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Search Results: 1 - 10 of 224617 matches for " Pamela C. Ronald "
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Lab to Farm: Applying Research on Plant Genetics and Genomics to Crop Improvement
Pamela C. Ronald
PLOS Biology , 2014, DOI: 10.1371/journal.pbio.1001878
Abstract: Over the last 300 years, plant science research has provided important knowledge and technologies for advancing the sustainability of agriculture. In this Essay, I describe how basic research advances have been translated into crop improvement, explore some lessons learned, and discuss the potential for current and future contribution of plant genetic improvement technologies to continue to enhance food security and agricultural sustainability.
Overexpression of the Endoplasmic Reticulum Chaperone BiP3 Regulates XA21-Mediated Innate Immunity in Rice
Chang-Jin Park,Rebecca Bart,Mawsheng Chern,Patrick E. Canlas,Wei Bai,Pamela C. Ronald
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0009262
Abstract: Recognition of pathogen-associated molecular patterns by pattern recognition receptors (PRRs) activates the innate immune response. Although PRR-mediated signaling events are critical to the survival of plants and animals, secretion and localization of PRRs have not yet been clearly elucidated. Here we report the in vivo interaction of the endoplasmic reticulum (ER) chaperone BiP3 with the rice XA21 PRR, which confers resistance to the Gram negative bacterium, Xanthomonas oryzae pv. oryzae (Xoo). We show that XA21 is glycosylated and is primarily localized to the ER and also to the plasma membrane (PM). In BiP3-overexpressing rice plants, XA21-mediated immunity is compromised, XA21 stability is significantly decreased, and XA21 proteolytic cleavage is inhibited. BiP3 overexpression does not affect the general rice defense response, cell death or brassinolide-induced responses. These results indicate that BiP3 regulates XA21 protein stability and processing and that this regulation is critical for resistance to Xoo.
An efficient method for visualization and growth of fluorescent Xanthomonas oryzae pv. oryzae in planta
Sang-Wook Han, Chang-Jin Park, Sang-Won Lee, Pamela C Ronald
BMC Microbiology , 2008, DOI: 10.1186/1471-2180-8-164
Abstract: A fluorescent X. oryzae pv. oryzae Philippine race 6 strain expressing green fluorescent protein (GFP) (PXO99GFP) was generated using the gfp gene under the control of the neomycin promoter in the vector, pPneo-gfp. The PXO99GFPstrain displayed identical virulence and avirulence properties as the wild type control strain, PXO99. Using fluorescent microscopy, bacterial multiplication and colonization were directly observed in rice xylem vessels. Accurate and rapid determination of bacterial growth was assessed using fluoremetry and an Enzyme-Linked ImmunoSorbant Assay (ELISA).Our results indicate that the fluorescent marker system is useful for assessing bacterial infection and monitoring bacterial multiplication in planta.Xanthomonas oryzae pv. oryzae, a yellow-pigmented Gram-negative bacterium, is the causal agent of bacterial blight disease of rice (Oryzae sativa L.) plants. X. oryzae pv. oryzae infection can cause yield loss of up to 50% in tropical Asia [1]. X. oryzae pv. oryzae infects rice leaves through natural openings such as hydathodes and/or wounded sites and then primarily colonizes the vascular tissues by propagating in the xylem. Increased extracellular polysaccharide secretion accompanies bacteria growth, eventually causing a block in the vascular system [2]. The early symptoms therefore start with wilting in the infected leaves and enlargement in length and width of the legions of leaf blight [3]. As the symptom progress, severe necrosis occurs along the interveinal regions. Eventually, the whole leaf becomes whitish and greyish, and then dies [2,4]. Over the last few decades, the challenge in elucidating biological phenomena has been met by advances in techniques, which have accelerated our understanding of biological events. In particular, useful tools have been developed to evaluate cellular dynamics in vivo. One of the best examples of a technique that has facilitated cell-based studies is marker systems that use fluorescent proteins (FPs). Since
A novel system for gene silencing using siRNAs in rice leaf and stem-derived protoplasts
Rebecca Bart, Mawsheng Chern, Chang-Jin Park, Laura Bartley, Pamela C Ronald
Plant Methods , 2006, DOI: 10.1186/1746-4811-2-13
Abstract: We have established a rice seedling protoplast system designed for the rapid characterization of large numbers of genes. We report optimized methods for protoplast isolation from 7–14 day old etiolated rice seedlings. We show that the reporter genes luciferase GL2 and GUS are maximally expressed approximately 20 h after polyethylene glycol (PEG)-mediated transformation into protoplasts. In addition we found that transformation efficiency varied significantly with plasmid size. Five micrograms of a 4.5 kb plasmid resulted in 60–70% transformation efficiency. In contrast, using 50 μg of a 12 kb plasmid we obtained a maximum of 25–30% efficiency. We also show that short interfering RNAs (siRNAs) can be used to silence exogenous genes quickly and efficiently. An siRNA targeting luciferase resulted in a significant level of silencing after only 3 hours and up to an 83% decrease in expression. We have also isolated protoplasts from cells prepared from fully green tissue. These green tissue-derived protoplasts can be transformed to express high levels of luciferase activity and should be useful for assaying light sensitive cellular processes.We report a system for isolation, transformation and gene silencing of etiolated rice leaf and stem-derived protoplasts. Additionally, we have extended the technology to protoplasts isolated from fully green tissue. The protoplast system will bridge the gap between hi-throughput assays and functional biology as it can be used to quickly study large number of genes for which the function is unknown.Genomics tools such as DNA sequencing, microarrays and yeast-two-hybrid assays have propelled the field of genetics forward at a remarkable rate, yet mechanisms for defining gene function lag behind. To date, even for model systems such as rice and Arabidopsis, only a fraction of the total genes have been studied in depth using classical genetics and molecular biology techniques [1]. Two common methods for gene characterization are 1) mutant
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.
Direct calibration of PICKY-designed microarrays
Hui-Hsien Chou, Arunee Trisiriroj, Sunyoung Park, Yue-Ie C Hsing, Pamela C Ronald, Patrick S Schnable
BMC Bioinformatics , 2009, DOI: 10.1186/1471-2105-10-347
Abstract: Using synthesized samples with known concentrations of specific oligonucleotides, a series of microarray experiments was conducted to evaluate microarrays designed by PICKY, an oligo microarray design software tool, and to test a direct microarray calibration method based on the PICKY-predicted, thermodynamically closest nontarget information. The complete set of microarray experiment results is archived in the GEO database with series accession number GSE14717. Additional data files and Perl programs described in this paper can be obtained from the website http://www.complex.iastate.edu webcite under the PICKY Download area.PICKY-designed microarray probes are highly reliable over a wide range of hybridization temperatures and sample concentrations. The microarray calibration method reported here allows researchers to experimentally optimize their hybridization conditions. Because this method is straightforward, uses existing microarrays and relatively inexpensive synthesized samples, it can be used by any lab that uses microarrays designed by PICKY. In addition, other microarrays can be reanalyzed by PICKY to obtain the thermodynamically closest nontarget information for calibration.PICKY is an optimal oligo microarray design software developed for large and complex genomes [1]. PICKY-estimated DNA annealing temperatures for probes can deviate from actual annealing temperatures because some potentially important parameters are unavailable to its design algorithms, such as variations in the salt composition of hybridization buffers, effects of partially immobilized probes on the microarray surface, nonlinear and multistage nontarget annealing with a probe, effects of incorporated dye molecules on transcript annealing efficiency with a probe, and effects of additional chemicals (e.g., SDS, formamide or DMSO) in the hybridization buffers. These parameters vary with lab environments, and their influence on hybridization kinetics can only be experimentally measured. Be
Plant and Animal Pathogen Recognition Receptors Signal through Non-RD Kinases
Christopher Dardick ,Pamela Ronald
PLOS Pathogens , 2006, DOI: 10.1371/journal.ppat.0020002
Abstract: Plants and animals mediate early steps of the innate immune response through pathogen recognition receptors (PRRs). PRRs commonly associate with or contain members of a monophyletic group of kinases called the interleukin-1 receptor-associated kinase (IRAK) family that include Drosophila Pelle, human IRAKs, rice XA21 and Arabidopsis FLS2. In mammals, PRRs can also associate with members of the receptor-interacting protein (RIP) kinase family, distant relatives to the IRAK family. Some IRAK and RIP family kinases fall into a small functional class of kinases termed non-RD, many of which do not autophosphorylate the activation loop. We surveyed the yeast, fly, worm, human, Arabidopsis, and rice kinomes (3,723 kinases) and found that despite the small number of non-RD kinases in these genomes (9%–29%), 12 of 15 kinases known or predicted to function in PRR signaling fall into the non-RD class. These data indicate that kinases associated with PRRs can largely be predicted by the lack of a single conserved residue and reveal new potential plant PRR subfamilies.
Correction: Rice XB15, a Protein Phosphatase 2C, Negatively Regulates Cell Death and XA21-Mediated Innate Immunity
Chang-Jin Park,Ying Peng,Xuewei Chen,Christopher Dardick,DeLing Ruan,Rebecca Bart,Patrick E. Canlas,Pamela C. Ronald
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.0060282
Rice Snl6, a Cinnamoyl-CoA Reductase-Like Gene Family Member, Is Required for NH1-Mediated Immunity to Xanthomonas oryzae pv. oryzae
Rebecca S. Bart equal contributor,Mawsheng Chern equal contributor,Miguel E. Vega-Sánchez,Patrick Canlas,Pamela C. Ronald
PLOS Genetics , 2010, DOI: 10.1371/journal.pgen.1001123
Abstract: Rice NH1 (NPR1 homolog 1) is a key mediator of innate immunity. In both plants and animals, the innate immune response is often accompanied by rapid cell death at the site of pathogen infection. Over-expression of NH1 in rice results in resistance to the bacterial pathogen, Xanthomonas oryzae pv. oryzae (Xoo), constitutive expression of defense related genes and enhanced benzothiadiazole (BTH)- mediated cell death. Here we describe a forward genetic screen that identified a suppressor of NH1-mediated lesion formation and resistance, snl6. Comparative genome hybridization and fine mapping rapidly identified the genomic location of the Snl6 gene. Snl6 is a member of the cinnamoyl-CoA reductase (CCR)-like gene family. We show that Snl6 is required for NH1-mediated resistance to Xoo. Further, we show that Snl6 is required for pathogenesis-related gene expression. In contrast to previously described CCR family members, disruption of Snl6 does not result in an obvious morphologic phenotype. Snl6 mutants have reduced lignin content and increased sugar extractability, an important trait for the production of cellulosic biofuels. These results suggest the existence of a conserved group of CCR-like genes involved in the defense response, and with the potential to alter lignin content without affecting development.
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