Biophotonics / Lorenzo Pavesi, Philippe M. Fauchet (Eds.)

Format:

Book

Contributor:

Pavesi, Lorenzo.

Fauchet, Philippe M.

Series:

Biological and medical physics, biomedical engineering

Language:

English

Subjects (All):

Photobiology.

Photonics.

Physical Description:

xxii, 336 pages : illustrations ; 24 cm.

Place of Publication:

Berlin ; [New York] : Springer, [2008]

Summary:

More profound understanding of the nature of light and light-matter interactions in biology has enabled many applications in the biology and medical fields. So a new discipline is born, namely biophotonics. The aim of this book is to review the current state-of-the-art of the field by means of authoritative chapters written by the world leaders of the respective fields. Biosensors, biochips, optical tomography, optical microsurgery, photodynamics therapy, bioactivation of gene, photobiology of skin, and nanobiophotonics are each introduced and recent advances presented. This book will be useful not only to physicians, biologists, physicists, chemists, materials scientists, and engineers but also to graduate students who are interested in these rapidly developing fields.

Contents:

1 Light Conversion in Photosynthetic Organisms / S. Frigerio, R. Bassi, G.M. Giacometti 1

1.2 Chloroplast Structure 2

1.3 Pigments and Light Absorption 3

1.4 Photosynthetic Apparatus 4

1.4.1 Photosystem II 6

1.4.2 Photosystem I 7

1.4.3 Cytochrome b[subscript 6]f 8

1.4.4 ATP Synthase 8

1.5 Cyclic Phosphorylation 9

1.6 Photoinhibition 13

2 Exploiting Photosynthesis for Biofuel Production / C. Govoni, T. Morosinotto, G. Giuliano, R. Bassi 15

2.1 Biological Production of Vehicle Traction Fuels: Bioethanol and Biodiesel 17

2.1.1 Bioethanol 17

2.1.2 Biodiesel 18

2.1.3 Biofuels Still Present Limitations Preventing Their Massive Utilization 18

2.2 Hydrogen Biological Production by Fermentative Processes 19

2.2.1 Hydrogen Production by Bacterial Fermentation 20

2.3 Hydrogen Production by Photosynthetic Organisms 21

2.3.1 Cyanobacteria 22

2.3.2 Eukaryotic Algae 23

2.4 Challenges in Algal Hydrogen Production 23

2.4.1 Oxygen Sensitivity of Hydrogen Production 23

2.4.2 Optimization of Light Harvesting in Bioreactors 25

3 In Between Photosynthesis and Photoinhibition: The Fundamental Role of Carotenoids and Carotenoid-Binding Proteins in Photoprotection / G. Bonente, L. Dall'Osto, R. Bassi 29

3.1 When Light Becomes Dangerous for a Photosynthetic Organism 29

3.2 Acclimation 31

3.3 State 1-State 2 Transitions 32

3.4 Carotenoids Play a Fundamental Role in Many Photoprotection Mechanisms 33

3.5 Analysis of Xanthophyll Function In Vivo 36

3.6 Nonphotochemical Quenching 38

3.7 Feedback Deexcitation of Singlet-Excited Chlorophylls: qE 39

3.8 [Delta]pH - Independent Energy Thermal Dissipation (qI) 40

3.9 Chlorophyll Triplet Quenching 41

3.10 Scavenging of Reactive Oxygen Species 41

4 Non-Linear Microscopy / D. Mazza, P. Bianchini, V. Caorsi, F. Cella, P.P. Mondal, E. Ronzitti, I. Testa, G. Vicidomini, A. Diaspro 47

4.2 Chronological Notes on MPE 48

4.3 Principles of Confocal and Two-Photon Fluorescence Microscopy 49

4.3.1 Fluorescence 49

4.3.2 Confocal Principles and Laser Scanning Microscopy 50

4.3.3 Point Spread Function of a Confocal Microscope 52

4.4 Two-Photon Excitation 55

4.5 Two-Photon Optical Sectioning 59

4.6 Two-Photon Optical Setup 60

4.7 Second Harmonic Generation (SHG) Imaging 63

5 Applications of Optical Resonance to Biological Sensing and Imaging: I. Spectral Self-Interference Microscopy / M.S. Unlu, A. Yalcin, M. Dogan, L. Moiseev, A. Swan, B.B. Goldberg, C.R. Cantor 71

5.1 High-Resolution Fluorescence Imaging 71

5.2 Self-Interference Imaging 71

5.3 Physical Model of SSFM 73

5.3.1 Classical Dipole Emission Model 73

5.4 Acquisition and Data Processing 75

5.4.1 Microscope Setup 75

5.4.2 Fitting Algorithm 76

5.5 Experimental Results 77

5.5.1 Monolayers of Fluorophores on Silicon Oxide Surfaces: Fluorescein, Quantum Dots, Lipid Films 77

5.5.2 Conformation of Surface-Immobilized DNA 79

5.6 SSFM in 4Pi Configuration 82

6 Applications of Optical Resonance to Biological Sensing and Imaging: II. Resonant Cavity Biosensors / M.S. Unlu, E. Ozkumur, D.A. Bergstein, A. Yalcin, M.F. Ruane, B.B. Goldberg 87

6.1 Multianalyte Sensing 87

6.2 Resonant Cavity Imaging Biosensor 88

6.2.1 Detection Principle 88

6.2.2 Experimental Setup, Data Acquisition, and Processing 90

6.2.3 Experimental Results 91

6.2.4 Spectral Reflectivity Imaging Biosensor 92

6.3 Optical Sensing of Biomolecules Using Microring Resonators 94

6.3.1 Basics on Microring Resonators 94

6.3.2 Setup and Data Acquisition 95

6.3.3 Data Analysis and Discussion 96

7 Biodetection Using Silicon Photonic Crystal Microcavities / P.M. Fauchet, B.L. Miller, L.A. DeLouise, M.R. Lee, H. Ouyang 101

7.1 Photonic Crystals: A Short Introduction 101

7.1.1 Electromagnetic Theory 101

7.1.2 One-Dimensional and Two-Dimensional PhC 103

7.1.3 Microcavities: Breaking the Periodicity 105

7.1.4 Computational Algorithms 106

7.2 One-Dimensional PhC Biosensors 107

7.2.1 Preparation and Selected Properties of Porous Silicon 107

7.2.2 Sensing Principle 109

7.2.3 One-Dimensional Biosensor Design and Performance 111

7.2.4 Fabrication of One-Dimensional PhC Biosensors 112

7.3 Selected Biosensing Results 114

7.3.1 DNA Detection 114

7.3.2 Bacteria Detection 114

7.3.3 Protein Detection 115

7.3.4 IgG Detection 117

7.4 Two-Dimensional PhC Biosensors 118

7.4.1 Sample Preparation and Measurement 118

7.4.2 Sensing Principle 119

7.4.3 Selected Biosensing Results 120

8 Optical Coherence Tomography with Applications in Cancer Imaging / S.A. Boppart 127

8.2 Principles of Operation 128

8.3 Optical Sources for Optical Coherence Tomography 133

8.4 Fourier-Domain Optical Coherence Tomography 133

8.5 Beam Delivery Instruments for Optical Coherence Tomography 135

8.6 Spectroscopic Optical Coherence Tomography 136

8.7 Applications to Cancer Imaging 138

8.7.1 Cellular Imaging for Tumor Cell Biology 138

8.7.2 Translational Breast Cancer Imaging 140

8.8 Optical Coherence Tomography Contrast Agents 141

8.9 Molecular Imaging using Optical Coherence Tomography 145

9 Coherent Laser Measurement Techniques for Medical Diagnostics / B. Kemper, G. von Bally 151

9.2 Electronic Speckle Pattern Interferometry (ESPI) 152

9.2.1 Double Exposure Subtraction ESPI 152

9.2.2 Spatial Phase Shifting (SPS) ESPI 153

9.3 Endoscopic Electronic Speckle Pattern Interferometry (ESPI) 156

9.3.1 Proximal Endoscopic ESPI 156

9.3.2 Distal Endoscopic ESPI 158

9.4 Microscopic (Speckle) Interferometry 161

9.5 Digital Holographic Microscopy 164

9.5.1 Principle and Measurement Setup 164

9.5.2 Nondiffractive Reconstruction 166

9.5.3 Resolution and Numerical Focus 170

9.5.4 Digital Holographic Phase Contrast Microscopy of Living Cells 171

10 Biomarkers and Luminescent Probes in Quantitative Biology / M. Zamai, G. Malengo, V.R. Caiolfa 177

10.1 Fluorophores and Genetic Dyes 177

10.1.1 Small Organic Dyes and Quantum Dots 177

10.1.2 Fluorescent Proteins 178

10.2 Microspectroscopy in Quantitative Biology: Where and How 183

10.2.1 Fluorescence Correlation Spectroscopy 183

10.2.2 Fluorescence Lifetime Imaging (FLIM) 188

10.2.3 Glossary of Molecular Biology 194

11 Fluorescence-Based Optical Biosensors / F.S. Ligler 199

11.2 Biological Recognition Molecules and Assay Formats 200

11.3 Displacement Immunosensors 203

11.4 Fiber Optic Biosensors 204

11.4.1 Fiber Optics for Biosensor Applications 205

11.4.2 Optrode Biosensors 207

11.4.3 Evanescent Fiber Optic Biosensors 207

11.5 Bead-Based Biosensors 209

11.6 Planar Biosensors 210

11.7 Critical Issues and Future Opportunities 212

12 Optical Biochips / P.

Seitz 217

12.1 Taxonomy of Optical Biochips 217

12.1.1 Basic Architecture of Optical Biochips 217

12.2 Analyte Classes for Optical Biochips 220

12.2.1 DNA (DNA Fragments, mRNA, cDNA) 220

12.2.2 Proteins (Antigens) 221

12.2.3 Specific Organic Molecules 221

12.2.4 Cell Gene Products (cDNA, Proteins) 221

12.2.5 Tissue 222

12.3 Optical Effects for Biochemical Sensors 222

12.3.1 Spectral Absorption 222

12.3.2 Phase Shift 223

12.3.3 Fluorescence 223

12.3.4 Luminescence 223

12.3.5 Raman Scattering 224

12.3.6 Nonlinear Optical (NLO) Effects 224

12.4 Preferred Sensing Principles for Optical Biochips 224

12.4.1 Evanescent Wave Sensing 225

12.4.2 Fluorescence Sensing 228

12.5 Readout Methods for Evanescent Wave Sensors 229

12.5.1 Angular Scanning 229

12.5.2 Wavelength Tuning 230

12.5.3 Grating Coupler Chirping 230

12.6 Substrates for Optical Biochips 230

12.7 Realization Example of an Optical Biosensor/Biochip: WIOS 231

12.8 Outlook: Lab-on-a-Chip Using Organic Semiconductors 232

12.8.1 Basics of Organic Semiconductors 233

12.8.2 Organic LEDs 233

12.8.3 Organic Lasers 234

12.8.4 Organic Photodetectors and Image Sensors 234

12.8.5 Organic Photovoltaic Cells 234

12.8.6 Organic Field Effect Transistors and Circuits 235

12.8.7 Monolithic Photonic Microsystems Using Organic Semiconductors 235

13 CMOS Single-Photon Systems for Bioimaging Applications / E. Charbon 239

13.2 Spectroscopy 240

13.3 Lifetime Imaging 242

13.4 Time-of-Flight in Bio- and Medical Imaging 244

13.5 System Considerations 245

14 Optical Trapping and Manipulation for Biomedical Applications / A. Chiou, M.-T. Wei, Y.-Q. Chen, T.-Y. Tseng, S.-L. Liu, A. Karmenyan, C.-H. Lin 249

14.2 Theoretical Models for the Calculation of Optical Forces 252

14.2.1 The Ray-Optics (RO) Model 252

14.2.2 Electromagnetic (EM) Model 255

14.3 Experimental Measurements of Optical Forces 255

14.3.1 Axial Optical Force as a Function of Position along the Optical Axis 255

14.3.2 Transverse Trapping Force Measured by Viscous Drag 257

14.3.3 Three-Dimensional Optical Force Field Probed by Particle Brownian Motion 257

14.3.4 Optical Forced Oscillation 261

14.4 Potential Biomedical Applications 265

14.4.1 Optical Forced Oscillation for the Measurement of Protein-Protein Interactions 266

14.4.2 Protein-DNA Interaction 267

14.4.3 Optical Trapping and Stretching of Red Blood Cells 269

15 Laser Tissue Welding in Minimally Invasive Surgery and Microsurgery / R. Pini, F. Rossi, P. Matteini, F. Ratto 275

15.2 Laser Welding in Ophthalmology 281

15.2.1 Laser Welding of the Cornea 281

15.2.2 Combing Femtosecond Laser Microsculpturing of the Cornea with Laser Welding 285

15.2.3 Laser Closure of Capsular Tissue 287

15.3 Applications in Microvascular Surgery 289

15.4 Potentials in Other Surgical Fields 291

15.4.1 Laser Welding of the Gastrointestinal Tract 291

15.4.2 Laser Welding in Gynaecology 291

15.4.3 Laser Welding in Neurosurgery 292

15.4.4 Laser Welding in Orthopaedic Surgery 292

15.4.5 Laser Welding of the Skin 292

15.4.6 Laser Welding in Urology 293

15.5 Perspectives of Nanostructured Chromophores for Laser Welding 293

16 Photobiology of the Skin / A.P. Pentland 301

16.1 Basics of Skin Structure: Cell Types, Skin Structures, and Their Function 301

16.2 Effects of Light Exposure on Skin 304

16.3 Sun Protection and Sunscreens 309

16.4 Phototherapy: Use of Light for Treatment for Skin Disease 311

17 Advanced Photodynamic Therapy / B.C. Wilson 315

17.2 Basic Principles and Features of "Standard PDT" 316

17.3 Novel PDT Concepts 319

17.3.1 Two-Photon PDT 319

17.3.2 Metronomic PDT 322

17.3.3 PDT Molecular Beacons 323

17.3.4 Nanoparticle-Based PDT 325

17.4 PDT Dosimetry Using Photonic Techniques 327

17.5 Biophotonic Techniques for Monitoring Response to PDT 330

17.6 Biophotonic Challenges and Opportunities in Clinical PDT 331.

Notes:

Includes bibliographical references and index.

ISBN:

9783540767794

3540767797

OCLC:

272307116