• Biomolecules & Therapeutics
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• v.27 no.2
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• pp.201-209
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• 2019

Mixed lineage leukemia proteins (MLL) are the key histone lysine methyltransferases that regulate expression of diverse genes. Aberrant activation of MLL promotes leukemia as well as solid tumors in humans, highlighting the urgent need for the development of an MLL inhibitor. We screened and isolated MLL1-binding ssRNAs using SELEX (${\underline{S}}ystemic$ ${\underline{E}}volution$ of ${\underline{L}}igands$ by ${\underline{E}}xponential$ enrichment) technology. When sequences in sub-libraries were obtained using next-generation sequencing (NGS), the most enriched aptamers-APT1 and APT2-represented about 30% and 26% of sub-library populations, respectively. Motif analysis of the top 50 sequences provided a highly conserved sequence: 5'-A[A/C][C/G][G/U][U/A]ACAGAGGG[U/A]GG[A/C] GAGUGGGU-3'. APT1, APT2, and APT5 embracing this motif generated secondary structures with similar topological characteristics. We found that APT1 and APT2 have a good binding activity and the analysis using mutated aptamer variants showed that the site information in the central region was critical for binding. In vitro enzyme activity assay showed that APT1 and APT2 had MLL1 inhibitory activity. Three-dimensional structure prediction of APT1-MLL1 complex indicates multiple weak interactions formed between MLL1 SET domain and APT1. Our study confirmed that NGS-assisted SELEX is an efficient tool for aptamer screening and that aptamers could be useful in diagnosis and treatment of MLL1-mediated diseases.

• The Korean Journal of Mycology
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• v.52 no.1
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• pp.61-71
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• 2024

Next-generation sequencing of shiitake, oyster, and king oyster spent mushroom substrates collected from Chun-cheon, Yeo-ju, Hong-cheon, Gwang-ju, Ui-ryeong, and A-san was performed. Metabarcoding analysis using amplicon sequence variants was performed to confirm the microbial content ratio in the medium after harvesting the collected mushrooms; the ratio of the contents of various microorganisms in the medium after mushroom harvest varied depending on the materials added to produce the mushroom medium. The WPGMA analysis of the similarity between microbial communities, which was based on the β-diversity, confirmed that the microbial communities in the substrates of the different mushroom varieties were similar.

• Horticultural Science & Technology
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• v.35 no.2
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• pp.149-164
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• 2017

Next generation sequencing (NGS) technologies have led to the rapid accumulation of genome sequences through whole-genome sequencing and re-sequencing of crop species. Genomic resources provide the opportunity for a new revolution in plant breeding by facilitating the dissection of complex traits. Among vegetable crops, reference genomes have been sequenced and assembled for several species in the Solanaceae and Cucurbitaceae families, including tomato, pepper, cucumber, watermelon, and melon. These reference genomes have been leveraged for re-sequencing of diverse germplasm collections to explore genome-wide sequence variations, especially single nucleotide polymorphisms (SNPs). The use of genome-wide SNPs and high-throughput genotyping methods has led to the development of new strategies for dissecting complex quantitative traits, such as genome-wide association study (GWAS). In addition, the use of multi-parent populations, including nested association mapping (NAM) and multiparent advanced generation intercross (MAGIC) populations, has helped increase the accuracy of quantitative trait loci (QTL) detection. Consequently, a number of QTL have been discovered for agronomically important traits, such as disease resistance and fruit traits, with high mapping resolution. The molecular markers for these QTL represent a useful resource for enhancing selection efficiency via marker-assisted selection (MAS) in vegetable breeding programs. In this review, we discuss current genomic resources and marker-trait association analysis to facilitate genome-assisted breeding in vegetable species in the Solanaceae and Cucurbitaceae families.

• Journal of the Korean Institute of Telematics and Electronics S
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• v.36S no.6
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• pp.9-16
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• 1999

In this paper, an efficient algorithm for generation do Lempel's D-homomorphism. This number of exclusive-or operations required to generate the next bit for de Bruijn sequences of order n from a de Bruijm function of order k is shown to be approximately $k(2^{W(n-k)}-1)$where W(r) is the number of one's in the binary representation of r: therefore, the number of required operations can reduced to k if the de Bruijn function is selected appropriately.

• Journal of Sensor Science and Technology
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• v.21 no.5
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• pp.359-366
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• 2012

Nanopore DNA sequencing is an emerging and promising technique that can potentially realize the goal of a low-cost and high-throughput method for analyzing human genome. Especially, solid-state nanopores have relatively high mechanical stability, simple surface modification, and facile fabrication process without the need for labeling or amplification of PCR (polymerized chain reaction) in DNA sequencing. For these advantages of solid-sate nanopores, the use of solid-state nanopores has been extensively considered for developing a next generation DNA sequencing technology. Solid-state nanopore sequencing technique can determine and count charged molecules such as single-stranded DNA, double-stranded DNA, or RNA when they are driven to pass through a membrane nanopore between two electrolytes of cis-trans chambers with applied bias voltage by measuring the ionic current which varies due to the existence of the charged particles in the nanopore. Recently, many researchers have suggested that nanopore-based sensors can be competitive with other third-generation DNA sequencing technologies, and may be able to rapidly and reliably sequence the human genome for under $1,000.

• Economic and Environmental Geology
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• v.4 no.2
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• pp.77-90
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• 1971

About four hundred deposits of iron, talc, fluorite, tungsten, molybdenum, lead, zinc and other polymetallic mineral deposits were plotted on the Ore Distribution Map of the Ockcheon Geosynclinal Area. These mineral deposits plotted on the map can be divided into the several metallogenic zones by the consideration of their geologic background including the sedimentary and tectonic cycles and the igneous activities in the geosynclinal evolution, as follows: a. Chungju iron and talc zones. b. Cheong-san copper bearing iron sulphide zone c. Kumsan-Muju fluorite-polymetallic zones. d. Cheong-an Puyong and Ein Suckseong gold zone e. Hwang-gan Seolcheon and Sangju gold zones. Chungju iron zone originated in the iron bed in the Kemyongsan Series corresponding to the Pre-Ockcheon Cycle of evolution history. In early period of the Ockcheon Cycle, Hyangsanri quartzite and Munjuri phyllitic formation corresponding to the lower terrigenous sequence were not mineralized while the next sequence of the Samsungsan basic igneous-metamorphic formation and the Changri limestone formation were mineralized by the copper bearing iron sulphide and the fluorite-polymetallic deposits respectively. Two generations of the gold zones are recognized. The earlier generation distributes directionaly in the outside of the Ockcheon sedimentary belt was followed by the earlier grantitic invasion of Jurasic in age, while the later generation scatters at random which was related to the nondirectional Cretaceous granitic intrusion of the Post-Ockcheon Cycle. Conclusively speaking, it was disclosed that the endogenic mineralization in the Ockcheon geosyn clinal zone was not conspicuous in its inner sedimentary belt except its limestone area but in its outer peripheral granitic or gneissic zones, and the related igneous activities occured in the Post-Ockcheon Cycle of evolution history.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.58-58
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• 2017

The advent of next generation sequencing technology has elicited plenty of sequencing data available in agriculturally relevant plant species. For most crop species, it is too expensive to obtain the whole genome sequence data with sufficient coverage. Thus, many approaches have been developed to bring down the cost of NGS. Genotyping-by-sequencing (GBS) is a cost-effective genotyping method for complex genetic populations. GBS can be used for the analysis of genomic selection (GS), genome-wide association study (GWAS) and constructing haplotype and genetic linkage maps in a variety of plant species. For efficiently dealing with plant GBS data, the TASSEL-GBS pipeline is one of the most popular choices for many researchers. TASSEL-GBS is JAVA based a software package to obtain genotyping data from raw GBS sequences. Here, we describe application of GBS and bioinformatics pipeline of TASSEL-GBS for analyzing plant genetics data.

• Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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• 2006.05a
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• pp.71-73
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• 2006

This research aims to develop a multiple channel electrochemical DNA chip using micro- fabrication technology. At first, we fabricated a high integrated type DNA chip array by lithography technology. Several probe DNAs consisting of thiol group at their 5-end were immobilized on the gold electrodes. Then target DNAs were hybridized by an electrical force. Redox peak of cyclic-voltammogram showed a difference between target DNA and mismatched DNA in the anodic peak current. Therefore. it is able to detect a various genes electrochemically after immobilization of a various probe DNA and hybridization of label-free DNA on the electrodes simultaneously. It suggested that this DNA chip could recognize the sequence specific genes.

• Journal of Digital Contents Society
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• v.8 no.3
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• pp.385-391
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• 2007

In this paper, we propose a frequency synchronization algorithm for S-DMT cable modem, which is practicable to the next-generation high capacity upstream physical layer in HFC networks. Analyzing several viable frequency synchronization algorithms of multicarrier systems, we proposed an algorithm using predetermined training sequence of repeated pattern in preamble field and residual frequency offset compensation with pilot signals. We verified that the simulation results of the proposed algorithm in AWGN showed good performance and suitability to the S-DMT upstream cable modem for fast frequency synchronization.

• Korean Journal of Plant Taxonomy
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• v.46 no.1
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• pp.60-64
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• 2016

Scopolia parviflora of the family Solanaceae is an endemic species of Korea and a traditional Korean medicinal plant. The plastid genome was sequenced by next-generation sequencing (NGS) method. The characterized cp genome is 156,193 bp in size; the large single-copy (LSC) region is 86,364 bp, the inverted repeat (IR) is 25,905 bp, and the small single copy (SSC) region is 18,019 bp. The overall GC content of the plastid genome amounts to 37.61%. The cp genome contains 113 genes and 21 introns, including 80 proteincoding genes, four RNA genes, 30 tRNA genes, 20 group II introns, and one group I intron. A phylogenetic analysis showed that Scopolia parviflora was closely related to Hyoscyamus niger.