47. Nicholson TL, Buboltz AM, Harvill ET, Brockmeier SL (2009) Microarray and functional analysis of growth phase-dependent gene regulation in Bordetella bronchiseptica. Infect. Immun. 77(10): 4221–4231. 48. Tusher V G, Tibshirani R Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. 98: 5116–5121. 49. Saeed AI, Sharov V, White J, Li, Liang W, et al. (2003) TM4: a free, open- source system for microarray data management and analysis. Biotechniques 34: 374–378. 50. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2-DDCT method. Methods 25: 402–408. CO2 Responsive Regulon in Bordetella 51. Cummings CA, Bootsma HJ, Relman DA, Miller JF (2006) Species- and Strain- Specific Control of a Complex, Flexible Regulon by Bordetella BvgAS. J. Bacteriol. 188: 1775–1785. 52. Yuk MH, Harvill ET, Cotter PA, Miller JF (2000) Modulation of host immune responses, induction of apoptosis and inhibition of NF-kappaB activation by the Bordetella type III secretion system. Mol. Microbiol. 35: 991–1004. 53. Cotter PA, Yuk MH, Mattoo S, Akerley BJ, Boschwitz J, et al. (1998) Filamentous hemagglutinin of Bordetella bronchiseptica is required for efficient establishment of tracheal colonization. Infect. Immun. 66(12): 5921–5929. 54. Mattoo S, Miller JF, Cotter PA (2000) Role of Bordetella bronchiseptica fimbriae in tracheal colonization and development of a humoral immune response. Infect. Immun. 68(4): 2024–2033. PLOS ONE | www.plosone.org 12 October 2012 | Volume 7 | Issue 10 | e47635