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16 results on '"Legaie, Roxane"'

2. Time-Series Transcriptomics Reveals That AGAMOUS-LIKE22 Affects Primary Metabolism and Developmental Processes in Drought-Stressed Arabidopsis

Author

Bechtold, Ulrike, Penfold, Christopher A., Jenkins, Dafyd J., Legaie, Roxane, Moore, Jonathan D., Lawson, Tracy, Matthews, Jack S.A., Vialet-Chabrand, Silvere R.M., Baxter, Laura, Subramaniam, Sunitha, Hickman, Richard, Florance, Hannah, Sambles, Christine, Salmon, Deborah L., Feil, Regina, Bowden, Laura, Hill, Claire, Baker, Neil R., Lunn, John E., Finkenstädt, Bärbel, Mead, Andrew, Buchanan-Wollaston, Vicky, Beynon, Jim, Rand, David A., Wild, David L., Denby, Katherine J., Ott, Sascha, Smirnoff, Nicholas, and Mullineaux, Philip M.

Published
2016

4. Arabidopsis Defense against Botrytis cinerea: Chronology and Regulation Deciphered by High-Resolution Temporal Transcriptomic Analysis

Author

Windram, Oliver, Madhou, Priyadharshini, McHattie, Stuart, Hill, Claire, Hickman, Richard, Cooke, Emma, Jenkins, Dafyd J., Penfold, Christopher A., Baxter, Laura, Breeze, Emily, Kiddle, Steven J., Rhodes, Johanna, Atwell, Susanna, Kliebenstein, Daniel J., Kim, Youn-sung, Stegle, Oliver, Borgwardt, Karsten, Zhang, Cunjin, Tabrett, Alex, Legaie, Roxane, Moore, Jonathan, Finkenstadt, Bärbel, Wild, David L., Mead, Andrew, Rand, David, Beynon, Jim, Ott, Sascha, Buchanan-Wollaston, Vicky, and Denby, Katherine J.

Published
2012

5. High-Resolution Temporal Profiling of Transcripts during Arabidopsis Leaf Senescence Reveals a Distinct Chronology of Processes and Regulation

Author

Breeze, Emily, Harrison, Elizabeth, McHattie, Stuart, Hughes, Linda, Hickman, Richard, Hill, Claire, Kiddle, Steven, Kim, Youn-sung, Penfold, Christopher A., Jenkins, Dafyd, Zhang, Cunjin, Morris, Karl, Jenner, Carol, Jackson, Stephen, Thomas, Brian, Tabrett, Alexandra, Legaie, Roxane, Moore, Jonathan D., Wild, David L., Ott, Sascha, Rand, David, Beynon, Jim, Denby, Katherine, Mead, Andrew, and Buchanan-Wollaston, Vicky

Published
2011

6. Enhancing Data Integration with Text Analysis to Find Proteins Implicated in Plant Stress Response

Author

Hassani-Pak Keywan, Legaie Roxane, Canevet Catherine, Berg Hugo A. van den, Moore Jonathan D., and Rawlings Christopher J.

Subjects
Biotechnology, TP248.13-248.65
Abstract

High throughput genomic studies can identify large numbers of potential candidate genes, which must be interpreted and filtered by investigators to select the best ones for further analysis. Prioritization is generally based on evidence that supports the role of a gene product in the biological process being investigated. The two most important bodies of information providing such evidence are bioinformatics databases and the scientific literature. In this paper we present an extension to the Ondex data integration framework that uses text mining techniques over Medline abstracts as a method for accessing both these bodies of evidence in a consistent way. In an example use case, we apply our method to create a knowledge base of Arabidopsis proteins implicated in plant stress response and use various scoring metrics to identify key protein-stress associations. In conclusion, we show that the additional text mining features are able to highlight proteins using the scientific literature that would not have been seen using data integration alone. Ondex is an open-source software project and can be downloaded, together with the text mining features described here, from www.ondex.org.

Published
2010
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7. The dynamic architecture of the metabolic switch in Streptomyces coelicolor

Author

Bonin Michael, Wild David L, Rand David A, Dijkhuizen Lubbert, Jansen Ritsert C, Challis Gregory L, Legaie Roxane, Gaze William H, Iqbal Mudassar, Thomas Louise, Nentwich Merle, Rodríguez-García Antonio, Juarez-Hermosillo Miguel A, Morrissey Edward R, Omara Walid AM, Moore Jonathan, Merlo Maria E, Alam Mohammad T, Sletta Håvard, Jakobsen Øyvind M, Wentzel Alexander, Bruheim Per, Herbig Alexander, Battke Florian, Nieselt Kay, Reuther Jens, Wohlleben Wolfgang, Smith Margaret CM, Burroughs Nigel J, Martín Juan F, Hodgson David A, Takano Eriko, Breitling Rainer, Ellingsen Trond E, and Wellington Elizabeth MH

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background During the lifetime of a fermenter culture, the soil bacterium S. coelicolor undergoes a major metabolic switch from exponential growth to antibiotic production. We have studied gene expression patterns during this switch, using a specifically designed Affymetrix genechip and a high-resolution time-series of fermenter-grown samples. Results Surprisingly, we find that the metabolic switch actually consists of multiple finely orchestrated switching events. Strongly coherent clusters of genes show drastic changes in gene expression already many hours before the classically defined transition phase where the switch from primary to secondary metabolism was expected. The main switch in gene expression takes only 2 hours, and changes in antibiotic biosynthesis genes are delayed relative to the metabolic rearrangements. Furthermore, global variation in morphogenesis genes indicates an involvement of cell differentiation pathways in the decision phase leading up to the commitment to antibiotic biosynthesis. Conclusions Our study provides the first detailed insights into the complex sequence of early regulatory events during and preceding the major metabolic switch in S. coelicolor, which will form the starting point for future attempts at engineering antibiotic production in a biotechnological setting.

Published
2010
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9. De novo transcriptome assembly for the spiny mouse (Acomys cahirinus)

Author

Mamrot, Jared, primary, Legaie, Roxane, additional, Ellery, Stacey J., additional, Wilson, Trevor, additional, Seemann, Torsten, additional, Powell, David R., additional, Gardner, David K., additional, Walker, David W., additional, Temple-Smith, Peter, additional, Papenfuss, Anthony T., additional, and Dickinson, Hayley, additional

Published
2017
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10. Clinical Utility of Circulating Tumor (ct)DNA Quantity and Kinetics in Patients Undergoing CAR T-Cell Therapy for Relapsed/Refractory Aggressive B-Cell Lymphoma

Author

Caldwell, Imogen, Yap, Yan Zhuang, Dowling, Mark R, Saghebi, Javad, Wong, Aaron Jun Ning, Legaie, Roxane, Arnolda, Rainier, Wilson, Clarissa, Ignacio, Danielle, O'Leary, Nicole, Yaung, Stephanie, Su, Bowdoin, Woestmann, Corinna, Dickinson, Michael, Thompson, Ella, and Blombery, Piers

Abstract

Background: CD19-targeted CAR T-cells are approved for relapsed and/or refractory (RR) aggressive B-cell lymphomas. While some patients experience durable remissions, others do not respond or relapse. Improved patient selection and early identification of patients who may need additional therapies are thus necessary. ctDNA is a promising biomarker for prognostication in DLBCL and has the potential to guide therapeutic decisions. We aimed to explore the possible clinical utility of ctDNA quantitation in patients with aggressive B-cell lymphomas undergoing CAR T-cell therapy.

Published
2023
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12. The dynamic architecture of the metabolic switch in Streptomyces coelicolor

Author

Nieselt, Kay, Battke, Florian, Herbig, Alexander, Bruheim, Per, Wentzel, Alexander, Jakobsen, Oyvind M., Sletta, Havard, Alam, Mohammad T., Merlo, Maria E., Moore, Jonathan, Omara, Walid A. M., Morrissey, Edward R., Juarez-Hermosillo, Miguel A., Rodriguez-Garcia, Antonio, Nentwich, Merle, Thomas, Louise, Iqbal, Mudassar, Legaie, Roxane, Gaze, William H., Challis, Gregory L., Jansen, Ritsert C., Dijkhuizen, Lubbert, Rand, David A., Wild, David L., Bonin, Michael, Reuther, Jens, Wohlleben, Wolfgang, Smith, Margaret C. M., Burroughs, Nigel J., Martin, Juan F., Hodgson, David A., Takano, Eriko, Breitling, Rainer, Ellingsen, Trond E., Wellington, Elizabeth M. H., Jakobsen, Øyvind M., Sletta, Håvard, Morrisey, E.R, Bioinformatics, Host-Microbe Interactions, and Faculty of Science and Engineering

Subjects
NITROGEN-METABOLISM, EXPRESSION, GENE-CLUSTER, lcsh:QH426-470, Cellular differentiation, lcsh:Biotechnology, PHASE, Streptomyces coelicolor, Computational biology, ANTIBIOTIC PRODUCTION, Microbiology, QH301, lcsh:TP248.13-248.65, PHOP, Gene expression, Gene cluster, Genetics, Cluster Analysis, Gene, SPORULATION, biology, IDENTIFICATION, Gene Expression Profiling, food and beverages, Gene Expression Regulation, Bacterial, biology.organism_classification, Flux balance analysis, Anti-Bacterial Agents, QR, Gene expression profiling, RNA, Bacterial, lcsh:Genetics, Genes, Bacterial, Multigene Family, Fermentation, DNA microarray, REGULATOR, A3(2), Biotechnology
Abstract

Background During the lifetime of a fermenter culture, the soil bacterium S. coelicolor undergoes a major metabolic switch from exponential growth to antibiotic production. We have studied gene expression patterns during this switch, using a specifically designed Affymetrix genechip and a high-resolution time-series of fermenter-grown samples. Results Surprisingly, we find that the metabolic switch actually consists of multiple finely orchestrated switching events. Strongly coherent clusters of genes show drastic changes in gene expression already many hours before the classically defined transition phase where the switch from primary to secondary metabolism was expected. The main switch in gene expression takes only 2 hours, and changes in antibiotic biosynthesis genes are delayed relative to the metabolic rearrangements. Furthermore, global variation in morphogenesis genes indicates an involvement of cell differentiation pathways in the decision phase leading up to the commitment to antibiotic biosynthesis. Conclusions Our study provides the first detailed insights into the complex sequence of early regulatory events during and preceding the major metabolic switch in S. coelicolor, which will form the starting point for future attempts at engineering antibiotic production in a biotechnological setting.

Published
2010

14. Multiple Secondary Genetic Events Inducing Histologic Progression (HP) of Non-MALT Marginal Zone Lymphoma (MZL): An Integrated Genomic Analysis of Genome-Wide Copy-Number-Changes (CNC) and Transcriptomic Data.

Author

Willems, Lise, primary, Briere, Josette, primary, Raharijaona, Mahatsangy, primary, Ballester, Benoit, primary, Quentin, Samuel, primary, Legaie, Roxane, primary, Rolland, Delphine, primary, Molina, Thierry Jo, primary, Brice, Pauline, primary, De Kerviler, Eric, primary, Gisselbrecht, Christian, primary, Berger, Francoise, primary, Traverse-glehen, Alexandra, primary, Baseggio, Lucile, primary, Felman, Pascale, primary, Salles, Gilles, primary, Coiffier, Bertrand, primary, Soulier, Jean, primary, Houlgatte, Remi, primary, and Thieblemont, Catherine, primary

Published
2008
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15. Metabolic Switches and Adaptations Deduced from the Proteomes of Streptomyces coelicolor Wild Type and phoP Mutant Grown in Batch Culture

Author

Thomas, Louise, Hodgson, David A., Wentzel, Alexander, Nieselt, Kay, Ellingsen, Trond E., Moore, Jonathan, Morrissey, Edward R., Legaie, Roxane, Wohlleben, Wolfgang, Rodríguez-García, Antonio, Martín, Juan F., Burroughs, Nigel J., Wellington, Elizabeth M. H., and Smith, Margaret C. M.

Abstract

Bacteria in the genus Streptomyces are soil-dwelling oligotrophs and important producers of secondary metabolites. Previously, we showed that global messenger RNA expression was subject to a series of metabolic and regulatory switches during the lifetime of a fermentor batch culture of Streptomyces coelicolor M145. Here we analyze the proteome from eight time points from the same fermentor culture and, because phosphate availability is an important regulator of secondary metabolite production, compare this to the proteome of a similar time course from an S. coelicolor mutant, INB201 (ΔphoP), defective in the control of phosphate utilization. The proteomes provide a detailed view of enzymes involved in central carbon and nitrogen metabolism. Trends in protein expression over the time courses were deduced from a protein abundance index, which also revealed the importance of stress pathway proteins in both cultures. As expected, the ΔphoP mutant was deficient in expression of PhoP-dependent genes, and several putatively compensatory metabolic and regulatory pathways for phosphate scavenging were detected. Notably there is a succession of switches that coordinately induce the production of enzymes for five different secondary metabolite biosynthesis pathways over the course of the batch cultures.

Published
2012

16. Metabolic Switches and Adaptations Deduced from the Proteomes of Streptomyces coelicolorWild Type and phoPMutant Grown in Batch Culture*

Author

Thomas, Louise, Hodgson, David A., Wentzel, Alexander, Nieselt, Kay, Ellingsen, Trond E., Moore, Jonathan, Morrissey, Edward R., Legaie, Roxane, Consortium, The STREAM, Wohlleben, Wolfgang, Rodríguez-García, Antonio, Martín, Juan F., Burroughs, Nigel J., Wellington, Elizabeth M.H., and Smith, Margaret C.M.

Abstract

Bacteria in the genus Streptomycesare soil-dwelling oligotrophs and important producers of secondary metabolites. Previously, we showed that global messenger RNA expression was subject to a series of metabolic and regulatory switches during the lifetime of a fermentor batch culture of Streptomyces coelicolorM145. Here we analyze the proteome from eight time points from the same fermentor culture and, because phosphate availability is an important regulator of secondary metabolite production, compare this to the proteome of a similar time course from an S. coelicolormutant, INB201 (ΔphoP), defective in the control of phosphate utilization. The proteomes provide a detailed view of enzymes involved in central carbon and nitrogen metabolism. Trends in protein expression over the time courses were deduced from a protein abundance index, which also revealed the importance of stress pathway proteins in both cultures. As expected, the ΔphoPmutant was deficient in expression of PhoP-dependent genes, and several putatively compensatory metabolic and regulatory pathways for phosphate scavenging were detected. Notably there is a succession of switches that coordinately induce the production of enzymes for five different secondary metabolite biosynthesis pathways over the course of the batch cultures.

Published
2012
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