• Animal Bioscience
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• 제35권9호
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• pp.1340-1350
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• 2022

Objective: Luxi Black Head sheep (LBH) is the first crossbreed specialized for meat production and was developed by crossbreeding Black Head Dorper sheep (DP) and Small Tailed Han sheep (STH) in the farming areas of northern China. Research on the genomic variations and selection signatures of LBH caused by continuous artificial selection is of great significance for identifying the genetic mechanisms of important traits of sheep and for the continuous breeding of LBH. Methods: We explored the genetic relationships of LBH, DP, and several Mongolian sheep breeds by constructing phylogenetic tree, principal component analysis and linkage disequilibrium analysis. In addition, we analysed 29 whole genomes of sheep. The genome-wide selection signatures have been scanned with four methods: heterozygosity (H_P), fixation index (F_ST), cross-population extended haplotype homozygosity (XP-EHH) and the nucleotide diversity (𝜃_π) ratio. Results: The genetic relationships analysis showed that LBH appeared to be an independent cluster closer to DP. The candidate signatures of positive selection in sheep genome revealed candidate genes for developmental process (HoxA gene cluster, BCL2L11, TSHR), immunity (CXCL6, CXCL1, SKAP2, PTK6, MST1R), growth (PDGFD, FGF18, SRF, SOCS2), and reproduction (BCAS3, TRIM24, ASTL, FNDC3A). Moreover, two signalling pathways closely related to reproduction, the thyroid hormone signalling pathway and the oxytocin signalling pathway, were detected. Conclusion: The selective sweep analysis of LBH genome revealed candidate genes and signalling pathways associated with developmental process, immunity, growth, and reproduction. Our findings provide a valuable resource for sheep breeding and insight into the mechanisms of artificial selection.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.207-207
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• 2022

Eating and cooking quality (ECQ) is one of the most complex quantitative traits in rice. The understanding of genetic regulation of transcript expression levels attributing to phenotypic variation in ECQ traits is limited. We integrated whole-genome resequencing, transcriptome, and phenotypic variation data from 84 Japonica accessions to build a transcriptome-wide association study (TWAS) based regulatory network. All ECQ traits showed a large phenotypic variation and significant phenotypic correlations among the traits. TWAS analysis identified a total of 285 transcripts significantly associated with six ECQ traits. Genome-wide mapping of ECQ-associated transcripts revealed 66,905 quantitative expression traits (eQTLs), including 21,747 local eQTLs, and 45,158 trans-eQTLs, regulating the expression of 43 genes. The starch synthesis-related genes (SSRGs), starch synthase IV-1 (SSIV-1), starch branching enzyme 1 (SBE1), granule-bound starch synthase 2 (GBSS2), and ADP-glucose pyrophosphorylase small subunit 2a (OsAGPS2a) were found to have eQTLs regulating the expression of ECQ associated transcripts. Further, in co-expression analysis, 130 genes produced at least one network with 22 master regulators. In addition, we developed CRISPR/Cas9-edited glbl mutant lines that confirmed the role of alpha-globulin (glbl) in starch synthesis to validate the co-expression analysis. This study provided novel insights into the genetic regulation of ECQ traits, and transcripts associated with these traits were discovered that could be used in further rice breeding.

• Journal of Animal Science and Technology
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• 제54권5호
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• pp.323-329
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• 2012

본 연구는 한우 거세우 266두에서 유전자형 결정이 완료된 4,522개의 SNP를 이용하여 한우 성장형질 (6, 12, 18 및 24개월령 체중)에 대한 양적형질좌위 (QTL)을 탐색 하였다. 각 SNP와 성장형질과의 연관성 분석은 회귀분석 (single marker regression)을 이용하여 수행하였으며, 통계적 유의성은 P-value (P<0.001)로 설정하였다. 그 결과, 6개월체중에서 3개 좌위, 12개월 체중에서는 5개 좌위, 18개월체중에서 5개좌위 그리고 24개월체중에서 4개 좌위가 통계적 유의차를 보였다. 통계적 유의차를 보인 SNP의 상가적 유전분산을 분석한 결과, 몇몇 SNP에서는 6~11% 정도의 상가적 유전효과를 보였으며, 대부분의 SNP들은 2~5%로 매우 작은 효과를 보였다.

• BMB Reports
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• 제48권5호
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• pp.243-248
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• 2015

Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of familial Parkinson's disease (PD). As such, functions and dysfunctions of LRRK2 in PD have been the subject of extensive investigation. In addition to PD, increasing evidence is suggesting that LRRK2 is associated with a wide range of diseases. Genome-wide association studies have implicated LRRK2 in Crohn's disease (CD) and leprosy, and the carriers with pathogenic mutations of LRRK2 show increased risk to develop particular types of cancer. LRRK2 mutations are rarely found in Alzheimer's disease (AD), but LRRK2 might play a part in tauopathies. The association of LRRK2 with the pathogenesis of apparently unrelated diseases remains enigmatic, but it might be related to the yet unknown diverse functions of LRRK2. Here, we reviewed current knowledge on the link between LRRK2 and several diseases, including PD, AD, CD, leprosy, and cancer, and discussed the possibility of targeting LRRK2 in such diseases. [BMB Reports 2015; 48(5): 243-248]

• Molecules and Cells
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• 제25권3호
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• pp.438-445
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• 2008

Leaf senescence is a highly regulated genetic process that constitutes the last stage of plant development and provides adaptive fitness by relocating metabolites from senescing leaves to reproducing seeds. Characterization of various senescence mutants, mostly in Arabidopsis, and genome-wide analyses of gene expression, have identified a wide array of regulatory components, including transcription factors and enzymes as well as signaling molecules mediating growth hormones and environmental stress responses. In this work we demonstrate that a membrane-associated NAC transcription factor, NTL9, mediates osmotic stress signaling in leaf senescence. The NTL9 gene is induced by osmotic stress. Furthermore, activation of the dormant, membrane-associated NTL9 is elevated under the same conditions. A series of senescence-associated genes (SAGs) were upregulated in transgenic plants overexpressing an activated form of NTL9, and some of them were slightly but reproducibly downregulated in a T-DNA insertional NTL9 knockout mutant. These observations indicate that NTL9 mediates osmotic stress responses that affect leaf senescence, providing a genetic link between intrinsic genetic programs and external signals in the control of leaf senescence.

• 대한한의학방제학회지
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• 제29권4호
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• pp.267-275
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• 2021

Objectives : Previously, we reported that compound K isolated from fermented ginseng by Aspillus oryzae has a wide biochemical and pharmacological effect, including anti-cancer activity in prostate cancer PC-3 cells. Despite these findings, its signaling pathway and gene expression pattern are not clearly understood. Methods : To confirm the gene expression study of treated with compound K in PC-3 cells, a cDNA microarray chip composed of 44K human cDNA probes was used. MTT assay, western blot analysis, propidium iodide staining, and annexin V/propidium iodide staining were analyzed. Results : We confirmed the differences of gene expression profiles. Then, we analyzed with the cell cycle arrest, cell death and cell proliferation related genes using DAVID database. Conclusions : Our finding should be useful for understanding genome-wide expression patterns of compound K-mediated cell cycle arrest toward induction of cell death and be helpful for finding future cancer therapeutic targets for prostate cancer cells.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.293-293
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• 2022

This study is to develop new wheat breeding material through wide hybridization with wild species harboring useful characteristics such as salt, heat, and drought tolerance. Leymus mollis, wild rye was used to improve wheat genetic quality. L. mollis, is a perennial plant harboring tolerance against salt, heat, and drought because L. mollis distributes on the seaside. The F₁ hybrids were produced by crossing between common wheat (Triticum aestivum L., Chinese Spring) and L. mollis. Genomic in situ hybridization revealed that the F₁ hybrids have L. mollis genome. For the evaluation of salt and drought tolerance, seeds from the F₂ were used. Under 2% NaCl solution, the F₃ wheat-Leymus addition plants with salt tolerance showed more tillering and longer roots than other F₃ plants without salt tolerance. Also, the F₃ plants with salt tolerance showed better shallow-rooted than other F₃ plants without salt tolerance. Finally, the F₃ plants with salt tolerance made seed-setting under 2% NaCl condition, but other F₃ plants without salt tolerance were not. Under drought conditions, the F₃ plants with drought tolerance showed longer culm and spike length than other F₃ plants without drought tolerance and even those of Chinese Spring under well-water conditions. We evaluated and selected the F₃ plants with salt or drought tolerance for generation advancement.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.231-231
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• 2022

The GASA protein (Gibberellic acid-stimulated Arabidopsis) are family of small cysteine-rich peptides found in plants. These GASA gene family mainly involved in biotic/abiotic stress responses and plant development. Despite being present in a wide plant species, their action and functions still remain unclear. In this study, using the in-silico analysis method we identified 41 GASA genes in peanuts (Arachis hypogaea L.). Based on the phylogenetic analysis 41 GASA genes are classified in the four major clusters and subclades. Mainly, clusters IV and III comprise the majority of GASA genes 15 and 11 genes respectively, followed by cluster I and cluster II with 9 and 6 genes respectively. Additionally, based on in-silico analysis we predicted the post-transcriptional and post-translational changes of GASA proteins under abiotic stresses such as drought and salt stress would aid our understanding of the regulatory mechanisms. Hence, a further study is planned to evaluate the expression of these GASA genes under stress in different plant tissues to elucidate the possible functional role of GASA genes in peanut plants. These findings might offer insightful data for peanut advancement.

• 동의신경정신과학회지
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• 제26권1호
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• pp.63-78
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• 2015

Objectives: Pinelliae Rhizoma has traditionally been used as an anti-depressant in oriental medicine. This study is to investigate the effect of Pinelliae Rhizoma extract (PRe) on psychological stress in genome wild expression of mice. Methods: After giving physical stress to mice, PRe was orally administered with 100 mg/kg/day for five days. After extracting whole brain tissue from the mice, their genome changes were observed by micorarray analysis method. The genome changes were analyzed by IMAGENE 4.0, TREEVIEW, FatiGo algorithems, BOND database, cytoscape program, etc. Results: 1. PRe administered group were remained at normal level; 60% of increase was shown in expressed genes by physical stress, and 65% of decrease was shown in expressed genes by psychological stress. 2. Genes with increased expression in control group that remained at a normal state in PRe administered group were involved with the gene of a cellular metabolic process on biological process, protein binding on molecular function, and cell part on cell composition. The pathway was found to be cytokin-cytokin receptor interaction. 3. Genes with decreased expression in control group that remained at a normal state in PRe administered group were involved with the gene of a cellular metabolic process on biologiacl detail and coupled ATPaes activity on molecular function. This gene related path was Ubiquintin mediated proteolysis etc. 4. Core node genes analyzed by protein interaction network were Vinculin, Cell sdivision cycle 42 homolog (S. cerevisiae) etc. They played an important role in maintaining cytoskeleton and controlling cell cycle. Conclusions: Several genes were up-regulated and down-regulated in response to psychological stress. The expression of most of the genes that were altered in response to psychological stress was restored to normal levels in PRe treated mice. When the interaction network information was analyzed, the recovery of the core node genes in PRe treated mice indicates that this final set of genes may be the effective target of PRe.

• 미생물학회지
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• 제46권2호
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• pp.213-218
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• 2010

Lactate dehydrogenases (LDHs)는 세포 내의 생화학적 대사경로에서 중요한 역할을 담당하는 효소로서 오랜 동안 많은 관심을 받았다. 본 연구에서는 다양한 미생물 genome database의 탐색을 통해 Bacillus cereus ATCC 14579 genome으로부터 LDH로 추정되는 3종의 유전자를 발견하고, 대장균에서 클로닝 및 대량 발현하였다. 모든 BcLDH 동질효소들의 상동부위 아미노산 잔기 대부분이 기존의 $NAD^+$-의존형 LDH와 높은 상동성을 보였다. 한편 314개의 아미노산으로 이루어진 BcLDH1과 2는 86%의 서열 상동성을 보였으나, BcLDH3와는 49%의 상동성을 나타냈다. 흥미롭게도 BcLDH1만이 $NAD^+$ 조효소 존재 하에서 L-lactate와 pyruvate 간의 상호전환 활성을 나타냈으며, 그 외의 동질효소들은 거의 활성을 보이지 않았다. 결론적으로 BcLDH1은 전형적인 $NAD^+$-의존형이며, L-lactate에 특이적인 dehydrogenase 효소임을 확인하였다.