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HDAC3 acts as a negative regulator of angiogenesis

Deokbum Park, Hyunmi Park, Youngmi Kim, Hyuna Kim, Dooil Jeoung
2014 BMB Reports  
Histone deacetylase-3 (HDAC3) is involved in cellular proliferation, apoptosis and transcriptional repression. However, the role of HDAC3 in angiogenesis remains unknown. HDAC3 negatively regulated the expression of angiogenic factors, such as VEGF and plasminogen activator inhibitor-1 (PAI-1). HDAC3 showed binding to promoter sequences of PAI-1. HDAC3 activity was necessary for the expression regulation of PAI-1 by HDAC3. VEGF decreased the expression of HDAC3, and the down-regulation of HDAC3
more » ... enhanced endothelial cell tube formation. HDAC3 negatively regulated tumor-induced angiogenic potential. We show the novel role of HDAC3 as a negative regulator of angiogenesis. [BMB Reports 2014; 47(4): 227-232]
doi:10.5483/bmbrep.2014.47.4.128 pmid:24286308 pmcid:PMC4163891 fatcat:2fk35e6l2rdu3oilulxlmiaowm

Giant nonlinear response of terahertz nanoresonators on VO_2 thin film

Jisoo Kyoung, Minah Seo, Hyeongryeol Park, Sukmo Koo, Hyun-sun Kim, Youngmi Park, Bong-Jun Kim, Kwangjun Ahn, Namkyoo Park, Hyun-Tak Kim, Dai-Sik Kim
2010 Optics Express  
Park, S. M. Koo, D. J. Park, J. H. Kang, O. K. Suwal, S. S. Choi, P. C. M. Planken, G. S. Park, N. K. Park, Q. H. Park, and D. S.  ...  Park, S. Koo, H. S. Kim, H. Bernien, B. J. Kim, J. H. Choe, Y. H. Ahn, H.-T. Kim, N. Park, Q. H. Park, K. Ahn, and D. S.  ... 
doi:10.1364/oe.18.016452 pmid:20721032 fatcat:wrzg77xxeze25au6dfeer3vpwm

Visualization of tyrosinase activity in melanoma cells by a BODIPY-based fluorescent probe

Tae-Il Kim, Jihye Park, Seonhwa Park, Yongdoo Choi, Youngmi Kim
2011 Chemical Communications  
Experimentals Materials All reagents were of the highest commercial quality and used as received without further purification. All solvents were spectral grade unless otherwise noted. Anhydrous CH 2 Cl 2 and THF were obtained as a sure-seal bottle from Aldrich Co. Inc. (Milwaukee, WI). Silica gel (40 m) was obtained from Merck Inc. Aqueous solutions were freshly prepared with deionized water from a water purification system (Human Corp. Korea). 2,4-Dimethylpyrrole (2),
more » ... yde (3), L-DOPA were purchased from Aldrich Co. Inc. (Milwaukee, WI). Tyrosinase (EC 1.14.18.1, 4276 U/mg) from mushroom and miconazole were purchased from Sigma. Kojic acid and anisaldehyde for inhibition assay were purchased from TCI Co. Inc. (Tokyo), and benzaldehyde and benzoic acid were purchased from Aldrich Co. Inc. (Milwaukee, WI), respectively. General methods, instrumentation and measurements Synthetic manipulations that required an inert atmosphere (where noted) were carried out under argon using standard Schlenk techniques. NMR ( 1 H, 13 C) spectra were recorded on Bruker 400 MHz or 500 MHz spectrometers. The chemical shift data for each signal are given in uni ts of δ (ppm) relative to tetramethylsilane (TMS) where δ (TMS) = 0, and referenced to the residual solvent resonances. Splitting patterns are denoted as s (singlet), d (doublet), t (triplet), q (quartet), m (multiplet), and br (broad). High-resolution FAB-MS or ESI-MS were obtained at national center for inter-university research facilities. Absorption spectra were obtained on a Shimadzu UV-2501 spectrophotometer. Fluorescence measurements were recorded on a Hitachi F-7000 fluorescence spectrophotometer using 10 mm quartz cuvettes with a path length of 1 cm. Fluorescence quantum yields were determined by standard methods, using fluorescein (Φ F = 0.95 in 0.1 N NaOH) as a standard. The reaction with tyrosinase was measured by monitoring changes in fluorescence intensity using a Synergy Mx Microplate Reader (BioTek, USA). Electronic Supplementary Material (ESI) for Chemical Communications This journal is
doi:10.1039/c1cc15061h pmid:22031105 fatcat:qyozt7px5racrfkznzfivsjzue

Nutrient intakes of infants with atopic dermatitis and relationship with feeding type

Youngshin Han, Youngmi Lee, Haeryun Park, Sunyoung Park, Kyunghee Song
2015 Nutrition Research and Practice  
The prevalence of atopic dermatitis in infants is increasing worldwide. However, the nutrient intake status of infants with atopic dermatitis has not been studied properly. This study was conducted to compare the nutrient intake status of infants in the weaning period with atopic dermatitis by feeding type. Feeding types, nutrient intake status and growth status of 98 infants with atopic dermatitis from age 6 to 12 months were investigated. Feeding types were surveyed using questionnaires, and
more » ... aily intakes were recorded by mothers using the 24-hour recall method. Growth and iron status were also measured. The result showed that breastfed infants consumed less energy and 13 nutrients compared to formula-fed or mixed-fed infants (p < 0.001). The breastfed group showed a significantly lower intake rate to the Dietary Reference Intakes for Koreans than the other two groups (p < 0.001). In addition, they consumed less than 75% of the recommended intakes in all nutrients, except for protein and vitamin A, and in particular, iron intake was very low, showing just 18.7% of the recommended intake. There was no significant difference in growth by feeding type, but breastfed infants showed a significantly higher rate of iron deficiency anemia (p < 0.001). Continuous management programs should be prepared for breastfed infants with atopic dermatitis, who are in a period when rapid growth takes place and proper nutrient intake is essential.
doi:10.4162/nrp.2015.9.1.57 pmid:25671069 pmcid:PMC4317481 fatcat:ekmcpba4hjeqvot2hu6zdni3x4

The Hyaluronic Acid–HDAC3–miRNA Network in Allergic Inflammation

Youngmi Kim, Sangkyung Eom, Deokbum Park, Hyuna Kim, Dooil Jeoung
2015 Frontiers in Immunology  
We previously reported the anti-allergic effect of high molecular weight form of hyaluronic acid (HMW-HA). In doing so, HA targets CD44 and inhibits FcεRI signaling and cross-talk between epidermal growth factor receptor (EGFR) and FcεRI. We previously reported the role of histone deacetylases (HDACs) in allergic inflammation and allergic inflammationpromoted enhanced tumorigenic potential. We reported regulatory role of HA in the expression of HDAC3. In this review, we will discuss molecular
more » ... chanisms associated with anti-allergic effect of HA in relation with HDACs. The role of microRNAs (miRNAs) in allergic inflammation has been reported. We will also discuss the role of miRNAs in allergic inflammation in relation with HA-mediated anti-allergic effects.
doi:10.3389/fimmu.2015.00210 pmid:25983734 pmcid:PMC4415435 fatcat:r4mo3uz5gzcmvelz6fev5halga

YouTube as a Source of Information and Education on Hysterectomy

Kyong-No Lee, Ga-Hyun Son, Sung-Ho Park, Youngmi Kim, Sung Taek Park
2020 Journal of Korean medical science  
Globally, YouTube is one of the most popular websites, and the content is not restricted to entertainment. The purpose of this study was to assess the quality of information in YouTube videos pertaining to hysterectomy. We explored YouTube using the search terms "hysterectomy" and "remove uterus." The videos that appeared were sorted using the filter "sort by view count." Of the initial 100 videos, the top 50 videos for each search term were included for review, as determined by the "relevance"
more » ... filter based on YouTube's algorithm. After excluding 34 videos for various reasons, 66 were included in the final analysis. Each video rated as "useful" was further analyzed for reliability and completeness of information; a set of pre-determined criteria were modified from a previous study and used to grade the quality of videos. The top 66 videos on hysterectomy had a total of 4,679,118 views. Based on authorship, the videos were categorized as follows: videos uploaded by patients, 37%; academic videos, 35%; videos uploaded by physicians, 13%; commercial videos, 4%; and videos uploaded by non-physicians, 2%. The type of content was also categorized: 50% of the videos recorded personal experiences, 23% recorded surgical techniques, 21% involved explanations of the surgery, and 4% were commercial videos. The majority of the videos made by patients were negatively biased toward hysterectomy surgery (71.72%), while the majority of those made by academics or physicians were surgical educational videos for doctors, not patients. YouTube is currently not an appropriate source for patients to gain information on hysterectomy. Physicians should be aware of the limitations and provide up-to-date and peer-reviewed content on the website.
doi:10.3346/jkms.2020.35.e196 pmid:32597042 pmcid:PMC7324264 fatcat:34gsyozgyrhlnexjtzj2aqx5uq

Erratum: Nutrient intakes of infants with atopic dermatitis and relationship with feeding type

Youngshin Han, Youngmi Lee, Haeryun Park, Sunyoung Park, Kyunghee Song
2015 Nutrition Research and Practice  
The authors apologize for any inconvenience this mistake may have caused.
doi:10.4162/nrp.2015.9.2.213 pmid:25861430 pmcid:PMC4388955 fatcat:3onz2hsgx5htlaxl6qqijpqnhy

HMMER web server: 2018 update

Simon C Potter, Aurélien Luciani, Sean R Eddy, Youngmi Park, Rodrigo Lopez, Robert D Finn
2018 Nucleic Acids Research  
The HMMER webserver [http://www.ebi.ac.uk/Tools/ hmmer] is a free-to-use service which provides fast searches against widely used sequence databases and profile hidden Markov model (HMM) libraries using the HMMER software suite (http://hmmer.org). The results of a sequence search may be summarized in a number of ways, allowing users to view and filter the significant hits by domain architecture or taxonomy. For large scale usage, we provide an application programmatic interface (API) which has
more » ... een expanded in scope, such that all result presentations are available via both HTML and API. Furthermore, we have refactored our JavaScript visualization library to provide standalone components for different result representations. These consume the aforementioned API and can be integrated into thirdparty websites. The range of databases that can be searched against has been expanded, adding four sequence datasets (12 in total) and one profile HMM library (6 in total). To help users explore the biological context of their results, and to discover new data resources, search results are now supplemented with cross references to other EMBL-EBI databases.
doi:10.1093/nar/gky448 pmid:29905871 pmcid:PMC6030962 fatcat:k3vsfblq5ba3tkdhcp57ufiq5q

A Computational Approach to Detect CNVs Using High-throughput Sequencing

Myungjin Moon, Jaegyoon Ahn, Youngmi Yoon, Chihyun Park, Sanghyun Park, Jeehee Yoon
2009 2009 Ninth IEEE International Conference on Bioinformatics and BioEngineering  
Copy-Number Variations (CNVs) can be defined as gains or losses that are greater than 1kbs of genomic DNA among phenotypically normal individuals. CNVs detected by microarray based approach are limited to medium or large sized ones because of its low resolution. Here we propose a novel approach to detect CNVs by aligning the short reads obtained by high-throughput sequencer to the previously assembled human genome sequence, and analyzing the distribution of the aligned reads. Application of our
more » ... algorithm demonstrates the feasibility of detecting CNVs of arbitrary length, which include short ones that microarray based algorithms cannot detect. Also, false positive and false negative rates of the results were relatively low compared to those of microarray based algorithms.
doi:10.1109/bibe.2009.13 dblp:conf/bibe/MoonAYPPY09 fatcat:xvvmpg3rjrafjclzgusokhxdxu

Integrative gene network construction for predicting a set of complementary prostate cancer genes

Jaegyoon Ahn, Youngmi Yoon, Chihyun Park, Eunji Shin, Sanghyun Park
2011 Computer applications in the biosciences : CABIOS  
Motivation: Diagnosis and prognosis of cancer and understanding oncogenesis within the context of biological pathways is one of the most important research areas in bioinformatics. Recently, there have been several attempts to integrate interactome and transcriptome data to identify subnetworks that provide limited interpretations of known and candidate cancer genes, as well as increase classification accuracy. However, these studies provide little information about the detailed roles of
more » ... ied cancer genes. Results: To provide more information to the network, we constructed the network by incorporating genetic interactions and manually curated gene regulations to the protein interaction network. To make our newly constructed network cancer specific, we identified edges where two genes show different expression patterns between cancer and normal phenotypes. We showed that the integration of various datasets increased classification accuracy, which suggests that our network is more complete than a network based solely on protein interactions. We also showed that our network contains significantly more known cancer-related genes than other feature selection algorithms. Through observations of some examples of cancer-specific subnetworks, we were able to predict more detailed and interpretable roles of oncogenes and other cancer candidate genes in the prostate cancer cells.
doi:10.1093/bioinformatics/btr283 pmid:21551151 fatcat:mxqlnuioa5astmaku2kxrea3ei

Nuclear localization signal domain of HDAC3 is necessary and sufficient for the expression regulation of MDR1

Hyunmi Park, Youngmi Kim, Deokbum Park, Dooil Jeoung
2014 BMB Reports  
Histone acetylation/deacetylation has been known to be associated with the transcriptional regulation of various genes. The role of histone deacetylase-3 in the expression regulation of MDR1 was investigated. The expression level of HDAC3 showed an inverse relationship with the expression level of MDR1. Wild-type HDAC3, but not catalytic mutant HDAC3 S424A , negatively regulated the expression of MDR1. Wild-type HDAC3, but not catalytic mutant HDAC3 S424A , showed binding to the promoter
more » ... es of HDAC3. HDAC3 regulated the expression level, and the binding of Ac-H3 K9/14 and Ac-H4 K16 around the MDR1 promoter sequences. The nuclear localization signal domain of HDAC3 was necessary, and sufficient for the binding of HDAC3 to the MDR1 promoter sequences and for conferring sensitivity to microtubule-targeting drugs. [BMB Reports 2014; 47(6): 342-347]
doi:10.5483/bmbrep.2014.47.6.169 pmid:24286324 pmcid:PMC4163870 fatcat:4wsso3gtcfb3lnhoqbsei6npiy

Drug voyager: a computational platform for exploring unintended drug action

Min Oh, Jaegyoon Ahn, Taekeon Lee, Giup Jang, Chihyun Park, Youngmi Yoon
2017 BMC Bioinformatics  
The dominant paradigm in understanding drug action focuses on the intended therapeutic effects and frequent adverse reactions. However, this approach may limit opportunities to grasp unintended drug actions, which can open up channels to repurpose existing drugs and identify rare adverse drug reactions. Advances in systems biology can be exploited to comprehensively understand pharmacodynamic actions, although proper frameworks to represent drug actions are still lacking. Results: We suggest a
more » ... ovel platform to construct a drug-specific pathway in which a molecular-level mechanism of action is formulated based on pharmacologic, pharmacogenomic, transcriptomic, and phenotypic data related to drug response (http://databio.gachon.ac.kr/tools/). In this platform, an adoption of three conceptual levels imitating drug perturbation allows these pathways to be realistically rendered in comparison to those of other models. Furthermore, we propose a new method that exploits functional features of the drug-specific pathways to predict new indications as well as adverse reactions. For therapeutic uses, our predictions significantly overlapped with clinical trials and an up-to-date drug-disease association database. Also, our method outperforms existing methods with regard to classification of active compounds for cancers. For adverse reactions, our predictions were significantly enriched in an independent database derived from the Food and Drug Administration (FDA) Adverse Event Reporting System and meaningfully cover an Adverse Reaction Database provided by Health Canada. Lastly, we discuss several predictions for both therapeutic indications and side-effects through the published literature. Conclusions: Our study addresses how we can computationally represent drug-signaling pathways to understand unintended drug actions and to facilitate drug discovery and screening.
doi:10.1186/s12859-017-1558-3 pmid:28241745 pmcid:PMC5329936 fatcat:cmca5i4npfdfpmzvlz5elceuk4

Noise-robust algorithm for identifying functionally associated biclusters from gene expression data☆

Jaegyoon Ahn, Youngmi Yoon, Sanghyun Park
2011 Information Sciences  
Biclusters are subsets of genes that exhibit similar behavior over a set of conditions. A biclustering algorithm is a useful tool for uncovering groups of genes involved in the same cellular processes and groups of conditions under which these processes take place. In this paper, we propose a polynomial time algorithm to identify functionally highly correlated biclusters. Our algorithm identifies (1) gene sets that simultaneously exhibit additive, multiplicative, and combined patterns and allow
more » ... high levels of noise, (2) multiple, possibly overlapped, and diverse gene sets, (3) biclusters that simultaneously exhibit negatively and positively correlated gene sets, and (4) gene sets for which the functional association is very high. We validate the level of functional association in our method by using the GO database, protein-protein interactions and KEGG pathways.
doi:10.1016/j.ins.2010.10.013 fatcat:gkowy6l7rzbepeh7f7blwr3vzm

The Mitogenic and Antiapoptotic Actions of Ghrelin in 3T3-L1 Adipocytes

Min Seon Kim, Cho Ya Yoon, Pil Geum Jang, Young Joo Park, Chan Soo Shin, Hye Sun Park, Je Won Ryu, Youngmi Kim Pak, Joong Yeol Park, Ki Up Lee, Seong Yeon Kim, Hong Kyu Lee (+2 others)
2004 Molecular Endocrinology  
RESULTS GHS-R Expression in 3T3-L1 Adipocytes When we assayed expression of the ghrelin receptor, GHS-R1a, in 3T3-L1 preadipocytes and differentiated adipocytes, we found that GHS-R1a mRNA and protein were present in 3T3-L1 cells, as well as in the rat hypothalamus and pituitary gland (Fig.
doi:10.1210/me.2003-0459 pmid:15178745 fatcat:e2btw36cefdobngqjibzbzxhse

Monolayer formation of PBLG–PEO block copolymers at the air–water interface

Youngmi Park, Young-Wook Choi, Sangwook Park, Chong Su Cho, Michael J. Fasolka, Daewon Sohn
2005 Journal of Colloid and Interface Science  
Park thanks Nano Science and Technology in Korea (KISTEP) for their support.  ... 
doi:10.1016/j.jcis.2004.09.023 pmid:15721901 fatcat:gn4c2aquqzcvjbildguejuazxq
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