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Kim, Yong-Seok,Yi, Hana,Kim, Myung Kyum,Seong, Chi-Nam,Kim, Wonyong,Jeon, Che Ok,Kim, Seung-Bum,Im, Wan-Taek,Joh, Kiseong,Cha, Chang-Jun The National Institute of Biological Resources 2020 Journal of species research Vol.9 No.4
In the project of a comprehensive investigation of indigenous prokaryotic species in Korea, a total of 39 bacterial strains phylogenetically belonging to the classes Betaproteobacteria and Gammaproteobacteria were isolated from various environmental sources such as soil, cultivated soil, sludge, seawater, marine sediment, algae, human, tree, moss, tidal flat, beach sand and lagoon. Phylogenetic analysis based on 16S rRNA gene sequences revealed that 39 strains showed the high sequence similarities (≥98.7%) to the closest type strains and formed robust phylogenetic clades with closely related species in the classes Betaproteobacteria and Gammaproteobacteria. In the present study, we report 14 species of 9 genera of four families of two orders in the class Betaproteobacteria and 25 species of 21 genera of 15 families of eight orders in the class Gammaproteobacteria, which have not been reported in Korea. Morphological, biochemical, and physiological characteristics, isolation sources, and NIBR deposit numbers are described in the species descriptions.
Cyclopropane Intermediates from Insertion Reactions of Platinum-Carbenes: A Route to Heterospiranes
Kim, Kiseong,Kim, Soyung,Oh, Chang Georg 2018 Synlett Vol. No.
<P>Heteroaromatic-anchored enynals with a pendent alkene group were successfully cyclized through a Huisgen-type [3+2] cycloaddition to give a tetracyclic Pt-carbene complex that underwent insertion into the C-H bond in the β-position to give fused cyclopropanes that are otherwise inaccessible. On heating, the cyclopropanes smoothly rearranged to form the corresponding heterospiranes with excellent levels of stereoselectivity and high yields.</P>
Coupling effects on turning points of infectious diseases epidemics in scale-free networks
Kim, Kiseong,Lee, Sangyeon,Lee, Doheon,Lee, Kwang Hyung BioMed Central 2017 BMC bioinformatics Vol.18 No.suppl7
<P><B>Background</B></P><P>Pandemic is a typical spreading phenomenon that can be observed in the human society and is dependent on the structure of the social network. The Susceptible-Infective-Recovered (SIR) model describes spreading phenomena using two spreading factors; contagiousness (β) and recovery rate (γ). Some network models are trying to reflect the social network, but the real structure is difficult to uncover.</P><P><B>Methods</B></P><P>We have developed a spreading phenomenon simulator that can input the epidemic parameters and network parameters and performed the experiment of disease propagation. The simulation result was analyzed to construct a new marker VRTP distribution. We also induced the VRTP formula for three of the network mathematical models.</P><P><B>Results</B></P><P>We suggest new marker VRTP (value of recovered on turning point) to describe the coupling between the SIR spreading and the Scale-free (SF) network and observe the aspects of the coupling effects with the various of spreading and network parameters. We also derive the analytic formulation of VRTP in the fully mixed model, the configuration model, and the degree-based model respectively in the mathematical function form for the insights on the relationship between experimental simulation and theoretical consideration.</P><P><B>Conclusions</B></P><P>We discover the coupling effect between SIR spreading and SF network through devising novel marker VRTP which reflects the shifting effect and relates to entropy.</P>
A report of 21 unreported bacterial species in Korea, belonging to the Betaproteobacteria
Kim, Pil Soo,Cha, Chang-Jun,Cho, Jang-Cheon,Chun, Jongsik,Im, Wan-Taek,Jahng, Kwang Yeop,Jeon, Che Ok,Joh, Kiseong,Kim, Seung Bum,Seong, Chi Nam,Yoon, Jung-Hoon,Bae, Jin-Woo The National Institute of Biological Resources 2016 Journal of species research Vol.5 No.1
As a subset investigation to discover indigenous prokaryotic species in Korea, a total of 21 bacterial strains assigned to the class Betaproteobacteria were isolated from a wide range of environmental samples which collected from fresh water, roots of plants, mineral water and soil from ginseng farm. Phylogenetic analysis based on 16S rRNA gene sequences indicated that 21 isolated strains were most closely related to the class Betaproteobacteria, with high 16S rRNA gene sequence similarity (>99.1%) and constructed a robust phylogenetic clade with the closest species in the class Betaproteobacteria. These isolated species have no previous report or publication in Korea; therefore 17 species in 14 genera of 6 families in the order Burkholderiales, 1 species in the order Methylophilales, 2 species in 2 genera of 1 family in the order Neisseriales are reported for betaproteobacterial species found in Korea. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are also described in the species description section and as an image.
Kim, Hyun Sik,Cha, Chang-Jun,Cho, Jang-Cheon,Im, Wan-Taek,Jahng, Kwang Yeop,Jeon, Che Ok,Joh, Kiseong,Kim, Seung Bum,Seong, Chi Nam,Kim, Wonyong,Yi, Hana,Lee, Soon Dong,Yoon, Jung-Hoon,Bae, Jin-Woo The National Institute of Biological Resources 2017 Journal of species research Vol.6 No.2
In an investigation of indigenous prokaryotic species in Korea, a total of 57 bacterial strains assigned to the classes Betaproteobacteria and Gammaproteobacteria were isolated from diverse environments. Samples were collected from fresh water, natural caves, soil, paddy fields, lakes, sea water, jeotgal (fermented seafood), salt flats, soil from abandoned mines, plant roots, digestive organs of both Japanese crested ibis (Nipponia nippon) and Burmese python (Python molurus bivittatus) and tidal flats. From the high 16S rRNA gene sequence similarity (>98.7%) and formation of robust phylogenetic clades with closely related species, it was determined that each strain belonged to an independent and predefined bacterial species within either the Betaproteobacteria or Gammaproteobacteria. There is no official report or publication that describes these 57 proteobacterial species in Korea. Overall, in the class Betaproteobacteria there were 16 species in 12 genera of 4 families in the order Burkholderiales and two species in two genera of one family in the order Neisseriales. Within the class Gammaproteobacteia, there were five species in four genera of four families in the order Alteromonadales, 12 species in 11 genera of one family in the order Enterobacteriales, four species in four genera of three families in the order Oceanospirillales, 11 species in four genera of two families in the order Pseudomonadales, two species in the order Vibrionales and five species in five genera of one family in the order Xanthomonadales. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source and strain IDs are described in the species description section.
Kim, Min Ji,Kim, Yeong Seok,Cha, Chang-Jun,Im, Wan-Taek,Jeon, Che Ok,Joh, Kiseong,Seong, Chi Nam,Yi, Hana,Kim, Seung Bum The National Institute of Biological Resources 2020 Journal of species research Vol.9 No.1
The phylum Bacteroidetes covers phenotypically diverse groups of Gram negative rods that do not form endospores, and currently includes 6 classes, 6 orders, 33 families and 380 genera. Members of Bacteroidetes can be aerobic and anaerobic heterotrophs, hydrogen utilizing chemolithotrophs, or methylotrophs. They can be isolated from diverse habitats including terrestrial and aquatic environments, environments with extreme physicochemical conditions, and animal and plant hosts. During a series of extensive surveys of prokaryotic species diversity in Korea, bacterial strains belonging to Bacteroidetes were isolated from various sources of aquatic and terrestrial environments. A total of 22 isolates were obtained, which represent 22 unrecorded species in Korea belonging to 14 genera of 6 families. Sixteen species among them were assigned to Flavobacteriaceae, two species were to Sphingobacteriaceae, and single species was to each of the families Bacteroidaceae, Balneolaceae, Chitinophagaceae and Cytophagaceae. At genus level, Chryseobacterium (5 species) and Flavobacterium (5 species) were the most abundant genera, and single species were obtained for the genera Bacteroides, Baloneola, Terrimonas, Dyadobacter, Aquimarina, Arenibacter, Gillisia, Gilvibacter, Salinimicrobium, Winogradskyella, Pedobacter and Sphingobacterium. The detailed descriptions of each unrecorded species are provided.
Kim, Dong-Uk,Seong, Chi-Nam,Jahng, Kwangyeop,Lee, Soon Dong,Cha, Chang-Jun,Joh, Kiseong,Jeon, Che Ok,Kim, Seung-Bum,Kim, Myung Kyum The National Institute of Biological Resources 2018 Journal of species research Vol.7 No.2
In 2016, as a subset study to discover indigenous prokaryotic species in Korea, a total of 15 bacterial strains were isolated and assigned to the class Betaproteobacteria. From the high 16S rRNA gene sequence similarity (>98.8%) and formation of a robust phylogenetic clade with the closest species, it was determined that each strain belonged to each independent and predefined bacterial species. There is no official report that these 15 species have been described in Korea; therefore, 1 strain of the Aquitalea, 5 strains of the Paraburkholderia, 2 strains of the Comamonas, 1 strain of the Cupriavidus, 1 strain of the Diaphorobacter, 2 strains of the Hydrogenophaga, 1 strain of the Iodobacter, 1 strain of the Massilia and 1 strain of the Rhodoferax within the Betaproteobacteria are described for unreported bacterial species in Korea. Gram reaction, colony and cell morphology, basic biochemical characteristics, and isolation sources are also described in the species description section.
A report of 26 unrecorded bacterial species in Korea, belonging to the Bacteroidetes and Firmicutes
Kim, Haneul,Yoon, Jung-Hoon,Cha, Chang-Jun,Seong, Chi Nam,Im, Wan-Taek,Jahng, Kwang Yeop,Jeon, Che Ok,Kim, Seung Bum,Joh, Kiseong The National Institute of Biological Resources 2016 Journal of species research Vol.5 No.1
An outcome of the study to discover indigenous prokaryotic species in Korea, a total of 26 bacterial species assigned to the classes Bacteroidetes and Firmicutes were isolated from diverse environmental samples collected from soil, tidal flat, freshwater, seawater, wetland, plant roots, and fermented foods. From the high 16S rRNA gene sequence similarity (>99.0%) and formation of a robust phylogenetic clade with the closest species, it was determined that each strain belonged to each independent and predefined bacterial species. There is no official report that these 26 species have been described in Korea; therefore 14 strains for the order Flavobacteriales and two strains for the order Cytophagales were assigned to the class Bacteroidetes, and 8 strains for the order Bacillales and 4 strains for the order Lactobacillales were assigned to the class Firmicutes are reported for new bacterial species found in Korea. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are also described in the species description section.