Ebook: Advances in Biophotonics

This volume is the result of the first NATO Advanced Study Institute (ASI) on the topic “Biophotonics: From Fundamental Principles to Health, Environment, Security and Defence Applications” held in Ottawa, Canada, September 29 – October 9, 2004. This ASI was particularly timely, since the field of biophotonics is rapidly emerging in both academia and industry: for example, the number of hits for “biophotonics” if it is entered in the internet search engine Google® has quadrupled in the last year. The meeting was notable for the extent of international attendance, with 116 participants from 18 different countries, including a very high representation from former Sovietbloc countries, demonstrating the intense interest in this topic. A full list of the speakers and topics covered at the ASI is given below.

What then is biophotonics? In the most general terms, it is the convergence of photonics and life sciences. Photonics – the science and technology of light generation, manipulation and measurement – has itself seen a remarkable expansion in the past 20 years, both in research and in commercialization, particularly in telecommunications. Despite, or perhaps partly because of, the downturn in this sector, there has been substantial transfer of photonic technologies in the past 5 years into biophotonics applications. Nowhere is this clearer than in the sub-surface tissue imaging technique of optical coherence tomography (discussed in the chapters by V.V. Tuchin and B.C. Wilson), in which many of the key components are taken straight from optical telecom (light sources, fiber splitters, optical circulators, etc). This technology transfer has greatly accelerated the development of biophotonic techniques and applications.

Conversely, the life sciences have an increasing need for new technologies to which photonics can make significant contributions. As biology and medicine move into the post-genomics era, it is increasingly important to have highly sensitive tools for probing cells, tissues and whole organism structure and functions. The optical spectrum (UV-visible-infrared) is well suited to this, since the quantum energy of optical photons is comparable to molecular energy levels of biomolecules, so that optical spectroscopies and imaging techniques provide rich biomolecular information. Examples are given in the chapters by J. Chan and colleagues and S. Lane et al. in biochemical analysis and in single-cell analysis, respectively, using Raman spectroscopy.

The sensitivity of modern optical techniques even allows measurements of single molecules, as discussed by T. Huser et al. Through photonic technologies such optical fibers, as discussed in the chapter by M. Ben-David and I. Gannot, and sensitive imaging detectors, these measurements can often be done in a non- or minimally-invasive way, which is tremendously valuable for clinical and remote-sensing applications. The technological elegance of photonics is illustrated both by this chapter and that by Cartwright in the domain of optical biosensors, which are becoming ubiquitous in many applications, including biomedical, environmental and bio/chemo security. This breadth of applications of specific optical techniques is well illustrated also in the chapter by V.M. Savov on chemiluminscence and bioluminescence.

At the same time, optical wavelengths are comparable to cellular/subcellular structure dimensions, so that imaging at very high spatial resolution is possible. Photonic technologies have thus revolutionized the field of optical microscopy, as illustrated in the chapters by H. Schneckenburger and by T. Huser et al.

In clinical medicine this ability to probe and image tissues is leading to a wide range of novel diagnostic methods. Examples of these techniques are given by Matthews and colleagues. In parallel, therapeutic applications of light have developed rapidly over the past 20 years, with many applications of surgical lasers operating by photothermal or photomechanical interactions with tissue. The application of photochemical interactions is presented in the chapter by B.C. Wilson on the specific technique of photodynamic therapy using light-activated drugs. The principles of photobiology that underlie these photothermal, photochemical and photomechanical effects are discussed in depth by P. Prasad. Complementing this, S. Tanev and colleagues provide an introduction to some exact modeling methods of tissue optics that determine how light energy is distributed in tissue, while V.V. Tuchin examines light propagation and interactions with blood, both theoretically and experimentally. Understanding these lighttissue interactions is key to optimizing the delivery of light to tissue, for both treatments and diagnostics.

Finally, the new field of nanotechnology is now penetrating into biophotonics. Examples include the use of nanoparticles such as metal nanospheres or rods and quantum dots for enhanced cell and tissue imaging and local light energy absorption. The chapter by C.E. Talley et al. discusses one specific implementation, namely the use of nanoparticles for enhancing Raman biospectroscopy.

As will be evident, this volume is not intended as a comprehensive text on biophotonics. Rather, it presents 'snapshots' of some of the most exciting developments, from a perspective of photonic technologies, and life-sciences applications. The editors hope that the reader will be equally excited and encouraged to pursue further in-depth reading, using the extensive references provide by the authors of each chapter.

The article reviews the basics and some of the applications of the three-dimensional finite-difference time-domain (FDTD) technique for simulation and modelling of light scattering by biological cells in an absorptive extra-cellular medium. The emphasis is on the details of the single particle light scattering version of FDTD approach including a comprehensive consideration of the far field transformation algorithm and the Uni-axial Perfectly Matched Layer (UPML) absorbing boundary conditions. As a demonstration, we consider two simulation scenarios. First, we consider the effect of absorption of the extra-cellular medium on the light scattering patterns from biological cells. The single cell scattering properties including scattering phase functions, extinction and absorption efficiencies are derived based on the volume integration of the internal fields. The simulation results show that absorption in the extra-cellular medium modify the light scattering patterns and need to be carefully taken into account. Second, we present some initial results on the application of the FDTD technique to study the nature of the optical clearing effect - the increased light transmission through biological cells due to the matching of the refractive indices of some of their components to that of the extra-cellular medium. We show that the FDTD approach has a significant potential for studying the control of biological tissue optical properties by external administration of chemical agents. The implications of the FDTD approach for biomedical diagnostics research is also discussed.

This chapter aims to review the recent results on the optical clearing of the naturally turbid biological tissues and blood using the optical immersion technique. Basic principles of the technique, its advantages, limitations, and future are discussed. The refractive index matching concept for enhancement of in-depth light penetration into tissues and blood is discussed on the basis of in vitro and in vivo studies of optical clearing using optical spectroscopy, polarization and coherence-domain techniques.

Photobiology deals with the interaction of light with biological matter. Hence, it forms the core of biophotonics which utilizes interactions of light with biological specimens. Here we discuss the interactions of various molecular, cellular and tissue components with light. The content is mostly taken from Chapter 6 of this author's monograph on biophotonics (Prasad, 2003). The various light-induced radiative and non-radiative processes are described, along with a discussion of the various photochemical processes. Photochemistry in cells and tissues can also be initiated by externally added exogenous substances, often called photosensitizers, which form the basis for photodynamic therapy. The various types of scattering processes occurring in a tissue as described here, together with light absorption, determine the penetration of light of a given wavelength into a particular type of tissue. Methods of measurement of optical reflection, absorption and scattering properties of a tissue are introduced. Some important manifestations of non-radiative processes in a tissue, used for a number of biophotonics applications such as laser tissue engineering and laser microdissection are thermal, photoablation, plasma- induced ablation and photodisruption. These processes are defined. An emerging area of biophotonics is in vivo imaging and spectroscopy for optical diagnosis. This topic is covered, along with the various methods of light delivery for in vivo photoexcitation. Another exciting in vivo biophotonics area is that of optical biopsy to detect the early stages of cancer. This topic is covered as well. Understanding of structure and functions at the single biomolecule and bioassembly levels is a major thrust of molecular and structural biology. This topic is also covered here. The use of novel optical techniques allows one to probe processes at the single molecule level.

Recent years have seen a growing interest in the use of Raman-based spectroscopy as an analytical tool for the chemical analysis of biological samples. Raman spectroscopy has found many applications in cellular and structural biology, biomedicine, and biodetection. Its attractiveness for live biological studies lies mainly in its high sensitivity to molecular interactions and small molecular scale conformational changes. In addition, the noninvasiveness of this approach permits both in-vitro and in-vivo studies. This increased interest has been a result of advances in both instrumentation and techniques that have enabled improved data acquisition and data interpretation. This chapter addresses recent advances in Raman-based techniques and highlights their uses in specific biological studies.

Surface-enhanced Raman scattering is a powerful tool for the investigation of biological samples. Following a brief introduction to Raman and surface-enhanced Raman scattering, several examples of biophotonic applications of SERS are discussed. The concept of nanoparticle-based sensors using SERS is introduced and the development of these sensors is discussed.

This chapter provides a basic introduction to single molecule fluorescence detection. A brief introduction provides the motivation for detecting fluorescence at the single molecule level and seeks to explain why single molecule spectroscopy has gained so much popularity, especially in the biosciences. A brief history of single molecule detection will discuss how single molecule sensitivity was achieved historically and how it has progressed since then. Details of the typical instrumentation are provided with an emphasis on reproducibility for newcomers to this field. We then discuss sample preparation for single molecule experiments, we will detail what evidence argues for the detection of single fluorescent molecules, and we will end with a brief outlook into the future of this field.

Information on the structure and metabolic changes of biological systems is accurately obtained by characterization of the molecular mechanisms of chemiluminescence (CL) and bioluminescence (BL). The applications of CL and BL in medicine, biotechnology, environment, military defense, agriculture and space research are discussed. The advantages, specifications and limitations of these methods in comparison to other physical and chemical approaches are described.

This chapter presents the basic sciences involved in photodynamic therapy, in terms of: the photophysical, photochemical and photobiological principles; the technologies of PDT light sources, delivery systems and dosimetry devices; and optical methods that are under development for monitoring the response of tissue to PDT. The current and potential medical applications are also indicated. The discussion includes both aspects of PDT that are well-established and new concepts in the science, technology or clinical applications, including work from the author's laboratory.

We present an overview of the research program of the Center for Biophotonics Science Technology (CBST) which is headquartered at the University of California at Davis. We define biophotonics as the application of photonic technologies their related scientific methods to medicine the biosciences. Our Center focuses on three grand-challenge-driven science technology themes: 1) advanced bioimaging 2) molecular cellular biophotonics 3) medical biophotonics. Examples of research within the advanced bioimaging theme include the development of structured illumination microscopy as a means to push image resolution up to five times the diffraction-limit ultra short pulse x-ray diffraction imaging to characterize single biomolecules. The molecular cellular theme projects use biophotonic techniques to investigate fundamental biological mechanisms (including those that relate to the pathogenesis of atherosclerosis cardiovascular disease) the photophysical behavior of phytochromes (fluorescent plant proteins) the molecular mechanisms of DNA damage recognitionrepair. In the medical theme area, we are developing applications for hyperspectral microscopy, optical biopsy methods and laser-activated shape memory polymers in image-guided surgery, cancer detection and vascular therapy, respectively. The Center actively supports and advocates the development of multidisciplinary research teams and areas of common technology development in all of its theme projects.