• Genomics & Informatics
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• 제6권2호
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• pp.64-67
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• 2008

The Korean Rice Ds-tagging lines Database (KRDD) is designed to provide information about Ac/Ds insertion lines and activation tagging lines using japonica rice. This database has provided information on 18,158 Ds lines, which includes the ID, description, photo image, sequence information, and gene characteristics. The KRDD is visualized using a web-based graphical view, and anonymous users can query and browse the data using the search function. It has four major menus of web pages: (i) a Blast Search menu of a mutant line; Blast from rice Ds-tagging mutant lines; (ii) a primer design tool to identify genotypes of Ds insertion lines; (iii) a Phenotype menu for Ds lines, searching by identification name and phenotype characteristics; and (iv) a Management menu for Ds lines.

• Tuberculosis and Respiratory Diseases
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• 제76권3호
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• pp.105-113
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• 2014

From January 2012 up until March 2013, many articles with huge clinical importance in asthma were published based on large numbered clinical trials or meta-analysis. The main subjects of these studies were the new therapeutic plan based on the asthma phenotype or efficacy along with the safety issues regarding the current treatment guidelines. For efficacy and safety issues, inhaled corticosteroid tapering strategy or continued long-acting beta agonists use was the major concern. As new therapeutic trials, monoclonal antibodies or macrolide antibiotics based on inflammatory phenotypes have been under investigation, with promising preliminary results. There were other issues on the disease susceptibility or genetic background of asthma, particularly for the "severe asthma" phenotype. In the era of genome and pharmacogenetics, there have been extensive studies to identify susceptible candidate genes based on the results of genome wide association studies (GWAS). However, for severe asthma, which is where most of the mortality or medical costs develop, it is very unclear. Moreover, there have been some efforts to find important genetic information in order to predict the possible disease progression, but with few significant results up until now. In conclusion, there are new on-going aspects in the phenotypic classification of asthma and therapeutic strategy according to the phenotypic variations. With more pharmacogenomic information and clear identification of the "severe asthma" group even before disease progression from GWAS data, more adequate and individualized therapeutic strategy could be realized in the future.

• 대한치과교정학회지
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• 제50권6호
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• pp.383-390
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• 2020

Objective: To investigate the distribution, side involvement, phenotype, and associated anomalies of Korean patients with craniofacial clefts (CFC). Methods: The samples consisted of 38 CFC patients, who were treated at Seoul National University Dental Hospital during 1998-2018. The Tessier cleft type, sex, side involvement, phenotype, and associated anomalies were investigated using non-parametric statistical analysis. Results: The three most common types were #7 cleft, followed by #0 cleft and #14 cleft. There was no difference between the frequency of male and female. Patients with #0 cleft exhibited nasal deformity, bony defect, and missing teeth in the premaxilla, midline cleft lip, and eye problems. A patient with #3 cleft (unilateral type) exhibited bilateral cleft lip and alveolus. All patients with #4 cleft were the bilateral type, including a combination of #3 and #4 clefts, and had multiple missing teeth. A patient with #5 cleft (unilateral type) had a posterior openbite. In patients with #7 cleft, the unilateral type was more prevalent than the bilateral type (87.0% vs. 13.0%, p < 0.001). Sixteen patients showed hemifacial microsomia (HFM), Goldenhar syndrome, and unilateral cleft lip and palate (UCLP). There was a significant match in the side involvement of #7 cleft and HFM (87.5%, p < 0.01). Patients with #14 cleft had plagiocephaly, UCLP, or hyperterorbitism. A patient with #30 cleft exhibited tongue tie and missing tooth. Conclusions: Due to the diverse associated craniofacial anomalies in patients with CFC, a multidisciplinary approach involving a well-experienced cooperative team is mandatory for these patients.

• Asian-Australasian Journal of Animal Sciences
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• 제15권5호
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• pp.732-739
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• 2002

Milk samples with different phenotype combination of $\{kappa}$-casein and ${\beta}$-lactoglobulin and different preheating temperatures of 30, 70, 75 and $80^{\circ}C$ were used for cheesemaking under laboratory conditions. For the 853 batches of cheese, mean composition was 59.64% total solids, 30.24% fat and 23.66% protein, and the whey contained 6.93% total solids, 0.30% fat and 0.87% protein. Least squares analysis of the data indicated that heating temperature of the milk and ${\kappa}$-CN/${\beta}$-LG phenotypes had significant effects on cheese and whey compositions. The total solids, fat and protein contents of cheese were negatively correlated with preheating temperatures of milk. Cheese from BB/BB phenotype milk had the highest and those from AA/AA phenotype milk had the lowest concentrations of total solids, fat and protein. Mean recoveries of milk components in the cheese were 53.71% of total solids, 87.15% of fat, and 80.32% of protein. For the 10 different types of milk, maximum recoveries of milk components in cheese occurred with preheating temperature of $70^{\circ}C$ or $75^{\circ}C$ and lowest recoveries occurred at $80^{\circ}C$. The whey averaged 6.94% total solids, 0.30% fat and 0.87% protein. Losses of milk components in the whey were lowest for milk preheated at $80^{\circ}C$ and for milk containing the BB/BB phenotype.

• 한국임상수의학회지
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• 제18권4호
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• pp.334-340
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• 2001

This study was conducted to investigate changes in blood properties of high potassium (HK) phenotype Jindo dogs (15kg$\pm$2kg) after daily oral administration with water celery extracts (10 ml/kg) for 7 days. Blood samples were collected for three days in a row before administration of water celery extracts. After water celery extracts administration, blood samples were collected at 3h, 6h, 9h and then on daily basis until day 10 post administration (PA). At day 15, final sample was collected. Blood samples were analyzed on the basis of red blood cell (RBC), white blood cell (WBC), packed cell volume (PCV), hemoglobin (Hb) concentration, mean corpuscular volume(MCV), mean corpuscular hemoglobin concentration(MCHC), gluthathione concentration(GSH) and met-hemoglobin(Met-Hb) concentration. The significant changes (p<0.01, p<0.05) of RBCs were shown at 3 h to day 5, and days 7 and 9 after administration. PCV values were decreased form 3 h to day 10 after administration. Mean Hb concentration showed significant increase as 3 h to day 3, and day 6 to day 9 after administration. The significant changes (p<0.05) of WBCs were shown at 9 h and day 1 after administration. The increased numbers of MCV were detected at days 6 to 9 after administration (p<0.05, p<0.01). The significant changes of MCHC were shown at 9h and day 1 after administration. The significant increases (p<0.01, p<0.05) of GSH concentration were detected at days 1, 6 and 7 after administration. In Met-Hb concentration, the significant increases (p<0.05) occurred at only 9h and day 7 after administration, The significant increases (p<0.01, p<0.05) of reticulocyte were detected at days 2, 4, 5, 6 and 7. Data from blood samples collected at day 15 after administration showed that all of blood analysis results returned to normal level, compared to controls.

• Toxicological Research
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• 제14권4호
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• pp.569-575
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• 1998

One of the most frequent dejects in human cancer is the uncontrolled activation of the ms-signaling pathways. Significant evidence has accumulated to directly implicate members of the matrix metalloproteinases (MMPs) in tumor invasion and metastasis formation. We have previously shown that MMP-9 expression was significantly enhanced in the ras-tranfected HT1080 human fibrosarcoma cells at the mRNA level. In the present study, we investigated the roles of MMP-2 and -9 on the H-ras-induced invasive phenotypes of MCF 10A human breast epithelial cells and HT 1080 human fibrosarcoma cells. We show that H-ras is able to induce or enhance a signaling pathway leading to the enhancement of an invasive phenotype in both MCF10A and HT1080 cells as determined by matrigel invasion assay. We then examined the effect of H-ras activation on the expression of MMP-2 and -9 by measuring enzymatic activities and mRNA levels. Our data clearly demonstrated that H-ras prominently induces expression of MMP-2 in MCF10A cells, while it efficiently up regulates MMP-9 in HT1080 cells. Taken together, these findings suggest that the correlation between ras-mediated invasiveness and enhanced expression of MMPs may be cell type-specific: MMP-9 is closely associated with the invasive phenotype induced by ras activation in fibrosarcoma cells, whereas MMP-2 is more likely associated with it in epithelial cells.

• Journal of Genetic Medicine
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• 제6권1호
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• pp.67-73
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• 2009

목 적 : 터너증후군 환자들에게는 다양한 핵형과 표현형이 나타나지만 우리나라에서는 그 연관성에 대한 연구가 미미한 실정이다. 그리하여 본 연구에서는 터너증후군으로 진단받은 환자들의 염색체 이상, 임상양상, 동반 질환에 대해 조사하였다. 대상 및 방 법 : 경북대학교병원에서 터너증후군으로 진단받은 환자 92명을 대상으로 염색체 핵형을 분류하였으며, 그 중 62명을 대상으로 임상 양상 및 동반 질환을 조사하였다. 결 과 : 핵형이 45,X인 환자는 54.3%였고. 섞임증 및 구조 이상이 나머지를 차지하였다. 섞임증의 경우 45,X에 비하여 Turner stigmata의 빈도가 낮았다. 46,X,del(Xp) 및 45,X/46,X,del(Xq)에서는 모두 골격 이상이 나타난 반면, 46,X, del(Xq)에서는 나타나지 않았다. 46,X,del(Xp)에서는 성적 유치증이 나타나지 않았지만, 46,X,del(Xq) 및 45,X/46,X,del(Xq)의 경우에는 이차 성징 지연이 지연 및 무월경이 나타났다. 46,X,i(Xq) 및 45,X/46,X,i(Xq)의 경우 이차 성징이 발현되지 않았고 모두 일차 무월경을 보였다. 그 외에 장완의 isochromosome이 있는 경우 청력 장애 및 갑상선 질환이 더 빈번하게 나타났다. 결 론 : 터너증후군 환자들의 핵형과 표현형 사이의 연관성을 조사하는 작업은 성염색체에 위치하는 유전자자리를 예측하는 정보를 얻을 수 있다는 점에서 중요하다고 생각한다.

• Genomics & Informatics
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• 제14권4호
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• pp.187-195
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• 2016

In genetic association studies with high-dimensional genomic data, multiple group testing procedures are often required in order to identify disease/trait-related genes or genetic regions, where multiple genetic sites or variants are located within the same gene or genetic region. However, statistical testing procedures based on an individual test suffer from multiple testing issues such as the control of family-wise error rate and dependent tests. Moreover, detecting only a few of genes associated with a phenotype outcome among tens of thousands of genes is of main interest in genetic association studies. In this reason regularization procedures, where a phenotype outcome regresses on all genomic markers and then regression coefficients are estimated based on a penalized likelihood, have been considered as a good alternative approach to analysis of high-dimensional genomic data. But, selection performance of regularization procedures has been rarely compared with that of statistical group testing procedures. In this article, we performed extensive simulation studies where commonly used group testing procedures such as principal component analysis, Hotelling's $T^2$ test, and permutation test are compared with group lasso (least absolute selection and shrinkage operator) in terms of true positive selection. Also, we applied all methods considered in simulation studies to identify genes associated with ovarian cancer from over 20,000 genetic sites generated from Illumina Infinium HumanMethylation27K Beadchip. We found a big discrepancy of selected genes between multiple group testing procedures and group lasso.

• 한국동물위생학회지
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• 제42권4호
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• pp.217-225
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• 2019

To detect Single nucleotide polymorphisms (SNP) markers associated with Bovine viral diarrhea virus (BVDV) and Bovine respiratory syncytial virus (BRSV) S/P ratio in Korean Holstein dairy cattle, Genome-wide association study (GWAS) was performed using Illumina BovineSNP50 Beadchip. The number of phenotype data and genotype data were 107, and 294. respectively. Phenotype data were collected for four periods (0 week, 1 week, 4 week, 24 week) after having vaccinated (0 week no vaccinated period). A total of 36,257 SNPs was remained after quality control had been done by PLINK. The result of GWAS showed 6 SNP markers (BTB-01704243, BTB-01594395, ARS-BFGL-NGS-118070, ARS-BFGL-NGS-111365, BTA-65410-no-rs, Hapmap38331-BTA-61256) under BVDV and 4 SNP markers (ARS-BFGL-NGS-109861, Hapmap53701-rs29017064, ARS-BFGL-NGS-71055, BTA-11232-no-rs) under BRSV. And also, 10 candidate genes found through 10 SNP markers (TBX18, CEP162, PAFAH1B1, METTL16, BRCA1, RND2, POLK, ENSBTAG00000051724, ADAM18, NRG3).

• Journal of Animal Science and Technology
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• 제63권4호
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• pp.751-758
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• 2021

The recessive white (locus c) phenotype observed in chickens is associated with three alleles (recessive white c, albino c^a, and red-eyed white c^re) and causative mutations in the tyrosinase (TYR) gene. The recessive white mutation (c) inhibits the transcription of TYR exon 5 due to a retroviral sequence insertion in intron 4. In this study, we genotyped and sequenced the insertion in TYR intron 4 to identify the mutation causing the unusual white plumage of Yeonsan Ogye chickens, which normally have black plumage. The white chickens had a homozygous recessive white genotype that matched the sequence of the recessive white type, and the inserted sequence exhibited 98% identity with the avian leukosis virus ev-1 sequence. In comparison, brindle and normal chickens had the homozygous color genotype, and their sequences were the same as the wild-type sequence, indicating that this phenotype is derived from other mutation(s). In conclusion, white chickens have a recessive white mutation allele. Since the size of the sample used in this study was limited, further research through securing additional samples to perform validation studies is necessary. Therefore, after validation studies, a selection system for conserving the phenotypic characteristics and genetic diversity of the population could be established if additional studies to elucidate specific phenotype-related genes in Yeonsan Ogye are performed.