• Korean Journal of Microbiology
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• v.41 no.2
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• pp.117-124
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• 2005

Two bacterial isolates obtained from rotifer and diseased olive flounder larvae, Paralichthys olivaceus, were identified as Vibrio ichthyoenteri based on the results of phenotypic characterization. In an attempt to develop rapid PCR method for the detection of V. ichthyoenteri, we examined the 16S-23S rRNA intergenic spacer region(ISR) of V. ichthyoenteri and developed species-specific primer for V. ichthyoenteri. Analysis of the ISR sequences showed that V. ichthyoenteri contains one type of polymorphic ISRs. The size of ISRs was 348 bp length and did not contain tRNA genes. Mutiple alignment of representative sequences from different V. species revealed several domains of high sequence variability, and allowed to design species-specific primer for detection of V. ichthyoenteri. The specificity of the primer was examined using genomic DNA prepared from 19 different V. species, isolated 18group Vibrio species and most similar sequence of other known Vibrio species. The results showed that the PCR reaction using species-specific primer designed in this study can be used to detect V. ichthyoenteri.

• The Korean Journal of Mycology
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• v.40 no.3
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• pp.174-176
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• 2012

We report morphological and physiological characteristics of newly isolated six kinds of yeasts which are new in Korean mycoflora. The yeasts were isolated from wild flowers in Daejeon city, Korea and identified by molecular analysis of the amplified internal transcribed space rDNA sequence or partial 18S rDNA sequence. Species of isolates were identified as Kuraishia capsulate, Lodderomyces elongisporus, Pseudozyma antarctica, Starmerella bombicola.

• Journal of fish pathology
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• v.23 no.3
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• pp.313-322
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• 2010

Edible tunicate Halocynthia roretzi, one of the most commercially important aquatic organisms in Korea, has been killed by tunic softness syndrome since last decade. The intracellular protistan parasite observed by the transmission electron microscope in hemocytes of the tunicate was considered to be the causative agent of the mass mortality. The goal of the present work is to examine the characteristic features of the parasite by identifying the 18S rDNA sequences of the parasite. The experiments conducted include amplification of presumptive 18S rDNA from diseased tunicate tissues with UNonMet-PCR and sequencing the product. A preliminary phylogenetic analysis was performed on the presumptive parasite rDNA. A digoxigenin labeled DNA probe was designed on the basis of the sequences of rDNA. Dig-ISH assay was conducted to diagnose the protistan parasite. A PCR using UNonMet-PCR primer generated 595 bp SSU rDNA fragment. Subsequently, PCRs with primer pair expended this sequence to 1542 bp. This is the first partial sequences of SSU rDNA gene to be published on the protistan parasite that has presumed causing the mass mortality of tunicate. Since the Dig-ISH technique demonstrated the presence of infection in hemocytes on the all host tissues, the fragment was confirmed to be the intracellular protistan parasite SSU rDNA. A phylogenetic analysis suggested that the protistan parasite may be a unique eukaryote that is closely related to Apicomplexa.

• ALGAE
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• v.35 no.3
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• pp.293-301
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• 2020

The applications of DNA barcoding have a wide range of uses, such as in taxonomic studies to help elucidate cryptic species and phylogenetic relationships and analyzing environmental samples for biodiversity monitoring and conservation assessments of species. After obtaining the DNA barcode sequences, sequence similarity-based homology analysis is commonly used. This means that the obtained barcode sequences are compared to the DNA barcode reference databases. This bioinformatic analysis necessarily implies that the overall quantity and quality of the reference databases must be stringently monitored to not have an adverse impact on the accuracy of species identification. With the development of next-generation sequencing techniques, a noticeably large number of DNA barcode sequences have been produced and are stored in online databases, but their degree of validity, accuracy, and reliability have not been extensively investigated. In this study, we investigated the extent to which the amount and types of erroneous barcode sequences were deposited in publicly accessible databases. Over 4.1 million sequences were investigated in three largescale DNA barcode databases (NCBI GenBank, Barcode of Life Data System [BOLD], and Protist Ribosomal Reference database [PR2]) for four major DNA barcodes (cytochrome c oxidase subunit 1 [COI], internal transcribed spacer [ITS], ribulose bisphosphate carboxylase large chain [rbcL], and 18S ribosomal RNA [18S rRNA]); approximately 2% of erroneous barcode sequences were found and their taxonomic distributions were uneven. Consequently, our present findings provide compelling evidence of data quality problems along with insufficient and unreliable annotation of taxonomic data in DNA barcode databases. Therefore, we suggest that if ambiguous taxa are presented during barcoding analysis, further validation with other DNA barcode loci or morphological characters should be mandated.

• Journal of Microbiology and Biotechnology
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• v.10 no.2
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• pp.143-146
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• 2000

This study was conducted to compare the cellular fatty acid composition and genotypic analysis of Bifidobacterium longum MK-G7 originated from Koreans with other commercial type strains of bifidobacteria. The cellular fatty acid of Bif. longum MK-G7 was shown to be composed of $C_{160FAME},C_{181\;c18DMA},C_{18.1\;CIS9\; FAME},C_{14.0FAME},C_{19\;0cye9,10 DMA},Feature7(C_{17.2 FAME), and Feature 10(C_{181\; Cll/t9/t6 FAME}$. Bif. longum MK-G7 showed 99.9% homology and the highest relatedness with Bif. longum ATCC 15707 type strain. Both Bif. longum MK-G7 and Bif. longum ATCC 15707 showed 153 bp products on RAPD (randomly amplified polymorphic DNA) analysis, however, they showed quite different band patterns on PFGE (pulsed-field gel electrophoresis) analysis. Consequently, our present study showed that Bif. longum MK-G7 was different from any commercial type strains of Bif. longum tested.

• Journal of Life Science
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• v.16 no.1
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• pp.71-75
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• 2006

We analyzed the phylogenic relationships of 23 partial 18S rDNA sequences of 22 species (1 species has 2 strains) belonging to Sarcorptiforms include 4 new sequences, using several tools. Although geographic distributions are quite far from, sequence similarity of two strains of Dermatophygoides pteronyssinus isolated from Japan and New Zealand were very high. This result suggests that mite migration by animals including human occurred in the two continents. We investigated the Endeostigmata taxonomic relationship between the Prostigmata and Oribatida subgroups using small fragments (340-400 bp) of their 185 rDNA sequences. But Endeostigmata was not grouped with Oribatida or Prostigmata. In conclusion, it is first reported phylogenic relationship for classified mites included in Sarcoptiformes using 185 rDNA sequence analysis and its system is a very powerful tool for classification of mites.

• Journal of Life Science
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• v.18 no.4
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• pp.447-453
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• 2008

Zinc is an essential trace element in Human Being. Highly zinc containing yeast strain isolated from the tropical fruit, rambutan and the zinc concentration in this yeast strain was 306 ppm (30.6 mg%)per dry matter basis. This strain was found to be a rounded type, normal size, and multi-polar budding. Phylogenetic analysis using the ITS1-5.85 rDNA sequences from isolated strain is most similar to yeast Saccharomyces cerevisiae at the level of nucleotide sequence identity at 99%. This strain was produced alcohol by about 12% using fully colonized koji-rice with Aspergillus oryzae. In conclusion, the isolated strain was found to be closely related to the S. cerevisiae based on its morphological and physiological properties, and alcohol fermentation. The phylogenetic analysis of strain FF-10 using ITS 5.8S rDNA sequence data also supported the closely related to the S. cerevisiae. Accordingly, the isolated yeast was named as S. cerevisiae FF-10. Further studies on the best culture conditions for zinc production from zinc-enriched S. cerevisiae FF-10 are under investigation.

• Animal cells and systems
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• v.2 no.4
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• pp.451-454
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• 1998

Gulgastrura reticulosa, first described by Yosii (1966) as a monotypic new genus from a Korean limestone cave, was reviewed for its systematic position by c1adistic analysis of morphological characteristics, investigation of its intermaulting period and reproductive cycle as well as allozyme and 18S rDNA analysis. The great extent of divergence was strongly suggested by its combined lack of sensory organs (third antennal organ, postantennal organ, eyes, pseudocelli) with simultaneous development of an 'apical organ'at the tip of the antennae. The obvious divergence from any existing Collembola families was additionally supported by the extremely prolonged intermoulting period as well as by the low strap value it showed with Onychiuridae as obtained by 18S DNA sequence analysis. All these were considered Justifying the creation of a new family, Gulgastruridae, but still revealing more allied to Onychiuvidae rather than to Hypogastruridae.

• Journal of Microbiology and Biotechnology
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• v.18 no.6
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• pp.1005-1010
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• 2008

The genus Burkholderia consists of extremely versatile bacteria that occupy diverse niches and are commonly encountered in the rhizosphere of crop plants. In this study, we characterized three plant growth promoting strains assigned as Burkholderia sp. using biochemical and molecular characterization. The Burkholderia spp. strains CBMB40, CBPB-HIM, and CBPB-HOD were characterized using biochemical tests, BIOLOG carbon substrate utilization, fatty acid methyl ester analysis, analysis of recA gene sequences, and DNA-DNA hybridization. The results from these studies indicated that the strains CBMB40, CBPB-HIM, and CBPB-HOD can be assigned under Burkholderia vietnamiensis, Burkholderia ubonensis, and Burkholderia pyrrocinia, respectively.

• Parasites, Hosts and Diseases
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• v.44 no.4 s.140
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• pp.313-320
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• 2006

In an effort to characterize, on the molecular scale, the Acanthamoeba initially isolated from the cornea of an amoebic keratitis patient associated with overnight-wear orthokeratology lens in Korea, we conducted mitochondrial DNA restriction fragment length polymorphism, 18S rDNA sequencing, and drug sensitivity analyses on the isolate (KA/PE1). The patient was treated with polyhexamethylene biguanide, chlorhexidine and oral itraconazole, which resulted in resolution of the patient's ocular inflammation. The majority of the molecular characteristics of the KA/PE1 were determined to be identical, or quite similar, to those of A. castellanii Ma strain, which had been isolated also from amoebic keratitis. The risk of Acanthamoeba keratitis as a potential complication of overnight orthokeratology is briefly discussed.