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Search Results: 1 - 10 of 43700 matches for " Chang-Kyu Lee "
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Round-robin test on thermal conductivity measurement of ZnO nanofluids and comparison of experimental results with theoretical bounds
Lee Wook-Hyun,Rhee Chang-Kyu,Koo Junemo,Lee Jaekeun
Nanoscale Research Letters , 2011,
Abstract: Ethylene glycol (EG)-based zinc oxide (ZnO) nanofluids containing no surfactant have been manufactured by one-step pulsed wire evaporation (PWE) method. Round-robin tests on thermal conductivity measurements of three samples of EG-based ZnO nanofluids have been conducted by five participating labs, four using accurate measurement apparatuses developed in house and one using a commercial device. The results have been compared with several theoretical bounds on the effective thermal conductivity of heterogeneous systems. This study convincingly demonstrates that the large enhancements in the thermal conductivities of EG-based ZnO nanofluids tested are beyond the lower and upper bounds calculated using the models of the Maxwell and Nan et al. with and without the interfacial thermal resistance.
Ground beetle (Coleoptera: Carabidae) assemblage in the urban landscape, Korea
Jong-Kook Jung,Seung-Tae Kim,Sue-Yeon Lee,Chang-Kyu Park
Journal of Ecology and Field Biology , 2012,
Abstract: This study was conducted with the intention of clarifying the effects of land-use types on a species of ground beetle’s richness,abundance, and composition; the study focused on urban landscapes. We also selected the potential bioindicatorsclassifying land-use types; eleven sites were selected from an urban landscape in Korea. Overall, land-use types in urbanlandscapes did not appear to cause significant decrease in species richness or the abundance of total ground beetle assemblage.According to habitat preferences, several land-use types and distances from the forest significantly affectedthe species richness and abundance, while the open-habitat species were not affected by these variables. Land-use typeswere classified into two major groups, forest and non-forest areas, based on ground beetle assemblage; several indicators,such as Dolichus halensis halensis and subfamily Carabinae species, were of particular consideration. In conclusion, environmentalchange by anthropogenic disturbance can cause different effects on ground beetle assemblages, and forestspecialists can be negatively affected.
Identification of the Porcine XIST Gene and Its Differential CpG Methylation Status in Male and Female Pig Cells
Jae Yeon Hwang, Eun Bae Kim, Hakhyun Ka, Chang-Kyu Lee
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0073677
Abstract: XIST, a long non-coding RNA, plays an important role in triggering X chromosome inactivation in eutherians, and is used extensively for qualifying stem cells and cloned embryos. However, a porcine XIST has not yet been thoroughly identified despite its biological importance in a wide variety of research fields. Here, we present a full-length porcine XIST sequence assembled using known sequences (GenBank), RNA-Seq data (NCBI SRA), and PCR/sequencing. The proposed porcine XIST gene model encodes a 25,215-bp transcript consisting of 7 exons, including two conserved and two porcine-specific repeat regions. Transcription covering the entire XIST region was observed specifically in female cells, but not in male cells. We also identified eight transcription starting sites (TSSs) and evaluated CpG methylation patterns in the upstream (+2.0 kb) and downstream (?2.0 kb) regions. Sixty-seven CG di-nucleotides identified in the target region were considered to be candidate CpG sites, and were enriched in the following two regions: ?284 to +53 bp (13 sites) and +285 to +1,727 bp (54 sites) from the selected TSS. Male 5` region of XIST (64.5 sites, 96.26%) had a higher level of CpG methylation than female DNA (33.4 sites, 49.85%). Taken together, our results revealed that the porcine XIST gene is expressed exclusively in female cells, which is influenced by the lower level of CpG methylation in the putative promoter region compared with male cells. The porcine XIST presented in this study represents a useful tool for related research areas such as porcine embryology and stem cell biology.
Epigenetic Changes of Lentiviral Transgenes in Porcine Stem Cells Derived from Embryonic Origin
Kwang-Hwan Choi, Jin-Kyu Park, Hye-Sun Kim, Kyung-Jun Uh, Dong-Chan Son, Chang-Kyu Lee
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0072184
Abstract: Because of the physiological and immunological similarities that exist between pigs and humans, porcine pluripotent cell lines have been identified as important candidates for preliminary studies on human disease as well as a source for generating transgenic animals. Therefore, the establishment and characterization of porcine embryonic stem cells (pESCs), along with the generation of stable transgenic cell lines, is essential. In this study, we attempted to efficiently introduce transgenes into Epiblast stem cell (EpiSC)-like pESCs. Consequently, a pluripotent cell line could be derived from a porcine-hatched blastocyst. Enhanced green fluorescent protein (EGFP) was successfully introduced into the cells via lentiviral vectors under various multiplicities of infection, with pluripotency and differentiation potential unaffected after transfection. However, EGFP expression gradually declined during extended culture. This silencing effect was recovered by in vitro differentiation and treatment with 5-azadeoxycytidine. This phenomenon was related to DNA methylation as determined by bisulfite sequencing. In conclusion, we were able to successfully derive EpiSC-like pESCs and introduce transgenes into these cells using lentiviral vectors. This cell line could potentially be used as a donor cell source for transgenic pigs and may be a useful tool for studies involving EpiSC-like pESCs as well as aid in the understanding of the epigenetic regulation of transgenes.
Analysis of Imprinted Gene Expression in Normal Fertilized and Uniparental Preimplantation Porcine Embryos
Chi-Hun Park, Kyung-Jun Uh, Brendan P. Mulligan, Eui-Bae Jeung, Sang-Hwan Hyun, Taeyoung Shin, Hakhyun Ka, Chang-Kyu Lee
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0022216
Abstract: In the present study quantitative real-time PCR was used to determine the expression status of eight imprinted genes (GRB10, H19, IGF2R, XIST, IGF2, NNAT, PEG1 and PEG10) during preimplantation development, in normal fertilized and uniparental porcine embryos. The results demonstrated that, in all observed embryo samples, a non imprinted gene expression pattern up to the 16-cell stage of development was common for most genes. This was true for all classes of embryo, regardless of parental-origins and the direction of imprint. However, several differentially expressed genes (H19, IGF2, XIST and PEG10) were detected amongst the classes at the blastocyst stage of development. Most interestingly and despite the fact that maternally and paternally expressed genes should not be expressed in androgenones and parthenogenones, respectively, both uniparental embryos expressed these genes when tested for in this study. In order to account for this phenomenon, we compared the expression patterns of eight imprinted genes along with the methylation status of the IGF2/H19 DMR3 in haploid and diploid parthenogenetic embryos. Our findings revealed that IGF2, NNAT and PEG10 were silenced in haploid but not diploid parthenogenetic blastocysts and differential methylation of the IGF2/H19 DMR3 was consistently observed between haploid and diploid parthenogenetic blastocysts. These results appear to suggest that there exists a process to adjust the expression status of imprinted genes in diploid parthenogenetic embryos and that this phenomenon may be associated with altered methylation at an imprinting control region. In addition we believe that imprinted expression occurs in at least four genes, namely H19, IGF2, XIST and PEG10 in porcine blastocyst stage embryos.
SAR Image Simulation in the Time Domain for Moving Ocean Surfaces
Takero Yoshida,Chang-Kyu Rheem
Sensors , 2013, DOI: 10.3390/s130404450
Abstract: This paper presents a fundamental simulation method to generate synthetic aperture radar (SAR) images for moving ocean surfaces. We have designed the simulation based on motion induced modulations and Bragg scattering, which are important features of ocean SAR images. The time domain simulation is able to obtain time series of microwave backscattering modulated by the orbital motions of ocean waves. Physical optics approximation is applied to calculate microwave backscattering. The computational grids are smaller than transmit microwave to demonstrate accurate interaction between electromagnetic waves and ocean surface waves. In this paper, as foundations for SAR image simulation of moving ocean surfaces, the simulation is carried out for some targets and ocean waves. The SAR images of stationary and moving targets are simulated to confirm SAR signal processing and motion induced modulation. Furthermore, the azimuth signals from the regular wave traveling to the azimuth direction also show the azimuthal shifts due to the orbital motions. In addition, incident angle dependence is simulated for irregular wind waves to compare with Bragg scattering theory. The simulation results are in good agreement with the theory. These results show that the simulation is applicable for generating numerical SAR images of moving ocean surfaces.
PPARα siRNA–Treated Expression Profiles Uncover the Causal Sufficiency Network for Compound-Induced Liver Hypertrophy
Xudong Dai ,Angus T. De Souza,Hongyue Dai,David L Lewis,Chang-kyu Lee,Andy G Spencer,Hans Herweijer,Jim E Hagstrom,Peter S Linsley,Douglas E Bassett,Roger G Ulrich,Yudong D He
PLOS Computational Biology , 2007, DOI: 10.1371/journal.pcbi.0030030
Abstract: Uncovering pathways underlying drug-induced toxicity is a fundamental objective in the field of toxicogenomics. Developing mechanism-based toxicity biomarkers requires the identification of such novel pathways and the order of their sufficiency in causing a phenotypic response. Genome-wide RNA interference (RNAi) phenotypic screening has emerged as an effective tool in unveiling the genes essential for specific cellular functions and biological activities. However, eliciting the relative contribution of and sufficiency relationships among the genes identified remains challenging. In the rodent, the most widely used animal model in preclinical studies, it is unrealistic to exhaustively examine all potential interactions by RNAi screening. Application of existing computational approaches to infer regulatory networks with biological outcomes in the rodent is limited by the requirements for a large number of targeted permutations. Therefore, we developed a two-step relay method that requires only one targeted perturbation for genome-wide de novo pathway discovery. Using expression profiles in response to small interfering RNAs (siRNAs) against the gene for peroxisome proliferator-activated receptor α (Ppara), our method unveiled the potential causal sufficiency order network for liver hypertrophy in the rodent. The validity of the inferred 16 causal transcripts or 15 known genes for PPARα-induced liver hypertrophy is supported by their ability to predict non-PPARα–induced liver hypertrophy with 84% sensitivity and 76% specificity. Simulation shows that the probability of achieving such predictive accuracy without the inferred causal relationship is exceedingly small (p < 0.005). Five of the most sufficient causal genes have been previously disrupted in mouse models; the resulting phenotypic changes in the liver support the inferred causal roles in liver hypertrophy. Our results demonstrate the feasibility of defining pathways mediating drug-induced toxicity from siRNA-treated expression profiles. When combined with phenotypic evaluation, our approach should help to unleash the full potential of siRNAs in systematically unveiling the molecular mechanism of biological events.
Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data
Chang-Kyu Lee, Susan M Sunkin, Chihchau Kuan, Carol L Thompson, Sayan Pathak, Lydia Ng, Chris Lau, Shanna Fischer, Marty Mortrud, Cliff Slaughterbeck, Allan Jones, Ed Lein, Michael Hawrylycz
Genome Biology , 2008, DOI: 10.1186/gb-2008-9-1-r23
Abstract: The analysis and interpretation of gene expression data from diverse expression profiling projects present formidable challenges. From a technology perspective, all gene expression profiling methods seek to measure some function of mRNA abundance, and the available platforms include RT-PCR, oligonucleotide and cDNA microarrays, and serial analysis of gene expression (SAGE) [1] and its variants. The recent availability of genomic scale colorimetric in situ hybridization (ISH) data [2] adds still another data modality to the mix, one for which strict quantification is more limited and comparison with existing gene expression data is challenging. To properly interpret data sets such as the Allen Brain Atlas (ABA) [3], it is essential to understand the utility and limits of non-radioactive colorimetric ISH signal and to determine the feasibility of comparing this data modality to the dominant gene expression platforms. This study undertakes this goal, and after a technique for relative signal measurement of colorimetric ISH data is presented, the ABA ISH data [2] are compared with publicly available expression data from two microarray sources [4,5] in six major structures of the C57Bl/6J adult mouse brain.ISH involves anatomic localization of labeled RNA or DNA probes that hybridize to target complementary RNA or DNA sequences in the cell. These hybrids are detected either by using an isotopic probe and emulsion autoradiography, or by non-isotopic methods using specific antibodies to detect a hapten incorporated into the probe [6]. One variation of this methodology involves using dual ISH to detect the expression of two different mRNAs within the same brain section, allowing for the identification of transcripts co-localized in the same cell [7]. Both radioactive and non-isotopic ISH have become powerful tools for detecting and localizing mRNA, particularly in complex tissues with non-uniform structure such as the brain [8,9]. Advantages of radioisotopic ISH are perceiv
Investigation of De Novo Unique Differentially Expressed Genes Related to Evolution in Exercise Response during Domestication in Thoroughbred Race Horses
Woncheoul Park, Jaemin Kim, Hyeon Jeong Kim, JaeYoung Choi, Jeong-Woong Park, Hyun-Woo Cho, Byeong-Woo Kim, Myung Hum Park, Teak-Soon Shin, Seong-Keun Cho, Jun-Kyu Park, Heebal Kim, Jae Yeon Hwang, Chang-Kyu Lee, Hak-Kyo Lee, Seoae Cho, Byung-Wook Cho
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0091418
Abstract: Previous studies of horse RNA-seq were performed by mapping sequence reads to the reference genome during transcriptome analysis. However in this study, we focused on two main ideas. First, differentially expressed genes (DEGs) were identified by de novo–based analysis (DBA) in RNA-seq data from six Thoroughbreds before and after exercise, here-after referred to as “de novo unique differentially expressed genes” (DUDEG). Second, by integrating both conventional DEGs and genes identified as being selected for during domestication of Thoroughbred and Jeju pony from whole genome re-sequencing (WGS) data, we give a new concept to the definition of DEG. We identified 1,034 and 567 DUDEGs in skeletal muscle and blood, respectively. DUDEGs in skeletal muscle were significantly related to exercise-induced stress biological process gene ontology (BP-GO) terms: ‘immune system process’; ‘response to stimulus’; and, ‘death’ and a KEGG pathways: ‘JAK-STAT signaling pathway’; ‘MAPK signaling pathway’; ‘regulation of actin cytoskeleton’; and, ‘p53 signaling pathway’. In addition, we found TIMELESS, EIF4A3 and ZNF592 in blood and CHMP4C and FOXO3 in skeletal muscle, to be in common between DUDEGs and selected genes identified by evolutionary statistics such as FST and Cross Population Extended Haplotype Homozygosity (XP-EHH). Moreover, in Thoroughbreds, three out of five genes (CHMP4C, EIF4A3 and FOXO3) related to exercise response showed relatively low nucleotide diversity compared to the Jeju pony. DUDEGs are not only conceptually new DEGs that cannot be attained from reference-based analysis (RBA) but also supports previous RBA results related to exercise in Thoroughbred. In summary, three exercise related genes which were selected for during domestication in the evolutionary history of Thoroughbred were identified as conceptually new DEGs in this study.
X-Linked Gene Transcription Patterns in Female and Male In Vivo, In Vitro and Cloned Porcine Individual Blastocysts
Chi-Hun Park, Young Hee Jeong, Yeun-Ik Jeong, Se-Yeong Lee, Yeon-Woo Jeong, Taeyoung Shin, Nam-Hyung Kim, Eui-Bae Jeung, Sang-Hwan Hyun, Chang-Kyu Lee, Eunsong Lee, Woo Suk Hwang
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0051398
Abstract: To determine the presence of sexual dimorphic transcription and how in vitro culture environments influence X-linked gene transcription patterns in preimplantation embryos, we analyzed mRNA expression levels in in vivo-derived, in vitro-fertilized (IVF), and cloned porcine blastocysts. Our results clearly show that sex-biased expression occurred between female and male in vivo blastocysts in X-linked genes. The expression levels of XIST, G6PD, HPRT1, PGK1, and BEX1 were significantly higher in female than in male blastocysts, but ZXDA displayed higher levels in male than in female blastocysts. Although we found aberrant expression patterns for several genes in IVF and cloned blastocysts, similar sex-biased expression patterns (on average) were observed between the sexes. The transcript levels of BEX1 and XIST were upregulated and PGK1 was downregulated in both IVF and cloned blastocysts compared with in vivo counterparts. Moreover, a remarkable degree of expression heterogeneity was observed among individual cloned embryos (the level of heterogeneity was similar in both sexes) but only a small proportion of female IVF embryos exhibited variability, indicating that this phenomenon may be primarily caused by faulty reprogramming by the somatic cell nuclear transfer (SCNT) process rather than in vitro conditions. Aberrant expression patterns in cloned embryos of both sexes were not ameliorated by treatment with Scriptaid as a potent HDACi, although the blastocyst rate increased remarkably after this treatment. Taken together, these results indicate that female and male porcine blastocysts produced in vivo and in vitro transcriptional sexual dimorphisms in the selected X-linked genes and compensation of X-linked gene dosage may not occur at the blastocyst stage. Moreover, altered X-linked gene expression frequently occurred in porcine IVF and cloned embryos, indicating that X-linked gene regulation is susceptible to in vitro culture and the SCNT process, which may eventually lead to problems with embryonic or placental defects.
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