• Genomics & Informatics
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• 제12권4호
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• pp.261-267
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• 2014

MicroRNAs (miRNAs) are known for their role in mRNA silencing via interference pathways. Repetitive elements (REs) share several characteristics with endogenous precursor miRNAs. In this study, 406 previously identified and 1,494 novel RE-derived miRNAs were sorted from the GENCODE v.19 database using the RepeatMasker program. They were divided into six major types, based on their genomic structure. More novel RE-derived miRNAs were confirmed than identified as RE-derived miRNAs. In conclusion, many miRNAs have not yet been identified, most of which are derived from REs.

• BMB Reports
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• 제53권1호
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• pp.3-9
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• 2020

The mitochondrial genome encodes 13 proteins that are components of the oxidative phosphorylation system (OXPHOS), suggesting that precise regulation of these genes is crucial for maintaining OXPHOS functions, including ATP production, calcium buffering, cell signaling, ROS production, and apoptosis. Furthermore, heteroplasmy or mis-regulation of gene expression in mitochondria frequently is associated with human mitochondrial diseases. Thus, various approaches have been developed to investigate the roles of genes encoded by the mitochondrial genome. In this review, we will discuss a wide range of techniques available for investigating the mitochondrial genome, mitochondrial transcription, and mitochondrial translation, which provide a useful guide to understanding mitochondrial gene expression.

• 한국미생물·생명공학회지
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• 제51권4호
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• pp.555-558
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• 2023

Staphylococcus aureus is a prominent multidrug-resistant pathogen known for its resistance to a variety of antibiotics. To combat this, a wide range of antibiotics, including quinolones, is utilized. While the efficacy of quinolones against S. aureus has been established, the rise in quinolone-resistant strains, particularly in methicillin-resistant S. aureus (MRSA), has necessitated a shift in their usage patterns. Genomic sequencing plays a crucial role as it offers insights into the genetic mechanisms of resistance. Thus, we report the complete genome sequence of an oxolinic acid-resistant strain of S. aureus isolated from sweet potato leaves, a crop commonly cultivated in Korea.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.139-139
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• 2017

The complete chloroplast genome sequence of Avena sterilis L., a dominant wild oat species in the family Poaceae, is first reported in this study. The complete cp genome sequence of A. sterilis is 135,887 bp in length with 38.5% overall GC content and exhibits a typical quadripartite structure comprising one pair of inverted repeats (21, 603 bp) separated by a small single-copy region (12,575 bp) and a large single-copy region (80,106). The A. sterilis cp genome encodes 111 unique genes, 76 of which are protein-coding genes, 4 rRNA genes, 30 tRNA genes and 18 duplicated genes in the inverted repeat region. Nine genes contain one or two introns. Pair-wise alignments of cp genome were performed for genome-wide comparison. This newly determined cp genome sequence of A. sterilis will provide valuable information for the future breeding programs of valuable cereal crops in the family Poaceae.

• Genomics & Informatics
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• 제10권2호
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• pp.69-73
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• 2012

The explosive development of genomics technologies including microarrays and next generation sequencing (NGS) has provided comprehensive maps of cancer genomes, including the expression of mRNAs and microRNAs, DNA copy numbers, sequence variations, and epigenetic changes. These genome-wide profiles of the genetic aberrations could reveal the candidates for diagnostic and/or prognostic biomarkers as well as mechanistic insights into tumor development and progression. Recent efforts to establish the huge cancer genome compendium and integrative omics analyses, so-called "integromics", have extended our understanding on the cancer genome, showing its daunting complexity and heterogeneity. However, the challenges of the structured integration, sharing, and interpretation of the big omics data still remain to be resolved. Here, we review several issues raised in cancer omics data analysis, including NGS, focusing particularly on the study design and analysis strategies. This might be helpful to understand the current trends and strategies of the rapidly evolving cancer genomics research.

• Genomics & Informatics
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• 제14권1호
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• pp.34-40
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• 2016

Due to advances in omics technologies, numerous genome-wide studies on human samples have been published, and most of the omics data with the associated clinical information are available in public repositories, such as Gene Expression Omnibus and ArrayExpress. While analyzing several public datasets, we observed that errors in gender information occur quite often in public datasets. When we analyzed the gender description and the methylation patterns of gender-specific probes (glucose-6-phosphate dehydrogenase [G6PD], ephrin-B1 [EFNB1], and testis specific protein, Y-linked 2 [TSPY2]) in 5,611 samples produced using Infinium 450K HumanMethylation arrays, we found that 19 samples from 7 datasets were erroneously described. We also analyzed 1,819 samples produced using the Affymetrix U133Plus2 array using several gender-specific genes (X (inactive)-specific transcript [XIST], eukaryotic translation initiation factor 1A, Y-linked [EIF1AY], and DEAD [Asp-Glu-Ala-Asp] box polypeptide 3, Y-linked [DDDX3Y]) and found that 40 samples from 3 datasets were erroneously described. We suggest that the users of public datasets should not expect that the data are error-free and, whenever possible, that they should check the consistency of the data.

• Mycobiology
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• 제42권4호
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• pp.322-330
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• 2014

The aim of this study was to identify and characterize new Flammulina velutipes laccases from its whole-genome sequence. Of the 15 putative laccase genes detected in the F. velutipes genome, four new laccase genes (fvLac-1, fvLac-2, fvLac3, and fvLac-4) were found to contain four complete copper-binding regions (ten histidine residues and one cysteine residue) and four cysteine residues involved in forming disulfide bridges, fvLac-1, fvLac-2, fvLac3, and fvLac-4, encoding proteins consisting of 516, 518, 515, and 533 amino acid residues, respectively. Potential N-glycosylation sites (Asn-Xaa-Ser/Thr) were identified in the cDNA sequence of fvLac-1 (Asn-454), fvLac-2 (Asn-437 and Asn-455), fvLac-3 (Asn-111 and Asn-237), and fvLac4 (Asn-402 and Asn-457). In addition, the first 19~20 amino acid residues of these proteins were predicted to comprise signal peptides. Laccase activity assays and reverse transcription polymerase chain reaction analyses clearly reveal that $CuSO_4$ affects the induction and the transcription level of these laccase genes.

• 미생물학회지
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• 제54권3호
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• pp.295-298
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• 2018

Lactobacillus plantarum은 그람 양성, 비운동성의 이형발효세균이며, 다양한 환경에서 서식하고 있다. L. plantarum SK151은 장관상피세포 흡착능이 우수한 균주로서, 김치로부터 분리되었다. SK151 균주의 유전체 길이는 3,231,249 염기쌍이며, G + C 함량은 44.6%이었다. SK151 균주의 유전체에는 비타민 B2 (리보플라빈) 생합성에 필요한 유전자군이 완벽하게 존재하고 있었으며, 세포 흡착과 관련된 유전자도 다수 존재하고 있었다.

• Asian-Australasian Journal of Animal Sciences
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• 제22권10호
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• pp.1359-1365
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• 2009

We performed a genome-wide linkage and quantitative trait locus (QTL) analysis to confirm the existence of QTL affecting Rous Sarcoma Virus (RSV) induced tumor regression, and to estimate their effects on phenotypic variance in an F2 resource population. The F2 population comprised 158 chickens obtained by crossing tumor regressive White Leghorn (WL) and tumor progressive Rhode Island Red (RIR) lines was measured for tumor formation after RSV inoculation. Forty-three tumor progressive and 28 tumor regressive chickens were then used for genome-wide linkage and QTL analysis using a total of 186 microsatellite markers. Microsatellite markers were mapped on 20 autosomal chromosomes. A significant QTL was detected with marker LEI0258 located within the MHC B region on chromosome 16. This QTL had the highest F ratio (9.8) and accounted for 20.1% of the phenotypic variation. Suggestive QTL were also detected on chromosomes 4, 7 and 10. The QTL on chromosome 4 were detected at the 1% chromosome-wide level explaining 17.5% of the phenotypic variation, and the QTLs on chromosome 7 and 10 were detected at the 5% chromosome-wide level and explained 11.1% and 10.5% of the phenotypic variation, respectively. These results indicate that the QTLs in the non-MHC regions play a significant role in RSV-induced tumor regression. The present study constitutes one of the first preliminary reports in domestic chickens for QTLs affecting RSV-induced tumor regression outside the MHC region.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 추계학술대회
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• pp.264-264
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• 2017