SEARCH · PubMed Health

Results for “Random Amplified Polymorphic DNA Technique”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2Linked to original sources

PubMed2001

Comparison of multilocus RFLPs and PCR-based marker systems for genetic analysis of the silkworm, Bombyx mori.

The utility of multilocus RFLPs and three PCR-based techniques, Random Amplified Polymorphic DNA (RAPD), Inter-Simple Sequence Repeat-PCR (ISSR-PCR) and simple sequence repeats (SSRs) for genetic characterization was examined using 13 diverse silkworm strains. All four approaches successfully discriminated the 13 silkworm varieties but differed in the amount of polymorphism detected. The usefulness of each system was examined in terms of number of loci revealed (effective multiplex ratio, EMR) and the amount of polymorphism detected (diversity index, DI). For example, the six multilocus RFLP probes produced 180 products of which 97% were polymorphic; 15 SSR loci gave rise to an average of 8 alleles each, of which 86% were polymorphic. The ISSR-PCR produced 39 fragments of which 76.98% were polymorphic. The highest diversity index was observed for ISSR-PCR (0.957) and the lowest for RAPDs (0.744). The RAPD, ISSR-PCR and RFLP assays clearly separated the diapausing and non-diapausing silkworm varieties. These results are discussed in terms of choice of appropriate marker technology for different aspects of silkworm genome analysis.

Animals↗

PubMed2006

[RAPD analysis on germplasm resources of different farm races of Morinda officinalis].

OBJECTIVE: To explore the genetic diversity of different farm races of Morinda officinalis on molecular level. METHODS: The molecular biological technique-random amplified polymorphic DNA (RAPD) were used. RESULTS: Of the 40-mer arbitary primers, 14 were found to amplify polymorphic products. 3-5 polymorphic bands were amplified by each polymorphic primer on the average. Using UPGMA method all the tested accesions can be clustered into two groups: 4 accessions of Daye were classified as one group, 1 accession of Xiaoye be another group. CONCLUSION: There actually existed much genetic diversity on molecular level among the different farm races of Morinda officinalis.

Cluster Analysis↗

PubMed2000

Extensive intra-tumor heterogeneity in primary human glial tumors as a result of locus non-specific genomic alterations.

Genomic changes are a hallmark of the neoplastic process. These range from alterations at specific loci and defined karyotypic changes which influence tumor behavior to generalized alterations exemplified by microsatellite instability. Generalized genomic changes within a tumor would be evidence in favor of the mutator hypothesis which postulates a role for such extensive changes during tumorigenesis. In this report, we have used the DNA fingerprinting technique of randomly amplified polymorphic DNA (RAPD) analysis to study genomic alterations within primary human astrocytic tumors (gliomas) in a locus non-specific manner. The RAPD fingerprinting profile of consecutive segments of tumors 2 mm across was studied; 17 astrocytic (high- and low-grade) tumors were sectioned end to end. Tissue from 50 consecutive sections, 40 microm thick (total 2 mm across), was pooled and taken to be a tumor compartment. DNA was subjected to RAPD amplification by 15 random 10-mer primers. A tumor segment was taken to have a DNA fingerprinting pattern different from others in the same specimen when its RAPD profile differed from others by at least one band of one RAPD reaction. All but one of the tumors showed compartments with a unique genetic profile, indicating genomic instability leading to widespread intra-tumor genetic heterogeneity. Eight tumors were also studied for loss of heterozygosity (LOH) of the p53 and D17S379 loci in the different segments as examples of alteration of specific tumor influencing loci. Three showed LOH of p53, which was limited to only one compartment of each tumor. The extensive intra-tumor genetic instability detected in this study is suggestive of the overall high rate of change in the genomes of tumors including those of a lower grade. It is hypothesized that some of these altered clones, which manifest as zones of heterogeneity in a solid tumor, may accumulate changes at loci known to influence tumor behavior, and thus clinical outcome.

Brain Neoplasms↗

PubMedDate not supplied

Genetic stability assessments of plantlets regenerated from cryopreserved in vitro cultured grape and kiwi shoot-tips using RAPD.

In vitro cultured shoot-tips of four grape (Vitis vinifera) cultivars and one kiwi (Actinidia deliciosa) cultivar were cryopreserved using the encapsulation-dehydration method. Genomic DNA of plantlets regenerated directly from cryopreserved shoot-tips was extracted and analyzed using the RAPD (Random Amplified Polymorphic DNA) technique. The RAPD profiles obtained were highly reproducible and no differences were found between the DNA patterns obtained with plantlets regenerated from control and cryopreserved plantlets. The RAPD technique therefore appears to be a fast, simple and efficient method for evaluating genetic stability of cryopreserved material, which can be used rapidly after the completion of a freezing experiment and will efficiently complement other genetic stability evaluation methods.

Actinidia↗

PubMed1996

A total DNA characterization in Proteocephalus exiguus and P. percae (Cestoda: Proteocephalidae): random amplified polymorphic DNA and hybridization techniques.

Two morphologically similar fish tapeworms, Proteocephalus exiguus and P. percae, were differentiated by the random amplified polymorphic DNA (RAPD) marker and Southern-blot hybridization techniques. Four geographic isolates of P. exiguus and two of P. percae were studied using eight arbitrary decamer oligonucleotides as primers. Species-specific RAPD fragments enabled reliable separation of the taxa studied. Generally, 1-3 fragments specific for P. percae and 1-4 P. exiguus-specific fragments were detected using individual primers. Intraspecific differences in P. percae depended on the primer used. The profiles generated by the primers OPA 04 and OPA 12 showed an intraspecific variation, whereas six other primers tested revealed indistinguishable banding patterns. On the other hand, intraspecific variability of P. exiguus, detected among four geographic isolates, was evident using all primers. Additionally, the utilization of two species-specific RAPD markers as effective probes was demonstrated. Distinct differences between P. exiguus and P. percae were revealed using each of the restriction enzyme/probe combinations.

Animals↗

PubMed1995

Phenotypic and genotypic analysis of variability in Aspergillus fumigatus.

Sixty-one isolates and collection strains of Aspergillus fumigatus were compared for their phenotypic (morphological features and isoenzyme profiles) and genotypic (restriction enzyme-generated mitochondrial DNA and ribosomal DNA profiles and random amplified polymorphic DNA patterns) features. The examined strains exhibited highly variable colony morphologies and growth rates at different temperatures, but their micromorphologies and conidial diameters were characteristic of the species. Of the isoenzymes studied, the beta-arylesterase and phosphatase patterns were the most divergent, and the 61 strains could be classified into seven groups. The glucose 6-phosphate dehydrogenase and catalase isoenzyme patterns displayed only a limited variability, while the profiles of superoxide dismutase, lactate dehydrogenase, and glutamate dehydrogenase were highly conserved. The HaeIII-generated mitochondrial DNA patterns and SmaI-digested repetitive DNA and ribosomal DNA hybridization patterns of almost all strains were also invariable. The level of variation was much higher when random amplified polymorphic DNA analysis was applied. Although the patterns of the strains were very similar with most of the primers, the application of some primers made it possible to cluster the A. fumigatus isolates into several groups. The results indicate that the random amplified polymorphic DNA technique could be used more efficiently than isoenzyme analysis for typing A. fumigatus isolates. A good correlation was found between the dendrograms obtained from the isoenzyme and random amplified polymorphic DNA data, but the isoenzyme and amplified DNA patterns did not correlate with the pathogenicity, pigment production, or geographical origin of the strains. One "A. fumigatus" strain (strain FRR 1266) exhibited unique isoenzyme, mitochondrial DNA, ribosomal DNA, and random amplified polymorphic DNA patterns; it is proposed that this strain represents a new species of the section Fumigati.

Aspergillus fumigatus↗

PubMed2003

Comparison of usefulness of randomly amplified polymorphic DNA and amplified-fragment length polymorphism techniques in epidemiological studies on nasopharyngeal carriage of non-typable Haemophilus influenzae.

Randomly amplified polymorphic DNA (RAPD) and automated amplified-fragment length polymorphism (AFLP) techniques with fluorescently labelled primers were used to type non-serotypable Haemophilus influenzae (NTHI) isolates. Eighty-seven isolates from healthy children attending day-care centres or living at orphanages in southern Poland were investigated. Through comparison of the AFLP data with RAPD analysis, it has been concluded that the discriminatory power of AFLP for NTHI typing is higher than RAPD. Generally, the NTHI isolates analysed were highly heterogeneous, as detected with a HindIII/TaqI AFLP genotyping scheme on intra/inter similarity levels of 94 and 96 % using Pearson's correlation coefficient. The range of similarity values found for isolates from children permanently residing at a particular day-care centre was much wider than that for isolates from orphanages. AFLP can efficiently access NTHI strain diversity and can monitor their turn-over for comparative typing in local and inter-local epidemiological investigations.

Bacterial Typing Techniques↗

PubMed1995

Evaluation of random amplified polymorphic DNA (RAPD)-PCR as a method to differentiate Lactobacillus acidophilus, Lactobacillus crispatus, Lactobacillus amylovorus, Lactobacillus gallinarum, Lactobacillus gasseri, and Lactobacillus johnsonii.

The technique random amplified polymorphic DNA (RAPD)-PCR was evaluated as a method to differentiate Lactobacillus acidophilus, Lactobacillus crispatus, Lactobacillus amylovorus, Lactobacillus gallinarum, Lactobacillus gasseri, and Lactobacillus johnsonii. Representative strains, including the type of each species, were selected from different clusters obtained by numerical analysis of total soluble cell protein patterns. Results obtained by RAPD-PCR corresponded well with results obtained by numerical analysis of total soluble cell protein patterns. The type strains of each species displayed different RAPD profiles. Strains with identical L(+)- nicotinamide adenine dinucleotide-dependent lactic dehydrogenase (nLDH) electrophoretic profiles could be distinguished on the basis of their RAPD profiles.

Base Sequence↗

PubMed1997

Effect of bacterial association on the phenotype and genotype of an Entamoeba histolytica clonal population.

A several-times-cloned population of Entamoeba histolytica trophozoites (clone MAVIII) was cultured under axenic (MAVIIIax), monoxenic (MAVIIImx) and polyxenic (MAVIIIpx) conditions. Clones MAVIIIax and MAVIIImx presented similar virulence in vitro, but differed in their virulence in vivo, whereas MAVIIIpx trophozoites were neither virulent in vitro or in vivo. The MAVIII clones maintained their zymodeme and exhibited three unusual glucose phosphate isomerase bands, absent in other E. histolytica strains studied. Similar patterns were shown by the three MAVIII clones in the signature of a 482-bp DNA fragment from the M17 gene (which encodes for a variable immunodominant antigen), obtained by low stringency single specific primer PCR technique. However, MAVIII clones displayed genotypic variability in the patterns obtained by the random amplified polymorphic DNA technique using total DNA as template. Results suggest that monomorphism is kept in certain regions of the genome, mainly in those carrying protein encoding genes, but a high polymorphism is present in total DNA of cloned trophozoites cultured under different conditions, confirming the plasticity of the E. histolytica genome.

Animals↗

PubMed2006

Differentiation of Candida species obtained from nosocomial candidemia using RAPD-PCR technique.

Thirteen strains of the genus Candida were isolated from catheter, urine and surgical wounds from individual patients of the Santa Casa de Misericórdia, Belo Horizonte, MG, Brazil. Ten strains were characterized as Candida albicans, two as Candida glabrata, and one as Candida parapsilosis. Isolates were evaluated for molecular relatedness by random amplified polymorphic DNA technique using 15 primers. The analysis of the genomic DNA obtained revealed a low intraspecific polymorphism and did not allow for the differentiation between strains of the same species obtained from distinct clinical sources (catheter, urine and surgical wounds). The RAPD profiles generated were able to differentiate among the species of Candida albicans, Candida parapsilosis and Candida glabrata strains isolated in this study.

Candida↗

PubMed1999

Evaluation of phenotypic and molecular typing techniques for determining diversity in Erwinia carotovora subspp. atroseptica.

A number of phenotypic and molecular fingerprinting techniques, including physiological profiling (Biolog), restriction fragment length polymorphism (RFLP), enterobacterial repetitive intergenic consensus (ERIC) and a phage typing system, were evaluated for their ability to differentiate between 60 strains of Erwinia carotovora ssp. atroseptica (Eca) from eight west European countries. These techniques were compared with other fingerprinting techniques, random amplified polymorphic DNA (RAPD) and Ouchterlony double diffusion (ODD), previously used to type this pathogen. Where possible, data were represented as dendrograms and groups/subgroups of strains identified. Simpson's index of diversity (Simpson's D) was used to compare groupings obtained with the different techniques which, with the exception of Biolog, gave values of 0.46 (RFLP), 0. 39 (ERIC), 0.83 (phage typing), 0.82 (RAPD) and 0.26 (ODD). Of the techniques tested, phage typing showed the highest level of diversity within Eca, and this technique will now form the basis of studies into the epidemiology of blackleg disease.

Bacterial Typing Techniques↗

PubMed2006

[Molecular typing of Listeria monocytogenes isolated from clinical and food samples].

INTRODUCTION: Listeria monocytogenes is an emergent foodborne pathogen acquired by the ingestion of contaminated food. This bacterium causes a disease called listeriosis, whose mortality rate world wide is around 20% to 30%, reaching up to 80% in cases of neonatal infections. The random amplified polymorphic DNA technique allows different isolates to be distinguished and characterized at the molecular level, which can provide useful information about the diversity of this pathogen in Colombia. OBJECTIVE: To molecularly characterize different L. monocytogenes isolates from food and clinical samples using this technique to determine possible relationships among these two origins. MATERIALS AND METHODS: Thirty eight L. monocytogenes isolates were analyzed; 22 from human clinical samples and 16 from food processing plants and food using two 10bp primers (HLW74, Arbitrary). The data were analyzed using Quantity One and SYN-TAX software. RESULTS: A high percentage of polymorphism was detected with both primers (HLWL-74, 81.81%; Arbitrary, 85.71%). Two major lineages were found, which were divided into four major clusters (A, B C and D) and great genetic diversity was observed. Most of the clinical isolates were grouped within the same cluster, and were more distantly related to the food isolates. CONCLUSION: The results of this study demonstrate a high degree of genetic diversity of DNA polymorphisms among the L. monocytogenes isolates circulating in Colombia, which could reflect phenotypic and pathogenic differences in these isolates.

Bacterial Typing Techniques↗

PubMed2002

Molecular typing techniques to characterize the development of a lactic acid bacteria community on vacuum-packaged beef.

The development of a community of lactic acid bacteria from vacuum-packaged beef was investigated during a 6-week storage trial at 2 degrees C. The lactic acid bacteria population was monitored by using molecular techniques to identify a random sample of isolates at biweekly intervals during the storage trial. The polymerase chain reaction and a randomly amplified polymorphic DNA technique were used to identify and distinguish populations of lactic acid bacteria that developed during the storage trial. At week 0, the population of lactic acid bacteria was 3.5 log cfu/120 cm2 and by week 6, the population reached a maximum of 7.6 log cfu/120 cm2. A sampling from the week 0 population indicated a mixed community of Lactobacillus curvatus, Lactobacillus sakei and Leuconostoc spp. However, the sampling from week 6 indicated the population composition had changed to one where a single Leuconostoc strain predominated. This strain demonstrated antagonism towards the growth of other lactic acid bacteria isolated during the study. Additionally, the strain inhibited the growth of foodborne pathogens Escherichia coli O157:H7 and Listeria monocytogenes. DNA sequence data from the 16S rRNA gene suggested that the isolate may be a Leuconostoc gelidum strain.

Animals↗

PubMed1996

Species, sub-species and hybrid populations of the blowflies Lucilia cuprina and Lucilia sericata (Diptera:Calliphoridae).

The blowflies Lucilia cuprina Wiedmann and Lucilia sericata Meigen (Diptera:Calliphoridae) are facultative ectoparasites of warm blooded vertebrates, particularly domestic sheep. Despite being similar in morphology and ecology, the two species and different populations of each species, are known to vary in their importance as pests in different regions of the world. To elucidate the genetic basis of these species and population level differences, flies were collected from sites in Africa, Europe, Australasia, North America and the islands of Hawaii, and examined using a combination of morphology, the random amplified polymorphic DNA technique and a complementary mitochondrial DNA analysis. The results confirm the species integrity of L. sericata and L. cuprina and support the existence of intra-specific genetic variation in L. cuprina, but not L. sericata.

Animals↗

PubMed2000

Analysis of genetic variability within the genus Petromyces.

Phenotypic and genotypic features of three teleomorphic species, Petromyces alliaceus, P. albertensis and P. muricartus and some related anamorphic Aspergillus species were compared. The dendrogram based on carbon source utilisation data revealed a close relationship between P. muricarus and the A. ochraceus strains examined. P. alliaceus and P. albertensis strains were very closely related to each other. A dendrogram with similar topology was obtained by analysing sequences of the intergenic transcribed spacer regions of representatives of these species. P. alliaceus and P. albertensis strains could only be distinguished by the random amplified polymorphic DNA technique. These strains possibly represent a single species closely related to Aspergillus section Flavi, while the anamorph of P. turicatus is a member of Aspergillus section Circumdati. Our results indicate that Aspergillus section Circumdati is in need of taxonomic revision.

Ascomycota↗

PubMed2001

Choice of methodology for assessing genetic impacts of environmental stressors: polymorphism and reproducibility of RAPD and AFLP fingerprints.

PCR-based multi-locus DNA fingerprints represent one of the most informative and cost-effective measures of genetic diversity and are useful population-level biomarkers of toxicologic and other anthropogenic impacts. However, concerns about reproducibility of DNA fingerprints have limited their wider use in environmental biology. We assessed polymorphism and reproducibility of two common fingerprinting techniques, RAPD (randomly amplified polymorphic DNA) and AFLP (amplified fragment length polymorphism), in pedigreed populations of rainbow trout (Oncorhynchus mykiss) to derive general rules for selective removal of problematic fingerprint bands. We found that by excluding bands that comprised less than 1% of total intensity, and by excluding the largest and smallest 10% of the bands, we could achieve nearly 100% reproducibility of AFLP fingerprints. Similar application of band exclusion criteria to RAPD fingerprints did not significantly enhance their reproducibility, and at least 15% of RAPD bands were not fully repeatable, heritable, or transmittable. The RAPD technique produced more polymorphic fingerprints than AFLP; however, considering that a substantial proportion of RAPD markers did not demonstrate Mendelian inheritance patterns, the AFLP methodology is to be preferred for future research.

Animals↗

PubMed1999

Detection of mitomycin C-induced genetic damage in fish cells by use of RAPD.

Concern about genetic alterations in fish populations arising from anthropogenic activities has led to the adaptation and/or development of new tests and techniques that shed light on these alterations. The high number and the reduced size of chromosomes and the long cell cycle associated with most fish species preclude the use of most accepted genotoxicity assays. The purpose of this work was to study the capability of the randomly amplified polymorphic DNA technique to show genotoxic effects induced by chemicals in fish cells. To do that we studied the effect of 0.5 microg/ml mitomycin C (MMC) on an established rainbow trout cell line (RTG-2). To increase the sensitivity of detecting altered copies of DNA and to avoid the presence of false positives and a lack of reproducibility, the amounts of DNA template and primer present in amplification reactions were studied and optimized after comparison between the control and exposed fingerprints for 4, 6 and 8 h. Results show that 5 ng of DNA template and 4 pM chosen primer were optimum to show differences between control and exposed cells and to obtain reproducible results. The results obtained, after optimum conditions were established, show that this system could be useful for the assessment of DNA alterations in in vitro genotoxicity studies.

Animals↗

PubMed1996

Nosocomial CDC group IV c-2 bacteremia: epidemiological investigation by randomly amplified polymorphic DNA analysis.

The CDC group IV c-2 bacterium is a gram-negative bacillus rarely isolated from clinical specimens. This organism caused catheter-related bacteremia in five immunocompromised children hospitalized in two distinct wards of our institution between November 1993 and October 1994. Three patients recovered on empiric antibacterial chemotherapy combining ceftazidime and amikacin, and a fourth patient required imipenem instead of ceftazidime. The fifth patient recovered without treatment. Catheter removal was never necessary. The randomly amplified polymorphic DNA technique with three different primers was applied to nine isolates recovered by culturing blood from the five children and showed that all of the patients harbored isolates of the same genotype. The source of the outbreak could not be determined.

Adolescent↗