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Life Sciences - Plant Sciences | Plant Chemical Genomics - Methods and Protocols

Plant Chemical Genomics

Methods and Protocols

Series: Methods in Molecular Biology, Vol. 1056

Hicks, Glenn R, Robert, Stéphanie (Eds.)

2014, XI, 269 p. 169 illus., 13 illus. in color.

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  • Offers overviews of technical approaches for utilizing small molecules in plant researhc
  • Provides methods highlighting specific applications applied to basic plan processes
  • Features notes on troubleshooting and avoiding known pitfalls

Plant Chemical Genomics: Methods and Protocols , expert researchers in the field detail many of the techniques used for identification of bioactive compounds from a large selection of fields in plant biology including plant pathogenesis, immune responses, small RNA processing, endomembrane trafficking, lipids, plant hormone signaling and cell wall. The presentation of these and other examples as well as synthetic chemistry, computation and target identification provides a comprehensive overview of the practical aspects of chemical biology that are possible in plant systems. Small molecules and natural products that produce a phenotype in plants have been known for decades. The agrichemical industry has utilized small molecules based on known natural molecules such as auxins, cytokinins, abscissic acid and other growth regulators. In recent years, the screening and characterization of novel small molecules has enhanced our understanding of protein function, metabolic, signaling and endomembrane pathways, and their interactions in basic plant research.

Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.

Content Level » Professional/practitioner

Keywords » ChemMine database - cell wall - chemical phenotypes - chemical screens - cognate gene targets of bioactive compounds - endomembrane trafficking - immune responses - lipids - phenotypic datasets - plant hormone signaling - plant pathogenesis - small RNA processing

Related subjects » Plant Sciences

Table of contents 

Section I: Automation and Imaging

1. Fully-automated Compound Screening in Arabidopsis thaliana Seedlings

Dominique Audenaert, Long Nguyen, Bert De Rybel, and Tom Beeckman


2. Time-profiling Fluorescent Reporters in the Arabidopsis Root

Antoine P. Larrieu, Andrew P. French, Tony P. Pridmore, Malcolm J. Bennett and Darren M. Wells


3. Screening for Bioactive Small Molecules by in vivo Monitoring of Luciferase-based Reporter Gene Expression in Arabidopsis thaliana

Christian Meesters and Erich Kombrink



Section II: Chemical Screening

4. Application of Yeast-two Hybrid Assay to Chemical Genomic Screens: A High-throughput System to Identify Novel Molecules Modulating Plant Hormone Receptor Complexes

Andrea Chini


5. High-throughput Screening of Small Molecule Libraries for Inducers of Plant Defense Responses

Colleen Knoth and Thomas Eulgem


6. Using a Reverse Genetics Approach to Investigate Small Molecule Activity

Siamsa M. Doyle and  Stéphanie Robert


7. Investigating the Phytohormone Ethylene Response Pathway by Chemical Genetics

Lee-Chung, Lin, Chiao-Mei Chueh, and Long-Chi Wang


8. Screening for Inhibitors of Chloroplast Galactolipid Synthesis Acting in membrano and in Planta

Laurence Boudière and Eric Maréchal


9. Forward Chemical Screening of Small RNA Pathways

Yifan Lii and Hailing Jin


10. Identification and Use of Fluorescent Dyes for Plant Cell Wall Imaging Using High-Throughput Screening

Charles T. Anderson and Andrew Carroll


11. High-throughput Identification of Chemical Endomembrane Cycling Disruptors Utilizing Tobacco Pollen

Michelle Q. Brown, Nolan Ung, Natasha V. Raikhel, and Glenn R. Hicks


12. Plant Chemical Genomics: Gravity Sensing and Response

Marci Surpin

 13. Screening Chemical Libraries for Compounds that Affect Protein Sorting to the Yeast Vacuole

Jan Zouhar


Section III: Cheminformatics

14. The use of Multi-drug Approach to Uncover New Players of the Endomembrane System Trafficking Machinery

Urbina D, Pérez-Henríquez P,  and Norambuena L

 15. Cheminformatic Analysis of High-Throughput Compound Screens

Tyler W. H. Backman and Thomas Girke


16. Endomembrane Dissection Using Chemically-Induced Bioactive Clusters

Natasha Worden, Thomas Girke, and Georgia Drakakaki

 17. Statistical Molecular Design: A Tool to Follow Up Hits From Small Molecule ScreeningAnders E. G. Lindgren, Andreas Larsson, Anna Linusson, and Mikael Elofsson



Section IV: Target Identification

18. Early Stage Hit Triage for Plant Chemical Genetic Screens and Target Site Identification

Terence A. Walsh


19. Screening for Gene Function using the FOX (Full-length cDNA OvereXpressor gene) Hunting System

Mieko Higuchi, Minami Matsui




Section V: Hormone Transport and Metabolite Profiling

20. Quantification of Stable Isotope Label in Metabolites via Mass Spectrometry

Jan Huege, Jan Goetze, Frederik Dethloff, Bjoern Junker, and Joachim Kopka


21. 1H NMR Based Metabolomics Methods for Chemical Genomics Experiments

Daniel J. Orr, Gregory A. Barding, Jr., Christiana E. Merrywell, Glenn R. Hicks, Natasha V. Raikhel, and Cynthia K. Larive


22. Determination of Auxin Transport Parameters on the Cellular Level

Jan Petrášek, Martina Laňková, and Eva Zažímalová


23. Analyzing the in vivo Status of Exogenously Applied Auxins: A HPLC-based Method to Characterize the Intracellularly Localized Auxin Transporters

Sibu Simon, Petr Skůpa, Petre I. Dobrev, Jan Petrášek, Eva Zažímalová, and Jiří Friml

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