• Journal of Plant Biotechnology
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• 제7권4호
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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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• 제23권11호
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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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• 제43권3호
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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.

• 정보처리학회논문지:소프트웨어 및 데이터공학
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• 제11권1호
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• pp.11-18
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• 2022

신약 디자인은 단백질 수용체와 같은 생물학적 표적과 상호작용할 수 있는 약물 후보물질을 식별하는 과정이다. 전통적인 신약 디자인 연구는 약물 후보 물질 탐색과 약물 개발 단계로 구성되어 있으나, 하나의 신약을 개발하기 위해서는 10년 이상의 장시간이 요구된다. 이러한 기간을 단축하고 효율적으로 신약 후보 물질을 발굴하기 위하여 심층 학습 기반의 방법들이 연구되고 있다. 많은 심층학습 기반의 모델들은 SMILES 문자열로 표현된 화합물을 재귀신경망을 통해 학습 및 생성하고 있으나, 재귀신경망은 훈련시간이 길고 복잡한 분자식의 규칙을 학습시키기 어려운 단점이 있어서 개선의 여지가 남아있다. 본 연구에서는 self-attention과 variational autoencoder를 활용하여 SMILES 문자열을 생성하는 딥러닝 모델을 제안한다. 제안된 모델은 최신 신약 디자인 모델 대비 훈련 시간을 1/26로 단축하는 것뿐만 아니라 유효한 SMILES를 더 많이 생성하는 것을 확인하였다.

• BMB Reports
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• 제49권12호
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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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• 제54권11호
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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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• 제17권3호
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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.

• 한국컴퓨터정보학회논문지
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• 제25권8호
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• pp.1-8
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• 2020

본 논문에서는 드노보 전사체 어셈블리의 수행시간을 단축하기 위해 RNA-seq 서열을 유전자계 정보를 활용하여 여러 노드로 분산이 가능한 방법을 제시한다. 제안하는 전사체 서열 데이터 분산기법의 성능을 측정하기 위해 애기장대의 리드를 4개의 데이터 셋(전체 비분류 리드, 완전 분류 리드, 모델 분류 리드, 무작위 분류 리드)으로 구성하여 실험을 수행하였다. 전체 비분류 데이터와 비교하여 생성된 유전자 콘티그(Contig)는 95% 일치하였고 동일한 리소스들을 사용하는 단일 노드에 비해 본 연구에서 제시하는 분산환경분산 환경 기반의 어셈블리 수행시간은 4.2배 단축되었다.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2018년도 춘계학술발표회
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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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• 제30권6호
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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.