• Title, Summary, Keyword: SNP

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Identification of SNP(Single Nucleotide Polymorphism) from MC1R, MITF and TYRP1 associated with Feather Color in Chicken (닭의 모색 연관 유전자인 MC1R, MITF, TYRP1의 SNP(Single Nucleotide Polymorphism) 규명)

  • Kim, Byung Ki;Byun, Youn-Hwa;Ha, Jea Jung;Jung, Daejin;Lee, Yoon-Seok;Hyeong, Ki-Eun;Yeo, Jung-Sou;Oh, Dong-Yep
    • Korean Journal of Poultry Science
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    • v.41 no.1
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    • pp.29-37
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    • 2014
  • The Feather Color of chicken is considered as most obvious, and the purpose of this study is to identify the genotype following the SNP of MC1R, MITF and TYRP1, which are genes related to Feather Color, and develop a SNP marker that can be classified per breed. When a haplotype is observed through the combination of markers, a Korean Native Chicken can especially be distinguished when it is a CGG type in the SNP combination of the MC1R gene. In case of the TAG, TGG and TAA types, only Araucana was identified, and for the CAA type, Leghorn could specifically be distinguished. In the SNP combination of TYRP1 gene, only Leghorn was differentiated in case of the TTTCA and CCTCA types, and only Silky Fowl was identified in case of the CTTTA type. The SNP combination of MC1R gene enabled for Korean Native Chicken, Leghorn, and Araucana to be distinguished and each of the SNP and combination of TYRP1 gene allowed for all 4 breeds to be classified. If many researches are conducted about genetic polymorphism between breeds, then it is considered that the differences between breeds will be understood from a molecular biological aspect instead of simply distinguishing the breeds through Feather Color.

p38 Kinase Regulates Nitric Oxide-induced Dedifferentiation and Cyclooxygenase-2 Expression of Articular Chondrocytes

  • Yu, Seon-Mi;Cheong, Seon-Woo;Cho, Sam-Rae;Kim, Song-Ja
    • IMMUNE NETWORK
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    • v.6 no.3
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    • pp.117-122
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    • 2006
  • Background: Caveolin, a family of integral membrane proteins are a principal component of caveolae membranes. In this study, we investigated the effect of p38 kinase on differentiation and on inflammatory responses in sodium nitroprusside (SNP)-treated chondrocytes. Methods: Rabbit articular chondrocytes were prepared from cartilage slices of 2-week-old New Zealand white rabbits by enzymatic digestion. SNP was used as a nitric oxide (NO) donor. In this experiments measuring SNP dose response, primary chondrocytes were treated with various concentrations of SNP for 24h. The time course of the SNP response was determined by incubating cells with 1mM SNP for the indicated time period $(0{\sim}24h)$. The cyclooxygenase-2 (COX-2) and type II collagen expression levels were determined by immunoblot analysis, and prostaglandin $E_2\;(PGE_2)$ assay was used to measure the COX-2 activity. The tyrosine phosphorylation of caveolin-1 was determined by immunoblot analysis and immunostaining. Results: SNP treatment stimulated tyrosine phosphorylation of caveolin-1 and activation of p38 kinase. SNP additionally caused dedifferentiation and inflammatory response. We showed previously that SNP treatment stimulated activation of p38 kinase and ERK-1/-2. Inhibition of p38 kinase with SB203580 reduced caveolin-1 tyrosine phosphorylation and COX-2 expression but enhanced dedifferentiation, whereas inhibition of ERK with PD98059 did not affect caveolin-1 tyrosine phosphorylation levels, suggesting that ERK at least is not related to dedifferentiation and COX-2 expression through caveolin-1 tyrosine phosphorylation. Conclusion: Our results indicate that SNP in articular chondrocytes stimulates dedifferentiation and inflammatory response via p38 kinase signaling in association with caveolin-1 phosphorylation.

SNP: A New On-Chip Communication Protocol for SoC (SNP : 시스템 온 칩을 위한 새로운 통신 프로토콜)

  • Lee Jaesung;Lee Hyuk-Jae;Lee Chanho
    • Journal of KIISE:Computer Systems and Theory
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    • v.32 no.9
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    • pp.465-474
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    • 2005
  • For high density SoC design, on-chip communication based on bus interconnection encounters bandwidth limitation while an NoC(Network-on-Chip) approach suffers from unacceptable complexity in its Implementation. This paper introduces a new on-chip communication protocol, SNP (SoC Network Protocol) to overcome these problems. In SNP, conventional on-chip bus signals are categorized into three groups, control, address, and data and only one set of wires is used to transmit all three groups of signals, resulting in the dramatic decrease of the number of wires. SNP efficiently supports master-master communication as well as master-slave communication with symmetric channels. A sequencing rule of signal groups is defined as a part of SNP specification and a phase-restoration feature is proposed to avoid redundant signals transmitted repeatedly over back-to-back transactions. Simulation results show that SNP provides about the same bandwidth with only $54\%$ of wires when compared with AMBA AHB.

Effect of Combining Multiple CNV Defining Algorithms on the Reliability of CNV Calls from SNP Genotyping Data

  • Kim, Soon-Young;Kim, Ji-Hong;Chung, Yeun-Jun
    • Genomics & Informatics
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    • v.10 no.3
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    • pp.194-199
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    • 2012
  • In addition to single-nucleotide polymorphisms (SNP), copy number variation (CNV) is a major component of human genetic diversity. Among many whole-genome analysis platforms, SNP arrays have been commonly used for genomewide CNV discovery. Recently, a number of CNV defining algorithms from SNP genotyping data have been developed; however, due to the fundamental limitation of SNP genotyping data for the measurement of signal intensity, there are still concerns regarding the possibility of false discovery or low sensitivity for detecting CNVs. In this study, we aimed to verify the effect of combining multiple CNV calling algorithms and set up the most reliable pipeline for CNV calling with Affymetrix Genomewide SNP 5.0 data. For this purpose, we selected the 3 most commonly used algorithms for CNV segmentation from SNP genotyping data, PennCNV, QuantiSNP; and BirdSuite. After defining the CNV loci using the 3 different algorithms, we assessed how many of them overlapped with each other, and we also validated the CNVs by genomic quantitative PCR. Through this analysis, we proposed that for reliable CNV-based genomewide association study using SNP array data, CNV calls must be performed with at least 3 different algorithms and that the CNVs consistently called from more than 2 algorithms must be used for association analysis, because they are more reliable than the CNVs called from a single algorithm. Our result will be helpful to set up the CNV analysis protocols for Affymetrix Genomewide SNP 5.0 genotyping data.

Modulation of Apoptosis and Differentiation by the Treatment of Sulfasalazine in Rabbit Articular Chondrocytes

  • Lee, Won Kil;Kang, Jin Seok
    • Toxicological Research
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    • v.32 no.2
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    • pp.115-121
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    • 2016
  • This study was conducted to examine the cellular regulatory mechanisms of sulfasalazine (SSZ) in rabbit articular chondrocytes treated with sodium nitroprusside (SNP). Cell phenotype was determined, and the MTT assay, Western blot analysis and immunofluorescence staining of type II collagen was performed in control, SNP-treated and SNP plus SSZ ($50{\sim}200{\mu}g/mL$) rabbit articular chondrocytes. Cellular proliferation was decreased significantly in the SNP-treated group compared with that in the control (p < 0.01). SSZ treatment clearly increased the SNP-reduced proliferation levels in a concentration-dependent manner (p < 0.01). SNP treatment induced significant dedifferentiation and inflammation compared with control chondrocytes (p < 0.01). Type II collagen expression levels increased in a concentration-dependent manner in response to SSZ treatment but were unaltered in SNP-treated chondrocytes (p < 0.05 and < 0.01, respectively). Cylooxygenase-2 (COX-2) expression increased in a concentration-dependent manner in response to SSZ treatment but was unaltered in SNP-treated chondrocytes (p < 0.05). Immunofluorescence staining showed that SSZ treatment increased type II collagen expression compared with that in SNP-treated chondrocytes. Furthermore, phosphorylated extracellular regulated kinase (pERK) expression levels were decreased significantly in the SNP-treated group compared with those in control chondrocytes (p < 0.01). Expression levels of pERK increased in a concentration-dependent manner by SSZ but were unaltered in SNP-treated chondrocytes. pp38 kinase expression levels increased in a concentration-dependent manner by SSZ but were unaltered in control chondrocytes (p < 0.01). In summary, SSZ significantly inhibited nitric oxide-induced cell death and dedifferentiation, and regulated extracellular regulated kinases 1 and 2 and p38 kinase in rabbit articular chondrocytes.

Pridict of Liver cirrhosis susceptibility using Decision tree with SNP (Decision Tree와 SNP정보를 이용한 간경화 환자의 감수성 예측)

  • Kim, Dong-Hoi;Uhmn, Saang-Yong;Cho, Sung-Won;Ham, Ki-Baek;Kim, Jin
    • Proceedings of the Korean Information Science Society Conference
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    • pp.63-66
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    • 2006
  • 본 논문에서는 SNP데이터를 이용하여 간경화에 대한 감수성을 예측하기 위해 의사결정 트리를 이용하였다. 데이터는 간경화 환자와 정상환자 총 116명의 데이터를 사용하였으며, Feature 값으로는 간질환과 밀접한 연관성을 갖는 28개의 SNP데이터를 사용하였다. 실험방법은 각각의 SNP에 대하여 의사결정트리로 분류율을 측정한 후 가장 높은 분류율을 가지는 SNP부터 조합해 나가는 방식으로 C4.5 의사결정트리를 이용 leave-one-out cross validation으로 간경화와 정상을 구분하는 정확도를 측정하였다. 실험결과 간 질환 관련 SNP중 IL1RN-S130S, IRNGR2-Q64R, IL-10(-592), IL1B_S35S 4개의 SNP조합에서 65.52%의 정확도를 얻을 수 있었다.

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Inference of kinship coefficients from Korean SNP genotyping data

  • Park, Seong-Jin;Yang, Jin Ok;Kim, Sang Cheol;Kwon, Jekeun;Lee, Sanghyuk;Lee, Byungwook
    • BMB Reports
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    • v.46 no.6
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    • pp.305-309
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    • 2013
  • The determination of relatedness between individuals in a family is crucial in analysis of common complex diseases. We present a method to infer close inter-familial relationships based on SNP genotyping data and provide the relationship coefficient of kinship in Korean families. We obtained blood samples from 43 Korean individuals in two families. SNP data was obtained using the Affymetrix Genome-wide Human SNP array 6.0 and the Illumina Human 1M-Duo chip. To measure the kinship coefficient with the SNP genotyping data, we considered all possible pairs of individuals in each family. The genetic distance between two individuals in a pair was determined using the allele sharing distance method. The results show that genetic distance is proportional to the kinship coefficient and that a close degree of kinship can be confirmed with SNP genotyping data. This study represents the first attempt to identify the genetic distance between very closely related individuals.

The Role of Nitric Oxide on the Growth Regulation of Chinese Cabbage (Brassica campestris L.) Primary Leaves (배추 (Brassica campestris L.) 제 1엽의 생장조절에 대한 Nitric Oxide의 역할)

  • Ham Jeong-Hun;Jin Chang-Duck
    • Journal of Plant Biotechnology
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    • v.32 no.4
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    • pp.293-300
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    • 2005
  • The possible role of nitric oxide (NO)-induced cell division was investigated to explain the physiologycal effects of a NO donor, sodium nitroprusside (SNP) on the growth of primary leaves in chinese cabbage seedling plants. Exogenous treatment of SNP to chinese cabbage plants for 8 days at different concentrations (0, 200, 500 and 1000 ${\mu}M$) affected the leaf growth in a concentration-dependent manner, showing a maximum growth at $200\;{\mu}M$. In accordance with leaf growth responses, the chlorophyll and soluble protein contents increased strongly to 142% and 134% of control at $200\;{\mu}M$ SNP, respectively. However, a very little decrease in chlorophyll and a 13%> decrease in protein were observed at $1000\;{\mu}M$ SNP. In addition, the content of DNA and RNA also increased maximumly to 142% and 139% of the control at $200\;{\mu}M$ SNP, respectively, whereas they decreased to 80% and 84% of the control at $1000\;{\mu}M$ SNP. With respect to the development of enzymes related to cell wall synthesis, $200\;{\mu}M$ SNP led to the maximum activities in both phenylalanine ammonia-lyase (212% of the control) and guaiacol peroxidase (134% of the control). However, the activities of both enzymes were not modified significantly at $1000\;{\mu}M$ SNP. In conclusion, these results suggest that the enhancement of leaf growth in chinese cabbage plants by SNP at the effective concentration was probably due to the NO ability in the induction of cell division.

Calpain-10 SNP43 and SNP19 Polymorphisms and Colorectal Cancer: a Matched Case-control Study

  • Hu, Xiao-Qin;Yuan, Ping;Luan, Rong-Sheng;Li, Xiao-Ling;Liu, Wen-Hui;Feng, Fei;Yan, Jin;Yang, Yan-Fang
    • Asian Pacific Journal of Cancer Prevention
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    • v.14 no.11
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    • pp.6673-6680
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    • 2013
  • Objective: Insulin resistance (IR) is an established risk factor for colorectal cancer (CRC). Given that CRC and IR physiologically overlap and the calpain-10 gene (CAPN10) is a candidate for IR, we explored the association between CAPN10 and CRC risk. Methods: Blood samples of 400 case-control pairs were genotyped, and the lifestyle and dietary habits of these pairs were recorded and collected. Unconditional logistic regression (LR) was used to assess the effects of CAPN10 SNP43 and SNP19, and environmental factors. Both generalized multifactor dimensionality reduction (GMDR) and the classification and regression tree (CART) were used to test gene-environment interactions for CRC risk. Results: The GA+AA genotype of SNP43 and the Del/Ins+Ins/Ins genotype of SNP19 were marginally related to CRC risk (GA+AA: OR = 1.35, 95% CI = 0.92-1.99; Del/Ins+Ins/Ins: OR = 1.31, 95% CI = 0.84-2.04). Notably, a high-order interaction was consistently identified by GMDR and CART analyses. In GMDR, the four-factor interaction model of SNP43, SNP19, red meat consumption, and smoked meat consumption was the best model, with a maximum cross-validation consistency of 10/10 and testing balance accuracy of 0.61 (P < 0.01). In LR, subjects with high red and smoked meat consumption and two risk genotypes had a 6.17-fold CRC risk (95% CI = 2.44-15.6) relative to that of subjects with low red and smoked meat consumption and null risk genotypes. In CART, individuals with high smoked and red meat consumption, SNP19 Del/Ins+Ins/Ins, and SNP43 GA+AA had higher CRC risk (OR = 4.56, 95%CI = 1.94-10.75) than those with low smoked and red meat consumption. Conclusions: Though the single loci of CAPN10 SNP43 and SNP19 are not enough to significantly increase the CRC susceptibility, the combination of SNP43, SNP19, red meat consumption, and smoked meat consumption is associated with elevated risk.

Novel SNP in the coding region of the FTO gene is associated with marbling score in Hanwoo (Korean cattle)

  • Chung, Eui-Ryong
    • Journal of Animal Science and Technology
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    • v.56 no.8
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    • pp.27.1-27.6
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    • 2014
  • The fat mass and obesity associated (FTO) gene plays an important role in the regulation of energy homeostasis, fat deposition and obesity. For this reason, the FTO gene is a physiological and functional candidate gene for carcass and meat quality traits in beef cattle. The objectives of this study were to identify SNPs in the exonic regions of FTO gene and to evaluate the association of these SNPs with carcass traits in Hanwoo (Korean cattle). In this study, we newly identified two exonic SNPs in Hanwoo population. The g.125550A > T SNP was located in exon 3 and the g.175675C > T SNP was located in exon 6. Genotyping of the two SNP markers was carried out using PCR-RFLP analysis in Hanwoo steers to evaluate their association with carcass traits. As a result, g.125550A > T SNP genotype was significantly associated with effects on marbling score. Animals with the AA and TT homozygous genotypes had a significantly higher marbling score (p < 0.001) than those with AT heterozygous genotype, and this was significant after Bonferroni correction of the significance threshold (p = 0.003). Dominance effect was also observed for the marbling score (P < 0.05) with higher marbling score of homozygous animals. However, no significant associations with meat quality traits were observed for the g.175675C > T SNP. Our results suggest that the exonic SNP g.125550A > T in the FTO gene may be used as a DNA marker for the selection of Hanwoo with higher marbling.