Functional Genomics and Proteomics in the Clinical Neurosciences

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