Handbook of Neurobehavioral Genetics and Phenotyping

Valter Tucci graduated in Psychology in 2000, at the University of Padua, studying the cardiovascular changes associated with NREM and REM sleep states in humans. During his Ph.D studies he investigated the physiological and cognitive traits of narcoleptic patients. Then he moved to Boston where he studied sleep physiology and cognitive processes in rhesus monkeys and zebrafish. In 2003, he moved to Oxford (UK). At this time, he switched to work on behavioural neurogenetics. He was awarded a Career Development Fellowship by the MRC Mammalian Genetics Unit in Harwell and was then promoted to the post of Investigator Scientist two years later. Valter Tucci is currently Team Leader of the Neurobehavioural Group at the Italian Institute of Technology (IIT). His research focuses on analysis of the effects that genetic and epigenetic mechanisms exert on sleep and cognition.

List of Contributors xix

Preface xxv

1 Genetic Screens in Neurodegeneration 1
Abraham Acevedo Arozena and Silvia Corrochano

Introduction 1

The Genetics of Neurodegenerative Disorders 2

Neurodegeneration Disease Models 4

Genetic Approaches to Discover New Genes Related to Neurodegeneration Using Disease Models 5

Saccharomyces cerevisiae 6

Caenorhabditis elegans 8

Drosophila melanogaster 9

Danio rerio 10

Mus musculus 11

Human Cellular Models and Post-mortem Material 14

The Future 14

Acknowledgments 15

References 15

2 Computational Epigenomics 19
Mattia Pelizzola

Background 19

Profiling and Analyzing the Methylation of Genomic DNA 19

Experimental Methods 20

Data Analysis 20

Array-based Methods 20

Sequencing-based Methods 20

Profiling and Analyzing Histone Marks 26

Experimental Methods 26

Data Analysis 27

Issues of Array-based Methods 27

Issues of NGS-based Methods 27

Integration with Other Omics Data 31

Chromatin States 32

Unraveling the Cross-talk Between Epigenetic Layers 33

References 33

3 Behavioral Phenotyping in Zebrafish: The First Models of Alcohol Induced Abnormalities 37
Robert Gerlai

Introduction 37

Alcohol Related Human Disorders: A Growing Unmet Medical Need 37

Unraveling Alcohol Related Mechanisms: The Importance of Animal Models 38

Face Validity: The First Step in Modeling a Human Disorder 39

Acute Effects of Alcohol in Zebrafish: A Range of Behavioral Responses 39

Chronic Alcohol Exposure Induced Behavioral Responses in Zebrafish 41

Effects of Embryonic Alcohol Exposure 42

Behavioral Phenotyping: Are We There Yet? 46

Assembling the Behavioral Test Battery 49

Concluding Remarks 50

References 50

4 How does Stress Affect Energy Balance? 53
Maria Razzoli, Cheryl Cero, and Alessandro Bartolomucci

Introduction 53

Stress 54

Energy Balance and Metabolic Disorders 55

Pro-adipogenic Stress Mediators 57

Pro-lipolytic Effect of Stress Mediators 57

How does Stress Affect Energy Balance? 57

Animal Models of Chronic Stress and their Impact on Energy Balance 58

Physical and Psychological (non-social) Chronic Stress Models 58

Mild Chronic Pain Models - Mild Tail Pinch, Foot Shock 58

Thermal Models - Cold and Heat Stress 64

Chronic Mild Stress Models: Chronic Mild Stress, Chronic Variable Stress, etc. 64

Restraint or Immobilization 65

Chronic Social Stress Models 66

Social Isolation, Individual Housing 66

Unstable Social Settings 66

Visible Burrow System 67

Intermittent Social Defeat (Resident/Intruder Procedure) 67

Chronic Psychosocial Stress, Sensory Contact, and Chronic Defeat stress 68

Stress, Recovery, and Maintenance: Insights on Adaptive and Maladaptive Effects of Stress 69

Molecular Mechanisms of Stress-Induced Negative and Positive Energy Balance 70

Serotonin (5-hydroxytryptamine, 5HT) 71

Orexin 71

Neuropeptide Y (NPY) 72

Ghrelin and Growth Hormone Secretagogue Receptor (GHSR) 72

Glucagon like Peptide 1 (GLP1) 73

Leptin 73

Amylin 74

Norepinephrine and ß3-Adrenergic Receptor 74

Conclusion 74

References 75

5 Interactions of Experience-Dependent Plasticity and LTP in the Hippocampus During Associative Learning 91
Agnès Gruart, Noelia Madroñal, María Teresa Jurado-Parras, and José María Delgado-García

Introduction: Study of Learning and Memory Processes in Alert Behaving Mammals 91

Changes in Synaptic Strength During Learning and Memory 92

Classical Conditioning 92

Instrumental Conditioning 95

Changes in Synaptic Strength Evoked by Actual Learning can be Modified by Experimentally Evoked Long-term Potentiation 96

Other Experimental Constraints on the Study of the Physiological Basis of Learning Processes 100

Factors Modifying Synaptic Strength (Environment, Aging, and Brain Degenerative Diseases) 101

Different Genetic and Pharmacological Manipulations Able to Modify Synaptic Strength 103

Functional Relationships Between Experimentally Evoked LTP and Associative Learning Tasks 106

Future Perspectives 108

Context and Environmental Constraints 108

Other Forms of Learning and Memory Processes 109

Cortical Circuits and Functional States During Associative Learning 109

References 110

6 The Genetics of Cognition in Schizophrenia: Combining Mouse and Human Studies 115
Diego Scheggia and Francesco Papaleo

Background 115

Genetics of Schizophrenia 116

Cognitive (dys)functions in Schizophrenia 117

Translating Cognitive Symptoms in Animal Models 119

Executive Control 120

Performance in Schizophrenia 122

Animal Models 124

Working Memory 125

Performance in Schizophrenia 126

Animal Models 127

Control of Attention 128

Performance in Schizophrenia 130

Animal Models 130

Concluding Remarks 131

References 132

7 The Biological Basis of Economic Choice 143
David Freestone and Fuat Balci

Introduction 143

Translating from Animals to Humans 144

Reinforcement Learning in the Brain 145

Subjective Value 146

The Midbrain Dopamine System Updates Value 147

From Stimulus Value to Action Value 150

Model Based Learning 150

The Prefrontal Cortex Encodes Value 152

The Basal Ganglia Selects Actions 153

Optimal Decisions: Benchmarks for the Analysis of Choice Behavior 155

The Drift Diffusion Model 157

Temporal Risk Assessment 158

Timed-response Inhibition for Reward-rate Maximization 160

Timed Response Switching 163

Temporal Bisection 164

Numerical Risk Assessment 166

Rodent Version of Balloon Analog Risk Task 167

Conclusion 167

Acknowledgments 168

References 168

8 Interval-timing Protocols and Their Relevancy to the Study of Temporal Cognition and Neurobehavioral Genetics 179
Bin Yin, Nicholas A. Lusk, and Warren H. Meck

Introduction 179

Application of a Timing, Immersive Memory, and Emotional Regulation (Timer) Test Battery 190

Neural Basis of Interval Timing 191

What Makes a Mutant Mouse "Tick"? 193

Proposal of a TIMER Test Battery and Its Application in Reverse Genetics 199

Behavioral Test Battery Applications in Forward Genetics 202

Order of Behavioral Tasks 205

Location and Time of Behavioral Testing 205

Summary 205

References 206

Appendix I 226

Limitations of the individual-trials analysis for data obtained in the peak-interval (PI) procedure 226

9 Toolkits for Cognition: From Core Knowledge to Genes 229
Giorgio Vallortigara and Orsola Rosa Salva

Introduction 229

Core Knowledge: The Domestic Chick as a System Model 230

Numerical Competence 230

Physical Properties 230

Geometry of Space 232

Animate Agents 232

A Comparative Perspective on the Genetic and Evolutionary Bases of Social Behavior 236

From Social Experience to Genes 239

From Genes to Social Behavior 241

Future Directions 243

Conserved Mechanisms for Social Core Knowledge 243

Interactions Between Experience and Genomic Information 243

Neurogenetic Basis of Social Predispositions 243

Epigenetics and the Development of the Social Brain 244

Spatial Cognition, Another Promising Core-knowledge Domain 244

References 245

10 Quantitative Genetics of Behavioral Phenotypes 253
Elzbieta Kostrzewa and Martien J.H. Kas

Human Studies of Quantitative Traits 253

Mouse Studies of Quantitative Traits 254

Classical Inbred Mice 254

Quantitative Trait Loci (QTL) Analysis 254

Knock-out (KO) Mouse Lines 256

Use of Mice as Animal Model for Complex Human Traits 257

Comparative Genomic Approaches 257

Evolutionarily Conserved Behavioral Phenotypes 257

Physical Activity - Definitions and Methods of Phenotypic Measurement 258

Current Results of Quantitative Genetic Basis of PA in Humans 259

Current Results of Quantitative Genetic Basis of PA in Mice 260

KO Studies 260

QTL Studies 261

An Overlap of Genetic Findings Between the Species 261

Conclusions 265

References 265

11 Behavioral Phenotyping in Genetic Mouse Models of Autism Spectrum Disorders: A Translational Outlook 271
Maria Luisa Scattoni, Caterina Michetti, Angela Caruso, and Laura Ricceri

Introduction 271

Measuring Social behavior in ASD Mouse Models 272

Social Interaction Tests 272

Male-female 277

Female-female 278

Male-male 278

Social-approach 279

Sociability Test Phase 280

Social Novelty 280

Social Recognition 280

Repetitive Behavior 281

Motor Stereotypies 281

Restricted Interests 281

Behavioral Inflexibility 282

Behavioral Tests Targeting other ASD Symptoms 282

Anxiety 282

Epilepsy 283

Behavioral Phenotyping in ASD Mouse Pups 283

Future Directions: ASD Mouse Models as a Resource for Gene-environment Interaction Studies 284

Acknowledgments 285

References 285

12 Genetics of Human Sleep and Sleep Disorders 295
Birgitte Rahbek Kornum

The Mystery of Human Sleep 295

Sleep is Essential for Mammalian Life 295

The Function of Sleep 296

Extended Wakefulness Induces Sleep 296

Homeostatic and Circadian Regulation of Sleep and Wake 297

Adenosine and Sleep Homeostasis 298

Resistance to Sleep Loss is a Stable Phenotype 299

Genetic Markers of Response to Sleep Loss 299

A Unique Activity Pattern Characterizes the Sleeping Brain 300

Sleep Stages and Sleep Cycles 300

Genetics of the Human Sleep Electroencephalography 301

Normal Sleep Architecture is Lost in Fatal Familial Insomnia 303

Circadian Regulation of Sleep and Associated Disorders 304

Circadian Regulation of Sleep 304

Molecular Regulation of the Circadian Clock 305

The Central Circadian Clock is Entrained By Light 306

Circadian Rhythm Sleep Disorders 307

Advanced Sleep Phase Syndromes 307

Delayed Sleep Phase Syndromes 308

Short Sleep Times in Healthy Individuals 308

Destabilization of Sleep States and Narcolepsy 309

Normal Regulation of Sleep Architecture 309

Wakefulness is Associated with Cortical Activation 309

The Preoptic Area Contains Sleep-promoting Neurons 309

Mutual Inhibition Regulates Transitions Between Wake and Sleep 310

Regulation of REM Sleep 311

Narcolepsy, A Disorder of Wakefulness and REM Sleep 311

Narcolepsy with Cataplexy is Caused By Hypocretin Deficiency 312

Autoimmunity Toward Hypocretin Neurons 312

Genetic Evidence Supports the Autoimmune Hypothesis of Narcolepsy 313

Restless Legs Syndrome, A Developmental Sleep Disorder 314

Restless Legs Syndrome, A Mysterious Urge to Move 314

Restless Legs Syndrome and Dopamine Disturbances 315

Iron Deficiency Exacerbates RLS Symptoms 315

Genetic Studies Suggest Developmental Defects 316

Unresolved Issues and Future Perspectives 316

What is the Molecular and Neuroanatomical Basis for the Ultradian Rhythm of NREM-REM Sleep? 317

What is the Genetic Basis for Individual Variation in Complex Sleep Features such as Sleep Spindles and K-Complexes? 317

What is the Basis for the Individual Differences in Resistance to Sleep Loss? 317

Are Homeostatic and Circadian Mechanisms Genuinely Independent or Are They Intimately Linked? 318

What Controls the Molecular and Anatomical Diversity of Sleep Regulatory Networks Across Species? 318

References 319

13 The Endocannabinoid System in the Control of Behavior 323
Edgar Soria-Gomez, Mathilde Metna, Luigi Bellocchio, Arnau Busquets-Garcia, and Giovanni Marsicano

Introduction 323

Cannabinoid Effects and Endocannabinoid Functions 324

Role of the ECS in Memory Processes 325

Memory: General Background 325

Role of the ECS in Synaptic Plasticity 325

Memory Impairment Produced by Exogenous Cannabinoids 326

Cannabinoid Regulation of Memory: Neurobiological Mechanisms 327

Role of the ECS in Fear Processes 329

Fear: General Background 329

The ECS as an Endogenous Regulator of Fear Responses 331

Cannabinoid Regulation of Fear: Neurobiological Mechanisms 332

Implication of the ECS in Fear Coping Behaviors 333

Role of the ECS in Feeding Behavior 336

Feeding Behavior: General Background 336

The ECS as an Endogenous Regulator of Feeding Behavior 337

The ECS and Food Reward Circuits 338

The ECS in the Hypothalamic Appetite Network 338

The ECS in the Caudal Brainstem and Gastrointestinal Tract 340

Bimodal Control of Stimulated Food Intake by the ECS in the Brain 341

Paraventricular Hypothalamus Versus Ventral Striatum in Hypophagia induced by the ECS 342

The Olfactory Bulb and the Hyperphagic Action of the ECS 342

Conclusions 343

References 344

14 Epigenetics in Brain Development and Disease 357
Elisabeth J. Radford, Anne C. Ferguson-Smith, and Sacri R. Ferrón

Introduction 357

Epigenetics and Neurodevelopment 358

Histone Modifications 358

DNA Methylation 361

Hydroxymethylation 364

Genomic Imprinting 364

Non-coding RNAs 365

Neurodevelopmental Disorders with an Epigenetic Basis 366

Rett Syndrome 366

Coffin-Lowry Syndrome 367

Rubinstein-Taybi Syndrome 367

Alpha-thalassemia Mental Retardation Syndrome 367

Imprinted Neurodevelopmental Disorders 368

Trinucleotide Repeat Disorders 368

Fragile X Syndrome 370

Friedreich's Ataxia 370

Myotonic Dystrophy 371

Huntington's Disease (HD) 371

Epigenetics of Neurodegenerative Disorders 372

Parkinson´s Disease (PD) 372

Alzheimer´s Disease (AD) 373

The Impact of the Environment on the Epigenome 374

Epigenetic Therapy in Neurodevelopment 375

Untargeted Treatment 375

Targeted Epigenetic Modulation 377

Concluding Remarks 377

Acknowledgments 377

References 378

15 Impact of Postnatal Manipulations on Offspring Development in Rodents 395
Diego Oddi, Alessandra Luchetti, and Francesca Romana D'Amato

Introduction 395

Early Postnatal Environment in Laboratory Altricial Rodents 396

Rodents' Responses to Postnatal Environment and Early Manipulations 397

Assessing Pups' Responses to Postnatal Environment and Early Manipulation 397

Neonatal Ultrasonic Calls: Isolation-induced Vocalizations and Maternal Potentiation 397

Searching for Social Contact: Homing and Huddling Behaviors 398

Early-life Environment and Stress-Response 398

Separation from the Mother 399

Mother's Stress 400

The Cross-fostering Paradigm 401

Repeated Cross-fostering as a Model of Early Maternal Environment Instability 403

Environmental Enrichment 405

Conclusions 406

References 407

16 Exploring the Roles of Genetics and the Epigenetic Mechanism DNA Methylation in Honey Bee (Apis Mellifera) Behavior 417
Christina M. Burden and Jonathan E. Bobek

Introduction 417

Genetics of Adult Honey Bee Biology and Behavior 418

Nurse to Forager Transition 418

Forager Preference 420

Techniques for Investigating the Genetic Bases of Behavior 420

QTL Mapping 421

RNA Techniques 421

Microarrays 421

RNA Sequencing 422

Experimentally Modulating the Genes Correlated with Specific Behaviors to Test Causality 422

DNA Methylation and Honey Bee Behavior 423

Honey Bee DNA Methylation Machinery and Genome-Wide Patterns 423

DNA Methylation and Task Specialization 424

DNA Methylation and Memory Consolidation 425

Techniques for Detecting and Assaying DNA Methylation 426

The Technological Bases for Most DNA Methylation Assays 426

Methylation-specific Restriction Endonucleases 426

Protein-mediated Precipitation of Methylated DNA 428

Bisulfite Conversion 428

Assaying Single CpGs, Short Sequences, and Target Regions 429

Analyzing Genome-wide DNA Methylation Patterns: Microarray-based Methodologies 431

Analyzing Genome-wide DNA Methylation Patterns: Sequencing-based Methodologies 432

Techniques for Manipulating DNA Methylation 434

Pharmacological Manipulation of DNA Methylation 434

RNA Interference as a DNMT Blockade 434

Concluding Remarks and Future Perspectives 435

References 436

17 Genetics and Neuroepigenetics of Sleep 443
Glenda Lassi and Federico Tinarelli

Defining Sleep 443

Sleep is Genetically Determined 445

EEG and Heritable Traits 445

Sleep Disorders and Genes 446

Sleep and Gene Expression 447

Epigenetics 448

DNA Methylation 450

Posttranslational Modifications (PTMs) 450

RNA interference 452

Neuroepigenetics 453

Two Neurodevelopmental Disorders with Opposing Imprinting Profiles and Opposing Sleep Phenotypes 453

Neuroepigenetics of Sleep 454

Fruit Fly 454

Rodent Models 454

Human Beings 456

Sleep and Parent-of-origin Effects 458

Conclusions 460

References 460

18 Behavioral Phenotyping Using Optogenetic Technology 469
Stephen Glasgow, Carolina Gutierrez Herrera, and Antoine Adamantidis

Introduction 469

Microbial Opsins 470

Fast Excitation Using Channelrhodopsin-2 and Its Variants 470

Fast Optical Silencing 474

Alternative strategies for cell-type specific modulation of neural activity 476

Targeting systems 476

Light Delivery in the Animal Brain 478

Recording Light-evoked Neuronal Activity 479

Behavioral Phenotyping 479

In-vivo Optogenetics: Defining Circuits 480

Perspectives 484

Acknowledgments 484

References 484

19 Phenotyping Sleep: Beyond EEG 489
Sibah Hasan, Russell G. Foster, and Stuart N. Peirson

Sleep Research 489

Phenotyping Sleep in Humans 490

Introduction 490

Actigraphy 490

Cardiorespiratory Signals 491

EEG 492

Phenotyping Sleep in Animal Models 494

Introduction 494

EEG 494

Introduction 494

Tethered EEG 496

Telemetered EEG 496

NeuroLogger EEG 498

Beyond EEG 498

Infrared Beam Break 499

Movement Based on Implanted Magnets 499

Piezo-electric Sensors 499

Video Tracking 500

Future Perspectives 501

Acknowledgements 502

References 502

20 A Cognitive Neurogenetics Screening System with a Data-Analysis Toolbox 507
C.R. Gallistel, Fuat Balci, David Freestone, Aaron Kheifets, and Adam King

Introduction 507

Mechanisms, Not Procedures 508

Functional Specificity 508

No Group Averages 509

Physiologically Meaningful Measures 509

Importance of Large-scale Screening and Minimal Handling 511

Utilizable Archived Data with Intact Data Trails 511

The System 512

The Toolbox 513

Core Commands 516

Powerful Graphics Commands 517

Results 518

Summary 523

References 524

21 Mapping the Connectional Architecture of the Rodent Brain with fMRI 527
Adam J. Schwarz and Alessandro Gozzi

Introduction 527

MRI Mapping of Functional Connectivity in the Rodent Brain 528

Networks of Functional Covariance 528

Connectivity of Neurotransmitter Systems 529

The Dopaminergic System 529

The Serotonergic System 531

Resting State BOLD fMRI 532

Connectivity Networks of the Rodent Brain 533

Do Rodent Brains have a Default Mode Network? 536

Use of Anesthesia and Other Methodological Considerations 539

Transgenic Models: Genetic Manipulation of Functional Connectivity Patterns 541

Future Perspectives 543

References 545

22 Cutting Edge Approaches for the Identification and the Functional Investigation of miRNAs in Brain Science 553
Emanuela de Luca, Federica Marinaro, Francesco Niola, and Davide De Pietri Tonelli

Introduction 553

History 553

Biology and Functions in the Brain 553

Identification of Novel MicroRNAs in the Brain 555

miRNA Extraction and Purification 556

miRNA Cloning 556

Computational Identification of Novel miRNAs 557

RNA Sequencing (RNA-Seq) 558

miRNA expression analysis in the brain 559

miRNA profiling 559

Analysis of miRNA Expression in Tissue 559

Target Identification 560

Computational Identification of Targets 561

Proteomics 561

RISC-associated miRNA Targets 562

RNomics 563

miRNA Manipulation/Target Validation 565

miRNA Inhibition 565

miRNA Over-expression 566

Target Validation 567

New Frontiers in Small RNA-based Technologies to Cure Nervous System Deficits 567

Use of miRNAs in Gene Therapy 567

Use of miRNAs in Gene Therapy in the Brain Requires Improved Delivery Strategies 571

Conclusion and Perspectives 572

Are Circulating miRNAs Novel Biomarkers for Brain Diseases? 572

Use of miRNAs in Cell Reprogramming Technology 573

Are miRNAs Just the "Tip of the Iceberg"? Emerging Classes of Noncoding RNAs and Novel Scenarios 574

Acknowledgments 575

Competing Financial Interests 575

References 575

Index 585