Index
A
ABI 370, 16
additives, 62–3
affinity Bio-chem-FETs, 208–9
schematic of beetle antenna-based, 210
schematic representation of Bio-FET for detection of proteins, 211
Affymetrix, 22
Affymetrix exon, 119
Affymetrix GeneChip probe array, 115
alcohol oxidase immobilization, 164
alkaline phosphatase (ALP), 135
allele-specific primer extension (ASPE), 99
allele-specific reverse transcriptase PCR, 12
Amerithrax, 8
ammonium acetate, 365
amperometric mode, 134–5
amplicons, 56
amplification
products, 76–7
strategies, 141
analyte, 224–6
purification, 222
AndoriDus CCD, 317
annotation data base
problems and some potential solutions, 35–6
anthrax attacks, 4–5
anti-pathogen antibodies
early detection of infection, 144
indicators of infection using electrochemical immunosensors, 144
antimicrobial peptides (AMP), 258
APTIMA Combo 2 Assay, 85
arginase-urease system, 160
arginine determination
biosensors, 159–61
aspartame injection, 162
ASPE assay, 110–11
Aspergillus niger, 169
assay development parameters, 99–100
assay optimization, 84
atomic dynamics, 297
atrazine detection, 181–2
Aval, 78–9
avian virus (H5N1), 267
B
B-pentamer, 265
Bacillus, 399
Bacillus pumilus, 401–2
Bacillus subtilis, 286
back-end processing, 222
bacterial cell lysis, 373–6
bacterial genetics, 28–30
bacterial nucleic acid characterization, 25
bacterial proteome
handling, processing and separation methods, 372–7
cell lysis and protein extraction, 373–6
protein separation techniques, 376–7
ballistics, 9
Bayesian probabilistic approach, 389
bead array technologies
applications, 115–21
nCounter Platform, 119–21
nucleic acid detection, 121
VeraCode Platform, 118–19
xMAP Platform, 115–18
genetic disease screening and microbial detection, 93–121
Illumina VeraCode, 108–11
Luminex xMAP Technology, 94–108
NanoString nCounter, 111–15
BeadXpress analysis, 119
BeadXpress reader, 109–10
BEBO, 60
BESt analyzer, 84
bio-chem-field effect transistors (FET)
biological sensing, 194–215
FET, 198–205
future trends, 215
chemical compounds and biological units as sensing elements, 205–12
affinity Bio-chem-FETs, 208–9
catalytic Bio-chem-FETs, 206–8
generic schematic diagram utilizing selective chemical or biological element, 206
history, 195–8
Clark enzyme membrane electrode design, 197
generation of potential across glass membrane, 196
key issues and terminology, 194–5
nanomaterials and nanoengineering in design, 212–15
schematic illustration of experimental setup with G-FETs, 214
silicon nanowires FET for ultrasensitive, direct and label-free detection, 214
Bio-Lidar
essentials, 336–8
use, 338–40
graphical depiction of bio-cloud surveillance in a rural area, 339
graphical depiction of bio-cloud surveillance in an urban area, 340
value-added, 341–2
absence of early warning and immediate action, 342
early warning, 341
bioaerosols determination, 144–6
combination of aerosol sampling cyclone with electrochemical immunosensor, 145
monitoring of viable cells of E. coli disseminated inside aerosol chamber, 146
bioanalysis, 132–40
biochemical lysis, 375
biodetection
LIDAR (LIght Detection And Ranging), 334–50
areas for improvement, 342–9
essentials of Bio-Lidar, 336–8
future trends, 350
integration, 349–50
use of Bio-Lidar, 338–40
value-added, 341–2
value of early warning, 335
bioforensics
combined microbiology and NGS, 10 sample testing, 11
bioinformatic analysis, 6–7
Biolog bacterial enzyme analyses, 401–2
biological element, 195
biological identification
electrochemical detection, 131–47
electrochemical sensors for pathogens, 141–6
electrochemical techniques for bioanalysis, 132–40
mass spectrometry-based proteomics, 370–420
analysis of double-blind bacterial mixtures, 406–19
analysis of MALDI-MS spectra, 400–6
bacterial proteome handling, processing and separation methods, 372–7
computational and bioinformatics approaches, 389–98
mass spectral proteomic methods, 386–9
peptide mass fingerprinting (PMF) and MALDI-MS/MS, 398–400
sample ionization and introduction for mass spectrometry (MS) analysis, 377–85
multiplexed, lateral flow, polymerase chain reaction (PCR) techniques, 54–67
considerations when developing realtime PCR assay, 63–4
development and description, 57–63
instrument platforms, 64–7
modifications, 57
overview of PCR, 55–6
Raman spectroscopy, 313–32
experimental methods used for intensive variability, 315–17
multivariate spectral analysis methods, 317–24
species-level biological identification results, 324–31
terahertz spectral characterization, 281–307
approach for computational modeling of vibrational frequencies and absorption spectra, 287–9
component-based model for Escherichia coli cells, 294–5
dissipation time scales, 291–3
experimental sub-terahertz spectroscopy of biological molecules and species, 295–305
fundamentals of terahertz vibrational spectroscopy of large biological molecules and species, 282–4
future trends, 306–7
overview, 284–6
problem with poor convergence of simulation, 289–91
recent and future trends, 286–7
statistical model for Escherichia coli DNA sequence, 293–4
biological sensing
bio-chem-field effect transistors (FET), 194–215
chemical compounds and biological units as sensing elements, 205–12
FET, 198–205
future trends, 215
nanomaterials and nanoengineering in design, 212–15
biological units, 205–12
biomolecules, 287–9
BioNanomatrix, 22
biosecurity, 3–15
biosensors
cyanide determination, 183
detection of diuron and atrazine, 181–2
dependence of tyrosinase residual activity, 182
formaldehyde determination, 163–5
glucose biosensors, 155–7
heavy metal ions determination, 178–80
lactose determination, 172–4
maltose determination, 174–6
nitrate determination, 169–71
organophosphorus pesticides determination, 176–8
phosphate determination, 167–8
proteins determination, 165–6
sucrose determination, 171–2
surfactants determination, 180–1
urea biosensors, 159
Bipolar Junction Transistor (BJT), 195
bottom-up method, 387–9
advantages, 387–8
disadvantages, 388–9
botulism toxin, 258
Boyle-Mariotte-PCR, 240
Bruker IFS66v, 297
Bruker spectrometer FS66v, 305
BsoBI, 78–9
C
calcium dipicolinic acid (CaDPA), 322
capillary electrophoresis, 8
capillary forces, 228
carbohydrate-based detection, 258–9
carbon-hydrogen, 317
carbon nanotubes (CNTs), 213
Cary 5000 UV-Vis spectrophotometer, 267
cascade rolling circle amplification (RCA), 82
catalytic Bio-chem-FETs, 206–8
penicillinase catalytic reaction for production of penicillinic acid, 207
rat neuron on electrolyte-oxide-silicon (EOS) field-effect transistor, 212
cell lysis, 222
Centers for Medicare and Medicaid Services (CMS), 7
cetyltrimethylammonium bromide (CTAB), 365
charge coupled device (CCD), 106
chemical adsorption, 205–6
chemical compounds, 205–12
chemical lysis, 374–5
chemical mutagenesis, 28
chemical oxygen demand (COD), 165
chemically modified field effect transistors (CHEMFETs), 203–4
chemically sensitive semiconductor devices (CSSDs), 203–4
chip-based analysis
nucleic acid-based analytes in microfluid devices, 235–45
image of instrument controlling magnetic bead-based purification and isolation, 240
relative intensity of fluorescence signal and graphical view of set of data, 244
schematic illustration of working principle of so-called Boyle-Mariotte-PCR, 242
schematic illustration of working principle of so-called flow-through PCR, 241
schematics of functionalization process in order to immobilize trapping biomolecule, 243
protein-based analytes in microfluidic devices, 226–37
fluorescent and colorimetric images, 236–7
functionalization process in order to immobilize trapping biomolecule, 227
graphs display background-corrected intensity of signals after incubation, 238
illustration of function of ELISA test chip and six arrays of spotted target molecules, 234
image of black COP ELISA detection test chip with two detection channels, 235
image of operation of test, 232–3
list of companies offering for pathogen analysis, 230–1
schematic representation of operation of disposable cartridge, 229
Chlorella vulgaris, 183
cholera toxin, 264–6
cholinesterase activity, 177
chromatography, 223
chronoamperometry, 134–5
clinical specimens (ClinSeq), 5
colorimetric test, 235–6
commercially available platforms
comparison, 19
metric and performance of next-generation DNA sequence vs data collected, 20
comparative proteomics, 370–1
complement fixation, 266
complementary DNA (cDNA), 64
complex samples
nucleic acid sequencing for characterising infectious and novel agents, 3–43
discovery of novel agents, 30–8
future trends, 38–43
known pathogens, 24–30
next-generation sequencing (NGS) technologies and sequencing landscape, 15–24
pathogen sequencing and applications in public health and biosecurity, 3–15
complicated primers, 71–3
complicated proteins, 71–3
component-based model, 294–5
computational modelling
approach of vibrational frequencies and absorption spectra of biomolecules, 287–9
absorption spectrum of poly[C]-Poly[G] thin film and modelling results, 289
concanavalin A, 259–60
conductometric biosensors, 153–88
based on direct analysis and for agrobusiness applications, 171–6
lactose determination, 172–4
maltose determination, 174–6
sucrose determination, 171–2
based on direct analysis and for biomedical applications, 155–63
arginine determination, 159–61
glucose biosensors, 155–7
testing protein denaturation, 161–3
urea biosensors, 157–9
based on direct analysis and for environmental applications, 163–71
formaldehyde determination, 163–5
nitrate determination, 169–71
nitrite determination, 168–9
phosphate determination, 167–8
proteins determination, 165–6
based on inhibition analysis, 176–83
cyanide determination, 183
detection of diuron and atrazine, 181–2
heavy metal ions determination, 178–80
nitrite determination, 182–3
organophosphorus pesticides determination, 176–8
surfactants determination, 180–1
conductometry in enzyme catalysis, 154–5
detection of microorganisms, 187
DNA-based, 186–7
characterization, 186
whole cell, 183–6
alkaline phosphatase and acetylcholinesterase activities, 185
conductometric enzyme biosensors
based on inhibition analysis, 176–83
direct analysis I, 155–63
biosensors for biomedical applications, 155–63
direct analysis II, 163–71
environmental applications, 163–71
direct analysis III, 171–6
agrobusiness applications, 171–6
conductometric microelectrodes, 162
conductometric transducers, 156
conductometric urease sensors, 158
conductometry, 154–5
constant temperature regime, 290–1
contamination, 63
continuous analysers, 381
continuous-flow PCR, 239
cope number variation, 8
coupling verification, 96
covalent attachment, 205–6
covalent entrapment, 205–6
covalent linkage, 135–6
Coxiella burnetii, 406
cross-correlation method, 401
cross-linking, 205–6
cross primers, 80
cross priming amplification (CPA), 80
cultural paradigm
legal framework, 41–3
cyanide determination
biosensors, 183
dependence of catalase residual activity on concentration of cyanide, 184
cyclic voltammogram, 136
cycling probe technology, 82
cyclo-olefin polymer (COP) chip, 233–4
D
D-amino acids oxidase, 158
data processing, 317–20
spectrum of sporulated BaS particle at data processing stages, 321
vegetative BaS spectra at data processing stages, 319
delayed extraction, 382
depolarization ratio, 343
depolarization Lidar, 343–4
detection test chip, 235–6
dielectrophoresis (DEP), 361
digital slipchip, 87
digitally controlled potentiostat (LMP91000), 132
distribution of particle spectra, 323
PLS loading vectors for sporulated organisms, 322
dimethyl sulfoxide (DMSO), 62–3
dipsticks, 221–2
direct hybridization assay, 96
direct population sequencing, 12–13
dissipation time scales, 291–3
diuron detection, 181–2
Dixon plots, 183
DNA arrays, 223
DNA-binding dyes, 59–60
DNA-DNA hybridization, 401–2
DNA samples, 13
domestic bioterrorism, 4
Doppler Radar sweep, 335
double-stranded DNA (dsDNA), 78–9
downstream ligation probe (DLP), 102
drain-to-source voltage, 199–200
dual-dye labelled hairpin probe, 79
E
E. coli, 5–7
E. coli O157:H7, 416
early warning, 335
electrical conductivity, 154–5
electrochemical detection
biological identification, 131–47
electrochemical sensors for pathogens, 141–6
electrochemical techniques for bioanalysis, 132–40
electrochemical immunoassays, 135
electrochemical impedance, 228
electrochemical impedance spectroscopy (EIS), 136
electrochemical measuring system, 132
electrochemical sensors, 224
pathogens, 141–6
determination of bioaerosols, 144–6
determination of microbes, 141–3
early detection of infection based on anti-pathogen antibodies, 144
electrochemical techniques
bioanalysis, 132–40
immunoassays, 135
immunosensors, 135–6
sensors based on hybridization of nucleic acids, 140
instrumentation and sensors, 132–5
Emstat potentiostat, 133
variability of screen-printed electrochemical sensors providing 1, 2, 4 and 8 electrodes, 134
electrochemiluminescence (ECL), 132
electromagnetic field, 283–4
electron capture dissociation (ECD), 386
electron microscopy, 22
electron transfer dissociation (ETD), 386
electrophoresis, 223
non-uniform electric field gradients, 360–4
AC fields for non-linear separation and electrodeless trapping to mitigate damage to DNA sample, 361
sample collection and preparation for nucleic acid preparation, 355–67
comparison of techniques, 364–6
future trends, 366–7
separation parameters, 356–7
uniform electric fields, 357–9
zone and field electrophoresis and isotachophoresis, 358
electrospray ionization (ESI), 378–9
application of, 379
nano-, source, 379
source and interface to a quadruple ion trap mass analyser, 378
ELISA analysis chip, 233–4
elongation step, 56
EmStat, 132
end-point detection, 84
energy minimization, 288–9
energy simulation protocol, 290–1
enteroaggregative E. coli (EAHEC) strain, 6
enterohemorrhagic E. coli (EHEC) strain, 6
enzymatic oxygen reaction, 157
enzyme catalysis, 154–5
enzyme immunoassay membrane tests, 266
cells, 294–5
DNA sequence, 293–4
Ethical, Legal and Social Implications (ELSI), 42–3
EvaGreen, 60
experimental sub-terahertz spectroscopy
biological molecules and species, 295–305
instrumentation for highly resolved vibrational spectroscopy for biological materials, 300–2
results from highly resolved vibrational spectroscopy for biological identification, 302–5
vibrational spectroscopy with moderate resolution of 0.25 cm−1, 295–300
exponential amplification, 56
exponential rolling circle amplification (RCA), 82
F
FAST assay, 116–17
femtosecond-resolved fluorescence spectroscopy, 304–5
field-able sequencing, 38–9
IonTorrent bus and Mini images, 39
field effect, 195
field effect transistor (FET), 198–205
converting a FET into Bio-chem-FET, 203–5
CHEMFET illustration, 204
main components, 198–201
Bio-chem-FET and chem-FET operate in saturation mode, 200
photograph of single FET, 200
role of semiconductors in design of Biochem-FETs, 201–3
potential development at Helmholtz layer of semiconductor membrane, 202
FilmArray BioSurveillance System, 65–6
FilmArray software, 65–6
filtration, 222
mechanisms, 223
fingerprint analysis, 9
Firmicutes, 394
first-generation sequencing technologies, 15–16
FLEXMAP 3D, 106
FlexmiR v2, 104–5
FlexScript, 102
flow cytometry, 115–16
fluorescence chemistries, 59
fluorescence microscopy, 22
fluorescence probes, 60–1
fluorescence resonance energy transfer (FRET), 257
fluorescent DNA-binding dyes, 59–60
fluorophores, 61
Fluvirin, 269–70
forensics
attribution, 7–10
current methods, 8
future issues, 9–10
modern methods and approaches, 8–9
identification of discriminatory mutations by comparison of draft sequence data sets, 10
formaldehyde determination
biosensors, 163–5
calibration curves, 164
calibration curves at various durations of alcohol oxidase immobilization, 165
formamide, 62–3
Fourier transform (FT)ICR mass spectrometer, 384–5
Fourier transform-infrared spectroscopy (FT-IR), 299
FT spectroscopy (FTS) system, 285
G
galvanostatic techniques, 132
gamma factor, 292–3
ganglioside, 265
gas phase fractionation (GPF), 408
Gastrointestinal Pathogen Panel, 117–18
gate-controlled diodes, 203
gate-to-source voltage, 199–200
GenBank data base, 40
Gene Expression assay, 112
genetic disease
bead array technologies for screening and microbial detection, 93–121
applications, 115–21
Illumina VeraCode, 108–11
Luminex xMAP Technology, 94–108
NanoString nCounter, 111–15
genetic fingerprinting, 12
genetic mapping, 28–9
genome-wide association, 118
genome wide association studies (GWAS), 29
genomic analysis, 9
genomic microbial DNA, 140
genomic standards, 27
genomic variations
deep sequencing in microbial populations, 11–13
genotyping viral populations for detection of rare variants, 12–13
rare variant detection in pooled DNA samples, 13
genomics, 7
genotyping viral populations, 12–13
glucose biosensors, 155–7
glucose sensors, 155–6
GoldenGate, 109
Grams 32, 267
graphene-based Bio-chem-FETs (G-FETs), 213
green tape technology, 158
GridION, 18
H
Haemophilus, 401
haemorrhagic uremic syndrome (HUS), 5
Halcyon Molecular, 22
Headwall Raman Explorer spectrograph, 317
heating, 364
heavy metal ions determination
biosensors, 178–80
calibration curves, 180
Helicos, 18
hemagglutinin (HA), 266–7
hierarchical cluster analysis (HCA), 390
high-performance liquid chromatography (HPLC), 377
high-density oligonucleotide microarrays, 30
high-performance liquid chromatography, 177–8
high-temperature denaturation step, 55
high-throughput analyses, 398
high-throughput sequencing (HTS), 30
highly resolved vibrational spectroscopy
instrumentation for biological materials, 300–2
results for biological identification, 302–5
absorption spectrum of protein thioredoxin from E. coli, 305
reproducibility of transmission spectrum of E. coli DNA, 303
transmission spectra of E. coli DNA with different amounts of material, 303
transmission spectrum of DNA nanosize monocrystal grown, 304
HincII, 78–9
Homeland Security Presidential Directive 21 (HSPD-21), 14
Honeybee Colony Collapse Disorder (CCD), 30
horseradish peroxidase (HRP), 135
Hot-start techniques, 62
human Genetics Programme, 42–3
hybrid devices, 194–5
Hybridase thermostable RNase H, 81–2
hybridization, 22
hybridization protection assay (HPA), 84–5
hybridization sequencing, 17
hydrolysis probes, 60–1
hyperbranched rolling circle amplification (RCA), 82
I
IDBA, 31–2
illumigene, 85
Illumina, See synthesis sequencing
Illumina VeraCode, 108–11
chemistries, 109–11
GoldenGate assay, 110
instrumentation, 111
technology, 108–9
immobilized nucleic acid probes, 140
immunochromatography, 266
ImmunoFET, 209
immunosensors, 135–6
electrochemical immunosensing and hybridization-based assays, 137
selected electrochemical affinity biosensors for assays of microbial pathogens, 138–9
inelastic neutron scattering, 292
infectious agents
nucleic acid sequencing for characterising novel agents in complex samples, 3–43
discovery of novel agents, 30–8
future trends, 38–43
known pathogens, 24–30
next-generation sequencing (NGS) technologies and sequencing landscape, 15–24
pathogen sequencing and applications in public health and biosecurity, 3–15
influenza virus, 266–74
infrared elastic backscatter, 343–4
inner primers, 75–6
inteins, 398
intelligent BioSystems, 21
intensity vector, 389
interdigitated electrode (IDE), 155
internal control (IC), 63–4
internal hydrogen bonds, 283
ion selective field effect transistors (ISFETs), 203–4
ion torrent draft sequence, 5
ion traps, 382
ionophore, 195
measured and calculated mass normalized coefficients of extinction and scattering, 347
irradiation
biological deactivation, 330–1
spectrum of B. anthracis Sterne viable versus B. anthracis Sterne gamma irradiated, 331
IsoAmp, 85
isotachophoresis, 359
isothermal amplification, 141
based on DNA polymerase, 74–84
ICAN, ICA, 81–2
LAMP and SmartAmp, 74–8
RCA and related technologies, 82–3
RPA and HDA, 83–4
SDA, NEAR, NEMA, CPA, 78–80
based on RNA polymerase, 84–5
future prospects, 85–7
clinical applications, 86
melting temperature (Tm) estimation and categories, 70–4
category of technologies, 72
equation, 71
LAMP and SmartAmp primer design scheme, 72
terminology for primer design, 73–4
specific sequences, 69–87
isothermal and chimeric primer-initiated amplification of nucleic acid (ICAN), 81–2
isothermal chain amplification (ICA), 81–2
isothermal nucleic acid amplification, 238–9
J
Jacalin, 263
K
kinetic energy, 381–2
Klenow exo-DNA polymerase, 78–9
known pathogens characterization traditional methods
bacterial nucleic acid, 25–6
viral nucleic acid, 26–7
L
lab-on-a-foil system, 87
lab on chip technology (LoC), 224
laboratory-developed tests (LDTs), 117
lactose, 172–4
biosensors, 172–4
calibration curves, 173
Langevin equation, 292
laserGen, 21
lateral flow devices, 245
lateral flow polymerase chain reaction (PCR) techniques
multiplexed PCR for biological identification, 54–67
considerations when developing realtime PCR assay, 63–4
real-time PCR development and description, 57–63
real-time PCR instrument platforms, 64–7
lateral-flow tests, 221–2
lattice vibration, 283–4
LC-MS/MS, 376
LIDAR (LIght Detection And Ranging)
biodetection, 334–50
areas for improvement, 342–9
essentials of Bio-Lidar, 336–8
future trends, 350
use of Bio-Lidar, 338–40
value-added, 341–2
value of early warning, 335
system consideration and atmospheric transmission, 348–9
value of integration, 349–50
networked Bio-Lidar ‘sweep-to-cue’ leverages UAV/UGV/point sensors, 350
ligation, 21–2
ligation-dependent assay (LDA), 101–2
light Cycler, 65
light-emitting diode (LED), 108
line probe assay (LiPA), 12–13
linear discriminant analysis (LDA), 324
linear ion trap (LIT), 383
2D, 383–4
schematic diagram, 384
QTRAP 4000 mass spectrometer, 385
linear regression equation, 168–9
lipopolysaccharide, 258–9
locus-specific oligo (LSO), 109
design of inner primers, 75
different detection methods, 77
Luer adapter, 235
Luer-Lock compatible interfaces, 222–3
Luminex 200, 106
Luminex website, 96
Luminex xMAP Technology, 94–108
chemistries, 95–106
capture of addressed targets onto precoupled beads, 99
direct hybridization illustration, 97
FlexmiR v2 illustration, 105
FlexScript LDA workflow, 103
LDA probe design, 104
used for addressed microsphere assays, 100
instrumentation, 106–8
Luminex analysers, 107
technology, 94–5
Lumistox device, 177–8
lysozyme, 375
M
magainin I, 258
MAGPIX, 106
MagPlex TAG Microspheres, 95
maltose determination
biosensors, 174–6
calibration curve, 175
selectivity, 176
MASCOT, 393
mass analysers, 381–5
mass spectrometry, 106
analysis of double-blind bacterial mixtures, 406–19
ABOID deconvolution, 411–15
case study, 410–11
classification and identification using peptide sequence information, 406–7
classification map of experimentally processed samples, 414
LC-ESI-MS/MS, 407–8
outer membrane protein vs whole cell analysis by bacterial strain, 415–19
phylogenetic profiles of amino acid sequences among taxa, 408–10
analysis of MALDI-MS spectra, 400–6
accurate mass assignment, 403
automated select mass extraction, 402
experimental condition variability, 406
experimental mass database, 403–4
experimental masses vs. on-line database, 402–3
growth media effect on mass spectra, 405
mass appearance variability, 405–6
microorganism differentiation, 404–5
molecular biology techniques, 401–2
positive and negative mode, 403
spectral cross-correlation, 401
visual fingerprint, 400–1
-based proteomics, for biological identification, 370–420
bacterial proteome handling, processing and separation methods, 372–7
peptide mass fingerprinting (PMF) and MALDI-MS/MS, 398–400
computational and bioinformatics approaches, 389–98
bacterial classification using pattern recognition, 389
data analysis pathway, 396
double-blind study of mixture of 7 organisms, 397
identification of agents of biological origin (ABOID), 393–8
multivariate linear least squares regression, 389–92
peptide analysis, 395
rapid analysis of mass spectra from bottom-up proteomics experiments, 392–3
schematic processing of data processing workflow, 391
mass spectral proteomic methods, 386–9
bottom-up method, 387–9
top-down method, 386–7
sample ionization and introduction for analysis, 377–85
application of ESI-MS/MS, 379
application of MALDI-MS, 379–80
electrospray ionization (ESI), 378–9
mass analysers, 381–5
matrices used in MALDI-MS, 380–1
nano-ESI source, 379
matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF)-MS, 371
application, 379–80
schematic diagram, 380
bacterial mapping, 400
matrices used, 380–1
matrix-assisted laser desorption/ionization tandem mass spectrometry (MALDI-MS/MS), 398–400
Maxam-Gilbert method, 15–16
median fluorescent intensity (MFI), 96
melting temperature (Tm), 70–4
metagenome sequencing, 30–1
limitations, 31–5
assembly vs read-based analysis, 31–2
depth and breadth of coverage of individual organisms in sample, 32–3
lack of reference genomes, 32
pathogen detection, 31
sample preparation, 33–5
metal oxide semiconductor capacitors, 203
Metal Oxide Semiconductor Field Effect Transistors (MOSFETs), 203
MetAmos, 31–2
MetaRay, 31–2
MetaVelvet, 31–2
Michaelis-Menten enzyme-substrate complex, 268
microbead-based RCA system, 87
microbes
determination, 141–3
selected assays of bacterial and viral pathogens based on hybridization of nucleic acids, 142–3
microbial detection, 259
bead array technologies for genetic disease screening, 93–121
applications, 115–21
Illumina VeraCode, 108–11
Luminex xMAP Technology, 94–108
NanoString nCounter, 111–15
microfluidic chip, 87
microfluidic devices
challenges and technical as well as commercial solutions, 221–4
schematic diagram of typical process steps in bioanalytical or diagnostic process, 223
rapid identification and characterization of pathogens, 220–45
analytes, 224–6
chip-based analysis of nucleic acid-based analytes, 235–45
chip-based analysis of protein-based analytes, 226–37
future trends, 244–5
microfluidic modules, 222
microorganisms detection, 187
MicroPlex TAG Microspheres, 95
microscopy, 22
Microsoft Excel, 102
mini-Luer, 222–3
mobile mode, 339
MODTRAN program, 348
molecular dynamics (MD), 288–9
molecular zipper, 83
Monte Carlo technique, 293
μStat, 132
multi-locus sequence typing (MLST), 25
multi-locus variable analysis (MLVA), 25
multi-locus variable nucleotide tandem repeat (VNTR), 25
multi-locus variable-number tandem repeat analysis (MLVA), 4
multi-priming, 81
multiplexed CodeSet, 111
multiplexed polymerase chain reaction (PCR) techniques
lateral flow PCR for biological identification, 54–67
considerations when developing realtime PCR assay, 63–4
real-time PCR development and description, 57–63
real-time PCR instrument platforms, 64–7
multivariate linear least squares regression, 389–92
Mycobacterium avium, 187
Mycobacterium tuberculosis, 404
N
NABsys, 22
Nafion, 168
nano-bio technology, 302–4
nanoengineering, 212–15
nanofibres (CNFs), 213
nanomaterials, 212–15
nanopores, 22–3
NanoString nCounter, 111–15
chemistries, 112–14
miRNA assay, 114
probe design illustration, 112
instrumentation, 114–15
technology, 111
nanotechnology, 212
National Human Genome Research Institute of National Institutes of Health (NHGRI-NIH), 19
National Research and Development Strategy for Microbial Forensics, 15
National Security Strategy, 14–15
National Strategy for Countering Biothreats, 14–15
nCounter Digital Analyser, 112–13
nCounter Gene Expression assay, 120–1
neuraminidase, 258
neuraminidase assay, 266
neuraminidase (NA), 266–7
next-generation sequencing (NGS), 359
next-generation sequencing (NGS) technologies
sequencing landscape, 15–24
data analysis challenge, 23–4
historical perspective, 15–19
technological innovations on horizon, 21–3
hybridization, 22
ligation, 21–2
microscopy, 22
nanopores, 22–3
pyrosequencing, 21
single molecule detection, 23
summary, 23
nicking enzyme amplification reaction (NEAR), 80
nicking enzyme mediated amplification (NEMA), 80
nitrate
biosensors, 169–71
calibration curves of MV/Nafion/NR electrode for increasing nitrate concentrations, 170
nitrite
calibration curve, 169
no template control (NTC), 63
normal mode analysis, 288–9
novel agents
discovery, 30–8
examples of metagenome sequencing to determine etiologic agents, 30–1
limitations of metagenome sequencing, 31–5
problems with annotation data base and some potential solutions, 35–6
nucleic acid sequencing for characterising infectious agents in complex samples, 3–43
future trends, 38–43
known pathogens, 24–30
next-generation sequencing (NGS) technologies and sequencing landscape, 15–24
pathogen sequencing and applications in public health and biosecurity, 3–15
nSolver Analysis Software, 115
nuclease protection assay chemistry, 104–5
nucleic acid amplification, 70–1
nucleic acid analysis
electrophoretic approaches to sample collection and preparation, 355–67
comparison of techniques, 364–6
future trends, 366–7
non-uniform electric field gradients, 360–4
separation parameters, 356–7
uniform electric fields, 357–9
nucleic acid assays, 95
nucleic acid-based analytes, 235–45
nucleic acid sequencing
characterising infectious and novel agents in complex samples, 3–43
discovery of novel agents, 30–8
future trends, 38–43
known pathogens, 24–30
next-generation sequencing (NGS) technologies and sequencing landscape, 15–24
pathogen sequencing and applications in public health and biosecurity, 3–15
nucleic acid template, 75–6
nucleoprotein antibody assay, 266
NucliSENS EasyQ, 85
O
Occupational Safety and Health Administration standards, 163
Ocean Optics spectrometer, 263
Ohm’s Law, 212–13
oligonucleotide duplex, 70
oligonucleotide ligation assay (OLA), 99
on-cartridge filtration, 227–8
open-source genomic analysis, 5
optical biodetection
binding of cells, 259–61
binding of cholera toxin, 264–6
change in 419 nm absorbance as function of cholera toxin concentration, 266
tetra-aminophenylporphyrin incorporated into presence and absence of CT, 265
binding of influenza, 266–74
absorbance change of immobilized siallyllactosamine-porphyrin complex, 269
absorbance changes of porphyrin-SLA slides upon exposure to bPIV3 vaccine, 270
absorbance spectrum of immobilized sialyllactosamine-porphyrin complex, 270
difference spectra of immobilized sialyllactose-porphyrin complex, 268
dose-response curve of change in 430 minus 405 nm absorbance vs NA concentration, 269
dose-response curve of immobilized sialyllactosamine-porphyrin complex, 271
binding of receptor to simulated toxin, 261
spectra of immobilized ConA with bound TPPS before and after exposure to glycophorin, 261
binding of simulated toxin to receptor, 262
absolute spectra of immobilized glycophorin with bound tetraphenylsulfonateporphyrin, 262
binding of specific antigen diagnostic of cancer to a receptor, 263–4
dose-response curve of 422 minus 470 nm absorbance change of TPPS, 264
immobilized ConA with TPPS before and after exposure to T-antigen, 263
immobilized jacalin with TPPS bound prior to and after exposure to T-antigen, 264
receptors and porphyrin-incorporated enzymes, 253–75
prior research and literature, 257–9
optimal assay conditions, 98
Orbitrap, 385
organic solid systems, 284
organophosphorus pesticides determination
biosensors, 176–8
calibration curves of AcChE for diisopropylfluorophosphate, 178
photodegradation of methyl parathion, 179
original equipment manufacturer (OEM), 132
Oseltamavir, 258
outer membrane protein
vs whole cell analysis by bacterial strain, 415–19
abbreviated nearest neighbor classification dendrograms, 418
nearest neighbour classification dendrograms, 417
Oxford Nanopore Technologies (ONT), See single molecule nanopore sequencing
Oxide Semiconductor Field Effect Transistors (OSFETs), 203
oxygen consumption, 211
P
p-aminophenyl phosphate (PAPP), 135
PacBio sequence data, 6
Pacific Biosciences, 17–18
padlock probes, See rolling circle amplification (RCA)
PalmSens, 132
parainfluenza, 271–2
partial least squares, 320
dimension reduction, 322
pathogen sequencing
applications in public health and biosecurity, 3–15
combined microbiology and NGS in bioforensics, 11
deep sequencing to look at genomic variations in microbial populations, 11–13
forensics and attribution, 7–11
need for rapid detection and genetic characterization by 2001 anthrax attacks, 4–5
policy drivers for NGS, 13–15
WGS in event caused by E. coli, 5–7
characterization, 24–30
changing landscape of bacterial genetics of WGS and linking phenotype to genotype, 28–30
genomic standards and viral characterization, 27
mutations, 28–30
traditional methods, 24–7
microfluidic devices for rapid identification and characterization, 220–45
analytes, 224–6
challenges and technical as well as commercial solutions, 221–4
chip-based analysis of nucleic acid-based analytes, 235–45
chip-based analysis of protein-based analytes, 226–35
future trends, 244–5
pattern recognition methods, 389
Pearson Correlation Coefficient, 120–1
peptide mass fingerprinting (PMF), 398–400
PeptideProphet algorithm, 410
peptides microencapsulation, 163
PG581, 132
pH-Field Effect Transistors (pH-FET), 205
phosphate determination
biosensors, 167–8
calibration curve, 167
physical adsorption, 205–6
plasmid curing process, 5
plateau phase, 58
PNA probe, 83
point of care (POC testing), 224–5
Polonator, 21–2
2D-polyacrylamide gel electrophoresis (PAGE), 372
polystyrene microspheres, 94–5
porphyrin-incorporated enzymes
optical biodetection using receptors, 253–75
binding of cells, 259–61
binding of cholera toxin, 264–6
binding of influenza, 266–74
binding of receptor to simulated toxin, 261
binding of simulated toxin to receptor, 262
binding of specific antigen diagnostic of cancer to a receptor, 263–4
prior research and literature, 257–9
porphyrin tetraphenylporphyrin sulfonate (TPPS), 259–60
portable real-time polymerase chain reaction (PCR) detection, 64–7
portable thermocyclers available from Idaho Technology Inc., 65–6
T-COR potable thermocyclers from Tetracore, Inc., 66–7
portable thermocyclers, 65–6
post-translational modifications (PTM), 386
potentiometric techniques, 132
Powersoil, 365
PREMIER Biosoft, 84–5
primer dimers, 84
primer generation rolling circle amplification (PG-RCA), 83
primer-template duplex, 70
primers, 61–2
Probe-On slides, 265
ProbeTec herpes Simplex Viruses Qx Amplified DNA Assays, 85
promoter primer, 84–5
protein, 376
databases, 395–7
extraction, 373–6
microencapsulation, 163
protein-based analytes, 226–37
protein denaturation testing
biosensors, 161–3
response curves of conductometric biosensor vs aspartame and BSA additions, 162
protein homologues, 35
proteinase K, 165
proteins determination
biosensors, 165–6
dependence of steady-state response on BSA concentration, 166
Proteobacteria, 394
proteomics technologies, 161
proton consumption, 157
Pseudomonas, 400
Pseudomonas putida, 390
PSTAT mini, 132
public health, 3–15
PubMed, 78
pulse field gel electrophoresis (PFGE), 25
pulsed-field electrophoresis, 359
pyrophosphate ions (PPi), 208
Q
quadrupole ion trap (QIT), 382–3
schematic diagram, 383
quantitative trait loci (QTL), 29
quartz crystal microbalance (QCM), 224
R
Raman micro-spectroscopy, 316–17
Raman spectroscopy, 314
biological identification, 313–32
experimental methods used for intensive variability, 315–17
bacterium sample preparation, 315–16
Raman micro-spectroscopy, 316–17
multivariate spectral analysis methods, 317–24
classification techniques, 323–4
data processing, 317–20
spectral analysis, 317
species-level biological identification results, 324–31
biological deactivation by irradiation, 330–1
filter performance parameters, 325
number of species in spectral data for each organism type, 325
spectral classification procedure, 325–30
ramification amplification, 82
rapid identification
microfluidic devices for characterization of pathogens, 220–45
analytes, 224–6
challenges and technical as well as commercial solutions, 221–4
chip-based analysis of nucleic acid-based analytes, 235–45
chip-based analysis of protein-based analytes, 226–37
future trends, 244–5
rare variant detection, 13
RAZOR EX, 65
RazorEdge, 317
read-based analysis, 32
reagent lysis, 374
real-time polymerase chain reaction (PCR), 106
considerations when developing assay, 63–4
contamination, 63
controls, 63–4
reverse transcription, 64
development and description, 57–63
chemistries, 59–61
kinetics, 58–9
reaction components, 61–3
instrument platforms, 64–7
portable detection, 64–7
receptors
optical biodetection using porphyrin-incorporated enzymes, 253–75
binding of cells, 259–61
binding of cholera toxin, 264–6
binding of influenza, 266–74
binding of receptor to simulated toxin, 261
binding of simulated toxin to receptor, 262
binding of specific antigen diagnostic of cancer to a receptor, 263–4
prior research and literature, 257–9
recombinase polymerase amplification (RPA), 83
reflectron, 382
RefSeq database, 35
relaxation times, 361
resonant frequencies, 283
Resource Effective Bio-identification System (REBS), 316
reverse hybridization, 12–13
reverse transcriptase polymerase chain reaction (RT-PCR) assay, 30
reverse transcription real-time polymerase chain reaction (PCR), 64
Ribonuclease H (RNAse H), 81
RNA, 356–7
RNA polymerase, 84–5
Roche-454-based whole genome pyrosequencing technology, 29–30
Roche Molecular Systems, 57
Ruggedized Advanced Pathogen Identification Device (R.A.P.I.D) Biodetection System, 65
S
sample processing, 222
sampling problem, 289–90
Sanger sequencing, 40
screen-printed electrodes (SPE), 133–4
self-assembled monolayers (SAM), 135–6
self-sustained sequence replication (3SR), 84–5
semi-conductor sequencing, 18–19
sensor sensitivity, 177
sequence-based typing method, 26
sequencing
diagnostic tool, 39–41
defining next standards for sequence-based references, 40–1
sequencing landscape, 15–24
serial interface, 132
sialic acid, 271
sialic acid-based receptors, 257
sialic acid-binding components, 273
sialyllactosamine (SLA), 267
single base chain extension (SBCE), 99
single base extension (SBE), 99
single genome sequencing (SGS), 12
single molecule detection, 23
single molecule nanopore sequencing, 18
single molecule sequencing, 17–18
Helicos, 18
Pacific Biosciences, 17–18
single-stranded DNA (ssDNA), 82
small acid soluble proteins (SASP), 399
smart amplification process (SmartAmp), 74–8
Smart Ct, 67
solution-based chemistries, 116
spectral analysis, 317
procedure for classification of measured spectrum, 318
spectral classification procedure, 325–30
biological/non-biological determination performance based on the LDA of the spectral space, 328
distribution of spectra in twodimensional PLS latent variable space, 327
organic/inorganic determination performance based on CH stretch filter results, 326
PLS loading vectors for biological particle filter, 326
species-level classification performance
based on combined classification, 330
based on the support vector machine analysis, 329
spore/non-spore determination performance based on the LDA of the spectral space, 328
Sphingomonas wittichii, 399
stand-off integrated bioaerosol active hyperspectral detection (SINBAHD) system, 345
staphylococcal enterotoxin B (SEB), 258
Staphylococcus, 411–12
Staphylococcus epidermis, 187
static mode, 339
statistical model
Escherichia coli DNA sequence, 293–4
model sequence for DNA from three different strains, 293
predicted sub-THz signatures of SNA from strains, 294
stem-loop forming region, 76
storage stability, 174
strong cation exchange (SCX), 376
sucrose, 171–2
biosensors, 171–2
calibration curves, 172
support vector machine (SVM), 345
surface acoustic waves (SAW), 224
surface plasmon resonance (SPR), 257
surfactants determination
biosensors, 180–1
procedure by conductometric enzyme biosensors, 181
suspension array assays, 115
‘sweep-to-cue’ approach, 349
SYBR Green I, 60
Synchronous Coefficient of Drag Alteration (SCODA), 362–4
schematic diagram, 362
synthesis sequencing, 17
T
T-antigen, 263
T-COR potable thermocyclers, 66–7
Taq polymerase, 62–3
target amplification, 84
target-specific polymerase chain reaction (TS-PCR), 99
target-specific primer extension (TSPE), 99
template switching, 81
terahertz resonance spectroscopy, 286–7
terahertz spectral characterization
biological identification, 281–307
absorption spectrum of DNA from sub-THz to UV, 282
approach for computational modeling of vibrational frequencies and absorption spectra, 287–9
component-based model for Escherichia coli cells, 294–5
dissipation time scales, 291–3
experimental sub-terahertz spectroscopy of biological molecules and species, 295–305
fundamentals of terahertz vibrational spectroscopy of large biological molecules and species, 282–4
future trends, 306–7
problem with poor convergence of simulation, 289–91
recent and future trends, 286–7
statistical model for Escherichia coli DNA sequence, 293–4
overview, 284–6
examples of transmission spectra from different materials in sub-THz range, 284
terahertz vibrational spectroscopy
fundamentals for biological identification of large biological molecules and species, 282–4
vibrations in THz frequency range, 283
The Institute for Genomic Research (TIGR), 16
thermal measurements, 224
thermocycling, 55
Thermus aquaticus, 56
thioredoxin, 290
Threat Identification and Detection System (TIDS) software, 389
time-of-flight (TOF) mass analysers, 381–2
advantages, 386
disadvantages, 386–7
TOTO-1, 60
tracer, 136
transcription mediated amplification (TMA), 84–5
transduction, 195
transistor, 195
transmission spectra, 302
trial-and-error method, 84
Triangle 4 vaccine, 268–9
TriZol, 33
true single molecule sequencing (tSMS), 18
Ty1HRT yeast system, 12
U
ultradeep pyrosequencing (UDPS), 12–13
ultrasonication, 373–4
Sonicator Continuous Flow Cell, 374
ultraviolet laser induced fluorescence (UV-LIF), 344–5
266 nm LIF measured from aerosolized 5 micron particles and interferents, 346
cross-sections for tryptophan, NADH and riboflavin, 344
ultraviolet (UV), 296
ultraviolet (UV) mutagenesis, 28
United States National Institutes of Health (NIH), 16
universal primer site, 102
upstream ligation probe (ULP), 102
urea biosensors, 157–9
urea hydrolysis, 154–5
urease-creatinase-creatininase, 158
US Food and Drug Administration, 65–6
US Joint Biological Agent Identification and Diagnostic System (JBAIDS), 65
V
Vibratess, 301
vibrational frequencies, 299
vibrational resonance spectroscopy, 282–3
vibrational spectroscopy
moderate resolution of 0.25 cm−1, 295–300
Bacillus subtilis spores, 298
reproducibility of spectral features in transmission spectra for E. coli samples, 298
sub-THz absorption spectra of E. coli and B. subtilis living cells, 300
viologens, 168
viral culture, 266
viral nucleic acid characterization, 26–7
voltammetric techniques, 132
W
Watson-Crick double-stranded configuration, 302–4
WeatherBug, 335
Whatman FTA filter, 365
whole cell conductometric biosensors, 183–6
whole genome sequencing (WGS), 4
Wizard, 365
World Health Organization, 42–3
X
X-ray crystallography, 267
xTAG Data Analysis Software (TDAS), 116
xTAG Respiratory Viral Panel (xTAG RVPv1), 116
xTAG Technology, 95
Y
Y. pestis CO92, 417–18
YOYO-1, 60
Z
Zanamavir, 258
zero-mode waveguide, 17–18
zone electrophoresis, 357–9
ZstatFlu detector, 273
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