Thematic serial volume focused on combining the basic methodology of genomics and proteomics with the current applications of such technologies in understanding psychiatric illnesses.
List of Contributors
Foreword
Functional Genomics and Proteomics in the Clinical
Neurosciences
Tissue preparation and banking
Introduction
Identifying subjects
Collection and harvesting tissue
Documenting
RNA integrity
Protein integrity
Conclusions
Functional genomic methodologies
Introduction
Input sources of RNA
Gene expression profiling: toward an informed choice
Level of sensitivity to detect the molecules of interest
Magnitude of expression-level changes in the brain
Minimum starting material for functional genomic analysis
Verification of expression-profiling analysis
Conventional methods of analyzing gene expression: Northern
hybridization
qPCR
Serial analysis of gene expression (SAGE)
Massive parallel signature sequencing (MPSS)
Total analysis of gene expression (TOGA)
Sequencing by hybridization (SBH)
Microarray platforms
Analyzing massive datasets
Regional and single cell assessment
RNA amplification strategies: aRNA amplification
Additional considerations
Conclusions
Methods for proteomics in neuroscience
Introduction
Subcellular fractionation
Expression proteomics
Functional proteomics
Mass spectrometry
Protein arrays
Conclusion
Functional genomics and proteomics in the clinical neurosciences:
data mining and bioinformatics
Introduction
Experimental methods
Data analysis
Statistical analysis and pattern classification
Microarray case study
Interpretation and validation
Reproducibility of microarray studies: concordance of current
analysis methods
Introduction
The data analysis pipeline
Assessment of data quality
Performance comparison
Validation
Implications for data mining
Summary and conclusions
The genomics of mood disorders
Introduction
Genetics of mood disorders: the progress
Neurobiological and neuroanatomical substrates of severe mood
disorders
The pathophysiology of severe mood disorders: insights from recent
gene profiling studies
Clues from animal models
Concluding remarks
Transcriptome alterations in schizophrenia: disturbing the
functional architecture of the dorsolateral prefrontal cortex
Dysfunction of the DLPFC in schizophrenia
Types of transcriptome alterations in the DLPFC in
schizophrenia
Causes of transcriptome alterations in the DLPFC in
schizophrenia
Consequences of transcriptome alterations in the DLPFC in
schizophrenia
Conclusions
Strategies for improving sensitivity of gene expression profiling:
regulation of apoptosis in the limbic lobe of schizophrenics and
bipolars
Introduction
Conclusions
Assessment of genome and proteome profiles in cocaine abuse
Introduction
Neuroanatomy of cocaine addiction
Functional genomics
Proteomics
Conclusion
Neuronal gene expression profiling: uncovering the molecular
biology of neurodegenerative disease
Introduction
Alzheimer's disease
Determination of RNA within senile plaques and neurofibrillary
tangles in AD
Single cell gene array analysis of hippocampal senile plaques in
AD
Single cell gene analysis of hippocampal NFTs in AD
Regional gene expression profiling in the hippocampus in AD
Regional gene expression profiling in frontal and temporal
neocortex in AD
Regional gene expression profiling in other AD-related brain
regions
Single cell analysis of cholinergic basal forebrain (CBF) neurons
in AD
Single cell profiling of galanin hyperinnervated CBF neurons in
AD
Summary of gene expression profiling in AD
Parkinson's disease
Regional gene profiling of the substantia nigra in PD
Gene expression profiling of Lewy body-containing SNpc neurons in
PD
Summary of gene expression profiling in PD
Schizophrenia
Regional gene expression profiling in frontal cortex in
schizophrenia
Single cell gene profiling in the entorhinal cortex in
schizophrenia
Multiple sclerosis
Gene profiling in multiple sclerosis
Creutzfeld–Jakob disease
Gene profiling in the aged brain
Single cell profiling of aged CA1 and CA3 hippocampal neurons
Gene regulation during the course of normal aging within the
frontal cortex
Conclusions
Abbreviations
Epileptogenesis-related genes revisited
Introduction
Methods
Results and discussion
Concluding remarks
Abbreviations
Functional genomics of sex hormone-dependent neuroendocrine
systems: specific and generalized actions in the CNS
Neural and genomic mechanisms for female mating behaviors
From lordosis to sexual arousal to generalized CNS arousal
From generalized CNS arousal to specific forms of arousal
Molecular biology of histamine receptors in CNS
α1B-Noradrenergic receptor signaling
μ and δ opioid receptor signaling
Summary and outlook
Abbreviations
Implications for the practice of psychiatry
Introduction
Proteomics
mRNA expression arrays (expressomics)
Whole genome SNP association studies
Use of convergent evidence
Future directions
Human brain evolution
Anatomical evolution
Protein sequence evolution
Gene expression evolution
Theory of gene expression evolution
Adaptive human brain evolution
Conclusion
Subject Index
Erratum to Progress in Brain Research Vol. 158 Functional Genomics
and Proteomics in the Clinical Neurosciences Scott E. Hemby and
Sabine Bahn
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