Echinococcus granulosus from Mexican pigs is the same strain as that in Polish pigs

AbstractSamples of Echinococcus granulosus from seven pigs from Mexico were compared with isolates of the parasite from pigs in Poland and representative strains and species of Echinococcus. Isolates from pigs in Mexico were found to be genetically identical to E. granulosus from Polish pigs and distinct from other major genotypes by sequencing part of the mitochondrial cytochrome c oxidase I (COI) mtDNA locus, restriction fragment length polymorphism (RFLP) of the polymerase chain reaction (PCR) amplified rDNA internal transcribed spacer (ITS) 1 using five different enzymes, and random amplified polymorphic DNA (RAPD) analysis. These results were complemented by data on hook morphology and together strengthen the view that Echinococcus maintained in a cycle involving pigs and dogs is a distinct strain that is conserved genetically in different geographical areas. The present study supports the close relationship of the cervid, camel and pig strains and raises the question of their taxonomic status.

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Comparison of repetitive-sequence-based polymerase chain reaction with random amplified polymorphic DNA analysis for rapid genotyping of nontuberculosis mycobacteria

Canadian Journal of Microbiology ◽

10.1139/w2012-068 ◽

2012 ◽

Vol 58 (8) ◽

pp. 953-964 ◽

Cited By ~ 6

Author(s):

Sara Christianson ◽

Joyce Wolfe ◽

Hafid Soualhine ◽

Meenu K. Sharma

Keyword(s):

Repetitive Sequence ◽

Dna Analysis ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Gene Sequencing ◽

Variable Number ◽

Outbreak Investigations ◽

Hsp65 Gene ◽

Polymerase Chain ◽

Clinically Significant

Nontuberculosis mycobacteria (NTM) are an important cause of human disease and infections. Though less notorious than tuberculosis, these infections are clinically significant and have been associated with outbreaks in various settings. To accommodate outbreak investigations for the numerous species of NTM, we evaluated a DiversiLab repetitive-sequence-based PCR (rep-PCR) kit for genotyping of mycobacteria. This kit was used to genotype both rapidly and slowly growing mycobacteria and was compared with other PCR-based genotyping methods, including random amplified polymorphic DNA (RAPD) analysis, hsp65 gene sequencing, and mycobacterial interspersed repetitive unit – variable number of tandem repeat (MIRU–VNTR) analysis. Compared with RAPD analysis, rep-PCR achieved better reproducibility in testing. When compared with hsp65 gene sequencing and MIRU–VNTR for Mycobacterium avium , rep-PCR provided results that agreed with these less discriminatory genotyping methods but provided a higher level of discrimination for situations such as outbreak investigations. We also evaluated the kit for its ability to identify closely related rapidly growing NTM. While rep-PCR was informative in some cases, a much larger library of isolates would be necessary to truly evaluate it as an identification tool. Overall, rep-PCR was able to provide improved reproducibility over RAPD and a discriminatory genotyping method for the isolates evaluated in this study.

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Molecular systematics and phylogeography of the genus Echinops (Compositae, Cardueae–Echinopsinae): focus on the Iranian centre of diversification

Phytotaxa ◽

10.11646/phytotaxa.297.2.1 ◽

2017 ◽

Vol 297 (2) ◽

pp. 101 ◽

Cited By ~ 1

Author(s):

SOMAYEH MONTAZEROLGHAEM ◽

ALFONSO SUSANNA ◽

JUAN ANTONIO CALLEJA ◽

VALIOLLAH MOZAFFARIAN ◽

MOHAMMAD REZA RAHIMINEJAD

Keyword(s):

Eastern Mediterranean ◽

Eastern Mediterranean Region ◽

Taxonomic Status ◽

Morphological Characters ◽

Molecular Dating ◽

Ancestral Area ◽

Close Relationship ◽

Taxonomic Changes ◽

High Level ◽

Relationship Of

A molecular phylogeny of the genus Echinops (Asteraceae, Cardueae) based on plastid and nuclear markers is presented. The study focuses on the Iranian representatives of the genus, which constitute a larger part of Echinops. The Bayesian cpDNA tree resulted in a large polytomy. However, the Bayesian ITS tree displayed a well-resolved topology more compatible with the taxonomic treatment generally accepted in Echinops. An ITS network illustrates a close relationship of haplotypes. Mapping diagnostic morphological characters onto the ITS tree revealed a high level of homoplasy among the studied taxa. Except for the life cycle, all other morphological characters evolved many times among the clades and most of them appeared to be of low taxonomical value. Based on the nucleotide polymorphism and haplotypes, the taxonomic status of some taxa was evaluated. The independent status of E. sect. Phaeochaete was confirmed by molecular analyses and morphological characters. The paraphyletic nature of E. sect. Echinops was confirmed. As for the molecular dating, our results suggest that the genus evolved in the early Miocene but the main speciation events took place in the Pliocene-Pleistocene. The biogeographic results do not support any specific ancestral area for Echinops, yet the model states that its current diversity originated in the Irano-Turanian Region and the Eastern Mediterranean region. Some taxonomic changes are suggested, in the synonymy and placement of some taxa.

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Contamination, Error, and Nonspecific Molecular Tools

Phytopathology ◽

10.1094/phyto.2000.90.6.565 ◽

2000 ◽

Vol 90 (6) ◽

pp. 565-567 ◽

Cited By ~ 18

Author(s):

Alan T. Dyer ◽

Kurt J. Leonard

Keyword(s):

Length Polymorphism ◽

Fragment Length ◽

Bacterial Contamination ◽

Fragment Length Polymorphism ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Molecular Tools ◽

Sequence Comparisons ◽

Aphanomyces Cochlioides ◽

Apparent Similarity

Random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) are widely used in studies of genetic variation. Although it is recognized that contamination should be avoided in DNA samples, little is known about the potential hazards of low level bacterial contamination of samples from which DNA is extracted for RAPD or AFLP analyses. We found that contamination of Aphanomyces cochlioides cultures with a prokaryote at visibly undetectable levels markedly altered the results of RAPD and AFLP analyses. The contamination resulted in seven contaminant-specific RAPD products and in the suppression of eight products characteristic of uncontaminated A. cochlioides cultures. Prokaryote contamination resulted in 39 contaminant-specific AFLP products, but did not cause suppression of AFLP products. Comparing A. cochlioides samples with outgroup A. euteiches did not clearly indicate the presence of contaminant DNA, because uneven product suppression in RAPD analysis increased the apparent similarity between contaminated samples and A. euteiches and because a high proportion of the contaminant-specific amplified products comigrated with products from A. euteiches in both RAPD and AFLP analyses. Work with organisms that are prone to contamination should employ techniques such as restriction fragment length polymorphism or DNA sequence comparisons rather than relying solely on RAPD or AFLP analyses.

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Application of Different Genotyping Methods forPseudomonas aeruginosa in a Setting of Endemicity in an Intensive Care Unit

Journal of Clinical Microbiology ◽

10.1128/jcm.37.11.3654-3661.1999 ◽

1999 ◽

Vol 37 (11) ◽

pp. 3654-3661 ◽

Cited By ~ 79

Author(s):

Han Speijer ◽

Paul H. M. Savelkoul ◽

Marc J. Bonten ◽

Ellen E. Stobberingh ◽

Jeroen H. T. Tjhie

Keyword(s):

Intensive Care Unit ◽

Intensive Care ◽

Gel Electrophoresis ◽

Fragment Length Polymorphism ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Pulsed Field Gel Electrophoresis ◽

Aflp Analysis ◽

Typing Method ◽

Strain Differentiation

Colonization with Pseudomonas aeruginosa was studied by taking serial swab specimens from the oropharynges and anuses and tracheal and gastric aspirates from patients in an intensive care unit during a 10-month period in a setting of endemicity. Nineteen (10%) of the 192 patients included in the study were colonized on admission, while another 30 (16%) patients acquired P. aeruginosawhile in the hospital. Typing of 353 isolates was performed by random amplified polymorphic DNA (RAPD) analysis, and 56 strains were selected for further typing by RAPD analysis, pulsed-field gel electrophoresis (PFGE), and amplified fragment length polymorphism (AFLP) analysis. By these methods, 42, 44, and 44 genotypes were found, respectively. Computer-aided cluster analysis indicated that similar groups of related isolates were obtained by each method. By taking admission periods into account, analysis of the typing results suggested cross-acquisition of P. aeruginosa for five patient pairs. The small number of transfers and the large number of genotypes found indicate that most P. aeruginosa strains were derived from the patients themselves. The numbers of observed typing patterns and band differences between related isolates were counted for each typing method. AFLP analysis with primers without a selective base proved to be the most discriminatory method, followed by PFGE, AFLP analysis (with one selective base), and RAPD analysis. On the basis of a comparison with established strain differentiation criteria for PFGE, the criteria for differentiation of P. aeruginosa by AFLP analysis are presented.

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Genetic variability of Pantaneiro horse using RAPD-PCR markers

Revista Brasileira de Zootecnia ◽

10.1590/s1516-35982007000400007 ◽

2007 ◽

Vol 36 (4) ◽

pp. 799-806 ◽

Cited By ~ 2

Author(s):

Andréa Alves do Egito ◽

Beatriz Helena Fuck ◽

Concepta McManus ◽

Samuel Rezende Paiva ◽

Maria do Socorro Maués Albuquerque ◽

...

Keyword(s):

Genetic Variability ◽

Random Amplified Polymorphic Dna ◽

Genetic Distances ◽

Jaccard Coefficient ◽

Mato Grosso ◽

Rapd Pcr ◽

Close Relationship ◽

Polymerase Chain ◽

Genic Diversity ◽

Mato Grosso Do Sul

Blood samples were collected from Pantaneiro Horses in five regions of Mato Grosso do Sul and Mato Grosso States. Arabian, Mangalarga Marchador and Thoroughbred were also included to estimate genetic distances and the existing variability among and within these breeds by RAPD-PCR (Random Amplified Polymorphic DNA - Polymerase Chain Reaction) molecular markers. From 146 primers, 13 were chosen for amplification and 44 polymorphic bands were generated. The analysis of molecular variance (AMOVA) indicated that the greatest portion of detected variability was due to differences between individuals within populations (75.47%). Analysis of the genetic variability between pairs of populations presented higher estimates for the five Pantaneiro populations with the Arabian breed, while lowest estimates were presented by pairs formed among the Pantaneiro populations with the Mangalarga Marchador. Highest genic diversity was shown by the Pantaneiro (0.3396), which also showed highest genetic distance with the Arabian and lowest with Mangalarga Marchador breed. UPGMA dendrogram showed distinct differences between naturalized (Pantaneiro and Mangalarga Marchador) and exotic (Arabian and Thoroughbred) breeds. In the dendrogram generated by UPGMA method, the similarity matrix generated by the Jaccard coefficient showed distinction between the naturalised breeds, Pantaneiro and Mangalarga Marchador, and the exotic breeds, Árab and English Thoroughbred. Results suggest that the Pantaneiro presents a higher genetic variability than the other studied breeds and has a close relationship with the Mangalarga Marchador.

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Sources of Potential Errors in the Application of Random Amplified Polymorphic DNAs in Cucumber

HortScience ◽

10.21273/hortsci.31.2.262 ◽

1996 ◽

Vol 31 (2) ◽

pp. 262-266 ◽

Cited By ~ 36

Author(s):

Jack Staub ◽

Jeffery Bacher ◽

Karl Poetter

Keyword(s):

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Inbred Lines ◽

Sphaerotheca Fuliginea ◽

Chain Reaction ◽

Banding Patterns ◽

Taq Dna Polymerase ◽

Polymerase Chain ◽

Stock Solutions ◽

Pcr Conditions

The influence of tissue age, pathogen infestation, intrapopulation contamination, and polymerase chain reaction (PCR) conditions were assessed as sources of error in random amplified polymorphic DNA (RAPD) analysis. DNA from young, uninfected tissue provided the most consistent results. Plants infected with Sphaerotheca fuliginea Schl. (ex Fr.) Poll. showed variation in RAPD banding patterns compared to those of uninfected plants. Differences in banding patterns were detectable when DNA from two inbred lines were mixed at dilution ratios of ≤20:1 but not ≥50:1. Differing lots of commercially available 10× reaction buffer, MgCl2 stock solutions, and Taq DNA polymerase affected RAPD banding patterns and overall yield. For reproducibility of RAPD assays, it may be necessary to optimize reactions for specific lots of PCR reagents from either commercial or in-house sources.

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Application of rps16 Intron and trnL-trnF Intergenic Spacer Sequences to Identify Rengas clone Riau

Biosaintifika Journal of Biology & Biology Education ◽

10.15294/biosaintifika.v9i2.9108 ◽

2017 ◽

Vol 9 (2) ◽

Author(s):

Dewi Indriyani Roslim ◽

Herman Herman

Keyword(s):

Intergenic Spacer ◽

Taxonomic Status ◽

Morphological Characters ◽

Molecular Technique ◽

Dna Barcodes ◽

Query Cover ◽

Blastn Analysis ◽

Total Dna ◽

Polymerase Chain ◽

Relationship Of

Rengas clone Riau has been identified using morphological characters and molecular technique with a psbA-trnH intergenic spacer, however, this method can only determine its taxonomic status at genus level, namely Gluta sp. This study reports application two DNA barcodes, i.e. rps16 intron and trnL-trnF intergenic spacer, to identify Rengas clone Riau. The methods included collection of the leaves from Kajuik Lake, total DNA isolation, electrophoresis, PCR (polymerase chain reaction), gel purification and sequencing. The rps16 intron size was 659 bp and the trnL-trnF intergenic spacer was 527 bp. The BLASTn analysis showed that sequences of the rps16 intron and the trnL-trnF intergenic spacer of Gluta sp clone Riau had 100% similarity to those of G. renghas deposited in GenBank. These results were supported by high max score, high total score, query cover = 100%, and E-value = 0. The dendrograms also showed the closest relationship of Gluta sp clone Riau with G. renghas deposited in GenBank compared to other species of Gluta. In conclusion, this study succeeded in identifying Rengas clone Riau as Gluta renghas by using sequences of the rps16 intron and the trnL-trnF intergenic spacer. A combination of DNA barcodes could be applied to identify various plants as long as the database for the DNA barcodes is available in public database such as GenBank.

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A DNA-Based Procedure for In Planta Detection of Fusarium oxysporum f. sp. phaseoli

Phytopathology ◽

10.1094/phyto.2002.92.3.237 ◽

2002 ◽

Vol 92 (3) ◽

pp. 237-244 ◽

Cited By ~ 48

Author(s):

Fernando M. Alves-Santos ◽

Brisa Ramos ◽

M. Asunción García-Sánchez ◽

Arturo P. Eslava ◽

José María Díaz-Mínguez

Keyword(s):

Common Bean ◽

Fusarium Oxysporum ◽

Scar Marker ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Rapd Marker ◽

In Planta ◽

Sequence Characterized Amplified Region ◽

Polymerase Chain ◽

Highly Virulent

We have characterized strains of Fusarium oxysporum from common bean fields in Spain that were nonpathogenic on common bean, as well as F. oxysporum strains (F. oxysporum f. sp. phaseoli) pathogenic to common bean by random amplified polymorphic DNA (RAPD) analysis. We identified a RAPD marker (RAPD 4.12) specific for the highly virulent pathogenic strains of the seven races of F. oxysporum f. sp. phaseoli. Sequence analysis of RAPD 4.12 allowed the design of oligonucleotides that amplify a 609-bp sequence characterized amplified region (SCAR) marker (SCAR-B310A280). Under controlled environmental and greenhouse conditions, detection of the pathogen by polymerase chain reaction was 100% successful in root samples of infected but still symptomless plants and in stem samples of plants with disease severity of ≥4 in the Centro Internacional de Agricultura Tropical (CIAT; Cali, Colombia) scale. The diagnostic procedure can be completed in 5 h and allows the detection of all known races of the pathogen in plant samples at early stages of the disease with no visible symptoms.

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Characterization of the Hyphal Swelling Group of Pythium: DNA Polymorphisms and Cultural and Morphological Characteristics

Plant Disease ◽

10.1094/pdis.1998.82.2.218 ◽

1998 ◽

Vol 82 (2) ◽

pp. 218-222 ◽

Cited By ~ 23

Author(s):

K. Kageyama ◽

H. Uchino ◽

M. Hyakumachi

Keyword(s):

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Morphological Characteristics ◽

Its Region ◽

Restriction Enzymes ◽

Dna Polymorphisms ◽

Banding Patterns ◽

Length Polymorphisms ◽

Polymerase Chain

The hyphal swelling (HS) group of Pythium species and P. ultimum were studied for cultural and morphological characteristics, restriction fragment length polymorphisms of the amplified internal transcribed spacer (ITS) region in nuclear rDNA, and random amplified polymorphic DNA (RAPD) analysis of genome DNA. The shape of sporangia was spherical to subspherical or lemoniform and averaged 18.1–23.0 μm. All isolates could grow at 5 to 35°C, and the rate at the optimal temperature, 30°C, was 29–34 mm/24 h. The size of the ITS region amplified by polymerase chain reaction and the banding patterns after digestion with the restriction enzymes showed no variation between the HS group and P. ultimum. No difference in banding patterns was shown between the HS group and P. ultimum by RAPD analysis with each of three primers. Isolates examined were from Japan, and results should be confirmed from other regions.

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