Pan-Genomics of Lactobacillus plantarum Revealed Group-Specific Genomic Profiles without Habitat Association

( Sukjung Choi ),( Gwi-deuk Jin ),( Jongbin Park ),( Inhwan You ),( Eun Bae Kim ) 한국미생물생명공학회(구 한국산업미생물학회) 2018 Journal of microbiology and biotechnology Vol.28 No.8

Lactobacillus plantarum is a lactic acid bacterium that promotes animal intestinal health as a probiotic and is found in a wide variety of habitats. Here, we investigated the genomic features of different clusters of L. plantarum strains via pan-genomic analysis. We compared the genomes of 108 L. plantarum strains that were available from the NCBI GenBank database. These genomes were 2.9-3.7 Mbp in size and 44-45% in G+C content. A total of 8,847 orthologs were collected, and 1,709 genes were identified to be shared as core genes by all the strains analyzed. On the basis of SNPs from the core genes, 108 strains were clustered into five major groups (G1-G5) that are different from previous reports and are not clearly associated with habitats. Analysis of group-specific enriched or depleted genes revealed that G1 and G2 were rich in genes for carbohydrate utilization (L-arabinose, L-rhamnose, and fructooligosaccharides) and that G3, G4, and G5 possessed more genes for the restrictionmodification system and MazEF toxin-antitoxin. These results indicate that there are critical differences in gene content and survival strategies among genetically clustered L. plantarum strains, regardless of habitats.

Draft genome sequence of Lactobacillus salivarius KLW001 isolated from a weaning piglet

진귀득,이준영,김은배,Jin, Gwi-Deuk,Lee, Jun-Yeong,Kim, Eun Bae The Microbiological Society of Korea 2017 미생물학회지 Vol.53 No.2

Lactobacillus salivarius KLW001, a species of lactic acid bacteria (LAB), was isolated from a weaning piglet in a swine farm, South Korea, to develop an antimicrobial probiotic strain for piglets. Herein, we report the draft genome sequence of the strain. The genome contains 2,326,706 bp with a G+C content of 33.0% in 166 contigs (${\geq}500bp$). From the genome, we found out 4 genes related to antibiotic resistance, 36 genes for phages, 3 genes for bile hydrolysis, and 27 CRISPR spacers. 이유자돈용 생균제 개발을 위해, 본 연구자들은 유산균의 일종인 Lactobacillus salivairus KLW001 균주를 대한민국 양돈가에서 사육 중인 이유자돈으로부터 분리하였다. 이 균주는 K88 antigen-positive Escherichia coli, Salmonella enterica serovar Typhimurium에 대한 항균 활성이 타 균주보다 우수하여, 우리는 이 균주의 유전체를 분석하였다. 유전체 초안 속의 166개 Contig (${\geq}500bp$)들에서, G+C content (%)가 33.0%였고, 2,326,706 bp 크기의 염기서열을 확보할 수 있었다. 유전체 초안으로부터 항생제 저항 유전자 4개, Phage 관련 유전자 36개, Bile 대사 유전자 3개, CRISPR Spacer 27개를 확인하였다.

Complete genome sequence and SNPs of <i>Raja pulchra</i> (Rajiformes, Rajidae) mitochondria

Hwang, Jae Yeon,Jin, Gwi-Deuk,Park, Jongbin,Kim, Heebal,Lee, Chang-Kyu,Kwak, Woori,Nam, Bo-Hye,An, Cheul Min,Park, Jung Youn,Park, Kyu-Hyun,Huh, Chul-Sung,Kim, Eun Bae Informa UK (Informa Healthcare) 2016 Mitochondrial DNA. Part A Vol.27 No.4

<P>Mitochondrial genomes were sequenced from five Raja pulchra individuals, and single-nucleotide polymorphisms (SNPs) were identified by comparing previously announced sequences in this study. Total 117 SNPs were detected and they were present in 2 rRNA genes, 9 tRNA genes, 13 protein coding genes and non-coding region. One deleted polymorphic site, which was located in 16S rRNA gene, was observed in two individuals. Six polymorphic sites were non-synonymous SNPs, which were distributed in ND1, ND2, ATP6 and ND4 gene. Phylogenic analysis validated current taxa. The genome sequences of R. pulchra mitochondria could be comparable information for understanding species divergence and genomic variation among the populations.</P>

Food components of dried Ulva lactuca and edible green lavers

Jun-Hyun Cho,Hyun-Gyu Nam,Yeong-Deuk Son,Seong-Gwi Ryu,Kwang-Soo Oh 한국수산해양기술학회(구 한국어업기술학회) 2017 한국수산해양기술학회 학술발표대회 Vol.2017 No.11

한국 전통유래식품(청국장)에서 분리한 Enterococcus faecium JB00008 (KACC 92186P) 유산균주의 유전체 분석

박종빈,진귀득,김은배,Park, Jongbin,Jin, Gwi-Deuk,Kim, Eun Bae The Microbiological Society of Korea 2018 미생물학회지 Vol.54 No.2

본 연구에서 이용된 Enterococcus faecium JB00008 (KACC 92186P) 균주는 전통발효식품인 청국장에서 분리되었다. 이 균주는 Escherichia coil에 대해 높은 항균활성능력을 보였다. 우리는 이 균주의 유전체의 염기 서열을 분석하였다. 유전체 초안은 500 bp 이상의 contig 34개로 조립되었으며, 크기가 2,847,295 bp이고, G + C 함량(%)는 37.84%이다. 유전체 초안에서 항균활성물질(bacteriocin) 중 하나인 enterocin과 연관된 유전자가 5개 확인되었다. Enterococcus faecium was commonly used as a probiotics and feed additives to human and animals because of their beneficial effects. We sequenced the genome of E. faecium JB00008 (KACC 92186P) isolated from a Korean fermented soybean paste (Cheonggukjang) that showed antibacterial activity against Escherichia coli. A 2,847,295-bp draft genome was obtained, and it has in 37.84% G + C content in 34 contigs (length, ${\geq}500bp$).

Draft genome sequence of Lactobacillus reuteri KLR3004 from a fattening pig

박종빈,이준영,진귀득,김은배,Park, Jongbin,Lee, Jun-Yeong,Jin, Gwi-Deuk,Kim, Eun Bae The Microbiological Society of Korea 2017 미생물학회지 Vol.53 No.2

국내 비육돈에서 분리된 Lactobacillus reuteri KLR3004 유산균주의 분석을 실시하였다. 이 유전체 초안은 크기가 1,996,237 bp이며 G+C content (%)는 38.75%이다. 이 초안속의 149개 contig들로부터 1,837개의 단백질 코딩 유전자가 예측되었다. We sequenced the genome of Lactobacillus reuteri KLR3004 strain isolated from a fattening pig in South Korea. The sequences were assembled into a draft genome containing 1,996,237 bp with a G+C content of 38.75% and 1,837 predicted protein-coding sequences in 149 contigs.

Pattern of Failure in Bladder Cancer Patients Treated with Radical Cystectomy: Rationale for Adjuvant Radiotherapy

Kim, Yong Bae,Hong, Sung Joon,Yang, Seung Cheol,Cho, Jae Ho,Choi, Young Deuk,Kim, Gwi Eon,Rha, Koon Ho,Han, Woong Kyu,Cho, Nam Hoon,Oh, Young Taek The Korean Academy of Medical Sciences 2010 JOURNAL OF KOREAN MEDICAL SCIENCE Vol.25 No.6

<P>Thus far, the role of adjuvant radiotherapy (RT) after radical cystectomy (RC) in urinary bladder cancer patients has yet to be defined. The purpose of this study is to analyze patterns of failure, and suggest the rationale for RT. Between 1986 and 2005, a total of 259 patients treated with RC and pelvic lymph node dissection was enrolled. The age range was 27-82 yr (median, 62 yr). Node positivity increased according to tumor staging. Patients were divided into the following two groups based on pathologic analysis: organ-confined disease group (n=135) and extravesical/lymph node-positive disease group (n=80). Pelvic failures (PF) were observed in 8 (4.9%) in organ-confined disease group, and 21 (21.7%) in extravesical/lymph node-positive disease group. Five-year PF-free survival rates were 91.2% in organ-confined disease group and 68.0% in extravesical/lymph node-positive disease group. Five-year cancer-specific survival rates were 86.2% in organ-confined disease group and 53.9% in extravesical/lymph node-positive disease group. In conclusion, a relatively high PF rate was observed in extravesical lymph node-negative and lymph node-positive disease patients in this study. Adjuvant pelvic RT may be considered to reduce pelvic failures in extravesical lymph node-positive bladder cancer. Future prospective trials are required to test the clinical benefit of adjuvant RT.</P>

투석용 동정맥루의 혈관성형술 중 발생한 정맥파열: 경피적 치료와 예후$^1$

구동억,김대호,이혜경,홍현숙,권귀향,최득린,Gu, Dong-Eok,Kim, Dae-Ho,Lee, Hye-Gyeong,Hong, Hyeon-Suk,Gwon, Gwi-Hyang,Choe, Deuk-Rin 대한영상의학회 2002 대한영상의학회지 Vol.46 No.3

목적: 기능부전 혈액투석 동정맥루의 혈관성형술 중 발생한 정맥파열의 경피적 치료 및 예후에 대하여 알아보고자 한다. 대상과 방법: 혈관성형술을 시행한 혈액투석 동정맥루 환자 814명 중 정맥파열이 발생한 63(7.7%)명을 대상으로 하였다. 남자 24명 여자 39명이며 나이는 20-78세(평균:55.8)였다. 정맥파열은 모두 말초정맥협착 환자였다. 혈관성형술 후 시행한 정맥조영술에서 조영제 누출이 있으면 정맥파열로 진단하였고 파열부위를 손으로 혈류를 감지하면서 3-5분간 압박하거나, 풍선카테터로 파열부위에서 혈류를 2-3기압으로 3-5분간 차단하였다. 1예는 파열부위에 스텐트를 삽입하였다. 성공적인 지혈 및 혈관성형술을 시행한 경우에서 Kaplan-Meier법으로 개통율을 조사하였다. 또한 말초정맥 파열 없이 혈관성형술을 실시한 경우와 비교하여 개통기간에 차이가 있는지 비교하였다. 결과: 파열부위는 두부정맥 (38), 상완정맥 (16), 기저정맥 (9)이었다. 63명중 54명(85.9%)에서 성공적인 혈관성형술을 시행하였다. 실패한 9명 중 5명은 출혈은 멎었지만 불충분한 확장을 보였고, 상완정맥 및 두부정맥 파열을 보인 2명은 유도철사로 파열부위에서 정맥경로를 찾지 못하였다. 상완정맥 파열로 출혈이 멎지 않은 1명과 두부정맥 파열로 신경압박 증상이 있는 1명은 수술을 하였다. 성공적인 혈관성형술을 시행한 54명에서 6개월의 1차 및 2차 개통율은 47.9, 81.2%이며 6.1개월 및 15.8개월의 평균 개통기간을 보였다. 정맥파열이 없는 경우는 9.6개월의 평균 개통기간을 보였고 (p=0.02)로 통계적인 차이를 보였다. 결론: 혈액투석 동정맥루의 혈관성형술 중 발생한 정맥파열은 경피적으로 치료할 수 있으며, 동정맥루의 기능을 유지할 수 있다. Purpose: To evaluate the usefulness of percutaneous management and prognosis in venous rupture during angioplasty of hemodialytic arteriovenous fistulas. Materials and Methods: Among 814 patients who underwent angioplasty on account of inadequate hemodialysis, 63[39 women and 24 men aged 20-78 (mean, 55.8) years] were included in this study. All 63 had peripheral venous stenosis. Venous rupture was diagnosed when contrast leakage was seen at venography after percutaneous angioplasty (PTA). In order to manage venous rupture, the sites at which this occurred were compressed manually for 3-5 minutes or blood flow was blocked with a balloon catheter for the same period. In one case, a stent was inserted at the rupture site. Using the Kaplan-Meier method, we investigated the patency rate of arteriovenous fistula (AVF) in cases of successful PTA. We also compared PTA patency rates in cases with and without peripheral venous rupture. Results: Venous rupture occurred in 38 cephalic, 16 brachial, and 9 basilic veins. In 63 patients, bleeding stopped and in 54 (85.7%) of these, PTA was successful. Among the nine failed cases, dilatation was incomplete in five, though bleeding had stopped. In patients with brachial and cephalic vein rupture, the venous tract at the rupture site was not located. Two patients underwent surgery: one of these experienced brachial venous rupture, with incontrollable bleeding, and the other had nerve compression symptoms due to hematoma. Among 54 patients in whom PTA was successful, the primary and secondary six-month rates for angioaccess were 47.9% and 81.2%, and the mean patency period was 6.1 and 15.8 months, respectively. In cases of non-venous rupture, the mean patency period was 9.6 months, significantly longer than in cases involving venous rupture (p=0.02). Conclusion: Venous rupture occurring during the PTA of hemodialytic AVF can be managed percutaneously.

하지 연부조직육종을 위한 방사선치료기술 별 선량평가 연구

이솔민,송성찬,현성은,박흥득,이재기,김영석,김귀언,Lee, SolMin,Song, Seongchan,Hyun, Sung Eun,Park, Heung Deuk,Lee, Jaegi,Kim, Young Suk,Kim, Gwi Eon 대한방사선치료학회 2016 대한방사선치료학회지 Vol.28 No.1

A dosimetric evaluation of volumetric modulated arc therapy, intensity modulated radiation therapy, and three-dimensional conformal radiation therapy for the lower extremity soft tissue sarcoma For the lower extremity soft tissue sarcoma, volumetric modulated arc therapy, intensity modulated radiation therapy, and three-dimensional conformal radiation therapy were evaluated to compare these three treatment planning technique. The mean doses to the planning target volume and the femur were calculated to evaluate target coverage and the risk of bone fracture during radiation therapy. Volumetric modulated arc therapy can reduce the dose to the femur without compromising target coverage and reduce the treatment time compared with intensity modulated radiation therapy. 본원에서 수술 후 방사선치료를 수행한 하지 연부조직육종 환자에 대해 용적세기조절회전치료(VMAT), 세기조절방사선치료(IMRT), 3차원입체조영방사선치료(3D-CRT)의 세 가지 치료계획을 수립하여 치료계획용적(PTV)과 대퇴골에 전달되는 방사선량을 각각 비교하였다. 세 치료계획방법 모두 치료계획용적에 전달되는 방사선량은 큰 차이를 보이지 않았으나 용적세기조절회전치료와 세기조절방사선치료의 경우 3차원입체조영방사선치료보다 대퇴골에 전달되는 방사선량을 줄일 수 있었다. 또한 용적세기조절회전치료의 경우 세기조절방사선치료 보다 치료에 필요한 monitor unit이 적어 치료시간 감소의 효과가 나타났다. 따라서 하지 연부조직육종 방사선치료 시 용적세기조절회전치료의 사용은 효과적인 방사선치료를 수행할 수 있을 것이라 사료된다.