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Ryu, Chung-Kyu,Lee, Yoonji,Park, Seul-gi,You, Hea-Jung,Lee, Ra-Young,Lee, Seung-Yon,Choi, Sun 이화여자대학교 약학연구소 2009 藥學硏究論文集 Vol.- No.19
The abnormal proliferation and migration of vascular smooth muscle cells (SMCs) play an important role in the pathology of coronary artery atherosclerosis and restenosis following angioplasty. It was reported that some heterocyclic quinone derivatives such as 6-arylamino-quinoxaline-5,8-diones and 6-arylamino-1H-benzo[d]imidazole-4,7-diones have inhibitory activity on rat aortic smooth muscle cell (RAoSMC) proliferation. To understand the structural basis for antiproliferative activity to design more potent agents, we generated pharmacophore models of representative molecules with high activity using Genetic Algorithm with Linear Assignment of Hypermolecular Alignment of Database (GALAHAD) and aligned a series of compounds to the selected pharmacophore model, then performed three-dimensional quantitative structure-activity relationship (3D-QSAR) studies using Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA). Good cross-validated correlations were obtained with CoMFA (resulting in q² of 0.734 and r² of 0.947) and CoMSIA (resulting in q² of 0.736 and r² of 0.913). The IC_(50) values of the heterocyclic quinone derivatives on RAoSMC exhibited a strong correlation with steric and hydrophobic fields of the 3D structure of the molecules, resulting in the reliable prediction of inhibitory activity of the series of compounds.
( Dooho Lee ),( Yeongkuk Kim ),( Yoonji Chung ),( Dongjae Lee ),( Dongwon Seo ),( Tae Jeong Choi ),( Dajeong Lim ),( Duhak Yoon ),( Seung Hwan Lee ) 한국축산학회 2021 한국축산학회지 Vol.63 No.6
Recently, the cattle genome sequence has been completed, followed by developing a commercial single nucleotide polymorphism (SNP) chip panel in the animal genome industry. In order to increase statistical power for detecting quantitative trait locus (QTL), a number of animals should be genotyped. However, a high-density chip for many animals would be increasing the genotyping cost. Therefore, statistical inference of genotype imputation (low-density chip to high-density) will be useful in the animal industry. The purpose of this study is to investigate the effect of the reference population size and marker density on the imputation accuracy and to suggest the appropriate number of reference population sets for the imputation in Hanwoo cattle. A total of 3,821 Hanwoo cattle were divided into reference and validation populations. The reference sets consisted of 50k (38,916) marker data and different population sizes (500, 1,000, 1,500, 2,000, and 3,600). The validation sets consisted of four validation sets (Total 889) and the different marker density (5k [5,000], 10k [10,000], and 15k [15,000]). The accuracy of imputation was calculated by direct comparison of the true genotype and the imputed genotype. In conclusion, when the lowest marker density (5k) was used in the validation set, according to the reference population size, the imputation accuracy was 0.793 to 0.929. On the other hand, when the highest marker density (15k), according to the reference population size, the imputation accuracy was 0.904 to 0.967. Moreover, the reference population size should be more than 1,000 to obtain at least 88% imputation accuracy in Hanwoo cattle.
Identification and Purity Test of Melon Cultivars and F₁ Hybrids Using Fluidigm-based SNP Markers
D.S. Kishor,Yoonji Noh,Woon-Ho Song,Gung Pyo Lee,Jin-Kee Jung,Eun-Jo Shim,Sang-Min Chung 한국원예학회 2020 원예과학기술지 Vol.38 No.5
In melon (Cucumis melo L.), the grow-out test (GOT) has been traditionally used as a genetic purity test. However, this method is time-consuming, space-demanding, and associated with ambiguous classification of the genotypes. Molecular markers have proved to be an efficient tool in genotyping analyses. In the present study, a total of 96 genome-wide single nucleotide polymorphism (SNP) markers differentiated 85 melon F₁ hybrid plants from their parental lines and six other PT melon breeding lines via high-throughput Fluidigm genotyping. Of these, 39 SNP markers showed polymorphism between the parents. Additionally, SNP analysis and population structure analysis showed that several F₁ hybrid plants were associated with outcrossing during the breeding program. Unweighted pair group method with arithmetic average (UPGMA) analysis revealed that most of the contaminated plants were closely sub-grouped with the 7_PT1 breeding line, suggesting possible outcrossing with 7_PT1. By combining with simple DNA extraction, the Fluidigm-based SNP marker analysis proved to be a simple and effective approach for the genetic purity analysis of F₁ hybrids and melon cultivars.
Association Study of Functional Candidate Genes for Meat Tenderness in Hanwoo Cattle
Phuong Thanh N. Dinh,Yoonji Chung,Dong Jae Lee,Dong-Hun Kang,Bo Hye Park,Ki-Yong Chung,이승환 한국동물유전육종학회 2021 한국동물유전육종학회지 Vol.5 No.4
Hanwoo (Korean cattle) is the most profitable cattle as meat-type one since 1960s with the cherished role in the food industry due to its palatability, which is performed by several characteristics such as tenderness, juiciness, or flavor. Meat tenderness is one of the most important features for the quality of meat and is affected subjectively and objectively by several factors. Therefore, it is essential to identify the distribution of potentially functional SNPs or candidate regions associated with tenderness. Starting from 12 candidate genes extracted from previous study, including CNOT3, OSCAR, NLRP5, PIBF1, ITBG3, COL11A1, COL1A, COL24A1, COL28A, COL2A1, COL4A3 and COL6A3, an association study for tenderness in 1161 Hanwoo beef cattle was performed using linear mixed model through MLMA module of GCTA software, fitting a genetic relationship matrix built from 11,227,701 SNPs of the whole genome and 7 environmental factors to predict the effects of 730 candidate SNPs. SNP that fitted to the model having the p-value < 0.01 will be in a significant association with the trait. 10 SNPs and 7 SNPs related to tenderness of semimembranosus area (S_SF) and longissimus dorsi area (D_SF) were detected, respectively. Most of them are phenotypic variations of collagen family genes, including: COL1A1, COL4A3, COL6A3 and COL11A1. This result suggests an attempt to explore effective biomarkers for meat tenderness trait in Hanwoo cattle.
Hou, Xiyan,Majik, MaheshS.,Kim, Kyunglim,Pyee, Yuna,Lee, Yoonji,Alexander, Varughese,Chung, Hwa-Jin,Lee, Hyuk Woo,Chandra, Girish,Lee, Jin Hee,Park, Seul-gi,Choi, Won Jun,Kim, Hea Ok,Phan, Khai,Gao, Z American ChemicalSociety 2012 Journal of medicinal chemistry Vol.55 No.1
<P>Truncated <I>N</I><SUP>6</SUP>-substituted-4′-oxo-and 4′-thioadenosine derivatives with C2 or C8 substitutionwere studied as dual acting A<SUB>2A</SUB> and A<SUB>3</SUB> adenosinereceptor (AR) ligands. The lithiation-mediated stannyl transfer andpalladium-catalyzed cross-coupling reactions were utilized for functionalizationof the C2 position of 6-chloropurine nucleosides. An unsubstituted6-amino group and a hydrophobic C2 substituent were required for highaffinity at the hA<SUB>2A</SUB>AR, but hydrophobic C8 substitutionabolished binding at the hA<SUB>2A</SUB>AR. However, most of synthesizedcompounds displayed medium to high binding affinity at the hA<SUB>3</SUB>AR, regardless of C2 or C8 substitution, and low efficacyin a functional cAMP assay. Several compounds tended to be full hA<SUB>2A</SUB>AR agonists. C2 substitution probed geometrically throughhA<SUB>2A</SUB>AR docking was important for binding in order of hexynyl> hexenyl > hexanyl. Compound <B>4g</B> was the most potentligand acting dually as hA<SUB>2A</SUB>AR agonist and hA<SUB>3</SUB>AR antagonist, which might be useful for treatment of asthma or otherinflammatory diseases.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jmcmar/2012/jmcmar.2012.55.issue-1/jm201229j/production/images/medium/jm-2011-01229j_0013.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/jm201229j'>ACS Electronic Supporting Info</A></P>