Fluorescence (cont.)
plate readers.................................................... 603, 605
reporter strains ............................................... 219, 221
G
Gene essentiality............................................................ 285
Gene expression ......................................... 168, 481, 482,
485, 487, 505, 507, 513, 514
Gene silencing ...................................................... 343–363
Genomic DNA
preparation ..................................................... 406, 411
sequencing ...................................................... 410, 524
Glycerol monomycolate (GroMM).................... 110, 119,
120, 124, 129, 130, 142, 143, 146
Glycopeptidolipids (GPL) .................................. 110, 114,
119, 125, 128, 143, 144
Growth analysis
measuring ATP levels .............................................. 639
measuring optical density .............................. 641, 643
measuring with resazurin.............................. 236, 237,
241, 242, 605, 613, 630, 638–640, 642, 643,
645, 646
Growth inhibition
measurements ........................................ 596, 703, 704
models...................................................................... 626
H
High content screening ....................................................vi
High throughput screening (HTS) ................... 611–632,
638, 645, 647, 650
Hypoxia models
model of persistence ...................................... 152, 206
I
Image analysis
imageJ software ....................................................... 189
Inducible gene expression
recombineering .............................................. 301–320
Infection models
Dictyostelium discoideum ............................. 183–201
macrophages ................................................... 167–182
L
Lipids
characterization ....................................................... 114
extraction ............................................... 549, 551, 556
isolation ................................................................... 110
purification ........................... 114, 116, 146, 551, 573
Lipoarabinomannan (LAM) ........................109–148, 550
Luminescence
microscopy............................................................... 198
reporter strains ..............................168, 371, 376, 640
M
Macrophage
activation ............................................... 170, 176, 179
alveolar ..................................................................... 168
bone marrow derived ..................................... 167, 181
in high-content screening....................................... 188
human monocyte derived THP-1 ................ 168, 262,
267, 666, 677, 678, 678, 679, 683, 686, 700
imaging .................................................................... 168
infection models ...................................................... 167
models............................................................. 167, 651
multiplicity of infection ........................ 264, 652, 700
phagosomes .................................................... 615, 686
viability................................................... 174, 175, 181
Matrix-Assisted Laser Desorption/Ionization-Time
of Flight mass spectrometry
(MALDI-TOF MS).......... 14, 114, 134, 401, 540
Media
carbon source .......................................................... 4, 8
detergents ....................................................... 278, 604
Dubos-tween-albumin ................................................ 5
growth .............................................. 5, 8, 52, 55, 207,
221, 269, 408, 604
Middlebrook 7H9......................................5, 250, 251
Middlebrook 7H10 ............................ 4, 34, 292, 293
Sauton’s ................................................ 142, 153, 154,
156, 157, 162, 163, 266, 571, 617
supplements.................................................... 5, 8, 100
Tween 80........................................................ 278, 604
Tyloxapol ............................................... 278, 604, 617
Metabolomics
activity-based metabolomic profiling
(ABMP) .......................... 580–582, 584, 588–590
carbon tracing ......................................................... 582
metabolite analysis ......................................... 583, 584
Multi-stress non-replicating assay ....................... 612, 615
Mycobacterium avium .......................................5, 6, 8, 12,
14, 20, 22, 59, 112, 125, 142, 143, 273, 275,
280, 363, 424, 432, 444
Mycobacterium leprae ............................... 2–4, 6, 8, 9, 12,
13, 27–30, 33–36, 40, 43–45, 47, 52, 54, 116,
426, 444
Mycobacterium marinum ................................5, 6, 14, 20,
22, 116, 183–201, 235, 273, 275, 363, 426
Mycobacterium smegmatis .................................5, 21, 102,
125, 134, 135, 143, 152, 153, 156–158, 163,
219, 221, 242, 274–279, 282, 286, 302, 304,
307, 315–317, 344, 346, 348, 350, 351, 357,
388, 389, 391, 394, 395, 431, 441, 514, 529,
531, 639, 640, 642, 643
Mycobacterium tuberculosis ............................... 1–6, 9–15,
20, 22, 23, 26, 30, 31, 34, 36–38, 44, 47–49, 53,
56, 59–73, 77–79, 81, 84, 85, 90, 99, 101–103,
734
MYCOBACTERIA PROTOCOLS
Index
plate readers.................................................... 603, 605
reporter strains ............................................... 219, 221
G
Gene essentiality............................................................ 285
Gene expression ......................................... 168, 481, 482,
485, 487, 505, 507, 513, 514
Gene silencing ...................................................... 343–363
Genomic DNA
preparation ..................................................... 406, 411
sequencing ...................................................... 410, 524
Glycerol monomycolate (GroMM).................... 110, 119,
120, 124, 129, 130, 142, 143, 146
Glycopeptidolipids (GPL) .................................. 110, 114,
119, 125, 128, 143, 144
Growth analysis
measuring ATP levels .............................................. 639
measuring optical density .............................. 641, 643
measuring with resazurin.............................. 236, 237,
241, 242, 605, 613, 630, 638–640, 642, 643,
645, 646
Growth inhibition
measurements ........................................ 596, 703, 704
models...................................................................... 626
H
High content screening ....................................................vi
High throughput screening (HTS) ................... 611–632,
638, 645, 647, 650
Hypoxia models
model of persistence ...................................... 152, 206
I
Image analysis
imageJ software ....................................................... 189
Inducible gene expression
recombineering .............................................. 301–320
Infection models
Dictyostelium discoideum ............................. 183–201
macrophages ................................................... 167–182
L
Lipids
characterization ....................................................... 114
extraction ............................................... 549, 551, 556
isolation ................................................................... 110
purification ........................... 114, 116, 146, 551, 573
Lipoarabinomannan (LAM) ........................109–148, 550
Luminescence
microscopy............................................................... 198
reporter strains ..............................168, 371, 376, 640
M
Macrophage
activation ............................................... 170, 176, 179
alveolar ..................................................................... 168
bone marrow derived ..................................... 167, 181
in high-content screening....................................... 188
human monocyte derived THP-1 ................ 168, 262,
267, 666, 677, 678, 678, 679, 683, 686, 700
imaging .................................................................... 168
infection models ...................................................... 167
models............................................................. 167, 651
multiplicity of infection ........................ 264, 652, 700
phagosomes .................................................... 615, 686
viability................................................... 174, 175, 181
Matrix-Assisted Laser Desorption/Ionization-Time
of Flight mass spectrometry
(MALDI-TOF MS).......... 14, 114, 134, 401, 540
Media
carbon source .......................................................... 4, 8
detergents ....................................................... 278, 604
Dubos-tween-albumin ................................................ 5
growth .............................................. 5, 8, 52, 55, 207,
221, 269, 408, 604
Middlebrook 7H9......................................5, 250, 251
Middlebrook 7H10 ............................ 4, 34, 292, 293
Sauton’s ................................................ 142, 153, 154,
156, 157, 162, 163, 266, 571, 617
supplements.................................................... 5, 8, 100
Tween 80........................................................ 278, 604
Tyloxapol ............................................... 278, 604, 617
Metabolomics
activity-based metabolomic profiling
(ABMP) .......................... 580–582, 584, 588–590
carbon tracing ......................................................... 582
metabolite analysis ......................................... 583, 584
Multi-stress non-replicating assay ....................... 612, 615
Mycobacterium avium .......................................5, 6, 8, 12,
14, 20, 22, 59, 112, 125, 142, 143, 273, 275,
280, 363, 424, 432, 444
Mycobacterium leprae ............................... 2–4, 6, 8, 9, 12,
13, 27–30, 33–36, 40, 43–45, 47, 52, 54, 116,
426, 444
Mycobacterium marinum ................................5, 6, 14, 20,
22, 116, 183–201, 235, 273, 275, 363, 426
Mycobacterium smegmatis .................................5, 21, 102,
125, 134, 135, 143, 152, 153, 156–158, 163,
219, 221, 242, 274–279, 282, 286, 302, 304,
307, 315–317, 344, 346, 348, 350, 351, 357,
388, 389, 391, 394, 395, 431, 441, 514, 529,
531, 639, 640, 642, 643
Mycobacterium tuberculosis ............................... 1–6, 9–15,
20, 22, 23, 26, 30, 31, 34, 36–38, 44, 47–49, 53,
56, 59–73, 77–79, 81, 84, 85, 90, 99, 101–103,
734
MYCOBACTERIA PROTOCOLS
Index