PubMed Central (PMC3 - NLM DTD)
(2,081,148 recursos)
Archive of life sciences journal literature at the U.S. National Institutes of Health (NIH), developed and managed by NIH's National Center for Biotechnology Information (NCBI) in the National Library of Medicine (NLM).
Mostrando recursos 121 - 140 de 50,776
121.
An Expression and Bioinformatics Analysis of the Arabidopsis Serine Carboxypeptidase-Like Gene Family1[w] - Fraser, Christopher M.; Rider, Lance W.; Chapple, Clint
The Arabidopsis (Arabidopsis thaliana) genome encodes a family of 51 proteins that are homologous to known serine carboxypeptidases. Based on their sequences, these serine carboxypeptidase-like (SCPL) proteins can be divided into several major clades. The first group consists of 21 proteins which, despite the function implied by their annotation, includes two that have been shown to function as acyltransferases in plant secondary metabolism: sinapoylglucose:malate sinapoyltransferase and sinapoylglucose:choline sinapoyltransferase. A second group comprises 25 SCPL proteins whose biochemical functions have not been clearly defined. Genes encoding representatives from both of these clades can be found in many plants, but have not...
122.
Major Signaling Pathways Modulate Arabidopsis Glucosinolate Accumulation and Response to Both Phloem-Feeding and Chewing Insects1 - Mewis, Inga; Appel, Heidi M.; Hom, Amanda; Raina, Ramesh; Schultz, Jack C.
Plant responses to enemies are coordinated by several interacting signaling systems. Molecular and genetic studies with mutants and exogenous signal application suggest that jasmonate (JA)-, salicylate (SA)-, and ethylene (ET)-mediated pathways modulate expression of portions of the defense phenotype in Arabidopsis (Arabidopsis thaliana), but have not yet linked these observations directly with plant responses to insect attack. We compared the glucosinolate (GS) profiles of rosette leaves of 4-week-old mutant and transgenic Arabidopsis (Columbia) plants compromised in these three major signaling pathways, and characterized responses by those plants to feeding by two phloem-feeding aphids (generalist Myzus persicae and specialist Brevicoryne brassicae)...
123.
Role of FRIGIDA and FLOWERING LOCUS C in Determining Variation in Flowering Time of Arabidopsis1[w] - Shindo, Chikako; Aranzana, Maria Jose; Lister, Clare; Baxter, Catherine; Nicholls, Colin; Nordborg, Magnus; Dean, Caroline
Arabidopsis (Arabidopsis thaliana) accessions provide an excellent resource to dissect the molecular basis of adaptation. We have selected 192 Arabidopsis accessions collected to represent worldwide and local variation and analyzed two adaptively important traits, flowering time and vernalization response. There was huge variation in the flowering habit of the different accessions, with no simple relationship to latitude of collection site and considerable diversity occurring within local regions. We explored the contribution to this variation from the two genes FRIGIDA (FRI) and FLOWERING LOCUS C (FLC), previously shown to be important determinants in natural variation of flowering time. A correlation of...
128.
Extension of the Visualization Tool MapMan to Allow Statistical Analysis of Arrays, Display of Coresponding Genes, and Comparison with Known Responses1 - Usadel, Björn; Nagel, Axel; Thimm, Oliver; Redestig, Henning; Blaesing, Oliver E.; Palacios-Rojas, Natalia; Selbig, Joachim; Hannemann, Jan; Piques, Maria Conceição; Steinhauser, Dirk; Scheible, Wolf-Rüdiger; Gibon, Yves; Morcuende, Rosa; Weicht, Daniel; Meyer, Svenja; Stitt, Mark
MapMan is a user-driven tool that displays large genomics datasets onto diagrams of metabolic pathways or other processes. Here, we present new developments, including improvements of the gene assignments and the user interface, a strategy to visualize multilayered datasets, the incorporation of statistics packages, and extensions of the software to incorporate more biological information including visualization of coresponding genes and horizontal searches for similar global responses across large numbers of arrays.
129.
Complex Organization and Evolution of the Tomato Pericentromeric Region at the FER Gene Locus1[w] - Guyot, Romain; Cheng, Xudong; Su, Yan; Cheng, Zhukuan; Schlagenhauf, Edith; Keller, Beat; Ling, Hong-Qing
Tomato (Lycopersicon esculentum) is a model species for molecular biology research and a candidate for large-scale genome sequencing. Pericentromeric heterochromatin constitutes a large portion of the tomato chromosomes. However, the knowledge of the structure, organization, and evolution of such regions remains very limited. Here, we report the analysis of a 198-kb sequence near the FER gene, located in a distal part of pericentromeric heterochromatin on the long arm of tomato chromosome 6. Nine genes, one pseudogene, and 55 transposable elements (TEs) were identified, showing a low gene density (19.8 kb/gene) and a high content of transposable elements (>45% of the...
130.
Serial Analysis of Gene Expression Study of a Hybrid Rice Strain (LYP9) and Its Parental Cultivars1[w] - Bao, JingYue; Lee, Sanggyu; Chen, Chen; Zhang, XiuQing; Zhang, Yu; Liu, SiQi; Clark, Terry; Wang, Jian; Cao, MengLiang; Yang, HuanMing; Wang, San Ming; Yu, Jun
Using the serial analysis of gene expression technique, we surveyed transcriptomes of three major tissues (panicles, leaves, and roots) of a super-hybrid rice (Oryza sativa) strain, LYP9, in comparison to its parental cultivars, 93-11 (indica) and PA64s (japonica). We acquired 465,679 tags from the serial analysis of gene expression libraries, which were consolidated into 68,483 unique tags. Focusing our initial functional analyses on a subset of the data that are supported by full-length cDNAs and the tags (genes) differentially expressed in the hybrid at a significant level (P < 0.01), we identified 595 up-regulated (22 tags in panicles, 228 in...
131.
Engineering Cytoplasmic Male Sterility via the Chloroplast Genome by Expression of ?-Ketothiolase1 - Ruiz, Oscar N.; Daniell, Henry
While investigating expression of the polydroxybutyrate pathway in transgenic chloroplasts, we addressed the specific role of ?-ketothiolase. Therefore, we expressed the phaA gene via the chloroplast genome. Prior attempts to express the phaA gene in transgenic plants were unsuccessful. We studied the effect of light regulation of the phaA gene using the psbA promoter and 5? untranslated region, and evaluated expression under different photoperiods. Stable transgene integration into the chloroplast genome and homoplasmy were confirmed by Southern analysis. The phaA gene was efficiently transcribed in all tissue types examined, including leaves, flowers, and anthers. Coomassie-stained gel and western blots confirmed...
132.
Laser Photoacoustic Detection Allows in Planta Detection of Nitric Oxide in Tobacco following Challenge with Avirulent and Virulent Pseudomonas syringae Pathovars1 - Mur, Luis A.J.; Santosa, I. Edi; Laarhoven, Lucas J.J.; Holton, Nicholas J.; Harren, Frans J.M.; Smith, Aileen R.
We demonstrate the use of laser photoacoustic detection (LPAD) as a highly sensitive method to detect in planta nitric oxide (.NO) production from tobacco (Nicotiana tabacum). LPAD calibration against .NO gas demonstrated a linear relationship over 2 orders of magnitude with a detection threshold of <20 pmol h?1 (1 part per billion volume [ppbv]). The specificity of the photoacoustic signal for .NO when adding gas or the .NO donor, sodium nitroprusside, on injection into plant leaves, was demonstrated by its abolition with O3 (.NO + O3 ? NO2 + O2). The utility of the LPAD method was shown by examination...
133.
The alc-GR System. A Modified alc Gene Switch Designed for Use in Plant Tissue Culture1[w] - Roberts, Gethin R.; Garoosi, G. Ali; Koroleva, Olga; Ito, Masaki; Laufs, Patrick; Leader, David J.; Caddick, Mark X.; Doonan, John H.; Tomsett, A. Brian
The ALCR/alcA (alc) two-component, ethanol-inducible gene expression system provides stringent control of transgene expression in genetically modified plants. ALCR is an ethanol-activated transcription factor that can drive expression from the ALCR-responsive promoter (alcA). However, the alc system has been shown to have constitutive expression when used in plant callus or cell suspension cultures, possibly resulting from endogenous inducer produced in response to lowered oxygen availability. To widen the use of the alc system in plant cell culture conditions, the receptor domain of the rat glucocorticoid receptor (GR) was translationally fused to the C terminus of ALCR to produce ALCR-GR, which...
134.
It's All GO for Plant Scientists1 - Clark, Jennifer I.; Brooksbank, Cath; Lomax, Jane
The Gene Ontology project (http://www.geneontology.org/) produces structured, controlled vocabularies and gene product annotations. Gene products are classified according to the cellular locations and biological process in which they act, and the molecular functions that they carry out. We annotate gene products from a broad range of model species and provide support for those groups that wish to contribute annotation of further model species. The Gene Ontology facilitates the exchange of information between groups of scientists studying similar processes in different model organisms, and so provides a broad range of opportunities for plant scientists.
135.
Plant Genome Resources at the National Center for Biotechnology Information - Wheeler, David L.; Smith-White, Brian; Chetvernin, Vyacheslav; Resenchuk, Sergei; Dombrowski, Susan M.; Pechous, Steven W.; Tatusova, Tatiana; Ostell, James
The National Center for Biotechnology Information (NCBI) integrates data from more than 20 biological databases through a flexible search and retrieval system called Entrez. A core Entrez database, Entrez Nucleotide, includes GenBank and is tightly linked to the NCBI Taxonomy database, the Entrez Protein database, and the scientific literature in PubMed. A suite of more specialized databases for genomes, genes, gene families, gene expression, gene variation, and protein domains dovetails with the core databases to make Entrez a powerful system for genomic research. Linked to the full range of Entrez databases is the NCBI Map Viewer, which displays aligned genetic,...
136.
KaPPA-View. A Web-Based Analysis Tool for Integration of Transcript and Metabolite Data on Plant Metabolic Pathway Maps1[w] - Tokimatsu, Toshiaki; Sakurai, Nozomu; Suzuki, Hideyuki; Ohta, Hiroyuki; Nishitani, Kazuhiko; Koyama, Tanetoshi; Umezawa, Toshiaki; Misawa, Norihiko; Saito, Kazuki; Shibata, Daisuke
The application of DNA array technology and chromatographic separation techniques coupled with mass spectrometry to transcriptomic and metabolomic analyses in plants has resulted in the generation of considerable quantitative data related to transcription and metabolism. The integration of omic data is one of the major concerns associated with research into identifying gene function. Thus, we developed a Web-based tool, KaPPA-View, for representing quantitative data for individual transcripts and/or metabolites on plant metabolic pathway maps. We prepared a set of comprehensive metabolic pathway maps for Arabidopsis (Arabidopsis thaliana) and depicted these graphically in Scalable Vector Graphics format. Individual transcripts assigned to...
137.
Munich Information Center for Protein Sequences Plant Genome Resources. A Framework for Integrative and Comparative Analyses1[w] - Schoof, Heiko; Spannagl, Manuel; Yang, Li; Ernst, Rebecca; Gundlach, Heidrun; Haase, Dirk; Haberer, Georg; Mayer, Klaus F.X.
With several plant genomes sequenced, the power of comparative genome analysis can now be applied. However, genome-scale cross-species analyses are limited by the effort for data integration. To develop an integrated cross-species plant genome resource, we maintain comprehensive databases for model plant genomes, including Arabidopsis (Arabidopsis thaliana), maize (Zea mays), Medicago truncatula, and rice (Oryza sativa). Integration of data and resources is emphasized, both in house as well as with external partners and databases. Manual curation and state-of-the-art bioinformatic analysis are combined to achieve quality data. Easy access to the data is provided through Web interfaces and visualization tools, bulk...
138.
The SOL Genomics Network. A Comparative Resource for Solanaceae Biology and Beyond1 - Mueller, Lukas A.; Solow, Teri H.; Taylor, Nicolas; Skwarecki, Beth; Buels, Robert; Binns, John; Lin, Chenwei; Wright, Mark H.; Ahrens, Robert; Wang, Ying; Herbst, Evan V.; Keyder, Emil R.; Menda, Naama; Zamir, Dani; Tanksley, Steven D.
The SOL Genomics Network (SGN; http://sgn.cornell.edu) is a rapidly evolving comparative resource for the plants of the Solanaceae family, which includes important crop and model plants such as potato (Solanum tuberosum), eggplant (Solanum melongena), pepper (Capsicum annuum), and tomato (Solanum lycopersicum). The aim of SGN is to relate these species to one another using a comparative genomics approach and to tie them to the other dicots through the fully sequenced genome of Arabidopsis (Arabidopsis thaliana). SGN currently houses map and marker data for Solanaceae species, a large expressed sequence tag collection with computationally derived unigene sets, an extensive database of...
140.
Surrogate Splicing for Functional Analysis of Sesquiterpene Synthase Genes1[w] - Wu, Shuiqin; Schoenbeck, Mark A.; Greenhagen, Bryan T.; Takahashi, Shunji; Lee, Sungbeom; Coates, Robert M.; Chappell, Joseph
A method for the recovery of full-length cDNAs from predicted terpene synthase genes containing introns is described. The approach utilizes Agrobacterium-mediated transient expression coupled with a reverse transcription-polydeoxyribonucleotide chain reaction assay to facilitate expression cloning of processed transcripts. Subsequent expression of intronless cDNAs in a suitable prokaryotic host provides for direct functional testing of the encoded gene product. The method was optimized by examining the expression of an intron-containing ?-glucuronidase gene agroinfiltrated into petunia (Petunia hybrida) leaves, and its utility was demonstrated by defining the function of two previously uncharacterized terpene synthases. A tobacco (Nicotiana tabacum) terpene synthase-like gene containing...
121.
