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Jo, Junghyun,Hwang, Sohyun,Kim, Hyung Joon,Hong, Soomin,Lee, Jeoung Eun,Lee, Sung-Geum,Baek, Ahmi,Han, Heonjong,Lee, Jin Il,Lee, Insuk,Lee, Dong Ryul Oxford University Press 2016 Nucleic acids research Vol.44 No.3
<P>Spermatogonial stem cells (SSCs) can spontaneously dedifferentiate into embryonic stem cell (ESC)-like cells, which are designated as multipotent SSCs (mSSCs), without ectopic expression of reprogramming factors. Interestingly, SSCs express key pluripotency genes such as <I>Oct4, Sox2, Klf4</I> and <I>Myc</I>. Therefore, molecular dissection of mSSC reprogramming may provide clues about novel endogenous reprogramming or pluripotency regulatory factors. Our comparative transcriptome analysis of mSSCs and induced pluripotent stem cells (iPSCs) suggests that they have similar pluripotency states but are reprogrammed via different transcriptional pathways. We identified 53 genes as putative pluripotency regulatory factors using an integrated systems biology approach. We demonstrated a selected candidate, <I>Positive cofactor 4</I> (<I>Pc4</I>), can enhance the efficiency of somatic cell reprogramming by promoting and maintaining transcriptional activity of the key reprograming factors. These results suggest that <I>Pc4</I> has an important role in inducing spontaneous somatic cell reprogramming via up-regulation of key pluripotency genes.</P>
Lee, Tak,Yang, Sunmo,Kim, Eiru,Ko, Younhee,Hwang, Sohyun,Shin, Junha,Shim, Jung Eun,Shim, Hongseok,Kim, Hyojin,Kim, Chanyoung,Lee, Insuk Oxford University Press 2015 Nucleic acids research Vol.43 No.d1
<P><I>Arabidopsis thaliana</I> is a reference plant that has been studied intensively for several decades. Recent advances in high-throughput experimental technology have enabled the generation of an unprecedented amount of data from <I>A. thaliana</I>, which has facilitated data-driven approaches to unravel the genetic organization of plant phenotypes. We previously published a description of a genome-scale functional gene network for <I>A. thaliana</I>, AraNet, which was constructed by integrating multiple co-functional gene networks inferred from diverse data types, and we demonstrated the predictive power of this network for complex phenotypes. More recently, we have observed significant growth in the availability of omics data for <I>A. thaliana</I> as well as improvements in data analysis methods that we anticipate will further enhance the integrated database of co-functional networks. Here, we present an updated co-functional gene network for <I>A. thaliana</I>, AraNet v2 (available at http://www.inetbio.org/aranet), which covers approximately 84% of the coding genome. We demonstrate significant improvements in both genome coverage and accuracy. To enhance the usability of the network, we implemented an AraNet v2 web server, which generates functional predictions for <I>A. thaliana</I> and 27 nonmodel plant species using an orthology-based projection of nonmodel plant genes on the <I>A. thaliana</I> gene network.</P>
Lee, Juyong,Lee, Kiho,Joung, InSuk,Joo, Keehyoung,Brooks, Bernard R,Lee, Jooyoung BioMed Central 2015 BMC bioinformatics Vol.16 No.-
<P><B>Background</B></P><P>In template-based modeling when using a single template, inter-atomic distances of an unknown protein structure are assumed to be distributed by Gaussian probability density functions, whose center peaks are located at the distances between corresponding atoms in the template structure. The width of the Gaussian distribution, the variability of a spatial restraint, is closely related to the reliability of the restraint information extracted from a template, and it should be accurately estimated for successful template-based protein structure modeling.</P><P><B>Results</B></P><P>To predict the variability of the spatial restraints in template-based modeling, we have devised a prediction model, Sigma-RF, by using the random forest (RF) algorithm. The benchmark results on 22 CASP9 targets show that the variability values from Sigma-RF are of higher correlations with the true distance deviation than those from Modeller. We assessed the effect of new sigma values by performing the single-domain homology modeling of 22 CASP9 targets and 24 CASP10 targets. For most of the targets tested, we could obtain more accurate 3D models from the identical alignments by using the Sigma-RF results than by using Modeller ones.</P><P><B>Conclusions</B></P><P>We find that the average alignment quality of residues located between and at two aligned residues, quasi-local information, is the most contributing factor, by investigating the importance of input features used in the RF machine learning. This average alignment quality is shown to be more important than the previously identified quantity of a local information: the product of alignment qualities at two aligned residues.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1186/s12859-015-0526-z) contains supplementary material, which is available to authorized users.</P>
( Lee Insuk ) 서울대학교 규장각한국학연구원 2010 Seoul journal of Korean studies Vol.23 No.1
The women known as kisaeng or “courtesans” played a key role as entertainers for the Korean Royal Court before 1910. The political and social situation of the colonial period (1910-1945), when Japanese culture was promoted and Western culture was also gradually introduced, influenced the traditional Korean performing arts as represented by kisaeng. As a consequence, the kisaeng can be seen as pivotal in the transition between the old and the modern in the Korean performing arts. Kisaeng at the Royal Court had to broaden their roles significantly from being performing artists to acting as sex workers. Due to an exaggerated emphasis on the prostitution aspect, kisaeng received a social stigma that made it necessary for them to hide their identities in contemporary Korea. In this article, I examine how kisaengs’ lives were linked to political, economic and ideological forces. I also explore how and why kisaeng organized their training system and expanded their performing repertoire by combining old traditions with new cultural influences in order to meet the expectations of their customers and the Korean public. A wide range of data, including resources on the Japanese colonial policies, the kisaeng school system, Japanese-produced kisaeng postcards, gramophone recordings, and the journal Changhan edited by kisaeng themselves, enables us to understand how and where kisaeng inherited the traditional performing arts and incorporated new trends in culture. I argue that the kisaeng’s experience in the colonial period should be re-evaluated in the light of the overall process of modernization in Korea.
Lee, Yoon Suk,Kim, Haeryoung,Kim, Hyoung Woo,Lee, Jong-Chan,Paik, Kyu-Hyun,Kang, Jingu,Kim, Jaihwan,Yoon, Yoo-Seok,Han, Ho-Seong,Sohn, Insuk,Cho, Jeonghee,Hwang, Jin-Hyeok Williams & Wilkins Co 2015 Medicine Vol.94 No.50
<▼1><P>Supplemental Digital Content is available in the text</P></▼1><▼2><P><B>Abstract</B></P><P>There is limited data on miRNA expression in pancreatic neuroendocrine tumors (PanNETs). In this study, we aimed to identify miRNAs that could be potential prognostic biomarkers of PanNETs in patients who underwent curative surgery.</P><P>For miRNA target screening, 2 primary PanNETs and corresponding liver metastases were screened for miRNA expression by the NanoString nCounter analysis. Candidate miRNAs were selected by ≥2-fold difference of expression between metastatic versus primary tumor. For miRNA target validation, quantitative real-time PCR was performed for candidate miRNAs on 37 PanNETs and matched nonneoplastic pancreata, and the miRNA levels were correlated with the clinicopathological features and patient survival data.</P><P>Eight miRNAs (miRNA-27b, -122, -142–5p, -196a, -223, -590–5p, -630, and -944) were selected as candidate miRNAs. Only miR-196a level was significantly associated with stage, and mitotic count. When PanNETs were stratified into high (n = 10) and low (n = 27) miRNA-196a expression groups, miRNA-196a-high PanNETs were significantly associated with advanced pathologic T stage (50.0% vs 7.4%), N stage (50.0% vs 3.7%), higher mitotic counts (60.0% vs 3.7%), and higher Ki-67-labeling indices (60.0% vs 22.2%). In addition, high miRNA-196a expression was significantly associated with decreased overall survival (<I>P</I> = 0.046) and disease-free survival (<I>P</I> < 0.001) during a median follow-up of 37.9 months with the hazard ratio for recurrence of 16.267 (95% confidence interval = 1.732–153.789; <I>P</I> = 0.015).</P><P>MiRNA-196a level may be a promising prognostic marker of recurrence in resected PanNETs, although further experimental investigation would be required.</P></▼2>
The Peculiar Response of DNA Hydrogel Fibers to a Salt and pH Stimulus
Lee, Sun Hee,Lee, Chang Kee,Shin, Su Ryon,Kim, Sun I.,So, Insuk,Kim, Seon Jeong WILEY-VCH Verlag 2009 Macromolecular Rapid Communications Vol.30 No.6
<P>DNA hydrogels which are composed of an entangled network without a crosslinker are synthesized and examined in regards to their sensitivity to salt and pH changes. The DNA hydrogel fibers only exhibited a marked response – that is a fast and large change in length – under biological conditions ([Na<SUP>+</SUP>] = 0.15 M at pH = 7) and are therefore suitable materials for bio-inspired devices.</P><P> <img src='wiley_img/10221336-2009-30-6-MARC200800677-gra001.gif' alt='wiley_img/10221336-2009-30-6-MARC200800677-gra001'> </P>
Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana
Lee, Insuk,Ambaru, Bindu,Thakkar, Pranjali,Marcotte, Edward M,Rhee, Seung Y Nature Publishing Group 2010 Nature biotechnology Vol.28 No.2
We introduce a rational approach for associating genes with plant traits by combined use of a genome-scale functional network and targeted reverse genetic screening. We present a probabilistic network (AraNet) of functional associations among 19,647 (73%) genes of the reference flowering plant Arabidopsis thaliana. AraNet associations are predictive for diverse biological pathways, and outperform predictions derived only from literature-based protein interactions, achieving 21% precision for 55% of genes. AraNet prioritizes genes for limited-scale functional screening, resulting in a hit-rate tenfold greater than screens of random insertional mutants, when applied to early seedling development as a test case. By interrogating network neighborhoods, we identify AT1G80710 (now DROUGHT SENSITIVE 1; DRS1) and AT3G05090 (now LATERAL ROOT STIMULATOR 1; LRS1) as regulators of drought sensitivity and lateral root development, respectively. AraNet (http://www.functionalnet.org/aranet/) provides a resource for plant gene function identification and genetic dissection of plant traits.
Slow relaxation of randomly packed hard spheres
Lee, Jongjin,Lee, Changwon,Yu, Insuk,Jung, Youngkyun,Lee, Jysoo IOP Pub 2007 Journal of Physics, Condensed Matter Vol.19 No.35
<P>We discover that the apparent weight and the electrical resistance of randomly packed stainless steel balls exhibit unusually slow relaxation behavior. It is found experimentally that these relaxations are due to structural change of the packing. Simultaneous measurements of the apparent weight and the electrical resistance show correlated time dependence. We have also performed two-dimensional molecular dynamics simulations and studied a possible mechanism for the slow relaxation behavior observed in experiments.</P>