• Journal of Plant Biotechnology
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• v.7 no.4
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• pp.267-272
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• 2005

Common bean (Phaseolus vulgaris L.) plants were regenerated via organogenesis from mature embryonic axes, cultured on MS medium supplemented with ildole-3-ecetic acid (IAA) and thidiazuron (TDZ) for one week in the dark. Embryonic axillary regions were excised, longitudinally cut to split the both sides, and cultured for two weeks on MS medium supplemented with IAA and TDZ. The combination 0.5 mg $l^{-1}$ TDZ/0.5 mg $l^{-1}$ IAA presented the higher efficiency in shoot regeneration and the combination 0.5 mg $l^{-1}$ TDZ/0.25 mg $l^{-1}$ IAA presented the higher efficiency in conversion of shoots to plants. Regenerating explants were transferred to MS medium containing 1 mg $l^{-1}$ BAP for shoot development. All elongated shoots were rooted in vitro, presented normal phenotype and produced viable seeds. Histological analysis confirmed the mode of regeneration as de novo shoot organogenesis.

• Journal of Microbiology and Biotechnology
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• v.23 no.11
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• pp.1569-1576
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• 2013

In mice, supplementation of t10,c12 conjugated linoleic acid (CLA) increases liver mass and hepatic steatosis via increasing uptake of fatty acids released from adipose tissues. However, the effects of t10,c12 CLA on hepatic lipid synthesis and the associated mechanisms are largely unknown. Thus, we tested the hypothesis that gut microbiota-producing t10,c12 CLA would induce de novo lipogenesis and triglyceride (TG) synthesis in HepG2 cells, promoting lipid accumulation. It was found that treatment with t10,c12 CLA ($100{\mu}M$) for 72 h increased neutral lipid accumulation via enhanced incorporation of acetate, palmitate, oleate, and 2-deoxyglucose into TG. Furthermore, treatment with t10,c12 CLA led to increased mRNA expression and protein levels of lipogenic genes including SREBP1, ACC1, FASN, ELOVL6, GPAT1, and DGAT1, presenting potential mechanisms by which CLA may increase lipid deposition. Most strikingly, t10,c12 CLA treatment for 3 h increased phosphorylation of mTOR, S6K, and S6. Taken together, gut microbiota-producing t10,c12 CLA activates hepatic de novo lipogenesis and TG synthesis through activation of the mTOR/SREBP1 pathway, with consequent lipid accumulation in HepG2 cells.

• Journal of Plant Biotechnology
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• v.43 no.3
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• pp.293-301
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• 2016

High-quality gene sets are necessary for functional research of genes. Although Perilla is a commonly cultivated oil crop and vegetable crop in Southeast Asia, the quality of its available gene set is insufficient. To construct a high-quality Perilla gene set, we sequenced mRNAs extracted from different tissues of Perilla citriodora, the wild species (2n = 20) of Perilla. To make a high-quality gene set for P. citriodora, we compared the quality of assemblies produced by Velvet and Trinity, the two well-known de novo assemblers, and improved the de novo assembly pipeline by optimizing k-mers and removing redundant sequences. We then selected representative transcripts for loci according to several criteria. The improved assembly yielded a total of 86,396 transcripts and 38,413 representative transcripts. We evaluated the assembled transcripts by comparing them to 638 homologous Arabidopsis genes involved in fatty acid and TAG biosynthesis pathways. High proportions of full-length genes and transcripts in the assembled transcripts matched known genes in other species, indicating that the P. citriodora gene set can be applied in future functional studies. Our study provides a reference P. citriodora gene set for further studies. It will serve as valuable genetic resource to elucidate the molecular basis of various metabolisms.

• KIPS Transactions on Software and Data Engineering
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• v.11 no.1
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• pp.11-18
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• 2022

De novo drug design is the process of developing new drugs that can interact with biological targets such as protein receptors. Traditional process of de novo drug design consists of drug candidate discovery and drug development, but it requires a long time of more than 10 years to develop a new drug. Deep learning-based methods are being studied to shorten this period and efficiently find chemical compounds for new drug candidates. Many existing deep learning-based drug design models utilize recurrent neural networks to generate a chemical entity represented by SMILES strings, but due to the disadvantages of the recurrent networks, such as slow training speed and poor understanding of complex molecular formula rules, there is room for improvement. To overcome these shortcomings, we propose a deep learning model for SMILES string generation using variational autoencoders with self-attention mechanism. Our proposed model decreased the training time by 1/26 compared to the latest drug design model, as well as generated valid SMILES more effectively.

• BMB Reports
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• v.49 no.12
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• pp.653-654
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• 2016

The human reference genome, maintained by the Genome Reference Consortium, is conceivably the most complete genome assembly ever, since its first construction. It has continually been improved by incorporating corrections made to the previous assemblies, thanks to various technological advances. Many currently-ongoing population sequencing projects have been based on this reference genome, heightening hopes of the development of useful medical applications of genomic information, thanks to the recent maturation of high-throughput sequencing technologies. However, just one reference genome does not fit all the populations across the globe, because of the large diversity in genomic structures and technical limitations inherent to short read sequencing methods. The recent success in de novo construction of the highly contiguous Asian diploid genome AK1, by combining single molecule technologies with routine sequencing data without resorting to traditional clone-by-clone sequencing and physical mapping, reveals the nature of genomic structure variation by detecting thousands of novel structural variations and by finally filling in some of the prior gaps which had persistently remained in the current human reference genome. Now it is expected that the AK1 genome, soon to be paired with more upcoming de novo assembled genomes, will provide a chance to explore what it is really like to use ancestry-specific reference genomes instead of hg19/hg38 for population genomics. This is a major step towards the furthering of genetically-based precision medicine.

• Clinical and Experimental Pediatrics
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• v.54 no.11
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• pp.470-472
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• 2011

Familial hyperkalemic periodic paralysis (HYPP) is an autosomal-dominant channelopathy characterized by transient and recurrent episodes of paralysis with concomitant hyperkalemia. Mutations in the skeletal muscle voltage-gated sodium channel gene $SCN4A$ have been reported to be responsible for this disease. Here, we report the case of a 16-year-old girl with HYPP whose mutational analysis revealed a heterozygous c.2111C>T substitution in the $SCN4A$ gene leading to a Thr704Met mutation in the protein sequence. The parents were clinically unaffected and did not have a mutation in the $SCN4A$ gene. A $de$ $novo$ $SCN4A$ mutation for familial HYPP has not previously been reported. The patient did not respond to acetazolamide, but showed a marked improvement in paralytic symptoms upon treatment with hydrochlorothiazide. The findings in this case indicate that a $de$ $novo$ mutation needs to be considered when an isolated family member is found to have a HYPP phenotype.

• Genomics & Informatics
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• v.17 no.3
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• pp.27.1-27.9
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• 2019

Supernumerary B chromosomes were found in Lilium amabile (2n = 2x = 24), an endemic Korean lily that grows in the wild throughout the Korean Peninsula. The extra B chromosomes do not affect the host-plant morphology; therefore, whole transcriptome analysis was performed in 0B and 1B plants to identify differentially expressed genes. A total of 154,810 transcripts were obtained from over 10 Gbp data by de novo assembly. By mapping the raw reads to the de novo transcripts, we identified 7,852 differentially expressed genes (log₂FC > |10|), in which 4,059 and 3,794 were up-and down-regulated, respectively, in 1B plants compared to 0B plants. Functional enrichment analysis revealed that various differentially expressed genes were involved in cellular processes including the cell cycle, chromosome breakage and repair, and microtubule formation; all of which may be related to the occurrence and maintenance of B chromosomes. Our data provide insight into transcriptomic changes and evolution of plant B chromosomes and deliver an informative database for future study of B chromosome transcriptomes in the Korean lily.

• Journal of the Korea Society of Computer and Information
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• v.25 no.8
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• pp.1-8
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• 2020

In this paper, we propose a gene family based RNA-seq read distribution method in means to accelerate the overal transcriptome assembly computation time. To measure the performance of our transcriptome sequence data distribution method, we evaluated the performance by testing four types of data sets of the Arabidopsis thaliana genome (Whole Unclassified Reads, Family-Classified Reads, Model-Classified Reads, and Randomly Classified Reads). As a result of de novo transcript assembly in distributed nodes using model classification data, the generated gene contigs matched 95% compared to the contig generated by WUR, and the execution time was reduced by 4.2 times compared to a single node environment using the same resources.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2018.04a
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• pp.5-5
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• 2018

Ginseng (Panax ginseng C.A. Meyer), one of the most widely used medicinal plants in traditional oriental medicine, is used for the treatment of various diseases. It has been classified according to its cultivation environment, such as field cultivated ginseng (FCG) and mountain cultivated ginseng (MCG). However, little is known about differences in gene expression in ginseng roots between field cultivated and mountain cultivated ginseng. In order to investigate the whole transcriptome landscape of ginseng, we employed High-Throughput sequencing technologies using the Illumina HiSeqTM2500 system, and generated a large amount of sequenced transcriptome from ginseng roots. Approximately 77 million and 87 million high-quality reads were produced in the FCG and MCG roots transcriptome analyses, respectively, and we obtained 256,032 assembled unigenes with an average length of 1,171 bp by de novo assembly methods. Functional annotations of the unigenes were performed using sequence similarity comparisons against the following databases: the non-redundant nucleotide database, the InterPro domains database, the Gene Ontology Consortium database, and the Kyoto Encyclopedia of Genes and Genomes pathway database. A total of 4,207 unigenes were assigned to specific metabolic pathways, and all of the known enzymes involved in starch and sucrose metabolism pathways were also identified in the KEGG library. This study indicated that alpha-glucan phosphorylase 1, putative pectinesterase/pectinesterase inhibitor 17, beta-amylase, and alpha-glucan phosphorylase isozyme H might be important factors involved in starch and sucrose metabolism between FCG and MCG in different environments.

• Bulletin of the Korean Chemical Society
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• v.30 no.6
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• pp.1313-1316
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• 2009

Cdc25 phosphatases have been considered as attractive drug targets for anticancer therapy due to the correlation of their overexpression with a wide variety of cancers. We have been able to identify five novel Cdc25 phosphatase inhibitors with micromolar activity by means of a structure-based de novo design method with a known inhibitor scaffold. Because the newly discovered inhibitors are structurally diverse and have desirable physicochemical properties as a drug candidate, they deserve further investigation as anticancer drugs. The differences in binding modes of the identified inhibitors in the active sites of Cdc25A and B are addressed in detail.