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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>
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>
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.
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)
사람과 로봇의 사회적 상호작용을 위한 로봇의 가치효용성 기반 동기-감정 생성 모델
이원형(Won Hyong Lee),박정우(Jeong Woo Park),김우현(Woo Hyun Kim),이희승(Hui Sung Lee),정명진(Myung Jin Chung) 제어로봇시스템학회 2014 제어·로봇·시스템학회 논문지 Vol.20 No.5
People would like to be socially engaged not only with humans but also with robots. One of the most common ways in the robotic field to enhance human robot interaction is to use emotion and integrate emotional concepts into robots. Many researchers have been focusing on developing a robot’s emotional expressions. However, it is first necessary to establish the psychological background of a robot’s emotion generation model in order to implement the whole process of a robot’s emotional behavior. Therefore, this article suggests a robot’s motivational emotion model with value effectiveness from a Higgins’ motivation definition, regulatory focus theory, and Circumplex model. For the test, a game with the best-two-out-of-three rule is introduced. Each step of the game was evaluated by the proposed model. As the results imply, the proposed model generated psychologically appropriate emotions for a robot in the given situation. The empirical survey remains for future work to prove that this research improves social human robot interaction.