• Title/Summary/Keyword: 28S rDNA

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Identification and Characterization of an Agarase- and Xylanse-producing Catenovulum jejuensis A28-5 from Coastal Seawater of Jeju Island, Korea (제주 연안해수로부터 한천 분해 효소 및 자일란 분해 효소를 생산하는 Catenovulum jejuensis A28-5의 동정 및 특성 규명)

  • Kim, Da Som;Jeong, Ga Ram;Bae, Chang Hwan;Yeo, Joo-Hong;Chi, Won-Jae
    • Microbiology and Biotechnology Letters
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    • v.45 no.2
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    • pp.168-177
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    • 2017
  • Strain A28-5, which can degrade xylan and agar in solid medium, was isolated from a coastal seawater sample collected from Jeju Island, South Korea. This strain was found to be a gram-negative, $Na^+$-requiring bacterial strain with a polar flagellum for motility. Additionally, the strain was tolerant to antibiotics such as ampicillin and thiostrepton. The G+C content of the genome was 43.96% and menaquinone-7 was found to be the predominant quinone. Major fatty acids constituting the cell wall of the strain were $C_{16:1}$ ${\omega}7c/iso-C_{15:0}$ 2-OH (23.32%), $C_{16:0}$ (21.83%), and $C_{18:1}$ ${\omega}7c$ (17.98%). The 16S rRNA gene sequence of the strain showed the highest similarity (98.94%) to that of Catenovulum agarivorans YM01, which was demonstrated by constructing a neighbor-joining phylogenetic tree. A28-5 was identified as a novel species of the genus Catenovulum via DNA-DNA hybridization with Catenovulum agarivorans YM01, and thus was named as Catenovulum jejuensis A28-5. The formation of tetramers and hexamers of xylooligosaccharides and (neo)agarooligosaccharides, respectively, were confirmed by thin-layer chromatography analysis using an enzyme reaction solution containing xylan or agarose with two crude enzymes prepared from the liquid culture of the strain.

Occurence of Powdery Mildew Caused by Podosphaera xanthii on Vigna nakashimae in Korea (Podosphaera xanthii에 의한 좀돌팥 흰가루병 발생)

  • Kyung-Gu, Min;Tae-Min, Park;Youn-Jin, Park;Myoung-Jun, Jang
    • Research in Plant Disease
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    • v.28 no.4
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    • pp.248-251
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    • 2022
  • In October 2022, common Asian cowpea (Vigna nakashimae) powdery mildew disease was investigated at Yesan-gun, Chungcheongnam-do, Korea (36°40'12.7"N,126°51'36.4"E). The disease mainly occurred on the front of the leaves, and weak powdery mildew disease occurred on the back side of leaf. The chasmothecia was identified on the back side of the leaf. Analysis of the internal transcribed spacer rDNA sequence and 28S large subunit sequence, along with the morphological characteristics of the anamorph and teleomorph of the causal fungus identified as Podosphaera xanthii. This is the first time in Korea to report common Asian cowpea (Vigna nakashimae) powdery mildew disease caused by Podospaera xanthii.

Morphological and molecular characteristics of Paralecithodendrium longiforme (Digenea: Lecithodendriidae) adults and cercariae from Chinese pipistrelle bats and viviparid snails in Thailand

  • Thitichai Arttra;Pheravut Wongsawad;Chalobol Wongsawad;Nattawadee Nantarat;Preeyaporn Butboonchoo;Jong-Yil Chai
    • Parasites, Hosts and Diseases
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    • v.62 no.1
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    • pp.85-97
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    • 2024
  • This study aimed to describe the morphological and molecular characteristics of Paralecithodendrium longiforme (Digenea: Lecithodendriidae) adults and cercariae isolated in Thailand. Adult flukes were isolated from the Chinese pipistrelle bat (Hypsugo sp.), and cercariae were detected in the viviparid snail (Filopaludina martensi martensi) from Chiang Mai province. The morphological characteristics were observed and described using conventional methods, and the molecular characteristics with internal transcribed spacer 2 (ITS2) and 28S rDNA gene sequences. The adult flukes were fusiform, 0.84-0.98 mm in length, and 0.37-0.49 mm in width, and were distinguishable from other species by the presence of longitudinal uterine coils. The cercariae were nonvirgulate xiphidiocercariae, with the oral sucker bigger than the acetabulum, the tail without fin fold, a body size of 117.5-138.3×48.3-52.2 ㎛, and a tail size of 100.7-103.7×15.0-18.9 ㎛. Molecular studies revealed that the adults and cercariae shared 99.3% (ITS2) and 99.6% (28S rDNA) homology with each other. They were phylogenetically close to P. longiforme with an identity of 94.5% for ITS2 and 98.7% for 28S rDNA. This study provides new information on the natural definitive host and first intermediate host of P. longiforme in Thailand. The discovery of its cercarial stage in Filopaludina snails highlights the importance of monitoring the associated second intermediate host and prevention and control of this potentially zoonotic trematode.

IDENTIFICATION OF PUTATIVE PATHOGENS IN ACUTE ENDODONTIC INFECTIONS BY PCR BASED ON 16S rDNA (중합효소연쇄반응법을 이용한 급성 치수 및 치근단 질환의 병원성 세균의 동정)

  • Kim, Ji-Hoon;Yoo, So-Young;Lim, Sun-A;Kook, Joong-Ki;Lim, Sang-Soo;Park, Seul-Hee;Hwang, Ho-Keel
    • Restorative Dentistry and Endodontics
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    • v.28 no.2
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    • pp.178-183
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    • 2003
  • The purpose of this study was to investigate the frequency of 7 putative pathogens in endodontic infections. The specimens were collected from infected pulpal tissue of patients who were referred for root canal treatment to the department of conservative dentistry, Chosun University Samples were collected aseptically using a barbed broach and a paper point. The cut barbed broaches and paper points were transferred to an eppendorf tube containing 500 ml of 1 X PBS. DNAs were extracted from the samples by direct DNA extraction method using lysis buffer (0.5% EDTA, 1% Triton X-100). Identification of 7 putative pathogens was performed by PCR based on 16S rDNA. The target species were as follows : Porphyromonas endodontalis, Porphyromonas gingivalis, Prevotella intermedia, Prevotella nigrescens, Bacteroides forsythus, Actinobacillus actinomycetemcomitans, and Treponema denticola. Our data revealed that the prevalence of P. endodontalis was found in 88.6% (39/54), P. ginivalis 52.3% (23/44), P. nigrescens 18.2% (8/44), P intermedia 15.9% (7/44) B. forsythus 18.2% (8/44), A. actinomycetemcomitans 3.3% (1/44), T. denticola 25% (l1/44) of the samples. The high prevalence of P. endodontalis and P. ginivalis suggests that they may play an important role in the etiology of endodontic infections.

Mariannaea samuelsii Isolated from a Bark Beetle-Infested Elm Tree in Korea

  • Tang, Longqing;Hyun, Min-Woo;Yun, Yeo-Hong;Suh, Dong-Yeon;Kim, Seong-Hwan;Sung, Gi-Ho;Choi, Hyung-Kyoon
    • Mycobiology
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    • v.40 no.2
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    • pp.94-99
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    • 2012
  • During an investigation of fungi from an elm tree infested with bark beetles in Korea, one isolate, DUCC401, was isolated from elm wood. Based on morphological characteristics and phylogenetic analysis of the internal transcribed spacer and 28S rDNA (large subunit) sequences, the isolate, DUCC401, was identified as Mariannaea samuelsii. Mycelia of the fungus grew faster on malt extract agar than on potato dextrose agar and oatmeal agar media. Temperature and pH for optimal growth of fungal mycelia were 25oC and pH 7.0, respectively. The fungus demonstrated the capacity to degrade cellobiose, starch, and xylan. This is the first report on isolation of Mariannaea samuelsii in Korea.

Characteristics of Heterotrophic Bacterial Population in the Artificial Lake Geumgang Near Estuary Barrage (금강 하구둑 인근에서 미생물군집의 특성)

  • Bae, Myoung-Sook;Park, Suhk-Hwan;Choi, Gang-Guk;Lee, Keun-Kwang;Lee, Geon-Hyoung
    • The Korean Journal of Ecology
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    • v.28 no.3
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    • pp.129-134
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    • 2005
  • The monthly variations of physico-chemical and microbiological water quality were investigate in the artificial Lake Geumgang near estuary barrage. Sixty heterotrophic bacteria were isolated and identified by amplification and sequencing of 16S rDNA. Water temperature, pH, and inorganic nutrients($NH_4$-N, $NO_2$-N, $NO_3$-N, $PO_4$-P) were measured. Concentrations of DO, BOD, and inorganic nutrients were lower than in the middle-stream of Geum river The population densities of heterotrophic bacteria and total coliforms varied from $4.1{\pm}1.0\times10^2$ to $6.7{\pm}1.1{\times}10^3\;cfu\;ml^{-1}$, and 0 to $2.3{\pm}0.6{\times}10^2\;cfu\;ml^{-1}$, respectively. Among the measured numbers of physiological groups of bacteria, cellulolytic bacteria showed higher population densities than those of other physiological groups. Bacterial community structure was analysed based on 16S rDNA partial sequencing. Among 60 isolates, dominant genus was Pseudomones (20 strains).

Sequence Analysis of the Internal Transcribed Spacer of Ribosomal DNA in the Genus Rhizopus

  • Park, You-Jung;Min, Byung-Re
    • Mycobiology
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    • v.33 no.2
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    • pp.109-112
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    • 2005
  • The internal transcribed spacer (ITS) regions including the 3'-end of 18S rRNA gene, 5.8S rRNA gene and the 5'-end of the 28S rRNA gene of Rhizopus spp. were amplified by PCR and analyzed by DNASIS program. Length polymorphism of these region ranged from 564 bp in R. oryzae to 789bp in R. stolonifer. The length and sequence of 5.8S was very conserved with $154{\sim}155\;bp$. The sequence of ITS2 was more variable than that of ITS1. The base substitution rates were ranged from 0 to 0.6069 per site, and higher rate was found in R. stolonifer. In general, transition was usually more frequent than transversion. On the basis of sequencing results, four groups were clustered with value of 61.9% similarity; R. oryzae, R. micros pores, R. homothallicus, and R. stolonifer groups.

Cytogenetical Study of Cynanchum wilfordii and Cynanchum auriculatum using Fluorescence In Situ Hybridization (FISH) (rDNA FISH를 이용한 큰조롱과 넓은잎큰조롱의 세포유전학적 연구)

  • Kim, Su Hyun;Kim, Woo Cheol;Kim, Hyun Hee;Heo, Kweon
    • Korean Journal of Medicinal Crop Science
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    • v.28 no.5
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    • pp.325-330
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    • 2020
  • Background: Dried tuberous roots of Cynanchum wilfordii are known to relieve menopause symptoms. However, the dried roots of C. wilfordii are morphologically similar to those of C. auriculatum, which makes it difficult to distinguish when used as a medicine. Various comparative studies have focused on chemical or molecular analysis of these roots. However, the differences between the two species at the cytogenetic level based on chromosome structure and composition remain to be elucidated. Methods and Results: For chromosome slides, the roots were fixed in 8-hydroxyquinoline, digested with enzyme mixture, and spread on slides. 5S and 45S rDNA were used as cytogenetic markers for the analysis of nuclear genomes by FISH. The chromosome number of the two species was 2n = 22, with a relatively short length, 1.13 ㎛ - 4.24 ㎛ and 1.00 ㎛ - 3.42 ㎛ with respect to each other. Both species represent one pair of 5S and 45S rDNA signal on chromosome 1, at the proximal region and peri-centromeric region, respectively. Conclusions: These preliminary cytogenetic data using FISH in C. wilfordii and C. auriculatum could be valuable for the comprehension of Cynanchum genome history.

Characteristics and Diagnostic Methods of Streptococcosis Causing Disease in Aquaculture (양식 어류에 질병을 유발하는 연쇄구균증의 특성 및 진단 방법)

  • Kim, Dong-Hwi;Heo, Moon-Soo
    • Journal of Life Science
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    • v.28 no.9
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    • pp.1118-1126
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    • 2018
  • In this study, investigated the general characteristics and diagnostic methods types of streptococcosis among various fish disease pathogens that caused a lot of economic damaged to aquaculture fish based on the previous research paper. Streptococcosis infection of fish is considered a reemerging disease affecting a variety of wild and cultured fish throughout the world. Calssifiacation of Gram positive cocci based on DNA-DNA hybridization coupled with 16S sequencing has shown that at least five different species are considered of significance as fish pathogens: Lactococcus garvieae, L. piscium, Streptococcus iniae, S. agalactiae, S. paruberis, Vagococcus salmoninarum. Symptoms of infection with streptococcosis disease such as body color change, eyeball abnormality, gill discoloration, bleeding, abdominal distension, swelling of the kidney and spleen. In addition, it usually occurs from June to October when the water temperature rise a lot of fish death. Currently, 16S rRNA, 16S-23S rRNA intergenic spacer region (ISR), Random Amplified polymorphic DNA (RAPD), Ribotyion (RT), Loop-mediated isothermal amplification (LAMP) are among the methods for diagnosing streptococcosis. Among them, the LAMP method, which is high applicable to the aquaculture farm has attracted the spotlight, but due to problems such as confirmation of results. This seems to minimize the economic loss of streptococcosis which complements the problem so that it can be easily used from the diagnosis to the results confirmation.

First Report of Three Didymella Species Isolated from Freshwater Ecosystem in Korea (담수환경에서 발굴된 Didymella속 3종의 국내 최초 보고)

  • Mun, Hye Yeon;Goh, Jaeduk;Oh, Yoosun;Jeong, Ae-Ran;Chung, Namil
    • The Korean Journal of Mycology
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    • v.46 no.1
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    • pp.1-8
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    • 2018
  • Three fungal isolates, NNIBRFG108, 1139, and 1480, were isolated from freshwater environments; NNIBRFG108 from plant litter in Samcheok, Gangwon and NNIBRFG1139 and 1480 from the soil in Jeju & Gimcheon, Gyeongbuk, Korea. Based on the morphological characteristics and phylogenetic analysis of internal tanscribed spacer (ITS), 28S rDNA region, and ${\beta}$-tubulin gene, NNIBRFG108, NNIBRFG1139, and NNIBRFG1480 isolates were confirmed as Didymella segeticola, D. ellipsoidea, and D. aeria, respectively. Neither species has previously been described in Korea.