Modern Neuroscience Research Protocol

Table of contents :
back to Contents……Page 0
Introduction……Page 1
Subprotocol 1: Fixation, Sectioning and Embedding……Page 2
Subprotocol 2: Ultrastructure……Page 9
Subprotocol 3: The Golgi Method……Page 13
Subprotocol 4: Single-Cell Methods……Page 17
References……Page 23
Introduction……Page 27
Subprotocol 1: Differential Display: Practical Approach……Page 30
Subprotocol 2: Serial Analysis of Gene Expression (SAGE): Practical Approach……Page 39
Subprotocol 3: Digestion of cDNA with Anchoring Enzyme……Page 43
Subprotocol 4: Binding to Magnetic Beads……Page 44
Subprotocol 5: Addition of Linkers……Page 45
Subprotocol 6: Tag Release by Digestion with Tagging Enzyme……Page 46
Subprotocol 8: Ligation to Ditags……Page 47
Subprotocol 9: PCR Amplification of Ditags……Page 48
Subprotocol 10: Ditag Isolation……Page 49
Subprotocol 11: Concatemerisation……Page 51
Subprotocol 12: Cloning Concatemers……Page 52
Subprotocol 13: Sequencing……Page 53
References……Page 55
Introduction……Page 57
Subprotocol 1: IN SITU HYBRIDIZATION OF CULTURED NEURONS……Page 58
Subprotocol 2: In Situ Hybridization at the Electron Microscopic Level……Page 65
Subprotocol 3: Single-Cell Differential mRNA Display……Page 75
Subprotocol 4: Functional Implications of mRNAs in Dendrites and Axons: Metabolic Labeling of Isolated Neurites……Page 81
Subprotocol 5: Intracellular Injection of mRNA……Page 84
References……Page 87
Introduction……Page 89
Materials……Page 102
Procedure……Page 103
Results……Page 115
Troubleshoot……Page 117
Comments……Page 122
References……Page 125
Introduction……Page 127
Subprotocol 1: General Arrangement and Preparation for Electrophysiological Recording and Data Acquisition……Page 128
Subprotocol 2: Extracellular Recording……Page 134
Subprotocol 3: Intracellular Recording with Sharp Electrodes……Page 146
Subprotocol 4: Intracellular Recording and Tracer Injection……Page 158
Summary and Conclusions……Page 165
Supplier List……Page 166
References……Page 168
Introduction……Page 173
Materials……Page 176
Procedure……Page 180
Results……Page 187
Comments……Page 188
Applications……Page 189
References……Page 191
Introduction……Page 193
Subprotocol 1: Microiontophoresis……Page 194
Subprotocol 2: Micropressure Ejection……Page 207
References……Page 209
Introduction……Page 213
A Philosophy of Modelling……Page 214
Formulation of Dendritic Model……Page 216
The Discrete Tree Equations……Page 226
Formal Solution of Matrix Equations……Page 237
Solution of the Discretised Cable Equations……Page 242
Generating Independent and Correlated Stochastic Spike Trains……Page 245
Equivalent Cable Construction……Page 254
Generalised Compartmental Models……Page 268
The Spectral Methodology……Page 277
Spectral and Exact Solution of an Unbranched Tree……Page 284
Spectral and Exact Solution of a Branched Tree……Page 290
References……Page 299
Notation and Definitions……Page 302
Appendix I……Page 304
In Vitro Models……Page 307
En bloc Preparations……Page 310
Brain Slices……Page 311
Determinants of Ex Vivo Brain Function……Page 318
Conclusions……Page 324
References……Page 325
Introduction……Page 327
Materials……Page 329
Procedure……Page 330
Results……Page 333
Comments……Page 334
References……Page 337
Abbreviations……Page 338
Introduction……Page 339
Outline……Page 340
Materials……Page 341
Procedure……Page 343
Results……Page 351
Troubleshoot……Page 352
Comments……Page 354
References……Page 357
Suppliers……Page 359
Glossary……Page 360
Introduction……Page 361
Outline……Page 362
Materials……Page 364
Procedure……Page 368
Results……Page 371
References……Page 376
Introduction……Page 378
Subprotocol 1: Harvest and Implantation of PN Grafts into the CNS……Page 382
Subprotocol 2: Schwann Cell Guidance Channels……Page 391
References……Page 405
Introduction……Page 409
Outline……Page 410
Subprotocol 1: Dissection of Embryonic/Fetal CNS Tissue……Page 411
Subprotocol 2: Preparation of Tissue/Cells……Page 418
Subprotocol 3: Transplantation into Adults……Page 420
Subprotocol 4: Transplantation into Neonates……Page 424
Subprotocol 5: Transplantation into Embryos……Page 426
References……Page 430
Subprotocol 1: Architectonics……Page 435
Subprotocol 2: Hodology……Page 440
Subprotocol 3: Histochemical Methods: Neurochemistry and Functional Neurohistology, Including the Molecular Biology of Neuron……Page 445
Subprotocol 4: Silver-Impregnation Methods in the Peripheral Nervous System……Page 450
References……Page 453
Introduction……Page 457
Outline……Page 467
Procedure……Page 469
Results……Page 475
Troubleshoot……Page 478
Comments……Page 482
References……Page 483
Abbreviations……Page 484
Introduction……Page 485
Subprotocol 1: Multi-Unit Recording……Page 486
Subprotocol 2: Examples of Analysis and Results……Page 494
References……Page 498
Suppliers……Page 499
Abbreviations……Page 500
Introduction……Page 501
Part 1: Time Domain Analysis of Neuronal Spike Train Data……Page 503
Part 2: Frequency Domain Analysis……Page 508
Part 3: Correlation Between Signals……Page 514
Part 4: Multivariate Analysis……Page 525
Part 5: Extended Coherence Analysis – Pooled Spectra and Pooled Coherence……Page 528
Part 6: A Maximum Likelihood Approach to Neuronal Interactions……Page 531
Results……Page 533
Concluding Remarks……Page 537
References……Page 539
Introduction……Page 542
The Neural Code……Page 544
Basics of Information Theory……Page 548
Random Continuous Time Signals……Page 552
Information Transmission with Continuous Time Signals……Page 554
Information Transmission – The Method……Page 557
Summary – the Practical Procedure……Page 560
Upper Bound to Information Rate and Coding Efficiency……Page 561
The Muscle Spindle: Experimental and Simulation Results……Page 563
Conclusions……Page 567
References……Page 568
Theory……Page 570
Procedures and Results……Page 576
Comments……Page 582
References……Page 584
Abbreviations……Page 585
Introduction……Page 586
Part 1: Static Linear Systems……Page 589
Part 2: Dynamic Linear Systems……Page 591
Part 3: Physical Components of Linear Systems……Page 593
Part 4: Laplace and Z Transform……Page 602
Part 5: System Identification and Parameter Estimation……Page 608
Part 6: Modeling The Nervous System Control……Page 612
Part 7: Modeling Nonlinear Systems with Linear Systems Description Tools……Page 615
References……Page 621
Introduction……Page 623
Outline……Page 624
Procedure……Page 625
Results……Page 633
References……Page 635
Part 1: Stationary Methods……Page 637
Part 2: Nonstationary Analyses……Page 650
Part 3: Phase Space Reconstruction……Page 656
Postscript……Page 659
References……Page 661
Abbreviations……Page 662
Glossary……Page 663
Part 1: Theoretical Backgrounds……Page 665
Part 2: Procedure and Results……Page 671
Concluding Remarks……Page 681
References……Page 682
Introduction……Page 684
Network Architecture and Operation……Page 686
Model Neurons, Connections and Network Dynamics……Page 687
Learning and Generalization……Page 692
References……Page 698
Introduction……Page 700
Part 1: Muscle Anatomy and Physiology……Page 701
Part 2: Signal Acquisition and Materials……Page 711
Part 3: Registration Procedures……Page 716
Part 4: Signal Processing……Page 717
Part 5: Results……Page 723
Part 6: Troubleshooting……Page 728
Part 7: Special Applications……Page 730
Applications……Page 738
References……Page 740
Abbreviations……Page 747
Appendix……Page 748
Introduction……Page 751
Outline……Page 753
Procedure……Page 754
Results……Page 761
Troubleshoot……Page 766
Comments……Page 768
References……Page 769
Abbreviations……Page 770
Outline……Page 771
Materials……Page 772
Procedure……Page 773
Results……Page 779
Suppliers……Page 780
Introduction……Page 781
Procedure……Page 782
Results……Page 792
References……Page 793
Introduction……Page 797
Materials……Page 798
Procedure……Page 802
Results……Page 808
Comments……Page 810
References……Page 811
Abbreviations……Page 813
Introduction……Page 814
External Force Measurements Using Force Platforms……Page 815
External Movement Measurements Using High-Speed Video……Page 817
Surface Electromyography……Page 818
Part 2: Internal Biomechanics……Page 823
Muscle Force Measurements……Page 824
Joint Contact Pressure Measurements……Page 827
Movement Measurements……Page 829
Theoretical Determination of Internal Forces……Page 831
Future Considerations……Page 837
References……Page 838
Introduction……Page 842
Principal Component Analysis Made Simple……Page 843
Application to Gait Analysis……Page 847
Force Fields and the Problem of Degrees of Freedom……Page 857
References……Page 859
Introduction……Page 861
Subprotocol 1: Apparatus and Mechanisms……Page 862
Subprotocol 2: EMG Recording and Analysis Protocol……Page 866
Applications……Page 868
References……Page 881
General Introduction……Page 884
Introduction……Page 887
Methods……Page 892
Introduction……Page 921
Imaging of Population Activity……Page 925
Methods……Page 933
Targeted Injection of Tracers into Pre-Defined Functional Domains……Page 948
Electrical Recordings from Pre-Defined Functional Domains……Page 949
Combining Micro-Stimulation and Optical Imaging……Page 950
Conclusions and Outlook……Page 951
References……Page 952
Introduction……Page 961
Subprotocol 1: EEG Recording……Page 964
Subprotocol 2: EEG Signal Analysis……Page 966
Subprotocol 3: Secondary EEG Analysis……Page 978
Subprotocol 4: Presentation of Results……Page 979
References……Page 981
General Introduction……Page 986
Part 1: Review of EP Processing Methods……Page 987
Processing Methods……Page 988
Part 2: Extraction of Trial-Varying EPS……Page 990
Layer 1: Unsupervised Learning Structure……Page 992
Layer 2: Decomposition of EP Waveform……Page 1001
Conclusion……Page 1010
References……Page 1011
Introduction……Page 1013
Materials……Page 1018
Procedure……Page 1022
Results……Page 1033
Troubleshoot……Page 1036
Applications……Page 1038
References……Page 1039
Suppliers……Page 1042
Introduction……Page 1043
Technical Aspects of MRI Data Acquisition……Page 1045
Data Evaluation and Visualization……Page 1051
Physiologic Aspects of Brain Activation……Page 1057
Paradigm Design……Page 1065
References……Page 1069
Introduction……Page 1071
Outline……Page 1075
Materials……Page 1076
Procedure……Page 1079
Results……Page 1081
Troubleshoot……Page 1083
References……Page 1084
Suppliers……Page 1085
Introduction……Page 1086
Technical Requirements and Methods……Page 1093
Applied MRS – Single-Voxel 1 H MRS……Page 1102
Results: Neurospectroscopy……Page 1106
Conclusions……Page 1124
References……Page 1126
Glossary……Page 1129
General Introduction……Page 1136
Stereotaxic Surgery on Small Rodents……Page 1138
Microdialysis Experiments on Awake Rats……Page 1142
Part 2: Implantable Sensors……Page 1145
Measuring Extracellular K + Ions by ISM……Page 1146
Amperometric Electrodes……Page 1149
Measurement of Dopamine by Chronoamperometry……Page 1150
Biosensors……Page 1152
Biosensor for Glucose……Page 1154
Cortical Cup Technique……Page 1157
Microdialysis……Page 1158
Determination of Dopamine Release by Microcolumn Liquid Chromatography with Electrochemical Detection (LCEC)……Page 1159
Determination of Serotonin in Microdialysis Samples by LCEC……Page 1161
Determination of Aspartate and Glutamate in Microdialysis Samples by HPLC with Fluorescence Detection……Page 1163
Determination of GABA in Microdialysis Samples by HPLC with Fluorescence (FL) and Electrochemical (EC) Detection……Page 1165
Determination of Physiological Amino Acids in Microdialysis Samples by Microcolumn HPLC with Gradient Elution and Fluorescence (FL) Detection……Page 1167
Determination of Acetylcholine in Microdialysis Samples by Microbore Liquid Chromatography/Electrochemistry on Peroxidase Redox Polymer Coated Electrodes……Page 1172
Microdialysis in the Human Brain……Page 1175
References……Page 1178
Suppliers……Page 1184
Introduction……Page 1186
Procedure……Page 1187
Troubleshoot……Page 1193
Suppliers……Page 1196
Introduction……Page 1198
Outline……Page 1200
Methods and Procedures……Page 1201
Experimental Examples……Page 1216
Concluding Remarks……Page 1224
References……Page 1225
Suppliers……Page 1227
Introduction……Page 1229
Methods……Page 1230
The Neurobehavioral Examination……Page 1233
Comments: Generalizing from Behavioral Analysis……Page 1255
References……Page 1257
Introduction……Page 1262
Outline……Page 1263
What is a Signal?……Page 1264
Noise……Page 1265
Amplification and Amplifiers……Page 1268
Fundamentals of Filtering and Filters……Page 1272
Digital or Analog Processing?……Page 1278
A/D Conversion……Page 1279
Implementations……Page 1281
Data Processing……Page 1283
Data Display……Page 1287
Part 5: Storage and Backup……Page 1290
Concluding Remarks……Page 1292
References……Page 1293
Glossary……Page 1294