Hypoxia: Methods and Protocols

Description

This volume details widely used and newer lab protocols for studying hypoxic responses in physiology and diseases. Chapters guide the reader through the application of hypoxic conditions, to the techniques of molecular biology, biochemical, cell biology, genomic,bioinformatic, metabolic, and animal studies. 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 tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Hypoxia: Methods and Protocols aims to provide a valuable set of tools that can be used to study hypoxia and beyond. Front Matter ....Pages i-xii Genetic Knockdown and Pharmacologic Inhibition of Hypoxia-Inducible Factor (HIF) Hydroxylases (Christina Pickel, Cormac T. Taylor, Carsten C. Scholz)....Pages 1-14 Kinetic Analysis of HIF Prolyl Hydroxylases (Peppi Koivunen, Johanna Myllyharju)....Pages 15-25 Mass Spectrometry and Bioinformatic Analysis of Hydroxylation-Dependent Protein-Protein Interactions (Javier Rodriguez, Alex von Kriegsheim)....Pages 27-36 Acquisition of Temporal HIF Transcriptional Activity Using a Secreted Luciferase Assay (Miguel A. S. Cavadas, Cormac T. Taylor, Alex Cheong)....Pages 37-44 Fluorescence Lifetime Imaging Microscopy (FLIM) as a Tool to Investigate Hypoxia-Induced Protein-Protein Interaction in Living Cells (Vera Schützhold, Joachim Fandrey, Katrin Prost-Fingerle)....Pages 45-53 Transcriptional Profiling Using RNA-Seq to Study Hypoxia-Mediated Gene Regulation (Surendra K. Shukla, Ryan J. King, Pankaj K. Singh)....Pages 55-66 Chromatin Immunoprecipitation of HIF-α in Breast Tumor Cells Using Wild Type and Loss of Function Models (Danielle L. Brooks, Tiffany N. Seagroves)....Pages 67-79 Evaluating the Metabolic Impact of Hypoxia on Pancreatic Cancer Cells (Divya Murthy, Enza Vernucci, Gennifer Goode, Jaime Abrego, Pankaj K. Singh)....Pages 81-93 Hypoxia-Induced Metabolomic Alterations in Pancreatic Cancer Cells (Venugopal Gunda, Sushil Kumar, Aneesha Dasgupta, Pankaj K. Singh)....Pages 95-105 Hypoxia-Mediated In Vivo Tumor Glucose Uptake Measurement and Analysis (Surendra K. Shukla, Scott E. Mulder, Pankaj K. Singh)....Pages 107-113 Measurement of Sensory Nerve Activity from the Carotid Body (Ying-Jie Peng, Nanduri R. Prabhakar)....Pages 115-124 Monitoring Functional Responses to Hypoxia in Single Carotid Body Cells (Ana María Muñoz-Cabello, Hortensia Torres-Torrelo, Ignacio Arias-Mayenco, Patricia Ortega-Sáenz, José López-Barneo)....Pages 125-137 Testing Acute Oxygen Sensing in Genetically Modified Mice: Plethysmography and Amperometry (Patricia Ortega-Sáenz, Candela Caballero, Lin Gao, José López-Barneo)....Pages 139-153 Immunohistochemistry of the Carotid Body (Jayasri Nanduri, Nanduri R. Prabhakar)....Pages 155-166 Hypoxia Signaling and Placental Adaptations (Damayanti Chakraborty, Regan L. Scott, Michael J. Soares)....Pages 167-183 Evaluation of Erythrocyte Changes After Normoxic Return from Hypoxia (Jihyun Song, Josef T. Prchal)....Pages 185-194 Hypoxic Treatment of Zebrafish Embryos and Larvae (Hiroyasu Kamei, Cunming Duan)....Pages 195-203 Microinjection of Antisense Morpholinos, CRISPR/Cas9 RNP, and RNA/DNA into Zebrafish Embryos (Yi Xin, Cunming Duan)....Pages 205-211 Western Blot Analysis of C. elegans Proteins (Dae-Eun Jeong, Yujin Lee, Seung-Jae V. Lee)....Pages 213-225 In Vivo Manipulation of HIF-1α Expression During Glioma Genesis (Patricia D. B. Tiburcio, Séan B. Lyne, L. Eric Huang)....Pages 227-235 In Vitro Assays of Breast Cancer Stem Cells (Debangshu Samanta, Gregg L. Semenza)....Pages 237-246 Fluorescence-Activated Cell Sorting of Murine Mammary Cancer Stem-Like Cell Subpopulations with HIF Activity (Danielle L. Brooks, Tiffany N. Seagroves)....Pages 247-263 Evaluation of Macrophage Polarization in Pancreatic Cancer Microenvironment Under Hypoxia (Kuldeep S. Attri, Kamiya Mehla, Pankaj K. Singh)....Pages 265-276 Detection of Hypoxia and HIF in Paraffin-Embedded Tumor Tissues (Fuming Li, Kyoung Eun Lee, M. Celeste Simon)....Pages 277-282 Analysis of Hypoxia and the Hypoxic Response in Tumor Xenografts (Nuray Böğürcü, Sascha Seidel, Boyan K. Garvalov, Till Acker)....Pages 283-300 Correlation of Glioma Proliferation and Hypoxia by Luciferase, Magnetic Resonance, and Positron Emission Tomography Imaging (Michael Karsy, David L. Gillespie, Kevin P. Horn, Lance D. Burrell, Jeffery T. Yap, Randy L. Jensen)....Pages 301-320 Back Matter ....Pages 321-323