• Journal of Microbiology and Biotechnology
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• 제27권8호
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• pp.1419-1427
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• 2017

As probiotics play an important role in maintaining a healthy gut flora environment through antitoxin activity and inhibition of pathogen colonization, they have been of interest to the medical research community for quite some time now. Probiotic bacteria such as Lactobacillus plantarum, which can be found in fermented food, are of particular interest given their easy accessibility. We performed whole-genome sequencing and genomic analysis on a GB-LP1 strain of L. plantarum isolated from Korean traditional fermented food; this strain is well known for its functions in immune response, suppression of pathogen growth, and antitoxin effects. The complete genome sequence of GB-LP1 is a single chromosome of 3,040,388 bp with 2,899 predicted open reading frames. Genomic analysis of GB-LP1 revealed two CRISPR regions and genes showing accelerated evolution, which may have antibiotic and antitoxin functions. The aim of the present study was to predict strain specific-genomic characteristics and assess the potential of this new strain as lactic acid bacteria at the genomic level using in silico analysis. These results provide insight into the L. plantarum species as well as confirm the possibility of its utility as a candidate probiotic.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2010년도 정기총회 및 추계학술발표회
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• pp.11-11
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• 2010

The Korean ginseng, Panax ginseng C. A. Meyer is a popular medicinal herb in Araliaceae. Genetic map in crops provides valuable information for breeding, genetic and genomic researches. However, little information is available for construction of genetic map in ginseng. Up to now, we have produced large amounts of expressed sequence tags (ESTs) from four ginseng cultivars (37Mb, 49Mb, 39Mb, 47Mb from Gopoong, Gumpoong, Chunpoong and Yunpoong respectively using pyrosequencing technique and 5Mb from normalized full-length cDNA library of Chunpoong) to obtain comprehensive information of gene expression, and constructed EST database including ESTs from public database. Till now, we designed 261 SSR primer sets using EST sequences and identified 106 intergenic polymorphic markers. And 44 of the 106 showed polymorphisms among panax ginseng cultivars. Among 44 markers, 27 SSR polymorphic markers were inspected to 51 $F_2$ population from Yunpoong x Chunpoong, which showed good at the fitness of Mendellian segregation ratio 1:2:1. To enrich the number of markers, and thus construct high resolution genetic map which can be used as frame map for further genome sequencing. we are planning to develop large scale EST-derived SNP markers which are available in the F2 population. This study provides genetic information as well as foundation for ginseng researches such as genetics, genomics, breeding, and the final goal for whole genome sequencing. This study was supported by Technology Development Program for Agriculture and Forestry, Ministry for Food, Agriculture, Forestry and Fisheries, Republic of Korea (Grant No. 609001-051SB210).

• 한국정보통신학회논문지
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• 제17권12호
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• pp.3009-3015
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• 2013

차세대 시퀀싱(NGS)은 암에서 전사체 싱글 뉴클레오티드 변형 발견과 모든 지놈 발견을 가능하게 한다. 어느 한 위치에서 배열된 다수의 짧은 리드 시퀀스로부터 개인의 유전자형을 결정하는 가장 기초적인 방법이다. Byesian 알고리즘은 사후 유전자형 확률을 사용하여 파라미터 추정한다. 또 다른 방법인 EM 알고리즘은 최대 가능성 추정 방법을 사용해서 관측된 데이터에서 파라미터를 추정한다. 본 논문에서는 새로운 유전자형 조사 시스템을 제안하고 시퀀싱 에러 비율과 체세포 돌연 변이 상태 그리고 유전자형 확률의 사후 추정치에 관한 샘플 크기(S = 50, 100, 500)의 영향을 비교 분석하였다. 그 결과 작은 샘플 크기 50에서도 Byesian 알고리즘을 사용하여 추정한 파라미터가 EM 알고리즘 보다 더 정확하게 실제 파라미터에 근접하였다.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.135-135
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• 2017

The Gramene database (http://www.gramene.org) is a powerful online resource for agricultural researchers, plant breeders and educators that provides easy access to reference data, visualizations and analytical tools for conducting cross-species comparisons. Learn the benefits of using Gramene to enrich your lectures, accelerate your research goals, and respond to your organismal community needs. Gramene's genomes portal hosts browsers for 44 complete reference genomes, including crops and model organisms, each displaying functional annotations, gene-trees with orthologous and paralogous gene classification, and whole-genome alignments. SNP and structural diversity data, available for 11 species, are displayed in the context of gene annotation, protein domains and functional consequences on transcript structure (e.g., missense variant). Browsers from multiple species can be viewed simultaneously with links to community-driven organismal databases. Thus, while hosting the underlying data for comparative studies, the portal also provides unified access to diverse plant community resources, and the ability for communities to upload and display private data sets in multiple standard formats. Our BioMart data mining interface enable complex queries and bulk download of sequence, annotation, homology and variation data. Gramene's pathway portal, the Plant Reactome, hosts over 240 pathways curated in rice and inferred in 66 additional plant species by orthology projection. Users may compare pathways across species, query and visualize curated expression data from EMBL-EBI's Expression Atlas in the context of pathways, analyze genome-scale expression data, and conduct pathway enrichment analysis. Our integrated search database and modern user interface leverage these diverse annotations to facilitate finding genes through selecting auto-suggested filters with interactive views of the results.

• Journal of Microbiology and Biotechnology
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• 제33권10호
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• pp.1292-1298
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• 2023

PAMB 00755^T, a bacterial strain, was isolated from Korean fir leaves. The strain exhibits yellow colonies and consists of Gram-negative, non-motile, short rods or ovoid-shaped cells. It displays optimal growth conditions at 20℃, 0% NaCl, and pH 6.0. Results of 16S rRNA gene-based phylogenetic analyses showed that strain PAMB 00755^T was most closely related to Sphingomonas chungangi MAH-6^T (97.7%) and Sphingomonas polyaromaticivorans B2-7^T (97.4%), and ≤96.5% sequence similarity to other members of the genus Sphingomonas. The values of average nucleotide identity (79.9-81.3%), average amino acid identity (73.3-75.9%), and digital DNA-DNA hybridization (73.3-75.9%) were significantly lower than the threshold values for species boundaries; these overall genome-related indexes (OGRI) analyses indicated that the strain represents a novel species. Genomic analysis revealed that the strain has a 4.4-Mbp genome encoding 4,083 functional genes, while the DNA G+C content of the whole genome is 66.1%. The genome of strain PAMB 00755^T showed a putative carotenoid biosynthetic cluster responsible for its antioxidant activity. The respiratory quinone was identified as ubiquinone 10 (Q-10), while the major fatty acids in the profile were identified as C_18:1ω7c and/or C_18:1ω6c (summed feature 8). The major polar lipids of strain PAMB 00755^T were diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, and phosphatidylcholine. Based on a comprehensive analysis of genomic, phenotypic, and chemotaxonomic characteristics, we proposed the name Sphingomonas abietis sp. nov. for this novel species, with PAMB 00755^T as the type strain (= KCTC 92781^T = GDMCC 1.3779^T).

• Animal cells and systems
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• 제1권2호
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• pp.363-370
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• 1997

RNase MRP is a ribonucleoprotein complex with a site-specific endonuclease activity. Its original substrate for cleavage is the small mitochondrial RNA near the mitochondrial DNA replication origin, thus it was proposed to generate the primer for mtDNA replication. Recently, it has been shown to have another substrate in the nucleus, such as pre-S.8S ribosomal RNA in nucleolus. The gene for the RNA component of RNase MRP (MRP RNA) was found to be encoded by the nucleus genome, suggesting an interesting intracellular trafficking of MRP RNA to both mitochondria and nucleolus after transcription in nucleus. In this study, genomic DNA encoding MRP RNA was microinjected into the nucleus of Xenopus oocytes, to analyze promoter regions involved in the transcription. It showed that the proximal sequence element and TATA box are important for basal level transcription; octamer motif and Sp1 binding sites are for elevated level transcription. Most of Xenopus MRP RNA was exported out to the cytoplasm following transcription in the nucleus. Utilizing various hybrid constructs, export of MRP RNA was found to be regulated by the promoter and the 5' half of the coding region of the gene. Interestingly, the transcription in nucleus seems to be coupled to the export of MRP RNA to cytoplasm. Intracellular transport of injected MRP RNA can be easily visualized by whole-mount in situ hybridization following microinjection; it also shows possible intra-nuclear sites for transcription and export of MRP RNA.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2003년도 생물공학의 동향(XIII)
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• pp.434-437
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• 2003

A new bacterial strain, was isolated from activated sludge, identified and named P. aeruginosa EMS1. The new strain produced surface-active rhamnolipids by batch cultivation in mineral salts medium with waste flying oils. The mutant strain KH7, designated P. aeruginosa EMS1, derived by random mutagenesis with N-methyl-N-nitro-N-nitrosogoanidine treatment producing high levels of the biosurfactants was selected by an ion-pair plate assay. The mutant strain KH7 showed 4-5 times more hydrocarbon emulsification as compared to the parent when grown on waste frying oils and various hydrocarbons. Furthermore, P. aeruginosa EMS1 and mutant strain KH7 was also able to use whey as a co-substrate for growth and biosurfactant production. As results of this study, mutant strain KH7 is a very efficient biosurfactant producer, and its culture conditions are relatively inexpensive and economical. Rhamnolipid is synthesized by the rhlAB-encoded rhamnosyltransferase. To be convinced of these genes, we performed PCR based on P. aeruginosa PAO1 whole-genome database. rhl gene cluster nucleotide and amino acid sequences were compared for both parent and mutant. Comparison of nucleotide sequence of rhlAB, there were usually terminal's codons exchange.

• 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.