• Proceedings of the Korean Society for Bioinformatics Conference
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• 2006.02a
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• pp.116-123
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• 2006

생물체의 cDNA를 유리기판위에 고밀도로 첨착 시킨 유전자 칩과 정량적인 방법으로 개별 유전자 발현을 진단 가능한 Real- time PCR (실시간 고분자중합연쇄반응 기술) 기법은 첨단 의학분야와 신약개발 및 독성유전체 연구분야에 활발히 도입되고 있는 기술이다. 본 발표의 첫 번째 부분에서는 유전자칩 에서 얻어진 유전자 발현패턴분석에 기반한 바이오마커 선정 및 real time PCR에 의한 확증 관련 기술 과 유전자칩에서 얻어지는 수많은 데이터를 재정렬 및 다양한 분석기법과 display기술을 활용하여 광범위한 화학물질에 대한 독성효과 분석을 가능하게 해주며, 특정 독성물질에 대한 관련유전자 그룹 발견 및 독성영향에 따른 분류방법에 관한 결과를 발표할 것이다. 또한 바이오마커 활용의 하나로 박테리아세포 기반 바이오센서 제작및 세포칩 개발등에 대한 결과도 추가될 것이다. 두 번째 부분에서는 non-model organism(유전체정보가 확보되지 않은 생물체)인 송사리를 이용하여 새로운 2K 유전자칩을 개발하고, 여기서 각종 화학물질에 대하여 얻어진 수많은 유전자칩 분석 데이타를 활용하여 각각의 화학물질이 보여주는 독성효과를 매우 효과적이고 쉽게 이해할 수 있는 display기술을 개발, 적용함으로써 유전자칩 발현에 기반한 화학물질 독성 screening 및 specificity discrimination을 가능케 하는 예가 발표될 것이다. 이 연구에서 개발한 송사리 유전자칩은 간조직의 RNA를 직접 cDNA화 하는 방식을 취하고 있어 전체 송사리의 유전정보를 필요로 하지 않아 비용 및 효율에서 전체 송사리의 유전정보를 얻는 비용과 노력을 취하지 않고 간에서 발생하는 독성학적 영향 및 유전자의 발현정도를 정밀하고 효율적인 방법으로 얻어 낸다. 현재 2000여개의 cDNA유전자중 50%이상의 유전자가 17베타에스트라디올, 페놀, 노닐페놀, 비스페놀, 감마레이조사, 잔류약품중 이보프란, 다이클로펜악, 농약중의 파라???R, 돌연변이 유발물질 중의 이티비알, 금속류중의 카드뮴을 통해 발현양상과 특정 캐미칼별 발현 특이성이 조사되었고, 이들 유전자는 염기서열 분석을 통해 염기서열이 분석되었으며, 미국 NCBI의 유전자 은행과의 비교를 통해 일부유전자는 새로운 유전자로 밝혀지고 있다. 또한 이 발표에서는 소염진통제계열 의약품인 dichlofenac 이 송사리의 각종 조직에 미치는 독성영향을 Real-time PCR을 이용하여 대표적 스트레스 유전자의 발현에 미치는 영향에 대한 분석 예가 발표될 것이다.

• Journal of Plant Biotechnology
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• v.43 no.2
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• pp.157-163
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• 2016

This study was conducted to investigate the potential use of New Zealand spinach (Tetragonia tetragonioides) as a new vegetable crop which will be cultivated in salt-affected soils such as reclaimed areas. New Zealand spinach ecotypes native to Korea were collected across the Southern, Western and Eastern seashore regions of the Korean peninsula, among which fifty-five accessions were later further propagated and evaluated genetically by using an AFLP (amplified fragment length polymorphism) marker. Based on the AFLP analysis performed to uncover the genetic diversity of the collected ecotypes, enzymatic cleavage of the extracted DNA was implemented based on 12 EcoRI and MseI combinations. A total of 1,279 alleles (107 alleles per EcoRI and MseI enzyme combination) were successfully amplified, among which 62 alleles per enzyme combination were polymorphic (58%). The AFLP analysis indicated that the rate of genetic dissimilarity was 29% among the New Zealand spinach collections, which were clustered into the 7 genetic diversity group. This is the first report on the genetic variation in the genus Tetragonia, and the basic information can be applied to select parental lines for enhancing the segregation spectrum of the new halophytic vegetable plant grown in salt-affected areas.

• Journal of Life Science
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• v.20 no.12
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• pp.1764-1771
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• 2010

Carthamus tinctorius L. (Compositae) is an herb primarily distributed throughout in the world. The species is regarded as ecologically important in the world. Safflower was used for medicines, as well as making red (carthamin) and yellow dyes. We have used the RAPD technique to investigate the phylogenetic relationships and genetic diversity of C. tinctorius. We obtained 123 bands from all the 26 cultivars. The average number of bands was 9.5 per primer. The genetic diversity of safflower is found among cultivars and there is a high among-cultivar differentiation. The OPC18-01 band is the specific marker for Syria cultivar, whereas no products were detected in individuals from other country cultivars. We found seven phenetic bands for determining the specific marker of cultivars with SCAR markers. Though the number of individuals sampled for analysis was small and probably not fully representative of the total available diversity in C. tinctorius, this study demonstrates that the regions (Morocco, Syria, and Turkey) of the Mediterranean Sea were more variable than other regions with the exception of India. In this result, although only simple result of RAPD is difficult to assert the center of species diversity of C. tinctorius, the regions of the Mediterranean Sea may be the most probable candidate for the origin of safflower. India was also the candidate of the center or secondary center of species diversity of C. tinctorius. RAPD markers were effective in classifying cultivar levels of safflower.

• Korean Journal of Plant Resources
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• v.31 no.5
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• pp.531-537
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• 2018

This study was carried to survey distribution of the nucleotide polymorphisms in heme-binding (HB) domain, which is highly conserved region between 1,210 and 1,240 bp of cytochrome P450, in domestic garlic cultivars. 120 garlic cultivars collected from Korea were classified into seven HB domain variation based on the nucleotide sequence of the domain. Northern type garlic cultivars, collected from Kyungpook, Chungnam, Chungpook and Kangwon province, showed 51.3% of KP2 type nucleotide sequence, 5'-TTT/GGC/GGT/GGA/CGG/AGA/ATA/TGT/CCT/GGA-3' with coding amino acid FGGGRRICPG, 13.7% of KP1, 11.3% of CP, 8.8% of CM and 5% of KW2 types. Southern type cultivars, collected from Kyungnam province, showed 52.5% of KM type nucleotide sequence, 5'-TTT/GGC/GCA/GGA/CGG/AGA/ATT/TGT/CCT/GGA-3' with coding amino acid FGAGRRICPG, 22.5% of KP2, 5.0% of KW2 and 2,5% of CP type nucleotide sequence. These results showed that Korean garlics were cultivated in highly mixed condition even in the same region.

• Journal of the korean veterinary medical association
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• v.25 no.10
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• pp.595-606
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• 1989

항원제시세포(APC)와 보조T세포 간의 협력작용에 의하여 활성화된 작동세포(NK세포, CTL, K세포, 대식세포, 과립구 등)의 종양세포, 이식장기 및 세포내기생세균에 감염된 각종 세포에 대한 세포독성작용은 생체방어를 위한 중요한 세포성면역기전이다. 지난 몇 년간 세포성면역기전에 관한 많은 연구에도 불구하고 T림파구매개성 세포독성작용의 면역생물학적기전은 확실히 밝혀있지 않다. 지금까지 알려진 중요한 연구내용을 요약하면 다음과 같다. 1. 세포독성작용을 나타내는 작동세포로는 NK세포, CTL, K세포, 대식세포/단핵구 및 과립구가 있다. 2. T세포의 세포표면항원분자군(CD)으로는 $CD_{2},\;CD_{3},\;CD_{4}[Ly_{3}T_{4}],\;CD_{5}[=Ly_{1}],\;CD_{7},\;CD_{8}[Ly_{2,3}]$가 있으며 $CD_{4}$는 보조Ttpvhdml 특이마커이고 $CD_{8}$는 세포독성 T세포 및 억압T세포의 특이마커이다. 주요 T세포수용체(TCR)는 $CD_{4}$ 또는 $CD_{8}$ 분자와 가까이 연합된 이향체($TCR-{\alpha}{\beta}/TCR-{\gamma}{\delta}$이며 보조 T세포 $CD_{4}$(마우스 $L_{3}T_{4}$)는 수용체와 연합되어 있는반면 억압 T세포 $CD_{8}(Ly+_{2,3})$는 항원수용체와 연합되어 있다. 3. T세포는 Ti-$CD_{3}$(항원/MHC) 복합체를 통한 '항원가교'에 의한 자극(항원인식)과 $CD_{2}$를 통한 비특이경로에 의하여 활성화(분화증식)된다. 비특이경로를 통한 활성경로에서 T세포($CD_{4}$ 및 $CD_{8}$)가 활성화되기 위하여는 보조T세포가 생산하는 IL-2을 요구하며 IL-2의 자극으로 분화증식된 $CD_{8}$는 세포독성능을 나타내지만 $CD_{4}^{+}$는 여전히 세포독성능을 나타내지 못한다. 4. 보조T세포는 class II MHC분자와 연합된 항원을 식별하는 반면 세포독성T세포는 class I MHC 분자와 연합된 항원을 식별한다. 5. 림파구 매개성 세포독성은 접촉(conjugati-on), 탈분극(depolarization), 용해계획(progra-mming), 용해(lysis) 및 재순환(recycling)의 단계를 거쳐 진행된다. 6. 표적세포살해매체로는 perforin / PFP / cy-tolysin, lymphopores, lymphotoxins, protone, cytolytic enzymes가 알려졌으며 세포독성작용은 이들 이외에도 여러 가지 매체를 통한 복합작용으로 추정된다. 7. CTL 매개성 표적세포의 주요 대사변화는 actomyocin ATPase의 증가, phosphocreatine과 ATPase의 소모, ATP 의존성 $Na^{+}/K^{+}$ 펌프작용의 중지, ATP 의존성 $Ca^{2+}$ 유출감소 및 세포내 축적이 관찰된다. 8. $Ca^{2+}$의 축적으로 세포막 교질 침투손상을 주어 수분의 유입을 증가시킴으로써 수포형성, 핵붕괴, 사립체팽화 및 정상세포 구조상실(Zeiosis)이 있다. 결론적으로 CTL 매개성 세포독성작용은 PFP, LT, TNF, 유사 TNF / LT 및 기타 매체를 통한 복합작용이며 세포살해기전은 지속적 대사소모와 정형적 세포구조(핵 및 세포질)의 파괴에 의한 것이다.

• Journal of Mushroom
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• v.15 no.3
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• pp.111-117
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• 2017

The mushroom species Cordyceps militaris has been studied and cultivated as a medicinal mushroom due to its multiple valuable biological and pharmaceutical activities. For breeding new strains of C. militaris, multiplex PCR assays were performed using primers specific for its mating type genes, MAT1-1 and MAT1-2. Mating types and mating status were confirmed, as evidenced by DNA bands at 233-bp and 191-bp for MAT1-1 and MAT1-2 respectively. The novel 'Dowonhongcho 2ho' was developed through mating; they were found to possess high-quality fruiting bodies when grown in artificial media. The stromata of the new strain were club-shaped, with a bright orange-red color, and measured 7.1 cm in length. They had an average cordycepin content of 0.33%. Compared to 'Dowonhongcho,' the new strain had a 7% higher yield, as well as firm fruiting bodies. The optimum temperature for mycelial growth was $20{\sim}25^{\circ}C$, and the optimum temperature for stroma development was $18{\sim}22^{\circ}C$. The fruiting bodies developed after 49.1 days from inoculation. The use of mating type molecular markers improved the breeding efficiency of the new strain 'Dowonhongcho 2ho.' Thus, they may be valuable for artificial cultivation and industrial-scale production of C. militaris with excellent characteristics.

• Journal of the Society of Cosmetic Scientists of Korea
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• v.44 no.1
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• pp.67-72
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• 2018

Green tea (Camellia sinensis L.) has been widely explored for its medicinal applications. However, most of the studies had targeted the green tea leaf, while other parts remained unexplored. In this study, protective effect of green tea root extract on Normal Human Epidermal Keratinocytes (NHEKs) against the damage induced by an external stimulant (PM2.5) was confirmed. Thirty-year-old green tea root samples were collected from Amorepacific's Dolsongi tea field and green tea root extract was prepared with 70% ethanol. Total crude saponin content in green tea root extract was 54%, which is much higher than that in ginseng extract. Our results suggest that green tea root extract can be used as a natural surfactant in cosmetics. For evaluating its protective effect against the damage induced by PM2.5, IL-36G was used as a biomarker. IL-36G mRNA expression level increased remarkable upon PM2.5 treatment in NHEKs. Moreover, IL-36G was recently reported to be expressed in psoriasis lesions. Results showed significant decrease of IL-36G expression by treatment of green tea root extract. In conclusion, thirty-year-old green tea root extract can be used as a natural surfactant with a high saponin content and may have protective effect against the damage induced by PM2.5.

• Weed & Turfgrass Science
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• v.4 no.3
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• pp.225-229
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• 2015

Echinochloa colona is one of the most problematic weeds in the paddy fields of the world. In recent years, this species is likely to be introduced in Korea due to global warming, the expansion of international trade including agricultural products, and increasing tourists. We tried to identify the species from Korean Echinochloa crus-galli and E. oryzicola in order to establish the control measures in case of the initial influx. For this study, Echinochloa colona collected from the National Plant Germplasm System, USA were examined and E. crus-galli and E. oryzicola were collected in Korea. It is, however, very difficult to identify for Echinochloa species using morphological characters because of numerous interspecific and intraspecific types found in nature. Thus, we barcoded the species using rbcL, matK, and ITS. All three markers identified E. colona very well from the others. ITS alone may be enough as a DNA barcode for E. colona identification, when considering cost and effectiveness. The barcode sequences were deposited to the National Center for Biotechnology Information database for public use.

• Korean Journal of Ichthyology
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• v.34 no.3
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• pp.208-217
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• 2022

We wanted to develop a real-time PCR assay capable of detecting Liobagrus obesus in environmental DNA (eDNA) extracted from freshwater samples using a pair of species-specific primers and probe for the endangered fish, L. obesus. The species-specific primers and probe were designed in consideration of single nucleotide polymorphisms between 65 species of freshwater fish living in the Republic of Korea within the cytochrome b (cytb) gene of mitochondrial DNA. The species-specific primers and probe, in the real-time PCR assay, showed high specificity as only the L. obesus genomic DNA (gDNA) was found to be positive in the specificity verification using 65 species gDNA of freshwater fish in the Republic of Korea. In addition, in the detection limit analysis using the serial dilution concentrations of L. obesus gDNA, it was found that it was possible to detect up to 0.2 pg, showing high sensitivity. Afterwards, using the species-specific primers and probe, real-time PCR assay was performed on freshwater samples obtained from 8 stations in the mid-upper basin of Geum River. As a result, the cytb gene of L. obesus was detected in total 5 stations including all 3 stations where this species was collected at the time of field survey. Therefore, the species-specific primers and probe developed in present study, and the real-time PCR assay using them, can accurately detect the cytb gene of L. obesus from eDNA samples, which can be utilized to monitor the existing habitats of this species and to discover potential new habitats.

• Applied Chemistry for Engineering
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• v.32 no.4
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• pp.461-466
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• 2021

In this article, a portable and cost-effective voltammetric biosensor with nanoparticles was developed for the measurements of heterogeneous nuclear ribonucleoprotein A1 protein (hnRNP A1) biomarker which can potentially be used for lung cancer diagnosis. Gold nanoparticles were first electrodeposited onto screen printed carbon electrode (SPCE) followed by immobilizing a single stranded DNA aptamer specific to hnRNP A1 onto the electrode surface. Ethanolamine was also used when immobilizing DNA aptamer on the surface to prevent signals from non-specific adsorption events. Sequential injection of hnRNP A1 biomarker and anti-hnRNP A1 conjugated with alkaline phosphatase (ALP) onto the aptamer chip surface allows to form the sandwich complex of DNA aptamer/hnRNP A1/ALP-anti-hnRNP A1 on the electrode surface which further reacted with 4-aminophenyl phosphate (APP). The electrocatalytic reaction of the enzyme, ALP, and the substrate, APP, resulting in the oxidative current response changes at -0.05 and -0.17 V (vs. Ag/AgCl) against the hnRNP A1 concentration was measured using cyclic and differential pulse voltammetry, respectively. The Au nanoparticles-integrated voltammetric biosensor was applied to analyze human normal serum solutions possibly suggesting potential applicability for lung cancer diagnosis.