• Journal of Korean Society of Forest Science
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• v.96 no.6
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• pp.667-675
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• 2007

The genetic diversity and the spatial structure in two populations of Abelia tyaihyoni in Yeongwol region were studied by employing I-SSR markers. In spite of the limited distribution and small population sizes of Abelia tyaihyoni, the amount of genetic diversity estimated at the individual level was comparable to other shrub species (S.I.=0.336, h=0.217). Genetic diversity at the genet level was very similar to that at individual level. (S.l.=0.339, h=0.219). About 18.7 percent of total variation was allocated between two populations, which was slightly higher or similar level as compared with other shrub species. Genotypic diversity estimated by the ratio of the number of genets ($N_G$) over the total number of individuals (N) and a modified Simpson's index ($D_G$) were also higher than those of other shrubs. The maximum diameter of a genet did not exceed 5.5 m. The high level of gene and genotypic diversity, and the relatively limited maximum diameter of a genet suggested that the clonal propagation is not the most dominant factor in determining the population structure of Abelia tyaihyoni. Spatial autocorrelation analysis revealed significant spatial genetic structure within 12 m and 18 m distances in two populations A and B, respectively. Autocorrelations among individuals at the both individual and genet levels in each population didn't show any considerable differences. As a sampling strategy for ex-situ conservation of populations showing continuous distribution, a minimum distance of 18 m between individuals was recommended. For the populations with many segments, it was considered very crucial to sample materials from as many segments as possible.

• Restorative Dentistry and Endodontics
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• v.22 no.1
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• pp.413-427
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• 1997

Porphyromonas endodontalis and Prevotella intermedia are black-pigmented anaerobic gram negative rods which have been isolated from infected root canals and submucous abscesses of endodontic origin. And they are associated with clinical symptoms such as pain, percussion, and foul odor. It has been reported that there are 3 serotypes according to capsule membrane in P. endodontalis and 2 DNA homology groups and 3 serotypes in P. intermedia, but there is no data available regarding genetic diversity for the species P. endodontalis and P. intermedia. The purpose of this study is to investigate genetic diversities between individual strains of P. endodontalis and P. intermedia which are indistinguishable by serotyping and biotyping using bacterial DNA restriction endonuclease analysis. 45 teeth with at least one clinical symptoms, with single canal, and with pulp necrosis were sampled. For sampling bacteria, access cavity was prepared after disinfecting tooth and its surroundings. Then the paper point was inserted to the apex of the canal, leave there for 15 seconds, and finally it was placed into PRAS Ringer's solution and PBS solution. P. endodontalis and P. intermedia were identified by biochemical test and IIF after subculturing black and brown colonies which were produced after 7 days of incubation on BAP in anaerobic chamber. P. endodontalis and P. intermedia strains were grown in BHI broth and whole genomic DNA was extracted by phenol-chloroform extraction technique and digested by restriction endonuclease, Eco RI and Pst I. The resulting DNA fragments were separated by agarose gel electrophoresis, stained with EtBr and photographed under UV light. The results were as follows : 1. In both P. endodontalis and P. intermedia, different serotypes could be found within a root canal of same patient. 2. There were obvious genetic heterogeneity within a patient and within a serotype in both P. endodontalis and P. intermedia. 3. P. endodontalis serotype c, isolated from different patients, exhibited limited genotypic diversity.

• Restorative Dentistry and Endodontics
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• v.25 no.4
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• pp.587-598
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• 2000

Urea in the oral cavity is hydrolyzed mainly by bacterial ureases to ammonia, which in turn, raises pH of the oral environment, maintaining oral pH homeostasis, thereby inhibiting dental caries. Streptococcus salivarius has been shown to be a major contribution to oral ureolysis. Synthesis of urease by S. salivarius appears to be constitutive, but can be greatly enhanced in the acidic environment. It has been presumed that ureolytic activity of S. salivarius strains isolated from caries-active site is greater than that of strains from caries-free site. However, no in vivo study has supported the presumption. The present study was performed to observe the ureolytic activity of S. salivarius strains isolated from different environments in the same individual, finding out whether the ureolytic activity is related to dental caries. For the purpose, S. salivarius strains were isolated from caries-active site (>C2), a caries-free site of the tooth, and the dorsum of the tongue of each of 50 patients having decayed teeth. The strains isolated from the patients who harbored S. salivarius in more than two sites were selected and then their ureolytic activities were measured. In order to examine clonal diversity of the strains, their ureC genes were amplified by polymerase chain reaction (PCR) and then restricted with EcoRV, and the protein profiles of the strains were compared by SDS-PAGE. The results were as follows: 1. Of 50 patients, 13 patients harbored S. salivarius in more than two sites; a total of 61 S. salivarius strain were isolated from the patients and selected for the study. 2. Of 17 isolates from the caries-active site of 9 patients harboring S. salivarius in more than two sites including carious lesion, 10 (58.8%) showed a high ureolytic activity (> 200 ${\mu}mol/min/mg$). While, 19 out of 44 isolates (43.2%) from the caries-free site of the teeth and the dorsum of the tongues of 13 patients were the strains with a high ureolytic activity. 3. Of 9 patients harboring S. salivarius in more than two sites including caries-active site. 6 patients were found to have the strains in the caries-active site showing a lower ureolytic activity than the strains in the other sites. 4. Of 34 isolates with ureolytic activity higher than 40 ${\mu}mol/min/mg$, 32 isolates produced 0.54-Kbp PCR products regardless of the sites of bacterial collection. In contrast, of 27 isolates with ureolytic activity lower than 40${\mu}mol/min/mg$, 26 isolates yielded 1.3-Kbp PCR products or none regardless of the sites. 5. Different clonal types of S. salivarius with relatively higher and lower ureolytic activities were found in the same individuals and even in the same sites. 6. None of strains showing different ureolytic activity appeared to be the same clonal type. The overall results suggest that ureolytic activity of the isolates does not appear to be related to differences of the environments but related to their own genetic traits.

• Korean Journal of Plant Resources
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• v.20 no.1
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• pp.79-85
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• 2007

The species in genus Saxifiraga distributed in circumpolar arctic are taxonomically difficult to study. RAPD analyses were performed to compare the genetic diversity of the 16 Saxifrages originated from the Norwegian Arctic Svalbard and Korea. The 12 accessions of URP primers were tested and 4 of which showed polymorphism were selected. Total 79 (44.8%) DNA bands were scored and analyzed by UPGMA cluster analysis. The results indicated that all of the 9 Saxifraga species from Svalbard showed high genetic diversity than those from Korea. The Similarity matrix and cluster analyses indicated that the Saxifraga species from Svalbard and Korea can be divided into two different subgroups. RAPDs of the Saxifraga species of Korea showed higher homologous patterns than those of Arctic Saxifrage. Among the Saxifraga species, we found that the morphological similarity reflects the genetic similarity. The geographic distance, clonal reproduction, and environmental condition may contribute the high level of genetic diversity between Saxifraga species from the two isolated regions.

• Journal of Periodontal and Implant Science
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• v.25 no.1
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• pp.89-98
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• 1995

P. intermedia are considered an important pathogen in adult periodontitis, rapidly progressing periodontitis, refractory periodontitis, pregnancy gingivitis, acute necrotizing ulcerative gingivitis, pubertal gingivitis. So far 2 DNA homology groups and 3 serotypes of P. intermedia have been reported but there is no data available as yet regarding genetic diversity for the species P. intermedia. The purpose of this study is to investigate, using bacterial DNA restriction endonuclease analysis, genetic diversity between individual strains of P. intermedia which are indistinguishable by serotyping and biotyping, occurrence of an intrafamilial transmission and genetic heterogeneity between P. intermedia strains isolated within a patient and within the same serotypes. The families who have had no systemic disease, no experience of periodontal treatment for the previous 1 year and no experience of antibiotics for the previous 6 months were selected and subgingival plaque was collected at 4 sites in each person and incubated in the anaerobic chamber. P. intermedia were identified by colony shape, gram stain, biochemical test, SK-I03(Sunstar Inc.) test and IIF using monoclonal antibody was perfomed for the determination of serotypes. P. intermedia strains were grown in BHI broth and whole genomic DNA was extracted and digested by restriction endonuclease. The resulting DNA fragments were separated by agarose gel electrophoresis, stained and photographed under UV. As the results of this study, intrafamilial vertial transmissions could be assessed in 2 families and horizintal transmissions in another 2 families. There were different DNA digest patterns within a patient, so P. intermedia showed that individuals could be colonized by multiple clonal types at anyone time. And different serotypes could be found within a patient and in the same serotype within a patient, obvius genetic heterogeneity could not be assessed. But in the same serotype in different famies, there were differences in the DNA digest patterns.

• Journal of Microbiology and Biotechnology
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• v.16 no.2
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• pp.193-199
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• 2006

Halotolerant spore-forming Gram-positive bacteria were isolated from the root, rhizosphere, and non-rhizosphere soil of Blutaparon portulacoides. The different isolates were characterized genetically using an amplified ribosomal DNA restriction analysis (ARDRA), and phenotypically based on their colonial morphology, physiology, and nutritional requirements. Three different 16S rRNA gene-based genotypes were observed at a 100% similarity using the enzymes HinfI, MspI, and RsaI, and the phenotypic results also followed the ARDRA groupings. Selected strains, representing the different ARDRA groups, were analyzed by 16S rDNA sequencing, and members of the genera Halobaeillus, Virgibacillus, and Oceanobacillus were found. Two isolates showed low 16S rDNA sequence similarities with the closest related species of Halobacillus, indicating the presence of new species among the isolates. The majority of the strains isolated in this study seemed to belong to the species O. iheyensis and were compared using an AP-PCR to determine whether they had a clonal origin or not. Different patterns allowed the grouping of the strains according to Pearson's coefficient, and the resulting dendrogram revealed the formation of two main clusters, denoted as A and B. All the strains isolated from the soil were grouped into cluster A, whereas cluster B was exclusively composed of the strains associated with the B. portulacoides roots. This is the first report on the isolation and characterization of halotolerant spore-forming Gram-positive bacteria that coexist with B. portulacoides. As such, these new strains may be a potential source for the discovery of bioactive compounds with industrial value.

• Journal of Plant Biotechnology
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• v.46 no.1
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• pp.1-8
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• 2019

The main goal of this study was to determine the genetic diversity among 36 grape cultivars grown in Palestine by using ISSR-polymerase chain reaction (PCR) fingerprints. Among the tested primers, 17 produced reasonable amplification products with high intensity and pattern stability. A total of 57 DNA fragments (loci) separated by electrophoresis on agarose gels were detected and they ranged in size, from 150 to 900 bp. Out of these fragments, 55 (88%) were polymorphic and 2 (3.5%) monomorphic. Our results also revealed an average of 3.1 loci per primer. A minimum of 1 and maximum of 10 DNA fragments were obtained (S-17, #820 and #841) and (S-31) primers, respectively. Therefore, the later primer (S-31) is considered to be the most powerful primer among the tested ones. The genetic distance matrix showed an average distance range of between 0.05 and 0.76. The maximum genetic distance value of 0.76 (24% similarity) was exhibited between the (Shami and Marawi.Hamadani.Adi) as well as (Bairuti and Marawi.Hamadani.Adi) genotypes. On the other hand, the lowest genetic distance of 0.05 (95% similarity) was exhibited between (Jandali.Tawel.Mofarad and Jandali. Kurawi.Mlzlz) along with (Shami.Aswad and Shami.mtartash. mlwn) genotypes. Furthermore, the UPGMA dendrogram generally clusters the grape cultivars into eight major clusters in addition to an isolated genotype. Based on these figures, the cultivars tested in this study could be characterized by large divergence at the DNA level. This is taking the assumption that our region has a very rich and varied clonal grape genetic structure.

• The Korean Journal of Ecology
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• v.15 no.2
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• pp.181-189
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• 1992

Dictyostelid cellular slime molds were quantitatibly isolated from the soils of mt.halla (above 900m in altitude), korea, according to the 'clonal isolation technique(cavender and raper, 1965a)'. Total fifteen species were found, including 1 new and 6 undescribed species.these are dictyostelium mucorodes, dictostelium minutem,polysphondylium pallidum fasciculatum, polysphondylium violaceum, dictyostelium flavidum,dictyostelium fasciculatum, polysphondylium violaceum, dictyostelium flavidum sp. n.(HL-1),dictyostelium aureo-stipes var. aureo-stipes, dictyostelium capitatum, dictyostelium giganteum,dictyostelium polycephalum,dictyostelium brefeldianum,dictyostelium macrocephalum, and dictyostelium sphaerocephalum, dictyostelium sp. (HL-2), dictyostelium sp. (CJ-9). D. mucoroides was the dominant species, and D. minutam,p.pallidum, d. fasciculatum, and p. violaceum were relatively common. d. polycephalum, d. brefeldianum, d. macrocephalum, dictyostelium sp. (HL-3), and d. sphaerocephalum were very rare. Species diversity appeared to be the highest in the deciduous broad-leaved forest from the soils of which 14 species were isolated. eight species were, including five undescribed species, isolated only from this forest soils. Number of isolates severely decrease at the forests above 1,500m in altitude.

• The Korean Journal of Ecology
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• v.27 no.5
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• pp.257-261
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• 2004

Juniperus chinensis var. sargentii Henry is a short and creeping evergreen shrub which reaches about 50㎝ in height and occurs in the northeast Asia and in high mountains over the South Korea. Its distribution is restricted, and the number of individuals are gradually decreasing. This study was conducted to estimate spatial pattern, genetic diversity and spatial genetic structure of J. chinensis var. sargentii. A total of 131 clumps were studied in the study area (40m × 60m). The spatial pattern of this population was random (Aggregation index R=1.031). In spite of the small number and the limited distribution, the level of genetic diversity (Shannon's index 1=0.463) was relatively high as compared with those of other plant species with similar ecological characteristics. ISSR genotypes of all individuals were investigated to find the genetic relationship of clumps and genets. Fifteen clumps were composed to be clones, and a total of 116 unique genotypes were composed by separate genets. Spatial autocorrelation analysis using Tanimoto distance showed that the genetic patch was established within 8m. The effect of clonal reproduction on genetic structure was almost nothing.

• Journal of Microbiology and Biotechnology
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• v.20 no.1
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• pp.169-178
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• 2010

The microbial community structure in Thailand soils contaminated with low and high levels of arsenic was determined by denaturing gradient gel electrophoresis. Band pattern analysis indicated that the bacterial community was not significantly different in the two soils. Phylogenetic analysis obtained by excising and sequencing six bands indicated that the soils were dominated by Arthrobacter koreensis and $\beta$-Proteobacteria. Two hundred and sixty-two bacterial isolates were obtained from arsenic-contaminated soils. The majority of the As-resistant isolates were Gramnegative bacteria. MIC studies indicated that all of the tested bacteria had greater resistance to arsenate than arsenite. Some strains were capable of growing in medium containing up to 1,500 mg/l arsenite and arsenate. Correlations analysis of resistance patterns of arsenite resistance indicated that the isolated bacteria could be categorized into 13 groups, with a maximum similarity value of 100%. All strains were also evaluated for resistance to eight antibiotics. The antibiotic resistance patterns divided the strains into 100 unique groups, indicating that the strains were very diverse. Isolates from each antibiotic resistance group were characterized in more detail by using the repetitive extragenic palindromic-PCR (rep-PCR) DNA fingerprinting technique with ERIC primers. The PCR products were analyzed by agarose gel electrophoresis. The genetic relatedness of 100 bacterial fingerprints, determined by using the Pearson product-moment similarity coefficient, showed that the isolates could be divided into four clusters, with similarity values ranging from 5-99%. Although many isolates were genetically diverse, others were clonal in nature. Additionally, the arsenic-resistant isolates were examined for the presence of arsenic resistance (ars) genes by using PCR, and 30% of the isolates were found to carry an arsenate reductase encoded by the arsC gene.