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Search Results: 1 - 10 of 11338 matches for " Peijian Cao "
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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.
Rosiglitazone Restores Endothelial Dysfunction in a Rat Model of Metabolic Syndrome through PPAR … - and PPAR … -Dependent Phosphorylation of Akt and eNOS
Zhigang Zhao,Zhidan Luo,Peijian Wang,Jing Sun,Hao Yu,Tingbing Cao,Yinxing Ni,Jing Chen,Zhencheng Yan,Daoyan Liu,Zhiming Zhu
PPAR Research , 2011, DOI: 10.1155/2011/291656
Abstract: Vascular endothelial dysfunction has been demonstrated in metabolic syndrome (MS). Chronic administration of rosiglitazone ameliorates endothelial dysfunction through PPARγ-mediated metabolic improvements. Recently, studies suggested that single dose of rosiglitazone also has direct vascular effects, but the mechanisms remain uncertain. Here we established a diet-induced rat model of MS. The impaired vasorelaxation in MS rats was improved by incubating arteries with rosiglitazone for one hour. Importantly, this effect was blocked by either inhibition of PPARγ or PPARδ. In cultured endothelial cells, acute treatment with rosiglitazone increased the phosphorylation of Akt and eNOS and the production of NO. These effects were also abolished by inhibition of PPARγ, PPARδ, or PI3K. In conclusion, rosiglitazone improved endothelial function through both PPARγ- and PPARδ-mediated phosphorylation of Akt and eNOS, which might help to reconsider the complex effects and clinical applications of rosiglitazone. 1. Introduction Metabolic syndrome is characterized by a combination of metabolic disorders that increase the risk of developing cardiovascular disease. Vascular endothelial dysfunction has been demonstrated in metabolic syndrome with and without hypertension or diabetes [1–3]. Thiazolidinediones (TZDs), which are a class of powerful insulin sensitizers, are ideal candidates for the early treatment of metabolic syndrome. There is also a growing body of in vivo evidence suggesting that TZDs improve endothelial function [4–7] and have a small reducing effect on blood pressure [8, 9]. The vascular protective effects might be a consequence of the metabolic changes that are mainly mediated by the transcription factor, peroxisome-proliferator-activated receptor (PPAR) γ [6, 8, 10, 11]. However, studies suggest that a single dose of rosiglitazone has a direct effect on endothelial function, which is independent of the metabolic improvement [12]. These studies imply that the short-term application of rosiglitazone might have endothelial benefits without any side effects, although the long-term intake of rosiglitazone is associated with an increased risk of heart failure. However, the mechanism by which rosiglitazone improves endothelial function remains uncertain. Although PPARγ in endothelial cells (ECs) is involved in the regulation of nitric oxide (NO) [13], the production of reactive oxygen species [14], and the synthesis of endothelin receptor [15], rosiglitazone also has PPARγ-independent effects in isolated vasculatures and cultured ECs [16]. Unlike PPARγ, the
A Genome-Wide Survey of Switchgrass Genome Structure and Organization
Manoj K. Sharma, Rita Sharma, Peijian Cao, Jerry Jenkins, Laura E. Bartley, Morgan Qualls, Jane Grimwood, Jeremy Schmutz, Daniel Rokhsar, Pamela C. Ronald
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0033892
Abstract: The perennial grass, switchgrass (Panicum virgatum L.), is a promising bioenergy crop and the target of whole genome sequencing. We constructed two bacterial artificial chromosome (BAC) libraries from the AP13 clone of switchgrass to gain insight into the genome structure and organization, initiate functional and comparative genomic studies, and assist with genome assembly. Together representing 16 haploid genome equivalents of switchgrass, each library comprises 101,376 clones with average insert sizes of 144 (HindIII-generated) and 110 kb (BstYI-generated). A total of 330,297 high quality BAC-end sequences (BES) were generated, accounting for 263.2 Mbp (16.4%) of the switchgrass genome. Analysis of the BES identified 279,099 known repetitive elements, >50,000 SSRs, and 2,528 novel repeat elements, named switchgrass repetitive elements (SREs). Comparative mapping of 47 full-length BAC sequences and 330K BES revealed high levels of synteny with the grass genomes sorghum, rice, maize, and Brachypodium. Our data indicate that the sorghum genome has retained larger microsyntenous regions with switchgrass besides high gene order conservation with rice. The resources generated in this effort will be useful for a broad range of applications.
Mechanisms of the Regulation of the Intestinal Exchanger NHE3
Peijian He,C. Chris Yun
Journal of Biomedicine and Biotechnology , 2010, DOI: 10.1155/2010/238080
Abstract: A major of Na
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.
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.
A Phenome-Based Functional Analysis of Transcription Factors in the Cereal Head Blight Fungus, Fusarium graminearum
Hokyoung Son equal contributor,Young-Su Seo equal contributor,Kyunghun Min,Ae Ran Park,Jungkwan Lee,Jian-Ming Jin,Yang Lin,Peijian Cao,Sae-Yeon Hong,Eun-Kyung Kim,Seung-Ho Lee,Aram Cho,Seunghoon Lee,Myung-Gu Kim,Yongsoo Kim,Jung-Eun Kim,Jin-Cheol Kim,Gyung Ja Choi,Sung-Hwan Yun,Jae Yun Lim,Minkyun Kim,Yong-Hwan Lee,Yang-Do Choi,Yin-Won Lee
PLOS Pathogens , 2011, DOI: 10.1371/journal.ppat.1002310
Abstract: Fusarium graminearum is an important plant pathogen that causes head blight of major cereal crops. The fungus produces mycotoxins that are harmful to animal and human. In this study, a systematic analysis of 17 phenotypes of the mutants in 657 Fusarium graminearum genes encoding putative transcription factors (TFs) resulted in a database of over 11,000 phenotypes (phenome). This database provides comprehensive insights into how this cereal pathogen of global significance regulates traits important for growth, development, stress response, pathogenesis, and toxin production and how transcriptional regulations of these traits are interconnected. In-depth analysis of TFs involved in sexual development revealed that mutations causing defects in perithecia development frequently affect multiple other phenotypes, and the TFs associated with sexual development tend to be highly conserved in the fungal kingdom. Besides providing many new insights into understanding the function of F. graminearum TFs, this mutant library and phenome will be a valuable resource for characterizing the gene expression network in this fungus and serve as a reference for studying how different fungi have evolved to control various cellular processes at the transcriptional level.
Hilbert Boundary Value Problem with an Unknown Function on Arbitrary Infinite Straight Line  [PDF]
Lixia Cao
Advances in Pure Mathematics (APM) , 2013, DOI: 10.4236/apm.2013.32033

We consider a Hilbert boundary value problem with an unknown parametric function on arbitrary infinite straight line passing through the origin. We propose to transform the Hilbert boundary value problem to Riemann boundary value problem, and address it by defining symmetric extension for holomorphic functions about an arbitrary straight line passing through the origin. Finally, we develop the general solution and the solvable conditions for the Hilbert boundary value problem.

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