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Search Results: 1 - 10 of 1162 matches for " Cheol-Goo Hur "
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Induction of Olfaction and Cancer-Related Genes in Mice Fed a High-Fat Diet as Assessed through the Mode-of-Action by Network Identification Analysis
Youngshim Choi, Cheol-Goo Hur, Taesun Park
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0056610
Abstract: The pathophysiological mechanisms underlying the development of obesity and metabolic diseases are not well understood. To gain more insight into the genetic mediators associated with the onset and progression of diet-induced obesity and metabolic diseases, we studied the molecular changes in response to a high-fat diet (HFD) by using a mode-of-action by network identification (MNI) analysis. Oligo DNA microarray analysis was performed on visceral and subcutaneous adipose tissues and muscles of male C57BL/6N mice fed a normal diet or HFD for 2, 4, 8, and 12 weeks. Each of these data was queried against the MNI algorithm, and the lists of top 5 highly ranked genes and gene ontology (GO)-annotated pathways that were significantly overrepresented among the 100 highest ranked genes at each time point in the 3 different tissues of mice fed the HFD were considered in the present study. The 40 highest ranked genes identified by MNI analysis at each time point in the different tissues of mice with diet-induced obesity were subjected to clustering based on their temporal patterns. On the basis of the above-mentioned results, we investigated the sequential induction of distinct olfactory receptors and the stimulation of cancer-related genes during the development of obesity in both adipose tissues and muscles. The top 5 genes recognized using the MNI analysis at each time point and gene cluster identified based on their temporal patterns in the peripheral tissues of mice provided novel and often surprising insights into the potential genetic mediators for obesity progression.
A computational approach for identifying pathogenicity islands in prokaryotic genomes
Sung Ho Yoon, Cheol-Goo Hur, Ho-Young Kang, Yeoun Hee Kim, Tae Kwang Oh, Jihyun F Kim
BMC Bioinformatics , 2005, DOI: 10.1186/1471-2105-6-184
Abstract: We present a computational method for detecting potential PAIs in complete prokaryotic genomes by combining sequence similarities and abnormalities in genomic composition. We first collected 207 GenBank accessions containing either part or all of the reported PAI loci. In sequenced genomes, strips of PAI-homologs were defined based on the proximity of the homologs of genes in the same PAI accession. An algorithm reminiscent of sequence-assembly procedure was then devised to merge overlapping or adjacent genomic strips into a large genomic region. Among the defined genomic regions, PAI-like regions were identified by the presence of homolog(s) of virulence genes. Also, GIs were postulated by calculating G+C content anomalies and codon usage bias. Of 148 prokaryotic genomes examined, 23 pathogenic and 6 non-pathogenic bacteria contained 77 candidate PAIs that partly or entirely overlap GIs.Supporting the validity of our method, included in the list of candidate PAIs were thirty four PAIs previously identified from genome sequencing papers. Furthermore, in some instances, our method was able to detect entire PAIs for those only partial sequences are available. Our method was proven to be an efficient method for demarcating the potential PAIs in our study. Also, the function(s) and origin(s) of a candidate PAI can be inferred by investigating the PAI queries comprising it. Identification and analysis of potential PAIs in prokaryotic genomes will broaden our knowledge on the structure and properties of PAIs and the evolution of bacterial pathogenesis.PAIs are distinct genetic elements of pathogens encoding various virulence factors such as protein secretion systems, host invasion factors, iron uptake systems, and toxins [1,2]. PAIs are a subset of genomic islands which have been transferred by horizontal gene transfer (HGT) event and confer virulence upon the recipient. PAIs can be identified by features such as the presence of virulence genes, biased G+C content and cod
Evolution of ribosomal DNA-derived satellite repeat in tomato genome
Sung-Hwan Jo, Dal-Hoe Koo, Jihyun F Kim, Cheol-Goo Hur, Sanghyeob Lee, Tae-jin Yang, Suk-Yoon Kwon, Doil Choi
BMC Plant Biology , 2009, DOI: 10.1186/1471-2229-9-42
Abstract: FISH analysis revealed that the satellite repeat showing homology with intergenic spacer (IGS) of rDNA present in the tomato genome. By comparing the sequences representing distinct stages in the divergence of rDNA repeat with those of canonical rDNA arrays, the molecular mechanism of the evolution of satellite repeat is described. Comprehensive sequence analysis and phylogenetic analysis demonstrated that a long terminal repeat retrotransposon was interrupted into each copy of the 18S rDNA and polymerized by recombination rather than transposition via an RNA intermediate. The repeat was expanded through doubling the number of IGS into the 25S rRNA gene, and also greatly increasing the copy number of type I subrepeat in the IGS of 25-18S rDNA by segmental duplication. Homogenization to a single type of subrepeat in the satellite repeat was achieved as the result of amplifying copy number of the type I subrepeat but eliminating neighboring sequences including the type II subrepeat and rRNA coding sequence from the array. FISH analysis revealed that the satellite repeats are commonly present in closely-related Solanum species, but vary in their distribution and abundance among species.These results represent that the dynamic satellite repeats were originated from intergenic spacer of rDNA unit in the tomato genome. This result could serve as an example towards understanding the initiation and the expansion of the satellite repeats in complex eukaryotic genome.The large variety of genome sizes found throughout the plant kingdom is mainly attributed to species-specific differences in ploidy and repetitive DNA content [1]. Repetitive DNA can be divided into two categories: interspersed repeats, which are individual repeat units that are distributed around the genome in an apparently random fashion, and tandem repeated DNA, whose repeat units are placed next to each other in an array. Several previous studies have uncovered interspersed repeats, the retrotransposons, whic
Pepper EST database: comprehensive in silico tool for analyzing the chili pepper (Capsicum annuum) transcriptome
Hyun-Jin Kim, Kwang-Hyun Baek, Seung-Won Lee, JungEun Kim, Bong-Woo Lee, Hye-Sun Cho, Woo Taek Kim, Doil Choi, Cheol-Goo Hur
BMC Plant Biology , 2008, DOI: 10.1186/1471-2229-8-101
Abstract: We built the Pepper EST database to mine the complexity of chili pepper ESTs. The database was built on 122,582 sequenced ESTs and 116,412 refined ESTs from 21 pepper EST libraries. The ESTs were clustered and assembled into virtual consensus cDNAs and the cDNAs were assigned to metabolic pathway, Gene Ontology (GO), and MIPS Functional Catalogue (FunCat). The Pepper EST database is designed to provide a workbench for (i) identifying unigenes in pepper plants, (ii) analyzing expression patterns in different developmental tissues and under conditions of stress, and (iii) comparing the ESTs with those of other members of the Solanaceae family. The Pepper EST database is freely available at http://genepool.kribb.re.kr/pepper/ webcite.The Pepper EST database is expected to provide a high-quality resource, which will contribute to gaining a systemic understanding of plant diseases and facilitate genetics-based population studies. The database is also expected to contribute to analysis of gene synteny as part of the chili pepper sequencing project by mapping ESTs to the genome.Pepper is a member of the family Solanaceae, which is one of the largest families in the plant kingdom and includes more than 3,000 species [1]. The Solanaceae family includes important crops, such as pepper, tomato, tobacco, potato, and eggplant and has been highly cultivated over the years for human nutrition and health. Capsicum species are consumed worldwide and are valued because of their unique color, pungency, and aroma. Capsicum peppers include C. annuum, C. chinense, C. baccatum, C. frutescens, and C. pubescens and are cultivated in different parts of the world. Of these, the varieties of the chili pepper plant species C. annuum, having a modest-sized diploid genome (2n = 24), are the most heavily consumed due to their nutritional value and spicy taste [2]. The chemical that is primarily responsible for the pungency of C. annuum has been identified as capsaicin [3], which elicits numerous b
Comparative analysis of pepper and tomato reveals euchromatin expansion of pepper genome caused by differential accumulation of Ty3/Gypsy-like elements
Minkyu Park, SungHwan Jo, Jin-Kyung Kwon, Jongsun Park, Jong Hwa Ahn, Seungill Kim, Yong-Hwan Lee, Tae-Jin Yang, Cheol-Goo Hur, Byoung-Cheorl Kang, Byung-Dong Kim, Doil Choi
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-85
Abstract: For sequence-level analysis, we generated 35.6 Mb of pepper genomic sequences from euchromatin enriched 1,245 pepper BAC clones. The comparative analysis of orthologous gene-rich regions between both species revealed insertion of transposons exclusively in the pepper sequences, maintaining the gene order and content. The most common type of the transposon found was the LTR retrotransposon. Phylogenetic comparison of the LTR retrotransposons revealed that two groups of Ty3/Gypsy-like elements (Tat and Athila) were overly accumulated in the pepper genome. The FISH analysis of the pepper Tat elements showed a random distribution in heterochromatic and euchromatic regions, whereas the tomato Tat elements showed heterochromatin-preferential accumulation.Compared to tomato pepper euchromatin doubled its size by differential accumulation of a specific group of Ty3/Gypsy-like elements. Our results could provide an insight on the mechanism of genome evolution in the Solanaceae family.The Solanaceae is an unusually divergent family consisting of approximately 90 genera and 3,000-4,000 species [1]. Members of the Solanaceae have evolved into extremely divergent forms, ranging from trees to annual herbs, and they occupy diverse habitats ranging from deserts to aquatic areas [1]. Such hyper-diversity in one family makes it useful to study plant adaptation and diversification. Despite this diversity, all Solanaceous species evolved during the last 40 million years [2]. Furthermore, almost all members share the same chromosome number (x = 12) [2].To date, diversity within the Solanaceae has been studied by comparative genome analyses using common genetic markers. As a result, we know that the Solanaceae genomes have undergone relatively small numbers of chromosomal rearrangements (e.g., about 5 rearrangements between potato and tomato and about 30 rearrangements between pepper and tomato), maintaining well-conserved gene content and order [3-8]. The conservation of the Solanaceae
Effect of Autologus Platelet-Rich Plasma on IL-6, MMP-3 and MCP-1 Expression in Synoviocytes from Osteoarthritic Patients Knees  [PDF]
Chang Ich Hur, Cheol Park, Hanlou Li, Jong Keun Seon, Hyun Keun Kim, Taek Rim Yoon, Eun-Kyoo Song
Open Journal of Regenerative Medicine (OJRM) , 2014, DOI: 10.4236/ojrm.2014.33008
Abstract: Nowadays, some studies reported promising results of platelet-rich plasma (PRP) for the treatment of osteoarthritis (OA). However, the effects of PRP on prevention of osteoarthritis in knee joints have been debated. The present study investigated the effects of PRP on osteoarthritis related inflammatory cytokines expressed in fibroblast-like synoviocytes (FLS) from osteoarthritic knees. The synovial tissues were harvested from eight osteoarthritic patients who had undertaken total knee arthroplasties (TKAs) and cultured in DMEM containing 10% FBS. Platelet-rich plasma releasate (PRPr) was made by clotting or activation of PRP by citrate. The levels of PDGF-AA and VEGF in PRPr and whole blood were measured with ELISA method. The FLS were isolated and cultured from osteoarthritic knees. The IL-1β stimulated FLS were cultivated with three different conditions (none, 1% and 10% of PRP). To determine the expression of IL-6, MMP-3, and MCP-1, we used reverse transcriptase polymerase chain reaction (RT-PCR). The concentrations of platelet count in PRP were about 7 to 9 times higher than those of whole blood. The levels of PDGF-AA in PRPr were approximately 3 to 4 times higher than those of whole blood. The levels of VEGF in PRPr were also significantly 7 to 18 times higher than those of whole blood. Without induction of the FLS with IL-1β, 1% or 10% PRPr did not reduce expressions of inflammatory proteins (MMP-3, MCP-1), except for IL-6. However, with induction of the FLS with IL-1β, both concentrations (1% and 10%) of PRPr reduced significantly all inflammatory protein expressions (IL-6, MMP-3, MCP-1). PRPr diminished inflammatory IL-1β-mediated effects on human osteoarthritic fibroblast-like synoviocytes. These results suggest that platelet-rich plasma can be a good therapeutic option for the treatment of osteoarthritis.
Effect of Liquid Ga on Metal Surfaces: Characterization of Morphology and Chemical Composition of Metals Heated in Liquid Ga
Eun Je Lee,Min Goo Hur,Jeong Mun Son,Jeong Hoon Park
Journal of Nanomaterials , 2013, DOI: 10.1155/2013/619682
Abstract:
Biomechanical Properties of Insect Wings: The Stress Stiffening Effects on the Asymmetric Bending of the Allomyrina dichotoma Beetle's Hind Wing
Ngoc San Ha, Quang Tri Truong, Nam Seo Goo, Hoon Cheol Park
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0080689
Abstract: Although the asymmetry in the upward and downward bending of insect wings is well known, the structural origin of this asymmetry is not yet clearly understood. Some researchers have suggested that based on experimental results, the bending asymmetry of insect wings appears to be a consequence of the camber inherent in the wings. Although an experimental approach can reveal this phenomenon, another method is required to reveal the underlying theory behind the experimental results. The finite element method (FEM) is a powerful tool for evaluating experimental measurements and is useful for studying the bending asymmetry of insect wings. Therefore, in this study, the asymmetric bending of the Allomyrina dichotoma beetle's hind wing was investigated through FEM analyses rather than through an experimental approach. The results demonstrated that both the stressed stiffening of the membrane and the camber of the wing affect the bending asymmetry of insect wings. In particular, the chordwise camber increased the rigidity of the wing when a load was applied to the ventral side, while the spanwise camber increased the rigidity of the wing when a load was applied to the dorsal side. These results provide an appropriate explanation of the mechanical behavior of cambered insect wings, including the bending asymmetry behavior, and suggest an appropriate approach for analyzing the structural behavior of insect wings.
An Evaluation of Relative Damage to the Powertrain System in Tracked Vehicles
Sang-Ho Lee,Jeong-Hwan Lee,Sang-Hwa Goo,Yong-Cheol Cho,Ho-Young Cho
Sensors , 2009, DOI: 10.3390/s90301845
Abstract: The objective of this study was to improve the reliability of the endurance test for the powertrain system of military tracked vehicles. The measurement system that measures the driving duty applied to the powertrain system caused by mobility on roads consists of eight analog channels and two pulse channels, including the propeller shaft output torques for the left and right sides. The data obtained from this measurement system can be used to introduce a new technology that produces the output torque of a torque converter and that can be applied to analyze the revolution counting for the endurance and road mobility in the front unit and represent the relative fatigue damages analysis technique and its results according to the driven roads through a cumulative fatigue method.
Comparison between the Therapeutic Effect of Metformin, Glimepiride and Their Combination as an Add-On Treatment to Insulin Glargine in Uncontrolled Patients with Type 2 Diabetes
Cheol-Young Park, Jun Goo Kang, Suk Chon, Junghyun Noh, Seung Joon Oh, Chang Beom Lee, Sung Woo Park
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0087799
Abstract: Aims To compare the commonly prescribed oral anti-diabetic drug (OAD) combinations to use as an add-on therapy with insulin glargine in patients with uncontrolled type 2 diabetes despite submaximal doses of OADs. Methods People with inadequately controlled type 2 diabetes (n = 99) were randomly assigned on a 1:1:1 basis to receive insulin glargin, with fixed doses of glimepiride, metformin, and glimepiride plus metformin. Outcomes assessed included HbA1c, the changes in fasting glucose levels, body weight, serum lipids values, insulin dose and symptomatic hypoglycemia. Results After 24 weeks, HbA1C levels improved from (mean ± SD) 8.5±0.9% to 7.7±0.8% (69.0±10.0 mmol/mol to 60.8±8.6 mmol/mol) with insulin glargine plus metformin, from 8.4±1.0% to 7.7±1.3% (68.8±10.6 mmol/mol to 61.1±14.4 mmol/mol) with insulin glargine plus glimepiride and from 8.7±0.9% to 7.3±0.6% (71.7±9.8 mmol/mol to 56.2±6.7 mmol/mol) with insulin glargine plus glimepirde plus metformin. The decrease in HbA1c was more pronounced with insulin glargine plus glimepiride plus metformin than with insulin glargine plus metformin (0.49% [CI, 0.16% to 0.82%]; P = 0.005) (5.10 mmol/mol [CI, 1.64 to 8.61]; P = 0.005) and insulin glargine plus glimepiride (0.59% [CI, 0.13% to 1.05%]; P = 0.012) (5.87 mmol/mol [CI, 1.10 to 10.64]; P = 0.012) (overall P = 0.02). Weight gain and the risk of hypoglycemia of any type did not significantly differ among the treatment groups. Conclusion The combination therapy of metformin and glimepiride plus glargine insulin resulted in a significant improvement in overall glycemic control as compared with the other combinations. Trial registration information ClinicalTrials.gov, NCT00708578. The approval number of Kangbuk Samsung hospital's institutional review board (IRB): C0825.
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