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Title:   Author  item
                                            Nicholson, Tracy
  Submitted to: BMC Genomics
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 12/1/2006
                                    Publication  Date: 7/6/2007
                                    Citation: Nicholson, T.L. 2007. Construction and validation of a first-generation long-oligonulceotide microarray by transcriptional of the Bordetella bronchiseptica Bvg regulon. Biomed Central (BMC) Genomics. 8(1):220.Interpretive Summary: Bordetella bronchiseptica is a bacterial respiratory pathogen that infects a broad range of mammals. Gene expression in Bordetella is controlled by a set of proteins, called BvgAS, which control the expression of a spectrum of phases transitioning between an infectious (Bvg+) phase and a non-infectious (Bvg-) phase. This report describes the design and construction of a method, termed DNA microarray, which allows people to tell whether or not a gene is expressed. The special aspect of this method is that gene activity, whether or not a gene is expressed, can be determined for the entire Bordetella genome in a single experiment. This method was tested and validated by comparing the gene activity between two different strains of Bordetella, one normal strain and the other altered so that the set of proteins called BvgAS were inactivated or no longer functioning. Data from this comparison revealed 1,667 genes that are regulated by BvgAS. The results presented here provide a comprehensive, genome-wide portrait of genes regulated by BvgAS, while also providing data validating the use of this method for studying gene expression in Bordetella, which will expedite the discovery of new potential targets for drug and vaccine therapy.
                                Technical Abstract: Background: Bordetella bronchiseptica is a bacterial respiratory pathogen that infects a broad range of mammals, causing chronic and often subclinical infections. Gene expression in Bordetella is regulated by a two-component sensory transduction system, BvgAS, which controls the expression of a spectrum of phenotypic phases transitioning between a virulent (Bvg+) phase and a non-virulent (Bvg-) phase.
Results:  Based on the genomic sequence and using the freely available software ArrayOligoSelector, a long oligonucleotide B.  bronchiseptica microarray was designed and assembled. This long-oligonucleotide microarray was subsequently tested and validated by comparing changes in the global expression profiles between B. bronchiseptica RB50 and its Bvg- phase-locked derivative, RB54. Data from this microarray analysis revealed 1,667 Bvg-regulated genes, which greatly expands the BvgAS regulon defined in previous reports. For previously reported Bvg-regulated transcripts, the gene expression data presented here is congruent with prior findings. Additionally, quantitative real-time PCR data provided an independent verification of the microarray expression values. 
Conclusion:  The results presented here provide a comprehensive, genome-wide portrait of transcripts encompassing the BvgAS regulon, while also providing data validating the long-oligonucleotide microarray described here for studying gene expression in Bordetella bronchiseptica.


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