• Journal of Microbiology and Biotechnology
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• v.14 no.4
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• pp.816-821
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• 2004

A reliable molecular phylogenetic method to identify Hericium erinaceum, the most industrially valuable species in the Hericium genus, was established. Sequencing and phylogenetic analyses of the PCR-amplified ITS and 5.8S rDNA from Hericium fungi, including 6 species and 23 isolates, showed that variation in nucleotide sequences and size exists in both ITS1 and ITS2 regions, but not in the 5.8S region. These two ITS regions provided different levels of information on the relationship of H. erinaceum to other Hericium species. Based on the ITS1 sequence, both the parsimony and neighbor joining trees clearly distinguished Asian H. erinaceum isolates from other Hericium species and isolates. The intraspecific divergence of the ITS2 region was suitable to dissect the Asian H. erinaceum isolates into a few groups.

• Animal Systematics, Evolution and Diversity
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• v.35 no.1
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• pp.33-36
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• 2019

The marine interstitial annelid Pharyngocirrus uchidai(Sasaki, 1981) has been only known from Japan. In this study, we report the occurrence of P. uchidai for the first time in four localities along the eastern coast of Korea: Bukmyeon, Gamchu, Gase, and Oeongchi. Species identification was confirmed by comparison of DNA barcoding sequences with morphological examination from the type locality, Oshoro, Japan. We generated a total of 25 sequences of a partial segment (580 bp) of the cytochrome c oxidase subunit I gene (COI), representing five specimens from each locality. Maximum intra-specific variation was 1.2% in terms of Kimura two-parameter (K2P) distance, observed between two individuals each from Gamchu (i.e., between two specimens from the single locality), Gamchu and Oeongchi, Gamchu and Oshoro, and Oeongchi and Oshoro. On the other hand, an identical haplotype was found in all the five localities, substantiating our species identification for the Korean populations. Inter-specific K2P distance between P. uchidai and an unidentified Saccocirrus sp. from Canada (based on public database entries) was 22.4-23.4%.

• Journal of KIISE:Software and Applications
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• v.26 no.11
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• pp.1350-1358
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• 1999

이 논문에서는 유전밴드 영상신호에 포함되어 있는 지형적 특징을 이용하여 밝기의 변화가 일정하지 않은 유전밴드를 인식하는 방법을 연구하였다. 유전밴드는 동일인을 식별하는데 있어서 지문보다 높은 신뢰성을 가지고 있으므로, 유전밴드 영상에서 유전밴드의 유무와 위치를 자동적으로 검출하는 것은 매우 중요하다. 레인내의 밝기의 변화가 일정한 유전밴드는 미분연산자에 의해 검출할 수 있지만, 밝기의 변화가 일정하지 않은 레인내의 유전밴드는 일반적인 인식방법에 의해서는 검출하기 어렵다. 따라서 유전밴드 영상으로부터 지형적 특징을 추출하고, 이것으로부터 계산한 곡률(curvature)의 크기에 의해 유전밴드를 인식함으로써 레인의 밝기가 변화하는 경우에도 효과적으로 인식하였다.Abstract This paper presents recognition of DNA band using the topographical features of DNA band images. The DNA band provides a more reliable way of identification than fingerprints. Recognition based on differentiation operators can easily detect the DNA band if the brightness of lane in the image is almost uniform. When the brightness of the lane changes gradually, the DNA bands are hard to be recognized. Using the curvature magnitude of the lane computed from topographic features extracted from DNA images, the DNA bands are efficiently recognized in the lane whose brightness changes.

• Korean Journal of Ecology and Environment
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• v.54 no.3
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• pp.247-256
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• 2021

Understanding the selective feeding behavior of zooplankton on phytoplankton is essential for evaluating the nutrient cycle and energy flow in the food web. Although many studies have been conducted regarding the feeding behaviors of zooplankton through gut content analyses, there are limitations in the visual identification of digested contents using a microscope. DNA techniques have been applied to overcome these limitations since they can detect and amplify small amounts of prey DNA remaining in the gut contents. We designed a method to extract prey DNA from the gut contents of the whole body of the copepod specimen and tested the resolution of DNA identification for the prey phytoplankton. The common brackish species, Sinocalanus tenellus, were collected from Saemangeum Reservoir in different sites and seasons, and gut content DNA was extracted using 2.5% bleach treatment for 2 min for removal of potential contamination sources existing in preserved specimens without dissolution of the body. The sequences of the extracted gut contents were confirmed using BLASTn suite based on the NCBI database. The phytoplankton species detected in the gut showed temporal and spatial differences. Although DNA analysis of small copepod gut contents has been suggested as an effective method to examine the dynamics of primary prey sources at the genus or species level, uncertainties such as misidentification and limitations in the detailed information of the composition still exist.

• Animal Systematics, Evolution and Diversity
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• v.34 no.3
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• pp.162-167
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• 2018

To confirm the genetic identification and phylogenetic relationships of unidentified 6 baleen whales by-caught from 2002 to 2016, a partial sequence of approximately 500 base pair (bp) of the mitochondrial DNA (mtDNA) control region was analyzed and compared to published sequence from Genbank. Our results indicated that the two individuals among 6 specimens are clustered with Omura's whale clade through phylogenetic analysis, which had only a single haplotype. Omura's whale was reclassified as a new species in 2003 and they had not been previously reported in Korean waters. This study firstly revealed existence of Omura's whale in Korean waters by molecular analysis based on mtDNA control region.

• Microbiology and Biotechnology Letters
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• v.22 no.6
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• pp.577-583
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• 1994

To classify Lactobacillus casei strains on the basis of difference in their chromosomal DNA sequence, we have performed polymerase chain reactions on their chromosomal DNA by using random primers, and followed by analyzing randomly amplified polymorphic DNA fragments. We also developed a mini-preparative method to isolate PCR-grade chromosomal DNA from Lacto- bacillus casei strains within 3 hours. Based on RAPD pattems by polymerase chain reactions with degenerated random primers, 4 Lactobacillus casei strains and 2 mutant strains were successfully discriminated. Results were very sensitive, strain-specific and reproducible. It was also reliable. These results suggest that RAPD may be applied efficiently for the identification of several Lactoba- cillus casei strains.

• 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.

• Mycobiology
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• v.50 no.4
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• pp.231-237
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• 2022

Penicillium species have been actively studied in various fields, and many new and unrecorded species continue to be reported in Korea. Moreover, unidentified and misidentified Korean Penicillium species still exist in GenBank. Therefore, it is necessary to revise the Korean Penicillium inventory based on accurate identification. We collected Korean Penicillium nucleotide sequence records from GenBank using the newly developed software, GenMine, and re-identified Korean Penicillium based on the maximum likelihood trees. A total of 1681 Korean Penicillium GenBank nucleotide sequence records were collected from GenBank. In these records, 1208 strains with four major genes (Internal Transcribed Spacer rDNA region, b-tubulin, Calmodulin and RNA polymerase II) were selected for Penicillium reidentification. Among 1208 strains, 927 were identified, 82 were identified as other genera, the rest remained undetermined due to low phylogenetic resolution. Identified strains consisted of 206 Penicillium species, including 156 recorded species and 50 new species candidates. However, 37 species recorded in the national list of species in Korea were not found in GenBank. Further studies on the presence or absence of these species are required through literature investigation, additional sampling, and sequencing. Our study can be the basis for updating the Korean Penicillium inventory.

• 보존과학연구
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• s.22
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• pp.27-40
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• 2001

DNA typing is often used to determine identity from human remains. Recently, the molecular biological analysis of ancient deposits has become possible since methods for the recovery of DNA conserved in bones or teeth from archaeological remains have been developed. In the field of archaeology, one of the most promising approaches is to identify the individuals present in a mass burial site. We performed nuclear DNA typing and mitochondrial DNA sequencing analysis based on PCR from a Korea ancient human remain excavated from Sa-chon Nuk-island and civilian access controlline(CACL). A femur bone were collected and successfully subjected to DNA extraction, quantification, PCR amplification, and subsequently typed for several shot tandem repeat(STR)loci. 4 types of STR systems used in this study were CTT multiplex(CSF1PO, TPOX, TH01), FFv multiplex(F13A01, FESFPS, vWA), Silver STRⅢ multiplex(D16S539, D7S820, D13S317), and amelogenin for sex determination. This studies are primarily concerned with the extraction, amplification, and DNA typing of ancient human bone DNA samples. Also, it is suggestive of importance about closely relationship between both fields of archaeology and molecular biology.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.12
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• pp.7091-7094
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• 2013

DNA repair capacity is crucial in maintaining cellular functions and homeostasis. However, it can be altered based on DNA sequence variations in DNA repair genes and this may lead to the development of many diseases including malignancies. Identification of genetic polymorphisms responsible for reduced DNA repair capacity is necessary for better prevention. Homologous recombination (HR), a major double strand break repair pathway, plays a critical role in maintaining the genome stability. The present study was performed to determine the frequency of the HR gene XRCC3 Exon 7 (C18067T, rs861539) polymorphisms in Saudi Arabian population in comparison with epidemiological studies by "MEDLINE" search to equate with global populations. The variant allelic (T) frequency of XRCC3 (C>T) was found to be 39%. Our results suggest that frequency of XRCC3 (C>T) DNA repair gene exhibits distinctive patterns compared with the Saudi Arabian population and this might be attributed to ethnic variation. The present findings may help in high-risk screening of humans exposed to environmental carcinogens and cancer predisposition in different ethnic groups.