• Genomics & Informatics
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• v.17 no.3
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• pp.28.1-28.9
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• 2019

Bar-code (tag) microarrays of yeast gene-deletion collections facilitate the systematic identification of genes required for growth in any condition of interest. Anti-sense strands of amplified bar-codes hybridize with ~10,000 (5,000 each for up-and down-tags) different kinds of sense-strand probes on an array. In this study, we optimized the hybridization processes of an array for fission yeast. Compared to the first version of the array (11 ㎛, 100K) consisting of three sectors with probe pairs (perfect match and mismatch), the second version (11 ㎛, 48K) could represent ~10,000 up-/ down-tags in quadruplicate along with 1,508 negative controls in quadruplicate and a single set of 1,000 unique negative controls at random dispersed positions without mismatch pairs. For PCR, the optimal annealing temperature (maximizing yield and minimizing extra bands) was 58℃ for both tags. Intriguingly, up-tags required 3× higher amounts of blocking oligonucleotides than down-tags. A 1:1 mix ratio between up- and down-tags was satisfactory. A lower temperature (25℃) was optimal for cultivation instead of a normal temperature (30℃) because of extra temperature-sensitive mutants in a subset of the deletion library. Activation of frozen pooled cells for >1 day showed better resolution of intensity than no activation. A tag intensity analysis showed that tag(s) of 4,316 of the 4,526 strains tested were represented at least once; 3,706 strains were represented by both tags, 4,072 strains by up-tags only, and 3,950 strains by down-tags only. The results indicate that this microarray will be a powerful analytical platform for elucidating currently unknown gene functions.

• Journal of Life Science
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• v.17 no.1 s.81
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• pp.24-30
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• 2007

Inter simple sequence repeat (ISSR) markers were performed in order to analyse the genetic relation-ships of both taxa of Gardenia jasminoides var. radicans and G. jasminoides for. grandifora. Over the 88 fragments, only one locus (ISSR-11-05) was specific to G. jasminoides var. radicans and only one (ISSR-09-05) G. jasminoides for. grandiflora. Although G. jasminoides var. radicans showed low levels of alleles and Shannon's information index than G. jasminoides for. Grandiflora, however, there was not significant differences (p > 0.05). For both taxa the mean genetic diversity of natural populations was higher than that of cultivation populations. It was suggested that domestication processes via artificial selection do not have eroded the high levels of genetic diversity. ISSR markers were more effective in classifying natural populations of wild G. jasminoides in East Asia as well as cultivated G. jasminoides. The information about the phylogenetic relationship of G. jasminoides var. radicans and its closely related species is very valuable of the systematics of genus Gardenia, the origin of cultivated G. jasminoides, and future G. jasminoides breeding.

• Journal of Ginseng Research
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• v.44 no.2
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• pp.312-320
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• 2020

Background: Ginseng (Panax ginseng Meyer) is an essential source of pharmaceuticals and functional foods. Ginseng productivity has been compromised by high light (HL) stress, which is one of the major abiotic stresses during the ginseng cultivation period. The genetic improvement for HL tolerance in ginseng could be facilitated by analyzing its genetic and molecular characteristics associated with HL stress. Methods: Genome-wide analysis of gene expression was performed under HL and recovery conditions in 1-year-old Korean ginseng (P. ginseng cv. Chunpoong) using the Illumina HiSeq platform. After de novo assembly of transcripts, we performed expression profiling and identified differentially expressed genes (DEGs). Furthermore, putative functions of identified DEGs were explored using Gene Ontology terms and Kyoto Encyclopedia of Genes and Genome pathway enrichment analysis. Results: A total of 438 highly expressed DEGs in response to HL stress were identified and selected from 29,184 representative transcripts. Among the DEGs, 326 and 114 transcripts were upregulated and downregulated, respectively. Based on the functional analysis, most upregulated and a significant number of downregulated transcripts were related to stress responses and cellular metabolic processes, respectively. Conclusion: Transcriptome profiling could be a strategy to comprehensively elucidate the genetic and molecular mechanisms of HL tolerance and susceptibility. This study would provide a foundation for developing breeding and metabolic engineering strategies to improve the environmental stress tolerance of ginseng.

• Korean Journal of Agricultural and Forest Meteorology
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• v.3 no.1
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• pp.37-43
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• 2001

Crop status monitoring and yield prediction at higher spatial resolution is a valuable tool in various decision making processes including agricultural policy making by the national and local governments. A prototype crop forecasting system was developed to project the size of rice crop across geographic areas nationwide, based on daily weather pattern. The system consists of crop models and the input data for 1,455 cultivation zone units (the smallest administrative unit of local government in South Korea called "Myun") making up the coterminous South Korea. CERES-rice, a rice crop growth simulation model, was tuned to have genetic characteristics pertinent to domestic cultivars. Daily maximum/minimum temperature, solar radiation, and precipitation surface on 1km by 1km grid spacing were prepared by a spatial interpolation of 63 point observations from the Korea Meteorological Administration network. Spatial mean weather data were derived for each Myun and transformed to the model input format. Soil characteristics and management information at each Myun were available from the Rural Development Administration. The system was applied to the forecasting of national rice production for the recent 3 years (1997 to 1999). The model was run with the past weather data as of September 15 each year, which is about a month earlier than the actual harvest date. Simulated yields of 1,455 Myuns were grouped into 162 counties by acreage-weighted summation to enable the validation, since the official production statistics from the Ministry of Agriculture and Forestry is on the county basis. Forecast yields were less sensitive to the changes in annual climate than the reported yields and there was a relatively weak correlation between the forecast and the reported yields. However, the projected size of rice crop at each county, which was obtained by multiplication of the mean yield with the acreage, was close to the reported production with the $r^2$ values higher than 0.97 in all three years.

• Microbiology and Biotechnology Letters
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• v.16 no.6
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• pp.522-525
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• 1988

A method to produce tissue type Plasminogen Activator (tPA) from normal human fibroblast is developed by cultivating cells in serum free media containing heparin as an inducer. Optimal dose of this inducer was 30$\mu$g/m$\ell$. The composition of serum free medium was also defined to fit to the industrial scale cultivation. 1.42 ug of tPA per 10$^5$ viable cells per ml was produced. 1.1 gram of tPA can be produced every day from this cell line under normal perfusion chemostat operations assuming that same productivity is maintained when the process is sealed up. This method could reduce pro-duction costs and simplify purification processes by using serum free medium. Tissue type PA produced from this cell line has high ability of dissolving clots, based upon fibrin lysis test showing 50mm$^2$ of clearing zones in agarose gel plate. These results were reproducible and in good agreement with results of ELISA assay. tPA from normal human cells will be safer than that from melanoma and recombinant cells in human clinical trials.

• Horticultural Science & Technology
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• v.34 no.1
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• pp.32-45
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• 2016

Fruit bagging has been widely practiced in peach cultivation to produce high quality and unblemished fruit. Moreover, fruit bagging has been utilized to study the effect of shading on the quality of fruit. We conducted a proteomic analysis on peach fruit to elucidate the biochemical and physiological events that characterize the effect of bagging treatment. Comparative analysis of 2D electrophoresis (2-DE) gels showed that relative protein levels differed significantly at 125 DAFB (days after full bloom), as well as at 133 DAFB in fruit that had been bagged until 125 DAFB, followed by exposure to sunlight. Most of the proteins with altered expression were identified by MALDI TOF/TOF. Twenty-one proteins with differential expression among the groups were identified at 125 DAFB, while thirty proteins with differential expression among the groups were identified at 133 DAFB. The analysis revealed that expression of proteins involved in photosynthesis, stress responses, and biochemical processes influencing metabolism were altered during bagging treatment, suggesting that regulation of the synthesis of carbohydrates, amino acids, and proteins influenced fruit size, solid/acid ratio, and peel color. This work provides the first characterization of proteomic changes in peach in response to fruit bagging treatment. Identifying and tracking protein changes may allow us to better understand the mechanisms underlying the effects of bagging treatment.

• Smart Media Journal
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• v.7 no.3
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• pp.51-56
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• 2018

Banana is the eighth most important crop in the world designated by the United Nations Food and Agriculture Organization (FAO). In terms of production, it is the fourth most harvested crop following wheat, rice, and corn, considered to be a promising food source for mankind as it is not only scrumptious but also rich in nutrients. However, abnormal cultivation methods that mankind has invented to breed bananas is currently pushing them to the state of extinction. The aim of this study is to develop information-rich digital contents that can easily and intriguingly convey information about steadily but certainly increasing risk of banana extinction. The end-users are middle and high school students who are assumed to be aware of the agricultural revolution through their school curriculum. The linear storytelling method was meant to encourage the end-users to be interested in the causes and processes in which banana has become endangered. For generating a natural interaction between the content and the end-users, a parallel, upper-lower structure was used, in which the relationship between the stories comprising several stages and the information graphic supporting each story is represented. This paper can support an information campaign about the endangered species.

• Korean Journal of Medicinal Crop Science
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• v.28 no.6
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• pp.445-454
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• 2020

Background: Culturing wild ginseng adventitious root using plant factory technology provides genetic safety and high productivity. This production technology is drawing attention in the fields of functional raw materials and product development. The cultivation method using elicitors is key technology for controlling biomass and increasing secondary metabolites. Methods and Results: Elicitor treatments using methyl jasmonate, pyruvic acid, squalene, β-sistosterol were performed to amplify total ginsenosides (Rb1, Rc, Rb2, Rb3, and Rd) of cultured wild ginseng adventitious root. Thereafter, fermentation and steaming processes were performed to convert total ginsenosides into minor molecular ginsenosides (Rg3, Rk1, and Rg5). The result indicated that methyl jasmonate minimizes the reduction in fresh weight of cultured wild ginseng adventitious root and maximizes total ginsenosides (sum of Rb1, Rc, Rb2, Rb3, and Rd). Ginsenoside conversion results showed a maximum degree of conversion of 131 mg/g. Conclusions: In this study, we demonstrated that the optimal elicitor treatment method increased the content of total ginsenosides, while the steaming and fermentation processing method increased the content of minor ginsenosides.

• Journal of Ginseng Research
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• v.46 no.2
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• pp.225-234
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• 2022

Background: Ginseng, officially known as Panax ginseng Meyer, has been traditionally used as a medicinal herb, particularly in Asia. Ginseng is propagated from seeds; however, seed germination is challenging, especially in its natural environment on farms. The seeds typically exhibit morphophysiological dormancy and require release from both morphological and physiological dormancy before germination. Although some studies have proposed methods for increasing seed germination rates, the underlying mechanisms of its dormancy release process remain unclear. Here, we investigated metabolic alterations during dehiscence in P. ginseng to determine their potential roles in dormancy release. Methods: We compared the ginseng seed metabolome before and after dehiscence and the ginsenoside and phytosterol compositions of the seeds in both periods in the presence of related enzymes. Results: After seed dehiscence, the sugar, amino acid, and squalene concentrations were significantly altered, phytosterols associated with the stigmasterol biosynthesis pathway were increased, while ginsenoside and brassinosteroid levels were not significantly altered. In addition, squalene epoxidase, cycloartenol synthase, 24-methylenesterol C-methyltransferase, and the stigmasterol biosynthesis pathway were activated. Conclusion: Overall, our findings suggest that morphological activities that facilitate ginseng seed growth are the primary phenomena occurring during the dehiscence process. This study improves the understanding of P. ginseng germination processes and promotes further research of its germination and cultivation.

• Journal of Forest and Environmental Science
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• v.38 no.2
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• pp.75-89
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• 2022

The negative impact of monoculture rubber plantations on biodiversity and associated ecological processes/ecosystem services has led to suggestions on the use of integrated land use systems for rubber cultivation and production in order to ensure environmental sustainability. However, there is paucity of information on the effect of such integrated land use systems on the diversity and abundance of the rubber plantation undergrowth. We evaluated and compared undergrowth plant species composition, richness, abundance, diversity and interaction, in three integrated systems (Rubber-Strelitzia reginae Integrated System - RSrIS, Rubber-Podocarpus nagi Integrated System - RPnIS & Naturally Managed Rubber Plantation - NMRP) with three Rubber Monoculture Plantations (RMP₁, RMP₂ & RMP₃) adjacent to the integrated systems, respectively, at the Investigation and Experiment Station of Tropical Crops, Danzhou, Hainan, China. Undergrowth species density was higher in the rubber monocultures than in the integrated systems except in RSrIS. Species richness and diversity were also higher in the monocultures except in NMRP. Species similarity/interaction between the monocultures and the integrated systems was highest between RMP₃ and NMRP. The NRMP proved to be the best model of natural rubber integrated system for the conservation of undergrowth species richness, diversity and interspecific interaction. However, the conservation of undergrowth species in other forms of integrated natural systems can be enhanced by considering the ecology of species to be integrated in terms of their growth characteristics, competitive nature, and ability to grow in association with other species.