• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.66-72
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• 2003

Toxicogenomics is now emerging as one of the most important genomics application because the toxicity test based on gene expression profiles is expected more precise and efficient than current histopathological approach in pre-clinical phase. One of the challenging points in Toxicogenomics is the construction of intelligent database management system which can deal with very heterogeneous and complex data from many different experimental and information sources. Here we present a new Toxicogenomics database developed as a part of 'Toxicogenomics for Efficient Safety Test (TEST) project'. The TEST database is especially focused on the connectivity of heterogeneous data and intelligent query system which enables users to get inspiration from the complex data sets. The database deals with four kinds of information; compound information, histopathological information, gene expression information, and annotation information. Currently, TEST database has Toxicogenomics information fer 12 molecules with 4 efficacy classes; anti cancer, antibiotic, hypotension, and gastric ulcer. Users can easily access all kinds of detailed information about there compounds and simultaneously, users can also check the confidence of retrieved information by browsing the quality of experimental data and toxicity grade of gene generated from our toxicology annotation system. Intelligent query system is designed for multiple comparisons of experimental data because the comparison of experimental data according to histopathological toxicity, compounds, efficacy, and individual variation is crucial to find common genetic characteristics .Our presented system can be a good information source for the study of toxicology mechanism in the genome-wide level and also can be utilized fur the design of toxicity test chip.

• BMB Reports
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• v.39 no.1
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• pp.76-83
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• 2006

Pyridoxine-5-P oxidase catalyses the terminal step in the biosynthesis of pyridoxal-S-P, the biologically active form of vitamin $B_6$ Which acts as an essential cofactor. Here, a human brain pyridoxine-5-P oxidase gene was fused with a gene fragment encoding the HIV-1 Tat protein transduction domain (RKKRRQRRR) in a bacterial expression vector to produce a genetic in-frame Tat-pyridoxine-5-P oxidase fusion protein. Expressed and purified Tat-pyridoxine-5-P oxidase fusion protein transduced efficiently into PC12 cells in a time- and dose-dependent manner when added exogenously to culture media. Once inside the cells, the transduced Tat-pyridoxine-5-P oxidase protein showed catalytic activity and was stable for 48 h. Moreover, the formation of pyridoxal-5-P was increased by adding exogenous Tat-pyridoxine-5-P oxidase to media pre-treated with the vitamin $B_6$ precursor pyridoxine. In addition, the intracellular concentration of pyridoxal-S-P was markedly increased when Tat-pyridoxal kinase was transduced together with Tat-pyridoxine-5-P oxidase into cells. These results suggest that the transduction of Tat-pyridoxine-5-P oxidase fusion protein presents a means of regulating the level of pyridoxal-5-P and of replenishing this enzyme in various neurological disorders related to vitamin $B_6$.

• The Plant Pathology Journal
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• v.24 no.2
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• pp.152-158
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• 2008

A peculiar virus-like disease of tomato showing yellow mosaic and necrotic spots on leaves and necrosis on veins, petioles and stems was observed at the Tomato Experimental Station (TES), Buyeo, Chungcheongnamdo, Korea. The disease incidence at TES fields ranged from 21 to 35% infecting different tomato cultivars. For this reason, to identify the virus infecting tomato and to characterize the virus based on biology, serology, cytology and at molecular level. Here, leaf samples were randomly collected from different infected tomato cultivars at TES fields and greenhouses and tested by ELISA using Pepper mottle virus (PePMoV) and Tomato mosaic virus (ToMV) antisera. Infected saps were mechanically inoculated in different host plants to test for pathogenicity, symptomatology and host ranges. Infected tissues and ultrathin sections were examined by electron microscopy. Finally, putative coat protein and 3'-untranslated region (CP/3'-UTR) fragment was amplified and cloned for sequence determination and analyzed its genetic relationship to existing PepMoV and PVY sequences at the Genbank. Results showed 69% of the samples were positive with PepMoV, 13% with ToMV and 19 % were doubly infected with PepMoV and ToMV. Symptoms greatly varied from different host plants inoculated with tomato leaf sap infected with PepMoV alone and discussed in detailed in this paper. Electron microscopy from infected tissues showed filamentous particles of 720-750nm in length, a typical morphology and size of PepMoV. In addition, cylindrical inclusion bodies, pinwheels, scrolls and laminates with masses of fibrillar inclusions were also found in ultrathin sections. Alignment of the sequences of the CP/3'-UTR revealed >96% sequence identity with PepMoV and only <61% with PVY. Taken together, all these evidences presented clearly indicated that the causal agent infecting tomato at TES was PepMoV and we designated this PepMoV infecting tomato as Tom-sd2 strain in this study.

• Microbiology and Biotechnology Letters
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• v.43 no.2
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• pp.134-141
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• 2015

An agarolytic marine bacterium (H9) was isolated from the coastal seawater of the West Sea, South Korea. The isolate, H9, was gram-negative and rod-shaped with a smooth surface and polar flagellum. Cells grew at 20-30℃, between pH 5.0 and 9.0, and in ASW-YP (Artificial Sea Water-Yeast extract, Peptone) media containing 1-5% (w/v) NaCl. The G+C content was 41.56 mol%. The predominant isoprenoid quinone in strain H9 was ubiquinone-8. The major fatty acids (>10%) were C_16:1ω7c (34.3%), C_16:0 (23.72%), and C_18:1ω7c (13.64%). Based on 16S rRNA gene sequencing, and biochemical and chemotaxonomic characterization, the strain was designated as Pseudoalteromonas sp. H9 (=KCTC23887). In liquid culture supplemented with 0.2% agar, the cell density and agarase activity reached a maximum level of OD = 4.32 (48 h) and OD = 3.87 (24 h), respectively. The optimum pH and temperature for the extracellular crude agarases of H9 were 7.0 and 40℃, respectively. Thin-layer chromatography analysis of the agarase hydrolysis products revealed that the crude agarases hydrolyze agarose into neoagarotetraose and neoagarohexaose. Therefore, the new agar-degrading strain, H9, can be applicable for the production of valuable neoagarooligosaccharides and for the complete degradation of agar in bio-industries.

• Microbiology and Biotechnology Letters
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• v.44 no.4
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• pp.550-556
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• 2016

Groundwater heat pump (GWHP) systems must consider phenomena such as clogging to improve system efficiency and maintenance. In this study, we evaluated the prokaryotic diversity in a boring slime sample obtained at a depth of 10 m, which represented an undisturbed sample not affected by aquifer drawdown. Bacteria belonging to the phyla Proteobacteria (20.8%), Acidobacteria (18.8%), Chloroflexi (16.9%), and Firmicutes (10.2%) were found. Additionally, 144 species were identified as belonging to the genus Koribacter. Archaeal phyla were detected including Thaumarchaeota (42.8%), Crenarchaeota (36.9%), and Euryarchaeota (17.4%) and the class level comprised the miscellaneous Crenarchaeota group (MCG), Finnish forest soil type B (FFSB), and Thermoplasmata, which collectively accounted for approximately 69.4% of the detected Archaea. Operational taxonomic units (OTUs) were analyzed to reveal 3,565 bacterial and 836 archaeal OTUs, with abundances of 7.81 and 6.68, and richnesses of 5.96E-4 and 2.86E-3, respectively. The distribution of the groundwater microbial community in the study area showed a higher proportion of non-classified or unidentified groups compared to typical communities in surface water and air. In addition, 135 (approx. 1.9%) reads were assigned to a bacterial candidate associated with clogging.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.21 no.7
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• pp.312-320
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• 2020

The objective of the study was to undertake a phylogenetic diversity census of ruminal archaea based on a meta-analysis of 16S rRNA gene sequences that were publicly available in the Ribosomal Database Project. A total of 8,416 sequences were retrieved from the Ribosomal Database Project (release 11, update 5) and included in the construction of a taxonomy tree. Species-level operational taxonomic units (OTUs) were analyzed at a 97% sequence similarity by using the QIIME program. Of the 8,416 sequences, 8,412 were classified into one of three phyla; however, the remaining four sequences could not be classified into a known phylum. The Euryarchaeota phylum was predominant and accounted for 99.8% of the archaeal sequences examined. Among the Euryarchaeota, 65.4% were assigned to Methanobrevibacter, followed by Methanosphaera (10.4%), Methanomassillicoccus (10.4%), Methanomicrobium (7.9%), Methanobacterium (1.9%), Methanimicrococcus (0.5%), Methanosarcina (0.1%), and Methanoculleus (0.1%). The 7,544 sequences that had been trimmed to the V2 and V3 regions clustered into 493 OTUs. Only 17 of those 493 OTUs were dominant groups and accounted for more than 1% of the 7,544 sequences. These results can help guide future research into the dominant ruminal methanogens that significantly contribute to methane emissions from ruminants, research that may lead to the development of anti-methanogenic compounds that inhibit these methanogens regardless of diet or animal species.

• Asian-Australasian Journal of Animal Sciences
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• v.13 no.10
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• pp.1359-1366
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• 2000

An experiment was carried out to study plasma levels of hormones and metabolites of crossbred Holstein cattle during late pregnancy (28 days pre partum), early lactation (30 days post partum), mid-lactation (120 days post partum) and late lactation (210 days post partum). Two breed types of Holstein $Friesian{\times}Red$ Sindhi (50:50 = 50%HF) and Holstein $Friesian{\times}Red$ Sindhi (87.5:12.5 = 87.5%HF) were divided into four groups of four animals each. Two groups of each breed were fed with either rice straw treated with 5% urea or pangola hay (Digitaria decumbens) as the source of roughage throughout the experiments. There were a substantial increases in the mean levels of total triiodothyronine ($T_3$), insulin and glucagon at the onset of lactation, and maintained in a high levels during lactation advance for all groups of experiments. The mean levels of prolactin and thyroxine ($T_4$) were not significantly different among groups of animals, but the plasma cortisol concentration was slightly higher in both groups of 50%HF in comparison with those of 87.5%HF animals. The mean levels of plasma growth hormone (GH) of both groups of 87.5%HF animals feeding on either hay or urea treated rice straw markedly rose in the early period of lactation and markedly reduced in mid- and late lactation. These changes were accompanied with changes of milk yield. In contrast to 50%HF animals, plasma GH levels were considerably higher in the late pregnant period than in the early period of lactation and it remained constant as its value at the early lactation throughout the experimental period. The high levels of both plasma progesterone and estradiol concentration significantly declined after parturition and remained low through lactating period. The plasma glucose level in the 50%HF animals feeding on either hay or urea treated rice straw was higher than the 87.5%HF animals in all periods of experiments. Changes in plasma FFA levels of both types of crossbred animals were depended on the endocrine status during late pregnancy and lactation. The levels of plasma FFA of 50%HF animals were significantly higher (p<0.05) than those of 87.5%HF animals during late pregnancy. Both plasma ${\beta}$-hydroxybutyrate and lactate concentrations were not affected by feeding on either hay or urea treated rice straw during late pregnancy and lactation. These data demonstrate that there were no differences in the physiological performances in the same crossbred animals fed either hay or urea treated rice straw. The 87.5%HF animal has the genetic potential for a high milk yield and homeorhetic adaptation for mammary function differed from 50%HF animals during periods of lactation. Altering lactation persistency in 87.5%HF is regulated mainly by chronically acting growth hormones through the period of lactation.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.11
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• pp.1537-1544
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• 2015

Meat and carcass quality attributes are of crucial importance influencing consumer preference and profitability in the pork industry. A set of 400 Berkshire pigs were collected from Dasan breeding farm, Namwon, Chonbuk province, Korea that were born between 2012 and 2013. To perform genome wide association studies (GWAS), eleven meat and carcass quality traits were considered, including carcass weight, backfat thickness, pH value after 24 hours (pH24), Commission Internationale de l'Eclairage lightness in meat color (CIE L), redness in meat color (CIE a), yellowness in meat color (CIE b), filtering, drip loss, heat loss, shear force and marbling score. All of the 400 animals were genotyped with the Porcine 62K SNP BeadChips (Illumina Inc., USA). A SAS general linear model procedure (SAS version 9.2) was used to pre-adjust the animal phenotypes before GWAS with sire and sex effects as fixed effects and slaughter age as a covariate. After fitting the fixed and covariate factors in the model, the residuals of the phenotype regressed on additive effects of each single nucleotide polymorphism (SNP) under a linear regression model (PLINK version 1.07). The significant SNPs after permutation testing at a chromosome-wise level were subjected to stepwise regression analysis to determine the best set of SNP markers. A total of 55 significant (p<0.05) SNPs or quantitative trait loci (QTL) were detected on various chromosomes. The QTLs explained from 5.06% to 8.28% of the total phenotypic variation of the traits. Some QTLs with pleiotropic effect were also identified. A pair of significant QTL for pH24 was also found to affect both CIE L and drip loss percentage. The significant QTL after characterization of the functional candidate genes on the QTL or around the QTL region may be effectively and efficiently used in marker assisted selection to achieve enhanced genetic improvement of the trait considered.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.2
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• pp.294-304
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• 2020

Objective: The study was conducted to evaluate the effects of the absorbent (a mixture of activated carbon and hydrated sodium calcium aluminosilicate) on growth performance, blood profiles and hepatic genes expression in broilers fed diets naturally contaminated with aflatoxin. Methods: A total of 1,200 one-day-old male chicks were randomly assigned to 6 treatments with 10 replicate cages per treatment. The dietary treatments were as follows: i) control (basal diets); ii) 50% contaminated corn; iii) 100% contaminated corn; iv) control+1% adsorbent; v) 50% contaminated corn+1% absorbent; vi) 100% contaminated corn+1% absorbent. Results: During d 1 to 21, feeding contaminated diets reduced (p<0.05) body weight (BW), average daily gain (ADG), and average daily feed intake (ADFI), but increased (p<0.05) feed-to-gain ratio (F/G). The absorbent supplementation increased (p<0.05) BW, ADG, and ADFI. There were interactions (p<0.05) in BW, ADG, and ADFI between contaminated corn and absorbent. Overall, birds fed 100% contaminated diets had lower (p<0.05) final BW and ADG, but higher (p<0.05) F/G compared to those fed control diets. The absorbent addition increased (p<0.05) serum albumin concentration on d 14 and 28 and total protein (TP) level on d 28, decreased (p<0.05) alanine transaminase activity on d 14 and activities of aspartate aminotransferase and alkaline phosphatase on d 28. Feeding contaminated diets reduced (p<0.05) hepatic TP content on d 28 and 42. The contaminated diets upregulated (p<0.05) expression of interleukin-6, catalase (CAT), and superoxide dismutase (SOD), but downregulated (p<0.05) glutathione S-transferase (GST) expression in liver. The absorbent supplementation increased (p<0.05) interleukin-1β, CAT, SOD, cytochrome P450 1A1 and GST expression in liver. There were interactions (p<0.05) in the expression of hepatic CAT, SOD, and GST between contaminated corn and absorbent. Conclusion: The results suggest that the naturally aflatoxin-contaminated corn depressed growth performance, while the adsorbent could partially attenuate the adverse effects of aflatoxin on growth performance, blood profiles and hepatic genes expression in broilers.

• Journal of Nutrition and Health
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• v.31 no.9
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• pp.1446-1456
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• 1998

Bones are important parts in sustaining the shape of the body, but they are also metabolic organs which undergo bone remodeling by constant bone resorption and formation. Osteoporosis, the typical metabolic bone disease, is characterized by a reduction in bone mineral density (BMD). Women more than men are at risk fir osteoporosis-related fractures, especially in the lumbar spine, wrist, and hip region. Risk of fracture depends on one's BMD, which open determined by the peak bone mass value achieved at skeletal maturity and followed by subsequent age-and menopause-related bone loss. Genetic and environmental factors are known to play a key role in bone metabolism and diet is considered as one of the important environmental factors. The purpose of the present study was to assess the status of BMD and bone mineral content(BMC) to clarify the relationships between dietary intakes and the risk of osteoporosis in adult women in Taegu. Subjects were 130 healthy females in between 20 and 69 years of age. BMD and BMC of the lumbar spine(venebrae L2-4) of the subjects were measured by dual energy X-ray absorptiometry. The average age of the subjects was 47.4${\pm}$11.7 years old, the average weight was 57.2${\pm}$8.4kg, the average age of menarche was 16.6${\pm}$1.9 years old and the average age of menopause was 48.4${\pm}$5.3 years old. The nutrient intakes of the subjects measured by the convenient method were generally lower than the level of RDA. The result of nutrient intake assessed has shown that the average energy intake was 1701${\pm}$316kca1 which is 85.1% of the RDA and the average calcium intake was 485.4${\pm}$172.3mg which is 69.3% of the RDA. The intakes of protein, vitamin A, vitamin B$_1$, niacin were greater than the RDA, whereas the remaining nutrient intakes were lower than the RDA. The average BMD of the subjects was shown to be 1.06${\pm}$1.09g/$\textrm{cm}^2$. The highest BMD of 1.24${\pm}$0.14g/$\textrm{cm}^2$ was noticed in the subjects of 30s compared to 20s, 40s, 50s, 60s. The BMD values were compared by the relative body weight(R3W) of the menopause subjects, and it was found that the underweight group had significant lower BMB while the rest of the groups did not have any differences in BMD. The most strongly correlated nutrient with BMD among the menopause subjects appeared to be calcium. The women whose Ca intakes were higher than 500mg showed the significantly higher BMD than those with Ca intakes lower than 500mg. This study suggests that the most effective way to prevent osteoporosis and to reduce the incidences of fractures seems to be minimizing bone loss through the adequate intake of calcium as well as avoiding underweight, especially in menopausal women. (Korean J Nutrition 31(9) . 1446-1456, 1998)