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Book Details
Abstract
Optogenetic tools have allowed significant advances in the understanding of biological problems, particularly in the neurosciences field. Biological tools as well as optical set-ups have evolved and a wide range of probes and light-controllable modules are now available.
The aim of this book is to give a flavour of illumination strategies and imaging with an overview of the different optogenetic tools and their main applications in cell biology. Based on examples covering the different aspects of cell biology, this book provides a practical approach for using light-emitting sensors and light-driven actuators.
Table of Contents
| Section Title | Page | Action | Price |
|---|---|---|---|
| Cover | Cover | ||
| COMPREHENSIVE SERIES IN PHOTOCHEMICAL AND PHOTOBIOLOGICAL SCIENCE | i | ||
| Preface | vii | ||
| References | ix | ||
| Contents | xi | ||
| Part I - Illumination strategies and imaging | 1 | ||
| Chapter 1 - Fast Volumetric Imaging Using Light-sheet Microscopy. Principles and Applications | 3 | ||
| 1.1.\rIntroduction | 5 | ||
| 1.2.\rFrom Classical Approaches to LSFM: the Question of Optical Sectioning | 5 | ||
| 1.2.1.\rConfocal Microscopy | 7 | ||
| 1.2.2.\rTwo-photon Microscopy | 7 | ||
| 1.2.3.\rLight-sheet Fluorescent Microscopy | 8 | ||
| 1.3.\rOptical Principles of Light-sheet Microscopy | 10 | ||
| 1.3.1.\rThe Origins of LSFM | 10 | ||
| 1.3.2.\rSpatial Resolution in LSFM | 11 | ||
| 1.3.2.1.\rBasics of Gaussian Optics.In light-sheet microscopy, a cylindrical or scanned spherical Gaussian beam is used to illuminate the ... | 11 | ||
| 1.3.2.2.\rResolution of the Light Sheet.In standard bright-field microscopy, the spatial resolution reflects the shape of the PSF (point-s... | 12 | ||
| 1.3.2.3.\rTrade-off Between the Field of View and the Axial Resolution.In light-sheet microscopy, any configuration therefore reflects a t... | 13 | ||
| 1.4.\rBuilding the Improved LSFM: Pushing the Limits | 13 | ||
| 1.4.1.\rIncreasing the Spatial Resolution | 13 | ||
| 1.4.2.\rHigh-speed Volumetric Imaging | 16 | ||
| 1.4.3.\rContrast Enhancement | 16 | ||
| 1.4.4.\rImaging Deeper in Semi-transparent Samples | 17 | ||
| 1.4.5.\rLight-sheet Microscopy with a Single Objective | 18 | ||
| 1.5.\rApplication: Light-sheet Imaging of Zebrafish Brain | 19 | ||
| 1.5.1.\rLight-sheet-based Whole-brain Functional Imaging in Zebrafish Larvae | 19 | ||
| 1.5.2.\rWhole-brain LSFM-based Functional Imaging to Study Sensorimotor Integration in the Vertebrate Brain | 20 | ||
| 1.6.\rLSFM in the Next Decade | 22 | ||
| References | 22 | ||
| Chapter 2 - Super-resolution Microscopy | 25 | ||
| 2.1.\rThe Diffraction Limit | 27 | ||
| 2.2.\rSuper-resolution via Localization Microscopy | 27 | ||
| 2.3.\rSingle-molecule Localization in 3D | 31 | ||
| 2.4.\rSuper-resolution via Correlation of Fluorescence Fluctuations | 32 | ||
| 2.5.\rSuper-resolution via Optical Non-linear Effects | 34 | ||
| 2.6.\rSuper-resolution Based on Structured Illumination | 36 | ||
| 2.7.\rConclusion | 38 | ||
| Acknowledgements | 38 | ||
| References | 39 | ||
| Part II - Light-emitting Sensors | 41 | ||
| Chapter 3 - The Glowing Panoply of Fluorogen-based Markers for Advanced Bioimaging | 43 | ||
| 3.1.\rIntroduction | 45 | ||
| 3.2.\rFluorogen-based Markers Engineered from Natural Photorec | 47 | ||
| 3.2.1.\rFlavin-binding Cyan–Green Fluorescent Proteins | 48 | ||
| 3.2.2.\rBiliverdin-binding Far-red and Infrared Fluorescent Pr | 49 | ||
| 3.2.3.\rBilirubin-binding Green Fluorescent Proteins | 51 | ||
| 3.3.\rSemi-synthetic Fluorogen-based Markers | 52 | ||
| 3.3.1.\rSemi-synthetic Fluorogen-based Protein Markers | 52 | ||
| 3.3.1.1.\rFluorogen-activating Proteins.Activating the fluores | 52 | ||
| 3.3.1.2.\rSelf-labeling Tags.Semi-synthetic fluorogen-based markers were also obtained by exploiting site-specific labeling systems such a... | 55 | ||
| 3.3.1.3.\rFluorescence-activating and Absorption-shifting Tag.Fluorescence-activating and absorption-shifting tag (FAST) is a small protei... | 56 | ||
| 3.3.2.\rSemi-synthetic Fluorogen-based RNA Markers | 57 | ||
| 3.4.\rConcluding Remarks | 58 | ||
| Acknowledgements | 58 | ||
| References | 58 | ||
| Chapter 4 - Optogenetic Reporters for Cell Biology and Neuroscience | 63 | ||
| 4.1.\rIntroduction to Optogenetic Reporters | 65 | ||
| 4.2.\rDesign Strategies | 66 | ||
| 4.2.1.\rBiFC | 66 | ||
| 4.2.2.\rDimerization-dependent FPs | 66 | ||
| 4.2.3.\rFRET | 68 | ||
| 4.2.4.\rEngineered Allosteric Effects | 69 | ||
| 4.2.5.\rEnhancement of Intrinsic FP Sensitivities | 71 | ||
| 4.3.\rApplications of Optogenetic Reporters | 72 | ||
| 4.3.1.\rCell Cycle | 72 | ||
| 4.3.2.\rpH Sensing | 74 | ||
| 4.3.3.\rProgrammed Cell Death | 75 | ||
| 4.3.3.1.\rApoptosis.Apoptosis is a highly regulated cell death process, which generally occurs to maintain or modulate cell populations in... | 76 | ||
| 4.3.3.2.\rNon-apoptotic PCD.Although apoptosis is the most thoroughly studied pathway of PCD, the mechanism and function of other types of... | 78 | ||
| 4.3.4.\rMessenger Molecules | 78 | ||
| 4.3.4.1.\rNeurotransmitters.Neurotransmitters are the chemical messengers that transmit signals across a chemical synapse from a neuron to... | 79 | ||
| 4.3.4.2.\rCalcium Ion.Ca2+ is a ubiquitous signaling ion – it regulates the activity of various proteins allosterically, acts in a wide ra... | 80 | ||
| 4.3.4.2.1\rFRET-based GECIs.The first class of GECIs, cameleons, were reported by Miyawaki and co-workers in the lab of Roger Y. Tsien in 1... | 80 | ||
| 4.3.4.2.2\rSingle FP-based GECIs.Single FP-based GECIs are engineered by coupling the conformational change of a Ca2+ sensing domain to mod... | 82 | ||
| 4.3.5.\rProtein Kinases | 83 | ||
| 4.3.6.\rMembrane Potential | 86 | ||
| 4.4.\rConclusions and Future Directions | 88 | ||
| Acknowledgements | 89 | ||
| References | 89 | ||
| Part III - Light-driven Actuators | 99 | ||
| Chapter 5 - Light-driven Actuators: Spatiotemporal Dynamics of Cellular Signaling Processes | 101 | ||
| 5.1.\rIntroduction | 103 | ||
| 5.2.\rExperimental Procedures | 103 | ||
| 5.2.1.\rPlasmid Construction | 103 | ||
| 5.2.2.\rCell Culture | 104 | ||
| 5.2.3.\rBioluminescence Assay | 104 | ||
| 5.2.4.\rDish Coating | 105 | ||
| 5.2.5.\rConfocal Laser Scanning Microscopy Imaging | 105 | ||
| 5.2.6.\rHalf-life Evaluation of Off Kinetics | 106 | ||
| 5.3.\rResults and Discussion | 106 | ||
| 5.3.1.\rTuning Switch-off Kinetics and Dimerization Efficiencies | 108 | ||
| 5.3.2.\rAssembly Method to Enhance the Performances of the Magnet System | 109 | ||
| 5.3.3.\rKinetic Study of the CAD–Magnet System | 110 | ||
| 5.3.4.\rOptical Control of Membrane Morphology by the CAD–Magnet System | 112 | ||
| 5.3.5.\rThe Induction of Cell Membrane Dynamics Using CAD–Magnet | 112 | ||
| 5.4.\rConclusion | 113 | ||
| References | 115 | ||
| Chapter 6 - Optogenetic Control of the Generation of Reactive Oxygen Species for Photoinducible Protein Inactivation and Cell Ablation | 117 | ||
| 6.1.\rIntroduction | 119 | ||
| 6.2.\rMolecular Mechanism of CALI | 119 | ||
| 6.2.1.\rPhotosensitization Mechanism | 120 | ||
| 6.2.2.\rROS Effects on Intracellular Molecules | 121 | ||
| 6.2.3.\rHow Specific is CALI | 122 | ||
| 6.3.\rDevelopment of CALI Agents and Their Application in Cell Biology | 122 | ||
| 6.3.1.\rChemical-based Photosensitizers | 122 | ||
| 6.3.2.\rGenetically Encoded Photosensitizers | 125 | ||
| 6.3.3.\rGenetically Encoded Photosensitizers for Photodynamic Therapy | 128 | ||
| 6.4.\rFuture Perspectives for CALI | 131 | ||
| References | 132 | ||
| Chapter 7 - Optogenetic Tools for Quantitative Biology: The Genetically Encoded PhyB–PIF Light-inducible Dimerization System and Its Application for Controlling Signal Transduction | 137 | ||
| 7.1.\rIntroduction | 139 | ||
| 7.2.\rLight-induced Dimerization (LID) Systems for Controlling Cell Signaling | 139 | ||
| 7.3.\rSynthesis of the Chromophore of Phytochrome | 141 | ||
| 7.4.\rPhyB–PIF LID system | 143 | ||
| 7.5.\rQuantitative Manipulation of Cell Signaling by the PhyB–PIF System | 143 | ||
| 7.6.\rConclusion | 145 | ||
| Acknowledgements | 146 | ||
| References | 146 | ||
| Chapter 8 - Quantitative Control of Kinase Activity with a Mathematical Model | 149 | ||
| 8.1.\rIntroduction | 151 | ||
| 8.2.\rExperimental Design of the PA-Akt System | 153 | ||
| 8.2.1.\rPrinciple of the PA-Akt System | 153 | ||
| 8.2.2.\rDesign of the Construction of the PA-Akt System | 154 | ||
| 8.2.3.\rNotes on Light Illumination Wavelength and Strength | 155 | ||
| 8.3.\rApplication of the PA-Akt System for Cellular Signaling Analysis | 157 | ||
| 8.3.1.\rOptogenetic Control of the PA-Akt System | 158 | ||
| 8.3.2.\rDissecting the Signaling Pathway by the PA-Akt System | 159 | ||
| 8.3.3.\rSpatial Regulation of Actin Remodeling by Localized Activation of PA-Akt | 159 | ||
| 8.3.4.\rPrediction of Light-induced Akt Activation Using a Mathematical Model | 161 | ||
| 8.4.\rConclusion | 165 | ||
| References | 166 | ||
| Chapter 9 - Light Control of Transcription in Cells | 169 | ||
| 9.1.\rIntroduction | 171 | ||
| 9.2.\rLight-inducible Transcription Systems | 171 | ||
| 9.3.\rLight-induced Oscillatory Versus Sustained Expression of Ascl1 | 173 | ||
| 9.4.\rLight-induced Oscillatory Expression of Dll1 | 175 | ||
| 9.4.1.\rDll1 Oscillations in Neurogenesis and Somitogenesis | 175 | ||
| 9.4.2.\rCell-to-Cell Transfer of Oscillatory Information via Dll1 Oscillations | 177 | ||
| 9.5.\rConclusion | 178 | ||
| References | 179 | ||
| Chapter 10 - Building Light-inducible Receptor Tyrosine Kinases | 181 | ||
| 10.1.\rIntroduction | 183 | ||
| 10.2.\rExperimental | 183 | ||
| 10.2.1.\rMaterials | 183 | ||
| 10.2.2.\rSample Preparation | 184 | ||
| 10.2.3.\rMicroscope Setup | 184 | ||
| 10.2.4.\rImage Analysis | 184 | ||
| 10.3.\rResults and Discussion | 185 | ||
| 10.3.1.\rScreening OptoRTKs with PHR | 185 | ||
| 10.3.2.\rActivation of Canonical Signaling Pathways | 186 | ||
| 10.3.3.\rFunctional Validation of Downstream Activation | 189 | ||
| 10.3.4.\rResponses to Different Light Conditions | 191 | ||
| 10.3.5.\rApplication of Diverse Actuators | 192 | ||
| 10.4.\rConclusions | 194 | ||
| Acknowledgements | 194 | ||
| References | 194 | ||
| Chapter 11 - Mechanotransduction and Optogenetics | 197 | ||
| 11.1.\rIntroduction | 199 | ||
| 11.2.\rOptogenetic Regulation of Mechanotransduction at the Tissue Level | 201 | ||
| 11.2.1.\rSmall Rho GTPases Are Key Regulators of Force Modulation in Tissues | 202 | ||
| 11.2.2.\rHow Can a Predefined Spatial Constraint Have an Impact on Tissue Dynamics | 204 | ||
| 11.3.\rPhotocontrol of Mechanotransduction Processes at the Cellular Level | 207 | ||
| 11.3.1.\rLight-sensitive Increases in Contractility Can Mimic the Initiation of Cytokinesis | 207 | ||
| 11.3.2.\rOptogenetics Regulation of Cell Migration | 208 | ||
| 11.3.2.1.\rCell Polarization During Migration Induced by Light-sensitive Small Rho GTPases.Several studies have used FRET-based biosensors ... | 210 | ||
| 11.3.2.2.\rCell Polarization During Migration Induced by Light-sensitive G-protein Coupled Receptors (GPCRs).GPCRs are inducers of cell mig... | 210 | ||
| 11.3.2.3.\rOptogenetic Probing Reveals a Different Ca2+ Pool Implicated in Cell Migration.Besides PI(3,4,5)P3 metabolism and small GTPase r... | 211 | ||
| 11.4.\rControlling the Individual Regulators of Mechanotransduction by Optogenetics | 212 | ||
| 11.4.1.\rOptogenetic Control of ECM Receptors, the Integrins | 213 | ||
| 11.4.2.\rOptogenetic Control of Signalling Elements Downstream of Integrins | 214 | ||
| 11.4.3.\rOptogenetic Control of Actin Remodelling | 215 | ||
| 11.5.\rOptogenetics Sheds Light on the Spatiotemporal Regulation of Signalling | 216 | ||
| 11.5.1.\rTemporal Regulation of a Signal Transduction | 216 | ||
| 11.5.2.\rSpatial Regulation of a Signal Transduction | 217 | ||
| 11.5.3.\rDiffusion of a Signal as a Feature of Spatial Regulation | 217 | ||
| Acknowledgements | 218 | ||
| References | 218 | ||
| Subject Index | 221 |