• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.72-77
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• 2005

Orthologs are genes having the same function across different species that specialize from a single gene in the last common ancestor of these species. Orthologous groups are useful in the genome annotation, studies on gene evolution, and comparative genomics. However, the construction of an orthologous group is difficult to automate and it takes so much time. It is also hard to guarantee the accuracy of the constructed orthologous groups. We propose a system to construct orthologous groups on many genomes automatically and rapidly. We utilize the grid computing to reduce the sequence alignment time, and we use clustering algorithm in the application of database to automate whole processes. We have generated orthologous groups for 20 complete prokaryotes genomes just in a day because of the grid computing. Furthermore, new genomes can be accommodated easily by the clustering algorithm and grid computing. We compared the generated orthologous groups with COGs (Clusters of orthologous Group of proteins) and KO (KEGG Ortholog). The comparison shows about 85 percent similarity compared with previous well-known orthologous databases.

• Animal Systematics, Evolution and Diversity
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• 제24권3호
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• pp.327-332
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• 2008

Soft coral Dendronephthya gigantea (Verrill, 1864) is a conspicuous species dominating shallow sea waters of Jejudo Island, Korea. Recently its whole mitochondrial genome sequencing was completed by us and the sequence information provided an opportunity to test the age of Octocorallia and time of evolutionary separation between some representative orders of the subclass Octocorallia. Molecular phylogenetic analyses based on 13 mitochondrial protein encoding genes revealed a polyphyletic relationship among octocorallians representing two orders (Alcyonacea and Gorgonacea) and four families (Alcyoniidae, Nephtheidae, Briareidae, and Gorgoniidae). Estimates of divergence times among octocorallians indicate that the first splitting might occur around end of or after Cretaceous period (50-79 million years ago (Ma)). The age is relatively young compared to the long history of stony sea corals (>240 Ma). Taken together our result suggests a possible relatively recent radiating evolution at least in the order Alcyonacea and Gorgonacea. Molecular dating and phylogenetic analysis based on much broader taxon sampling and many genes might give an insight into this interesting hypothesis.

• Journal of Microbiology and Biotechnology
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• 제17권7호
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• pp.1083-1089
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• 2007

Because of their selectivity and catalytic efficiency, BVMOs are highly valuable biocatalysts for the chemoenzymatic synthesis of a broad range of useful compounds. In this study, we investigated the microbial Baeyer-Villiger oxidation and sulfoxidation of thioanisole and bicyclo[3.2.0]hept-2-en-6-one using whole Escherichia coli cells that recombined with each of the Baeyer-Villiger monooxygenases originated from Pseudomonas aeruginosa PAOl and two from Streptomyces coelicolor A3(2). The three BVMOs were identified in the microbial genome database by a recently described protein sequence motif; e.g., BVMO motif(FXGXXXHXXXW). The reaction products were identified as (R)-/(S)-sulfoxide and 2-oxabicyclo/3-oxabicyclo[3.3.0]oct-6-en-2-one by GC-MS analysis. Consequently, this study demonstrated that the three enzymes can indeed catalyze the Baeyer-Villiger reaction as a biocatalyst, and effective annotation tools can be efficiently exploited as a source of novel BVMOs.

• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2006년도 한국컴퓨터종합학술대회 논문집 Vol.33 No.1 (A)
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• pp.43-45
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• 2006

Unlike RNA interference, whose usage is limited to eukaryotic cells, Peptide Nucleic Acid (PNA) technique is applicable to both eukaryotic and prokaryotic cells. PNA has been proven to be an effective agent for blocking gene expressions and has several advantages over other antisense techniques. Here we developed a parallel computing software that provides the ideal sequences to design PNA oligos to prevent any off-target effects. We applied a new approach in our location-finding algorithm that finds a target gene from the whole genome sequence. Message Passing Interface (MPI) was used to perform parallel computing in order to reduce the calculation time. The software will help biologists design more accurate and effective antisense PNA by minimizing the chance of off-target effects.

• 한국컴퓨터정보학회논문지
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• 제25권8호
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• pp.1-8
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• 2020

본 논문에서는 드노보 전사체 어셈블리의 수행시간을 단축하기 위해 RNA-seq 서열을 유전자계 정보를 활용하여 여러 노드로 분산이 가능한 방법을 제시한다. 제안하는 전사체 서열 데이터 분산기법의 성능을 측정하기 위해 애기장대의 리드를 4개의 데이터 셋(전체 비분류 리드, 완전 분류 리드, 모델 분류 리드, 무작위 분류 리드)으로 구성하여 실험을 수행하였다. 전체 비분류 데이터와 비교하여 생성된 유전자 콘티그(Contig)는 95% 일치하였고 동일한 리소스들을 사용하는 단일 노드에 비해 본 연구에서 제시하는 분산환경분산 환경 기반의 어셈블리 수행시간은 4.2배 단축되었다.

• 한국미생물·생명공학회지
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• 제49권4호
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• pp.493-500
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• 2021

Argyrins are a group of anticancer and antibacterial octapeptide bioactive substances isolated from myxobacteria. In this study, we showed that the myxobacterium Archangium gephyra MEHO_001, isolated in Korea, produces argyrins A and B. MEHO_001 cells tend to aggregate when cultured in liquid media. Hence, a dispersion mutant, MEHO_002, was isolated from MEHO_001. The MEHO_002 strain produced approximately 3.5 times more argyrins than that produced by the wild-type strain MEHO_001. We determined the whole-genome sequence of A. gephyra MEHO_002 and identified a putative argyrin biosynthetic gene cluster comprising five genes, arg1-arg5, encoding non-ribosomal peptide synthases and tailoring enzymes. Inactivation of arg2 by plasmid insertion disrupted argyrin production. The amino acid sequences of the proteins encoded by arg2-arg5 of A. gephyra MEHO_002 were 90-98% similar to those encoded by the argyrin biosynthetic genes of Cystobacter sp. SBCb004, an argyrin-producing myxobacterium with identical domain organization.

• Journal of Microbiology and Biotechnology
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• 제30권7호
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• pp.974-981
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• 2020

Sequence type 410 (ST410) of Escherichia coli is an extraintestinal pathogen associated with multi drug resistance. In this study, we aimed to investigate the horizontal propagation pathway of a high-risk clone of E. coli ST410 that produces Klebsiella pneumoniae carbapenemase (KPC). blaKPC-encoding E. coli and K. pneumoniae isolates were evaluated, and complete sequencing and comparative analysis of blaKPC-encoding plasmids from E. coli and K. pneumoniae, antimicrobial susceptibility tests, polymerase chain reaction, multilocus sequence typing, and conjugal transfer of plasmids were performed. Whole-genome sequencing was performed for plasmids mediating KPC-2 production in E. coli and K. pneumoniae clinical isolates. Strains E. coli CPEc171209 and K. pneumoniae CPKp171210 were identified as ST410 and ST307, respectively. CPEc171209 harbored five plasmids belonging to serotype O8:H21, which is in the antimicrobial-resistant clade C4/H24. The CPKp171210 isolate harbored three plasmids. Both strains harbored various additional antimicrobial resistance genes. The IncX3 plasmid pECBHS_9_5 harbored blaKPC-2 within a truncated Tn4401a transposon, which also contains blaSHV-182 with duplicated conjugative elements. This plasmid displayed 100% identity with the IncX3 plasmid pKPBHS_10_3 from the K. pneumoniae CPKp171210 ST307 strain. The genes responsible for the conjugal transfer of the IncX3 plasmid included tra/trb clusters and pil genes coding the type IV pilus. ST410 can be transmitted between patients, posing an elevated risk in clinical settings. The emergence of a KPC-producing E. coli strain (ST410) is concerning because the blaKPC-2-bearing plasmids may carry treatment resistance across species barriers. Transgenic translocation occurs among carbapenem-resistant bacteria, which may spread rapidly via horizontal migration.

• 미생물학회지
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• 제41권2호
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• pp.93-98
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• 2005

Sphingomonas chungbukensis DJ77의 유전체 서열분식 과정에서 969개의 nucleotide로 구성된 sphingosine kinase 유전자를 동정하였다. 이 sphingosine kinase 단백질의 아미노산 서열은 Zymomonas mobilis subsp. mobilis ZM4의 sphingosine kinase 아미노산 서열과 $55\%$의 상동성을 보였다. 또한 다중서열정렬을 통해 각각 진핵세포의 sphingosine kinase의 C2, C3, C5 domain에 속하는 3개의 conserved sequence를 발견하였다. 그 중 하나는 sphingosine kinase에서 ATP-binding site일 것으로 예상되어지는nucleotide-binding motif(GGDG)였고 나머지 둘은 아직 기능이 알려지지 않은 conserved sequences 였다. 이러한 다중서열정렬을 바탕으로 계통수를 그려본 결과, S. chungbukensis DJ77의 sphingosine kinase (SPK)는 COG1597 그룹과 유사했으며, COG1597 내에서 동일종의 diacylglycerol kinase와는 서로 다른 그룹에 속하는 것으로 나타났다. 재조합 SPK는 이종(異種)세포인 Escherichia coli내에서 성공적으로 과발현 되었으나, 세포 내에서 불용성 복합체(inclusion body)를 형성하였다.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.259-259
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• 2022

Soil salinity is a major factor that reduces crop yields. The amount of soil affected by salinity is about 83 million hectares (FAO 2000), which is increasing due to the effects of climate change. In soybean [Glycine max (L.) Merr.], nutritional properties such as protein, starch, and sucrose content together with biomass and yield tends to reduce due to excessive salt. As a result of QTL mapping using the 169 F_2:3 population from the KA-1285 (salt-tolerant) × Daepung (salt-sensitive) in a previous study, two major QTLs (Gm03_39796778 and Gm03_40600088) related to salt tolerance were found on chromosome 3. In this study, the CDS region of the Gmsalt3 gene was analyzed using the ABI 3730x1 DNA Analyzer (Macrogen, Korea). The sequence of Gmsalt3 gene in KA-1285 was compared with Williams 82.a4.vl and PI483463 (Glycine soja). Two transversions were found at exon6 in KA-1285 and PI483463. Currently, whole genome sequencing and variation analysis using the Illumine Novaseq 6000 machine (Illumina, USA) are in progress. The results of this study can provide useful molecular markers for the selection of salt-tolerant soybeans and can be used as basic data for future salt-tolerant gene research.

• Journal of Microbiology and Biotechnology
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• 제25권10호
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• pp.1621-1628
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• 2015

Chlamydia possesses a conserved 7.5 kb plasmid that is known to play an important role in chlamydial pathogenesis, since some chlamydial organisms lacking the plasmid are attenuated. The chlamydial transformation system developed recently required the use of plasmid-free organisms. Thus, the generation and identification of plasmid-free organisms represent a key step in understanding chlamydial pathogenic mechanisms. A tricolor immunofluorescence assay for simultaneously detecting the plasmid-encoded Pgp3 and whole organisms plus DNA staining was used to screen C. muridarum organisms selected with novobiocin. PCR was used to detect the plasmid genes. Next-generation sequencing was then used to sequence the genomes of plasmid-free C. muridarum candidates and the parental C. muridarum Nigg strain. We generated five independent clones of plasmid-free C. muridarum organisms by using a combination of novobiocin treatment and screening plaque-purified clones with anti-Pgp3 antibody. The clones were confirmed to lack plasmid genes by PCR analysis. No GlgA protein or glycogen accumulation was detected in cells infected with the plasmid-free clones. More importantly, whole-genome sequencing characterization of the plasmid-free C. muridarum organism and the parental C. muridarum Nigg strain revealed no additional mutations other than loss of the plasmid in the plasmid-free C. muridarum organism. Thus, the Pgp3-based immunofluorescence assay has allowed us to identify authentic plasmid-free organisms that are useful for further investigating chlamydial pathogenic mechanisms.