• Journal of Wetlands Research
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• v.14 no.4
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• pp.489-502
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• 2012

Biogeochemical processes in groundwater-stream water mixing zone are recently of great interest because biodegradation and natural attenuation of aquatic contaminants may occur through the processes. The objectives of this study are to investigate the hydrologic and biogeochemical processes at the groundwater-stream water mixing zone through which surface water-driven nitrate may be naturally attenuated, and to examine the effect of the vertical flow exchange flux on biogeochemical processes using correlation analysis. To examine the direction of vertical water flow in the zone, vertical hydraulic gradients were measured at several depths using mini-piezometers. Microbial populations in soil samples of the zone were also analyzed by means of the polymerase chain reaction (PCR) and Cloning methods. In addition, partial correlations among vertical flow exchange, nitrate concentration and microbial activity was investigated to examine their mutual interaction. The results showed the significant interaction among the three parameters, resulting in natural attenuation of nitrate. This study showed an example of the biogeochemical fuction of groundwater-stream water mixing zone, which can be predictable from the examination of the interaction among microbial activities, concentration of contamination and vertical flow exchange flux. temperature show a significant difference in adjacent streambed, Also, the results shows that distribution of temperature was more affected by groundwater direction than intensity of flux.

• Journal of the Korea Computer Graphics Society
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• v.10 no.2
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• pp.1-9
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• 2004

본 논문에서는 바이러스와 같은 생화학 물질의 분자구조를 3 차원 모델로 시각화하여 관찰하고, 그 분자모델을 직관적인 방법으로 조작하기 위한 가상 현실 분자 모델링 시스템을 제안한다. 이 시스템을 사용하면, 입체영상 디스플레이 장치와 데이터 글러브 및 동작 추적 장치를 사용하여 3 차원 분자 모델을 실감나게 조작할 수 있어서 효율적으로 분자들을 관찰하고 결합, 분리하는 등의 분자 모델링 작업이 가능하다. 사용자들은 마우스나 키보드 등의 장비 대신에 자연스러운 몸 동작이나 손 동작을 이용하여 분자 모델링 작업을 위한 동작을 하게 된다. 분자들의 결합을 화학적으로 정확하게, 그리고 실시간으로 시뮬레이션 하기 위해서 에너지 계산 알고리즘을 구현하였으며 이러한 작업이 가능하도록 분자 구조를 표현하는 새로운 자료구조를 제안하였다. 본 연구에서 제안하는 동작 기반의 VR 분자 모델링 시스템의 타당성을 검증하기 위하여 HIV 바이러스 분자를 가지고 분자 모델링 작업을 수행하였고, 사용자 테스트를 실시하여 기존의 방식과 작업 성능 및 사용자 만족도를 비교하였다.

• Microbiology and Biotechnology Letters
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• v.17 no.3
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• pp.219-223
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• 1989

Effect of antifoam agents, silicone oil and neolin 302, was investigated on the production of prodnisolone by microbial $\Delta$$^1$-Dehydrogenation of hydrocortisone. The microbial process was conduct-ed by using a pseudo-crystallofermentation. By the hydrophobic-hydrophobic interaction, the steroid crystals aggregated with the antifoam agents. The aggregation resulted in a decrease of total mass transter area of substrate particles which is proportional to the dissolution rate of the solid substrate, and it consequently led to a significant decrease of the bioconversion rate. The bioconversion with neolin proceeded more slowly than with silicone oil. Increase of the concentration of the antifoam agents also yielded a significant decrease of the bioconversion rate.

• Bulletin of the Korean Chemical Society
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• v.26 no.8
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• pp.1203-1208
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• 2005

A computational study based on molecular dynamics (MD) simulations was performed in order to explain the difference in aqueous solubilities of two flavonoid/$\beta$-cyclodextrin ($\beta$-CD) complexes, hesperetin/$\beta$-CD and naringenin/$\beta$-CD. The aqueous solubility of each flavonoid/$\beta$-CD complex could be characterized by complexwater interaction not by flavonoid-CD interaction. The radial distribution of water around each inclusion complex elucidated the difference of an experimentally observed solubility of each flavonoid/$\beta$-CD complex. The analyzed results suggested that a bulky hydrophobic moiety (-$OCH_3$) of B-ring of hesperetin nearby primary rim of $\beta$-CD was responsible for lower aqueous solubility of the hesperetin/$\beta$-CD complex.

• Bulletin of the Korean Chemical Society
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• v.24 no.11
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• pp.1627-1631
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• 2003

Molecular modeling was performed to comprehend the chiral recognition of ${\alpha}$-methoxy-${\alpha}$-trifluoromethylphenylacetic acid (MTPA) enantiomers by cyclomaltoheptaose (${\beta}$-cyclodextrin,${\beta}$-CD) and 6-amino-6-deoxy-cyclomaltoheptaose (am-${\beta}$-CD). Monte Carlo (MC) docking coupled to constant temperature molecular dynamics (MD) simulations was applied to the investigation for the ${\alpha}$-methoxy-${\alpha}$-trifluoromethylphenylacetic acid complexation with two different CDs in terms of the relative distribution of the interaction energies. The calculated results are finely correlated with the experimental observations in chiral recognition thermodynamics. Am-${\beta}$-CD as a host showed the superior enantio-discrimination ability to the native ${\beta}$-CD where the amino group of am-${\beta}$-CD was critically involved in enhancing the ability of chiral discrimination via the Coulombic interaction with MTPA.

• IMMUNE NETWORK
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• v.21 no.3
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• pp.19.1-19.18
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• 2021

Clinical and molecular phenotypes of asthma are complex. The main phenotypes of adult asthma are characterized by eosinophil and/or neutrophil cell dominant airway inflammation that represent distinct clinical features. Upper and lower airways constitute a unique system and their interaction shows functional complementarity. Although human upper airway contains various indigenous commensals and opportunistic pathogenic microbiome, imbalance of this interactions lead to pathogen overgrowth and increased inflammation and airway remodeling. Competition for epithelial cell attachment, different susceptibilities to host defense molecules and antimicrobial peptides, and the production of proinflammatory cytokine and pattern recognition receptors possibly determine the pattern of this inflammation. Exposure to environmental factors, including infection, air pollution, smoking is commonly associated with asthma comorbidity, severity, exacerbation and resistance to anti-microbial and steroid treatment, and these effects may also be modulated by host and microbial genetics. Administration of probiotic, antibiotic and corticosteroid treatment for asthma may modify the composition of resident microbiota and clinical features. This review summarizes the effect of some environmental factors on the upper respiratory microbiome, the interaction between host-microbiome, and potential impact of asthma treatment on the composition of the upper airway microbiome.

• Journal of Microbiology and Biotechnology
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• v.18 no.5
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• pp.852-858
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• 2008

An extracellular protease (Mc1) was isolated from the nematode-trapping fungus Monacrosporium cystosporium by gel filtration, anion-exchange, and hydrophobic interaction chromatographies. This protease had a molecular mass of approximately 38 kDa and displayed an optimal activity at pH 7-9 and $56^{\circ}C$ (over 30 min). Its proteolytic activity was highly sensitive to the serine protease inhibitor PMSF (phenylmethylsulfonylfluoride, 0.1 mM), indicating that it belonged to the serine-type peptidase group. The Michaelis constant ($K_m$) and $V_max$ for substrate N-Suc-Ala-Ala-Pro-Phe-pNA were $1.67{\times}10^{-4}\;M$ and 0.6071 $OD_{410}$ per 30 s, respectively. This protease could degrade a broad range of substrates including casein, gelatin, BSA (bovine serum albumin), and nematode cuticle. Moreover, the enzyme could immobilize the free-living nematode Panagrellus redivivus and the pine wood nematode Bursaphelenchus xylophilus, suggesting that it might playa role in infection against nematodes. The encoding gene of Mc1 was composed of one intron and two exons, coding for a polypeptide of 405 amino acid residues. The deduced amino acid sequence of Mcl showed 61.4-91.9% identity to serine proteases from other nematode-trapping fungi. Our results identified that Mcl possessed biochemical properties including optimal reaction condition and substrate preference that are different from previously identified serine proteases.

• Journal of Microbiology and Biotechnology
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• v.12 no.2
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• pp.286-291
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• 2002

Histone deacetylase I (HDAC1) works as one of the components in a nucleosome remodeling (NuRD) complex that consists of several proteins, including metastasis-associated protein 1 (MTA1). Since the protein-protein interaction of HDAC1 and MTA1 would appear to be important for both the integrity and functionality of the HDAC1 complex, the interruption of the HDAC1 and MTA1 interaction may be an efficient way to regulate the biological function of the HDAC1 complex. Based on this idea, a yeast two-hybrid system was constructed with HDAC1 and MTA1 expressing vectors in the DNA binding and activation domains, respectively. To verify the efficiency of the assay system, 3,500 microbial metabolite libraries were tested using the paper disc method, and KB0699 was found to inhibit the HDAC1 and MTA1 interaction without any toxicity to the wild-type yeast. Furthermore, KB0699 blocked the interaction of HDAC1 and MTA1 in an in vitro GST pull down assay and induced morphological changes in B16/BL6 melanoma cells, indicating the interruption of the HDAC1 complex function. Accordingly, these results demonstrated that the yeast assay strain developed in this study could be a valuable tool for the isolation of a HDAC1 complex disruptor.

• Journal of Microbiology and Biotechnology
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• v.33 no.2
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• pp.180-187
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• 2023

The skin is a dynamic ecosystem on which diverse microbes reside. The interkingdom interaction between microbial species in the skin microbiota is thought to influence the health and disease of the skin although the roles of the intra- and interkingdom interactions remain to be elucidated. In this context, the interactions between Malassezia and Staphylococcus, the most dominant microorganisms in the skin microbiota, have gained attention. This study investigated how the interaction between Malassezia and Staphylococcus affected the antifungal susceptibility of the fungus to the azole antifungal drug ketoconazole. The susceptibility was significantly decreased when Malassezia was co-cultured with Staphylococcus. We found that acidification of the environment by organic acids produced by Staphylococcus influenced the decrease of the ketoconazole susceptibility of M. restricta in the co-culturing condition. Furthermore, our data demonstrated that the significant increased ergosterol content and cell membrane and wall thickness of the M. restricta cells grown in the acidic environment may be the main cause of the altered azole susceptibility of the fungus. Overall, our study suggests that the interaction between Malassezia and Staphylococcus influences the antifungal susceptibility of the fungus and that pH has a critical role in the polymicrobial interaction in the skin environment.

• Journal of Microbiology and Biotechnology
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• v.29 no.12
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• pp.1957-1968
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• 2019

Tetraselmis is a green algal genus, some of whose species are important in aquaculture as well as biotechnology. In algal culture, fluorescent lamps, traditional light source for culturing algae, are now being replaced by a cost-effective light-emitting diodes (LEDs). In this study, we investigated the effect of LED light of different wavelengths (white, red, yellow, and blue) on the growth of Tetraselmis suecica and its associated microbial community structures using the next-generation sequencing (NGS). The fastest growth rate of T. suecica was shown in the red light, whereas the slowest was in yellow. The highest OTUs (3426) were identified on day 0, whereas the lowest ones (308) were found on day 15 under red light. The top 100 OTUs associated with day 0 and day 5 cultures of T. suecica under the red and yellow LED were compared. Only 26 OTUs were commonly identified among four samples. The highest numbers of unique OTUs were identified at day 0, indicating the high degree of initial microbial diversity of the T. suecica inoculum. The red light-unique OTUs occupied 34.98%, whereas the yellow-specific OTUs accounted for only 2.2%. This result suggested a higher degree of interaction in T. suecica culture under the red light, where stronger photosynthesis occurs. Apparently, the microbial community associated with T. suecica related to the oxygen produced by algal photosynthesis. This result may expand our knowledge about the algae-bacteria consortia, which would be useful for various biotechnological applications including wastewater treatment, bioremediation, and sustainable aquaculture.