Detail View

CONTENTS
Foreword to the Second Edition = xiii
Foreword to the First Edition = xv
Preface to the Second Edition = xvii
Preface to the First Edition = xix
Introduction = xxiii
1. Whole-Brain Imaging
 Structural Brain Imaging Techniques = 2
  Cerebral Angiography = 3
  Computerized Tomography = 4
  Magnetic Resonance Imaging = 6
  Diffusion MRI = 12
 Functional Brain Imaging Techniques = 14
  Functional Magnetic Resonance Imaging = 14
  Positron Emission Tomography = 17
  Single-Proton Emission Computerized Tomography = 19
  Electroencephalography = 20
  Magnetoencephalography = 20
  Optical Imaging = 22
 Functional Imaging Experimental Design and Analysis = 24
  Planning the Experiment = 25
  Conducting the Experiment = 29
  Manipulating Neural Activity during an Experiment = 31
  Postexperimental Data Analysis = 32
 Conclusion = 35
 Suggested Reading and References = 37
2. Animal Behavior
 Considerations for Choosing and Performing a Behavioral Assay = 40
  Choosing an Appropriate Model Organism = 40
  Choosing an Appropriate Behavioral Paradigm = 41
  Variability in Individuals = 42
  Using Animal Behavior as a Model for Human Behavior = 43
 Rodent Behavioral Paradigms = 44
  Locomotor Activity = 44
  Motor Coordination and Balance = 45
  Sensory Function = 48
  Nociception = 50
  Spatial Learning and Memory = 52
  Nonspatial Learning and Memory = 54
  Attention and Impulsivity = 56
  Reward-Related Behaviors = 56
  Social Behaviors = 57
  Anxiety = 58
  Depression = 60
 Drosophila Behavioral Paradigms = 61
  Locomotor Behavior = 62
  Flight = 62
  Sensory Function = 63
  Learning and Memory = 65
  Social Behaviors = 65
 Caenorhabditis elegans Behavioral Paradigms = 65
  Locomotor Behavior = 66
  Sensory Behavior = 66
 Nonhuman Primate Behavioral Paradigms = 67
 Conclusion = 69
 Suggested Reading and References = 69
3. Stereotaxic Surgeries and In Vivo Techniques
 Stereotaxic Surgeries = 74
  Stereotaxic Surgeries in Rodents = 76
  Stereotaxic Surgeries in Nonhuman Primates = 79
 Implants for Long-Term Access to the Brain = 80
  Sealable Chambers = 80
  Cannulae = 80
  Cranial Windows = 81
  Measuring Neural Activity In Vivo = 81
  Electrophysiology = 81
  Fluorescent Activity Indicators = 82
  Measuring Neural Chemistry In Vivo = 82
  Microdialysis = 82
  Voltammetry and Amperometry = 84
 Manipulating Neural Activity In Vivo = 86
 Conclusion = 86
 Suggested Reading and References = 86
4. Electrophysiology
 A Brief Review of the Electrical Properties of Neurons = 90
 The Electrophysiology Rig = 92
 Categories of Electrophysiology Recordings = 93
  Extracellular Recording = 99
  Intracellular Recording = 105
  Patch Clamp Techniques = 105
 Electrophysiology Tissue Preparations = 108
  In Vitro Recordings = 108
  In Vivo Recordings = 112
 Manipulating Neural Activity during Electrophysiology Experiments = 113
 Conclusion = 114
 Suggested Reading and References = 114
5. Microscopy
 Essential Principles of Microscopy = 118
  Fundamental Parameters in Microscopy = 118
  The Design of a Compound Microscope = 121
  The Design of a Stereomicroscope = 125
 Light Microscopy = 126
 Fluorescence Microscopy = 128
  Epifluorescent Microscopy = 129
  Confocal Microscopy = 129
  Two-Photon Microscopy = 132
  Total Internal Reflection Fluorescence Microscopy = 132
 Electron Microscopy = 133
  Transmission Electron Microscopy = 134
  Scanning Electron Microscopy = 134
  Electron Tomography = 135
 Preparing and Interpreting Microscopy Data = 136
  Image Processing = 136
  Interpreting Images = 137
 Conclusion = 139
 Suggested Reading and References = 143
6. Visualizing Neural Structure
 Tissue Preparation = 146
  Fixation = 146
  Embedding = 147
  Sectioning = 147
 Visualizing Morphology = 150
  Cell Body Stains = 150
  Fiber Stains = 152
  Golgi Stain = 152
  Intracellular and Juxtacellular Labeling = 153
 Visualizing Gene and Protein Expression = 156
  In Situ Hybridization = 156
  Immunohistochemistry = 158
  Enzymatic Histochemistry = 160
  Reporter Genes = 160
 Visualizing Circuitry = 162
  Anterograde and Retrograde Tracers = 162
  Transsynaptic Labeling = 164
 Conclusion = 165
 Suggested Reading and References = 165
7. Visualizing Neural Function
 Static Markers of Activity = 168
  Assaying Neural Activity in Fixed Tissue = 168
  Assaying Cellular Function in Fixed Tissue = 169
 Visualizing Neural Activity = 171
  Imaging Voltage = 171
  Imaging Calcium Dynamics = 173
  Imaging Synaptic Transmission = 176
 Visualizing Protein Function = 177
  Time-Lapse Imaging with Reporter Genes = 177
  Fluorescence Resonance Energy Transfer = 177
  Bimolecular Fluorescence Complementation = 180
  Fluorescence Recovery after Photobleaching = 180
  Photoactivation and Photoconversion = 180
 Conclusion = 181
 Suggested Reading and References = 181
8. Manipulating Neural Activity
 Experimental Logic of Manipulating Neural Activity = 186
 Physical Manipulation = 187
  Ablation = 187
  Thermal Cooling = 188
 Electrical Manipulation = 189
 Pharmacological Manipulation = 189
 Genetic Manipulation = 191
 Pharmacogenetic Manipulation = 192
 Optogenetic Manipulation = 193
  Optogenetic Transgenes = 193
  Methods of Delivering Light to the Nervous System = 195
  Strategies for Studying Neural Circuits Using Optogenetics = 196
 Neuromodulation Techniques Used in Humans = 197
 Conclusion = 197
 Suggested Reading and References = 200
9. Identifying Genes and Proteins of Interest
 A Brief Review of Genes and Proteins = 204
  The Central Dogma of Molecular Biology = 204
  Deoxyribonucleic Acid = 204
  Transcription = 206
  Translation = 208
 Genetic Screens = 209
  Forward Genetic Screen = 210
  Reverse Genetic Screen = 213
 In Silico Screens = 214
  BLAST = 214
  Ensembl = 214
 Molecular Screens = 214
  cDNA Microarray Screen = 215
  RNAi Screen = 216
 Conclusion = 216
 Suggested Reading and References = 217
10. Molecular Cloning and Recombinant DNA Technology
 Isolating DNA Fragments = 220
  Restriction Enzymes = 220
  Polymerase Chain Reaction = 221
  Isolation and Characterization of DNA Fragments Using Gel Electrophoresis = 226
 Cloning DNA = 227
  Vectors = 227
  Ligation = 229
  Transformation = 231
  Purifying DNA from Host Cells = 231
 Identifying DNA = 231
  DNA Sequencing = 233
  Nucleic Acid Hybridization Techniques = 234
 Conclusion = 236
 Suggested Reading and References = 236
11. Gene Delivery Strategies
 Physical Gene Delivery = 239
  Microinjection = 240
  Electroporation = 241
  Biolistics = 243
 Chemical Gene Delivery = 244
  Calcium Phosphate Transfection = 244
  Lipid Transfection = 246
 Viral Gene Delivery = 247
  Adenovirus = 248
  Canine Adenovirus = 248
  Herpes Simplex Virus = 249
  Adeno-Associated Virus = 250
  Lentivirus = 250
 Conclusion = 250
 Suggested Reading and References = 251
12. Making and Using Transgenic Organisms
 Transgenes = 254
  Reporter Genes = 254
  Genes Used to Measure Neural Activity = 254
  Genes Used to Manipulate Neural Activity = 256
  Genes Used to Ablate Neurons = 257
  Genes Used to Disrupt Endogenous Gene Function = 257
  Overexpression of Endogenous Genes = 258
 The Transgenic Construct = 258
 Binary Transgenic Systems = 261
  The Gal4／UAS System = 262
  The Cre／Lox System = 263
  The Flp／Frt System = 264
  The Tet-off／Tet-on System = 264
 Making Transgenic Organisms = 265
  Making Transgenic Mice = 265
  Making Transgenic Flies = 267
  Making Transgenic Worms = 267
  Making Other Transgenic Organisms = 269
 Conclusion = 269
 Suggested Reading and References = 270
13. Manipulating Endogenous Genes
 Classical Gene Targeting Methods = 274
  Knockout Mouse = 275
  Knockin Mouse = 282
  Conditional Knockout Mouse = 282
 Nuclease-Based Gene Targeting Methods = 284
 Disrupting Gene Products = 287
  RNA Interference(RNAi) = 287
  Morpholinos = 289
  Dominant Negatives = 290
 Conclusion = 291
 Suggested Reading and References = 291
14. Cell Culture Techniques
 Cell Culture Equipment and Reagents = 296
  Equipment = 296
  Culture Media = 298
 Immortalized Cell Lines = 298
 Primary Cell and Tissue Culture = 301
  Slice Cultures = 302
  Explant Cultures = 303
  Dissociated Cell Cultures = 303
 Stem Cell Cultures = 304
  Embryonic Stem Cells = 304
  Neural Stem Cells = 305
  Induced Pluripotent Stem Cells = 306
 Manipulating Cells in Culture = 307
  Transfection and Infection = 307
  Co-Culture Systems = 307
  Pharmacology = 308
  Antibody Interference = 308
 Conclusion = 308
 Suggested Reading and References = 309
15. Biochemical Assays and Intracellular Signaling
 Introduction to Signal Transduction and Intracellular Signaling = 313
 Fundamental Tools Used to Study Proteins = 313
  Making and Using Antibodies = 314
  Purifying Proteins = 318
 Investigating Protein Expression = 320
  Western Blot = 320
  Enzyme-Linked Immunosorbent Assay = 323
  Radioimmunoassay = 324
  Immunohistochemistry = 325
  Immunoelectron Microscopy = 326
  Reporter Proteins = 327
 Investigating Protein-Protein Interactions = 327
  Co-Immunoprecipitation = 327
  Protein Affinity Chromatography = 328
  Yeast Two-Hybrid Assay = 330
 Investigating Posttranslational Modifications = 331
  PTM-Specific Assays = 336
  PTM-Specific Antibodies = 337
 Investigating Protein-DNA Interactions = 337
  Electrophoretic Mobility Shift Assay = 338
  Chromatin Immunoprecipitation = 339
  Luciferase Assay = 341
 Conclusion = 342
 Suggested Reading and References = 342
Glossary = 345
Index = 377