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Search Results: 1 - 10 of 3066 matches for " Jong Bhak "
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Identification and Characterization of MicroRNAs in Normal Equine Tissues by Next Generation Sequencing
Myung-Chul Kim, Seung-Woo Lee, Doug-Young Ryu, Feng-Ji Cui, Jong Bhak, Yongbaek Kim
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0093662
Abstract: The role of microRNAs (miRNAs) as a post-transcriptional gene regulator has been elucidated in a broad range of organisms including domestic animals. Characterization of miRNAs in normal tissues is an important step to investigate the functions of miRNAs in various physiological and pathological conditions. Using Illumina Next Generation Sequencing (NGS) technology, we identified a total of 292 known and 329 novel miRNAs in normal horse tissues including skeletal muscle, colon and liver. Distinct sets of miRNAs were differentially expressed in a tissue-specific manner. The miRNA genes were distributed across all the chromosomes except chromosomes 29 and 31 in the horse reference genome. In some chromosomes, multiple miRNAs were clustered and considered to be polycistronic transcript. A base composition analysis showed that equine miRNAs had a higher frequency of A+U than G+C. Furthermore, U tended to be more frequent at the 5′ end of miRNA sequences. This is the first experimental study that identifies and characterizes the global miRNA expression profile in normal horse tissues. The present study enriches the horse miRNA database and provides useful information for further research dissecting biological functions of miRNAs in horse.
Gene Expression Pattern in Transmitochondrial Cytoplasmic Hybrid Cells Harboring Type 2 Diabetes-Associated Mitochondrial DNA Haplogroups
Seungwoo Hwang, Soo Heon Kwak, Jong Bhak, Hae Sun Kang, You Ri Lee, Bo Kyung Koo, Kyong Soo Park, Hong Kyu Lee, Young Min Cho
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0022116
Abstract: Decreased mitochondrial function plays a pivotal role in the pathogenesis of type 2 diabetes mellitus (T2DM). Recently, it was reported that mitochondrial DNA (mtDNA) haplogroups confer genetic susceptibility to T2DM in Koreans and Japanese. Particularly, mtDNA haplogroup N9a is associated with a decreased risk of T2DM, whereas haplogroups D5 and F are associated with an increased risk. To examine functional consequences of these haplogroups without being confounded by the heterogeneous nuclear genomic backgrounds of different subjects, we constructed transmitochondrial cytoplasmic hybrid (cybrid) cells harboring each of the three haplogroups (N9a, D5, and F) in a background of a shared nuclear genome. We compared the functional consequences of the three haplogroups using cell-based assays and gene expression microarrays. Cell-based assays did not detect differences in mitochondrial functions among the haplogroups in terms of ATP generation, reactive oxygen species production, mitochondrial membrane potential, and cellular dehydrogenase activity. However, differential expression and clustering analyses of microarray data revealed that the three haplogroups exhibit a distinctive nuclear gene expression pattern that correlates with their susceptibility to T2DM. Pathway analysis of microarray data identified several differentially regulated metabolic pathways. Notably, compared to the T2DM-resistant haplogroup N9a, the T2DM-susceptible haplogroup F showed down-regulation of oxidative phosphorylation and up-regulation of glycolysis. These results suggest that variations in mtDNA can affect the expression of nuclear genes regulating mitochondrial functions or cellular energetics. Given that impaired mitochondrial function caused by T2DM-associated mtDNA haplogroups is compensated by the nuclear genome, we speculate that defective nuclear compensation, under certain circumstances, might lead to the development of T2DM.
PanSNPdb: The Pan-Asian SNP Genotyping Database
Chumpol Ngamphiw, Anunchai Assawamakin, Shuhua Xu, Philip J. Shaw, Jin Ok Yang, Ho Ghang, Jong Bhak, Edison Liu, Sissades Tongsima, and the HUGO Pan-Asian SNP Consortium
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0021451
Abstract: The HUGO Pan-Asian SNP consortium conducted the largest survey to date of human genetic diversity among Asians by sampling 1,719 unrelated individuals among 71 populations from China, India, Indonesia, Japan, Malaysia, the Philippines, Singapore, South Korea, Taiwan, and Thailand. We have constructed a database (PanSNPdb), which contains these data and various new analyses of them. PanSNPdb is a research resource in the analysis of the population structure of Asian peoples, including linkage disequilibrium patterns, haplotype distributions, and copy number variations. Furthermore, PanSNPdb provides an interactive comparison with other SNP and CNV databases, including HapMap3, JSNP, dbSNP and DGV and thus provides a comprehensive resource of human genetic diversity. The information is accessible via a widely accepted graphical interface used in many genetic variation databases. Unrestricted access to PanSNPdb and any associated files is available at: http://www4a.biotec.or.th/PASNP.
Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection
Andrés F Flórez, Daeui Park, Jong Bhak, Byoung-Chul Kim, Allan Kuchinsky, John H Morris, Jairo Espinosa, Carlos Muskus
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-484
Abstract: We have predicted the protein interaction network of Leishmania major by using three validated methods: PSIMAP, PEIMAP, and iPfam. Combining the results from these methods, we calculated a high confidence network (confidence score > 0.70) with 1,366 nodes and 33,861 interactions. We were able to predict the biological process for 263 interacting proteins by doing enrichment analysis of the clusters detected. Analyzing the topology of the network with metrics such as connectivity and betweenness centrality, we detected 142 potential drug targets after homology filtering with the human proteome. Further experiments can be done to validate these targets.We have constructed the first protein interaction network of the Leishmania major parasite by using a computational approach. The topological analysis of the protein network enabled us to identify a set of candidate proteins that may be both (1) essential for parasite survival and (2) without human orthologs. These potential targets are promising for further experimental validation. This strategy, if validated, may augment established drug discovery methodologies, for this and possibly other tropical diseases, with a relatively low additional investment of time and resources.Leishmaniasis is a complex infectious disease caused by several species of the Leishmania genus, affecting more than 2 million of people around the world in 88 countries. In addition to endemic countries, there have been increasing numbers of cases in non-endemic countries due to tourism [1-5]. The parasite is transmitted to human or animal reservoirs by the female insect of the genus Lutzomyia in the New World and Phlebotomus in the Old World [1]. Leishmaniasis has three main clinical presentations: cutaneous, mucocutaneous and visceral. The visceral form affects mainly children, who can die if adequate treatment is not provided in a timely manner. The cutaneous and mucocutaneous forms can cause severe disabilities in adults, affecting productivity
A protein domain interaction interface database: InterPare
Sungsam Gong, Changbum Park, Hansol Choi, Junsu Ko, Insoo Jang, Jungsul Lee, Dan M Bolser, Donghoon Oh, Deok-Soo Kim, Jong Bhak
BMC Bioinformatics , 2005, DOI: 10.1186/1471-2105-6-207
Abstract: We introduce a large-scale protein domain interaction interface database called InterPare http://interpare.net webcite. It contains both inter-chain (between chains) interfaces and intra-chain (within chain) interfaces. InterPare uses three methods to detect interfaces: 1) the geometric distance method for checking the distance between atoms that belong to different domains, 2) Accessible Surface Area (ASA), a method for detecting the buried region of a protein that is detached from a solvent when forming multimers or complexes, and 3) the Voronoi diagram, a computational geometry method that uses a mathematical definition of interface regions. InterPare includes visualization tools to display protein interior, surface, and interaction interfaces. It also provides statistics such as the amino acid propensities of queried protein according to its interior, surface, and interface region. The atom coordinates that belong to interface, surface, and interior regions can be downloaded from the website.InterPare is an open and public database server for protein interaction interface information. It contains the large-scale interface data for proteins whose 3D-structures are known. As of November 2004, there were 10,583 (Geometric distance), 10,431 (ASA), and 11,010 (Voronoi diagram) entries in the Protein Data Bank (PDB) containing interfaces, according to the above three methods. In the case of the geometric distance method, there are 31,620 inter-chain domain-domain interaction interfaces and 12,758 intra-chain domain-domain interfaces.Proteins are the most important class of molecules in a cell. Most proteins function by interacting with other molecules, especially other proteins. The interactions among proteins are highly regulated and tightly conserved throughout evolution, [1,2] mainly because unnecessary or unsatisfactory interaction (misinteraction) triggered by random mutations can lead to molecular dysfunction. Therefore, interaction interface regions are under p
Gene Flow between the Korean Peninsula and Its Neighboring Countries
Jongsun Jung,Hoyoung Kang,Yoon Shin Cho,Ji Hee Oh,Min Hyung Ryu,Hye Won Chung,Jeong-Sun Seo,Jong-Eun Lee,Bermseok Oh,Jong Bhak,Hyung-Lae Kim
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0011855
Abstract: SNP markers provide the primary data for population structure analysis. In this study, we employed whole-genome autosomal SNPs as a marker set (54,836 SNP markers) and tested their possible effects on genetic ancestry using 320 subjects covering 24 regional groups including Northern ( = 16) and Southern ( = 3) Asians, Amerindians ( = 1), and four HapMap populations (YRI, CEU, JPT, and CHB). Additionally, we evaluated the effectiveness and robustness of 50K autosomal SNPs with various clustering methods, along with their dependencies on recombination hotspots (RH), linkage disequilibrium (LD), missing calls and regional specific markers. The RH- and LD-free multi-dimensional scaling (MDS) method showed a broad picture of human migration from Africa to North-East Asia on our genome map, supporting results from previous haploid DNA studies. Of the Asian groups, the East Asian group showed greater differentiation than the Northern and Southern Asian groups with respect to Fst statistics. By extension, the analysis of monomorphic markers implied that nine out of ten historical regions in South Korea, and Tokyo in Japan, showed signs of genetic drift caused by the later settlement of East Asia (South Korea, Japan and China), while Gyeongju in South East Korea showed signs of the earliest settlement in East Asia. In the genome map, the gene flow to the Korean Peninsula from its neighboring countries indicated that some genetic signals from Northern populations such as the Siberians and Mongolians still remain in the South East and West regions, while few signals remain from the early Southern lineages.
Predicting the Interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service
Jeong-Gu Kim, Daeui Park, Byoung-Chul Kim, Seong-Woong Cho, Yeong Kim, Young-Jin Park, Hee Cho, Hyunseok Park, Ki-Bong Kim, Kyong-Oh Yoon, Soo-Jun Park, Byoung-Moo Lee, Jong Bhak
BMC Bioinformatics , 2008, DOI: 10.1186/1471-2105-9-41
Abstract: A PPI network in Xoo proteome was predicted by bioinformatics algorithms: PSIMAP, PEIMAP, and iPfam. We present the resultant species specific interaction network and host-pathogen interaction, XooNET. It is a comprehensive predicted initial PPI data for Xoo. XooNET can be used by experimentalists to pick up protein targets for blocking pathological interactions. XooNET uses most of the major types of PPI algorithms. They are: 1) Protein Structural Interactome MAP (PSIMAP), a method using structural domain of SCOP, 2) Protein Experimental Interactome MAP (PEIMAP), a common method using public resources of experimental protein interaction information such as HPRD, BIND, DIP, MINT, IntAct, and BioGrid, and 3) Domain-domain interactions, a method using Pfam domains such as iPfam. Additionally, XooNET provides information on network properties of the Xoo interactome.XooNET is an open and free public database server for protein interaction information for Xoo. It contains 4,538 proteins and 26,932 possible interactions consisting of 18,503 (PSIMAP), 3,118 (PEIMAP), and 8,938 (iPfam) pairs. In addition, XooNET provides 3,407 possible interaction pairs between two sets of proteins; 141 Xoo proteins that are predicted as membrane proteins and rice proteomes. The resultant interacting partners of a query protein can be easily retrieved by users as well as the interaction networks in graphical web interfaces. XooNET is freely available from http://bioportal.kobic.kr/XooNET/ webcite.Proteins constitute 50 percent or more of the dry weight of living organisms. They have the most diverse biological roles. They function by interacting with other molecules including proteins themselves. Usually, protein-protein interactions are the key mechanisms of normal and pathological functions of living cells. Recently, genomic-scale identification of PPI in model organisms such as Saccharomyces cerevisiae [1-3] and Escherichia coli [4] have been reported to map the network protein-protein i
The association of Alu repeats with the generation of potential AU-rich elements (ARE) at 3' untranslated regions.
Hyeong Jun An, Doheon Lee, Kwang Hyung Lee, Jonghwa Bhak
BMC Genomics , 2004, DOI: 10.1186/1471-2164-5-97
Abstract: Interspersed in the human genome, Alu repeats occupy 5% of the 3' UTR of mRNA sequences. Alu has poly-adenine (poly-A) regions at its end, which lead to poly-thymine (poly-T) regions at the end of its complementary Alu. It has been found that AREs are present at the poly-T regions. From the 3' UTR of the NCBI's reference mRNA sequence database, we found nearly 40% (38.5%) of ARE (Class I) were associated with Alu sequences (Table 1) within one mismatch allowance in ARE sequences. Other ARE classes had statistically significant associations as well. This is far from a random occurrence given their limited quantity. At each ARE class, random distribution was simulated 1,000 times, and it was shown that there is a special relationship between ARE patterns and the Alu repeats.AREs are mediating sequence elements affecting the stabilization or degradation of mRNA at the 3' untranslated regions. However, AREs' mechanism and origins are unknown. We report that Alu is a source of ARE. We found that half of the longest AREs were derived from the poly-T regions of the complementary Alu.Varying more than ten-fold, messenger RNA degradation is essential for the regulation of gene expression [1,2]. Differential mRNA decay rates were determined by specific cis-acting sequences within mRNA. For example, the mRNA sequences of yeast, many mammalians, and other eukaryotes contain AU-rich elements or AREs at their 3' untranslated regions (UTR) [3,4]. For example, in yeast, AREs stimulated the shortening of poly adenine (poly A), and two kinds of degradation pathways followed. One is 5'-to-3' exonuclease access by removal of the 5' cap structure. The other is 3'-to-5' digestion by a complex of exonucleases called exosome [5,6]. Genes required for these steps have been identified in yeast and were found to be conserved among eukaryotes. Although the mechanisms of AREs enhanced mRNA degradation are unknown, several groups provided evidence that 3'-to-5' degradation by the exosome may be
Empowering Teachers for Innovations: The Case of Online Teacher Learning Communities  [PDF]
Onno De Jong
Creative Education (CE) , 2012, DOI: 10.4236/ce.2012.38B026
Abstract: Implementing innovations in classrooms often evokes a variety of recurrent difficulties, especially feelings of resistance among experienced teachers. Modern teacher education aims at reducing their opposition by empowering these teachers for developing new knowledge, beliefs, and skills. A growing number of these teacher courses is designed as teacher learning communities (TLC-s). A specific category of them, online networks, is the scope of the present paper. Main values and attributes of these communities are addressed. This is followed by presenting some leading principles for designing TLC-s. Important principles are: (i) creating subcommunities within large-scale online networks, (ii) combining online activities with face-to-face meetings, and, (iii) facilitating more equality in online group participation. These principles are illustrated by examples of real practices. Finally, main conditions for successful new online TLC-s are presented. Prospects for advanced studies of practices of these communities are also given.
Biphenyl- and carvone-induced protein expression patterns in Rhodococcus sp. ACS  [PDF]
Jong-Shik Kim
Journal of Agricultural Chemistry and Environment (JACEN) , 2013, DOI: 10.4236/jacen.2013.23010
Abstract: Protein expression patterns in the polychlorinated biphenyl (PCB)-degrading Rhodococcussp. strain ACS were examined following growth on two substrates capable of inducing the enantioselective biotransformation of PCBs via different degradation pathways. Eleven
inducible proteins were identified by SDS-PAGE and characterized by LC-MS/MS. Four of the peptides, a spore coat protein, an extracellular serine protease, a spoVP, and a molecular chaperonin from Bacillus subtilis, were identified as being unique to biphenyl-induced cells, whereas anextracellular serine protease from B. subtilis was identified as being unique to carvone-induced cells.
None of the peptides identified had sequences that corresponded to known dioxygenases or other PCB-degrading enzymes of this Gram- positive bacterium, suggesting that the identified induced proteins may be involved in either PCB degradation or adaptive responses that protect cells from toxicity.


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