NF-kappa B

Part I: Standard Approaches to Detect NF-kappaB Pathway 1. Electrophoretic Mobility Shift Assay Analysis of NF- kB DNA Binding Sitharam Ramaswami and Matthew S. Hayden M.D 2. Detection of IkB Degradation Dynamics and IkB-a Ubiquitination Petro Starokadomskyy and Ezra Burstein 3. Measurement of NF-kappaB Transcriptional Activity and Identification of NF-kappaB cis-regulatory Elements using Luciferase Assays Patricia E. Collins, Christine O'Carroll, and Ruaidhri J. Carmody Part II: Detection and Analysis of NF-kappaB Signaling 4. Assessing Sites of NF-kappaB DNA Binding using Chromatin Immunoprecipitation Amy Colleran, Patricia E. Collins, and Ruaidhri J. Carmody 5. IKK Kinase Assay for Assessment of Canonical NF-kB Activation in Neurons Anca B Mihalas and Mollie K Meffert 6. Analysis of Epidermal Growth Factor-induced NF-kB Signaling Changying Jiang and Xin Lin 7. Methods to Assess the Activation of the Alternative (non-canonical) NF-kB Pathway by Non-death TNF Receptors Caroline Remouchamps and Emmanuel Dejardin 8. Systematic Detection of Non-canonical NF-kappaB Activation Zhaoxia Qu and Gutian Xiao 9. Non-canonical NF-kappaB activation and SDF-1 expression in Human Endothelial Cells Kelly A. McCorkell and Michael J. May 10. Stable Reconstitution of IKK-deficient Mouse Embryonic Fibroblasts Carolyn M. Gray and Michael J. May 11. Dissecting NF-kappaB Signaling Induced by Genotoxic Agents Via Genetic Complementation of NEMO-deficient 1.3E2 Cells Shawn S. Jackson and Shigeki Miyamoto Part III: Methods to Study the Control of NF-kappaB Signalling 12. Visualizing TCR induced POLKADOTS Formation and NF-kappaB Activation in the D10 T Cell Clone and Mouse Primary Effector T cells Suman Paul and Brian C Schaefer 13. Detection of Recombinant and Cellular MALT1 Paracaspase Activity Daniel Nagel and Daniel Krappmann 14. TRAF Protein Function In Non-Canonical NF-kappaB Signaling Anna D. Reichardt, Jose Pindado Rodriguez, Shivam A. Zaver, Genhong Cheng 15. Roles of c-IAP Proteins in TNF Receptor Family Activation of NF-kB Signaling Eugene Varfolomeev, Tatiana Goncharov, and Domagoj Vucic 16. Elucidating Dynamic Protein-protein Interactions and Ubiquitination in NF-kB Signaling Pathways Noula Shembade and Edward W. Harhaj 17. Immunoblot Analysis of Linear Polyubiquitination of NEMO Yoshiteru Sasaki, Hiroaki Fujita, Misa Nakai, and Kazuhiro Iwai 18. In vitro Detection of NEMO-Ubiquitin Binding using DELFIA and Microscale Thermophoresis Assays Michelle Vincendeau, Daniel Krappmann, and Kamyar Hadian 19. Use of Fluorescence Spectroscopy For Quantitative Investigations Of Ubiquitin Interactions with the Ubiquitin-Binding Domains of NEMO Virginie Dubosclard, Elisabeth Fontan, and Fabrice Agou 20. Generation of a Proteolytic Signal: E3/E2-mediated Polyubiquitination of IkappaBalpha Robert A. Chong, Kenneth Wu, Jordan Kovacev, and Zhen-Qiang Pan 21. Control of NF-kappaB Subunits by Ubiquitination Patricia E. Collins, Amy Colleran, and Ruaidhri J. Carmody 22. Methodology to Study NF-kB/RelA Ubiquitination in vivo Haiying Li, Petro Starokadomskyy, and Ezra Burstein 23. Using Sequential Immunoprecipitation and Mass Spectrometry to Identify Methylation of NF-kB Tao Lu and George R. Stark 24. Methods to Detect NF-kB Acetylation and Methylation JinJing Chen and Lin-Feng Chen Part IV : Analyzing and Targeting NF-kappaB Activity in Disease 25. A Method for the Quantitative Analysis of Stimulation-Induced Nuclear Translocation of the p65 subunit of NF-kB from Patient-Derived Dermal Fibroblasts Alex W. Wessel and Eric P. Hanson 26. Methods for Assessing the In Vitro Transforming Activity of NF-kappaB Transcription Factor c-Rel and Related Proteins Thomas D. Gilmore and Celine Gelinas 27. Using RNA Interference in Lung Cancer Cells to Target the IKK-NF-kappaB Pathway Daniela S. Basseres and Albert S. Baldwin 28. Immunohistochemical Analysis of NF-kB in Human Tumor Tissue Clint T. Allen and Carter Van Waes 29. Assessment of Canonical NF-kB Activity in Canine Diffuse Large B-Cell Lymphoma Anita Gaurnier-Hausser and Nicola J. Mason 30. NEMO Binding Domain Peptide Inhibition of Inflammatory Signal-Induced NF-kappaB Activation In Vivo Kelly A. McCorkell and Michael J. May 31. Regulation of NFkappaB Signaling in Osteoclasts and Myeloid Progenitors Gaurav Swarnkar and Yousef Abu-Amer 32. NF-kappaB Activation with Aging: Characterization and Therapeutic Inhibition Jing Zhao, Xuesen Li, Sara McGowan, Laura J. Niedernhofer, and Paul D. Robbins 33. The "Sneaking-ligand" Approach: Cell-type Specific Inhibition of the Classical NF-kB Pathway Bettina Sehnert, Harald Burkhardt, Stefan Dubel, and Reinhard E. Voll 34. Sneaking-ligand Fusion Proteins Attenuate Serum Transfer Arthritis by Endothelium-targeted NF-kB inhibition Bettina Sehnert, Harald Burkhardt, Michael J. May, Jochen Zwerina, and Reinhard E. Voll 35. Analysis of NF-kB Activation in Mouse Intestinal Epithelial Cells Helena Shaked, Monica Guma, and Michael Karin Part V: Bioinformatics and Modeling Approaches to Study NF-kappaB 36. Characterizing the DNA Binding Site Specificity of NF-kB with Protein Binding Microarrays (PBMs) Trevor Siggers, Thomas D. Gilmore, Brian Barron, and Ashley Penvose 37. Methods for Analyzing the Evolutionary Relationship of NF-kB Proteins Using Free, Web-driven Bioinformatics and Phylogenetic Tools John Finnerty and Thomas D. Gilmore 38. Studying NFkB Signaling with Mathematical Models Simon Mitchell, Rachel Tsui, and Alexander Hoffmann