• Genomics & Informatics
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• v.21 no.1
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• pp.7.1-7.11
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• 2023

The gram-positive bacterium Listeria monocytogenes is an important foodborne intracellular pathogen that is widespread in the environment. The functions of hypothetical proteins (HP) from various pathogenic bacteria have been successfully annotated using a variety of bioinformatics strategies. In this study, a HP Imo0888 (NP_464414.1) from the Listeria monocytogenes EGD-e strain was annotated using several bioinformatics tools. Various techniques, including CELLO, PSORTb, and SOSUIGramN, identified the candidate protein as cytoplasmic. Domain and motif analysis revealed that the target protein is a PemK/MazF-like toxin protein of the type II toxin-antitoxin system (TAS) which was consistent with BLASTp analysis. Through secondary structure analysis, we found the random coil to be the most frequent. The Alpha Fold 2 Protein Structure Prediction Database was used to determine the three-dimensional (3D) structure of the HP using the template structure of a type II TAS PemK/MazF family toxin protein (DB ID_AFDB: A0A4B9HQB9) with 99.1% sequence identity. Various quality evaluation tools, such as PROCHECK, ERRAT, Verify 3D, and QMEAN were used to validate the 3D structure. Following the YASARA energy minimization method, the target protein's 3D structure became more stable. The active site of the developed 3D structure was determined by the CASTp server. Most pathogens that harbor TAS create a crucial risk to human health. Our aim to annotate the HP Imo088 found in Listeria could offer a chance to understand bacterial pathogenicity and identify a number of potential targets for drug development.

• Genomics & Informatics
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• v.21 no.3
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• pp.42.1-42.23
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• 2023

Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, one of the most deadly infections in humans. The emergence of multidrug-resistant and extensively drug-resistant Mtb strains presents a global challenge. Mtb has shown resistance to many frontline antibiotics, including rifampicin, kanamycin, isoniazid, and capreomycin. The only licensed vaccine, Bacille Calmette-Guerin, does not efficiently protect against adult pulmonary tuberculosis. Therefore, it is urgently necessary to develop new vaccines to prevent infections caused by these strains. We used a subtractive proteomics approach on 23 virulent Mtb strains and identified a conserved membrane protein (MmpL4, NP_214964.1) as both a potential drug target and vaccine candidate. MmpL4 is a non-homologous essential protein in the host and is involved in the pathogen-specific pathway. Furthermore, MmpL4 shows no homology with anti-targets and has limited homology to human gut microflora, potentially reducing the likelihood of adverse effects and cross-reactivity if therapeutics specific to this protein are developed. Subsequently, we constructed a highly soluble, safe, antigenic, and stable multi-subunit vaccine from the MmpL4 protein using immunoinformatics. Molecular dynamics simulations revealed the stability of the vaccine-bound Tolllike receptor-4 complex on a nanosecond scale, and immune simulations indicated strong primary and secondary immune responses in the host. Therefore, our study identifies a new target that could expedite the design of effective therapeutics, and the designed vaccine should be validated. Future directions include an extensive molecular interaction analysis, in silico cloning, wet-lab experiments, and evaluation and comparison of the designed candidate as both a DNA vaccine and protein vaccine.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2022.09a
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• pp.51-51
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• 2022

Water dropwort (Oenanthe stolonifera DC.) is a perennial herbaceous plant that grows wild throughout Korea. As of 2020, 24,819 tons (51.7% of open field, 48.3% of facility) are produced in 1,278 ha (59.9% of open field, 40.1% of facility) nationwide. Water dropwort, which is rich in nutrients such as vitamins and iron, is mainly cultivated by vegetative propagation method using local traditional species, however, seed propagation and breeding of cultivars are insufficient so far. Since securing, propagating and continuous characterization of various genetic resources are required to breed new cultivars, this study was conducted to compare the main characteristics of domestic genetic resources and to improve their utilization. Growth characteristics such as plant height, fresh weight, plant type, and flowering date were investigated for the 89 varieties of genetic resources owned by Jeollabuk-do Agricultural Research and Extension Services after vegetative propagation in the individual pots. Also, the morphological image information of leaves and flowers was constructed. Genetic resources were collected nationwide and originated in 30 regions including Hwaseong, Siheung and Jeju. Their plant types could be classified into straight, intermediate and creeping types according to their morphological characteristics, and at this time, the number of intermediate types accounted for the largest proportion. Flowering was carried out under high-temperature and long-day conditions in summer. According to the flowering date, they could be classified into early, middle and late flowering varieties, and at this time, the middle flowering varieties occupied the largest proportion. As a result of the investigation of vegetative growth characteristics, varieties with long plant height, heavy fresh weight and thick stem thickness were identified. Along with this result, it is thought that classification and selection of genetic resources for various purposes will be possible through additional investigations such as analysis of components and antioxidant activity. Moreover, it is judged that such results can be used as basic data for breeding new water dropwort cultivars in the future.

• The Korean Society of Law and Medicine
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• v.18 no.1
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• pp.237-264
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• 2017

With the onset of the Human Genome Project, social concerns about 'genetic information discrimination' have been raised, but the problem has not yet been highlighted in Korea. However, non-medical institutions' genetic testing which is related to disease prevention could be partially allowed under the revised "Bioethics and Safety Act" from June 30, 2016. In the case of one domestic insurance company, DTC genetic testing was provided for the new customer of cancer insurance as a complimentary service, which made the social changes related to the recognition of the genetic testing. At a time when precision medicine is becoming a new standard for medical care, discipline on genetic information discrimination has become a problem that can not be delayed anymore. Article 46 and 67 of the Bioethics Act stipulate the prohibition of discrimination on grounds of genetic information and penalties for its violation. However, these broad principles alone can not solve the problems in specific genetic information utilization areas such as insurance and employment. The United States, Canada, the United Kingdom, and Germany have different regulations that prohibit genetic information based discrimination. In the United States, Genetic Information Non-Discrimination Act takes a form that adds to the existing law about the prohibition of genetic information discrimination. In addition, the range of genetic information includes the results of genetic tests of individuals and their families, including "family history". Canada has recently enacted legislation in 2017, expanding coverage to general transactions of goods or services in addition to insurance and employment. The United Kingdom deals only with 'predictive genetic testing results of individuals'. In the case of insurance, the UK government and Association of British Insurers (ABI) agree to abide by a policy framework ('Concordat') for cooperation that provides that insurers' use of genetic information is transparent, fair and subject to regular reviews; and remain committed to the voluntary Moratorium on insurers' use of predictive genetic test results until 1 November 2019, and a review of the Concordat in 2016. In the case of employment, The ICO's 'Employment Practices Code (2011)' is used as a guideline. In Germany, Human Genetic Examination Act(Gesetz ${\ddot{u}}ber$ genetische Untersuchungen bei Menschen) stipulates a principle ban on the demand for genetic testing and the submission of results in employment and insurance. The evaluation of the effectiveness of regulatory framework, as well as the form and scope of the discipline is different from country to country. In light of this, it would be desirable for the issue of genetic information discrimination in Korea to be addressed based on the review of related regulations, the participation of experts, and the cooperation of stakeholders.

• Proceedings of the Korea Society of Environmental Toocicology Conference
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• 1997.12a
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• pp.105-105
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• 1997

• Horticultural Science & Technology
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• v.33 no.5
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• pp.806-806
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• 2015

• Proceedings of the PSK Conference
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• 2001.10a
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• pp.219.2-219.2
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• 2001

• Proceedings of the Korean Society of Plant Pathology Conference
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• 1999.10a
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• pp.45.2-45
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• 1999

• Horticultural Science & Technology
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• v.31 no.6
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• pp.764-771
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• 2013

Recently, Cucumber mosaic virus (CMV)-P1 infection in pepper cultivation is very serious problem, which causes low marketability and yield. In this research, 56 domestic pepper cultivars including 20 PR (Phytophthora resistance) cultivars, 31 foreign pepper lines collected from USA and 112 genetic pepper resources form RDA Genebank were used for CMV-P1 resistance evaluation. Resistance evaluation was performed at 24 days and 51 days after artificial inoculation of peppers by enzyme-linked immunosorbent assay (ELISA). Among the 36 domestic cultivars 'Muhanjilju' were resistant to CMV-P1. All 20 PR cultivars and 29 foreign peppers except 'NuMex Twilight' and 'Chainese Giant' were susceptible. Among 112 pepper lines from RDA Genebank, nine pepper lines were resistant, and 17 pepper lines were moderately resistant, and 86 pepper lines were susceptible. Almost all domestic peppers on the market were highly susceptible to CMV-P1, whereas 17.2% of foreign pepper cultivars and genetic pepper lines from RDA Genebank were resistant or moderately resistant. Resistant pepper lines selected in this study can be used as genetic sources for breeding CMV-P1 resistant pepper.

• Journal of Korea Society of Industrial Information Systems
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• v.10 no.3
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• pp.21-29
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• 2005

The most of automated negotiation systems are dependent upon negotiators' offers, as negotiation is going on. Particularly, the preference, evaluation function and negotiation strategy are variously changed at every negotiation round by the negotiator and have an effect on the counter offers. Therefore, this study proposed the automated negotiation methodology or negotiation model which makes the negotiator's participation minimize. To minimize negotiator's participation, the preference of negotiator was predicted by the ratio of seller and buyer's count offers and the evaluation function of negotiator was also predicted by least squares approximation method at every negotiation round. The predicted evaluation function was evaluated and selected by $R^2$ value, coefficient of determination. Finally the optimal counter offers were generated by the genetic algorithm using the predicted preference and value function.