobacillus strains. The reverse oligonucleotide was designed in the region where the sequences were homologous for the six strains. The expected size of the amplification product was +/-1000 bp. The specificity of the method was tested on total chromosomal DNA. For five out of the six strains, the amplification of the fragment was strain-specific and the method was directly applicable to colonies. For the strain L. casei ATCC393, an additional argument to the classification of this bacteria in the paracasei group could be proposed. Validation of the developed method was performed by applying it to six Lactobacillus reference strains and to various species of bacteria.     

Emulsion PCR-based method to detect Y chromosome microdeletions

Deletions in Y chromosome are thought to be pathologically involved in some cases of male infertility associated with azoospermia or oligozoospermia. An emulsion-based multiplex PCR method was developed for detecting Y chromosome microdeletions in infertile men and a plasma sample of pregnant women carrying a male fetus. The sensitivity of multiplex PCR in emulsion was evaluated. Conventional PCR was also carried out for comparison. A total of 13 sequence-tagged sites (STSs) distributed in the AZF region were analyzed simultaneously with this method. The SRY gene was also detected as the inner control. Results showed that Y chromosome microdeletions were found in 4 of 19 infertile patients. Also, in 1 of 63 samples collected from pregnant women, microdeletions were found in some of the detected sites. It is suggested that the emulsion PCR assay was proven to be a promising diagnostic tool and could be widely used in further clinical and academic research.     

A PCR-RFLP based diagnostic technique to rapidly identify Seiridium species causing cypress canker

Seiridium cardinale, S. cupressi and S. unicorne represent three distinct species of fungi that cause cankers on Cupressus species and the disease collectively known as cypress canker. These fungi cannot be distinguished reliably from each other using morphological characters or ribosomal DNA sequence data. Here we describe a RFLP assay based on digesting β-tubulin amplicons with a single endonuclease, HaeIII, which easily can be used to distinguish among these three species. This RFLP assay provides an inexpensive and simple means of identifying Seiridium species, which include some of the most serious threats to trees in Cupressaceae.     

A method to detect and quantify Phaeomoniella chlamydospora and Phaeoacremonium aleophilum DNA in grapevine-wood samples

Grapevines are sensitive to a wide range of fungal pathogens, including agents such as Phaeomoniella chlamydospora and Phaeoacremonium aleophilum that cause tracheomycosis. In the present study, a procedure for DNA extraction from grapevine woody tissue is first evaluated and shown to be suitable for quantitative analysis. Next, a multiplex real-time PCR method targeting the β-tubulin gene of the pathogens and the actin gene of plant material is developed and its quantitative capability is verified. This protocol was evaluated in inoculated grapevine-wood samples and in young vines from a nursery and was found to be reliable and highly specific. Results obtained from inoculated cuttings show that the fungal colonization process must be considered regardless of the wood phenotype. An analysis of samples of young vines from the nursery shows that a high rate of contamination occurs at the basis of plants and that this contamination is associated with low quantitative values. This finding provides evidence that in vine nurseries, these fungi may be efficient soil-borne pathogens.     

Taxonomy ofPuccinia species causing rust diseases on sugarcane

A taxonomic revision ofPuccinia species causing rust diseases on sugarcane was conducted to clarify their morphological characteristics. Specimens including previously reported species,Puccinia melanocephala, P. kuehnii andPuccinia sp.sensu Muta, 1987, were collected in Japan and the Philippines and borrowed from various herbaria worldwide. Morphological characteristics of these specimens were examined under light and scanning electron microscopes. Comparative morphological studies of the specimens showed that rust fungi infecting sugarcane could be classified into two species,Puccinia melanocephala andP. kuehnii. Puccinia sp.sensu Muta was morphologically identical withP. kuehnii. Results of this study corroborate previous phylogenetic analysis results of D1/D2 regions of LSU rDNA gene. Contribution No. 157, Laboratory of Plant Parasitic Mycology, Institute of Agriculture and Forestry, University of Tsukuba     

Developments in serological methods to detect and identify plant viruses

Plant Cell, Tissue and Organ Culture (PCTOC) -     

PCR-based detection of Mycoplasma species

In this study, we describe our newly-developed sensitive two-stage PCR procedure for the detection of 13 common mycoplasmal contaminants (M. arthritidis, M. bovis, M. fermentans, M. genitalium, M. hominis, M. hyorhinis, M. neurolyticum, M. orale, M. pirum, M. pneumoniae, M. pulmonis, M. salivarium, U. urealyticum). For primary amplification, the DNA regions encompassing the 16S and 23S rRNA genes of 13 species were targeted using general mycoplasma primers. The primary PCR products were then subjected to secondary nested PCR, using two different primer pair sets, designed via the multiple alignment of nucleotide sequences obtained from the 13 mycoplasmal species. The nested PCR, which generated DNA fragments of 165-353 bp, was found to be able to detect 1-2 copies of the target DNA, and evidenced no cross-reactivity with the genomic DNA of related microorganisms or of human cell lines, thereby confirming the sensitivity and specificity of the primers used. The identification of contaminated species was achieved via the performance of restriction fragment length polymorphism (RFLP) coupled with Sau3AI digestion. The results obtained in this study furnish evidence suggesting that the employed assay system constitutes an effective tool for the diagnosis of mycoplasmal contamination in cell culture systems.     

New strategy to detect single nucleotide polymorphisms

A great effort has been made to identify and map a large set of single nucleotide polymorphisms. The goal is to determine human DNA variants that contribute most significantly to population variation in each trait. Different algorithms and software packages, such as PolyBayes and PolyPhred, have been developed to address this problem. We present strategies to detect single nucleotide polymorphisms, using chromatogram analysis and consensi of multiple aligned sequences. The algorithms were tested using HIV datasets, and the results were compared with those produced by PolyBayes and PolyPhred using the same dataset. Our algorithms produced significantly better results than these two software packages.     

PCR-based positive hybridization to detect genomic diversity associated with bacterial secondary metabolism

A PCR-based positive hybridization (PPH) method was developed to explore toxic-specific genes in common between toxigenic strains of Anabaena circinalis, a cyanobacterium able to produce saxitoxin (STX). The PPH technique is based on the same principles of suppression subtractive hybridization (SSH), although with the former no driver DNA is required and two tester genomic DNAs are hybridized at high stringency. The aim was to obtain genes associated with cyanobacterial STX production. The genetic diversity within phylogenetically similar strains of A.circinalis was investigated by comparing the results of the standard SSH protocol to the PPH approach by DNA-microarray analysis. SSH allowed the recovery of DNA libraries that were mainly specific for each of the two STX-producing strains used. Several candidate sequences were found by PPH to be in common between both the STX-producing testers. The PPH technique performed using unsubtracted genomic libraries proved to be a powerful tool to identify DNA sequences possibly transferred laterally between two cyanobacterial strains that may be candidate(s) in STX biosynthesis. The approach presented in this study represents a novel and valid tool to study the genetic basis for secondary metabolite production in microorganisms.     

Phylogenetic and morphological re-evaluation of the Botryosphaeria species causing diseases of Mangifera indica

Species of Botryosphaeria are among the most serious pathogens that affect mango trees and fruit. Several species occur on mangoes, and these are identified mainly on the morphology of the anamorphs. Common taxa include Dothiorella dominicana, D. mangiferae (= Natrassia mangiferae), D. aromatica and an unidentified species, Dothiorella 'long'. The genus name Dothiorella, however, is acknowledged as a synonym of Diplodia. This study aimed to characterize and name the Botryosphaeria spp. associated with disease symptoms on mangoes. To achieve this isolates representing all four Dothiorella spp. mentioned above were compared with the anamorphs of known Botryosphaeria spp., based on conidial morphology and DNA sequence data. Two genomic regions were analyzed, namely the ITS rDNA and beta-tubulin regions. The morphological and molecular results confirmed that the fungi previously identified from mango as species of Dothiorella belong to Fusicoccum. Dothiorella dominicana isolates were identical to isolates of F. parvum (teleomorph = B. parva). A new epithet, namely F. mangiferum, is proposed for isolates previously treated as D. mangiferae or N. mangiferae. Isolates of D. aromatica were identified as F. aesculi (teleomorph = B. dothidea). A fourth Fusicoccum sp. also was identified as those isolates previously known as Dothiorella 'long'. A key is provided to distinguish these species based on anamorph morphology in culture. This study provides a basis for the identification of Botryosphaeria species from mango, which is important for disease control and to uphold quarantine regulations.     

PCR-based species identification of Agriotes larvae

Click beetle larvae within the genus Agriotes (Coleoptera: Elateridae), commonly known as wireworms, are abundant ground-dwelling herbivores which can inflict considerable damage to field crops. In Central Europe up to 20 species, which differ in their distribution, ecology and pest status, occur in arable land. However, the identification of these larvae based on morphological characters is difficult or impossible. This hampers progress towards controlling these pests. Here, we present a polymerase chain reaction (PCR)-based approach to identify, for the first time, 17 Agriotes species typically found in Central Europe. Diagnostic sequence information was generated and submitted to GenBank, allowing the identification of these species via DNA barcoding. Moreover, multiplex PCR assays were developed to identify the nine most abundant species rapidly within a single-step reaction: Agriotes brevis, A. litigiosus, A. obscurus, A. rufipalpis, A. sordidus, A. sputator, A. ustulatus, A. lineatus and A. proximus. The latter two species remain molecularly indistinguishable, questioning their species status. The multiplex PCR assays proved to be highly specific against non-agrioted elaterid beetles and other non-target soil invertebrates. By testing the molecular identification system with over 900 field-collected larvae, our protocol proved to be a reliable, cheap and quick method to routinely identify Central European Agriotes species.     

多基因遗传病基因研究的策略和方法

基因在决定个体表型方面起着决定性的作用。虽然单基因疾病的致病基因的克隆工作取得了显著的进展,但对于多基因疾病来说,仍然存在许多问题,同时也是巨大的挑战。本文综述了多基因疾病的遗传特点和多基因疾病易感基因识别、分离和克隆的一般步骤和存在的问题,介绍了人类基因组计划在此过程中的作用和单核苷酸多态性的应用前景,提出 了最有可能克隆出多基因疾病易感基因的策略和方法。     

PCR-based methods for identification of Enterococcus species

Two DNA-based techniques were used for species identification of enterococci.PvuII digestion of the genus-specific PCR product yielded four different restriction profiles among 20 enterococcal species; one of them was species-specific forE. faecium. In the second case, 32 reference strains belonging to 20 enterococcal species were divided to 12 groups by amplification of internal transcribed spacer of rRNA operon. Interspecies and some intraspecies profile variability was determined. Both methods gave similar results.     

Genes causing inherited cancer as beacons to identify the mechanisms of chemoresistance

Mechanisms of resistance to cancer chemotherapy are poorly understood. Molecular pathways involving genes associated with inherited cancer syndromes could represent mechanisms of chemoresistance. Microarray techniques can identify simultaneous alterations in the mRNA expression of multiple genes, but identification of the exact mechanism responsible for a particular phenotype, including resistance to a specific drug, remains problematic. Genes in which mutations cause inherited cancers play vital roles in apoptosis, growth arrest and/or DNA repair, and are inactivated by somatic mutations, deletions or hypermethylation in most cancer tissues. Similarities between carcinogenic injury and cell damage created by chemotherapeutics suggests that somatic inactivation of such genes is crucially important to drug sensitivity.     

PCR-based strategy for construction of multi-site-saturation mutagenic expression library

There is an increasing demand for efficient and effective methods to engineer protein variants for industrial applications, structural biology and drug development. We describe a PCR-based strategy that produces multi-site-saturation mutagenic expression library using a circular plasmid carrying the wild-type gene. This restriction digestion- and ligation-independent method involves three steps: 1) synthesis of the degenerate oligonucleotide primers, 2) incorporation of the mutations through PCR, 3) transformation into the expression host. Our strategy is demonstrated through successful construction of an E. coli K12 malic enzyme expression library that contains members with simultaneous mutations on amino acid residues G311, D345 and G397. This method is in principle compatible with any circular vector that can be propagated with a dam(+)E. coli host to generate protein variant library with multiple changes, including mutation, short sequence deletion and insertion, or any mix of them.