• BMB Reports
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• v.36 no.5
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• pp.427-432
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• 2003

Jute is the principal coarse fiber for commercial production and use in Bangladesh. Therefore, the development of a high-yielding and environmental-stress tolerant jute variety would be beneficial for the agro economy of Bangladesh. Two molecular fingerprinting techniques, random-amplified polymorphic DNA (RAPD) and amplified-fragment length polymorphism (AFLP) were applied on six jute samples. Two of them were cold-sensitive varieties and the remaining four were cold-tolerant accessions. RAPD and AFLP fingerprints were employed to generate polymorphism between the cold-sensitive varieties and cold-tolerant accessions because of their simplicity, and also because there is no available sequence information on jute. RAPD data were obtained by using 30 arbitrary oligonucleotide primers. Five primers were found to give polymorphism between the varieties that were tested. AFLP fingerprints were generated using 25 combinations of selective-amplification primers. Eight primer combinations gave the best results with 93 polymorphic fragments, and they were able to discriminate the two cold-sensitive and four cold-tolerant jute populations. A cluster analysis, based on the RAPD and AFLP fingerprint data, showed the population-specific grouping of individuals. This information could be useful later in marker-aided selection between the cold-sensitive varieties and cold-tolerant jute accessions.

• Plant Biotechnology Reports
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• v.2 no.3
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• pp.191-198
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• 2008

Germplasm characterization and evolutionary process in viable populations are important links between the conservation and utilization of plant genetic resources. Here, an investigation is made, based on molecular and biochemical techniques for assessing and exploiting the genetic variability in germplasm characterization of taro, which would be useful in plant breeding and ex situ conservation of taro plant genetic resources. Geographical differentiation and phylogenetic relationships of Indian taro, Colocasia esculenta (L.) Schott, were analyzed by random amplified polymorphic DNA (RAPD) and isozyme of seven enzyme systems with specific reference to the Muktakeshi accession, which has been to be proved resistant to taro leaf blight caused by P. colocasiae. The significant differentiations in Indian taro cultivars were clearly demonstrated by RAPD and isozyme analysis. RAPD markers showed higher values for genetic differentiation among taro cultivars and lower coefficient of variation than those obtained from isozymes. Genetic differentiation was evident in the taro accessions collected from different regions of India. It appears that when taro cultivation was introduced to a new area, only a small fraction of genetic variability in heterogeneous taro populations was transferred, possibly causing random differentiation among locally adapted taro populations. The selected primers will be useful for future genetic analysis and provide taro breeders with a genetic basis for selection of parents for crop improvement. Polymorphic markers identified in the DNA fingerprinting study will be useful for screening a segregating population, which is being generated in our laboratory aimed at developing a taro genetic linkage map.

• Journal of Microbiology and Biotechnology
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• v.13 no.1
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• pp.15-21
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• 2003

Two microbial communities of activated sludge in the same municipal wastewater, but treated with different systems, were studied and compared using molecular microbiological approaches. The bacterial 16S rDNA sequences from 124 clones were analyzed, however, the majority of them were not closely related to any known species, and found to belong to 8 different phylogenetic groups and 3 different unidentified groups. The relative frequencies of each group were similar between the two microbial communities. Fingerprinting using terminal restriction fragment length polymorphism (T-RFLP) showed that the putative Nitrospira-related populations were more diverse and quantitatively higher in the KNR process system than in the other system using a conventional activated sludge process. The relationship between the bacterial community composition and the higher removal efficiency of nitrogen and phosphorus in the KNR process is discussed.

• Parasites, Hosts and Diseases
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• v.48 no.4
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• pp.303-307
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• 2010

Stellantchasmus falcatus is a minute intestinal fluke in the family Heterophyidae. Metacercariae, the infective stage, were reported in a marine fish, mullet Liza subviridis, and a fresh water fish, Dermopgenus pusillus, in Thailand. Adults were found in chicks, rats, cats, and humans. Morphological studies were done for comparing Stellantchasmus sp. worms found in 2 different fish hosts; their shapes and organ arrangements were very similar except for the prepharynx length. Therefore, the present study aimed to compare their DNA fingerprints using the HAT-RAPD method for both types of Stellantchasmus and several other related species. Ten arbitrarily selected primers (OPA-04, OPA-09, OPN-02, OPN-03, OPN-09, OPN-12, OPP-11, OPR-15, OPX-13, and OPAD-01) were used. It was found that OPA-09, OPN-03, and OPAD-01 were able to generate S. falcatus specific fragments in mullets which consisted of 200, 760, and 280 bp, respectively. In addition, the results of morphologic, DNA fingerprinting, and phylogenetic analyses strongly suggest that the fresh water and marine specimens of Stellantchamus may be different species.

• The Journal of Korean Society of Virology
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• v.29 no.1
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• pp.39-44
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• 1999

Warts, or verrucae, are benign epithelial proliferations of the skin and mucosa caused by infection with human papillomaviruses (HPV). It is now recognized that there are many different HPV types. Especially type3 is most frequently observed in flat wart. Other types, such as type2, 10, 14, 27, 28, 29, 38, and 41 are rarely encounted in flat wart. We describe here a simple and economic method for detection and identification of epidermodysplasia verruciformis-associated HPV. The method is based on polymerase chain reaction (PCR) amplification and restriction analysis. The method has been developed with cloned HPV DNA and DNA from clinical samples. Clinical samples are from either frozen tissue or paraffin-embedded tissue. Genomic fragments were obtained from two different HPV types (3 and 10). The amplification fragments were identified by a form of miniature fingerprinting, with a set of restriction enzymes that gave a unique digestion pattern for each HPV type. We have tested 74 clinical samples. Only type3 among these clinical samples is detected, and one sample is involved in neither type3 nor type10.

• Korean Journal of Plant Resources
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• v.9 no.3
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• pp.305-310
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• 1996

Five edible mountain vegetables(Saussurea sp. Aster tataricus, A. scaber. Synurus deltoides, Ligularia fischeri) were investigated on the basis of amplified DNA polymorphisms resulted from PCR (polymerase chain reaction) analysis. The sampled plants consisted of 38 individuals in 5 taxa. Only 10 primers out of 62 primers (60 random [10-mer] primers, two 15-mer [M13 core sequence, and (GGAT) sequence]) tested gave rise to polymorphisms in all of the tested plants, producing 176 DAN fragments amplified. Intraspecific polymorphisms found in each taxa showed intraspecies constancy (31.1-61.1%) in the banding patterns of individual plants: Saussurea sp. 31.1%, 15 bands, Aster tataricus, 40.9%, 18 bands, A. scaber. 38.5%, 15 bands. Synurus deltoides, 34.7%, 17 bands, and Ligularia fischeri, 61.1%, 22 brands, respectively. All five species were well classified from each other at the 0.93 level of similarity index value. Intraspecific and interspecific variations were appeared at the levels ranging from 0.62 to 0.99. Based on these results, our PCR analyses support the previous data derived from external morphology of the 5 edible mountain vegetables, but very low levels o intraspecific variations were detected in all of these taxa.

• Journal of Microbiology and Biotechnology
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• v.20 no.4
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• pp.683-692
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• 2010

Morphologically, nine different slow-growing protoclones were screened from regenerated protoplasts of heterokaryotic Agaricus bisporus. As such, the present study is the first report on differentiating homo- and heterokaryotic protoclones using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. Among 80 primers tested, the seven ISSR and seven RAPD primers selected for the analysis generated a total of 94 ISSR and 52 RAPD fragments, respectively. The ISSR fingerprinting also detected more polymorphic loci (38.29%) than the RAPD fingerprinting (34.61%). A principal coordinate analysis (PCA) was employed to evaluate the resolving power of the markers as regards differentiating protoclones. As a result, the mean polymorphism information content (PIC) for each marker system (i.e., 0.787 for RAPD and 0.916 for ISSR) suggested that ISSR is more effective for determining polymorphisms. The dendrograms constructed using RAPD, ISSR, and an integrated RAPD and ISSR marker system were highly correlated with one another as revealed by a high Mantel correlation (r= 0.98). The pairwise similarity index values also ranged from 0.64 to 0.95 (RAPD), 0.67 to 0.98 (ISSR), and 0.67 to 0.98 (RAPD and ISSR), whereas the mean similarity index values of 0.82, 0.81, and 0.84 were obtained for the RAPD, ISSR, and combined data, respectively. As there was a good correspondence between the RAPD and ISSR similarity matrices, ISSR would appear to be an effective alternative to RAPD in the genetic diversity assessment and accurate differentiation of homo- and heterokaryotic protoclones of A. bisporus.

• Journal of Preventive Medicine and Public Health
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• v.38 no.2
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• pp.182-188
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• 2005

Objectives: This study was undertaken to investigate the source of infection and mode of transmission of shigellosis, which occurred sporadically among residents and students in a subcounty of Cheongwon county, Chungbuk province, Korea, from June 4 to July 3 2003. Methods: 692 subjects completed a questionnaire and provided a swab for microbiological examinations,and 7 environmental specimens were examined for bacterial organisms. PFGE (pulsed-field gel electrophoresis) and fingerprinting were performed to find the genetic relationship among the temporally associated sporadic isolates. Results: A total of 29 patients had symptoms consistent with the case definition, with 13 confirmed and 16 suspected cases. The frequency of diarrhea was 6 times or more a day (80.8%), with a duration of 1 to 4 days (88.5%) in most cases. The most common symptoms accompanying the diarrhea were fever (80.9%) followed by abdominal pain (76.9%), headache (65.4%), chill (61.5%), vomiting (46.2%) and tenesmus (15.4%). The epidemic curve was characteristic of a person-to-person transmission. The PFGE and fingerprinting demonstrated identical or similar DNA patterns among the 3 Shigella sonnei isolates (A51, A53 and A61 types) found in this outbreak. Conclusion: A genetically identical strain of S. sonnei was estimated to be the cause of this outbreak, and the mode of transmission was most likely person-to-person.

• Journal of Aquaculture
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• v.20 no.4
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• pp.255-259
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• 2007

Genetic diversity among four populations of Chinese shrimp Fenneropenaeus chinensis from Narodo, Yeonggwang, Taean and Chinese Bohai Bay was assessed by amplified fragment length polymorphism (AFLP) DNA fingerprinting. Total numbers of AFLP bands generated (ranging from 251 to 254) and average percent of polymorphic bands (27.1 to 28.1 %) were similar in the four populations. Heterozygosity and genetic diversity within or among the populations were very low for the populations with average values ranging from 0.1177 to 0.1288 and from 0.1099 to 0.1194, respectively. Analyses of pairwise distance, Fst index and genetic similarity among the populations also revealed the similar results with very low genetic differentiation each other. These results suggest that all the wild populations tested in the present analysis may be belonging to the same genetic origin, and also that they may have a close relationship in genetic structure without any significant differentiation.

• Korean Journal Plant Pathology
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• v.14 no.4
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• pp.308-313
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• 1998

Reverse transcription and polymerase chain reaction (RT-PCR) techiniques were used to identification and differentiation of cucumber mosaic virus isolated from Forsythia koreana (CMV-Fk). RT-PCT used by two set of 20-mer primers one was CMV-common primers and another was CMV subgroup I-specific primers designed in a conserved region of the 3' end of CMV RNA3, amplified about 490 bp and 200 bp DNA fragments from CMV-Fk, respectively. CMV could be detected by RT-PCR at a dilution as low as 10-4 in forsythia crude sap extracts. Restriction enzyme analysis of RT-PCR products using EcoRI and MspI showed that CMV-Fk belonged to CMV subgroup I. But, analysis of RNA fingerprinting by arbitrarily primed polymerase chain reaction (RAP-PCR) showed heterogeneity of RNA3 between CMV-Fk and CMV-Y as a member of subgroup I.