In this, the Post-Genomic Age, our knowledge of biological systems continues to expand and progress. As the research becomes more focused, so too does the data. Genomic research progresses to proteomics and brings us to a deeper understanding of the behavior and function of protein clusters. And now proteomics gives way to neuroproteomics as we begin to unravel the complex mysteries of neurological diseases that less than a generation ago seemed opaque to our inquiries, if not altogether intractable.

Edited by Dr. Oscar Alzate, Neuroproteomics is the newest volume in the CRC Press Frontiers of Neuroscience series. With an extensive background in mathematics and physics, Dr. Alzate exemplifies the newest generation of biological systems researchers. He organizes research and data contributed from all across the world to present an overview of neuroproteomics that is practical and progressive.

Bolstered by each new discovery, researchers employing multiple methods of inquiry gain a deeper understanding of the key biological problems related to brain function, brain structure, and the complexity of the nervous system. This in turn is leading to new understanding about diseases of neurological deficit such as Parkinson’s and Alzheimer’s.

Approaches discussed in the book include mass spectrometry, electrophoresis, chromatography, surface plasmon resonance, protein arrays, immunoblotting, computational proteomics, and molecular imaging. Writing about their own work, leading researchers detail the principles, approaches, and difficulties of the various techniques, demonstrating the questions that neuroproteomics can answer and those it raises.

New challenges await, not the least of which is the identification of potential methods to regulate the structures and functions of key protein interaction networks. Ultimately, those building on the foundation presented here will advance our understanding of the brain and show us ways to abate the suffering caused by neurological and mental diseases.

Contents

• Series Preface
• Foreword
• Preface
• Editor
• Contributors
• 1. Neuroproteomics
  Oscar Alzate.
  • 1.1 INTRODUCTION
  • 1.2 NEUROPROTEOMICS
  • 1.3 EXPERIMENTAL TECHNIQUES CURRENTLY USED IN NEUROPROTEOMICS
  • 1.4 CHALLENGES
  • 1.5 ORGANIZATION OF BOOK
  • 1.6 FINAL REMARKS
  • REFERENCES
• 2. Banking Tissue for Neurodegenerative Research
  John F. Ervin.
  • 2.1 INTRODUCTION
  • 2.2 TISSUE PROCUREMENT AND STORAGE
  • 2.3 OTHER CONSIDERATIONS
  • REFERENCES
• 3. Multidimensional Techniques in Protein Separations for Neuroproteomics
  Carol Haney Ball and Petra Levine Roulhac.
  • 3.1 SUMMARY
  • 3.2 INTRODUCTION
  • 3.3 SAMPLE PREPARATIONS
  • 3.4 INTACT PROTEIN OFF-LINE MULTIDIMENSIONAL APPROACHES
  • 3.5 INTACT PROTEIN ON-LINE MULTIDIMENSIONAL APPROACHES
  • 3.6 PEPTIDE MULTIDIMENSIONAL APPROACHES AND QUANTITATIVE ANALYSES
  • 3.7 CONCLUSIONS AND FUTURE DIRECTIONS
  • ABBREVIATIONS
  • REFERENCES
• 4. 2-D Fluorescence Difference Gel Electrophoresis (DIGE) in Neuroproteomics
  Roberto Diez, Michael Herbstreith, Cristina Osorio, and Oscar Alzate.
  • 4.1 INTRODUCTION
  • 4.2 TWO-DIMENSIONAL GEL ELECTROPHORESIS
  • 4.3 TWO-DIMENSIONAL DIFFERENCE GEL ELECTROPHORESIS
  • 4.4 BENEFITS OF DIGE FOR IMAGE ANALYSIS
  • 4.5 VIRTUES OF DIGE
  • 4.6 SAMPLE PREPARATION
  • 4.7 ORTHOGONAL TECHNIQUES
  • 4.8 APPLICATIONS IN NEUROPROTEOMICS
  • 4.9 SATURATION DYES
  • 4.10 ORGANIZATIONS
  • 4.11 CONCLUSIONS
  • REFERENCES
• 5. Mass Spectrometry for Proteomics
  Carol E. Parker, Maria R. Warren, and Viorel Mocanu.
  • 5.1 INTRODUCTION
  • 5.2 MS SOURCE DESIGN
  • 5.3 LIQUID CHROMATOGRAPHY-MASS SPECTROMETRY CONSIDERATIONS
  • 5.4 MASS ANALYZERS
  • 5.5 DETECTOR TECHNOLOGY
  • 5.6 HYBRID INSTRUMENTS
  • 5.7 COLLISION CELLS: GAS-PHASE SEQUENCING BY MS/MS (TANDEM MASS SPECTROMETRY)
  • 5.8 NEW FRAGMENTATION TECHNIQUES
  • 5.9 GEL-BASED PROTEIN IDENTIFICATION
  • 5.10 COMPUTERS AND DATABASES
  • 5.11 CONCLUSION
  • REFERENCES
• 6. Mass Spectrometry for Post-Translational Modifications
  Carol E. Parker, Viorel Mocanu, Mihaela Mocanu, Nedyalka Dicheva, and Maria R. Warren.
  • 6.1 INTRODUCTION
  • 6.2 GENERAL CONSIDERATIONS
  • 6.3 DATABASE SEARCH CONSIDERATIONS
  • 6.4 MS/MS-BASED MODIFICATION SITE DETERMINATION
  • 6.5 ACETYLATION AND FORMYLATION
  • 6.6 PHOSPHORYLATION
  • 6.7 TYROSINE SULFATION
  • 6.8 BIOTINYLATION
  • 6.9 NITROSYLATION
  • 6.10 UBIQUITINATION
  • 6.11 COLLISIONAL-INDUCED DISSOCIATION-CLEAVABLE MODIFICATIONS
  • 6.12 GLYCOSYLATION
  • 6.13 CONCLUSION
  • REFERENCES
• 7. MALDI Imaging and Profiling Mass Spectrometry in Neuroproteomics
  Main Andersson, Per Andren, and Richard M. Caprioli.
  • 7.1 SUMMARY
  • 7.2 INTRODUCTION
  • 7.3 MS TECHNOLOGY
  • 7.4 MALDI IMAGING MASS SPECTROMETRY OF THE BRAIN
  • 7.5 IMAGING MASS SPECTROMETRY OF NEUROPEPTIDES
  • 7.6 MALDI PROFILING AND IMAGING OF EXPERIMENTAL NEURODEGENERATIVE DISORDERS
  • 7.7 THREE-DIMENSIONAL IMAGING MASS SPECTROMETRY OF THE BRAIN
  • 7.8 IMAGING WITH TANDEM MASS SPECTROMETRY
  • 7.9 QUANTITATION
  • 7.10 IDENTIFICATION OF PROTEINS
  • 7.11 INTEGRATING HISTOLOGY AND IMAGING MASS SPECTROMETRY
  • 7.12 CELL ISOLATION BY LASER CAPTURE MICRODISSECTION AND ANALYSIS BY IMS
  • 7.13 LIMITATIONS OF TECHNOLOGY
  • 7.14 PERSPECTIVES
  • REFERENCES
• 8. Protein Interaction Networks
  Alexei Vazquez.
  • 8.1 INTRODUCTION
  • 8.2 NETWORK PROPERTIES
  • 8.3 NETWORK EVOLUTION
  • 8.4 FUNCTION PREDICTION
  • 8.5 SUMMARY AND OUTLOOK
  • REFERENCES
• 9. Knowledge-Based Analysis of Protein Interaction Networks in Neurodegenerative Diseases
  Minoru Kanehisa, Vachiranee Limviphuvadh, and Mao Tanabe.
  • 9.1 INTRODUCTION
  • 9.2 OVERVIEW OF KEGG
  • 9.3 NETWORK ANALYSIS OF NEURODEGENERATIVE DISEASES
  • 9.4 CONCLUDING REMARKS
  • REFERENCES
• 10. Redox Proteomics of Oxidatively Modified Brain Proteins in Mild Cognitive Impairment
  Tanea T. Reed, Rukhsana Sultana, and D. Allan Butterfield.
  • 10.1 MILD COGNITIVE IMPAIRMENT
  • 10.2 OXIDATIVE STRESS
  • 10.3 POST-TRANSLATIONAL MODIFICATIONS
  • 10.4 PROTEIN CARBONYLATION
  • 10.5 HNE MODIFICATION
  • 10.6 PROTEIN NITRATION
  • 10.7 OXIDATIVE DAMAGE IN MCI BRAIN
  • 10.8 REDOX PROTEOMICS
  • 10.9 ENZYME ASSAYS
  • 10.10 ENERGY-RELATED PROTEINS
  • 10.11 NEUROPLASTICITY
  • 10.12 MITOCHONDRIAL DYSFUNCTION
  • 10.13 ANTIOXIDANT DEFENSE
  • 10.14 STRUCTURAL DYSFUNCTION
  • 10.15 SIGNAL TRANSDUCTION
  • 10.16 PROTEIN SYNTHESIS
  • 10.17 CONCLUSIONS
  • REFERENCES
• 11. Neuroproteomics in the Neocortex of Mammals: Molecular Fingerprints of Cortical Plasticity
  Lieselotte Cnops, Tjing-Tjing Hu, Gert Van den Bergh, and Lutgarde Arckens.
  • 11.1 Introduction
  • 11.2 FACTS ABOUT CAT VISUAL SYSTEM
  • 11.3 NEUROPROTEOMICS OF CAT VISUAL CORTEX PLASTICITY
  • 11.4 CRMPS AND CORTICAL PLASTICITY
  • 11.5 DYNAMIN I AND MATURE CELL SHAPE
  • 11.6 SYNAPTOTAGMIN I AND CORTICAL PLASTICITY
  • 11.7 CONCLUSION
  • 11.8 FUTURE CHALLENGES
  • REFERENCES
• 12. A Neuroproteomic Approach to Understanding Visual Cortical Development
  Leonard E. White.
  • 12.1 SUMMARY
  • 12.2 INTRODUCTION
  • 12.3 CIRCUIT CONSTRUCTION IN VISUAL CORTICAL DEVELOPMENT
  • 12.4 ORIENTATION AND DIRECTION SELECTIVITY IN VISUAL CORTEX
  • 12.5 ROLE FOR SENSORY EXPERIENCE IN DEVELOPMENT OF ORIENTATION AND DIRECTION SELECTIVITY IN VISUAL CORTEX
  • 12.6 UNITING SYSTEMS NEUROSCIENCE AND NEUROPROTEOMICS FOR UNDERSTANDING DEVELOPMENT OF ORIENTATION AND DIRECTION SELECTIVITY IN VISUAL CORTEX
  • 12.7 TOWARD A COMPREHENSIVE VIEW OF EXPERIENCE-DEPENDENT BRAIN DEVELOPMENT
  • REFERENCES
• 13. Behaviorally Regulated mRNA and Protein Expression in the Songbird Brain
  Miriam V. Rivas and Erich D. Jarvis.
  • 13.1 INTRODUCTION
  • 13.2 AUDITORY AND VOCAL PATHWAYS
  • 13.3 EXPRESSION OF SINGING-REGULATED GENES AND THEIR PROTEINS
  • 13.4 RNA AND PROTEIN CONCORDANCE
  • 13.5 DIFFERENCES BETWEEN VOCAL AND AUDITORY PATHWAYS
  • 13.6 PROPOSED HYPOTHESIS OF SINGING-REGULATED GENES AND PROTEINS
  • 13.7 FUTURE NEEDS
  • REFERENCES
• 14. Proteomics of Experience-Dependent Plasticity in the Songbird Auditory Forebrain
  Raphael Pinaud, Oscar Alzate, and Liisa A. Tremere.
  • 14.1 INTRODUCTION
  • 14.2 BRAIN SUBSTRATES OF SONG LEARNING AND PRODUCTION
  • 14.3 BRAIN SUBSTRATES FOR AUDITORY PROCESSING
  • 14.4 NCM SELECTIVITY, PLASTICITY, AND POTENTIAL ROLES IN MEMORY FORMATION
  • 14.5 KNOWN PROTEIN REGULATORY EVENTS IN NCM
  • 14.6 QUANTITATIVE PROTEOMICS SCREENING IN NCM: A METHODOLOGICAL SUMMARY
  • 14.7 EXPERIENCE-REGULATED PROTEINS IN NCM
  • 14.8 CALCIUM-DRIVEN PLASTICITY: ACTIVATION OF THE EXTRACELLULAR-SIGNAL REGULATED KINASE PATHWAY
  • 14.9 CONCLUDING REMARKS
  • REFERENCES
• 15. Applications of Proteomics to Nerve Regeneration Research
  Mark W. Massing, Grant A. Robinson, Christine E. Marx, Oscar Alzate, and Roger D. Madison.
  • 15.1 PERIPHERAL NERVE INJURY: BACKGROUND AND CLINICAL SIGNIFICANCE
  • 15.2 FEMORAL NERVE REGENERATION MODEL
  • 15.3 ROLE OF PROTEOMICS IN IDENTIFYING MEDIATORS OF AXONAL REGENERATION AND PREFERENTIAL MOTOR REINNERVATION
  • 15.4 DISCOVERY OF TROPHOMORPHIC MEDIATORS WITH 2D-DIGE
  • 15.5 SUMMARY AND FUTURE DIRECTIONS
  • REFERENCES

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