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At least 19 recordsLinked to original sources
PubMed1994

Characterization of Bacillus licheniformis with the RAPD technique (randomly amplified polymorphic DNA).

RAPD technique (randomly amplified polymorphic DNA) was used for epidemiological subtyping of Bacillus licheniformis and other Bacillus spp. Within 46 isolates of B. licheniformis, up to 10 strain types could be determined when two 10-mer primers were used. RAPD patterns, which were found in eight further strains of Bacillus spp., clearly differed from those of B. licheniformis. Thus RAPD technique proved to be a promising tool for characterization of Bacillus spp.

Bacillus↗
PubMed2002

Random amplified polymorphic DNA technique for identification and differentiation of old world Leishmania species.

The random amplified polymorphic DNA technique may be used to explore parasite DNA polymorphisms. We assessed its applicability to identification of Old World Leishmania species. A set of 6 random decamer primers (Al, A4, A5, A7, A10, and A15) was applied to a panel of DNA from 57 representatives of different Old World Leishmania species. The amplification profiles allowed discrimination among species belonging to different taxonomic complexes. Two criteria were used to analyze the profiles: the presence of consistent amplicons at the same electrophoretic position for isolates of the same species, and the presence of distinct amplicons for isolates of different species. Three primers--Al, A7 and A10--rendered such products.

Animals↗
PubMed1993

Random amplified polymorphic DNA technique for the identification of Trichinella species.

The random amplified polymorphic DNA (RAPD) technique was successfully used to produce genetic fingerprints distinguishing between Trichinella spiralis and Trichinella britovi. The same patterns were obtained from purified and crude DNA preparations of pooled and single muscle larvae. RAPD fingerprinting was applied to muscle larvae preserved under different conditions and recovered from different hosts. Larvae recovered from fresh and frozen meat and stored at -20 degrees C for a long time or under 70% ethyl alcohol at room temperature for 30 d gave good and reproducible results. Single larvae recovered from a naturally infected wild boar and from a human biopsy gave fingerprints congruent to those obtained from T. britovi reference strains. The results prove that RAPD analysis is a quick method to distinguish between the autochthonous Trichinella species of Central-Southern Europe in less than 1 d after the detection of the infection. If necessary, the biological material can be frozen or stored under 70% ethyl alcohol at room temperature and sent to laboratories able to perform the RAPD analysis. The RAPD technique requires no prior knowledge of the molecular biology of the organism to be investigated and therefore appears to be a promising tool in parasitology for the identification of sibling species.

Animals↗
PubMed2005

Optimization of random amplified polymorphic DNA techniques for use in genetic studies of Cuban Triatominae.

Random amplified polymorphic DNA (RAPD) technique is a simple and reliable method to detect DNA polymorphism. Several factors can affect the amplification profiles, thereby causing false bands and non-reproducibility of assay. In this study, we analyzed the effect of changing the concentration of primer, magnesium chloride, template DNA and Taq DNA polymerase with the objective of determining their optimum concentration for the standardization of RAPD technique for genetic studies of Cuban Triatominae. Reproducible amplification patterns were obtained using 5 pmoL of primer, 2.5 mM of MgCl2, 25 ng of template DNA and 2 U of Taq DNA polymerase in 25 microL of the reaction. A panel of five random primers was used to evaluate the genetic variability of T. flavida. Three of these (OPA-1, OPA-2 and OPA-4) generated reproducible and distinguishable fingerprinting patterns of Triatominae. Numerical analysis of 52 RAPD amplified bands generated for all five primers was carried out with unweighted pair group method analysis (UPGMA). Jaccard's Similarity Coefficient data were used to construct a dendrogram. Two groups could be distinguished by RAPD data and these groups coincided with geographic origin, i.e. the populations captured in areas from east and west of Guanahacabibes, Pinar del Río. T. flavida present low interpopulation variability that could result in greater susceptibility to pesticides in control programs. The RAPD protocol and the selected primers are useful for molecular characterization of Cuban Triatominae.

Animals↗
PubMed2002

Optimization of random amplified polymorphic DNA techniques for its use in genetic studies of Trichomonas vaginalis isolates.

The random amplified polymorphic DNA (RAPD) technique is a simple method to detect DNA polymorphism. Several factors can affect the amplification profiles causing the presence of false bands and assay non-reproducibility. In this study, we analyzed the effect of changing concentrations of the primer, template DNA and Taq DNA polymerase with the goal of determining their optimum concentration for the standardization of the RAPD technique for genetic studies of Trichomonas vaginalis, a parasite that is of major epidemiological relevance in Cuba.

Animals↗
PubMed1998

Comparative genetic analysis of tritrichomonadid protozoa by the random amplified polymorphic DNA technique.

The taxonomic classification within the genus Tritrichomonas is a subject of controversy, and, potentially, separation of the tritrichomonads from cattle and swine on the species level is not valid. To tackle this hypothesis we comparatively assessed several isolates of protozoan parasites from the three Tritrichomonas species T. foetus, T. suis, and T. mobilensis by the RAPD (random amplified polymorphic DNA) technique. In this method with 20 different primers, all T. foetus and T. suis isolates resulted in identical genomic fingerprints, thus yielding additional evidence for the genetic identity of T. foetus and T. suis. In contrast, it turned out that the species T. mobilensis isolated from the squirrel monkey is genetically distinct and can clearly be discriminated from the other tritrichomonads. Consequently, the results obtained in this study support a possible future revision of the taxonomic classification of the genus Tritrichomonas.

Animals↗
PubMed1996

Analysis of Heterodera avenae populations by the random amplified polymorphic DNA technique.

Eleven populations of the Heterodera avenae complex (four Spanish, two British, two French, and three Swedish) were studied by random amplified polymorphic DNA analysis. From 5 to 11 fragments were obtained with each of 14 random primers, with fragment size ranging from 200 to 2200 bp. Cluster analysis of the 11 populations, using 108 scorable markers, separate these populations into two main groups. These groups coincide with what is known as the "true" H. avenae and the "Gotland strain" or "British pathotype 3" of H. avenae. The results also clarify the relationships among some members of the H. avenae complex established previously using morphological and biochemical criteria.

Animals↗
PubMed1998

Differentiation of Cryptosporidium parvum isolates by a simplified randomly amplified polymorphic DNA technique.

Genomic DNA was isolated from Cryptosporidium parvum oocysts by a specific immunomagnetic separation-in vitro excystation procedure and subjected to randomly amplified polymorphic DNA analysis using sequence-independent primers. An estuary C. parvum isolate was easily differentiated from several bovine isolates, while five bovine isolates of the same origin were indistinguishable from each other.

Animals↗
PubMed1994

Comparative genetic analysis of Swiss and Spanish isolates of Echinococcus granulosus by southern hybridization and Random Amplified Polymorphic DNA technique.

Swiss and Spanish isolates of Echinococcus granulosus were compared using different molecular biological techniques: Genomic DNAs isolated from parasites originating from various intermediate hosts were subjected to Southern hybridization with different probes, the same source of DNA was used for DNA amplification using the Random Amplified Polymorphic DNA (RAPD) technique. With both methods the various isolates (metacestodes) of E. granulosus exhibited characteristic banding patterns which allowed us to assign them to the following groups of homologous profiles: (a) isolates of horse and donkey origin from Spain and Switzerland; (b) isolates of cattle origin from Switzerland; (c) isolates of sheep, cattle and human origin from Spain; (d) isolates of pig origin from Spain and Switzerland and of goat origin from Spain. By RAPD (Southern hybridization not examined) two isolates of human origin from Switzerland were showing banding patterns distinct from groups (a-d). The results provide further evidence that the morphological and biological differences of several strains of E. granulosus are also detectable on the genetic level using molecular biological techniques.

Animals↗
PubMed1993

Application of the random amplified polymorphic DNA technique for the detection of polymorphism among wild and cultivated tetraploid wheats.

Development of a high-density genetic linkage map of cultivated wheats using conventional molecular markers has lagged behind the other major food crops such as rice and tomato because of the large genome size and limited levels of genetic polymorphisms. Recently, random amplified polymorphic DNAs (RAPDs) have been suggested to provide an alternative to visualize more polymorphism. For the construction of a genetic linkage map in tetraploid wheats, one can use a strategy of intersubspecific crosses between the most dissimilar wild and cultivated tetraploid wheats that are easy to hybridize and result in fertile progeny. An assessment of the level of RAPDs among different accessions and varieties of wild and cultivated tetraploid wheats is required to fulfill this objective. We present here the data obtained using RAPD analysis of 40 primers in 20 accessions of wild tetraploid emmer wheats (Triticum turgidum L. ssp. dicoccoides) and 10 genotypes of cultivated tetraploid durum wheats (Triticum turgidum L. ssp. durum) selected from geographically diverse locations. We have observed a higher level of polymorphism among different accessions of wild emmer wheat from Israel. Turkey, and Jordan than the group of cultivated American, Turkish, and Syrian durum wheats. These data have been used to generate a dendrogram suggesting the genetic relationships among these genotypes, and the most dissimilar genotypes are identified for future mapping and gene tagging work.

Base Sequence↗
PubMed1999

Technical aspects of random amplified polymorphic DNA (RAPD) technique in genotyping of bacterial strains.

Random Amplified Polymorphic DNA (RAPD) method became widely applied for sensitive, efficient and fast distinguishing of different isolates of a given species, if pure culture is available. Problems with reproducibility and discriminatory power, frequently cited in the literature, can be overcome by precise optimization procedure allowing to achieve reliable conditions for each species analysed. Basing on two examples of different species, H. pylori and E. faecium, particular parameters of RAPD fingerprinting were evaluated with respect to selection of best working primers generating medium-complex profiles, using only high quality DNA samples and evaluation optimum for every reaction reagent. Stable and informative amplification patterns were obtained with different best working primers which could discriminate between all H. pylori and E. faecium strains tested. For both analysed species different optima were found, suggesting species-specific need of precise RAPD conditions evaluation. This study proved high sensitivity and efficiency of optimized RAPD profiling applicable for searching the epidemiology traces for both species.

Bacterial Typing Techniques↗
PubMed1996

Use of random amplified polymorphic DNA (RAPD) technique in inheritance studies of Plasmodium falciparum.

Effectiveness of random amplified polymorphic DNA (RAPD), a technique using 1 10-base primer to amplify random segments of genomic DNA, and some of its possible uses were tested in the A + T-rich genome of Plasmodium falciparum. The best concentrations of MgCl2, 60% G + C primer, and DNA were determined to be 4.0 mM, 0.4 microM, and 90-180 ng/15 microliters reaction, respectively. Use of 30% G + C primers did not allow amplification to occur. Application of RAPD to DNA of parent and progeny clones from a P. falciparum cross showed that polymorphisms identified in the parentals and tracked in the progeny were inherited in a Mendelian fashion and that RAPD-identified polymorphisms could be used as genetic markers. Some of these polymorphic markers were located on more than 1 chromosome, whereas others were specific for a single chromosome. Two of these markers, each located on chromosome 3 of 1 of the parental parasites, were missing from 2 of the 18 progeny, suggesting that deletions, or crossover events had occurred. RAPD markers also identified a higher number of nonparental-type progeny than expected, thus confirming previous observations for high genetic variability in malaria parasites.

Animals↗
PubMed2003

The possible effect of a sanitization program on intraspecies differentiation of Listeria monocytogenes strains isolated from a fish processing plant.

Forty-seven Listeria monocytogenes strains isolated during a year in a selected Polish fish-processing plant as well as 7 L. monocytogenes strains of different origins (including a reference strain) were analyzed in our studies. Strains were isolated from raw fish fillets (flounder), frozen coated flounder fillets, coating ingredients, and the processing environment. Isolation of strains covered the period of a sanitization program introduced in the plant. L. monocytogenes was identified using conventional microbiological methods and the PCR technique. RAPD (random amplified polymorphic DNA) technique for fingerprinting was applied to analyze the intraspecies diversity. Six RAPD types (A-F) and seven unique strains were revealed as a result of fingerprinting with one persistent type isolated from July 1999 to February 2000. It was detected for the first time after one month of sanitization. Its occurrence could have been promoted by clone selection either due to ineffective disinfection or to resistance against the disinfectant. As L. monocytogenes mostly occurred on frozen products, this indicates that contamination could start during product freezing, cold storage, or handling. The results revealed that there is a crucial need for preparing sanitization schemes precisely targeted at L. monocytogenes to avoid its recurrence as persistent 'in-house' strains. The possibility of incorrect interpretations of classical microbiological test results as well as the necessity to introduce assays based on nucleic acid analysis into epidemiological investigations were emphasized.

Animals↗
PubMed2005

Use of RAPD and killer toxin sensitivity in Saccharomyces cerevisiae strain typing.

AIMS: Two different strain characterization techniques, random amplified polymorphic DNA (RAPD) and killer toxin sensitivity (KTS), were compared to assess their typing performance using a set of 30 certified Saccharomyces cerevisiae strains. METHODS AND RESULTS: A sequential random resampling procedure was employed to subdivide the 32 descriptors in eight sets, in order to compare the differential performances of the two techniques with diverse number of characters. Results showed that RAPD performs better than killer, although the complete differentiation of the strains under study could be obtained only by combining profiles from the two techniques. CONCLUSIONS: The combination of different typing techniques was useful when discriminating similar organisms. In such cases, the introduction of a second typing technique can be more advantageous than increasing the number of characters obtained with a single method. SIGNIFICANCE AND IMPACT OF THE STUDY: The distribution of among-strains pairwise distances and the relative performance of the two techniques has implications for the study of biodiversity, taxonomy and microbial ecology.

DNA, Fungal↗
PubMed2001

Evaluation of molecular techniques for the genetic characterization of Saccharomyces cerevisiae strains.

The applicability of different PCR-based techniques, random amplified polymorphic DNA, cleaved amplified polymorphic sequence and SSRs (simple sequence repeats) to genetically identify, typify and discriminate among Saccharomyces cerevisiae strains, was investigated. The analysis and comparison of the genetic profiles obtained for each of the techniques allowed determination of the degree of polymorphism, genetic diversity and relationships among the strains. Consequently, the discriminatory power and usefulness of the molecular techniques assayed was established. SSR analysis was the most effective method due to its high level of polymorphism, the ease of interpretation of the genetic profiles obtained, and the speed of use.

Genetic Techniques↗
PubMed1995

Genetic characterization of Toxoplasma gondii strains by random amplified polymorphic DNA polymerase chain reaction.

The technique of Random Amplified Polymorphic DNA (RAPD) PCR has been used to detect DNA polymorphisms among Toxoplasma gondii strains. Seven arbitrary oligonucleotides (10-mer) were used as primers to amplify total genomic DNAs and significant genetic heterogeneity was detected among 11 T. gondii strains with different virulence for mice. The polymorphisms observed allowed relationship dendrograms of T. gondii strains to be constructed by PHYLIP and PAUP analyses. The genetic relationships of the T. gondii strains generated by 2 analyses using completely different assumptions were similar. Both analyses revealed 2 groups of T. gondii strains, one formed by the 6 virulent strains and the other formed by the 5 avirulent strains. This suggests that the genus Toxoplasma may actually contain 2 groups, correlated with their virulence, which have probably evolved independently following their initial separation. Significant polymorphisms were also detected between 2 different laboratory stocks of the T. gondii RH strain.

Animals↗
PubMed2001

Polyphasic investigation of the diversity within Lactobacillus plantarum related strains revealed two L. plantarum subgroups.

The diversity of 140 strains related to Lactobacillus plantarum was investigated using a polyphasic approach combining two molecular techniques: randomly amplified polymorphic DNA fingerprinting (RAPD) and Southern hybridisation with a pyr probe on BglI digests of chromosomal DNA, as well as phenotypic characterization. The RAPD technique allowed us to classify a subset of 60 representative strains into four groups. One group belonged to Lactobacillus paraplantarum, the second to Lactobacillus pentosus and the two remaining groups to L. plantarum (G(L)p1 and G(L)p2). The Southern hybridisation technique (F. Bringel, M.-C. Curk and J.-C. Hubert, Int. J. Syst. Bacteriol. 46: 588-594, 1996) revealed nine groups of profiles (I to IX). Results indicated an excellent convergence between RAPD and hybridisation classifications for more than 93% (56/60) of the strains studied. When we compared the fermentation patterns of the L. plantarum strains, three differences were found. Melezitose fermentation was not fermented by the G(L)p2 RAPD group, unlike the G(L)p1 RAPD group which included L. plantarum type strain NCIMB11974T. Second, alpha-methyl-D-mannoside was fermented by a majority of the strains of the G(L)p1 RAPD group but by none of the strains in the G(L)p2 RAPD group. Third, dulcitol was catabolized by nearly half of the strains of the G(L)p2 RAPD group but by none of the strains in the G(L)p1 RAPD group. Molecular diversity within L. plantarum was confirmed using Southern profiles, PCR amplification and subsequent sequencing of these PCR products. A 773 bp sequence overlapping the pyrDF genes showed high homology: at least 97% identical in L. plantarum strains (V to IX) and 99.9% identical in hybridisation groups VII and VIII. The same G-T transversion which destroyed the pyrF BglI site was found in 11 strains (hybridisation groups VI, VII and VIII). DNA rearrangements were identified downstream from the pyr genes, by PCR amplification and Southern hybridisation profile analysis in three strains of hybridisation groups VIII and IX, two of which also harboured the G-T transversion.

Blotting, Southern↗