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FIREPOWER IN THE LAB: Automation in the Fight Against Infectious Diseases and Bioterrorism
FIREPOWER IN THE LAB
Automation in the Fight Against Infectious Diseases and Bioterrorism
Scott I. Layne, Tony J. Beugelsdijk, and C. Kumar N. Patel, Editors
JOSEPH HENRY PRESS
Washington, D.C.
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FIREPOWER IN THE LAB: Automation in the Fight Against Infectious Diseases and Bioterrorism
Joseph Henry Press
2101 Constitution Avenue, N.W. Washington, D.C. 20418
The Joseph Henry Press, an imprint of the National Academy Press, was created with the goal of making books on science, technology, and health more widely available to professionals and the public. Joseph Henry was one of the founders of the National Academy of Sciences and a leader of early American science.
This volume is based on a colloquium “Automation in Threat Reduction and Infectious Disease Research: Needs and New Directions,” held in Washington, D.C., on April 29-30, 1999. Financial support for this project was provided by the Centers for Disease Control and Prevention, the U.S. Department of Energy, the U.S. Department of Health and Human Services Office of Emergency Preparedness, and the Los Alamos National Laboratory. Additional sponsorship was provided by the Association for Laboratory Automation, the Institute of Medicine, the National Academy of Engineering, and the University of California, Los Angeles.
The contents of this volume are based on presentations and discussions that took place during the colloquium. Authors had the opportunity to update references up to the date of publication. Any opinions, findings, conclusions, or recommendations expressed in this volume are those of the editors or authors and do not necessarily reflect the views of the National Academies or the organizations that provided support for the project.
Library of Congress Cataloging-in-Publication Data
Firepower in the lab : automation in the fight against infectious diseases and bioterrorism / Scott P. Layne, Tony J. Beugelsdijk, and C. Kumar N. Patel, editors.
p. ; cm.
Includes bibliographical references and index.
ISBN 0-309-06849-5 (alk. paper)
1. Medical laboratories—Automation—Congresses. 2. Medicine—Research—United States. 3. Laboratories—Technological innovations—United States. 4. Bioterrorism. I. Layne, Scott P. II. Beugelsdijk, Tony J., 1949- III. Patel, C. Kumar N.
[DNLM: 1. Automation—Congresses. 2. Communicable Disease Control—Congresses. 3. Containment of Biohazards—Congresses. 4. Food Contamination—prevention & control—Congresses. 5. Laboratory Infection—prevention & control—Congresses. QY 23 F523 2001]
R858.A2 F55 2001
610′.285—dc21
2001024533
Copyright 2001 by the National Academy of Sciences. All rights reserved.
Printed in the United States of America.
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FIREPOWER IN THE LAB: Automation in the Fight Against Infectious Diseases and Bioterrorism
CONTENTS
Preface
vii
1 Where the Bucks Stop: A Case for Intermediate-Scale Grants
C. Kumar N. Patel
1
2 Tackling Grand Challenges with Powerful Technologies
Scott P. Layne, Tony J. Beugelsdijk, and C. Kumar N. Patel
5
Part I:
Infectious Diseases
3 The Application of Mathematical Models in Infectious Disease Research
Roy M. Anderson
31
4 Expanding the Worldwide Influenza Surveillance System and Improving the Selection of Strains for Vaccines
Nancy J. Cox
47
5 Addressing Emerging Infectious Diseases, Food Safety, and Bioterrorism: Common Themes
James M. Hughes
55
6 Laboratory Firepower for AIDS Research
Scott P. Layne and Tony J. Beugelsdijk
61
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FIREPOWER IN THE LAB: Automation in the Fight Against Infectious Diseases and Bioterrorism
7 Input/Output of High-Throughput Biology: Experience of the National Center for Biotechnology Information
David J. Lipman
85
8 Applications of Modern Technology to Emerging Viral Infections and Vaccine Development
Gary J. Nabel
93
9 Next Steps in the Global Surveillance for Anti-Tuberculosis Drug Resistance
Ariel Pablos-Mendez
101
10 Antibiotic Discovery by Microarray-Based Gene Response Profiling
Gary K. Schoolnik and Michael A. Wilson
113
11 Sequencing Influenza A from the 1918 Pandemic, Investigating Its Virulence, and Averting Future Outbreaks
Jeffery K. Taubenberger
123
Part II:
Food Supply
12 Ensuring Safe Food: An Organizational Perspective
John C. Bailar III
133
13 Foodborne Pathogen and Toxin Diagnostics: Current Methods and Needs Assessment from Surveillance, Outbreak Response, and Bioterrorism Preparedness Perspectives
Susan E. Maslanka, Gerald Zirnstein, Jeremy Sobel, and Bala Swaminathan
143
14 Food Safety: Data Needs for Risk Assessment
Joseph V. Rodricks
165
Part III:
Bioterrorism and Biowarfare
15 Biological Weapons: Past, Present, and Future
Ken Alibek
177
16 National Innovation to Combat Catastrophic Terrorism
Ashton Carter
187
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FIREPOWER IN THE LAB: Automation in the Fight Against Infectious Diseases and Bioterrorism
17 Flow Cytometry Analysis Techniques for High-Throughput Biodefense Research
James H. Jett, Hong Cai, Robert C. Habbersett, Richard A. Keller, Erica J. Larson, Babetta L. Marrone, John P. Nolan, Xuedong Song, Basil Swanson, and Paul S. White
193
18 Forensic Perspective on Bioterrorism and the Proliferation of Bioweapons
Randall S. Murch
203
19 Biological Warfare Scenarios
William Patrick III
215
Part IV:
Further Applications and Technologies
20 Integration of New Technologies in the Future of the Biological Sciences
David J. Galas and T. Gregory Dewey
227
21 New Standards and Approaches for Integrating Instruments into Laboratory Automation Systems
Torsten A. Staab and Gary W. Kramer
243
22 High-Throughput Sequencing, Information Generation, and the Future of Biology
J. Craig Venter
261
23 Summary and Next Steps
Scott P. Layne, Tony J. Beugelsdijk, and C. Kumar N. Patel
267
APPENDIXES
A Contributors
271
B Automation in Threat Reduction and Infectious Disease Research: Needs and New Directions (Agenda of the April 1999 Colloquium)
277
Index
283
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FIREPOWER IN THE LAB: Automation in the Fight Against Infectious Diseases and Bioterrorism
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FIREPOWER IN THE LAB: Automation in the Fight Against Infectious Diseases and Bioterrorism
PREFACE
In April 1999 a group of 200 experts in the fields of infectious diseases, food safety, bioterrorism mitigation, and molecular medicine gathered for a colloquium at the National Academy of Sciences in Washington, D.C. What brought this diverse group of individuals together was the understanding that each of their various disciplines must contend with certain “grand” problems that require enormous quantities of laboratory-based data to make progress. The various scientific challenges discussed during the meeting included (1) fighting deadly infectious diseases such as influenza A epidemics, multidrug-resistant tuberculosis, and the human immunodeficiency virus; (2) ensuring safe food by reducing risks, detecting pathogens and toxins, and investigating infectious disease outbreaks; (3) mitigating bioterrorism and biowarfare by preventing attacks, characterizing agents, and minimizing aftermaths; and (4) facilitating work on human genetics and molecular medicine, especially in predicting cancers, diagnosing diseases, and tailoring medications.
Meeting participants identified the various needs in their disciplines as well as the accomplishments that would be possible if such needs were met with high-throughput laboratory and informatics resources. Participants emphasized problems involving large populations of people and/or significant numbers of genetic variations that, because of their sheer size, justify focused efforts to create and analyze enormous quantities of laboratory-based data. Within several years the associated databases are envisioned to grow to ~1015 bits (petabits); thus, the limiting factor is that humans, unaided, are not capable of producing such vast inventories of data.
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FIREPOWER IN THE LAB: Automation in the Fight Against Infectious Diseases and Bioterrorism
Specialists surveyed the available building blocks for establishing petabit-generating user facilities—including robotics, laboratory automation, lab-on-a-chip, informatics, Internet, and process control innovations. They noted that, for the first time, all of the necessary pieces are available for building flexible and programmable laboratory firepower (a capability referred to as “mass customized testing via the Internet”). Although petabit-generating labs are available to medical and biological researchers in industry, they are not available to researchers in academic institutions. Such allocation of resources is currently shifting large-scale undertakings into the private sector and away from the public domain.
Policymakers noted that few, if any, government grants are available for intermediate-cost research efforts (e.g., user facilities), although grants are available for many small-cost (e.g., individual-investigator) and certain large-cost projects (e.g., human genome). Herein lies the most significant obstacle to obtaining adequate funding. User facilities that are dedicated to tackling grand problems will likely cost $20 million to start up over a 2-year period and $5 million to supply and operate annually. Yet no single government agency offers grants for such intermediate-cost research efforts, and frequently it is impossible to coordinate major funding across two or more agencies. Major philanthropic foundations may be a more realistic source of funds.
Meeting participants also discussed what approaches might be effective in surmounting such funding obstacles. One practical idea that gained wide support at the colloquium was that if researchers start with an especially compelling problem—such as a widespread and potentially catastrophic infectious disease—government agencies ultimately might be persuaded to offer much needed medium-level grants.
The chapters in this volume come from invited talks at the colloquium. They are arranged according to the four scientific challenges—infectious diseases, food safety, bioterrorism, and genomics—discussed during the meeting, with more detailed “technology” chapters interspersed between “scientific” chapters. The second chapter, “Tackling Grand Challenges with Powerful Technologies” offers an overview and perspective on the key topics in this volume. The last chapter, “Summary and Next Steps,” offers unofficial, yet important, conclusions and recommendations that emerged from the meeting.
We wish to thank the colloquium's sponsors for institutional and financial support: Association for Laboratory Automation; Centers for Disease Control and Prevention; U.S. Department of Energy; U.S. Department of Health and Human Services Office of Emergency Preparedness; Institute of Medicine; Los Alamos National Laboratory; National Academy of Engineering; and the University of California, Los Angeles. We also thank the members of the organizing committee for their help in
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FIREPOWER IN THE LAB: Automation in the Fight Against Infectious Diseases and Bioterrorism
building the program: Donald S. Burke, Irvin S. Y. Chen, Raymond E. Dessy, Robin A. Felder, Maurice Hilleman, James M. Hughes, Gary W. Kramer, David J. Lipman, Michael Osterholm, William E. Paul, Robert T. Schooley, and Alejandro C. Zaffaroni. We especially thank Jonathan Davis and Andrew Pope at the Institute of Medicine for their interests and extra efforts. Finally, we acknowledge and thank Kathi E. Hanna for her expert editorial assistance in preparing this volume.
SCOTT P. LAYNE,
TONY J. BEUGELSDIJK, and
C. KUMAR N. PATEL, Editors
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FIREPOWER IN THE LAB: Automation in the Fight Against Infectious Diseases and Bioterrorism
FIREPOWER IN THE LAB
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