Modern Techniques In Neuroscience Research Windhorst Johansson

Cytological Staining Methods......Page 13
Subprotocol 1: Fixation, Sectioning and Embedding......Page 14
Subprotocol 2: Ultrastructure......Page 21
Subprotocol 3: The Golgi Method......Page 25
Subprotocol 4: Single-Cell Methods......Page 29
References......Page 35
Application of Differential Display and Serial Analysis of Gene Expression in the Nervous System......Page 39
Subprotocol 1: Differential Display: Practical Approach......Page 42
Subprotocol 2: Serial Analysis of Gene Expression (SAGE): Practical Approach......Page 51
Subprotocol 3: Digestion of cDNA with Anchoring Enzyme......Page 55
Subprotocol 4: Binding to Magnetic Beads......Page 56
Subprotocol 5: Addition of Linkers......Page 57
Subprotocol 6: Tag Release by Digestion with Tagging Enzyme......Page 58
Subprotocol 8: Ligation to Ditags......Page 59
Subprotocol 9: PCR Amplification of Ditags......Page 60
Subprotocol 10: Ditag Isolation......Page 61
Subprotocol 11: Concatemerisation......Page 63
Subprotocol 12: Cloning Concatemers......Page 64
Subprotocol 13: Sequencing......Page 65
References......Page 67
Methods Towards Detection of Protein Synthesis in Dendrites and Axons......Page 69
Subprotocol 1: IN SITU HYBRIDIZATION OF CULTURED NEURONS......Page 70
Subprotocol 2: In Situ Hybridization at the Electron Microscopic Level......Page 77
Subprotocol 3: Single-Cell Differential mRNA Display......Page 87
Subprotocol 4: Functional Implications of mRNAs in Dendrites and Axons: Metabolic Labeling of Isolated Neurites......Page 93
Subprotocol 5: Intracellular Injection of mRNA......Page 96
References......Page 99
Optical Recording from Individual Neurons in Culture......Page 101
Materials......Page 114
Procedure......Page 115
Results......Page 127
Troubleshoot......Page 129
Comments......Page 134
References......Page 137
Electrical Activity of Individual Neurons In Situ: Extra- and Intracellular Recording......Page 139
Subprotocol 1: General Arrangement and Preparation for Electrophysiological Recording and Data Acquisition......Page 140
Subprotocol 2: Extracellular Recording......Page 146
Subprotocol 3: Intracellular Recording with Sharp Electrodes......Page 158
Subprotocol 4: Intracellular Recording and Tracer Injection......Page 170
Summary and Conclusions......Page 177
Supplier List......Page 178
References......Page 180
Electrical Activity of Individual Neurons: Patch-Clamp Techniques......Page 185
Materials......Page 188
Procedure......Page 192
Results......Page 199
Comments......Page 200
Applications......Page 201
References......Page 203
Microiontophoresis and Pressure Ejection......Page 205
Subprotocol 1: Microiontophoresis......Page 206
Subprotocol 2: Micropressure Ejection......Page 219
References......Page 221
An Introduction to the rinciples of Neuronal Modelling......Page 225
A Philosophy of Modelling......Page 226
Formulation of Dendritic Model......Page 228
The Discrete Tree Equations......Page 238
Formal Solution of Matrix Equations......Page 249
Solution of the Discretised Cable Equations......Page 254
Generating Independent and Correlated Stochastic Spike Trains......Page 257
Equivalent Cable Construction......Page 266
Generalised Compartmental Models......Page 280
The Spectral Methodology......Page 289
Spectral and Exact Solution of an Unbranched Tree......Page 296
Spectral and Exact Solution of a Branched Tree......Page 302
References......Page 311
Notation and Definitions......Page 314
Appendix I......Page 316
In Vitro Models......Page 319
En bloc Preparations......Page 322
Brain Slices......Page 323
Determinants of Ex Vivo Brain Function......Page 330
Conclusions......Page 336
References......Page 337
Culturing CNS Neurons: A Practical Approach to Cultured Embryonic Chick Neurons......Page 339
Materials......Page 341
Procedure......Page 342
Results......Page 345
Comments......Page 346
References......Page 349
Abbreviations......Page 350
Neural Stem Cell Isolation, Characterization and Transplantation......Page 351
Outline......Page 352
Materials......Page 353
Procedure......Page 355
Results......Page 363
Troubleshoot......Page 364
Comments......Page 366
References......Page 369
Suppliers......Page 371
Glossary......Page 372
In Vitro Reconstruction of Neuronal Circuits: A Simple Model System Approach......Page 373
Outline......Page 374
Materials......Page 376
Procedure......Page 380
Results......Page 383
References......Page 388
Grafting of Peripheral Nerves and Schwann Cells into the CNS to Support Axon Regeneration......Page 390
Subprotocol 1: Harvest and Implantation of PN Grafts into the CNS......Page 394
Subprotocol 2: Schwann Cell Guidance Channels......Page 403
References......Page 417
Cell and Tissue Transplantation in the Rodent CNS......Page 421
Outline......Page 422
Subprotocol 1: Dissection of Embryonic/Fetal CNS Tissue......Page 423
Subprotocol 2: Preparation of Tissue/Cells......Page 430
Subprotocol 3: Transplantation into Adults......Page 432
Subprotocol 4: Transplantation into Neonates......Page 436
Subprotocol 5: Transplantation into Embryos......Page 438
References......Page 442
Subprotocol 1: Architectonics......Page 447
Subprotocol 2: Hodology......Page 452
Subprotocol 3: Histochemical Methods: Neurochemistry and Functional Neurohistology, Including the Molecular Biology of Neuron......Page 457
Subprotocol 4: Silver-Impregnation Methods in the Peripheral Nervous System......Page 462
References......Page 465
Optical Recording from Populations of Neurons in Brain Slices......Page 469
Outline......Page 479
Procedure......Page 481
Results......Page 487
Troubleshoot......Page 490
Comments......Page 494
References......Page 495
Abbreviations......Page 496
Recording of Electrical Activity of Neuronal Populations......Page 497
Subprotocol 1: Multi-Unit Recording......Page 498
Subprotocol 2: Examples of Analysis and Results......Page 506
References......Page 510
Suppliers......Page 511
Abbreviations......Page 512
Time and Frequency Domain Analysis of Spike Train and Time Series Data......Page 513
Part 1: Time Domain Analysis of Neuronal Spike Train Data......Page 515
Part 2: Frequency Domain Analysis......Page 520
Part 3: Correlation Between Signals......Page 526
Part 4: Multivariate Analysis......Page 537
Part 5: Extended Coherence Analysis – Pooled Spectra and Pooled Coherence......Page 540
Part 6: A Maximum Likelihood Approach to Neuronal Interactions......Page 543
Results......Page 545
Concluding Remarks......Page 549
References......Page 551
Information-Theoretical Analysis of Sensory Information......Page 554
The Neural Code......Page 556
Basics of Information Theory......Page 560
Random Continuous Time Signals......Page 564
Information Transmission with Continuous Time Signals......Page 566
Information Transmission – The Method......Page 569
Summary – the Practical Procedure......Page 572
Upper Bound to Information Rate and Coding Efficiency......Page 573
The Muscle Spindle: Experimental and Simulation Results......Page 575
Conclusions......Page 579
References......Page 580
Theory......Page 582
Procedures and Results......Page 588
Comments......Page 594
References......Page 596
Abbreviations......Page 597
Linear Systems Description......Page 598
Part 1: Static Linear Systems......Page 601
Part 2: Dynamic Linear Systems......Page 603
Part 3: Physical Components of Linear Systems......Page 605
Part 4: Laplace and Z Transform......Page 614
Part 5: System Identification and Parameter Estimation......Page 620
Part 6: Modeling The Nervous System Control......Page 624
Part 7: Modeling Nonlinear Systems with Linear Systems Description Tools......Page 627
References......Page 633
Nonlinear Analysis of Neuronal Systems......Page 635
Outline......Page 636
Procedure......Page 637
Results......Page 645
References......Page 647
Part 1: Stationary Methods......Page 649
Part 2: Nonstationary Analyses......Page 662
Part 3: Phase Space Reconstruction......Page 668
Postscript......Page 671
References......Page 673
Abbreviations......Page 674
Glossary......Page 675
Part 1: Theoretical Backgrounds......Page 677
Part 2: Procedure and Results......Page 683
Concluding Remarks......Page 693
References......Page 694
Neural Networks and Modeling of Neuronal Networks......Page 696
Network Architecture and Operation......Page 698
Model Neurons, Connections and Network Dynamics......Page 699
Learning and Generalization......Page 704
References......Page 710
Acquisition, Processing and Analysis of the Surface Electromyogram......Page 712
Part 1: Muscle Anatomy and Physiology......Page 713
Part 2: Signal Acquisition and Materials......Page 723
Part 3: Registration Procedures......Page 728
Part 4: Signal Processing......Page 729
Part 5: Results......Page 735
Part 6: Troubleshooting......Page 740
Part 7: Special Applications......Page 742
Applications......Page 750
References......Page 752
Abbreviations......Page 759
Appendix......Page 760
Decomposition and Analysis of Intramuscular Electromyographic Signals......Page 763
Outline......Page 765
Procedure......Page 766
Results......Page 773
Troubleshoot......Page 778
Comments......Page 780
References......Page 781
Abbreviations......Page 782
Outline......Page 783
Materials......Page 784
Procedure......Page 785
Results......Page 791
Suppliers......Page 792
Long-term Cuff Electrode Recordings from Peripheral Nerves in Animals and Humans......Page 793
Procedure......Page 794
Results......Page 804
References......Page 805
Microneurography in Humans......Page 809
Materials......Page 810
Procedure......Page 814
Results......Page 820
Comments......Page 822
References......Page 823
Abbreviations......Page 825
Biomechanical Analysis of Human and Animal Movement......Page 826
External Force Measurements Using Force Platforms......Page 827
External Movement Measurements Using High-Speed Video......Page 829
Surface Electromyography......Page 830
Part 2: Internal Biomechanics......Page 835
Muscle Force Measurements......Page 836
Joint Contact Pressure Measurements......Page 839
Movement Measurements......Page 841
Theoretical Determination of Internal Forces......Page 843
Future Considerations......Page 849
References......Page 850
Detection and classifcation of synergies in multijoint movement with applications to gait analysis......Page 854
Principal Component Analysis Made Simple......Page 855
Application to Gait Analysis......Page 859
Force Fields and the Problem of Degrees of Freedom......Page 869
References......Page 871
Magnetic Stimulation of the Nervous System......Page 873
Subprotocol 1: Apparatus and Mechanisms......Page 874
Subprotocol 2: EMG Recording and Analysis Protocol......Page 878
Applications......Page 880
References......Page 893
In-vivo Optical Imaging of Cortical Architecture and Dynamics......Page 896
Introduction......Page 899
Methods......Page 904
Introduction......Page 933
Imaging of Population Activity......Page 937
Methods......Page 945
Targeted Injection of Tracers into Pre-Defined Functional Domains......Page 960
Electrical Recordings from Pre-Defined Functional Domains......Page 961
Combining Micro-Stimulation and Optical Imaging......Page 962
Conclusions and Outlook......Page 963
References......Page 964
Electroencephalography......Page 973
Subprotocol 1: EEG Recording......Page 976
Subprotocol 2: EEG Signal Analysis......Page 978
Subprotocol 3: Secondary EEG Analysis......Page 990
Subprotocol 4: Presentation of Results......Page 991
References......Page 993
Modern Techniques in ERP Research......Page 998
Part 1: Review of EP Processing Methods......Page 999
Processing Methods......Page 1000
Part 2: Extraction of Trial-Varying EPS......Page 1002
Layer 1:  Unsupervised Learning Structure......Page 1004
Layer 2: Decomposition of EP Waveform......Page 1013
Conclusion......Page 1022
References......Page 1023
Magnetoencephalography......Page 1025
Materials......Page 1030
Procedure......Page 1034
Results......Page 1045
Troubleshoot......Page 1048
Applications......Page 1050
References......Page 1051
Suppliers......Page 1054
Magnetic Resonance Imaging of Human Brain Function......Page 1055
Technical Aspects of MRI Data Acquisition......Page 1057
Data Evaluation and Visualization......Page 1063
Physiologic Aspects of Brain Activation......Page 1069
Paradigm Design......Page 1077
References......Page 1081
Positron Emission Tomography of the Human Brain......Page 1083
Outline......Page 1087
Materials......Page 1088
Procedure......Page 1091
Results......Page 1093
Troubleshoot......Page 1095
References......Page 1096
Suppliers......Page 1097
Magnetic Resonance Spectroscopy of the Human Brain......Page 1098
Technical Requirements and Methods......Page 1105
Applied MRS – Single-Voxel 1 H MRS......Page 1114
Results: Neurospectroscopy......Page 1118
Conclusions......Page 1136
References......Page 1138
Glossary......Page 1141
Monitoring Chemistry of Brain Microenvironment: Biosensors, Microdialysis and Related Techniques......Page 1148
Stereotaxic Surgery on Small Rodents......Page 1150
Microdialysis Experiments on Awake Rats......Page 1154
Part 2: Implantable Sensors......Page 1157
Measuring Extracellular K + Ions by ISM......Page 1158
Amperometric Electrodes......Page 1161
Measurement of Dopamine by Chronoamperometry......Page 1162
Biosensors......Page 1164
Biosensor for Glucose......Page 1166
Cortical Cup Technique......Page 1169
Microdialysis......Page 1170
Determination of Dopamine Release by Microcolumn Liquid Chromatography with Electrochemical Detection (LCEC)......Page 1171
Determination of Serotonin in Microdialysis Samples by LCEC......Page 1173
Determination of Aspartate and Glutamate in Microdialysis Samples by HPLC with Fluorescence Detection......Page 1175
Determination of GABA in Microdialysis Samples by HPLC with Fluorescence (FL) and Electrochemical (EC) Detection......Page 1177
Determination of Physiological Amino Acids in Microdialysis Samples by Microcolumn HPLC with Gradient Elution and Fluorescence (FL) Detection......Page 1179
Determination of Acetylcholine in Microdialysis Samples by Microbore Liquid Chromatography/Electrochemistry on Peroxidase Redox Polymer Coated Electrodes......Page 1184
Microdialysis in the Human Brain......Page 1187
References......Page 1190
Suppliers......Page 1196
Invasive Techniques in Humans: Microelectrode Recordings and Microstimulation......Page 1198
Procedure......Page 1199
Troubleshoot......Page 1205
Suppliers......Page 1208
Psychophysical Methods......Page 1210
Outline......Page 1212
Methods and Procedures......Page 1213
Experimental Examples......Page 1228
Concluding Remarks......Page 1236
References......Page 1237
Suppliers......Page 1239
Analysis of Behavior in Laboratory Rodents......Page 1241
Methods......Page 1242
The Neurobehavioral Examination......Page 1245
Comments: Generalizing from Behavioral Analysis......Page 1267
References......Page 1269
Data Acquisition, Processing and Storage......Page 1274
Outline......Page 1275
What is a Signal?......Page 1276
Noise......Page 1277
Amplification and Amplifiers......Page 1280
Fundamentals of Filtering and Filters......Page 1284
Digital or Analog Processing?......Page 1290
A/D Conversion......Page 1291
Implementations......Page 1293
Data Processing......Page 1295
Data Display......Page 1299
Part 5: Storage and Backup......Page 1302
Concluding Remarks......Page 1304
References......Page 1305
Glossary......Page 1306