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Search Results: 1 - 10 of 42197 matches for " Ki-Hong Jung "
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The Rice Oligonucleotide Array Database: an atlas of rice gene expression
Peijian Cao, Ki-Hong Jung, Daeseok Choi, Daehee Hwang, Jun Zhu, Pamela C. Ronald
Rice , 2012, DOI: 10.1186/1939-8433-5-17
Abstract: In this study, we developed the Rice Oligonucleotide Array Database (ROAD, http://www.ricearray.org webcite) to explore gene expression across 1,867 publicly available rice microarray hybridizations. The ROAD’s user-friendly web interface and variety of visualization tools facilitate the extraction of gene expression profiles using gene and microarray element identifications. The ROAD supports meta-analysis of genes expressed in different tissues and at developmental stages. Co-expression analysis tool provides information on co-regulation between genes under general, abiotic and biotic stress conditions. Additionally, functional analysis tools, such as Gene Ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthology, are embedded in the ROAD. These tools facilitate the identification of meaningful biological patterns in a list of query genes.The Rice Oligonucleotide Array Database provides comprehensive gene expression profiles for all rice genes, and will be a useful resource for researchers of rice and other grass species.
Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research
Rita Sharma,Peijian Cao,Ki-Hong Jung,Manoj K. Sharma,Pamela C. Ronald
Frontiers in Plant Science , 2013, DOI: 10.3389/fpls.2013.00330
Abstract: Glycoside hydrolases (GH) catalyze the hydrolysis of glycosidic bonds in cell wall polymers and can have major effects on cell wall architecture. Taking advantage of the massive datasets available in public databases, we have constructed a rice phylogenomic database of GHs (http://ricephylogenomics.ucdavis.edu/cellwalls/gh/). This database integrates multiple data types including the structural features, orthologous relationships, mutant availability, and gene expression patterns for each GH family in a phylogenomic context. The rice genome encodes 437 GH genes classified into 34 families. Based on pairwise comparison with eight dicot and four monocot genomes, we identified 138 GH genes that are highly diverged between monocots and dicots, 57 of which have diverged further in rice as compared with four monocot genomes scanned in this study. Chromosomal localization and expression analysis suggest a role for both whole-genome and localized gene duplications in expansion and diversification of GH families in rice. We examined the meta-profiles of expression patterns of GH genes in twenty different anatomical tissues of rice. Transcripts of 51 genes exhibit tissue or developmental stage-preferential expression, whereas, seventeen other genes preferentially accumulate in actively growing tissues. When queried in RiceNet, a probabilistic functional gene network that facilitates functional gene predictions, nine out of seventeen genes form a regulatory network with the well-characterized genes involved in biosynthesis of cell wall polymers including cellulose synthase and cellulose synthase-like genes of rice. Two-thirds of the GH genes in rice are up regulated in response to biotic and abiotic stress treatments indicating a role in stress adaptation. Our analyses identify potential GH targets for cell wall modification.
The Effect of Money Supply on the Volatility of Korean Stock Market  [PDF]
Ki-Hong Choi, Seong-Min Yoon
Modern Economy (ME) , 2015, DOI: 10.4236/me.2015.65052
Abstract: We examined the potential relationships between changes in the money supplies of Korea and the United States and volatility of the Korean stock market using the GARCH, GJR-GARCH, and EGARCH models. We did not identify any such relationships, implying that changes in money supply do not influence the flow of information to the market. However, we found that the asymmetric effect of bad news on volatility was higher when contemporaneous changes in Korean and US money supply variables were included in the models. This indicates that changes in money supply did not affect Korean stock volatility directly. Finally, the results based on a variance model indicated that the money supply of the two countries had no effect on the Korean stock market. This formal study suggests that there is no significant forecasting power of past changes in money supply. Although stock returns and volatility are not directly affected by changes in the money supply, the influence of supply on macroeconomic activity should not be disregarded.
A two-genome microarray for the rice pathogens Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola and its use in the discovery of a difference in their regulation of hrp genes
Young-Su Seo, Malinee Sriariyanun, Li Wang, Janice Pfeiff, Jirapa Phetsom, Ye Lin, Ki-Hong Jung, Hui Hsien Chou, Adam Bogdanove, Pamela Ronald
BMC Microbiology , 2008, DOI: 10.1186/1471-2180-8-99
Abstract: Three biological replicates of the microarray experiment to compare global gene expression in representative strains of Xoo and Xoc grown in PSB vs. XOM2 were carried out. The non-specific error rate and the correlation coefficients across biological replicates and among duplicate spots revealed that the microarray data were robust. 247 genes of Xoo and 39 genes of Xoc were differentially expressed in the two media with a false discovery rate of 5% and with a minimum fold-change of 1.75. Semi-quantitative-RT-PCR assays confirmed differential expression of each of 16 genes each for Xoo and Xoc selected for validation. The differentially expressed genes represent 17 functional categories.We describe here the construction and validation of a two-genome microarray for the two pathovars of X. oryzae. Microarray analysis revealed that using representative strains, a greater number of Xoo genes than Xoc genes are differentially expressed in XOM2 relative to PSB, and that these include hrp genes and other genes important in interactions with rice. An exception was the rax genes, which are required for production of the host resistance elicitor AvrXa21, and which were expressed constitutively in both pathovars.The rice pathogens Xanthomonas oryzae pathovar oryzae (Xoo) and Xanthomonas oryzae pathovar oryzicola (Xoc) cause economically significant disease in many rice-growing regions of the world [1]. Xoo invades rice vascular tissue to cause bacterial leaf blight, whereas Xoc colonizes the mesophyll parenchyma tissue to cause bacterial leaf streak. Xoo gains access to the xylem through wounds or natural openings such as hydathodes, while Xoc, in contrast, enters the leaf mainly through stomata [2]. Xoo and Xoc are closely related, infect the same host, and are often both established in the same rice fields. The complete genome sequences of Japanese Xoo strain T7174 (also called MAFF311018) and Korean Xoo strain KACC10331 have been published [3,4]. The genome sequences of a t
Relationship between Trading Volume and Asymmetric Volatility in the Korean Stock Market  [PDF]
Ki-Hong Choi, Zhu-Hua Jiang, Sang Hoon Kang, Seong-Min Yoon
Modern Economy (ME) , 2012, DOI: 10.4236/me.2012.35077
Abstract: We investigated the relationship between return volatility and trading volume as a proxy for the arrival of information to the market, based on Korean stock market (KSM) data from January 2000 to December 2010. We measured the rela- tionship between return volatility and trading volume using the GJR-GARCH and exponential GARCH (EGARCH) models. We found a positive relationship between trading volume and volatility, suggesting that trading volume influ- ences the flow of information to the market. This finding supports the validity of the mixture of distributions hy-pothesis. Considering that trading volume can also explain volatility asymmetry, we conclude that trading volume is a useful tool for predicting the volatility dynamics of the KSM.
Cross-Family Translational Genomics of Abiotic Stress-Responsive Genes between Arabidopsis and Medicago truncatula
Daejin Hyung, Chaeyoung Lee, Jin-Hyun Kim, Dongwoon Yoo, Young-Su Seo, Soon-Chun Jeong, Jai-Heon Lee, Youngsoo Chung, Ki-Hong Jung, Douglas R. Cook, Hong-kyu Choi
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0091721
Abstract: Cross-species translation of genomic information may play a pivotal role in applying biological knowledge gained from relatively simple model system to other less studied, but related, genomes. The information of abiotic stress (ABS)-responsive genes in Arabidopsis was identified and translated into the legume model system, Medicago truncatula. Various data resources, such as TAIR/AtGI DB, expression profiles and literatures, were used to build a genome-wide list of ABS genes. tBlastX/BlastP similarity search tools and manual inspection of alignments were used to identify orthologous genes between the two genomes. A total of 1,377 genes were finally collected and classified into 18 functional criteria of gene ontology (GO). The data analysis according to the expression cues showed that there was substantial level of interaction among three major types (i.e., drought, salinity and cold stress) of abiotic stresses. In an attempt to translate the ABS genes between these two species, genomic locations for each gene were mapped using an in-house-developed comparative analysis platform. The comparative analysis revealed that fragmental colinearity, represented by only 37 synteny blocks, existed between Arabidopsis and M. truncatula. Based on the combination of E-value and alignment remarks, estimated translation rate was 60.2% for this cross-family translation. As a prelude of the functional comparative genomic approaches, in-silico gene network/interactome analyses were conducted to predict key components in the ABS responses, and one of the sub-networks was integrated with corresponding comparative map. The results demonstrated that core members of the sub-network were well aligned with previously reported ABS regulatory networks. Taken together, the results indicate that network-based integrative approaches of comparative and functional genomics are important to interpret and translate genomic information for complex traits such as abiotic stresses.
Identification and Functional Analysis of Light-Responsive Unique Genes and Gene Family Members in Rice
Ki-Hong Jung,Jinwon Lee,Chris Dardick,Young-Su Seo,Peijian Cao,Patrick Canlas,Jirapa Phetsom,Xia Xu,Shu Ouyang,Kyungsook An,Yun-Ja Cho,Geun-Cheol Lee,Yoosook Lee,Gynheung An,Pamela C. Ronald
PLOS Genetics , 2008, DOI: 10.1371/journal.pgen.1000164
Abstract: Functional redundancy limits detailed analysis of genes in many organisms. Here, we report a method to efficiently overcome this obstacle by combining gene expression data with analysis of gene-indexed mutants. Using a rice NSF45K oligo-microarray to compare 2-week-old light- and dark-grown rice leaf tissue, we identified 365 genes that showed significant 8-fold or greater induction in the light relative to dark conditions. We then screened collections of rice T-DNA insertional mutants to identify rice lines with mutations in the strongly light-induced genes. From this analysis, we identified 74 different lines comprising two independent mutant lines for each of 37 light-induced genes. This list was further refined by mining gene expression data to exclude genes that had potential functional redundancy due to co-expressed family members (12 genes) and genes that had inconsistent light responses across other publicly available microarray datasets (five genes). We next characterized the phenotypes of rice lines carrying mutations in ten of the remaining candidate genes and then carried out co-expression analysis associated with these genes. This analysis effectively provided candidate functions for two genes of previously unknown function and for one gene not directly linked to the tested biochemical pathways. These data demonstrate the efficiency of combining gene family-based expression profiles with analyses of insertional mutants to identify novel genes and their functions, even among members of multi-gene families.
Joint Filter Design of Alternate MIMO AF Relaying Networks with Interference Alignment
Ki-Hong Park,Mohamed-Slim Alouini
Mathematics , 2012,
Abstract: We study in this paper a two-hop relaying network consisting of one source, one destination, and three amplify-and-forward (AF) relays operating in a half-duplex mode. In order to compensate for the inherent loss of capacity pre-log factor 1/2 in a half-duplex mode, we consider alternate transmission protocol among three relays where two relays and the other relay alternately forward messages from source to destination. We consider a multiple-antenna environment where all nodes have $M$ antennas. Aligning the inter-relay interference due to the alternate transmission is utilized to make additional degrees of freedom (DOFs) and recover the pre-log factor loss. It is shown that the proposed relaying scheme can achieve $\frac{3M}{4}$ DOFs compared with the $\frac{M}{2}$ DOFs of conventional AF relaying. In addition, suboptimal linear filter designs for a source and three relays are proposed to maximize the system achievable sum-rate for different fading scenarios when the destination utilizes a linear minimum mean-square error filter for decoding. We verify from our selected numerical results that the proposed filter designs give significant improvement over a naive filter or conventional relaying schemes.
Towards Establishment of a Rice Stress Response Interactome
Young-Su Seo,Mawsheng Chern,Laura E. Bartley,Muho Han,Ki-Hong Jung,Insuk Lee,Harkamal Walia,Todd Richter,Xia Xu,Peijian Cao,Wei Bai,Rajeshwari Ramanan,Fawn Amonpant,Loganathan Arul,Patrick E. Canlas,Randy Ruan,Chang-Jin Park,Xuewei Chen,Sohyun Hwang,Jong-Seong Jeon,Pamela C. Ronald
PLOS Genetics , 2011, DOI: 10.1371/journal.pgen.1002020
Abstract: Rice (Oryza sativa) is a staple food for more than half the world and a model for studies of monocotyledonous species, which include cereal crops and candidate bioenergy grasses. A major limitation of crop production is imposed by a suite of abiotic and biotic stresses resulting in 30%–60% yield losses globally each year. To elucidate stress response signaling networks, we constructed an interactome of 100 proteins by yeast two-hybrid (Y2H) assays around key regulators of the rice biotic and abiotic stress responses. We validated the interactome using protein–protein interaction (PPI) assays, co-expression of transcripts, and phenotypic analyses. Using this interactome-guided prediction and phenotype validation, we identified ten novel regulators of stress tolerance, including two from protein classes not previously known to function in stress responses. Several lines of evidence support cross-talk between biotic and abiotic stress responses. The combination of focused interactome and systems analyses described here represents significant progress toward elucidating the molecular basis of traits of agronomic importance.
Refinement of Light-Responsive Transcript Lists Using Rice Oligonucleotide Arrays: Evaluation of Gene-Redundancy
Ki-Hong Jung, Christopher Dardick, Laura E. Bartley, Peijian Cao, Jirapa Phetsom, Patrick Canlas, Young-Su Seo, Michael Shultz, Shu Ouyang, Qiaoping Yuan, Bryan C. Frank, Eugene Ly, Li Zheng, Yi Jia, An-Ping Hsia, Kyungsook An, Hui-Hsien Chou, David Rocke, Geun Cheol Lee, Patrick S. Schnable, Gynheung An, C. Robin Buell, Pamela C. Ronald
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0003337
Abstract: Studies of gene function are often hampered by gene-redundancy, especially in organisms with large genomes such as rice (Oryza sativa). We present an approach for using transcriptomics data to focus functional studies and address redundancy. To this end, we have constructed and validated an inexpensive and publicly available rice oligonucleotide near-whole genome array, called the rice NSF45K array. We generated expression profiles for light- vs. dark-grown rice leaf tissue and validated the biological significance of the data by analyzing sources of variation and confirming expression trends with reverse transcription polymerase chain reaction. We examined trends in the data by evaluating enrichment of gene ontology terms at multiple false discovery rate thresholds. To compare data generated with the NSF45K array with published results, we developed publicly available, web-based tools (www.ricearray.org). The Oligo and EST Anatomy Viewer enables visualization of EST-based expression profiling data for all genes on the array. The Rice Multi-platform Microarray Search Tool facilitates comparison of gene expression profiles across multiple rice microarray platforms. Finally, we incorporated gene expression and biochemical pathway data to reduce the number of candidate gene products putatively participating in the eight steps of the photorespiration pathway from 52 to 10, based on expression levels of putatively functionally redundant genes. We confirmed the efficacy of this method to cope with redundancy by correctly predicting participation in photorespiration of a gene with five paralogs. Applying these methods will accelerate rice functional genomics.
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