• Journal of Microbiology
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• v.43 no.2
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• pp.144-151
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• 2005

During the past ten years, Archaea have been recognized as a widespread and significant component of marine picoplankton assemblages. More recently, the presence of novel archaeal phylogenetic lineages has been discovered in coastal marine environments, freshwater lakes, polar seas, and deep-sea hydrothermal vents. Therefore, we conducted an investigation into the archaeal community existing in tidal flat sediment collected from Ganghwa Island, Korea. Phylogenetic analysis of archaeal 16S rDNA amplified directly from tidal flat sediment DNA revealed the presence of two major lineages, belonging to the Crenarchaeota ($53.9\%$) and Euryarchaeota ($46.1\%$) phyla. A total of 102 clones were then sequenced and analyzed by comprehensive phylogenetic analysis. The sequences determined in our samples were found to be closely related to the sequences of clones which had been previously obtained from a variety of marine environments. Archaeal clones exhibited higher similarities ($83.25 - 100\%$) to sequences..from other environments in the public database than did those ($75.22 - 98.46\%$) of previously reported bacterial clones obtained from tidal flat sediment. The results of our study suggest that the archaeal community in tidal flat sediment is remarkably diverse.

• Proceedings of the Korean Information Science Society Conference
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• 2006.06a
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• pp.43-45
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• 2006

Unlike RNA interference, whose usage is limited to eukaryotic cells, Peptide Nucleic Acid (PNA) technique is applicable to both eukaryotic and prokaryotic cells. PNA has been proven to be an effective agent for blocking gene expressions and has several advantages over other antisense techniques. Here we developed a parallel computing software that provides the ideal sequences to design PNA oligos to prevent any off-target effects. We applied a new approach in our location-finding algorithm that finds a target gene from the whole genome sequence. Message Passing Interface (MPI) was used to perform parallel computing in order to reduce the calculation time. The software will help biologists design more accurate and effective antisense PNA by minimizing the chance of off-target effects.

• Journal of Korean Society on Water Environment
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• v.22 no.1
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• pp.83-90
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• 2006

Performance and operation of BAC in ozone-BAC advanced water treatment process were investigated using the pilot scale test plant built in D water purification plant. The performance was evaluated by the removal efficiencies of DOC, BDOC, ammonia nitrogen and THMs. The effect of EBCT on DOC removal was experimented for an effective operating condition, and the amount of attached biofilm was analyzed in various water temperatures and position of BAC. Two removal mechanisms, adsorption and biological decomposition by attached biofilm, were predominant to decrease the concentration of various contaminants. DOC was removed 40%, and the removal rate was decreased in winter time due to the lowered activity of attached biofilm. BDOC was effectively removed. THMs and ammonia nitrogen were mainly removed not in ozonation process but in BAC. Water temperature deeply influenced in removal efficiency of ammonia nitrogen. The amount of attached biofilm depended on water temperature and height of packed activated carbon column. Considering DOC removal efficiency and design EBCT of commercial BAC plant, the proper EBCT was 12.5 minutes.

• Biotechnology and Bioprocess Engineering:BBE
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• v.9 no.3
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• pp.156-165
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• 2004

Concentrations of substrates, glucose, and ammionia in biological processes have been on-line monitored by using glucose-flow injection (FIA) and ammonia-FIA systems. Based on the on-line monitored data the concentrations of substrates have been controlled by an on-off controller, a PID controller, and a neural network (NN) based controller. A simulation program has been developed to test the control quality of each controller and to estimate the control parameters. The on-off controller often produced high oscillations at the set point due to its low robustness. The control quality of a PID controller could have been improved by a high analysis frequency and by a short residence time of sample in a FIA system. A NN-based controller with 3 layers has been developed, and a 3(input)-2(hidden)-1(output) network structure has been found to be optimal for the NN-based controller. The performance of the three controllers has been tested in a simulated process as well as in a cultivation process of Saccharomyces cerevisiae, and the performance has also been compared to simulation results. The NN-based controller with the 3-2-1 network structure was robust and stable against some disturbances, such as a sudden injection of distilled water into a biological process.

• Advances in environmental research
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• v.1 no.3
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• pp.201-210
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• 2012

The bioavailability of sorbed organic contaminants is one of the most important factors used to determine their fate in the environment. This study was conducted to evaluate the bioavailability of slow-desorbable naphthalene in soils. An air sparging system was utilized to remove dissolved (or desorbed) naphthalene continuously and to limit the bacterial utilization of dissolved naphthalene. A biological air sparging system (air sparging system with bacteria) was developed to evaluate the bioavailability of the slow-desorption fraction in soils. Three different strains (Pseudomonas putida G7, Pseudomonas sp. CZ6 and Burkholderia sp. KM1) and two soils were used. Slow-desorbable naphthalene continuously decreased under air sparging; however, a greater decrease was observed in response to the biological air sparging system. Enhanced bioavailability was not observed in the Jangseong soil. Overall, the results of this study suggests that the removal rate of slow-desorbable contaminants may be enhanced by inoculation of degrading bacteria into an air sparging system during the remediation of contaminated soils. However, the enhanced bioavailability was found to depend more on the soil properties than the bacterial characteristics.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.9 no.8
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• pp.1828-1833
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• 2005

The Integration of biological databases is critically important because of the interconnectedness of biological research. But it's not easy to integrate these databases for the different formats and designers in heterogeneous environments. So initial design is indispensable to integrate heterogeneous databases. In this paper, after we performed conceptual modeling on a popular nucleotide database, GenBank and a protein database, Swiss-Prot and integrated them by considering cross-reference. we also propose the integration system architecture called Bio-Gateway System, which can help users query closely linked information between two biological databases within one system differently from existing systems as well as query easily on condition that user knows fine condition for less effort.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.4 no.4
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• pp.739-744
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• 2000

As DNA sequences have been known through the Genome project the techniques for dealing with molecule-level gene information are being made researches briskly. It is also urgent to develop new computer algorithms for making databases and analyzing it efficiently considering the vastness of the information for known sequences. In this respect, this paper studies the association rule search algorithms for finding out the characteristics shown by means of the association between promoter sequences and genes, which is one of the important research areas in molecular biology. This paper treat biological data, while previous search algorithms used transaction data. So, we design a transformed association rule algorithm that covers data types and biological properties. These research results will contribute to reducing the time and the cost for biological experiments by minimizing their candidates.

• Mycobiology
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• v.47 no.1
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• pp.50-58
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• 2019

Agarum clathratum, a brown macroalgae species, has recently become a serious environmental problem on the coasts of Korea. In an effort to solve this problem, fungal diversity associated with decaying A. clathratum was investigated and related ${\beta}$-glucosidase and endoglucanase activities were described. A total of 233 fungal strains were isolated from A. clathratum at 15 sites and identified 89 species based on morphology and a multigene analysis using the internal transcribed spacer region (ITS) and protein-coding genes including actin (act), ${\beta}$-tubulin (benA), calmodulin (CaM), and translation elongation factor (tef1). Acremonium, Corollospora, and Penicillium were the dominant genera, and Acremonium fuci and Corollospora gracilis were the dominant species. Fifty-one species exhibited cellulase activity, with A. fuci, Alfaria terrestris, Hypoxylon perforatum, P. madriti, and Pleosporales sp. Five showing the highest enzyme activities. Further enzyme quantification confirmed that these species had higher cellulase activity than P. crysogenum, a fungal species described in previous studies. This study lays the groundwork for bioremediation using fungi to remove decaying seaweed from populated areas and provides important background for potential industrial applications of environmentally friendly processes.

• Journal of Korean Society on Water Environment
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• v.27 no.5
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• pp.646-653
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• 2011

The combined system of sequencing batch biofilm reactor (SBBR) and membrane SBR (MSBR) was operated with sewage to evaluate the COD utilization for biological nutrient removal (BNR). The SBBR was operated for nitrification reactor, while denitrifying PAO (dPAO) was cultivated in MSBR with anaerobic-anoxic operation. In the SBBR and MSBR system, the enhanced biological phosphorus removal (EBPR) was successfully achieved with higher N removal. The COD utilization in combined SBBR-MSBR system was significantly reduced compared to ordinary BNR (up to 3.1 g SCOD/g (N+P) and 1.6 g SCOD/g (N+P) with different C/N/P ratio). The results suggest that a dPAO process could effectively reduce carbon energy (=COD) requirement. The combination of oxic-SBBR and anaerobic-anoxic MSBR for dPAO utilization could be an attractive alternative to upgrade the process performance in weak sewage.

• Journal of the Korean Society of Mechanical Technology
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• v.20 no.6
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• pp.770-775
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• 2018

In this study, the characteristics of muscle relaxation were analyzed by the experimental and numerical method. A skin tissue was produced by imitational biological tissue using the agar powder, saline solution and sugar. The tissue was exposed to three types of wavelength-blue visible radiation(410 nm), red visible radiation(635 nm), and infrared ray(830 nm). The temperature results along the depth of tissue were measured according to the variation of light wavelength and irradiation time. The temperature change of the tissue shown up similar pattern regardless of the light wavelength kinds. The wavelength of infrared ray penetrated strongly into tissue between 3.2 mm and 11.4 mm. Also, the temperature change with the irradiation time was small, and the temperature value of the infrared ray was the largest. As a result, the muscle relaxation will occur mainly at the infrared wavelength.