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Lee, Youn Yeop,Lee, Jae Kook,Park, Kwan Ho,Kim, Seo-Yeon,Roh, Seong Woon,Lee, Sang-Beom,Choi, Youngcheol,Lee, Sung-Jae International Union of Microbiological Societies 2013 International journal of systematic and evolutiona Vol.63 No.11
<P>A novel Gram-stain-negative, facultatively anaerobic, non-motile and short rod-shaped bacterium, strain KBL009<SUP>T</SUP>, was isolated from the larval gut of <I>Hermetia illucens</I>. Strain KBL009<SUP>T</SUP> grew optimally at 37 °C, at pH 6.0 and with 1–2 % (w/v) NaCl. The 16S rRNA gene sequence of strain KBL009<SUP>T</SUP> showed 97.6 % similarity to that of <I>Paenalcaligenes hominis</I> CCUG 53761A<SUP>T</SUP> indicating its classification with the genus <I>Paenalcaligenes</I>. The major fatty acids were cyclo-C<SUB>17 : 0</SUB>, C<SUB>16 : 0</SUB> and summed feature 2 (comprising C<SUB>14 : 0</SUB> 3-OH/iso-C<SUB>16 : 1</SUB>). The respiratory quinones were ubiquinone-8 (Q-8), predominating, and a minor amount of Q-7. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unknown aminolipid and five unknown polar lipids. The polyamine pattern contained predominantly putrescine and relatively high amounts of spermidine. The betaproteobacterial-specific 2-hydroxyputrescine could only be detected in trace amounts. The G+C content of genomic DNA was 56.1 mol%. Results from DNA–DNA hybridization with <I>P. hominis</I> KCTC 23583<SUP>T</SUP> unambiguously demonstrated that strain KBL009<SUP>T</SUP> represents a novel species in the genus <I>Paenalcaligenes</I>. Based on phenotypic, genotypic and phylogenetic characterization, the novel species <I>Paenalcaligenes hermetiae</I> sp. nov. is proposed. The type strain is KBL009<SUP>T</SUP> ( = KACC 16840<SUP>T</SUP> = JCM 18423<SUP>T</SUP>). An emended description of the genus <I>Paenalcaligenes</I> is also provided.</P>
Lee, Sang-Yeop,Oh, Man Hwan,Yun, Sung Ho,Choi, Chi-Won,Park, Edmond Changkyun,Song, Hyun Seok,Lee, Hayoung,Yi, Yoon-Sun,Shin, Juhyun,Chung, Chaeuk,Moon, Jae Young,Lee, Je Chul,Kim, Gun-Hwa,Kim, Seung Elsevier 2018 INFECTION GENETICS AND EVOLUTION Vol.65 No.-
<P><B>Abstract</B></P> <P>Extensively drug-resistant (XDR) <I>Acinetobacter baumannii</I> strains have emerged rapidly worldwide. The antibiotic resistance characteristics of XDR <I>A. baumannii</I> strains show regional differences; therefore, it is necessary to analyze both genomic and proteomic characteristics of emerging XDR <I>A. baumannii</I> clinical strains isolated in Korea to elucidate their multidrug resistance. Here, we isolated new sequence type of XDR <I>A. baumannii</I> clinical strain (KAB03) from Korean hospitals and performed comprehensive genome analyses. The strain belongs to new sequence type, ST451. Single nucleotide polymorphism (SNP) analysis with other types of <I>A. baumannii</I> strains revealed that KAB03 has unique SNP pattern in the regions of <I>gyrB</I> and <I>gpi</I> of MLST profiles. <I>A. baumannii</I> KAB03 harbours three antibiotic resistance islands (AbGRI1, 2, and 3). AbGRI1 harbours two copies of Tn<I>2006</I> containing <I>bla</I> <SUB>OXA-23</SUB>, which play an important role in antibiotic resistance. AbGRI2 possesses aminoglycoside resistant gene <I>aph(3′)-Ic</I> and class A β-lactamase <I>bla</I> <SUB>TEM</SUB>. AbGIR3 has macrolide resistant genes and aminoglycoside resistant gene <I>armA</I>. <I>A. baumannii</I> KAB03 harbours mutations in <I>pmrB</I> and <I>pmrC</I>, which are believed to confer colistin resistance. In addition, proteomic and transcriptional analysis of KAB03 confirmed that β-lactamases (ADC-73 and OXA-23), Ade efflux pumps (AdeIJK), outer membrane proteins (OmpA and OmpW), and colistin resistance genes (PmrCAB) were major proteins responsible for antibiotic resistance. Our proteogenomic results provide valuable information for multi-drug resistance in emerging XDR <I>A. baumannii</I> strains belonging to ST451.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Whole genome of an XDR <I>A. baumannii</I> KAB03 belonging to ST451, isolated in South Korea, was analyzed </LI> <LI> <I>A.s baumannii</I> strains belonging to ST451 have unique SNP pattern in the regions of <I>gyrB</I> and <I>gpi</I> of MLST profiles </LI> <LI> Antibiotic resistance proteins of <I>A. baumannii</I> KAB03 were suggested by proteomic and transcriptomic analysis </LI> </UL> </P>
Lee, Sang-Yeop,Yun, Sung Ho,Lee, Yeol Gyun,Choi, Chi-Won,Leem, Sun-Hee,Park, Edmond Changkyun,Kim, Gun-Hwa,Lee, Je Chul,Kim, Seung Il Oxford University Press 2014 The Journal of antimicrobial chemotherapy Vol.69 No.6
<P><B>Objectives</B></P><P>To determine the genomic sequence of extensively drug-resistant <I>Acinetobacter baumannii</I> DU202 and to perform proteomic characterization of antibiotic resistance in this strain using genome data.</P><P><B>Methods</B></P><P>The genome sequence of <I>A. baumannii</I> DU202 was determined using the Hi-Seq 2000 system and comparative analysis was performed to determine the unique characteristics of <I>A. baumannii</I> DU202. Previous proteomic results from the cell wall membrane fraction by one-dimensional electrophoresis and liquid chromatography combined with mass spectrometry analysis (1DE-LC-MS/MS), using the <I>A. baumannii</I> ATCC 17978 genome as a reference, were reanalysed to elucidate the resistance mechanisms of <I>A. baumannii</I> DU202 using strain-specific genome data. Additional proteomic data from the cytosolic fraction were also analysed.</P><P><B>Results</B></P><P>The genome of <I>A. baumannii</I> DU202 consists of 3660 genes and is most closely related to the Korean <I>A. baumannii</I> 1656-2 strain. More than 144 resistance genes were annotated in the <I>A. baumannii</I> DU202 genome, of which 72 that encoded proteins associated with antibiotic resistance were identified in the proteomic analysis of <I>A. baumannii</I> DU202 cultured in tetracycline, imipenem and Luria–Bertani broth (control) medium. Strong induction of β-lactamases, a multidrug resistance efflux pump and resistance–nodulation–cell division (RND) multidrug efflux proteins was found to be important in the antibiotic resistance responses of <I>A. baumannii</I> DU202.</P><P><B>Conclusions</B></P><P>Combining genomic and proteomic methods provided comprehensive information about the unique antibiotic resistance responses of <I>A. baumannii</I> DU202.</P>
Ho Yeop Lee,Byeong Chang Sim,Ha Thi Nga,Ji Sun Moon,Jingwen Tian,Nguyen Thi Linh,Sang Hyeon Ju,Dong Wook Choi,Daiki Setoyama,이현승 대한내분비학회 2022 Endocrinology and metabolism Vol.37 No.6
Background: An excess of thyroid hormones in Graves’ disease (GD) has profound effects on systemic energy metabolism that are currently partially understood. In this study, we aimed to provide a comprehensive understanding of the metabolite changes that occur when patients with GD transition from hyperthyroidism to euthyroidism with methimazole treatment. Methods: Eighteen patients (mean age, 38.6±14.7 years; 66.7% female) with newly diagnosed or relapsed GD attending the endocrinology outpatient clinics in a single institution were recruited between January 2019 and July 2020. All subjects were treated with methimazole to achieve euthyroidism. We explored metabolomics by performing liquid chromatography-mass spectrometry analysis of plasma samples of these patients and then performed multivariate statistical analysis of the metabolomics data. Results: Two hundred metabolites were measured before and after 12 weeks of methimazole treatment in patients with GD. The levels of 61 metabolites, including palmitic acid (C16:0) and oleic acid (C18:1), were elevated in methimazole-naïve patients with GD, and these levels were decreased by methimazole treatment. The levels of another 15 metabolites, including glycine and creatinine,were increased after recovery of euthyroidism upon methimazole treatment in patients with GD. Pathway analysis of metabolomics data showed that hyperthyroidism was closely related to aminoacyl-transfer ribonucleic acid biosynthesis and branched-chain aminoacid biosynthesis pathways. Conclusion: In this study, significant variations of plasma metabolomic patterns that occur during the transition from hyperthyroidism to euthyroidism were detected in patients with GD via untargeted metabolomics analysis.
Current Status of Colloid Formation and Migration International Joint Research Phase IV (2019–2023)
Sang-Ho Lee,Jin-Seok Kim,Seung Yeop Lee,Jang-Soon Kwon 한국방사성폐기물학회 2023 한국방사성폐기물학회 학술논문요약집 Vol.21 No.2
The Colloid Formation and Migration (CFM) international joint research initiative continues as a part of the GTS’s Radionuclide Retardation Programme, which has been in progress since 1984. This project focuses on examining the formation of colloids from a bentonite-engineered barrier system and exploring how these colloids impact the migration of radionuclides in fractured host rock when subjected to advective flow. Phase 1 of the project was launched in 2004 and concluded in early 2008, focusing on preliminary studies related to in-situ boundary conditions, predicting models, and supplementary lab works. Following that, Phase 2 spanned from 2008 to 2013 and aimed at fortifying the field setup by adding three new monitoring boreholes and suitable instrumentation in both the boreholes and tunnel. This phase also tested the system’s resilience while mapping the flow domain. Phase 3 kicked off in January 2014 and extended until December 2018. During this period, the Long-term In-situ Test (LIT) was introduced in May 2014, featuring a set of compacted bentonite rings laced with radionuclide tracers. These were placed in a borehole to serve as a colloid and radionuclide source. CFM Phase 4 initiative commenced in January 2019, marking the successful deployment of the i-BET (In-situ Bentonite Erosion Test). This project component involves placing approximately 50 kg of compacted bentonite in a natural water-conducting shear zone. Korea Atomic Energy Research Institute (KAERI) joined CFM in 2008 to examine the behavior of colloid generation and migration with radionuclides in the Underground Research Laboratory. The fourth phase of the CFM project was also scheduled to include a post-mortem evaluation of the LIT and additional tracer experiments in the well-mapped MI shear zone. This study aims to provide an interim update on the ongoing i-BET, a key component of Phase 4 of the CFM project. We will also discuss the current status of the post-mortem analysis for the LIT experiment. In addition, we will outline plans for the forthcoming Phase VI of the project. These plans will continue to advance our understanding of radionuclide migration and the influence of bentonite-based disposal systems.