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RAPD
About: RAPD is a research topic. Over the lifetime, 15960 publications have been published within this topic receiving 360391 citations.
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TL;DR: Investigation of RAPDs using Brassica, Sinapis and Raphanus taxa revealed the classical U triangle relationship between diploid and amphidiploid Brassica taxa and suggested at least ten primers are needed to adequately portray these relationships.
Abstract: The potential use of RAPDs for taxonomic studies were investigated using Brassica, Sinapis and Raphanus taxa. Principal coordinate analysis of 284 RAPD bands revealed the classical U triangle relationship between diploid and amphidiploid Brassica taxa. Raphanus sativus and S. alba were distinct from the Brassica taxa. It appears that at least ten primers with approximately 100 total bands are needed to adequately portray these relationships. Cultivars of cabbage and cauliflower were separated by RAPDs. Analysis of RAPDs from individual plants of B. carinata cv. dodola resulted in 69 RAPDs, with 91.7% monomorphic and 8.3% polymorphic bands. RAPDs appear to be useful for taxonomic studies at levels ranging from populations to species and perhaps genera.
269 citations
TL;DR: In plant I, the same RAPD type (RAPD type 12) was found over a 4-year period, indicating that an established in-house flora persisted and was not eliminated by routine hygienic procedures, and indicates that persistent strains may be avoided by rigorous cleaning and sanitation.
Abstract: The contamination routes of Listeria monocytogenes in cold-smoked salmon processing plants were investigated by analyzing 3,585 samples from products (produced in 1995, 1996, 1998, and 1999) and processing environments (samples obtained in 1998 and 1999) of two Danish smokehouses. The level of product contamination in plant I varied from 31 to 85%, and no L. monocytogenes was found on raw fish (30 fish were sampled). In plant II, the levels of both raw fish and product contamination varied from 0 to 25% (16 of 185 raw fish samples and 59 of 1,000 product samples were positive for L. monocytogenes). A total of 429 strains of L. monocytogenes were subsequently compared by random amplified polymorphic DNA (RAPD) profiling, and 55 different RAPD types were found. The RAPD types detected on the products were identical to types found on the processing equipment and in the processing environment, suggesting that contamination of the final product (cold-smoked salmon) in both plants (but primarily in plant I) was due to contamination during processing rather than to contamination from raw fish. However, the possibility that raw fish was an important source of contamination of the processing equipment and environment could not be excluded. Contamination of the product occurred in specific areas (the brining and slicing areas). In plant I, the same RAPD type (RAPD type 12) was found over a 4-year period, indicating that an established in-house flora persisted and was not eliminated by routine hygienic procedures. In plant II, where the prevalence of L. monocytogenes was much lower, no RAPD type persisted over long periods of time, and several different L. monocytogenes RAPD types were isolated. This indicates that persistent strains may be avoided by rigorous cleaning and sanitation; however, due to the ubiquitous nature of the organism, sporadic contamination occurred. A subset of strains was also typed by using pulsed-field gel electrophoresis and amplified fragment length polymorphism profiling, and these methods confirmed the type division obtained by RAPD profiling.
269 citations
TL;DR: AFLP bands scored indicate that AFLPs are a promising marker for mapping important genes in rice, and could be mapped to specific chromosomes, and these appeared to be distributed throughout the rice genome.
Abstract: Amplified fragment length polymorphism (AFLP) has been proposed as a valuable tool for gene mapping in plant species. We compared the levels of polymorphism for AFLP, RAPD, and microsatellite markers on 12 japonica and 2 indica rice cultivars. For AFLPs, seven EcoRI and seven MseI primers used in 18 primer combinations generated a total of 529 bands, of which 147 were clearly polymorphic among the accessions. The 21 RAPD primers produced 103 bands of which 43 were polymorphic. For the microsatellite markers the number of alleles per locus ranged from one (1 locus) to six. All marker types gave the same classification of the rice accessions into subspecies. Within japonica cultivars, the average percent polymorphism between any two accessions was 22% for AFLP, 24% for RAPD, and 36% for microsatellite markers (monomorphic bands excluded). The average percent polymorphism between indica and japonica accessions was 65, 35, and 76%, for AFLP, RAPD, and microsatellite markers, respectively. The total number of polymorphic bands was much higher for AFLPs, averaging over eight per gel. Seven AFLP primer combinations were assayed on 80 F2 plants of an indica x japonica cross previously mapped with RFLP markers. Of 54 AFLP bands scored, 50 could be mapped to specific chromosomes, and these appeared to be distributed throughout the rice genome. This indicates that AFLPs are a promising marker for mapping important genes in rice.
265 citations
TL;DR: Increasing use of carbapenems and ciprofloxacin (selective pressure) as well as clonal dissemination might have contributed to the wide spread of PDRAB in this hospital.
Abstract: The rapid emergence (from 0% before 1998 to 6.5% in 2000) of pandrug-resistant Acinetobacter baumannii (PDRAB) was noted in a university hospital in Taiwan. To understand the epidemiology of these isolates, we studied 203 PDRAB isolates, taken from January 1999 to April 2000: 199 from 73 hospitalized patients treated at different clinical settings in the hospital and 4 from environmental sites in an intensive-care unit. Pulsed-field gel electrophoresis analysis and random amplified polymorphic DNA (RAPD) generated by arbitrarily primed polymerase chain reaction of these 203 isolates showed 10 closely related genotypes (10 clones). One (clone 5), belonging to pulsotype E and RAPD pattern 5, predominated (64 isolates, mostly from patients in intensive care). Increasing use of carbapenems and ciprofloxacin (selective pressure) as well as clonal dissemination might have contributed to the wide spread of PDRAB in this hospital.
262 citations
TL;DR: The rapid screening and identification of tightly linked markers to the target genes demonstrated the potential of RAPD markers for saturating genetic maps.
Abstract: Near-isogenic lines were used to identify restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) markers linked to genes for resistance to downy mildew (Dm) in lettuce. Two pairs of near-isogenic lines that differed for Dm1 plus Dm3 and one pair of near-isogenic lines that differed for Dm11 were used as sources of DNA. Over 500 cDNAs and 212 arbitrary 10-mer oligonucleotide primers were screened for their ability to detect polymorphism between the near-isogenic lines. Four RFLP markers and four RAPD markers were identified as linked to the Dm1 and Dm3 region. Dm1 and Dm3 are members of a cluster of seven Dm genes. Marker CL922 was absolutely linked to Dm15 and Dm16, which are part of this cluster. Six RAPD markers were identified as linked to the Dm11 region. The use of RAPD markers allowed us to increase the density of markers in the two Dm regions in a short time. These regions were previously only sparsely populated with RFLP markers. The rapid screening and identification of tightly linked markers to the target genes demonstrated the potential of RAPD markers for saturating genetic maps.
261 citations