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4 results on '"Elizabeth Purdom"'

1. Cell Wall Compositions of Sorghum bicolor Leaves and Roots Remain Relatively Constant Under Drought Conditions

Author

Tess Scavuzzo-Duggan, Nelle Varoquaux, Mary Madera, John P. Vogel, Jeffery Dahlberg, Robert Hutmacher, Michael Belcher, Jasmine Ortega, Devin Coleman-Derr, Peggy Lemaux, Elizabeth Purdom, Henrik V. Scheller, Translational microbial Evolution and Engineering (TIMC-TrEE), Translational Innovation in Medicine and Complexity / Recherche Translationnelle et Innovation en Médecine et Complexité - UMR 5525 (TIMC ), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), and Université Grenoble Alpes (UGA)

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], Plant Biology, Biomass, Plant Science, drought, 7. Clean energy, 01 natural sciences, SB1-1110, Cell wall, Transcriptome, 03 medical and health sciences, Affordable and Clean Energy, Enzymatic hydrolysis, Botany, biomass conversion and expansion factor, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Rhizosphere, biology, fungi, Root microbiome, Plant culture, food and beverages, pre-flowering, 15. Life on land, Sorghum bicolor, Biorefinery, Sorghum, biology.organism_classification, post-flowering, Climate Action, 13. Climate action, biomass conversion and expansion factor (BCEF), cell wall, 010606 plant biology & botany
Abstract

Renewable fuels are needed to replace fossil fuels in the immediate future. Lignocellulosic bioenergy crops provide a renewable alternative that sequesters atmospheric carbon. To prevent displacement of food crops, it would be advantageous to grow biofuel crops on marginal lands. These lands will likely face more frequent and extreme drought conditions than conventional agricultural land, so it is crucial to see how proposed bioenergy crops fare under these conditions and how that may affect lignocellulosic biomass composition and saccharification properties. We found that while drought impacts the plant cell wall of Sorghum bicolor differently according to tissue and timing of drought induction, drought-induced cell wall compositional modifications are relatively minor and produce no negative effect on biomass conversion. This contrasts with the cell wall-related transcriptome, which had a varied range of highly variable genes (HVGs) within four cell wall-related GO categories, depending on the tissues surveyed and time of drought induction. Further, many HVGs had expression changes in which putative impacts were not seen in the physical cell wall or which were in opposition to their putative impacts. Interestingly, most pre-flowering drought-induced cell wall changes occurred in the leaf, with matrix and lignin compositional changes that did not persist after recovery from drought. Most measurable physical post-flowering cell wall changes occurred in the root, affecting mainly polysaccharide composition and cross-linking. This study couples transcriptomics to cell wall chemical analyses of a C4 grass experiencing progressive and differing drought stresses in the field. As such, we can analyze the cell wall-specific response to agriculturally relevant drought stresses on the transcriptomic level and see whether those changes translate to compositional or biomass conversion differences. Our results bolster the conclusion that drought stress does not substantially affect the cell wall composition of specific aerial and subterranean biomass nor impede enzymatic hydrolysis of leaf biomass, a positive result for biorefinery processes. Coupled with previously reported results on the root microbiome and rhizosphere and whole transcriptome analyses of this study, we can formulate and test hypotheses on individual gene candidates’ function in mediating drought stress in the grass cell wall, as demonstrated in sorghum.

Published
2021
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2. Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics

Author

Peggy G. Lemaux, Siwen Deng, Daniel F. Caddell, Nelle Varoquaux, Mary Lou Guerinot, Dawn Chiniquy, Ling Xu, Heidi M.-L. Wipf, Jeffery A. Dahlberg, Mary Madera, John W. Taylor, Elizabeth Purdom, Spencer Diamond, Cheng Gao, Zhaobin Dong, Robert B. Hutmacher, Devin Coleman-Derr, Tuesday Simmons, Jillian F. Banfield, Grady Pierroz, Adam M. Deutschbauer, University of California [Berkeley], University of California, China State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University (CAU), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), USDA-ARS : Agricultural Research Service, Translational microbial Evolution and Engineering (TIMC-TrEE), Translational Innovation in Medicine and Complexity / Recherche Translationnelle et Innovation en Médecine et Complexité - UMR 5525 (TIMC ), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), University of California [Davis] (UC Davis), and Dartmouth College [Hanover]

Subjects
0106 biological sciences, 0301 basic medicine, Acclimatization, [SDV]Life Sciences [q-bio], General Physics and Astronomy, 01 natural sciences, Plant Roots, 2.1 Biological and endogenous factors, RNA-Seq, Aetiology, Soil Microbiology, 2. Zero hunger, Genetics, Rhizosphere, Multidisciplinary, Microbiota, food and beverages, Crop Production, Droughts, Actinobacteria, Soil microbiology, Plant molecular biology, Science, Iron, Physiological, Drought tolerance, Biology, Stress, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Stress, Physiological, parasitic diseases, Microbe, Microbiome, Sorghum, Comparative genomics, Drought, Human Genome, fungi, Root microbiome, General Chemistry, 15. Life on land, biology.organism_classification, 030104 developmental biology, 13. Climate action, Metagenomics, Food Security, 010606 plant biology & botany
Abstract

Recent studies have demonstrated that drought leads to dramatic, highly conserved shifts in the root microbiome. At present, the molecular mechanisms underlying these responses remain largely uncharacterized. Here we employ genome-resolved metagenomics and comparative genomics to demonstrate that carbohydrate and secondary metabolite transport functionalities are overrepresented within drought-enriched taxa. These data also reveal that bacterial iron transport and metabolism functionality is highly correlated with drought enrichment. Using time-series root RNA-Seq data, we demonstrate that iron homeostasis within the root is impacted by drought stress, and that loss of a plant phytosiderophore iron transporter impacts microbial community composition, leading to significant increases in the drought-enriched lineage, Actinobacteria. Finally, we show that exogenous application of iron disrupts the drought-induced enrichment of Actinobacteria, as well as their improvement in host phenotype during drought stress. Collectively, our findings implicate iron metabolism in the root microbiome’s response to drought and may inform efforts to improve plant drought tolerance to increase food security., Advances in omics provide a tool to understand mechanisms for plant–microbial interactions under stress. Here the authors apply genome-resolved metagenomics to investigate sorghum and its microbiome responses to drought, identifying an unexpected role of iron metabolism.

Published
2021
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3. A pipeline to analyse time-course gene expression data

Author

Nelle Varoquaux, Elizabeth Purdom, Translational Innovation in Medicine and Complexity / Recherche Translationnelle et Innovation en Médecine et Complexité - UMR 5525 (TIMC ), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Génomique et Évolution des Microorganismes (TIMC-IMAG-GEM ), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications Grenoble - UMR 5525 (TIMC-IMAG), and Université Grenoble Alpes (UGA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )

Subjects
0301 basic medicine, Normalization (statistics), Differential expression analysis, General Immunology and Microbiology, business.industry, Computer science, [SDV]Life Sciences [q-bio], Functional data analysis, General Medicine, Computational biology, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Workflow, Software, Time course, Gene expression, General Pharmacology, Toxicology and Pharmaceutics, business, Cluster analysis, 030217 neurology & neurosurgery
Abstract

International audience; The phenotypic diversity of cells is governed by a complex equilibrium between their genetic identity and their environmental interactions: Understanding the dynamics of gene expression is a fundamental question of biology. However, analysing time-course transcriptomic data raises unique challenging statistical and computational questions, requiring the development of novel methods and software. This workflow provides a step-by-step tutorial of the methodology used to analyse time-course data: (1) quality control and normalization of the dataset; (2) differential expression analysis using functional data analysis; (3) clustering of time-course data; (4) interpreting clusters with GO term and KEGG pathway enrichment analysis. As a case study, we apply this workflow to time-course transcriptomic data from mice exposed to four strains of influenza to showcase every step of the pipeline.

Published
2020
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4. Subtype and pathway specific responses to anticancer compounds in breast cancer

Author

Heidi S. Feiler, Eric A. Collisson, Joel Greshock, Mary Ann Hardwicke, Elizabeth Purdom, Gordon B. Mills, Bryan T. Hennessy, Lakshmi Jakkula, Pete Smith, Yinghui Guan, James E. Korkola, John W. Park, Joe W. Gray, Nicholas J. Wang, William J. Gibb, Kurtis E. Bachman, Denise M. Wolf, Lyubomir T. Vassilev, Henrik Bengtsson, Kenneth Wood, Stephen C. Benz, Zhi Hu, Anguraj Sadanandam, Nora Bayani, François Pepin, Frances Tong, Terence P. Speed, Laura M. Heiser, Sam Ng, Steffen Durinck, Theodore C. Goldstein, Joshua M. Stuart, Wen-Lin Kuo, Richard M. Neve, Paul T. Spellman, Jessica Billig, David Haussler, Sophia Lewis, Safiyyah Ziyad, Richard Wooster, Andrea Dueregger, Pierre Neuvial, Laurence J. Marton, Life Science Division [LBNL Berkeley], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Department of Biomolecular Engineering, University of California [Santa Cruz] (UCSC), University of California-University of California, Center for Biomolecular Science and Engineering, Department of Statistics [Berkeley], University of California [Berkeley], Laboratoire Statistique et Génome (SG), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Department of Epidemiology and Biostatistics, University of California, San Francisco, University of California [San Francisco] (UCSF), Cytokinetics Inc, Oncology, Millenium Pharmaceuticals, Hoffmann-La Roche Ltd, Department of Systems Biology, The University of Texas MD Anderson Cancer Center, The University of Texas M.D. Anderson Cancer Center [Houston], GlaxoSmithKline, Glaxo Smith Kline, Division of Hematology-Oncology, Progen Pharmaceuticals, The Walter and Eliza Hall Institute of Medical Research (WEHI), The Walter and Eliza Hall Institute of Medical Research, Howard Hughes Medical Institute [Santa Cruz] (HHMI), Center for Biomolecular Science & Engineering, Department of Computer Science [Alabama], University of Alabama [Tuscaloosa] (UA), University of California-University of California-Howard Hughes Medical Institute (HHMI), University of California [Santa Cruz] (UC Santa Cruz), University of California (UC)-University of California (UC), University of California [Berkeley] (UC Berkeley), University of California [San Francisco] (UC San Francisco), F. Hoffmann-La Roche [Basel], and Howard Hughes Medical Institute (HHMI)-University of California [Santa Cruz] (UC Santa Cruz)

Subjects
Transcription, Genetic, [SDV]Life Sciences [q-bio], Gene Dosage, Antineoplastic Agents, Breast Neoplasms, Genomics, Biology, Pharmacology, Models, Biological, Gene dosage, 03 medical and health sciences, 0302 clinical medicine, Breast cancer, Breast cancer cell line, Transcription (biology), Cell Line, Tumor, medicine, Drug response, Humans, Breast Cancer Special Feature, 030304 developmental biology, 0303 health sciences, Multidisciplinary, medicine.disease, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 3. Good health, Cell culture, 030220 oncology & carcinogenesis, Cancer research, Female, Drug Screening Assays, Antitumor, Signal transduction, Signal Transduction
Abstract

International audience; Breast cancers are comprised of molecularly distinct subtypes that may respond differently to pathway-targeted therapies now under development. Collections of breast cancer cell lines mirror many of the molecular subtypes and pathways found in tumors, suggesting that treatment of cell lines with candidate therapeutic compounds can guide identification of associations between molecular subtypes, pathways, and drug response. In a test of 77 therapeutic compounds, nearly all drugs showed differential responses across these cell lines, and approximately one third showed subtype-, pathway-, and/or genomic aberration-specific responses. These observations suggest mechanisms of response and resistance and may inform efforts to develop molecular assays that predict clinical response.

Published
2012

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