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Transcribed Spacer Regions (transcribed + spacer_regions)

Distribution by Scientific Domains
Life Sciences50%
Medical Sciences33%

Kinds of Transcribed Spacer Regions

  • internal transcribed spacer regions
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    Selected Abstracts

    Genetic diversity of the hyperparasite Sphaerellopsis filum on Melampsora willow rusts

    FOREST PATHOLOGY, Issue 5 2004
    M. Liesebach
    Summary The non-specific rust hyperparasite Sphaerellopsis filum occurs naturally on Melampsora rusts of many species of the genus Salix as well as on a large range of other rust genera worldwide. To study the genetic diversity of the hyperparasitic fungus 77 S. filum isolates collected from rusts on willow clones from plantations, clone collections and natural habitats of different sites were investigated using polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP) analysis of the rDNA internal transcribed spacer regions including 5.8S rDNA and sequence analysis. Additionally, strains from Melampsora poplar rusts (4) and strains of Puccinia abrupta from Parthenium hysterophorus (5) and of P. obscura from Bellis perennis (1) were used for comparisons. Results of genetic analysis demonstrated distinct variation within the S. filum isolates. Two main groups with more than 32% difference between their nucleotide sequences were distinguished, indicating two taxa within S. filum. Within the first main group three profiles (I, II, III) were detected. The differences between these profiles were about 12%. The variation within each profile was very low (less than 2%). The second main group comprised two profiles (IV, V), which differed in 12 to 16% of their nucleotide positions. The isolates of group IV possessed a higher variation (up to 5%) within the group than those of the first main group (I, II, III). Group V was only represented by a single isolate. Neither interrelations between the S. filum profiles and the Melampsora genotypes nor a spatial distribution could be detected. It is remarkable that the six strains of S. filum from Puccinia rusts belong to one subgroup. Résumé Sphaerellopsis filum est un hyperparasite non spécifique des rouilles qui se rencontre naturellement sur les Melampsora affectant le genre Salix ainsi que sur une large gamme d'autres genres de rouille dans le monde entier. Pour caractériser la diversité de ce champignon hyperparasite, 77 isolats de S. filum, récoltés à partir de lésions de rouille sur des clones de plantation, des collections de clones et dans des sites naturels, ont étéétudiés par analyse PCR-RFLP des régions ITS de l'ADNr, incluant le 5.8S rDNA, et par analyse de séquences. Des souches provenant de Melampsora des peupliers (4), de Puccinia abrupta sur Parthenium hysterophorus (5) et de P. obscura sur Bellis perennis (1) ont également été utilisées pour comparaison. L'analyse génétique démontre une variation entre isolats de S. filum. Deux groupes principaux, avec plus de 32% de différence dans leur séquence nucléotidique, se distinguent, indiquant l'existence de deux taxons au sein de S. filum. A l'intérieur du premier groupe, trois profils (I, II, III) sont mis en évidence, avec une différence d'environ 12% entre profils mais très peu de variation (moins de 2%) à l'intérieur d'un profil. Le deuxième groupe comprend deux profils (IV, V) qui différent de 12 à 16% pour leur séquence nucléotidique. Les isolats du groupe IV présentent une variation intra-groupe plus importante (jusqu'à 5%) que ceux des groupes I, II et III. Le groupe V n'est représenté que par un isolat. Aucune relation n'a pu être établié entre les profils de S. filum et les génotypes de Melampsora ou la distribution spatiale. Il est à noter que les six isolats de S. filum provenant de rouilles àPuccinia appartiennent à un seul sous-groupe. Zusammenfassung Der Hyperparasit Sphaerellopsis filum kommt natürlich auf Melampsora -Rostpilzen bei Salicaceae und auf zahlreichen anderen Rostgattungen weltweit vor. Um die genetische Vielfalt dieses hyperparasitischen Pilzes zu untersuchen, wurden 77 S. filum -Proben, die von Weidenrosten in Plantagen, Klonsammlungen und von verschiedenen natürlichen Standorten stammen, isoliert. Die 5.8S-ITS-Abschnitte der rDNA wurden mit Hilfe der PCR-RFLP untersucht und Sequenzen analysiert. Zum Vergleich wurden vier Isolate von Pappelrosten sowie fünf Isolate von Puccinia abrupta von Parthenium hysterophorus und ein Isolat von Puccinia obscura von Bellis perennis herangezogen. Die Ergebnisse der genetischen Untersuchungen zeigten eine deutliche Variation zwischen den S. filum -Isolaten. Zwei Gruppen mit über 32% Unterschied in der Nukleotid-Sequenz ließen sich unterscheiden. Dies deutet auf zwei taxonomische Einheiten von Sphaerellopsis hin. Die erste Gruppe ließ sich in drei Untergruppen (I, II, III) einteilen, deren 5.8S-ITS-Profile im Mittel 12% Unterschied aufwiesen. Die Variation innerhalb dieser drei Profile war sehr gering (,2%). Die zweite Gruppe umfasste zwei Profile (IV, V), die sich an 12 bis 16% Positionen ihrer Nukleotid-Abfolge unterschieden. Die Variation innerhalb von Profil IV war höher (bis 5%) als die der Untergruppen I - III, Profil V war nur durch ein Isolat vertreten. Eine Beziehung des S. filum -Genotyps zum Melampsora -Genotyp der Weide oder der Pappel ließ sich bei dem untersuchten Material nicht nachweisen, ebenso konnte keine geographische Differenzierung gefunden werden. Auffällig ist, dass alle sechs Puccinia -Isolate einer Untergruppe angehörten. [source]

    Occurrence of Toxic Hexadepsipeptides in Preharvest Maize Ear Rot Infected by Fusarium poae in Poland

    JOURNAL OF PHYTOPATHOLOGY, Issue 1 2007
    J. Che, kowski
    Abstract Twenty-seven preharvest maize ears affected by Fusarium poae rot (disease score 36,100%) were selected in 1998 and 1999 in Poland and examined for the occurrence of toxic hexadepsipeptides: beauvericin (BEA), enniatin A, enniatin B and enniatin B1. The identification of F. poae was confirmed by sequence analysis of variable internal transcribed spacer regions and compared with NCBI gene bank DNA sequences. Chemical analyses were performed by HPLC-MS. In 27 ears infected by F. poae were detected: BEA (trace to 46 ,g/g) in 18 samples, enniatin A (trace to 37 ,g/g) in nine samples, enniatin B (trace to 47 ,g/g) in 15 samples and enniatin B1 (trace to 25 ,g/g) in 12 samples. When 20 strains of F. poae isolated from these samples were cultured on rice, all produced BEA (1.9,75 ,g/g), three enniatin A (1.8,2 ,g/g), 12 enniatin B (1.1,5.1 ,g/g) and eight enniatin B1 (1.2,5.2 ,g/g). Occurrence and quantification of enniatin A, enniatin B and enniatin B1 and their co-occurrence with BEA in maize kernels is reported for the first time. [source]

    Survival of inoculated Saccharomyces cerevisiae strain on wine grapes during two vintages

    LETTERS IN APPLIED MICROBIOLOGY, Issue 3 2006
    F. Comitini
    Abstract Aims:, To investigate the influence of a specific ecological niche, the wine grape, on the survival and development of Saccharomyces cerevisiae. Methods and Results:, A strain with a rare phenotype was sprayed onto the grape surfaces and monitored through two vintages using a specific indicative medium and analysing the internal transcribed spacer regions in the 5·8S rDNA. During the ripening process, there was a progressive colonization of the surface of the undamaged and damaged grapes by epiphytic yeasts, up to the time of harvest. The damaged wine grapes showed a much greater epiphytic yeast population. However, the inoculated S. cerevisiae strain showed a scarce persistence on both undamaged and damaged wine grapes, and the damaged grapes did not appear to improve the grape surface colonization of this strain. Conclusions:, Results indicated that wine grape is not a favourable ecological niche for the development and colonization of S. cerevisiae species. Significance and Impact of the Study:, Results of this work are further evidence that S. cerevisiae is not specifically associated with natural environments such as damaged and undamaged wine grapes. [source]

    Identification of Candida fabianii as a cause of lethal septicaemia

    MYCOSES, Issue 4 2006
    Giuseppe Valenza
    Summary Infections caused by rare fungal species of low pathogenic potential become increasingly common in hospital settings. The identification of these species presents a major challenge for the clinical mycology laboratory. We describe a case of fatal septicaemia caused by Candida fabianii. The use of common biochemical approaches led to misidentification of the isolate as Candida utilis. Sequencing of the internal transcribed spacer regions (ITS1 and ITS2) allowed unequivocal species identification. [source]

    Identification, distribution and current taxonomy of Botryosphaeriaceae species associated with grapevine decline in New South Wales and South Australia

    AUSTRALIAN JOURNAL OF GRAPE AND WINE RESEARCH, Issue 1 2010
    W.M. PITT
    Abstract Background and Aims:, Botryosphaeriaceae species are recognised as important pathogens of grapevines both in Australia and overseas. The identity, prevalence and distribution of Botryosphaeriaceae species in vineyards throughout the major winegrowing regions of New South Wales (NSW) and South Australia (SA) was determined to provide a foundation for improved disease prevention and management. Methods and Results:, Field surveys from 91 vineyards across NSW and SA resulted in the collection of 2239 diseased wood samples and subsequent isolation of 1258 Botryosphaeriaceae isolates. Morphological identification along with phylogenetic analysis of ribosomal DNA internal transcribed spacer regions (ITS1-5.8S-ITS2) and partial sequences of the translation elongation factor 1-, gene (EF1-,) showed that eight Botryosphaeriaceae species from four phylogenetic lineages occur on grapevines in eastern Australia, including Diplodia seriata, Diplodia mutila, Lasiodiplodia theobromae, Neofusicoccum parvum, Neofusicoccum australe, Botryosphaeria dothidea, Dothiorella viticola and Dothiorella iberica. Conclusions:, The prevalence of individual species varied according to geography and climate. Species of Diplodia and Dothiorella, characterised by thick-walled, pigmented conidia were the most prevalent and were distributed widely throughout both NSW and SA. Species with hyaline conidia, such as Neofusicoccum and Fusicoccum, were isolated less frequently and displayed more limited geographic ranges, whilst only a single isolate of Lasiodiplodia was recovered, this being from the northern most region of NSW. Significance of the Study:, The identification of eight taxa within the Botryosphaeriaceae, and their distributions throughout south-eastern Australia was established and discussed in context with climate, reported optimum growth temperatures, and more recent taxonomic and nomenclatural revisions. We established a sound base for control strategies based on the prevailing species in Australian viticultural regions. [source]

    Diagnosis of common dermatophyte infections by a novel multiplex real-time polymerase chain reaction detection/identification scheme

    BRITISH JOURNAL OF DERMATOLOGY, Issue 4 2007
    M. Arabatzis
    Summary Background, In the absence of a functional dermatophyte-specific polymerase chain reaction (PCR), current diagnosis of dermatophytoses, which constitute the commonest communicable diseases worldwide, relies on microscopy and culture. This combination of techniques is time-consuming and notoriously low in sensitivity. Objectives, Recent dermatophyte gene sequence records were used to design a real-time PCR assay for detection and identification of dermatophytes in clinical specimens in less than 24 h. Patients and methods, Two assays based on amplification of ribosomal internal transcribed spacer regions and on the use of probes specific to relevant species and species-complexes were designed, optimised and clinically evaluated. One assay was for detecting the Trichophyton mentagrophytes species complex plus T. tonsurans and T. violaceum. The second assayed for the T. rubrum species complex, Microsporum canis and M. audouinii. Results, The analytical sensitivity of both assays was 0·1 pg DNA per reaction, corresponding to 2·5,3·3 genomes per sample. The protocol was clinically evaluated over 6 months by testing 92 skin, nail and hair specimens from 67 patients with suspected dermatophytosis. Real-time PCR detected and correctly identified the causal agent in specimens from which T. rubrum, T. interdigitale, M. audouinii or T. violaceum grew in culture, and also identified a dermatophyte species in an additional seven specimens that were negative in microscopy and culture. Conclusions, This highly sensitive assay also proved to have high positive and negative predictive values (95·7% and 100%), facilitating the accurate, rapid diagnosis conducive to targeted rather than empirical therapy for dermatophytoses. [source]