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Grimontia marina sp. nov., a Marine Bacterium Isolated from the Yellow Sea
최아영,김경미,강일남,윤석현,서영상,이윤,조장천 한국미생물학회 2012 The journal of microbiology Vol.50 No.1
A novel species belonging to the genus Grimontia is described in this study. A Gram-negative, chemoheterotrophic, obligately aerobic, catalase- and oxidase-positive, motile by a single polar flagellum, and rod-shaped bacterium, designated IMCC5001T, was isolated from surface seawater of the Yellow Sea. Strain IMCC5001T grew optimally at 30°C in the presence of 3.5% NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate was related most closely to Grimontia hollisae with a sequence similarity of 95.8%, and formed a robust phyletic lineage with Grimontia hollisae. Differential physiological characteristics between the new strain and Grimontia hollisae KCCM 41680T and chemotaxonomic characterization including determination of DNA G+C content, fatty acid methyl esters, quinone composition, and polar lipid profiles justified the assignment of strain IMCC5001T to the genus Grimontia as a novel species. In conclusion, strain IMCC5001T represents a new species, for which the name Grimontia marina sp. nov. is proposed, with the type strain IMCC5001T (=KCTC 22666T =NBRC 105794T).
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Complete genome sequence of Amylibacter sp. IMCC11727 isolated from the East Sea, South Korea
김수민,임연정,강일남,조장천 한국미생물학회 2023 미생물학회지 Vol.59 No.2
The genus Amylibacter belonging to the family Rhodobacteraceae of the class Alphaproteobacteria is known as Gram-negative, aerobic, and rod-shaped bacterium. In this study, we report the complete genome sequence of Amylibacter sp. IMCC11727 (= KCTC 52246 = KACC 18775), isolated from the East Sea of South Korea. The genome of strain IMCC11727 was sequenced using the PacBio RSII platform and subsequently assembled into a single circular contig with a size of 3,452,935 bp and a G + C content of 53.7%. The genome encoded 3,474 proteincoding sequences and genes for 3 rRNAs and 38 tRNAs. Strain IMCC11727 is suggested to be a candidate for a novel species in the genus Amylibacter, with metabolic potential for cobalamin biosynthesis and dimethylsulfoniopropionate (DMSP) degradation.
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Shan-Hui Li,송재호,강일남,Juchan Hwang,Jang-Cheon Cho 한국미생물학회 2020 The journal of microbiology Vol.58 No.6
A Gram-stain-negative, rod-shaped, obligately aerobic, nonflagellated, and chemoheterotrophic bacterium, designated IMCC3088T, was isolated from coastal seawater of the Yellow Sea. The 16S rRNA gene sequence analysis indicated that this strain belonged to the family Halieaceae which shared the highest sequence similarities with Luminiphilus syltensis NOR5-1BT (94.5%) and Halioglobus pacificus S1-72T (94.5%), followed by 92.3–94.3% sequence similarities with other species within the aforementioned family. Phylogenetic analyses demonstrated that strain IMCC3088T was robustly clustered with Luminiphilus syltensis NOR5-1BT within the family Halieaceae. However, average amino acid identity (AAI), percentages of conserved proteins (POCP), average nucleotide identity (ANI), and alignment fraction (AF) between strain IMCC3088T and Luminiphilus syltensis NOR5-1BT were 54.5%, 47.7%, 68.0%, and 16.5%, respectively, suggesting that they belonged to different genera. Whole-genome sequencing of strain IMCC3088T revealed a 3.1 Mbp genome size with a DNA G + C content of 51.7 mol%. The genome encoded diverse metabolic pathways including sulfur oxidation, phenol degradation, and proteorhodopsin phototrophy. Mono-unsaturated fatty acids were found to be the predominant cellular fatty acid components in the strain. Phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol were the primarily identified polar lipids, and ubiquinone-8 was identified as a major respiratory quinone. The taxonomic data collected herein suggested that strain IMCC3088T represented a novel genus and species of the family Halieaceae, for which the name Aequoribacter fuscus gen. nov., sp. nov. is proposed with the type strain (= KACC 15529T = NBRC 108213T).
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이정훈,Sooryun Cheong,Hee-Jung Lee,Miye Kwon,강일남,Eun-Gyoung Oh,Hong-Sik Yu,Soon-Bum Shin,Sang-Jong Kim 한국미생물학회 2010 The journal of microbiology Vol.48 No.5
Noroviruses (NoV) are the key cause of acute epidemic gastroenteritis, and oysters harvested from NoVpolluted sea areas are considered as the significant vectors of viral transmission. To improve NoV detection from oyster using nested reverse transcription-polymerase chain reaction (RT-PCR), we evaluated the sensitivity and specificity of previously published primer pairs and the efficiency of different RNA extraction procedures. Among the primer pairs used for RT-PCR, the sensitivity of GIF1/GIR1-GIF2/GIR1 and GIIF1/GIIR1-GIIF2/GIIR1 was higher than that of other primer pairs used in nested RT-PCR for the detection of NoV genogroup I (NoV GI) and NoV GII from both NoV-positive stool suspension and NoVseeded oyster concentrates, respectively; the resulting products showed neither unspecific bands in the positive samples nor false-positive bands in the negative controls. The extraction of NoV RNA from oyster samples using a QIAamp® Viral RNA Mini kit with a QIAshredderTM Homogenizer pretreatment afforded more efficient recovery (mean recovery for NoV GI and GII, 6.4%) and the procedure was less time consuming (<30 min) than most other RNA extraction procedures. The results of RNA extraction procedure and primer pairs evaluated by nested RT-PCR assay in this study can be useful for monitoring NoV contamination in oysters, which is an indicator of possible public health risks.
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