will not show the presence of other contaminants however and
should not replace UV spectrometry. If RNA is present, repeat
RNase A treatment of the sample. To remove other contaminants present, repeat the gDNA extraction process proceeding
from the chloroform–isoamyl alcohol step.
References
1. Somerville W, Thibert L, Schwartzman K et al
(2005) Extraction of Mycobacterium tuberculosis DNA: a question of containment. J Clin
Microbiol 43(6):2996–2997
2. Amaro A, Duarte E, Amado A et al (2008)
Comparison of three DNA extraction methods
for Mycobacterium bovis, Mycobacterium tuberculosis and Mycobacterium avium subsp avium.
Lett Appl Microbiol 47(1):8–11
3. Aldous WK, Pounder JI, Cloud JL et al (2005)
Comparison of six methods of extracting Mycobacterium tuberculosis DNA from processed
sputum for testing by quantitative real-time
PCR. J Clin Microbiol 43(5):2471–2473
4. Englund S, Bolske G, Ballagi-Pordany A et al
(2001) Detection of Mycobacterium avium
subsp. paratuberculosis in tissue samples by single, fluorescent and nested PCR based on the
IS900 gene. Vet Microbiol 81(3):257–271
5. Hosek J, Svastova P, Moravkova M, Pavlik I,
Bartos M (2006) Methods of mycobacterial
DNA isolation from different biological material: a review. Vet Med 51(2):180–192
6. Belisle J, Mahaffey S, Hill P (2008) Isolation of
Mycobacterium species genomic DNA. In:
Parish T, Brown A (eds) Methods in molecular
biology: mycobacteria protocols, 2nd edn.
Humana Press, New York
7. Bemer-Melchior P, Drugeon HB (1999) Inactivation of Mycobacterium tuberculosis for DNA
typing analysis. J Clin Microbiol 37
(7):2350–2351
8. Zwadyk P Jr, Down JA, Myers N et al (1994)
Rendering of mycobacteria safe for molecular
diagnostic studies and development of a lysis
method for strand displacement amplification
and PCR. J Clin Microbiol 32(9):2140–2146
9. Galas DJ, Schmitz A (1978) DNAse footprinting: a simple method for the detection of
protein-DNA binding specificity. Nucleic
Acids Res 5(9):3157–3170
10. Revzin MGA (1986) The use of gel electrophoresis to detect and study nucleic acid–protein interactions. Trends Biochem Sci 11
(10):395–396
11. Gade P, Kalvakolanu DV (2012) Chromatin
immunoprecipitation assay as a tool for
analyzing transcription factor activity. Methods
Mol Biol 809:85–104
12. Minch KJ, Rustad TR, Peterson EJ et al (2015)
The DNA-binding network of Mycobacterium
tuberculosis. Nat Commun 6:5829
13. Rodrigue S, Brodeur J, Jacques PE et al (2007)
Identification of mycobacterial sigma factor
binding sites by chromatin immunoprecipitation assays. J Bacteriol 189(5):1505–1513
14. Rustad TR, Minch KJ, Ma S et al (2014)
Mapping and manipulating the Mycobacterium
tuberculosis transcriptome using a transcription
factor overexpression-derived regulatory network. Genome Biol 15(11):502
15. AlqaSeer K, Turapov O, Barthe P et al (2019)
Protein kinase B controls Mycobacterium tuberculosis growth via phosphorylation of the transcriptional regulator Lsr2 at threonine 112.
Mol Microbiol 112(6):1847–1862
16. Blasco B, Chen JM, Hartkoorn R et al (2012)
Virulence regulator EspR of Mycobacterium
tuberculosis is a nucleoid-associated protein.
PLoS Pathog 8(3):e1002621
17. Sala C, Haouz A, Saul FA et al (2009)
Genome-wide regulon and crystal structure of
BlaI (Rv1846c) from Mycobacterium tuberculosis. Mol Microbiol 71(5):1102–1116
18. Muller AU, Imkamp F, Weber-Ban E (2018)
The mycobacterial LexA/RecA-independent
DNA damage response is controlled by PafBC
and the pup-proteasome system. Cell Rep 23
(12):3551–3564
19. Sales ML, Fonseca Junior AA, Orzil L et al
(2014) Validation of a real-time PCR assay for
the molecular identification of Mycobacterium
tuberculosis.
Braz
J
Microbiol
45
(4):1363–1369
20. Jabbar A, Phelan JE, de Sessions PF et al
(2019) Whole genome sequencing of drug
resistant Mycobacterium tuberculosis isolates
from a high burden tuberculosis region of
North West Pakistan. Sci Rep 9(1):14996
21. Yates TA, Khan PY, Knight GM et al (2016)
The transmission of Mycobacterium tuberculosis
in high burden settings. Lancet Infect Dis 16
(2):227–238
74
Heena Jagatia and Daire Cantillon
should not replace UV spectrometry. If RNA is present, repeat
RNase A treatment of the sample. To remove other contaminants present, repeat the gDNA extraction process proceeding
from the chloroform–isoamyl alcohol step.
References
1. Somerville W, Thibert L, Schwartzman K et al
(2005) Extraction of Mycobacterium tuberculosis DNA: a question of containment. J Clin
Microbiol 43(6):2996–2997
2. Amaro A, Duarte E, Amado A et al (2008)
Comparison of three DNA extraction methods
for Mycobacterium bovis, Mycobacterium tuberculosis and Mycobacterium avium subsp avium.
Lett Appl Microbiol 47(1):8–11
3. Aldous WK, Pounder JI, Cloud JL et al (2005)
Comparison of six methods of extracting Mycobacterium tuberculosis DNA from processed
sputum for testing by quantitative real-time
PCR. J Clin Microbiol 43(5):2471–2473
4. Englund S, Bolske G, Ballagi-Pordany A et al
(2001) Detection of Mycobacterium avium
subsp. paratuberculosis in tissue samples by single, fluorescent and nested PCR based on the
IS900 gene. Vet Microbiol 81(3):257–271
5. Hosek J, Svastova P, Moravkova M, Pavlik I,
Bartos M (2006) Methods of mycobacterial
DNA isolation from different biological material: a review. Vet Med 51(2):180–192
6. Belisle J, Mahaffey S, Hill P (2008) Isolation of
Mycobacterium species genomic DNA. In:
Parish T, Brown A (eds) Methods in molecular
biology: mycobacteria protocols, 2nd edn.
Humana Press, New York
7. Bemer-Melchior P, Drugeon HB (1999) Inactivation of Mycobacterium tuberculosis for DNA
typing analysis. J Clin Microbiol 37
(7):2350–2351
8. Zwadyk P Jr, Down JA, Myers N et al (1994)
Rendering of mycobacteria safe for molecular
diagnostic studies and development of a lysis
method for strand displacement amplification
and PCR. J Clin Microbiol 32(9):2140–2146
9. Galas DJ, Schmitz A (1978) DNAse footprinting: a simple method for the detection of
protein-DNA binding specificity. Nucleic
Acids Res 5(9):3157–3170
10. Revzin MGA (1986) The use of gel electrophoresis to detect and study nucleic acid–protein interactions. Trends Biochem Sci 11
(10):395–396
11. Gade P, Kalvakolanu DV (2012) Chromatin
immunoprecipitation assay as a tool for
analyzing transcription factor activity. Methods
Mol Biol 809:85–104
12. Minch KJ, Rustad TR, Peterson EJ et al (2015)
The DNA-binding network of Mycobacterium
tuberculosis. Nat Commun 6:5829
13. Rodrigue S, Brodeur J, Jacques PE et al (2007)
Identification of mycobacterial sigma factor
binding sites by chromatin immunoprecipitation assays. J Bacteriol 189(5):1505–1513
14. Rustad TR, Minch KJ, Ma S et al (2014)
Mapping and manipulating the Mycobacterium
tuberculosis transcriptome using a transcription
factor overexpression-derived regulatory network. Genome Biol 15(11):502
15. AlqaSeer K, Turapov O, Barthe P et al (2019)
Protein kinase B controls Mycobacterium tuberculosis growth via phosphorylation of the transcriptional regulator Lsr2 at threonine 112.
Mol Microbiol 112(6):1847–1862
16. Blasco B, Chen JM, Hartkoorn R et al (2012)
Virulence regulator EspR of Mycobacterium
tuberculosis is a nucleoid-associated protein.
PLoS Pathog 8(3):e1002621
17. Sala C, Haouz A, Saul FA et al (2009)
Genome-wide regulon and crystal structure of
BlaI (Rv1846c) from Mycobacterium tuberculosis. Mol Microbiol 71(5):1102–1116
18. Muller AU, Imkamp F, Weber-Ban E (2018)
The mycobacterial LexA/RecA-independent
DNA damage response is controlled by PafBC
and the pup-proteasome system. Cell Rep 23
(12):3551–3564
19. Sales ML, Fonseca Junior AA, Orzil L et al
(2014) Validation of a real-time PCR assay for
the molecular identification of Mycobacterium
tuberculosis.
Braz
J
Microbiol
45
(4):1363–1369
20. Jabbar A, Phelan JE, de Sessions PF et al
(2019) Whole genome sequencing of drug
resistant Mycobacterium tuberculosis isolates
from a high burden tuberculosis region of
North West Pakistan. Sci Rep 9(1):14996
21. Yates TA, Khan PY, Knight GM et al (2016)
The transmission of Mycobacterium tuberculosis
in high burden settings. Lancet Infect Dis 16
(2):227–238
74
Heena Jagatia and Daire Cantillon