• Genomics & Informatics
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• v.10 no.2
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• pp.99-105
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• 2012

Dyslipidemia, mainly characterized by high triglyceride (TG) and low high-density lipoprotein cholesterol (HDL-C) levels, is an important etiological factor in the development of cardiovascular disease (CVD). Considering the relationship between childhood obesity and CVD risk, it would be worthwhile to evaluate whether previously identified lipid-related variants in adult subjects are associated with lipid variations in a childhood obesity study (n = 482). In an association analysis for 16 genome-wide association study (GWAS)-based candidate loci, we confirmed significant associations of a genetic predisposition to lipoprotein concentrations in a childhood obesity study. Having two loci (rs10503669 at LPL and rs16940212 at LIPC) that showed the strongest association with blood levels of TG and HDL-C, we calculated a genetic risk score (GRS), representing the sum of the risk alleles. It has been observed that increasing GRS is significantly associated with decreased HDL-C (effect size, $-1.13{\pm}0.07$) compared to single nucleotide polymorphism combinations without two risk variants. In addition, a positive correlation was observed between allelic dosage score and risk allele (rs10503669 at LPL) on high TG levels (effect size, $10.89{\pm}0.84$). These two loci yielded consistent associations in our previous meta-analysis. Taken together, our findings demonstrate that the genetic architecture of circulating lipid levels (TG and HDL-C) overlap to a large extent in childhood as well as in adulthood. Post-GWAS functional characterization of these variants is further required to elucidate their pathophysiological roles and biological mechanisms.

• Journal of Periodontal and Implant Science
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• v.38 no.4
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• pp.579-588
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• 2008

Purpose: The purpose of this study was to investigate the association of generalized aggressive periodontitis with IL-6 promoter gene single nucleotide polymorphisms(SNP). Material and Methods: The study population consisted of 52 generalized aggressive periodontitis patients(GAP) and 30 periodontally healthy control subjects, who were systemically healthy non-smokers. Genomic DNA was obtained from buccal swab. The IL-6 promotor SNP at the positions of -597, -572, and -174 were genotyped by amplifying the polymorphic region using polymerase chain reaction(PCR), restriction enzyme digestion and gel electrophoresis. Result: The genotype distributions for G/G, G/A and A/A genotypes of IL-6 -597 were 30.8%, 40.4%, and 28.8% in the GAP group and 53.3%, 40%, and 6.7% in the control group and were statistically different between 2 groups(p<0.05). Allele 2 frequency of IL-6 -597 were significantly higher in the GAP group than the control group(p<0.01). At the position of IL-6 -572, the distribution for C/C, C/G and G/G genotypes were 23.1%, 55.8% and 21.2% in the GAP group and 20%, 33.3%, and 46.7% in the control group. In female subjects, the genotype distribution were significantly different between 2 groups(p<0.01). In male subjects, allele 2 frequency of IL-6-572 was significantly lower in the GAP group than the control group(p<0.05). The genotype distribution of IL-6 -174 in the GAP group were 96.2%, 3.8% for G/G, G/C genotypes whereas only the G/G genotype was detected in the control group. Conclusion: In conclusion, significant associations were found in IL-6 gene promoter(-597, -572) polymorphisms and generalized aggressive periodontitis. Further cohort study will be necessary in larger population.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.9
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• pp.1319-1326
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• 2007

Fructose-1,6-bisphosphatase (FBP1) is a key regulatory enzyme of gluconeogenesis that catalyzes the hydrolysis of fructose-1,6-bisphosphate to generate fructose-6-phosphate and inorganic phosphate. Deficiency of fructose-1, 6-bisphosphatase is associated with fasting hypoglycemia and metabolic acidosis. The enzyme has been shown to occur in bacteria, fungi, plants and animals. The bovine FBP1 gene was cloned and characterized in this study. The full length (1,241 bp) FBP1 mRNA contained an open reading frame (ORF) encoding a protein of 338 amino acids, a 63 bp 5' untranslated region (UTR) and a 131 bp 3' UTR. The bovine FBP1 gene was 89%, 85%, 82%, 82% and 74% identical to the orthologs of pig, human, mouse, rat and zebra fish at mRNA level, and 97%, 96%, 94%, 93% and 91% identical at the protein level, respectively. This gene was broadly expressed in cattle with the highest level in testis, and the lowest level in heart. An intronic single nucleotide polymorphism (SNP) (A/G) was identified in the $5^{th}$ intron of the bovine FBP1 gene. Genotyping of 133 animals from four beef breeds revealed that the average frequency for allele A (A-base) was 0.7897 (0.7069-0.9107), while 0.2103 (0.0893-0.2931) for allele B (G-base). Our preliminary association study indicated that this SNP is significantly associated with traits of Average Daily Feed Intake (ADFI) and Carcass Length (CL) (p<0.01). In addition, the FBP1 gene was assigned on BTA8 by a hybrid radiation (RH) mapping method.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.6
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• pp.765-773
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• 2009

Sterol regulatory element binding factor 1 (SREBF1) and fatty acid synthase (FASN) genes play an important role in the biosynthesis of fatty acids and cholesterol, and in lipid metabolism. This study used polymorphisms in the intron 5 of bovine SREBF1 and in the thioesterase (TE) domain of FASN genes to evaluate their associations with beef fatty acid composition. A previously identified 84-bp indel (L: insertion/long type and S: deletion/short type) of the SREBF1 gene in Korean cattle had significant associations with the concentration of stearic (C18:0), linoleic (C18:2) and polyunsaturated fatty acids (PUFA). The stearic acid concentration was 6.30% lower in the SS than the LL genotype (p<0.05), but the linoleic and PUFA contents were 11.06% and 12.20% higher in SS compared to LL (p<0.05). Based on the sequence analysis, five single nucleotide polymorphisms (SNPs) g.17924G>A, g.18043C>T, g.18440G>A, g.18529G>A and g.18663C>T in the TE domain of the FASN gene were identified among the different cattle breeds studied. Among these, only g.17924 G>A and g.18663C>T SNPs were segregating in the Hanwoo population. The g.17924G>A SNP is a non-synonymous mutation (thr2264ala) and was significantly associated with the contents of palmitic (C16:0) and oleic acid (C18:1). The oleic acid concentration was 3.18% and 2.79% higher in Hanwoo with the GG genotype than the AA and AG genotypes, respectively (p<0.05), whereas the GG genotype had 3.8% and 4.01% lower palmitic acid than in those cattle with genotype AA and AG, respectively (p<0.05). Tissue expression data showed that SREBFI and FASN genes were expressed in a variety of tissues though they were expressed preferentially in different muscle tissues. In conclusion, the 84-bp indel of SREBF1 and g.17924G>A SNP of the FASN gene can be used as DNA markers to select Hanwoo breeding stock for fatty acid composition.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.5
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• pp.770-777
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• 2020

Objective: This study was conducted to determine early hereditary endowment to establish a short-term feeding program. Methods: Hanwoo steers (n = 140) were equally distributed into four groups (35/group) based on genetic meat yield index (MYI) viz. the greatest, great, low, and the lowest at Jukam Hanwoo farm, Goheung. All animals were fed in group pens (5 animals/pen) with similar feed depending on the growth stage. Rice straw was provided ad libitum, whereas concentrate was fed at 5.71 kg during the growing period (6 to 13 mo) and 9.4 kg during the fattening period (13 to 28 mo). Body weight (BW) was measured at two-month intervals, whereas carcass weight was determined at slaughtering at about 31 months of age. The Affymetrix Bovine Axiom Array 640K single nucleotide polymorphism (SNP) chip was used to determine the meat quantity-related gene in the blood. Results: After 6 months, the highest (p<0.05) BW was observed in the greatest MYI group (190.77 kg) and the lowest (p<0.05) in the lowest MYI group (173.51 kg). The great MYI group also showed significantly (p<0.05) higher BW than the lowest MYI group. After 16 and 24 months, the greatest MYI group had the highest BW gain (p<0.05) and were therefore slaughtered the earliest. Carcass weight was significantly (p<0.05) higher in the greatest and the great MYI groups followed by the low and the lowest MYI groups. Back-fat thickness in the greatest MYI group was highly correlated to carcass weight and marbling score. The SNP array analysis identified the carcass-weight related gene BTB-01280026 with an additive effect. The steers with the allele increasing carcass weight had heavier slaughter weight of about 12 kg. Conclusion: Genetic MYI is a potential tool for calf selection, which will reduce the slaughter age while simultaneously increasing carcass weight, back-fat thickness, and marbling score.

• Biomolecules & Therapeutics
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• v.23 no.2
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• pp.189-194
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• 2015

P450 1A2 is responsible for the metabolism of clinically important drugs and the metabolic activation of environmental chemicals. Genetic variations of P450 1A2 can influence its ability to perform these functions, and thus, this study aimed to characterize the functional significance of three P450 1A2 allelic variants containing nonsynonymous single nucleotide polymorphisms (P450 $1A2^*8$, R456H; $^*15$, P42R; $^*16$, R377Q). Variants containing these SNPs were constructed and the recombinant enzymes were expressed and purified in Escherichia coli. Only the P42R variant displayed the typical CO-binding spectrum indicating a P450 holoenzyme with an expression level of ~ 170 nmol per liter culture, but no P450 spectra were observed for the two other variants. Western blot analysis revealed that the level of expression for the P42R variant was lower than that of the wild type, however the expression of variants R456H and R377Q was not detected. Enzyme kinetic analyses indicated that the P42R mutation in P450 1A2 resulted in significant changes in catalytic activities. The P42R variant displayed an increased catalytic turnover numbers ($k_{cat}$) in both of methoxyresorufin O-demethylation and phenacetin O-deethylation. In the case of phenacetin O-deethylation analysis, the overall catalytic efficiency ($k_{cat}/K_m$) increased up to 2.5 fold with a slight increase of its $K_m$ value. This study indicated that the substitution P42R in the N-terminal proline-rich region of P450 contributed to the improvement of catalytic activity albeit the reduction of P450 structural stability or the decrease of substrate affinity. Characterization of these polymorphisms should be carefully examined in terms of the metabolism of many clinical drugs and environmental chemicals.

• Korean Journal of Poultry Science
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• v.41 no.3
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• pp.191-196
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• 2014

The identification and utilization of potential candidate genes with significant effects on economically important traits have become increasingly important in poultry breeding programs. The ovocalyxin-32 (OCX-32) gene is located chromosome 9 in chicken, plays an important role in eggshell formation. This study was performed to assess the association between single nucleotide polymorphisms (SNPs) of OCX-32 gene and egg production traits in the Korean native chicken. Four Korean native chicken population (n = 181; including 46 females of Ogol, 46 females of white, 43 females of gray and 46 females of black) were used to analyze two SNPs (c.494A>C and c.267T>G) in the OCX-32 gene by PCR-RFLP (Polymerase Chain Reaction-Restricted Fragment Length Polymorphism). We measured egg production traits of age at first egg, first egg weight, egg production ratio and egg weight. The SNP c.494A>C was significantly associated with egg production ratio in Korean Ogol chickens (p<0.001) and egg weight in Korean white chickens (p<0.05). SNP c.267T>C was significantly associated with egg weight in Korean Ogol chickens (p<0.05). But there was no significant association in Korean gray and black chickens. Results suggest the possibility of using molecular markers in OCX-32 gene as a tool for performance and egg production traits in Korean native chicken breeding program.

• The Journal of the Korea Contents Association
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• v.16 no.10
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• pp.435-442
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• 2016

Obesity extends the global economic burden and it causes that the failure of a reduction of physical activity, and diet management. In this work, nutritional information and personalized diet based on calorie supply system and is discriminatory utilized the obesity-related SNP information in order to recommend a personalized functional foods. This study performed a GWAS analysis for the excavation of a Korean-specific and obesity-related SNP, which utilizes genetic information were recommended by entering a personalized diet in accordance with the SNP genotype-phenotype information. In addition, we integrated Database with relation of nutrient for utilizing the USDA Food information and it was applied to recommend with Sickdanome. As a result, the obesity-related SNP information was confirmed in the sample which has the normal value BMI. In this study, we have recognized that the phenotype information related obesity, BMI is inconsistent with the SNP genotype information. This result is shown that it is necessary to provide the personalized dietary SickdanOme recommendation based on the both pheotype-genotype information.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.1
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• pp.123-127
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• 2014

A recent study summarized several published genome-wide association studies (GWASs) of cancer and reported two pleiotropic loci at 6p21.1 and 7p15.3 contributing to multiple cancers including lung cancer, noncardia gastric cancer (NCGC), and esophageal squamous-cell carcinoma (ESCC) in Han Chinese. However, it is not known whether such genetic variants have similar effects on the risk of gynecologic cancers, such as ovarian cancer. Hence, we explored associations between genetic variants in 6p21.1 and 7p15.3 and ovarian cancer risk in Han Chinese women. We performed an independent case-control study by genotyping the two loci (rs2494938 A > G at 6p21.1 and rs2285947 A > G at 7p15.3) in a total of 377 ovarian cancer cases and 1,034 cancer-free controls using TaqMan allelic discrimination assay. We found that rs2285947 at 7p15.3 was significantly associated with risk of ovarian cancer with per allele odds ratio (OR) of 1.33 [95% confidence interval (CI): 1.08-1.64, P=0.008]. However, no significant association was observed between rs2494938 and ovarian cancer risk. Our results showed that rs2285947 at 7p15.3 may also contribute to the development of ovarian cancer in Han Chinese women, further suggesting pleiotropy of 7p15.3 in multiple cancers.

• Journal of Conservation Science
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• v.30 no.4
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• pp.409-416
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• 2014

Most human bones of Joseon Dynasty period are so good condition that we can do research in physical anthropology, genetics and chemistry with them. In this study, we analyzed DNA typing using 6 human bones of Joseon dynasty period excavated at Janggi-dong, Gimpo. The DNA typing was mitochondrial DNA haplotype, Y-chromosome haplotype and sex determination. Prior to DNA analysis, we distinguished histological index of 6 human bones. As the result of mitochondrial DNA analysis, most of bones were confirmed as haplogroup G, R11, M7, A5, etc. As the result of sex determination, 4 human bones were female and 2 human bones were male. The male haplogroup was confirmed as haplogroup O by the single nucleotide polymorphism analysis of Y chromosome. For extensive ancient human bone analysis, researchers need to apply a histological index to select ancient human bones and explain a relationship among ancient human bones with various analyses of mitochondrial and nuclear DNA.