Microspectroscopy. Synchrotron Infrared. RSC PublishingteaJf. Biomedical Applications of. Synchrotron Light Germany. David Moss.

Transcription

1 Biomedical Applications of Synchrotron Infrared Microspectroscopy Edited by David Moss Synchrotron Light Germany Source ANKA, Karlsruhe Research Center, Karlsruhe, RSC PublishingteaJf

2 Contents Section 1: Fundamentals Chapter 1 Vibrational Spectroscopy: What Does the Clinician Need? 3 Sheila E. Fisher, Andrew T Harris, Nitish Khanna and Josep Sule-Suso 1.1 Introduction Vibrational Spectroscopy in Cancer Introduction Screening, Early Diagnosis and Surveillance Therapy Vascular Disease Introduction Pathophysiology Vibrational Spectroscopy in Vascular Disease Microbiology and Infective Disease Conclusions 20 References 20 Chapter 2 Mid-infrared Spectroscopy: The Basics 29 John M. Chalmers 2.1 Introduction Mid-infrared Radiation and Mid-infrared Spectroscopy Electromagnetic Radiation: What is it? Mid-infrared Radiation: What is it? What is Mid-infrared Spectroscopy? Quantitative Mid-infrared Spectroscopy: The Basics 34 RSC Analytical Spectroscopy Monographs No. 11 Biomedical Applications of Synchrotron Infrared Microspectroscopy Edited by David Moss Royal Society of Chemistry 2011 Published by the Royal Society of Chemistry, xiii

3 xiv Contents 2.3 Mid-infrared Spectroscopy Instrumentation What is FT-IR? Why FT-IR? FT-IR Microscopy Why Synchrotron-sourced Mid-infrared FT-IR Microspectroscopy? Mid-infrared Spectroscopy: Sampling Techniques and Practices Transmission Sampling Technique Transflection Sampling Technique Attenuated Total Reflection (ATR) Technique ATR Microspectroscopy Near-field FT-IR Microscopy FT-IR Mapping and Imaging Techniques Mid-infrared Spectroscopy: Data Analysis Techniques How Does Mid-infrared Spectroscopy Differ from Near-infrared, Relate to and Far-infrared and Raman Spectroscopy? Fundamental Molecular Vibrations: Mid-infrared and Raman Bands Near-infrared Spectroscopy Far-infrared/THz Spectroscopy Raman Spectroscopy 62 References 63 Chapter 3 Infrared Synchrotron Radiation Beamlines: High Brilliance Tools for IR Spectromicroscopy 67 Auguslo Marcelli and Gianfelice Cinque 3.1 Introduction Infrared Synchrotron Radiation: Historical Background Basic Principles of Synchrotron Radiation Synchrotron Radiation Properties Brilliance Collimation Polarization Stability Time Structure What is an SR Beamline? SR Beamlines and IR Instrumentation for Spectroscopy and Microscopy IR Spectromicroscopy Synchrotron Radiation and Imaging IR Biomedical Applications at IRSR Beamlines Status and Perspectives of IRSR Facilities 94

4 a Content.'! xv 3,9 Conclusions 99 References 100 Chapter 4 Raman Microscopy: Complement or Competitor? 105 Hugh J. Byrne, Ganesh D. Sockalingum and Nick Stone 4.1 Introduction Raman Spectroscopy Brief History What is Raman Spectroscopy? How is Raman Scattering Measured? System Calibration Raman Spectroscopy for Diagnostics and Biochemical - Analysis Raman Microscopy and Imaging at Cellular and Subcellular Levels Comparison to FTIR Pros and Cons Physical Principles Spatial Resolution Fluorescence and Scattering Photodegradation Signal to Noise Conclusions 137 References 139 Addendum A Raman Calibration Procedure 142 Section 2: Technical Aspects Chapter 5 Preparation of Tissues and Cells for Infrared and Raman Spectroscopy and Imaging 147 Fiona Lyng, Ehsan Gazi and Peter Gardner 5.1 Introduction Tissue Preparation Introduction to Tissue Preparation Methods Fresh and Cryopreserved Tissue Chemical Fixation of Tissue Paraffin Embedded Tissue Cell Preparation Introduction to Cell Preparation Methods Chemical Fixation of Cells Cell Preparation for Biomechanistic Studies Growth Medium and Substrate Effects on Spectroscopic Examination of Cells Preparation of Living Cells for FTIR and Raman Studies 177

5 xvi Contents FTIR Studies Raman Studies Conclusions 183 References 185 Chapter 6 Data Acquisition and Analysis in Biomedical Vibrational Spectroscopy 192 Peter Lasch and Wolfgang Petrich 6.1 Introduction Standardisation of the Infrared Spectral Measurements Assessing the Quality of the Obtained Spectra Spectral Pre-processing Data Analysis: Quantitative Analysis Data Analysis: Classification Unsupervised Classification Analysis Supervised Classification Analysis The DPR Approach The Role of Independent Validation Conclusions Acknowledgements 221 Appendix A: Noise and Reproduction Error 221 Appendix B: Differentiation Indices 223 References 223 Chapter 7 Synchrotron Radiation as a Source for Infrared Microspectroscopic Imaging with 2D Multi-Element Detection 226 G. L. Carr, L. M. Miller and P. Dumas 7.1 Introduction Optical Issues for Infrared Microspectroscopy The Standard Infrared Microspectrometer The Schwarzschild Microscope Objective The FPA Infrared Microspectrometer The Synchrotron Infrared Source Basic Properties of the Synchrotron Infrared Source Infrared Microspectroscopy using the Synchrotron Source Imaging at the Diffraction Limit Imaging and the Point Spread Function Performance with the Synchrotron Source and a Single-Element Detector Comparing Synchrotron IR Imaging with Internal Source-based FPA Imaging 240

6 Contents xvii Diffraction Effects and Issues for PSF Decon volution Focal Plane Array IR Microspectroscopy with the Synchrotron Source Matching the Dipole Bend Source to the FPA Microspectrometer Initial Results using the Synchrotron Source and FPA Basic PSF Deconvolution with FPA Microspectrometers Opportunities for Advanced 2D Image Deconvolution Conclusions 255 References 256 Chapter 8 Scattering in Biomedical Infrared Spectroscopy 260 Paul Bassan and Peter Gardner 8.1 Introduction to Scattering in Infrared Spectroscopy Mie Scattering Complex Refractive Index The Imaginary Refractive Index, k The Real Refractive Index, n Resonant Mie Scattering (RMieS) Extended Multiplicative Signal Correction (EMSC) Resonant Mie Scattering Correction using the Extended Multiplicative Signal Correction (RMieS-EMSC) Construction of Mie Scattering Efficiency Database Decomposition of the Resonant Mie Scattering Efficiency Database, Q Evaluation of the RMieS-EMSC Algorithm Correction of Real Spectra Conclusions 274 References 275 Section 3: Case Studies Chapter 9 Synchrotron Based FTIR Spectroscopy in Lung Cancer. Is there a Niche? 279 Josep Sule-Suso 9.1 Introduction Lung Cancer Screening 280

7 xviii Contents 9.3 Lung Cancer Diagnosis Treatment of Lung Cancer Conclusions 287 References 287 Chapter 10 Head and Neck Cancer: Observations from Synchrotron-sourced Mid-infrared Spectroscopy Investigations 291 Mark J. Tobin, John M. Chalmers, Andrew T. Harris and Sheila E. Fisher 10.1 Introduction Experimental Work Mid-infrared Synchrotron Radiation FT-IR Studies of Oral Tissue Sections Mid-infrared Synchrotron Radiation FT-IR Studies of Cultured Cells Raman Studies of H&N Samples Conclusions 313 References 314 Chapter 11 Single Cell Analysis of TSE-infected Neurons 315 Ariane Kretlow, Janina Kneipp, Peter Laseh, Michael Beekes, Lisa Miller and Dieter Naumann 11.1 Introduction IR-Spectroscopy and the Composition of Complex Biological Material Why apply Synchrotron FTIR Microspectroscopy (SFTIRM)? Materials and Methods The Study Design Animal Experiments and Sample Preparation Data Acquisition Techniques Data Evaluation Techniques Results Assessment, Discussion and Conclusions 330 Acknowledgements 333 References 333

8 Contents xix Chapter 12 Monitoring the Effects of Cisplatin Uptake in Rat Glioma Cells: A Preliminary Study Using Fourier Transform Infrared Synchrotron Microspectroscopy 339 K. R. Bambery, B. R. Wood, E. Schiiltke, B. H. J. Juwlink, T. May and D. McNaughton 12.1 Introduction Methodology Cell Culture, Cisplatin Preparation and Treatment Synchrotron FTIR Microspectroscopy Neural Network Classification Results Discussion Conclusions 348 References 349 Chapter 13 Mid-Infrared Reflectivity of Mouse Atheromas: A Case Study 351 Hoi- Ying N. Holman and Francis G. Blankenberg 13.1 Introduction Existing Diagnostic Methods Pathologic and Biochemical Features of Vulnerable Plaques Concept of Mid-infrared Reflectivity of Atherosclerotic Aorta Mid-infrared Reflectivity of Experimental Atherosclerosis Discussion 362 Acknowledgements 366 References 366 Subject Index 369