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 New PCR Primer Pairs Specific for Cryptococcus neoformans Serotype A or B Prepared on the Basis of Random Amplified Polymorphic DNA Fingerprint Pattern Analyses

1999 ◽  
Vol 37 (2) ◽  
pp. 315-320 ◽  
Author(s):  
Francisco Hideo Aoki ◽  
Tamae Imai ◽  
Reiko Tanaka ◽  
Yuzuru Mikami ◽  
Hideaki Taguchi ◽  
...  
Keyword(s):  
Cryptococcus Neoformans ◽  
Dna Sequences ◽  
Random Amplified Polymorphic Dna ◽  
Pcr Primers ◽  
Dna Fingerprint ◽  
Serotype A ◽  
Specific Pcr ◽  
Fingerprint Pattern ◽  
Serotype B ◽  
Pcr Primer

Thirty-three strains of Cryptococcus neoformans were isolated from clinical specimens, including specimens from AIDS patients in Brazil, and were classified into two serotypes; we detected 31 and 2 strains of serotypes A and B, respectively. Random amplified polymorphic DNA (RAPD) fingerprint pattern analyses of these strains of serotypes A and B showed that the patterns were similar for strains of each serotype when three 10-mer primers were used as the RAPD primers. Comparative studies of the fingerprint patterns of the study isolates with those of the reference strains also showed that the RAPD patterns for strains of each serotype were related and that most of the fingerprint bands existed commonly for all strains of each serotype tested. The common RAPD bands (an approximately 700-bp band for serotype A and an approximately 450-bp band for serotype B) were extracted and the DNA sequences were determined. Using this information, we prepared two and one PCR primer pairs which were expected to be specific for C. neoformans serotypes A and B, respectively. Use of each PCR primer combination thus prepared for serotype A or B was 100% successful in identifying the respectiveC. neoformans serotypes, including the 33 clinical isolates tested in the present study. Among these combinations, one for serotype A was found to amplify DNA from C. neoformans serotype B as well as serotype A. Serotype B-specific PCR primer pairs amplified DNA from not only serotype B strains but also from serotype C strains. The usefulness of other serotype-specific PCR primers for clinical C. neoformans isolates is discussed.

scholarly journals Molecular Epidemiological Study ofHaemophilus influenzae Serotype b Strains Obtained from Children with Meningitis in Japan

1999 ◽  
Vol 37 (8) ◽  
pp. 2548-2552 ◽  
Author(s):  
Toshihiro Mitsuda ◽  
Haruo Kuroki ◽  
Nobuyasu Ishikawa ◽  
Tomoyuki Imagawa ◽  
Schuichi Ito ◽  
...  
Keyword(s):  
Epidemiological Study ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Rflp Analysis ◽  
Vaccine Failure ◽  
Long Pcr ◽  
Pcr Ribotyping ◽  
Dna Restriction ◽  
Ofhaemophilus Influenzae ◽  
Serotype B

We report an epidemiological study of 30 Haemophilus influenzae serotype b (Hib) strains derived from the cerebrospinal fluid of children with meningitis. The Hib strains were biotyped, tested for β-lactamase production, and genotyped by long PCR-ribotyping, random amplified polymorphic DNA (RAPD) analysis, and genomic DNA restriction fragment length polymorphism (RFLP) analysis by pulsed-field gel electrophoresis (PFGE). The phenotypic study characterized 22 of the strains (73%) as biotype I. A genotypic study using long PCR-ribotyping withHaeIII restriction digestion showed no polymorphisms among these 30 Hib strains, but RAPD analysis with two sets of primers demonstrated two distinctive subtypes: one typical of the strains of biotype group II and the second characteristic of the strains of biotype groups I and IV. Each RAPD group was subtyped into several genotypic groups by PFGE-RFLP with SmaI digestion. The genotyping of clinically isolated Hib strains may help to elucidate transmission routes in community infections, endemicity, and the reasons for vaccine failure.

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.

scholarly journals The RAPD analysis of several cultivars of grapevine (Vitis viniferaL.) and their clones

2011 ◽  
Vol 31 (No. 4) ◽  
pp. 136-139 ◽  
Author(s):  
H. Vlastníková ◽  
K. Moravcová ◽  
M. Pidra
Keyword(s):  
Rapd Markers ◽  
Rapd Analysis ◽  
Pinot Noir ◽  
The Other ◽  
Banding Patterns ◽  
Rapd Profile ◽  
Other Hand ◽  
Rapd Pattern

Nine identification RAPD markers (Moravcová et al. 2003) were used to distinguish 24 clones and grapevine cultivars. No polymorphism was detected among all the tested clones of Chardonnay, Pinot gris and Zweigeltrebe from Polešovice. Pinot noir, Pinot gris, Pinot blanc and Pinot Meunier were indistinguishable within clones, they also showed the identical RAPD profile within cultivars (except discussed sample No. 26). On the other hand, Auxerrois as a relative to cultivars of Pinot group showed unique patterns and may be classified as a different cultivar. Some irregularities within the cultivars of Pinot family from Oblekovice were also found, several of them gave different results from those expected: Pinot blanc sample 26 has the RAPD profile typical of Chardonnay. A new abnormal RAPD pattern as a marker of typical Chardonnay and Pinot profiles was observed in two cases. While RAPD banding patterns could not distinguish between the known clones, they were useful for distinguishing between phenotypically similar cultivars and for assessing the origins of cultivars thought to have originated as sports.    

scholarly journals Random amplified polymorphic DNA (RAPD) analysis of Pasteurella multocida and Manheimia haemolytica strains isolated from cattle, sheep and goats

2012 ◽  
Vol 49 (No. 3) ◽  
pp. 65-69 ◽  
Author(s):  
G. Ozbey ◽  
A. Kilic ◽  
H. B Ertas ◽  
A. Muz
Keyword(s):  
Genetic Heterogeneity ◽  
Pasteurella Multocida ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Mannheimia Haemolytica ◽  
Random Primer ◽  
Sheep And Goats ◽  
Distinct Band ◽  
Cattle And Sheep

n this study, 30, 15 and 1 strains of <i>Pasteurella multocida</i> and 9, 8 and 6 strains of <i>Mannheimia haemolytica</i> from cattle, sheep and goats isolated in Elazig province located in the East of Turkey, respectively were typed by random amplified polymorphic DNA (RAPD) assay using a random primer (OPA-11). By RAPD assay, two and three distinct band profiles were obtained in the examination of <i>P. multocida</i> isolates from cattle and sheep, respectively. However, <i>M. haemolytica</i> isolates from cattle, sheep and goats showed only one profile and these strains were not discriminated by RAPD. This study showed that little genetic heterogeneity exists among <i>P. multocida</i> and <i>M. haemolytica</i> isolates from lungs of cattle, sheep and goats.

scholarly journals Pulsed-Field Gel Electrophoresis Is More Efficient than Ribotyping and Random Amplified Polymorphic DNA Analysis in Discrimination of Pasteurella haemolytica Strains

1999 ◽  
Vol 37 (2) ◽  
pp. 380-385 ◽  
Author(s):  
Angeli Kodjo ◽  
Laurence Villard ◽  
Chantal Bizet ◽  
Jean-Louis Martel ◽  
Richard Sanchis ◽  
...  
Keyword(s):  
Gel Electrophoresis ◽  
Dna Analysis ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Geographic Origin ◽  
Pulsed Field Gel Electrophoresis ◽  
Pasteurella Haemolytica ◽  
Pulsed Field ◽  
Rapd Pattern ◽  
Almost All

One hundred thirty-three strains of Pasteurella haemolytica of both biotypes (90 and 43 strains of biotypes A and T, respectively) and almost all the serotypes were subjected to ribotyping, random amplified polymorphic DNA (RAPD) analysis, and pulsed-field gel electrophoresis (PFGE) analysis for epidemiological purposes. A total of 15 patterns recorded as ribotypes HA to HO were found for the P. haemolytica biotype A strains, with ribotypes HA, HC, and HD being encountered most often (66 strains [74%]); and 20 ribotypes, designated HA′ to HT′, that were clearly distinct from those observed for biotype A strains were observed for strains of biotype T. RAPD analysis generated a total of 44 (designated Rp1 to Rp44) and 15 (designated Rp1′ to Rp 15′) unique RAPD patterns for biogroup A and biogroup T, respectively. Analysis of the data indicated that a given combined ribotype-RAPD pattern could be observed for biotype A strains of different serotypes, whatever the zoological or geographic origin, whereas this was not the case for biotype T strains. PFGE appeared to be more efficient in strain discrimination since selected strains from various zoological or geographical origins harboring the same ribotype-RAPD group were further separated into unique entities.

scholarly journals Genetic Characterization by RAPD Analysis of Isolates of Fusarium oxysporum f. sp. erythroxyli Associated with an Emerging Epidemic in Peru

1997 ◽  
Vol 87 (12) ◽  
pp. 1220-1225 ◽  
Author(s):  
Amy J. Nelson ◽  
Karol S. Elias ◽  
E. Arévalo G. ◽  
Lee C. Darlington ◽  
Bryan A. Bailey
Keyword(s):  
Fusarium Oxysporum ◽  
Dna Fingerprinting ◽  
Genetic Characterization ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Dna Fingerprint ◽  
Pathogenicity Test ◽  
Vascular Wilt ◽  
Genetic Complexity ◽  
Rapd Pattern

An epidemic of vascular wilt caused by Fusarium oxysporum f. sp. erythroxyli is currently occurring on Erythroxylum coca var. coca in the coca-growing regions of the Huallaga Valley in Peru. Random amplified polymorphic DNA (RAPD) analysis of isolates of the pathogen was undertaken to elucidate its genetic complexity, as well as to identify a specific DNA fingerprint for the pathogen. Two hundred isolates of Fusarium were collected from 10 coca-growing regions in Peru. Of these, 187 were confirmed to be F. oxysporum, and 143 of the F. oxysporum were shown to be pathogens of coca by a root-dip pathogenicity test. The pathogens could be grouped into two subpopulations based on RAPD analysis, and no polymorphism in RAPD pattern was observed among isolates of either subpopulation. Both subpopulations were present in the central Huallaga Valley, where earliest reports of the epidemic occurred. RAPD analysis could easily distinguish the isolates of F. oxysporum f. sp. erythroxyli from the nonpathogenic isolates of F. oxysporum from E. coca var. coca, indicating its utility in DNA fingerprinting.

Comparative assessment of genetic diversity among twenty varieties of Brassica juncea [L.] Czern & Coss using RAPD and ISSR markers

2012 ◽  
Vol 2 (4) ◽  
pp. 166-176
Author(s):  
Javed Ahmad ◽  
Salim Khan ◽  
Gohar Taj Khan
Keyword(s):  
Genetic Diversity ◽  
Brassica Juncea ◽  
Genetic Similarity ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Issr Markers ◽  
Rapd Profile ◽  
Inter Simple Sequence Repeats ◽  
Rapd And Issr ◽  
Simple Sequence

PCR based molecular markers such as RAPD (random amplified polymorphic DNA) and ISSR (inter simple sequence repeats) were employed for the evaluation of genetic diversity among twenty varieties of Brassica juncea. Mean polymorphism information content (PIC) value was greater for RAPD (0.4195) as compared to ISSR (0.2602). In RAPD analysis, 98.9% loci were polymorphic whereas in ISSR, 94.8 % were polymorphic. The number of loci in RAPD profile ranged from 7 to 10 with an average of 9.3 per primer whereas in ISSR, these were from 3 to 12 with an average of 6.8 loci per primer. RAPD based genetic similarity ranged from 0.224 to 0.842 whereas ISSR derived genetic similarity 0.467 to 0.880. The mental test between two Jaccard’s similarity matrices gave r = 0.89, showing good fit correlation in between ISSR‐ and RAPD‐based similarities. The results obtained from the consensus tree constructed from RAPD+ISSR marker more likely support the distribution of the twenty genotypes of B. juncea based on ISSR analysis. The twenty varieties were clustered into three main clusters 1, 2, and 3 respectively. In combined dendrogram study, each cluster has 13, 3, and 4 varieties.

Molecular Characterization ofStreptococcus PyogenesIsolates to investigate an outbreak of Puerperal Sepsis

2005 ◽  
Vol 26 (5) ◽  
pp. 455-461 ◽  
Author(s):  
Josette Raymond ◽  
Laurent Schlegel ◽  
Fabien Garnier ◽  
Anne Bouvet
Keyword(s):  
Molecular Characterization ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Index Patient ◽  
Restriction Pattern ◽  
Microbiological Characteristics ◽  
Rapd Pattern ◽  
Close Relationship ◽  
Different Strains ◽  
Predominant Strain

AbstractObjective:To describe microbiological characteristics and epidemiologic features of an outbreak of postpartum endometritis.Methods:Various markers were investigated in five patients and three throat carriage isolates ofStreptococcus pyogenesobtained during an outbreak of endometritis occurring in a 13-week period. Molecular characterization included biotyping, T-serotyping,emmgene sequence and restriction, pulsed-field gel electrophoresis (PFGE), and random amplified polymorphic DNA (RAPD) analysis.Results:Biotype, T-serotype, and genotypic data (emmanalysis, PFGE, and RAPD analysis) revealed a close relationship among the isolates from three patients, suggesting that cross-contamination had occurred. These isolates were biotype 1, T type 28, andemmtype 28. The isolates from one patient and one carrier differed from those of the index patient by minor variations of theemmamplicon restriction pattern, PFGE pattern, or RAPD pattern. The remaining isolates were phenotypically and genetically different.Conclusion:Identification of different isolates demonstrated that different strains may circulate simultaneously during a true outbreak and that the predominant strain might persist for several months.

EVALUATION OF PTYCHOBOTHRIDEAN CESTODES USING RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD) MARKERS FROM FRESH WATER FISHES IN GODAVARI BASIN (M.S.) INDIA

2017 ◽  
Vol 23 (2) ◽  
Author(s):  
SUNITA BORDE ◽  
ASAWARI FARTADE ◽  
AMOL THOSAR ◽  
RAHUL KHAWAL
Keyword(s):  
Fresh Water ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Band Pattern ◽  
Genomic Variation ◽  
Polymorphic Band ◽  
Rapd Profile ◽  
Band Size ◽  
Pcr Product ◽  
The Common

Ptychobothridean genera like Senga and Circumoncobothrium are the common parasites of fresh water fishes. The genotypic study of these parasites was taken by RAPD. The RAPD profile of these two parasites were not similar to each other as depicted by the band pattern in picture. These results suggest the presence of inter-specific polymorphism among cestode parasites of two different genera for RAPD analysis. The present study demonstrated that genetic differentiation of cestode parasites could be accomplished on the basis of genomic variation with polymorphic band pattern using RAPD. All the detected bands (PCR product) were polymorphic and band size ranged from 500-5000 bp in length. The RAPD of profiles using GBO-31, GBO-32, GBO-33, GBO-34, GBO-35 and GBO-36. Primers were able to characterize inter-specific polymorphism among the two genus ( Senga and Circumoncobothrium ). Genetic analysis suggests that Senga and Circumoncobothrium show genetic diversity with respect to RAPD patterns using all the six primers used for the present study. The genetic distance between the analyzed genuses ranged from 0.14 to 0.80. The differentiation of the two parasites on the basis of genetic markers could greatly facilitate study on the biology of these parasites.

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