In Silico Evaluation of Deleterious SNPs in Chicken TLR3 and TLR4 Genes

Donghyun Shin,Ki-Duk Song 한국가금학회 2018 韓國家禽學會誌 Vol.45 No.3

The innate immune recognition is based on the detection of microbial products. Toll-like receptors (TLRs) located on the cell surface and the endosome senses microbial components and nucleic acids, respectively. Chicken TLRs mediate immune responses by sensing ligands from pathogens, have been studied as immune adjuvants to increase the efficacy of vaccines. Single nucleotide polymorphisms (SNPs) of TLR3 and TLR4 genes in chicken were associated with resistance and susceptibility to viral infection. In this study, SNPs of chTLR3 and chTLR4 genes were retrieved from public database and annotated with chicken reference genome. Three-dimensional models of the chTLR3 and chTLR4 proteins were built using a Swiss modeler. We identified 35 and 13 nsSNPs in chTLR3 and chTLR4 genes respectively. Sorting Intolerant from Tolerant (SIFT) and Polymorphism Phenotyping v2 (Polyphen-2) analyses, suggested that, out of 35 and 13 nsSNPs, 4 and 2 SNPs were identified to be deleterious in chTLR3 and chTLR4 gene respectively. In chTLR3, 1 deleterious SNP was located in ectodomain and 3 were located in the Toll / IL-1 receptor (TIR) domain. Further structural model of chTLR3-TIR domain suggested that 1 deleterious SNP be present in the B-B loop region, which is important for TIR-TIR domain interactions in the downstream signaling. In chTLR4, the deleterious SNPs were located both in the ectodomain and TIR domain. SNPs predicted for chTLR3 and chTLR4 in this study, might be related to resistance or susceptible to viral infection in chickens. Results from this study will be useful to develop the effective measures in chicken against infectious diseases.

Heritability Estimated Using 50K SNPs Indicates Missing Heritability Problem in Holstein Breeding

Shin, Donghyun,Park, Kyoung-Do,Ka, Sojoeng,Kim, Heebal,Cho, Kwang-hyeon Korea Genome Organization 2015 Genomics & informatics Vol.13 No.4

Previous studies in Holstein have shown 35% to 51.8% heritability in milk production traits, such as milk yield, fat, and protein, using pedigree data. Other studies in complex human traits could be captured by common single-nucleotide polymorphisms (SNPs), and their genetic variations, attributed to chromosomes, are in proportion to their length. Using genome-wide estimation and partitioning approaches, we analyzed three quantitative Holstein traits relevant to milk production in Korean Holstein data harvested from 462 individuals genotyped for 54,609 SNPs. For all three traits (milk yield, fat, and protein), we estimated a nominally significant (p = 0.1) proportion of variance explained by all SNPs on the Illumina BovineSNP50 Beadchip ($h^2_G$). These common SNPs explained approximately most of the narrow-sense heritability. Longer genomic regions tended to provide more phenotypic variation information, with a correlation of 0.46~0.53 between the estimate of variance explained by individual chromosomes and their physical length. These results suggested that polygenicity was ubiquitous for Holstein milk production traits. These results will expand our knowledge on recent animal breeding, such as genomic selection in Holstein.

태양광 발전의 그리드 패리티 결정요인 분석: 126개국 가정용 태양광을 중심으로

( Donghyun Shin ),( Hyungwoo Lim ),( Hahyun Jo ) 한국국제경제학회 2019 국제경제연구 Vol.25 No.1

본 연구는 그리드 패리티 관련 선행연구를 바탕으로 태양광 그리드 패리티 달성에 영향을 미치는 주요 요인을 선정한 후, 2011년 126개 국가의 횡단면 분석을 통해 태양광 그리드 패리티 달성을 위한 결정요인을 회귀분석하였다. 분석결과 태양광 및 신재생에너지 산업 수준, 태양광 시스템의 효율성 개선, 낮은 자본조달비용, 높은 R&D 투자, 적극적인 신재생에너지 목표 설정이 태양광 그리드 패리티 달성에 주요한 요인으로 나타났다. 강건성 검증을 위해 모형평균방법, 순서형 프로빗 및 GMM 모형을 활용하여 추가적인 분석을 진행한 결과, 태양광 산업, 일조량, 정책 강도, 실질 소득, 자본조달비용 등 주요 변수의 유의성 및 영향정도는 유사했다. 이상의 분석을 통해 그리드 패리티 달성에 있어 자연적 요인뿐 아니라 태양광 산업 및 금융시장 발전, R&D 투자 등 거시경제적, 정책적 변수 역시 주요한 요인임을 보였다. Based on the previous studies on grid parity, this study selected major factors influencing the achievement of solar grid parity. We analyzed 126 countries to determine the factors for achieving solar grid parity in 2011. As a result, we concluded that the growth of solar and renewable energy industry, the efficiency of solar power system, the low cost of capital, the high R&D investment, and the aggressiveness of renewable energy goal leads to the grid parity. For robustness, we conducted additional analysis using the model average method, ordered probit and GMM, and the results were similar. This study shows that not only the solar radiation but also macroeconomic and policy variables such as solar industry growth, financial market development, renewable energy policy, and R&D investment are important factors for achieving grid parity.

Performance Enhancement of Emergency Rescue System using Surface Correlation Technology

Shin, Beomju,Lee, Jung Ho,Shin, Donghyun,Yu, Changsu,Kyung, Hankyeol,Lee, Taikjin 항법시스템학회 2020 Journal of Positioning, Navigation, and Timing Vol.9 No.3

In emergency rescue situations, the localization accuracy of the rescue requestor is a very important factor in determining the success or failure of the rescue. Indoors where Global Navigation Satellite System (GNSS) is not operated, there is no choice but to use Wi-Fi or LTE signals. However, the performance of the current emergency rescue system utilizing those RF signals is exceedingly low. In this study, the effectiveness of the surface correlation technology using the accumulated signal pattern of RF signals was verified in relation to the emergency localization technology. To validate the proposed system, we configured and tested an emergency rescue scenario in multi-floors building. When the emergency rescue was requested, it was confirmed that the initial localization error was large owing to the short length of the accumulated signal pattern. However, the localization error decreased over time, which eventually led to the accurate location information being delivered to the rescuer.

A Study on Altitude Estimation using Smartphone Pressure Sensor for Emergency Positioning

Shin, Donghyun,Lee, Jung Ho,Shin, Beomju,Yu, Changsu,Kyung, Hankyeol,Choi, Dongwook,Kim, Yeji,Lee, Taikjin 항법시스템학회 2020 Journal of Positioning, Navigation, and Timing Vol.9 No.3

This paper introduces a study to estimate the user altitude in need of rescue in an emergency. The altitude is estimated by using the barometric pressure sensor embedded in the smartphone. Compared to GPS, which is degraded in urban or indoor environments, it has the advantage of not having spatial restrictions. With the endless development of smartphone hardware, it is possible to estimate the absolute altitude using the measured value if only the bias of the embedded barometric pressure sensor is applied. The altitude information of the person in need of rescue in an emergency is a great help in reducing rescue time. Since time is tight, we propose online calibration that provides the barometric pressure sensor bias used for altitude estimation through database. Furthermore, experiments were conducted to understand the characteristics of the barometric pressure sensor, which is greatly affected by wind. At the end, the altitude estimation performance was confirmed through an actual field tests in various floors in the building.

Epitaxial growth of single-crystalline AlN layer on Si(111) by DC magnetron sputtering at room temperature

Shin, In-Su,Kim, Jongmyeong,Lee, Donghyun,Kim, Donghyun,Park, Yongjo,Yoon, Euijoon Institute of Pure and Applied Physics 2018 Japanese Journal of Applied Physics Vol. No.

<P>The epitaxial growth of an AlN layer on a Si(111) substrate at room temperature by DC magnetron sputtering was investigated. The predeposition of a 5-nm-thick Al layer on the Si substrate before the AlN deposition was found to be crucial for the epitaxial growth of the AlN layer. The orientation relationships of AlN/Al/Si were observed to be AlN[1 (1) over bar 00] parallel to Al [0 (1) over bar1] parallel to Si[11 (2) over bar] and AlN[11 (2) over bar0] parallel to Al[011] parallel to Si[1 (1) over bar0], indicating the epitaxial growth of the AlN layer on the Si(111) substrate. This epitaxial growth of the AlN layer was attributed to the smaller lattice mismatches between AlN[1 (1) over bar 00] and Al[0 (1) over bar1] and AlN[11 (2) over bar0] and Al[011] than that between AlN[11 (2) over bar0] and Si[1 (1) over bar0]. (C) 2018 The Japan Society of Applied Physics</P>

In Silico Evaluation of Deleterious SNPs in Chicken TLR3 and TLR4 Genes

Shin, Donghyun,Song, Ki-Duk The Korean Society of Poultry Science 2018 韓國家禽學會誌 Vol.45 No.3

The innate immune recognition is based on the detection of microbial products. Toll-like receptors (TLRs) located on the cell surface and the endosome senses microbial components and nucleic acids, respectively. Chicken TLRs mediate immune responses by sensing ligands from pathogens, have been studied as immune adjuvants to increase the efficacy of vaccines. Single nucleotide polymorphisms (SNPs) of TLR3 and TLR4 genes in chicken were associated with resistance and susceptibility to viral infection. In this study, SNPs of chTLR3 and chTLR4 genes were retrieved from public database and annotated with chicken reference genome. Three-dimensional models of the chTLR3 and chTLR4 proteins were built using a Swiss modeler. We identified 35 and 13 nsSNPs in chTLR3 and chTLR4 genes respectively. Sorting Intolerant from Tolerant (SIFT) and Polymorphism Phenotyping v2 (Polyphen-2) analyses, suggested that, out of 35 and 13 nsSNPs, 4 and 2 SNPs were identified to be deleterious in chTLR3 and chTLR4 gene respectively. In chTLR3, 1 deleterious SNP was located in ectodomain and 3 were located in the Toll / IL-1 receptor (TIR) domain. Further structural model of chTLR3-TIR domain suggested that 1 deleterious SNP be present in the B-B loop region, which is important for TIR-TIR domain interactions in the downstream signaling. In chTLR4, the deleterious SNPs were located both in the ectodomain and TIR domain. SNPs predicted for chTLR3 and chTLR4 in this study, might be related to resistance or susceptible to viral infection in chickens. Results from this study will be useful to develop the effective measures in chicken against infectious diseases.

Minimally Invasive Pancreatoduodenectomy Combined with Major Venous Vascular Resection

Donghyun Shin 대한외과학회 2023 대한외과학회 학술대회 초록집 Vol.2023 No.5

Extent of linkage disequilibrium and effective population size of the Landrace population in Korea

Shin, Donghyun,Kim, Sung-Hoon,Park, Joowan,Lee, Hak-Kyo,Song, Ki-Duk Asian Australasian Association of Animal Productio 2018 Animal Bioscience Vol.31 No.8

Objective: The genetic diversity of the Landrace population, a representative maternal pig breed in Korea, is important for genetic improvement. Previously, the effective population size (Ne) has been used to infer the genetic diversity of a population of interest. In this study, we aimed to use single nucleotide polymorphism (SNP) data to characterize linkage disequilibrium (LD) and the Ne of the Korean Landrace population. Methods: We genotyped 1,128 Landrace individuals from three representative Korean major grand-grand-parent (GGP) farms using the Illumina PorcineSNP60 version2 BeadChip, which covers >61,565 SNPs located across all autosomes and mitochondrial and sex chromosomes. We estimated the expected LD and current Ne, as well as ancestral Ne. Results: In the Korean Landrace population, the mean LD ($r^2$) of 3.698 million SNP pairs was $0.135{\pm}0.204$. The mean $r^2$ decreased slowly with as the distance between SNPs increased, and remained constant beyond 3 Mb. According to the $r^2$ calculations, 8,085 of 3.698 million SNP pairs were in complete LD. The current Ne (${\pm}$standard deviation) of the Korean Landrace population is approximately 92.27 [79.46; 105.07] individuals. The ancestral Ne exhibited a slow and steady decline from 186.61 to 92.27 over the past 100 generations. Additionally, we observed more a rapid Ne decrease from the past 20 to 10 generations ago, compared with other intervals. Conclusion: We have presented an overview of LD and the current and ancestral Ne values in the Korean Landrace population. The mean LD and current Ne for the Korean Landrace population confirm the genetic diversity and reflect the history of this pig population in Korea.

In silico approaches to identify the functional and structural effects of non-synonymous SNPs in selective sweeps of the Berkshire pig genome

Shin, Donghyun,Oh, Jae-Don,Won, Kyeong-Hye,Song, Ki-Duk Asian Australasian Association of Animal Productio 2018 Animal Bioscience Vol.31 No.8

Objective: Non-synonymous single nucleotide polymorphisms (nsSNPs) were identified in Berkshire selective sweep regions and then were investigated to discover genetic nsSNP mechanisms that were potentially associated with Berkshire domestication and meat quality. We further used bioinformatics tools to predict damaging amino-acid substitutions in Berkshire-related nsSNPs. Methods: nsSNPs were examined in whole genome resequencing data of 110 pigs, including 14 Berkshire pigs, generated using the Illumina Hiseq2000 platform to identify variations that might affect meat quality in Berkshire pigs. Results: Total 65,550 nsSNPs were identified in the mapped regions; among these, 319 were found in Berkshire selective-sweep regions reported in a previous study. Genes encompassing these nsSNPs were involved in lipid metabolism, intramuscular fatty-acid deposition, and muscle development. The effects of amino acid change by nsSNPs on protein functions were predicted using sorting intolerant from tolerant and polymorphism phenotyping V2 to reveal their potential roles in biological processes that may correlate with the unique Berkshire meat-quality traits. Conclusion: Our nsSNP findings confirmed the history of Berkshire pigs and illustrated the effects of domestication on generic-variation patterns. Our novel findings, which are generally consistent with those of previous studies, facilitated a better understanding of Berkshire domestication. In summary, we extensively investigated the relationship between genomic composition and phenotypic traits by scanning for nsSNPs in large-scale whole-genome sequencing data.