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Spie Press Book

An Engineering Introduction to Biotechnology
Author(s): J. Patrick Fitch
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Book Description

This tutorial will help technical professionals in optics determine whether their technologies have potential application in the life sciences. It also is useful as a 'prep class' for more detailed books on biology and biotechnology, filling the gap between fundamental and high-level approaches.

Book Details

Date Published: 10 January 2002
Pages: 144
ISBN: 9780819444974
Volume: TT55

Table of Contents
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Preface 5
Part I Introduction to Biology 8
Chapter 1 Basic Biology 9
1.1 Life 9
1.2 Cells-Eukarya, Archae, and Bacteria 11
1.3 Viruses, viroids, and prions 17
Chapter 2 Nucleic Acids as the Blueprint 19
2.1 Genetics to genomics 19
2.2 DNA 21
2.3 RNA 23
2.4 How DNA codes for protein 23
2.5 Genetic regulation 27
2.6 Mutations and disease 29
Chapter 3 Manipulating Nucleic Acids and Proteins 32
3.1 Sizing DNA and Protein 32
3.2 Blots 33
3.3 Cutting DNA and protein 34
3.4 Copying DNA 36
3.5 Genetic engineering 38
3.6 Protein expression 41
Chapter 4 An Integrated Approach for Biological Discovery 44
Part II Applications and Instrumentation 50
Chapter 5 DNA Sequencing 51
5.1 Sequencing approaches 51
5.2 Instruments 52
5.3 Automation 56
Chapter 6 Detecting Nucleic Acids 59
6.1 Environmental detection chips 59
6.2 Gene expression microarrays 60
6.3 Multi affinity assays 63
Chapter 7 Protein Structure 67
7.1 Nuclear magnetic resonance 67
7.2 X-ray crystallography 69
7.3 Computational structure prediction 71
Chapter 8 Appendix A: Units and Measures 73
8.1 Definitions 73
8.2 Order of magnitude calculations 74
Chapter 9 Appendix B: Nonscientific Issues 75
9.1 Safety 75
9.2 Ethical, legal and social issues 76
Recommended Reading 77
Index 78


Biology is usually presented differently than engineering and physical science. The physical sciences strongly promote a reductive approach that decomposes complex phenomena into simpler subsystems that can be incorporated into models. As an example, consider the high-energy physics community's pursuit of subatomic particles. The expectation is that models increase in accuracy with the goal of becoming predictive of the phenomena. Biology has been an observational science. The quantification and reduction of the complex phenomena observed in biology has not usually allowed a reductive approach. This can be a source of frustration for nonbiologists that often conclude the science is only a memorization activity with vocabulary and experimental anecdotes in place of models and predictive theories. One of the goals of this book is to present introductory biotechnology from the perspective of someone trained as a physical scientist.

This book is for technical professionals engineers, physical scientists, and technical managers and marketers. The goal is to create the opportunity for these professionals to evaluate if their technologies and organizations have relevant application in the life sciences. The plan is to introduce the basic concepts of biology emphasizing "omic" or "whole mass" approaches; showcase large-scale applications like DNA sequencing; and demonstrate technical successes with a few case studies of bioinstrumentation. The subtitle might be "omic" technologies for "ohmic" engineers. We do not attempt to present the detailed biochemistry, safety, or ethical issues that are also important components of biotechnology. Hopefully this approach will appeal to the reader, will facilitate new discoveries through the interaction of disciplines, and will enable follow-on reading of existing molecular biotechnology texts. The canonical reader of the book is an engineer that has not had biology or chemistry for a while. This book is offered as a "Prep Class" for the more detailed books on biology and biotechnology. I hope this book fills the gap and makes texts like Molecular Biotechnology by Glick and Pasternak reachable.

There are many ways to define biotechnology. Sometimes biotechnology is considered to be the use of engineering principles in biology. Two examples are producing new enzymes for laundry detergent and brewing beer constrained by safety, consumer appeal, and business considerations. Sometimes biotechnology is meant as the technical or engineering part of a life science program. This might include instrumentation and software for applications including drug discovery and DNA sequencing. One common interpretation is that biotechnology is synonymous to genetic engineering where functions are added or removed by modifying the nucleic acids in an organism.

In this book, biotechnology is any technique, technology or application that depends on or benefits from information obtained through the ability to extract, copy, modify, or reintroduce the nucleic acids of an organism.

Many people have enabled this writing endeavor and deserve acknowledgements. I am grateful to my family for their loving support and donating many nights and weekends required for this project. Thanks to the biologists at Lawrence Livermore National Laboratory that have encouraged me especially T. Carrano, L. Ashworth, J. Felton, P. McCready, and L. Stubbs. I have enjoyed collaborating with many exceptional engineers, computer scientists, and physical scientists including T. Slezak, J. Balch, and C. Davidson. Thanks to the staff at the SPIE for encouraging the Introduction to Genomics short courses and then this writing endeavor.

A special thanks to Bahrad Sokhansanj, a Ph.D. candidate at the time of this writing, for his many contributions and discussions and for his enthusiastic pursuit of our joint projects. Our paper together "Genomic engineering: moving beyond DNA sequence to function," Proceedings of IEEE, vol. 88, No. 12, pp.

1949-1971, Dec. 2000, was an excellent starting point for collecting the thoughts
presented in this book and for revising the SPIE short course.

There were also several people that provided significant input on drafts of the manuscript in particular, Janine Garnham, Beth Vitalis, and Tom Kuczmarski. A special thank you to Kathy Fitch for helping review every version of the manuscript.

I would also like to acknowledge the Public Health Image Library PHIL provided at the Centers for Disease Control (CDC) web site The CDC provided in the public domain the PHIL images used in this book. I have included the PHIL identification number and the source acknowledgement (organization and scientist) when available. Some of this work was performed under the auspices of the U.S. Department of Energy by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48.

An additional dedication to the heroic people aboard UA93 on September

11, 2001 is appropriate. As one of many people in the Washington, DC area that
day, thank you. May the knowledge derived from and the activities that follow this book honor your memory through applications beneficial to humanity

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