Plant Argonaute Proteins: Methods and Protocols, Carbonell Alberto

1. Methodological Advances in Auxin and Cytokinin Biology
   Andrej Hurnэ and Eva Benkovб

2. Analytical Determination of Auxins and Cytokinins
   Petre I. Dobrev, Klбra Hoyerovб, and Jan Petrбsek

3. Manipulation of Auxin and Cytokinin Balance During the Plasmodiophora brassicae: Arabidopsis thaliana Interaction
   Jutta Ludwig-Mьller, Susann Auer, Sabine Jьlke, and Sabine Marschollek

4. Microbial Manipulation of Auxin and Cytokinins in Plants
   Anwar Hussain, Uhsan Ullah, and Shahida Hasnain

5. A Standardized Method to Assess Infection Rates of Root-Knot and Cyst Nematodes in Arabidopsis thaliana Mutants with Alterations in Root Development Related to Auxin and Cytokinin Signaling
   Rocнo Olmo, Ana Clбudia Silva, Fernando E. Dнaz-Manzano, Javier Cabrera, Carmen Fenoll, and Carolina Escobar

6. Reconstruction of an Immune Dynamic Model to Simulate the Contrasting Role of Auxin and Cytokinin in Plant Immunity
   Martin Kaltdorf, Dandekar Thomas, and Muhammad Naseem

7. Interplay between Auxin and Cytokinin and its Impact on Mitogen Activated Protein Kinase (MAPK)
   Pallavi Singh and Alok Krishna Sinha

8. Quantification of Cytokinin Levels and Responses in Abiotic Stresses
   Alfonso Albacete

9. Assessment of Cytokinin-Induced Immunity through Quantification of Hyaloperonospora arabidopsidis Infection in Arabidopsis thaliana
   Ruth A. Watson and Cris T. Argueso

10. Real-Time Genetic Manipulations of the Cytokinin Pathway: A Tool for Laboratory and Field Studies
    Martin Schдfer and Stefan Meldau

11. Modulating the Levels of Plant Hormone Cytokinins at the Host-Pathogen Interface
    Muhammad Naseem, Shabana Shams, and Thomas Roitsch

12. Analyzing Cytokinin Responses during Plant-Nematode Interactions
    Florian M.W. Grundler and Shahid Siddique

13. Examining H₂O₂ Production in Arabidopsis Leaves Upon Challenge by Cytokinin
    Shahjahan Shabbir Ahmed, Ihsan Ullah, Shazia Irfan, and Nazeer Ahmed

14. A Systems Biology Methodology Combining Transcriptome and Interactome Datasets to Assess the Implications of Cytokinin Signaling for Plant Immune Networks
    Meik Kunz, Thomas Dandekar, and Muhammad Naseem

15. Monitoring of Crosstalk between Jasmonate and Auxin in the Framework of Plant Stress Responses of Roots
    Vнctor Carrasco Loba, Marta-Marina Pйrez Alonso, and Stephan Pollmann

16. High-Throughput Protoplast Trans-Activation (PTA) Screening to Define Transcription Factors in Auxin-Mediated Gene Regulation
    Nora Whner, Jцrn Herfert, Wolfgang Drцge-Laser, and Christoph Weiste
    

3. Metaanalysis of Genome-Wide Chromatin Data

4. Localization of Mirnas by In Situ Hybridization in Plants using Conventional Oligonucleotide Probes

5. COBRA (Combined Bisulfite Restriction Analysis) Assay for the Analysis of Locus-Specific Changes in Methylation Patterns

6. Analysis of Global Genome Methylation Using the Cytosine-Extension Assay

Andriy Bilichak and Igor Kovalchuk

7. In Situ Analysis Of DNA Methylation in Plants

Palak Kathiria and Igor Kovalchuk

8. Analysis of DNA Hydroxymethylation in Arabidopsis Using Colorimetric Assay

Andrey Golubov and Igor Kovalchuk

9. Analysis of DNA Cytosine Methylation Patterns using Methylation Specific Amplification Polymorphism (MSAP)

Marнa Бngeles Guevara, Nuria De Marнa, Enrique Sбez-Laguna, Marнa Dolores Vйlez, Marнa Teresa Cervera, and Josй Antonio Cabezas

10. Differentially Methylated Region - Representational Difference Analysis (DMR-RDA): A Powerful Method to Identify Dmrs in Uncharacterized Genomes

11. Analysis of Small RNA Populations Using Hybridization to DNA Tiling Arrays

Martine Boccara, Alexis Sarazin, Bernard Billoud, Agnes Bulski, Louise Chapell, David Baulcombe, and Vincent Colot

12. Northern Blotting Techniques for Small RNAs

Todd Blevins

13. Stem-Loop QRT-PCR for the Detection of Plant Micrornas

Erika Varkonyi-Gasic

14. Profiling New Small RNA Sequences

Masayuki Tsuzuki and Yuichiro Watanabe

15. Small RNA Library Preparation and Illumina Sequencing in Plants

Andriy Bilichak, Andrey Golubov, and Igor Kovalchuk

16. Bioinformatics Analysis of Small RNA Transcriptomes - The Detailed Work Flow

Slava Ilnytskyy and Andriy Bilichak

17. Increasing a Stable Transformation Efficiency of Arabidopsis by Manipulating the Endogenous Gene Expression using Virus-Induced Gene Silencing

18. The Random Oligonucleotide-Primed Synthesis Assay for the Quantification of DNA Strand Breaks

Andriy Bilichak and Igor Kovalchuk

19. Profiling Transposable Elements and their Epigenetic Effects in Non-Model Species

Christian Parisod

1. Epigenetics and RNA Processing: Connections to Drought, Salt and ABA?

Min May Wong, Geeng Loo Chong and Paul Verslues

2. The Fundamental Role Of Reactive Oxygen Species In Stress Response

Michael Liebthal and Karl-Josef Dietz

3. Role of Long Non-coding RNAs on Plant Stress Tolerance

Yuepeng Song and Deqiang Zhang

4. Towards a Resilient, Functional Microbiome: Drought Tolerance-Alleviating Microbes for Sustainable Agriculture

Part II: Methodology Chapters

5. Mining and Quantifying In Vivo Molecular Interactions in Abiotic Stress Acclimation

Thorsten Seidel and Derya Kirasi

6. Generation of a Stress-inducible Luminescent Arabidopsis and Its Use in Genetic Screening for Stress-responsive Gene Deregulation Mutants

Si-in Yu and Byeong-ha Lee

Ibtisam Al Harrasi, Rashid Al-Yahyai and Mahmoud W Yaish

8. ChIP-seq Analysis for Identifying Genome-wide Histone Modifications Associated With Stress-responsive Genes in Plants

Guosheng Li, Guru Jagadeeswaran, Andrew Mort, and Ramanjulu Sunkar

9. Isolation of Polysomal RNA for Analyzing Stress-Responsive Genes Regulated at the Translational Level in Plants

Yong-Fang Li, Ramamurthy Mahalingam, and Ramanjulu Sunkar

10. Global Proteomic Profiling and Identification of Stress-Responsive Proteins using Two-dimensional Gel Electrophoresis

Pragya Barua, Deepak Gayen, Nilesh Vikram Lande, Subhra Chakraborty, and Niranjan Chakraborty

11. Phosphoproteomics Analysis for Probing Plant Stress Tolerance

Christof Rampitsch

12. Probing Posttranslational Redox Modifications

Patrick Treffon, Michael Liebthal, Wilena Telman, and Karl-Josef Dietz

13. Zymographic Method for Distinguishing Different Classes of Superoxide Dismutases in Plants

Ashwini R. Jamdhade, Ramanjulu Sunkar, and Vandana K. Hivrale

14. Determination of Enzymes Associated with Sulfite Toxicity in Plants: Kinetic Assays For SO, APR, SiR and in-gel SiR Activity

Galina Brychkova, Assylay Kurmanbayeva, Aizat Bekturova, Inna Khozin, Dominic Standing, Dmitry Yarmolinsky, and Moshe Sagi

15. Determination of Total Sulfur, Sulfate, Sulfite, Thiosulfate, and Sulfolipids in Plants

Assylay Kurmanbayeva, Galina Brychkova, Aizat Bekturova, Inna Khozin, Dominic Standing, Dmitry Yarmolinsky, and Moshe Sagi

16. Determining Glutathione Levels in Plans

Smita Sahoo, Jay Prakash Awasthi, Ramanjulu Sunkar, and Sanjib Kumar Panda

17. Porous Graphitic Carbon Liquid Chromatography-Mass Spectrometry Analysis of Drought Stress-responsive Raffinose Family Oligosaccharides in Plant Tissues

Tiago F. Jorge, Maria H. Florкncio^, and Carla Antуnio

18. Profiling Abscisic Acid Induced Changes in Fatty Acid Composition in Mosses

Suhas Shinde, Shivakumar Devaiah and Aruna Kilaru

Xiaoqing Gong and Jihong Liu

20. Determination of Polyamines by Dansylation, Benzoylation, and Capillary Electrophoresis

G. Veeranagamallaiah and Chinta Sudhakar

21. Rapid Quantification of Abscisic Acid by GC-MS/MS for studies of Abiotic Stress Response

Paul E. Verslues

Contributing Authors...

1. From Genes to Networks: Characterizing Gene-Regulatory Interactions in Plants

Kerstin Kaufmann and Dijun Chen

Part I Experimental Approaches to Study Plant Gene-Regulatory Networks

2. Inducible Promoter Systems for Gene Perturbation Experiments in Arabidopsis
Bennett Thomson, Emmanuelle Graciet, and Frank Wellmer

3. Cell Type-Specific Gene Expression Profiling Using Fluorescence-Activated Nuclear Sorting
Daniel Slane and Martin Bayer

4. Characterization of Cell Type-Specific DNA Binding Sites of Plant Transcription Factors using Chromatin Immunoprecipitation
On Sun Lau

5. Yeast One and Two Hybrid High-Throughput Screenings using Arrayed Libraries
Rocнo Sбnchez-Montesino and Luis Oсate-Sбnchez

6. SELEX-Seq: A Method to Determine DNA-Binding Specificities of Plant Transcription Factors
Cezary Smaczniak, Gerco C. Angenent and Kerstin Kaufmann

7. Analysis of a Plant Transcriptional Regulatory Network using Transient Expression Systems
Sara Dнaz-Triviсo, Yuchen Long, Ben Scheres, and Ikram Blilou

8. Analysis of In Vivo Chromatin and Protein Interactions of Arabidopsis Transcript Elongation Factors
Alexander Pfab, Wojciech Antosz, Philipp Holzinger, Astrid Bruckmann, Joachim Griesenbeck, and Klaus D. Grasser

9. Characterization of Mediator Complex and its Associated Proteins from Rice
Subhasis Samanta and Jitendra Kumar Thakur

10. DNase I SIM: A Simplified In-Nucleus Method for DNase I Hypersensitive Site Sequencing
Sergei A. Filichkin and Molly Megraw

11. In Situ Hi-C Library Preparation for Plants to Study their Three-Dimensional Chromatin Interactions on a Genome-Wide Scale
Chang Liu

12. Multiplexed Transcriptional Activation or Repression in Plants using CRISPR-dCas9 Based Systems
Levi G. Lowder, Joseph W. Paul III, and Yiping Qi

13. Generation of dTALEs and Libraries of Synthetic TALE-Activated Promoters for Engineering of Gene Regulatory Networks in Plants
Tom Schreiber and Alain Tissier

Part II Computational Approaches to Study Plant Gene-Regulatory Networks

14. Design of Knowledge Bases for Plant Gene Regulatory Networks
Eric Mukundi, Fabio Gomez-Cano, Wilberforce Zachary Ouma, and Erich Grotewold

15. AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species
Tak Lee and Insuk Lee

16. Integration of Genome-Wide TF Binding and Gene Expression Data to Characterize Gene Regulatory Networks in Plant Development
Dijun Chen and Kerstin Kaufmann

17. Predicting Transcription Factor-Binding Sites and their Cognate Transcription Factors using Gene Expression Data
Chun-Ping Yu and Wen-Hsiung Li

18. Computational Approaches to Study Gene Regulatory Networks
Nooshin Omranian and Zoran Nikoloski

19. Boolean Dynamic Modeling Approaches to Study Plant Gene Regulatory Networks: Integration, Validation and Prediction
J. Davila-Velderrain, J.C. Martinez-Garcia, and R.E. Alvarez Buylla

20. ODE-Based Modeling of Complex Regulatory Circuits
Daniel D. Seaton

Simon Schiml, Friedrich Fauser, and Holger Puchta

2. User Guide for the LORE1 Insertion Mutant Resource

Terry Mun, Anna Malolepszy, Niels Sandal, Jens Stougaard, and Stig U. Andersen

Xiaofei Cheng, Nick Krom, Shulan Zhang, Kirankumar S. Mysore, Michael Udvardi, and Jiangqi Wen

Daniele L. Filiault, Danelle K. Seymour, Ravi Maruthachalam, and Julin N. Maloof

Part II: Phenotypes

5. Assessing Distribution and Variation of Genome-wide DNA Methylation using Short Read Sequencing

Jцrg Hagmann and Claude Becker

6. Circular Chromosome Conformation Capture in Plants

Stefan Grob

7. Genome Wide Profiling of Histone Modifications and Histone Variants in Arabidopsis thaliana and Marchantia polymorpha

Ramesh Yelagandula, Akihisa Osakabe, Elin Axelsson, Frederic Berger, and Tomokazu Kawashima

8. Tissue-Specific Transcriptome Profiling in Arabidopsis Roots

Erin E. Sparks and Philip N. Benfey

9. Sample Preparation Protocols for Protein Abundance, Acetylome and Phosphoproteome Profiling of Plant Tissues

10. Automated High-throughput Root Phenotyping of Arabidopsis thaliana under Nutrient Deficiency Conditions

Santosh B. Satbhai, Christian Göschl, and Wolfgang Busch

11. Large-scale Phenotyping of Root Traits in the Model Legume Lotus japonicus

Marco Giovannetti, Anna Malolepszy, Christian Goeschl, and Wolfgang Busch

12. Long-term Confocal Imaging of Arabidopsis thaliana Roots for Simultaneous Quantification of Root Growth and Fluorescent Signals

Delyana Stoeva, Christian Gцschl, and Wolfgang Busch

Part III: Molecular Bases of Phenotypes

13. Identification of Protein-DNA Interactions Using Enhanced Yeast One-Hybrid Assays and a Semi-Automated Approach

Allison Gaudinier, Michelle Tang, Anne-Maarit Bеgman, and Siobhan M. Brady

14. Mapping Protein- protein Interaction using High-throughput Yeast-2-Hybrid

Jessica Lopez and M. Shahid Mukhtar

15. Mapping Protein-protein Interactions using Affinity Purification and Mass Spectrometry

Chin-Mei Lee, Christopher Adamchek, Ann Feke, Dmitri A. Nusinow, and Joshua M. Gendron

16. Measuring Protein Movement, Oligomerization State, and Protein-Protein Interaction in Arabidopsis Roots Using Scanning Fluorescence Correlation Spectroscopy (scanning FCS)
Natalie M. Clark and Rosangela Sozzani

17. Studying Protein-Protein Interactions in planta using Advanced Fluorescence Microscopy

18. Chemiluminescence Based Detection of Peptide Activity and Peptide-Receptor Binding in Plants

Mari Wildhagen, Markus Albert, and Melinka A. Butenko

19^. Application of Chemical Genomics to Plant-Bacteria Communication: A High-Throughput System to Identify Novel Molecules Modulating the Induction of Bacterial Virulence Genes by Plant Signals

Elodie Vandelle, Maria Rita Puttilli, Andrea Chini, Giulia Devescovi, Vittorio Venturi, and Annalisa Polverari