Biomedical Applications of Synchrotron Infrared Microspectroscopy

by Moss, David

• ISBN13: 9780854041541
• ISBN10: 0854041540
• Edition: 1st
• Format: Hardcover
• Copyright: 2011-01-06
• Publisher: Royal Society of Chemistry

Summary

Focusing on biomedical IR spectroscopy, this volume presents a practical 'how to' guide for those new to the field of biomedical synchrotron IR microspectroscopy and imaging. The text describes the fundamentals of synchrotrons and FTIR spectroscopy.

Table of Contents

Fundamentals
Vibrational Spectroscopy: What Does the Clinician Need?	p. 3
Introduction	p. 3
Vibrational Spectroscopy in Cancer	p. 6
Introduction	p. 6
Screening, Early Diagnosis and Surveillance	p. 7
Therapy	p. 9
Vascular Disease	p. 13
Introduction	p. 13
Pathophysiology	p. 13
Vibrational Spectroscopy in Vascular Disease	p. 15
Microbiology and Infective Disease	p. 17
Conclusions	p. 20
References	p. 20
Mid-infrared Spectroscopy: The Basics	p. 29
Introduction	p. 29
Mid-infrared Radiation and Mid-infrared Spectroscopy	p. 30
Electromagnetic Radiation: What is it?	p. 30
Mid-infrared Radiation: What is it?	p. 31
What is Mid-infrared Spectroscopy?	p. 32
Quantitative Mid-infrared Spectroscopy: The Basics	p. 34
Mid-infrared Spectroscopy Instrumentation	p. 35
What is FT-IR? Why FT-IR?	p. 35
FT-IR Microscopy	p. 41
Why Synchrotron-sourced Mid-infrared FT-IR Microspectroscopy?	p. 42
Mid-infrared Spectroscopy: Sampling Techniques and Practices	p. 43
Transmission Sampling Technique	p. 46
Transflection Sampling Technique	p. 47
Attenuated Total Reflection (ATR) Technique	p. 48
ATR Microspectroscopy	p. 51
Near-field FT-IR Microscopy	p. 52
FT-IR Mapping and Imaging Techniques	p. 54
Mid-infrared Spectroscopy: Data Analysis Techniques	p. 55
How Does Mid-infrared Spectroscopy Relate to and Differ from Near-infrared, Far-infrared and Raman Spectroscopy?	p. 56
Fundamental Molecular Vibrations: Mid-infrared and Raman Bands	p. 56
Near-infrared Spectroscopy	p. 61
Far-infrared/THz Spectroscopy	p. 61
Raman Spectroscopy	p. 62
References	p. 63
Infrared Synchrotron Radiation Beamlines: High Brilliance Tools for IR Spectromicroscopy	p. 67
Introduction	p. 67
Infrared Synchrotron Radiation: Historical Background	p. 69
Basic Principles of Synchrotron Radiation	p. 72
Synchrotron Radiation Properties	p. 73
Brilliance	p. 74
Collimation	p. 75
Polarization	p. 76
Stability	p. 76
Time Structure	p. 77
What is an SR Beamline?	p. 78
SR Beamlines and IR Instrumentation for Spectroscopy and Microscopy	p. 82
IR Spectromicroscopy	p. 83
Synchrotron Radiation and Imaging IR	p. 87
Biomedical Applications at IRSR Beamlines	p. 88
Status and Perspectives of IRSR Facilities	p. 94
Conclusions	p. 99
References	p. 100
Raman Microscopy: Complement or Competitor?	p. 105
Introduction	p. 105
Raman Spectroscopy - a Brief History	p. 106
What is Raman Spectroscopy?	p. 108
How is Raman Scattering Measured?	p. 112
System Calibration	p. 118
Raman Spectroscopy for Diagnostics and Biochemical Analysis	p. 122
Raman Microscopy and Imaging at Cellular and Subcellular Levels	p. 127
Comparison to FTIR - Pros and Cons	p. 129
Physical Principles	p. 129
Spatial Resolution	p. 130
Fluorescence and Scattering	p. 133
Photodegradation	p. 134
Signal to Noise	p. 135
Conclusions	p. 137
References	p. 139
Addendum A - Raman Calibration Procedure	p. 142
Technical Aspects
Preparation of Tissues and Cells for Infrared and Raman Spectroscopy and Imaging	p. 147
Introduction	p. 147
Tissue Preparation	p. 148
Introduction to Tissue Preparation Methods	p. 148
Fresh and Cryopreserved Tissue	p. 150
Chemical Fixation of Tissue	p. 152
Paraffin Embedded Tissue	p. 155
Cell Preparation	p. 158
Introduction to Cell Preparation Methods	p. 158
Chemical Fixation of Cells	p. 159
Cell Preparation for Biomechanislic Studies	p. 168
Growth Medium and Substrate Effects on Spectroscopic Examination of Cells	p. 171
Preparation of Living Cells for FTIR and Raman Studies	p. 177
FTIR Studies	p. 177
Raman Studies	p. 180
Conclusions	p. 183
References	p. 185
Data Acquisition and Analysis in Biomedical Vibrational Spectroscopy	p. 192
Introduction	p. 192
Standardisation of the Infrared Spectral Measurements	p. 193
Assessing the Quality of the Obtained Spectra	p. 204
Spectral Pre-processing	p. 206
Data Analysis: Quantitative Analysis	p. 209
Data Analysis: Classification	p. 210
Unsupervised Classification Analysis	p. 210
Supervised Classification Analysis	p. 214
The DPR Approach	p. 216
The Role of Independent Validation	p. 217
Conclusions	p. 220
Acknowledgements	p. 221
Noise and Reproduction Error	p. 221
Differentiation Indices	p. 223
References	p. 223
Synchrotron Radiation as a Source for Infrared Microspec-troscopic Imaging with 2D Multi-Element Detection	p. 226
Introduction	p. 226
Optical Issues for Infrared Microspectroscopy	p. 228
The Standard Infrared Microspectrometer	p. 228
The Schwarzschild Microscope Objective	p. 229
The FPA Infrared Microspectrometer	p. 230
The Synchrotron Infrared Source	p. 232
Basic Properties of the Synchrotron Infrared Source	p. 233
Infrared Microspectroscopy using the Synchrotron Source	p. 234
Imaging at the Diffraction Limit	p. 235
Imaging and the Point Spread Function	p. 235
Performance with the Synchrotron Source and a Single-Element Detector	p. 238
Comparing Synchrotron IR Imaging with Internal Source-based FPA Imaging	p. 240
Diffraction Effects and Issues for PSF Deconvolution	p. 244
Focal Plane Array IR Microspectroscopy with the Synchrotron Source	p. 248
Matching the Dipole Bend Source to the FPA Microspectrometer	p. 249
Initial Results using the Synchrotron Source and FPA	p. 250
Basic PSF Deconvolution with FPA Microspectrometers	p. 253
Opportunities for Advanced 2D Image Deconvolution	p. 254
Conclusions	p. 255
References	p. 256
Scattering in Biomedical Infrared Spectroscopy	p. 260
Introduction to Scattering in Infrared Spectroscopy	p. 260
Mie Scattering	p. 262
Complex Refractive Index	p. 262
The Imaginary Refractive Index, k	p. 262
The Real Refractive Index, n	p. 263
Resonant Mie Scattering (RMieS)	p. 264
Extended Multiplicative Signal Correction (EMSC)	p. 266
Resonant Mie Scattering Correction using the Extended Multiplicative Signal Correction (RMieS-EMSC)	p. 268
Construction of Mie Scattering Efficiency Database	p. 269
Decomposition of the Resonant Mie Scattering Efficiency Database, Q	p. 270
Evaluation of the RMieS-EMSC Algorithm	p. 271
Correction of Real Spectra	p. 272
Conclusions	p. 274
References	p. 275
Case Studies
Synchrotron Based FTIR Spectroscopy in Lung Cancer. Is there a Niche?	p. 279
Introduction	p. 279
Lung Cancer Screening	p. 280
Lung Cancer Diagnosis	p. 283
Treatment of Lung Cancer	p. 286
Conclusions	p. 287
References	p. 287
Head and Neck Cancer: Observations from Synchrotron-sourced Mid-infrared Spectroscopy Investigations	p. 291
Introduction	p. 291
Experimental Work	p. 293
Mid-infrared Synchrotron Radiation FT-IR Studies of Oral Tissue Sections	p. 295
Mid-infrared Synchrotron Radiation FT-IR Studies of Cultured Cells	p. 308
Raman Studies of H&N Samples	p. 312
Conclusions	p. 313
References	p. 314
Single Cell Analysis of TSE-infected Neurons	p. 315
Introduction	p. 315
IR-Spectroscopy and the Composition of Complex Biological Material	p. 316
Why apply Synchrotron FTIR Microspectroscopy (SFTIRM)?	p. 321
Materials and Methods	p. 322
The Study Design	p. 322
Animal Experiments and Sample Preparation	p. 322
Data Acquisition Techniques	p. 323
Data Evaluation Techniques	p. 324
Results	p. 326
Assessment, Discussion and Conclusions	p. 330
Acknowledgements	p. 333
References	p. 333
Monitoring the Effects of Cisplatin Uptake in Rat Glioma Cells: A Preliminary Study Using Fourier Transform Infrared Synchrotron Microspectroscopy	p. 339
Introduction	p. 339
Methodology	p. 341
Cell Culture, Cisplatin Preparation and Treatment	p. 341
Synchrotron FTIR Microspectroscopy	p. 341
Neural Network Classification	p. 342
Results	p. 343
Discussion	p. 346
Conclusions	p. 348
References	p. 349
Mid-Infrared Reflectivity of Mouse Atheromas: A Case Study	p. 351
Introduction	p. 351
Existing Diagnostic Methods	p. 353
Pathologic and Biochemical Features of Vulnerable Plaques	p. 354
Concept of Mid-infrared Reflectivity of Atherosclerotic Aorta	p. 356
Mid-infrared Reflectivity of Experimental Atherosclerosis	p. 358
Discussion	p. 362
Acknowledgements	p. 366
References	p. 366
Subject Index	p. 369
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