• Journal of Forest and Environmental Science
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• v.25 no.2
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• pp.93-100
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• 2009

In Malaysia, Labisia pumila Benth & Hook f, popularly known as 'Kacip Fatimah' has been used traditionally to treat various elements of the woman's health in Malay community. The objective of this study was to develop randomly amplified polymorphic DNA (RAPD) based DNA markers for the identification of L. pumila and to distinguish its three varieties from each other. Total DNA from nine accessions of L. pumila was extracted by CTAB method and polymerase chain reactions (PCR) were carried out to amplify the segments of DNA using different primers to develop DNA barcode using RAPD technique. To find out variety-specific DNA marker/s, twenty different 10-mer primer sequences with annealing temperature from 36-$40^{\circ}C$ were evaluated in triplicate. Out of 20 random primers, two primers (OPA-1 and OPA-2/A10) were selected which produced reliable RAPD band patterns. To have DNA based handle, two RAPD amplification products were cloned and sequenced to determine the identity of the DNA. RAPD analysis using two random primers generated 72 discrete bands ranging in size 200 bp-3,000 bp. Fifty nine of these were polymorphic loci (82%) and thirteen were non-polymorphic loci (18%). A total of 32 bands polymorphic loci (72%) were amplified with primer OPA-1 and analyzed by cluster analysis and UPGMA (Unweighted Pair Group Method with Arithmetic) to present a dendogram depicting the degree of genetic relationship among nine accessions of L. pumila. Our results shows the reasonable genetic diversity among the L. pumila varieties and within varieties; and two RAPD marker sequences obtained could be used to identify L. pumila at species level.

• 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 Forest and Environmental Science
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• v.28 no.4
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• pp.278-281
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• 2012

Comparative sequence analyses were conducted on complete mtDNA sequences from four small mammal species in Korea and revealed the presence of 30 well conserved sequences in various regions of the complete mtDNA sequences. The conserved sequences were found in 9 regions in protein coding genes, 10 regions in tRNA genes, 10 in rRNA genes, one region in replication origin and 2 regions in D loop. They could be used to design primers for amplifying complete mtDNA sequences of small mammals.

• Journal of Microbiology and Biotechnology
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• v.13 no.2
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• pp.236-242
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• 2003

A culture-independent and -dependent survey of the bacterial community structure in the rhizosphere and soil samples from hot pepper plants was conducted using 16S rDNA clone library and FAME analyses. Out of the 78 clones sequenced, 56% belonged to Proteobacteria, 4% to high G+C Gram- positive group, 3% to Cytophyga-Flexibacter-Bacreroides, and 32% could not be grouped with any known taxonomic division. Among the 127 FAME isolates identified, 66% belonged to low G+C Gram-positive bacteria (Baciilus spp.) and 26% to high G+C Gram-positive bacteria. In a cluster analysis, the results for both methods were found to be strikingly dissimilar. The current study is the first comparative study of FAME and 165 rDNA clonal analyses performed on the same set of soil, rhizosphere soil, and root samples.

• Ocean and Polar Research
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• v.38 no.4
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• pp.295-301
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• 2016

The nomenclature of the sea nettle jellyfish from Korea was initially described as Dactylometra quinquecirrha Agassiz, 1862. However its identity has been questioned on the basis of its local distribution and molecular data. Here, we examined morphology and DNA sequences of nuclear rDNA using specimens collected from southern Korean waters in August 2014. Based on morphological characteristics (bell size, umbrella pattern, number of tentacles and lappets) and distribution locality, we reassign the Korean D. quinquecirrha to Chrysaora pacifica (Goette, 1886), and provide a re-description accordingly. The molecular identity of C. pacifica was further confirmed by comparison of nuclear ribosomal DNA sequences.

• Journal of Microbiology and Biotechnology
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• v.17 no.4
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• pp.668-672
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• 2007

A microcosmal experiment using a metagenomic technique was designed to assess the effect of BTEX (benzene, toluene, ethylbenzene, and xylenes) on an indigenous bacterial community in a Daejeon forest soil. A compositional shift of bacterial groups in an artificial BTEX-contaminated soil was examined by the 16S rDNA PCR-DGGE method. Phylogenetic analysis of 16S rDNAs in the dominant DGGE bands showed that the number of Actinobacteria and Bacillus populations increased. To confirm these observations, we performed PCR to amplify the 23S rDNA and 16S rDNA against the sample metagenome using Actinobacteria-targeting and Bacilli-specific primer sets, respectively. The result further confirmed that a bacterial community containing Actinobacteria and Bacillus was affected by BTEX.

• Proceedings of the Korean Society of Toxicology Conference
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• 2001.10a
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• pp.26-26
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• 2001

8-Hydroxyguanine(oh$\^$8/Gua), an oxidative DNA adduct is a most easily and abundantly formed base modification. What we have known about oh$\^$8/Gua so far is that this DNA adduct mediates the mutagenesis and it is used as a useful marker of oxidative DNA damage. We found additional evidence and here present them: 1) oh$\^$8/Gua in DNA can trigger cell death by inducing cell cycle arrest and apoptosis and 2) it can be used to assess the oxidative damage of each individual gene.(omitted)

• Proceedings of the Korean Society of Toxicology Conference
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• 2003.10b
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• pp.126-126
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• 2003

Welding fume (WF) induces pulmonary disease including pneumoconiosis. To investigate whether reactive oxygen species-induced oxidative DNA damage occurs during welding fume exposure and the upregulation of DNA repair mechanisms is accompanied, SPF SD rats were exposed to welding fumes with the concentrations of 65.6${\pm}$2.9 mg/㎥(low dose) and 116.8${\pm}$3.9 mg/㎥ (high dose) of total suspended particulate for 2 hrs per day in an inhalation chamber for a total of 2hrs, 15 or 30 days.(omitted)

• Toxicological Research
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• v.12 no.1
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• pp.17-20
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• 1996

The effect of Fumonisin B1, a mycotoxin produced by Fusarium moniliforme on bacterial viruses P1 and Lambda, was investigated by the virus plaque assay. Fumonisin B1 inhibited the P1 viral multiplication in the concentration range from $100{\mu}g$/ml to $400{\mu}g$/ml. The inhibition was Fumonisin B1 concentration-dependent. Another bacterial virus Lambda multiplication was also inhibited by lower concentration of Fumonisin B1 ($10{\mu}g$/ml~$50{\mu}g$/ml). This inhibition was dependent on Fumonisin B1 and on virus-Fumonisin B1 reaction time. Sensitivity of bacteriophage Lambda to Fumonisin B1 was higher than that of P1 virus. Lambda vital DNA was treated in vitro with Fumonisin B1 at various concentration. Significant DNA fragmentation by Fumonisin 191 was observed in the agarose gel electrophoresis. Lambda viral DNA was partially digested even in the Fumonisin B1 $10{\mu}g$ and the level of its fragmentation was dependent on Fumonisin B1 amount up to $30{\mu}g$ per assay.

• Animal Systematics, Evolution and Diversity
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• v.36 no.3
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• pp.258-263
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• 2020

The aim of this study is to report monotypic species, Nonparahalosydna pleiolepis(Marenzeller, 1879) for the first time from Korean waters with its DNA barcoding data. We collected individuals of the species from the subtidal zone of southern coast of Korea through scuba diving. To estimate DNA barcoding gap, the pairwise genetic distances were calculated between N. pleiolepis and its congeners (Halosydna brevisetosa Kinberg, 1856 and Lepidonotus squamatus (Linnaeus, 1758)) based on the cytochrome c oxidase subunit I gene (COI). Inter-specific genetic distances ranged from 18.7% to 24.6%, while intra-specific genetic distance within N. pleiolepis ranged from 0.3% to 0.5%. The maximum intra-specific genetic distance among the three species was 1.4%. The morphological diagnosis of N. pleiolepis with a taxonomic note on the species were also provided.