• Genomics & Informatics
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• 제5권4호
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• pp.188-193
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• 2007

The Functional Element SNPs Database (FESD) categorizes functional elements in human genic regions and provides a set of single nucleotide polymorphisms (SNPs) located within each area. Users may select a set of SNPs in specific functional elements with haplotype information and obtain flanking sequences for genotyping. Our previous version of FESD has been improved in several ways. We regenerated all the data in FESD II from recently updated source data such as HapMap, UCSC GoldenPath, dbSNP, OMIM, and $TRANSFAC^{(R)}$. Users can obtain information about tagSNPs and simulate LD blocks for each gene from four ethnicities in the HapMap project on the fly. FESD II employs a Java/JSP web interface for better platform portability and higher speed than PHP in the previous version. As a result, FESD II provides its users with more powerful information about functional element SNPs of human ethnicities.

• 한국응용약물학회:학술대회논문집
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• 한국응용약물학회 1994년도 춘계학술대회 and 제3회 신약개발 연구발표회
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• pp.286-286
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• 1994

Thrombin (0.25 U/ml : TB), 소-피부 collagen (200 $\mu\textrm{g}$/ml : CG), adenosine 5'-diphesphate (4,0 $\times$ $10^{-5}$M : ADP), 및 epinephrine (4,0 $\times$ 10 $^{-5}$M : EPI)의 가토-혈소판 응집과 단백인산화작용에 미치는 PDE-I (3-isobutyl-1-methylxanthine : IBMX, 및 KR 30075), amitriptyline (AP), chlorpromazine (CP), 및 sodium nitrogrosside (SNP)의 염향을 비교-검토하였다. 그 결과, KR은 2,2 $\times$ $10^{-7}$M 이하의 $IC_{50}$/에서 EPI > ADP > CG > TB 순으로 각각을 억제하였으며, SNP 보다도 강하였고; KR-30075보다 약하나 IBMX, AP, 및 CP도 각 응집재의 작용을 억제하였으며 특히 EPI에 대하여 $10^{-8}$M 이하의 $IC_{50}$/에서 유의한 억제력을 보였다. 각 응집제들은 41 kD 인산화는 유의하게 증가시키며 47 kD와 20 kD 단백인산화는 감소시켰는데; 모든 항응집성 약물이 41 kD 인산화-증가는 유의하게 억제하였다, 아울러, AP와 CP는 47 kD 단백인산화-감소에 영향을 미치지 않았으나 20 kD 단백인산화-감소는 억제하였다. PDE-I (IBMX와 KR)와 SNP는 47 kD와 20 kD 단백인산화-감소를 다소 약화시켰으며, 43 kD와 22 kD 단백인산화를 KR > IBMX > SNP순으로 유의하게 증가시켰고, KR의 22 kD 단백인산화작용은 현저하였다.

• Biomolecules & Therapeutics
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• 제21권5호
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• pp.364-370
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• 2013

Resveratrol (trans-3,4'-trihydroxystillbene), a naturally occurring polyphenolic antioxidant found in grapes and red wine, elicits diverse biochemical responses and demonstrates anti-aging, anti-inflammatory, and anti-proliferative effects in several cell types. Previously, resveratrol was shown to regulate differentiation and inflammation in rabbit articular chondrocytes, while the direct production of nitric oxide (NO) in these cells by treatment with the NO donor sodium nitroprusside (SNP) led to apoptosis. In this study, the effect of resveratrol on NO-induced apoptosis in rabbit articular chondrocytes was investigated. Resveratrol dramatically reduced NO-induced apoptosis in chondrocytes, as determined by phase-contrast microscopy, the MTT assay, FACS analysis, and DAPI staining. Treatment with resveratrol inhibited the SNP-induced expression of p53 and p21 and reduced the expression of procaspase-3 in chondrocytes, as detected by western blot analysis. SNP-induced degradation of I-kappa B alpha ($I{\kappa}B-{\alpha}$) was rescued by resveratrol treatment, and the SN50 peptide-mediated inhibition of NF-kappa B (NF-${\kappa}B$) activity potently blocked SNP-induced caspase-3 activation and apoptosis. Our results suggest that resveratrol inhibits NO-induced apoptosis through the NF-${\kappa}B$ pathway in articular chondrocytes.

• Asian-Australasian Journal of Animal Sciences
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• 제25권1호
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• pp.28-32
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• 2012

In the present study, we evaluated the informativeness of SNPs genotyped by the Illumina Bovine SNP50K assay in different cattle breeds. To investigate these on a genome-wide scale, we considered 52,678 SNPs spanning the whole autosomal and X chromosomes in cattle. Our study samples consists of six different cattle breeds. Across the breeds approximately 72 and 6% SNPs were found polymorphic and fixed or close to fix in all the breeds, respectively. The variations in the average minor allele frequency (MAF) were significantly different between the breeds studied. The level of average MAF observed in Hanwoo was significantly lower than the other breeds. Hanwoo breed also displayed the lowest number of polymorphic SNPs across all the chromosomes. More importantly, this study indicated that the Bovine SNP50K assay will have reduced power for genome-wide association studies in Hanwoo as compared to other cattle breeds. Overall, the Bovine SNP50K assay described in this study offer a useful genotyping platform for mapping quantitative trait loci (QTLs) in the cattle breeds. The assay data represent a vast and generally untapped resource to assist the investigation of the complex production traits and the development of marker-assisted selection programs.

• Genomics & Informatics
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• 제5권2호
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• pp.68-76
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• 2007

Due to the increasing interest in SNPs and mutational hot spots for disease traits, it is becoming more important to define and understand the relationship between SNPs and their flanking sequences. To study the effects of flanking sequences on SNPs, statistical approaches are necessary to assess bias in SNP data. In this study we mainly applied Markov chains for SNP sequences, particularly those located in intronic regions, and for analysis of in-del data. All of the pertaining sequences showed a significant tendency to generate particular SNP types. Most sequences flanking SNPs had lower complexities than average sequences, and some of them were associated with microsatellites. Moreover, many Alu repeats were found in the flanking sequences. We observed an elevated frequency of single-base-pair repeat-like sequences, mirror repeats, and palindromes in the SNP flanking sequence data. Alu repeats are hypothesized to be associated with C-to-T transition mutations or A-to-I RNA editing. In particular, the in-del data revealed an association between particular changes such as palindromes or mirror repeats. Results indicate that the mechanism of induction of in-del transitions is probably very different from that which is responsible for other SNPs. From a statistical perspective, frequent DNA lesions in some regions probably have effects on the occurrence of SNPs.

• 원예과학기술지
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• 제31권2호
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• pp.219-223
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• 2013

DNA markers can determine the genotype of many species. Single nucleotide polymorphism (SNP) detection is difficult without sequencing but it becomes easier with sdCAPS method. Here an experiment was performed for developing molecular markers using two SNPs, CSatpB-SNP and CSycf1-SNP, of chloroplast in cucumber plants. Properly designed primers with nucleotide sequences for restriction enzymes proved success of PCR and efficacy of digestion by the restriction enzymes. Then these markers were used to study the genotyping of cucumber breeding lines and cultivars obtained from various sources in respect of their chilling stress response. We confirmed that a U.S. cucumber line, 'NC76' known to possess a nuclear factor for the chilling tolerance showed the chloroplast genotypes related to chilling tolerance. However all Korean cucumber cultivars tested in this study showed the chloroplast genotypes related to chilling susceptibility. In conclusion, to develop chilling tolerant cucumber, both maternal and a nuclear factors related to chilling tolerance should be transferred from 'NC76' when 'NC76' is used as a female source and other elite lines as recurrent parents.

• Asian-Australasian Journal of Animal Sciences
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• 제24권4호
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• pp.457-462
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• 2011

The purpose of this study was to detect QTL for carcass quality on bovine chromosome (BTA) 6 using a high density SNP map in a Hanwoo population. The data set comprised 45 sires and their 427 Hanwoo steers that were born between spring of 2005 and fall of 2007. The steers that were used for progeny testing in the Hanwoo Improvement Center in Seosan, Korea, were genotyped with the 2,535SNPs on BTA6 that were embedded in the Illumina bovine SNP 50K chip. Four different linkage disequilibrium (LD) mapping models were applied to detect significant SNPs for carcass quality traits; the fixed model with a single marker, the random model with a single marker, the random model with haplotype effects using two adjacent markers, and the random model at hidden state. A total of twelve QTL were detected, for which four, one, three and four SNPs were detected on BTA6 under the respective models (p<0.001). Among the detected QTL, four, two, five and one QTL were associated with carcass weight, backfat thickness, longissimus dorsi muscle area, and marbling score, respectively (p<0.001). Our results suggest that the use of multiple LD mapping approaches may be beneficial in increasing power to detect QTL given a limited sample size and magnitude of QTL effect.

• International Journal of Oral Biology
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• 제40권4호
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• pp.211-216
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• 2015

Nitric Oxide (NO) is an important signaling molecule in the nociceptive process. Our previous study suggested that high concentrations of sodium nitroprusside (SNP), a NO donor, induce a membrane hyperpolarization and outward current through large conductances calcium-activated potassium ($BK_{ca}$) channels in substantia gelatinosa (SG) neurons. In this study, patch clamp recording in spinal slices was used to investigate the sources of $Ca^{2+}$ that induces $Ca^{2+}$-activated potassium currents. Application of SNP induced a membrane hyperpolarization, which was significantly inhibited by hemoglobin and 2-(4-carboxyphenyl) -4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide potassium salt (c-PTIO), NO scavengers. SNP-induced hyperpolarization was decreased in the presence of charybdotoxin, a selective $BK_{Ca}$ channel blocker. In addition, SNP-induced response was significantly blocked by pretreatment of thapsigargin which can remove $Ca^{2+}$ in endoplasmic reticulum, and decreased by pretreatment of dentrolene, a ryanodine receptors (RyR) blocker. These data suggested that NO induces a membrane hyperpolarization through $BK_{ca}$ channels, which are activated by intracellular $Ca^{2+}$ increase via activation of RyR of $Ca^{2+}$ stores.

• Communications for Statistical Applications and Methods
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• 제16권6호
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• pp.915-923
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• 2009

광범위 유전자 연관(genome-wide association) 연구에서는 무수히 많은 유전자들 중에 인간의 질병에 관련된 유전자를 찾아왔다. 기존의 인간 질병에 관련된 유전자를 찾는 방법에서 이렇게 많은 유전자들 중에서 우수한 유전자를 찾는데 직접 이용할 시에는 계산이 복잡해지고 비용이 많이 들어가며 시간이 오래 걸린다는 단점이 생긴다. 따라서 이번 수많은 유전자들 중 주요 유전자 그룹을 찾는 방법으로 SNPHarvester가 개발되였다. 본 연구에서는 인간의 질병이 아닌 한우의 여러 경제형질에 관련된 우수 유전자를 SNPHarvester를 이용하여 17 개의 SNP들 중에서 우수한 유전자 그룹을 찾았고 의사결정나무(decision tree)를 이용하여 한우의 여러 경제형질을 높일 수 있는 SNP 그룹 내의 우수 유전자형도 함께 규명할 수 있었다.

• International Journal of Oral Biology
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• 제31권2호
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• pp.67-72
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• 2006

Nitric oxide(NO) is a labile, uncharged, reactive radical that functions as a sensitive mediator of intercellular communication in diverse tissues. It has been reported that NO is produced by osteoblast and these results may suggest that NO is integrally involved in the regulation of osteoclast formation and osteoclast resorption activity by osteoblastic cells. We examined the effect of cytokines on NO release by mouse bone marrow cell. We also examined the effects of cytokines and sodium nitroprusside(SNP) on the formation of osteoclast-like cell from mouse bone marrow cells in culture. Cytokines stimulated NO production of mouse bone marrow cells, and N-nitro-L-arginine methyl ester, a specific inhibitor of NO synthase, suppressed the cytokine-induced NO production. SNP showed dual action in the generation of osteoclasts. The addition of $30{\mu}M$ SNP inhibited the formation of tartrate resistant acid phosphatase(TRAP)(+) multinucleated cell, whereas lower concentration($3{\mu}M$) of SNP enhanced it. Although the precise action of NO remains to be elucidated in detail, the action of NO in osteoclast generation in our studies seems to be associated, at least in part, with bone metabolism and bone pathophysiology.