• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2002년도 추계학술대회
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• pp.22-26
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• 2002

There are a number of ways in which environmental microbiology and microbial ecology will benefit from DNA micro array technology. These include community genome arrays, SSU rDNA arrays, environmental functional gene arrays, population biology arrays, and there are clearly more different applications of microarray technology that can be applied to relevant problems in environmental microbiology. Two types of the applications, bacterial identification chip and functional gene detection chip, will be presented. For the bacterial identification chip, a new approach employing random genome fragments that eliminates the disadvantages of traditional DNA-DNA hybridization is proposed to identify and type bacteria based on genomic DNA-DNA similarity. Bacterial genomes are fragmented randomly, and representative fragments are spotted on a glass slide and then hybridized to test genomes. Resulting hybridization profiles are used in statistical procedures to identify test strains. Second, the direct binding version of microarray with a different array design and hybridization scheme is proposed to quantify target genes in environmental samples. Reference DNA was employed to normalize variations in spot size and hybridization. The approach for designing quantitative microarrays and the inferred equation from this study provide a simple and convenient way to estimate the target gene concentration from the hybridization signal ratio.

• Journal of Microbiology and Biotechnology
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• 제31권7호
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• pp.903-911
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• 2021

Previous studies have modified microbial genomes by introducing gene cassettes containing selectable markers and homologous DNA fragments. However, this requires several steps including homologous recombination and excision of unnecessary DNA regions, such as selectable markers from the modified genome. Further, genomic manipulation often leaves scars and traces that interfere with downstream iterative genome engineering. A decade ago, the CRISPR/Cas system (also known as the bacterial adaptive immune system) revolutionized genome editing technology. Among the various CRISPR nucleases of numerous bacteria and archaea, the Cas9 and Cas12a (Cpf1) systems have been largely adopted for genome editing in all living organisms due to their simplicity, as they consist of a single polypeptide nuclease with a target-recognizing RNA. However, accurate and fine-tuned genome editing remains challenging due to mismatch tolerance and protospacer adjacent motif (PAM)-dependent target recognition. Therefore, this review describes how to overcome the aforementioned hurdles, which especially affect genome editing in higher organisms. Additionally, the biological significance of CRISPR-mediated microbial genome editing is discussed, and future research and development directions are also proposed.

• 정보처리학회논문지A
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• 제16A권3호
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• pp.143-152
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• 2009

최근 생물정보학 분야의 연구는 하나하나의 유전자를 연구하던 예전의 방법에서 유전자들간의 관계를 알아보는 연구들로 변해가고 있다. 이러한 유전자들 간의 연구 중 하나가 유전자 팀(gene team)을 연구하는 것이다. 유전자 팀이란 몇몇 염색체들 사이의 유전자들이 보존되어 있는 것을 말하며, 닫힌 영역 안에 보존되어 있는 유전자들의 집합으로 볼 수 있다. 이들은 진화과정을 거치면서, 유전자 팀 내의 유전자들의 위치나 그 종류가 변한다. 이러한 유전자 팀을 찾기 위해 많은 연구들이 이루어져왔다. 본 논문은 생물정보학 분야에서 많이 사용되는 계층적 클러스터링(hierarchical clustering)방법을 변형하여 전체 유전체(whole genome) 쌍내에서의 의미 있는 영역을 찾고, 영역 내에서 gene team을 찾을 수 있는 방법을 소개한다. 본 연구 방법을 이용하면, 복잡한 구조의 두 유전체 사이의 연관 유전자들이나 유사 영역들의 맵(map)을 단계별로 간략화 하여 나타낼 수 있다.

• 한국미생물생명공학회:학술대회논문집
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• 한국미생물생명공학회 2005년도 2005 Annual Meeting & International Symposium
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• pp.264-265
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• 2005

• Genomics & Informatics
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• 제7권3호
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• pp.178-180
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• 2009

A few bioinformatics tools have been used to find out conserved regions as probes. We have developed a system based on a heuristic method with web interfaces to find out conserved regions against microbial genomes. The system runs in real time by using relative entropy in limited narrow regions and detecting similar regions between pair regions with local alignment. The system could be useful to find out conserved regions as genome-wide scale.

• 미생물학회지
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• 제38권4호
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• pp.267-275
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• 2002

미생물 유전체 프로젝트의 결과인 유전체 서열에 대해, 비교 유전체 분석을 수행할 수 있는 분석 도구인 GComp를 개발하였다. 이 도구는 국부 상동성 계산을 BLAST나 FASTA를 사용하여 수행한 후에 그 결과를 받아들여, 상동성을 보이는 부분을 분석하고 위치 파악 및 연결한 뒤, 두 유전체간의 상동성 정도를 일목요연하게 보여줄 수 있는 테이블과 파일들을 생성한다. 한편. 그 결과를 그래픽으로 표시하고 전체를 살펴볼 수 있는 인터페이스 기능을 구현하였다. 시험 데이터로 기존의 미생물 유전체 서열을 상대로 분석하면서, 유전체 서열의 핵산 및 단백질 수준에서의 비교분석 결과를 통해 두 유전체에 대한 비교 정보를 효과적으로 확인할 수 있었고, 보다 다양한 분석을 위한 도구 개발의 기준을 설정할 수 있었다.

• Journal of Microbiology and Biotechnology
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• 제34권6호
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• pp.1276-1286
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• 2024

The environment has been identified as an origin, reservoir, and transmission route of antibiotic resistance genes (ARGs). Among diverse environments, freshwater environments have been recognized as pivotal in the transmission of ARGs between opportunistic pathogens and autochthonous bacteria such as Aeromonas spp. In this study, five environmental strains of Aeromonas spp. exhibiting multidrug resistance (MDR) were selected for whole-genome sequencing to ascertain their taxonomic assignment at the species-level and to delineate their ARG repertoires. Analyses of their genomes revealed the presence of one protein almost identical to AhQnr (A. hydrophila Qnr protein) and four novel proteins similar to AhQnr. To scrutinize the classification and taxonomic distribution of these proteins, all Aeromonas genomes deposited in the NCBI RefSeq genome database (1,222 genomes) were investigated. This revealed that these Aeromonas Qnr (AQnr) proteins are conserved intrinsic resistance determinants of the genus, exhibiting species-specific diversity. Additionally, structure prediction and analysis of contribution to quinolone resistance by AQnr proteins of the isolates, confirmed their functionality as quinolone resistance determinants. Given the origin of mobile qnr genes from aquatic bacteria and the crucial role of Aeromonas spp. in ARG dissemination in aquatic environments, a thorough understanding and strict surveillance of AQnr families prior to the clinical emergence are imperative. In this study, using comparative genome analyses and functional characterization of AQnr proteins in the genus Aeromonas, novel Aeromonas ARGs requiring surveillance has suggested.

• Asian-Australasian Journal of Animal Sciences
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• 제17권6호
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• pp.877-884
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• 2004

Although gut microbial functions have been analyzed through cultivation of isolated microbes, molecular analysis without cultivation is becoming a popular approach in recent years. Gene cloning studies have partially revealed the mechanisms involved in fiber digestion of individual microbe. The molecular approach finally made it possible to analyze full genomes of the representative rumen cellulolytic bacteria Fibrobacter and Ruminococcus. The coming database may contain useful information such as regulation of gene expression relating to fiber digestion. Meanwhile, unculturable bacteria are still poorly characterized, even though they are main constituents of gut microbial ecosystem. The molecular analysis is essential to initiating the studies on these unculturable bacteria. The studies dealing with rumen and large intestine are revealing considerable complexity of the microbial ecosystems with many undescribed bacteria. These bacteria are being highlighted as possibly functional members contributing to feed digestion. Manipulation of gut bacteria and gut ecology for improving animal production is still at challenging stage. Bacteria newly introduced in the rumen, whether they are genetically modified or not, suffer from poor survival. In one of these attempts, Butyrivibrio fibrisolvens expressing a foreign dehalogenase was successfully established in sheep rumen to prevent fluoroacetate poisoning. This expands choice of forages in tropics, since many tropic plants are known to contain the toxic fluoroacetate. This example may promise the possible application of molecular breeding of gut bacteria to the host animals with significance in their health and nutrition. When inoculation strategies for such foreign bacteria are considered, it is obvious that we should have more detailed information of the gut microbial ecology.

• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2002년도 추계학술대회
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• pp.90-93
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• 2002

The revolution in molecular biology has given us greatly increased ability to obtain and to modify biological resources and to use them for the benefit of all humankind. The sequencing and the associated analysis of gene functions for a growing number of genomes will have an unprecedented effect on the uses of biological resources and the need for access to them. To investigate the diversity of microbial community in swamp, molecular systematic methods were applied. By amplified rDNA restriction analysis (ARDRA) and rDNA partial sequence analysis, $75\%$ of the isolates were known species. In case of uncultured analysis, almost all the selected clones were new species candidate. Especially archea and uncultured bacterial analyses, all clones were new taxon candidates. As for the eukaryotic diversity, several yeast form cultures were isolated from various samples of swamp. Among them, about $60\%$ of the isolates were easily identified. In case of a new species candidate, most strain were included in hymenomycetal yeasts.

• Journal of Microbiology
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• 제43권5호
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• pp.411-416
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• 2005

The high-throughput sequencing of microbial genomes has resulted in the relatively rapid accumulation of an enormous amount of genomic sequence data. In this context, the problem posed by the detection of promoters in genomic DNA sequences via computational methods has attracted considerable research attention in recent years. This paper addresses the development of a predictive model, known as the dependence decomposition weight matrix model (DDWMM), which was designed to detect the core promoter region, including the -10 region and the transcription start sites (TSSs), in prokaryotic genomic DNA sequences. This is an issue of some importance with regard to genome annotation efforts. Our predictive model captures the most significant dependencies between positions (allowing for non­adjacent as well as adjacent dependencies) via the maximal dependence decomposition (MDD) procedure, which iteratively decomposes data sets into subsets, based on the significant dependence between positions in the promoter region to be modeled. Such dependencies may be intimately related to biological and structural concerns, since promoter elements are present in a variety of combinations, which are separated by various distances. In this respect, the DDWMM may prove to be appropriate with regard to the detection of core promoter regions and TSSs in long microbial genomic contigs. In order to demonstrate the effectiveness of our predictive model, we applied 10-fold cross-validation experiments on the 607 experimentally-verified promoter sequences, which evidenced good performance in terms of sensitivity.