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Whole-genome resequencing analysis of 20 Micro-pigs
Da‑Hye Son,Nam‑Hyun Hwang,Won‑Hyong Chung,Ha‑Seung Seong,Hyungbum Lim,Eun‑Seok Cho,Jung‑Woo Choi,Kyung‑Soo Kang,Yong‑Min Kim 한국유전학회 2020 Genes & Genomics Vol.42 No.3
Background Miniature pigs have been increasingly used as mammalian model animals for biomedical research because of their similarity to human beings in terms of their metabolic features and proportional organ sizes. However, despite their importance, there is a severe lack of genome-wide studies on miniature pigs. Objective In this study, we performed whole-genome sequencing analysis of 20 Micro-pigs obtained from Medi Kinetics to elucidate their genomic characteristics. Results Approximately 595 gigabase pairs (Gb) of sequence reads were generated to be mapped to the swine reference genome assembly (Sus scrofa 10.2); on average, the sequence reads covered 99.15% of the reference genome at an average of 9.6-fold coverage. We detected a total of 19,518,548 SNPs, of which 8.7% were found to be novel. With further annotation of all of the SNPs, we retrieved 144,507 nonsynonymous SNPs (nsSNPs); of these, 5968 were found in all 20 individuals used in this study. SIFT prediction for these SNPs identified that 812 nsSNPs in 402 genes were deleterious. Among these 402 genes, we identified some genes that could potentially affect traits of interest in Micro-pigs, such as RHEB and FRAS1. Furthermore, we performed runs of homozygosity analysis to locate potential selection signatures in the genome, detecting several loci that might be involved in phenotypic characteristics in Micro-pigs, such as MSTN, GDF5, and GDF11. Conclusion In this study, we identified numerous nsSNPs that could be used as candidate genetic markers with involvement in traits of interest. Furthermore, we detected putative selection footprints that might be associated with recent selection applied to miniature pigs.
Solution-phase synthesis of rubidium lead iodide orthorhombic perovskite nanowires
Lim, Da-Hye,Ramasamy, Parthiban,Kwak, Do-Hyun,Lee, Jong-Soo IOP 2017 Nanotechnology Vol.28 No.25
<P>Recently, metal halide perovskite nanocrystals have demonstrated outstanding properties in various optoelectronic applications. Cesium lead halides (CsPbX<SUB>3</SUB>) are the most studied perovskites in nanoscale dimensions. However, halide perovskite nanocrystals with other cations have rarely been reported. It is important to develop new perovskite compositions to further expand their application in various fields. In this paper, we first report the synthesis of colloidal rubidium lead iodide (RbPbI<SUB>3</SUB>) nanowires (NWs). RbPbI<SUB>3</SUB> NWs have an orthorhombic crystal structure and are single-crystalline in nature. The diameter of the NWs is around 32 nm with lengths up to several tens of micrometers. RbPbI<SUB>3</SUB> NWs absorb strongly below 450 nm. RbPbI<SUB>3</SUB> devices exhibited good photoresponsive behavior, suggesting a potential use in optoelectronics.</P>
Kim, Da Yeon,Kim, So-Hyun,Ahn, Hye Min,Lim, Sa Rang,Oh, Junsang,Choi, Seulgi,Lee, Hong-Jin,Auh, Joong-Hyuck,Choi, Hyung-Kyoon The Korean Society for Applied Biological Chemistr 2015 Applied Biological Chemistry (Appl Biol Chem) Vol.58 No.1
Highbush blueberries (Vaccinium corymbosum L.) are cultivated worldwide for their fruit with unique taste and potential health benefits. Blueray, Bluecrop, and Spartan are prominent among the various blueberry cultivars. We performed gas chromatography-mass spectrometry (GC-MS)-based metabolic profiling to differentiate the fruits of these three cultivars, and built an optimal partial least squares-discriminant analysis (PLS-DA) model to separate them. Amino acids, fatty acids, organic acids, phenolic compounds, and sugars were identified in the fruits. The optimized PLS-DA model for different cultivars of the fruits was obtained by selecting variables based on a variable importance in the projection (VIP) cut-off value of 1.0. Caffeic acid, aspartic acid, acetic acid, threonolactone, inositol, xylose, glucoside, linolenic acid, mannose, altrose, glycine alanine, and valine were found to be relevant and contributing compounds for differentiating cultivars. In addition, a hierarchical cluster analyses dendrogram pattern was correlated with the PLS-DA. This study suggested that GC-MS-based metabolic profiling coupled with multivariate statistical analysis could be used to differentiate the fruits of three major highbush blueberry cultivars.
Sun-Hyung Lim,Sun-Hwa Ha,MinJi Choi,Da-Hye Kim,SangKyu Park,Jong-Yeol Lee,Young-Mi Kim 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07
Anthocyanins, providing the bright red-orange to blue-violet colors, flavonoid-derived pigments with strong antioxidant activity that have benefits for human health. We isolated RsMYB1, which encodes an R2R3 MYB transcription factor (TF), from red radish plants (Raphanus sativus L.) that accumulate high levels of anthocyanins. RsMYB1 shows higher expression in red radish than in common white radish, in both leaves and roots, at different growth stages. regulatory genes. Transient expression of RsMYB1 in tobacco showed that RsMYB1 is a positive regulator of anthocyanin production. Also, the synergistic effect of RsMYB1 with B-Peru was larger than the effect of Arabidopsis plants stably expressing RsMYB1 produced red pigmentation throughout the plant, accompanied by up-regulation of the six structural and two regulatory genes for anthocyanin production. This broad transcriptional activation of anthocyanin biosynthetic machinery in Arabidopsis included up-regulation of TRANSPARENT TESTA 8, which encodes a bHLH-type TF. These results suggest that overexpression of RsMYB1 promotes anthocyanin production by triggering the expression of endogenous bHLH genes as potential binding partners for RsMYB1. In addition, RsMYB1-overexpressing Arabidopsis plants had a higher antioxidant capacity than did non-transgenic control plants. Taken together, RsMYB1 is an actively positive regulator for anthocyanins biosynthesis in radish plants and it might be one of the best targets for anthocyanin production by single gene manipulation being applicable in diverse plant species.