• Journal of Microbiology and Biotechnology
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• 제33권8호
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• pp.1030-1038
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• 2023

Lactiplantibacillus plantarum, previously named Lactobacillus plantarum, is a facultative, homofermentative lactic acid bacterium widely distributed in nature. Several Lpb. plantarum strains have been demonstrated to possess good probiotic properties, and Lpb. plantarum HOM3204 is a potential probiotic strain isolated from homemade pickled cabbage plants. In this study, whole-genome sequencing was performed to acquire genetic information and predict the function of HOM3204, which has a circular chromosome of 3,232,697 bp and two plasmids of 48,573 and 17,060 bp, respectively. Moreover, various oxidative stress-related genes were identified in the strain, and its antioxidant activity was evaluated in vitro and in vivo. Compared to reference strains, the intracellular cell-free extracts of Lpb. plantarum HOM3204 at a dose of 10¹⁰ colony-forming units (CFU)/ml in vitro exhibited stronger antioxidant properties, such as total antioxidant activity, 2,2-diphenyl-1-picrylhydrazyl radical scavenging rate, superoxide dismutase activity, and glutathione (GSH) content. Daily administration of 10⁹ CFU Lpb. plantarum HOM3204 for 45 days significantly improved the antioxidant function by increasing the glutathione peroxidase activity in the whole blood and GSH concentration in the livers of D-galactose-induced aging mice. These results suggest that Lpb. plantarum HOM3204 can potentially be used as a food ingredient with good antioxidant properties.

• Genomics & Informatics
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• 제20권3호
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• pp.36.1-36.6
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• 2022

BLAST, a basic bioinformatics tool for searching local sequence similarity, has been one of the most widely used bioinformatics programs since its introduction in 1990. Users generally use the web-based NCBI-BLAST program for BLAST analysis. However, users with large sequence data are often faced with a problem of upload size limitation while using the web-based BLAST program. This proves inconvenient as scientists often want to run BLAST on their own data, such as transcriptome or whole genome sequences. To overcome this issue, we developed NBLAST, a graphical user interface-based BLAST program that employs a two-way system, allowing the use of input sequences either as "query" or "target" in the BLAST analysis. NBLAST is also equipped with a dot plot viewer, thus allowing researchers to create custom database for BLAST and run a dot plot similarity analysis within a single program. It is available to access to the NBLAST with http://nbitglobal.com/nblast.

• Journal of Animal Science and Technology
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• 제62권6호
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• pp.948-951
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• 2020

Treponema phagedenis KS1, a fastidious anaerobe, was isolated from a bovine digital dermatitis (BDD)-infected dairy cattle in Chungnam, Korea. Initial data indicated that T. phagedenis KS1 exhibited putative virulent phenotypic characteristics. This study reports the whole genome assembly and annotation of T. phagedenis KS1 (KCTC14157BP) to assist in the identification of putative pathogenicity related factors. The whole genome of T. phagedenis KS1 was sequenced using PacBio RSII and Illumina HiSeqXTen platforms. The assembled T. phagedenis KS1 genome comprises 16 contigs with a total size of 3,769,422 bp and an overall guanine-cytosine (GC) content of 40.03%. Annotation revealed 3,460 protein-coding genes, as well as 49 transfer RNA- and 6 ribosomal RNA-coding genes. The results of this study provide insight into the pathogenicity of T. phagedenis KS1.

• 미생물학회지
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• 제54권4호
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• pp.465-467
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• 2018

퇴비로부터 분리한 Niabella ginsenosidivorans $BS26^T$ 균주의 유전체서열을 분석하였다. 균주 $BS26^T$의 유전체는 G + C 비율이 44.48%이며, 4,800개의 유전자와 4,704개의 단백질 코딩 유전자, 85개의 위유전자 그리고49개의 RNA유전자를 포함한 단일 원형 염색체로 구성되었으면 그 크기는 5,627,734 bp였다. 균주 $BS26^T$는 인삼사포닌의 당 분해에 관여하는 여러 타입의 글라이코시다제 유전자를 가지고 있었다. 이러한 유전체 분석은 주요 진세노사이드 전환에 관여하는 유전자 특징을 이해하는데 큰 기여가 되었다.

• Genomics & Informatics
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• 제11권1호
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• pp.38-45
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• 2013

In cancer genome studies, the annotation of newly detected oncogene/tumor suppressor gene candidates is a challenging process. We propose using concept lattice analysis for the annotation and interpretation of genes having candidate somatic mutations in whole-exome sequencing in acute myeloid leukemia (AML). We selected 45 highly mutated genes with whole-exome sequencing in 10 normal matched samples of the AML-M2 subtype. To evaluate these genes, we performed concept lattice analysis and annotated these genes with existing knowledge databases.

• 식물병연구
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• 제22권2호
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• pp.65-71
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• 2016

Cymbidium mosaic virus (CymMV) is a major virus infecting orchid plants and causing economic loss. In this study, the incidence of viral infection in Calanthe spp. at the Korean Institute of Calanthe was investigated using reverse transcription polymerase chain reaction. The CymMV infection rate was 42%, and the two viruses Odontoglossum ringspot virus and Cucumber mosaic virus had frequencies of 8% and 2%, respectively. Additionally, we characterized an isolate of CymMV, CymMV-GW, using biological tests and examined the nucleotide sequence properties of its complete genome. CymMV-GW induced chlorotic ringspots and chlorotic spot symptoms in inoculated leaves of Chenopodium amaranticolor and Nicotiana benthamiana, respectively. In this study, we have for the first complete genome sequence of CymMV-GW in Korea. The CymMV-GW genome was 6,225 nucleotides in length, excluding the poly-(A) tail, and showed whole-genome nucleotide and amino acid sequence identities of 97.7% and 100%, respectively, with the NJ-1 isolate of CymMV. Here, we report the complete genome sequence of the CymMV-GW isolate and viral infection rates for Calanthe spp. in Korea.

• 미생물학회지
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• 제53권1호
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• pp.55-57
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• 2017

한국 발효식품의 보존성을 높이기 위한 스타터 균주를 얻기 위하여 고추장에서 Bacillus subtilis BS16045를 분리하였다. B. subtilis BS16045에 대한 유전체 분석을 실시하였으며, G+C 비율이 43.6%인 4,165,121 bp 크기의 염기서열을 얻었다. 또한 이 유전체로부터 항진균 및 항균 활성에 연관이 있는 surfactin, kanosamine, bacillaene, plipastatin, subtilosin A, bacilysin 생산 유전자들을 확인하였다. 이러한 결과들을 통해 B. subtilis BS16045는 장류 제조시설에서 유해균의 오염문제를 해결할 수 있는 스타터로 이용될 수 있을 것으로 보인다.

• Molecules and Cells
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• 제38권5호
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• pp.466-473
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• 2015

Over the last 30 years, Hanwoo has been selectively bred to improve economically important traits. Hanwoo is currently the representative Korean native beef cattle breed, and it is believed that it shared an ancestor with a Chinese breed, Yanbian cattle, until the last century. However, these two breeds have experienced different selection pressures during recent decades. Here, we whole-genome sequenced 10 animals each of Hanwoo and Yanbian cattle (20 total) using the Illumina HiSeq 2000 sequencer. A total of approximately 3.12 and 3.07 billion sequence reads were mapped to the bovine reference sequence assembly (UMD 3.1) at an average of approximately 10.71- and 10.53-fold coverage for Hanwoo and Yanbian cattle, respectively. A total of 17,936,399 single nucleotide polymorphisms (SNPs) were yielded, of which 22.3% were found to be novel. By annotating the SNPs, we further retrieved numerous nonsynonymous SNPs that may be associated with traits of interest in cattle. Furthermore, we performed whole-genome screening to detect signatures of selection throughout the genome. We located several promising selective sweeps that are potentially responsible for economically important traits in cattle; the PPP1R12A gene is an example of a gene that potentially affects intramuscular fat content. These discoveries provide valuable genomic information regarding potential genomic markers that could predict traits of interest for breeding programs of these cattle breeds.

• 한국유기농업학회지
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• 제31권4호
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• pp.395-412
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• 2023

광식성 난방제 해충인 미국흰불나방(Hyphantria cunea)의 친환경 방제를 위한 바이러스 살충제의 소재 활용을 위해서 국내에서 분리된 미국흰불나방 핵다각체병바이러스(H. cunea nucleopolyhedrovirus W1: HycuNPV-W1)의 다각체 형태 및 전장 유전체 서열을 결정하고 분석하였다. HycuNPV-W1의 다각체는 1.5-2.2 um 크기의 사면체에 가까운 부정형으로 확인되었다. 전장 유전체의 염기서열을 결정한 결과, 기존에 보고된 HycuNPV와 비교할 때 1,606 bp 더 짧은 131,353 bp로 확인되었다. 그러나 G+C 함량은 45%였으며 상동반복영역은 6개로 기존에 보고된 HycuNPV와 차이는 확인할 수 없었다. ORF 분석에서는 HycuNPV-W1은 기존의 HycuNPV와 비교할 때 3개의 ORF가 더 적은 145개를 가졌으나, HycuNPV-W1에만 존재하는 2개의 ORF가 확인되었다. 이들 ORF의 기능은 현재까지 밝혀지지 않았으나 바이러스의 생물학적 특성에 큰 영향을 주지 않을 것으로 추정되었다. 유전체의 vista 분석 결과에서는 HycuNPV-W1과 기존 HycuNPV의 전체 염기서열 유사도가 매우 높은 것으로 확인되었다. 국내에서 처음으로 분석한 HycuNPV-W1의 전장 유전체는 기존의 HycuNPV와 매우 유사한 것으로 나타났으나, 독자적인 특성을 가진 서로 다른 분리주로 국내 고유자원임을 확인할 수 있었다.

• Molecules and Cells
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• 제38권6호
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• pp.475-481
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• 2015

Programmable nucleases, which include zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and RNA-guided engineered nucleases (RGENs) repurposed from the type II clustered, regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system are now widely used for genome editing in higher eukaryotic cells and whole organisms, revolutionising almost every discipline in biological research, medicine, and biotechnology. All of these nucleases, however, induce off-target mutations at sites homologous in sequence with on-target sites, limiting their utility in many applications including gene or cell therapy. In this review, we compare methods for detecting nuclease off-target mutations. We also review methods for profiling genome-wide off-target effects and discuss how to reduce or avoid off-target mutations.