• The Korean Journal of Physiology and Pharmacology
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• v.18 no.1
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• pp.25-32
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• 2014

Nitric oxide (NO) is recognized as a mediator and regulator of inflammatory responses. NO is produced by nitric oxide synthase (NOS), and NOS is abundantly expressed in the human dental pulp cells (HDPCs). NO produced by NOS can be cytotoxic at higher concentrations to HDPCs. However, the mechanism by which this cytotoxic pathway is activated in cells exposed to NO is not known. The purpose of this study was to elucidate the NO-induced cytotoxic mechanism in HDPCs. Sodium nitroprusside (SNP), a NO donor, reduced the viability of HDPCs in a dose- and time-dependent manner. We investigated the in vitro effects of nitric oxide on apoptosis of cultured HDPCs. Cells showed typical apoptotic morphology after exposure to SNP. Besides, the number of Annexin V positive cells was increased among the SNP-treated HDPCs. SNP enhanced the production of reactive oxygen species (ROS), and N-acetylcysteine (NAC) ameliorated the decrement of cell viability induced by SNP. However, a soluble guanylate cyclase inhibitor (ODQ) did not inhibited the decrement of cell viability induced by SNP. SNP increased cytochrome c release from the mitochondria to the cytosol and the ratio of Bax/Bcl-2 expression levels. Moreover, SNP-treated HDPCs elevated activities of caspase-3 and caspase-9. While pretreatment with inhibitors of caspase (z-VAD-fmk, z-DEVD-fmk) reversed the NO-induced apoptosis of HDPCs. From these results, it can be suggested that NO induces apoptosis of HDPCs through the mitochondria-dependent pathway mediated by ROS and Bcl-2 family, but not by the cyclic GMP pathway.

• Journal of Life Science
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• v.14 no.5
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• pp.847-854
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• 2004

Allergy is a multi-factorial disease influenced by genetic and environmental factors. As the number of allergy-affected people is increasing in developed countries, there is an increasing interest in genetic predisposition to the allergy. A number of genes and chromosomal region have been identified to be linked to allergy including rhinitis, asthma and atopy. In order to understand the genetic background for the allergy-affected people, we investigated genetic predisposition among students enrolled in Busan Science Academy. Among 138 students, about 30% students had some allergy-related disorder including rhinitis, asthma and atopy. We analyzed several single nucleotide polymorphisms (SNPs) within two genes, Inter-leukin-4(IL-4) and Interleukin-4 receptor(IL-4R), which are involved in the induction of allergy reaction with the Th2 immunity. For 96 samples obtained from students, we analyzed 9 SNPs including -590 C/T and -34 C/T in IL-4, and I75V, Q576R, E375A, e406R, 5411L, S761P and S727A in IL-4R. From the analysis, these SNPs showed slight differences among normal and allergy-affected students, but these differences was not enough to predict the predisposition to the allergy. In contrast to previous reports, we could not find SNP(s) related with allergy. These results suggest that genetic tests recently performed in Korea widely have to be reassessed for its validity of genetic predisposition. [Supported by grants from MOST]

• Journal of Life Science
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• v.25 no.11
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• pp.1304-1310
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• 2015

The period circadian clock gene 3 (PER3) plays a role in the mammalian circadian clocksystem. A regular exercise regime may affect the PER3 transcription in skeletal muscle. Although the effects of day length on circadian and circannual processes are well established in humans and mice, the influence of exercise on these processes in the horse has not been investigated. The present study investigated the expression of the PER3 gene following exercise in a thoroughbred breed of Korean horse. In addition, a comprehensive in silico nonsynonymous single nucleotide polymorphism (nsSNP) analysis of the horse PER3 gene and predicted effects of nsSNPs on proteins were examined. The expression of PER3 in skeletal muscle was significantly upregulated after exercise. Four nsSNPs were functionally annotated and analyzed by computational prediction. The total free energy and RMSD values of PER3 gene showed causative mutations. The results showed that nsSNP s395916798 (G72R) was associated with residues that have stabilizing effects on structure and function of PER3 gene. This study documented role of PER3 gene in phenotypic adaptation related to exercise in skeletal muscle. Further, the SNPs in PER3 could serve as useful biomarkers of early recovery after exercise in racehorses.

• Journal of Korean Dental Science
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• v.5 no.1
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• pp.7-12
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• 2012

Purpose: To examine the antibacterial effectiveness of silver nanoparticles (SNP) mixed with commercial orthodontic adhesives. Materials and Methods: SNP was prepared by dissolving silver perchlorate in an organic solvent and reducing it with ultraviolet radiation. SNP was then mixed with four commercial orthodontic adhesives (Light Bond, Blugloo, Transbond XT, and Fuji Ortho LC) (0.05 wt %), which were then formed into disc-shape specimens ($8.0mm{\times}3.0mm$). Commercial orthodontic adhesives containing no SNP were used as the control groups. Specimens of the four experimental and four control groups were incubated with streptococcus mutans and the medium turbidity was assessed at 3, 6, 9, 12, and 24 hours after incubation. The agar diffusion test was also performed to examine the growth inhibition zone of these groups. The data were statistically analyzed using a Wilcoxon rank sum test and t-test with a Bonferroni's correction (P<0.05). Result: The SNP containing groups had a superior antibacterial effect compared to the control groups. In the agar diffusion test, the control groups without SNP did not produce an inhibition zone, whereas the SNP containing groups showed inhibition zone of 10~13 mm. Conclusion: The incorporation of SNP into orthodontic adhesives can inhibit cariogenic bacterial growth.

• The Korean Journal of Malacology
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• v.26 no.2
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• pp.185-188
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• 2010

The Web-based the genus Haliotis SNP database was constructed on the basis of Intel Server Platform ZSS130 dual Xeon 3.2 GHz cpu and Linux-based (Cent OS) operating system. Haliotis related sequences (2,830 nucleotide sequences, 9,102 EST sequences) were downloaded through NCBI taxonomy browser. In order to eliminate vector sequences, we conducted vector masking step using cross match software with vector sequence database. In addition, poly-A tails were removed using Trimmest software from EMBOSS package. The processed sequences were clustered and assembled by TGICL package (TIGR tools) equipped with CAP3 software. A web-based interface (Haliotis SNP Database, http://www.haliotis.or.kr) was developed to enable optimal use of the clustered assemblies. The Clustering Res. menu shows the contig sequences from the clustering, the alignment results and sequences from each cluster. And also we can compare any sequences with Haliotis related sequences in BLAST menu. The search menu is equipped with its own search engine so that it is possible to search all of the information in the database using the name of a gene, accession number and/or species name. Taken together, the Web-based SNP database for Haliotis will be valuable to develop SNPs of Haliotis in the future.

• Journal of the Korean Data and Information Science Society
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• v.25 no.5
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• pp.1095-1106
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• 2014

Symbolic data analysis extends the data mining and exploratory data analysis to the knowledge mining, we can suggest the SDA tree model on clinical and genomic data with new knowledge mining SDA approach. Using SDA application for huge genomic SNP data, we can get the correlation the availability of understanding of hidden structure of HCC data could be proved. We can confirm validity of application of SDA to the tree structured progression model and to quantify the clinical lab data and SNP data for early diagnosis of HCC. Our proposed model constructs the representative model for HCC survival time and causal association with their SNP gene data. To fit the simple and easy interpretation tree structured survival model which could reduced from huge clinical and genomic data under the new statistical theory of knowledge mining with SDA.

• Korean Journal of Plant Resources
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• v.34 no.5
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• pp.443-450
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• 2021

Peach flesh color is commercially important criteria for classification and has implications for nutritional quality. To breed new yellow-fleshed peach cultivar many cross seedlings and generations should be maintained. Therefore it is necessary to develop early selection molecular markers for screening cross seedlings and germplasm with economically important traits to increase breeding efficiency. For the comparison of transcription profiles in peach varieties with a different flesh color expression, two cDNA libraries were constructed. Differences in gene expression between yellow-fleshed peach cultivar, 'Changhowon Hwangdo' and white-fleshed peach cultivar, 'Mibaekdo' were analyzed by next-generation sequencing (NGS). Expressed sequence tag (EST) of clones from the two varieties was selected for nucleotide sequence determination and homology searches. Putative single nucleotide polymorphisms (SNPs) were screened from peach EST contigs by high resolution melting (HRM) analysis, SNP ID ppa002847m:cds and ppa002540m:cds displayed specific difference between 17 yellow-fleshed and 21 white-fleshed peach varieties. The SNP markers for distinguishing yellow and white fleshed peach varieties by HRM analysis offers the opportunity to use early selection. This SNP markers could be useful for marker assisted breeding and provide a good reference for relevant research on molecular mechanisms of color variation in peach varieties.

• Journal of Animal Science and Technology
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• v.49 no.5
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• pp.549-558
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• 2007

C4B and BAT2, assigned to the SLA class III region, were recently reported on relation with human diseases. The primers for RT-PCR and RACE-PCR for CDS analysis of these genes of pig were designed by aligning the CDSs of humans and mice from GenBank. After we amplified and sequenced with these primers and cDNAs, the full-length CDSs of pig were determined. The CDS lengths of C4B and BAT2 were shown as 5226 bp and 6501 bp. In addition, the identities of nucleotide sequences with human and mouse were 76% to 87%, and the identities of amino acids were 72% to 90%. After we carried out the alignment with determined CDSs in this study and pig genomic sequences from GenBank, the primers for cSNP detection in genome were designed in intron regions that flanked one or more exons. Then, we amplified and directly sequenced with genomic DNAs of six pig breeds. Four cSNPs from C4B and three 3 cSNPs from BAT2 were identified. In addition, amino acid substitution occurred in six cSNP positions except for C4248T of C4B. By the Multiplex-ARMS method, we genotyped seven cSNPs with DNA samples used for direct sequencing. We verified that this result was the same as that analyzed using direct sequencing. To demonstrate recrudescence, we performed both direct sequencing and Multiplex-ARMS on two randomly selected DNA samples. The genotype of each sample showed the same result from both methods. Therefore, seven cSNPs were identified from C4B and BAT2 and could be used as the basic data for haplotype analysis of SLA class III region. Moreover, the Multiplex-ARMS method should be powerful for genotyping of genes assigned to the whole SLA region for the xenograft study.

• Journal of Animal Science and Technology
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• v.54 no.5
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• pp.323-329
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• 2012

Genome-wide association study was performed on data from 266 Hanwoo steers derived from 66 sires using bovine 10K mapping chip in Hanwoo (Korean cattle). SNPs were excluded from the analysis if they failed in over 5% of the genotypes, had median GC scores below 0.6, had GC scores under 0.6 in less than 90% of the samples, deviated in heterozygosity more than 3 standard deviations from the other SNPs and were out of Hardy-Weinberg equilibrium for a cut-off p-value of $1^{-15}$. Unmapped and SNPs on sex chromosomes were also excluded. A total of 4,522 SNPs were included in the analysis. To test an association between SNP and QTL, a single marker regression analysis was implemented in this study. SNP was assumed to be in LD with QTL in close proximity and the effect evaluated was additive effect (QTL allele substitution effect). The number of significant SNP at a threshold of P<0.001 was 3, 5, 5 and 4 loci for live weight at 6, 12, 18 and 24 months, respectively. For live weight at different ages, significant SNP were spread out across chromosome but some of significant SNP (rs29012453 and rs29012456 on BTA24) had shown highly significant effects. As for the distribution of size of SNP effects, few loci for live weight at different age had moderate effects (6~11%) but most of significant loci had small effects (2 to 5% of additive genetic variance) against total additive genetic variance. In conclusion, live weight at different age might be affected by few loci with moderate effect and many loci with small effects across genome in Hanwoo.

• Journal of Acupuncture Research
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• v.21 no.6
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• pp.19-36
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• 2004

Objective : The purpose of this study was to investigate the effect of Bee Venom and Melittin Solution on the lipopolysaccharide(LPS) and sodium nitroprusside(SNP)-induced expression of prostaglandin $E_2(PGE_2)$, cyclooxygenase-2(COX-2), nuclear factor kappa B($NF-{\kappa}B$) and nuclear factor kappa B($NF-{\kappa}B$) dependent luciferase activity in RAW 264.7 cells, a murine macrophage cell line. Methods : The expression of PGE2 was determined by determination of $PEG_2$, COX-2 was by western blotting with corresponding antibodies, $NF-{\kappa}B$ was by gel mobility shift assay method and $NF-{\kappa}B$ dependent luciferase activity was investigated by luciferase assay in RAW 264.7 cells. Results : 1. LPS and SNP-induced expression of $PEG_2$ was significant after 24hour. 2. The 0.5, 1 and $5{\mu}g/mL$ of bee venom and the 5 and $10{\mu}g/mL$ of melittin solution inhibited significantly LPS-induced expression of $PEG_2$ and, the $5{\mu}g/mL$ of bee venom and the 5 and $10{\mu}g/mL$ of melittin solution inhibited significantly SNP-induced expression of $PEG_2$ compared with control, respectively. The 0.5 and $1{\mu}g/mL$ of bee venom could not significantly inhibit SNP-induced expression of $PEG_2$ compared with control. 3. The $5{\mu}g/mL$ of bee venom and the 5 and $10{\mu}g/mL$ of melittin solution inhibited significantly LPS and SNP-induced expression of COX-2 compared with control, respectively. The 0.5 and $1{\mu}g/mL$ of bee venom inclined to decrease LPS and SNP-induced expression of COX-2 compared with control. 4. The 0.5, 1 and $5{\mu}g/mL$ of bee venom and the 5 and $10{\mu}g/mL$ of melittin solution inhibited significantly LPS and SNP-induced expression of $NF-{\kappa}B$ compared with control, respectively. 5. The 0.5, 1 and $5{\mu}g/mL$ of bee venom and the 5 and $10{\mu}g/mL$ of melittin solution inhibited significantly LPS-induced expression of $NF-{\kappa}B$ dependent luciferase activity and the 1 and $5{\mu}g/mL$ of bee venom and the 5 and $10{\mu}g/mL$ of melittin solution inhibited significantly SNP-induced expression of $NF-{\kappa}B$ dependent luciferase activity compared with control, respectively. The $NF-{\kappa}B$ inhibitor also inhibited significantly LPS and SNP-induced expression of $NF-{\kappa}B$ dependent luciferase activity compared with control. 6. The 0.5, 1 and $5{\mu}g/mL$ of bee venom and the 5 and $10{\mu}g/mL$ of melittin solution inhibited significantly LPS + IFN-${\gamma}$, TNF-${\alpha}$ and LPS + TNF-${\alpha}$-induced expression of $NF-{\kappa}B$ dependent luciferase activity compared with control, respectively. The $NF-{\kappa}B$ inhibitor also inhibited significantly LPS and SNP-induced expression of $NF-{\kappa}B$ dependent luciferase activity compared with control. Conclusions : These results suggest the inhibitory action of bee venom and melittin solution on the inflammatory mediators such as $PEG_2$, COX-2 and $NF-{\kappa}B$.