Active-X controls, 249
Acute respiratory distress syndrome, 57
Adaptive response, 115-116, 117
Adenoviral vector boost, 96
Advanced diagnostics
influenza, 21
microtechnologies, 20-21, 152, 153-154
point-of-use devices, 20-21
public health system, 196
sensitivity, 20
Affymetrix, Inc., 155
Africa
influenza surveillance, 52
Age
and mass immunizations, 40-41
and influenza, 48, 124, 128, 129
and spread of epidemics, 39
Agri-Screen, 152
AIDS. See HIV/AIDS
Alaskan wilderness, 124
Alert (ELISA system), 151
American Academy of Pediatrics, 58
American Society for Microbiology, 262
American Society for Testing and Materials (ASTM), 16, 17, 69, 244-245
Anthrax, 178, 179, 181, 183, 203-204, 222
Antibiotics.
See also Antimicrobial drug resistance
CDC guidelines for use, 58
discovery applications of high-throughput automated laboratories, 119-120
effect on normal flora, 119
microarray-based gene response profiling for, 113-120
mode of action, 117-118
pathway-specific inhibitors, 118
tissue-specific growth inhibitors, 115, 118-119
Antibodies
anti-hemagglutinin, 124
cross-sectional serological surveys, 37-38, 39
saliva-based tests, 41
Antigenic shift and drift, influenza viruses, 123, 124, 126, 127, 129
Antimicrobial drug resistance, 55
adherence to treatment and, 101
beta-lactamase-producing bacteria, 34, 35
in bioweapons agents, 179, 180, 183
and costs of treatment, 110
disease control programs and, 101, 102, 104, 107-108, 109
global situation, 103-104
isoniazid, 101-102, 104, 105, 106, 109, 114
laboratory issues, 102, 105-107, 109-110
malaria, 264
microarray gene response profiling, 114
pathway-specific inhibitors, 118
penicillin, 57
prevalence, 103-104
research recommendations, 108
response strategies, 58
rifampin, 101-102, 105, 106, 110, 155
Staphylococcus aureus,
surveillance, 21, 102, 105-107, 101-110
susceptibility testing of drugs, 8, 21, 102, 105-107, 109, 110, 155, 156-157
tuberculosis, 5, 8, 9, 18, 101-110, 114, 155
volume of drug use and, 35, 58, 101, 109
Antiviral strategies.
See also Vaccines
HIV/AIDS, 10, 61, 62, 72, 73, 80
recombinant DNA techniques and, 98-99
AOAC International, 173
Applied biology, 239-240
Applied Biosystems, 264
Arabidopsis genome, 263
Argentina, 104
Asia
influenza surveillance, 52
spread of infectious agents in, 32-34
tuberculosis, 103-104
Association for Laboratory Automation, 16-17
Association of Public Health Laboratories, 150
ASTM E1989-98. See Laboratory Equipment Control Interface Specification
Aum Shinrikyo cult, 59, 181, 221-222
Auto3-P Communications with Automated Clinical Laboratory Systems, Instruments, Devices, and Information Systems standard, 249
Avian influenza, 5, 9, 52, 124, 127, 268
Bacillus globigii (BG), 218, 223
Bacteriological Analytical Manual,
Barcode applications, 22
Batch science.
See also High-throughput automated laboratories assay scripts, 65, 66, 70, 74, 75
HIV/AIDS research, 65-69, 70, 72-75, 77-82
hierarchy of machines, 22-23, 71
implementation, 77-82
Influenza A prediction/aversion, 129-130
process control tools, 21-22, 66, 67, 69, 70, 74, 77
Bead-based assays, 19, 157-158, 195, 198-199, 200
Bennington, Vermont, 146
Bernoulli, Daniel, 32
BIACORE system, 153-154
Biocomputing.
See also Mathematical modeling
cell-sims, 232-233
and genome sequencing, 261, 264-266
Biocontainment facilities, 77, 150, 207, 209
Biodefense.
See also Bioforensics
flow cytometry applications, 19, 193-200
medical, 184-185
security strategy, 187-188, 205
Biodirected crystallization, 234
Bioforensics
collaboration at federal level, 208-209
critical components, 209-211
defined, 205-206
DNA technology, 198, 208, 210-211
national network, 204-206
needs, 206-208
Biological and Toxin Weapons Convention, 178, 179, 190-191
Biological sciences
data avalanche in, 236-237
discovery and technological change in, 228-234
Biology
applied, 239-240
as information science, 234-236
Biomedical databases, 85-86
Biosensor assays, 143, 153-154
Bioterrorism/biowarfare.
See also Biodefense;
Bioweapons;
Weapons of mass destruction
catastrophic, 187-191
challenges in mitigating, 13-15, 25-26, 140, 267
European concerns, 31
food contamination, 135, 139-140, 147-148, 149, 150, 153, 154, 160, 177, 181
forensic perspective on, 203-212
institutional coordination of response, 13, 141, 150, 160, 190, 206
interdisciplinary perspective, 13, 140, 190
international infrastructure for, 188-189
laboratory issues, 14-15
mathematical modeling applications, 31-32
New York City subway system scenario, 223
offensive components, 215-216
plants as targets, 263
preparedness and response strategies, 5-6, 13, 14-15, 21, 58-59, 148, 150, 153, 154, 184-185, 187-188, 189-191, 204, 262
religious cults and, 147, 181, 204, 221-222
San Francisco scenario, 218-220
simulations, 215-223
small attacks, 5
U.S. vulnerability to attacks, 58, 139-140, 180-181, 188-189, 203-204, 218-220
Biotinylated oligonucleotide probes, 157-158
Bioweapons
agents, 59, 178-179, 180, 181, 183, 203-204
convention/ban, 178, 179, 180, 190-191
costs and ease of production, 14, 177, 181
deployment/dissemination modes, 177-178, 215-218
dual-use production equipment/research, 182-183, 185
enforcement of bans on, 13, 180, 183, 190-191, 205
human-animal studies, 220-221
medical defense against, 184-185
nonproliferation assays, 198
operational, 179
proliferation risks, 14, 181-183, 203-212, 220-221
Soviet program, 13-14, 178-180, 181-183, 203
strategic, 179
terrorist threat, 180-181
U.S. program, 14, 178, 179, 222
Black Death. See Plague
BLAST (Basic Local Alignment Search Tool), 88
Bomb Data Center, 206
Botulism, 158
Bovine spongiform encephalopathy (BSE), 42-45
Bristol-Myers Squibb (BMS), 249, 258
Brown, Patrick, 114
Brucellosis, 179
Burke, Edmund, 136
Burke, John, 58
Campylobacter jejuni,
Canada, 55
Cancer Genome Anatomy Project, 90-91
cDNA
labeling and hybridization, 18, 113, 114-115, 155
Celera, 265
Cell-sims, 232-233
Center for Food Safety and Applied Nutrition, 140
Centers for Disease Control and Prevention (CDC)
bioterrorism response, 150, 208
emerging-infections initiative, 56, 57-58, 59
guidelines for antibiotic use, 58
influenza projections, 8
and WHO influenza surveillance, 10, 47, 49
Central Intelligence Agency, 190
Chain terminating amplification and gel electrophoresis, 18
Chargaff, Erwin, 228
Chemokine receptors, 61
Chicken pox, 39-40
tuberculosis, 103-104, 106, 107
Cholera toxin detection, 199-200
CJISWAN, 211
Claremont College, 239-240
Clostridium difficile Toxin A test, 152-153
Cocolithophoids, 234
CODIS (Combined DNA Indexing System), 210-211
Collaboratories, 61-62
Collaborating centers for influenza, 49, 50, 53
Color multiplexing, 19
Common Command Set, 244-245
Computational power, 6, 64, 233, 265
Computer science, and microtechnologies, 20, 64
Congenital rubella syndrome, 41
Consortia
bioforensic, 208-209
genome mapping centers, 89
industry-academic partnerships, 77-78
Consortium on Automated Analytical Laboratory Systems (CAALS), 244, 245, 249-250
Coordination of threat response
bioterrorism, 13, 141, 150, 160, 190, 206, 208-209
in bioforensics, 208-209
food safety, 12-13, 133-141, 144, 147, 150, 160
CORBA (Common Request Broker Architecture), 249, 252, 257
Cost-benefit models, 41-43
Coxiella burnetti,
Creutzfeldt-Jakob disease, 31, 43-44
Cross-sectional serological surveys for antibodies, 37-38, 39
Cyclospora gastroenteritis, 55, 57
Cytotoxic cellular epitopes, 61
Cytotoxic T lymphocyte assays, 68, 72, 74-75
Czech Republic, 103
Databases
benchmark storage facilities, 64
biomedical, 85-86
cancer genomes, 90
challenges in developing, 87
costs, 86
genome sequence, 51, 77, 88-89, 90, 236-237, 265
for high-throughput automated laboratories, 23-25
intellectual property issues, 24-25
interconnectivity and interoperability, 210, 211, 231
location, 23
object-oriented systems, 23, 24, 231, 232
pathogen molecular fingerprints, 12, 19, 14, 21, 57-58
relational systems, 23-24, 231
re-releases, 88
search engines, 86, 88, 89, 211
security issues, 24
self-proofing software, 231
size, 6
syntax and semantics issues, 87-88
transcript map, 88
types and forms of data, 23
validation of information for, 86
XML standard, 24
DCOM (Distributed Component Object Model), 249, 257
Device Capability Dataset (DCD)
access and location, 252
origins, 249-250
representation and access, 251-252
static vs. nonstatic data, 251
status and directions, 252, 258
Diagnostics. See Advanced diagnostics
Diarrhea and dysentery, 55, 146
Directly observed therapies (DOT), 8, 9, 102, 104, 107, 108
Discovery, and technological change, 228-234
DNA
cloning technology, 228
computer, 234
fragment sizing flow cytometry, 195-198
hybridization, 228
labeling, 19
ligase, 228
restriction digest of single molecules of single chromosomes, 264
sequencing, 228;
see also Genome sequencing
synthesis, 229
DNA Data Bank of Japan, 77, 88
Dose, defined, 168 n.2
DOTS-Plus Working Group, 108
Drosophila genome, 237
Drug resistance. See Antimicrobial drug resistance
Dual-use technologies, 182-183, 185
Dugway Proving Ground, 218
Ebola virus/hemorrhagic fever, 55, 94-98, 99, 179
EcoCyc project, 117
Economic costs
of databases, 86
of antimicrobial drug resistance, 110
of foodborne illnesses, 144, 145
of high-throughput automated laboratories, 1, 4, 78-79
Effector cell:target cell assays, 74
Eia Foss system, 151
Emerging diseases.
See also Foodborne illnesses;
Infectious diseases;
Pathogens;
specific diseases andpathogens
antimicrobial resistance considerations, 56, 58
bioterrorism considerations, 31, 58-59
contributing factors, 56-57
defined, 56
Ebola model, 94-98
European concerns, 31
evolution of, 32-33, 123, 125, 262
IOM landmark report, 56-57
outbreaks, 55-56, 94, 95, 101, 106, 123-124
re-emergence of ancient strains, 264
surveillance systems, 10-11, 56, 57-58
technology applications, 93-100
transmission of, 144-145
Endoplasmic reticulum trafficking signals, 98
Engineering in biology, 232-233
Enzyme-linked immunosorbent assays (ELISA), 19, 151-152, 153, 157
Epidemics.
See also Pandemics
chains of transmission, 37-38
plotting curves, 35-38
saturation, 37
critical vaccine coverage, 37
Epidemiologic modeling, 26-27
Epidemiologic perspectives
in foodborne illness, 144-147, 159
in high-throughput automated laboratories, 15, 23, 27
ErgoTech Systems, Inc., 249, 258
Escherichia coli,
gene cluster analysis, 117
malaria clones, 264
molecular fingerprinting, 198
O157:H7, 12, 31, 55, 57, 145, 146, 147, 148, 158
Estonia, 104
Europe, 53
outbreaks of emerging diseases, 94, 95, 101, 124, 125
European Bioinformatics Institute, 89
European Molecular Biology Laboratory, 77, 88
Evanascent wave technology, 154
Exposure, defined, 168 n.2
Expressed sequence tags (ESTs), 89, 90, 91, 261
Extensible Markup Language (XML), 24, 252
Fachhochschule Wiesbaden (FHW) University of Applied Sciences, 250, 252, 257-258
Federal Bureau of Investigation (FBI), 190, 203-204, 206, 210-211
Fermentation, 170
Finland, antibiotic resistance in bacteria, 35
Flow cytometry
antibiotic susceptibility testing, 156-157
bacterial species and strain identification, 196-198
in biodefense research, 19, 193-200
capabilities, 193-194
DNA fragment sizing, 195-198
foodborne pathogen detection, 19-20, 156-157
future directions, 200
in high-throughput automated laboratories, 19-20, 75, 195, 198, 200
in HIV/AIDS research, 75
microsphere-based assays, 19, 195, 198-200
principles of operation, 19, 156, 193-195
sensitivity, 19, 193, 195-196, 198
Food and Drug Administration, 12, 140, 173
Food chemistry, 170-171
Food contaminants/contamination
agents, 147
categories of constituents, 171-172
early detection of, 148
numbers of, 173
sources of risks, 170-172
terrorist events, 135, 139-140, 147-148, 149, 150, 153, 154, 160, 177, 181
testing for, 137-139, 151-157, 172-173
tolerances, 172
Food preservation, 170
Food processing, 170
Food safety
challenges in ensuring, 11-13, 267
defined, 133-134
enforcement of rules and regulations, 12, 160
evaluation, 172-173
federal approaches, 12-13, 140-141, 144, 147, 150, 160
high-throughput automated labs, 19-20, 137-139, 173
informatics resources, 12
inspection program, 136-137, 138, 140
interdisciplinary nature of, 140
organizational perspective, 133-141, 144, 160
risk assessment data, 27-28, 168-173
risk-based decision making, 166, 167, 172
sampling considerations, 137
supply of food and, 133, 134-136
Food Safety and Inspection Service, 137, 138, 140
Food supply
Foodborne illnesses
epidemiological trends, 144-147, 159
investigation of, 12-13, 147, 148, 149-150, 151, 153, 154, 158
mortality and morbidity, 11, 144
outbreaks, 12-13, 55, 56, 57, 145, 147, 148, 149-150, 151, 153, 154, 158
public health response to, 148-149
surveillance, 12, 58, 146, 147, 148-150, 154, 159, 160
transmission of, 144-145
Foodborne pathogens.
See also individual pathogens
biosensor assays, 143, 153-154
detection of, 157-158
“fingerprint” database, 12, 19, 57-58, 159
flow cytometry analysis, 19-20, 156-157
hydroxyapatite recovery of, 157
infectivity of contaminated foods, 44, 148
known agents, 11, 31, 144, 145
magnetic-bead capture of, 157-158
microarray technology, 19, 143, 154-156, 159
microtiter immunoassay-based methods, 20, 143, 151-152
rapid, immunoassay-based kits, 152-153
screening approaches, 143, 149-150, 158-159
universal platform for scrrening, 158-159
Forensics.
See Bioforensics
France, 89
Francicsella tularensis,
Functional genomics, 113
Gabon, 55
GenBank, 86-88
GeneChip Instrument System, 155
Gene cluster analysis, 117
GeneMachines microarray printer, 155-156
GenePix 4000A microarray scanner, 156
General Equipment Interface Specification (GEIS), 245
Genetic diversity, 93, 94, 208, 262, 265
Genomic sequencing annotation, 113
automated sequencers, 261, 264-265
biocomputing and, 261, 264-266
chain terminating amplification and gel electrophoresis, 18
cDNA oligomer applications, 18
databases, 51, 77, 88-89, 90, 236-237, 265
DNA restriction digest of single molecules of single chromosomes, 264
expressed sequence tag method, 89, 90, 91, 261
human, 6, 15, 26, 88-89, 233, 236-237, 261, 265
influenza viruses, 18-19, 25, 50, 52, 124-128, 268
microbial, 18, 19-20, 26, 113, 261-264
mouse, 265
technologies for, 18-19, 26, 261, 264-265
transposon maps, 263
Whole Genome Shotgun Strategy, 261, 264
and whole-organism transposon mutagenesis, 263
Genotyping
and high-throughput automated laboratories, 15, 18-19, 23, 27
HIV, 62, 63, 68, 72, 73-74, 75
mass tagging technology, 238
and technological change, 237-239
Gibbs entropy, 236
Global Project on Anti-Tuberculosis Drug Resistance Surveillance, 102-108
Glycosylation motifs, 98
gp160, 96
Grand challenges
bioterrorism/biowarfare mitigation, 5, 13-15, 25-26, 267
common themes, 6-7
defined, 1
high-throughput automated labs, 1, 10-11
human genetics, 15-16
infectious diseases, 1, 8-10, 25-26, 267
molecular medicine, 15-16, 25-26, 267
pharmaceutical screening, 15-16
problems for science, 6-7
technologies and approaches, 6, 16-28
Grants, 1-5, 24, 57, 76, 267-268
Great Britain, BSE epidemic, 43-45, 89, 180
Hazard Analysis and Critical Control Points (HACCP) programs, 160
Hazardous Materials Response Unit (HMRU), 206
Healthy People 2000, influenza vaccination objectives, 52
Hemagglutinin (HA) surface protein, 50, 124, 125, 126, 127-128
Hemagglutination inhibition (HI) test, 50
Hemolytic uremic syndrome, 57, 146
Hemophilus influenzae,
Hemorrhagic colitis, 57
Hepatitis B, 55
Hepatitis E, 146
“Herald” wave, 126
Herd immunity profiling, 40, 41, 42
Herpesvirus, 96
Hewlett-Packard Gene Array Scanner, 155
High-throughput automated laboratories.
See also Batch science
adapting science, 77
advantages, 7, 11, 14-15, 53, 75, 138-139, 267-268
and antimicrobial drug resistance surveillance, 102, 105-107, 109-110
bioterrorism response capabilities, 14-15
commercially available systems for, 17, 62
containment facilities, 77
databases for, 23-25
disadvantages, 137-138
drug discovery applications, 119-120
epidemiologic perspective, 15, 23, 27
first application, 268
flow cytometry applications in, 19-20, 75, 195, 198, 200
food safety applications, 19-20, 137-139, 173
genotypic perspective, 15, 18-19, 23, 27
HIV/AIDS research, 10, 62-63, 69-75
influenza surveillance, 9, 10-11, 18-19, 21, 53
infomatics tools, 25-26, 28, 229-230
immunologic testing instruments, 151-152
integration of hardware, 16, 17-18, 22, 23, 69, 77, 243-258
interconnection standards for, 16, 17-18, 69, 77, 243-258
Internet-accessible mass customized testing, ;
see also Batch science
and microarray-based gene response profiling, 119-120
miniaturization and, 20, 229-230
modular systems design, 23, 69, 71, 72, 77, 151-152, 230, 253
and molecular medicine, 15-16, 267
obstacles, 268
overview, 7
pharmaceutical screening, 15
phenotypic perspective, 15, 23, 27
sample characterization capabilities, 19-20
resource requirements, 78-79, 80, 82
run capacity, 22
statistical issues, 137-138
tuberculosis applications, 9, 18
validation of methods, 173
HIV/AIDS
antiretroviral therapies, 10, 61, 62, 72, 73, 80
asymptomatic phase, 93
cellular immunity and, 74-75
clades, 94
genetic variability, 93, 94, 208
genome, 79-80
genotyping, 62, 63, 68, 72, 73-74, 75
intervention success, 37
mortality and morbidity, 10, 32, 36, 55, 61
multidrug resistance, 10, 45, 72, 73
prevalence/pandemic, 8, 10, 36-37, 44, 61
projections, 93
spread of, 93-94
in sub-Saharan Africa, 32
surveillance, 94
tuberculosis co-infection, 9, 101, 107
vaccine development, 10, 61, 62, 65-66, 96
HIV/AIDS research
batch science, 65-69, 70, 72-75, 77-82
cytotoxic T lymphocyte assays, 68, 72, 74-75
flow cytometry, 75
high-throughput automated laboratories, 10, 62-63, 69-72
intellectual property issues, 70, 75-77
interdisciplinary perspective, 64
intermediate-scale “collaboratories,”
Internet applications, 70, 77-82
limitations of current laboratories, 64-65
molecular sequencing, 62, 63, 68, 72, 73-74, 75, 77, 79-80
reproduction measurements, 74
standardization of assays, 75
viral infectivity assays, 68, 69, 72-73, 75
HLA-restricted T cells, 74
HIV Sequence Database, 77
Hong Kong, 106
“chicken” (H5N1) flu, 8, 51, 56, 125, 127, 129, 268
Human Genome Project, 82, 237, 261
Human genome sequencing
genetic diversity, 265
infomatics and, 26, 229, 236-237
map, 88-89
medical applications, 6, 15, 265-266
Hydrodynamic focusing, 19
Hydroxyapatite, pathogen adherence to, 157
IAsys Auto+ Advantage, 154
IEEE 1394 (Firewire) interface, 244
Image processing of microarray scans, 116
Immune response, 93, 96-97, 98
Immunization
age considerations, 40-41
influenza rates, 52
and transmission dynamics, 41
Immunoassay cards, 152-153
Immunologic testing instruments, 151-152
Immunomagnetic separation methods, 151
Immunosuppressive bioweapons agents, 179, 180
India, 32, 48, 55, 103-104, 107, 110, 145-146
Infectious diseases.
See also Emerging diseases;
Mathematical modeling of infectious diseases;
Pathogens;
individual diseases
chains of transmission, 37-38, 41
challenges in fighting, 8-10, 25-26, 267
control and threat reduction, 18-19, 59, 101, 102, 104, 107-108, 109
cross-sectional serological surveys for antibodies, 37-38, 39
data collection, 27
diagnostic innovations, 20-21
incidence calculations, 44
incubation period, 44
leading killers, 55
mortality, 55
pathogenicity, 96
Influenza
A-strain viruses, 8, 51, 56, 123, 124-128
age factors, 48, 124, 128, 129
antigenic relatedness of strains, 50-52, 123, 124, 126, 127, 129
avian viruses, 5, 9, 52, 124, 127, 268
batch science and, 129-130
B-strain viruses, 51
challenges in fighting, 8-9, 10-11, 26, 129
clades, 126
collaborating centers for, 49, 50, 53
database, 51
diagnostic technologies, 21
economic and societal impacts, 8, 48
evolution, 123, 124, 126, 127, 129
genome sequencing, 18-19, 25, 50, 52, 124-128, 268
HA surface protein, 50, 124, 125, 126, 127-128
hemagglutination inhibition (HI) test, 50
“herald” wave, 126
high-throughput automated labs, 9, 10-11, 18-19, 21, 53, 268
Hong Kong H5N1, 8, 51, 56, 125, 127, 129, 268
immunization rates, 52
interpandemic periods, 48, 129
interspecies movement, 52, 125
mortality and morbidity, 8, 47-48, 123-124, 126-127, 129
national centers for, 49, 50, 53
neuraminidase surface protein, 124
neutralization test, 53
pandemics, 8, 47, 48, 123-124, 125-129, 268
patterns of circulation, 49
and pneumonia, 124, 125, 126-127
predicting/averting, 26, 27, 129-130
projections, 8
reservoir (natural), 124-125, 129
special investigations, 52-53
surveillance, 8, 9, 10-11, 18-19, 21, 49, 50, 52-53, 129
threat of pandemics, 128-129
in vivo titers, 21
WHO global surveillance system, 8, 10-11, 20, 21, 47, 49, 50-53
Infomatics.
See also Databases
and DNA shuffling, 28
and drug discovery process, 116-117
food safety applications, 12
long-term tasks, 25
short-term tasks, 25
tools for high-throughput automated laboratories, 25-26, 28, 229-230
and vaccine development, 98
Information science, biology as, 234-236
Inhibition assays, 50, 153-154
Institute for Genomic Research, 261
Institute of Medicine, Emerging Infections report, 56-57
Integration of technologies
education and training and, 239-240
forms of, 227
genotyping example, 237-239
instruments into laboratory automation systems, 16, 17-18, 22, 23, 69, 77, 243-258
interconnection standards and, 16, 17-18, 69, 77
interdisciplinary perspective, 7, 20, 239-240
into life sciences, 227-236
miniaturization and, 20, 229-230
Intellectual property
AIDS/HIV investigators, 70, 75-77
commercial/proprietary ownership (closed category), 24, 75-76
consortium ownership, 24-25, 76-77
databases, 24-25
principal investigator ownership, 24, 76
Interconnection standards.
See also Laboratory Equipment Control Interface Specification
Auto3-P Communications with Automated Clinical Laboratory Systems, Instruments, Devices, and Information Systems standard, 249
capability dataset approach, 253, 254, 255, 256, 257
Common Command Set, 244-245
control flow interactions, 246, 247-248
descriptive, 243
General Equipment Interface Specification, 245
IEEE 1394 (Firewire) interface, 244
implementation, 249
data and interface modeling languages, 249, 252, 256-257
local/remote control mode, 247
for mass customized testing via Internet, 22, 23, 77
optional interactions, 246
Open Systems Interconnection reference model, 244
prescriptive, 243
required interactions, 246
USB, 244
Interdisciplinary perspective
on bioterrorism preparedness and response, 13, 140, 190, 207
on education and training, 239-240
on food safety, 140
HIV/AIDS research, 64
cooperative problem solving, 240
on microtechnologies, 20
on technological development, 7, 20, 227-228, 239-240
Interepidemic periods, 40, 48, 129
Interface Definition Language (IDL), 249, 252, 257
Intermediate-scale research, 2, 61-63
International Union Aqainst Tuberculosis and Lung Disease, 102-104, 107-108
Internet.
See also Batch science
information resources, 89;
see also Databases
mass customized testing via, 7, 21-23
non-real-time operations, 65, 66
Introns, 263
Investigator-initiated research, 1-2, 24, 61
Iran, 182
Iraq, 182
ISO10313 (STEP), 256-257
Isoniazid, 9, 101-102, 104, 105, 106, 109, 114
Ivanovo Oblast, Russia, 103
Japan, 55, 56, 59, 89, 145, 178, 181
Japanese encephalitis, 179
Junin virus (Argentinian hemorrhagic fever), 179
Keck Graduate Institute of Applied Life Sciences, 239-240
Korean Institute of Tuberculosis, 105-106
Lab Automation '99 conference, 17, 250
Laboratories, conventional.
See also High-throughput automated laboratories
overview, 7
quality assurance and quality control issues, 102, 105-106
response to bioterrorist attacks, 14-15
safety issues, 105
work force limitations, 11, 14-15, 64
Laboratories-on-a-chip (LOC), 20
Laboratory Response Network for Biological Terrorism, 150
Lassa fever, 179
Lawrence Livermore National Laboratory, 90
LECIS (Laboratory Equipment Control Interface Specification)
control paradigm, 17-18, 244, 245-246
interaction categories, 246
manufacturer support for, 17
origins, 244-245
primary interactions, 246-248
secondary interactions, 248
status and directions, 249
TCP/IP-based reference implementation, 249
Lentiviruses, 98
Leptospirosis, 55
Libya, 182
Lipopolysaccharide biosynthesis, 262
Listeria monocytogenes,
Listeria Rapid Test, 152
Los Alamos National Laboratory, 51, 196, 249, 258
Los Angeles, 57
Luciferase, 118
Luminex Corporation, 200
Lyapounov functions, 236
Machupo virus (Bolivian hemorrhagic fever), 179, 183
Macromolecular structure, 228
Mass customized testing, Internet and, 7, 21-23.
See also Batch science
Mathematical modeling
applications, 31-32
cost-benefit constructs, 41-43
for data collection prioritizing, 27
epidemiologic, 26-27
evolution of infectious agents, 34-35, 261
experimental systems in biology, 45, 230-231, 241
first application for infectious diseases, 32
immune response predictions, 98
limits of, 38-41
Mad Cow disease, 43-45
in mass customized testing environments, 22
overview, 26-27
pandemic forecasting, 27, 25-28
phase space organization and mapping, 27
plotting epidemic curves, 35-38
spread of diseases, 32-34
vaccine valuation for childhood diseases, 39-41
Mega-cities, and spread of infectious agents, 32-34
Message-passing communication protocols, 244, 245
Microarrays
antibiotic discovery by gene response profiling, 113-120
analysis of data, 116-117
experimental design, 115-116
fabrication and hybridization, 114-115
foodborne pathogen detection, 19, 143, 154-156, 159
gene chip method, 155
gene cluster analysis, 117
image processing of scans, 116, 155, 156
laboratory automation, 119-120
limitations in conventional labs, 18
pathogen strain identification, 106
printers, 155-156
probes, 155
size of dataset, 116-117
Microbial sequencing, 261-264
Microcapillary structures, 18
Microsphere-based assays, 19, 195, 198-200
Microtechnologies
diagnostic applications, 20-21, 153-154
interdisciplinary nature of, 20
LOC, 20
Milwaukee, Wisconsin, 146
Molecular biology
mathematical modeling in, 230-231
technological change and, 228-229
Molecular breeding, 28
Molecular evolution in vitro, 233
Molecular fingerprinting of pathogens, 12, 14, 19, 21, 57-58, 106, 159, 196-198
Molecular medicine
grand challenges, 15-16, 25-26, 267
high-throughput automated laboratory applications, 15-16, 267
Monoclonal antibody methods, 228
Morexella catarrhalis,
Mortality and morbidity
infectious diseases, 55
influenza, 8, 47-48, 123-124, 126-127, 129
Multiplexing of assays, 19, 200
Mycobarteriophage, 106
Mycobacterium tuberculosis, .
See also Tuberculosis
Mycoplasma genitalium,
Mycoplasma pneumoniae,
Mycotoxin detection, 152-153
Myristoylation sites, 98
Nanogen, 156
National Center for Biotechnology Information
Cancer Genome Anatomy Project, 90-91
data ownership, 77
GenBank, 86-88
human genome map, 88-89
Medline/PubMed system, 85-86
National centers for influenza surveillance, 49, 50, 53
National Committee for Clinical Laboratory Standards (NCCLS), 249
National Food Safety Initiative, 144, 147, 160
National Human Genome Research Institute, 2
National Institutes of Health, 2, 3, 94, 261, 263, 264
National Library of Medicine, 85
National Institute of Standards and Technology (NIST), 244, 250, 252, 257-258
National Reference Laboratories (NRLs), 102, 105-106
National Research Council, 4
National Science Foundation, 3, 263
Nerve gas, 59
Neuraminidase, 124
New York City
HIV infection, 37
outbreaks of emerging diseases, 56, 146
public health department, 57
New Zealand, 103
Nicaragua, 55
Nipah virus, 56
Nixon, Richard, 179
Nosocomial infections, 57
North America, influenza pandemic, 124
Nunn, Sam, 204
Object Database Management Group, 23
Official Methods of Analysis of AOACInternational,
Oklahoma City bombing, 58, 188
Open reading frames, identification and functional identification 113, 115, 116
Open Systems Interconnection (OSI) reference model, 244
Osama bin Laden, 181
Outbreaks of infectious diseases
emerging diseases, 55-56, 94, 95, 101, 106, 123-124, 125, 146
foodborne, 12-13, 55, 56, 57, 145, 147, 148, 149-150, 151, 153, 154, 158
investigation of, 12-13, 147, 148, 149-150, 151, 153, 154, 158, 196
Pacific islands, 124
Pandemics.
See also Epidemics
“herald” wave, 126
HIV/AIDS, 8, 10, 36-37, 44, 61
influenza, 8, 47-48, 123-124, 125-129, 268
mathematical modeling of, 27, 25-28
threat of, 128-129
Pathogens.
See also Foodborne pathogens;
Infectious diseases;
Influenza;
specific pathogens
beta-lactamase-producing, 34, 35
bioweapon agents, 59, 178-179, 180, 181, 183, 203-204
evolution, 1, 32-33, 34-35, 42, 45, 51, 123, 124, 125, 126, 127, 129, 261-262, 263
genomic sequencing, 18-19, 25, 50, 52, 124-128, 261-266
molecular fingerprints, 12, 14, 19, 21, 57-58
strain (phenotype) structure considerations, 41-42
Perry, William, 188
Persian Gulf War, 181
Pharmaceutical screening
industry-academic partnerships, 77-78
scientific needs, 15-16
Pharmacogenomics, 238-239, 265-266
Phenotypes
laboratory automation perspective, 15, 23, 27
structure considerations, 41-42
and vaccine development, 49, 50-53
Physics, and microtechnologies, 20, 64
Plague, 8, 35-36, 55, 178, 179, 183
Pneumonia, 48, 55, 57, 124, 125, 126-127
POLARA laboratory automation software, 249
Polio, 5
Polymerase chain reaction (PCR), 106, 114, 158, 229
Population factors, in spread of infectious diseases, 1, 32-33
Primer 3 (software), 114
Principal investigators
Probe multiplexing, 19
Process control tools (PCTs), 21-22, 66, 67, 69, 70, 74, 77, 230
Protease inhibitors, 61, 72, 80
Protein and Nucleic Acid Core facility, 114
Public health system
diagnostic methods, 196
response to foodborne illnesses, 148-149
PubMed system, 85-86
Pulsed-field gel electrophoresis, 196
PulseNet, 58
Pyrazinamide, 9
Quality assurance and quality control
in bioforensic laboratories, 209
in drug susceptibility testing, 102, 105-106
in food contaminant analysis, 173
Radiation Hybrid Database (RHdb), 89
Radiometric BACTEC 460 method, 105, 106
Rajneeshee cult, 181
Rapid, immunoassay-based kits, 152-153
Recombinant DNA technologies and antiviral treatments, 98-99
and bioweapons production, 182, 185
Research Institute of Tuberculosis (Tokyo), 106
Reservoir of infection, 94
Resonant mirror technology, 154
Restriction enzyme technology, 228
Restriction fragment length polymorphism DNA fingerprinting, 106
REVEAL test, 152
Reverse transcriptase inhibitors, 61, 72, 80
Reverse transcription reaction, 115
Rice genome, 263
Ricin, 203-204
RIDASCREEN, 151
Rifampin, 9, 101-102, 105, 106, 110, 155
Rift Valley fever, 56
Risk, defined, 27
Risk assessment
analytical technologies and, 172-173
decision making based on, 166, 167, 172
content of, 168-170
defined, 165-166
dose-response evaluation, 169
food safety context, 27-28, 168-173
hazard identification, 168-169
human exposure assessment, 169
methodologies, 165
overview, 27-28
process, 167-169
safety in context of, 166-168
social goal, 166
traditional uses, 27
uncertainties, 165
Risk characterization, 168
Riverside, California, 146
Rubella, 40-41
Russian spring-summer encephalitis, 179
Safety, defined, 166-168
Saliva-based antibody tests, 41
detection methods, 153, 157, 158
S. enteritidis,
S. typhimurium,
terrorists attacks, 181
Sandia National Laboratory, Intelligent Systems and Robotics Center 245
Saudi Arabia, 56
Schuler, Greg, 89
Screening approaches
foodborne pathogens, 143, 149-150, 158-159
universal platform, 158-159
Security issues
biodefense strategies, 187-188, 205
databases, 24
Serratia marcescens,
Shannon information, 236
Shigella dysenteriae,
Signal averaging, 19
Signal sequences, 98
Signal-to-noise ratios, 19
Singapore, 56
Single-gene mutations, 6
Single nucleotide polymorphisms (SNPs), 6, 15, 18, 199, 265
Smallpox, 5, 32, 147, 178, 179, 261, 263, 264
Somalia, 56
South America, 52
Soviet Union (former)
bioweapons program, 13-14, 178-180, 181-182, 203
Special investigations
influenza vaccines, 52-53
limiting factors, 52-53
Stalin, Joseph, 189
Standard Laboratory Modules (SLMs), 69, 71, 72, 77, 253
Standardization of assays, 75, 150
Stanford University, 114
Staphylococcus aureus,
Streptomycin, 102
Subnanomolar-scale reactions, 20
Supranational Reference Laboratories (SRLs), 102, 105-106, 107
Surface plasmon resonance, 153
Surveillance
antimicrobial drug resistance, 21, 102, 105-107, 101-110
emerging diseases, 10-11, 56, 57-58
foodborne illnesses, 12, 58, 146, 147, 148-150, 154, 159, 160
funding for, 147
importance of, 56
HIV, 94
influenza, 8, 9, 10-11, 18-19, 21, 49, 50, 52-53, 129
saliva-based antibody tests, 41
Syria, 182
System Capability Dataset (SCD)
components, 254-255
configuration and status component, 254
creation timeline, 255-256
dependencies component, 255
events component, 255
functionality component, 254
geometry and location component, 254
identification and description component, 254
implementation, 257
maintenance and calibration component, 254
metadata component, 254-255
representation, 256-257
static and dynamic contents, 255
status and directions, 257-258
Symbolic Query Language, 23-24
System Support Modules (SSMs), 253
Task Sequence Controllers (TSCs), 69, 71, 77
T-cell immunity, 96
Technological change.
See also Integration of technologies
data acquisition and, 229-230
discovery, and
genotyping example, 237-239
and grand challenges, 6
interdisciplinary nature of, 227
TECRA MINILYSER processor, 151
TECRA SET ID VIA kit, 151
Thailand, 106
Thermodynamic analysis of biomolecular interactions, 154
Tissue databases, 90
Tokyo subway system attack, 59
Toxins, 147, 148, 151, 152-153, 154, 195, 199-200
Toxoplasma, 11
Transia Card, 152
Transia Elisamatic II, 151
Transposon maps, 263
Travel, and spread of infectious diseases, 34, 144-145
Tuberculosis
challenges in fighting, 9, 107-108
drug susceptibility testing, 105-107, 109-110
global incidence, 110
high-throughput automated laboratory applications, 9, 18
latent infections, 9
management strategies, 9, 102, 107-108, 109-110
mortality and morbidity, 9, 55
multidrug resistance, 5, 8, 9, 18, 101-110, 114, 155
Oshkosh strain, 264
recent transmission vs. reactivation, 106-107
research needs, 108
sequencing, 264
surveillance, 18, 102, 107, 109-110
transmissibility and virulence, 108
vaccine development, 96
virulence and infectivity, 264
Typhoid fever, 145-146, 178-179
UniGene, 90
United Kingdom.
See Great Britain
United States
biodefense strategy, 187-188
bioweapons program, 14, 178, 179, 222
deaths from infectious diseases, 55
food supply trends, 133, 134-136
genome mapping centers, 89
influenza surveillance network, 10, 49
influenza projections, 8
outbreaks of emerging diseases, 55, 56, 101, 124
population age distribution, 48
vulnerability to bioterrorist attacks, 58, 180-181, 188-189, 203, 218-220
Universal microtiter plate handling device, 249
Universal Serial Bus (USB), 244
Urethritis, 262-263
U.S. Army Medical Institute of Infectious Disease, 208
U.S. Department of Agriculture, 58, 138, 208
U.S. Deparment of Defense (DOD), 2, 4, 150, 187, 190, 264
U.S. Department of Energy (DOE), 2, 208
U.S. Environmental Protection Agency, 140, 144, 173
Vaccinia, 263
Vaccines
biodefense role, 184
cost effectiveness, 41
critical coverage, 37
herpesvirus, 96
information technologies and, 98
malaria, 96
modeling potential value of, 39-40
strain selection, 50-53
Venezuelan equine encephalomyelitis, 179
Veratox and Veratox HS, 152
Viral encephalitis, 181
Virulence of pathogens
bioweapons alterations, 182
Vitek Immuno Diagnostic Assay System (VIDAS), 152
Washington University, 90-91
Water supply, 135
Waterborne diseases, 57, 145-146, 147-148, 160, 177
Weapons of mass destruction, 13, 177.
See also Bioweapons;
Catastrophic terrorism
West Nile encephalitis, 56
Whitehead Institute, 114
World Health Organization, 82
anti-tuberculosis drug resistance surveillance, 102-104
Global Tuberculosis Program, 102
influenza surveillance network, 8, 10-11, 20, 21, 47, 49, 50-53
tuberculosis treatment recommendations, 107-108
Western Pacific Regional Office, 105-106
World Trade Center bombing, 58, 188
World War I, 124
World War II, 178
Wulf, William A., 61
Yellow fever, 179
Yeltsin, Boris, 180
Zaire, 55
Zoster, 39-40