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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
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.
Assessing probe-specific dye and slide biases in two-color microarray data
Ruixiao Lu, Geun-Cheol Lee, Michael Shultz, Chris Dardick, Kihong Jung, Jirapa Phetsom, Yi Jia, Robert H Rice, Zelanna Goldberg, Patrick S Schnable, Pamela Ronald, David M Rocke
BMC Bioinformatics , 2008, DOI: 10.1186/1471-2105-9-314
Abstract: We develop a procedure for quantifying the extent of probe-specific dye and slide bias in two-color microarrays. The primary output is a graphical diagnostic of the extent of the bias which called ECDF (Empirical Cumulative Distribution Function), though numerical results are also obtained.We show that the dye and slide biases were high for human and rice genomic arrays in two gene expression facilities, even after the standard intensity-based normalization, and describe how this diagnostic allowed the problems causing the probe-specific bias to be addressed, and resulted in important improvements in performance. The R package LMGene which contains the method described in this paper has been available to download from Bioconductor.One of the major tasks in the analysis of high-dimensional biological assay data such as gene expression arrays is to detect differential expression from a comparative experiment. Using two-color microarrays is supposed to adjust for the noise introduced by many factors on the same slide including spot size and conformation. Standard data pre-processing methods for two-color data include the normalization of the differences between two dye channels, after which most users believe the dye bias has effectively been removed and that the normalized measurements are now relatively free of dye bias. However, probe specific dye-bias and slide-bias can be high even after standard normalization, which may cause problems when one expects to identify many statistically significantly differentially expressed genes.This dye bias has received some recent attention [1-8]. These papers generally provide computational methods to detect and correct for dye bias, at least in some circumstances. Correction can include use of gene-specific dye bias terms in an ANOVA, for example. Even when this is done, dye bias may still cause significant harm by introducing large amounts of noise that prevent identification of significantly differentially expressed genes. We
Annual Review of Education, Communication and Language Sciences , 2008,
Abstract: Success in learning a second or a foreign language, unlike success in first language acquisition, is very variable. Learner strategies, as conscious actions in learning and using a second or a foreign language, are one of the variable factors that have profound effects on how individual learners approach language learning and how successful they are. The more we learn about learner strategies, the more we gain a sense of the complex system of language learning and teaching. This paper critically reviews previous research on learner strategies and the implications of learner strategies for language teaching will be addressed. It aims to give some ideas to language teachers or administrators of how to: (1) explicitly involve learner strategies in a language curriculum, (2) provide language learners with a menu of the strategies that they can choose and adapt to different language learning tasks, and (3) create habits of good language learners.
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.
Hydrogen Peroxide Toxicity Induces Ras Signaling in Human Neuroblastoma SH-SY5Y Cultured Cells
Jirapa Chetsawang,Piyarat Govitrapong,Banthit Chetsawang
Journal of Biomedicine and Biotechnology , 2010, DOI: 10.1155/2010/803815
Abstract: It has been reported that overproduction of reactive oxygen species occurs after brain injury and mediates neuronal cells degeneration. In the present study, we examined the role of Ras signaling on hydrogen peroxide-induced neuronal cells degeneration in dopaminergic neuroblastoma SH-SY5Y cells. Hydrogen peroxide significantly reduced cell viability in SH-SY5Y cultured cells. An inhibitor of the enzyme that catalyzes the farnesylation of Ras proteins, FTI-277, and a competitive inhibitor of GTP-binding proteins, GDP-beta-S significantly decreased hydrogen peroxide-induced reduction in cell viability in SH-SY5Y cultured cells. The results of this study might indicate that a Ras-dependent signaling pathway plays a role in hydrogen peroxide-induced toxicity in neuronal cells.
Copper-Alginate Encapsulation of Crude laccase from Lentinus polychrous Lev. and their Effectiveness in Synthetic Dyes Decolorizations
J. Phetsom,S. Khammuang,P. Suwannawong,R. Sarnthima
Journal of Biological Sciences , 2009,
Abstract: Crude laccase from Lentinus polychrous Lev. was entrapped in alginate beads for application in decolorization of synthetic dyes. The percentages of alginate, types and concentrations of bivalent cations (Cu2+, Zn2+, Ca2+) influenced on immobilized enzyme activity as well as immobilized yield. The sensitivity of the immobilized Cu-alginate enzyme towards pH change was lowest when compared to the immobilized enzymes of other bivalent cations including free enzyme. By using ABTS substrate, the optimum temperature of the Ca-, Cu- and Zn-alginate enzymes were 60, 55 and 55°C, respectively while the optimum temperature of the free enzyme was 50°C. The Cu- and Zn-alginate enzymes were well stabilized for a week in all tested pH values except for pH 8.0 (0.1 M Tris-HCl). The Cu- and Zn-alginate enzymes revealed better temperature stability than the Ca-alginate and the free enzymes. Decolorizations of four structurally different synthetic dyes by the immobilized Cu-alginate enzymes in a continuous pack-bed approach were reported. The Cu-alginate enzymes were being able to repeated use effectively more than two times in dye removal experiments.
(E)-3-(Anthracen-9-yl)-1-(furan-2-yl)prop-2-en-1-oneThis paper is dedicated to His Majesty King Bhumibol Adulyadej of Thailand (King Rama IX) for his sustainable development of the country.
Jirapa Horkaew,Thitipone Suwunwong,Suchada Chantrapromma,Chatchanok Karalai
Acta Crystallographica Section E , 2010, DOI: 10.1107/s1600536810005982
Abstract: In the molecule of the title heteroaryl chalcone derivative, C21H14O2, the almost planar prop-2-en-1-one unit [r.m.s. deviation = 0.0087 (1) ] forms dihedral angles of 5.81 (7) and 49.85 (6)°, respectively, with the furan ring and anthracene ring system. In the crystal structure, the molecules are linked into a two-dimensional network parallel to (100) by C—H...O hydrogen bonds and π...π interactions involving the furan rings [centroid–centroid distance = 3.7205 (6) ].
User-Feedback for Road Traffic Information using Mobile Phone
Jirapa Jaroenjanyakul,Wasan Pattara-Atikom,Satidchoke Phosaard,Weerapong Polnigongit
Lecture Notes in Engineering and Computer Science , 2008,
Jirapa Horkaew,Suchada Chantrapromma,Nisakorn Saewan,Hoong-Kun Fun
Acta Crystallographica Section E , 2010, DOI: 10.1107/s1600536810032514
Abstract: In the title compound, C17H16O3, the carbonyl group is in an s-cis configuration with respect to the olefinic double bond. The dihedral angle between the two benzene rings is 2.85 (3)°. The prop-2-en-1-one bridge makes dihedral angles of 4.77 (4) and 4.15 (4)°, respectively, with the 2-hydroxyphenyl and 4-ethoxyphenyl rings. The ethoxy group is coplanar with the attached phenyl ring [Car—O—C—C = 179.72 (5)°]. An intramolecular O—H...O hydrogen bond generates an S(6) ring motif. In the crystal structure, molecules are stacked in an antiparallel manner to form columns along the b axis. The columnar structure is stabilized by C—H...π interactions involving the 2-hydroxyphenyl ring.
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