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Guide to Research Techniques in Neuroscience

ISBN-10: 0123748496
ISBN-13: 9780123748492
Edition: 2010
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Description: Neuroscience is by definition a multidisciplinary field: some scientists study genes and proteins at the molecular level while others study neural circuitry. A single topic such as the auditory system can be studied using techniques from genetics,  More...

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Book details

Copyright year: 2010
Publisher: Elsevier Science & Technology Books
Publication date: 9/22/2009
Binding: Paperback
Pages: 408
Size: 6.00" wide x 9.00" long x 0.75" tall
Weight: 1.430
Language: English

Neuroscience is by definition a multidisciplinary field: some scientists study genes and proteins at the molecular level while others study neural circuitry. A single topic such as the auditory system can be studied using techniques from genetics, imaging, biochemistry, or electrophysiology. A young scientist must learn how to read the primary literature and then develop their own experiments. This book offers that scientist an overview of mainstream research techniques, provides guidelines on how to choose one technique over another, offers tips on analyzing data, and provides a list of references for additional detailed study. This book can also assist an experienced scientist understand published studies conducted outside their own subfield.*Written by Stanford University graduate students in neuroscience to provide a "hands-on" approach for other neuroscience graduate students *Techniques within one field will be compared so that user can select best technique for their experiment *Chapters include references (key articles, books, protocols) for additional detailed study *Data Analysis boxes in each chapter help with data interpretation and offer guidelines on how best to represent results *"Walk-through" boxes guide students through the experiment step-by-step

Matt Carter, PhD, is currently Assistant Professor of Biology at Williams College. His previous position was as a post-doctoral fellow in Richard Palmiter's lab at the University of Washington using optogenetic techniques to study neural circuitry. He has authored the first edition of this book (Elsevier, 2009) as well as Designing Science Presentations: A Visual Guide to Figures, Papers, Slides, Posters, and More (Elsevier, 2012). He was the awardee of Stanford University's Walter J. Gores Award for Excellence in Teaching, and two-time recipient of the Stanford School of Medicine's Excellence in Teaching Award. He currently teaches courses at Williams in both Topics in Neuroscience as well as Neural Systems and Circuits. Former: carterme@u.washington.edu

Preface
Foreword
Introduction
Whole Brain Imaging
Structural Brain Imaging Techniques
Cerebral Angiography
Computerized Tomography (CT)
Magnetic Resonance Imaging (MRI)
Diffusion Magnetic Resonance imaging (diffusion MRI)
Functional Brain Imaging Techniques
Functional Magnetic Resonance Imaging (FMRI)
Positron Emission Tomography (PET)
Single-Proton Emission Computerized Tomography (SPECT)
Electroencephalography (EEC)
Magnetoencephalography (MEG)
Optical Imaging
Functional Imaging Experimental Design and Analysis
Planning the Experiment
Conducting the Experiment
Manipulating Neural Activity during an Experiment
Postexperimental Data Analysis
Conclusion
Suggested Reading and References
Animal Behavior
Considerations for Choosing and Performing a Behavioral Assay
Choosing an Appropriate Model Organism
Choosing an Appropriate Behavioral Paradigm
Variability in Individuals
Using Animal Behavior as a Model for Human Behavior
Rodent Behavioral Paradigms
Locomotor Activity
Motor Coordination and Balance
Sensory Function
Nociception
Spatial Learning and Memory
Nonspatial Learning and Memory
Social Behaviors
Anxiety
Depression
Drosophila Behavioral Paradigms
Locomotor Behavior
Flight
Sensory Function
Learning and Memory
Social Behaviors
C. elegans Behavioral Paradigms
Locomotor Behavior
Sensory Behavior
Nonhuman Primate Behavioral Paradigms
Conclusion
Suggested Reading and References
Stereotaxic Surgeries and In Vivo Techniques
Stereotaxic Surgeries
Stereotaxic Surgeries in Rodents
Stereotaxic Surgeries in Nonhuman Primates
Implants for Long-Term Access to the Brain
Sealable Chambers
Cannulae
Cranial Windows
Measuring Neural Activity In Vivo
Electrophysiology
Fluorescent Activity Indicators
Measuring Neurochemistry in Vivo
Microdialysis
Voltammetry and Amperometry
Manipulating the Brain In Vivo
Physical Manipulation
Pharmacological Manipulation
Electrical Manipulation
Genetic Manipulation
Conclusion
Suggested Reading and References
Electrophysiology
A Brief Review of the Electrical Properties of Neurons
The Electrophysiology Rig
Types of Electrophysiology Recordings
Extracellular Recording
Intracellular Recording
Patch Clamp Techniques
Electrophysiology Tissue Preparations
In Vitro Recordings
In Vivo Recordings
Methods of Manipulating Neurons During Electrophysiology Experiments
Conclusion
Suggested Reading and References
Microscopy
Essential Principles of Microscopy
Fundamental Parameters in Microscopy
The Design of a Compound Microscope
The Design of a Stereomicroscope
Light Microscopy
Fluorescence Microscopy
Epifluorescent Microscopy
Confocal Microscopy
Two-Photon Microscopy
Total Internal Reflection Fluorescence (TIRF) Microscopy
Electron Microscopy
Transmission Electron Microscopy (TEM)
Scanning Electron Microscopy (SEM)
Electron Tomography (ET)
Preparing and Interpreting Microscopy Data
Image Processing
Interpreting Images
Conclusion
Suggested Reading and References
Visualizing Nervous System Structure
Tissue Preparation
Fixation
Embedding
Sectioning
Visualizing Morphology
Cell Body Stains
Fiber Stains
Golgi Stain
Intracellular and Juxtacellular Labeling
Fluorescent Labels
Chromogenic/Colorimetric Labels
Radioactive Labels
Cold Labels
Visualizing Gene and Protein Expression
In Situ Hybridization
Immunohistochemistry
Enzymatic Histochemistry
Reporter Genes
Visualizing Circuitry
Anterograde and Retrograde Tracers
Transsynaptic Labeling
Conclusion
Suggested Reading and References
Visualizing Nervous System Function
Static Markers of Activity
Assaying Neural Activity in Fixed Tissue
Assaying Cellular Function in Fixed Tissue
Visualizing Neural Activity
Imaging Voltage
Imaging Calcium
Imaging Synaptic Transmission
Optically Manipulating Neural Activity
Stimulation through Uncaging of Molecules
Light-Activated Channels
Visualizing Protein Function
Time-Lapse Imaging with Reporter Genes
Fluorescence Resonance Energy Transfer (FRET)
Bimolecular Fluorescence Complementation (BiFC)
Fluorescence Recovery after Photo bleaching (FRAP)
Photoactivation and Photoconversion
Optically Manipulating Protein Function
Photoactivation/Photo-uncaging
Photoinactivation
Conclusion
Suggested Reading and References
Identifying Genes and Proteins of Interest
A Brief Review of Genes and Proteins
The Central Dogma of Molecular Biology
DNA
Transcription
Translation
Genetic Screens
Forward Genetic Screen
Reverse Genetic Screen
In Silico Screens
Blast
Ensembl
Molecular Screens
cDNA Microarray Screen
RNAi Screen
Conclusion
Suggested Reading and References
Molecular Cloning and Recombinant DNA Technology
Isolating DNA Fragments
Restriction Enzymes
Polymerase Chain Reaction (PCR)
Cloning DNA
Vectors
Ligation
Transformation
Purifying DNA
Isolation and Characterization of DNA Fragments Using Gel Electrophoresis
Purifying DNA from Host Cells
Identifying DNA
DNA Sequencing
Nucleic Acid Hybridization Techniques
Conclusion
Suggested Reading and References
Gene Delivery Strategies
Physical Gene Delivery
Microinjection
Electroporation
Biolistics
Chemical Gene Delivery
Calcium Phosphate Transfection
Lipid Transfection
Viral Gene Delivery
Adenovirus
Adeno-Associated Virus (AAV)
Lentivirus
Herpes Simplex Virus (HSV)
Conclusion
Suggested Reading and References
Making and Using Transgenic Organisms
Transgenes
Reporter Genes
Genes Used to Ablate Neurons
Genes Used to Measure Neural Activity
Genes Used to Manipulate Neural Activity
Genes Used to Disrupt Endogenous Gene Function
Overexpression or Misexpression of Endogenous Genes
The Transgenic Construct
Binary Transgenic Systems
The Gal4/UAS System
The Cre/Lox System
The Flp/Frt System
TheTet-off/Tet-on System
Making Transgenic Organisms
Making Transgenic Mice
Making Transgenic Flies
Making Transgenic Worms
Making Other Transgenic Organisms
Conclusion
Suggested Reading and References
Manipulating Endogenous Genes
Genetic Targeting
Knockout
Knockin
Conditional Knockout
Disrupting Gene Products
RNA Interference (RNAi)
Morpholtnos
Dominant Negatives
Conclusion
Suggested Reading and References
Cell Culture Techniques
Cell Culture Equipment and Reagents
Equipment
Culture Media
Immortalized Cell Lines
Primary Cell and Tissue Culture
Dissociated Cell Cultures
Slice Cultures
Explant Cultures
Stem Cell Cultures
Embryonic Stem Cells
Neural Stem Cells
Induced Plurrpotent Stem Cells
Manipulating Cells in Culture
Transfection
Coculture Systems
Pharmacology
Antibody Interference
Conclusion
Suggested Reading and References
Biochemical Assays and Intracellular Signaling
Introduction to Signal Transduction and Intracellular Signaling
Fundamental Tools for Studying Proteins
Making and Using Antibodies
Purifying Proteins
Immunoprecipitation (IP)
Investigating Protein Expression
Western Blot (WB)
Enzyme-Linked Immunosorbent Assay (ELISA)
Radioimmunoassay (RIA)
Immunohistochemistry (IHC)
Immunoelectron Microscopy (IEM)
Reporter Proteins
Investigating Protein-Protein Interactions
Coimmunoprecipitation (Co-IP)
Protein Affinity Chromatography
Yeast Two-Hybrid Assay
Investigating Posttranslational Modifications
PTM-Specific Assays
PTM-Specific Antibodies
Investigating Protein-DNA Interactions
Electrophoretic Mobility Shift Assay (EMSA)
Chromatin Immunoprecipitation (ChIp)
Luciferase Assay
Conclusion
Suggested Reading and References
Glossary
Index

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