• 한국약용작물학회지
• /
• 제23권6호
• /
• pp.489-499
• /
• 2015

Background : Plants belonging to 5 species of the genus Eleutherococcus are currently distributed in the Korean peninsula. The traditional medicine 'Ogapi', derived from Eleutherococcus sessiliflorus and other related species, and 'Gasiogapi', derived from Eleutherococcus senticosus, are frequently mixed up and marketed. Therefore, accurated identification of their origins in urgently required. Methods and Results : Candidate genes from nuclear ribosomal DNA (nrDNA) and chloroplast DNA (cpDNA) of Eleutherococcus plants were analyzed. Whereas the nrDNA-internal transcribed spacer (ITS) regions were useful in elucidating the phylogenetic relationships among the plants, the cpDNA regions were not as effective. Therefore, a combined analysis with nrDNA-ITS was performed. Various combinations of nrDNA and matK were effective for discriminating among the plants. However, the matK and rpoC1 combination was ineffective for discriminating among some species. Based on these results, it was found that OG1, OG4, OG5, OG7, GS1, GS2, and GS3 were derived from E. sessiliflorus. In particular, it was confirmed that GS1, GS2, and GS3 were not derived from E. senticosus. However, more samples need to be analyzed because identification of the origins of OG2, OG3, OG6 and GS4 was not possible. Conclusion : The ITS2, ITS5a, and matK combination was the most effective in identifying the phylogenetic relationship among Eleutherococcus plants and traditional medicines based on Eleutherococcus.

• 한국지능시스템학회:학술대회논문집
• /
• 한국퍼지및지능시스템학회 2003년도 ISIS 2003
• /
• pp.322-325
• /
• 2003

In this paper, we propose n new fuzzy model identification of time series system using wavelet transform and genetic DNA code. Generally, it is well known that the DNA coding method is more diverse in the knowledge expression and better in the optimization performance than the genetic algorithm (GA) because it can encode more plentiful genetic information based on the biological DNA. The proposed method can construct a fuzzy model using the wavelet transform, in which the coefficients are identified by the DNA coding method. Thus, we can effectively get the fuzzy model of the nonlinear system by using the advantages of both wavelet transform and DNA coding method. In order to demonstrate the superiority of the proposed method, it is compared with modeling method using the conventional GA.

• Weed & Turfgrass Science
• /
• 제4권1호
• /
• pp.26-34
• /
• 2015

최근에 전 세계적으로 동물, 식물뿐만 아니라 균류, 해조류 등에서 활발하게 이용하는 DNA 바코드는 게놈 DNA의 단편을 이용해 종들 간의 DNA 변이를 발견하여 형태적 지식 없이 정확하게 종을 동정하고 분류하는 방법이다. 고등식물에서는 단일마커로 바코드 조건을 충족할 수 없어 엽록체 DNA의 rbcL과 matK 유전자를 표준마커로 이용하고 있다. 본 연구는 식물 표준 바코드마커와 핵 DNA의 ITS 부위를 이용하여 국내 벼과 식물 252 분류군 중 주로 농경지에서 발생하는 잡초 총 84분류군 403생태형을 바코드하여 데이터베이스를 구축하기 위하여 수행하였다. 바코드 결과 PCR 증폭과 염기서열 분석 성공률은 rbcL에서 가장 높았으며 matK에서 가장 낮았다. 그러나 바코드 갭과 종식별 해상력은 matK에서 가장 높았다. 80.9%의 염기서열 분석 성공률을 보인 ITS는 matK와의 조합에서 92.9% 까지 종 식별 해상력을 높일 수 있어 벼과 바코드에 매우 유용한 조합이었다. 벼과의 바코드데이터는 미국의 국립생물공학정보센터에 기탁하여 genbank 번호를 부여받아 공개하였다. 그러므로 형태적으로 동정이 어려운 벼과 잡초를 matK와 ITS 부위의 염기서열을 분석하여 미국의 국립생물공학정보센터에 기탁한 데이터와 비교함으로써 쉽고 간편하게 동정할 수 있게 되었다.

• 대한의생명과학회지
• /
• 제24권4호
• /
• pp.292-304
• /
• 2018

Microbes is becoming increasingly forensic possibility as a consequence of advances in massive parallel sequencing (MPS) and bioinformatics. Human DNA typing is the best identifier, but it is not always possible to extract a full DNA profile namely its degradation and low copy number, and it may have limitations for identical twins. To overcome these unsatisfactory limitations, forensic potential for bacteria found in evidence could be used to differentiate individuals. Prokaryotic cells have a cell wall that better protects the bacterial nucleoid compared to the cell membrane of eukaryotic cells. Humans have an extremely diverse microbiome that may prove useful in determining human identity and may even be possible to link the microbes to the person responsible for them. Microbial composition within the human microbiome varies across individuals. Therefore, MPS of human microbiome could be used to identify biological samples from the different individuals, specifically for twins and other cases where standard DNA typing doses not provide satisfactory results due to degradation of human DNA. Microbial forensics is a new discipline combining forensic science and microbiology, which can not to replace current STR analysis methods used for human identification but to be complementary. Among the fields of microbial forensics, this paper will briefly describe information on the current status of microbiome research such as metagenomic code, salivary microbiome, pubic hair microbiome, microbes as indicators of body fluids, soils microbes as forensic indicator, and review microbial forensics as the feasibility of microbiome-based human identification.

• Animal cells and systems
• /
• 제16권6호
• /
• pp.488-497
• /
• 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.

• Journal of Ecology and Environment
• /
• 제46권2호
• /
• pp.126-135
• /
• 2022

Background: Pollinators are important ecological elements due to their role in the maintenance of ecosystem health, wild plant reproduction, crop production and food security. The pollinator-plant interaction supports the preservation of plant and animal populations and it also improves the yield in pollination dependent crops. Having knowledge about the plant-pollinator interaction is necessary for development of pesticide risk assessment of pollinators and conservation of endangering species. Results: Traditional methods to discover the relatedness of insects and plants are based on tracing the visiting pollinators by field observations as well as palynology. These methods are time-consuming and needs expert taxonomists to identify different groups of pollinators such as insects or identify flowering plants through palynology. With pace of technology, using molecular methods become popular in identification and classification of organisms. DNA metabarcoding, which is the combination of DNA barcoding and high throughput sequencing, can be applied as an alternative method in identification of mixed origin environmental samples such as pollen loads attached to the body of insects and has been used in DNA-based discovery of plant-pollinator relationship. Conclusions: DNA metabarcoding is practical for plant-pollinator studies, however, lack of reference sequence in online databases, taxonomic resolution, universality of primers are the most crucial limitations. Using multiple molecular markers is preferable due to the limitations of developed universal primers, which improves taxa richness and taxonomic resolution of the studied community.

• Journal of Microbiology and Biotechnology
• /
• 제17권6호
• /
• pp.879-890
• /
• 2007

The identification of tumor antigens is essential for the development of anticancer therapeutic vaccines and clinical diagnosis of cancer. SEREX (serological analysis of recombinant cDNA expression libraries) has been used to identify such tumor antigens by screening sera of patients with cDNA expression libraries. SEREX-defined antigens provide markers for the diagnosis of cancers. Potential diagnostic values of these SEREX-defined antigens have been evaluated. SEREX is also a powerful method for the development of anticancer therapeutics. The development of anticancer vaccines requires that tumor antigens can elicit antigen-specific antibodies or T lymphocytes. More than 2,000 antigens have been discovered by SEFEX. Peptides derived from some of these antigens have been evaluated in clinical trials. This review provides information on the application of SEREX for identification of tumor-associated antigens (TAA) for the development of cancer diagnostics and anticancer therapeutics.

• The Plant Pathology Journal
• /
• 제25권2호
• /
• pp.184-188
• /
• 2009

Identification of differently expressed genes under specific tissues and/or environments provides insights into the nature and underlying mechanisms of cellular processes. Although cDNA-AFLP (Amplified Fragment Length Polymorphism) is a powerful method for analyzing differentially expressed genes, its use has been limited to the requirement of radioactive isotope use and the difficulty of isolating the bands of interest from a gel. Here, we describe a modified method for cDNA-AFLP that uses a fluorescence dye for detection and isolation of bands directly from a small size polyacrylamide gel. This method involves three steps: (i) preparation of cDNA templates, (ii) PCR amplification and differential display, and (iii) identification of differentially expressed genes. To demonstrate its utility and efficiency, differentially expressed genes during vegetative growth and appressorial development of Magnaporthe oryzae were analyzed. This method could be applied to compare gene expression profiles in a diverse array of organisms.

• Asian-Australasian Journal of Animal Sciences
• /
• 제24권12호
• /
• pp.1637-1643
• /
• 2011

Korean native chickens are a very valuable chicken population in Korea and their prices are higher than that of commercial broilers. In order to discriminate two commercial Korean native chicken populations (CCP1 and CCP2), single nucleotide polymorphisms (SNPs) from mitochondrial (mt) DNA D-loop sequences and LEI0258 marker polymorphisms in the major histocompatibility complex (MHC) region were investigated. A total of 718 birds from nine populations were sampled and 432 mtDNA sequences were obtained. Of these, two commercial Korean native chicken populations (363 birds) were used for investigation of their genetic relationship and breed differentiation. The sequence data classified the chickens into 20 clades, with the largest number of birds represented in clade 1. Analysis of the clade distribution indicated the genetic diversity and relation among the populations. Based on the mtDNA sequence analysis, three selected SNPs from mtDNA polymorphisms were used for the breed identification. The combination of identification probability (Pi) between CCP1 and CCP2 using SNPs from mtDNA and LEI0258 marker polymorphisms was 86.9% and 86.1%, respectively, indicating the utility of these markers for breed identification. The results will be applicable in designing breeding and conservation strategies for the Korean native chicken populations and also used for the development of breed identification markers.

• 한국어병학회지
• /
• 제30권2호
• /
• pp.79-88
• /
• 2017

현재 양식장에서는 Aeromonad를 비롯한 다양한 병원균에 의한 전염병으로 인해 많은 경제적 손실을 겪고 있다. 연어과 어류뿐만 아니라 담수 및 해수어류에도 치명적인 감염을 야기하는 Aeromonas 종은 적어도 26종 이상이 보고되어왔으며, 전염병을 유발하는 유비쿼터스 세균이다. Aeromonas 종을 확인하기 위해 16S rDNA 및 하우스 키핑 유전자의 핵산 서열을 기반으로 한 분자생물학적 기술이 사용될 수 있다. 본 연구에서 Aeromonas 종은 강원도 16개 양식장의 연어과 어류로부터 분리되었으며 Aeromonad의 16S rDNA와 하우스 키핑 유전자의 서열, 즉 RNA polymerase sigma factor ${\sigma}^{70}$ (rpoD) 또는 DNA gyrase subunit B (gyrB)를 기반으로 계통 발생 학적으로 동정했다. 그 결과 대서양 연어 (Salmo salar), 은연어 (Oncorhynchus keta), 산천어 (Oncorhynchus masou masou), 무지개송어 (Oncorhynchus mykiss)에서 96 개의 균주가 수집되었으며, 36개의 균주가 16S rDNA 분석에 의해 Aeromonas 속으로 확인되었다. 확인된 Aeromonas 속 균주는 rpoD 또는 gyrB 유전자 서열을 기반으로 추가 분석되어 Aeromonas salmonicida (24 균주), A. sobria (10 균주), A. media (1 균주) 및 A. popoffii (1 균주)로 검출되었으며, 이 것은 Aeromonas salmonicida가 강원도의 연어과 어류에서 주요 감염균임을 나타낸다. 또 하우스 키핑 유전자의 서열에 기초한 Aeromonas 종의 계통발생학적 동정은 16S rDNA 서열보다 더 정확하다는 것이 또한 증명되었다.