• Title/Summary/Keyword: DNA barcode

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An integrated DNA barcode assay microdevice for rapid, highly sensitive and multiplex pathogen detection at the single-cell level

  • Jung, Jae Hwan;Cho, Min Kyung;Chung, So Yi;Seo, Tae Seok
    • Proceedings of the Korean Vacuum Society Conference
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    • pp.276-276
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    • 2013
  • Here we report an integrated microdevice consisting of an efficient passive mixer, a magnetic separation chamber, and a capillary electrophoretic microchannel in which DNA barcode assay, target pathogen separation, and barcode DNA capillary electrophoretic analysis were performed sequentially within 30 min for multiplex pathogen detection at the single-cell level. The intestine-shaped serpentine 3D micromixer provides a high mixing rate to generate magnetic particle-pathogenic bacteria-DNA barcode labelled AuNP complexes quantitatively. After magnetic separation and purification of those complexes, the barcode DNA strands were released and analyzed by the microfluidic capillary electrophoresis within 5 min. The size of the barcode DNA strand was controlled depending on the target bacteria (Staphylococcus aureus, Escherichia coli O157:H7, and Salmonella typhimurium), and the different elution time of the barcode DNA peak in the electropherogram allows us to recognize the target pathogen with ease in the monoplex as well as in the multiplex analysis. In addition, the quantity of the DNA barcode strand (~104) per AuNP is enough to be observed in the laser-induced confocal fluorescence detector, thereby making single-cell analysis possible. This novel integrated microdevice enables us to perform rapid, sensitive, and multiplex pathogen detection with sample-in-answer-out capability to be applied for biosafety testing, environmental screening, and clinical trials.

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An assessment of the taxonomic reliability of DNA barcode sequences in publicly available databases

  • Jin, Soyeong;Kim, Kwang Young;Kim, Min-Seok;Park, Chungoo
    • 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.

Identification of bird species and their prey using DNA barcode on feces from Korean traditional village groves and forests (maeulsoop)

  • Joo, Sungbae;Park, Sangkyu
    • Animal cells and systems
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    • v.16 no.6
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    • pp.488-497
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    • 2012
  • A DNA barcode based on 648 bp of cytochrome c oxidase I (COI) gene aims to build species-specific libraries for animal groups. However, it is hard to recover full-length (648 bp) barcode gene from environmental fecal samples due to DNA degradation. In this study, we designed a new primer set (K_Bird), which amplifies a 226 bp fragment targeted an inner position of full-length COI barcode based on 102 species of Korean birds to improve amplification success, and we attempted to identify bird species from 39 avian fecal samples collected during 4 months from Jinan, South Korea. Simultaneously, we conducted a dietary analysis using a universal DNA mini-barcode (Uni_Minibar) from same fecal samples. In silico analysis on newly designed mini-barcode represented that genetic distances were 0.5% in species and 9.1% in genera. Intraspecific variations of 149 species out of 174 species (86%) between Korea and North America were within the threshold (5.3% threshold in this study). From environmental fecal samples collected in Jinan, we identified seven avian species, which have high similarity (99-100%) with registered COI sequences in GenBank. Eight kinds of prey species, such as moth, spider, fly, and dragonfly, were identified in dietary analysis. We suppose that our strategy applying mini-barcode for environmental fecal samples, might be a useful and convenient tool for species identification and dietary analysis for birds.

Food Fraud Monitoring of Commercial Sciaenidae Seafood Product Using DNA Barcode Information (DNA barcode를 이용한 민어과 수산가공품 진위판별 모니터링)

  • Park, Eun-Ji;Jo, Ah-Hyeon;Kang, Ju-Yeong;Lee, Han-Cheol;Park, Min-Ji;Yang, Ji-Young;Shin, Ji-Young;Kim, Gun-Do;Kim, Jong-Oh;Seo, Yong-Bae;Kim, Jung-Beom
    • Journal of Food Hygiene and Safety
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    • v.35 no.6
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    • pp.574-580
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    • 2020
  • In this study we sought to determine the food fraud by discriminating species of commercial seafood product such as Larimichthys polyactis, Larimichthys crocea, Pennahia argentatus, and Miichthys miiuy, which are difficult to morphologically discriminate. After amplifying the mitochondrial cytochrome c oxidase subunit I gene of the reference fish, the DNA sequences of the amplified PCR products were analyzed. As a result, a 655 bp sequence for species identification was selected for use as DNA barcodes. To confirm the DNA data and primer set, the DNA barcode sequence of each fish was compared to that in that in the NCBI. All of the DNA barcode data were matched with the gene sequence of each fish in the NCBI. A total of 32 processed seafood products (8 L. polyactis, 12 L. crocea, 3 Pennahia argentatus, and 9 Miichthys miiuy) were investigated. Homology of 97% or more in DNA sequences was judged as the same species. As a result of the monitoring, there were no discovered cases of forgery or alteration. However, the use of a raw material name having no matching standard name in the Korea Food Code may cause consumer confusion. Therefore, it is suggested that the standard name or scientific name be co-labeled with the raw material name on seafood products to prevent consumer confusion.

Error Correcting using the Check digit on Barcode, and the present and future of Barcode (바코드에 있어서 체크숫자를 이용한 오류수정과 바코드의 현재와 미래)

  • Kim, Hwa-Joon
    • Journal for History of Mathematics
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    • v.21 no.2
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    • pp.103-118
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    • 2008
  • Barcode technology is becoming an essential tool for every companies, and this makes help us to gain time, analysis of goods, an inventory control, a prevention of burglar and so on. In this paper, we have treated about the history of barcode, its error correcting using the check digit, and the present and future of barcode. We wish roles of mathematician on new barcode system which it bring on an economical efficiency and stability.

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DNA barcoding of Euphorbiaceae in Korea

  • Kim, Kyeonghee;Park, Ki-Ryong;Lim, Chae Eun
    • Journal of Species Research
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    • v.9 no.4
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    • pp.413-426
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    • 2020
  • The Euphorbiaceae family features some of the most economically important plants that are sources of foods, oils, waxes, and medicines. The accurate identification of Euphorbiaceae species is critical in sustainable utilization of plant resources. We examined 234 sequences of nrDNA ITS, cpDNA rbcL and matK loci from 20 species in Euphorbiaceae in Korea and three outgroup taxa to develop efficient DNA barcodes. The three barcode loci were successfully amplified and sequenced for all Euphorbiaceae species. nrDNA ITS locus showed the highest mean interspecific K2P distance (0.3034), followed by cpDNA matK (0.0830), and rbcL (0.0352) locus. The degree of species resolution for individual barcode loci ranged from 75% (rbcL and matK) to 80% (ITS). The degree of species resolution was not enhanced with the different combinations of three barcode loci. The combined data set of the three loci(ITS+rbcL+matK) provided 80% of species resolution. These results confirm that ITS locus, as a single barcode, is the best option for barcoding of the Euphorbiaceae in Korea.

Identification of Korean Poaceae Weeds Based on DNA Sequences (DNA 염기서열에 기초한 벼과 잡초의 분자생물학적 동정)

  • Lee, Jeongran;Kim, Chang-Seok;Lee, In-Yong;Oh, Hyun-Ju;Kim, Jung Hyun;Kim, Sun Yu
    • Weed & Turfgrass Science
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    • v.4 no.1
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    • pp.26-34
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    • 2015
  • Korean Poaceae includes approximately 80 species of the agricultural weeds. Precise species identification is the first step for more effective weed management in the agricultural fields. However, the identification of species in Poaceae is not easy without the assistance of taxonomists or identification experts although they are relatively easy to distinguish from the plants of the other family by the unique characteristics of caryopsis. Thus, DNA barcode was suggested as an alternative powerful technique for species identification by using short sections of DNA from a specific region of the genome. Two standard barcode markers of vascular plants, chloroplast rbcL and matK, and a supplementary nuclear ribosomal Internal Transcribed Spacer (ITS) region were used for barcode of major Korean Poaceae weeds, 403 individuals of 84 taxa. All the barcode markers revealed a good level of sequencing success with the lowest 73.7% for matK and the highest 88.8% for rbcL. The barcode sequences were deposited to the National Center for Biotechnology Information (NCBI) database for public use. Combined matK and ITS showed very high resolving power with 92.9%. Besides the identification of weeds for weed managment, the generated DNA barcode data could be used for many other applications such as rapid biodiversity assessment and conservation prioritization.

Food Fraud Monitoring of Raw Materials for Commercial Seafood Products Using DNA Barcode Information (DNA Barcode를 이용한 수산가공품 원재료 진위판별)

  • Park, Eun-Ji;Kang, Ju-Yeong;Lee, Han-Cheol;Park, Min-Ji;Yang, Ji-Young;Shin, Ji-Young;Kim, Gun-Do;Kim, Jong-Oh;Seo, Yong-Bae;Kim, Jung-Beom
    • Journal of Food Hygiene and Safety
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    • v.36 no.4
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    • pp.331-341
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    • 2021
  • DNA barcode sequences of commercial seafood products, which are difficult to morphologically discriminate, were analyzed to determine cases of food fraud. The gene sequences were analyzed by amplifying the COX I (cytochrome C oxidase subunit I) gene region of mitochondrial DNA, which is mainly used for species identification. The DNA barcode sequences were compared with the gene sequence of each fish registered in the US National Center for Biotechnology. A total of 46 processed seafood products (12 Pagrus majo, 4 Oplegnathus fasciatus, 7 Dentex tumifrons, 2 Acanthopagrus schlegelii, 7 Oreochromis niloticus, 6 Branchiostegus japonicus, 8 Branchiostegus albus) were investigated. Having DNA sequence identity of more than 97% was judged as the same species. As a result of this study, no cases of forgery and alteration were detected. However, some disparities in the commercial names used in local markets and the standard names given in the Korea Food Code were found, which may cause confusion for consumers. It is therefore suggested that the standard name or scientific name be displayed on seafood product labels.

Phylogenetic analysis of 14 Korean Araliaceae species using chloroplast DNA barcode analysis (엽록체 DNA 바코드 분석을 통한 한국산 두릅나무과 식물 14종의 유연관계 분석)

  • Hwang, Hwan Su;Choi, Yong Eui
    • Journal of Plant Biotechnology
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    • v.43 no.1
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    • pp.82-90
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    • 2016
  • Most Araliaceae plant species distributed in Korea are economically important because of their high medicinal values. This study was conducted to develop barcode markers from sequence analysis of chloroplast DNA in 14 taxa of Araliaceae species grown in South Korea. Sequencing of seven chloroplast DNA regions was performed to establish the DNA barcode markers, as suggested by the Consortium for the Barcode of Life (CBOL). From the sequence analysis of chloroplast DNA, we identified specific sequences and nucleotides that allowed us to discriminate among each other 14 Korean Araliaceae species. The sequence in the region of psbA-trnH revealed the most frequent DNA indels and substitutions of all 7 regions studied. This psbA-trnH marker alone can discriminate among all 14 species. There are no differences between Korean and Chinese Panax ginseng in all seven sequenced chloroplast DNA regions. A phylogenetic tree constructed using the seven chloroplast DNA regions revealed that Tetrapanax papyriferus should be classified as an independent clade. The Aralia and Panax genera showed a close phylogenetic relationship. Five species in the Eleutherococcus genus were more closely related to Kalopanax septemlobus than to any Panax species.

DNA barcoding of Schisandraceae in Korea (한국산 오미자과의 DNA 바코드)

  • Youm, Jung Won;Han, Sang-Wook;Seo, Seon Won;Lim, Chae Un;Oh, Sang-Hun
    • Korean Journal of Plant Taxonomy
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    • v.46 no.3
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    • pp.273-282
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    • 2016
  • The establishment of a DNA barcode database at the regional scale and assessments of the utility of DNA barcodes are crucial for conservation biology and for the sustainable utilization of biological resources. Schisandraceae is a small family consisting of ca. 45 species. It contains many economically important species, such as Schisandra chinensis, which is widely used as a source in tonic beverages and in oriental medicine. In Korea, three species, S. chinensis, S. repanda, and Kadsura japonica, are distributed. We evaluated the level of variation of the DNA sequences of rbcL, matK, and the ITS regions from 13 accessions representing the distributional range of the three species. The three DNA barcode regions were easily amplified and sequenced. The minimum values of the interspecific genetic distances among S. chinensis, S. repanda, and K. japonica either separately or in combination are 4- to 23-fold higher than the maximum value of the intraspecific distance, showing that there is a clear DNA barcoding gap in the regions for Korean Schisandraceae. Phylogenetic analyses of the three DNA barcode regions, separately and simultaneously, indicate that all of the DNA barcode regions are useful for identifying a species of Schisandraceae in Korea. The distinctiveness of the three species of Schisandraceae was also supported at the species level when Chinese and Japanese populations were added. The results of this study indicate that three concatenated regions constitute the best option for DNA barcoding in Schisandraceae in Korea.