Environmental Responses in Plants: Methods and Protocols

PaPart I Tropisms

1.11. Hydrotropism: Analysis of the Root Response to a Moisture Gradient
Regina Antoni, Daniela Dietrich, Malcolm J. Bennett, and Pedro L. Rodriguez

2. Assessing Gravitropic Responses in Arabidopsis
Richard Barker, Benjamin Cox, Logan Silber, Arah Sangari, Amir Assadi, and Patrick Masson

3. Physiological Analysis of Phototropic Responses in Arabidopsis
Mathias Zeidler

4. Automatic Chloroplast Movement Analysis
Henrik Johansson and Mathias Zeidler

5. Micro

scopic and Biochemical Visualization of Auxins in Plant Tissues
Joshua J. Blakeslee and Angus S. Murphy

6. Immunolocalization of PIN and ABCB Transporters in Plants
Nicola Carraro and Wendy A. Peer

Part II Photoperiodism and Circasian Rhythms

7. Analysis of Circadian Leaf Movements
Niels A. Müller and José M. Jimémez-Gómez

8. Sample Preparation of Arabidopsis Thaliana Shoot Apices for Expression Studies of Photoperiod-Induced Genes
Fernando Andrés, Stefano Torti, Coral Vincent, and George Coupland

9. A Luciferase-Based Assay to Test Whether Gene Expression Responses to Environmental Inputs are

Temporally Restricted by the Circadian Clock
Amaury de Montaigu, Markus C. Berns, and Geroge Coupland

10. Identification of Arabidopsis Transcriptional Regulators by Yeast One-Hyrbid Screens Using a Transcription Factor ORFeome
Ghislain Breton, Steve A. Kay, and José L. Pruneda-Paz

11. Monitoring Alternative Splicing Changes in Arabidopsis Circadian Clock Genes
Craig G. Simpson, John Fuller, Cristiane P. G. Calixto, Jim McNicol, Clare Booth, John W. S. Brown, and Dorothee Staiger

12. Assessing the Impact of Photosynthetic Sugars in the Arabidopsis Circadian Clock
Michael J. Haydon and Alex A. R. Webb

13. Assessing Protein Stability Under Different Light and Circadian Conditions
Takatoshi Kiba and Rossana Henriques

Part III Abiotic Stress Responses

14. Screening for Abiotic Stress Tolerance in Rice: Salt, Cold, and Drought
Diego M. Almeida, M. Cecília Almadanim, Tiago Louren

ço, Isabel A. Abreu, Nelson J. M. Saibo, and M. Margarida Oliveira

15. Basic Techniques to Assess Seed Germination Responses to Abiotic Stress in Arabidopsis Thaliana
Urszula Piskurewicz and Luis Lopez-Molina

16. Assessing Tolerance to Heavy-Metal Stress in Arabidopsis Thaliana Seedings
Estelle Remy and Paula Duque

17. Assessing Drought Responses Using Thermals Infrared Imaging
Ankush Prashar and Hamlyn G. Jones

18. Generating Targeted Gene Knockout Lines in Physcomotrella Patens to Study Evolution of Stress- Responsive Mechanisms
Monika Maronova and Maria Kalyna

19. Screening Stress Tolerance Traits in Arabidopsis Cell Cultures
Imma P. Salamó, Bogáta Boros, and L

ászló Szabados

20. Using Arabidopsis Protoplasts to Study Cellular responses to Environmental Stress
Ana Confraria and Elena Baena-González

21. Construction of Artificial miRNAs to Prevent Drought Stress in Solanum Tuberosum
Anna Wyrzykowska, Marcin Pieczynski, and Zofia Szweykowska-Kulinska

Part IV Plant-Pathogen Interactions

22. Virus-Induced Gene Silencing for Gene Function Studies in Barley
Maria Barciszewska-Pacak, Artur Jarmolowski, and Andrzej Pacak

23. Methods for Long-Term Stable Storage of Colletotrichum Species
Kei Hiruma and Yusuke Saijo

24. Plant Inoculation with the Fungal Leaf Pathogen Colletotrichum Higginsianum
Kei Hiruma and Yusuke Saijo

25. Tracing Plant Defense Responses in Roots Upon MAMP/DAMP Treatment
Kei Hiruma and Yusuke Saijo

26. Analysis of the Immunity=Related Oxidative Bursts by a Luminol-Based Assay
Marco Trujillo

27. Quantitative Analysis of Microbe-Associated-Molecular-Pattern (MAMP)-Induced Ca²⁺ Transients in Plants
Fabian Trempel, Stefanie Ranf, Dierk Scheel, and Justin Lee

28. Rapid Assessment of DNA Methylation Changes in Response to Salicylic Acid by Chop-qPCR
Stephanie Rausch and Sascha Laubinger

29. Determining Nucleosome Position at Individual Loci after Biotic Stress Using MNase-qPCR
Margaux Kaster and Sascha Laubinger

30. Phosphoprotein Enrichment Combined with Phosphopeptide Enrichment to Identify Putative Phosphoproteins During Defense Response in Arabidopsis Thaliana
Ines Lassowskat, Wolfgang Hoehenwarter, Justin Lee, and Dierk Scheel

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