• Journal of the Korean Institute of Intelligent Systems
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• v.25 no.6
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• pp.529-535
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• 2015

Biological networks have been handled with the static concept. However, life phenomena in cells occur depending on the cellular state and the external environment, and only a few proteins and their interactions are selectively activated. Therefore, we should adopt the dynamic network concept that the structure of a biological network varies along the flow of time. This concept is effective to analyze the progressive transition of the disease. In this paper, we applied the proposed method to Alzheimer's disease to analyze the structural and functional characteristics of the disease network. Using gene expression data and protein-protein interaction data, we constructed the sub-networks in accordance with the progress of disease (normal, early, middle and late). Based on this, we analyzed structural properties of the network. Furthermore, we found module structures in the network to analyze the functional properties of the sub-networks using the gene ontology analysis (GO). As a result, it was shown that the functional characteristics of the dynamics network is well compatible with the stage of the disease which shows that it can be used to describe important biological events of the disease. Via the proposed approach, it is possible to observe the molecular network change involved in the disease progression which is not generally investigated, and to understand the pathogenesis and progression mechanism of the disease at a molecular level.

• Korean Chemical Engineering Research
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• v.48 no.2
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• pp.147-156
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• 2010

There are four key factors for gas-phase biofilters; biocatalysts(microorganisms), packing materials, design/operating techniques, and diagnosis/management techniques. Biofilter performance is significantly affected by microbial community structures as well as loading conditions. The microbial studies on biofilters are mostly performed on basis of culture-dependent methods. Recently, advanced methods have been proposed to characterize the microbial community structure in environmental samples. In this study, the physiological, biochemical and molecular methods for profiling microbial communities are reviewed, and their applicability to biofilters is discussed. Community-level physiological profile is based on the utilization capability of carbon substrate by heterotrophic community in environmental samples. Phospholipid fatty acid analysis method is based on the variability of fatty acids present in cell membranes of different microorganisms. Molecular methods using DNA directly extracted from environmental samples can be divided into "partial community DNA analysis" and "whole community DNA analysis" approaches. The former approaches consist in the analysis of PCR-amplified sequence, the genes of ribosomal operon are the most commonly used sequences. These methods include PCR fragment cloning and genetic fingerprinting such as denaturing gradient gel electrophoresis, terminal-restriction fragment length polymorphism, ribosomal intergenic spacer analysis, and random amplified polymorphic DNA. The whole community DNA analysis methods are total genomic cross-DNA hybridization, thermal denaturation and reassociation of whole extracted DNA and extracted whole DNA fractionation using density gradient.

• Applied Microscopy
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• v.29 no.2
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• pp.177-187
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• 1999

Ultrastructure of gametes in the three-spine stickleback, Gasterosteus aculeatus aculeatus was observed, utilizing light, scanning and transmission electron microscopes. The egg of three-spine stickleback is spherical and demersal type. The eggs are highly adhesived to each other but not to substrates. There are many oil droplets in vitelline membrane. The outer surface of egg envelope is arranged by mushroom-like structures and pore canals. The egg have a micropyle, sperm entry site, in the area of the animal pole. The egg envelope consists of three layers, an outer layer with high electron density, a middle layer consisting two layers and an inner layer consisting of 16 to 20 layers. In the fertilized egg envelope, the molecular weights of these components ranged from 14 kDa to 205 kDa. The molecular weights of nam protein bands are 19.4 kDa, 36.7 KDa, 39.4 kDa, 42.9 kDa, 46.1 kDa and 53.0 kDa. The head of spermatozoa is spherical shape and the acrosome is absent. The mitochondria in midpiece are arranged from one to three layers and separated from the axoneme by the cytoplasmic canal. The tail has two lateral fins and the axoneme is of the 9+2 structure.

• Journal of Microbiology and Biotechnology
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• v.17 no.2
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• pp.253-261
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• 2007

Molecular and cultivation techniques were used to characterize the bacterial communities of biobead reactor biofilms in a sewage treatment plant to which an Aerated Up-Flow Biobead process was applied. With this biobead process, the monthly average values of various chemical parameters in the effluent were generally kept under the regulation limits of the effluent quality of the sewage treatment plant during the operation period. Most probable number (MPN) analysis revealed that the population of denitrifying bacteria was abundant in the biobead #1 reactor, denitrifying and nitrifying bacteria coexisted in the biobead #2 reactor, and nitrifying bacteria prevailed over denitrifying bacteria in the biobead #3 reactor. The results of the MPN test suggested that the biobead #2 reactor was a transition zone leading to acclimated nitrifying biofilms in the biobead #3 reactor. Phylogenetic analysis of 16S rDNA sequences cloned from biofilms showed that the biobead #1 reactor, which received a high organic loading rate, had much diverse microorganisms, whereas the biobead #2 and #3 reactors were dominated by the members of Proteobacteria. DGGE analysis with the ammonia monooxygenase (amoA) gene supported the observation from the MPN test that the biofilms of September were fully developed and specialized for nitrification in the biobead reactor #3. All of the DNA sequences of the amoA DGGE bands were very similar to the sequence of the amoA gene of Nitrosomonas species, the presence of which is typical in the biological aerated filters. The results of this study showed that organic and inorganic nutrients were efficiently removed by both denitrifying microbial populations in the anaerobic tank and heterotrophic and nitrifying bacterial biofilms well-formed in the three functional biobead reactors in the Aerated Up-Flow Biobead process.

• Proceedings of the Korean Society of Tribologists and Lubrication Engineers Conference
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• 2001.06a
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• pp.162-177
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• 2001

The hydrolysis rates of seven kinds of polyol ester base oils 〔POEs〕 of different branch shape were investigated by using a simple apparatus under mild acidic condition. Seven polyol ester base oils were made of poly hydric alcohols of two-four valence, normal or branched fatty acids of different carbon number. p-Toluene sulfonic acid was used as acid catalyst to accelerate the rate of hydrolysis. Partial esters and fatty acid produced by sequential hydrolysis of POEs were identified and their concentrations were determined by calibrated-internal standard method using Gas Chromatography. The rate constants of each step in sequential hydrolysis were determined by the least square method from rate equation and the concentration of each component, were compared with one another. It was shown that the rate of hydrolysis of POEs was strongly affected by whether molecular structure of fatty acid was straight chain or branch chain and which position was branched. The hydrolysis stability for all the POEs can be reasonably explained by using a steric hindrance effect anticipated fi:om their molecular structures affecting as water molecule makes an attack on the carbonyl carbon of POEs.

• Proceedings of the Korean Vacuum Society Conference
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• 2010.02a
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• pp.14-15
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• 2010

Recently there has been growing interest in topological insulators or the quantum spin Hall (QSH) phase, which are insulating materials with bulk band gaps but have metallic edge states that are formed topologically and robust against any non-magnetic impurity [1]. In a three-dimensional material, the two-dimensional surface states correspond to the edge states (topological metal) and their intriguing nature in terms of electronic and spin structures have been experimentally observed in bulk Bi1-xSbx single crystals [2,3,4]. However, if we want to know the transport properties of these topological metals, high purity samples as well as very low temperature will be needed because of the contribution from bulk states or impurity effects. In a recent report, it was also shown that an intriguing coupling between the surface and bulk states will occur [5]. A simple solution to this bothersome problem is to prepare a topological metal on an ultrathin film, in which the surface-to-bulk ratio is drastically increased. Therefore in the present study, we have investigated if there is a method to make an ultrathin Bi1-xSbx film on a semiconductor substrate. From reflection high-energy electron diffraction observation, it was found that single crystal Bi1-xSbx films (0${\sim}30\;{\AA}A$ can be prepared on Si(111)-$7{\times}7$. The transport properties of such films were characterized by in situ monolithic micro four-point probes [6]. The temperature dependence of the resistivity for the x=0.1 samples was insulating when the film thickness was $240\;{\AA}A$. However, it became metallic as the thickness was reduced down to $30\;{\AA}A$, indicating surface-state dominant electrical conduction. Figure 1 shows the Fermi surface of $40\;{\AA}A$ thick Bi0.92Sb0.08 (a) and Bi0.84Sb0.16 (b) films mapped by angle-resolved photoemission spectroscopy. The basic features of the electronic structure of these surface states were shown to be the same as those found on bulk surfaces, meaning that topological metals can be prepared at the surface of an ultrathin film. The details will be given in the presentation.

• Journal of Life Science
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• v.17 no.3 s.83
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• pp.318-327
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• 2007

This study presents the molecular phylogenetic analysis of Korean Aurelia aurita Linnaeus collected from Yeosu in the southern waters of Korea using nuclear ITS1 region and mitochondrial COI gene sequences. The use of oligonucleotide primers F5 (forward) and R5 (reverse) targeted to ITS1 and LCO1490 (forward) and HCO2198 (reverse) targeted to COI amplified 267 bp and 643 bp fragments, respectively. The shortest genetic distance towards the ITS1 region is estimated at 0.023 when comparing Korean A. aurita to Aurelia sp. collected from California, USA. In particular, Korean and American/Swedish A. aurita were located far away in terms of genetic distance, ranging from 0.393 to 0.395. On the other hand, the genetic distance between Korean and English/Turkish/Swedish/American A. aurita regarding the mitochondrial DNA COI gene ranged from 0.201 to 0.205. However, a sister-ship with Korean and American A. aurita showed an extremely high bootstrap value (100%). The predicted secondary RNA structure of the mitochondrial DNA COI gene showed many different folding structures with a similar energy between Korean and American A. aurita. These results suggest that ITS1 and the mitochondrial DNA COI gene could be used as genetic markers for identification of the biogeographic populations.

• Journal of Life Science
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• v.15 no.6 s.73
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• pp.1005-1012
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• 2005

Endophytic Bacillus sp. CY22 was previously isolated from the interior of balloon flower root and showed strong antifungal activity against phytopathogenic fungi such as Rhizoctonia solnni, Fusarium oxysporum, and Phythium ultimum. Many Bacillus strains produce antifungal compound such as iturin, fengycin, and mycosubtilin. We isolated and identified antifungal compound from cell supernatant of the endophytic strain. By the MALDI-TOF mass result, the antifungal compound was similar to the known antifungal lipopeptide iturin. It was found that the purified iturin had three isoforms with protonated masses of m/z 1,043.39, 1,057.42, and 1,071.42 and different structures in combination with $Na^{+}$ ion using MALDI-TOF MS. The ita22 gene, which transacylase gene is associated with production of antifungal iturin, had an open reading frame (ORF) of 1,200 bp encoding 400 amino acids. Results of deduced amino acids sequence homology search, Ita22 was homologous with FenF (BAB69697) of Bacillus subtilis 168.

• Journal of Soil and Groundwater Environment
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• v.19 no.6
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• pp.59-71
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• 2014

We investigated soil contamination depending on the land use by examining the contamination levels and distribution characteristics of 16 polycyclic aromatic hydrocarbons (PAHs) in the national soil. Total PAHs (the sum of 16 PAH concentrations) and carcinogenic PAHs (the sum of seven carcinogenic PAH concentrations) were $8.50{\sim}3,437.16{\mu}g/kg$ and $2.94{\sim}2,136.96{\mu}g/kg$, respectively. The concentration of benzo(a)pyrene, one of the contaminants regulated by the soil quality standard in the nation, was $ND{\sim}924.73{\mu}g/kg$. Its maximum value of $924.73{\mu}g/kg$ was detected in railroad (Region 3) and is approximately 13% of the standard value for Region 3 (i.e., 7 mg/kg). We also investigated the characteristics of contamination sources of PAHs in soil of the upland, forests, roads, and railroads, examining the fraction distribution of PAHs concentration by the number of benzene rings against the total PAHs concentration. The results demonstrate that the mean fraction of 4~6-ring PAHs against total PAHs concentration in soil was in the range of 51.8~80.7% with relative abundance of high-molecular PAHs, showing that the origin of contamination is under the category of combustion sources. When the molecular indices (Flu/(Flu/Pyr), Ant/(Ant+Phe), InP/(InP+BP), and BaA/(BaA+Chr)) were applied, they were also categorized as petroleum-based combustion sources. The individual PAH concentrations in soil by the land use were grouped into Regions 1, 2, and 3, which are statistically treated and are the parts of the national category system of soil quality standard. As a result, the concentration level of 16 PAHs was $0.02{\sim}2.63{\mu}g/kg$ in Region 1, $0.05{\sim}4.26{\mu}g/kg$ in Region 2, and $2.36{\sim}178.27{\mu}g/kg$ in Region 3. The concentration level of 6 carcinogenic PAHs was 14.2~320.4% against that of benzo(a)pyrene in Region 3 and sites of recycling waste sleepers. Considering that there were similarities among PAHs in terms of structures and toxicities, it would be recommended to review other types of carcinogenic PAHs together with benzo(a)pyrene when developing the soil quality standards in the nation.

• Particle and aerosol research
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• v.17 no.4
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• pp.125-132
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• 2021

Fresh PM_2.5 smokes emitted from combustion of four biomass materials (pellet, palm fruit fiber (PFF), PKS, and sawdust) in a laboratory-controlled environment were characterized using an attenuated total reflectance-fourier transform infrared (ATR-FTIR) technique. In smoke samples emitted from combustion of pellets, PFF and PKS, which is being used as boiler fuels for greenhouses in rural areas, the organic carbon/elemental carbon (OC/EC) ratios in PM_2.5 were very high (14.0-35.5), whereas in sawdust smoke samples they were significantly low (<4.0) due to the combustion method close to flaming combustion. ATR-FTIR analysis showed that OH(3400-3250 cm^-1), CH₃(2958-2840 cm^-1), CH₂(2910 cm^-1 and 2850 cm^-1), ketone(1726-1697 cm^-1), C=C(1607-1606 cm^-1 and 1515-1514 cm^-1), lignin (1463-1462 cm^-1 and 1430-1428 cm^-1) and -NO₂(1360-1370 cm^-1) peaks were identified in all biomass burning (BB) smoke samples. However, additional peaks appeared depending on the type of biomass. Among the four types of biomass materials, an additional peak of the methylene group CH₃(2872-2870 cm^-1) appeared only in PFF and PKS smoke samples, and a peak of C=O(1685 cm^-1) was also confirmed. And in the case of PKS smoke samples, a peak of aromatic C=C(1593 cm^-1 and 1476 cm^-1) that did not appear in other BB samples was also observed. This indicates that the molecular structure of organic compounds emitted during BB differs depending on the type of biomass materials. The results of this study are expected to provide valuable information to more specifically reveal the effect of BB on PM_2.5 collected in the atmospheric environment.