Oxygen biology and hypoxia / edited by Helmut Sies and Bernard Brüne.

Format:

Book

Contributor:

Sies, H. (Helmut), 1942-

Brüne, Bernard.

Series:

Methods in enzymology ; v. 435.

Methods in enzymology ; v. 435

Language:

English

Subjects (All):

Oxygen in the body.

Anoxemia.

Physical Description:

xlviii, 543 pages, 18 unnumbered pages of plates : illustrations (some color) ; 24 cm.

Place of Publication:

Amsterdam ; Oxford : Academic, 2007.

Contents:

Section I Hypoxia-Inducible Factor 1

1 Hypoxia-Inducible Factors P[superscript ER]/ARNT/S[superscript IM] Domains: Structure and Function / Thomas H. Scheuermann, Jinsong Yang, Lei Zhang, Kevin H. Gardner, Richard K. Bruick 3

2 Delineation of the HIF PAS Domains 5

3 Expression and Characterization of HIF PAS Domains 7

4 Assessing PAS Domain Protein-Protein Interactions 11

2 Hypoxia-Inducible Factor Prolyl-Hydroxylase: Purification and Assays of PHD2 / Kirsty S. Hewitson, Christopher J. Schofield, Peter J. Ratcliffe 25

2 Preparation of Purified PHD2 from a Bacterial Source 28

3 Assaying of PHD2 Activity 29

4 Indirect Measurements of PHD2 Activity 29

5 Direct Measurements of PHD2 Hydroxylation Activity 35

6 Binding Assays 37

7 Comparison of Assay Formats 38

3 Determination and Modulation of Prolyl-4-Hydroxylase Domain Oxygen Sensor Activity / Renato Wirthner, Kuppusamy Balamurugan, Daniel P. Stiehl, Sandra Barth, Patrick Spielmann, Felix Oehme, Ingo Flamme, Dorthe M. Katschinski, Roland H. Wenger, Gieri Camenisch 43

2 Production of Functionally Active PHDs 48

3 Determination of PHD by VHL Binding to Peptides Derived from the HIF-1[alpha] ODD Domain 48

4 Determination of Prolyl-4-Hydroxylation by Oxidative Decarboxylation of 2-Oxoglutarate 51

5 Crude Tissue Extracts are not a Suitable Source of PHD Activity for the 2-Oxoglutarate Conversion Assay 53

6 Thin Layer Chromatography to Assess the Purity of [5-[superscript 14] C]2-Oxoglutarate 53

7 Application of the 2-Oxoglutarate Conversion Assay to Protein Targets 55

4 Characterization of Ankyrin Repeat-Containing Proteins as Substrates of the Asparaginyl Hydroxylase Factor Inhibiting Hypoxia-Inducible Transcription Factor / Sarah Linke, Rachel J. Hampton-Smith, Daniel J. Peet 61

2 Experimental Techniques 65

5 Transgenic Models to Understand Hypoxia-Inducible Factor Function / Andrew Doedens, Randall S. Johnson 87

2 Hypoxia Response Pathway Genes and Development 90

3 HIF in Physiology 93

4 HIF Function in Tumor Biology 98

6 The Silencing Approach of the Hypoxia-Signaling Pathway / Edurne Berra, Jacques Pouyssegur 107

1 A Brief History of RNAi 108

2 The Hypoxia-Signaling Pathway 109

3 HIF-[alpha] Stability 110

4 HIF Activity 114

5 HIF-1/HIF-2 Target Gene Specificity 116

6 RNAi as a New Potential Therapeutic Strategy 116

7 Cellular and Developmental Adaptations to Hypoxia: A Drosophila Perspective / Nuria Magdalena Romero, Andres Dekanty, Pablo Wappner 123

2 Drosophila melanogaster as a Model System to Study Physiological Responses to Hypoxia 124

3 Experimental Advantages of the Model System 125

4 The Drosophila Respiratory System 126

5 Occurrence of a Drosophila System Homologous to Mammalian HIF 128

6 Regulation of Sima by Oxygen Levels 131

7 Role of Sima and Fatiga in Drosophila Development 132

8 Hypoxia-Inducible Genes and the Adaptation of Drosophila to Oxygen Starvation 134

9 Regulation of Sima by the PI3K and TOR Pathways 134

10 Role of the HIF System in Growth Control and Cell Size Determination 136

Section II Erythropoietin 145

8 Constitutively Overexpressed Erythropoietin Reduces Infarct Size in a Mouse Model of Permanent Coronary Artery Ligation / Giovanni G. Camici, Thomas Stallmach, Matthias Hermann, Rutger Hassink, Peter Doevendans, Beat Grenacher, Alain Hirschy, Johannes Vogel, Thomas F. Luscher, Frank Ruschitzka, Max Gassmann 147

2 Material and Methods 149

3 Results 151

9 Use of Gene-Manipulated Mice in the Study of Erythropoietin Gene Expression / Norio Suzuki, Naoshi Obara, Masayuki Yamamoto 157

2 Materials 161

3 Methods and Results 163

10 Control of Erythropoietin Gene Expression and its Use in Medicine / Wolfgang Jelkmann 179

2 Native EPO Gene Expression and its Pharmacologic Stimulation 180

3 EPO Gene Transfer 184

4 Recombinant EPOS 187

11 Role of Hypoxia-Inducible Factor-2[alpha] in Endothelial Development and Hematopoiesis / Osamu Ohneda, Masumi Nagano, Yoshiaki Fujii-Kuriyama 199

2 Vasculogenesis/Angiogenesis and HIFs 200

3 HIF-1[beta]/ARNT Null Mice 204

4 Neovascularization and HIFs 205

5 Hematopoiesis and HIFs 211

Section III Hypoxia and Adaptation 219

12 Organ Protection by Hypoxia and Hypoxia-Inducible Factors / Wanja M. Bernhardt, Christina Warnecke, Carsten Willam, Tetsuhiro Tanaka, Michael S. Wiesener, Kai-Uwe Eckardt 221

2 From Ischemic to Hypoxic Preconditioning 222

3 Hypoxia-Inducible Transcription Factors 223

4 Strategies to Activate HIF and HIF Target Genes 227

5 Hypoxic Preconditioning and HIF 231

6 HIF in Chronic Hypoxic/Ischemic Diseases 236

13 Hypoxia and Regulation of Messenger RNA Translation / Marianne Koritzinsky, Bradly G. Wouters 247

2 Changes in Global mRNA Translation During Hypoxia 249

3 Molecular Mechanisms that Regulate mRNA Translation During Hypoxia 251

4 Methods Employed to Study mRNA Translation During Hypoxia 256

5 Protocols 268

14 Hypoxia and the Unfolded Protein Response / Constantinos Koumenis, Meixia Bi, Jiangbin Ye, Douglas Feldman, Albert C. Koong 275

2 Methods Employed in Detecting Hypoxic Induction of ER Stress 282

Section IV Hypoxia and Tumor Biology 295

15 Tumor Hypoxia in Cancer Therapy / J. Martin Brown 297

1 Hypoxia in Human Tumors 298

2 The Dynamic Nature of Hypoxia in Tumors 300

3 Consequences of Tumor Hypoxia for Cancer Treatment 300

4 Size of the Oxygen Effect with Radiation 302

5 The Influence of Tumor Hypoxia on Cancer Treatment by Radiotherapy 303

6 Influence of Tumor Hypoxia on Response to Chemotherapy 307

7 Exploiting Hypoxia in Cancer Treatment 308

16 HIF Gene Expression in Cancer Therapy / Denise A. Chan, Adam J. Krieg, Sandra Turcotte, Amato J. Giaccia 323

2 Experimental Procedures 326

17 Analysis of Hypoxia-Inducible Factor-1[alpha] Expression and its Effects on Invasion and Metastasis / Balaji Krishnamachary, Gregg L. Semenza 347

2 Protocol 1: HIF-1[alpha] Immunohistochemistry 349

3 Protocol 2: Invasion Assay 350

4 Protocol 3: Transepithelial Resistance Measurement of Cell-Cell Adhesion 351

5 Protocol 4: Analysis of MRNA Expression by QRT-PCR 351

18 Macrophage Migration Inhibitory Factor Manipulation and Evaluation in Tumoral Hypoxic Adaptation / Millicent Winner, Lin Leng, Wayne Zundel, Robert A. Mitchell 355

2 Modulation of MIF Levels by Targeted shRNAs and Assessment of Knockdown Efficiency 357

3 Analysis of MIF-Dependent CSN5 and COP9 Signalosome Function 362

4 Determination of Tumor-Associated MIF Expression and MIF Polymorphic Disparity 364

19 The Von Hippel-Lindau Tumor Suppressor Protein: An Update / William G.

Kaelin, Jr. 371

2 Regulation of Epithelial Differentiation by pVHL 373

3 Crosstalk Between c-Met and VHL 374

4 Regulation of Neuronal Apoptosis by pVHL 375

5 Possible Links Between p53 and pVHL 376

6 Regulation of pVHL by Phosphorylation 376

7 Polyubiquitylation of pVHL 377

8 Mouse Models for Studying pVHL Function 377

20 Hypoxia-Inducible Factor 1 Inhibitors / Giovanni Melillo 385

2 Cell-Based High Throughput Screens 387

3 Cell-Free Assays 393

4 Bioassay-Directed Isolation of Natural Product HIF-1 Inhibitors 398

Section V Hypoxia and Inflammatory Mediators 403

21 Regulation of Hypoxia-Inducible Factors During Inflammation / Stilla Frede, Utta Berchner-Pfannschmidt, Joachim Fandrey 405

2 Regulation of HIF at the Transcriptional Level 408

3 Regulation of HIF at the Translational Level 410

4 Regulation of HIF-1[alpha] at the Posttranslational Level 411

5 Regulation of HIF-1 Activity 413

22 Superoxide and Derived Reactive Oxygen Species in the Regulation of Hypoxia-Inducible Factors / Agnes Gorlach, Thomas Kietzmann 421

2 Reactive Oxygen Species Act as Signaling Molecules 423

3 HIFs are Sensitive to Oxygen 424

4 Reactive Oxygen Species Modulate HIF 425

5 How are HIFs Regulated by Reactive Oxygen Species? 427

8 The Cytochrome C Reduction Assay for Detection of Extracellular Reactive Oxygen Species 431

9 Chemiluminescence Assay for Detection of Extracellular Reactive Oxygen Species 432

10 Measuring Intracellular Production of Reactive Oxygen Species using Fluorescent Dyes 433

11 Detection of Reactive Oxygen Species by Electron Paramagnetic Resonance 436

23 Genetics of Mitochondrial Electron Transport Chain in Regulating Oxygen Sensing / Eric L. Bell, Navdeep S. Chandel 447

2 Detecting HIF-1[alpha] Protein Levels 449

3 Detecting Intracellular ROS Levels 452

4 Method 1: Examining Hypoxic Stabilization of HIF-1[alpha] Protein in Cells Containing RNAI against the Rieske Fe-S Protein 454

5 Method 2: Examining the Role of ROS Generated from Mitochondrial Electron Transport in Hypoxic Stabilization of HIF-1[alpha] Protein 458

24 Hypoxia-Inducible Factor-1[alpha] Under the Control of Nitric Oxide / Bernhard Brune, Jie Zhou 463

1 HIF-1 and Oxygen Sensing 464

2 Nitric Oxide: A Multifunctional Messenger 465

3 Accumulation of HIF-1[alpha] and Activation of HIF-1 by NO 467

4 Superoxide Stabilizes HIF-1[alpha] but Antagonizes NO Actions 470

5 Hypoxic Signal Transmission is Antagonized by NO 472

25 Hypoxic Regulation of NF-[kappa]B Signaling / Eoin P. Cummins, Katrina M. Comerford, Carsten Scholz, Ulrike Bruning, Cormac T. Taylor 479

2 Treatment Protocols for Cellular Hypoxia Studies 481

3 Measurement of NF-[kappa]B Activity in Cultured Cells 484.

Notes:

Includes bibliographical references and indexes.

ISBN:

9780123739704

0123739705

OCLC:

171547259