• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2008년도 International Meeting of the Microbiological Society of Korea
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• pp.118-118
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• 2008

The phylogenetic diversity of microbial communities in calcareous mats from Spearfish Creek, a freshwater stream located in the Black Hills of South Dakota, was examined using PCR-based 16S rDNA sequence analysis. In this study, two types of calcareous mats were compared: mature mats formed on the natural substrate of rock surfaces and developing mats on an artificial substrate of glass slides. Among 63 unique isolates from a clone library of 16S rRNA genes from mature mat samples, there were 8 phyla of Bacteria represented. The predominant phylum was Proteobacteria (48%), with the $\beta$ subclass being the largest group. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA genes from slide samples collected at intervals for four months showed considerable diversity of the microbial community from the earliest stages of community development. Amplicons isolated from DGGE gels and sequenced indicated that community succession has occurred without increasing microbial diversity. However, light microscopic analysis revealed a significant increase in microbial cell density throughout the community development. Scanning electron microscopy of mat samples provides evidence that diatoms are also important members of calcareous mat communities.

• Journal of Microbiology and Biotechnology
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• 제23권5호
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• pp.602-613
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• 2013

This paper aims at an investigation of the features of bacterial communities in surface sediments of the South China Sea (SCS). In particular, biogeographical distribution patterns and the phylogenetic diversity of bacteria found in sediments collected from a coral reef platform, a continental slope, and a deep-sea basin were determined. Bacterial diversity was measured by an observation of 16S rRNA genes, and 18 phylogenetic groups were identified in the bacterial clone library. Planctomycetes, Deltaproteobacteria, candidate division OP11, and Alphaproteobacteria made up the majority of the bacteria in the samples, with their mean bacterial clones being 16%, 15%, 12%, and 9%, respectively. By comparison, the bacterial communities found in the SCS surface sediments were significantly different from other previously observed deep-sea bacterial communities. This research also emphasizes the fact that geographical factors have an impact on the biogeographical distribution patterns of bacterial communities. For instance, canonical correspondence analyses illustrated that the percentage of sand weight and water depth are important factors affecting the bacterial community composition. Therefore, this study highlights the importance of adequately determining the relationship between geographical factors and the distribution of bacteria in the world's seas and oceans.

• Journal of Microbiology and Biotechnology
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• 제23권9호
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• pp.1187-1196
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• 2013

Global warming will have far-reaching effects on our ecosystem. However, its effects on Antarctic soils have been poorly explored. To assess the effects of warming on microbial abundance and community composition, we sampled Antarctic soils from the King George Island in the Antarctic Peninsula and incubated these soils at elevated temperatures of $5^{\circ}C$ and $8^{\circ}C$ for 14 days. The reduction in total organic carbon and increase in soil respiration were attributed to the increased proliferation of Bacteria, Fungi, and Archaea. Interestingly, bacterial ammonia monooxygenase (amoA) genes were predominant over archaeal amoA, unlike in many other environments reported previously. Phylogenetic analyses of bacterial and archaeal amoA communities via clone libraries revealed that the diversity of amoA genes in Antarctic ammonia-oxidizing prokaryotic communities were temperature-insensitive. Interestingly, our data also showed that the amoA of Antarctic ammonia-oxidizing bacteria (AOB) communities differed from previously described amoA sequences of cultured isolates and clone library sequences, suggesting the presence of novel Antarctic-specific AOB communities. Denitrification-related genes were significantly reduced under warming conditions, whereas the abundance of amoA and nifH increased. Barcoded pyrosequencing of the bacterial 16S rRNA gene revealed that Proteobacteria, Acidobacteria, and Actinobacteria were the major phyla in Antarctic soils and the effect of short-term warming on the bacterial community was not apparent.

• Journal of Microbiology and Biotechnology
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• 제26권1호
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• pp.99-109
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• 2016

We investigated the relation between the presence of geosmin in water and the bacterial community structure within the granular activated carbon (GAC) system of water treatment plants in South Korea. GAC samples were collected in May and August of 2014 at three water treatment plants (Sungnam, Koyang, and Yeoncho in Korea). Dissolved organic carbon and geosmin were analyzed before and after GAC treatment. Geosmin was found in raw water from Sungnam and Koyang water treatment plants but not in that from Yeoncho water treatment plant. Interestingly, but not surprisingly, the 16S rRNA clone library indicated that the bacterial communities from the Sungnam and Koyang GAC systems were closely related to geosmin-degrading bacteria. Based on the phylogenetic tree and multidimensional scaling plot, bacterial clones from GAC under the influence of geosmin were clustered with Variovorax paradoxus strain DB 9b and Comamonas sp. DB mg. In other words, the presence of geosmin in water might have inevitably contributed to the growth of geosmin degraders within the respective GAC system.

• Journal of Microbiology and Biotechnology
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• 제19권9호
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• pp.881-887
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• 2009

Forty-four eicosapentaenoic acid (EPA)-producing microbial strains were isolated from the intestines of marine fishes. Among them, one strain showing a maximum level of EPA (4.78% of total fatty acids) was identified as Shewanella sp. BR-2 on the basis of its 168 rRNA sequence. The EPA content reached a maximum level during the mid-exponential phase of cell growth, and gradually decreased with further growth of the cells. A cosmid DNA including the EPA biosynthesis gene cluster consisting of pfaA-E was isolated from a cosmid library of genomic DNA of Shewanella sp. BR-2, named pCosEPA-BR2. An E. coli clone harboring pCosEPA-BR2 produced EPA at a maximum level of 7.5% of total fatty acids, confirming the EPA biosynthesis activity of the cloned gene cluster.

• 상하수도학회지
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• 제26권3호
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• pp.399-408
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• 2012

The overall goal of this study was to characterize and quantify ammonia-oxidizing bacteria (AOB) in four different full-scale sequence batch reactor (SBR) wastewater treatment plants. Also, this study focused on assessing the occurrence of the alternative ammonia-oxidizing microbes such as anammox (anaerobic ammonia oxidation) bacteria (AMX) and ammonia-oxidizing archaea (AOA) in these systems. Based on total AOB numbers and the estimated cell density in the mixed liquor samples, AOB constituted 0.3 - 1.8% of the total bacterial population in the four WWTPs. Based on clone library, Nitrosomonas ureae-like AOB were dominant in plant A and B, while plant C and D had Nitrosomonas nitrosa-like AOB as major AOB group. The four different AMX primer sets targeting AMX 16S rRNA gene produced PCR amplicons distantly related to Chlamydia and Planctomycetales group bacteria. However, it was not clear these groups of bacteria perform anammox reaction in the SBR plants. Also, molecular evidence of AOA was found in one of the SBR plants, with a sequence located in the deep branch of the sediment creanarchaeota group.

• International Journal of Oral Biology
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• 제39권4호
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• pp.215-220
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• 2014

Toothbrushes play an essential role in oral hygiene. However, they can be significant in microbial transmission and can increase the risk of infection, since they can serve as a reservoir for microorganisms in healthy, oral-diseased and medically ill adults. This study was conducted to evaluate toothbrush contamination in six toothbrushes donated from four people. Two participants each supplied two toothbrushes - one used in the bathroom and one used in the workplace. The other two people each donated two toothbrushes used in the workplace. Polymerase chain reaction was used to construct a 16S rRNA clone library. Sequences of cloned DNA were compared with those from the reference organisms provided by GenBank. A total 120 clones, representing 20 clones for each toothbrush, were analyzed. They are composed of six pylum, 46 genera and 79 species. The most dominant species were Streptococcus oralis, Streptococcus parasanguinis and Haemophilus parainfluenzae. Enterobacter and Escherichia were recovered from toothbrushes used domestically. Toothbrushes used in the workplace did not contain Enterobacteria.

• Journal of Microbiology and Biotechnology
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• 제23권12호
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• pp.1717-1725
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• 2013

Traditional soybean paste from Shandong Liangshan and Tianyuan Jiangyuan commercial soybean paste were chosen for analysis and comparison of their bacterial and fungal dynamics using denaturing gel gradient electrophoresis and 16S rRNA gene clone libraries. The bacterial diversity results showed that more than 20 types of bacteria were present in traditional Shandong soybean paste during its fermentation process, whereas only six types of bacteria were present in the commercial soybean paste. The predominant bacteria in the Shandong soybean paste were most closely related to Leuconostoc spp., an uncultured bacterium, Lactococcus lactis, Bacillus licheniformis, Bacillus spp., and Citrobacter freundii. The predominant bacteria in the Tianyuan Jiangyuan soybean paste were most closely related to an uncultured bacterium, Bacillus licheniformis, and an uncultured Leuconostoc spp. The fungal diversity results showed that 10 types of fungi were present in the Shandong soybean paste during the fermentation process, with the predominant fungi being most closely related to Geotrichum spp., an uncultured fungal clone, Aspergillus oryzae, and yeast species. The predominant fungus in the commercial soybean paste was Aspergillus oryzae.

• Radiation Oncology Journal
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• 제17권2호
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• pp.151-157
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• 1999

목적 : HL60 세포주에서 PMA(phorbol 12-myrisate 13-acetate) 및 DMSO(dlmethyisulfoxlde) 에 의해 분화가 유도될 때 감소되는 특성을 보이는 K872 클론에 대한 염기 서열, 조직 분포, 단백 분리 등을 시행하였다. 재료 및 방법 QIA plasmid extraction kit(Qiagen GmbH, Germany)를 이용하여 사람의 모유두 세포 pBluescript phagemid cDNA library로부터 K872 클론을 추출하였다. Sanger's dideoxy nucleotide chain-termination method을 이용하여, 추출한 K872 클론의 염기 서열을 분석하였다. BLAST(Basic Local Alignment Search Tools) 프로그램으로 유전자은행의 염기 서열과의 상동성을 검색하였다. K872 클론으로 만든 probe로 다양한 인간 조직 및 암세포주로부터 분리한 RNA에 대하여 nothern blot을 시행하였다. His-Patch Thifusion expression system을 이용하여 대장균 배지에 0.1mM IPTG(Isopropyl-$\beta$-thlogalactopyranoslde) 를 첨가해서 결합단백의 유전자 발현을 유도하였다. 결합단백이 함유된 용출액을 SDS-PAGE에 걸어서 발현된 단백을 확인하였다. 결과 : K872 클론은 675개의 코딩 영역과 280개의 코딩과 관련없는 영역으로 구성된 1006개의 염기로 구성됨을 관찰하였다. 해독틀로 추정되는 부분은 시작 코돈을 포함하여 길6개의 아미노산을 형성하고 단백 산물의 분자량은 25,560 Da으로 추정되었다. 추정 아미노산 배열은 쥐의 glutathlone S-transferase kappa 1(rGSTKl) 의 아미노산 배열과 70$\%$의 상동성을 보였다. nothern blot에 따른 발현 양상은 심장, 수의근, 말초혈액 백혈구 등의 조직에서 높은 발현을 보였으며 방사선 내성과 관련지어 볼 때 대장암 및 흑색종 세포주에서 발현이 높았던 점은 특기할 만하였다. 결론 : 상동성 검색 결과 K872 유전자는 항암제 및 방사선 내성과 관련이 있는 rGSTK1에 대한 사람의 상동유전자로 사료되며 향후 이와 관련한 기능 분석이 필요할 것으로 사료된다

• 식물조직배양학회지
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• 제25권5호
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• pp.341-346
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• 1998

색소유전자의 전이를 통하여 새로운 색소발현체계를 가진 품종을 육종하기 위한 기초연구로 stock (Matthiola incana R. Br.)의 꽃봉오리로부터 cDNA-library를 합성하였고 screening을 통하여 anthocyanin 합성경로의 중요효소의 하나인 DFR (dihydroflavonol 4-reductase) 유전자를 분리하였다. 염기서열분석을 수행하여 분리유전자의 크기가 1450bp 이며 이중 coding region은 1029 bp 임을 확인하였다. 이미 밝혀진 다른 식물체의 DFR 유전자와 서로 염기서열의 일치성을 비교해 본 결과 외자엽식물인 옥수수와 보리와는 각각 61%를 보였으며, 쌍자엽식물인 페튜니아, 금어초, 거베라, 과꽃 그리고 카네이션 등 과는 66%-67%의 일치성을 나타내었다. 아울러 염기서열의 G/C 함량분석을 통하여 쌍자엽식물의 G/C 함량은 외자엽식물의 그것에 비해 매우 낮은 수치를 나타내었다. 분리유전자의 발현을 확인하기 위하여 인위적으로 기내에서의 전사와 해석을 수행한 결과 42-44 kd 크기의 단백질을 확인하였다. Southern blot 분석의 결과 DFR 유전자는 stock의 genome에 다른 대부분의 식물체와 유사하게 한 개가 존재하며 야생종과 돌연변이종의 stock을 분리 DFR 유전자를 probe 로 Northern blot 분석을 수행하여 돌연변이종인 lineK17b가 DFR 돌연변이임을 확인하였다.