• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.17-20
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• 2000

Structural genomics aims to provide a good experimental structure or computational model of every tractable protein in a complete genome. Underlying this goal is the immense value of protein structure, especially in permitting recognition of distant evolutionary relationships for proteins whose sequence analysis has failed to find any significant homolog. A considerable fraction of the genes in all sequenced genomes have no known function, and structure determination provides a direct means of revealing homology that may be used to infer their putative molecular function. The solved structures will be similarly useful for elucidating the biochemical or biophysical role of proteins that have been previously ascribed only phenotypic functions. More generally, knowledge of an increasingly complete repertoire of protein structures will aid structure prediction methods, improve understanding of protein structure, and ultimately lend insight into molecular interactions and pathways. We use computational methods to select families whose structures cannot be predicted and which are likely to be amenable to experimental characterization. Methods to be employed included modern sequence analysis and clustering algorithms. A critical component is consultation of the presage database for structural genomics, which records the community's experimental work underway and computational predictions. The protein families are ranked according to several criteria including taxonomic diversity and known functional information. Individual proteins, often homologs from hyperthermophiles, are selected from these families as targets for structure determination. The solved structures are examined for structural similarity to other proteins of known structure. Homologous proteins in sequence databases are computationally modeled, to provide a resource of protein structure models complementing the experimentally solved protein structures.

• Journal of Microbiology and Biotechnology
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• 제19권1호
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• pp.99-107
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• 2009

Strain PUPC1 produces an antifungal protease as well as plant growth promoting enzymes such as 1-aminocyclopropane-1-carboxylate (ACC) deaminase and phosphatase. Morphological, cultural, and physiological characteristics as well as 16S rRNA gene-sequence-based phylogenetic analysis confirmed the taxonomic affiliation of PUPC1 as Chryseobacterium aquaticum. The optimum growth of PUPC1 was observed at pH 6.0 and $30^{\circ}C$, and maximum protease production was observed in medium B amended with 1% tryptone, 0.5% sucrose, and 0.005% $MnCl_2$. The protease was purified by ammonium sulfate precipitation, Sephadex G-75 gel filtration chromatography, and electroelution from preparative SDS-PAGE. The protease had a molecular mass of 18.5 kDa. The optimum pH and temperature stability of the protease were pH 5.0-10.0 and temperature $40-70^{\circ}C$. Chryseobacterium aquaticum PUPC1 and its protease showed a broad-spectrum antifungal activity against phytopathogenic fungi. Strain PUPC1 also exhibited plant growth promoting traits. The objective of the present investigation was to isolate a strain for agricultural application for plant growth promotion and biocontrol of fungal diseases.

• Journal of Species Research
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• 제5권2호
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• pp.235-240
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• 2016

To investigate the indigenous prokaryotic species diversity in Korea, various environmental samples from diverse ecosystems were examined taxonomically. The isolated bacterial strains were identified based on 16S rRNA gene sequences, and those exhibiting at least 98.7% sequence similarity with known bacterial species but never reported in Korea were selected as unrecorded species. As an outcome of this study, 10 unrecorded bacterial species belonging to the phylum Firmicutes were discovered from various sources such as soil, tidal flat, fresh water, sea water, kimchi and gut of Fulvia mutica. The unrecorded species were assigned to 7 different genera of 5 families, namely Bacillus and Ornithinibacillus of Bacillaceae, Exiguobacterium of Exiguobacteriaceae, Brevibacillus and Paenibacillus of Paenibacillaceae, Staphylococcus of Staphylococcaceae, and Lactococcus of Streptococcaceae. The selected isolates were subjected to further taxonomic characterization including the analysis of Gram reaction, cellular and colonial morphology, biochemical activities, and phylogenetic trees. The descriptive information on the 10 unrecorded species are provided.

• The Plant Pathology Journal
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• 제38권4호
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• pp.304-312
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• 2022

Boxwood is a representative ornamental shrub that is widely used in landscaping horticulture. After pruning, damaged leaves or stems of boxwoods are unavoidably vulnerable to infection by various plant pathogens. Several boxwood diseases caused by fungi, such as Volutella blight and Macrophoma leaf spot, have been reported worldwide including Republic of Korea. In this study, we isolated and identified fungal pathogens of boxwood diseases that occurred in Korea and characterized their morphological and taxonomic characteristics. Boxwood samples showing blight symptoms were collected in Seoul, Republic of Korea, and the putative fungal pathogens Pseudonectria buxi, P. foliicola, and Neofusicoccum buxi were successfully identified. Investigation of the morphological features of the field isolates, including mycelial growth and conidial morphology, and phylogenetic analysis of multiple DNA barcode loci revealed that there were some morphological and genetic variations among isolates, but all of the analyzed isolates were closely related to the corresponding reference strains. We also found that P. foliicola strains were more virulent than P. buxi, and the N. buxi strains isolated in this study were weak pathogens or saprophytes. The results of our study will contribute to the development of control strategies for boxwood diseases caused by fungi and accelerate research on the complex ecology of boxwood diseases.

• 환경생물
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• 제41권4호
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• pp.657-665
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• 2023

The root-lesion nematode Pratylenchus spp. is the most important plantparasitic nematode due to its worldwide distribution, wide host ranges, and migratory endoparasitic characteristics. One population of Pratylenchus collected from the giant pussy willow (Salix chaenomeloides Kimura) in the Andong area as part of a nematode survey in Korea was characterized morphologically and by molecular methods. The analysis of morphological measurements and morphometric characteristics, as well as DNA sequencing of the rRNA large subunit (LSU) D2/D3 expansion segments and the internal transcribed spacer (ITS) gene sequence, confirmed the identity of this population as P. hippeastri. This study is the first report of P. hippeastri associated with Salix chaenomeloides in Korea and worldwide. Further studies on distribution and pathogenicity in different P. hippeastri host crops, such as grapevines, strawberries, and apples, are necessary. The taxonomic keys to 16 Pratylenchus species in Korea are provided.

• 한국균학회지
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• 제52권1호
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• pp.35-54
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• 2024

With a history spanning 9,000 years, yeast has played a central role in the traditional production of fermented foods, particularly alcohol and bakery. Recent research has highlighted the versatility of yeast in various industries, including the production of bioactive compounds, bioethanol, pigments, and enzymes, and as a host for molecular biology studies. In Korea, yeast isolation has traditionally focused on traditional fermented foods such as soybean paste. However, there is a growing trend in the isolation and characterization of yeasts from natural environments such as flowers and fruits for industrial applications. In this study, we isolated and identified 12 yeasts from various natural environments in Korea, including botanical gardens and parks that are not listed on the National Species List of Korea (NSLK). These newly discovered species included Sakaguchia oryzae, Cystobasidium raffinophilum, Meira argovae, Kazachstania humilis, Meyerozyma smithsonii, Anthracocystis trispicatae, Naganishia brisbanensis, Tremella yokohamensis, Kwoniella shandongensis, Kwoniella newhampshirensis, Aureobasidium proteae, and Rhodotorula dairenensis.

• 한국균학회지
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• 제43권3호
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• pp.149-157
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• 2015

장류와 주류 제조를 위하여 국내에서 유통되는 하경발효의 황국균(HK1), 수원발효의 황국균(SW101), 백국균(SW201), 충무발효의 된장용 황국균(CF1001), 간장용 황국균(CF1002), 청주용 황국균(CF1003), 주류용 백국균(CF1005)과 전통 메주에서 분리하여 산업화 준비를 하고 있는 황국균(KACC 93210)의 분류학적 특성과 안전성을 조사하였다. 공시한 6균주의 황국균은 모두 A. oryzae로 동정되었으며 이중 HK1, SW101, CF1001, CF1003은 분생포자를 생성하는 대(stipe)의 길이가 중간크기($711{\sim}1,121{\mu}m$, 중모(中毛))로써 서로 유사한 형태적 및 분자계통학적 특성을 나타내었으나 청주용인 CF1003이 다른 3균주에 비하여 포자를 다소 적게 그리고 균사를 다소 많이 생성하였다. 간장제조용인 CF1002는 대의 길이가 평균 $543{\mu}m$로서 짧았으며(단모(短毛)) omtA 유전자 분석에서 다른 황국균이 ICAo 그룹에 위치하는 반면에 IBLB-그룹에 소속되어 명쾌히 구분되었다. 전통메주에서 분리되어 산업화 과정에 있는 황국균 KACC93210 균주는 대(stipe)가 평균 $270{\mu}m$로 매우 짧았으며(초단모(超短毛)) 다른 황국균이 양털모양의 집락을 형성하는 반면 벨벳모양의 집락을 형성하여 형태적으로 쉽게 구분되었고 omtA 유전자에서도 공시한 황국균은 물론 세계적으로 보고된 어떤 황국균과도 염기서열이 서로 달랐다. 수원발효의 백국균(SW201)과 충무발효의 백국균(CF1005)은 모두 A. luchuensis (또는 A. luchuensis mut. kawachii)로 동정되었으며 집락 형태가 다소 상이하였으나 기타의 형태적 특징과 분자계통학적 특징에서 서로 구분되지 않았다. 황국균 6균주는 aflatoxin, cyclopiazonic acid, sterigmatocystin의 곰팡이 독소를 생성하지 않았고 백국균(A. luchuensis)은 유해한 독소를 생성하지 않는 것으로 이미 보고되었으므로 국내에 유통되는 황국균과 백국균은 모두 곰팡이독소에서 안전한 곰팡이임이 입증되었다.

• 한국미생물·생명공학회지
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• 제18권5호
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• pp.511-516
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• 1990

토양으로부터 분리한 효모는 내당성, 내알콜성이 있으며 알콜발효능이 우수한 균주를 분리하여 Saccharomyces cerevisiae로 동정하였다. 이 균의 특성을 살펴 본 결과 당농도가 60 배지에서도 생육이 가능한 내당성의 특징과 15(v/v) 이상의 에탄올이 함유된 배지에서는 생육할 수 없고 15(v/v) 에탄올에 2일 침적 후 알콜에 의한 알콜발효능의 저해율은 39.1 저해받았으며 8.0의 생존률을 나타내는 내알콜성특징과 2.0mM의 구리가 함유된 배지에서도 생육할 수 있는 내구리성의 특성을 갖고 있었다. 또한 분리균주의 알콜발효특성을 조사한 결과 배지 초기 pH는 4.5, 배양온도는 $30^{\circ}C$, 초기 당농도는 30일 때가 좋았으며 30 당농도의 배지를 사용하여$30^{\circ}C$ 3일 진탕배양에 의해 50.5의 발효수율이 증가한 14.0(w/v)의 알콜을 생산하였다.

• 한국환경과학회지
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• 제8권4호
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• pp.451-456
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• 1999

Microorganisms utilizing petroleum as substrate were screened from the seawater in Pusan coastal area. Among them, fifty strains utilized bunker-A oil as a sole carbon and energy source. Five of these fifty strains were selected to experiment this study. According to the taxonomic characteristics of its morphological, cultural and biochemical properties, the selected stains were named Pseudomonas sp. EL-12, Flavobacterium sp. EL-15, Acinetobacter sp. EL-18, Enterobacter sp. EL-27 and Micrococcus sp. EL-43, respectively. The optimal medium compositions and cultural conditions for assimilation of bunker-A oil by the selected strains were 1.5-2% bunker-A oil, 0.1% $NH_4NO_3$, 1-1.5% $MgSO_4$.$7H_2O$, 0.05-0.15% KCl, 0.1-0.15% $CaCl_2$.$2H_2O$, 2.5-3.5% NaCl, initial pH 8-9, temperature 3$0^{\circ}C$ and aeration, respectively. The utilization and degradation characteristics on the various hydrocarbons by the selected stains were showed that bunker oil, n-alkane and branched alkane compounds were highly activity than cyclic alkane and aromatic hydrocarbon compounds.

• Journal of Microbiology and Biotechnology
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• 제30권6호
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• pp.804-810
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• 2020

The profitability of the dairy and beef industries is largely affected by the actually achieved reproductive efficiency. Although a large proportion of cows worldwide are bred by artificial insemination (AI) services, many potential factors affecting the outcome of pregnancy by AI remain to be addressed. In the present study, we investigated the vaginal microbiota by high-throughput sequencing of 16S rRNA gene and analyzed their association with differential pregnancy outcomes (i.e., pregnant vs. nonpregnant) of multiple AI services in dairy cows. Sequencing of the V3-V4 region totally produced 512,046 high-quality sequences that were computationally clustered into 2,584 operational taxonomic units (OTUs). All OTUs were taxonomically assigned to 10 bacterial phyla. There were statistically significant differences among the three AI service times (T1, T2 and T3) with respect to the Shannon index and number of observed OTUs (p < 0.05). Bray-Curtis distance-based PCoA analysis also revealed that T2 group could be significantly distinguished from T1 and T3. However, no significant difference between the pregnant and nonpregnant cows was found in confidence regarding both alpha diversity and beta diversity. These results could help us better understand the possible influence of vaginal microbial community on pregnancy outcomes of AI service in cows.