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Results for “Random Amplified Polymorphic DNA Technique”

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PubMed2002

[Genetic analysis and identification of three groups three-line hybrid rice and their parents by RAPD markers].

A total of 248 arbitrary 10-mer oligonucleotide primers were screened using RAPD (random amplified polymorphic DNA) techniques with the genome DNA of three groups of three-line hybrid rice and their parents. Thirteen primers produced 43 polymorphism fragments. Six primers of them produced 20 obviously repeatable polymorphic markers among rice lines tested. Using this RAPD markers,the hybrid rice combinations (sterile-line, maintainer-line, restorer-line and F1) can be effectively identified, and the genetic relationship among them can be shown.

English Abstract↗

PubMed2005

[Influences of enteral nutrition combined with probiotics on the gut microecology and barrier function of the rats with abdominal infection].

OBJECTIVE: To investigate the influences of enteral nutrition (EN), parenteral nutrition (PN) and probiotics supplement on the intestinal microecology, and barrier function of the rats with abdominal infection. METHODS: Twenty-one Sprague-Dawley (SD) rats with abdominal infection were randomly divided into three groups, and received PN (PN group, n=7), PN+ EN (PN+ EN group, n=7) or PN+ EN+ probiotics (probiotics group, n=7) respectively with isonitrogen and isocaloric nutrition. The rats were sacrificed after six days. The feces in cecum were cultured for anaerobic bacterial growth and DNA fingerprint spectrum was analyzed by randomly amplified polymorphic DNA technique. The transmembrane binding protein (occludin) and IgA levels in colon and terminal ileum were detected by immunohistochemistry method. The bacterial translocation rate and endotoxin level were also measured. RESULTS: The germ numbers of different species were both higher in PN+ EN and probiotic group than those in PN group. The bands of DNA fingerprint spectrum were significantly decreased in PN group, but the bands in both PN+ EN group and probiotic group were similar to that in the normal rats. The expression levels of occludin and IgA in the intestine and colorectum were higher in both PN+ EN group and probiotic group compared with those of PN group (P< 0.05, P< 0.01, respectively), the expression level of occludin was higher in probiotic group than that in PN+ EN group (P< 0.05). The overall bacterial translocation rates and endotoxin levels were significantly reduced in both probiotic and PN+ EN group (P< 0.05), but there was no difference between probiotic group and EN group. CONCLUSION: EN combined with probiotics can increase occluding and IgA expressions, improve the intestinal microecology,maintain the gut barrier function, and decrease the incidence of gut bacterial translocation.

Abdominal Cavity↗

PubMed1997

Trichinella nelsoni in carnivores from the Serengeti ecosystem, Tanzania.

A survey of trichinellosis among sylvatic carnivore mammals from the Serengeti ecosystem (Tanzania) demonstrated the presence of Trichinella nelsoni in 5 of 9 species examined. Muscle samples were collected from carcasses of 56 carnivores from 1993 to 1995 and frozen before transport and examination. Following artificial digestion of the samples, collected larvae were analyzed by the random amplified polymorphic DNA technique. Trichinella nelsoni was identified in 1 bat-eared fox (Otocyon megalotis), 1 cheetah (Acinonyx jubatus), 1 leopard (Panthera pardus), 3 lions (Panthera leo), and 3 spotted hyenas (Crocuta crocuta). The numbers of bat-eared foxes (6), cheetahs (5), and leopards (3) examined were too small to reveal the roles of these carnivore species in the ecology of T. nelsoni. The numbers of lions and spotted hyenas examined, with a prevalence of 12% and 23%, respectively, suggest that these species may be reservoirs of T. nelsoni in the area under study.

Acinonyx↗

PubMed2000

Identification and characterization of Malaysian river catfish, Mystus nemurus (C&V): RAPD and AFLP analysis.

This work represents the first application of the amplified fragment length polymorphism (AFLP) technique and the random amplified polymorphic DNA (RAPD) technique in the study of genetic variation within and among five geographical populations of M. nemurus. Four AFLP primer combinations and nine RAPD primers detected a total of 158 and 42 polymorphic markers, respectively. The results of AFLP and RAPD analysis provide similar conclusions as far as the population clustering analysis is concerned. The Sarawak population, which is located on Borneo Island, clustered by itself and was thus isolated from the rest of the populations located in Peninsular Malaysia. Both marker systems revealed high genetic variability within the Universiti Putra Malaysia (UPM) and Sarawak populations. Three subgroups each from the Kedah, Perak, and Sarawak populations were detected by AFLP but not by RAPD. Unique AFLP fingerprints were also observed in some unusual genotypes sampled in Sarawak. This indicates that AFLP may be a more efficient marker system than RAPD for identifying genotypes within populations.

Animals↗

PubMed2005

[Genetic diversity of Hepatacodium miconioides natural populations in Zhejiang Province].

Hepatacodium miconioides is the Class II protected plant species in China. This paper studied the genetic diversity and differentiation of its nine natural populations in Zhejiang Province by using random amplified polymorphic DNA (RAPD) technique. Twelve random primers were selected in the amplification, and 164 repetitive loci were produced. The percentage of polymorphic loci in each H. miconioides population ranged from 14.60% to 27.44%, with an average of 20.73%. Among the test populations, Kuochangshan population had the highest percentage of polymorphic loci, Simingshan population took the second place, and Guanyinping population had the lowest one. As estimated by Shannon index, the genetic diversity within H. miconioides populations accounted for 27.28% of the total genetic diversity, while that among H. miconioides populations accounted for 72.72%. The genetic differentiation among H. miconioides populations as estimated by Nei index was 0.7157. The genetic differentiation estimated by Nei index was generally consistent with that estimated by Shannon index, i.e., the genetic differentiation among populations was relatively high, but that within populations was relatively low. The gene flow among H. miconioides populations was relatively low (0.1987), and the genetic similarity ranged from 0.6557 to 0.8119, with an average of 0.7306. The highest genetic distance among populations was 0.4229, while the lowest one was 0.2083. All the results showed that there was a distinct genetic differentiation among H. miconioides populations. The genetic distance matrix of nine test populations was calculated by using the method, and the clustering analysis was made by using the unweighted pair group method with arithmetic mean (UPGMA). The cluster analysis suggested that the nine populations of H. miconioides in Zhejiang Province could be divided into two groups, i.e., eastern Zhejiang group and western Zhejiang group.

Caprifoliaceae↗

PubMed2006

The random amplified polymorphic DNA (RAPD) assay and related techniques applied to genotoxicity and carcinogenesis studies: a critical review.

More than 9000 papers using the random amplified polymorphic DNA (RAPD) or related techniques (e.g. the arbitrarily primed polymerase chain reaction (AP-PCR)) have been published from 1990 to 2005. The RAPD method has been initially used to detect polymorphism in genetic mapping, taxonomy and phylogenetic studies and later in genotoxicity and carcinogenesis studies. Despite their extensive use, these techniques have also attracted some criticisms, mainly for lack of reproducibility. In the light of their widespread applications, the objectives of this review are to (1) identify the potential factors affecting the optimisation of the RAPD and AP-PCR assays, (2) critically describe and analyse these techniques in genotoxicity and carcinogenesis studies, (3) compare the RAPD assay with other well used methodologies, (4) further elucidate the impact of DNA damage and mutations on the RAPD profiles, and finally (5) provide some recommendations/guidelines to further improve the applications of the assays and to help the identification of the factors responsible for the RAPD changes. It is suggested that after proper optimisation, the RAPD is a reliable, sensitive and reproducible assay, has the potential to detect a wide range of DNA damage (e.g. DNA adducts, DNA breakage) as well as mutations (point mutations and large rearrangements) and therefore can be applied to genotoxicity and carcinogenesis studies. Nevertheless, the interpretation of the changes in RAPD profiles is difficult since many factors can affect the generation of RAPD profiles. It is therefore important that these factors are identified and taken into account while using these assays. On the other hand, further analyses of the relevant bands generated in RAPD profile allow not only to identify some of the molecular events implicated in the genomic instability but also to discover genes playing key roles, particularly in the initiation and development of malignancy. Finally, to elucidate the potential genotoxic effects of environmental contaminants, a powerful strategy could be firstly to use the RAPD assay as a screening method and secondly to apply more specific methods measuring for instance DNA adducts, gene mutations or cytogenetic effects. It is also envisaged that these assays (i.e. RAPD and related techniques), which reflect effects at whole genome level, would continue to complement the use of emerging technologies (e.g. microarrays which aim to quantify expression of individual genes).

Animals↗

PubMed2003

Amplification-based nucleic acid scanning techniques to assess genetic polymorphism in Candida.

Opportunistic pathogen Candida causes common fungal infections that manifest both superficially and systemically, especially in compromised patients. Although C. albicans is by far the main etiological agent of candidosis, the frequency of isolation of other non-albicans species such as C. glabrata and C. krusei is increasing at an alarming rate. Therefore, the epidemiology, pathogenicity, and diagnosis of infections due to these organisms are of great importance. Of a variety of genotyping methods utilized for strain delineation of these Candida species, amplification-based techniques such as randomly amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), restriction digestion-mediated PCR (RFLP-PCR), and single-stranded conformational polymorphism (SSCP) and microsatellite PCR (interrepeat PCR, IR-PCR) are the most popular and widely used. In the last decade or so these techniques have helped unravel the clinical epidemiological features of pathogenicity, diversity, microevolution, and natural heterozygosity in Candida species. Here we review in detail the basic principles of RAPD, the nature of the primer and factors influencing its selection, and the limitations of RAPD assays as well as analysis and interpretation of banding profiles generated using the software programs. In addition, the principles of other RAPD-based amplification techniques (AFLP, RFLP-PCR, SSCP, and IR-PCR) and their application in molecular epidemiologic studies of Candida species in particular and other fungi in general are also reviewed. It is concluded that these methods have wide applicability in genotyping fungi, although they differ greatly in their resolution and have advantages and drawbacks depending on the task in question.

Candida↗

PubMed2000

A random amplified polymorphic DNA polymerase chain reaction technique that differentiates between Neospora species.

Neospora caninum is a recently described coccidial parasite that was first isolated from a dog in 1988 and has subsequently been shown to infect a wide range of mammals. Neospora hughesi, a new species of this genus, has recently been isolated from the spinal cord of horses showing clinical signs of equine protozoal myeloencephalitis. The random amplified polymorphic DNA polymerase chain reaction technique is capable of differentiating between N. caninum and N. hughesi.

Animals↗

PubMed2004

[Genetic diversity analysis of brown cotton and green cotton].

Genetic diversity analysis of brown cotton Xincai 1 and Xincai 2 and green cotton Xincai 3 and Xincai 4 and other 47 color cottons was conducted by the random amplified polymorphism DNA (RAPD) techniques, using 6 random primers. Cluster and similarity analysis of these cottons showed that the differences in genetic relationship and similarity among the brown cottons, green cottons and brown-green cottons are not remarkable. The results also reflect that the genetic bases of the brown and green cottons are narrow, and they are at the same genetic diversity level. These results are probably due to the same basic germplasms, the same breeding aims and the similar breeding approaches.

Cluster Analysis↗

PubMed2000

The differentiation of Carnobacterium divergens using the random amplification of polymorphic DNA polymerase chain reaction technique.

The potential of the randomly amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) technique to differentiate Carnobacterium divergens from other members of the genus Carnobacterium was examined. A numerical analysis of the genomic profiles obtained demonstrated that it was possible to differentiate the C. divergens strains from other Carnobacterium strains using this technique. The heterogeneity observed in the representatives of the species C. piscicola adds further weight to the suggestion in other taxonomic studies that subspecies of this species exist.

Bacteria↗

PubMed1998

Random amplification of polymorphic DNA and microsatellite genotyping of pre- and posttreatment isolates of Candida spp. from human immunodeficiency virus-infected patients on different fluconazole regimens.

Twelve patients infected with the human immunodeficiency virus (HIV) and with CD4 cell counts below 100 cells/microliter received fluconazole daily (200 mg; five patients) or weekly (400 mg; seven patients) for fungal prophylaxis during a 6-month period. Oropharyngeal swabs were taken at regular intervals in order to detect colonization with Candida spp. All yeast isolates were examined with respect to the development over time of fluconazole resistance. Genetic diversity among the strains was assessed in order to discriminate between selection of a resistant subclone and patient recolonization. Genotyping was performed through random amplification of polymorphic DNA (RAPD) analysis. Specific site polymorphisms were assayed by tracking length variability in several microsatellite loci. Finally, to maximize resolution, one of these loci (ERK1) was analyzed by nucleotide sequencing. Although the number of strains analyzed was too small to allow statistical verification, it appeared that when fluconazole was given weekly, a smaller fraction of the strains showed diminished sensitivity than when it was given daily. Genetic analyses allowed three different scenarios to be discerned. Resistance development in an otherwise apparently unchanged strain was seen for 1 of the 12 patients. Clear strain replacement was observed for 3 of the remaining 11 patients. For all other patients minor differences were seen in either the RAPD genotype or the microsatellite allele composition during the course of treatment. In general, microsatellite sequence data is in agreement with data obtained by other methods, but occasionally within-patient heterogeneity is indicated. The present results show that during fluconazole treatment colonizing strains can remain identical, be replaced by clearly different strains, or undergo small changes. Within a patient there may be different levels of intrastrain variation.

AIDS-Related Opportunistic Infections↗

PubMed2000

[Phylogenetic study of Artemia from China using RAPD and AFLP markers].

We have applied the techniques of RAPD (random amplified polymorphic DNA) and AFLP (amplified fragment length polymorphism) to the analysis of the relationships among Artemia species and strains. RAPD markers were successfully employed to detect diversity and genetic differentiation among four species of brine shrimp: A. franciscana, A. urmiana, A. sinica, and A. parthenogenetica. Seventy, ten-base synthetic oligonucleotides were used to amplify a total of 458 distinct fragments. DNA polymorphisms were found in all the species examined; The highest percentage of polymorphic bands found in A. parthenogenetica, was 28.8 per cent. There are significant differences between bisexual sibling species and parthenogenetic populations. A. parthenogenetica provided 94 specific molecular markers, while bisexual sibling species gave 27 specific molecular markers. A. sinica is a species distinct from the other Old World bisexual species. AFLP were used to analyze 15 Artemia species and strains for genetic diversity. They are extremely sensitive to even a small sequence variation and more polymorphism than RAPD. Using only 10 pairs of primer combinations, we detected 580 AFLP bands of which were polymerphic. The RAPD and AFLP techniques are powerful DNA fingerprinting methods for classification of Artemia species and strains.

Animals↗

PubMed2004

ARDRA and RAPD analyses of human and animal isolates of Streptococcus gallolyticus.

A total of 23 Streptococcus gallolyticus strains, consisting of 12 strains from feces of healthy animals and 11 from clinical cases of human or cow mastitis milk, were examined genealogically. Four strains of S. bovis "biotype II/1" and 3 strains of S. equinus, the closely related organisms to S. gallolyticus, were also analyzed for outgroup comparison. Neither the amplified ribosomal DNA restriction analysis (ARDRA) nor the randomly amplified polymorphic DNA (RAPD) analysis that had been designed to recognize S. gallolyticus strains virulent in pigeons could differentiate clinical strains from the others of S. gallolyticus. No correspondence between the DNA profile in either analysis and the host animal species was detected.

Animals↗

PubMed2005

Inter-alu PCR detects high frequency of genetic alterations in glioma cells exposed to sub-lethal cisplatin.

Increased genomic instability contributes to higher frequency of secondary drug resistance and neoplastic progression in tumors as well as in cells exposed to sub-lethal concentrations of chemotherapeutic agents. We have used PCR based DNA fingerprinting techniques of randomly amplified polymorphic DNA (RAPD) and inter-alu PCR to study this phenomenon in the tumor genome. The choice of the primer, either random (for RAPD) or specific (inter-alu PCR) can determine the nature of alterations being assessed. We have compared the inter-alu PCR and RAPD profiles of U87MG glioblastoma cells exposed to sequentially increasing low doses of cisplatin for 24 passages to that of untreated controls. Inter-alu PCR, with 2 primers, demonstrated a number of alterations in the treated cells, in the form of loss / gain and changes in the intensity of bands. No changes were observed by RAPD analysis with 5 primers, however, indicating a preferential increase in the alu mediated recombination frequency in the treated cells (p = 1.866 x 10(-4)). The number of changes observed with respect to the corresponding leucocyte DNA in the inter-alu PCR profile of 26 primary tumors (Grade II = 13; Grade IV = 13), resected before chemotherapy, for the 2 inter-alu primers was very small. We present a novel application of the inter-alu PCR in detecting alterations in long term cultured cells at low dose exposure to a chemotherapeutic agent. Our results suggest that alu mediated recombination may be important in cells exposed to sub-lethal doses of cisplatin but not in the genesis of primary glioma.

Alu Elements↗

PubMed2005

The use of RAPD to characterize Bipolaris sorokiniana isolates.

Bipolaris sorokiniana is a phytopathogenic fungus causing diseases of cereal crops such as common root rot, the leaf spot disease, seedling blight, and black point of the grain. Random-amplified polymorphic DNA (RAPD) assay was used to investigate the genetic diversity of 20 isolates collected from different cultivars in wheat-producing regions in Brazil. Seventy primers, with random nucleotide sequences, were tested. Reproducibility to amplify the genomic DNA of isolates was found for 30 of the 70 primers tested, generating between 1 and 17 fragments ranging from 0.35 to 2.0 kb (average size). The degree of similarity between samples was calculated through simple association and the dendrogram was assessed using the unweighted pair group method with arithmetical average. After the RAPD analyses 19 isolates were closely grouped, having a similarity coefficient of >or= 78%. Isolate I017 showed very low similarity coefficients, ranging between 38 and 46%. The RAPD analyses provided important information as to the degree of genetic variability and the relationship between the isolates investigated, revealing polymorphism and establishing electrophoretic profiles useful to characterize the phytopathogen.

Ascomycota↗

PubMed2000

Potential utility of random amplified polymorphic DNA (RAPD) and restriction endonuclease assay (REA) as typing systems for Madurella mycetomatis.

Two molecular methods were compared, random amplified polymorphic DNA (RAPD) and restriction endonuclease analysis (REA), in order to evaluate their ability to discriminate, and to characterize Madurella mycetomatis strains isolated from human mycetomas in different parts of the world. Both methods were able to cluster the Madurella mycetomatis isolates into the same number of distinct typing groups. However, RAPD, presenting several advantages over REA such as its rapidity, simplicity, and the accessibility for implementation in the laboratory, is a more sensitive and reproducible tool for the study of Madurella mycetomatis epidemiology than REA.

DNA Restriction Enzymes↗

PubMed2004

Screening of a RAPD marker tightly linked to Co gene in apple and the SCAR marker conversion.

A DNA marker linked to the columnar gene (Co) in apple (Malus domestica) was explored based on the population of 105 progenies of 'Spur Fuji' x 'Telamon' by bulk segregant analysis (BSA) and Random Amplified Polymorphic DNA (RAPD) technique. A total of 300 random primers were screened and a RAPD marker (S1142(682)) closely linked to Co gene (2.86 cM) was identified and then sequenced. Four specific PCR primers (two forward primers and two reverse primers) were designed,and the products of SCAR-PCR indicated that all the four pairs of primers could amplify polymorphic bands between columnar and non-columnar traits, so any of them could serve as the specific SCAR primers. One pair of these specific primers was chosen to amplify each individual in the population, and the result showed that the co-segregation pattern of this SCAR marker and Co gene was the same as that of the RAPD marker. Furthermore, it was found that the nucleotide sequence of the RAPD marker fragment contained an open reading frame (ORF) that could encode 68 deduced amino acid residues at the position of +45 - +251.

Amino Acid Sequence↗

PubMed1997

Genetic diversity among isolates of Aspergillus fumigatus in patients with cystic fibrosis.

Strains of Aspergillus fumigatus (n = 24) were isolated from the sputa of six patients with cystic fibrosis during periods from 3 to 11 months. The genetic polymorphisms of the strains were studied using the random amplified polymorphic DNA (RAPD) assay with three single oligonucleotides and pairwise combined primers. The analysis of RAPD patterns resulted in 15 different RAPD types. In four patients, the colonizing type changed, whereas in two others the same types were detected over periods between 3 and 11 months. The genetic diversity as well as the shift of the colonizing strains found in some patients might be important for the epidemiology of Aspergillus infections in patients with cystic fibrosis.

Adult↗