Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (338K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Talaat, A. M.
Right arrow Articles by Johnston, S. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Talaat, A. M.
Right arrow Articles by Johnston, S. A.
Related Collections
Right arrow RNA characterisation and manipulation
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2002, Vol. 30, No. 20 e104
© 2002 Oxford University Press

Genomic DNA standards for gene expression profiling in Mycobacterium tuberculosis

Adel M. Talaat, Susan T. Howard1, Walker Hale IV, Rick Lyons1, Harold Garner and Stephen Albert Johnston*

Center for Biomedical Inventions and Departments of Medicine, Microbiology and Biochemistry, University of Texas–Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8573, USA and 1 Department of Internal Medicine, University of New Mexico Health Science Center, 915 Camino de Salud, Albuquerque, NM 87131, USA

*To whom correspondence should be addressed. Tel: +1 214 648 1415; Fax: +1 214 648 1298; Email: stephen.johnston{at}utsouthwestern.edu
Present address:
Adel M. Talaat, Department of Animal Health and Biomedical Sciences, University of Wisconsin, Madison, WI 53706, USA

A fundamental problem in DNA microarray analysis is the lack of a common standard to compare the expression levels of different samples. Several normalization protocols have been proposed to overcome variables inherent in this technology. As yet, there are no satisfactory methods to exchange gene expression data among different research groups or to compare gene expression values under different stimulus–response profiles. We have tested a normalization procedure based on comparing gene expression levels to the signals generated from hybridizing genomic DNA (genomic normalization). This procedure was applied to DNA microarrays of Mycobacterium tuberculosis using RNA extracted from cultures growing to the logarithmic and stationary phases. The applied normalization procedure generated reproducible measurements of expression level for 98% of the putative mycobacterial ORFs, among which 5.2% were significantly changed comparing the logarithmic to stationary growth phase. Additionally, analysis of expression levels of a subset of genes by real time PCR technology revealed an agreement in expression of 90% of the examined genes when genomic DNA normalization was applied instead of 29–68% agreement when RNA normalization was used to measure the expression levels in the same set of RNA samples. Further examination of microarray expression levels displayed clusters of genes differentially expressed between the logarithmic, early stationary and late stationary growth phases. We conclude that genomic DNA standards offer advantages over conventional RNA normalization procedures and can be adapted for the investigation of microbial genomes.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 MicrobiologyHome page
H. K. Janagama, T. M. A. Senthilkumar, J. P. Bannantine, G. M. Rodriguez, I. Smith, M. L. Paustian, J. A. McGarvey, and S. Sreevatsan
Identification and functional characterization of the iron-dependent regulator (IdeR) of Mycobacterium avium subsp. paratuberculosis
Microbiology, November 1, 2009; 155(11): 3683 - 3690.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
C. B. Walker, Z. He, Z. K. Yang, J. A. Ringbauer Jr., Q. He, J. Zhou, G. Voordouw, J. D. Wall, A. P. Arkin, T. C. Hazen, et al.
The Electron Transfer System of Syntrophically Grown Desulfovibrio vulgaris
J. Bacteriol., September 15, 2009; 191(18): 5793 - 5801.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
J. P. Monteiro, K. V. Clemons, L. F. Mirels, J. A. Coller Jr, T. D. Wu, J. Shankar, C. R. Lopes, and D. A. Stevens
Genomic DNA microarray comparison of gene expression patterns in Paracoccidioides brasiliensis mycelia and yeasts in vitro
Microbiology, August 1, 2009; 155(8): 2795 - 2808.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
S. Even, C. Charlier, S. Nouaille, N. L. Ben Zakour, M. Cretenet, F. J. Cousin, M. Gautier, M. Cocaign-Bousquet, P. Loubiere, and Y. Le Loir
Staphylococcus aureus Virulence Expression Is Impaired by Lactococcus lactis in Mixed Cultures
Appl. Envir. Microbiol., July 1, 2009; 75(13): 4459 - 4472.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
K. Pohl, P. Francois, L. Stenz, F. Schlink, T. Geiger, S. Herbert, C. Goerke, J. Schrenzel, and C. Wolz
CodY in Staphylococcus aureus: a Regulatory Link between Metabolism and Virulence Gene Expression
J. Bacteriol., May 1, 2009; 191(9): 2953 - 2963.
[Abstract] [Full Text] [PDF]

Home page
 Infect. Immun.Home page
K. Poirier, S. P. Faucher, M. Beland, R. Brousseau, V. Gannon, C. Martin, J. Harel, and F. Daigle
Escherichia coli O157:H7 Survives within Human Macrophages: Global Gene Expression Profile and Involvement of the Shiga Toxins
Infect. Immun., November 1, 2008; 76(11): 4814 - 4822.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
S. K. Ward, E. A. Hoye, and A. M. Talaat
The Global Responses of Mycobacterium tuberculosis to Physiological Levels of Copper
J. Bacteriol., April 15, 2008; 190(8): 2939 - 2946.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
S. M. Caffrey, H. S. Park, J. Been, P. Gordon, C. W. Sensen, and G. Voordouw
Gene Expression by the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough Grown on an Iron Electrode under Cathodic Protection Conditions
Appl. Envir. Microbiol., April 15, 2008; 74(8): 2404 - 2413.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
V. K. Singh, S. Utaida, L. S. Jackson, R. K. Jayaswal, B. J. Wilkinson, and N. R. Chamberlain
Role for dnaK locus in tolerance of multiple stresses in Staphylococcus aureus
Microbiology, September 1, 2007; 153(9): 3162 - 3173.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
S. M. Caffrey, H.-S. Park, J. K. Voordouw, Z. He, J. Zhou, and G. Voordouw
Function of Periplasmic Hydrogenases in the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough
J. Bacteriol., September 1, 2007; 189(17): 6159 - 6167.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
A. M. Talaat, S. K. Ward, C.-W. Wu, E. Rondon, C. Tavano, J. P. Bannantine, R. Lyons, and S. A. Johnston
Mycobacterial Bacilli Are Metabolically Active during Chronic Tuberculosis in Murine Lungs: Insights from Genome-Wide Transcriptional Profiling
J. Bacteriol., June 1, 2007; 189(11): 4265 - 4274.
[Abstract] [Full Text] [PDF]

Home page
 Infect. Immun.Home page
C.-w. Wu, M. Livesey, S. K. Schmoller, E. J. B. Manning, H. Steinberg, W. C. Davis, M. J. Hamilton, and A. M. Talaat
Invasion and Persistence of Mycobacterium avium subsp. paratuberculosis during Early Stages of Johne's Disease in Calves
Infect. Immun., May 1, 2007; 75(5): 2110 - 2119.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
T. Wecke, B. Veith, A. Ehrenreich, and T. Mascher
Cell Envelope Stress Response in Bacillus licheniformis: Integrating Comparative Genomics, Transcriptional Profiling, and Regulon Mining To Decipher a Complex Regulatory Network
J. Bacteriol., November 1, 2006; 188(21): 7500 - 7511.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H. Charles, F. Calevro, J. Vinuelas, J.-M. Fayard, and Y. Rahbe
Codon usage bias and tRNA over-expression in Buchnera aphidicola after aromatic amino acid nutritional stress on its host Acyrthosiphon pisum
Nucleic Acids Res., September 11, 2006; 34(16): 4583 - 4592.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
S. Jordan, A. Junker, J. D. Helmann, and T. Mascher
Regulation of LiaRS-Dependent Gene Expression in Bacillus subtilis: Identification of Inhibitor Proteins, Regulator Binding Sites, and Target Genes of a Conserved Cell Envelope Stress-Sensing Two-Component System.
J. Bacteriol., July 1, 2006; 188(14): 5153 - 5166.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. Biol.Home page
T. Sakamaki, M. C. Casimiro, X. Ju, A. A. Quong, S. Katiyar, M. Liu, X. Jiao, A. Li, X. Zhang, Y. Lu, et al.
Cyclin d1 determines mitochondrial function in vivo.
Mol. Cell. Biol., July 1, 2006; 26(14): 5449 - 5469.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
C. A. Cummings, H. J. Bootsma, D. A. Relman, and J. F. Miller
Species- and Strain-Specific Control of a Complex, Flexible Regulon by Bordetella BvgAS.
J. Bacteriol., March 1, 2006; 188(5): 1775 - 1785.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
S. R. Chhabra, Q. He, K. H. Huang, S. P. Gaucher, E. J. Alm, Z. He, M. Z. Hadi, T. C. Hazen, J. D. Wall, J. Zhou, et al.
Global Analysis of Heat Shock Response in Desulfovibrio vulgaris Hildenborough.
J. Bacteriol., March 1, 2006; 188(5): 1817 - 1828.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Microbiol.Home page
T. Koessler, P. Francois, Y. Charbonnier, A. Huyghe, M. Bento, S. Dharan, G. Renzi, D. Lew, S. Harbarth, D. Pittet, et al.
Use of Oligoarrays for Characterization of Community-Onset Methicillin-Resistant Staphylococcus aureus.
J. Clin. Microbiol., March 1, 2006; 44(3): 1040 - 1048.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
Séb. P. Faucher, S. Porwollik, C. M. Dozois, M. McClelland, and F. Daigle
Transcriptome of Salmonella enterica serovar Typhi within macrophages revealed through the selective capture of transcribed sequences
PNAS, February 7, 2006; 103(6): 1906 - 1911.
[Abstract] [Full Text] [PDF]

Home page
 J. Mol. Diagn.Home page
M. Steinau, M. S. Rajeevan, and E. R. Unger
DNA and RNA References for qRT-PCR Assays in Exfoliated Cervical Cells
J. Mol. Diagn., February 1, 2006; 8(1): 113 - 118.
[Abstract] [Full Text] [PDF]

Home page
 Infect. Immun.Home page
M. Korem, Y. Gov, M. D. Kiran, and N. Balaban
Transcriptional Profiling of Target of RNAIII-Activating Protein, a Master Regulator of Staphylococcal Virulence
Infect. Immun., October 1, 2005; 73(10): 6220 - 6228.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
K. Veit, C. Ehlers, and R. A. Schmitz
Effects of Nitrogen and Carbon Sources on Transcription of Soluble Methyltransferases in Methanosarcina mazei Strain Go1
J. Bacteriol., September 1, 2005; 187(17): 6147 - 6154.
[Abstract] [Full Text] [PDF]

Home page
 Infect. Immun.Home page
R. C. LaRocque, J. B. Harris, M. Dziejman, X. Li, A. I. Khan, A. S. G. Faruque, S. M. Faruque, G. B. Nair, E. T. Ryan, F. Qadri, et al.
Transcriptional Profiling of Vibrio cholerae Recovered Directly from Patient Specimens during Early and Late Stages of Human Infection
Infect. Immun., August 1, 2005; 73(8): 4488 - 4493.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
Q. Gao, K. E. Kripke, A. J. Saldanha, W. Yan, S. Holmes, and P. M. Small
Gene expression diversity among Mycobacterium tuberculosis clinical isolates
Microbiology, January 1, 2005; 151(1): 5 - 14.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
B. A. Williams, R. M. Gwirtz, and B. J. Wold
Genomic DNA as a cohybridization standard for mammalian microarray measurements
Nucleic Acids Res., June 9, 2004; 32(10): e81 - e81.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
R. J. Belland, G. Zhong, D. D. Crane, D. Hogan, D. Sturdevant, J. Sharma, W. L. Beatty, and H. D. Caldwell
Genomic transcriptional profiling of the developmental cycle of Chlamydia trachomatis
PNAS, July 8, 2003; 100(14): 8478 - 8483.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. Bina, J. Zhu, M. Dziejman, S. Faruque, S. Calderwood, and J. Mekalanos
ToxR regulon of Vibrio cholerae and its expression in vibrios shed by cholera patients
PNAS, March 4, 2003; 100(5): 2801 - 2806.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
Q. Xu, M. Dziejman, and J. J. Mekalanos
Determination of the transcriptome of Vibrio cholerae during intraintestinal growth and midexponential phase in vitro
PNAS, February 4, 2003; 100(3): 1286 - 1291.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.