• Genomics & Informatics
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• v.6 no.4
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• pp.231-234
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• 2008

Precise and reliable identification of CNV is still important to fully understand the effect of CNV on genetic diversity and background of complex diseases. SNP marker has been used frequently to detect CNVs, but the analysis of SNP chip data for identifying CNV has not been well established. We compared various normalization methods for CNV analysis and suggest optimal normalization procedure for reliable CNV call. Four normal Koreans and NA10851 HapMap male samples were genotyped using Affymetrix Genome-Wide Human SNP array 5.0. We evaluated the effect of median and quantile normalization to find the optimal normalization for CNV detection based on SNP array data. We also explored the effect of Robust Multichip Average (RMA) background correction for each normalization process. In total, the following 4 combinations of normalization were tried: 1) Median normalization without RMA background correction, 2) Quantile normalization without RMA background correction, 3) Median normalization with RMA background correction, and 4) Quantile normalization with RMA background correction. CNV was called using SW-ARRAY algorithm. We applied 4 different combinations of normalization and compared the effect using intensity ratio profile, box plot, and MA plot. When we applied median and quantile normalizations without RMA background correction, both methods showed similar normalization effect and the final CNV calls were also similar in terms of number and size. In both median and quantile normalizations, RMA backgroundcorrection resulted in widening the range of intensity ratio distribution, which may suggest that RMA background correction may help to detect more CNVs compared to no correction.

• Journal of Animal Science and Technology
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• v.58 no.10
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• pp.38.1-38.6
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• 2016

Background: Despite the importance of relationships between somatic cell score (SCS) and currently selected traits (milk, fat and protein yield) of Holstein cows, there was a lack of comprehensive literature for it in Iran. Therefore we tried to examine heritabilities and relationships between these traits using a fixed-regression animal model and Bayesian inference. The data set consisted of 1,078,966 test-day observations from 146,765 primiparous daughters of 1930 sires, with calvings from 2002 to 2013. Results: Marginal posterior means of heritability estimates for SCS ($0.03{\pm}0.002$) were distinctly lower than those for milk ($0.204{\pm}0.006$), fat ($0.096{\pm}0.004$) and protein ($0.147{\pm}0.005$) yields. In the case of phenotypic correlations, the relationships between production and SCS were near zero at the beginning of lactation but become increasingly negative as days in milk increased. Although all environmental correlations between production and SCS were negative ($-0.177{\pm}0.007$, $-0.165{\pm}0.008$ and $-0.152{\pm}0.007$ between SCS and milk, fat, and protein yield, respectively), slightly antagonistic genetic correlations were found; with posterior mean of relationships ranging from $0.01{\pm}0.039$ to $0.11{\pm}0.036$. This genetic opposition was distinctly higher for protein than for fat. Conclusion: Although small, the positive genetic correlations suggest some genetic antagonism between desired increased milk production and reduced SCS (i.e., single-trait selection for increased milk production will also increase SCS).

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.22
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• pp.9643-9647
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• 2014

Background: Several studies have been performed to investigate the association of the HER2 Ile655Val polymorphism and breast cancer risk. However, the results were inconsistent. To understand the precise relationship, a meta-analysis was here conducted. Materials and Methods: A search of PubMed conducted to investigate links between the HER2 Ile655Val polymorphism and breast cancer, identified a total of 32 studies, of which 29, including 14,926 cases and 15,768 controls, with odds ratios (ORs) with 95% confidence intervals were used to assess any association. Results: In the overall analysis, the HER2 Ile655Val polymorphism was associated with breast cancer in an additive genetic model (OR=1.136, 95% CI 1.043-1.239, p=0.004) and in a dominant genetic (OR=1.118, 95% CI 1.020-1.227, p=0.018), while no association was found in a recessive genetic model. On subgroup analysis, an association with breast cancer was noted in the additive genetic model (OR=1.111, 95% CI: 1.004-1.230, p=0.042) for the Caucasian subgroup. No significant associations were observed in Asians and Africans in any of the genetic models. Conclusions: In summary, our meta-analysis findings suggest that the HER2 Ile655Val polymorphism is marginally associated with breast cancer susceptibility in worldwide populations with additive and dominant models, but not a recessive model.

• Journal of Ginseng Research
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• v.42 no.2
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• pp.158-164
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• 2018

Background: The study was carried out to assess the genetic variability present in ashwagandha and to examine the nature of associations of various traits to the root yield of the plant. Methods: Fifty-three diverse genetic stocks of ashwagandha (Withania somnifera) were evaluated for 14 quantitative characteristics. Analysis of variance, correlation, and path coefficient analysis were performed using the mean data of 2 years. Results: Analysis of variance revealed that the genotypes differed significantly for all characteristics studied. High heritability in conjunction with high genetic advance was observed for fresh root weight, 12 deoxywithastramonolide in roots, and plant height, which indicated that selection could be effective for these traits. Dry root weight has a tight linkage with plant height and fresh root weight. Further, in path coefficient analysis, fresh root weight, total alkaloid (%) in leaves, and 12 deoxywithastramonolide (%) in roots had the highest positive direct effect on dry root weight. Conclusion: Therefore, these characteristics can be exploited to improve dry root weight in ashwagandha genotypes and there is also scope for the selection of promising and specific chemotypes (based on the alkaloid content) from the present germplasm.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.9
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• pp.3759-3765
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• 2015

Background: Approaches in disruption of MDM2-p53 interactions have now emerged as an important therapeutic strategy in resurrecting wild type p53 functional status. The present study highlights virtual screening strategies in identification of high affinity small molecule non-peptidic inhibitors. Nutlin3A and RG7112 belonging to compound class of Cis-imidazoline, MI219 of Spiro-oxindole class and Benzodiazepine derived TDP 665759 served as query small molecules for similarity search with a threshold of 95%. The query molecules and the similar molecules corresponding to each query were docked at the transactivation binding cleft of MDM2 protein. Aided by MolDock algorithm, high affinity compound against MDM2 was retrieved. Patch Dock supervised Protein-Protein interactions were established between MDM2 and ligand (query and similar) bound and free states of p53. Compounds with PubCid 68870345, 77819398, 71132874, and 11952782 respectively structurally similar to Nutlin3A, RG7112, Mi219 and TDP 665759 demonstrated higher affinity to MDM2 in comparison to their parent compounds. Evident from the protein-protein interaction studies, all the similar compounds except for 77819398 (similar to RG 7112) showed appreciable inhibitory potential. Of particular relevance, compound 68870345 akin to Nutlin 3A had highest inhibitory potential that respectively showed 1.3, 1.2, 1.16 and 1.26 folds higher inhibitory potential than Nutilin 3A, MI 219, RG 7112 and TDP 1665759. Compound 68870345 was further mapped for structure based pharamacophoric features. In the study, we report Cis-imidazoline derivative compound; Pubcid: 68870345 to have highest inhibitory potential in blocking MDM2-p53 interactions hitherto discovered.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.4
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• pp.2145-2150
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• 2016

Background: Infection with hepatitis B virus (HBV) is a major global public health problem, with a wide spectrum of clinical manifestations. Human cytosolic glutathione-S-transferases (GSTs) include several classes such as alpha (A), mu (M), pi (P), sigma (S), zeta (Z), omega (O) and theta (T). The present study aimed to investigate the role of GST omega genes (GSTO1 and GSTO2) in different groups of patients infected with HBV. Materials and Methods: HBV groups were classified according to clinical history, serological tests and histological analysis into normal carriers (N), acute (A), chronic (CH), cirrhosis (CI) and hepatocellular carcinoma (HCC) cases. The study focused on determination of the genotypes of GST omega genes (GSTO1 and GSTO2) and GST activity and liver function tests. Results: The results showed that GSTO1 (A/A) was decreased in N, A, CH, CI and HCC groups compared to the C-group, while, GSTO1 (C/A) and GSTO1(C/C) genotypes were increased significantly in N, A, CH, CI and HCC groups. GSTO2 (A/A) was decreased in all studied groups as compared to the C-group but GSTO2(A/G) and GSTO2(G/G) genotypes were increased significantly. In addition, GST activities, albumin and TP levels were decreased in all studied groups compared to the C-group, while the activities of transaminases were increased to differing degrees. Conclusions: The results indicate that GSTO genetic polymorphisms may be considered as biomarkers for determining and predicting the progression of HBV infection.

• Nutrition Research and Practice
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• v.10 no.3
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• pp.265-273
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• 2016

BACKGROUND/OBJECTIVES: The inhibitory effect of Hijikia fusiforme (HF) extracts on degenerative osteoarthritis was examined in primary cultured rat cartilage cells and a monosodium iodoacetate (MIA)-induced osteoarthritis rat model. MATERIALS/METHODS: In vitro, cell survival and the expression of matrix metalloproteinases (MMPs), collagen type I, collagen type II, aggrecan, and tissue inhibitor of metalloproteinases (TIMPs) was measured after $H_2O_2$ ($800{\mu}M$, 2 hr) treatment in primary chondrocytes. In vivo animal study, osteoarthritis was induced by intra-articular injection of MIA into knee joints of rats, and then RH500, HFE250 and HFE500 were administered orally once a day for 28 days. To determine the anti-inflammatory effects of HFE, nitric oxide (NO), prostaglandin $E_2$ ($PGE_2$) expression were measured. In addition, real-time PCR was performed to measure the genetic expression of MMPs, collagen type I, collagen type II, aggrecan, and TIMPs. RESULTS: In the in vitro assay, cell survival after $H_2O_2$ treatment was increased by HFE extract (20% EtOH). In addition, anabolic factors (genetic expression of collagen type I, II, and aggrecan) were increased by HFE extract (20% EtOH). However, the genetic expression of MMP-3 and 7, known as catabolic factors were significantly inhibited by treatment with HFE extract (20% EtOH). In the in vivo assay, anabolic factors (genetic expression of collagen type I, II, aggrecan, and TIMPs) were increased by oral administration of HFE extract. However, the genetic expression of MMP-3 and 7, known as catabolic factors, and production of NO and $PGE_2$ were significantly inhibited by treatment with oral administration of HFE extract. CONCLUSION: HFE extract inhibited articular cartilage degeneration through preventing extracellular matrix degradation and chondrocyte injury.

• Journal of Ginseng Research
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• v.39 no.2
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• pp.141-147
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• 2015

Background: Adipocytes, which are the main cellular component of adipose tissue, are the building blocks of obesity. The nuclear hormone receptor $PPAR{\gamma}$ is a major regulator of adipocyte differentiation and development. Obesity, which is one of the most dangerous yet silent diseases of all time, is fast becoming a critical area of research focus. Methods: In this study, we initially aimed to investigate whether the ginsenoside Rf, a compound that is only present in Panax ginseng Meyer, interacts with $PPAR{\gamma}$ by molecular docking simulations. After we performed the docking simulation the result has been analyzed with several different software programs, including Discovery Studio, Pymol, Chimera, Ligplus, and Pose View. All of the programs identified the same mechanism of interaction between $PPAR{\gamma}$ and Rf, at the same active site. To determine the drug-like and biological activities of Rf, we calculate its absorption, distribution, metabolism, excretion, and toxic (ADMET) and prediction of activity spectra for substances (PASS) properties. Considering the results obtained from the computational investigations, the focus was on the in vitro experiments. Results: Because the docking simulations predicted the formation of structural bonds between Rf and $PPAR{\gamma}$, we also investigated whether any evidence for these bonds could be observed at the cellular level. These experiments revealed that Rf treatment of 3T3-L1 adipocytes downregulated the expression levels of $PPAR{\gamma}$ and perilipin, and also decreased the amount of lipid accumulated at different doses. Conclusion: The ginsenoside Rf appears to be promising compound that could prove useful in antiobesity treatments.

• Journal of Ginseng Research
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• v.39 no.4
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• pp.322-330
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• 2015

Background: UV-irradiated keratinocytes secrete various proinflammatory cytokines. UV-induced skin damage is mediated by growth factors and proinflammatory cytokines such as granulocyte macrophage colony stimulating factor (GM-CSF). In a previous study, we found that the saponin of Korean Red Ginseng (SKRG) decreased the expression of GM-CSF in UVB-irradiated SP-1 keratinocytes. In this study, we attempted to find the inhibitory mechanism of SKRG on UVB-induced GM-CSF expression in SP-1 keratinocytes. Methods: We investigated the inhibitory mechanism of SKRG and ginsenosides from Panax ginseng on UVB-induced GM-CSF expression in SP-1 keratinocytes. Results: Treatment with SKRG decreased the expression of GM-CSF mRNA and protein induced by irradiation of UVB in SP-1 keratinocytes. The phosphorylation of ERK was induced by UVB at 10 min, and decreased with SKRG treatment in SP-1 keratinocytes. In addition, treatment with SKRG inhibited the UVB-induced phosphorylation of epidermal growth factor receptor (EGFR), which is known to be an upstream signal of ERK. From these results, we found that the inhibition of GM-CSF expression by SKRG was derived from the decreased phosphorylation of EGFR. To identify the specific compound composing SKRG, we tested fifteen kinds of ginsenosides. Among these compounds, ginsenoside-Rh3 decreased the expression of GM-CSF protein and mRNA in SP-1 keratinocytes. Conclusion: Taken together, we found that treatment with SKRG decreased the phosphorylation of EGFR and ERK in UVB-irradiated SP-1 keratinocytes and subsequently inhibited the expression of GM-CSF. Furthermore, we identified ginsenoside-Rh3 as the active saponin in Korean Red Ginseng.

• Journal of Radiation Protection and Research
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• v.42 no.4
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• pp.212-221
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• 2017

Background: This study aims to calculate detector positions as a design of a radioactive source localizing radiation portal monitor (RPM) system using an improved genetic algorithm. Materials and Methods: To calculate of detector positions for a source localizing RPM system optimization problem is defined. To solve the problem, a modified iterative genetic algorithm (MIGA) is developed. In general, a genetic algorithm (GA) finds a globally optimal solution with a high probability, but it is not perfect at all times. To increase the probability to find globally optimal solution rather, a MIGA is designed by supplementing the iteration, competition, and verification with GA. For an optimization problem that is defined to find detector positions that maximizes differences of detector signals, a localization method is derived by modifying the inverse radiation transport model, and realistic parameter information is suggested. Results and Discussion: To compare the MIGA and GA, both algorithms are implemented in a MATLAB environment. The performance of the GA and MIGA and that of the procedures supplemented in the MIGA are analyzed by computer simulations. The results show that the iteration, competition, and verification procedures help to search for globally optimal solutions. Further, the MIGA is more robust against falling into local minima and finds a more reliably optimal result than the GA. Conclusion: The positions of the detectors on an RPM for radioactive source localization are optimized using the MIGA. To increase the contrast of the measurements from each detector, a relationship between the source and the detectors is derived by modifying the inverse transport model. Realistic parameters are utilized for accurate simulations. Furthermore, the MIGA is developed to achieve a reliable solution. By utilizing results of this study, an RPM for radioactive source localization has been designed and will be fabricated soon.