Página 1 dos resultados de 21 itens digitais encontrados em 0.011 segundos

VirtualPlant: A Software Platform to Support Systems Biology Research1[W][OA]

Katari, Manpreet S.; Nowicki, Steve D.; Aceituno, Felipe F.; Nero, Damion; Kelfer, Jonathan; Thompson, Lee Parnell; Cabello, Juan M.; Davidson, Rebecca S.; Goldberg, Arthur P.; Shasha, Dennis E.; Coruzzi, Gloria M.; Gutiérrez, Rodrigo A.
Fonte: American Society of Plant Biologists Publicador: American Society of Plant Biologists
Tipo: Artigo de Revista Científica
Publicado em /02/2010 EN
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Data generation is no longer the limiting factor in advancing biological research. In addition, data integration, analysis, and interpretation have become key bottlenecks and challenges that biologists conducting genomic research face daily. To enable biologists to derive testable hypotheses from the increasing amount of genomic data, we have developed the VirtualPlant software platform. VirtualPlant enables scientists to visualize, integrate, and analyze genomic data from a systems biology perspective. VirtualPlant integrates genome-wide data concerning the known and predicted relationships among genes, proteins, and molecules, as well as genome-scale experimental measurements. VirtualPlant also provides visualization techniques that render multivariate information in visual formats that facilitate the extraction of biological concepts. Importantly, VirtualPlant helps biologists who are not trained in computer science to mine lists of genes, microarray experiments, and gene networks to address questions in plant biology, such as: What are the molecular mechanisms by which internal or external perturbations affect processes controlling growth and development? We illustrate the use of VirtualPlant with three case studies, ranging from querying a gene of interest to the identification of gene networks and regulatory hubs that control seed development. Whereas the VirtualPlant software was developed to mine Arabidopsis (Arabidopsis thaliana) genomic data...

Systems Biology Update: Cell Type-Specific Transcriptional Regulatory Networks

Pu, Li; Brady, Siobhan
Fonte: American Society of Plant Biologists Publicador: American Society of Plant Biologists
Tipo: Artigo de Revista Científica
Publicado em /02/2010 EN
Relevância na Pesquisa
1018.7797%

Systems Biology of Organ Initiation at the Shoot Apex

Traas, Jan; Monéger, Françoise
Fonte: American Society of Plant Biologists Publicador: American Society of Plant Biologists
Tipo: Artigo de Revista Científica
Publicado em /02/2010 EN
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1018.7797%

Subcellular Flux Analysis of Central Metabolism in a Heterotrophic Arabidopsis Cell Suspension Using Steady-State Stable Isotope Labeling1[W][OA]

Masakapalli, Shyam K.; Le Lay, Pascaline; Huddleston, Joanna E.; Pollock, Naomi L.; Kruger, Nicholas J.; Ratcliffe, R. George
Fonte: American Society of Plant Biologists Publicador: American Society of Plant Biologists
Tipo: Artigo de Revista Científica
Publicado em /02/2010 EN
Relevância na Pesquisa
918.12336%
The presence of cytosolic and plastidic pathways of carbohydrate oxidation is a characteristic feature of plant cell metabolism. Ideally, steady-state metabolic flux analysis, an emerging tool for creating flux maps of heterotrophic plant metabolism, would capture this feature of the metabolic phenotype, but the extent to which this can be achieved is uncertain. To address this question, fluxes through the pathways of central metabolism in a heterotrophic Arabidopsis (Arabidopsis thaliana) cell suspension culture were deduced from the redistribution of label in steady-state 13C-labeling experiments using [1-13C]-, [2-13C]-, and [U-13C6]glucose. Focusing on the pentose phosphate pathway (PPP), multiple data sets were fitted simultaneously to models in which the subcellular compartmentation of the PPP was altered. The observed redistribution of the label could be explained by any one of three models of the subcellular compartmentation of the oxidative PPP, but other biochemical evidence favored the model in which the oxidative steps of the PPP were duplicated in the cytosol and plastids, with flux through these reactions occurring largely in the cytosol. The analysis emphasizes the inherent difficulty of analyzing the PPP without predefining the extent of its compartmentation and the importance of obtaining high-quality data that report directly on specific subcellular processes. The Arabidopsis flux map also shows that the potential ATP yield of respiration in heterotrophic plant cells can greatly exceed the direct metabolic requirements for biosynthesis...

Systematic Localization of the Arabidopsis Core Cell Cycle Proteins Reveals Novel Cell Division Complexes1[W][OA]

Boruc, Joanna; Mylle, Evelien; Duda, Maria; De Clercq, Rebecca; Rombauts, Stephane; Geelen, Danny; Hilson, Pierre; Inzé, Dirk; Van Damme, Daniel; Russinova, Eugenia
Fonte: American Society of Plant Biologists Publicador: American Society of Plant Biologists
Tipo: Artigo de Revista Científica
Publicado em /02/2010 EN
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908.43414%
Cell division depends on the correct localization of the cyclin-dependent kinases that are regulated by phosphorylation, cyclin proteolysis, and protein-protein interactions. Although immunological assays can define cell cycle protein abundance and localization, they are not suitable for detecting the dynamic rearrangements of molecular components during cell division. Here, we applied an in vivo approach to trace the subcellular localization of 60 Arabidopsis (Arabidopsis thaliana) core cell cycle proteins fused to green fluorescent proteins during cell division in tobacco (Nicotiana tabacum) and Arabidopsis. Several cell cycle proteins showed a dynamic association with mitotic structures, such as condensed chromosomes and the preprophase band in both species, suggesting a strong conservation of targeting mechanisms. Furthermore, colocalized proteins were shown to bind in vivo, strengthening their localization-function connection. Thus, we identified unknown spatiotemporal territories where functional cell cycle protein interactions are most likely to occur.

AtMetExpress Development: A Phytochemical Atlas of Arabidopsis Development[W][OA]

Matsuda, Fumio; Hirai, Masami Y.; Sasaki, Eriko; Akiyama, Kenji; Yonekura-Sakakibara, Keiko; Provart, Nicholas J.; Sakurai, Tetsuya; Shimada, Yukihisa; Saito, Kazuki
Fonte: American Society of Plant Biologists Publicador: American Society of Plant Biologists
Tipo: Artigo de Revista Científica
Publicado em /02/2010 EN
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922.97805%
Plants possess many metabolic genes for the production of a wide variety of phytochemicals in a tissue-specific manner. However, the metabolic systems behind the diversity and tissue-dependent regulation still remain unknown due to incomplete characterization of phytochemicals produced in a single plant species. Thus, having a metabolome dataset in addition to the genome and transcriptome information resources would enrich our knowledge of plant secondary metabolism. Here we analyzed phytochemical accumulation during development of the model plant Arabidopsis (Arabidopsis thaliana) using liquid chromatography-mass spectrometry in samples covering many growth stages and organs. We also obtained tandem mass spectrometry spectral tags of many metabolites as a resource for elucidation of metabolite structure. These are part of the AtMetExpress metabolite accumulation atlas. Based on the dataset, we detected 1,589 metabolite signals from which the structures of 167 metabolites were elucidated. The integrated analyses with transcriptome data demonstrated that Arabidopsis produces various phytochemicals in a highly tissue-specific manner, which often accompanies the expression of key biosynthesis-related genes. We also found that a set of biosynthesis-related genes is coordinately expressed among the tissues. These data suggested that the simple mode of regulation...

Large-Scale Reverse Genetics in Arabidopsis: Case Studies from the Chloroplast 2010 Project1[C][W][OA]

Ajjawi, Imad; Lu, Yan; Savage, Linda J.; Bell, Shannon M.; Last, Robert L.
Fonte: American Society of Plant Biologists Publicador: American Society of Plant Biologists
Tipo: Artigo de Revista Científica
Publicado em /02/2010 EN
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910.33695%
Traditionally, phenotype-driven forward genetic plant mutant studies have been among the most successful approaches to revealing the roles of genes and their products and elucidating biochemical, developmental, and signaling pathways. A limitation is that it is time consuming, and sometimes technically challenging, to discover the gene responsible for a phenotype by map-based cloning or discovery of the insertion element. Reverse genetics is also an excellent way to associate genes with phenotypes, although an absence of detectable phenotypes often results when screening a small number of mutants with a limited range of phenotypic assays. The Arabidopsis Chloroplast 2010 Project (www.plastid.msu.edu) seeks synergy between forward and reverse genetics by screening thousands of sequence-indexed Arabidopsis (Arabidopsis thaliana) T-DNA insertion mutants for a diverse set of phenotypes. Results from this project are discussed that highlight the strengths and limitations of the approach. We describe the discovery of altered fatty acid desaturation phenotypes associated with mutants of At1g10310, previously described as a pterin aldehyde reductase in folate metabolism. Data are presented to show that growth, fatty acid, and chlorophyll fluorescence defects previously associated with antisense inhibition of synthesis of the family of acyl carrier proteins can be attributed to a single gene insertion in Acyl Carrier Protein4 (At4g25050). A variety of cautionary examples associated with the use of sequence-indexed T-DNA mutants are described...

A Systems Model of Vesicle Trafficking in Arabidopsis Pollen Tubes[W][OA]

Kato, Naohiro; He, Hongyu; Steger, Alexander P.
Fonte: American Society of Plant Biologists Publicador: American Society of Plant Biologists
Tipo: Artigo de Revista Científica
Publicado em /02/2010 EN
Relevância na Pesquisa
1019.4341%
A systems model that describes vesicle trafficking during pollen tube growth in Arabidopsis (Arabidopsis thaliana) was constructed. The model is composed of ordinary differential equations that connect the molecular functions of genes expressed in pollen. The current model requires soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptors (SNAREs) and small GTPases, Arf or Rab, to reasonably predict tube growth as a function of time. Tube growth depends on vesicle trafficking that transports phospholipid and pectin to the tube tip. The vesicle trafficking genes identified by analyzing publicly available transcriptome data comprised 328 genes. Fourteen of them are up-regulated by the gibberellin signaling pathway during pollen development, which includes the SNARE genes SYP124 and SYP125 and the Rab GTPase gene RABA4D. The model results adequately fit the pollen tube growth of both previously reported wild-type and raba4d knockout lines. Furthermore, the difference of pollen tube growth in syp124/syp125 single and double mutations was quantitatively predicted based on the model analysis. In general, a systems model approach to vesicle trafficking arguably demonstrated the importance of the functional connections in pollen tube growth and can help guide future research directions.

Plant Systems Biology

Joyard, Jacques; McCormick, Sheila
Fonte: American Society of Plant Biologists Publicador: American Society of Plant Biologists
Tipo: Artigo de Revista Científica
Publicado em /02/2010 EN
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1122.70516%

Epigenetic Regulation of Gene Programs by EMF1 and EMF2 in Arabidopsis1[W][OA]

Kim, Sang Yeol; Zhu, T.; Sung, Z. Renee
Fonte: American Society of Plant Biologists Publicador: American Society of Plant Biologists
Tipo: Artigo de Revista Científica
Publicado em /02/2010 EN
Relevância na Pesquisa
806.4114%
The EMBRYONIC FLOWER (EMF) genes are required to maintain vegetative development in Arabidopsis (Arabidopsis thaliana). Loss-of-function emf mutants skip the vegetative phase, flower upon germination, and display pleiotropic phenotypes. EMF1 encodes a putative transcriptional regulator, while EMF2 encodes a Polycomb group (PcG) protein. PcG proteins form protein complexes that maintain gene silencing via histone modification. They are known to function as master regulators repressing multiple gene programs. Both EMF1 and EMF2 participate in PcG-mediated silencing of the flower homeotic genes AGAMOUS, PISTILLATA, and APETALA3. Full-genome expression pattern analysis of emf mutants showed that both EMF proteins regulate additional gene programs, including photosynthesis, seed development, hormone, stress, and cold signaling. Chromatin immunoprecipitation was carried out to investigate whether EMF regulates these genes directly. It was determined that EMF1 and EMF2 interact with genes encoding the transcription factors ABSCISIC ACID INSENSITIVE3, LONG VEGETATIVE PHASE1, and FLOWERING LOCUS C, which control seed development, stress and cold signaling, and flowering, respectively. Our results suggest that the two EMFs repress the regulatory genes of individual gene programs to effectively silence the genetic pathways necessary for vegetative development and stress response. A model of the regulatory network mediated by EMF is proposed.

Systems Biology Uncovers the Foundation of Natural Genetic Diversity1

Kliebenstein, Daniel J.
Fonte: American Society of Plant Biologists Publicador: American Society of Plant Biologists
Tipo: Artigo de Revista Científica
Publicado em /02/2010 EN
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1018.7797%

AGRONOMICS1: A New Resource for Arabidopsis Transcriptome Profiling1[W][OA]

Rehrauer, Hubert; Aquino, Catharine; Gruissem, Wilhelm; Henz, Stefan R.; Hilson, Pierre; Laubinger, Sascha; Naouar, Naira; Patrignani, Andrea; Rombauts, Stephane; Shu, Huan; Van de Peer, Yves; Vuylsteke, Marnik; Weigel, Detlef; Zeller, Georg; Hennig, Lars
Fonte: American Society of Plant Biologists Publicador: American Society of Plant Biologists
Tipo: Artigo de Revista Científica
Publicado em /02/2010 EN
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917.1295%
Transcriptome profiling has become a routine tool in biology. For Arabidopsis (Arabidopsis thaliana), the Affymetrix ATH1 expression array is most commonly used, but it lacks about one-third of all annotated genes present in the reference strain. An alternative are tiling arrays, but previous designs have not allowed the simultaneous analysis of both strands on a single array. We introduce AGRONOMICS1, a new Affymetrix Arabidopsis microarray that contains the complete paths of both genome strands, with on average one 25mer probe per 35-bp genome sequence window. In addition, the new AGRONOMICS1 array contains all perfect match probes from the original ATH1 array, allowing for seamless integration of the very large existing ATH1 knowledge base. The AGRONOMICS1 array can be used for diverse functional genomics applications such as reliable expression profiling of more than 30,000 genes, detection of alternative splicing, and chromatin immunoprecipitation coupled to microarrays (ChIP-chip). Here, we describe the design of the array and compare its performance with that of the ATH1 array. We find results from both microarrays to be of similar quality, but AGRONOMICS1 arrays yield robust expression information for many more genes, as expected. Analysis of the ATH1 probes on AGRONOMICS1 arrays produces results that closely mirror those of ATH1 arrays. Finally...

Complete Transcriptome of the Soybean Root Hair Cell, a Single-Cell Model, and Its Alteration in Response to Bradyrhizobium japonicum Infection1[C][W][OA]

Libault, Marc; Farmer, Andrew; Brechenmacher, Laurent; Drnevich, Jenny; Langley, Raymond J.; Bilgin, Damla D.; Radwan, Osman; Neece, David J.; Clough, Steven J.; May, Gregory D.; Stacey, Gary
Fonte: American Society of Plant Biologists Publicador: American Society of Plant Biologists
Tipo: Artigo de Revista Científica
Publicado em /02/2010 EN
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912.75266%
Nodulation is the result of a mutualistic interaction between legumes and symbiotic soil bacteria (e.g. soybean [Glycine max] and Bradyrhizobium japonicum) initiated by the infection of plant root hair cells by the symbiont. Fewer than 20 plant genes involved in the nodulation process have been functionally characterized. Considering the complexity of the symbiosis, significantly more genes are likely involved. To identify genes involved in root hair cell infection, we performed a large-scale transcriptome analysis of B. japonicum-inoculated and mock-inoculated soybean root hairs using three different technologies: microarray hybridization, Illumina sequencing, and quantitative real-time reverse transcription-polymerase chain reaction. Together, a total of 1,973 soybean genes were differentially expressed with high significance during root hair infection, including orthologs of previously characterized root hair infection-related genes such as NFR5 and NIN. The regulation of 60 genes was confirmed by quantitative real-time reverse transcription-polymerase chain reaction. Our analysis also highlighted changes in the expression pattern of some homeologous and tandemly duplicated soybean genes, supporting their rapid specialization.

Hope for Humpty Dumpty: Systems Biology of Cellular Signaling1

Assmann, Sarah M.
Fonte: American Society of Plant Biologists Publicador: American Society of Plant Biologists
Tipo: Artigo de Revista Científica
Publicado em /02/2010 EN
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1018.7797%

Signaling between Chloroplasts and the Nucleus: Can a Systems Biology Approach Bring Clarity to a Complex and Highly Regulated Pathway?

Jung, Hou-Sung; Chory, Joanne
Fonte: American Society of Plant Biologists Publicador: American Society of Plant Biologists
Tipo: Artigo de Revista Científica
Publicado em /02/2010 EN
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1018.7797%

Bioinformatic and Systems Biology Tools to Generate Testable Models of Signaling Pathways and Their Targets1

Pitzschke, Andrea; Hirt, Heribert
Fonte: American Society of Plant Biologists Publicador: American Society of Plant Biologists
Tipo: Artigo de Revista Científica
Publicado em /02/2010 EN
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1018.7797%

Gene Expression Analysis, Proteomics, and Network Discovery1

Baginsky, Sacha; Hennig, Lars; Zimmermann, Philip; Gruissem, Wilhelm
Fonte: American Society of Plant Biologists Publicador: American Society of Plant Biologists
Tipo: Artigo de Revista Científica
Publicado em /02/2010 EN
Relevância na Pesquisa
806.4114%

Metabolic Networks: How to Identify Key Components in the Regulation of Metabolism and Growth1

Stitt, Mark; Sulpice, Ronan; Keurentjes, Joost
Fonte: American Society of Plant Biologists Publicador: American Society of Plant Biologists
Tipo: Artigo de Revista Científica
Publicado em /02/2010 EN
Relevância na Pesquisa
806.4114%

A Systems View of Responses to Nutritional Cues in Arabidopsis: Toward a Paradigm Shift for Predictive Network Modeling1

Ruffel, Sandrine; Krouk, Gabriel; Coruzzi, Gloria M.
Fonte: American Society of Plant Biologists Publicador: American Society of Plant Biologists
Tipo: Artigo de Revista Científica
Publicado em /02/2010 EN
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911.7958%

AraGEM, a Genome-Scale Reconstruction of the Primary Metabolic Network in Arabidopsis1[W]

de Oliveira Dal'Molin, Cristiana Gomes; Quek, Lake-Ee; Palfreyman, Robin William; Brumbley, Stevens Michael; Nielsen, Lars Keld
Fonte: American Society of Plant Biologists Publicador: American Society of Plant Biologists
Tipo: Artigo de Revista Científica
Publicado em /02/2010 EN
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923.8717%
Genome-scale metabolic network models have been successfully used to describe metabolism in a variety of microbial organisms as well as specific mammalian cell types and organelles. This systems-based framework enables the exploration of global phenotypic effects of gene knockouts, gene insertion, and up-regulation of gene expression. We have developed a genome-scale metabolic network model (AraGEM) covering primary metabolism for a compartmentalized plant cell based on the Arabidopsis (Arabidopsis thaliana) genome. AraGEM is a comprehensive literature-based, genome-scale metabolic reconstruction that accounts for the functions of 1,419 unique open reading frames, 1,748 metabolites, 5,253 gene-enzyme reaction-association entries, and 1,567 unique reactions compartmentalized into the cytoplasm, mitochondrion, plastid, peroxisome, and vacuole. The curation process identified 75 essential reactions with respective enzyme associations not assigned to any particular gene in the Kyoto Encyclopedia of Genes and Genomes or AraCyc. With the addition of these reactions, AraGEM describes a functional primary metabolism of Arabidopsis. The reconstructed network was transformed into an in silico metabolic flux model of plant metabolism and validated through the simulation of plant metabolic functions inferred from the literature. Using efficient resource utilization as the optimality criterion...