• Journal of Ginseng Research
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• 제40권2호
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• pp.176-184
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• 2016

Background: Wild ginseng, Panax ginseng Meyer, is an endangered species of medicinal plants. In the present study, we analyzed variations within the ribosomal DNA (rDNA) cluster to gain insight into the genetic diversity of the Oriental ginseng, P. ginseng, at artificial plant cultivation. Methods: The roots of wild P. ginseng plants were sampled from a nonprotected natural population of the Russian Far East. The slides were prepared from leaf tissues using the squash technique for cytogenetic analysis. The 18S rDNA sequences were cloned and sequenced. The distribution of nucleotide diversity, recombination events, and interspecific phylogenies for the total 18S rDNA sequence data set was also examined. Results: In mesophyll cells, mononucleolar nuclei were estimated to be dominant (75.7%), while the remaining nuclei contained two to four nucleoli. Among the analyzed 18S rDNA clones, 20% were identical to the 18S rDNA sequence of P. ginseng from Japan, and other clones differed in one to six substitutions. The nucleotide polymorphism was more expressed at the positions 440-640 bp, and distributed in variable regions, expansion segments, and conservative elements of core structure. The phylogenetic analysis confirmed conspecificity of ginseng plants cultivated in different regions, with two fixed mutations between P. ginseng and other species. Conclusion: This study identified the evidences of the intragenomic nucleotide polymorphism in the 18S rDNA sequences of P. ginseng. These data suggest that, in cultivated plants, the observed genome instability may influence the synthesis of biologically active compounds, which are widely used in traditional medicine.

• 한국지하수토양환경학회:학술대회논문집
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• 한국지하수토양환경학회 2000년도 창립총회 및 춘계학술발표회
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• pp.92-95
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• 2000

A mixed bacterial culture capable of mineralizing methyl tort-butyl ether (MTBE), other fuel oxygenates ethers, tertiary carbon alcohols, benzene and toluene was used to inoculate batch reactor and sequence batch reactor (SBR) to treat gasoline contaminated ground water containing about 60 mg/L MTBE, 5 mg/L benzene, 5 mg/L toluene, and low concentrations of several other aromatic and aliphatic hydrocarbons. Respirometery studies showed that MTBE degrading mixed culture could treat MTBE contaminated ground water with addition of nitrogen and phosphate. SBR was operated to demonstrate the feasibility of using suspended growth activated system for the treatment of ground water and to confirm that the respirometry derived kinetics and stoichiometric coefficients were useful for predicting reactor performance. Theoretical performance of the reactor was predicted using mathematical models calibrated with biokinetic parameters derived from respirometry studies.

• 한국지하수토양환경학회:학술대회논문집
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• 한국지하수토양환경학회 2005년도 총회 및 춘계학술발표회
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• pp.139-142
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• 2005

Kim and Lee(2005) suggested Minimum Entropy Deconvolution(MED) to estimate the temporal sequence of the relative recharge. However this study by Kim and Lee(2005) was just related to the verification of the conceptual approach with MED. In this study, we try to characterize the applicability of MED in the case of spatially heterogeneous recharge (distance from recharge area). Simulated results were recorded with some specific sampling points. Estimated results from this study show higher than 0.8 in cross-correlation with the original recharge sequence.

• Journal of Species Research
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• 제13권2호
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• pp.142-146
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• 2024

The purpose of this study was to isolate and identify wild yeasts from soil collected in Daegu City and Cheongyang County, Republic of Korea. Among 11 strains isolated in this study, nine strains were previously reported and two strains were unreported in Republic of Korea. To identify wild yeast strains, pairwise sequence comparisons of the D1/D2 region of the 26S rRNA gene sequence were done using Basic Local Alignment Search Tool (BLAST). The cell morphologies were observed by phase contrast microscope and assimilation test are done using API 20C AUX kit. All strains were assigned to the phylum Basidiomycota. Of the two unrecorded yeast strains, CY-9-10C belongs to the genus Mrakia (family Mrakiaceae, order Cystofilobasidiales, class Tremellomycetes) and PG3-4-10C belongs to the genus Slooffia (family Chrysozymaceae, order Microbotryomycetes incertae sedis, class Microbotryomycetes). Both strains had oval-shaped and polar budding cells. This research described the morphological and biochemical properties of the two unreported yeast species that had not officially reported in Korea.

• Journal of Microbiology and Biotechnology
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• 제16권1호
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• pp.153-157
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• 2006

A soil metagenomic library was constructed using an E. coli-fosmid cloning system with environmental DNAs extracted from Kwangreung forest topsoil. We targeted the genes involved in the biosynthesis of bacterial polyketides. Initially, a total of 36 clone pools (10,800 clones) were explored by the PCR-based method using the metagenomic DNAs from each pool and a degenerate primer set, which has been designed based on the highly conserved regions among ketoacyl synthase (KS) domains in actinomycete type I polyketide synthases (PKS Is). Six clone pools were tentatively selected as positive and further examined through a hybridization-based method for selecting a fosmid clone containing PKS I genes. Colony hybridization was performed against fosmid clones from the 6 positive pools, and finally 4 clones were picked out and confirmed to contain the conserved DNA fragment of KS domains. In this study, we present a simple and feasible sorting method for a desired clone from metagenomic libraries.

• Journal of Microbiology and Biotechnology
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• 제13권6호
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• pp.942-948
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• 2003

Soil samples were obtained from 5 sites contaminated with polycyclic aromatic hydrocarbons (PAHs). These soil samples were cultured in using phenanthrene as a sole carbon and energy source, and 36 strains of phenanthrene-degrading bacteria were isolated from 3 sites. Most of them degraded 500 ppm of phenanthrene within 8 to 10 days, and these isolates could degrade a few other PAHs other than phenanthrene. Their genotypes were determined by restriction digests of the l6S rRNA genes [amplified ribosomal DNA restriction analysis (ARDRA)]. It was found that all the phenanthrene degrading isolates were included in 4 ARDRA types, and they showed a strict site endemism. l6S rDNAs of 12 strains selected from different sites were sequenced, and they were all confirmed as Sphingomonas strains. Their l6S rDNA sequences were compared for phylogenetic analysis; their sequence showed a similar result to ARDRA typing, thus indicating that these heterotrophic soil bacteria are not regionally mixed. In addition, it was found that the microbial diversity among sampling sites could be monitored by l6S rDNA PCR-RFLP pattern alone, which is simpler and easier to perform, without l6S rDNA sequence analysis.

• Journal of Microbiology and Biotechnology
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• 제17권6호
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• pp.913-918
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• 2007

A Gram-positive, aerobic, rod-shaped, nonmotile, endospore-forming bacterium, designated Gsoil $349^T$, was isolated from soil of a ginseng field and characterized using a polyphasic approach. Comparative analysis of 16S rRNA gene sequences revealed that the strain Gsoil $349^T$ belongs to the family Paenibacillaceae, and the sequence showed closest similarity with Cohnella thermotolerans DSM $17683^T$ (94.1%) and Cohnella hongkongensis DSM $17642^T$ (93.6%). The strain showed less than 91.3% 16S rRNA gene sequence similarity with Paenibacillus species. In addition, the presence of MK-7 as the major menaquinone and $anteiso-C_{15:0},\;iso-C_{16:0},\;and\;C_{16:0}$ as major fatty acids suggested its affiliation to the genus Cohnella. The G+C content of the genomic DNA was 53.4 mol%. On the basis of its phenotypic characteristics and phylogenetic distinctiveness, strain Gsoil $349^T$ should be treated as a novel species within the genus Cohnella for which the name Cohnella panacarvi sp. nov. is proposed. The type strain is Gsoil $349^T\;(=KCTC\;13060^T=\;DSM\;18696^T)$.

• 미생물학회지
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• 제52권4호
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• pp.500-502
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• 2016

박테리아 종들은 정교한 효소 시스템의 존재로 인해 이온화 방사선 처리 후에 생존할 수 있는 것으로 보고되어 왔고 몇몇 내생 포자를 생산하는 박테리아 또한 두꺼운 포자껍질의 존재 때문에 방사선에 저항할 수 있다. 이 연구에서는 방사선이 조사된 토양의 시료에서 추출된 Paenibacillus swuensis $DY6^T$의 완전한 게놈 서열을 분석하였다. 이 게놈은 G+C 함량이 49.93%인 5,012,599 bp으로 구성되어 있고 단백질 정보를 암호화한 유전자 4,463개와 133개 RNA 유전자를 포함하고 있다.

• 미생물학회지
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• 제53권4호
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• pp.326-328
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• 2017

Betaproteobacteria에 속하는 Herbaspirillum sp. meg3을 제주도 토양으로부터 분리하였다. 본 연구에서는 대략 5.47 Mb의 크기와 57.1%의 평균 G + C 함량을 가진 meg3 균주의 완전한 유전체를 보고한다. 유전체는 4,816개의 코딩 서열, 9개의 리보솜 RNA 및 51개의 전사 RNA 유전자가 존재하며, 두 개의 불완전한 프로파지 영역이 발견되었다. 또한 유전체 분석 결과는 meg3 균주가 방향족 화합물에 대한 분해능을 가지고 있음을 제시하고 있다.

• Journal of Microbiology and Biotechnology
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• 제26권10호
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• pp.1717-1722
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• 2016

A novel phytase of Acidobacteria was identified from a soil metagenome, cloned, overexpressed, and purified. It has low sequence similarity (<44%) to all the known phytases. At the optimum pH (2.5), the phytase shows an activity level of 1,792 μmol/min/mg at physiological temperature (37℃) and could retain 92% residual activity after 30 min, indicating the phytase is acidophilic and acidostable. However the phytase shows poor stability at high temperatures. To improve its thermal resistance, the enzyme was redesigned using Disulfide by Design 2.0, introducing four additional disulfide bridges. The half-life time of the engineered phytase at 60℃ and 80℃, respectively, is 3.0× and 2.8× longer than the wild-type, and its activity and acidostability are not significantly affected.