Methods in Bioengineering: 3D Tissue Engineering
Francois Berthiaume, Rutgers University and Jeffrey Morgan, Brown University, Editors

Chapter 1 - Chemical Modification of Porous Scaffolds Using Plasma Polymers
Chapter 2 - Three-Dimensional Cultures in Soft Self-Assembling Nanofibers
Chapter 3 - 3D Fibrin Matrices as Scaffold for Depot and Release of Bioactive Molecules
Chapter 4 - Designer Self-Assembling Peptide Scaffolds for 3D Tissue Cell Cultures
Chapter 5 - Chip-Based Tissue Engineering in Microbioreactors
Chapter 6 - Affinity-Binding Alginate Scaffolds for the Controlled Delivery of Multiple Heparin-Binding Proteins
Chapter 7 - Self-Assembly of Cell-Laden Hydrogels on the Liquid-Air Interface
Chapter 8 - 3D Encapsulation of Cells in Hydrogels Using Radical and Addition Cross-Linking
Chapter 9 - Micromolded Nonadhesive Hydrogels for the Self-Assembly of Scaffold-Free 3D Cellular Microtissues
Chapter 10 - On-Demand 3D Freeform Fabrication of Tissue Structures Using Bioprinting
Chapter 11 - Three-Dimensional Neuronal Cultures
Chapter 12 - Engineering Cartilage Tissue with Zonal Properties
Chapter 13 - Cartilage and Synovial Joint Regeneration by Cell Homing in Bioprinted, Anatomically Correct 3D Scaffolds
Chapter 14 - Integration of Experimental and Computational Microfluidics in 3D Tissue Engineering

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Methods in Bioengineering: Alternative Technologies to Animal Testing
Tim Maguire and Eric Novik, Editors

Chapter 1 - Current Methods for Prediction of Human Hepatic Clearance Using In Vitro Intrinsic Clearance
Chapter 2 - Use of Permeability from Cultured Cell Lines and PAMPA System and Absorption from Experimental Animals for the Prediction of Absorption in Humans
Chapter 3 - Aggregating Brain Cell Cultures for Neurotoxicity Tests
Chapter 4 - Approaches Towards a Multiscale Model of Systemic Inflammation in Humans
Chapter 5 - A Liposome Assay for Evaluating the Ocular Toxicity of Chemicals
Chapter 6 - Prediction of Potential Drug Myelotoxicity by In Vitro Assays on Hematopoietic Progenitors
Chapter 7 - Epigenetically Stabilized Primary Hepatocyte Cultures: A Potential Sensitive Screening Tool for Nongenotoxic Carcinogenicity
Chapter 8 - A Statistical Method to Reduce In Vivo Product Testing Using Related In Vitro Tests and ROC Analysis
Chapter 9 - Application of the Benchmark Approach in the Correlation of In Vitro and In Vivo Data in Developmental Toxicity
Chapter 10 - Three-Dimensional Cell Culture of Canine Uterine Glands
Chapter 11 - Markers for an In Vitro Skin Substitute
Chapter 12 - 3D Culture of Primary Chondrocytes, Cartilage, and Bone/Cartilage Explants in Simulated Microgravity
Chapter 13 - Alternatives for Absorption Testing
Chapter 14 - A 3D Model of the Human Epithelial Airway Barrier
Chapter 15 - Experimental Wear Assessment of Tibial Inserts for Total Knee Replacement

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Methods in Bioengineering: Biomicrofabrication and Biomicrofluidics
Jeffrey D. Zahn, Rutgers University, Editor

Chapter 1 - Microfabrication Techniques for Microfluidic Devices
Chapter 2 - Micropumping and Microvalving
Chapter 3 - Micromixing Within Microfluidic Devices
Chapter 4 - On-Chip Electrophoresis and Isoelectric Focusing Methods for Quantitative Biology
Chapter 5 - Electrowetting
Chapter 6 - Dielectrophoresis for Particle and Cell Manipulations
Chapter 7 - Optical Microfluidics for Molecular Diagnostics
Chapter 8 - Neutrophil Chemotaxis Assay from Whole Blood Samples
Chapter 9 - Microfluidic Immunoassays
Chapter 10 - Droplet Based Microfluidics by Shear-Driven Microemulsions
Chapter 11 - MicroFACS System
Chapter 12 - Optical Flow Characterization—Microparticle Image Velocimetry (μPIV)
Chapter 13 - Microtubule Motors in Microfluidics

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Methods in Bioengineering: Systems Analysis of Biological Networks
Arul Jayaraman and Juergen Hahn, Texas A&M University

Chapter 1 - Quantitative Immunofluorescence for Measuring Spatial Compartmentation of Covalently-Modified Signaling Proteins
Chapter 2 - Development of Green Fluorescent Protein-Based Reporter Cell Lines for Dynamic Profiling of Transcription Factor and Kinase Activation
Chapter 3 - Comparison of Algorithms for Analyzing Fluorescence Microscopy Images and Computation of Transcription Factor Profiles
Chapter 4 - Data-driven, Mechanistic Modeling of Biochemical Reaction Networks
Chapter 5 - Construction of Phenotype-Specific Gene Network by Synergy Analysis
Chapter 6 - Genome Scale Analysis of Metabolic Networks
Chapter 7 - Modeling the Dynamics of Cellular Networks
Chapter 8 - Steady State Sensitivity Analysis of Biochemical Networks: A Brief Review and new Methods
Chapter 9 - Determining Metabolite Production Capabilities of Engineered Saccharomyces cerevisiae using Dynamic Flux Balance Analysis
Chapter 10 - Experimental Design for Parameter Identifiability in Biological Signal Transduction Modeling
Chapter 11 - Parameter Identification with Adaptive Sparse Grid-based Optimization for Models of Cellular Processes
Chapter 12 - Reverse Engineering of Biological Networks
Chapter 13 - Transcriptome Analysis of Regulatory Networks
Chapter 14 - A Workflow From Time Series Gene Expression Profiling to Transcriptional Regulatory Networks

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Methods in Bioengineering: Nanoscale Bioengineering and Nanomedicine
Kaushal Rege, Arizona State University and Igor L. Medintz, U.S. Naval Research Laboratory

Chapter 1 - Preparation and Characterization of Carbon Nanotube-Protein Conjugates
Chapter 2 - Peptide-Nanoparticle Assemblies
Chapter 3 - Nanoparticle-Enzyme Hybrids as Bioactive Materials
Chapter 4 - Self-Assembled QD-Protein Bioconjugates and their Use in Fluorescence Resonance Energy Transfer
Chapter 5 - Tracking Single Biomolecules in Live Cells using Quantum Dot Nanoparticles
Chapter 6 - Designer Self-assembling Peptides Scaffolds for 3-dimensional Tissue Cell Cultures
Chapter 7 - Nanoparticles as Biodynamic Substrates for Engineering Cell Fates
Chapter 8 - Magnetic cell separation to enrich for rare cells
Chapter 9 - Magnetic Nanoparticles for Drug Delivery
Chapter 10 - Imaging and Therapy of Atherosclerotic Lesions with Theranostic Nanoparticles
Chapter 11 - Biomedical Applications Of Metal Nanoshells
Chapter 12 - Environmentally-Responsive Multifunctional Liposomes
Chapter 13 - Biodegradable, Targeted Polymeric Nanoparticle Drug Delivery Formulation for Cancer Therapy
Chapter 14 - Porous Silicon Particles for Multi-Stage Delivery
Chapter 15 - Mathematical Modeling of Nanoparticle Targeting
Chapter 16 - Techniques for the Characterization of Nanoparticle-Bioconjugates

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Methods in Bioengineering: Microdevices in Biology and Medicine
Yaakov Nahmias, Mass General Hospital/Harvard Medical School and Sangeeta Bhatia, MIT

Chapter 1 - Immunoaffinity Capture of Cells from Whole Blood
Chapter 2 - Dynamic Gene Expression Analysis in a Living Cell Array
Chapter 3 - Micromechanical Control of Cell-Cell Interactions
Chapter 4 - Mechanotransduction and the Study of Cellular Forces
Chapter 5 - A Microfluidic Tool for Immobilizing C. Elegans
Chapter 6 - Osmolality Control for Microfluidic Embryo Cell Culture using Hybrid poly(dimethylsiloxane) (PDMS)-Parylene Membranes
Chapter 7 - Image-Based Cell Sorting using Microscale Electrical and Optical Actuation
Chapter 8 - Pharmacokinetic-Pharmacodynamic Models on a Chip
Chapter 9 - Lab-on-a-chip Impedance Detection of Microbial and Cellular Activity
Chapter 10 - Controlling the Cellular Microenvironment
Chapter 11 - Subtractive Methods for Forming Microfluidic Gels of Extracellular Matrix Proteins

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Methods in Bioengineering: Stem Cell Bioengineering
Biju Parekkadan and Martin Yarmush, Mass General Hospital/Harvard Medical School, Editors

Chapter 1 - Somatic Cell Nuclear Transfer and Derivation of Embryonic Stem Cells
Chapter 2 - Derivation of Mouse Parthenogenetic Embryonic Stem Cells
Chapter 3 - Generation of Mice from Embryonic Stem Cells using Tetraploid Embryos as Hosts
Chapter 4 - Bioreactor Design and Implementation
Chapter 5 - Extracellular Matrix Microarrays and Stem Cell Fate
Chapter 6 - Microfluidic Culture Platform for Investigating the Proliferation and Differentiation of Stem Cells
Chapter 7 - Analysis of Mouse Hematopoietic Stem and Progenitor Cells
Chapter 8 - Skeletal Stem Cells and the Hematopoietic Microenvironment: Biology and Assays
Chapter 9 - Targeting the Stem Cell Niche In Vivo
Chapter 10 - Parabiosis in Aging Research and Regenerative Medicine
Chapter 11 - Utilization of the Mixed Lymphocyte Reaction (MLR) Assay to Determine Stem Cell Immunogenicity and Suppression
Chapter 12 - A Novel Method for the Preservation of Embryonic Stem Cells Using a Quartz Capillary Freezing System
Chapter 13 - In vivo MR Tracking of hESC-Derived Oligodendrocyte Precursors in Mouse Brain

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