112 results on '"Suman Lee"'
Search Results
2. Epigenetic analysis in rheumatoid arthritis synoviocytes
- Author
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Seokjin Ham, Jae-Bum Bae, Suman Lee, Bong-Jo Kim, Bok-Ghee Han, Seung-Ki Kwok, and Tae-Young Roh
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Medicine ,Biochemistry ,QD415-436 - Abstract
Rheumatoid arthritis: Understanding the regulation of disease-relevant genes Whole genome analysis of synoviocytes, specialized cells in the joint-lubricating synovial fluid, sheds light on the pathogenic mechanisms of rheumatoid arthritis (RA). Around 350 million people worldwide suffer joint pain and stiffness due to RA, but the inheritance pattern of the disease remains unclear. A study led by Tae-Young Roh at Pohang University of Science and Technology, South Korea, reveals a distinct pattern of chemical tags on the DNA of synoviocytes from RA patients. Differences in methyl group tags in over 500 regions of the genome influenced the expression of RA-associated genes and of microRNAs, small RNA molecules that are also involved in the regulation of gene expression. These differentially methylated sites may not only represent potential disease biomarkers, but also offer new insights into the regulation of RA-relevant genes.
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- 2019
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3. UPF1 Inhibits Hepatocellular Carcinoma Growth through DUSP1/p53 Signal Pathway
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Suman Lee, Yukyung Hwang, Tae Hun Kim, Jaemin Jeong, Dongho Choi, and Jungwook Hwang
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UPF1 ,hepatocellular carcinoma ,posttranscriptional regulation ,DUSP1 ,Biology (General) ,QH301-705.5 - Abstract
Human hepatocellular carcinoma (HCC) has a high mortality rate because of the dearth of effective treatments. Multiple studies have shown that overexpression of UPF1, a key nonsense-mediated mRNA decay (NMD) factor, reduces HCC growth through various cell signaling pathways. However, the mechanism by which UPF1 expression retards HCC proliferation through the regulation of RNA stability remains unclear. By employing various UPF1 variants and transcriptome analysis, we revealed that overexpression of UPF1 variants, not UPF1-mediated NMD, reduces HCC tumorigenesis. Additionally, UPF1 variant overexpression reduced tumorigenesis in xenografted mice. Transcriptome analysis indicated that the level of dual specificity phosphatase 1 (DUSP1) was increased by UPF1 variants via posttranscriptional regulation. The UPF1 overexpression-mediated increase of DUSP1 activated tumor suppressor signaling, ultimately inhibiting cell growth. In this study, we highlighted the function of UPF1 as a tumor suppressor in HCC growth.
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- 2022
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4. Differential DNA methylation of MSI2 and its correlation with diabetic traits.
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Jae-Pil Jeon, In-Uk Koh, Nak-Hyun Choi, Bong-Jo Kim, Bok-Ghee Han, and Suman Lee
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Medicine ,Science - Abstract
Differential DNA methylation with hyperglycemia is significantly associated with Type 2 Diabetes (T2D). Longtime extended exposure to high blood glucose levels can affect the epigenetic signatures in all organs. However, the relevance of the differential DNA methylation changes with hyperglycemia in blood with pancreatic islets remains unclear. We investigated differential DNA methylation in relation to glucose homeostasis based on the Oral Glucose Tolerance Test (OGTT) in a population-based cohort. We found a total of 382 differential methylation sites from blood DNA in hyperglycemia and type 2 diabetes subgroups using a longitudinal and cross-sectional approach. Among them, three CpG sites were overlapped; they were mapped to the MSI2 and CXXC4 genes. In a DNA methylation replication study done by pyrosequencing (n = 440), the CpG site of MSI2 were shown to have strong associations with the T2D group (p value = 2.20E-16). The differential methylation of MSI2 at chr17:55484635 was associated with diabetes-related traits, in particular with insulin sensitivity (QUICKI, p value = 2.20E-16) and resistance (HOMA-IR, p value = 1.177E-07). In human pancreatic islets, at the single-base resolution (using whole-genome bisulfite sequencing), the 292 CpG sites in the ±5kb at chr17:55484635 were found to be significantly hypo-methylated in donors with T2D (average decrease = 13.91%, 95% confidence interval (CI) = 4.18~ 17.06) as compared to controls, and methylation patterns differed by sex (-9.57%, CI = -16.76~ -6.89) and age (0.12%, CI = -11.17~ 3.77). Differential methylation of the MSI2 gene (chr17:55484635) in blood and islet cells is strongly related to hyperglycemia. Our findings suggest that epigenetic perturbation on the target site of MSI2 gene in circulating blood and pancreatic islets should represent or affect hyperglycemia.
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- 2017
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5. The genetic variation in Monocarboxylic acid transporter 2 (MCT2) has functional and clinical relevance with male infertility
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Jinu Lee, Dong Ryul Lee, and Suman Lee
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3′ UTR ,male infertility ,monocarboxylic acid transporter 2 ,single nucleotide polymorphism ,sperm ,Diseases of the genitourinary system. Urology ,RC870-923 - Abstract
Monocarboxylic acid transporter 2 (MCT2) transports pyruvate and lactate outside and inside of sperms, mainly as energy sources and plays roles in the regulation of spermatogenesis. We investigated the association among genetic variations in the MCT2 gene, male infertility and MCT2 expression levels in sperm. The functional and genetic significance of the intron 2 (+28201A > G, rs10506398) and 3' untranslated region (UTR) single nucleotide polymorphism (SNP) (+2626G > A, rs10506399) of MCT2 variants were investigated. Two MCT2 polymorphisms were associated with male infertility (n = 471, P < 0.05). In particular, the MCT2-3' UTR SNP (+2626 G > A) had a strong association with the oligoasthenoteratozoospermia (OAT) group. The +2626GG type had an almost 2.4-fold higher sperm count than that of the +2626AA type (+2626GG; 66 × 10 6 vs +2626AA; 27 × 10 6 , P < 0.0001). The MCT2-3' UTR SNP may be important for expression, as it is located at the MCT2 3' UTR. The average MCT2 protein amount in sperm of the +2626GG type was about two times higher than that of the +2626AA type. The results suggest that genetic variation in MCT2 has functional and clinical relevance with male infertility.
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- 2014
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6. DNA-Binding Motif of the Imprinted Transcription Factor PEG3.
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Suman Lee, An Ye, and Joomyeong Kim
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Medicine ,Science - Abstract
Peg3 is an imprinted gene that is predicted to encode a DNA-binding zinc finger protein. This was previously demonstrated through Chromatin ImmunoPrecipitation-based Sequencing experiments. In the current study, we reanalyzed the previous ChIP-Seq results and further characterized the DNA-binding motif of PEG3. According to the results, PEG3 binds to the promoters and enhancers of a subset of genes that are closely associated with the known functions of Peg3. Some of these identified targets include Tufm, Mrpl45, Cry2, Per1, Slc25a29 and Slc38a2. With this set of targets, we derived a DNA-binding motif of PEG3, 5'-GTGGCAGT-3', which also provides a tabulated matrix that can be used for predicting other unknown genomic targets. Among the newly identified targets, we analyzed in detail the two loci, Slc38a2 and Slc38a4, which are known to be involved in neutral amino acid transport. The results indicated that PEG3 likely functions as a transcriptional repressor for these two loci. Overall, the current study provides a set of genomic targets and also redefines the DNA-binding motif for the imprinted transcription factor PEG3.
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- 2015
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7. A Time-Series Analysis of International Public Relations Expenditure and Economic Outcome.
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Suman Lee and Byungwook Kim
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- 2018
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8. Globalization of the public relations agency industry: a country-level analysis of global public relations agencies and environmental factors
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Suman Lee, Surin Chung, and Euirang Lee
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Strategy and Management ,Communication - Abstract
PurposeThe present study examined the status of globalization of the public relations (PR) agency industry and its environmental factors by analyzing 101 countries.Design/methodology/approachData were constructed from content analysis and multiple archival sources. Cluster analysis and multiple regressions were used for data analysis.FindingsThe present study identified the four distinctive groups of countries in the number of global PR agencies per country. These groups are (1) globalized top countries, (2) globalized major countries, (3) globalizing countries and (4) peripheral countries. The study also found that the degree of globalization of the PR agency industry in a country was associated with its democracy, economic system (gross domestic product (GDP) and foreign direct investment inflow), legal system (rule of law), cultural system (power distance and long-term orientation) and media system (Internet penetration rate) factors.Originality/valueThe previous studies on the global PR agency industry was limited to investigating a few leading agencies, but this study analyzed 114 global PR agencies and their diffusion in 101 countries and explored the influence of each country's characteristics (i.e. political, economic, legal, cultural and media factors) identified as the global PR environment factors.
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- 2023
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9. Exploring Country-of-Origin Perceptions and Ethnocentrism: The Case of U.S. Dairy Marketing in China
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Richard Clancy, Suman Lee, Xiaohan Xu, and Maria Leonora G. Comello
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Marketing ,Ethnocentrism ,Perception ,media_common.quotation_subject ,Food products ,Business ,Product (category theory) ,Business and International Management ,China ,Country of origin ,Food Science ,media_common - Abstract
We examined variables relevant to food products marketing in foreign markets: perceptions of a product’s country-of-origin (which may provide a “halo effect” if positive), and consumers’ tendencies...
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- 2020
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10. The genetic and epigenetic association of LDL Receptor Related Protein 1B (LRP1B) gene with childhood obesity
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Suman Lee
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Male ,0301 basic medicine ,Pediatric Obesity ,Adolescent ,Genotype ,LRP1B ,lcsh:Medicine ,Single-nucleotide polymorphism ,Biology ,Polymorphism, Single Nucleotide ,Article ,Body Mass Index ,Epigenesis, Genetic ,03 medical and health sciences ,0302 clinical medicine ,Gene Frequency ,Humans ,Exome ,Epigenetics ,lcsh:Science ,Genetic association ,Genetics ,Multidisciplinary ,Waist-Hip Ratio ,lcsh:R ,Lipoprotein receptor-related protein ,DNA Methylation ,Introns ,Gene Expression Regulation, Neoplastic ,030104 developmental biology ,Receptors, LDL ,LRP1B Gene ,CpG site ,LDL receptor ,Female ,lcsh:Q ,030217 neurology & neurosurgery - Abstract
Low-density lipoprotein Receptor Related Protein 1B (LRP1B) is homologous to the gigantic lipoprotein receptor-related protein 1 that belongs to the family of Low-density lipoprotein receptors. Previous genetic association studies of the LRP1B gene have shown its genetic association with obesity. Through exome sequencing of the LRP1B gene from a childhood severe obesity cohort (n = 692), we found novel single nucleotide polymorphism (rs431809) in intron 4, which has been significantly correlated with both body mass index (BMI) and waist-hip-ratio (WHR). Three methylations of CpG sites (cg141441481, cg01852095 and cg141441470) in the same intron were also significantly correlated with BMI and WHR. All CpG methylations had bimodal patterns, and were dependent on rs431809 genotypes. The genetic influences of obesity on the LRP1B gene may be linked to the interplay of CpG methylations in the same intron. Heritability of SNP interacts with epigenetic crosstalk in LRP1B. Genetic and epigenetic crosstalk of LRP1B gene may be implicated in the prevention and therapeutic approach to childhood obesity.
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- 2019
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11. The Influence of International Education Experience on Host Country-Related Outcomes: An Analysis of Chinese Students’ Relationships with South Korean Universities
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Suman Lee, Hyehyun Hong, and Qianqian Tian
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higher education institutions ,Higher education ,Geography, Planning and Development ,TJ807-830 ,050801 communication & media studies ,Management, Monitoring, Policy and Law ,TD194-195 ,Renewable energy sources ,Globalization ,International education ,0508 media and communications ,Political science ,0502 economics and business ,GE1-350 ,Practical implications ,Student perceptions ,Government ,Environmental effects of industries and plants ,Renewable Energy, Sustainability and the Environment ,business.industry ,05 social sciences ,university–student relationship ,attitude toward the country ,policy support ,Public relations ,Public diplomacy ,Environmental sciences ,Host country ,international education experience ,business ,050203 business & management - Abstract
Recognizing the globalization of higher education institutions, this study examined the influence of university&ndash, student relationships on host country-related outcomes, including student attitudes, purchase intentions, and policy support. A survey was conducted with Chinese students who had studied or who were currently studying at South Korean universities. Its results showed a significant positive association between Chinese student perceptions of their relationships with host universities and their attitudes toward South Korea. In addition, their positive attitudes led to (i) intentions to purchase Korean products and (ii) policy support for the Korean government. The theoretical and practical implications of study findings are discussed from the perspectives of public diplomacy and the university&rsquo, s role in a highly globalized education system.
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- 2020
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12. Globally altered epigenetic landscape and delayed osteogenic differentiation in H3.3-G34W-mutant giant cell tumor of bone
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Simon Haas, Denis Kusevic, Florian Grünschläger, Jozef Zustin, Felix Rosemann, Suman Lee, Dieter Weichenhan, Daniela Mancarella, Maren Kirstin Schuhmacher, Christoph Plass, Kersten Breuer, Anna Jauch, Jinyeong Lim, Simin Öz, Albert Jeltsch, Matthias Schlesner, Dominik Vonficht, Chao Jiang, Reka Toth, Udo Oppermann, Jörg Fellenberg, Yoon Jung Park, Anand Mayakonda, Pavlo Lutsik, Mark Hartmann, Viet Ha Nguyen, Joschka Hey, Florian Haller, Joo Hyun Park, Umut H. Toprak, Alexander Kühn, Anders Lindroth, and Annika Baude
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0301 basic medicine ,Genome instability ,Epigenomics ,Cancer Research ,Stromal cell ,Science ,Mutation, Missense ,General Physics and Astronomy ,Bone Neoplasms ,General Biochemistry, Genetics and Molecular Biology ,Article ,Epigenesis, Genetic ,Histones ,03 medical and health sciences ,0302 clinical medicine ,Osteogenesis ,Cancer genomics ,Bone cancer ,Humans ,Epigenetics ,ddc:610 ,lcsh:Science ,Data mining ,Giant Cell Tumor of Bone ,Multidisciplinary ,DNA methylation ,biology ,Mesenchymal stem cell ,General Chemistry ,Chromatin ,Cell biology ,030104 developmental biology ,Histone ,biology.protein ,lcsh:Q ,030217 neurology & neurosurgery - Abstract
The neoplastic stromal cells of giant cell tumor of bone (GCTB) carry a mutation in H3F3A, leading to a mutant histone variant, H3.3-G34W, as a sole recurrent genetic alteration. We show that in patient-derived stromal cells H3.3-G34W is incorporated into the chromatin and associates with massive epigenetic alterations on the DNA methylation, chromatin accessibility and histone modification level, that can be partially recapitulated in an orthogonal cell line system by the introduction of H3.3-G34W. These epigenetic alterations affect mainly heterochromatic and bivalent regions and provide possible explanations for the genomic instability, as well as the osteolytic phenotype of GCTB. The mutation occurs in differentiating mesenchymal stem cells and associates with an impaired osteogenic differentiation. We propose that the observed epigenetic alterations reflect distinct differentiation stages of H3.3 WT and H3.3 MUT stromal cells and add to H3.3-G34W-associated changes., Helmholtz Association, Korean National Cancer Center, Korean National Research Fund, Oxford NIHR BRC, Arthritis Research UK, Projekt DEAL
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- 2020
13. Globally altered epigenetic landscape and lagging osteogenic differentiation in H3.3-G34W-mutant giant cell tumor of bone
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Kersten Breuer, Suman Lee, Anand Mayakonda, Viet Ha Nguyen, Jinyeong Lim, Chao Jiang, Florian Haller, Denis Kusevic, Jozef Zustin, Umut H. Toprak, Maren Kirstin Schuhmacher, Udo Oppermann, Annika Baude, Daniela Mancarella, Dieter Weichenhan, Simin Öz, Simon Haas, Yoon Jung Park, Felix Rosemann, Mark Hartmann, Florian Grünschläger, Christoph Plass, Albert Jeltsch, Dominik Vonficht, Matthias Schlesner, Joo Hyun Park, Jörg Fellenberg, Reka Toth, Joschka Hey, Alexander Kühn, Anders Lindroth, Anna Jauch, and Pavlo Lutsik
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Genome instability ,Histone ,Stromal cell ,biology ,Mesenchymal stem cell ,DNA methylation ,biology.protein ,medicine ,Epigenetics ,medicine.disease ,Giant-cell tumor of bone ,Cell biology ,Chromatin - Abstract
The neoplastic stromal cells of giant cell tumor of bone (GCTB) carry a mutation in H3F3A, leading to a mutant histone variant, H3.3-G34W, as a sole recurrent genetic alteration. We show that in patient-derived stromal cells H3.3-G34W is incorporated into the chromatin and associates with massive epigenetic alterations on the DNA methylation, chromatin accessibility and histone modification level that can be partially recapitulated in an orthogonal cell line system by the introduction of H3.3-G34W. These epigenetic alterations affect mainly heterochromatic and bivalent regions and provide possible explanations for the genomic instability as well as the osteolytic phenotype of GCTB. The mutation occurs in differentiating mesenchymal stem cells and associates with an impaired osteogenic differentiation. We propose that the observed epigenetic alterations reflect distinct differentiation stages of H3.3 WT and H3.3 MUT stromal cells and add to H3.3-G34W associated changes. Important abbreviations H3.3-G34W, mutated histone variant; H3.3 MUT, stromal cells expressing H3.3-G34W; H3.3 WT, stromal cells expressing wildtype H3.3
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- 2020
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14. Cybersecurity Breach and Crisis Response: An Analysis of Organizations’ Official Statements in the United States and South Korea
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Suman Lee and Nahyun Kim
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media_common.quotation_subject ,05 social sciences ,Economics, Econometrics and Finance (miscellaneous) ,050801 communication & media studies ,Crisis response ,Data breach ,Computer security ,computer.software_genre ,Corporate reputation ,0508 media and communications ,0502 economics and business ,Business, Management and Accounting (miscellaneous) ,Business ,computer ,Know-how ,050203 business & management ,Reputation ,media_common ,Crisis communication - Abstract
Cybersecurity breaches have rapidly become a high-impact crisis for many corporations. Thus, it is critically important for corporations to know how to protect their reputation through effective crisis communication. Considering the scarcity of empirical research on cybersecurity breaches in crisis communication, the current study attempts to fill this research gap. This study compared 108 official statements issued by organizations in the United States and South Korea when cybersecurity breaches threatened the reputations of various corporations. The characteristics of an apology (responsibility admittance, sympathetic expression, reassurance, compensation) and other features of crisis response (use of excuses, functions of apology, and organizational representation) were examined. This study found that the features of the official statements differed by cultural dimension (individualism vs. collectivism, small vs. large power distance) and by communication style (low-context vs. high-context communication).
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- 2018
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15. Crisis Management and Corporate Apology: The Effects of Causal Attribution and Apology Type on Publics’ Cognitive and Affective Responses
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Suman Lee and Surin Chung
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Distrust ,media_common.quotation_subject ,05 social sciences ,Economics, Econometrics and Finance (miscellaneous) ,050801 communication & media studies ,Cognition ,Crisis management ,Anger ,Publics ,0508 media and communications ,0502 economics and business ,Sympathy ,Business, Management and Accounting (miscellaneous) ,Attribution ,Psychology ,Social psychology ,050203 business & management ,media_common - Abstract
This study examined how corporate apologies influence cognitive and affective public responses (public anger, negative impression, distrust) during an aviation crisis. A total of 192 participants were exposed to one of the two types of causal attribution (internal vs. external) and one of the two types of corporate apology (responsibility-oriented vs. sympathy-oriented). This study found that a responsibility-oriented apology significantly more reduced public anger, negative impression, and distrust of an airline company than a sympathy-oriented apology in an internal/controllable crisis situation. Theoretical and practical implications as well as directions for future research are discussed.
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- 2017
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16. Positive correlation of cg16672562 methylation with obesity-related traits in childhood obesity, and its independence with underlying HIF3A (hypoxia-inducible factor 3a) genetic background
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Sohee Han, Suman Lee, Sang-Ick Park, Ho-Yeong Yu, Juyoung Lee, Hyo-Jin Kim, Mi Yeong Hwang, and Jae-Pil Jeon
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0301 basic medicine ,Genetics ,obesity ,cis-meQTL ,Single-nucleotide polymorphism ,Methylation ,Biology ,cg16672562 ,medicine.disease ,Obesity ,HIF3A ,Childhood obesity ,03 medical and health sciences ,030104 developmental biology ,Oncology ,CpG site ,DNA methylation ,CpG methylation ,medicine ,Body mass index ,Exome sequencing ,Research Paper - Abstract
// Suman Lee 1 , Hyo Jin Kim 2 , Sohee Han 1 , Jae-Pil Jeon 1 , Sang-Ick Park 2 , Ho-Yeong Yu 1 , Mi Yeong Hwang 1 and Juyoung Lee 1 1 Center for Genome Science, National Institute of Health, Chungju, Chungcheongbuk-do, 361-951, Republic of Korea 2 Center for Biomedical Sciences, National Institute of Health, Chungju, Chungcheongbuk-do, 361-951, Republic of Korea Correspondence to: Suman Lee, email: smnl93@gmail.com Keywords: cg16672562, HIF3A , obesity, CpG methylation, cis-meQTL Received: January 16, 2017 Accepted: May 27, 2017 Published: June 27, 2017 ABSTRACT Differential methylations of the HIF3A (hypoxia-inducible factor 3a) gene have been linked to body mass index (BMI). To explore the association of these methylations to childhood obesity, we measured 5 CpG methylation sites (cg27146050, cg46801562, cg22891070, cg16672562 and cg46801675) in intron 1 of the HIF3A gene by pyrosequencing, in the Korean population (mean age: 13.9 yrs, 305 obese cases and 387 controls). Two CpG methylations, cg46801562 and cg16672562, had statistically significant association with childhood obesity ( P = 2.09E-9 and 1.66E-7, respectively). Notably, in the case of cg16672562, all correlations were significantly positive with BMI ( beta = 0.285, P = 1.652E-13), waist-hip ratio ( beta = 0.0028, P = 1.42E-15) and fasting plasma glucose level ( beta = 0.0645, P = 2.61E-4), when analyzed by linear regression, with age and sex as covariates. We investigated any genetic effect of cg16672562 methylation by using 14 single nucleotide polymorphisms (SNP) identified by exome sequencing of the HIF3A locus . cg16672562 methylation showed no statistically significant changes due to the 14 polymorphisms. In this study, we show that cg16672562 is the most significant blood DNA methylation marker for childhood obesity in the Korean population, and might be independent of any underlying HIF3A genetic background.
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- 2017
17. Epigenetic analysis in rheumatoid arthritis synoviocytes
- Author
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Tae-Young Roh, Bok-Ghee Han, Jae-Bum Bae, Seokjin Ham, Seung-Ki Kwok, Suman Lee, and Bong-Jo Kim
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0301 basic medicine ,Clinical Biochemistry ,Bisulfite sequencing ,lcsh:Medicine ,Biology ,Biochemistry ,Article ,Epigenesis, Genetic ,Collagen fibril organization ,lcsh:Biochemistry ,Arthritis, Rheumatoid ,03 medical and health sciences ,0302 clinical medicine ,microRNA ,Humans ,lcsh:QD415-436 ,Gene Regulatory Networks ,RNA, Messenger ,Molecular Biology ,Gene ,Transcription factor ,Epigenomics ,Regulation of gene expression ,Gene Expression Profiling ,lcsh:R ,Genetic Variation ,DNA Methylation ,Synoviocytes ,3. Good health ,MicroRNAs ,030104 developmental biology ,Gene Expression Regulation ,030220 oncology & carcinogenesis ,DNA methylation ,Cancer research ,Molecular Medicine ,CpG Islands - Abstract
Rheumatoid arthritis (RA) is a complex chronic systematic disease with progressive destruction of the joints by invasive synoviocytes. To characterize the key regulators involved in the development of RA, we obtained multilayer epigenomics data including DNA methylation by whole-genome bisulfite sequencing, miRNA profiles, genetic variations by whole-exome sequencing, and mRNA profiles from synoviocytes of RA and osteoarthritis (OA) patients. The overall DNA methylation patterns were not much different between RA and OA, but 523 low-methylated regions (LMRs) were specific to RA. The LMRs were preferentially localized at the 5′ introns and overlapped with transcription factor binding motifs for GLI1, RUNX2, and TFAP2A/C. Single base-scale differentially methylated CpGs were linked with several networks related to wound response, tissue development, collagen fibril organization, and the TGF-β receptor signaling pathway. Further, the DNA methylation of 201 CpGs was significantly correlated with 27 expressed miRNA genes. Our interpretation of epigenomic data of the synoviocytes from RA and OA patients is an informative resource to further investigate regulatory elements and biomarkers responsible for the pathophysiology of RA and OA., Rheumatoid arthritis: Understanding the regulation of disease-relevant genes Whole genome analysis of synoviocytes, specialized cells in the joint-lubricating synovial fluid, sheds light on the pathogenic mechanisms of rheumatoid arthritis (RA). Around 350 million people worldwide suffer joint pain and stiffness due to RA, but the inheritance pattern of the disease remains unclear. A study led by Tae-Young Roh at Pohang University of Science and Technology, South Korea, reveals a distinct pattern of chemical tags on the DNA of synoviocytes from RA patients. Differences in methyl group tags in over 500 regions of the genome influenced the expression of RA-associated genes and of microRNAs, small RNA molecules that are also involved in the regulation of gene expression. These differentially methylated sites may not only represent potential disease biomarkers, but also offer new insights into the regulation of RA-relevant genes.
- Published
- 2019
18. SIRT7 mediates L1 elements transcriptional repression and their association with the nuclear lamina
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Simon J. Newkirk, Lourdes Serrano, Jay A. Tischfield, Nicolas G. Simonet, Joshua K. Thackray, Berta N. Vazquez, Wenfeng An, Alejandro Vaquero, Suman Lee, Noriko Kane-Goldsmith, Sanjay Chahar, Michael P. Verzi, and Jinchuan Xing
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Genome instability ,Male ,Chromatin Immunoprecipitation ,Transcription, Genetic ,Retrotransposon ,Biology ,Cell Line ,Epigenesis, Genetic ,Histones ,Cromatina ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Cell Line, Tumor ,Heterochromatin ,Testis ,Regulació genètica ,Genetics ,Animals ,Humans ,Sirtuins ,Epigenetics ,Psychological repression ,030304 developmental biology ,Mice, Knockout ,0303 health sciences ,Genome ,Nuclear Lamina ,Genetic regulation ,Myocardium ,Gene regulation, Chromatin and Epigenetics ,Fibroblasts ,Lamin Type A ,Epigenètica ,Chromatin ,Cell biology ,Long Interspersed Nucleotide Elements ,Liver ,Nuclear lamina ,K562 Cells ,Chromatin immunoprecipitation ,030217 neurology & neurosurgery ,Lamin - Abstract
Long interspersed elements-1 (LINE-1, L1) are retrotransposons that hold the capacity of self-propagation in the genome with potential mutagenic outcomes. How somatic cells restrict L1 activity and how this process becomes dysfunctional during aging and in cancer cells is poorly understood. L1s are enriched at lamin-associated domains, heterochromatic regions of the nuclear periphery. Whether this association is necessary for their repression has been elusive. Here we show that the sirtuin family member SIRT7 participates in the epigenetic transcriptional repression of L1 genome-wide in both mouse and human cells. SIRT7 depletion leads to increased L1 expression and retrotransposition. Mechanistically, we identify a novel interplay between SIRT7 and Lamin A/C in L1 repression. Our results demonstrate that SIRT7-mediated H3K18 deacetylation regulates L1 expression and promotes L1 association with elements of the nuclear lamina. The failure of such activity might contribute to the observed genome instability and compromised viability in SIRT7 knockout mice. Overall, our results reveal a novel function of SIRT7 on chromatin organization by mediating the anchoring of L1 to the nuclear envelope, and a new functional link of the nuclear lamina with transcriptional repression.
- Published
- 2019
19. Crisis Communication Strategy on Social Media and the Public’s Cognitive and Affective Responses: A Case of Foster Farms Salmonella Outbreak
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Surin Chung and Suman Lee
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Communication ,05 social sciences ,Outbreak ,050801 communication & media studies ,Technical translation ,Crisis response ,Cognition ,0508 media and communications ,0502 economics and business ,Social media ,Public acceptance ,Psychology ,Social psychology ,050203 business & management ,Crisis communication - Abstract
This study examined an organization’s crisis communication strategy (i.e., crisis response strategy and technical translation strategy) on social media and the public’s cognitive and affective responses. Twenty crisis communication messages posted by Foster Farms regarding a salmonella outbreak and 349 public responses were analyzed. The results showed that a technical translation strategy generated more public acceptance of the message and more positive emotions than a crisis response strategy. A crisis response strategy generated more public rejections of the message and more negative emotions than a technical translation strategy.
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- 2016
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20. Innate Color Preference of Zebrafish and Its Use in Behavioral Analyses
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Hae Jin Kang, Tae-Ik Choi, Cheol-Hee Kim, Suman Lee, Jae-Ho Ryu, Young-Ki Bae, and Jong-Su Park
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0301 basic medicine ,Male ,animal structures ,genetic structures ,Color vision ,Tyrosinase ,autism ,Color ,Biology ,Article ,03 medical and health sciences ,Applied Behavior Analysis ,0302 clinical medicine ,Preference test ,Sensation ,medicine ,color blindness ,Animals ,Molecular Biology ,Zebrafish ,Hypopigmentation ,Genetics ,behavioral analysis ,Retinal pigment epithelium ,Behavior, Animal ,fungi ,Cell Biology ,General Medicine ,medicine.disease ,biology.organism_classification ,zebrafish ,Oculocutaneous albinism ,color preference ,030104 developmental biology ,medicine.anatomical_structure ,Female ,medicine.symptom ,030217 neurology & neurosurgery - Abstract
Although innate color preference of motile organisms may provide clues to behavioral biases, it has remained a longstanding question. In this study, we investigated innate color preference of zebrafish larvae. A cross maze with different color sleeves around each arm was used for the color preference test (R; red, G; green, B; blue, Y; yellow). The findings showed that 5 dpf zebrafish larvae preferred blue over other colors (B > R > G > Y). To study innate color recognition further, tyrosinase mutants were generated using CRISPR/Cas9 system. As a model for oculocutaneous albinism (OCA) and color vision impairment, tyrosinase mutants demonstrated diminished color sensation, indicated mainly by hypopigmentation of the retinal pigment epithelium (RPE). Due to its relative simplicity and ease, color preference screening using zebrafish larvae is suitable for high-throughput screening applications. This system may potentially be applied to the analysis of drug effects on larval behavior or the detection of sensory deficits in neurological disorder models, such as autism-related disorders, using mutant larvae generated by the CRISPR/Cas9 technique.
- Published
- 2016
21. What's the Beef in South Korea Protests?: The Technical, Psychometric, and Sociocultural Dimensions of News Coverage of Risk
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Lulu Rodriguez and Suman Lee
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021110 strategic, defence & security studies ,Economic growth ,Government ,030505 public health ,Information Systems and Management ,media_common.quotation_subject ,0211 other engineering and technologies ,02 engineering and technology ,Newspaper ,Risk perception ,Scarcity ,03 medical and health sciences ,Content analysis ,Economics ,Normative ,0305 other medical science ,Sociocultural evolution ,Agronomy and Crop Science ,Outrage ,Food Science ,media_common - Abstract
Millions of South Koreans took to the streets for more than 2 months in 2008 ostensibly in protest over their government's handling of beef imports from the United States. This study examines the technical, psychometric, and sociocultural dimensions of these public protests by conducting a content analysis of the coverage of the English language daily newspaper The Korea Herald. The results suggest that the scarcity of technical risk assessment information and the preponderance of normative or outrage factors in the newspaper's coverage (lack of trust in government, perceptions of inequity, and unequal benefits accruing to both nations) may have fueled public anxiety and anger. The findings also point to social, cultural, and historical factors that may explain why allowing U.S. beef into the Korean market elicited strong public reactions.
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- 2016
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22. What Can Be Gleaned From News Coverage to Improve Science Reporting and Enhance Public Literacy About Agricultural Biotechnology in Ghana?
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Lulu Rodriguez and Suman Lee
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Government ,Information Systems and Management ,Food security ,business.industry ,media_common.quotation_subject ,05 social sciences ,04 agricultural and veterinary sciences ,Agricultural communication ,Agricultural biotechnology ,Public relations ,Food safety ,040401 food science ,Literacy ,0404 agricultural biotechnology ,Agriculture ,0502 economics and business ,050207 economics ,business ,Agronomy and Crop Science ,News media ,Food Science ,media_common - Abstract
A content analysis of print and online sources was conducted to assess the performance of the Ghanaian news media in reporting about agricultural biotechnology. The findings show the dominant presence of food security and food safety issues in the coverage of genetically modified organisms that was overwhelmingly negative toward genetic engineering and its agricultural products. Members of the food industry and government officials (mainly politicians) were the most commonly cited information sources. A qualitative examination of news discourse suggests ways to strengthen the effectiveness of communicating agricultural information that will enhance public literacy and foster intelligent decision making about this controversial topic.
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- 2016
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23. NGS-based deep bisulfite sequencing
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Suman Lee and Joomyeong Kim
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0301 basic medicine ,Genetics ,DNA methylation ,Clinical Biochemistry ,Bisulfite sequencing ,Biology ,Genome ,Deep sequencing ,03 medical and health sciences ,Medical Laboratory Technology ,chemistry.chemical_compound ,PCR, polymerase chain reaction ,030104 developmental biology ,chemistry ,Biochemistry, Genetics and Molecular Biology ,NGS ,Epigenomes ,Illumina Methylation Assay ,NGS, Next-Generation-Sequencing ,Methylated DNA immunoprecipitation ,DNA ,Illumina dye sequencing ,ComputingMethodologies_COMPUTERGRAPHICS - Abstract
Graphical abstract, We have developed an NGS-based deep bisulfite sequencing protocol for the DNA methylation analysis of genomes. This approach allows the rapid and efficient construction of NGS-ready libraries with a large number of PCR products that have been individually amplified from bisulfite-converted DNA. This approach also employs a bioinformatics strategy to sort the raw sequence reads generated from NGS platforms and subsequently to derive DNA methylation levels for individual loci. The results demonstrated that this NGS-based deep bisulfite sequencing approach provide not only DNA methylation levels but also informative DNA methylation patterns that have not been seen through other existing methods.•This protocol provides an efficient method generating NGS-ready libraries from individually amplified PCR products.•This protocol provides a bioinformatics strategy sorting NGS-derived raw sequence reads.•This protocol provides deep bisulfite sequencing results that can measure DNA methylation levels and patterns of individual loci.
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- 2016
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24. 459 CMV Antibody Level is an Independent Risk Factor for MACCE and Death in the General Population
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Suman Lee, N. van den Berg, Matthew Knuiman, Girish Dwivedi, Frank M Sanfilippo, and M. Divitini
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Pulmonary and Respiratory Medicine ,Oncology ,medicine.medical_specialty ,education.field_of_study ,CMV antibody level ,business.industry ,Internal medicine ,Population ,medicine ,Risk factor ,Cardiology and Cardiovascular Medicine ,business ,education - Published
- 2020
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25. The association of genetically controlled CpG methylation (cg158269415) of protein tyrosine phosphatase, receptor type N2 (PTPRN2) with childhood obesity
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Suman Lee
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0301 basic medicine ,Male ,medicine.medical_specialty ,Pediatric Obesity ,Adolescent ,lcsh:Medicine ,Biology ,Childhood obesity ,Article ,03 medical and health sciences ,0302 clinical medicine ,Internal medicine ,Genotype ,medicine ,Humans ,Genetic Predisposition to Disease ,Receptor-Like Protein Tyrosine Phosphatases, Class 8 ,Epigenetics ,Allele ,lcsh:Science ,Child ,Genetic Association Studies ,Multidisciplinary ,lcsh:R ,Methylation ,DNA Methylation ,medicine.disease ,Obesity ,030104 developmental biology ,Endocrinology ,CpG site ,DNA methylation ,lcsh:Q ,CpG Islands ,Female ,030217 neurology & neurosurgery - Abstract
Protein tyrosine phosphatase, receptor type N2 (PTPRN2) encodes a major islet autoantigen in type-1 diabetes. Previous genetic studies have shown its significant association with obesity. PTPRN2 plays an important role in epigenetic regulation of metabolic diseases and cancers. We investigated CpG methylations (cg17429772 and cg158269415) in PTPRN2 by pyrosequencing from blood samples of childhood obesity (n = 638). cg158269415 had significant positive correlations with body mass index (BMI) and waist-hip ratio (WHR). Case-control analysis showed that cg158269415 methylation in blood sample was significantly more hypermethylated in obese cases (n = 252), an average of 2.93% more than that that in controls (n = 386). The cg158269415 methylation has a trimodal distribution pattern with strong dependency on nearby located rs1670344 G > A genotype. Correlations of cg158269415 with BMI and WHR were significant and strong in major G allele carriers (GG + GA). Our study showed that an epigenetic association of PTPRN2 gene with childhood obesity was under certain genetic background. The genetic and epigenetic interplay of PTPRN2 gene may implicate a mechanism of childhood obesity. Whether these small changes in DNA methylation from whole blood are causally or consequently related to childhood obesity outcome and their clinical relevance remains to be determined. However, this study presents a promising obesity risk marker that warrants further investigation.
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- 2018
26. Epigenetic instability at imprinting control regions in a KrasG12D-induced T-cell neoplasm
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Ingeborg M. Langohr, Joomyeong Kim, Corey L. Bretz, and Suman Lee
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Genetic Markers ,0301 basic medicine ,Cancer Research ,Bisulfite sequencing ,Mice, Inbred Strains ,Kaplan-Meier Estimate ,Lymphoma, T-Cell ,medicine.disease_cause ,Epigenesis, Genetic ,Proto-Oncogene Proteins p21(ras) ,Genomic Imprinting ,Mice ,03 medical and health sciences ,0302 clinical medicine ,Combined bisulfite restriction analysis ,GNAS complex locus ,medicine ,Animals ,Epigenetics ,Molecular Biology ,RNA-Directed DNA Methylation ,Genetics ,biology ,DNA Methylation ,030104 developmental biology ,030220 oncology & carcinogenesis ,DNA methylation ,Disease Progression ,Cancer research ,biology.protein ,sense organs ,Carcinogenesis ,Genomic imprinting ,Research Paper - Abstract
Although aberrant DNA methylation within imprinted domains has been reported in a variety of neoplastic diseases, it remains largely uncharacterized in the context of carcinogenesis. In this study, we induced T-cell lymphoma in mice by employing a breeding scheme involving mouse strains, LSL-Kras(G12D) and MMTV-Cre. We then systematically surveyed imprinted domains for DNA methylation changes during tumor progression using combined bisulfite restriction analysis and NGS-based bisulfite sequencing. We detected hyper- or hypo-methylation at the imprinting control regions (ICRs) of the Dlk1, Peg10, Peg3, Grb10, and Gnas domains. These DNA methylation changes at ICRs were more prevalent and consistent than those observed at the promoter regions of well-known tumor suppressors, such as Mgmt, Fhit, and Mlh1. Thus, the changes observed at these imprinted domains are the outcome of isolated incidents affecting DNA methylation settings. Within imprinted domains, DNA methylation changes tend to be restricted to ICRs as nearby somatic differentially methylated regions and promoter regions experience no change. Furthermore, detailed analyses revealed that small cis-regulatory elements within ICRs tend to be resistant to DNA methylation changes, suggesting potential protection by unknown trans-factors. Overall, this study demonstrates that DNA methylation changes at ICRs are dynamic during carcinogenesis and advocates that detection of aberrant DNA methylation at ICRs may serve as a biomarker to enhance diagnostic procedures.
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- 2015
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27. A Time-Series Analysis of International Public Relations Expenditure and Economic Outcome
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Byung Wook Kim and Suman Lee
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Linguistics and Language ,business.industry ,Communication ,05 social sciences ,050801 communication & media studies ,Foreign direct investment ,Public relations ,Outcome (game theory) ,Language and Linguistics ,Power (social and political) ,0508 media and communications ,Country level ,Granger causality ,0502 economics and business ,Agency (sociology) ,Economics ,Time series ,business ,050203 business & management - Abstract
This study tested a causal relationship between international public relations (PR) expenditure and its economic outcome at the country level by using a time-series analysis. International PR expenditures of four client countries (Japan, Colombia, Belgium, and the Philippines) were collected from the semi-annual reports of the Foreign Agency Registration Act (FARA) from 1996 to 2009. Economic outcome was measured by U.S. imports from the client countries and U.S. foreign direct investment (FDI) toward them. This study found that the past PR expenditure holds power in forecasting future economic outcomes for Japan, Belgium, and the Philippines except Colombia.
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- 2015
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28. Trp250-hK2 is defective in intracellular trafficking and activates the unfolded protein response
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Jinu Lee, Suman Lee, Eun-Ju Choi, and Sei Mee Yoon
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Male ,Biological Transport, Active ,Golgi Apparatus ,Polymorphism, Single Nucleotide ,HeLa ,symbols.namesake ,Exon ,Prostate cancer ,Genetics ,medicine ,Humans ,Genetic Association Studies ,biology ,HEK 293 cells ,Prostatic Neoplasms ,Cell Biology ,Transfection ,Golgi apparatus ,biology.organism_classification ,medicine.disease ,Molecular biology ,HEK293 Cells ,Unfolded Protein Response ,Unfolded protein response ,symbols ,Kallikreins ,Intracellular ,HeLa Cells - Abstract
hK2, a member of the kallikrein protease family encoded by KLK2, is expressed exclusively in prostate and is a putative adjunct tumor marker for prostate cancer screening. The T allele of rs198977, a single nucleotide polymorphism in exon 5 of KLK2, codes for W-hK2 and is associated with lower serum hK2 levels and higher risk of prostate cancer than the C allele encoding R-hK2. To elucidate the mechanism that underlies this SNP's function, we transfected plasmids expressing R-hK2 or W-hK2 into PC3, HeLa and HEK293A cells and measured the hK2 level in cell lysates and conditioned media. The level of W-hK2 was lower than R-hK2 in conditioned media but was not different from R-hK2 in cell lysates. W-hK2 was hardly colocalized with Golgi-targeted fluorescent protein whereas R-hK2 colocalized. Reporter assays related to the unfolded protein response (UPR) and phospho-eIF2α immunoblot showed that W-hK2 increased UPR activity more than R-hK2. These results indicated that W-hK2 had a defect in cellular trafficking from the ER to the Golgi complex due to its misfolding and that it activated the UPR, suggesting a mechanism to explain the association of the T allele with higher prostate cancer risk.
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- 2015
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29. The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery
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Sergio Abrignani, David Adams, Melanie de Almeida, ALTUCCI, Lucia, Viren Amin, Ido Amit, Stylianos E, Antonarakis, Samuel Aparicio, Takahiro Arima, Laura Arrigoni, Rob Arts, Vahid Asnafi, Manel Esteller, Jae Bum Bae, Kevin Bassler, Stephan Beck, Benjamin Berkman, Bradley E, Bernstein, Mikhail Bilenky, Adrian Bird, Christoph Bock, Bernhard Boehm, Guillaume Bourque, Charles E, Breeze, Benedikt Brors, David Bujold, Oliver Burren, Marion J, Bussemakers, Adam Butterworth, Elias Campo, Enrique Carrillo de Santa Pau, Lisa Chadwick, Kui Ming Chan, Wei Chen, Tom H, Cheung, Luca Chiapperino, Nak Hyen Choi, Ho Ryun Chung, Laura Clarke, Joseph M, Connors, Philippe Cronet, John Danesh, Manolis Dermitzakis, Gerard Drewes, Pawel Durek, Stephanie Dyke, Tomasz Dylag, Connie J, Eaves, Peter Ebert, Roland Eils, Jürgen Eils, Catherine A, Ennis, Tariq Enver, Elise A, Feingold, Bärbel Felder, Anne Ferguson Smith, Jude Fitzgibbon, Paul Flicek, Roger S, Y, Foo, Peter Fraser, Mattia Frontini, Eileen Furlong, Sitanshu Gakkhar, Nina Gasparoni, Gilles Gasparoni, Daniel H, Geschwind, Petar Glažar, Thomas Graf, Frank Grosveld, Xin Yuan Guan, Roderic Guigo, Ivo G, Gut, Alf Hamann, Bok Ghee Han, R, Alan Harris, Simon Heath, Kristian Helin, Jan G, Hengstler, Alireza Heravi Moussavi, Karl Herrup, Steven Hill, Jason A, Hilton, Benjamin C, Hitz, Bernhard Horsthemke, Ming Hu, Joo Yeon Hwang, Nancy Y, Takashi Ito, Biola Maria Javierre, Sasa Jenko, Thomas Jenuwein, Yann Joly, Steven J, M, Jones, Yae Kanai, Hee Gyung Kang, Aly Karsan, Alexandra K, Kiemer, Song Cheol Kim, Bong Jo Kim, Hyeon Hoe Kim, Hiroshi Kimura, Sarah Kinkley, Filippos Klironomos, In Uk Koh, Myrto Kostadima, Christopher Kressler, Roman Kreuzhuber, Anshul Kundaje, Ralf Küppers, Carolyn Larabell, Paul Lasko, Mark Lathrop, S, Lee, Suman Lee, Hans Lehrach, Elsa Leitão, Thomas Lengauer, Åke Lernmark, David Leslie, Gilberto K, K, Leung, Danny Leung, Markus Loeffler, Yussanne Ma, Antonello Mai, Thomas Manke, Eric R, Marcotte, Marco A, Marra, Joost H, A, Martens, Jose Ignacio Martin Subero, Karen Maschke, Christoph Merten, Aleksandar Milosavljevic, Saverio Minucci, Totai Mitsuyama, Richard A, Moore, Fabian Müller, Andrew J, Mungall, Mihai G, Netea, Karl Nordström, Irene Norstedt, Hiroaki Okae, Vitor Onuchic, Francis Ouellette, Willem Ouwehand, Massimiliano Pagani, Vera Pancaldi, Thomas Pap, Tomi Pastinen, Ronak Patel, Dirk S, Paul, Michael J, Pazin, Pier Giuseppe Pelicci, Anthony G, Phillips, Julia Polansky, Bo Porse, J, Andrew Pospisilik, Shyam Prabhakar, Dena C, Procaccini, Andreas Radbruch, Nikolaus Rajewsky, Vardham Rakyan, Wolf Reik, Bing Ren, David Richardson, Andreas Richter, Daniel Rico, David J, Roberts, Philip Rosenstiel, Mark Rothstein, Abdulrahman Salhab, Hiroyuki Sasaki, John S, Satterlee, Sascha Sauer, Claudia Schacht, Florian Schmidt, Gerd Schmitz, Stefan Schreiber, Christopher Schröder, Dirk Schübeler, Joachim L, Schultze, Ronald P, Schulyer, Marcel Schulz, Martin Seifert, Katsuhiko Shirahige, Reiner Siebert, Thomas Sierocinski, Laura Siminoff, Anupam Sinha, Nicole Soranzo, Salvatore Spicuglia, Mikhail Spivakov, Christian Steidl, Seth Strattan, Michael Stratton, Peter Südbeck, Hao Sun, Narumi Suzuki, Yutaka Suzuki, Amos Tanay, David Torrents, Frederick L, Tyson, Thomas Ulas, Sebastian Ullrich, Toshikazu Ushijima, Alfonso Valencia, Edo Vellenga, Martin Vingron, Chris Wallace, Stefan Wallner, Jörn Walter, Huating Wang, Stephanie Weber, Nina Weiler, Andreas Weller, Andrew Weng, Steven Wilder, Sam M, Wiseman, Angela R, Zhenguo Wu, Jieyi Xiong, Yasuhiro Yamashita, Xinyi Yang, Desmond Y, Yap, Kevin Y, Yip, Stephen Yip, Jae Il Yoo, Daniel Zerbino, Gideon Zipprich, Antonarakis, Stylianos, International Human Epigenome Consortium, [0000-0002-8682-6748], Apollo - University of Cambridge Repository, Centro Nacional de Análisi Genómico (CNAG), Centro Nacional de Análisis Genómico, Radboud University Medical Center [Nijmegen], Technologies avancées pour le génôme et la clinique (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Hematology, University of Groningen and University Medical Center Groningen, CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Universitat de Barcelona, Sergio, Abrignani, David, Adam, Melanie de, Almeida, Altucci, Lucia, Viren, Amin, Ido, Amit, Stylianos, E, Antonarakis, Samuel, Aparicio, Takahiro, Arima, Laura, Arrigoni, Rob, Art, Vahid, Asnafi, Manel, Esteller, Jae Bum, Bae, Kevin, Bassler, Stephan, Beck, Benjamin, Berkman, Bradley, E, Bernstein, Mikhail, Bilenky, Adrian, Bird, Christoph, Bock, Bernhard, Boehm, Guillaume, Bourque, Charles, E, Breeze, Benedikt, Bror, David, Bujold, Oliver, Burren, Marion, J, Bussemakers, Adam, Butterworth, Elias, Campo, Enrique Carrillo de Santa, Pau, Lisa, Chadwick, Kui Ming, Chan, Wei, Chen, Tom, H, Cheung, Luca, Chiapperino, Nak Hyen, Choi, Ho Ryun, Chung, Laura, Clarke, Joseph, M, Connors, Philippe, Cronet, John, Danesh, Manolis, Dermitzaki, Gerard, Drewe, Pawel, Durek, Stephanie, Dyke, Tomasz, Dylag, Connie, J, Eaves, Peter, Ebert, Roland, Eil, Jürgen, Eil, Catherine, A, Ennis, Tariq, Enver, Elise, A, Feingold, Bärbel, Felder, Anne Ferguson, Smith, Jude, Fitzgibbon, Paul, Flicek, Roger, S, Y, Foo, Peter, Fraser, Mattia, Frontini, Eileen, Furlong, Sitanshu, Gakkhar, Nina, Gasparoni, Gilles, Gasparoni, Daniel, H, Geschwind, Petar, Glažar, Thomas, Graf, Frank, Grosveld, Xin Yuan, Guan, Roderic, Guigo, Ivo, G, Gut, Alf, Hamann, Bok Ghee, Han, R, Alan, Harri, Simon, Heath, Kristian, Helin, Jan, G, Hengstler, Alireza Heravi, Moussavi, Karl, Herrup, Steven, Hill, Jason, A, Hilton, Benjamin, C, Hitz, Bernhard, Horsthemke, Ming, Hu, Joo Yeon, Hwang, Nancy, Y, Ip, Takashi, Ito, Biola Maria, Javierre, Sasa, Jenko, Thomas, Jenuwein, Yann, Joly, Steven, J, M, Jone, Yae, Kanai, Hee Gyung, Kang, Aly, Karsan, Alexandra, K, Kiemer, Song Cheol, Kim, Bong Jo, Kim, Hyeon Hoe, Kim, Hiroshi, Kimura, Sarah, Kinkley, Filippos, Klironomo, In Uk, Koh, Myrto, Kostadima, Christopher, Kressler, Roman, Kreuzhuber, Anshul, Kundaje, Ralf, Küpper, Carolyn, Larabell, Paul, Lasko, Mark, Lathrop, S, Lee, Suman, Lee, Hans, Lehrach, Elsa, Leitão, Thomas, Lengauer, Åke, Lernmark, David, Leslie, Gilberto, K, K, Leung, Danny, Leung, Markus, Loeffler, Yussanne, Ma, Antonello, Mai, Thomas, Manke, Eric, R, Marcotte, Marco, A, Marra, Joost, H, A, Marten, Jose Ignacio Martin, Subero, Karen, Maschke, Christoph, Merten, Aleksandar, Milosavljevic, Saverio, Minucci, Totai, Mitsuyama, Richard, A, Moore, Fabian, Müller, Andrew, J, Mungall, Mihai, G, Netea, Karl, Nordström, Irene, Norstedt, Hiroaki, Okae, Vitor, Onuchic, Francis, Ouellette, Willem, Ouwehand, Massimiliano, Pagani, Vera, Pancaldi, Thomas, Pap, Tomi, Pastinen, Ronak, Patel, Dirk, S, Paul, Michael, J, Pazin, Pier Giuseppe, Pelicci, Anthony, G, Phillips, Julia, Polansky, Bo, Porse, J, Andrew, Pospisilik, Shyam, Prabhakar, Dena, C, Procaccini, Andreas, Radbruch, Nikolaus, Rajewsky, Vardham, Rakyan, Wolf, Reik, Bing, Ren, David, Richardson, Andreas, Richter, Daniel, Rico, David, J, Roberts, Philip, Rosenstiel, Mark, Rothstein, Abdulrahman, Salhab, Hiroyuki, Sasaki, John, S, Satterlee, Sascha, Sauer, Claudia, Schacht, Florian, Schmidt, Gerd, Schmitz, Stefan, Schreiber, Christopher, Schröder, Dirk, Schübeler, Joachim, L, Schultze, Ronald, P, Schulyer, Marcel, Schulz, Martin, Seifert, Katsuhiko, Shirahige, Reiner, Siebert, Thomas, Sierocinski, Laura, Siminoff, Anupam, Sinha, Nicole, Soranzo, Salvatore, Spicuglia, Mikhail, Spivakov, Christian, Steidl, Seth, Strattan, Michael, Stratton, Peter, Südbeck, Hao, Sun, Narumi, Suzuki, Yutaka, Suzuki, Amos, Tanay, David, Torrent, Frederick, L, Tyson, Thomas, Ula, Sebastian, Ullrich, Toshikazu, Ushijima, Alfonso, Valencia, Edo, Vellenga, Martin, Vingron, Chris, Wallace, Stefan, Wallner, Jörn, Walter, Huating, Wang, Stephanie, Weber, Nina, Weiler, Andreas, Weller, Andrew, Weng, Steven, Wilder, Sam, M, Wiseman, Angela, R, Wu, Zhenguo, Wu, Jieyi, Xiong, Yasuhiro, Yamashita, Xinyi, Yang, Desmond, Y, Yap, Kevin, Y, Yip, Stephen, Yip, Jae Il, Yoo, Daniel, Zerbino, and Gideon, Zipprich
- Subjects
Epigenomics ,0301 basic medicine ,[SDV]Life Sciences [q-bio] ,ADN ,lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4] ,Medizin ,Biology ,Genoma humà ,General Biochemistry, Genetics and Molecular Biology ,Epigenesis, Genetic ,World Wide Web ,03 medical and health sciences ,Human health ,0302 clinical medicine ,Blueprint ,Databases, Genetic ,Humans ,Disease ,ddc:576.5 ,DNA methylation ,databases, genetic ,disease ,histone code ,humans ,epigenesis, genetic ,epigenomics ,genome, human ,biochemistry, genetics and molecular biology (all) ,Molecular Biology ,ComputingMilieux_MISCELLANEOUS ,030304 developmental biology ,Genetics ,0303 health sciences ,Human genome ,Genome, Human ,DNA ,Epigenome ,DNA Methylation ,Human cell ,Epigenètica ,Histone Code ,030104 developmental biology ,030220 oncology & carcinogenesis ,Epigenetics - Abstract
Item does not contain fulltext The International Human Epigenome Consortium (IHEC) coordinates the generation of a catalog of high-resolution reference epigenomes of major primary human cell types. The studies now presented (see the Cell Press IHEC web portal at http://www.cell.com/consortium/IHEC) highlight the coordinated achievements of IHEC teams to gather and interpret comprehensive epigenomic datasets to gain insights in the epigenetic control of cell states relevant for human health and disease. PAPERCLIP.
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- 2016
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30. Intact piRNA pathway prevents L1 mobilization in male meiosis
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Alysson R. Muotri, Fred H. Gage, Maria C. Marchetto, Nicole Vanden Berg, Cathryn A. Hogarth, Simon J. Newkirk, Michael D. Griswold, James M. Rosser, Fiorella C. Grandi, Alex Bortvin, Suman Lee, Valeriya Gaysinskaya, Ping Ye, Wenfeng An, and Jef D. Boeke
- Subjects
0301 basic medicine ,Male ,Polymerase Chain Reaction ,Transgenic ,Histones ,Mice ,0302 clinical medicine ,Spermatocytes ,LINE-1 reporter transgene ,Testis ,Developmental ,Transgenes ,Genetics ,Multidisciplinary ,Meiosis ,Histone ,Phenotype ,PNAS Plus ,030220 oncology & carcinogenesis ,DNA methylation ,Stem Cell Research - Nonembryonic - Non-Human ,endocrine system ,Retroelements ,DNA damage ,Transgene ,Piwi-interacting RNA ,Biology ,Small Interfering ,Methylation ,Insertional mutagenesis ,Promoter Regions ,03 medical and health sciences ,Open Reading Frames ,Prophase ,Genetic ,retrotransposition ,Humans ,Animals ,Codon ,Spermatogenesis ,urogenital system ,Human Genome ,RNA ,DNA Methylation ,Stem Cell Research ,PIWI-interacting RNA ,meiotic arrest ,030104 developmental biology ,Germ Cells ,Long Interspersed Nucleotide Elements ,Gene Expression Regulation ,biology.protein ,Generic health relevance ,5' Untranslated Regions - Abstract
The PIWI-interacting RNA (piRNA) pathway is essential for retrotransposon silencing. In piRNA-deficient mice, L1-overexpressing male germ cells exhibit excessive DNA damage and meiotic defects. It remains unknown whether L1 expression simply highlights piRNA deficiency or actually drives the germ-cell demise. Specifically, the sheer abundance of genomic L1 copies prevents reliable quantification of new insertions. Here, we developed a codon-optimized L1 transgene that is controlled by an endogenous mouse L1 promoter. Importantly, DNA methylation dynamics of a single-copy transgene were indistinguishable from those of endogenous L1s. Analysis of Mov10l1-/- testes established that de novo methylation of the L1 transgene required the intact piRNA pathway. Consistent with loss of DNA methylation and programmed reduction of H3K9me2 at meiotic onset, the transgene showed 1,400-fold increase in RNA expression and consequently 70-fold increase in retrotransposition in postnatal day 14 Mov10l1-/- germ cells compared with the wild-type. Analysis of adult Mov10l1-/- germ-cell fractions indicated a stage-specific increase of retrotransposition in the early meiotic prophase. However, extrapolation of the transgene data to endogenous L1s suggests that it is unlikely insertional mutagenesis alone accounts for the Mov10l1-/- phenotype. Indeed, pharmacological inhibition of reverse transcription did not rescue the meiotic defect. Cumulatively, these results establish the occurrence of productive L1 mobilization in the absence of an intact piRNA pathway but leave open the possibility of processes preceding L1 integration in triggering meiotic checkpoints and germ-cell death. Additionally, our data suggest that many heritable L1 insertions originate from individuals with partially compromised piRNA defense.
- Published
- 2017
31. Differential DNA methylation of MSI2 and its correlation with diabetic traits
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Bok-Ghee Han, Suman Lee, Bong-Jo Kim, Nak-Hyun Choi, In-Uk Koh, and Jae-Pil Jeon
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0301 basic medicine ,Male ,endocrine system diseases ,Physiology ,Bisulfite sequencing ,lcsh:Medicine ,Biochemistry ,Epigenesis, Genetic ,Endocrinology ,Medicine and Health Sciences ,Glucose homeostasis ,Insulin ,Homeostasis ,Longitudinal Studies ,Prospective Studies ,lcsh:Science ,Multidisciplinary ,DNA methylation ,RNA-Binding Proteins ,Methylation ,Middle Aged ,Chromatin ,Blood Sugar ,Body Fluids ,Type 2 Diabetes ,Nucleic acids ,Blood ,CpG site ,Epigenetics ,Female ,Anatomy ,DNA modification ,Chromatin modification ,Research Article ,Chromosome biology ,Adult ,medicine.medical_specialty ,Cell biology ,Endocrine Disorders ,Blood sugar ,Biology ,03 medical and health sciences ,Islets of Langerhans ,Internal medicine ,medicine ,Genetics ,Diabetes Mellitus ,Humans ,Aged ,Diabetic Endocrinology ,Biology and life sciences ,lcsh:R ,DNA ,Glucose Tolerance Test ,Hormones ,030104 developmental biology ,Cross-Sectional Studies ,Diabetes Mellitus, Type 2 ,Metabolic Disorders ,Hyperglycemia ,Case-Control Studies ,lcsh:Q ,CpG Islands ,Gene expression ,Physiological Processes ,Epigenetics of diabetes Type 2 - Abstract
Differential DNA methylation with hyperglycemia is significantly associated with Type 2 Diabetes (T2D). Longtime extended exposure to high blood glucose levels can affect the epigenetic signatures in all organs. However, the relevance of the differential DNA methylation changes with hyperglycemia in blood with pancreatic islets remains unclear. We investigated differential DNA methylation in relation to glucose homeostasis based on the Oral Glucose Tolerance Test (OGTT) in a population-based cohort. We found a total of 382 differential methylation sites from blood DNA in hyperglycemia and type 2 diabetes subgroups using a longitudinal and cross-sectional approach. Among them, three CpG sites were overlapped; they were mapped to the MSI2 and CXXC4 genes. In a DNA methylation replication study done by pyrosequencing (n = 440), the CpG site of MSI2 were shown to have strong associations with the T2D group (p value = 2.20E-16). The differential methylation of MSI2 at chr17:55484635 was associated with diabetes-related traits, in particular with insulin sensitivity (QUICKI, p value = 2.20E-16) and resistance (HOMA-IR, p value = 1.177E-07). In human pancreatic islets, at the single-base resolution (using whole-genome bisulfite sequencing), the 292 CpG sites in the +/- 5kb at chr17: 55484635 were found to be significantly hypo-methylated in donors with T2D (average decrease = 13.91%, 95% confidence interval (CI) = 4.18 similar to 17.06) as compared to controls, and methylation patterns differed by sex (-9.57%, CI = -16.76 similar to -6.89) and age (0.12%, CI = -11.17 similar to 3.77). Differential methylation of the MSI2 gene (chr17: 55484635) in blood and islet cells is strongly related to hyperglycemia. Our findings suggest that epigenetic perturbation on the target site of MSI2 gene in circulating blood and pancreatic islets should represent or affect hyperglycemia.
- Published
- 2017
32. Establishment of a bone-specific col10a1:GFP transgenic zebrafish
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Mi Sun Lee, Kwan-Hee You, Yong-Il Kim, Seong-Kyu Choe, Raekil Park, Seung Hyun Jung, Kyeong-Won Yoo, Cheol-Hee Kim, Joon No Lee, Jung Hwa Choi, Hyun-Taek Kim, SeongAe Kwak, Sang-Yeob Yeo, and Suman Lee
- Subjects
Period (gene) ,Green Fluorescent Proteins ,Genomics ,Biology ,Genome ,Animals, Genetically Modified ,Chondrocytes ,Osteogenesis ,Arabidopsis ,Brassica rapa ,Animals ,Promoter Regions, Genetic ,Molecular Biology ,Gene ,Zebrafish ,Southern blot ,Genetics ,Osteoblasts ,Shotgun sequencing ,food and beverages ,Articles ,Cell Biology ,General Medicine ,Zebrafish Proteins ,biology.organism_classification ,Collagen Type X - Abstract
During skeletal development, both osteogenic and chondrogenic programs are initiated from multipotent mesenchymal cells, requiring a number of signaling molecules, transcription factors, and downstream effectors to orchestrate the sophisticated process. Col10a1, an important downstream effector gene, has been identified as a marker for maturing chondrocytes in higher vertebrates, such as mammals and birds. In zebrafish, this gene has been shown to be expressed in both osteoblasts and chondrocytes, but no study has reported its role in osteoblast development. To initially delineate the osteogenic program from chondrogenic lineage development, we used the zebrafish col10a1 promoter to establish a transgenic zebrafish expressing a GFP reporter specifically in osteoblast-specific bone structures that do not involve cartilaginous programs. A construct harboring a -2.2-kb promoter region was found to be sufficient to drive the reporter gene in osteoblast-specific bone structures within the endogenous col10a1 expression domain, confirming that separable cis-acting elements exist for distinct cell type-specific expression of col10a1 during zebrafish skeletal development. The -2.2-kb col10a1:GFP transgenic zebrafish marking only bone structures derived from osteoblasts will undoubtedly be an invaluable tool for identifying and characterizing molecular events driving osteoblast development in zebrafish, which may further provide a differential mechanism where col10a1 is involved in the development of chondrocytes undergoing maturation in other vertebrate systems.
- Published
- 2013
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33. The Influence of Mood and Symbolic Value on the Evaluation of Destination Logos
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Lulu Rodriguez, Suman Lee, Sela Sar, and Supathida Kulpavaropas
- Subjects
Negative mood ,Mood ,Communication ,mental disorders ,Cognition ,Psychology ,Logos Bible Software ,behavioral disciplines and activities ,Practical implications ,Social psychology ,Elaboration ,Education - Abstract
This study examined the effects of mood and symbolic value on the evaluation of destination logos. It hypothesized that mood differences activate either holistic or analytic cognitive processing styles that, in turn, influence country logo evaluations. An experiment using a 2 × 3 between-subjects factorial design was conducted with undergraduate students as participants. The results showed that people in a positive mood engaged in holistic elaboration and consequently evaluated country logos more favorably than those in a negative mood. Mood had a great effect on the evaluation of logos with a low symbol-meaning congruence. The findings also suggested that processing style mediated the influence of mood on logo evaluations. Theoretical and practical implications are discussed.
- Published
- 2013
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34. Aglycone of Rh4Inhibits Melanin Synthesis in B16 Melanoma Cells: Possible Involvement of the Protein Kinase A Pathway
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Jong Hyuk Sung, Tien Lam Tran, Won Keun Oh, Suman Lee, Sang Hyun Sung, Kyeol Bae, Wang Kyun Kim, and Yun Mi Jeong
- Subjects
Ginsenosides ,Tyrosinase ,Melanoma, Experimental ,Panax ,Biology ,Applied Microbiology and Biotechnology ,Biochemistry ,Analytical Chemistry ,Melanin ,Mice ,Cell Line, Tumor ,Cyclic AMP ,medicine ,Animals ,Phosphorylation ,Cyclic AMP Response Element-Binding Protein ,Protein kinase A ,neoplasms ,Molecular Biology ,Melanins ,Microphthalmia-Associated Transcription Factor ,integumentary system ,Monophenol Monooxygenase ,Plant Extracts ,Binding protein ,Melanoma ,Colforsin ,Organic Chemistry ,General Medicine ,medicine.disease ,Microphthalmia-associated transcription factor ,Antineoplastic Agents, Phytogenic ,Cyclic AMP-Dependent Protein Kinases ,Gene Expression Regulation, Neoplastic ,Plant Leaves ,alpha-MSH ,Cell culture ,Signal Transduction ,Biotechnology - Abstract
To our knowledge, there is no report that directly shows an inhibitory effect of ginsenoside on melanin synthesis in B16 melanoma cells. Hence, we investigated whether the aglycone of Rh(4) (A-Rh4) inhibits melanin synthesis in B16 melanoma cells, and determined the mechanism of melanin inhibition. We isolated 12 ginsenoside compounds from leaves of Panax ginseng and tested them in B16 melanoma cells. It significantly reduced melanin content and tyrosinase activity under alpha-melanocyte stimulating hormone- and forskolin-stimulated conditions. It significantly reduced the cyclic AMP (cAMP) level in B16 melanoma cells, and this might be responsible for the regulation down of MITF and tyrosinase. Phosphorylation of a downstream molecule, a cAMP response-element binding protein, was significantly decreased according to Western blotting and immunofluorescence assay. These data suggest that A-Rh4 has an anti-melanogenic effect via the protein kinase A pathway.
- Published
- 2013
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35. Obesity-related CpG Methylation (cg07814318) of Kruppel-like Factor-13 (KLF13) Gene with Childhood Obesity and its cis-Methylation Quantitative Loci
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Hye-Ja Lee, Joo-Yeon Hwang, Nak-Hyun Choi, Suman Lee, and In-Uk Koh
- Subjects
0301 basic medicine ,Male ,Pediatric Obesity ,Adolescent ,Quantitative Trait Loci ,Kruppel-Like Transcription Factors ,Single-nucleotide polymorphism ,Cell Cycle Proteins ,Biology ,Polymorphism, Single Nucleotide ,Article ,Body Mass Index ,Cohort Studies ,03 medical and health sciences ,0302 clinical medicine ,Humans ,Exome ,Epigenetics ,Gene ,Exome sequencing ,Genetic Association Studies ,Genetics ,Multidisciplinary ,Methylation ,Sequence Analysis, DNA ,DNA Methylation ,Repressor Proteins ,030104 developmental biology ,CpG site ,030220 oncology & carcinogenesis ,DNA methylation ,CpG Islands ,Female - Abstract
The cg07814318 hypermethylation of Kruppel-like factor 13 (KLF13) gene has been reported for its relevancy with Body Mass Index (BMI) from European origin. We explored the cg07814318 methylation and its cis-meQTL (cis-methylation quantitative loci) of KLF13 from a childhood obesity cohort. The cg07814318 methylation in blood was significantly associated with obesity and correlated with several obesity-related physical and biochemical traits. We examined the same loci from purified three human cell types (n = 47), i.e., pre-adipocytes, adipocytes and islets. The cg07814318 methylation pattern in pre-adipocytes and islets were significant higher in cells from subjects with a higher BMI compared with control subjects. By exome sequencing of KLF13 gene in blood with the same cohort, we found nine SNPs (single nucleotide polymorphisms) within its gene body, and two SNPs (rs11537749 and rs12595641) were as cis-meQTL of cg07814318. There was the 2.01% methylation change of cg07814318 between homozygous dominant and recessive genotypes, especially, in rs12595641. The sequencing variations within KLF13 genes could drive dynamic modifications of obesity-related CpG methylation. Differential DNA methylation patterns in the KLF13 gene determined from separate blood samples showed that this criterion could be used as a surrogate for representing overall epigenetic changes in cells related to obesity.
- Published
- 2016
36. The influence of logo design on country image and willingness to visit: A study of country logos for tourism
- Author
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Lulu Rodriguez, Suman Lee, and Sela Sar
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Marketing ,Organizational Behavior and Human Resource Management ,Communication ,Nation branding ,Logo ,Advertising ,Sociology ,Logos Bible Software ,Object (philosophy) ,Tourism - Abstract
This study examines the influence of tourism logo design on people's country image and their intention to visit the country being promoted. In an online survey, undergraduate students were exposed to the tourism logos of Australia, Kenya, and Malawi. The results show that students’ evaluations of a country's logo significantly affected their image of the country and their willingness to visit it after controlling for pre-existing knowledge and attitude toward the object country.
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- 2012
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37. The Sulfated Polysaccharide Fucoidan Stimulates Osteogenic Differentiation of Human Adipose-Derived Stem Cells
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Soojeong Park, Dae-Seog Lim, Kyo Won Lee, and Suman Lee
- Subjects
medicine.medical_treatment ,Cellular differentiation ,Cell ,Subcutaneous Fat ,Gene Expression ,Adipose tissue ,chemistry.chemical_compound ,Calcification, Physiologic ,Antigens, CD ,Osteogenesis ,Polysaccharides ,medicine ,Humans ,Osteopontin ,Cells, Cultured ,biology ,Fucoidan ,Growth factor ,Mesenchymal stem cell ,Cell Differentiation ,Mesenchymal Stem Cells ,Cell Biology ,Hematology ,Alkaline Phosphatase ,Extracellular Matrix ,Cell biology ,Adult Stem Cells ,Phenotype ,medicine.anatomical_structure ,Biochemistry ,chemistry ,biology.protein ,Stem cell ,Developmental Biology - Abstract
Human adipose-derived stem cells (hADSCs) are an attractive source for cell therapies, because they can be obtained from aspirated adipose tissues with the capacity of proliferation and differentiation into several mesenchymal lineages under certain conditions. Sulfated polysaccharides, including heparin, modulate osteogenic differentiation of stem cells through the regulation of growth factor binding and signaling pathways. Here, we examined the effects of the sulfated polysaccharide fucoidan on osteogenic differentiation of hADSCs. Strikingly, fucoidan treatment resulted in increased alkaline phosphatase (ALP) activity and alizarin red and von Kossa staining. At the molecular level, fucoidan treatment enhanced the expression of osteogenesis-specific marker genes, including ALP, osteopontin, type I collagen, Runt-related transcription factor 2, and osteocalcin. Furthermore, fucoidan also promoted the osteogenic differentiation of another mesenchymal cell lineage, human amniotic fluid stem cells. These findings strongly suggest that fucoidan enhances osteogenic differentiation of hADSCs and possibly other mesenchymal cell lineages, indicating that it may be a potential candidate for promoting bone regeneration.
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- 2012
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38. Single Nucleotide Polymorphism in the Promoter Region of H1 Histone Family Member N, Testis-specific (H1FNT) and Its Association Study with Male Infertility
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Jinu Lee, Suman Lee, and Seung Hee Yang
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Genetics ,Health Informatics ,Promoter ,Single-nucleotide polymorphism ,Biology ,medicine.disease ,Molecular biology ,Male infertility ,DNA binding site ,Histone ,Histone H1 ,medicine ,biology.protein ,SNP ,Gene ,Ecology, Evolution, Behavior and Systematics - Abstract
The H1 histone family, member N, testis-specific (H1FNT) is exclusively expressed in the testis, and had its possible role for sperm chromatin formation. The pur-pose of this study is to investigate any genetic associa-tion of H1FNT gene with male infertility, especially at the promoter region. We examined the promoter single nu-cleotide polymorphisms (SNP) of H1FNT gene which is located within transcription factor binding site for its as-sociation with male infertility. The statistical analysis showed that the −1129A>T polymorphism was pres-ent at a statistically significance in male infertility (p= 0.0059 and 0.0349 for hetero and risk type, re-spectively). The dual-luciferase promoter assay was per-formed to examine the polymorphic effect of this pro-moter SNP by the cloning of promoter region (1700bp fragment) into pGL3-basic vector. In our plasmid based reporter system, there is no big difference between wild and risk type. In conclusion, H1FNT −1129A>T pro-moter SNP is statistically significant with male infertility, especially with subfertile (non-azoospermia) group. Further analysis of its functional polymorphic effect in vivo may provide the biological significance of tes-tis-specific histone with spermatogenesis.Keywords: H1FNT, male infertility, single nucleotide polymorphism
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- 2010
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39. Return on investment (ROI) of international public relations: A country-level analysis
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Suman Lee and Youngmin Yoon
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Marketing ,Organizational Behavior and Human Resource Management ,Country level ,business.industry ,Communication ,Return on investment ,Economics ,Foreign direct investment ,Public relations ,Investment (macroeconomics) ,business ,Outcome (game theory) - Abstract
The purpose of this study is to examine the relationship between economic outcome and international public relations investment by other countries in the U.S. Based on country-level data analysis, this study found that the number of international public relations contracts by other countries in the U.S. was positively related to (1) U.S. imports from those countries, (2) U.S. direct investment to those countries, and (3) the number of U.S. tourists visiting those countries, after controlling for economic size.
- Published
- 2010
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40. Undifferentiated hematopoietic cells are characterized by a genome-wide undermethylation dip around the transcription start site and a hierarchical epigenetic plasticity
- Author
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Yun Shin Chung, Hye Joung Kim, Sungwhan An, Suman Lee, Kyung-Rim Kwon, Il-Hoan Oh, Jung-Hoon Park, Sung-Hyun Hong, and Tae-Min Kim
- Subjects
Cellular differentiation ,Blotting, Western ,Immunology ,Antigens, CD34 ,Biology ,Biochemistry ,Epigenesis, Genetic ,Mice ,medicine ,Animals ,Humans ,Epigenetics ,Promoter Regions, Genetic ,Acetylation ,Cell Differentiation ,Promoter ,Cell Biology ,Hematology ,DNA Methylation ,Hematopoietic Stem Cells ,Molecular biology ,Chromatin ,Mice, Inbred C57BL ,Trichostatin A ,CpG site ,DNA methylation ,CpG Islands ,Transcription Initiation Site ,Stem cell ,medicine.drug - Abstract
Evidence for the epigenetic regulation of hematopoietic stem cells (HSCs) is growing, but the genome-wide epigenetic signature of HSCs and its functional significance remain unclear. In this study, from a genome-wide comparison of CpG methylation in human CD34+ and CD34− cells, we identified a characteristic undermethylation dip around the transcription start site of promoters and an overmethylation of flanking regions in undifferentiated CD34+ cells. This “bivalent-like” CpG methylation pattern around the transcription start site was more prominent in genes not associated with CpG islands (CGI−) than CGI+ genes. Undifferentiated hematopoietic cells also exhibited dynamic chromatin associated with active transcription and a higher turnover of histone acetylation than terminally differentiated cells. Interestingly, inhibition of chromatin condensation by chemical treatment (5-azacytidine, trichostatin A) enhanced the self-renewal of “stimulated” HSCs in reconstituting bone marrows but not “steady-state” HSCs in stationary phase bone marrows. In contrast, similar treatments on more mature cells caused partial phenotypic dedifferentiation and apoptosis at levels correlated with their hematopoietic differentiation. Taken together, our study reveals that the undifferentiated state of hematopoietic cells is characterized by a unique epigenetic signature, which includes dynamic chromatin structures and an epigenetic plasticity that correlates to level of undifferentiation.
- Published
- 2009
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41. Functional polymorphism in H2BFWT‐5′UTR is associated with susceptibility to male infertility
- Author
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Hwan Hee Kim, Suman Lee, Yeo Jin Yun, Hee Suk Park, Jinu Lee, and Dong Ryul Lee
- Subjects
Male ,Five prime untranslated region ,Translational efficiency ,Blotting, Western ,Single-nucleotide polymorphism ,Polymerase Chain Reaction ,Male infertility ,Genotype ,Upstream open reading frame ,medicine ,Humans ,Genes in Pathology ,Infertility, Male ,DNA Primers ,Genetics ,Polymorphism, Genetic ,Base Sequence ,biology ,Cell Biology ,medicine.disease ,Molecular biology ,Sperm ,Histone ,Case-Control Studies ,biology.protein ,Molecular Medicine ,5' Untranslated Regions - Abstract
H2B histone family, member W, testis-specific (H2BFWT) gene encodes a testis-specific histone that becomes incorporated into sperm chromatin. A male infertility-associated single nucleotide polymorphism (-9CT) within the 5' untranslated region (5'UTR) of the H2BFWT gene was identified by direct sequencing. Statistical association studies showed the polymorphism significantly associated with male infertility (n = 442, P = 0.0157), especially in non-azoospermia (n = 262, P = 0.018). Furthermore, this polymorphism is also associated with sperm parameters, especially sperm count (n = 164, P = 0.0127) and vitality (n = 164, P = 0.0076). We investigated how the genetic variant at 5'UTR confers susceptibility to non-azoospermia. Western blotting of His-tag H2BFWT revealed a difference at the translational level between -9T and the wild-type -9C in the absence of change at the transcriptional level. Reporter assays showed that this reducing translational change originated from an upstream open reading frame (uORF) generated by the -9C to -9T change. Finally, in vivo H2BFWT expression in sperm was significantly dependent on the -9CT genotype from non-azoospermia (P = 0.0061). Therefore, this polymorphism could affect the translational efficiency of a quantitatively important histone protein by the uORF. Our data implicate H2BFWT as a susceptibility factor for male infertility, possibly with other genetic and environmental factors.
- Published
- 2009
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42. Effect of folate deficiency on placental DNA methylation in hyperhomocysteinemic rats
- Author
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Suman Lee, Ji Hye Lee, Namsoo Chang, Ji-Myung Kim, and Kyungju Hong
- Subjects
Vitamin ,medicine.medical_specialty ,Homocysteine ,Placenta ,Endocrinology, Diabetes and Metabolism ,Clinical Biochemistry ,Hyperhomocysteinemia ,Folic Acid Deficiency ,Biology ,Biochemistry ,Rats, Sprague-Dawley ,chemistry.chemical_compound ,Pregnancy ,Internal medicine ,medicine ,Animals ,Vitamin B12 ,Cyanocobalamin ,Molecular Biology ,Nutrition and Dietetics ,Methionine ,Methylation ,DNA Methylation ,Rats ,Endocrinology ,medicine.anatomical_structure ,chemistry ,DNA methylation ,Female - Abstract
We report that the maternal folate status can influence folate-mediated one-carbon metabolism and DNA methylation in the placenta. Thirty-six female Sprague-Dawley rats were divided into the following three dietary groups: folate-supplemented (FS; 8 mg/kg folic acid, n=12), homocystine- and folate-supplemented (HFS; 0.3% homocystine and 8 mg/kg folic acid, n=12) and homocystine-supplemented and folate-deficient (HFD; 0.3% homocystine and no folic acid, n=12). The animals were fed their experimental diets from 4 weeks prior to mating until Day 20 of pregnancy (n=7-9 per group). The HFS diet increased the plasma homocysteine and placental DNA methylation but did not affect plasma folate, vitamin B-12, S-adenosyl methionine (SAM) or S-adenosyl homocysteine (SAH) levels, or the SAM/SAH ratio in the liver and placenta compared with the FS diet. The HFD diet induced severely low plasma folate concentrations, with plasma homocysteine levels increasing up to 100 micromol/L, and increased hepatic SAH and decreased placental SAM levels and SAM/SAH ratio in both tissues, with a concomitant decrease in placental DNA methylation. Placental DNA methylation was significantly correlated with placental (gamma=0.819), hepatic (gamma=0.7) and plasma (gamma=0.752) folate levels; plasma homocysteine level (gamma=-0.688); hepatic SAH level (gamma=-0.662) and hepatic SAM/SAH ratio (gamma=0.494). These results suggest that the maternal folate status in hyperhomocysteinemic rats influences the homeostasis of folate-mediated one-carbon metabolism and the methyl pool, which would, in turn, affect placental DNA methylation by altering the methylation potential of the liver.
- Published
- 2009
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43. Cognitive categorisation and routes of national reputation formation: US opinion leaders' views on South Korea
- Author
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Suman Lee, Hochang Shin, and Elizabeth L Toth
- Subjects
Marketing ,International relations ,Government ,business.industry ,Strategy and Management ,media_common.quotation_subject ,Social change ,Opinion leadership ,International community ,Public relations ,Public diplomacy ,Economics ,business ,News media ,Reputation ,media_common - Abstract
Taking an exploratory case study approach, this paper will identify why some factors of national reputation formation toward South Korea are more important than others among US opinion leaders, based on a cognitive process of categorisation. It will also identify which communication channels can facilitate this cognitive process. In-depth interviews were conducted with business leaders, journalists, government officials, other professional experts and college students. Findings revealed that the Korean War and economic success were the primary factors people identified, exceeding other factors in importance with respect to South Korea's national reputation. Personal experience and news media, along with entertainment content, were the main routes in reputation formation. Knowing this mechanism and the central channels of national reputation formation will be essential in building strategic public relations by governments to promote and manage a positive national reputation in the international community.
- Published
- 2008
- Full Text
- View/download PDF
44. Association between folate metabolism-related gene polymorphisms and methylation of p16INK4A and hMLH1 genes in spontaneously aborted embryos with normal chromosomal integrity
- Author
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Hye Mi Park, Suman Lee, Doyeun Oh, Dong Hee Choi, Seung Ju Shin, and Nam Keun Kim
- Subjects
Adult ,Adolescent ,Gestational Age ,Reductase ,Risk Assessment ,Thymidylate synthase ,Young Adult ,Folic Acid ,Asian People ,Gene Frequency ,Pregnancy ,parasitic diseases ,Genotype ,Odds Ratio ,Humans ,Child ,Enhancer ,Gene ,Cyclin-Dependent Kinase Inhibitor p16 ,Methylenetetrahydrofolate Reductase (NADPH2) ,Adaptor Proteins, Signal Transducing ,Aged ,Retrospective Studies ,Aged, 80 and over ,Genetics ,Korea ,Polymorphism, Genetic ,biology ,Infant ,Nuclear Proteins ,Obstetrics and Gynecology ,Thymidylate Synthase ,Methylation ,DNA Methylation ,Middle Aged ,digestive system diseases ,Genotype frequency ,Abortion, Spontaneous ,Reproductive Medicine ,Case-Control Studies ,Child, Preschool ,Methylenetetrahydrofolate reductase ,biology.protein ,Female ,MutL Protein Homolog 1 - Abstract
Objective To assess prevalent polymorphisms of 5,10-methylenetetrahydrofolate reductase (MTHFR) and thymidylate synthase enhancer region (TSER) and methylation patterns of p16 INK4A and hMLH1 genes in spontaneously aborted embryos (SAEs) with normal chromosomal integrity. Design Retrospectively analyzed, prospectively obtained database. Setting Bundang CHA General Hospital in South Korea. Patient(s) Fifty-nine SAEs ( Intervention(s) None. Main Outcome Measure(s) Genotype frequency of MTHFR, TSER polymorphisms, and methylation status of p16 INK4A and hMLH1 genes in SAEs with normal chromosomal integrity. Result(s) The distribution of the MTHFR 677C>T polymorphism differed significantly between SAEs with normal chromosomal integrity and the two control groups. Also, the frequency of combined MTHFR 677 and TSER genotypes was significantly different between the aborted embryos and the adult control group. However, the MTHFR 677C>T and 1298A>C and TSER polymorphisms were not associated with the methylation status of p16 INK4A and hMLH1 genes in SAEs with normal chromosomal integrity. Conclusion(s) Association between the MTHFR 677C>T polymorphism and the risk of SAEs with normal chromosomal integrity in the Korean population.
- Published
- 2008
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45. The association of 4a4b polymorphism of endothelial nitric oxide synthase (eNOS) gene with the sperm morphology in Korean infertile men
- Author
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Jung Hoon Park, Suman Lee, Yeo-Jin Yun, and Seung-Hun Song
- Subjects
Male ,Nitric Oxide Synthase Type III ,Y chromosome microdeletion ,medicine.medical_treatment ,Semen ,Semen analysis ,Polymorphism, Single Nucleotide ,Risk Assessment ,Male infertility ,Andrology ,Risk Factors ,Enos ,Prevalence ,medicine ,Humans ,Genetic Predisposition to Disease ,Infertility, Male ,Azoospermia ,Korea ,Assisted reproductive technology ,biology ,medicine.diagnostic_test ,Obstetrics and Gynecology ,medicine.disease ,biology.organism_classification ,Spermatozoa ,Sperm ,Reproductive Medicine - Abstract
Objective To investigate the association between three polymorphism sites of endothelial nitric oxide synthase (eNOS; −786T>C, 4a4b, and 894G>T) with nonobstructive male infertility. Design Prospective case-control study. Setting University-based hospital. Patient(s) Three hundred seventy-one nonobstructive infertile men in azoospermia (n = 184) or ejaculate semen (n = 187) group were enrolled in this study. Two hundred twenty fertile men who had at least one child without any history of requiring assisted reproductive technology were included as the nationwide control group. Intervention(s) Semen analysis according to the World Health Organization guidelines and cytogenetic and Y chromosome microdeletion assay. Main Outcome Measure(s) Three eNOS polymorphisms were investigated to assess its association with male infertility by pyrosequencing and gel electrophoresis. Result(s) The statistical analysis of three eNOS polymorphisms showed no significant association between the polymorphisms of the control and infertile group. We investigated the sperm parameters depending on the genotypes of the ejaculate semen group. The sperm morphology was found to be significantly associated with the 4a4b polymorphism of eNOS. Conclusion(s) Endothelial nitric oxide synthase may be important to sperm morphology in infertile men.
- Published
- 2008
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46. Application of multiplex bead array assay for Yq microdeletion analysis in infertile males
- Author
-
Saswati Paul, Jin-Wook Jung, Hye-Jung Yeom, Young-Sun Her, Suman Lee, Mi-Seon Park, Seung Yong Hwang, Moon-Ju Oh, and Jong-Pil Yeoun
- Subjects
Male ,Chromosomes, Human, Y ,Reproducibility of Results ,Cell Biology ,Biology ,Flow Cytometry ,medicine.disease ,Y chromosome ,Polymerase Chain Reaction ,Sensitivity and Specificity ,Molecular biology ,Male infertility ,Sequence-tagged site ,genomic DNA ,Testis determining factor ,Multiplex polymerase chain reaction ,medicine ,Humans ,Multiplex ,Chromosome Deletion ,Primer (molecular biology) ,Molecular Biology ,Infertility, Male ,Sequence Tagged Sites - Abstract
The purpose of this study was to apply the multiplex bead array as a diagnostic tool for male infertility. The multiplex bead array offers a new platform in high-throughput nucleic acid detection. Six loci, including sex-determining regions on the Y (SRY) chromosome as a control and five sequence-tagged sites (STS) in azoospermia-factor regions, were used in this system. Extracted genomic DNA from infertile male blood was used for multiplex polymerase chain reaction (PCR). After multiplex PCR using specific Cy3-labeled primer sets, the PCR product was hybridized with capture probes. A multiplexed PCR-liquid bead was arrayed for simultaneous detection using the Luminex system. This assay system correctly identified the presence or deletion of the Y chromosome. Therefore, this method provides a sensitive and high-throughput method for probing the deletion of the Y chromosome, and offers a completely new approach to male infertility screening.
- Published
- 2008
- Full Text
- View/download PDF
47. International public relations as a predictor of prominence of US news coverage
- Author
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Suman Lee
- Subjects
Marketing ,Organizational Behavior and Human Resource Management ,business.industry ,Communication ,Advertising ,Media relations ,Public relations ,Public diplomacy ,Newspaper ,Test (assessment) ,Content analysis ,Political science ,business ,Social significance ,News media - Abstract
This study aims to test the public relations efforts of other countries as a predictor of their newsworthiness in the US news media, after controlling for national traits and social significance. Based on a content analysis of US newspaper and television news coverage ( New York Times , Washington Post , ABC , NBC , CBS , and CNN ) of 97 countries, this study found that the public relations of other countries’ governments is a significant predictor of these countries’ prominence in the US news coverage.
- Published
- 2007
- Full Text
- View/download PDF
48. DNA-Binding Motif of the Imprinted Transcription Factor PEG3
- Author
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An Ye, Joomyeong Kim, and Suman Lee
- Subjects
Chromatin Immunoprecipitation ,Amino Acid Transport System A ,Kruppel-Like Transcription Factors ,lcsh:Medicine ,Peptide Elongation Factor Tu ,Biology ,Mitochondrial Proteins ,Genomic Imprinting ,03 medical and health sciences ,0302 clinical medicine ,Neutral amino acid transport ,Animals ,Enhancer ,lcsh:Science ,Transcription factor ,030304 developmental biology ,Genetics ,Zinc finger ,0303 health sciences ,Binding Sites ,Multidisciplinary ,lcsh:R ,Promoter ,DNA ,Period Circadian Proteins ,Cryptochromes ,Mice, Inbred C57BL ,030220 oncology & carcinogenesis ,lcsh:Q ,Genomic imprinting ,Sequence motif ,Chromatin immunoprecipitation ,Research Article ,Transcription Factors - Abstract
Peg3 is an imprinted gene that is predicted to encode a DNA-binding zinc finger protein. This was previously demonstrated through Chromatin ImmunoPrecipitation-based Sequencing experiments. In the current study, we reanalyzed the previous ChIP-Seq results and further characterized the DNA-binding motif of PEG3. According to the results, PEG3 binds to the promoters and enhancers of a subset of genes that are closely associated with the known functions of Peg3. Some of these identified targets include Tufm, Mrpl45, Cry2, Per1, Slc25a29 and Slc38a2. With this set of targets, we derived a DNA-binding motif of PEG3, 5'-GTGGCAGT-3', which also provides a tabulated matrix that can be used for predicting other unknown genomic targets. Among the newly identified targets, we analyzed in detail the two loci, Slc38a2 and Slc38a4, which are known to be involved in neutral amino acid transport. The results indicated that PEG3 likely functions as a transcriptional repressor for these two loci. Overall, the current study provides a set of genomic targets and also redefines the DNA-binding motif for the imprinted transcription factor PEG3.
- Published
- 2015
49. Somewhere in the Middle: The Measurement of Third Culture
- Author
-
Suman Lee
- Subjects
Cultural Studies ,Future study ,Transcendence (philosophy) ,Communication ,Scale (social sciences) ,Dimension (data warehouse) ,Psychology ,Intercultural communication ,Social psychology - Abstract
This study explores the concept of “third culture,” which has not been tested by quantified measures since it was introduced. This study develops the 10-item measurement of third culture based on three dimensions—equality, commonality, and transcendence. Two hundred and fifteen international married individuals from 42 countries participated in a self-administered email survey. The findings indicated that the new scale is reliable and functions as a single dimension instead of as three subdimensions. Suggestions for future study as well as several implications on theory and methodology are discussed, drawing on the experience of this study.
- Published
- 2006
- Full Text
- View/download PDF
50. Analysis of Korean Infertile Males by PDMS Microchip Gel Electrophoresis
- Author
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Suman Lee, Seong Ho Kang, Seoungkwon Back, Yongseong Kim, Chungmu Kang, Ki Wha Chung, and Byung-Ok Choi
- Subjects
medicine.medical_specialty ,Family medicine ,medicine ,General Chemistry ,General hospital - Abstract
Division of Natural Science, Kyungnam University, Masan 631-701, Korea. E-mail: kimys@kyungnam.ac.kr College of Medicine, EWHA Womans University, Seoul 120-750, Korea CHA Research Institute, Department of Urology, Department of Medicine CHA General Hospital, Pochon CHA University, Seoul 135-081, Korea Department of Biological Science, Kongju National University, Kongju 314-701, Korea Department of Chemistry, Chonbuk National University, Jeonju 561-756, Korea Received November 15, 2005
- Published
- 2006
- Full Text
- View/download PDF
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