• The Plant Pathology Journal
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• 제34권3호
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• pp.250-255
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• 2018

Pine wilt disease, caused by the nematode Bursaphelenchus xylophilus, is one of the most devastating conifer diseases decimating several species of pine trees on a global scale. Here, we report the draft genome of Raoultella ornithinolytica MG, which is isolated from mountain-cultivated ginseng plant as an bacterial endophyte and shows nematicidal activity against B. xylophilus. Our analysis of R. ornithinolytica MG genome showed that it possesses many genes encoding potential nematicidal factors in addition to some secondary metabolite biosynthetic gene clusters that may contribute to the observed nematicidal activity of the strain. Furthermore, the genome was lacking key components of avermectin gene cluster, suggesting that nematicidal activity of the bacterium is not likely due to the famous anthelmintic agent of wide-spread use, avermectin. This genomic information of R. ornithinolytica will provide basis for identification and engineering of genes and their products toward control of pine wilt disease.

• 한국발생생물학회지:발생과생식
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• 제23권4호
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• pp.385-390
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• 2019

Upon gene inactivation in animal models, the zebrafish (Danio rerio) has become a useful model organism for many reasons, including the fact that it is amenable to various forms of genetic manipulation. Genome editing is a type of genetic engineering in which DNA is inserted, deleted, modified, or replaced in the genome of a living organism. Mainly, CRISPR (clustered regularly interspaced short palindromic repeats) Cas9 (CRISPR-associated protein 9) is a technology that enables geneticists to edit parts of the genome. In this study, we utilized this technology to generate an mmp15b mutant by using zebrafish as an animal model. MMP15 is the membrane-type MMP (MT-MMP) which is a recently identified matrix metalloproteinase (MMP) capable of degrading all kinds of extracellular matrix proteins as well as numerous bioactive molecules. Although the newly-established mmp15b zebrafish mutant didn't exhibit morphological phenotypes in the developing embryos, it might be further utilized to understand the role of MMP15 in liver-related diseases, such as liver fibrosis, and associated pathogeneses in humans.

• Journal of Microbiology and Biotechnology
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• 제28권6호
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• pp.1030-1036
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• 2018

Bacillus strains produce various types of antibiotics, and random mutagenesis has traditionally been used to overproduce these natural metabolites. However, this method leads to the accumulation of unwanted mutations in the genome. Here, we rationally designed a single nucleotide substitution in the degU gene to generate a B. subtilis strain displaying increased plipastatin production in a foreign DNA-free manner. The mutant strain (BS1028u) showed improved antifungal activity against Pythium ultimum. Notably, pps operon deletion in BS1028u resulted in complete loss of antifungal activity, suggesting that the antifungal activity strongly depends on the expression of the pps operon. Quantitative real-time PCR and lacZ assays showed that the point mutation resulted in 2-fold increased pps operon expression, which caused the increase in antifungal activity. Likewise, commercial Bacillus strains can be improved to display higher antifungal activity by rationally designed simple modifications of their genome, rendering them more efficient biocontrol agents.

• 정보처리학회논문지:소프트웨어 및 데이터공학
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• 제2권2호
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• pp.107-112
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• 2013

인간 유전체 지도 완성 후 NGS 기술의 발달로 대용량 유전체 데이터 분석에 대한 요구가 증대하였다. NGS 데이터는 대용량의 단편서열로 구성되므로 효과적인 분석을 위해 고성능 컴퓨팅 기술의 지원이 요구된다. 본 연구에서는 HPC 환경에서 NGS 데이터로부터 SNP를 탐색하는 유전체 분석 파이프라인을 구축하였다. 각 분석 단계의 CPU 이용률 분석을 통해 분석 단계 중 서열 정렬 단계가 연산 작업의 비율이 가장 높은 것을 확인하고, 공개된 병렬화 서열 정렬 도구들의 성능을 분석하여 유전체 분석를 위한 매니코어 프로세서의 활용 가능성을 확인하였다.

• Mycobiology
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• 제49권6호
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• pp.599-603
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• 2021

CRISPR/Cas9 genome editing systems have been established in a broad range of eukaryotic species. Herein, we report the first method for genetic engineering in pyogo (shiitake) mushrooms (Lentinula edodes) using CRISPR/Cas9. For in vivo expression of guide RNAs (gRNAs) targeting the mating-type gene HD1 (LeA1), we identified an endogenous LeU6 promoter in the L. edodes genome. We constructed a plasmid containing the LeU6 and glyceraldehyde-3-phosphate dehydrogenase (LeGPD) promoters to express the Cas9 protein. Among the eight gRNAs we tested, three successfully disrupted the LeA1 locus. Although the CRISPR-Cas9-induced alleles did not affect mating with compatible monokaryotic strains, disruption of the transcription levels of the downstream genes of LeHD1 and LeHD2 was detected. Based on this result, we present the first report of a simple and powerful genetic manipulation tool using the CRISPR/Cas9 toolbox for the scientifically and industrially important edible mushroom, L. edodes.

• Proceedings of the National Institute of Ecology of the Republic of Korea
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• 제5권3호
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• pp.86-93
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• 2024

Unintentional dispersal of organisms has explosively increased due to expansion of human activities. Among introduced organisms, some organisms are categorized as invasive species because of their effects on environmental risk, economic loss, and human health. In 2023, a leopard slug (Limax maximus) was reported in Suwon, Republic of Korea. This slug was designated as a potential invasive species because a wide range of plant species were identified as food sources for this slug in its original habitats. However, it is difficult to investigate the ecological risk of this newly introduced slug in Republic of Korea. Therefore, the potential ecological risk from this newly introduced slug was estimated by meta-genome analyses of its feces. Through meta-genome analyses, 22 Families, 28 Genera, and 26 Species of land plants were identified. Among these 26 identified plant species, six economically important crops - squash (Cucurbita maxima), tomato (Solanum lycopersicum), potato (Solanum tuberosum), cowpea (Vigna unguiculata), rice (Oryza sativa), and oriental melon (Cucumis melo) - were identified. Therefore, leopard slugs potentially could cause economic losses in Republic of Korea. Further study is required to build a control strategy against leopard slugs.

• Biotechnology and Bioprocess Engineering:BBE
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• 제10권5호
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• pp.408-417
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• 2005

Increasing numbers of value added chemicals are being produced using microbial fermentation strategies. Computational modeling and simulation of microbial metabolism is rapidly becoming an enabling technology that is driving a new paradigm to accelerate the bioprocess development cycle. In particular, constraint-based modeling and the development of genome-scale models of industrial microbes are finding increasing utility across many phases of the bioprocess development workflow. Herein, we review and discuss the requirements and trends in the industrial application of this technology as we build toward integrated computational/experimental platforms for bioprocess engineering. Specifically we cover the following topics: (1) genome-scale models as genetically and biochemically consistent representations of metabolic networks; (2) the ability of these models to predict, assess, and interpret metabolic physiology and flux states of metabolism; (3) the model-guided integrative analysis of high throughput 'omics' data; (4) the reconciliation and analysis of on- and off-line fermentation data as well as flux tracing data; (5) model-aided strain design strategies and the integration of calculated biotransformation routes; and (6) control and optimization of the fermentation processes. Collectively, constraint-based modeling strategies are impacting the iterative characterization of metabolic flux states throughout the bioprocess development cycle, while also driving metabolic engineering strategies and fermentation optimization.

• Journal of Microbiology and Biotechnology
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• 제34권4호
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• pp.978-984
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• 2024

Genome-scale metabolic model (GEM) can be used to simulate cellular metabolic phenotypes under various environmental or genetic conditions. This study utilized the GEM to observe the internal metabolic fluxes of recombinant Escherichia coli producing gamma-aminobutyric acid (GABA). Recombinant E. coli was cultivated in a fermenter under three conditions: pH 7, pH 5, and additional succinic acids. External fluxes were calculated from cultivation results, and internal fluxes were calculated through flux optimization. Based on the internal flux analysis, glycolysis and pentose phosphate pathways were repressed under cultivation at pH 5, even though glutamate dehydrogenase increased GABA production. Notably, this repression was halted by adding succinic acid. Furthermore, proper sucA repression is a promising target for developing strains more capable of producing GABA.

• Journal of Animal Science and Technology
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• 제44권1호
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• pp.31-38
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• 2002

양적형질 유전자좌위(Quantitative trait loci; QTL) 연관지도 작성을 위해 regression interval mapping method에 의해 Berkshire종과 Yorkshire종간 교배를 통해 생산된 $F_2$ 집단에서 실시하였다. 염색체내 QTL 위치를 결정하기 위해 regression 모델을 통해 계산된 검정통계량(F-statistic)에 대한 유의적인 threshold 수준의 설정은 permutation test 및 Lander와 kruglyak (1995)에 의해 제시된 방법으로 산출하였다. 525두 $F_2$ 개체에 대해 조사된 기록 중 5형질(도체중, 등심 단면적, 근내지방 교잡도, 콜레스테롤 함량, 척추 늑골 등지방 두께) 기록을 분석에 이용하였고 genome 전체에 걸친 125개의 microsatellite marker에 대해 3세대 집단 모두 개체에 대해 유전자형을 조사하였다. 회귀분석 모형에 따라 additive 및 dominance 효과를 추정하였으며 이때 모든 회귀계수 값과 F-검정 통계량은 각각 1cM 단위로 추정하였다. 각 형질별, 염색체별로 10,000회의 permutation에 의해 genome-wise 및 chromosome-wise threshold를 추정하였다. Lander와 Kruglyak(1995)에 의해 제시된 방법으로 산출된 threshold 값은 매우 높게 추정되어 이러한 threshold의 적용시 실제로 QTL 존재 여부를 인정할 수 있는 경우의 수가 permutation에 의해 유도된 threshold를 적용했을 때보다 상대적으로 적은 결과를 보였다. 5% genome-wise threshold의 경우 형질별로 다소 상이한 경향을 나타냈으며 분석에 활용된 5개 형질에 대해 총 4개의 QTL이 5% genome-wise 수준에서 검색되었다.

• Journal of Plant Biotechnology
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• 제48권1호
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• pp.34-43
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• 2021

CRISPR/Cas9에 의한 유전자 교정 기술은 유용 형질을 갖는 작물 및 임목의 육성에 있어 널리 사용되고 있는 핵심 기술이다. 유전자 교정 임목 육성에는 아그로박테리움에 의한 형질전환 방법이 높은 효율로 시행된 연구가 많았고 따라서 형질전환에 사용된 플라스미드 서열이 식물 유전체 안에 존재한다는 문제가 남아 있었다. 본 연구에서는 CRISPR/Cas9을 사용하여 유전자 교정 임목을 육성하는 데 기존에 알려진 벡터 도입 기술이 아닌, 단일 가닥 가이드 RNA (sgRNA)와 Cas9 단백질을 혼합하여 만든 리보핵산단백질을 현사시나무 원형질체에 도입하는 방법을 기술하였다. 염 스트레스 내성 관련 인자 PagSAP1 유전자를 표적으로 하는 3종류의 sgRNA를 디자인하고, 각 sgRNA와 Cas9 단백질을 혼합하여 만든 리보핵산단백질을 원형질체에 도입하였다. 표적화 딥시퀀싱을 통해 리보핵산단백질 형성 시 sgRNA와 Cas9 단백질을 혼합하고 일정 시간 배양하여 안정화되는 시간이 필요한 것을 확인하였다. 또한 sgRNA3의 리보핵산단백질이 sgRNA1, sgRNA2의 리보핵산단백질보다 높은 교정 효율을 보이는 것을 확인하였다. 본 실험을 통해 리보핵산단백질을 이용한 유전자 교정 기술이 임목에도 적용될 수 있음이 확인되었고, 이는 외래 유전자 없이 유전자 교정 임목을 육성하는 데 활용할 수 있을 것으로 사료된다.