• Asian Pacific Journal of Cancer Prevention
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• v.16 no.13
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• pp.5211-5217
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• 2015

Background: We earlier used PCR-dHPLC for mutation analysis of BRCA1 and BRCA2. In this article we report application of targeted resequencing of 30 genes involved in hereditary cancers. Materials and Methods: A total of 91 patient samples were analysed using a panel of 30 genes in the Illumina HiScan SQ system. CLCBio was used for mapping reads to the reference sequences as well as for quality-based variant detection. All the deleterious mutations were then reconfirmed using Sanger sequencing. Kaplan Meier analysis was conducted to assess the effect of deleterious mutations on disease free and overall survival. Results: Seventy four of the 91 samples had been run earlier using the PCR-dHPLC and no deleterious mutations had been detected while 17 samples were tested for the first time. A total of 24 deleterious mutations were detected, 11 in BRCA1, 4 in BRCA2, 5 in p53, one each in RAD50, RAD52, ATM and TP53BP1. Some 19 deleterious mutations were seen in patients who had been tested earlier with PCR-dHPLC [19/74] and 5/17 in the samples tested for the first time, Together with our earlier detected 21 deleterious mutations in BRCA1 and BRCA2, we now had 45 mutations in 44 patients. BRCA1c.68_69delAG;p.Glu23ValfsX16 mutation was the most common, seen in 10/44 patients. Kaplan Meier survival analysis did not show any difference in disease free and overall survival in the patients with and without deleterious mutations. Conclusions: The NGS platform is more sensitive and cost effective in detecting mutations in genes involved in hereditary breast and/or ovarian cancers.

• Journal of Biosystems Engineering
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• v.41 no.3
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• pp.208-220
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• 2016

Purpose: Fusel oil is a potent volatile aroma compound found in many alcoholic beverages. At low concentrations, it makes an essential contribution to the flavor and aroma of fermented alcoholic beverages, while at high concentrations, it induced an off-flavor and is thought to cause undesirable side effects. In this work, we introduce Fourier transform near-infrared (FT-NIR) spectroscopy as a rapid and nondestructive technique for the quantitative determination of fusel oil in the Korean alcoholic beverage "soju". Methods: FT-NIR transmittance spectra in the 1000-2500 nm region were collected for 120 soju samples with fusel oil concentrations ranging from 0 to 1400 ppm. The calibration and validation data sets were designed using data from 75 and 45 samples, respectively. The net analyte signal (NAS) was used as a preprocessing method before the application of the partial least-square regression (PLSR) and principal component regression (PCR) methods for predicting fusel oil concentration. A novel variable selection method was adopted to determine the most informative spectral variables to minimize the effect of nonmodeled interferences. Finally, the efficiency of the developed technique was evaluated with two different validation sets. Results: The results revealed that the NAS-PLSR model with selected variables ($R^2_{\upsilon}=0.95$, RMSEV = 100ppm) did not outperform the NAS-PCR model (($R^2_{\upsilon}=0.97$, RMSEV = 7 8.9ppm). In addition, the NAS-PCR shows a better recovery for validation set 2 and a lower relative error for validation set 3 than the NAS-PLSR model. Conclusion: The experimental results indicate that the proposed technique could be an alternative to conventional methods for the quantitative determination of fusel oil in alcoholic beverages and has the potential for use in in-line process control.

• Molecules and Cells
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• v.23 no.2
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• pp.192-197
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• 2007

Bulb color in onions (Allium cepa) is an important trait whose complex inheritance mechanism involves epistatic interactions among major color-related loci. Recent studies revealed that inactivation of dihydroflavonol 4-reductase (DFR) in the anthocyanin synthesis pathway was responsible for the color differences between yellow and red onions, and two recessive alleles of the anthocyanidin synthase (ANS) gene were responsible for a pink bulb color. Based on mutations in the recessive alleles of these two genes, PCR-based markers for allelic selection were developed. In this study, genotype analysis of onions from segregating populations was carried out using these PCR-based markers. Segregating populations were derived from the cross between yellow and red onions. Five yellow and thirteen pink bulbs from one segregating breeding line were genotyped for the two genes. Four pink bulbs were heterozygous for the DFR gene, which explains the continuous segregation of yellow and pink colors in this line. Most pink onions were homozygous recessive for the ANS gene, except for two heterozygotes. This finding indicated that the homozygous recessive ANS gene was primarily responsible for the pink color in this line. The two pink onions, heterozygous for the ANS gene, were also heterozygous for the DFR gene, which indicated that the pink color was produced by incomplete dominance of a red color gene over that of yellow. One pink line and six other segregating breeding lines were also analyzed. The genotyping results matched perfectly with phenotypic color segregation.

• Journal of the Korean Chemical Society
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• v.46 no.4
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• pp.309-317
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• 2002

A spectrofluorimetric method for the simultaneous determination of amino acids (tryptophan and tyrosine) based on the application of multivariate calibration method such as principal component regression and partial least squares (PLS) to luminescence measurements has been studied. Emission spectra of synthetic mixtures of two amino acids were obtained at excitation wavelength of 257 ㎚. The calibration model in PCR and PLS was obtained from the spectral data in the range of 280-500 ㎚ for each standard of a calibration set of 32 standards, each containing different amounts of two amino acids. The relative standard error of prediction ($RSEP_a$) was obtained to assess the model goodness in quantifying each analyte in a validation set. The overall relative standard error of prediction ($RSEP_m$) for the mixture obtained from the results of a validation set, formed by 6 independent mixtures was also used to validate the present method.

• Journal of Sericultural and Entomological Science
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• v.50 no.2
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• pp.122-125
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• 2012

This study was aimed for a development of a useful gene promoter which has a transcript expressional specificity in the early embryonic period of the silkworm, Bombyx mori. To select a useful gene expressed in the early embryonic stage, we constructed and analyzed a PCR-base subtraction cDNA library. In subtractive hybridization analysis, we confirmed four clones as differently expressed genes(BmNanos-like, BmNanos-P, BmNanos-O, BmVasa mRNAs). Northern hybridization and real time PCR results reveled that the BmNanos-like gene promoter is suitable for the silkworm transgenic vector system. Further defined studies on molecular functions and biological roles of their promoters will give us well-fined information and its application.

• Microbiology and Biotechnology Letters
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• v.49 no.3
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• pp.305-315
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• 2021

The cotton leafworm, Spodoptera littoralis, is a major pest in Egypt and many countries worldwide, and causes heavy economic losses. As a result, management measures to control the spread of the worm are required. S. littoralis nucleopolyhedrovirus (SpliNPV) is one of the most promising bioagents for the efficient control of insect pests. In this study, a chitinase gene (chitA) of a 1.8 kb DNA fragment was cloned and fully characterized from SpliNPV-EG1, an Egyptian isolate. A sequence of 601 amino acids was deduced when the gene was completely sequenced with a predicted molecular mass of 67 kDa for the preprotein. Transcriptional analyses using reverse transcription polymerase chain reaction (RT-PCR) revealed that chitA transcripts were detected first at 12 h post infection (hpi) and remained detectable until 168 hpi, suggesting their transcriptional regulation from a putative late promoter motif. In addition, quantitative analysis using quantitative RT-PCR showed a steady increase of 7.86-fold at 12 hpi in chitA transcription levels, which increased up to 71.4-fold at 120 hpi. An approximately 50 kDa protein fragment with chitinolytic activity was purified from ChitA-induced bacterial culture and detected by western blotting with an anti-recombinant SpliNPV chitinase antibody. Moreover, purification of the expressed ChitA recombinant protein showed in vitro growth inhibition of two different fungi species, Fusarium solani and F. oxysporum, confirming that the enzyme assembly and activity was correct. The results supported the potential role and application of the SpliNPV-ChitA protein as a synergistic agent in agricultural fungal and pest control programs.

• Mycobiology
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• v.47 no.1
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• pp.59-65
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• 2019

Agrobacterium tumefaciens-mediated transformation (ATMT), as a simple and versatile method, achieves successful transformation in the yeast-like cells (YLCs) of Tremella fuciformis with lower efficiency. Establishment of a more efficient transformation system of YLCs is important for functional genomics research and biotechnological application. In this study, an enzymolysis-assisted ATMT method was developed. The degradation degree of YLCs depends on the concentration and digestion time of Lywallzyme. Lower concentration (${\leq}0.1%$) of Lywallzyme was capable of formation of limited wounds on the surface of YLCs and has less influence on their growth. In addition, there is no significant difference of YLCs growth among groups treated with 0.1% Lywallzyme for different time. The binary vector pGEH under the control of T. fuciformis glyceraldehyde-3-phosphate dehydrogenase gene (gpd) promoter was utilized to transform the enzymolytic wounded YLCs with different concentrations and digestion time. The results of PCR, Southern blot, quantitative real-time PCR (qRT-PCR) and fluorescence microscopy revealed that the T-DNA was integrated into the YLCs genome, suggesting an efficient enzymolysis-assisted ATMT method of YLCs was established. The highest transformation frequency reached 1200 transformants per $10^6$ YLCs by 0.05% (w/v) Lywallzyme digestion for 15 min, and the transformants were genetically stable. Compared with the mechanical wounding methods, enzymolytic wounding is thought to be a tender, safer and more effective method.

• Korean Journal of Veterinary Service
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• v.30 no.4
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• pp.557-562
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• 2007

This study was carried out to discriminate Hanwoo from the milking and hybrid cattle by detection of MC1R gene related to bovine hair color. One hundred sixty six samples were collected from the abattoir (n = 106) and local market (n = 60). The beef from abattoir were originated from Hanwoo (n=27), Holstein (n=29), Hybrid (n=45) and imported cattle (n=5), respectively. The beef from market consisted of Hanwoo (n=36), Holstein (n=7) and imported ones (n=17). Commercialized screening kit (Kogenebiotec, Korea) was used for MC1R gene analysis. As a result, Hanwoo was discriminated from Holstein. However, 9 of 45 hybrid and 11 of 22 imported beef samples were indistinguishable from Hanwoo. It could be explained by second generation of crossing of Hanwoo with Holstein or the cattle with silver or yellow hair. This results suggest that additional tests as well as MC1R gene detection be needed to confirm Hanwoo beef among cattle beef.

• Journal of Soil and Groundwater Environment
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• v.19 no.5
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• pp.9-17
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• 2014

This paper reported the use of real-time polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE), and the culture-based method in the intrinsic bioremediation study at a petroleum contaminated site. The study showed that phenol hydroxylase gene was detected in groundwater contaminated with benzene, toluene, ethylbenzene, xylene isomers (BTEX) and methyl tert-butyl ether (MTBE). This indicated that intrinsic bioremediation occurred at the site. DGGE analyses revealed that the petroleum-hydrocarbon plume caused the variation in microbial communities. MTBE degraders including Pseudomonas sp. NKNU01, Bacillus sp. NKNU01, Klebsiella sp. NKNU01, Enterobacter sp. NKNU01, and Enterobacter sp. NKNU02 were isolated from the contaminated groundwater using the cultured-based method. Among these five strains, Enterobacter sp. NKNU02 is the most effective stain at degrading MTBE without the addition of pentane. The MTBE biodegradation experiment indicated that the isolated bacteria were affected by propane. Biodegradation of MTBE was decreased but not totally inhibited in the mixtures of BTEX. Enterobacter sp. NKNU02 degraded about 60% of MTBE in the bioreactor study. Tert-butyl alcohol (TBA), acetic acid, 2-propanol, and propenoic acid were detected using gas chromatography/mass spectrometry during MTBE degraded by the rest cells of Enterobacter sp. NKNU02. The effectiveness of bioremediation of MTBE was assessed for potential field-scale application.

• Proceedings of the SCSK Conference
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• 2003.09a
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• pp.285-290
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• 2003

Living cells are continuously subject to all sorts of stress such as ultraviolet rays on skin cells. Tests made in various laboratories show that when young fibroblasts (Le. at the beginning of their proliferate life) were repeatedly put under stress at subletal doses, they acquired a phenotype similar to Senescence Induced Prematurely by Stress (SIPS). The work presented hereafter was made on a new model of senescence induced prematurely by stress from ultraviolet Brays (UVB). The human fibroblast model was put under repeated UVB stress, causing SIPS. Several ageing biomarkers were used in order to characterise the cells that underwent stress:. an increase in the proportion of positive cells with senescence associated $\beta$-galactosidase activity (SA $\beta$-gal) measured by a specific coloration,. the proportion in the different morphological stages that fibroblasts undergo during culture visualised by microscopic observation,. the expression of genes known for overexpressing during senescence, particularly fibronectin and apolipoprotein J, measured by Real Time-PCR,. the common deletion of 4,977 bp in mitochondrial DNA, evaluated by nested PCR. Studying the variation of these 4 biomarkers, we have evaluated the protective effect of a Laminaria digitata extract (LDE) that can be used as a natural active ingredient for anti-ageing cosmetics.