Journal of Proteome Research Paramithiotis, E. Intracellular adaptation of Brucella abortus. J. Proteome Res. 2009, 8 (3), 1594–609. (24) Letesson, J. J.; Tibor, A.; van Eynde, G.; Wansard, V.; Weynants, V.; Denoel, P.; Saman, E. Humoral immune responses of Brucella- infected cattle, sheep, and goats to eight puriﬁed recombinant Brucella proteins in an indirect enzyme-linked immunosorbent assay. Clin. Diagn. Lab. Immunol. 1997, 4 (5), 556–64. (25) Lindler, L. E.; Hadﬁeld, T. L.; Tall, B. D.; Snellings, N. J.; Rubin, F. A.; Van De Verg, L. L.; Hoover, D.; Warren, R. L. Cloning of a Brucella melitensis group 3 antigen gene encoding Omp28, a protein recognized by the humoral immune response during human brucellosis. Infect. Immun. 1996, 64 (7), 2490–9. (26) Mayﬁeld, J. E.; Bricker, B. J.; Godfrey, H.; Crosby, R. M.; Knight, D. J.; Halling, S. M.; Balinsky, D.; Tabatabai, L. B. The cloning, expression, and nucleotide sequence of a gene coding for an immuno- genic Brucella abortus protein. Gene 1988, 63 (1), 1–9. (27) Rolan, H. G.; den Hartigh, A. B.; Kahl-McDonagh, M.; Ficht, T.; Adams, L. G.; Tsolis, R. M. VirB12 is a serological marker of Brucella infection in experimental and natural hosts. Clin. Vaccine Immunol. 2008, 15 (2), 208–14. (28) Roop, R. M., 2nd; Fletcher, T. W.; Sriranganathan, N. M.; Boyle, S. M.; Schurig, G. G. Identiﬁcation of an immunoreactive Brucella abortus HtrA stress response protein homolog. Infect. Immun. 1994, 62 (3), 1000–7. (29) Tibor, A.; Weynants, V.; Denoel, P.; Lichtfouse, B.; De Bolle, X.; Saman, E.; Limet, J. N.; Letesson, J. J. Molecular cloning, nucleotide sequence, and occurrence of a 16.5-kilodalton outer membrane protein of Brucella abortus with similarity to pal lipoproteins. Infect. Immun. 1994, 62 (9), 3633–9. (30) Yang, X.; Hudson, M.; Walters, N.; Bargatze, R. F.; Pascual, D. W. Selection of protective epitopes for Brucella melitensis by DNA vaccination. Infect. Immun. 2005, 73 (11), 7297–303. (31) Rossetti, O. L.; Arese, A. I.; Boschiroli, M. L.; Cravero, S. L. Cloning of Brucella abortus gene and characterization of expressed 26- kilodalton periplasmic protein: potential use for diagnosis. J. Clin. Microbiol. 1996, 34 (1), 165–9. (32) Baker, P. J.; Wilson, J. B. Hypoferremia in mice and its application to the bioassay of endotoxin. J. Bacteriol. 1965, 90 (4), 903–10. (33) Kittelberger, R.; Hilbink, F. Sensitive silver-staining detection of bacterial lipopolysaccharides in polyacrylamide gels. J. Biochem. Biophys. Methods 1993, 26 (1), 81–6. (34) Karkhanis, Y. D.; Zeltner, J. Y.; Jackson, J. J.; Carlo, D. J. A new and improved microassay to determine 2-keto-3-deoxyoctonate in lipopolysaccharide of Gram-negative bacteria. Anal. Biochem. 1978, 85 (2), 595–601. (35) Lamontagne, J.; Butler, H.; Chaves-Olarte, E.; Hunter, J.; Schirm, M.; Paquet, C.; Tian, M.; Kearney, P.; Hamaidi, L.; Chelsky, D.; Moriyon, I.; Moreno, E.; Paramithiotis, E. Extensive cell envelope modulation is associated with virulence in Brucella abortus. J. Proteome Res. 2007, 6 (4), 1519–29. (36) Lamontagne, J.; Beland, M.; Forest, A.; Cote-Martin, A.; Nassif, N.; Tomaki, F.; Moriyon, I.; Moreno, E.; Paramithiotis, E. Proteomics- based conﬁrmation of protein expression and correction of annotation errors in the Brucella abortus genome. BMC Genomics 2010, 11, 300. (37) Baldi, P.; Hatﬁeld, G. W. DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling; Cambridge University Press: Oxford, 2002. (38) Sundaresh, S.; Doolan, D. L.; Hirst, S.; Mu, Y.; Unal, B.; Davies, D. H.; Felgner, P. L.; Baldi, P. Identiﬁcation of humoral immune responses in protein microarrays using DNA microarray data analysis techniques. Bioinformatics 2006, 22 (14), 1760–6. (39) Sundaresh, S.; Randall, A.; Unal, B.; Petersen, J. M.; Belisle, J. T.; Hartley, M. G.; Duﬃeld, M.; Titball, R. W.; Davies, D. H.; Felgner, P. L.; Baldi, P. From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis. Bioinformatics 2007, 23 (13), i508–18. (40) Durbin, B. P.; Hardin, J. S.; Hawkins, D. M.; Rocke, D. M. A variance-stabilizing transformation for gene-expression microarray data. Bioinformatics 2002, 18 (Suppl 1), S105–10. ARTICLE (41) Huber, W.; von Heydebreck, A.; Sultmann, H.; Poustka, A.; Vingron, M. Variance stabilization applied to microarray data calibration and to the quantiﬁcation of diﬀerential expression. Bioinformatics 2002, 18 (Suppl 1), S96–104. (42) Kreil, D. P.; Karp, N. A.; Lilley, K. S. DNA microarray normal- ization methods can remove bias from diﬀerential protein expression analysis of 2D diﬀerence gel electrophoresis results. Bioinformatics 2004, 20 (13), 2026–34. (43) Baldi, P.; Brunak, S. R. Bioinformatics: the machine learning approach; MIT Press: Cambridge, MA, 2001. (44) Long, A. D.; Mangalam, H. J.; Chan, B. Y.; Tolleri, L.; Hatﬁeld, G. W.; Baldi, P. Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J. Biol. Chem. 2001, 276 (23), 19937–44. (45) Benjamini, Y.; Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Statist. Soc., Ser. B 1995, 57 (1), 289–300. (46) Moller, S.; Croning, M. D.; Apweiler, R. Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics 2001, 17 (7), 646–53. (47) Bendtsen, J. D.; Nielsen, H.; von Heijne, G.; Brunak, S. Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 2004, 340 (4), 783–95. (48) Gardy, J. L.; Laird, M. R.; Chen, F.; Rey, S.; Walsh, C. J.; Ester, M.; Brinkman, F. S. PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics 2005, 21 (5), 617–23. (49) Girosi, F. An Equivalence Between Sparse Approximation and Support Vector Machines. Neural Comput. 1998, 10 (6), 1455–80. (50) Ciftci, C.; Ozturk, F.; Oztekin, A.; Karaoglan, H.; Saba, R.; Gultekin, M.; Mamikoglu, L. Comparison of the serological tests used for the laboratory diagnosis of brucellosis. Mikrobiyol. Bul. 2005, 39 (3), 291–9. (51) Sisirak, M.; Hukic, M. Evaluation and importance of selected microbiological methods in the diagnosis of human brucellosis. Bosn. J. Basic Med. Sci. 2009, 9 (3), 198–203. (52) Dasgupta, A.; Sureka, K.; Mitra, D.; Saha, B.; Sanyal, S.; Das, A. K.; Chakrabarti, P.; Jackson, M.; Gicquel, B.; Kundu, M.; Basu, J. An oligopeptide transporter of Mycobacterium tuberculosis regulates cyto- kine release and apoptosis of infected macrophages. PLoS One 2010, 5 (8), e12225. (53) Skendros, P.; Pappas, G.; Boura, P. Cell-mediated immunity in human brucellosis. Microbes Infect. 2011, 13 (2), 134–42. (54) Paschos, A.; den Hartigh, A.; Smith, M. A.; Atluri, V. L.; Sivanesan, D.; Tsolis, R. M.; Baron, C. An in vivo high-throughput screening approach targeting the type IV secretion system component VirB8 identiﬁed inhibitors of Brucella abortus 2308 proliferation. Infect. Immun. 2011, 79 (3), 1033–43. (55) Wick, M. J.; Pfeifer, J. D.; Findlay, K. A.; Harding, C. V.; Normark, S. J. Compartmentalization of deﬁned epitopes expressed in Escherichia coli has only a minor inﬂuence on eﬃciency of phagocytic processing for presentation by class I and class II major histocompat- ibility complex molecules to T cells. Infect. Immun. 1993, 61 (11), 4848–56. (56) Salih-Alj Debbarh, H.; Cloeckaert, A.; Bezard, G.; Dubray, G.; Zygmunt, M. S. Enzyme-linked immunosorbent assay with partially puriﬁed cytosoluble 28-kilodalton protein for serological diﬀerentiation between Brucella melitensis-infected and B. melitensis Rev.1-vaccinated sheep. Clin. Diagn. Lab. Immunol. 1996, 3 (3), 305–8. (57) Tibor, A.; Saman, E.; de Wergifosse, P.; Cloeckaert, A.; Limet, J. N.; Letesson, J. J. Molecular characterization, occurrence, and im- munogenicity in infected sheep and cattle of two minor outer membrane proteins of Brucella abortus. Infect. Immun. 1996, 64 (1), 100–7. (58) Domingo, G. J.; Caivano, A.; Sartorius, R.; Barba, P.; Backstrom, M.; Piatier-Tonneau, D.; Guardiola, J.; De Berardinis, P.; Perham, R. N. Induction of speciﬁc T-helper and cytolytic responses to epitopes displayed on a virus-like protein scaﬀold derived from the pyruvate 4823 dx.doi.org/10.1021/pr200619r |J. Proteome Res. 2011, 10, 4813–4824