• 한국균학회소식:학술대회논문집
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• 2018.05a
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• pp.19-19
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• 2018

Fungal pathogens have huge impact on health and economic wellbeing of human by causing life-threatening mycoses in immune-compromised patients or by destroying crop plants. A key determinant of fungal pathogenesis is their ability to undergo developmental change in response to host or environmental factors. Genetic pathways that regulate such morphological transitions and adaptation are therefore extensively studied during the last few decades. Given that epigenetic as well as genetic components play pivotal roles in development of plants and mammals, contribution of microbial epigenetic counterparts to this morphogenetic process is intriguing yet nearly unappreciated question to date. To bridge this gap in our knowledge, we set out to investigate histone modifications among epigenetic mechanisms that possibly regulate fungal adaptation and processes involved in pathogenesis of a model plant pathogenic fungus, Magnaporthe oryzae. For functional and comparative analysis of histone modifications, a web-based database (dbHiMo) was constructed first to archive and analyze histone modifying enzymes from eukaryotic species whose genome sequences are available. Based on the database entries, we carried out functional analysis of genes encoding histone modifying enzymes. Here I provide examples of such analyses that show how histone acetylation and methylation is implicated in regulating important aspects of fungal pathogenesis. Current analysis of histone modifying enzymes is followed by ChIP-seq and RNA-seq experiments to pinpoint the genes that are controlled by particular histone modifications. We anticipate that our work will provide not only the significant advances in our understanding of epigenetic mechanisms operating in microbial eukaryotes but also basis to expand our perspective on regulation of development in fungal pathogens.

• Mycobiology
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• v.48 no.5
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• pp.373-382
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• 2020

Laccases (EC 1.10.3.2), a group of multi-copper oxidases (MCOs), play multiple biological functions and widely exist in many species. Fungal laccases have been extensively studied for their industrial applications, however, there was no database specially focused on fungal laccases. To provide a comparative genomics platform for fungal laccases, we have developed a comparative genomics platform for laccases and MCOs (http://laccase.riceblast.snu.ac. kr/). Based on protein domain profiles of characterized sequences, 3,571 laccases were predicted from 690 genomes including 253 fungi. The number of putative laccases and their properties exhibited dynamic distribution across the taxonomy. A total of 505 laccases from 68 genomes were selected and subjected to phylogenetic analysis. As a result, four clades comprised of nine subclades were phylogenetically grouped by their putative functions and analyzed at the sequence level. Our work would provide a workbench for putative laccases mainly focused on the fungal kingdom as well as a new perspective in the identification and classification of putative laccases and MCOs.

• Nuclear Engineering and Technology
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• v.53 no.4
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• pp.1199-1209
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• 2021

The detection of unexpected loose parts in the primary coolant system in a nuclear power plant remains an extremely important issue. It is essential to develop a methodology for the localization and mass estimation of loose parts owing to the high prediction error of conventional methods. An effective approach is presented for the localization and mass estimation of a loose part using machine-learning and deep-learning algorithms. First, a methodology was developed to estimate both the impact location and the mass of a loose part at the same times in a real structure in which geometric changes exist. Second, an impact database was constructed through a series of impact finite-element analyses (FEAs). Then, impact parameter prediction modes were generated for localization and mass estimation of a simulated metallic loose part using machine-learning algorithms (artificial neural network, Gaussian process, and support vector machine) and a deep-learning algorithm (convolutional neural network). The usefulness of the methodology was validated through blind tests, and the noise effect of the training data was also investigated. The high performance obtained in this study shows that the proposed methodology using an FEA-based database and deep learning is useful for localization and mass estimation of loose parts on site.

• Mass Spectrometry Letters
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• v.13 no.4
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• pp.106-114
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• 2022

A rapid and reliable approach to the identification of microorganisms is a critical requirement for large-scale culturomics analysis. MALDI-TOF MS is a suitable technique that can be a better alternative to conventional biochemical and gene sequencing methods as it is economical both in terms of cost and labor. In this review, the applications of MALDI-TOF MS for the comprehensive identification of microorganisms and bacterial strain typing for culturomics-based approaches for various environmental studies including bioremediation, plant sciences, agriculture and food microbiology have been widely explored. However, the restriction of this technique is attributed to insufficient coverage of the mass spectral database. To improve the applications of this technique for the identification of novel isolates, the spectral database should be updated with the peptide mass fingerprint (PMF) of type strains with not only microbes with clinical relevance but also from various environmental sources. Further, the development of enhanced sample processing methods and new algorithms for automation and de-replication of isolates will increase its application in microbial ecology studies.

• Journal of Ocean Engineering and Technology
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• v.35 no.3
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• pp.173-182
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• 2021

The maneuvering performance of a ship on the actual sea is very different from that in calm water due to wave-induced motion. Enhancement of a ship's maneuverability in waves at the design stage is an important way to ensure that the ship navigates safely. This paper focuses on the maneuvering prediction of a Russian trawler in wind and irregular waves. First, a unified seakeeping and maneuvering analysis of a Russian trawler is proposed. The hydrodynamic forces acting on the hull in calm water were estimated using empirical formulas based on a database containing information on several fishing vessels. A simulation of the standard maneuvering of the Russian trawler was conducted in calm water, which was checked using the International Maritime Organization (IMO) standards for ship maneuvering. Second, a unified model of seakeeping and maneuvering that considers the effect of wind and waves is proposed. The wave forces were estimated by a three-dimensional (3D) panel program (ANSYS-AQWA) and used as a database when simulating the ship maneuvering in wind and irregular waves. The wind forces and moments acting on the Russian trawler are estimated using empirical formulas based on a database of wind-tunnel test results. Third, standard maneuvering of a Russian trawler was conducted in various directions under wind and irregular wave conditions. Finally, the influence of wind and wave directions on the drifting distance and drifting angle of the ship as it turns in a circle was found. North wind has a dominant influence on the turning trajectory of the trawler.

• Herbal Formula Science
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• v.31 no.3
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• pp.171-182
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• 2023

Objectives : Saposhnikoviae Radix (SR) and Glehniae Radix (GR) have been frequently used in traditional medicine to treat diseases related to 'wind' syndrome, but there have been cases where it has been mixed in a state where the plant of origin is not clear. In this study, to select materials for conducting preclinical cerebral infarction research, the network pharmacology analysis method was used to select suitable medicinal materials for the study. Methods : In this study, a Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) based network pharmacology analysis method was used, and oral bioavailability (OB), drug likeness (DL), Caco-2 and BBB permeability were utilized to select compounds with potential activity. For the values of each variable used in this study, OB ≥ 20%, DL ≥ 0.18, Caco-2 ≥ 0, and BBB ≥ -0.3 were applied, then networks of bioactive compounds, target proteins, and target diseases was constructed. STRING database was used to construct a protein-protein interaction network. Results : It was confirmed that SR rather than GR has various target proteins and target diseases based on network pharmacological analysis using TCMSP database. And it was analyzed that the bioactive compounds only in SR act more on neurovascular diseases, and both drugs are expected to be effectively used for cardiovascular diseases. Conclusions : In our future study, SR will be used in an ischemic stroke mouse model, and the mechanism of action will be explored focusing on apoptosis and cell proliferation.

• Journal of the Korean Society of Environmental Restoration Technology
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• v.2 no.1
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• pp.48-57
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• 1999

This study was aimed to establish biotop unit of the mixed rural city for the method and process of the biotop mapping system. Survey site was Maejuri of Seunghwan(158ha), Gisanri of Mokchon(132ha) and Namkwanri, Pungsemeon(214ha). So the main process was divided by 4 schemes such as Biosphere, Geosphere, Antrosphere and Evaluation. Also the GIS(geographic information system) was used to make the database of the biotop and biotop complex, analyze the cross-combinations and analyze the characters of the biotop. Biotop mapping system had 5 steps which were proceeded with research goals, constructing the spatial database and attribute database, classifying the 3 types of biotop such as tree/shrub biotop, grass biotop and wetland biotop, cross-analyzing 3 biotop types with land use, habitat characters, relief characters and danger/disturbance elements and evaluating the 3 types of biotop. The results of applicating the biotop mapping system on the research site as followings : The distributions of the land uses in Maejuri, Seunghwan eup in Chonan city were recorded by forest(29.8%), orchard(14.1%) and landscaping around building site(9.0%). Gisanri, Mokchonmeon were composed of forest(64.5%), farm(12.8%) and Namkwanri, Pungsemeon were concentrated rice field(39.6%), dwell district(22.4%). The Tree/Shrub biotop type was reclassed by the forest type, natural and artificial decidous type with natural coniferous. The Grass biotop type was reclassed by the wild grassland type, garden type and peddy field with wild grassland. The distributions of the wet land were pointed high at the wet land type with reed marsh and edge vegetation around wet land in reservoir and river. The evaluation of the mapped bitopes was completed to the following aspect, "amenity" and "environmental education". A high value of 7.13%(1 class) was shown Maejuri, Seunghwan eup. The regions which were studied synthetically are divided to three parts ; the area where have nature and art mixed(Seunghwan), the area which is more artificial because people inhabit there for a long time(Pungsemeon) and the area that ecological environment is threatened by development pressure(Mokchonmeon). Therefore, ecological restoration plan which depends on specific property of the regions should be established. Also the interdisplinary researches were needed to develop the BMS(Biotop Mapping System) in Korea because of the differences with Germany, England's ecological habitat conditions.

• Journal of Plant Biotechnology
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• v.44 no.4
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• pp.372-378
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• 2017

For comparison of the transcription profiles in apple (Malus domestica L.) cultivars differing in flesh color expression, two cDNA libraries were constructed. Differences in gene expression between red flesh apple cultivar, 'Redfield' and white flesh apple cultivar, 'Granny Smith' were investigated by next-generation sequencing (NGS). Expressed sequence tag (EST) of clones from the red flesh apple cultivar and white flesh apple cultivar were selected for nucleotide sequence determination and homology searches. High resolution melting (HRM) technique measures temperature induced strand separation of short PCR amplicons, and is able to detect variation as small as one base difference between red flesh apple cultivars and white flesh apple cultivars. We applied high resolution melting (HRM) analysis to discover single nucleotide polymorphisms (SNP) based on the predicted SNP information derived from the apple EST database. All 103 pairs of SNPs were discriminated, and the HRM profiles of amplicons were established. Putative SNPs were screened from the apple EST contigs by HRM analysis displayed specific difference between 10 red flesh apple cultivars and 11 white flesh apple cultivars. In this study, we report an efficient method to develop SNP markers from an EST database with HRM analysis in apple. These SNP markers could be useful for apple marker assisted breeding and provide a good reference for relevant research on molecular mechanisms of color variation in apple cultivars.

• Journal of Plant Biotechnology
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• v.45 no.4
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• pp.289-298
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• 2018

The Biosafety Division of the National Academy of Agricultural Science has developed a 'Crop Composition DB' that provides analytical data on commercialized crops. It can be used as a reference in the 'Comparative Evaluation by Compositional Analysis' for the safety assessment of genetically modified (GM) crops. This database provides the composition of crops cultivated in Korea, and thus upgrades the data to check the extent of changes in the compositional content depending on the cultivated area, varieties and year. The database is a compilation of data on the antioxidant, nutrient and secondary metabolite compositions of rice and capsicum grown in two or more cultivation areas for a period of more than two years. Data analysis was conducted under the guidelines of the Association of Official Analytical Chemists or methods previously reported on papers. The data was provided as average, minimum and maximum values to assess whether the statistical differences between the GM crops and comparative non-GM crops fall within the biological differences or tolerances of the existing commercial crops. The Crop Composition DB is an open-access source and is easy to access based on the query selected by the user. Moreover, functional ingredients of colored crops, such as potatoes, sweet potatoes and cauliflowers, were provided so that food information can be used and utilized by general consumers. This paper introduces the feature and usage of 'Crop Composition DB', which is a valuable tool for characterizing the composition of conventional crops.

• The Plant Pathology Journal
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• v.32 no.3
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• pp.201-208
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• 2016

The main areas for field-grown vegetable production in Iran were surveyed during the years of 2012-2014 to determine the occurrence of begomoviruses infecting these crops. A total of 787 leaf samples were collected from vegetables and some other host plants showing virus-like symptoms and tested by an enzymelinked immunosorbent assay (ELISA) using polyclonal antibodies produced against Tomato yellow leaf curl virus (TYLCV). According to the ELISA results, 81 samples (10.3%) positively reacted with the virus antibodies. Begomovirus infections were confirmed by polymerase chain reaction (PCR) using previously described TYLCV-specific primer pair TYLCV-Sar/TYLCV-Isr or universal primer pair Begomo-F/Begomo-R. The PCR tests using the primer pair TYLCV-Sar/TYLCV-Isr resulted in the amplification of the expected fragments of ca. 0.67-kb in size for ELISA-positive samples tested from alfalfa, pepper, spinach and tomato plants, confirming the presence of TYLCV. For one melon sample, having a week reaction in ELISA and no reaction in PCR using TYLCV-specific primers, the PCR reaction using the primer pair Begomo-F/Begomo-R resulted in the amplification fragments of the expected size of ca. 2.8 kb. The nucleotide sequences of the DNA amplicons derived from the isolate, Kz-Me198, were determined and compared with other sequences available in GenBank. BLASTN analysis confirmed the begomovirus infection of the sample and showed 99% identities with Tomato leaf curl New Delhi virus (ToLCNDV); phylogenetic analysis supported the results of the database searches. This study reports the natural occurrence of TYLCV in different hosts in Iran. Our results also reveal the emergence of ToLCNDV in Iranian cucurbit crops.