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Search Results: 1 - 10 of 4710 matches for " Jae-Geun Yoon "
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Comprehensive Analysis of MGMT Promoter Methylation: Correlation with MGMT Expression and Clinical Response in GBM
Nameeta Shah,Biaoyang Lin,Zita Sibenaller,Timothy Ryken,Hwahyung Lee,Jae-Geun Yoon,Steven Rostad,Greg Foltz
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0016146
Abstract: O6-methylguanine DNA-methyltransferase (MGMT) promoter methylation has been identified as a potential prognostic marker for glioblastoma patients. The relationship between the exact site of promoter methylation and its effect on gene silencing, and the patient's subsequent response to therapy, is still being defined. The aim of this study was to comprehensively characterize cytosine-guanine (CpG) dinucleotide methylation across the entire MGMT promoter and to correlate individual CpG site methylation patterns to mRNA expression, protein expression, and progression-free survival. To best identify the specific MGMT promoter region most predictive of gene silencing and response to therapy, we determined the methylation status of all 97 CpG sites in the MGMT promoter in tumor samples from 70 GBM patients using quantitative bisulfite sequencing. We next identified the CpG site specific and regional methylation patterns most predictive of gene silencing and improved progression-free survival. Using this data, we propose a new classification scheme utilizing methylation data from across the entire promoter and show that an analysis based on this approach, which we call 3R classification, is predictive of progression-free survival (HR = 5.23, 95% CI [2.089–13.097], p<0.0001). To adapt this approach to the clinical setting, we used a methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) test based on the 3R classification and show that this test is both feasible in the clinical setting and predictive of progression free survival (HR = 3.076, 95% CI [1.301–7.27], p = 0.007). We discuss the potential advantages of a test based on this promoter-wide analysis and compare it to the commonly used methylation-specific PCR test. Further prospective validation of these two methods in a large independent patient cohort will be needed to confirm the added value of promoter wide analysis of MGMT methylation in the clinical setting.
Massively Parallel Signature Sequencing and Bioinformatics Analysis Identifies Up-Regulation of TGFBI and SOX4 in Human Glioblastoma
Biaoyang Lin,Anup Madan,Jae-Geun Yoon,Xuefeng Fang,Xiaowei Yan,Taek-Kyun Kim,Daehee Hwang,Leroy Hood,Gregory Foltz
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0010210
Abstract: A comprehensive network-based understanding of molecular pathways abnormally altered in glioblastoma multiforme (GBM) is essential for developing effective therapeutic approaches for this deadly disease.
The SOX2 response program in glioblastoma multiforme: an integrated ChIP-seq, expression microarray, and microRNA analysis
Xuefeng Fang, Jae-Geun Yoon, Lisha Li, Wei Yu, Jiaofang Shao, Dasong Hua, Shu Zheng, Leroy Hood, David R Goodlett, Gregory Foltz, Biaoyang Lin
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-11
Abstract: We show that knockdown of the SOX2 gene in LN229 GBM cells reduces cell proliferation and colony formation. We then comprehensively characterize the SOX2 response program by an integrated analysis using several advanced genomic technologies including ChIP-seq, microarray profiling, and microRNA sequencing. Using ChIP-seq technology, we identified 4883 SOX2 binding regions in the GBM cancer genome. SOX2 binding regions contain the consensus sequence wwTGnwTw that occurred 3931 instances in 2312 SOX2 binding regions. Microarray analysis identified 489 genes whose expression altered in response to SOX2 knockdown. Interesting findings include that SOX2 regulates the expression of SOX family proteins SOX1 and SOX18, and that SOX2 down regulates BEX1 (brain expressed X-linked 1) and BEX2 (brain expressed X-linked 2), two genes with tumor suppressor activity in GBM. Using next generation sequencing, we identified 105 precursor microRNAs (corresponding to 95 mature miRNAs) regulated by SOX2, including down regulation of miR-143, -145, -253-5p and miR-452. We also show that miR-145 and SOX2 form a double negative feedback loop in GBM cells, potentially creating a bistable system in GBM cells.We present an integrated dataset of ChIP-seq, expression microarrays and microRNA sequencing representing the SOX2 response program in LN229 GBM cells. The insights gained from our integrated analysis further our understanding of the potential actions of SOX2 in carcinogenesis and serves as a useful resource for the research community.The SOX (SRY-like HMG box) gene family represents a family of transcriptional factors characterized by the presence of a homologous sequence called the HMG (high mobility group) box. The HMG box is a DNA binding domain that is highly conserved throughout eukaryotic species. So far, twenty SOX genes have been identified in humans and mice and they can be divided into 10 subgroups on the basis of sequence similarity and genomic organization [1,2]. SOX genes b
High-Temperature Stable Operation of Nanoribbon Field-Effect Transistors
Choi Chang-Young,Lee Ji-Hoon,Koh Jung-Hyuk,Ha Jae-Geun
Nanoscale Research Letters , 2010,
Abstract: We experimentally demonstrated that nanoribbon field-effect transistors can be used for stable high-temperature applications. The on-current level of the nanoribbon FETs decreases at elevated temperatures due to the degradation of the electron mobility. We propose two methods of compensating for the variation of the current level with the temperature in the range of 25–150°C, involving the application of a suitable (1) positive or (2) negative substrate bias. These two methods were compared by two-dimensional numerical simulations. Although both approaches show constant on-state current saturation characteristics over the proposed temperature range, the latter shows an improvement in the off-state control of up to five orders of magnitude ( 5.2 × 10 6).
Plant Settlement Patterns and Their Effects on Breeding Sites of Little Terns (Sterna albifrons) on Sand Bars on Ganwol Lake
Nam, Jong Min,Jihyun Yoon,Heungtae Kim,Jae Geun Kim
Journal of Ecology and Field Biology , 2008,
Abstract: We analyzed soil characteristics, soil seed banks, and plant communities in a small islet inGanwol Lake from May 2005 to August 2006 to examine the forces driving plant settlement on sand bars andthe effects of plant settlement patterns on nesting sites of little terns (Sterna albifrons). The soil nutrientscontents in a site where the feces of wintering birds accumulate (N: 15.4 mg/kg, P: 10.5 mg/kg, LOI: 0.51%,pH: 6.8) and a site where organic sediments accumulate (N: 20.7 mg/kg, P: 16.4 mg/kg, LOI: 0.40%, pH: 6.6)were much higher those of a control site which was not affected by bird feces and organic sediments (N: 4.1mg/kg, P: 5.4 mg/kg, LOI: 0.41%, pH: 6.7). However, a seed bank was formed only on the site withaccumulated organic sediments. Plant settlement was accelerated by feces from wintering birds and organicsediment accumulation on sand bars in Ganwol Lake. The percentage of area disturbed by human activitiesincreased from 0.2% in May 2005 to 13.9% in August 2006, and the percentage of annual communitiesincreased from 27.5% to 43.3%, but the percentage of open area decreased from 55.2% to 28.0% from May2005 to August 2006. These increases in disturbed area and annual communities decreased the open areafor breeding of little terns. The enlargement of P. communis and T. angustata communities was suppressedby irregular flooding. These results provide useful information for the management of little tern breeding sitesfor conservation purposes.
Optimal environmental range for Juncus effusus, an important plant species in an endangered insect species (Nannopya pygmaea) habitat in Korea
Jihyun Yoon,Heungtae Kim,Jong Min Nam,Jae Geun Kim
Journal of Ecology and Field Biology , 2011,
Abstract: Juncus effusus is mostly found in freshwater wetlands and is widely used for landscaping and creating artificial wetlandsdue to its high ecological value. J. effusus tends to dominate during the early stage (3-10 years) of the second successionin abandoned paddy fields. This study focused on the environmental characteristics of J. effusus to create habitat for anendangered species, Nannopya pygmaea, which lives in wetlands dominated by J. effusus. Considering the distributionof J. effusus and N. pygmaea, 63 quadrats at eight wetlands were investigated between May and June 2006 during thecritically dry period. Fifty-three species from 28 families co-occurred with J. effusus, and Persicaria thunbergii was themost abundant (63.5%). The optimal ranges of distribution (ORD) for the water variables were water depth, -2 to 10 cm;dissolved oxygen, 0.99-3.55 mg/kg, conductivity (CON), 23.40-115.40 μs/cm, total dissolved solid, 12.53-57.60 mg/L;pH, 5.00-6.87; K+, 0.11-1.46 mg/L; Ca2+, 1.53-5.85 mg/L; Na+, 3.16-7.47 mg/L; Mg2+, 0.11-1.96 mg/L; NO3-N, < 0.001-0.072mg/L; NH4-N, 0.005-0.097 mg/L; and PO4-P, 0.006-0.047 mg/L. ORDs for the soil variables were water content, 1.05-2.96%; loss-on ignition method (LOI), 5.07-7.81%; CON, 23.70-59.70 μs/cm; pH, 4.40-5.16; extracted (e) K+, 4.34-15.73cmol/kg; eCa2+, 31.56-191.56 cmol/kg; eNa+, < 0.01-2.61 cmol/kg; eMg, 0.04-19.82 cmol/kg; eNO3-N, 0.514-1.175 mg/kg;eNH4-N, 0.033-0.974 mg/kg, ePO4-P, 0.491-11.552 mg/kg; total nitrogen, 0.016-0.200%; and total carbon, 1.06-2.37%. Theappearance of rush during early succession indicated relatively lower levels of these physicochemical parameters, andthat ORDs should be maintained for the J. effusus community.
Monitoring of non-point source pollutants load from a mixed forest land use

Sung Wan Yoon,Se Woong Chung,Dong Geun Oh,Jae Woon Lee,

环境科学学报(英文版) , 2010,
Abstract: The aim of this study was to determine the unit load of NPS (non-point source) pollutants including organic variables such as BOD (biochemical oxygen demand), COD (chemical oxygen demand) and DOC (dissolved organic carbon), nitrogen and phosphorus constituents, and suspended solids (SS) and their event mean concentration (EMC) of runoff flows from a water-shed of mixed forest land use by intensive field experiments. Field monitoring for continuous measurements of rainfall, flow, and water quality was conducted over 12 storm events during 2008-2009 using automated and manual sampling methods. The EMCs of individual runoff event were estimated for each water quality constituent based on the flow rate and concentration data of runoff discharge. The average EMCs of BOD, COD, DOC, SS, TN (total nitrogen), NH4+-N, NO3--N, TP (total phosphorus), PO43--P from the mixed forest land were 1.794, 3.498, 1.462, 10.269, 0.862, 0.044, 0.634, 0.034, and 0.005 mg/L, respectively. The annual unit loads of BOD, COD, DOC, SS, TN, MV-N, NO3--N, TP and PO43--P were estimated as 66.9, 133.2, 55.5, 429.8, 36.5, 1.6, 26.9, 1.3 and 0.1 kg/(ha·yr), respectively. In addition, affecting parameters on the EMCs were investigated by statistic analysis of the field data. As a result, significant correlations with precipitation, rainfall intensity, and total runoff flows were found in most constituents.
Accumulated organic matter, litterfall production, and decomposition tell us the status of litter dynamics in forests
Jae Geun Kim
Journal of Ecology and Field Biology , 2012,
Abstract: Litterfall dynamics in forests are assessed by estimating biomass production and decomposition. However, there havebeen few studies on how litter dynamics impact the health and management of ecosystems. Here, a new approach tomeasure and assess ecosystem function is presented based on conventional methods using littertraps, litterbags, andthe mass on the forest floor. To assess the status of litter dynamics, the decay rate (k) was estimated from a litterbag experiment,and removal rates (ki) were determined from mass balance on the forest floor at 21 sites on three mountainsin South Korea. The k3 (organic mass ratio of Oi and Oe + Oa + A horizons in November) values in an equilibrium state inSouth Korea were within the range of k ± 0.174 when considering the annual variation of litterfall production. This studyalso suggests that sampling sites for these types of studies should be in the middle, not at the ends, of steady slopes onthe forest floor.
Heavy Metal Accumulation in Oxyloma hirasei from the Upo Wetland
Kim, Heungtae,Jae Geun Kim
Journal of Ecology and Field Biology , 2007,
Abstract: Human activities have enhanced the influx of heavy metals to aquatic ecosystem and changed theabiotic environment such as the sediments supporting benthic organisms. The levels of heavy metals (Cd, Cr,Cu, Ni, Pb and Zn) in the benthic gastropod Oxyloma hirasei and the sediments around their habitat wereinvestigated to examine heavy metal levels and the potential of the gastropod as a bioindicator. We detecteddifferent levels of heavy metals in the sediments of two wetland areas, Upo and Mokpo, in the relativelywell-conserved Upo wetland, Ramsar Convention Area. Oxyloma hirasei had higher concentrations of heavymetals except Cr and Ni in their soft tissues than in their shells (Cd: 2.10~3.16, Cu: 19.73~28.66, Pb: 0.67~1.17, Zn: 216.1~285.7 μg/g dry weight in the soft tissues; Cr: 1.19~2.58, Ni: 0.47~1.16 μg/g dry weight inthe shells). Differences in the Cd, Cu, Ni and Pb concentrations in O. hirasei soft tissues reflected differencesin heavy metal concentrations in the sediments at the sampling sites. The coefficients of variation for Cd, Cuand Pb were lower than those for other metals in the soft tissues. Levels of Cd in the tissues of O. hirasei werethe highest among the metals examined in this study. Therefore, the soft tissue of O. hirasei appears to be apromising bioindicator particularly for Cd.
GSTT2 promoter polymorphisms and colorectal cancer risk
Sang-Geun Jang, Il-Jin Kim, Hio Chung Kang, Hye-Won Park, Sun-A Ahn, Hyun-Ju Yoon, Kun Kim, Hai-Rim Shin, Jin Soo Lee, Jae-Gahb Park
BMC Cancer , 2007, DOI: 10.1186/1471-2407-7-16
Abstract: A total of 436 colorectal cancer patients and 568 healthy controls were genotyped for three GSTT2 promoter SNPs (-537G>A, -277T>C and -158G>A), using real-time TaqMan assay and direct sequencing. An electrophoretic mobility shift assay (EMSA) was performed to determine the effects of polymorphisms on protein binding to the GSTT2 promoter.The -537A allele (-537G/A or A/A) was significantly associated with colorectal cancer risk (OR = 1.373, p = 0.025), while the -158A allele (-158G/A or A/A) was involved in protection against colorectal cancer (OR = 0.539, p = 0.032). Haplotype 2 (-537A, -277T, -158G) was significantly associated with colorectal cancer risk (OR = 1.386, p = 0.021), while haplotype 4 (-537G, -277C, -158A) protected against colorectal cancer (OR = 0.539, p = 0.032). EMSA data revealed lower promoter binding activity in the -537A allele than its -537G counterpart.Our results collectively suggest that SNPs and haplotypes of the GSTT2 promoter region are associated with colorectal cancer risk in the Korean population.Colorectal cancer (CRC), a predominant cause of tumor-related death in Western nations, is becoming more prevalent in Asian countries such as Korea [1,2]. Genetic and environmental factors are modulators of the carcinogenesis process [3]. Studies on the contribution of genetic polymorphisms to cancer development have examined numerous genes, including oncogenes, tumor suppressors, DNA repair genes and those encoding Phase I and Phase II enzymes [4]. Phase II enzymes attach to additional substrates in an attempt to detoxify the activated metabolite in preparation for final breakdown or excretion. Glutathione-S-transferases (GSTs) are a family of Phase II detoxification enzymes that protect cellular macromolecules by catalyzing the conjugation of glutathione (GSH) to a wide variety of endogenous and exogenous electrophilic compounds [5]. GSTs are divided into at least six classes (alpha, mu, pi, theta, omega and zeta), each of which consists of
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