INDEX
A
Anhydrotetracycline (ATC) ................................ 305, 307,
309, 315, 325, 327, 334, 340, 344, 345, 347, 354
Antibiotics
hygromycin..................................................... 274, 286
hygromycin resistance .................................... 274, 288
kanamycin ....................................................... 274, 286
kanamycin resistance ............................................... 282
metronidazole ........................................248–250, 612
Arabinogalactan.......................................... 110, 124, 235,
385, 387, 550, 551
ATP measurement
for antimicrobial susceptibility testing ................... 638
B
Bioinformatics ............................................ 400, 412–414,
417, 434, 485, 488, 504, 514, 534, 549, 552,
556, 579
Biomarkers......................................................78, 533, 534
Biosafety level 3 containment....................................... 335
C
cDNA
libraries .................................................. 485, 514, 522
synthesis ........................................355, 484, 492, 493,
514, 516, 520, 521
Cell disruption
bead beater ....................................................... 81, 586
French Press ............................................................ 104
probe sonication...................................................... 588
Cell wall
analyses .................................................................... 110
efflux .............................................. 232, 235–237, 441
permeability .......................... 232, 235–237, 273, 441
transport .................................................................. 232
Chromatin immunoprecipitation .............................60, 61
Clumping.............................................265, 281, 282, 627
Colony forming units (CFUs) determination ............198,
237, 242, 613, 622, 725
Culture
anaerobic............................... 251, 254, 255, 257, 258
clumping .....................................................6, 278, 730
media ............................................2, 9, 16, 18, 63, 79,
85, 100, 163, 164, 174, 176, 251, 252, 254, 255,
257, 258, 264, 265, 269, 278–280, 282, 309,
327, 354, 355, 357, 391, 477, 571, 588, 601,
620, 621, 625, 646, 667–671, 706, 716, 723
seed cultures ............................................................ 722
96-well format...................... 618, 619, 621, 622, 625
384-well format......................................618–621, 625
Culture filtrate
analyses .................................................................... 534
components ............................................................... 86
preparation ................................................................ 87
D
Diagonal measurement of n-way drug interactions
(DiaMOND) ............................................ 703–712
Dictyostelium discoideum .................................... 183–187,
189–193, 195–201
DNA
cDNA libraries......................................................... 485
isolation of genomic DNA ................................60, 61,
65, 68–69, 72, 406
pair-end sequencing ................................................ 412
single-end sequencing........................... 435, 484, 506
strand-specific sequencing ............................. 361, 528
E
Efflux
ethidium bromide (EtBr) ............. 232–235, 237–243
inhibitors ....................................... 232–235, 237–240
measurements ................................................. 241, 243
Electroporation
arcing ..................................................... 281, 282, 317
conditions ................................................................ 280
glycine treatment........................................... 274, 276,
280, 291, 292, 295, 296, 305, 309
recombination ......................................................... 274
transformation efficiencies .................... 274, 280, 283
Electrospray ionization (ESI)-MS................................ 114
F
Fatty acids ........................................................8, 110, 111,
114, 116, 124, 126, 129, 141, 144, 145, 385,
550, 574, 595, 596, 615
Fluorescence
microscopy.................................9, 197, 390, 392–395
Tanya Parish and Anuradha Kumar (eds.), Mycobacteria Protocols, Methods in Molecular Biology, vol. 2314,
https://doi.org/10.1007/978-1-0716-1460-0, © Springer Science+Business Media, LLC, part of Springer Nature 2021
733
A
Anhydrotetracycline (ATC) ................................ 305, 307,
309, 315, 325, 327, 334, 340, 344, 345, 347, 354
Antibiotics
hygromycin..................................................... 274, 286
hygromycin resistance .................................... 274, 288
kanamycin ....................................................... 274, 286
kanamycin resistance ............................................... 282
metronidazole ........................................248–250, 612
Arabinogalactan.......................................... 110, 124, 235,
385, 387, 550, 551
ATP measurement
for antimicrobial susceptibility testing ................... 638
B
Bioinformatics ............................................ 400, 412–414,
417, 434, 485, 488, 504, 514, 534, 549, 552,
556, 579
Biomarkers......................................................78, 533, 534
Biosafety level 3 containment....................................... 335
C
cDNA
libraries .................................................. 485, 514, 522
synthesis ........................................355, 484, 492, 493,
514, 516, 520, 521
Cell disruption
bead beater ....................................................... 81, 586
French Press ............................................................ 104
probe sonication...................................................... 588
Cell wall
analyses .................................................................... 110
efflux .............................................. 232, 235–237, 441
permeability .......................... 232, 235–237, 273, 441
transport .................................................................. 232
Chromatin immunoprecipitation .............................60, 61
Clumping.............................................265, 281, 282, 627
Colony forming units (CFUs) determination ............198,
237, 242, 613, 622, 725
Culture
anaerobic............................... 251, 254, 255, 257, 258
clumping .....................................................6, 278, 730
media ............................................2, 9, 16, 18, 63, 79,
85, 100, 163, 164, 174, 176, 251, 252, 254, 255,
257, 258, 264, 265, 269, 278–280, 282, 309,
327, 354, 355, 357, 391, 477, 571, 588, 601,
620, 621, 625, 646, 667–671, 706, 716, 723
seed cultures ............................................................ 722
96-well format...................... 618, 619, 621, 622, 625
384-well format......................................618–621, 625
Culture filtrate
analyses .................................................................... 534
components ............................................................... 86
preparation ................................................................ 87
D
Diagonal measurement of n-way drug interactions
(DiaMOND) ............................................ 703–712
Dictyostelium discoideum .................................... 183–187,
189–193, 195–201
DNA
cDNA libraries......................................................... 485
isolation of genomic DNA ................................60, 61,
65, 68–69, 72, 406
pair-end sequencing ................................................ 412
single-end sequencing........................... 435, 484, 506
strand-specific sequencing ............................. 361, 528
E
Efflux
ethidium bromide (EtBr) ............. 232–235, 237–243
inhibitors ....................................... 232–235, 237–240
measurements ................................................. 241, 243
Electroporation
arcing ..................................................... 281, 282, 317
conditions ................................................................ 280
glycine treatment........................................... 274, 276,
280, 291, 292, 295, 296, 305, 309
recombination ......................................................... 274
transformation efficiencies .................... 274, 280, 283
Electrospray ionization (ESI)-MS................................ 114
F
Fatty acids ........................................................8, 110, 111,
114, 116, 124, 126, 129, 141, 144, 145, 385,
550, 574, 595, 596, 615
Fluorescence
microscopy.................................9, 197, 390, 392–395
Tanya Parish and Anuradha Kumar (eds.), Mycobacteria Protocols, Methods in Molecular Biology, vol. 2314,
https://doi.org/10.1007/978-1-0716-1460-0, © Springer Science+Business Media, LLC, part of Springer Nature 2021
733