The potential for application of foodborne salmonella gene expression profiling assays in postharvest poultry processing

Perspectives on Food-Safety Issues of Animal-Derived Foods

Volumn , Issue , 2010, Pages 195-222

  Sirsat, Sujata A ^a   Muthaiyan, Arunachalam ^a   Dowd, Scot E ^a   Kwon, Young Min ^b   Ricke, Steven C ^a  

^a UNIVERSITY OF ARKANSAS   (United States)

^b Research and Testing Laboratory   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84872283815     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (136)

1. Alpuche-Aranda, C. M., E. L. Racoosin, J. A. Swanson, and S. I. Miller. 1994. Salmonella stimulate macrophage macropinocytosis and persist within spacious phagosomes. J. Exp. Med. 179:601-608.
2. Altier, C. 2005. Genetic and environmental control of Salmonella invasion. J. Microbiol. 43:85-92.
3. Alvarez, J., S. Porwollik, I. Laconcha, V. Gisakis, A. B. Vivanco, I. Gonzalez, S. Echenagusia, N. Zabala, F. Blackmer, M. McClelland, A. Rementeria, and J. Garaizar. 2003. Detection of a Salmonella enterica serovar California strain spreading in Spanish feed mills and genetic characterization with DNA microarrays. Appl. Environ. Microbiol. 69:7531-7534.
4. Ambion Inc. 2007. RNA later tissue collection: RNA stabilization solution. At http://www.ambion.com/techlib/prot/bp-7020.pdf. 2007. Accessed October 1, 2007.
5. Bader, M. W., W. W. Navarre, W. Shiau, H. Nikaido, J. G. Frye, M. McClelland, F. C. Fang, and S. I. Miller. 2003. Regulation of Salmonella typhimurium virulence gene expression by cationic antimicrobial peptides. Mol. Microbiol. 50:219-230.
6. Bajaj, V., C. Hwang, and C. A. Lee. 1995. hilA is a novel ompR/toxR family member that activates the expression of Salmonella typhimurium invasion genes. Mol. Microbiol. 18:715-727.
7. Bajaj, V., R. L. Lucas, C. Hwang, and C. A. Lee. 1996. Co-ordinate regulation of Salmonella typhimurium invasion genes by environmental and regulatory factors is mediated by control of hilA expression. Mol. Microbiol. 22:703-714.
8. Bäumler, A. J. 1997. The record of horizontal gene transfer in Salmonella. Trends Microbiol. 5:318-322.
9. Bäumler, A. J., R. M. Tsolis, T. A. Ficht, and L. G. Adams. 1998. Evolution of host adaptation in Salmonella enterica. Infect. Immun. 66:4579-4587.
10. Bäumler, A. J., R. M. Tsolis, and F. Heffron. 1996. Contribution of fimbrial operons to attachment to and invasion of epithelial cell lines by Salmonella typhimurium. Infect. Immun. 64:1862-1865.
11. Bearson, S., B. Bearson, and J. W. Foster. 1997. Acid stress responses in enterobacteria. FEMS Microbiol. Lett. 147:173-180.
12. Bedná, M. 2000. DNA microarray technology and application. Med. Sci. Monit. 6:796-800.
13. Behlau, I., and S. I. Miller. 1993. A PhoP-repressed gene promotes Salmonella typhimurium invasion of epithelial cells. J. Bacteriol. 175:4475-4484.
14. Blanc-Potard, A. B., and E. A. Groisman. 1997. The Salmonella selC locus contains a pathogenicity island mediating intramacrophage survival. EMBO J. 16:5376-5385.
15. Boyd, E. F., S. Porwollik, F. Blackmer, and M. McClelland. 2003. Differences in gene content among Salmonella enterica serovar Typhi isolates. J. Clin. Microbiol. 41:3823- 3828.
16. Brul, S., and P. Coote. 1999. Preservative agents in foods: mode of action and microbial resistance mechanisms. Int. J. Food Microbiol. 50:1-17.
17. Bryan, F. L., and M. P. Doyle. 1995. Health risks and consequences of Salmonella and Campylobacter jejuni in raw poultry. J. Food Prot. 58:326-344.
18. Burpo, F. J. 2001. A critical review of PCR primer design algorithms and cross-hybridization case study. At http://cmgm.stanford.edu/biochem218/ Projects%202001/Burpo.pdf. Accessed October 9, 2007.
19. Bustin, S. A. 2002. Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): Trends and problems. J. Mol. Endocrinol. 29:23-39.
20. Butte, A. 2002. The use and analysis of microarray data. Nat. Rev. Drug Discov. 1:951-960.
21. Campbell, A. 2003. The future of bacteriophage biology. Nat. Rev. Genet. 4:471-477.
22. Castillo, A., L. M. Lucia, K. J. Goodson, J. W. Savell, and G. R. Acuff. 1998. Use of hot water for beef carcass decontamination. J. Food Prot. 61:19-25.
23. Chan, K., S. Baker, C. C. Kim, C. S. Detweiler, G. Dougan, and S. Falkow. 2003. Genomic comparison of Salmonella enterica serovars and Salmonella bongori by use of an Senterica serovar Typhimurium DNA microarray. J. Bacteriol. 185:553-563.
24. Chen, L.-M., S. Hobbie, and J. E. Galán. 1996. Requirement of CDC42 for Salmonellainduced cytoskeletal and nuclear responses. Science 274:2115-2118.
25. Cheung, V. G., M. Morley, F. Aguilar, A. Massimi, R. Kucherlapati, and G. Childs. 1999. Making and reading microarrays. Nat. Genet. 21:15-19.
26. Cirillo, D. M., R. H. Valdivia, D. M. Monack, and S. Falkow. 1998. Macrophage-dependent induction of the Salmonella pathogenicity island 2 type III secretion system and its role in intracellular survival. Mol. Microbiol. 30:175-188.
27. Clements, M. O., S. Eriksson, A. Thompson, S. Lucchini, J. C. D. Hinton, S. Normark, and M. Rhen. 2002. Polynucleotide phosphorylase is a global regulator of virulence and persistency in Salmonella enterica. Proc. Natl. Acad. Sci. USA 99:8784-8789.
28. Collazo, C. M., and J. E. Galán. 1997. The invasion-associated type-III protein secretion system in Salmonella-a review. Gene 192:51-59.
29. Conway, T., and G. K. Schoolnik. 2003. Microarray expression profiling: capturing a genome-wide portrait of the transcriptome. Mol. Microbiol. 47:879-889.
30. Cummings, C. A., and D. A. Relman. 2000. Using DNA microarrays to study hostmicrobe interactions. Emerg. Infect. Dis. 6:513-525.
31. Darwin, K. H., and V. L. Miller. 1999. Molecular basis of the interaction of Salmonella with the intestinal mucosa. Clin. Microbiol. Rev. 12:405-428.
32. Davidson, P. M., and M. A. Harrison. 2002. Resistance and adaptation to food antimicrobials, sanitizers, and other process controls. Food Technology 56:69-78.
33. Davis, A. O., J. O. O'Leary, A. Muthaiyan, M. J. Langevin, A. Delgado, A. T. Abalos, A. R. Fajardo, J. Marek, B. J. Wilkinson, and J. E. Gustafson. 2005. Characterization of Staphylococcus aureus mutants expressing reduced susceptibility to common housecleaners. J. Appl. Microbiol. 98:364-372.
34. De Keersmaecker, S. C. D., K. Marchal, T. L. Verhoeven, K. Engelen, J. Vanderleyden, and C. S. Detweiler. 2005. Microarray analysis and motif detection reveal new targets of the Salmonella enterica Serovar Typhimurium HilA regulatory protein, including hilA itself. J. Bacteriol. 187:4381-4391.
35. Debouck, C., and P. N. Goodfellow. 1999. DNA microarrays in drug discovery and development. Nat. Genet. 21:48-50.
36. Denyer, S. P. 1995. Mechanisms of action of antibacterial biocides. International Biodeterioration & Biodegradation 36:227-245.
37. Denyer, S. P., and G. S. A. B. Stewart. 1998. Mechanisms of action of disinfectants. International Biodeterioration & Biodegradation 41:261-268.
38. Dopazo, J., E. Zanders, I. Dragoni, G. Amphlett, and F. Falciani. 2001. Methods and approaches in the analysis of gene expression data. J. Immunol. Methods 250:93-112.
39. Dowd, S. E., K. Killinger-Mann, J. Blanton, M. San Francisco, and M. Brashears. 2007. Positive adaptive state: microarray evaluation of gene expression in Salmonella enterica Typhimurium exposed to nalidixic acid. Foodborne Pathog. Dis. 4:187-200.
40. Dunkley, K. D., J. L. McReynolds, M. E. Hume, C. S. Dunkley, T. R. Callaway, L. F. Kubena, D. J. Nisbet, and S. C. Ricke. 2007. Molting in Salmonella Enteritidis-challenged laying hens fed alfalfa crumbles. I. Salmonella Enteritidis colonization and virulence gene hilA response. Poult. Sci. 86:1633-1639.
41. Eichelberg, K., and J. E. Galán. 1999. Differential regulation of Salmonella typhimurium type III secreted proteins by pathogenicity island 1 (SPI-1)-encoded transcriptional activators InvF and HilA. Infect. Immun. 67:4099-4105.
42. Eisen, M. B., P. T. Spellman, P. O. Brown, and D. Botstein. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. U.S.A 95:14863- 14868.
43. Ellebracht, E. A., A. Castillo, L. M. Lucia, R. K. Miller, and G. R. Acuff. 1999. Reduction of pathogens using hot water and lactic acid on beef trimmings. J. Food Sci. 64:1094-1099.
44. Enoch, J. S. 2007. Fourth peanut butter death reported. At http://www.consumeraffairs.com/news04/2007/03/peanut-butter-recall15.html. Accessed January 24, 2008.
45. Ernst, L. A., R. K. Gupta, R. B. Mujumdar, and A. S. Waggoner. 1989. Cyanine dye labeling reagents for sulfhydryl groups. Cytometry 10:3-10.
46. Farkas, J. 2007. Physical methods of food preservation. Pages 685-712 in Food microbiology: fundamentals and frontiers. 3rd ed. M. P. Doyle and L. R. Beuchat, eds. ASM Press, Washington, DC.
47. Fey, A., S. Eichler, S. Flavier, R. Christen, M. G. Höfle, and C. A. Guzmán. 2004. Establishment of a real-time PCR-based approach for accurate quantification of bacterial RNA targets in water, using Salmonella as a model organism. Appl. Environ. Microbiol. 70:3618-3623.
48. Francis, C. L., T. A. Ryan, B. D. Jones, S. J. Smith, and S. Falkow. 1993. Ruffles induced by Salmonella and other stimuli direct macropinocytosis of bacteria. Nature 364:639-642.
49. Francis, C. L., M. N. Starnbach, and S. Falkow. 1992. Morphological and cytoskeletal changes in epithelial cells occur immediately upon interaction with Salmonella typhimurium grown under low-oxygen conditions. Mol. Microbiol. 6:3077-3087.
50. Gahan, C. G. M., and C. Hill. 1999. The relationship between acid stress responses and virulence in Salmonella typhimurium and Listeria monocytogenes. Int. J. Food Microbiol. 50:93-100.
51. Galán, J. E. 1996. Molecular and cellular bases of Salmonella entry into host cells. Curr. Top. Microbiol. Immunol. 209:43-60.
52. Galán, J. E., and R. Curtiss. 1990. Expression of Salmonella typhimurium genes required for invasion is regulated by changes in DNA supercoiling. Infect. Immun. 58:1879-1885.
53. Gantois, I., R. Ducatelle, F. Pasmans, F. Haesebrouck, I. Hautefort, A. Thompson, J. C. Hinton, and F. Van Immerseel. 2006. Butyrate specifically down-regulates Salmonella pathogenicity island 1 gene expression. Appl. Environ. Microbiol. 72:946-949.
54. 2+ as an extracellular signal: environmental regulation of Salmonella virulence. Cell 84:165-174.
55. Garcia-del Portillo, F., J. W. Foster, and B. B. Finlay. 1993. Role of acid tolerance response genes in Salmonella typhimurium virulence. Infect. Immun. 61:4489-4492.
56. Giannella, R. A., O. Washington, P. Gemski, and S. B. Formal. 1973. Invasion of HeLa cells by Salmonella typhimurium: A model for study of invasiveness of Salmonella. J. Infect. Dis. 128:69-75.
57. Giulietti, A., L. Overbergh, D. Valckx, B. Decallonne, R. Bouillon, and C. Mathieu. 2001. An overview of real-time quantitative PCR: Applications to quantify cytokine gene expression. Methods 25:386-401.
58. Goldschmidt, M. C. 2006. The use of biosensor and microarray techniques in the rapid detection and identification of salmonellae. J. AOAC Int. 89:530-537.
59. Goldsmith, Z. G., and N. Dhanasekaran. 2004. The microrevolution: Applications and impacts of microarray technology on molecular biology and medicine (review). Int. J. Mol. Med. 13:483-495.
60. Hanna, S. E., C. J. Connor, and H. H. Wang. 2005. Real-time polymerase chain reaction for the food microbiologists: Technologies, applications, and limitations. J. Food Sci. 70:49-53.
61. Hensel, M., J. E. Shea, S. R. Waterman, R. Mundy, T. Nikolaus, G. Banks, A. Vazquez-Torres, C. Gleeson, F. C. Fang, and D. W. Holden. 1998. Genes encoding putative effector proteins of the type III secretion system of Salmonella pathogenicity island 2 are required for bacterial virulence and proliferation in macrophages. Mol. Microbiol. 30:163-174.
62. Holmstrøm, K., T. Tolker-Nielsen, and S. Molin. 1999. Physiological states of individual Salmonella typhimurium cells monitored by in situ reverse transcription-PCR. J. Bacteriol. 181:1733-1738.
63. Huang, X., H. Xu, X. Sun, K. Ohkusu, Y. Kawamura, and T. Ezaki. 2007. Genome-wide scan of the gene expression kinetics of Salmonella enterica serovar Typhi during hyperosmotic stress. Int. J. Mol. Sci. 8:116-135.
64. Hueck, C. J., M. J. Hantman, V. Bajaj, C. Johnston, C. A. Lee, and S. I. Miller. 1995. Salmonella typhimurium secreted invasion determinants are homologous to Shigella Ipa proteins. Mol. Microbiol. 18:479-490.
65. Jacob, F., D. Perrin, C. Sanchez, and J. Monod. 2005. The operon: A group of genes with expression coordinated by an operator. C.R. Acad. Sci. Paris 250 (1960):1727-1729.
66. Jacob, F., D. Perrin, C. Sanchez, and J. Monod. 2005. The operon: A group of genes with expression coordinated by an operator. C. R. Biol. 328:514-520.
67. Jay, J. M. 2000. Modern food microbiology. 6th ed. Aspen Publishing, Gaithersburg, MD.
68. Joerger, R. D. 2003. Alternatives to antibiotics: bacteriocins, antimicrobial peptides and bacteriophages. Poult. Sci. 82:640-647.
69. Johnston, C., D. A. Pegues, C. J. Hueck, C. A. Lee, and S. I. Miller. 1996. Transcriptional activation of Salmonella typhimurium invasion genes by a member of the phosphorylated response-regulator superfamily. Mol. Microbiol. 22:715-727.
70. Jones, B. D., N. Ghori, and S. Falkow. 1994. Salmonella typhimurium initiates murine infection by penetrating and destroying the specialized epithelial M cells of the Peyer's patches. J. Exp. Med. 180:15-23.
71. Jordan, J. 2005. Undercooked turkey blamed for Salmonella outbreak. At http://www.marlerblog.com/2005/06/articles/case-news/undercooked-turkey-blamed- forsalmonella-outbreak/. Accessed January 24, 2008.
72. Kemp, G. K., M. L. Aldrich, and A. L. Waldroup. 2000. Acidified sodium chlorite anti - microbial treatment of broiler carcasses. J. Food Prot. 63:1087-1092.
73. Klein, D. 2002. Quantification using real-time PCR technology: Applications and limitations. Trends Mol. Med. 8:257-260.
74. Kodadek, T. 2001. Protein microarrays: prospects and problems. Chem. Biol. 8: 105-115.
75. Kubori, T., Y. Matsushima, D. Nakamura, J. Uralil, M. Lara-Tejero, A. Sukhan, J. E. Galán, and S.-I. Aizawa. 1998. Supramolecular structure of the Salmonella typhimurium type III protein secretion system. Science 280:602-605.
76. Kundinger, M. M., I. B. Zabala-Díaz, V. I. Chalova, W.-K. Kim, R. W. Moore, and S. C. Ricke. 2007. Characterization of rsmC as a potential reference gene for Salmonella Typhimurium gene expression during growth in spent media. Sensing and Instrumentation for Food Quality and Safety 1:99-103.
77. Kwon, Y. M., S. Y. Park, S. G. Birkhold, and S. C. Ricke. 2000. Induction of resistance of Salmonella typhimurium to environmental stresses by exposure to short-chain fatty acids. J. Food Sci. 65:1037-1040.
78. Kwon, Y. M., and S. C. Ricke. 1998. Induction of acid resistance of Salmonella typhimurium by exposure to short-chain fatty acids. Appl. Environ. Microbiol. 64:3458-3463.
79. Lander, E. S. 1999. Array of hope. Nat. Genet. 21:3-4.
80. Lawhon, S. D., J. G. Frye, M. Suyemoto, S. Porwollik, M. McClelland, and C. Altier. 2003. Global regulation by CsrA in Salmonella typhimurium.Mol. Microbiol. 48:1633-1645.
81. Leistner, L. 2000. Basic aspects of food preservation by hurdle technology. Int. J. Food Microbiol. 55:181-186.
82. Leistner, L., and L. G. M. Gorris. 1995. Food preservation by hurdle technology. Trends Food Sci. Technol. 6:41-46.
83. Leyer, G. J., and E. A. Johnson. 1993. Acid adaptation induces cross-protection against environmental stresses in Salmonella typhimurium. Appl. Environ. Microbiol. 59:1842-1847.
84. Li, X., W. Gu, S. Mohan, and D. J. Baylink. 2002. DNA microarrays: Their use and misuse. Microcirculation 9:13-22.
85. Liu-Stratton, Y., S. Roy, and C. K. Sen. 2004. DNA microarray technology in nutraceutical and food safety. Toxicol. Lett. 150:29-42.
86. Lockhart, D. J., H. Dong, M. C. Byrne, M. T. Follettie, M. V. Gallo, M. S. Chee, M. Mittmann, C. Wang, M. Kobayashi, H. Horton, and E. L. Brown. 1996. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 14:1675-1680.
87. Lockhart, D. J., and E. A. Winzeler. 2000. Genomics, gene expression and DNA arrays. Nature 405:827-836.
88. Lucchini, S., A. Thompson, and J. C. D. Hinton. 2001. Microarrays for microbiologists. Microbiology 147:1403-1414.
89. MacBeath, G. 2002. Protein microarrays and proteomics. Nat. Genet. 32 Suppl:526-532.
90. Marcus, S. L., J. H. Brumell, C. G. Pfeifer, and B. B. Finlay. 2000. Salmonella pathogenicity islands: big virulence in small packages. Microbes Infect. 2:145-156.
91. Mead, P. S., L. Slutsker, V. Dietz, L. F. McCaig, J. S. Bresee, C. Shapiro, P. M. Griffin, and R. V. Tauxe. 1999. Food-related illness and death in the United States. Emerg. Infect. Dis. 5:607-625.
92. Miller, S. I., and D. A. Pegues. 2000. Salmonella species, including Salmonella typhi. Pages 2344-2363 in Principles and practice of infectious diseases. Churchill Livingstone, Philadelphia, PA.
93. Monsieurs, P., S. DeKeersmaecker, W. W. Navarre, M. W. Bader, F. De Smet, M. McClelland, F. C. Fang, B. De Moor, J. Van der leyden, and K. Marchal. 2005. Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimurium. J. Mol. Evol. 60:462-474.
94. Mullis, K. B. 1990. Target amplification for DNA analysis by the polymerase chain reaction. Ann. Biol. Clin. Paris 48:579-582.
95. Muthaiyan, A., J. A. Silverman, R. K. Jayaswal, and B. J. Wilkinson. 2008. Transcriptional profiling reveals that daptomycin induces the Staphylococcus aureus cell wall stress stimulon and genes responsive to membrane depolarization. Antimicrob. Agents Chemother. 52:980-990.
96. Nakaya, H., A. Yasuhara, K. Yoshimura, Y. Oshihoi, H. Izumiya, and H. Watanabe. 2003. Life-threatening infantile diarrhea from fluoroquinolone- resistant Salmonella enterica Typhimurium with mutations in both gyrA and parC. Emerg. Infect. Dis. 9:255-257.
97. Neergaard, L. 2008. Food poisoning can be long-term problem. At http://www.uspharmd.com/health/2008-01-22.html#Food-poisoning-can-be-longterm- problem. Accessed February 6, 2008.
98. Nguyen, D. V., A. B. Arpat, N. Wang, and R. J. Carroll. 2002. DNA microarray experiments: biological and technological aspects. Biometrics 58:701-717.
99. Pegues, D. A., M. J. Hantman, I. Behlau, and S. I. Miller. 1995. PhoP/PhoQ transcriptional repression of Salmonella typhimurium invasion genes: evidence for a role in protein secretion. Mol. Microbiol. 17:169-181.
100. Pelludat, C., R. Prager, H. Tschäpe, W. Rabsch, J. Schuchhardt, and W.-D. Hardt. 2005. Pilot study to evaluate microarray hybridization as a tool for Salmonella enterica serovar Typhimurium strain differentiation. J. Clin. Microbiol. 43:4092-4106.
101. Piddock, L. J. V., D. G. White, K. Gensberg, L. Pumbwe, and D. J. Griggs. 2000. Evidence for an efflux pump mediating multiple antibiotic resistance in Salmonella enterica serovar Typhimurium, Antimicrob. Agents Chemother. 44:3118-3121.
102. Porwollik, S., R. M.-Y. Wong, and M. McClelland. 2002. Evolutionary genomics of Salmonella: gene acquisitions revealed by microarray analysis. Proc. Natl. Acad. Sci. USA 99:8956-8961.
103. Prouty, A. M., I. E. Brodsky, J. Manos, R. Belas, S. Falkow, and J. S. Gunn. 2004. Transcriptional regulation of Salmonella enterica serovar Typhimurium genes by bile. FEMS Immunol. Med. Microbiol. 41:177-185.
104. Quackenbush, J. 2001. Computational analysis of microarray data. Nat. Rev. Genet. 2:418-427.
105. Rahn, K., S. A. DeGrandis, R. C. Clarke, S. A. McEwen, J. E. Galán, C. Ginocchio, R. Curtiss III, and C. L. Gyles. 1992. Amplification of an invA gene sequence of Salmonella typhimurium by polymerase chain reaction as a specific method of detection of Salmonella.Mol. Cell. Probes. 6:271-279.
106. Ramsay, G. 1998. DNA chips: state-of-the art. Nat. Biotechnol. 16:40-44.
107. Reen, F. J., E. F. Boyd, S. Porwollik, B. P. Murphy, D. Gilroy, S. Fanning, and M. McClelland. 2005. Genomic comparisons of Salmonella enterica serovar Dublin, Agona, and Typhimurium strains recently isolated from milk filters and bovine samples from Ireland, using a Salmonella microarray. Appl. Environ. Microbiol. 71:1616-1625.
108. Ricke, S. C. 2003. Perspectives on the use of organic acids and short chain fatty acids as antimicrobials. Poult. Sci. 82:632-639.
109. Ricke, S. C., M. M. Kundinger, D. R. Miller, and J. T. Keeton. 2005. Alternatives to antibiotics: chemical and physical antimicrobial interventions and foodborne pathogen response. Poult. Sci. 84:667-675.
110. Ronning, I. E., and H. A. Frank. 1987. Growth inhibition of putrefactive anaerobe 3679 caused by stringent-type response induced by protonophoric activity of sorbic acid. Appl. Environ. Microbiol. 53:1020-1027.
111. Saeed, A. I., V. Sharov, J. White, J. Li, W. Liang, N. Bhagabati, J. Braisted, M. Klapa, T. Currier, M. Thiagarajan, A. Sturn, M. Snuffin, A. Rezantsev, D. Popov, A. Ryltsov, E. Kostukovich, I. Borisovsky, Z. Liu, A. Vinsavich, V. Trush, and J. Quackenbush. 2003. TM4: A free, open-source system for microarray data management and analysis. Bio Techniques 34:374-378.
112. Sambrook, J., and D. W. Russell. 2001. Molecular cloning: A laboratory manual. 3rd ed. Cold Spring Harbor Laboratory Press, New York, NY.
113. Sampathkumar, B., G. G. Khachatourians, and D. R. Korber. 2003. High pH during trisodium phosphate treatment causes membrane damage and destruction of Salmonella enterica serovar Enteritidis. Appl. Environ. Microbiol. 69:122-129.
114. San Martin, M. F., G. V. Barbosa-Cánovas, and B. G. Swanson. 2002. Food processing by high hydrostatic pressure. Crit. Rev. Food Sci. Nutr. 42:627-645.
115. Schechter, L. M., S. M. Damrauer, and C. A. Lee. 1999. Two AraC/XylS family members can independently counteract the effect of repressing sequences upstream of the hilA promoter. Mol. Microbiol. 32:629-642.
116. Schena, M., D. Shalon, R. W. Davis, and P. O. Brown. 1995. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470.
117. Schulze, A., and J. Downward. 2001. Navigating gene expression using microarrays-a technology review. Nat. Cell. Biol. 3:E190-E195.
118. Singh, M., S. M. Simpson, H. R. Mullins, and J. S. Dickson. 2006. Thermal tolerance of acid-adapted and non-adapted Escherichia coli O157:H7 and Salmonella in ground beef during storage. Foodborne Pathog. Dis. 3:439-446.
119. Sirsat, S. A., S. E. Dowd, V. I. Chalova, A. Muthaiyan, and S. C. Ricke. 2007. Effect of temperature stress on gene expression of Salmonella Typhimurium. Abstract # 298P. Page 528 in 107th General Meeting American Society of Microbiology.
120. Smith, I. L., K. Halpin, D. Warrilow, and G. A. Smith. 2001. Development of a fluorogenic RT-PCR assay (TaqMan) for the detection of Hendra virus. J. Virol. Methods 98:33-40.
121. Stekel, D. 2003. Microarray bioinformatics. Press Syndicate of University of Cambridge, UK.
122. Suárez, M., and H. Rüssmann. 1998. Molecular mechanisms of Salmonella invasion: The type III secretion system of the pathogenicity island 1. Int. Microbiol. 1:197-204.
123. Taitt, C. R., Y. S. Shubin, R. Angel, and F. S. Ligler. 2004. Detection of Salmonella enterica serovar Typhimurium by using a rapid, array-based immunosensor. Appl. Environ. Microbiol. 70:152-158.
124. Tavazoie, S., J. D. Hughes, M. J. Campbell, R. J. Cho, and G. M. Church. 1999. Systematic determination of genetic network architecture. Nat. Genet. 22:281-285.
125. Terai, S., M. Yamasaki, S. Igimi, and F. Amano. 2005. Expression and degradation of SEp22, a pathogenicity-related protein of Salmonella Dps, in Salmonella enterica serovar Enteritidis isolated from the poultry farms in Japan. Bioscience Microflora 24:113-118.
126. Trayhurn, P. 1996. Northern blotting. Proc. Nutr. Soc. 55:583-589.
127. USDA-FSIS. 1996. The final rule on pathogen reduction and hazard analysis and critical control point (HACCP) systems. At http://www.fsis.usda.gov/oa/ background/finalrul.htm#PERFORMANCE%20STANDARDS. Accessed August 19, 2007.
128. Vaitilingom, M., F. Gendre, and P. Brignon. 1998. Direct detection of viable bacteria, molds, and yeasts by reverse transcriptase PCR in contaminated milk samples after heat treatment. Appl. Environ. Microbiol. 64:1157-1160.
129. Van Asten, F. J. A. M., H. G. C. J. M. Hendriks, J. F. J. G. Koninkx, B. A. Van der Zeijst, and W. Gaastra. 2000. Inactivation of the flagellin gene of Salmonella enterica serotype Enteritidis strongly reduces invasion into differentiated Caco-2 cells. FEMS Microbiol. Lett. 185:175-179.
130. Wawrik, B., J. H. Paul, and F. R. Tabita. 2002. Real-time PCR quantification of rbcL (ribulose- 1, 5-bisphosphate carboxylase/oxygenase) mRNA in diatoms and pelagophytes. Appl. Environ. Microbiol. 68:3771-3779.
131. Weld, R. J., C. Butts, and J. A. Heinemann. 2004. Models of phage growth and their applicability to phage therapy. J. Theor. Biol. 227:1-11.
132. Wong, K.-K., M. McClelland, L. C. Stillwell, E. C. Sisk, S. J. Thurston, and J. D. Saffer. 1998. Identification and sequence analysis of a 27-kilobase chromosomal fragment containing a Salmonella pathogenicity island located at 92 minutes on the chromosome map of Salmonella enterica serovar Typhimurium LT2. Infect. Immun. 66:3365-3371.
133. Wood, M. W., M. A. Jones, P. R. Watson, S. Hedges, T. S. Wallis, and E. E. Galyov. 1998. Identification of a pathogenicity island required for Salmonella enteropathogenicity. Mol. Microbiol. 29:883-891.
134. Woods, L. F. J., J. M. Wood, and P. A. Gibbs. 1981. The involvement of nitric oxide in the inhibition of the phosphoroclastic system in Clostridium sporogenes by sodium nitrite. J. Gen. Microbiol. 125:399-406.
135. Xiang, Z., Y. Yang, X. Ma, and W. Ding. 2003. Microarray expression profiling: Analysis and applications. Curr. Opin. Drug Discov. Devel. 6:384-395.
136. Zipper, H., H. Brunner, J. Bernhagen, and F. Vitzthum. 2004. Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications. Nucleic Acids Res. 32:e103.