106, 111–114, 116, 125, 128, 135, 136, 140,
142–144, 152–154, 157, 158, 162, 163,
167–182, 184, 219, 221, 224–226, 235, 236,
242, 243, 247, 248, 262, 264, 265, 269,
273–278, 280, 282, 286, 288, 291, 292, 298,
301–320, 323–325, 327, 328, 340, 343–346,
349, 350, 353–357, 361, 365–382, 386, 388,
395, 403, 408, 418, 424, 432, 440–444,
459–479, 481–511, 514, 529, 531, 534, 538,
551, 552, 554–556, 571–574, 579–591,
595–597, 601, 603–605, 607, 611–632,
637–643, 649–701, 704–706, 715–731
Mycobacterium ulcerans ................................3–5, 8, 9, 12,
20, 23, 116, 427, 444
Mycolic acids (MA)
mero-mycolic acid (mero-MA) .............................. 113
mycolic acid methyl ester (MAME) ....................... 142
mycolic acyl (MA) chains........................................ 109
N
Nitrate reduction.......................................................14, 20
Nitric oxide................................................. 247, 367, 369,
371, 615, 630, 631, 652, 662, 688, 689
Non-replicating persistence (NRP)
hypoxia............................................................ 247–259
multi-stress ..................................................... 611–632
nutrient starvation................................................... 258
Nontuberculous mycobacteria (NTM).................. 1, 2, 4,
6, 7, 9, 12, 15, 59, 60, 62, 64, 69, 70, 72, 73, 78,
441, 442
O
Oligo-mediated Recombineering followed by
BxB1 Integrase Targeting (ORBIT) ...... 303–307,
312–316, 319, 343
Oxygen
consumption................................................................ 7
P
Permeability.....................................................6, 231–244,
273, 441
Phagocytosis ........................................184, 190, 269, 683
Phenolic glycolipids (PGL) ................................ 110, 111,
113, 114, 116, 119, 128, 143, 144, 551, 558
Phosphatidyl inonsitol mannosides (PIM) .................110,
114, 137, 143, 144, 146, 556
Phthiocerol dimycocerosate (PDIM)
virulence .................................................................. 113
Promoter replacement
gene silencing .......................................................... 343
gene switching................................................ 287, 288
homologous recombination ................................... 286
PROSPECT.......................................................... 324–326
Protein
analyses ..........................................138, 227, 270, 534
extractions .................................. 79, 94, 96, 101, 137
fractionation ............................................................ 138
hydrophilic.............................................. 83–84, 97–99
hydrophobic ................................................... 138, 385
Triton X-114 partitioning ........................... 83, 97–98
Protein fractionation
cell lysates ................................................................ 544
sub-cellular fractionation ...................................81–82,
95–96, 544
Protein quantitations .................................................... 100
Protein separation
hydrophobic interaction chromatography............. 138
Proteolysis............................................................... 89, 325
R
Recombination
homologous recombination .........274, 285, 286, 297
recombineering .............................................. 302, 304
Reporter strains
fluorescent ............................................................... 206
luminescent.............................................................. 168
RNA
extraction .................................. 48, 74, 357, 408, 529
sequencing ...............................................60, 408, 461,
481–511, 513
S
Saponification ............................................. 110, 113, 124,
127, 134, 141, 144, 145, 551
Sequencing
platforms........................................................ 338, 400,
408–410, 482–485, 497, 513, 514
reference genomes......................................... 415, 435,
442, 482, 485
from sputum...........................................298, 459–479
transcription start sites ............................................ 513
transcription start sites (TSS)
mapping ............................................................. 513
transcriptomes ...............................481, 482, 484, 485
whole genomes..........................................60, 62, 298,
399, 400, 404, 444
Single-cell analysis ....................................... 184, 221, 696
Sulfoglycolipids .......................................... 110, 113, 116,
143, 551, 556, 560, 562, 563
T
Time lapse microscopy......................................... 205–227
Transcriptional regulation ............................................ 513
Transcriptional silencing ...................................... 348, 355
MYCOBACTERIA PROTOCOLS
Index 735
142–144, 152–154, 157, 158, 162, 163,
167–182, 184, 219, 221, 224–226, 235, 236,
242, 243, 247, 248, 262, 264, 265, 269,
273–278, 280, 282, 286, 288, 291, 292, 298,
301–320, 323–325, 327, 328, 340, 343–346,
349, 350, 353–357, 361, 365–382, 386, 388,
395, 403, 408, 418, 424, 432, 440–444,
459–479, 481–511, 514, 529, 531, 534, 538,
551, 552, 554–556, 571–574, 579–591,
595–597, 601, 603–605, 607, 611–632,
637–643, 649–701, 704–706, 715–731
Mycobacterium ulcerans ................................3–5, 8, 9, 12,
20, 23, 116, 427, 444
Mycolic acids (MA)
mero-mycolic acid (mero-MA) .............................. 113
mycolic acid methyl ester (MAME) ....................... 142
mycolic acyl (MA) chains........................................ 109
N
Nitrate reduction.......................................................14, 20
Nitric oxide................................................. 247, 367, 369,
371, 615, 630, 631, 652, 662, 688, 689
Non-replicating persistence (NRP)
hypoxia............................................................ 247–259
multi-stress ..................................................... 611–632
nutrient starvation................................................... 258
Nontuberculous mycobacteria (NTM).................. 1, 2, 4,
6, 7, 9, 12, 15, 59, 60, 62, 64, 69, 70, 72, 73, 78,
441, 442
O
Oligo-mediated Recombineering followed by
BxB1 Integrase Targeting (ORBIT) ...... 303–307,
312–316, 319, 343
Oxygen
consumption................................................................ 7
P
Permeability.....................................................6, 231–244,
273, 441
Phagocytosis ........................................184, 190, 269, 683
Phenolic glycolipids (PGL) ................................ 110, 111,
113, 114, 116, 119, 128, 143, 144, 551, 558
Phosphatidyl inonsitol mannosides (PIM) .................110,
114, 137, 143, 144, 146, 556
Phthiocerol dimycocerosate (PDIM)
virulence .................................................................. 113
Promoter replacement
gene silencing .......................................................... 343
gene switching................................................ 287, 288
homologous recombination ................................... 286
PROSPECT.......................................................... 324–326
Protein
analyses ..........................................138, 227, 270, 534
extractions .................................. 79, 94, 96, 101, 137
fractionation ............................................................ 138
hydrophilic.............................................. 83–84, 97–99
hydrophobic ................................................... 138, 385
Triton X-114 partitioning ........................... 83, 97–98
Protein fractionation
cell lysates ................................................................ 544
sub-cellular fractionation ...................................81–82,
95–96, 544
Protein quantitations .................................................... 100
Protein separation
hydrophobic interaction chromatography............. 138
Proteolysis............................................................... 89, 325
R
Recombination
homologous recombination .........274, 285, 286, 297
recombineering .............................................. 302, 304
Reporter strains
fluorescent ............................................................... 206
luminescent.............................................................. 168
RNA
extraction .................................. 48, 74, 357, 408, 529
sequencing ...............................................60, 408, 461,
481–511, 513
S
Saponification ............................................. 110, 113, 124,
127, 134, 141, 144, 145, 551
Sequencing
platforms........................................................ 338, 400,
408–410, 482–485, 497, 513, 514
reference genomes......................................... 415, 435,
442, 482, 485
from sputum...........................................298, 459–479
transcription start sites ............................................ 513
transcription start sites (TSS)
mapping ............................................................. 513
transcriptomes ...............................481, 482, 484, 485
whole genomes..........................................60, 62, 298,
399, 400, 404, 444
Single-cell analysis ....................................... 184, 221, 696
Sulfoglycolipids .......................................... 110, 113, 116,
143, 551, 556, 560, 562, 563
T
Time lapse microscopy......................................... 205–227
Transcriptional regulation ............................................ 513
Transcriptional silencing ...................................... 348, 355
MYCOBACTERIA PROTOCOLS
Index 735