scholarly journals Identification of Legionella Species by Random Amplified Polymorphic DNA Profiles

1998 ◽  
Vol 36 (11) ◽  
pp. 3193-3197 ◽  
Author(s):  
François Lo Presti ◽  
Serge Riffard ◽  
François Vandenesch ◽  
Jerome Etienne
Keyword(s):  
New Species ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Species Level ◽  
Clinical Isolates ◽  
Reproducible Technique ◽  
Legionella Species ◽  
Species Specific ◽  
Dna Profiles ◽  
Type Strains

Random amplified polymorphic DNA (RAPD) was used for the identification of Legionella species. Primer SK2 (5′-CGGCGGCGGCGG-3′) and standardized RAPD conditions gave the technique a reproducibility of 93 to 100%, depending on the species tested. Species-specific patterns corresponding to the 42Legionella species were consequently defined by this method; the patterns were dependent on the recognition of a core of common bands for each species. This specificity was demonstrated by testing 65 type strains and 265 environmental and clinical isolates. No serogroup-specific profiles were obtained. A number of unidentifiedLegionella isolates potentially corresponding to new species were clustered in four groups. RAPD analysis appears to be a rapid and reproducible technique for identification ofLegionella isolates to the species level without further restriction or hybridization.

Morphological and systematic study of the tribe Australiosomatini (Diplopoda:Polydesmida:Paradoxosomatidea:Paradoxosomatidae) and a revision of the genus Australiosoma Brölemann

2006 ◽  
Vol 20 (5) ◽  
pp. 527 ◽  
Author(s):  
Melissah Rowe ◽  
Petra Sierwald
Keyword(s):  
New Species ◽  
Species Level ◽  
Data Matrix ◽  
Adult Males ◽  
Ecological Studies ◽  
Additional Species ◽  
The Family ◽  
Two New Species ◽  
Three New Species ◽  
Species Specific

The collection of several paradoxosomatid species in the context of ecological studies prompted an investigation into the morphology and species-level characteristics of Australian millipedes in the tribe Australiosomatini Brölemann, 1916 (Polydesmida : Paradoxosomatidae). Three new species are described: Akamptogonus caragoon, sp. nov., Australiosoma fulbrighti, sp. nov. and Australiosoma combei, sp. nov. Notes or re-descriptions are provided for nine additional species belonging to the tribe. Scanning electron microscopy was utilised to examine details of the antennal sensory fields, the fifth sternite lamella and associated pores. The presence of the fifth sternite lamella in adult males is considered a synapomorphy for the family Paradoxosomatidae, whereas the prominent tubercle on the first femur in males (adenostyle) represents a synapomorphy of the subfamily Australiosomatinae. With the description of two new species in the genus Australiosoma Brölemann, 1913 a revision of the genus was undertaken with the purpose of constructing a species-level phylogeny. The most commonly described and utilised species-specific characteristics were scored in a data matrix and analysed using PAUP. The analysis resulted in a single, fully resolved tree of the following structure: Hoplatria clavigera ((A. clavigerum, A. inusitatum) (((A. rainbowi, A. nodulosum) A. michelseni) (A. laminatum (A. combei, A. fulbrighti))).

scholarly journals Random amplified polymorphic DNA (RAPD) analysis of Ornithobacterium rhinotracheale strains isolated from chickens in Turkey

2012 ◽  
Vol 50 (No. 12) ◽  
pp. 526-530 ◽  
Author(s):  
G. Ozbey ◽  
Ertas HB ◽  
A. Muz
Keyword(s):  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Random Primer ◽  
Serotype A ◽  
Dna Assay ◽  
Rapd Profile ◽  
Rapd Pattern ◽  
Serotype B ◽  
Dna Profiles ◽  
Ornithobacterium Rhinotracheale

Six field strains of Ornithobacterium rhinotracheale isolated from chickens in Elazig province located in the East of Turkey were typed by serotyping and random amplified polymorphic DNA assay using a random primer (OPG-11). Using the AGP test used for serotyping, serotype A was found to be the predominant serotype, only one strain was serotyped as serotype B. By RAPD assay, the tested ORT strains were found to have different RAPD profiles. In addition, the RAPD assay showed almost similar DNA profiles among the tested strains of the serotypes A, B, D and E. The strain of serotype C did give a different RAPD profile. Within strains of the same serotype (A), different profiles were found but the strain of serotype (B) had an identical profile as strains of serotype A. This study suggests that more genotypes of ORT strains are present within the same serotype and thus that no relationship exists between the RAPD pattern of ORT and their serotype.

scholarly journals Differentiation Among Rodentibacter Species Based on 16S–23S rRNA Internal Transcribed Spacer Analysis

2020 ◽  
Vol 70 (6) ◽  
pp. 487-491
Author(s):  
Laurentiu Benga ◽  
Peter M Benten ◽  
Eva Engelhardt ◽  
Karl Köhrer ◽  
Barbara Hueber ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Reliable Method ◽  
Species Level ◽  
23S Rrna ◽  
Its Sequence ◽  
Specific Identification ◽  
Laboratory Rodents ◽  
Sequence Variations ◽  
Species Specific ◽  
Type Strains

The internal transcribed spacer (ITS) regions of Rodentibacter pneumotropicus, R. heylii, R. rarus, R. ratti, and R. heidelbergensis and of a Rodentibacter- related β-hemolytic Pasteurellaceae taxon isolated from laboratory rodents were studied for their feasibility to discriminate among these species. The 6 species analyzed showed species-specific ITS patterns that were shared by the type strains and clinical isolates and that allowed their identification. Nevertheless, differentiating between the ITS band patterns of R. pneumotropicus and R. ratti is visually challenging. In all species tested, sequence analysis of the ITS fragments revealed a larger ITSile+ala, which contained the genes for tRNAIle(GAU) and tRNA Ala(UGC), and a smaller ITSglu with the tRNAGlu(UUC) gene. The ITS sequences varied among the 6 species evaluated, displaying identity levels ranging from 62% to 86% for ITSile+ala and 68% to 90% for ITSglu. Overall, ITS amplification proved to be a reliable method to differentiate among these important Pasteurellaceae species of laboratory rodents. Moreover, the ITS sequence variations recorded here might facilitate the design of probes for specific identification of these species. The ability to diagnose these organisms to the species level could increase our understanding of their clinical significance.

scholarly journals CDC Group IV c-2: a New RalstoniaSpecies Close to Ralstonia eutropha

1999 ◽  
Vol 37 (6) ◽  
pp. 1777-1781 ◽  
Author(s):  
Didier Moissenet ◽  
Christophe P. Goujon ◽  
Antoine Garbarg-Chenon ◽  
Hoang Vu-Thien
Keyword(s):  
16S Rdna ◽  
Biochemical Characterization ◽  
Ralstonia Eutropha ◽  
Rapd Analysis ◽  
Group Iv ◽  
Clinical Isolates ◽  
Rdna Sequences ◽  
Rdna Sequencing ◽  
16S Rdna Sequences ◽  
Type Strains

CDC group IV c-2, an environmental gram-negative bacillus recently proposed for inclusion in the genus Ralstonia, has been isolated in several human infections. Biochemical characterization and 16S ribosomal DNA (rDNA) sequencing with phylogenetic analysis were used to characterize eight clinical isolates and four type strains. Other typing tools, such as pulsed-field gel electrophoresis (PFGE) and randomly amplified polymorphic DNA (RAPD) analysis, were also used. PFGE typing of clinical isolates was unsuccessful because the DNA was degraded, and RAPD analysis was poorly discriminatory. In contrast, the type strains were clearly distinguished with both PFGE and RAPD analysis. All of the 16S rDNA sequences were identical. Comparison of the 16S rDNA sequences to the GenBank sequences showed that they were consistent with CDC group IV c-2 belonging to the genusRalstonia. The closest matches were obtained withRalstonia eutropha. However, four differences in 32 biochemical tests separated R. eutropha from CDC group IV c-2, which suggests that CDC group IV c-2 is a new species of the genusRalstonia.

Molecular Characterization of Five Medicinally Important Species of Typhonium (Araceae) through Random Amplified Polymorphic DNA (RAPD)

2005 ◽  
Vol 60 (7-8) ◽  
pp. 600-604 ◽  
Author(s):  
Laxmikanta Acharya ◽  
Arup Kumar Mukherjee ◽  
Pratap Chandra Panda ◽  
Premananda Das
Keyword(s):  
Molecular Characterization ◽  
Genetic Similarity ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Similarity Index ◽  
The Other ◽  
Important Species ◽  
Species Specific ◽  
Maximum Similarity

The interrelationship of five medicinally important species of Typhonium (Araceae) including T. venosum, which was previously placed under the genus Sauromatum, was inferred by analysis of random amplified polymorphic DNA (RAPD). DNA from pooled leaf samples was isolated and RAPD analysis was performed using 20 decamer oligonucleotide primers. Out of a total of 245 bands amplified, 12 were found to be monomorphic while 233 bands were polymorphic including 86 species-specific bands. The genetic similarities were analyzed from the dendrogram constructed by the pooled RAPD data using a similarity index. The dendrogram showed two distinct clades, one containing T. roxburghii, T. trilobatum and T. venosum and the other containing the remainder two species, i.e. T. diversifolium and T. flagelliforme. Both the clusters shared a common node approx. at 23.7% level of similarity. The maximum similarity of 31.2% was observed between T. venosum and T. trilobatum. In view of its close genetic similarity with other members of Typhonium, transfer of Sauromatum venosum to the genus Typhonium and merger of the two genera was supported.

Species-diagnostic and species-specific DNA sequences evenly distributed throughout pine and spruce chromosomes

Genome ◽  
2010 ◽  
Vol 53 (10) ◽  
pp. 769-777 ◽  
Author(s):  
Melanie Mehes-Smith ◽  
Paul Michael ◽  
Kabwe Nkongolo
Keyword(s):  
Dna Sequences ◽  
Random Amplified Polymorphic Dna ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Pinus Monticola ◽  
The Family ◽  
Species Specific ◽  
Rapd And Issr ◽  
Specific Sequences

Genome organization in the family Pinaceae is complex and largely unknown. The main purpose of the present study was to develop and physically map species-diagnostic and species-specific molecular markers in pine and spruce. Five RAPD (random amplified polymorphic DNA) and one ISSR (inter-simple sequence repeat) species-diagnostic or species-specific markers for Picea mariana , Picea rubens , Pinus strobus , or Pinus monticola were identified, cloned, and sequenced. In situ hybridization of these sequences to spruce and pine chromosomes showed the sequences to be present in high copy number and evenly distributed throughout the genome. The analysis of centromeric and telomeric regions revealed the absence of significant clustering of species-diagnostic and species-specific sequences in all the chromosomes of the four species studied. Both RAPD and ISSR markers showed similar patterns.

scholarly journals Strain Typing of Trichosporon asahii Clinical Isolates by Random Amplification of Polymorphic DNA (RAPD) Analysis

2021 ◽  
Author(s):  
Thayanidhi Premamalini ◽  
Vijayaraman Rajyoganandh ◽  
Ramaraj Vijayakumar ◽  
Hemanth Veena ◽  
Anupma Jyoti Kindo ◽  
...  
Keyword(s):  
Genetic Relatedness ◽  
Rapd Analysis ◽  
Clinical Isolates ◽  
Clinical Samples ◽  
Strain Typing ◽  
Trichosporon Asahii ◽  
Pcr Fingerprinting ◽  
Specific Pcr ◽  
Rapd Primer ◽  
Random Amplification

Abstract Objective The aim of this study was to identify and isolate Trichosporon asahii (T. asahii) from clinical samples and to assess the genetic relatedness of the most frequently isolated strains of T. asahii using random amplification of polymorphic DNA (RAPD) primers GAC-1 and M13. Methods All the clinical samples that grew Trichosporon species, identified and confirmed by polymerase chain reaction (PCR) using Trichosporon genus-specific primers, were considered for the study. Confirmation of the species T. asahii was carried out by T. asahii-specific PCR. Fingerprinting of the most frequently isolated T. asahii isolates was carried out by RAPD using random primers GAC-1 and M13. Results Among the 72 clinical isolates of Trichosporon sp. confirmed by Trichosporon-specific PCR, 65 were found to be T. asahii as identified by T. asahii-specific PCR. Fingerprinting of the 65 isolates confirmed as T. asahii using GAC-1 RAPD primer yielded 11 different patterns, whereas that of M13 primer produced only 5 patterns. The pattern I was found to be the most predominant type (29.2%) followed by pattern III (16.9%) by GAC-1 primer. Conclusions This study being the first of its kind in India on strain typing of T. asahii isolates by adopting RAPD analysis throws light on genetic diversity among the T. asahii isolates from clinical samples. Fingerprinting by RAPD primer GAC-1 identified more heterogeneity among the T. asahii isolates than M13.

scholarly journals SNP and SCAR Markers for Specific Discrimination of Antler-Shaped Ganoderma lucidum

2019 ◽  
Vol 7 (1) ◽  
pp. 12 ◽  
Author(s):  
O-Chul Kwon ◽  
Chang-Soo Lee ◽  
Young-Jin Park
Keyword(s):  
Ganoderma Lucidum ◽  
Gene Sequence ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Morphological Characteristics ◽  
Pcr Analysis ◽  
Scar Markers ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Specific Fragment

In this study we identified single nucleotide polymorphism (SNP) and sequence characteristic amplification region (SCAR) markers for specific identification of antler-shaped Ganoderma lucidum strains. When the partial mitochondrial SSU rDNA gene sequence of various antler- and kidney-shaped G. lucidum strains were analyzed and aligned, an SNP was found only in the antler-shaped G. lucidum strain at position 456 bp. In addition, this SNP of antler-shaped strains was digested by HinfI restriction enzyme. We further analyzed the polymorphism of various G. lucidum strains by random amplified polymorphic DNA (RAPD) analysis. In RAPD analysis, we isolated and sequenced a fragment, specific for antler-shaped G. lucidum strains. Based on this specific fragment sequence, two sets of specific primer pairs for antler-shaped G. lucidum strains were designed. PCR analysis revealed that two specific bands were observed only from antler-shaped strains. These two molecular markers will be helpful for identification of morphological characteristics of G. lucidum.

Corrigendum to: Lamprothamnium in Australia (Characeae, Charophyceae)

2013 ◽  
Vol 26 (6) ◽  
pp. 475
Author(s):  
Michelle T. Casanova
Keyword(s):  
New Species ◽  
Species Level ◽  
Type Material ◽  
Review Of The Literature ◽  
Comprehensive Review ◽  
The Past

Charophytes in the genus Lamprothamnium exhibit a large amount of diversity, particularly in the examples from Australia, although little of that variation has been recognised at species level in the past. The Australian members of the genus are revised here on the basis of extensive new collections, examination of specimens in herbaria and comprehensive review of the literature and available type material. The existing species Lamprothamnium macropogon (A.Braun) Ophel, L. inflatum (Fil. & G.O.Allen ex Fil.) A.García & Karol and L. heraldii A.García & Casanova are retained, eight new species are described (L. australicum Casanova, L. beilbyae Casanova, L. capitatum Casanova, L. compactum Casanova, L. coorongense Casanova, L. diminutum Casanova, L. macroanthum Casanova and L. stipitatum Casanova) and two taxa variously treated at infraspecific rank in Lychnothamnus are transferred to Lamprothamnium at species rank (L. cockajemmyense Casanova, L. tasmanicum (A.Braun) Casanova). Neither L. papulosum (Wallr.) J.Groves nor L. succinctum (A.Braun) R.D.Wood are confirmed for Australia after examination of the type material of these species. Species are distinguished by the arrangement of the gametangia, morphology of the fertile whorls and characteristics of the oospores. Four of these species are dioecious and nine are monoecious, which supports published conjectures concerning the biogeography of charophyte species (Proctor (1980): J. Phycol. 16, 218–233, doi:10.1111/j.1529-8817.1980.tb03023.x).

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