• Asian-Australasian Journal of Animal Sciences
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• 제31권11호
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• pp.1691-1699
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• 2018

Objective: In Korea, there are three main cattle breeds, which are distinguished by coat color: Brown Hanwoo (BH), Brindle Hanwoo (BRH), and Jeju Black (JB). In this study, we sought to compare the genetic diversity and divergence among there Korean cattle breeds using a BovineHD chip genotyping array. Methods: Sample data were collected from 168 cattle in three populations of BH (48 cattle), BRH (96 cattle), and JB (24 cattle). The single-nucleotide polymorphism (SNP) genotyping was performed using the Illumina BovineHD SNP 777K Bead chip. Results: Heterozygosity, used as a measure of within-breed genetic diversity, was higher in BH (0.293) and BRH (0.296) than in JB (0.266). Linkage disequilibrium decay was more rapid in BH and BRH than in JB, reaching an average $r^2$ value of 0.2 before 26 kb in BH and BRH, whereas the corresponding value was reached before 32 kb in JB. Intra-population, interpopulation, and Fst analyses were used to identify candidate signatures of positive selection in the genome of a domestic Korean cattle population and 48, 11, and 11 loci were detected in the genomic region of the BRH breed, respectively. A Neighbor-Joining phylogenetic tree showed two main groups: a group comprising BH and BRH on one side and a group containing JB on the other. The runs of homozygosity analysis between Korean breeds indicated that the BRH and JB breeds have high inbreeding within breeds compared with BH. An analysis of differentiation based on a high-density SNP chip showed differences between Korean cattle breeds and the closeness of breeds corresponding to the geographic regions where they are evolving. Conclusion: Our results indicate that although the Korean cattle breeds have common features, they also show reliable breed diversity.

• Journal of Radiation Protection and Research
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• 제42권1호
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• pp.33-41
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• 2017

Background: Phosphate rock and its by-product are widely used in various industries to produce phosphoric acid, gypsum, gypsum board, and fertilizer. Owing to its high level of natural radioactive nuclides (e.g., $^{238}U$ and $^{226}Ra$), the radiological safety of workers who work with phosphate rock should be systematically managed. In this study, $^{238}U$, $^{232}Th$, $^{226}Ra$, and $^{40}K$ levels were measured to analyze the transport characteristics of these radionuclides in the production cycle of phosphate rock. Materials and Methods: Energy dispersive X-ray fluorescence and gamma spectrometry were used to determine the activity of $^{238}U$, $^{232}Th$, $^{226}Ra$, and $^{40}K$. To evaluate the extent of secular disequilibrium, the analytical results were compared using statistical methods. Finally, the distribution of radioactivity across different stages of the phosphate rock production cycle was evaluated. Results and Discussion: The concentration ratios of $^{226}Ra$ and $^{238}U$ in phosphate rock were close to 1.0, while those found in gypsum and fertilizer were extremely different, reflecting disequilibrium after the chemical reaction process. The nuclide with the highest activity level in the production cycle of phosphate rock was $^{40}K$, and the median $^{40}K$ activity was $8.972Bq{\cdot}g^{-1}$ and $1.496Bq{\cdot}g^{-1}$, respectively. For the $^{238}U$ series, the activity of $^{238}U$ and $^{226}Ra$ was greatest in phosphate rock, and the distribution of activity values clearly showed the transport characteristics of the radionuclides, both for the byproducts of the decay sequences and for their final products. Conclusion: Although the activity of $^{40}K$ in k-related fertilizer was relatively high, it made a relatively low contribution to the total radiological effect. However, the activity levels of $^{226}Ra$ and $^{238}U$ in phosphate rock were found to be relatively high, near the upper end of the acceptable limits. Therefore, it is necessary to systematically manage the radiological safety of workers engaged in phosphate rock processing.

• Childhood Kidney Diseases
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• 제14권1호
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• pp.51-61
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• 2010

목 적 : 최근 Chemokine (C-C motif) ligand-2 (CCL-2; also known as MCP-1)와 CCL-5 (also known as RANTES)가 다양한 염증성 및 비염증성 신질환과 연관성을 보인다는 연구결과들이 보고되고 있다. 이에 본 저자들은 CCL-2 및 CCL-5 유전자의 단일염기다형성(single nucleotide polymorphism; SNP)가 소아 IgA 신병증의 발생 및 임상양상과 어떠한 연관성을 보이는지 알아보기 위하여 본 연구를 시행하였다. 방 법 : 경희의료원 소아청소년과에서 학교 검뇨상 이상소견을 보여 전원된 환아 중 신생검을 통해 IgA 신병증으로 확진된 196명의 소아환아와 285명의 건강한 대조군을 대상으로 geneotyping을 통해 6 개의 SNP 대립 유전자 빈도를 조사하여 분석하였다. 또한, 단백뇨(>4 mg/$m^2$/hour), 병리 소견 상 족세포의 족돌기 융합과 병리학적 진행성 병변의 유무에 따라 환자군을 다시 세 개의 하위그룹으로 세분화하여 비교하였다. 결 과 : IgA 신병증 환아 및 대조군의 SNP 대립 유전자 빈도를 분석하였을 때, CCL-2 및 CCL-5 유전자 모두에서 질환의 발생과 연관성을 보이는 SNP는 발견되지 않았다. 두 개의 linkage disequilibrium block이 형성되었으나 하플로타입 분석에서는 유의한 하플로타입을 찾을 수 없었다. 또한, 환자의 하위그룹을 비교하였을 때에도 단백뇨, 병리 소견 상 족세포의 족돌기 융합과 병리학적 진행성 병변과 연관성을 보이는 SNP는 발견되지 않았다. 결 론 : 한국 소아 환자를 대상으로 시행한 본 연구에서 CCL-2 및 CCL-5유전자 다형성과 IgA 신병증의 임상병리 양상 간에 유의한 연관성은 없었다.

• Genes and Genomics
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• 제40권12호
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• pp.1373-1382
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• 2018

Hanwoo and Chikso are classified as Korean native cattle breeds that are currently registered with the Food and Agriculture Organization. However, there is still a lack of genomic studies to compare Hanwoo to Chikso populations. The objective of this study was to perform genome-wide analysis of Hanwoo and Chikso populations, investigating the genetic relationships between these two populations. We genotyped a total of 319 cattle including 214 Hanwoo and 105 Chikso sampled from Gangwon Province Livestock Technology Research Institute, using the Illumina Bovine SNP50K Beadchip. After performing quality control on the initially generated datasets, we assessed linkage disequilibrium patterns for all the possible SNP pairs within 1 Mb apart. Overall, average $r^2$ values in Hanwoo (0.048) were lower than Chikso (0.074) population. The genetic relationship between the populations was further assured by the principal component analysis, exhibiting clear clusters in each of the Hanwoo and Chikso populations, respectively. Overall heterozygosity for Hanwoo (0.359) was slightly higher than Chikso (0.345) and inbreeding coefficient was also a bit higher in Hanwoo (-0.015) than Chikso (-0.035). The average $F_{ST}$ value was 0.036 between Hanwoo and Chikso, indicating little genetic differentiation between those two breeds. Furthermore, we found potential selection signatures including LRP1B and NTRK2 genes that might be implicated with meat and reproductive traits in cattle. In this study, the results showed that both Hanwoo and Chikso populations were not under severe level of inbreeding. Although the principal component analysis exhibited clear clusters in each of the populations, we did not see any clear evidence that those two populations are highly differentiated each other.

• Genomics & Informatics
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• 제15권4호
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• pp.178-182
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• 2017

Next-generation sequencing (NGS) technology has become a trend in the genomics research area. There are many software programs and automated pipelines to analyze NGS data, which can ease the pain for traditional scientists who are not familiar with computer programming. However, downstream analyses, such as finding differentially expressed genes or visualizing linkage disequilibrium maps and genome-wide association study (GWAS) data, still remain a challenge. Here, we introduce a dockerized web application written in R using the Shiny platform to visualize pre-analyzed RNA sequencing and GWAS data. In addition, we have integrated a genome browser based on the JBrowse platform and an automated intermediate parsing process required for custom track construction, so that users can easily build and navigate their personal genome tracks with in-house datasets. This application will help scientists perform series of downstream analyses and obtain a more integrative understanding about various types of genomic data by interactively visualizing them with customizable options.

• Genomics & Informatics
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• 제12권3호
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• pp.121-126
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• 2014

Medication adherence is generally defined as the extent of voluntary cooperation of a patient in taking medicine as prescribed. Adherence to long-term treatment with chronic disease is essential for reducing disease comorbidity and mortality. However, medication non-adherence in chronic disease averages 50%. This study was conducted a genome-wide association study to identify the genetic basis of medication adherence. A total of 235 medication non-adherents and 1,067 medication adherents with hypertension or diabetes were used from the Korean Association Resource project data according to the self-reported treatment status of each chronic disease, respectively. We identified four single nucleotide polymorphisms with suggestive genome-wide association. The most significant single nucleotide polymorphism was rs6978712 (chromosome 7, $p=4.87{\times}10^{-7}$), which is located proximal to the GCC1 gene, which was previously implicated in decision-making capability in drug abusers. Two suggestive single nucleotide polymorphisms were in strong linkage disequilibrium ($r^2$ > 0.8) with rs6978712. Thus, in the aspect of decision-making in adherence behavior, the association between medication adherence and three loci proximal to the GCC1 gene seems worthy of further research. However, to overcome a few limitations in this study, defining the standardized phenotype criteria for self-reported adherence should be performed before replicating association studies.

• 한국발생생물학회:학술대회논문집
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• 한국발생생물학회 2001년도 발생공학 국제심포지움 및 학술대회 발표자료집
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• pp.14-17
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• 2001

Positional clonging (map-based cloning) of mutations or genetic variations has been served as an invaluable tool to understand in-vivo functions of genes and to identify molecular components underlying phenotypes of interest. Mice homozygous for the cerebellar deficient folia (cdf) mutation are ataxic, with cerebellar hypoplasia and abnormal lobulation of the cerebellum. In the cdf mutant cerebellum approximately 40% of Purkinje cells are ectopically located within the white matter and the inner granule cell layer (IGL). To identify the cdf gene, a high-resolution genetic map for the cdf-gene-encompassing region was constructed using 1997 F2 mice generated from C3H/HeSnJ-cdf/cdf and CAST/Ei intercross. The cdf gene showed complete linkage disequilibrium with three tightly linked markers D6Mit208, D6Mit359, and D6Mit225. A contig using YAC, BAC, and P1 clones was constructed for the cdf critical region to identify the gene. A deletion in the cdf critical region on chromosome 6 that removes approximately 150 kb of DNA selection. cdf mutant mice with the transgenic copy of the identified gene restored the brain abnormalities of the mutant mice. The positional cloning of cdf gene provides a good example showing the identification of a gene could lead to finding a new component of important molecular pathways.

• International Journal of Vascular Biomedical Engineering
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• 제2권2호
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• pp.16-26
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• 2004

The object of this study is to develop a mathematical model of the hemodialysis system including the mechanism of solute kinetics, water exchange and also cardiovascular dynamics. The cardiovascular system model used in this study simulates the short-term transient and steady-state hemodynamic responses such as hypotension and disequilibrium syndrome (which are main complications to hemodialysis patients) during hemodialysis. It consists of a 12 lumped-parameter representation of the cardiovascular circulation connected to set-point models of the arterial baroreflexes, a kinetic model (hemodialysis system model) with 3 compartmental body fluids and 2 compartmental solutes. We formulate mathematically this model in terms of an electric analog model. All resistors and most capacitors are assumed to be linear. The control mechanisms are mediated by the information detected from arterial pressoreceptors, and they work on systemic arterial resistance, heart rate, and systemic venous unstressed volume. The hemodialysis model includes the dynamics of urea, creatinine, sodium and potassium in the intracellular and extracellular pools as well as fluid balance equations for the intracellular, interstitial, and plasma volumes. Model parameters are largely based on literature values. We have presented the results on the simulations performed by changing some model parameters with respect to their basal values. In each case, the percentage changes of each compartmental pressure, heart rate (HR), total systemic resistance (TSR), ventricular compliance, zero pressure filling volume and solute concentration profiles are represented during hemodialysis.

• 한국광물학회지
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• 제8권1호
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• pp.1-12
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• 1995

옥천 변성대 남서부 지역에서 산출되는 변성 니질암에서는 muscovite, biotite 및 chlorite를 주로하는 phyllosilicate가 서로 intergrowth 또는 interlayer를 이루는 것이 편광현미경 관찰, EPMA 분석, Back Scattered Electron (BSE) image 관찰 및 Transmission Electron Micro-scope(TEM) 관찰을 통하여 확인되었다. 이들 광물들은 편광현미경 관찰에서 흔히 각각의 입자를 식별할 수 없을 정도의 미세 규모로 서로 intergrow 되어 있으며BSE image에서는 0.1$\mu\textrm{m}$ 이하의 아주 작은 크기에서부터 10.0$\mu\textrm{m}$ 정도 크기까지 다양한 규모의 intergrow를 형성하고 있음이 관찰되었다. TEM scale에서는 개별 layer 크기(약 10$\AA$)에서부터 수십 개 layer 크기의 interlayering을 보여준다. 이와 같은 intergrowth 또는 interlayering의 결과로 EPMA 분석에서 종종 보기에는 규진(homogeneous)한 입자라 하더라도 두 개 이상의 광물 성분이 섞여 있는 분석값을 나타내며 이러한 nonstoichiometry는 BSE image에서 interlayer(또는 intergrow) 된 것으로 관찰되는 부분에서 더욱 두드러진다.Chlorite zone에서는 chlorite와 muscovite의 interlayering (C/M)이 주로 발견되며 biotite zone과 garnet zone에서는 chlorite와 biotite의 interlayer (C/B)가 주로 관찰된다. 이는 chlorite zone에서는 속성작용에서 보편적으로 나타나는 C/M으로부터 chlorite가 분리되는 광물반응이 일어나는데 반해서 biotite zone과 garnet zone에서는 chlorite로부터 C/B를 거쳐 biotite를 생성하는 광물반응이 일어나는 것을 의미한다. 이와 같은 현상은 변성작용에서 phollosilicate의 광물반응의 엄밀한 의미에서는 평형(equilibrium) 상태에서 균질한 광물을 생성하기보다는 비평형(disequilibrium) 반응으로 일어난다는 것을 의미한다.

• Asian-Australasian Journal of Animal Sciences
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• 제23권7호
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• pp.833-847
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• 2010

In the past decade, there have been many advances in whole-genome sequencing in domestic animals, as well as the development of "next-generation" sequencing technologies and high-throughput genotyping platforms. Consequently, these advances have led to the creation of the high-density SNP array as a state-of-the-art tool for genetics and genomics analyses of domestic animals. The emergence and utilization of SNP arrays will have significant impacts not only on the scale, speed, and expense of SNP genotyping, but also on theoretical and applied studies of quantitative genetics, population genetics and molecular evolution. The most promising applications in agriculture could be genome-wide association studies (GWAS) and genomic selection for the improvement of economically important traits. However, some challenges still face these applications, such as incorporating linkage disequilibrium (LD) information from HapMap projects, data storage, and especially appropriate statistical analyses on the high-dimensional, structured genomics data. More efforts are still needed to make better use of the high-density SNP arrays in both academic studies and industrial applications.