• ALGAE
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• 제31권3호
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• pp.205-217
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• 2016

Freshwater red tides due to dinoflagellates have caused spectacular and regular “summer reddening” in recent years in Baishihai Lake, a temperate, meromictic, meso- or oligotrophic, high-altitude, landslide-dammed, deep lake located at the eastern edge of Tibetan Plateau in China. Based on morphological and molecular analyses, the causative organism has been identified as a new woloszynskioid dinoflagellate, Tovellia diexiensis Q. Zhang et G. X. Liu sp. nov. The vegetative cells are 20-32 μm long and 16-24 μm wide. They have a hemispherical episome and a broadly rounded hyposome with a short characteristic antapical spine. Usually cells are bright red due to the presence of numerous red-pigmented bodies, which often masked the yellowish green discoid chloroplasts. The amphiesma of motile cells comprise mainly quadrilateral, pentagonal or hexagonal thin plates, arranged in 4-5 latitudinal series on the episome, 1 in the cingulum and 4 on the hyposome. Molecular phylogenies based on small subunit ribosomal DNA and large subunit ribosomal DNA (LSU) indicate T. diexiensis from Baishihai Lake to belong to the family Tovelliaceae, which was monophyletic in our LSU phylogenies. During the bloom-forming period in 2005, cell density of T. diexiensis reached 9.15 × 10⁵ cells L⁻¹. Astaxanthin and its diester were found to be the major pigments in T. diexiensis, resulting in a characteristic blood-red color of the water in Baishihai Lake.

• Journal of Yeungnam Medical Science
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• 제34권2호
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• pp.270-274
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• 2017

A nodular density was detected on a chest radiograph taken from a 57-year-old Korean woman who was visiting a hospital for a routine check. Chest computed tomography revealed a 4.8 cm lobulated mass in the right lung and another focal nodular lesion in the left lung; biopsies of both lungs revealed adenocarcinoma. We conducted DNA sequencing and peptide nucleic acid clamping to investigate the potential double primary lung cancer. The results verified that the mass in the right lung had a mutation in the epidermal growth factor receptor, whereas the nodule in the left lung had a wild-type sequence, showing that these two were genetically different cancers from one another. Thus, we demonstrate that genetic testing is useful in determining double primary lung cancer, and we herein report on this case.

• 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.

• 디지털융복합연구
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• 제11권11호
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• pp.409-414
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• 2013

Naive Bayesian classifiers 네이브 베이지안 분류기는 샘플 데이터로부터 쉽게 구현될 수 있는 강력하고도 많이 사용되는 형식의 분류기다. 그러나 강한 조건부 독립성으로 인하여 효율이 저하되는 분류 결과를 초래한다. 일반적으로 네이브 베이지안 분류기는 연속성을 가진 특징 데이터의 우도를 처리하기 위해 가우시안 분산을 사용한다. 속성들의 확률밀도는 항상 가우시안 분산에 적합한 것만은 아니다. 또 다른 형식의 분류기는 지도학습을 통해 퍼지 규칙과 퍼지집합을 학습할 수 있는 퍼지신경망이다. 퍼지신경망과 네이브 베이지안 분류기간에는 구조적 유사성을 가지고 있기 때문에 퍼지신경망으로 학습된 분산 그래프를 네이브 베이지안 분류기에 적용하고자 하는 방안이 본 연구의 목적이다. 따라서 네이브 베이지안 분류기에 가우시안 분산 그래프를 사용한 결과와 퍼지 분산 그래프를 사용한 결과를 비교하였다. 이를 위해 leukemia와 colon의 DNA 마이크로어레이 데이터를 적용하여 분류하였다. 네이브 베이지안 분류기에 퍼지 분산 그래프를 사용한 결과 가우시안 분산 그래프를 사용한 결과보다 더 신뢰성이 있음을 보여주었다.

• Journal of Ecology and Environment
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• 제29권4호
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• pp.399-404
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• 2006

This study was carried out to investigate the population densities, R/S ratios, and identification of heterotrophic bacteria on the rhizosphere soil of halophyte Suaeda japonica found on the western and southern mudflats of Korea. The population densities of aerobic and anaerobic heterotrophic bacteria on the rhizosphere soil of Suaeda japonica were in the range of $1.3\;{\pm}\;0.3\;{\times}\;10^6\;{\sim}\;6.3\;{\pm}\;3.3\;{\times}\;10^7\;and\;2.8\;{\pm}\;1.3\;{\times}\;10^4\;{\sim}\;1.8\;{\pm}\;0.7\;{\times}\;10^7\;cfu\;g^{-1}\;d.\;wt.$, respectively. In case of physiologically specific bacteria, population densities of amylolytic bacteria on the rhizosphere soil of Suaeda japonica were in the range of $4.4\;{\pm}\;0.6\;{\times}\;10^6\;{\sim}\;2.5\;{\pm}\;1.2\;{\times}\;10^7\;cfu\;g^{-1}\;d.\;wt.$, those of cellulolytic bacteria were from $8.5\;{\pm}\;6.0\;{\times}\;10^4\;{\sim}\;2.3\;{\pm}\;1.6\;{\times}\;10^6\;cfu\;g^{-1}\;d.\;wt.$, and those of proteolytic bacteria were from $3.8\;{\pm}\;1.8\;{\times}\;10^5\;{\sim}\;4.2\;{\pm}\;2.9\;{\times}\;10^6\;cfu\;g^{-1}\;d.\;wt.$, respectively. The R/S ratios were ranged from 2.33 to 2.39. Among eleven isolates from the roots of halophyte Suaeda japonica of Goheung bay by using 16S rDNA analysis, five clones were closely related to ${\gamma}-Proteobacteria$ group and six clones were closely related to ${\alpha}-Proteobacteria$ group. Among four isolates from Suncheon bay, two strains were related to ${\gamma}-Proteobacteria$ group and another two were related to Actinobacteria and Bacilli group, respectively.

• 식물병연구
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• 제11권1호
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• pp.48-55
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• 2005

Cylindrocarpon destructans는 인삼 및 수목에 뿌리썩음병을 일으키는 토양 전염병 식물병원균이다. 신속 정확한 검출 가능성을 알아보기 위하여 종 특이적인 primer와 nested PCR 기법을 활용하여 인삼 유묘로부터 뿌리썩음 병균 C. destructans로 2차 PCR증폭을 실시한 결과 병원성이 확인된 C.destructans에서만 400bp의 종특이적 증폭산물을 얻을 수 있었다. 종 특이성 primer 와 nested PCR 기법을 이용한 인삼뿌리썩음병균 DNA에 대한 반응 민감도는 최저 약 1fg으로 나타나 단 몇 개의 포자만 존재해도 검출이 가능하였다. 또한, nested PCR 기법은 실제 이병토양에 심었을 경우에도 C.destructans 에 감염된 인삼 유묘로부터만 정확하게 병원균을 검출해 내었다. 종특이적 primer 와 nested PCR 기법을 이용한 본 연구 결과는 실제 재배농가에서 인삼 경작시 뿌리썩음병 진단에 매우 유용하게 활용될 수 있을 것으로 판단된다.

• 한국토양비료학회지
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• 제48권5호
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• pp.442-450
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• 2015

This study was conducted to investigate the effect of Psy-2A-CrtI (PAC), a genetically modified (GM) rice with enhanced ${\beta}$-carotene, on the soil microbial community. The soil used to cultivate GM rice and its wild-type, Nakdong, was analyzed for population density, denaturing gradient gel electrophoresis (DGGE), and pyrosequencing. It was found that the bacterial, fungal and actinomycetes population densities of the PAC soils were within the range of those of the non-GM rice cultivar, Nakdong. The DGGE banding patterns of the GM and non-GM soils were also similar, suggesting that the bacterial community structures were stable within a given month and were unaffected by the presence of a GM plant. The pyrosequencing result showed a temporal difference in microorganism taxon and distribution ratio, but no significant difference between GM and non-GM was found. The persistence of the transgene DNA in the plant and surrounding soil were investigated for different time periods. There were differences in the persistence within the plant depending on the gene, but they could not be detected after 5 weeks. Also the transgenes were not detected in the surrounding soil. These results indicate that soil microbial communities are unaffected by the cultivation of a PAC rice within the experimental time frame.

• The Plant Pathology Journal
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• 제38권6호
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• pp.656-664
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• 2022

Pectobacterium odoriferum is the primary causative agent in Kimchi cabbage soft-rot diseases. The pathogenic bacteria Pectobacterium genera are responsible for significant yield losses in crops. However, P. odoriferum shares a vast range of hosts with P. carotovorum, P. versatile, and P. brasiliense, and has similar biochemical, phenotypic, and genetic characteristics to these species. Therefore, it is essential to develop a P. odoriferumspecific diagnostic method for soft-rot disease because of the complicated diagnostic process and management as described above. Therefore, in this study, to select P. odoriferum-specific genes, species-specific genes were selected using the data of the P. odoriferum JK2.1 whole genome and similar bacterial species registered with NCBI. Thereafter, the specificity of the selected gene was tested through blast analysis. We identified novel species-specific genes to detect and quantify targeted P. odoriferum and designed specific primer sets targeting HAD family hydrolases. It was confirmed that the selected primer set formed a specific amplicon of 360 bp only in the DNA of P. odoriferum using 29 Pectobacterium species and related species. Furthermore, the population density of P. odoriferum can be estimated without genomic DNA extraction through SYBR Green-based real-time quantitative PCR using a primer set in plants. As a result, the newly developed diagnostic method enables rapid and accurate diagnosis and continuous monitoring of soft-rot disease in Kimchi cabbage without additional procedures from the plant tissue.

• Journal of Periodontal and Implant Science
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• 제26권2호
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• pp.469-490
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• 1996

The initial events required for periodontal regeneration is the attachment, spreading, and proliferation of appropriated cells at the healing sites. These have been reported that minocycline stimulates the attachment of periodontal ligament cells, and also $TGF-{\beta}1$ enhances the proliferation of periodontal ligament cells. The purpose of the present study was to evaluate the effects of $TGF-{\beta}1$ on the cellular activity of minocycline treated human periodontal ligament cells. Periodontal ligament cells were obtained from the explants of healthy periodontal ligaments of extracted 3rd molars or premolar teeth extracted from the patients for orthodontic treatment. The cells were cultured in minimal essential medium(${\alpha}-MEM$) supplemented with 10.000units/ml penicillin, $10,000{\mu}g/ml$ streptomycin and 10% FBS(fetal bovine serum) at $37^{\circ}C$ in a humidified atmosphere of 5% carbon dioxide and the 5th to the 8th passages of the cells were used. To evaluate the effect of minocycline on cell attachment, the cells were seeded at a cell density of $1.5{\times}10^4$ cells/well in 24-well culture plates and treated with $20{\mu}g/ml$ and $100{\mu}g/ml$ of minocycline for 1.5 h. After trypsinization, the cells were counted with hemocytometer and were taken photographs for observation of cellular morphology. To evaluate the effect of $TGF-{\beta}1$ on minocycline-pretreated periodontal ligament cells, the cells were seeded at a cell density of $1{\times}10^4$ cells/ well in 24-well culture plates and treated with $20{\mu}g/ml$ and $100{\mu}g/ml$ of minocycline for 1.5 h. After incubation, 1 and 10ng/ml of $rh-TGF-{\beta}1$ were also added to the each well and incubated for 1 and 2 days, respectively. Then, MTT assay, DNA synthesis($^3H-thymidine\;assay$), and protein and collagen assay(3H-proline assay) were carried out. In the MIT assay, after 200ul MTT solutionlconeentration of 5mg/ml) were added to the each well of the 24-well plates and incubated for 3 hours, and 200 ul DMSO were added so as to dissolve insoluble blue formazan crystals which was formed in incubated period. Then it read plates on a ELISA reader. For mitogenic assay, 1 uCi/ml $^3H-thymidine$ was added to each well for the final 2 hours of the incubation periods. After labeling, the wells were washed 3 times with ice cold PBS and 4 times with 5% TCA to remove unincorporated label and precipitate the cellular DNA. DNA, with the incorporated $^3H-thymidine$, was solubilized with 500 ul of 0.1% NaOH/0.1% SDS. A 250 ul aliquot was removed from each well and placed in a scintillation vial with 4ml of scintillation cocktail. Using an liguid scintillation counter, counts per minute(CPM) were determined for each samples. 3 uCi/ml $^3H-proline$ was added to each well for the final 4 hours of the incubation periods and total protein and percent collagen synthesis were carried out. The results indicate that minocycline treated group with $100{\mu}g/ml$ concentration for 1.5 hours significantly increased than that of control in cell attachment, and cell process is also evident compared with that of control in cell morphology, and the cellular activity and DNA synthesis rate of cells treated minocycline and $TGF-{\beta}1$ significantly increased than that of control values, but were below to values of the $TGF-{\beta}1$ only treated group in MIT assay and $^3H-thymidine\;assay$, and the total protein synthesis of minocycline and $TGF-{\beta}1$ treated group also significantly increased than that of control values, but the percent collagen synthesis of tested group significantly decreased to compared with control. On the above the findings, the tested group of minocycline and $TGF-{\beta}1$ did not increase the effect on the cell activity than $TGF-{\beta}1$ only tested group and the tested group of minocycline inhibited cell activity. This results indicate that minocycline was effective on cell attachment in early stage, but it is harmful to cell activity, that inhibitory effect of minocycline was compensated with stimulatory effect of $TGF-{\beta}1$.

• 한국산림과학회지
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• 제112권1호
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• pp.40-56
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• 2023

사시나무속 수종은 생장이 빠르고 우수한 탄소흡수 능력을 보여주며, 환경정화 효과가 큰 수종으로 이상기후 및 환경오염 문제에 대응하는 기후적응성 품종개발 및 육종집단 조성에 적합하다. 따라서 유전연관지도 작성 및 양적형질 유전자좌 탐색을 통하여 포플러 육종을 신속하게 진행할 수 있을 것이다. 본 연구에서는 차세대 염기서열 분석기술 방법인 genotyping-by-sequencing 기법을 이용해 인공교배 차대에 대한 고밀도 유전연관 지도를 작성하였다. 또한 사시나무의 수고와 근원경 생장 그리고 해충피해에 대한 회복력 형질을 조사하여 유전연관지도에 위치한 양적형질 유전자좌를 탐색하였다. 서울대학교 학술림에 조성된 사시나무 4년생 육종집단(오대19 × 봉현4 인공교배 차대집단)에서 수고 및 근원경 생장을 조사하였으며, 식엽성 해충인 꼬마버들재주나방 유충의 피해를 받은 후 이에 대해 회복 능력을 조사하였다. 잎 시료의 DNA 추출 후 5개 microsatellite 마커를 이용하여 유전자형을 확인하였으며 친자로 확인된 개체만을 연구재료로 사용하였다. 친자 확인이 완료된 시료의 DNA는 제한효소를 이용해 절단하였으며, 이렇게 얻은 DNA 조각들은 GBS 라이브러리로 제작하여 염기서열을 분석하였다. 분석된 결과는 Populus trichocarpa를 참조유전체로 하여 정렬하였다. 정렬된 SNP 마커는 총 58,040개였으며, 그 가운데 17,755개의 SNP 마커를 유전연관지도 작성에 사용하였다. 유전연관지도는 19개의 연관군으로 나누어졌으며, 전체 길이는 2,129.54 cM으로 나타났다. 조사된 세 가지 형질에 대한 양적형질 유전자좌 분석을 실시한 결과, 수고와 근원경 생장과 연관된 양적형질 유전자좌는 찾을 수 없었으나 전장유전체연관연구(GWAS)를 통하여 4번 연관군(염색체)에 해충피해 회복력과 관련이 있을 것으로 추정되는 유전자를 확인하였다.