Copyright â Springer - 2016
Part I: Systems Biology of Multifactorial Diseases: Alzheimers Disease
Chapter 1: Alzheimer’s as a Systems-Level Disease Involving the Interplay of Multiple Cellular Networks
1 Systems Biology of Multifactorial Diseases: Alzheimer’s Disease
1.1 Alzheimer’s Disease: A Complex Multifactorial Disease
2 Susceptibility and Dynamic Interplay of Impaired and Homeostatic Networks Underlying the Onset and Progression of Alzheimer’s Disease
3 Potentiation of Homeostatic Networks at the Early Stages of AD May Delay the Onset, Arrest, or Even Reverse the Progression of the Disease
4 Implementing a Systems Biology Approach to AD
4.1 The Need for Standardization of Techniques and Data Records
4.2 From Single-ưCelled Models to Humans
5 Conclusions: Future perspectives
Chapter 2: Application of Systems Theory in Longitudinal Studies on the Origin and Progression of Alzheimer’s Disease
2 The Need for Longitudinal Studies
3 Systems Biology of Alzheimer’s Disease
3.3 Metabolomics and Lipidomics
4 Molecular Networks in Alzheimer’s Disease
Part II: Alzheimers Disease: Main Underlying Pathways and Networks
Chapter 3: The APP Proteolytic System and Its Interactions with Dynamic Networks in Alzheimer’s Disease
2 Overview of Alzheimer’s Disease (AD)
3 Basic Background for Biomolecular Networks
3.5 Protein Modifications
3.8 Environmental Factors
3.9 Describing Protein Interactions
4 Networks and Their Analysis as Tools to Investigate Complexity in Molecular Pathways
5 APP: A Dynamic and Complex Proteolytic System
6 Modeling the APP Proteolytic System. Practical Considerations
7 Applying Systems Biology Approaches in Other Areas
7.1 Pattern Recognition and the Early Diagnosis of AD
7.2 The Human Connectome Project
8 Relating the Systems Biology of APP to Normal Cognition and Disease Progression in AD
Chapter 4: Effects of Mild and Severe Oxidative Stress on BACE1 Expression and APP Amyloidogenic Processing
2.1 Preparation of Murine Primary Cortical Culture Components
2.1.3 Buffers and Reagents
2.2 Hydrogen Peroxide Treatment Components
2.5 Sodium Dodecyl Sulfate-ưPolyacrylamide Gel Electrophoresis (SDS-PAGE) and Immunoblotting Components
2.5.2 Buffers and Reagents
3.1 Preparation of Murine Primary Cortical Cells
3.1.2 Procedure for Neuronal Cell Preparation
3.2 Induction of Oxidative Stress with Hydrogen Peroxide
3.2.2 Treatment Procedure
3.3 Assessing the Cell Viability by the MTT Assay
3.4 Assessing Intracellular Free Radical Generation by the DCF Assay
3.5 SDS-PAGE and Immunoblotting for BACE1 and APP/APP-CTFs
Chapter 5: Advanced Assay Monitoring APP-Carboxyl-Terminal Fragments as Markers of APP Processing in Alzheimer Disease Mouse Models
2.2 Preparation of Soluble and Insoluble Brain Protein Fractions
2.3 Western Blot Analysis
2.3.1 Protein Sample Preparation
2.3.3 Immunoblotting Components: Transfer to Membrane
2.3.4 Antibodies Incubation
2.3.5 Imaging and Quantification
3.1 Preparation of Soluble and Insoluble Brain Protein Fractions
3.2 Western Blot Analysis
3.2.1 Protein Sample Preparation
3.2.2 Electrophoresis: Running Conditions
3.2.3 Transfer to Membrane
3.2.4 Antibodies Incubation
3.2.5 Imaging and Quantification
Chapter 6: Optical Super-Resolution Imaging of β-Amyloid Aggregation In Vitro and In Vivo: Method and Techniques
1.1 Optical Super-ưResolution Imaging
1.2 Multi-Parametric Imaging
3.1 Peptide Solutions Preparation
3.2 Conversion of Monomeric Protein to Fibrils In Vitro
3.3 Super-Resolution Fluorescence Microscopy by Single Molecule Localization (dSTORM Imaging)
3.3.1 Photoswitching Buffer Preparation
3.3.2 Imaging of Amyloid Fibrils with dSTORM In Vitro
3.3.3 Imaging of Amyloid Fibrils with dSTORM in Cells
3.4 Data Analysis for dSTORM
3.6 Fluorescence Lifetime Imaging
Chapter 7: Protocols for Monitoring the Development of Tau Pathology in Alzheimer’s Disease
1.1 Tau Neuropathological Staging of Alzheimer’s Samples. Staining Techniques
1.2 Monitoring Alterations in Dendritic Spines
1.3 Characterization of Phosphorylated Tau in Detergent-Insoluble Protein Aggregates
2.1 Brain Tissue Fixation for Preparation of Sections
2.2 Selection of Tissue Samples for Tau Neuropathological Staging
2.3 AT8 Immunohistoưchemistry. Phospho-Tau Immunostaining (See Notes 3 and 4)
2.4 Gallyas Silver Staining (See Notes 5
9)
2.5 Reagents and Materials for Dendritic Spines and Biochemistry Analysis
2.5.3 Secondary Antibodies
2.6 Reagents and Materials for Characterization of Tau Aggregates and Tau Phosphorylation State
3.1 Brain Tissue Samples. Fixation and Preparation of Sections
3.2 Immunochemiưstry. Phospho-Tau Immunostaining (See Notes 3, 4, and 10–12)
3.3 Gallyas Silver Staining (See Notes 5–9, and 13–16)
3.4 Monitoring Alterations in Dendritic Spines (See Notes 17–20)
3.4.1 Intracellular Injections (See Note 17)
3.4.2 Reconstruction and Morphometric Analysis of Pyramidal Neurons Labeled with LY
3.4.3 Combination of Iintracellular Injection with Immunohistochemiưstry and Histochemistry
3.5 Characterization of Tau Aggregates and Tau Phosphorylation State
3.5.1 Isolation of Brain Cell Extracts
3.5.2 Isolation of Detergent-ưInsoluble Tau Aggregates
3.5.3 Visualization of Insoluble Tau Aggregates by Immunoelectron Microscopy
3.5.4 Transmission Electron Microscopy
3.5.5 Western Blot Analysis
Chapter 8: LC3-II Tagging and Western Blotting for Monitoring Autophagic Activity in Mammalian Cells
Chapter 9: Advanced Mitochondrial Respiration Assay for Evaluation of Mitochondrial Dysfunction in Alzheimer’s Disease
1.1 Aβ and Tau Induce Mitochondrial Toxicity
1.2 Synergistic Mode of Action of Aβ and Tau
1.3 High-Resolution Respirometry in Isolated Mitochondria to Evaluate OXPHOS Capacity
2.1 Solutions for Isolated Mitochondria Preparation
2.2 Solutions for Mitochondrial Respiration Assay
3.1 Isolated Mitochondria Preparation
3.2 Mitochondrial Respiration Measurement: Preparations
3.3 Mitochondrial Respiration Measurement: High-Resolution Respirometry
Chapter 10: Analysis of Microglial Proliferation in Alzheimer’s Disease
2.1.1 Mouse/Rat Tissue Samples
2.1.2 Human Tissue Samples
2.2 Buffers and Solutions
2.3 Reagents and Other Components
2.4 Primary and Secondary Antibodies
2.4.1 Primary Antibodies (Recommended)
2.4.2 Secondary Antibodies
3.1 Immunoưhistochemical Detection of Microglial Proliferation in AD Mouse Models
3.2 Immunoưhistochemical Detection of Microglial Proliferation in Post-mortem Tissue from AD Patients
Part III: Comprehensive Disease Models Recapitulating Alzheimers Disease Features: From Cellular Models to Human
Chapter 11: Yeast as a Model for Alzheimer’s Disease: Latest Studies and Advanced Strategies
1 Yeast as a Model System
2 Approaches to Modeling Aβ Toxicity in Yeast
2.1 Amyloid Precursor Protein (APP) Processing
3 Yeast Approaches to Study Tau Biology
4 Concluding Remarks and Future Perspectives
Chapter 12: Yeast as a Model for Studies on Aβ Aggregation Toxicity in Alzheimer’s Disease, Autophagic Responses, and Drug Screening
2.3 Transformation of Yeast and Cultivation
2.4 Chemicals to Screen for Compounds Targeting Aβ
3.1 Transformation of Yeast Cells and Cultivation
3.2 Addition of Chemicals to Screen for Compounds Targeting Aβ
3.3 Flow Cytometry and Data Analysis
3.4 Screening for Compounds Targeting Aβ: Interpretation of Results
Chapter 13: Drosophila melanogaster as a Model for Studies on the Early Stages of Alzheimer’s Disease
2.5 Immunohistoưchemistry
3.2 Soluble and Insoluble Fraction of Total Aβ Peptide in the Fly Brain
3.5 Immunohistoưchemistry
Chapter 14: Chronic Mild Stress Assay Leading to Early Onset and Propagation of Alzheimer’s Disease Phenotype in Mouse Models
2.1 AD Animal Models. Transgenic Mice
2.2 Materials, Mild Stressors for the CMS Procedure
3.2 Chronic Mild Stress (CMS) Procedure
Chapter 15: Gene Expression Studies on Human Trisomy 21 iPSCs and Neurons: Towards Mechanisms Underlying Down’s Syndrome and Early Alzheimer’s Disease-Like Pathologies
2 Methodological Considerations for iPSC Studies
3 Defining Mechanisms Underlying Early Alzheimer’s Disease-Like Pathologies in Down’s Syndrome
3.1 Pathology and Gene Expression of AD iPSC-Derived Neurons
3.2 DS iPSCs as a Model of Early AD
3.3 Gene Expression Changes in DS Related to AD
Chapter 16: Cortical Differentiation of Human Pluripotent Cells for In Vitro Modeling of Alzheimer’s Disease
3.1 Plating Mouse Embryonic Fibroblasts
3.2 Culturing Human Pluripotent Cells
3.5 Transferring Neuroepithelial Sheet to Laminin Substrate
3.6 Passaging Neural Progenitor Cells
3.7 Freezing and Thawing Neural Progenitors
3.8 Final Plating of PSC Derived Cortical Neurons
3.9 Immunofluoưrescent Analysis of PSC Derived Cortical Neurons
3.10 Measuring Abeta Peptide Production by Stem Cell-ưDerived Neurons
Part IV: Experimental Systems Biology: Next Generation Molecular and High-Throughput Methods for the Study of Disease Susceptibility and Networks Dynamics Interplay in Complex Diseases
Chapter 17: Next Generation Sequencing in Alzheimer’s Disease
2 Next-Generation Sequencing to Identify Novel Disease Genes
3 Next-Generation Sequencing in Alzheimer’s Disease Research to Date
3.1 NGS for Resequencing of Alzheimer’s Disease Candidate Genes
3.1.1 NGS for Resequencing Mendelian AD Genes
3.1.2 NGS for Resequencing AD Susceptibility Genes
3.2 Whole-Exome Sequencing Studies in Alzheimer's Disease
3.3 Whole-Genome Sequencing Studies in Alzheimer’s Disease
4 Conclusions and Outlook
Chapter 18: Pooled-DNA Sequencing for Elucidating New Genomic Risk Factors, Rare Variants Underlying Alzheimer’s Disease
2.1 DNA Quantification and Pooling Components
2.2 PCR Amplification, Purification, Quantification, and Pooling Components
2.3 Library Preparation Components
3.1 DNA Quantification and Pooling
3.2 PCR Amplification, Purification, Quantification, and Pooling
3.8 Add Stop Ligase Mix STL
3.10 Enrich DNA Fragments
3.9 Purify Ligation Products
3.11 Preparation for Illumina Sequencing
3.12 Sequencing Data Analysis (See Note 11)
Chapter 19: New Genome-Wide Methods for Elucidation of Candidate Copy Number Variations (CNVs) Contributing to Alzheimer’s Disease Heritability
3 Data Analysis Workflows
3.1 Workflow for SNP Array Data
3.1.1 Quality Control (QC)
3.1.2 Population Substructure/Admixture by the SNP Dataset
3.1.3 LogR Ratio Calculation
3.1.4 Numeric Array Data or Segmentation
3.1.5 Test of Association
3.1.6 Visualization of Log2 Ratio Data
3.2 Workflow for aCGH Data
3.2.1 Quality Control (QC)
3.2.2 Population Substructure/Admixture by the SNP Dataset
3.2.3 Log2 Ratio Calculation
3.2.4 Numeric Array Data or Segmentation
3.2.5 Test of Association
3.2.6 Visualization of Log2 Ratio Data
Chapter 20: RNA-Sequencing to Elucidate Early Patterns of Dysregulation Underlying the Onset of Alzheimer’s Disease
1.1 Transcriptome Studies in Alzheimer’s Disease
3.1.1 Purification and Fragmentation of mRNA
3.1.2 First Strand cDNA Synthesis
3.1.3 Second Strand cDNA Synthesis
3.1.5 Addition of Adenine Bases
3.1.7 Amplification of cDNA Templates (See Note 6)
3.1.8 Library Quality Assessment
3.2.1 Fragmentation of RNA
3.2.2 Synthesis of First Strand cDNA
3.2.3 Synthesis of Second Strand cDNA
3.2.4 Double-Stranded cDNA Purification
3.2.6 AMPure Bead Preparation
3.2.8 Removal of Small Fragments
3.2.9 Library Quality Assessment
Chapter 21: Systems Biology Approaches to the Study of Biological Networks Underlying Alzheimer’s Disease: Role of miRNAs
1.2 miRNAs in Alzheimer’s Disease
2.1 miRNAs Detection Methods
2.2 Technical Considerations and Challenges in the Field
2.4 Reverse Transcription Quantitative Real Time PCR (RT-qPCR)
2.5 Next-Generation Sequencing (NGS)
2.6 Detection Methods. Concluding Remarks
3 Computational Systems Biology
3.1 Networks Construction
3.2 Network Inference and Analysis
Chapter 22: The Emerging Role of Metalloproteomics in Alzheimer’s Disease Research
1 Metal Hypothesis of Alzheimer’s Disease
2 Iron, Copper and Zinc in Alzheimer’s Disease
3 Principles of Metalloproteomics and Implications for Alzheimer’s Disease
4 Application of Metalloproteomics to Alzheimer’s Disease Research
Chapter 23: Redox Proteomics in Human Biofluids: Sample Preparation, Separation and Immunochemical Tagging for Analysis of Protein Oxidation
2.2 Sample Preparation and Iso-ưelectrofocusing (IEF)
2.3 SDS-ưPolyacrylamide Gel Electrophoresis (SDS-PAGE)
2.4 Immunochemical Detection of Oxidized Proteins
2.5 Image Analyses Equipment and Tools
2.7 Peptide Extraction and Clean-up
3.1.1 Cerebrospinal Fluid (CSF) Sample (See Note 6)
3.1.2 Plasma/Serum Sample
3.2 Iso-ưelectrofocusing (IEF). Separation by Isoelectric Point (pI)
3.3 SDS-ưPolyacrylamide Gel Electrophoresis (SDS-PAGE). Separation by Size
3.4 Transfer of Proteins onto Nitrocellulose Membranes
3.5 Post-ưderivatization of Membranes for Protein Carbonyl Detection (See Note 17)
3.6 Immunochemical Detection of Oxidized Proteins
3.8 Protein Digestion with Trypsin (See Note 27)
3.10 Clean-up, Concentration and Purification of Sample Using ZipTip Pipette Tips (See Note 5)
Chapter 24: Advanced Shotgun Lipidomics for Characterization of Altered Lipid Patterns in Neurodegenerative Diseases and Brain Injury
2.1 Equipment (See Note 1)
2.2 Reagents and Solutions
3.1 Cellular Lipid Extraction and Sample Preparation
3.2 Mass Spectrometric Analysis
3.3.1 Establishment of the Database of Lipid Classes and Individual Molecular Species
3.3.2 Automated Data Processing to Identify and Quantify Individual Lipid Species of a Specific Class
Chapter 25: AlzPathway, an Updated Map of Curated Signaling Pathways: Towards Deciphering Alzheimer’s Disease Pathogenesis
3.1 Collection of Review Articles and Manual Curation
3.3 Web Service of AlzPathway
3.4 Overview of AlzPathway
3.5 AlzPathway Applications
3.5.1 Key Molecules Discovery
3.5.2 Pathway-Based Drug Discovery
3.5.3 Cross-Pathway Analysis Between Neurodegenerative Diseases
Part V: Computational Systems Biology, Network Biology: Next Generation Computational and Integrative Network Biology Approaches for the Study of Modules, Network Dynamics, and Their Interplay in Complex Diseases
Chapter 26: A Computational Network Biology Approach to Uncover Novel Genes Related to Alzheimer’s Disease
1.1 Protein Interaction Networks and Disease
1.2 Overview of the Protocol
2.1 Alzheimers Disease Genes
2.3 Protein Interaction Data
2.4 Network Analysis Tools
2.5 Functional Annotations
3.1 AD Interactome Building
3.2 Functional Analysis of Candidates Based on Their Local Connectivity
3.3 Global Analysis: The Modular Structure of the AD Interactome
Chapter 27: Network Approaches to the Understanding of Alzheimer’s Disease: From Model Organisms to Humans
2 Why Do We Need a New Approach to Understand LOAD?
3 What Is a Network Approach?
3.1 Compilation or Curation of Existing Data from Literature
3.2 Computational Predictions Based on Available Information
3.3 Direct Measurements in High-ưThroughput Experiments
4 Differential Networks and Their Application to AD
4.1 What Network Approaches Are Currently Being Used to Study AD?
4.2 Databases and Repositories
4.4 Statistical Analysis of Networks
4.5 Experimental Validation of Networks and Nodes
5 Network Approaches to AD: Looking to the Future
Chapter 28: Characterization of Genetic Networks Associated with Alzheimer’s Disease
3.1 Architecture of a Multiscale Network Modeling Approach to Characterize Genetic Networks
3.2 Association Analysis of DNA, mRNA and Clinical Data
3.3 Constructing Tissue-Specific and Multi-Tissue Co-expression Networks
3.4 Differential Network Analysis
3.5 Determination of Module Relevance to LOAD Pathology
3.6 Reconstruction of the Bayesian Causal Networks
3.7 Identification of Key Causal Regulators
3.8 Prioritization of Subnetworks/Modules and Key Drivers
3.9 Summary and Future Work
Chapter 29: Network-Based Analysis for Uncovering Mechanisms Underlying Alzheimer’s Disease
2.1 Gene Expression Profiles of Alzheimer’s Disease
2.2 The Human Protein
Protein Interaction Data
3.1 Construction of the Gene Co-expression Network
3.2 Construction of the Protein Interaction Network
3.4 Application Using a Genetic Interaction Network
3.5 Application Using a Protein Interaction Network
Chapter 30: The SDREM Method for Reconstructing Signaling and Regulatory Response Networks: Applications for Studying Disease Progression
2.3 Optional Input Data (Defaults Available)
Part VI: Systems Biology of Alzheimers Disease in Practice: From Systems Biology to Early Diagnostics and Systems Medicine
Chapter 31: Advanced Neuroimaging Methods Towards Characterization of Early Stages of Alzheimer’s Disease
1 Alzheimer’s Disease Is a Network Disease: Need for Network-Wise Approaches
2 Disruption of Functional Brain Networks in AD
3 Characterization of Pathological Brain Networks with PET Imaging in AD
Chapter 32: Plasma Proteomics Biomarkers in Alzheimer’s Disease: Latest Advances and Challenges
3.1 Enzyme-Linked Immunosorbent Assay (ELISA)
3.2 Luminex xMAP Platform
3.3.1 Clinical Challenges
3.3.2 Analytical Challenges
Chapter 33: A Practical Guide for Exploring Opportunities of Repurposing Drugs for CNS Diseases in Systems Biology
1.1 Unmet Medical Needs and Complex Mechanisms of CNS Diseases
1.2 Therapeutic Challenge: Rethinking the Strategy for CNS Diseases
2.1 Network Biology: Impact and Approach
2.2 Application of Network Approach to Pharmacology
3.1 Step 1: Building and Visualizing a Multi-level Integrative Network
3.2 Step 2: Understanding the Disease Mechanism and Repositioning Opportunities for CNS Rare Diseases Using the Integrative Network
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