• Title/Summary/Keyword: RAPD

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Isolations of the Orchid mycorrhizal Fungi from the Roots of the Korean native Orchids and Inoculations of the Isolates to Four different Orchids (한국 자생란에 난 균근균의 분리와 유묘난에 접종)

  • 이상선;오창호;백기엽;이태수
    • Korean Journal Plant Pathology
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    • v.14 no.5
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    • pp.536-542
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    • 1998
  • Ten isolates of the orchid mycorrhizal fungi were isolated from the roots of Korean native orchid plants (Cymbidium goeringii) which inhabitate mainly in southern and western areas of Korea. The growth rates and color of the isolates in potato dextrose agar (PDA) were various. Microscopic observations of the hyphae isolated were identified as Rhizoctonia repens and R. endophytica var endophytica or their related species. R. repens was isolated from the roots of the Korean native orchids, but R. endophytica var endophyica was only isolated from the roots of the commercial orchids introduced from foreign countries. Also, the polymorephic patterns of genomic DNA extracted from selected isolates were compared with those of DNA extracted from the orchid mycorrhizal fungi isolated previously and similar band patterns were observed among those isolates. Five isolates of R. repens were selected and cultured at the oatmeal agar for investigating their symbiosis with orchid plants. The symbiotic specificity between orchid plants and isolated orchid mycorrhizal fungi was observe by growing orchids about six months in the greenhouse. The symbiotic responses of the commercial orchid plants with selected isolates were quite different form different isolates due to the genetic variations.

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Effects of Genotypes on In Vitro Maturation and Fertilization of Frozen-Thawed Porcine Oocytes

  • Jia Y. H.;Jin H. J.;Wee M. S.;Cheong H. T.;Yang B. K.;Park C. K.
    • Reproductive and Developmental Biology
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    • v.29 no.4
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    • pp.207-212
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    • 2005
  • In the present study, we investigated the effects of genotypes on in vitro maturation and fertilization in porcine fresh/frozen-thawed oocytes. The porcine cumulus-oocyte complexes (COCs) were divided into four groups according to whether they were: (1) in vitro matured; (2) cryopreserved and in vitro matured; (3) in vitro fertilized and (4) cryopreserved, and in vitro fertilized. Maturation of porcine COCs was accomplished by incubation in NCSU23 medium. Immature oocytes were cryopreserved by Open Pulled Straws (OPS) method according to Vajta et al., (1998). Oocytes stained by Acetic-Orcein method were observed under the microscope. DNA extracted from the ovaries was analyzed by RAPD (random amplified polymorphic DNA) and SSCP (single strand conformational polymorphisrrt) method. The rates of oocytes maturation and fertilization were significantly high in AA genotype. The results indicated that in vitro maturation and fertilization in porcine fresh/frozen-thawed oocytes may be affected by genotypes in pigs.

Genetic Variation of Rice Populations Estimated Using nrDNA ITS Region Sequence

  • Wang, Dong;Hong, Soon-Kwan
    • Korean Journal of Plant Resources
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    • v.27 no.3
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    • pp.249-255
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    • 2014
  • The rice belonging to Oryza sativa is not only has significant economic importance, for it is the major source of nutrition for about 3 billion all around the world. But also plays a vital role as a model organism, because it has a number of advantages to be a model plant, such as efficient transformation system and small genome size. Many methods and techniques have been conducted to attempt to distinguish different Oryza sativa species, such as amplified fragment length polymorphism (AFLP), random amplified polymorphic DNA (RAPD), simple sequence repeat (SSR) and so on. However, studies using sequence analysis of internal transcribed spacer (ITS), a region of ribosomal RNA has not been reported until now. This study was undertaken with an aim to understand the phylogenetic relationships among sixteen isolates of Oryza sativa collected from abroad and fifteen isolates collected from Korea, using ribosomal RNA (rRNA) internal transcribed spacer (ITS) sequences to compare the phylogeny relationships among different Oryza sativa species. The size variation obtained among sequenced nuclear ribosomal DNA (nrDNA) ITS region ranged from 515bp to 1000bp. The highest interspecific genetic distance (GD) was found between Sfejare 45 (FR12) and Anapuruna (FR15). Taebong isolate showed the least dissimilarity of the ITS region sequence with other thirty isolates. This consequence will help us further understanding molecular diversification in intra-species population and their phylogenetic analysis.

Genomic Fingerprinting of Antituberculosis Agents-Resistant Lactobacillus ruminus SPM0211 Using the Microbial $Uniprimer^{TM}$ Kit

  • Kang, Byung-Yong;Song, Moon-Seok;Kim, Yun-A;Park, So-Hee;Chung, Myung-Jun;Kim, Soo-Dong;Baek, Dae-Heoun;Kim, Kyung-Jae;Ha, Nam-Joo
    • Archives of Pharmacal Research
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    • v.28 no.7
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    • pp.854-858
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    • 2005
  • A Lactobacillus isolate was collected from the feces of a healthy Korean individual and named as Lactobacillus ruminus SPM0211. It was further characterized by subjecting it to an antibiotic resistance test and genetic analysis. In the antibiotic resistance test, all tested Lactobacillus spp. were classified as 'high resistance' for multiple antibiotics, such as isoniazid, ethambutol, cycloserine, and vancomycin. L. ruminus SPM0211 was classified as 'high resistance' for streptomycin also, while the other tested Lactobacillus spp. were classified as low resistance. This suggests that the antimicrobial spectra may be a good indicator in the discrimination of this strain among the tested Lactobacillus spp. In a polymerase chain reaction-random amplified polymorphic DNA (PCR-RAPD) analysis using the Microbial Uniprimer kit, L. ruminus SPM0211, and L. suebicus were clustered as a group with a 74.3% similarity level, suggesting that these two species are genetically related. Thus, our data suggest that the PCR-RADP method using the Microbial Uniprimer kit may be valuable in discriminating L. ruminus SPM0211 from other Lactobacillus spp.

Genetic Relationships among Typhula ishikariensis Varieties from Wisconsin

  • Chang, Seog-Won
    • Weed & Turfgrass Science
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    • v.4 no.2
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    • pp.135-143
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    • 2015
  • Typhula ishikariensis Imai is a causal agent of Typhula snow mold, one of the most important turfgrass diseases in northern regions of the United States. Within Wisconsin isolates, there are three district groups clustered with known isolates of T. ishikariensis var. ishikariensis, var. canadensis and var. idahoensis as identified by RAPD markers. To further investigate the genetic relationship among these groups (varieties), monokaryon-monokaryon and dikaryon-monokaryon mating experiments were conducted. Mating types from var. ishikariensis, var. canadensis and var. idahoensis isolates were paired in all possible combinations. Pairings between var. canadensis and var. idahoensis were highly compatible, while no compatibility was detected between var. ishikariensis and either var. canadensis or var. idahoensis. These results indicate that var. ishikariensis is genetically separated from var. canadensis and var. idahoensis, whereas var. canadensis and var. idahoensis appeared to be genetically related to each other as a taxonomic unit. In the genetic relationship with the known biological species, var. ishikariensis and var. canadensis were genetically related to biological species I and II, respectively. However, var. idahoensis was not compatible with any of the biological species, suggesting that the pathogen may be in the process of biological speciation from var. canadensis.

Purification and Characterization of a Major Fibrinolytic Enzyme from Bacillus amyloliquefaciens MJ5-41 Isolated from Meju

  • Jo, Hyeon-Deok;Lee, Hwang-A;Jeong, Seon-Ju;Kim, Jeong-Hwan
    • Journal of Microbiology and Biotechnology
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    • v.21 no.11
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    • pp.1166-1173
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    • 2011
  • Meju is a traditional Korean fermented soy product used as a key element for soy sauce and doenjang. Bacilli with antimicrobial activity were isolated from meju prepared by traditional methods at Sunchang county, Jeollabukdo, Korea. Six isolates were identified as Bacillus amyloliquefaciens by recA gene sequencing and RAPD-PCR. One isolate, B. amyloliquefaciens MJ5-41, showed the strongest fibrinolytic activity. A 27 kDa active fibrinolytic enzyme, AprE5-41, was purified from the culture supernatant of MJ5-41 grown on LB by chromatographic methods. The optimum pH and temperature for purified AprE5-41 were 7.0 and $45^{\circ}C$, respectively. AprE5-41 quickly degraded $A{\alpha}$ and $B{\beta}$ chains but not the ${\gamma}$-chain of fibrinogen. AprE5-41 exhibited the highest specificity for N-succinyl-Ala-Ala-Pro-Phe p-nitroanilide, a known substrate for ${\alpha}$-chymotrypsin, cathepsin G, and subtilisin BPN'. The structural gene, aprE5-41, was cloned by PCR and successfully expressed in B. subtilis.

Evaluation of the Coal-Degrading Ability of Rhizobium and Chelatococcus Strains Isolated from the Formation Water of an Indian Coal Bed

  • Singh, Durgesh Narain;Tripathi, Anil Kumar
    • Journal of Microbiology and Biotechnology
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    • v.21 no.11
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    • pp.1101-1108
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    • 2011
  • The rise in global energy demand has prompted researches on developing strategies for transforming coal into a cleaner fuel. This requires isolation of microbes with the capability to degrade complex coal into simpler substrates to support methanogenesis in the coal beds. In this study, aerobic bacteria were isolated from an Indian coal bed that can solubilize and utilize coal as the sole source of carbon. The six bacterial isolates capable of growing on coal agar medium were identified on the basis of their 16S rRNA gene sequences, which clustered into two groups; Group I isolates belonged to the genus Rhizobium, whereas Group II isolates were identified as Chelatococcus species. Out of the 4 methods of whole genome fingerprinting (ERIC-PCR, REP-PCR, BOX-PCR, and RAPD), REP-PCR showed maximum differentiation among strains within each group. Only Chelatococcus strains showed the ability to solubilize and utilize coal as the sole source of carbon. On the basis of 16S rRNA gene sequence and the ability to utilize different carbon sources, the Chelatococcus strains showed maximum similarity to C. daeguensis. This is the first report showing occurrence of Rhizobium and Chelatococcus strains in an Indian coal bed, and the ability of Chelatococcus isolates to solubilize and utilize coal as a sole source of carbon for their growth.

Phylogenetic Analysis of the Genus Dendronephthya (Nephtheidae, Alcyonacea) Based on Internal Transcribed Spacer Sequences of Nuclear rDNA

  • Lee, Young-Ja;Song, Jun-Im
    • Animal cells and systems
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    • v.4 no.4
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    • pp.319-324
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    • 2000
  • Species boundaries among the Alcyonacean soft coral, the genus Dendronephthya, are often obscured by inter- and intraspecific morphological variations. In the present study, we attempted to infer the genetic relationships of eight dendronephthians based on their molecular characters, the internal transcribed spacer (ITS) regions of ribosomal DNA, and then compared this result together with the random amplified polymorphic DNA (RAPD) data from our previous investigation. Dendronephthya. putteri and D. suensoni formed a divaricate form - VI grade specific clade, whereas D. castanea, D. gigantea, D. aurea and D. spinifera, formed a umbellate and glomerate form - IV and III grade specific clade. Therefore, we confirmed that the main characters the growth form and the anthocodial grade and formula, are important in identification of the species in dendronephthians despite some problems. Also, the relationships of the growth form are clarified as the glomerate form is much closer to the umbellate form than to the divaricate form based on two sets of independent molecular data. However, we cannot determine the molecular markers which limit the species boundaries among this genus with ITS sequences.

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Genetic Diversity of the Pear Scab Fungus Venturia nashicola in Korea

  • Choi, Eu Ddeum;Kim, Gyoung Hee;Park, Sook-Young;Song, Jang Hoon;Lee, Young Sun;Jung, Jae Sung;Koh, Young Jin
    • Mycobiology
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    • v.47 no.1
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    • pp.76-86
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    • 2019
  • Scab disease caused by Venturia nashicola is of agroeconomic importance in cultivation of Asian pear. However, little is known about the degree of genetic diversity in the populations of this pathogen. In this study, we collected 55 isolates from pear scab lesions in 13 major cultivation areas in Korea and examined the diversity using sequences of internal transcribed spacer (ITS) region, ${\beta}$-tubulin (TUB2), and translation elongation factor-$1{\alpha}$ ($TEF-1{\alpha}$) genes as molecular markers. Despite a low level of overall sequence variation, we found three distinctive subgroups from phylogenetic analysis of combined ITS, TUB2, and $TEF-1{\alpha}$ sequences. Among the three subgroups, subgroup 1 (60% of isolates collected) was predominant compared to subgroup 2 (23.6%) or subgroup 3 (16.4%) and was distributed throughout Korea. To understand the genetic diversity among the subgroups, RAPD analysis was performed. The isolates yielded highly diverse amplicon patterns and none of the defined subgroups within the dendrogram were supported by bootstrap values greater than 30%. Moreover, there is no significant correlation between the geographical distribution and the subgroups defined by molecular phylogeny. Our data suggest a low level of genetic diversification among the populations of V. nashicola in Korea.

Microscopical observation and randomly amplified polymorphic DNA (RAPD) analysis of artificially cultivated Ganoderma applanatum

  • Woo-Sik Jo;Young-Hyun Rew;Seung-Chun Park
    • Journal of Mushroom
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    • v.22 no.2
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    • pp.48-52
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    • 2024
  • This study investigated the microscopic characteristics and genetic relationships of Ganoderma applanatum fruiting bodies. Basidiospores were brown, ellipsoid, and had one or two large vacuoles and a double wall. The surface of basidiospores was smooth or wrinkled and most had numerous small and shallow holes. The length and width of basidiospores of Ganoderma applanatum isolates GBGA-01, GBGA-02, ASI 50167, ASI 52821, ASI 52822, ASI 52823, and ASI 53399 were on average 7.6×4.8 ㎛, 7.9×4.6 ㎛, 7.7×4.9 ㎛, 8.2×5.3 ㎛, 7.7×5.0 ㎛, 8.0×4.9 ㎛, and 7.9×4.9 mm, respectively. In contrast, the basidiospores of Ganoderma lucidum isolate ASI 7125 were 7.7×5.2 ㎛. Using the universal ITS1/ITS4 primer set, the ITS region of the isolates were amplified and sequenced. The ITS sequences were very closely related to G. applantum isolate GBGA-01, GBGA-02, ASI 50167, ASI 52821, ASI 52822, ASI 52823 and ASI 53399, but were not the same species. Whereas, G. lucidum isolate ASI 7125 belongs to different group.