In d e x [link.springer.com]978-1-60761-971...313 A Acetaldehyde 236, 238, 241–248 Acylated...
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313 A Acetaldehyde .......................................... 236, 238, 241–248 Acylated homoserine lactone (AHL) antibodies ........................................................ 308–309 extraction ......................................................... 162, 165 N-butyryl HSL or N-(butanoyl)-L-HSL (C 4 -HSL) ...............................................4, 102, 147 N-hexanoyl HSL (C 6 -HSL)........................................ 4 N-3-oxo-dodecanoyl HSL (3-oxo-C 12 -HSL) ..... 4, 102 N-3-oxo-hexanoyl homoserine lactone (3-oxo-C 6 -HSL).....................................4, 165, 166 N-3-oxo-octanoyl HSL (3-oxo-C 8 -HSL) ................... 4 hydrolysis .......................................... 276, 285, 291–298 inhibition assay ........................................................ 296 lactonases .......................................... 275–289, 293, 297 purification ....................................... 162, 165, 275–289 synthesis ........................... 114, 159, 161–162, 300, 304 Affymetrix GeneChip ................................................... 173 AIR ........................................................ 236, 238, 242, 248 Alcohol dehydrogenase................... 236, 238, 245–247, 249 Alginate ................................................................. 149–152 Alkaline protease ............................................................. 22 Antibiotic resistance .......................................................... 4 Antibody promiscuity ...................................................... 85 Apoptosis............................................................... 134, 220 Autoinducer. See Acylated homoserine lactone Autoinducer 2 (AI-2) DPD .................................................................... 36, 43 furanosyl borate diester (BAI-2) ...............32, 36, 39–44 (2S,4S)-2-methyl-2,3,3,4-tetrahydroxyte trahydrofuran-borate ........................................... 32 Autoinducing peptide (AIP) ................. 48–50, 54, 56, 300, 302, 303, 307 Autoinduction ......................................................... 52, 114 B Bacteria gram-negative Agrobacterium tumefaciens .................. 3–17, 114, 116 Aeromonas hydrophila ...........................................116 Burkholderia cepacia .............................................266 Burkholderia glumae ..................................... 266, 267 Burkholderia pseudomallei ................................. 22, 61 Burkholderia thailandensis ......................................61 Campylobacter jejuni...............................................72 Chromobacterium violaceum........................ 3–17, 116 Escherichia coli ............................... 32, 44, 72, 75, 76, 115–117, 121, 135, 149, 151, 152, 155, 161, 168, 169, 191, 192, 195, 196, 203, 209, 277, 279–280 Klebsiella pneumonia ............................................. 72 Pseudomonas aureofaciens ........................................ 5 Pseudomonas aeruginosa ............ PAO1, 9, 12, 23, 24, 103, 106, 118, 121, 148, 254, 255, 257, 259, 260 Pseudomonas putida ............................................ 114 Ralstonia solanacearum ....................................... 266 Rhodobacter capsulatus......................................... 208 Serratia marscesens .................................................. 5 Sinorhizobium meliloti ........................................ 208 Vibrio anguillarum................................................ 71 Vibrio cholerae ............................................. 189–206 Vibrio fischeri ................................... 3, 114, 116, 149 Vibrio harveyi .................................... 3, 1, 42, 72, 84 gram-positive Bacillus cereus ...........................................................2 Bacillus thuringiensis ............................................276 Staphylococcus aureus ........................... 48, 55, 57, 301 Streptococcus godonii ...............................................72 Streptococcus mutans ...............................................72 Streptococcus pneumonia ..........................................72 Streptococcus pyogenes ............................................ 72 Bioassay plate-based........................................................... 11–14 strains, used for ................................. 5, 6, 11, 13, 15, 17 Biofilm dispersal ....................................................220, 223, 225 formation .................... 4, 22, 72, 87, 102, 103, 134, 190, 219–232, 253, 260 maturation ..................................................21, 220, 221 Bioluminescence ........................... 28, 29, 32, 72, 73, 75, 77 Bioreporter b-galactosidase (lacZ) .................................................. 6 b-lactamase reporter cell assay ................................... 56 Biosensor acoustic wave biosensor ...................... 84–87, 90, 91, 98 AQ................................................................. 23, 26–29 fluorescence resonance energy transfer (FRET).......................................................... 31–45 Brominated furanones ....................................................... 4 Kendra P. Rumbaugh (ed.), Quorum Sensing: Methods and Protocols, Methods in Molecular Biology, vol. 692, DOI 10.1007/978-1-60761-971-0, © Springer Science+Business Media, LLC 2011 INDEX
Transcript of In d e x [link.springer.com]978-1-60761-971...313 A Acetaldehyde 236, 238, 241–248 Acylated...
![Page 1: In d e x [link.springer.com]978-1-60761-971...313 A Acetaldehyde 236, 238, 241–248 Acylated homoserine lactone (AHL) antibodies 308–309 extraction 162, 165 N-butyryl HSL or N-(butanoyl)-L-HSL](https://reader034.fdocuments.in/reader034/viewer/2022042113/5e900a5292d56e5bbc096084/html5/thumbnails/1.jpg)
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A
Acetaldehyde ..........................................236, 238, 241–248Acylated homoserine lactone (AHL)
antibodies ........................................................ 308–309extraction ......................................................... 162, 165N-butyryl HSL or N-(butanoyl)-L-HSL
(C4-HSL) ...............................................4, 102, 147N-hexanoyl HSL (C6-HSL) ........................................ 4N-3-oxo-dodecanoyl HSL (3-oxo-C12-HSL) ..... 4, 102N-3-oxo-hexanoyl homoserine lactone
(3-oxo-C6-HSL) .....................................4, 165, 166N-3-oxo-octanoyl HSL (3-oxo-C8-HSL) ................... 4hydrolysis ..........................................276, 285, 291–298inhibition assay ........................................................ 296lactonases ..........................................275–289, 293, 297purification .......................................162, 165, 275–289synthesis ........................... 114, 159, 161–162, 300, 304
Affymetrix GeneChip ................................................... 173AIR ........................................................ 236, 238, 242, 248Alcohol dehydrogenase ................... 236, 238, 245–247, 249Alginate ................................................................. 149–152Alkaline protease ............................................................. 22Antibiotic resistance .......................................................... 4Antibody promiscuity ...................................................... 85Apoptosis ............................................................... 134, 220Autoinducer. See Acylated homoserine lactoneAutoinducer 2 (AI-2)
DPD .................................................................... 36, 43furanosyl borate diester (BAI-2) ...............32, 36, 39–44(2S,4S)-2-methyl-2,3,3,4-tetrahydroxyte
trahydrofuran-borate ........................................... 32Autoinducing peptide (AIP) ................. 48–50, 54, 56, 300,
302, 303, 307Autoinduction ......................................................... 52, 114
B
Bacteriagram-negative
Agrobacterium tumefaciens ..................3–17, 114, 116Aeromonas hydrophila ...........................................116Burkholderia cepacia .............................................266Burkholderia glumae .....................................266, 267Burkholderia pseudomallei .................................22, 61Burkholderia thailandensis ......................................61
Campylobacter jejuni ...............................................72Chromobacterium violaceum ........................3–17, 116Escherichia coli ............................... 32, 44, 72, 75, 76,
115–117, 121, 135, 149, 151, 152, 155, 161, 168, 169, 191, 192, 195, 196, 203, 209, 277, 279–280
Klebsiella pneumonia ............................................. 72Pseudomonas aureofaciens ........................................ 5Pseudomonas aeruginosa ............PAO1, 9, 12, 23, 24,
103, 106, 118, 121, 148, 254, 255, 257, 259, 260Pseudomonas putida ............................................ 114Ralstonia solanacearum ....................................... 266Rhodobacter capsulatus ......................................... 208Serratia marscesens .................................................. 5Sinorhizobium meliloti ........................................ 208Vibrio anguillarum ................................................ 71Vibrio cholerae ............................................. 189–206Vibrio fischeri ...................................3, 114, 116, 149Vibrio harveyi ....................................3, 1, 42, 72, 84
gram-positiveBacillus cereus ...........................................................2Bacillus thuringiensis ............................................276Staphylococcus aureus ...........................48, 55, 57, 301Streptococcus godonii ...............................................72Streptococcus mutans ...............................................72Streptococcus pneumonia ..........................................72Streptococcus pyogenes ............................................ 72
Bioassayplate-based ........................................................... 11–14strains, used for ................................. 5, 6, 11, 13, 15, 17
Biofilmdispersal ....................................................220, 223, 225formation ....................4, 22, 72, 87, 102, 103, 134, 190,
219–232, 253, 260maturation ..................................................21, 220, 221
Bioluminescence ........................... 28, 29, 32, 72, 73, 75, 77Bioreporter
b-galactosidase (lacZ) .................................................. 6b-lactamase reporter cell assay ................................... 56
Biosensoracoustic wave biosensor ......................84–87, 90, 91, 98AQ ................................................................. 23, 26–29fluorescence resonance energy transfer
(FRET) .......................................................... 31–45Brominated furanones ....................................................... 4
Kendra P. Rumbaugh (ed.), Quorum Sensing: Methods and Protocols, Methods in Molecular Biology, vol. 692,DOI 10.1007/978-1-60761-971-0, © Springer Science+Business Media, LLC 2011
Index
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314 Quorum SenSing
Index
C
Candida albicans ......................................................219–232cDNA
fragmentation .......................................................... 181synthesis ................................... 174, 175, 180–182, 186
Cell culture mediaLuria-Bertani (LB) .................................................... 33tryptic soy broth (TSB) ............................................. 49
Cell free supernatant.......................... 10, 41, 43, 72–75, 77, 78, 81, 196, 197, 204
Cell phone ........................................................84, 235, 236Chemically orthogonal antibodies ................................... 86Cholerae autoinducer 1 (CAI-1) ........................... 189, 204Chromatogram ..............13, 64, 65, 107, 108, 212, 213, 293Chromatography
flash chromatography ...................................... 269–271high performance liquid chromatography
(HPLC) ...........................23, 50, 54, 55, 62, 64, 66, 68, 104, 107, 127, 161, 162, 164, 166, 167, 208, 209, 212–213, 216, 292–293, 295–297
liquid chromatography/mass spectrometry (LC/MS) .......... 61–69, 104, 107–109, 60–162, 167, 301
thin layer chromatography (TLC) ........... 6, 8, 10, 13–14, 23–28, 208–212, 216agar overlays ................................................... 11–12
Combinatorial libraries .................................................. 267COMSTAT ........................................................... 222, 230Conformational change ................ 32, 33, 84, 87, 88, 91, 98Cystic fibrosis (CF) ................................102, 103, 134, 149
D
Dissociation constant ...................................................... 85Delisea pulchra ............................................................... 254
E
Elastase ............................................................................ 22Enzyme kinetics ............................................................ 276Exotoxin .................................................................... 22, 48Expression analysis ................................................ 173–186Extracellular matrix ........................................219, 226, 231
F
Farnesol .......................................... 220, 221, 223, 225–231Flow cell ................................ 103–106, 109, 110, 151, 224,
255–256, 258–260, 262Fluorescence
detection .............................................................. 35–36flurophore maturation .......................................... 39–40proteins (GFP, CFP and YFP) .................................. 32
G
Gel electrophoresis ..............................................35–36, 52, 138–139, 179, 181–183, 185, 278–279, 308
Gene conjugation .............................................................. 5Global regulator ............................................................. 173
H
Halogenated furanones .................................................. 254High-throughput parallel sequencing ............................ 174
I
Immunoconjugate .................................................. 300–304In vitro synthesis ........................................................ 73, 77In vivo ............................... 48, 147–155, 220, 224, 231, 300
L
Lectins ............................................................................. 22Ligand ............................................... 32, 36, 39–41, 43, 44,
96, 99, 114, 140, 142Lipopolysaccharide (LPS) .....................133–136, 138–140,
142, 143, 209, 210, 214–215, 266LIVE/DEAD viability staining ..................................... 260Luciferase ....................................... 116, 117, 124, 193, 204Luminescent reporter ............................................ 113–129
M
Macrophages ..................................133, 136–138, 141–143MAP kinase................................................................... 142Mass spectrometry (MS)
matrix-assisted laser desorption/ ionization mass spectrometry (MALDI-MS) ............................... 54
Membrane vesicles (MV) .............................................. 208Metalloprotease ............................................................... 32Metalloprotein ............................................................... 275Microarray ..................................... 173–176, 180, 182, 185,
192, 254, 257, 258, 260–261Microscopy
confocal scanning laser microscopy (CSLM) ......................... 150–152, 155, 228–230, 232, 257, 258, 260
epifluorescence microscopy ...............150, 152, 155, 222Molecular recognition ........................ 84, 87, 91, 96, 98, 99Monoclonal antibodies
(mAbs) ................................... 85, 96, 300, 301, 307Morphology..................................... 32, 155, 220, 225, 228,
229, 231Mouse model ................................................................. 149mRNA ................................... 117, 182, 184, 185, 190–192,
194, 198, 201–205
N
Neural-network based systems .................................. 89–90NF-kappa B (NF-kB) ........................................... 133–136Northern blot .......................... 47, 49–51, 53–56, 190–192,
198–201, 205Nuclear magnetic resonance
(NMR) ................................. 22, 268, 269, 271, 272
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Quorum SenSing
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Index
P
Paraoxonase (PON) ............................................... 291–298Pathogen-associated molecular patterns
(PAMPs) ........................................................... 133Patulin ............................................ 117, 123, 128, 129, 254Periplasmic-binding proteins (bPBP) .............................. 32Phenotype ......................................................4, 5, 220, 254Pigment
pyocyanin ...................22, 26, 28, 29, 208, 302, 308–309violacein ........................................................6, 7, 11, 13
Polymerase chain reaction (PCR)colony PCR ............................................................. 195product purification ..........................122, 195, 198, 279real-time PCR ............................ 50, 174, 176, 182–186reverse transciptase PCR (RT-PCR) ........47, 49, 51–52
Protein expression .......................................75–76, 163, 164Protein purification ..............................37, 76–77, 277, 280Pseudomonas quinolone signal (PQS). See QuinolonesPulmonary infection model ........................................... 147
Q
Quadrature amplitude modulation (QAM) ............... 85, 86Quinolones
2-alkyl-4-quinolones (AQ) .................................. 21–292-heptyl-3-hydroxy-4-quinolone
(PQS) ................................ 22–24, 26–29, 207–2162-heptyl-4-quinolone
(HHQ) ........22–24, 26–29, 115, 208, 209, 212–2162-heptyl-4-quinolone N-oxide
(HQNO) ................................................. 22, 63–674-hydroxy-2-alkylquinolines
(HAQ) ........................................................... 63, 662-nonyl-4-quinolone (NHQ) .................................... 22
Quorum sensing (QS)agonists .....................................................116, 124, 128analogues ..................................................267, 299, 300antagonists ....................................................... 125, 267genes and proteins
agr ...................................................................47–58AiiA ........................................................... 277–280CqsA ................................................................. 189CqsS .................................................................. 189cviI ..................................................................... 6, 7cviR .............................................................6, 12, 15HapR .......................... 190, 192–194, 198, 202, 203las box ................................................................ 115lasI ..........................1, 102, 115–118, 121, 124, 129,
147, 161, 168, 169lasR .......... 21, 22, 102, 113–129, 147, 151, 254, 255lux box ............................................................... 114luxI ................................ 4–6, 13, 114, 147, 151, 266luxN ...............................................32, 72, 87, 96–98LuxO ............................ 95, 189, 190, 197, 202, 203luxP ....................................... 32, 33, 36, 39, 43, 189
luxQ ..........................................................87, 97, 98luxR ....................................... 4–6, 13, 15, 114, 115,
147, 149, 151, 265luxS ................ 32, 33, 36, 39, 42–45, 71, 75, 98, 189LuxU ..............................................87, 95, 189, 190MvfR ................................................................. 207pqsA ............................................. 23, 26, 28, 29, 210pqsH .............................................................208, 210PqsR .................................................................. 207rhlI ...................................................21, 22, 102, 115rhlR .......................................................22, 115, 147rsaL ..............................................115–118, 121, 128traI .......................................................................5–7traR .....................................................................4–6vsqR .....................................................................115
inhibitors (QSI) ............................4, 151, 254, 257–262QSI monitor screen ................................... 254–255
mimic ....................................................................... 116quenching ................................................................ 300
R
Radio frequency identification device (RFID) .......................................... 90–91, 99
Rhamnolipid ............................................................ 22, 148RNA
contamination .......................................................... 185isolation ..............................................50, 173–178, 184purification .............................................................. 177small RNA (sRNA) ......................................... 189–206
RNAIII ............................................................... 48, 50–57RNAIII activating protein (RAP) ....................... 48, 54–56RNAIII inhibiting peptide (RIP) .................. 48, 54, 55, 57
S
Siderophores .................................................................... 32Site-directed mutagenesis ...................... 117, 118, 190, 192,
202–204Splicing by overlap extension (SOE) ..................... 193–195State-space mapping.......................................85, 91–95, 98Superoxide dismutase ...................................................... 22Synthetic biology ........................................................... 235Synthetic ecosystem ....................................................... 235
T
Temporal regulation .............................................47, 51, 52Tetramic acid ..........................................101–110, 127, 300Toll-like receptor ............................................133, 140, 142Transcriptome ............................................................... 174Type III secretion ............................................................ 32
V
Virulence ....................................4, 21, 22, 72, 87, 102, 113, 116, 134, 149, 190, 208, 253, 254, 275
Vibrio harveyi two-component model.............................. 84
