• Title/Summary/Keyword: r-DNA

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DNA Barcoding for Diophrys quadrinucleata (Ciliophora: Euplotia) from South Korea

  • Chae, Kyu-Seok;Min, Gi-Sik
    • Animal Systematics, Evolution and Diversity
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    • v.38 no.4
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    • pp.274-278
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    • 2022
  • One marine ciliate, Diophrys quadrinucleata Zhang et al., 2020 was newly recorded from South Korea in this study. We provided morphological diagnosis and images of the Korean D. quadrinucleata population. We determined the small subunit ribosomal DNA (SSU rDNA) and cytochrome oxidase subunit I (CO1) sequence data of D. quadrinucleata, and then the sequences were compared with other Diophrys species. Intra-specific variation between the Korean and type (Chinese) populations was identical in the SSU rDNA, while the inter-specific variations between seven Diophrys species were 0.3-3.8% in the SSU rDNA and 12.6-18.2% in the CO1. In this study, we obtained 18S and CO1 data from species with identified morphology. As the importance of securing 18S and CO1 based on morphology increases in current studies, this study will contribute to ciliate studies.

Comparison of Nucleotide Sequences of 28S rDNA from Two Viviparid Snail Species in Korea : Cipangopaludina chinensis malleata and C. Japanica (한국산 논우렁이와 큰논우렁이의 28S rDNA 유전자 염기서열 분석)

  • Park, Gab-Man;Younghun Jung;Kim, Jae-Jin;Chung, Pyung-Rim
    • The Korean Journal of Malacology
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    • v.13 no.2
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    • pp.91-96
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    • 1997
  • 한국산 논우렁이(CIpangopaludina chinensis malleata)와 큰논우렁이 (C. japomica)는 형태학적으로 유사하여 그 감별이 용이치 않다. 본 연구는 이 두 종을 대상으로 28S rDNA DI유전자를 7종의 제한효소로 처리하여 PCR-RDLP기법으로 그 절편을 비교하였다. 절편 상호간에는 차이점을 관찰할 수 없었으나, 두 종으로부터 분석된 28S rDNA DI 유전자의 염기서열에서는 4 부위에서 종간 차이를 보였다.

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Isolation of Myxobacteria from Soil and RFLP Analysis of 16S rDNA Fragments. (토양으로부터 Myxobacteria의 분리 및 165 rDNA RFLP분석)

  • 김수광;최병현;김종균;이병규;강희일
    • Korean Journal of Microbiology
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    • v.39 no.3
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    • pp.187-191
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    • 2003
  • In an attempt to isolate myxobacteria from soil samples, we isolated swarm and fruiting body forming bacteria that have bacteriolytic activity on Coli-spot agar plate. For the classification of myxobacteria, 16S rDNA RFLP patterns were analyzed. Amplified 16S rDNAs of myxobacteria type strains (Family I, II, III and IV), negative control strains and soil-isolates were restricted with HaeIII, EcoRI and EcoRV, respectively. We found that the soil-isolates belongs to myxobacteria Family I, II, III.

Drug Resistance in Fish-Pathogenic Bacteria

  • Aoki, Takashi
    • Journal of fish pathology
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    • v.6 no.1
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    • pp.57-64
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    • 1993
  • The properties and DNA structures of R plasmids differ depending on the species of the fish-pathogens Aeromonas hydrophila, A. salmonicida, Edwardsiella tarda, Enterococcus seriolicida, Pasteurella piscicida and Vibrio anguillarum. However, some R plasmids with the same resistance markers in similar DNA structures were found in A. hydrophila and E. tarda, as well as in A. hydrophila and A. salmonicida. R plasmids from V. anguillarum were classified into three groups according to their DNA structures. The first group was detected before 1977, the second from 1980 to 1983, and the third from 1989 to 1991. R plasmids have been retained within P. piscieida having the same DNA structures and detected at various locations and times. E. seriolicida strains carrying the same R plasmids, which were encoded with resistance to macrolide antibiotics(MLs), lincomycin(LIM), and TC, and to MLs, LIM, and CP. were distributed in yellowtail farms in various districts. The chloramphenicol-resistance(cat) gene of the R plasmids of P. piscicida was classified as CAT type I. The cat of the R plasmids of E, tarda. A. salmonicida was classified as type II. The cat of R plasmids of V. anguillarum was classified into two types. One type detected before 1977, was classified as CAT IV and the other type, detected after 1980, was classified as CAT II. Tetracycline-resistance (tet) V. anguillarum, isolated before 1977 and after 1981, was classified as Tet B and Tet G, respectively. The class D tet gene was widely distributed in R plasmids from fish-pathogens A. hydrophila, E. tarda, P. piscicida, and also V. anguillarum isolated after 1989.

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Karyotype Analysis and Physical Mapping of rDNAs in Bupleurum longeradiatum (개시호 (Bupleurum longeradiatum)의 핵형분석과 rDNAs의 Physical Mapping)

  • Koo, Dal-Hoe;Seong, Nak-Sul;Seong, Jong-Suk;Bang, Kyong-Hwan;Bang, Jae-Wook
    • Korean Journal of Medicinal Crop Science
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    • v.11 no.5
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    • pp.402-407
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    • 2003
  • Karyotype analysis and chromosomal localization of 5S and 45S rDNAs using multi-color fluorescence in situ hybridization (McFISH) technique were carried out in Bupleurum longeradiatum. Somatic metaphase chromosome number was 2n=12. Karyotype was composed of three pairs of metacentrics (No.3, 4 and 6) and three pairs of submetacentrics (No. 1, 2 and 5). The length of somatic prometaphase chromosomes ranges from 2.55 to $5.05{\mu}m$ with total length of $18.15\;{\mu}m$. In FISH experiment, one pair of 5S rDNA signals was detected on the pericentromeric region of chromosome 4 and one pair of 45S rDNA signals was detected on the telomeric region of chromosome 2.

Morphology and Sequence Analysis of Nuclear 18S rDNA from the Summer Strain of Porphyra suborbiculata (Rhodophyta) in Korea (여름철 서식 한국산 홍조류 둥근돌김 (Porphyra suborbiculata)의 형태 및 18S rDNA 염기서열 분석)

  • JIN Long-Guo;KIM Myung-Sook;CHOI Jae-Suk;CHO Ji-Young;JIN Hyung-Joo;HONG Yong-Ki
    • Korean Journal of Fisheries and Aquatic Sciences
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    • v.33 no.6
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    • pp.489-495
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    • 2000
  • The 185 ribosomal RNA gene (185 rDNA) of the marine alga Porphyra sp. 723 (Bangiales, Rhodophyta) was amplified using the polymerase chain reaction and its sequence was analysed. The Porphyra species was a summer strain collected on rocks in upper intertidal zone at Ikidae, Pusan on 23rd July 1999. The fronds were $1{\~}5 cm$ long, monostromatic, and orbicular or ovate shaped, They had spinulate processes at margin of the frond, Comparison of this 185 rDNA sequence with the other Forphyra species indicates that Porphyra sp. 723 has the same 185 rDNA sequence derived from Porphyra suborbiculata (NCBI access number; AB 013180) except one base pair substitution in 2327 base pairs.

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Detection and Molecular Characterization of a Stolbur Phytoplasma in Lilium Oriental Hybrids

  • Chung, Bong-Nam;Jeong, Myeong-Il
    • The Plant Pathology Journal
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    • v.19 no.2
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    • pp.106-110
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    • 2003
  • Stolbur Phytoplasma was detected from Lilium Oriental hybrids showing flattened stem and flower clustering. The presence of phytoplasma was demonstrated using polymerase chain reaction(PCR) assays with phyto-plasma-universal(P1/P6)and stolbur phytoplasma-specific 16F1/R1-S primer pairs amplifying phytoplasma 16S rDNA regions. Nucleotide suquences of the phytoplasma 16S rDNA were determined. Nucleic acid extracted from lily amplified 1.5 kb DNA with a phytoplasma universal primer pair. In nested PCR, 1.1 kb PCR product was obtained using specific primer pair, indicating an isolate of stolbur phytoplasma. Nucleotide sequence of phytoplasma 16S rDNA reported in this study showed 99.5% and 99.1% identities with two known stolbur phytoplamas (16Sr XII-A). Also, it exhibited a sequence homology of 98.0% with phormium yellow leaf (16Sr XII-B), and 97.9% with Australian grapevine yellows (16Sr XII-B). Meanwhile, it showed 98.1% identity with strawberry green petal phytoplama, (16Sr1-C), and 94.7 % with American aster yellows (16Sr1-B). Homology percentage of the 16S rDNA nucleotide sequence suggests that this phytoplama could be classified into the stolbur phytoplasma, subgroup A (16Sr XII-A), as a type strain stolbur.

Comparison of metabolic diversity by sole carbon source utilization and genetic diversity by restriction patterns of amplified 16S rDNA (ARDRA)in soil bacterial communities. (토양세균 군집의 대사 다양성과 16S rDNA의 제한효소 지문분석에 의한 유전적 다양성의 비교)

  • 송인근;최영길;김유영;조홍범
    • Korean Journal of Microbiology
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    • v.35 no.1
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    • pp.72-77
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    • 1999
  • To investigate soil bacterial diversity according to vegelalioo types, utilizing ability of sole carbon sources and restriction enzyme patterns of 16s rDNA were analyzed. From the both results; five kinds of soil microbial communities were grouped as forest soil (Quercus mongolica and Pinus densi&ra vegetation), grass-agricultured soil and microbial communities of naked soil. But, both soil microbial communities of directily exlracted from ths soil and indirectly extracted from heterotrophic bacteria that cultured soil in LB medium showed very different similarity.

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Isolation of Lactococci Inhibiting Listeria monocytogenes from Kimchi Habitat and Its Identification by 16S rDNA Analysis (김치 서식처에서 Listeria monocytogenes를 억제하는 lactococci의 분리와 16S rDNA분석에 의한 동정)

  • 박은주;한홍의;민봉희
    • The Korean Journal of Ecology
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    • v.22 no.1
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    • pp.45-50
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    • 1999
  • A bacteriocin-producing strain was isolated from kimchi at the early stage of kimchi fermentation. It was identified as Lactococcus lactis by morphological, cultural and physiological characteristics and partial sequence of 16S rDNA. The bacteriocin from isolate had antimicrobial activity against gram positive pathogenic bacteria, such as Listeria monocytogenes. Staphylococcus aureus and several strains of lactic acid bacteria but not to gram negative bacteria, Yersinia enterocolitica. The bacteriocin was sensitive to protease, protease ⅩⅣ, a-chymotrypsin and pepsin but not to lipase, trypsin and lysozyme. The bacteriocin activity was stable at pH 2-11 and temperature of 100 for 10 min. Thus, Listeria monocytogenes could be inhibited by Lactococcus lactis at early stage of fermentation.

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Combined Effect of Ganciclovir and Vidarabine on the Replication, DNA Synthesis, and Gene Expression of Acyclovir-resistant Herpes Simplex Virus (Acyclovir저항성 Herpes Simplex Virus의 복제, DNA합성 및 형질 발현에 미치는 Ganciclovir 및 Vidarabine의 병용효과에 관한 연구)

  • Yang, Young-Tai;Cheong, Dong-Kyun;Mori, Masakazu
    • The Korean Journal of Pharmacology
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    • v.25 no.1
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    • pp.115-134
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    • 1989
  • Combined effects of ganciclovir (GCV) and vidarabine (ara-A) on the replication, DNA synthesis, and gene expression of wild type-1 herpes simplex virus (HSV-1) and three acyclovir (ACV)-resistant HSV-1 mutants were studied. These mutants include a virus expressing no thymidine kinase $(ACV^r)$, a virus expressing thymidine kinase with altered substrate specificity $(IUdR^r)$, and a mutant expressing altered DNA polymerase $(PAA^r5)$. GCV, an agent activated by herpesvirus specific thymidine kinase, showed potent antiviral activity against the wild type HSV-1(KOS) and DNA polymerase mutant $(PAA^r5)$. The ACV-resistant mutants with thymidine kinase gene $(ACV^r\;and\;IUdR^r)$ were resistant to GCV. All tested wild type HSV-1 or ACV-resistant HSV-1 mutants did not display resistance to vidarabine (are-A). Combined GCV and ara-A showed potentiating synergistic antiviral activity against wild type KOS and $PAA^r5$, and showed subadditive combnined ativiral activity against thymidine kinase mutants. Combined GCV and ara-A more significantly inhibited the viral DNA synthesis in wild type KOS and $PAA^r5-infected$ cells to a greater extent than either agent alone, but the synergism was not determined in $ACV^r$ or $IUdR^r-infected$ cells. These data clearly indicate that combined GCV and ara-A therapy might be useful for the treatment of infections caused by wild type HSV-1 or ACV-resistant HSV-1 with DNA polymerase mutation. ACV-resistant viruses with the mutation in thymidine kinase gene are also, resistant to GCV, but susecptible to ara-A, indicating that ara-A would the drug of choice for the treatment of ACV-resistant HSV-1 which does not express thymidine kinase or expresses thymidine kinase with altered substrate specificity. While the synthesis of viral ${\alpha}-proteins$ of wild type HSV-1 was not affected by ACV, GCV, ara-A, or combined GCV and ara-A, the synthesis of ${\beta}-proteins$ was slightly but significantly increased at the later stage of viral infection by the antiviral agents. The synthesis of ${\gamma}-proteins$ of wild type HSV- 1 was significantly inhibited by ACV, GCV, ara-A, and combined GCV and ara-A. Combined GCV $(5-{\mu}M)$ and ara-A $(100-{\mu}M)$ also significantly altered the expression of viral ${\beta}-and$ ${\gamma}-proteins$, of which efffct was similar to that of GCV $(10-{\mu}M)$ alone. Although ACV at the concentration of $10-{\mu}M$ did not alter the expression of ${\alpha}-$, ${\beta}-$, and ${\gamma}-proteins$ of ACV-resistant $PAA^r5$, GCV and ara-A significantly alter the epression of ${\beta}-and$ ${\gamma}-proteins$, not ${\alpha}-protein$, as same manner as they altered the expression of those proteins in cells inffcted with wild type HSV-1. Combined GCV $(5-{\mu}M)$ and ara-A $(100-{\mu}M)$ altered the expression ${\beta}-and$ ${\gamma}-proteins$ in $PAA^r5$ infected cells, and the effect of combined regimen was comparable of that of GCV $(10-{\mu}M)$. These data indicate that the alteration in the expression of ${\beta}-and$ ${\gamma}-proteins$ in wild type HSV-1 or $PAA^r5$ infected cells could be more significantly affected by combined GCV and are-A than individual GCV or ara-A. In view of the fact that (a) viral ${\alpha}-$, ${\beta}-$, and ${\gamma}-proteins$ are synthesized in a cascade manner; (b) ${\beta}-proteins$ are essential for the synthesis of viral DNA; (c) the synthesis of ${\beta}-proteins$ are inhibited by ${\gamma}-proteins$; and (d) most ${\gamma}-proteins$ are made from the newly synthesized progeny virus, it is suggested that GCV and ara-A, alone or in combination, primarily inhibit the synthesis of viral DNA, and by doing so might exhibit their antiherpetic activity. The alteration in viral protein synthesis in the presence of tested antiviral agents could result from the alteration in viral DNA synthesis. From the present study, it can be concluded that (a) combined GCV and ara-A therapy would be beneficial for the control of inffctions caused by wild type HSV-1 or ACV-resistant DNA polymerase mutants; (b) the combined synergistic activity of GCV and ara-A is due to further decrease in the viral DNA by the combined regimen; (c) ara-A is the drug of choice for the infection caused by ACV-resistant HSV-1 with thymidine kinase mutation; and (d) the alteration in viral protein synthesis by GCV and ars-A, alone or in combination, is mostly due to the decreased synthesis of viral DAN.

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