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Kim M.K.,Seoul Womens University | Back C.-G.,National Institute of Horticultural and Herbal Science | Jung H.-Y.,Kyungpook National University | Srinivasan S.,Seoul Womens University
Journal of Biotechnology | Year: 2015

Spirosoma radiotolerans is a Gram-negative, short rod-shaped and gamma-radiation-resistant bacterium isolated from rice field in South Korea (GPS; 37°34'30″. N, 127°00'30″. E). The complete genome of S. radiotolerans consists of a chromosome (7,029,352. bp). From the genome sequence database, we have identified the cluster of genes responsible for DNA recovery from ionizing radiation. The key enzymes for the nucleotide excision repair (NER) were investigated and were identified, suggesting that S. radiotolerans DG5A use (NER) pathways for efficient removal of pyrimidine dimers which are the most abundant type of UV-induced damage. Complete genome information enables further studies on the DNA repair mechanisms during the ionizing radiation. © 2015 Elsevier B.V.


Kim S.,Chonnam National University | Yoon M.-K.,National Institute of Horticultural and Herbal Science
Current Genetics | Year: 2010

To study genetic relatedness of two male sterility-inducing cytotypes, the phylogenetic relationship among three cytotypes of onions (Allium cepa L.) was assessed by analyzing polymorphisms of the mitochondrial DNA organization and chloroplast sequences. The atp6 gene and a small open reading frame, orf22, did not differ between the normal and CMS-T cytotypes, but two SNPs and one 4-bp insertion were identified in CMS-S cytotype. Partial sequences of the chloroplast ycf2 gene were integrated in the upstream sequence of the cob gene via short repeat sequence-mediated recombination. However, this chloroplast DNA-integrated organization was detected only in CMS-S. Interestingly, disruption of a group II intron of cox2 was identified for the first time in this study. Like other trans-splicing group II introns in mitochondrial genomes, fragmentation of the intron occurred in domain IV. Two variants of each exon1 and exon2 flanking sequences were identified. The predominant types of four variants were identical in both the normal and the CMS-T cytotypes. These predominant types existed as sublimons in CMS-S cytotypes. Altogether, no differences were identified between normal and CMS-T, but significant differences in gene organization and nucleotide sequences were identified in CMS-S, suggesting recent origin of CMS-T male-sterility from the normal cytotype. © 2010 Springer-Verlag.


Kim J.G.,Gyeongsang National University | Kim H.L.,National Institute of Horticultural and Herbal Science | Kim S.J.,National Institute of Horticultural and Herbal Science | Park K.-S.,National Institute of Horticultural and Herbal Science
Journal of Zhejiang University: Science B | Year: 2013

Blueberry fruits from 45 commercial cultivars (39 northern highbush and 6 half highbush blueberry) grown in Suwon, Korea were analyzed for fruit size, soluble solids content, titratable acidity, total anthocyanin content, total phenolic content, and antioxidant activity. Fruit characteristics varied widely among the 45 blueberry cultivars. Fruit weight ranged from 0.9 to 3.6 g, soluble solids content from 8.3 to 14.3 Brix, and titratable acidity from 0.8% to 3.6%. Antioxidant activity ranged from 0.7 to 2.1 mg of quercetin equivalents per gram of fresh berries in different blueberry cultivars. Among the 45 blueberry cultivars, high amounts of anthocyanins and polyphenols, and high antioxidant activity were observed in 'Elliott', 'Rubel', 'Rancocas', and 'Friendship'. © 2013 Zhejiang University and Springer-Verlag Berlin Heidelberg.


Li X.,Chungnam National University | Ramchiary N.,Chungnam National University | Ramchiary N.,Gauhati University | Ramchiary N.,Jawaharlal Nehru University | And 6 more authors.
DNA Research | Year: 2013

Brassica rapa is an important crop species that produces vegetables, oilseed, and fodder. Although many studies reported quantitative trait loci (QTL) mapping, the genes governing most of its economically important traits are still unknown. In this study, we report QTL mapping for morphological and yield component traits in B. rapa and comparative map alignment between B. rapa, B. napus, B. juncea, and Arabidopsis thaliana to identify candidate genes and conserved QTL blocks between them. A total of 95 QTL were identified in different crucifer blocks of the B. rapa genome. Through synteny analysis with A. thaliana, B. rapa candidate genes and intronic and exonic single nucleotide polymorphisms in the parental lines were detected from whole genome resequenced data, a few of which were validated by mapping them to the QTL regions. Semi-quantitative reverse transcriptase PCR analysis showed differences in the expression levels of a few genes in parental lines. Comparative mapping identified five key major evolutionarily conserved crucifer blocks (R, J, F, E, and W) harbouring QTL for morphological and yield components traits between the A, B, and C subgenomes of B. rapa, B. juncea, and B. napus. The information of the identified candidate genes could be used for breeding B. rapa and other related Brassica species. © 2012 The Author. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.


Yang S.-O.,Chung - Ang University | Shin Y.-S.,National Institute of Horticultural and Herbal Science | Hyun S.-H.,Chung - Ang University | Cho S.,Chung - Ang University | And 4 more authors.
Journal of Pharmaceutical and Biomedical Analysis | Year: 2012

Ginseng is an important herbal resource worldwide, and the adulteration or falsification of cultivation age has been a serious problem in the commercial market. In this study, ginseng (Panax ginseng) roots, which were cultivated for 2-6years under GAP standard guidelines, were analyzed by NMR-based metabolomic techniques using two solvents. At first, ginseng root samples were extracted with 50% methanol, and analyzed by NMR with D 2O as the NMR dissolution solvent. The 2-, 3-, 4-, and 5/6-year-old ginseng root samples were separated in PLS-DA-derived score plots. However, 5- and 6-year-old ginseng roots were not separated by the solvent system. Therefore, various solvents were tested to differentiate the 5- and 6-year-old ginseng root samples, and 100% methanol-d 4 was chosen as the direct extraction and NMR dissolution solvent. In the PLS model using data from the 100% methanol-d 4 solvent, 5- and 6-year-old ginseng roots were clearly separated, and the model was validated using internal and external data sets. The obtained RMSEE and RMSEP values suggested that the PLS model has strong predictability for discriminating the age of 5- and 6-years-old ginseng roots. The present study suggests that the age of ginseng could be successfully predicted using two solvents, and the developed method in this study can be used as a standard protocol for discriminating and predicting the ages of ginseng root samples. © 2011 Elsevier B.V.


Sharma K.,Konkuk University | Assefa A.D.,Konkuk University | Kim S.,Konkuk University | Ko E.Y.,Konkuk University | And 2 more authors.
Journal of the Science of Food and Agriculture | Year: 2014

BACKGROUND: Onion is undoubtedly one of the major sources of flavonoids. However, there exists a varietal difference in composition, concentration and beneficial activities of onion, on the basis of cultivars, day length sensitivity/ripening and types. To characterise such differences, 18 onion cultivars from Korean were evaluated for their total phenolics, flavonoids and antioxidant activity. Simultaneous quantification of quercetin, quercetin-3,4'-O-diglucoside, quercetin-4'-O-monoglucoside and isorhamnetin-3-glucoside was made in methanol and 75% ethanol. RESULTS: Total phenolic content was examined spectrophotometrically with the Folin-Ciocalteu phenol reagent and total antioxidant activity were studied by the ferric reducing antioxidant power (FRAP) and diphenyl picryl hydrazyl (DPPH) methods. The cultivar 'Sunpower' showed the highest level of total phenolics [5016±30.0 μg gallic acid equivalents g-1 dry weight (DW)] and flavonoids (2873.95±60.01 μg Q g-1 DW) among the 18 cultivars in methanol. However, there were fewer total phenolics and flavonoids in ethanol extracts. The antioxidant activity for cultivar Sunpower was highest in ethanol extracts 24.12±1.00 and 16.13±0.35 μmol L-1 Trolox equivalents g-1 DW with FRAP and DPPH, respectively. CONCLUSION: Among the 18 cultivars, Sunpower is the most promising in terms of total phenolics, total flavonoids and antioxidant activity. Our results suggest that day length sensitivity/ripening among the cultivars do not play any significant role for high values of total phenolics, flavonoids and antioxidant activity. © 2013 Society of Chemical Industry.


Chun J.-A.,Dong - A University | Lee J.-W.,Dong - A University | Yi Y.-B.,Dong - A University | Hong S.-S.,National Institute of Horticultural and Herbal Science | Chung C.-H.,Dong - A University
Starch/Staerke | Year: 2010

Starch can be exploited as an abundant resource for sustainable production of diverse chemical intermediates such as hydroxymethylfurfural (HMF). We present a simple process of producing HMF from starches using an ionic liquid, 1-octyl-3-methylimidazolium chloride ([OMIM]Cl), and CrCl2 catalyst. The addition of HCl and CrCl2 significantly affected the yields of HMF on the whole. CrCl2 increased the yields of HMF by approximately two-folds on average. The synthesis of HMF was most effective between 60 and 90 min reaction time at both concentrations of 0.3 and 0.5 M HCl. Starch concentration had influence on the productivity of HMF. At 20% starch concentration with 0.3 and 0.5 M HCl, its productivity was greatest (2.8 folds high). Eight starch sources (corn, wheat, rice, potato tuber, sweet potato, tapioca, acorn, and kudzu starch) were tested for the synthesis of HMF. The highest yields of HMF (73.0 ± 3.8 wt%) were obtained in tapioca starch dissolved in 0.5 M HCl. © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Yoon J.-Y.,Seoul Womens University | Chung B.-N.,National Institute of Horticultural and Herbal Science | Choi G.-S.,National Institute of Horticultural and Herbal Science | Choi S.-K.,National Institute of Horticultural and Herbal Science
Virus Genes | Year: 2012

The variability in the nucleotide (nt) and amino acid (aa) sequences of the coat protein (CP) of Cymbidium mosaic virus (CymMV), which naturally infects orchids worldwide, was investigated. The CP genes of 55 CymMV isolates originating from different locations in Korea were amplified using RT-PCR and sequenced. The encoded CP consists of 223 aa. The CP sequences of the Korean isolates were compared with those of previously published Cym-MV isolates originating from different countries at both nt and aa levels. The Korean isolates shared 74.9-98.3 and 52.7-100% CP homology with CymMV isolates from other countries at the nt and aa levels, respectively. No particular region of variability could be found in either grouping of viruses. In the deduced CymMV CP aa sequence, the C-terminal region was more divergent than the N-terminal. The phylogenetic tree analysis based on nt sequence diversity of CP genes of CymMV isolates supported the hypothesis that CymMV isolates were divided into two subgroups. However, these subgroups were not formed by phylogenetic tree analysis of CP aa sequences. There was no distinct correlation between geographical locations and specific sequence identity, while recombination analysis revealed that there were no intra-specific recombination events among CymMV isolates. © Springer Science+Business Media, LLC 2011.


Ahn Y.K.,National Institute of Horticultural and Herbal Science | Park T.-H.,Daegu University
Acta Agriculturae Scandinavica Section B: Soil and Plant Science | Year: 2013

Potato is one of the most important crops in the world and the common scab caused by Streptomyces species is a serious disease. To control the disease, agronomical, chemical and biological methods are commonly applied; however, the introduction of resistance into cultivated potatoes has been considered to be the most promising approach. Therefore, in this study, the authors identified resistant breeding lines derived from somatic hybrids that were produced by protoplast fusions between Solanum brevidens and Solanum tuberosum. Initially, in vitro assay was applied to select resistant interspecific hybrids, but field assays were also performed to develop resistant breeding lines and populations. Although chromosome number and crossability were not completely recovered back to the cultivated potatoes on somatic hybrids and backcross populations, breeding lines and populations with resistance to common scab that could be used for further breeding were developed. Finally, four BC2 populations were selected and tested for resistance to the common scab and for productivity. There were variations in resistance to the common scab within each line and in productivity between lines, but the average percentages of tuber surface area with disease symptom in BC2 lines were approximately 85% and 46% less than the commercial parent controls, 'Dejiam' and 'Superior', respectively and the productivities of two populations recovered by 80-103% and 90-115% relative to 'Dejiam' and 'Superior', respectively. The results obtained in this study may contribute genetic analysis and further breeding for resistance to the common scab. © 2013 © 2013 Taylor & Francis.


Park M.-H.,National Institute of Horticultural and Herbal Science | Kim J.-G.,National Institute of Horticultural and Herbal Science
Postharvest Biology and Technology | Year: 2015

Ultraviolet (UV) irradiation is used to control postharvest diseases and delays deterioration related to the ripening of fresh produce. Here, we investigated the effect of UV-C on the quality and functional properties of peeled garlic during storage. UV-C-treated garlic cloves remained firmer than the controls during storage. After 15 days at room temperature, hue values were lower for UV-C-treated garlic cloves than for the controls, which developed a yellow coloration. We also found that aerobic microbial populations were lower in 2kJm-2 UV-C-treated garlic than in untreated controls when stored at room temperature for 15 days (6.78log CFU vs. 6.10log CFU); however, treated garlic stored at 0°C showed a one-log reduction in the microbial population after 30 days. In addition, total polyphenol and flavonoid content was high in 2kJm-2 UV-C-treated garlic after 15 days storage at 0°C and total flavonoid content was significantly higher in UV-treated cloves than in the control cloves up to 10 days storage at room temperature. Apigenin and quercetin levels also increased in UV-C treated garlic under cold storage. Thus, UV-C irradiation could be used to reduce the microbial population and maintain or increase antioxidant levels in peeled garlic cloves. © 2014.

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