• Title/Summary/Keyword: 25S rDNA

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Distribution and Molecular Phylogeny of the Toxic Benthic Dinoflagellate Ostreopsis sp. in the Coastal Waters off Jeju Island, Korea (춘계 제주 연안에서 유독 저서성 와편모류 Ostreopsis sp.의 분포와 분자계통학적 위치)

  • KIM, SUNJU;SEO, HYOJEONG
    • The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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    • v.24 no.2
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    • pp.236-248
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    • 2019
  • We investigated occurrence and molecular phylogeny of the toxic epiphytic dinoflagellate Ostreopsis at seven sampling sites in the coastal waters off Jeju Island of Korea in April, 2017. During the sampling period, surface water temperature ranged from 15.7 to $18.3^{\circ}C$ and salinity was relatively constant, ranging from 33.4 to 34.9. Of a total of 13 macroalgal species collected from all sampling sites, Ostreopsis cells were observed from 8 macroalgal species and the highest cell abundance ($157.5cells\;g^{-1}$) was recorded on the red alga Grateloupia filicina at St. 6. LSU rDNA D8/D10 sequences of all Korean Ostreopsis strains isolated from the 4 sampling sites were 100% identical. Molecular phylogentic analyses (BI and ML) inferred from LSU rDNA alignment showed that the Korean Ostreopsis strains placed into the previously described the Ostreopsis sp. 1 clade, which contained strains isolated from the temperate coastal waters of Japan. The Korean Ostreopsis sp. 1 strain grew in a wide range of temperature ($10-30^{\circ}C$) and salinity (25-30), with its maximum growth rate of $0.49d^{-1}$ at $25^{\circ}C$ and salinity of 30, indicating that they can be tolerated in temperate areas.

Characterization of Antimicrobial Substance Produced by Lactobacillus paraplantarum KNUC25 Isolated from Kimchi (김치로부터 분리된 Lactobacillus paraplantarum KNUC25가 만드는 항균 물질의 특성)

  • Kim, Ma-Rie;Lee, Su-Jin;Seul, Keyung-Jo;Park, Yu-Mi;Ghim, Sa-Youl
    • Microbiology and Biotechnology Letters
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    • v.37 no.1
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    • pp.24-32
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    • 2009
  • The KNUC25 strain isolated from over-fermented whole Chinese cabbage kimchi was examined for its physiological characteristics using API 50 CHL system assay and identified as Lactobacillus paraplantarum by analysis of whole-cell protein SDS-PAGE pattern assay and similarity of 16S rDNA sequence. L. paraplantarum KNUC25 had a broad antimicrobial activity spectrum from Gram positive to Gram negative bacteria. Scanning electron micrograph analysis showed that KNUC25 might attack to cell surface of indicator cells and destruction can lead to inhibition of the cell growth. The antimicrobial substance of the KNUC25 strain was stable to various degrading enzymes and at high temperature and not a plasmid-born matter. Resistance to proteolytic enzymes showed that an antimicrobial activity of KNUC25 might not be caused by proteinous substance. Maximum production of antimicrobial substance was the exponential growth phase at $30^{\circ}C$.

Molecular Systematics of the Genus Megoura (Hemiptera: Aphididae) Using Mitochondrial and Nuclear DNA Sequences

  • Kim, Hyojoong;Lee, Seunghwan
    • Molecules and Cells
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    • v.25 no.4
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    • pp.510-522
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    • 2008
  • To construct the molecular systematics of the genus Megoura (Hemiptera: Aphididae), DNA based-identification was performed using four mitochondrial and three nuclear DNA regions: partial cytochrome c oxidase I (COI), partial tRNA-leucine + cytochrome c oxidase II (tRNA/COII), cytochrome b (CytB), partial 12S rRNA + tRNA-valine + 16S rRNA (12S/16S), elongation factor-1 alpha ($EF1{\alpha}$), and the internal transcribed spacers 1 and 2 (ITS1, ITS2). Pairwise sequence divergences between taxa were compared, and phylogenetic analyses were performed based on each DNA region separately, and the combined datasets. COI, CytB, $EF1{\alpha}$, ITS1, and ITS2 were relatively effective in determining species and resolving their relationships. By contrast, the sequences of tRNA/COII and 12S/16S were not able to separate the closely related species. CytB and $EF1{\alpha}$ gave better resolution with higher average sequence divergences (4.7% for CytB, 5.2% for $EF1{\alpha}$). The sequence divergence of COI (3.0%) was moderate, and those of the two ITS regions (1.8% for ITS1, 2.0% for ITS2) were very low. Phylogenetic trees were constructed by minimum evolution, maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses. The results indicated that the phylogenetic relationships between Megoura species were associated with their host preferences. Megoura brevipilosa and M. lespedezae living on Lespedeza were closely related, and M. nigra, monophagous on Vicia venosa, was rather different from M. crassicauda, M. litoralis, and M. viciae, which are oligophagous on Lathyrus and Vicia. The three populations of M. crassicauda formed a clade separated from M. litoralis and M. viciae. Nevertheless M. litoralis and M. viciae, which are morphologically similar, were not separated due to negligible sequence divergence. We discuss the phylogenetic relationships of the Megoura, and the usefulness of the seven DNA regions for determining the species level phylogeny of aphids.

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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Desmutagenic Activity of Heated Mountain Herb Juices (산채류(山菜類) 가열즙(加熱汁)의 돌연변이 억제 작용에 관(關)한 연구(硏究))

  • Ham, Seung-Shi
    • Applied Biological Chemistry
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    • v.31 no.1
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    • pp.38-45
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    • 1988
  • Potential mutagenicity of ten heated edible mountain herbs were examined with spore recassay, Ames test and DNA breaking test. Samples of edible mountain herbs were prepared with water extraction at $100^{\circ}C$ for 20 minutes. With the rec-assay, no significant mutagengic activity could be obtained from all of the samples, but among the eight of metal ions added to sample solution, $Pb^{2+}$ to R. crispus heated juice, $Zn^{2+}$ to L. fischeri and S. bracycarpa heated juice increased mutagenic activity of the samples. With the Ames test and DNA breaking test, all of the samples did not show mutagenicity. However, breaking action was activated on heated L. fischeri, P. japonicus. A. triphylla and A. tataricus juices in the presence of 25mM $Cu^{2+}$. But heated A. elata, H. aurantiaca, A. triphylla, S. bracycarpa and A. scaber juices were inactivated in the presence of 25mM $Fe^{2+}$. Desmutagenic activities against benzo$({\alpha})$pyrene significantly increased as increasing concentration of the heated edible mountain herb juices.

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New record of three oxytrichid ciliates (Ciliophora: Oxytrichidae) from South Korea

  • Kyu-Seok, Chae;Gi-Sik, Min
    • Journal of Species Research
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    • v.11 no.4
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    • pp.287-295
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    • 2022
  • Three oxytrichid ciliates, Oxytricha lithofera Foissner, 2016, Pleurotricha curdsi (Shi et al., 2002) Gupta et al., 2003 and Sterkiella tetracirrata Kumar et al., 2015, were isolated from soils and confirmed as new to South Korea. Oxytricha lithofera was identified based on lithosomes, cortical granules, 21-33 adoral zone membranelles, one left (14-21 cirri) and one right (15-18) marginal rows and 5 transverse cirri. Pleurotricha curdsi was identified based on the possession of 2 macronuclear nodules, 2-3 micronuclei, 46-53 adoral zone membranelles, 3 frontal cirri, 5 frontoventral cirri, 5-7 postoral ventral cirri, 2-3 right marginal rows and 5 transverse cirri. Sterkiella tetracirrata was identified with respect 4 macronuclear nodules, 3-6 micronuclei, 25-40 adoral zone membranelles, 3 frontal cirri, 3 postoral ventral cirri, 2 pretransverse cirri, one left (21-30 cirri) and one right (24-30) marginal row and 4 transverse cirri. On the basis of 18S rDNA sequence analyses, we describe the phylogenetic positions of the three species.

Causal Agents of Blossom Blight of Kiwifruit in Korea

  • Lee, Young-Sun;Han, Hyo-Shim;Kim, Gyoung-Hee;Koh, Young-Jin;Hur, Jae-Seoun;Jung, Jae-Sung
    • The Plant Pathology Journal
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    • v.25 no.3
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    • pp.220-224
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    • 2009
  • The causal agents of bacterial blossom blight in kiwifruit were isolated from flowers displaying symptoms in Korea. The pathogens were characterized by biochemical and physiological tests, and identified on the basis of 16S rDNA and 16S-23S internal transcribed spacer (ITS) sequences. Pathogenicity tests demonstrated that the blossom blight of kiwifruit in Korea is caused by two pathogens, Pseudomonas syringae pv. syringae and P. fluorescens. Carbon source utilization and DNA-DNA hybridization experiments confirmed P. fluorescens as one of the causal agents of blossom blight of kiwifruit. P. syringae pv. syringae and P. fluorescens can be distinguished from each other by the symptoms they produce in flowers. P. syringae pv. syringae primarily affected the stamen, while P. fluorescens caused rotting of all internal tissues of buds or flowers.

Cytogenetic Analyses of Angelica Plants Using Feulgen Staining and Multicolor Fluorescence in Situ Hybridization (Multicolor FISH와 Feulgen 염색법을 이용한 Angelica속 식물의 세포유전학적 분석)

  • Koo, Dal-Hoe;Kim, Soo-Young;Bang, Kyong-Hwan;Seong, Nak-Sul;Bang, Jae-Wook
    • Journal of Plant Biotechnology
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    • v.30 no.2
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    • pp.123-127
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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 two Angelica species. The numbers of diploid chromosomes were the same in two same in two species as 2n=22, however the lengths of chromosomes were varied from 4.25 to 6.50 ${\mu}{\textrm}{m}$ in A gigas and 4.95 to 8.50 ${\mu}{\textrm}{m}$ in A acutiloba. The chromosomes of A. gigas were composed of five metacentric and six submetacentric pairs, while those of A. acutiloba were six metacentic, one submetacentric and four subtelocentric paris. In FISH experiments, the numbers and size of 45S rDNA signals were varied between two species, however dach signal of the 5S rDNA was observed in two species.

Ocurrence of Clubroot Caused by Plasmodiophora brassicae on Kohlrabi in Korea (Plasmodiophora brassicae에 의한 콜라비 뿌리혹병 발생)

  • Song, MinA;Choi, InYoung;Song, JeongHeub;Lee, KuiJae;Shin, HyeonDong;Galea, Victor
    • Research in Plant Disease
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    • v.25 no.1
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    • pp.33-37
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    • 2019
  • From 2016 to 2018, approximately 15% of kohlrabi were observed displaying significant clubroot symptoms in farmer's fields in Jeju, Korea. The initial infection appeared as hypertrophy of root hairs, and as the disease progressed, galls formation occurred on the main roots, finally disease progress resulted in yellowing and wilting of leaves. Pathogenicity was proven by artificial inoculation of plants with resting spore suspension, fulfilling Koch's postulates. The resting spore is one-celled, spherical and subspherical, colorless, and $3-5{\mu}m$ in diameter. On the basis of the morphological characteristics and phylogenetic analyses of internal transcribed spacer rDNA, the causal agent was identified as Plasmodiophora brassicae. To our knowledge, this is the first report on the occurrence of P. brassicae on kohlrabi in Korea.

Isolation and Identification of Wild Yeasts from Freshwaters and Soils of Nakdong and Yeongsan River, Korea, with Characterization of Two Unrecorded Yeasts (낙동강과 영산강 담수와 주변 토양으로부터 야생효모의 분리 및 동정)

  • Han, Sang-Min;Kim, Ha-Kun;Lee, Hyang-Burm;Lee, Jong-Soo
    • The Korean Journal of Mycology
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    • v.44 no.4
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    • pp.350-354
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    • 2016
  • Diverse wild yeast were isolated from freshwaters and soils of Nakdong and Yeongsan rivers in Korea and identified by the comparison of polymerase chain reaction-amplified nucleotide sequences of the internal transcribed spacer region (including the 5.8S rRNA) and D1/D2 regions of 26S rDNA, using BLAST. In total, 15 strains belonging to 9 species were isolated from 25 samples, out of which Aureobasidium pullulans and Cryptococcus bestiolae were dominant. Candida ghanaensis JSF0127 and Meira geulakonigii JSF0130 were identified as unrecorded yeasts, for which their mycological characteristics were investigated. These unrecorded yeasts formed ascospores and grew in yeast extract peptone dextrose medium containing 5% NaCl.