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Chung, Won-Hyong,Jeong, Namhee,Kim, Jiwoong,Lee, Woo Kyu,Lee, Yun-Gyeong,Lee, Sang-Heon,Yoon, Woongchang,Kim, Jin-Hyun,Choi, Ik-Young,Choi, Hong-Kyu,Moon, Jung-Kyung,Kim, Namshin,Jeong, Soon-Chun Oxford University Press 2014 DNA research Vol.21 No.2
<P>Despite the importance of soybean as a major crop, genome-wide variation and evolution of cultivated soybeans are largely unknown. Here, we catalogued genome variation in an annual soybean population by high-depth resequencing of 10 cultivated and 6 wild accessions and obtained 3.87 million high-quality single-nucleotide polymorphisms (SNPs) after excluding the sites with missing data in any accession. Nuclear genome phylogeny supported a single origin for the cultivated soybeans. We identified 10-fold longer linkage disequilibrium (LD) in the wild soybean relative to wild maize and rice. Despite the small population size, the long LD and large SNP data allowed us to identify 206 candidate domestication regions with significantly lower diversity in the cultivated, but not in the wild, soybeans. Some of the genes in these candidate regions were associated with soybean homologues of canonical domestication genes. However, several examples, which are likely specific to soybean or eudicot crop plants, were also observed. Consequently, the variation data identified in this study should be valuable for breeding and for identifying agronomically important genes in soybeans. However, the long LD of wild soybeans may hinder pinpointing causal gene(s) in the candidate regions.</P>
Design of long oligonucleotide probes for functional gene detection in a microbial community
Chung, Won-Hyong,Rhee, Sung-Keun,Wan, Xiu-Feng,Bae, Jin-Woo,Quan, Zhe-Xue,Park, Yong-Ha Oxford University Press 2005 Bioinformatics Vol.21 No.22
<P><B>Motivation:</B> Analysis of the functions of microorganisms and their dynamics in the environment is essential for understanding microbial ecology. For analysis of highly similar sequences of a functional gene family using microarrays, the previous long oligonucleotide probe design strategies have not been useful in generating probes.</P><P><B>Results:</B> We developed a Hierarchical Probe Design (HPD) program that designs both sequence-specific probes and hierarchical cluster-specific probes from sequences of a conserved functional gene based on the clustering tree of the genes, specifically for analyses of functional gene diversity in environmental samples. HPD was tested on datasets for the <I>nirS</I> and <I>pmoA</I> genes. Our results showed that HPD generated more sequence-specific probes than several popular oligonucleotide design programs. With a combination of sequence-specific and cluster-specific probes, HPD generated a probe set covering all the sequences of each test set.</P><P><B>Availability:</B> http://brcapp.kribb.re.kr/HPD/</P><P><B>Contact:</B> yhpark@kribb.re.kr</P><P><B>Supplementary information:</B> http://brcapp.kribb.re.kr/HPD/HPD_Supplementary.doc</P>
Improved Optimization of Indirubin Production from Bioreactor Culture of Polygonum tinctorium
Chung, Choong Sik,Kim, Kyung Il,Bae, Geun Won,Lee, Youn Hyung,Lee, Hyong Joo,Chae, Young Am,Chung, In Sik 한국응용생명화학회 2000 Journal of Applied Biological Chemistry (J. Appl. Vol.43 No.2
Effect of the two-stage operation and cell concentration on indirubin production was investigated using bioreactor culture of Polygonum tinctorium. Two-stage culture was operated successfully for 110 days without any adverse effects on continuous indirubin production. Maximum indirubin concentration was found to be at 80 mg/bioreactor. Initial cell concentration significantly affected indirubin production. The indirubin production at 29.2% PCV was improved by 845%, compared to that at 5% PCV. For high-density bioreactor culture of P. tinctorium, a maximum production rate of 10.2 mg indirubin/L day was obtained. Indirubin recovery for bioreactor operation was also examined using XAD-2, XAD-4, XAD-7, and solid silicon. XAD-4 was 1.6-fold more effective than that for solid silicon in indirubin recovery.
올리고뉴클레오타이드 제작을 위해 효율적이고 차별적인 시드를 고르는 방법에 대한 고찰
정원형(Won-Hyong Chung),박성배(Seong-Bae Park) 한국정보과학회 2009 정보과학회논문지 : 시스템 및 이론 Vol.36 No.1
생물정보분야에서 올리고뉴클레오타이드(oligonucleotide)를 제작하는 문제는 시간을 많이 소모하는 문제이다. 이 문제를 해결하기 위하여 해시를 이용한 가속계산이 주로 쓰이고 있고 BLAST란 프로그램이 대표적으로 생물정보분야에서 사용되고 있다. BLAST류의 프로그램들은 DNA서열의 특성에 따라 시드를 변형하여 해시를 개선하는 알고리즘을 적용하여 서열간의 유사도가 높은 부분을 찾는다. 그러나 이 프로그램들은 원래 올리고뉴클레오타이드 제작을 위해서가 아닌 지역정렬 문제를 해결하기 위한 방법들로써 발전하여 왔으므로 본 문제에 효율적인가에 대한 검증이 아직까지 이루어지지 않았다. 우리는 BLAST류의 프로그램에서 사용된 시드(seed)들이 올리고뉴클레오타이드 제작에 효과적인가를 판단할 수 있는 효율적이고 차별적인 잣대를 제시하고 이에 따라 다섯 종류의 대표적인 시드를 평가하였다. 평가에서 spaced seed라는 시드가 가장 좋은 결과를 보임을 정량적으로 계산할 수 있었다. Oligonucleotide design is known as a time-consuming work in Bioinformatics. In order to accelerate the oligonucleotide design process, one of the most widely used approaches is the prescreening unreliable regions using hashing(or seeding) method represented by BLAST. Since the seeding is originally proposed to increase the sensitivity for local alignment, the specificity should be considered as well as the sensitivity for the oligonucleotide design problem. However, a measure of evaluating the seeds regarding how adequate and efficient they are in the oligo design is not yet proposed. we propose a novel measure of evaluating the seeding algorithms based on the discriminability and the efficiency. By the proposed measure, five well-known seeding algorithms are examined. The spaced seed is recorded as the best efficient discriminative seed for oligo design.
복강경하 저위전방절제술 전 병소위치 표시를 위한 점묵으로 파종된 직장암 1예
강형주 ( Hyong Ju Kang ),이보인 ( Bo In Lee ),김병욱 ( Byung Wook Kim ),최황 ( Hwang Choi ),조세현 ( Se Hyun Cho ),최규용 ( Kyu Yong Choi ),채현석 ( Hiun Suk Chae ),한석원 ( Seok Won Han ),정인식 ( In Sik Chung ),김경미 ( Kyoung 대한장연구학회 2005 Intestinal Research Vol.3 No.2
Endoscopic mucosal resection is accepted standard treatment of early gastrointestinal cancer, defined as cancer with involvement confined to the mucosa without lymph node metastasis. Under the therapeutic endoscopy, submucosal saline injection minimize the risks of transmural burn, perforation, bleeding. As laparoscopic colectomy became popular recently, colonoscopic tattooing of lesions to assist for localization in surgical field is in the spotlight. Four submucosal saline injections around the lesion, performed with an injection needle to test for the possibility of EMR, showed an obvious ‘non-lifting sign’. Therefore we performed endoscopic tattooing, and then experienced tumor cell seeding on tattooing site. Manipulation of cancerous tissue with submucosal saline injection or tattooing can have a risk of tumor cell seeding on injection sites at any time. Furthermore, if bowel wall is perforated, peritoneal metastasis or seeding are possible. In this case, we approached and injected saline carefully for prevention of cancer penetration. (Intestinal Research 2005;3:150-153)