• Molecules and Cells
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• v.39 no.4
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• pp.316-321
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• 2016

The receptor activator of nuclear factor ${\kappa}B$ (RANK) and its ligand RANKL are key regulators of osteoclastogenesis and well-recognized targets in developing treatments for bone disorders associated with excessive bone resorption, such as osteoporosis. Our previous work on the structure of the RANK-RANKL complex revealed that Loop3 of RANK, specifically the non-canonical disulfide bond at the tip, performs a crucial role in specific recognition of RANKL. It also demonstrated that peptide mimics of Loop3 were capable of interfering with the function of RANKL in osteoclastogenesis. Here, we reported the structure-based design of a smaller peptide with enhanced inhibitory efficiency. The kinetic analysis and osteoclast differentiation assay showed that in addition to the sharp turn induced by the disulfide bond, two consecutive arginine residues were also important for binding to RANKL and inhibiting osteoclastogenesis. Docking and molecular dynamics simulations proposed the binding mode of the peptide to the RANKL trimer, showing that the arginine residues provide electrostatic interactions with RANKL and contribute to stabilizing the complex. These findings provided useful information for the rational design of therapeutics for bone diseases associated with RANK/RANKL function.

• Horticulture, Environment, and Biotechnology : HEB
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• v.59 no.6
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• pp.909-917
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• 2018

Quercetin and its glycoside derivatives were identified and quantified using high-performance liquid chromatograph (HPLC) and liquid chromatograph/mass spectrometer/mass spectrometer (LC/MS/MS) in the leaves, flowers, and fruits of 22 Malus genotypes. In all genotypes, small amounts of quercetin aglycone were present, with water-soluble glycoside forms were the most abundant in different Malus plant tissues, including quercetin-3-galactoside, quercetin-3-rutinoside, quercetin-3-glucoside, quercetin-3-xyloside, quercetin-3-arabinoside, and quercetin-3-rhamnoside. Among these six quercetin glycosides, quercetin-3-galactoside was the common form in Malus plants, except in the leaves and flowers of M. ceracifolia and M. magdeburgensis, and in the fruits of M. micromalus 'Haihong Fruit', where there was a higher concentration of quercetin3-glucoside. Among the different tissues tested, leaves contained the highest concentration of quercetin and its glycosides, while fruits contained the lowest concentrations of these compounds. Among the genotypes we analyzed, no specific genotype consistently contained the highest concentration of quercetin and its glycoside derivatives. M. domestica 'Honeycrisp' had the highest total compound concentration (approximately $1600mg\;kg^{-1}$), whereas M. hupehensis contained the lowest in its fruits. In contrast, the concentration of total quercetin and its glycosides was more than $5000mg\;kg^{-1}$ in the leaves of eight genotypes and greater than $2500mg\;kg^{-1}$ in the flowers of seven species. In general, the concentration of quercetin and its glycoside derivatives depended on the species and tissue type. These results may provide useful information for the evaluation and selection of edible Malus fruits and the materials for quercetin glycoside extraction.

• Journal of Ginseng Research
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• v.48 no.2
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• pp.229-235
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• 2024

Background: Plant health is directly related to the change in native microbial diversity and changes in soil health have been implicated as one of the main cause of root rot. However, scarce information is present regarding allelopathic relationship of Panax notoginseng root exudates and pathogenic fungi Fusarium oxysporum in a continuous cropping system. Methods: We analyzed P. notoginseng root exudate in the planting soil for three successive years to determine phenolic acid concentration using GC-MS and HPLC followed by effect on the microbial community assembly. Antioxidant enzymes were checked in the roots to confirm possible resistance in P. notoginseng. Results: Total 29 allelochemicals in the planting soil extract was found with highest concentration (10.54 %) of p-hydroxybenzoic acid. The HPLC showing a year-by-year decrease in p-hydroxybenzoic acid content in soil of different planting years, and an increase in population of F. oxysporum. Moreover, community analysis displayed negative correlation with 2.22 mmol. L^-1 of p-hydroxybenzoic acid correspond to an 18.1 % population of F. oxysporum. Furthermore, in vitro plate assay indicates that medium dose of p-hydroxybenzoic acid (2.5-5 mmol. L^-1) can stimulate the growth of F. oxysporum colonies and the production of macroconidia, as well as cell wall-degrading enzymes. We found that 2-3 mmol. L^-1 of p-hydroxybenzoic acid significantly increased the population of F. oxysporum. Conclusion: In conclusion, our study suggested that p-hydroxybenzoic acid have negative effect on the root system and modified the rhizosphere microbiome so that the host plant became more susceptible to root rot disease.

• Fisheries and Aquatic Sciences
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• v.27 no.2
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• pp.100-110
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• 2024

Biometric evaluation and reproductive biology of Oreochromis niloticus were studied from Geray Reservoir. Between November 2021 and August 2022, 316 O. niloticus specimens were collected from this reservoir. The observed male to female sex ratio was 1:1.14, which was statistically insignificant compared with the hypothetical 1:1 sex ratio (X² = 1.27, p > 0.05). The length-weight relationship was curvilinear with allometric growth (b < 3) and statistically significant from the expected isometric growth pattern (b = 3). The regression equation for females was TW = 0.0264TL^2.72 (r² = 0.90, n = 168), males (TW = 0.0183TL^2.79, r² = 0.93, n = 148), and combined sexes (TW = 0.0229TL^2.76, r² = 0.91, n = 316). Gonadosomatic index (GSI) ranged from 0.8 to 1.4 (males) and 1.8 to 4.9 (females). The breeding season lasted from March to June, with a GSI peak in April. Fecundity ranged from 279 to 1,528 eggs./fish, with a mean of 1,025 eggs./fish. The correlation between absolute fecundity and length was more significant (F = 0.76TL^2.8, R² = 0.94, p < 0.05) than with weight (F = 17.683TW^0.71, R² = 0.92, p < 0.05). This study provides basic information on the biology of O. niloticus in the Geray Reservoir for future fishery management tools for the conservation and utilization of this valuable freshwater fish.

• BMB Reports
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• v.43 no.2
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• pp.79-90
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• 2010

Mouse models are crucial for the functional annotation of human genome. Gene modification techniques including gene targeting and gene trap in mouse have provided powerful tools in the form of genetically engineered mice (GEM) for understanding the molecular pathogenesis of human diseases. Several international consortium and programs are under way to deliver mutations in every gene in mouse genome. The information from studying these GEM can be shared through international collaboration. However, there are many limitations in utility because not all human genes are knocked out in mouse and they are not yet phenotypically characterized by standardized ways which is required for sharing and evaluating data from GEM. The recent improvement in mouse genetics has now moved the bottleneck in mouse functional genomics from the production of GEM to the systematic mouse phenotype analysis of GEM. Enhanced, reproducible and comprehensive mouse phenotype analysis has thus emerged as a prerequisite for effectively engaging the phenotyping bottleneck. In this review, current information on systematic mouse phenotype analysis and an issue-oriented perspective will be provided.

• Bioinformatics and Biosystems
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• v.2 no.2
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• pp.46-51
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• 2007

In the proteomics research using mass spectrometry, the protein database search gives the protein information from the peptide sequences that show the best match with the tandem mass spectra. The protein sequence database has been a powerful knowledgebase for this protein identification. However, as we accumulate the protein sequence information in the database, the database size gets to be huge. Now it becomes hard to consider all the protein sequences in the database search because it consumes much computing time. For the high-throughput analysis of the proteome, usually we have used the non-redundant refined database such as IPI human database of European Bioinformatics Institute. While the non-redundant database can supply the search result in high speed, it misses the variation of the protein sequences. In this study, we have concerned the proteomics data in the point of protein similarities and used the network analysis tool to build a new analysis method. This method will be able to save the computing time for the database search and keep the sequence variation to catch the modified peptides.

• Korean journal of applied entomology
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• v.33 no.3
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• pp.153-158
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• 1994

Vegetation rather than soil types, is the predominant factor in determining density and distribution of Dreponotermes tarnminensis (Hill) mounds within the Durokoppin Nature Reserve m Westem Austral~an wheatbelt D tomminensis mounds reach the hlghest densities m Woodland (dominated by Eucalyptus cap~llosa) and Casuarina (dominated by Allocasuarino campestris) vegetation assoc~ations. There appears to be no influence of soil type on mound dishibut~on. although higher mound densities tend to be found on the Booraan soil type.

• Proceedings of the Zoological Society Korea Conference
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• 1997.10a
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• pp.42-57
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• 1997

The multicriterion matrix technique (MM-technique) was proposed for a method of monitoring and assessment about vegetation naturalness. Four criteria and 10 subcriteria were selected and two evaluation indices such as VN-value and VN-class were used. The criteria were characterized by syntaxonomical informations of hemeroby concept and potential natural vegetation, hierarchical system between criteria, and ordinal scale of VN-values. VN-values were classified into 11 ordinal levels and condensed to five VN-classes for facilitating practical use. A vegetation map of naturalness described by combination o( two indices was proposed as an alternative resolution of the DGN map. We also discuss the organization of the map content which is a matter of grid size (unit-area). In the case study, a grid size proper to show a full account of real information of actual vegetation is less 250-grid (250 $\times$ 250 $m^2$) in a medium size of city area containing relatively fragmented ecosystems. In conclusion, it was recognized that this new assessment technique was useful and vegetation assessment was accomplished with the smaller grid size in Korea.

• The Magazine of the IEIE
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• v.24 no.10
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• pp.63-72
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• 1997

Application of MEMS to biologic system mainly categorized into bio-electronics and micro-medical systems, Bio-electronics concerns on the biocompatible electronic device, in-vivo sensors, the sensors based on biological materials, biological materials for electronics and optics, the concepts and materials Inspired by biology and useful for electronics, the algorithm inspired by biology, artificial sense, and the biologic-inorganic hybrids. Micro-medical systems are utilited into the drug delivery systems, micro patient monitoring systems, micro prosthesis and artificial organs, cardiology related prothesis, analysis systems, and the minimal invasive surgery tools based on the m icrom achining technology.

• Korean Journal of Environmental Biology
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• v.23 no.2 s.58
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• pp.184-190
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• 2005

A taxonomic survey of the dinoflagellate family Prorocentraceae Stein was conducted on 17 locations off the coast of Korea. This monograph is the result of the microscopic analyses. A total of eight species have been identified and described, of which Prorocentrum concavum Fukuyo is new record for Korea.