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Intro -- Preface -- Contents -- About the Editor-in-Chief -- Section Editors -- Contributors -- Part I: Introduction -- 1 Introduction to Cell Biosensors Through 55 Years of Scientific Production -- Introduction -- What Is a Cell Biosensor? -- Evolution of the Research Topics from 1965 to 2020 -- The ``Ideal´´ Bibliography -- Conclusions and Future Directions -- References -- References Related to Fig. 3 -- 1965-1990 -- 1991-2000 -- 2001-2010 -- 2011-2020 -- Part II: Fundamentals and Genetics for Cell Biosensors Applications -- 2 Stress Response-Based Whole-Cell Biosensor Development: Sentinels, Serendipity, and Circuitry -- Introduction -- Foundation -- Precedents -- Baltimore -- New Haven -- Palo Alto -- Wilmington, DE -- Other Technologies Were also Advancing -- Serendipity Intervened in the Form of the Sulfonylurea Herbicides -- The Heat Shock Response -- Environmental Biotechnology -- State of the Art -- The Ames Test (Ames et al. 1973) -- Microtox (Blaise et al. 1994) -- Metal-Detecting Biosensors -- Stress Response Induction -- Conceptual Protection of Wastewater Treatment Plant Bacterial Flora -- Concept Validation -- Expanding the Paradigm at DuPont -- Parallel Efforts -- Advantages of lux-Based Whole-Cell Biosensors -- Screening for Stress-Responsive Promoters -- An Ordered Array of E. coli Promoter::lux Whole-Cell Biosensors -- Comparison of Whole-Cell Biosensor and Nucleic Acid Hybridization Measures of Gene Expression -- Coda -- References -- 3 Engineering Autobioluminescent Eukaryotic Cells as Tools for Environmental and Biomedical Surveillance -- Introduction -- Whole-Cell Bioluminescent Bioreporters -- The Transition from Bioluminescence to Autobioluminescence -- Environmental Surveillance Using Autobioluminescent Yeast Bioreporters -- Biomedical Surveillance Using Autobioluminescent Human Cell Lines.
Conclusions and Future Directions -- References -- 4 Biosensors of the Well-being of Cell Cultures -- Introduction -- Current Paradigms for Measurement in Bioproduction -- Sensor Architectures -- Cell Stress Signaling -- I Am Well Generally -- Stress from the External Environment -- Stress from Internal Processes -- Biosensors of Metabolites -- Conclusions and Future Directions -- References -- 5 Systematic Design of a Quorum Sensing-Based Biosensor for the Detection of Metal Ions in Escherichia coli -- Introduction -- The Basic Principles of Quorum Sensing -- Design Example of QS-Based Metal Ion Biosensor -- Construction of QS-Based Metal Ion Biosensor -- Mathematical Model of QS-Based Metal Ion Biosensor -- Design Specifications for QS-Based Metal Ion Biosensor -- Design Procedure for the QS-Based Metal Ion Biosensor -- Experimental Results -- Conclusion -- Appendix -- Component Libraries -- References -- 6 Riboswitches as Sensor Entities -- Introduction -- Development of Riboswitches Responsive to Small Molecule Analytes -- Aptamer Selection -- Riboswitch Selection In Vivo -- Reengineering Natural Riboswitches -- Riboswitch Selection In Vitro -- Rational and Computational Design of Synthetic Riboswitches -- Riboswitch Detection Systems -- Monitoring Functionality of Synthetic Riboswitches -- Coupling Synthetic Riboswitches with New Reporter Systems -- Riboswitch Optimization toward Sensing Requirements -- Selectivity, but at a Cost -- Biological Circuits -- Riboswitch Circuitry -- Corollary Advantages of Signal Amplification -- Tandem Riboswitches -- Applications of Synthetic Riboswitches -- Conclusions -- References -- 7 Integration of Sensor Cells into Hardware Platforms -- Introduction -- Hardware Platforms for Sensor Cells -- Platform Substrate Material -- Platform Fabrication Approach -- Platform Architecture and Geometry.
Sensor Cells Immobilization onto Hardware Platforms -- Sensor Cells Immobilization Method -- Covalent Attachment -- Cross-Linking -- Affinity Binding -- Electrostatic, Van der Waals, Hydrophobic, and Ionic Interactions -- Entrapment -- Immobilization Method Biocompatibility -- Sensor Cells Bio-response Transduction to Bioelectronic Signals -- Electrochemical Transducers -- Potentiometric Transducers -- Amperometric Transducers -- Impedometric Transducers -- Optical Transducers -- Colorimetric Transducers -- Chemiluminescent Transducers -- Fluorescent Transducers -- Bioluminescent Transducers -- Mechanical Transducers -- Sensor Cells-Integrated Platform Modeling -- Sensor Cell Biological Response -- Bioelectronic Interface and Physicochemical Transducer Responses -- Conclusions and Future Directions -- References -- 8 Whole-Cell-Based Fiber-Optic Biosensors -- Introduction -- Whole-Cell-Based Fiber-Optic Biosensors -- Biosensors as Analytical Tools -- Fiber-Optic Transducers -- Whole-Cell Bioreporters -- Immobilization Approaches -- Biosensors for Toxicity Monitoring -- Determining Chemicals in Water -- Determining Chemicals in Soil -- Determining Chemicals in Air -- Conclusions and Future Directions -- References -- 9 Optical Approaches to Visualization of Cellular Activity -- Introduction -- Biosensors and Whole-Cell Biosensors -- Bioreporters Utilizing Natural Whole Cells -- Bioreporters Utilizing Genetically Modified Whole Cells -- Optical Detectors -- Commonly Used Reporter Genes -- Fluorescent Proteins -- Bacterial Luciferase (Lux) -- Firefly Luciferase (luc) -- β-galactosidase (lacZ) -- Multiple Reporter Proteins Within a Bioreporter Cell -- Optical Detector for Monitoring Bioreporters -- Photomultiplier Tube (PMT) -- Charge-Coupled Device (CCD) or Complementary Metal-Oxide-Semiconductor (CMOS) -- Conclusions and Future Prospects -- References.
10 Digital and Analogue Approaches to Whole-Cell Sensor Design -- Introduction -- Digital Computing -- Analog Circuits -- Mixed Signals -- Conclusions and Future Directions -- References -- 11 Engineering of Sensory Proteins with New Ligand-Binding Capacities -- Introduction: What Are Bioreporters -- Sensor Elements for Bioreporters -- Strategies for Obtaining New Sensory Proteins -- Mutagenesis and Selection of Mutant Transcription Activators -- Periplasmic Binding Proteins and Selection -- Bacterial Bioreporters Based on Methylaccepting Chemotaxis Proteins -- Conclusions -- References -- 12 Cell-Free Biosensors: Synthetic Biology Without Borders -- Introduction -- Background -- Accessibility of Biosensor Infrastructure -- Storage and Distribution -- Companion Devices -- Rapid Prototyping and Sensor Programmability -- Definition of Cell-Free Biosensing -- Isothermal Amplification-Based Diagnostics -- Nucleic Acid Sequence-Based Amplification (NASBA) -- Loop-Mediated Isothermal Amplification (LAMP) -- Recombinase Polymerase Amplification (RPA) -- Drawbacks of Using Isothermal Amplification Strategies for Sensing -- CFPE-Based Biosensors -- Recognition Components in Biosensors -- Riboregulators, Riboswitches, and Fluorogenic Aptamers -- Riboswitches for Nucleic Acid Sensing -- Riboswitches for Small Molecule and Protein Sensing -- Fluorogenic Aptamers and Sensor Systems -- CRISPR-Enabled Nucleic Acid Detection -- Functional DNA Molecules for Biosensing -- Functional DNA Molecules for Nucleic Acid and Protein Detection -- Amplification and Polymorphism Detection Using Dynamic DNA Nanotechnology -- DNA/Antibody Hybrid Systems for Protein and Small Molecule Detection -- Light-Sensitive Transcription Factors and Promoters -- Conclusion and Future Directions -- References -- 13 Engineering Prokaryote Synthetic Biology Biosensors -- Introduction.
Synthetic Biology as an Enabling Platform for Rapid Construction and Optimization of Prokaryotic Biosensors -- A Streamlined Approach to Developing Novel Prokaryotic Biosensors -- Efficient Sensor Optimization by Standardized and Modularized Genetic Parts -- Biosensor Improvement by Directed Evolution -- Development of New Sensing Modules -- Part Mining -- Antibody-Derived Domains as Universal Sensing Modules -- Tools and Strategies from Synthetic Biology for Optimizing Biosensor Performance -- Properties of a Biosensor -- Strategies for Enhancing Selectivity -- Strategies for Lowering the Limit of Detection (LOD) -- LOD Improvement by Tuning Receptor Densities -- LOD Improvement by Tuning Intracellular Ligand Densities -- Strategies for Increasing Output Dynamic Range -- Strategies for Reducing Leakiness -- Managing Leakiness on a Transcriptional Level -- Receptor and Promoter Engineering -- Antisense Transcription -- Managing Leakiness on a Translational Level -- Managing Leakiness on a Post-translational Level -- Functional Expansion of Biosensors by Synthetic Biology -- Memory Devices -- Toggle Switches -- Recombinase-Based Memory Devices -- CRISPR/Cas-Based Memory Devices -- Other Notable Memory Devices -- Computation Modules to Integrate Signals -- Modules to Reshape Response Function -- Reporter Modules for Interfacing with Different Detection Platforms -- Biosafety Enhancing Modules -- Conclusions and Future Directions -- References -- 14 Cell-Free Synthetic Biology Biosensors -- Introduction -- Cell-Free Protein Expression Platforms -- E. coli Cell-Free Systems -- Variety of Available Platforms -- Sensing Methods -- Protein-Based Sensing -- Nucleotide-Based Sensing -- Regulation with Synthetic Gene Networks -- Output -- Deployment -- Sample Processing -- Stability -- Encapsulation -- Conclusions and Future Directions -- References.
15 Genetic Circuit Design Principles.
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Handbook of cell biosensors / / Gérald Thouand, editor-in-chief
