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Gevab: a prototype genome variation analysis browsing server
Kim, Woo-Yeon,Kim, Sang-Yoon,Kim, Tae-Hyung,Ahn, Sung-Min,Byun, Ha Na,Kim, Deokhoon,Kim, Dae-Soo,Lee, Yong Seok,Ghang, Ho,Park, Daeui,Kim, Byoung-Chul,Kim, Chulhong,Lee, Sunghoon,Kim, Seong-Jin,Bhak, BioMed Central 2009 BMC bioinformatics Vol.10 No.suppl15
<P><B>Background</B></P><P>The first Korean individual diploid genome sequence data (KOREF) was publicized in December 2008.</P><P><B>Results</B></P><P>A Korean genome variation analysis and browsing server (Gevab) was constructed as a database and web server for the exploration and downloading of Korean personal genome(s). Information in the Gevab includes SNPs, short indels, and structural variation (SV) and comparison analysis between the NCBI human reference and the Korean genome(s). The user can find information on assembled consensus sequences, sequenced short reads, genetic variations, and relationships between genotype and phenotypes.</P><P><B>Conclusion</B></P><P>This server is openly and publicly available online at http://koreagenome.org/en/ or directly http://gevab.org.</P>
( Youngdeuk Lee ),( Eunyoung Jo ),( Yeon-ju Lee ),( Sachithra Amarin Hettiarachchi ),( Gun-hoo Park ),( Su-jin Lee ),( Soo-jin Heo ),( Do-hyung Kang ),( Chulhong Oh ) 한국미생물생명공학회(구 한국산업미생물학회) 2018 Journal of microbiology and biotechnology Vol.28 No.5
The agarase gene gaa16a was identified from a draft genome sequence of Gilvimarinus agarilyticus JEA5, an agar-utilizing marine bacterium. Recently, three agarase-producing bacteria, G. chinensis, G. polysaccharolyticus, and G. agarilyticus, in the genus Gilvimarinus were reported. However, there have been no reports of the molecular characteristics and biochemical properties of these agarases. In this study, we analyzed the molecular characteristics and biochemical properties of agarases in Gilvimarinus. Gaa16A comprised a 1,323-bp open reading frame encoding 441 amino acids. The predicted molecular mass and isoelectric point were 49 kDa and 4.9, respectively. The amino acid sequence of Gaa16A showed features typical of glycosyl hydrolase family 16 (GH16) β-agarases, including a GH16 domain, carbohydrate-binding region (RICIN domain), and signal peptide. Recombinant Gaa16A (excluding the signal peptide and carbohydrate-binding region, rGaa16A) was expressed as a fused protein with maltose-binding protein at its N-terminus in Escherichia coli. rGaa16A had maximum activity at 55°C and pH 7.0 and 103 U/mg of specific activity in the presence of 2.5 mM CaCl2. The enzyme hydrolyzed agarose to yield neoagarotetraose as the main product. This enzyme may be useful for industrial production of functional neoagaro-oligosaccharides.
Comparison of Two PCR Assays for Trichomonas vaginalis
노창석,김상수,박성열,문홍상,Yeon-ChulHONG,류재숙 대한기생충학ㆍ열대의학회 2019 The Korean Journal of Parasitology Vol.57 No.1
PCR is known to be the most sensitive method for diagnosing Trichomonas vaginalis infections. This study aimed to compare the sensitivity of a PCR assay for trichomoniasis (HY-PCR) developed in Hanyang University with the use of a Seeplex Ace Detection Kit®, using urine collected from four Korean men with prostatic disease. Overall, HY-PCR was more sensitive than the Seeplex Kit. The use of Chelex 100 is recommended for DNA isolation in order to increase the sensitivity of the PCR test.
The First Case of Cutaneous Acanthamoebiasis Caused by Acanthamoeba triangularis in Korea
최미수,명나혜,서민,장석빈,윤대관,염규진,정동일,박병철,Yeon-ChulHONG,김명화 대한피부과학회 2023 Annals of Dermatology Vol.35 No.-
A 62-year-old man with multiple myeloma visited our clinic with multiple painful erythem- atous to purpuric nodules on his whole body. He received a skin biopsy which showed septal and lobular inf lammation with vasculitis, and multiple amoebic organisms were found. Polymerase chain reaction and culture were performed and an Acanthamoeba triangularis infection was diagnosed. This is the first report on cutaneous acanthamoebiasis caused by A. triangularis, suggesting that A. triangularis should be regarded as a clinical pathogen that can cause ocular as well as disseminated infection.
( Youngdeuk Lee ),( Taeho Kim ),( Won-kyu Lee ),( Yong-kyun Ryu ),( Ji Hyung Kim ),( Younsik Jeong ),( Areumi Park ),( Yeon-ji Lee ),( Chulhong Oh ),( Do-hyung Kang ) 한국미생물생명공학회(구 한국산업미생물학회) 2021 Journal of microbiology and biotechnology Vol.31 No.2
Leptolyngbya sp. KIOST-1 (LK1) is a newly isolated cyanobacterium that shows no obvious cytotoxicity and contains high protein content for both human and animal diets. However, only limited information is available on its toxic effects. The purpose of this study was to validate the safety of LK1 powder. Following Organisation for Economic Co-operation and Development (OECD) guidelines, a single-dose oral toxicity test in Sprague Dawley rats was performed. Genotoxicity was assessed using a bacterial reverse mutation test with Salmonella typhimurium (strains TA98, TA100, TA1535, and TA1537) and Escherichia coli WP2 uvrA, an in vitro mammalian chromosome aberration test using Chinese hamster lung cells, and an in vivo mammalian erythrocyte micronucleus test using Hsd:ICR (CD-1) SPF mouse bone marrow. After LK1 administration (2,500 mg/kg), there were no LK1-related body weight changes or necropsy findings. The reverse mutation test showed no increased reverse mutation upon exposure to 5,000 μg/plate of the LK1 powder, the maximum tested amount. The chromosome aberration test and micronucleus assay demonstrated no chromosomal abnormalities and genotoxicity, respectively, in the presence of the LK1 powder. The absence of physiological findings and genetic abnormalities suggests that LK1 powder is appropriate as a candidate biomass to be used as a safe food ingredient.
Su-Min Song,Hae Soo Yun,Dorene Van Bik,Hyun Ha Chang,Sang-Ah Lee,Shin-WooKim,Nam Hee Ryoo,Dong Yeub Eun,이난영,Youn-Kyoung Goo,Yeon-ChulHONG,Meesun Ock,차희재,Dong-Il Chung 대한기생충학ㆍ열대의학회 2019 The Korean Journal of Parasitology Vol.57 No.4
From October 2015 to August 2018, tapeworm proglottids were obtained from 10 patients who were residents of Daegu and Gyeongbuk provinces and had a history of raw beef consumption. Most of them had no overseas travel experience. The gravid proglottids obtained from the 10 cases had 15-20 lateral uterine branches. A part of internal tran- scribed spacer 1 (ITS1) DNA of the 10 cases, amplified by polymerase chain reaction (PCR) and digested with AleI restric- tion enzyme, produced the same band pattern of Taenia saginata, which differentiated from T. asiatica and T. solium. Se- quences of ITS1 and cytochrome c oxidase subunit 1 (cox1) showed higher homology to T. saginata than to T. asiatica and T. solium. Collectively, these 10 cases were identified as T. saginata human infections. As taeniasis is one of the im- portant parasitic diseases in humans, it is necessary to maintain hygienic conditions during livestock farming to avoid public health concerns.