• Journal of Microbiology and Biotechnology
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• 제15권5호
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• pp.952-964
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• 2005

The diesel-degrading activities of biofilms sampled from petroleum-contaminated groundwaters in urban subway drainage systems were examined in liquid cultures, and the microbial populations of the biofilms were characterized by denaturing gel gradient electrophoresis (DGGE) and 16S rDNA sequence analysis. Biofilm samples derived from two sites (19 K and 20 K) at subway Station N and Station I could degrade around $80\%$ of applied diesel within 20 and 40 days, respectively, at $15^{\circ}C$, and these results were strongly correlated with the growth patterns of the biofilms. The closest phylogenetic neighbor of a dominant component in the 19 K biofilm was Thiothrix fructosivorans strain Q ($100\%$ similarity). Four dominant strains in the 20 K biofilm were closely related to Thiothrix fructosivorans strain Q ($100\%$ similarity), Thiothrix sp. CC-5 ($100\%$ similarity), Sphaerotilus sp. IF14 ($99\%$ similarity), and Cytophaga-Flexibacter-Bacterioides (CFB) group bacterium RW262 ($98\%$ similarity). Three dominant members in the Station I biofilms were very similar to uncultured Cytophagales clone CRE-PA82 ($91\%$ similarity), Pseudomonas sp. WDL5 ($97\%$ similarity), and uncultured CFB group bacterium LCK-64 ($94\%$ similarity). The microbial components of the biofilms differed depending on the sampling site. This is the first report on the isolation of clones highly similar to Thiothrix fructosivorans and Thiothrix sp. from biofilms in petroleum-polluted groundwaters, and the first evidence that these organisms may play major roles in petroleum degradation and/or biofilm-development.

• 상하수도학회지
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• 제14권1호
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• pp.84-98
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• 2000

Control of Trihalomethanes(THMs) is a major concern of many water treatment plants. A number of researchers have studied the effectiveness of activated carbon adsorption process in removing THMs or organic halogen compounds. Recently, attention has been paid to the biological activated carbon (BAC) treatment of THM precursors as an alternative to the carbon adsorption treatment because of its effectiveness as well as its low running cost. In this study, changes of THM formation potential(THMFP) and removal of substrates in the SBR effluent were investigated in an attempt to clarify the mechanisms of the decrease/increase of THMFP in the BAC treatment. The increase and decrease of THMFP concentrations were observed in effluents during prolonged operation. When PCP or DBS was feeded as substrate contained in SBR effluent, the THMFPs were easyly removed with TOCs removal. But the case of SBR effluent containing SDS or glycine was introduced, and when microbial growth came to its near steady state, the THMFPs of treated effluents were increased more or less in comparison to those in the influents. Such increases of THMFP coincided with the increase in microbial growth within the activated carbon fiber(ACF) column. In the case of only sucrose was feeded as substrate on ACF colume, THMFP concentrations of effluent were higher than those of influent. The THMFP concentration was significantly increased on inlet part of ACF column, which biomass inhabits abundantly, then they were decreased gradually. These increases mean production of the secondary THM precursors by biological activities, which can be removed by adsorption and biological degradation on ACF column.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.13-16
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• 2000

Microorganisms have been widely employed for the production of useful bioproducts including primary metabolites such as ethanol, succinic acid, acetone and butanol, secondary metabolites represented by antibiotics, proteins, polysaccharides, lipids and many others. Since these products can be obtained in small quantities under natural condition, mutation and selection processes have been employed for the improvement of strains. Recently, metabolic engineering strategies have been employed for more efficient production of these bioproducts. Metabolic engineering can be defined as purposeful modification of cellular metabolic pathways by introducing new pathways, deleting or modifying the existing pathways for the enhanced production of a desired product or modified/new product, degradation of xenobiotics, and utilization of inexpensive raw materials. Metabolic flux analysis and metabolic control analysis along with recombinant DNA techniques are three important components in designing optimized metabolic pathways, This powerful technology is being further improved by the genomics, proteomics, metabolomics and bioinformatics. Complete genome sequences are providing us with the possibility of addressing complex biological questions including metabolic control, regulation and flux. In silico analysis of microbial metabolic pathways is possible from the completed genome sequences. Transcriptome analysis by employing ONA chip allows us to examine the global pattern of gene expression at mRNA level. Two dimensional gel electrophoresis of cellular proteins can be used to examine the global proteome content, which provides us with the information on gene expression at protein level. Bioinformatics can help us to understand the results obtained with these new techniques, and further provides us with a wide range of information contained in the genome sequences. The strategies taken in our lab for the production of pharmaceutical proteins, polyhydroxyalkanoate (a family of completely biodegradable polymer), succinic acid and me chemicals by employing metabolic engineering powered by genomics, proteomics, metabolomics and bioinformatics will be presented.

• Ocean and Polar Research
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• 제27권2호
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• pp.205-214
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• 2005

From ancient Antarctic glacier ice, we extracted total genomic DNA that was suitable for prokaryotic 16S rDNA gene cloning and sequencing, and bacterial artificial chromosome (BAC) library and end-sequencing. The ice samples were from the Dry Valley region. Age dating by $^{40}Ar/^{39}Ar$ analysis on the volcanic ashes deposited in situ indicated the ice samples are minimum 100,000-300,000 yr (sample DLE) and 8 million years (sample EME) old. Further assay proved the ice survived freeze-thaw cycles or other re-working processes. EME, which was from a small lobe of the basal Taylor glacier, is the oldest known ice on Earth. Microorganisms, preserved frozen in glacier ice and isolated from the rest of the world over a geological time scale, can provide valuable data or insight for the diversity, distribution, survival strategy, and evolutionary relationships to the extant relatives. From the 16S gene cloning study, we detected no PCR amplicons with Archaea-specific primers, however we found many phylotypes belonging to Bacteria divisions, such as Actinobacteria, Acidobacteria, Proteobacteria $({\alpha},\;{\beta},\;and\;{\gamma})$, Firmicutes, and Cytophaga-Flavobacterium-Bacteroid$. BAC cloning and sequencing revealed protein codings highly identical to phenylacetic acid degradation protein paaA, chromosome segregation ATPases, or cold shock protein B of present day bacteria. Throughput sequencing of the BAC clones is underway. Viable and culturable cells were recovered from the DLE sample, and characterized by their 16S rDNA sequences. Further investigation on the survivorship and functional genes from the past should help unveil the evolution of life on Earth, or elsewhere, if any.

• KSBB Journal
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• 제29권1호
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• pp.50-57
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• 2014

NF-${\kappa}B$ is a transcriptional factor which is involved in many biological processes including immunity, inflammation, and cell survival. Many investigators studied on the mechanism involved in activation of NF-${\kappa}B$ signalling pathway via ubiquitination and degradation of $I{\kappa}B$ regarding skin disease. Some specific molecules including Akt, MEK, p38 MAP Kinase, Stat3, et al. represent convergence points and key regulatory proteins in signaling pathways controlling cellular events such as growth and differentiation, energy homeostasis, and the response to stress and inflammation. Ultraviolet (UV) irradiation has many adverse effects on skin, including inflammation, alteration in the extracellular matrix, cellular senescence, apoptosis and skin cancer. Prunus mume, a naturally derived plant extract, has beneficial biological activities as blood fluidity improvement, anti-fatigue action, antioxidative and free radical scavenging activities, inhibiting the motility of Helicobacter pyolri. Previous reports on various beneficial function prompted us to investigate UVB-induced or other immunostimulated biological marker regarding P. mume extract. P. mume extract suppresses UVB-induced cyclooxygenase-2 (COX-2) expression in mouse skin epidermal JB6 P+ cells. The activation of activator protein-1 and nuclear factor-${\kappa}B$ induced by UVB was dose-dependently inhibited by P. mume extract treatment. This results suggest that P. mume extracts might be used as a potential agents for protection of inflammation or UVB induced skin damage.

• 생명과학회지
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• 제13권6호
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• pp.970-975
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• 2003

생촉매 및 생물막 반응기를 이용한 TCE 생분해는 TCE를 무해한 최종산물로 처리할 수 있는 환경친화적 방법이며, 초기 시설비와 운영비도 낮아 경제성도 우수한 기술로 평가할 수 있다. 그러나, TCE 및 독성 분해산물로 인하여 생촉매 불활성화가 일어나서 장기간 안정된 반응기 운전이 어렵고, TCE와 성장기질사이의 경쟁적 저해로 인하여 처리효율이 저하된다는 단점이 있다. 이러한 문제점을 극복하기 위하여 TCE 처리 단계와 생촉매 재활성화 단계를 구분시킨 2단계 CSTR/TBF 시스템에 대하여 TCE 연속처리용 시스템으로써의 실규모 적용 가능성을 평가해 보았다. B. cepacia 및 M. trichosporium을 생촉매로 사용한 2단계 CSTR/TBF 시스템은 고농도 유입 TCE와 다양한 운전조건에서도 28∼525mg TCE/1$.$day수준의 높은 TCE 처리효율을 안정되게 유지할 수 있어 산업폐가스 처리를 위한 실규모 처리 시스템으로 적용 가능성이 높다고 평가할 수 있었다.

• The Korean Journal of Ecology
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• 제21권5_3호
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• pp.695-702
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• 1998

This study was carried out to investigate to determine seasonal variation of dehydrogenase activity, phosphatase activity, adenosine tri-phosphate content and some physicochemical properties, such as soil pH, moisture content, organic matter and several heavy metal concentrations from Apr. 1997 to jan. 1998 in Pinus densiflora and Quercus mongolica forest in Mt. Nam, to explain a relationship between enzyme activity and the soil factors. There were ranges of 4.03-4.65 in soil pH, 18.65-51.09% in moisture content and 6.69-95.95% in orgainc matter. The organic matter content decreased with soil horizon, showing the higher values in Q. mongolica forest. In comparison to the results of Kawngneung site as control area, there were slightly differences due to a development level of forest ecosystem and microbial degradation of organic matter. The heavy metal concentrations showed 32.50-75.55 ${\mu}g/g$ in Cu, 69.33-134.84 ${\mu}g/g$ in Zn, 57.02-150.32 ${\mu}g/g$ in Pb, and 0.36-1.00 ${\mu}g/g$ in Mt. Nam. These values are higher than in Kwangneung site because of long-term exposure to air pollutants from central city. On the other hand, ATP contents in Mt. Nam were lower than in Kawngneung site in relation to soil organic matter, moisture content and relatively high heavy metal concentrations. ATP contents per soil weight was largest in F+H layer and in spring time of other seasons. Dehydrogenase activity as an index of soil microbial activity had a ranges of 170.67-1,221.66 ${\mu}g$ TPF/g that showed lower values than in Kawngneung site. However, phophatase activity had a contray tendency due to P fertilization for a continuous management. Those values increased through spring to a maximum in the summer and fall in autumn. This is basically caused by metabolic state of soil on the biological activity and several and several factors, such as aeration, soil temperature, vegetation and microflora.

• 한국축산식품학회지
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• 제41권4호
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• pp.701-714
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• 2021

In this study, the microbial community succession and the protein hydrolysis of donkey meat during refrigerated (4℃) storage were investigated. 16S rDNA sequencing method was used to analyze the bacteria community structure and succession in the level of genome. Meanwhile, the volatile base nitrogen (TVB-N) was measured to evaluate the degradation level of protein. After sorting out the sequencing results, 1,274,604 clean data were obtained, which were clustered into 2,064 into operational taxonomic units (OTUs), annotated to 32 phyla and 527 genus. With the prolonging of storage time, the composition of microorganism changed greatly. At the same time, the diversity and richness of microorganism decreased and then increased. During the whole storage period, Proteobacteria was the dominant phyla, and the Photobacterium, Pseudompnas, and Acinetobacter were the dominant genus. According to correlation analysis, it was found that the abundance of these dominant bacteria was significantly positively correlated with the variation of TVB-N. And Pseudomonas might play an important role in the production of TVB-N during refrigerated storage of donkey meat. The predicted metabolic pathways, based on PICRUSt analysis, indicated that amino metabolism in refrigerated donkey meat was the main metabolic pathways. This study provides insight into the process involved in refrigerated donkey meat spoilage, which provides a foundation for the development of antibacterial preservative for donkey meat.

• Journal of Ecology and Environment
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• 제46권4호
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• pp.282-291
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• 2022

Background: The Arctic permafrost stores enormous amount of carbon (C), about one third of global C stocks. However, drastically increasing temperature in the Arctic makes the stable frozen C stock vulnerable to microbial decomposition. The released carbon dioxide from permafrost can cause accelerating C feedback to the atmosphere. Soil organic matter (SOM) composition would be the basic information to project the trajectory of C under rapidly changing climate. However, not many studies on SOM characterization have been done compared to quantification of SOM stocks. Thus, the purpose of our study is to determine soil properties and molecular compositions of SOM in four different Arctic regions. We collected soils in different soil layers from 1) Cambridge Bay, Canada, 2) Council, Alaska, USA, 3) Svalbard, Norway, and 4) Zackenberg, Greenland. The basic soil properties were measured, and the molecular composition of SOM was analyzed through pyrolysis-gas chromatography/mass spectrometry (py-GC/MS). Results: The Oi layer of soil in Council, Alaska showed the lowest soil pH and the highest electrical conductivity (EC) and SOM content. All soils in each site showed increasing pH and decreasing SOC and EC values with soil depth. Since the Council site was moist acidic tundra compared to other three dry tundra sites, soil properties were distinct from the others: high SOM and EC, and low pH. Through the py-GC/MS analysis, a total of 117 pyrolysis products were detected from 32 soil samples of four different Arctic soils. The first two-axis of the PCA explained 38% of sample variation. While short- and mid-hydrocarbons were associated with mineral layers, lignins and polysaccharides were linked to organic layers of Alaska and Cambridge Bay soil. Conclusions: We conclude that the py-GC/MS results separated soil samples mainly based on the origin of SOM (plants- or microbially-derived). This molecular characteristics of SOM can play a role of controlling SOM degradation to warming. Thus, it should be further investigated how the SOM molecular characteristics have impacts on SOM dynamics through additional laboratory incubation studies and microbial decomposition measurements in the field.

• 현장농수산연구지
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• 제3권1호
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• pp.132-141
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• 2001

옥수수 알곡(whole corn)을 분쇄(ground corn; GC), 파쇄(cracked corn; CC), 박편(flaked corn; FC) 및 수침(soaked corn; SC)등 가공방법을 달리하여 처리하였을 때 반추가축에 있어서 미생물의 부착양상에 미치는 영향을 구명하고자 한 본 연구의 요약은 다음과 같다. 1. 한우의 반추위내에 각 처리별 옥수수를 12 및 24시간 배양하여 주사 전자현미경을 이용하여 반추 미생물의 부착양상과 사료 기질의 형태를 조사하였다. 2. 분쇄 및 파쇄 옥수수에서 가장 많은 미생물들이 부착되어 있는 것이 관찰되었고 옥수수 알곡 및 수침 옥수수는 전분입자에 미생물의 부착을 관찰 할 수 없었으며, 단지 배양시간이 경과함에 따라 옥수수의 외피에 많은 미생물이 부착되었고 외피의 분해가 일어나는 것이 관찰되었다. 3. SEM 결과를 통하여, 옥수수의 입자가 작게 가공처리 될수록 미생물 군락의 형성이 용이하여, 반추위내 옥수수의 분해율을 향상시킨다고 판단된다.