• Genomics & Informatics
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• v.4 no.2
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• pp.77-79
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• 2006

In order to identify novel proapoptotic genes, we screened approximately 1,000 hypothetical genes whose functions are completely unknown. After these genes were transiently expressed in HeLa cells, their nuclei images were captured using automated high-speed fluorescence microscope, through which the ratio of apoptotic nuclei was estimated. We selected genes that induce greater than 3-fold increase in apoptotic nuclei compared to that of the vector control. The candidate proapoptotic genes were sequenced and their effects on cell death were further confirmed by the additional assay, DNA fragmentation ELISA. Finally, we were able to identify 4 full-length hypo-thetical genes with proapoptotic activity.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.4
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• pp.480-488
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• 2018

Objective: Average daily gain (ADG) is an important target trait of pig breeding programs. We aimed to identify single nucleotide polymorphisms (SNPs) and genomic regions that are associated with ADG in the Duroc pig population. Methods: We performed a genome-wide association study involving 390 Duroc boars and by using the PorcineSNP60K Beadchip and two linear models. Results: After quality control, we detected 3,5971 SNPs, which included seven SNPs that are significantly associated with the ADG of pigs. We identified six quantitative trait loci (QTL) regions for ADG. These QTLs included four previously reported QTLs on Sus scrofa chromosome (SSC) 1, SSC5, SSC9, and SSC13, as well as two novel QTLs on SSC6 and SSC16. In addition, we selected six candidate genes (general transcription factor 3C polypeptide 5, high mobility group AT-hook 2, nicotinamide phosphoribosyltransferase, oligodendrocyte transcription factor 1, pleckstrin homology and RhoGEF domain containing G4B, and ENSSSCG00000031548) associated with ADG on the basis of their physiological roles and positional information. These candidate genes are involved in skeletal muscle cell differentiation, diet-induced obesity, and nervous system development. Conclusion: This study contributes to the identification of the casual mutation that underlies QTLs associated with ADG and to future pig breeding programs based on marker-assisted selection. Further studies are needed to elucidate the role of the identified candidate genes in the physiological processes involved in ADG regulation.

• BMB Reports
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• v.41 no.12
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• pp.846-851
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• 2008

This study was conducted to identify marbling-related candidate genes in M. longissimus dorsi of high- and low-marbled Hanwoo. The longissimus dorsi muscles were selected for gene expression from eight Hanwoo steer carcasses based on crude fat content. In the analysis of variance, gene expression of five candidate genes, FABP4, SCD, $PPAR\gamma$, Titin and Nebulin was determined to be significantly different between high- and low-marbled Hanwoo steers (P < 0.0001). The Pik-4 and CaMK II genes were also shown to have a significant effect on crude fat content (P < 0.01). In the analysis of the differential expression between high- and low marbled groups, FABP4 gene expression was approximately 2 times higher in the high marbled group relative to the low marbled group. However, the $PPAR\gamma$ and SCD gene were highly expressed in the low marbled group. In addition, Titin and Nebulin were highly expressed in the low marbled group when placed under relatively high shear force. Finally, the Pik-4 and CaM K II gene also displayed a high expression pattern in the low marbled group.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.8
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• pp.1075-1083
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• 2015

Adipose tissue deposited within muscle fibers, known as intramuscular fat (IMF or marbling), is a major determinant of meat quality and thereby affects its economic value. The biological mechanisms that determine IMF content are therefore of interest. In this study, 48 genes involved in the bovine peroxisome proliferator-activated receptor signaling pathway, which is involved in lipid metabolism, were investigated to identify candidate genes associated with IMF in the longissimus dorsi of Hanwoo (Korean cattle). Ten genes, retinoid X receptor alpha, peroxisome proliferator-activated receptor gamma (PPARG), phospholipid transfer protein, stearoyl-CoA desaturase, nuclear receptor subfamily 1 group H member 3, fatty acid binding protein 3 (FABP3), carnitine palmitoyltransferase II, acyl-Coenzyme A dehydrogenase long chain (ACADL), acyl-Coenzyme A oxidase 2 branched chain, and fatty acid binding protein 4, showed significant effects with regard to IMF and were differentially expressed between the low- and high-marbled groups (p<0.05). Analysis of the gene co-expression network based on Pearson's correlation coefficients identified 10 up-regulated genes in the high-marbled group that formed a major cluster. Among these genes, the PPARG-FABP4 gene pair exhibited the strongest correlation in the network. Glycerol kinase was found to play a role in mediating activation of the differentially expressed genes. We categorized the 10 significantly differentially expressed genes into the corresponding downstream pathways and investigated the direct interactive relationships among these genes. We suggest that fatty acid oxidation is the major downstream pathway affecting IMF content. The PPARG/RXRA complex triggers activation of target genes involved in fatty acid oxidation resulting in increased triglyceride formation by ATP production. Our findings highlight candidate genes associated with the IMF content of the loin muscle of Korean cattle and provide insight into the biological mechanisms that determine adipose deposition within muscle.

• BMB Reports
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• v.47 no.6
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• pp.348-353
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• 2014

The speed of sound (SOS) value is an indicator of bone mineral density (BMD). Previous genome-wide association (GWA) studies have identified a number of genes, whose variations may affect BMD levels. However, their biological implications have been elusive. We re-analyzed the GWA study dataset for the SOS values in skeletal sites of 4,659 Korean women, using a gene-set analysis software, GSA-SNP. We identified 10 common representative GO terms, and 17 candidate genes between these two traits (PGS < 0.05). Implication of these GO terms and genes in the bone mechanism is well supported by the literature survey. Interestingly, the significance levels of some member genes were inversely related, in several gene-sets that were shared between two skeletal sites. This implies that biological process, rather than SNP or gene, is the substantial unit of genetic association for SOS in bone. In conclusion, our findings may provide new insights into the biological mechanisms for BMD.

• Reproductive and Developmental Biology
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• v.34 no.2
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• pp.111-115
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• 2010

Erythropoietin (EPO), a glycoprotein hormone produced from primarily cells of the peritubular capillary endothelium of the kidney, is responsible for the regulation of red blood cell production. We have been investigating the roles of glycosylation site added in the biosynthesis and function of recombinant protein. In this study, we analyzed by immunohistochemical methods adaptive mechanisms to excessive erythrocytosis in transgenic (tg) mice expressing dimeric human erythropoietin (dHuEPO) gene. Splenomegaly was observed over 11~21 times in the tg mice. The 2,672 candidate spleen-derived genes were identified through the microarray analysis method, and decreased genes were higher than increased genes in the spleen. The specific proteins in the increased and decreased genes were analyzed by immunohistochemical methods. Our results demonstrate that problems of abnormal splenomegaly would solve in tg mice overexpressing dHuEPO gene.

• Animal cells and systems
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• v.7 no.3
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• pp.249-253
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• 2003

Abnormalities in fibrinolysis system is associated with risk of hypertension. In this report, the Alu repeat insertion/deletion (I/D) polymorphism of tissue plasminogen activator (t-PA) and the Hind III RFLP of plasminogen activator inhibitor-1 (PAI-1) genes were investigated in 115 normotensives and 83 patients with hypertension, and their association with anthropometrical data and plasma biochemical parameters were analyzed. There were no significant differences in the gene frequencies of the two candidate genes between normotensives and hypertensives, respectively. Our results indicate lack of associations between the two polymorph isms in t-PA and PAI-1 genes and risk of hypertension in the population under study. However, the Hind III RFLP of PAI-1 gene was significantly associated with plasma glucose level, suggesting its role in glucose metabolism. It needs to be tested whether this RFLP of PAI-1 gene is associated with insulin resistance syndrome or non-insulin dependent diabetes mellitus (NIDDM) in the Korean population.

• Genomics & Informatics
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• v.9 no.2
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• pp.45-51
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• 2011

How personality forms and whether personality genes exist are long-studied questions. Various concepts and theories have been presented for centuries. Personality is a complex trait and is developed through the interaction of genes and the environment. Twin and family studies have found that there are critical genetic and environmental components in the inheritance of personality traits, and modern advances in genetics are making it possible to identify specific variants for personality traits. Although genes that were found in studies on personality have not provided replicable association between genetic and personality variability, more and more genetic variants associated with personality traits are being discovered. Here, we present the current state of the art on genetic research in the personality field and finally list several of the recently published research highlights. First, we briefly describe the commonly used self-reported measures that define personality traits. Then, we summarize the characteristics of the candidate genes for personality traits and investigate gene variants that have been suggested to be associated with personality traits.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• v.24 no.1
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• pp.1-6
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• 2021

Next-generation sequencing (NGS) technologies have changed the process of genetic diagnosis from a gene-by-gene approach to syndrome-based diagnostic gene panel sequencing (DPS), diagnostic exome sequencing (DES), and diagnostic genome sequencing (DGS). A priori information on the causative genes that might underlie a genetic condition is a prerequisite for genetic diagnosis before conducting clinical NGS tests. Theoretically, DPS, DES, and DGS do not require any information on specific candidate genes. Therefore, clinical NGS tests sometimes detect disease-related pathogenic variants in genes underlying different conditions from the initial diagnosis. These clinical NGS tests are expensive, but they can be a cost-effective approach for the rapid diagnosis of rare disorders with genetic heterogeneity, such as the glycogen storage disease, familial intrahepatic cholestasis, lysosomal storage disease, and primary immunodeficiency. In addition, DES or DGS may find novel genes that that were previously not linked to human diseases.

• Genomics & Informatics
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• v.10 no.4
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• pp.244-248
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• 2012

Oxidative stress, which results in an excessive product of reactive oxygen species (ROS), is one of the fundamental mechanisms of the development of hypertension. In the vascular system, ROS have physical and pathophysiological roles in vascular remodeling and endothelial dysfunction. In this study, ROS-hypertension-related genes were collected by the biological literature-mining tools, such as SciMiner and gene2pubmed, in order to identify the genes that would cause hypertension through ROS. Further, single nucleotide polymorphisms (SNPs) located within these gene regions were examined statistically for their association with hypertension in 6,419 Korean individuals, and pathway enrichment analysis using the associated genes was performed. The 2,945 SNPs of 237 ROS-hypertension genes were analyzed, and 68 genes were significantly associated with hypertension (p < 0.05). The most significant SNP was rs2889611 within MAPK8 (p = $2.70{\times}10^{-5}$; odds ratio, 0.82; confidence interval, 0.75 to 0.90). This study demonstrates that a text mining approach combined with association analysis may be useful to identify the candidate genes that cause hypertension through ROS or oxidative stress.