• Journal of Platform Technology
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• 제6권4호
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• pp.87-95
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• 2018

개인 전장 유전체 분석 가격의 하락으로 많은 국가들이 10만명에서 100만명까지의 대량 전장 유전체 분석과 엑솜 시퀀싱을 진행하고 있다. 하지만 많은 대형 프로젝트에서 대량의 데이터를 처리할 수 있는 프로그램이나 시스템의 부족으로 많은 비용이 클러스터 구축 및 시스템 구매 비용으로 소비되고 있다. 본 연구에서는 자체 서버나 클러스터 환경을 구축하지 않고도 동시에 수백 개 이상의 전장 유전체 및 엑솜에 대한 단일 염기 다형성(Single Nucleotide Polymorphism; SNP) 분석을 수행할 수 있고, 생물학자들도 쉽게 설치하여 운영할 수 있는 클라이언트 프로그램인 NGSOne을 개발하였다. 대표적인 SNP 분석 도구인 DRAGEN, BWA/GATK 및 Isaac/Strelka2를 선택하여 분석할 수 있고, 3개 툴에서 실행 시간 및 에러의 개수 면에서는 DRAGEN이 가장 좋은 성능을 보였다. 또한 NGSOne은 SNP 분석뿐만 아니라 다양한 분석 도구의 자동적인 실행을 위한 확장이 가능하다.

• Biomolecules & Therapeutics
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• 제27권2호
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• pp.201-209
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• 2019

Mixed lineage leukemia proteins (MLL) are the key histone lysine methyltransferases that regulate expression of diverse genes. Aberrant activation of MLL promotes leukemia as well as solid tumors in humans, highlighting the urgent need for the development of an MLL inhibitor. We screened and isolated MLL1-binding ssRNAs using SELEX (${\underline{S}}ystemic$ ${\underline{E}}volution$ of ${\underline{L}}igands$ by ${\underline{E}}xponential$ enrichment) technology. When sequences in sub-libraries were obtained using next-generation sequencing (NGS), the most enriched aptamers-APT1 and APT2-represented about 30% and 26% of sub-library populations, respectively. Motif analysis of the top 50 sequences provided a highly conserved sequence: 5'-A[A/C][C/G][G/U][U/A]ACAGAGGG[U/A]GG[A/C] GAGUGGGU-3'. APT1, APT2, and APT5 embracing this motif generated secondary structures with similar topological characteristics. We found that APT1 and APT2 have a good binding activity and the analysis using mutated aptamer variants showed that the site information in the central region was critical for binding. In vitro enzyme activity assay showed that APT1 and APT2 had MLL1 inhibitory activity. Three-dimensional structure prediction of APT1-MLL1 complex indicates multiple weak interactions formed between MLL1 SET domain and APT1. Our study confirmed that NGS-assisted SELEX is an efficient tool for aptamer screening and that aptamers could be useful in diagnosis and treatment of MLL1-mediated diseases.

• 보존과학회지
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• 제37권4호
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• pp.357-361
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• 2021

In order to determine the changes in microbial community due to termites, soil microorganisms surrounding the termites were investigated. First, bacterial communities from soil with termites collected at Seonamsa temple, Suncheon city, Korea were compared by next-generation sequencing (NGS, Illumina Miseq). The bacterial composition of soil from Daeungjeon without termites and the soil from Josadang, Palsangjeon, and Samjeon with termites were compared. Next, the bacterial composition of these soils was also compared with that of humus soil cultured with termites. A total high-quality sequences of 71,942 and 72,429 reads were identified in Seonamsa temple's soil and humus soil, respectively. The dominant phyla in the collected Seonamsa temple's soil were Proteobacteria (27%), Firmicutes (24%) and Actinobacteria (21%), whereas those in the humus soil were Bacteriodetes (56%) and Proteobacteria (37%). Using a two-dimensional plot to explain the principal coordinate analysis of operational taxonomic unit compositions of the soil samples, it was confirmed that the samples were divided into soil with and without termites, and it was especially confirmed that the Proteobacteria phylum was increased in humus soil with termites than in humus soil without termites.

• Journal of Microbiology and Biotechnology
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• 제28권9호
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• pp.1473-1481
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• 2018

A cellulase hyperproducing mutant strain, JNDY-13, was obtained using the ARTP mutation system and with Trichoderma reesei RUT-C30 as the parent strain. Whole-genome sequencing of JNDY-13 confirmed that 105 of the 653 SNPs were point mutations, 336 mutations were deletions and 165 were insertions. Moreover, 99 mutations were insertions and duplications. Among all the mutations, the one that occurred in the galactokinase gene might be related to the production of cellulases in T. reesei JNDY-13. Moreover, the up-regulation of cellulase and hemicellulase genes in JNDY-13 might contribute to higher cellulases production. Under optimal conditions, the highest cellulase activity by batch fermentation reached 4.35 U/ml, and the highest activity of fed-batch fermentation achieved was 5.40 U/ml.

• Journal of Microbiology and Biotechnology
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• 제34권3호
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• pp.580-588
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• 2024

Microbial communities in mangrove forests have recently been intensively investigated to explain the ecosystem function of mangroves. In this study, the soil microbial communities under young (<11 years-old) and old (>17 years-old) mangroves have been studied during dry and wet seasons. In addition, biogeochemical properties of sediments and methane emission from the two different mangrove ages were measured. The results showed that young and old mangrove soil microbial communities were significantly different on both seasons. Seasons seem to affect microbial communities more than the mangrove age does. Proteobacteria and Chloroflexi were two top abundant phyla showing >15%. Physio-chemical properties of sediment samples showed no significant difference between mangrove ages, seasons, nor depth levels, except for TOC showing significant difference between the two seasons. The methane emission rates from the mangroves varied depending on seasons and ages of the mangrove. However, this did not show significant correlation with the microbial community shifts, suggesting that abundance of methanogens was not the driving factor for mangrove soil microbial communities.

• 원예과학기술지
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• 제31권4호
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• pp.473-482
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• 2013

효율적인 선발방법으로서 분자표지는 실제적인 고추(Capsicum annuum L.) 육종 과정에 사용되어 왔다. 최근에는 고추의 양적 형질로 알려진 매운맛, 색소 및 당 함량 등에 관한 다수의 유전분석 연구가 세계적으로 수행되고 있다. 또한 양적형질과 연관된 분자표지를 개발하기 위해서는 QTL mapping이 필수적이라고 보고되고 있다. 본 연구에서는 하나의 새로운 방법으로, 양친의 NGS resequencing을 통해 고추 유전자지도 상의 위치가 알려져 있는 분자표지를 일부 선발하여 SNP(HRM) 분자표지로 개발한 후 이를 이용하여 고추 유전체 전체를 포함하는 유전자지도 작성을 제안하고자 하였다. 식물재료는 C. annuum 'NB1'(모친)과 C. chinense 'Jolokia'(부친) 및 이들의 $F_2$ 세대 94개체를 사용하였다. 양친에 대해 NGS resequencing을 수행하여 각각 4.6Gbp와 6.2Gbp의 염기서열을 얻었다. 'NB1'과 'Jolokia' 간의 총 SNP 수는 429만개였으며, 그 중 확실한 SNP 수는 176만개였다. 이 중에서 고추 유전자지도 내 위치를 고려하여 145개의 SNP(HRM) 분석용 프라이머를 디자인하였으며, 그 중 116개가 성공적으로 다형성을 보여 유전자지도 작성에 사용되었다. 총 연관거리는 1,167.9cM였고, 연관군 수는 고추의 기본염색체 수와 일치하는 12개였다. 결과적으로 본 연구에서 제시된 방법은 시간적인 효율성과 예측의 정확성 면에서 새로운 고추 유전자지도 작성에 매우 적합함은 물론 작성된 유전자지도는 양친에서 차이를 보이는 특정 형질에 대한 QTL 분석을 하는데 바로 사용될 수 있을 것으로 판단되었다.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.58-58
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• 2017

The advent of next generation sequencing technology has elicited plenty of sequencing data available in agriculturally relevant plant species. For most crop species, it is too expensive to obtain the whole genome sequence data with sufficient coverage. Thus, many approaches have been developed to bring down the cost of NGS. Genotyping-by-sequencing (GBS) is a cost-effective genotyping method for complex genetic populations. GBS can be used for the analysis of genomic selection (GS), genome-wide association study (GWAS) and constructing haplotype and genetic linkage maps in a variety of plant species. For efficiently dealing with plant GBS data, the TASSEL-GBS pipeline is one of the most popular choices for many researchers. TASSEL-GBS is JAVA based a software package to obtain genotyping data from raw GBS sequences. Here, we describe application of GBS and bioinformatics pipeline of TASSEL-GBS for analyzing plant genetics data.

• Journal of Plant Biotechnology
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• 제46권2호
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• pp.71-78
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• 2019

The objective of this study was to use 'Danta PR', NGS (Next Generation Sequencing) technology for genome resequencing to develop polymorphic makers between Chinese oriental melon, 'Hyangseo 1' and Korean oriental melon. From the resequencing data that covered about 81 times of the genome size, 104,357 of SSR motifs and Indel, and 1,092,436 of SNPs were identified. 299 SSR and 307 Indel markers were chosen to cover each chromosome with 25 markers. These markers were subsequently used to identify genotypes of 'Danta PR' BC1 (F1 x 'Danta PR') population and a genetic linkage map was constructed. SSR, Indel, and SNPs identified in this study would be useful as a breeding tool to develop new oriental melon varieties.

• 한국콘텐츠학회:학술대회논문집
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• 한국콘텐츠학회 2015년도 춘계 종합학술대회 논문집
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• pp.231-232
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• 2015

최근 유전체학, NGS(Next Generation Sequencing) 기술, IT/NT 장비의 발전 등에 따라 방대한 양의 바이오-메디컬 데이터가 생산되고, 이에 따라 빅데이터를 활용한 헬스케어 산업이 급속히 발달하고 있으며, 이와 관련된 빅데이터 기술은 국민의 건강 증대와 건강한 고령 삶을 제공하는 핵심 기술로 급부상하고 있다. 패스웨이는 단백질, 유전자, 세포 등의 생체적 요소 간의 역학관계 혹은 상호작용 등을 네트워크 형식으로 표현한 생물학적 심층지식으로, 바이오-메디컬 빅데이터 분석에 있어서 널리 활용되고 있다. 하지만 패스웨이는 매우 다양한 형태를 갖고 용량이 매우 큰 빅데이터로 이를 분석하는데 많은 시간이 소요된다. 그래서 본 논문에서는 세계적으로 가장 우수하고 방대한 양의 패스웨이를 제공하는 KEGG 패스웨이 데이터베이스로부터 사용자가 관심 갖는 패스웨이만을 자동 수집하고 패스웨이 간 계층구조를 기반으로 네트워크를 구성 후, 해당 패스웨이 네트워크에 대한 클러스터링과 핵심 패스웨이 선정을 통해 패스웨이 간의 역학관계 또는 상호작용을 직관적으로 분석할 수 시스템을 제안했다.

• 한국환경복원기술학회지
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• 제23권2호
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• pp.69-89
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• 2020

Scientific trust and quantification of traditional species investigation and results that have been used in ecology for decades has always been a problem and concern for ecologists. Global ecologists have proposed DNA-based species investigation studies to find answers to problems. In this study, we reviewed the global trend of research on environmental DNA(eDNA), which is a method for monitoring species by detecting DNA of organisms naturally mixed in environmental samples such as water, soil, and feces. The first eDNA research confirmed the possibility of species investigation at the molecular level, and commercialization of NGS(Next Generation Sequencing) and DNA metabarcoding elicits efficient and quantitative species investigation results, and eDNA research is increasing in the filed of ecology. In this study, mammals and birds were detected using MiMammal universal primers from 23 samples(3 natural reserves; 20 water bowls) out of 4 patches to verify eDNA for urban ecosystems in Suwon, and eDNA was verified by performing camera trapping and field survey. Most terrestrial species were detected through eDNA, and particularly, mice(Mus musculus), and Vinous-throated Parrotbill (Sinosuthora webbiana) were identified only with eDNA, It has been confirmed to be highly effective by investigating techniques for small and internal species. However, due to the lack of resolution of the primer, weasels(Mustela sibirica) and squirrels(Melanochromis auratus) were not detected, and it was confirmed that the traditional investigation method was effective only for a few species, such as Mogera robusta(Mogera robusta). Therefore, it is judged that the effects of species investigation can be maximized only when eDNA is combined with traditional field survey and Camera trapping to complement each other.