Scallan E, Hoekstra RM, Angulo FJ, Tauxe RV, Widdowson MA, Roy SL, Jones JL, Griffin PM. Foodborne illness acquired in the United States--major pathogens. Emerg Infect Dis. 2011;17(1):7–15.
Article
PubMed
PubMed Central
Google Scholar
Scallan E, Hoekstra RM, Mahon BE, Jones TF, Griffin PM. An assessment of the human health impact of seven leading foodborne pathogens in the United States using disability adjusted life years. Epidemiol Infect. 2015;143(13):2795–804.
Article
CAS
PubMed
Google Scholar
Karaffova V, Bobikova K, Husakova E, Levkut M, Herich R, Revajova V, Levkutova M, Levkut M. Interaction of TGF-beta4 and IL-17 with IgA secretion in the intestine of chickens fed with E. faecium AL41 and challenged with S. Enteritidis. Res Vet Sci. 2015;(100):75–9.
Gomez TM, Motarjemi Y, Miyagawa S, Kaferstein FK, Stohr K. Foodborne salmonellosis. World Health Stat Q. 1997;50(1-2):81–9.
CAS
PubMed
Google Scholar
Foley SL, Lynne AM. Food animal-associated Salmonella challenges: pathogenicity and antimicrobial resistance. J Anim Sci. 2008;86(14 Suppl):E173–87.
CAS
PubMed
Google Scholar
Bosilevac JM, Guerini MN, Kalchayanand N, Koohmaraie M. Prevalence and characterization of salmonellae in commercial ground beef in the United States. Appl Environ Microbiol. 2009;75(7):1892–900.
Article
CAS
PubMed
PubMed Central
Google Scholar
Berndt A, Wilhelm A, Jugert C, Pieper J, Sachse K, Methner U. Chicken cecum immune response to Salmonella enterica serovars of different levels of invasiveness. Infect Immun. 2007;75(12):5993–6007.
Article
CAS
PubMed
PubMed Central
Google Scholar
Samiullah, Chousalkar KK, Roberts JR, Sexton M, May D, Kiermeier A. Effects of egg shell quality and washing on Salmonella Infantis penetration. Int J Food Microbiol. 2013;165(2):77–83.
Article
CAS
PubMed
Google Scholar
Guarnieri DJ, DiLeone RJ. MicroRNAs: a new class of gene regulators. Ann Med. 2008;40(3):197–208.
Article
CAS
PubMed
Google Scholar
Ebert MS, Sharp PA. Roles for microRNAs in conferring robustness to biological processes. Cell. 2012;149(3):515–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yang C, Wei W. The miRNA expression profile of the uveal melanoma. Sci China Life Sci. 2011;54(4):351–8.
Article
CAS
PubMed
Google Scholar
Zhou R, O’Hara SP, Chen XM. MicroRNA regulation of innate immune responses in epithelial cells. Cell Mol Immunol. 2011;8(5):371–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Takeuchi O, Akira S. Pattern recognition receptors and inflammation. CELL. 2010;140(6):805–20.
Article
CAS
PubMed
Google Scholar
Schulte LN, Eulalio A, Mollenkopf HJ, Reinhardt R, Vogel J. Analysis of the host microRNA response to Salmonella uncovers the control of major cytokines by the let-7 family. EMBO J. 2011;30(10):1977–89.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sharbati S, Sharbati J, Hoeke L, Bohmer M, Einspanier R. Quantification and accurate normalisation of small RNAs through new custom RT-qPCR arrays demonstrates Salmonella-induced microRNAs in human monocytes. BMC Genomics. 2012;13:23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bao H, Kommadath A, Plastow GS, Tuggle CK, Guan LL, Stothard P. MicroRNA buffering and altered variance of gene expression in response to Salmonella infection. PLoS ONE. 2014;9(4):e94352.
Article
PubMed
PubMed Central
Google Scholar
Lawless N, Foroushani AB, McCabe MS, O’Farrelly C, Lynn DJ. Next generation sequencing reveals the expression of a unique miRNA profile in response to a gram-positive bacterial infection. PLoS ONE. 2013;8(3):e57543.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rathjen T, Pais H, Sweetman D, Moulton V, Munsterberg A, Dalmay T. High throughput sequencing of microRNAs in chicken somites. Febs Lett. 2009;583(9):1422–6.
Article
CAS
PubMed
Google Scholar
Wang Y, Brahmakshatriya V, Zhu H, Lupiani B, Reddy SM, Yoon BJ, Gunaratne PH, Kim JH, Chen R, Wang J, et al. Identification of differentially expressed miRNAs in chicken lung and trachea with avian influenza virus infection by a deep sequencing approach. BMC Genomics. 2009;10:512.
Article
PubMed
PubMed Central
Google Scholar
Kinsella RJ, Kahari A, Haider S, Zamora J, Proctor G, Spudich G, Almeida-King J, Staines D, Derwent P, Kerhornou A, et al. Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database (Oxford). 2011;2011:r30.
Article
Google Scholar
Wu G, Dawson E, Duong A, Haw R, Stein L. ReactomeFIViz: a Cytoscape app for pathway and network-based data analysis. F1000Res. 2014;3:146.
PubMed
PubMed Central
Google Scholar
Maudet C, Mano M, Eulalio A. MicroRNAs in the interaction between host and bacterial pathogens. FEBS Lett. 2014;588(22):4140–7.
Article
CAS
PubMed
Google Scholar
Maudet C, Mano M, Sunkavalli U, Sharan M, Giacca M, Forstner KU, Eulalio A. Functional high-throughput screening identifies the miR-15 microRNA family as cellular restriction factors for Salmonella infection. Nat Commun. 2014;5:4718.
Article
CAS
PubMed
Google Scholar
Staedel C, Darfeuille F. MicroRNAs and bacterial infection. Cell Microbiol. 2013;15(9):1496–507.
Article
CAS
PubMed
Google Scholar
Wu G, Liu L, Qi Y, Sun Y, Yang N, Xu G, Zhou H, Li X. Splenic gene expression profiling in White Leghorn layer inoculated with the Salmonella enterica serovar Enteritidis. Anim Genet. 2015;46(6):617–26.
Article
CAS
PubMed
Google Scholar
Ghorai A, Ghosh U. miRNA gene counts in chromosomes vary widely in a species and biogenesis of miRNA largely depends on transcription or post-transcriptional processing of coding genes. Front Genet. 2014;5:100.
Article
PubMed
PubMed Central
Google Scholar
Sevignani C, Calin GA, Nnadi SC, Shimizu M, Davuluri RV, Hyslop T, Demant P, Croce CM, Siracusa LD. MicroRNA genes are frequently located near mouse cancer susceptibility loci. Proc Natl Acad Sci U S A. 2007;104(19):8017–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Uribe JH, Collado-Romero M, Zaldivar-Lopez S, Arce C, Bautista R, Carvajal A, Cirera S, Claros MG, Garrido JJ. Transcriptional analysis of porcine intestinal mucosa infected with Salmonella Typhimurium revealed a massive inflammatory response and disruption of bile acid absorption in ileum. Vet Res. 2016;47:11.
Article
PubMed
PubMed Central
Google Scholar
Wang Y, Brahmakshatriya V, Lupiani B, Reddy SM, Soibam B, Benham AL, Gunaratne P, Liu HC, Trakooljul N, Ing N, et al. Integrated analysis of microRNA expression and mRNA transcriptome in lungs of avian influenza virus infected broilers. BMC Genomics. 2012;13:278.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nat. 2005;433(7027):769–73.
Article
CAS
Google Scholar
Matarese G, La Cava A. The intricate interface between immune system and metabolism. Trends Immunol. 2004;25(4):193–200.
Article
CAS
PubMed
Google Scholar
Dumortier O, Hinault C, Van Obberghen E. MicroRNAs and metabolism crosstalk in energy homeostasis. Cell Metab. 2013;18(3):312–24.
Article
CAS
PubMed
Google Scholar
Rottiers V, Naar AM. MicroRNAs in metabolism and metabolic disorders. Nat Rev Mol Cell Biol. 2012;13(4):239–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Johnston CE, Hartley C, Salisbury AM, Wigley P. Immunological changes at point-of-lay increase susceptibility to Salmonella enterica Serovar enteritidis infection in vaccinated chickens. PLoS ONE. 2012;7(10):e48195.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wigley P, Hulme SD, Powers C, Beal RK, Berchieri AJ, Smith A, Barrow P. Infection of the reproductive tract and eggs with Salmonella enterica serovar pullorum in the chicken is associated with suppression of cellular immunity at sexual maturity. Infect Immun. 2005;73(5):2986–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Adams J. The proteasome: structure, function, and role in the cell. Cancer Treat Rev. 2003;29 (Suppl 1):3–9.
Article
CAS
PubMed
Google Scholar
Song R, Harding CV. Roles of proteasomes, transporter for antigen presentation (TAP), and beta 2-microglobulin in the processing of bacterial or particulate antigens via an alternate class I MHC processing pathway. J Immunol. 1996;156(11):4182–90.
CAS
PubMed
Google Scholar
Kruger E, Kuckelkorn U, Sijts A, Kloetzel PM. The components of the proteasome system and their role in MHC class I antigen processing. Rev Physiol Biochem Pharmacol. 2003;148:81–104.
CAS
PubMed
Google Scholar
Lo WF, Ong H, Metcalf ES, Soloski MJ. T cell responses to Gram-negative intracellular bacterial pathogens: a role for CD8+ T cells in immunity to Salmonella infection and the involvement of MHC class Ib molecules. J Immunol. 1999;162(9):5398–406.
CAS
PubMed
Google Scholar
Kubori T, Galan JE. Temporal regulation of salmonella virulence effector function by proteasome-dependent protein degradation. Cell. 2003;115(3):333–42.
Article
CAS
PubMed
Google Scholar
Maksymowych WP, Ikawa T, Yamaguchi A, Ikeda M, McDonald D, Laouar L, Lahesmaa R, Tamura N, Khuong A, Yu DT, et al. Invasion by Salmonella typhimurium induces increased expression of the LMP, MECL, and PA28 proteasome genes and changes in the peptide repertoire of HLA-B27. Infect Immun. 1998;66(10):4624–32.
CAS
PubMed
PubMed Central
Google Scholar
Christoffersen NR, Shalgi R, Frankel LB, Leucci E, Lees M, Klausen M, Pilpel Y, Nielsen FC, Oren M, Lund AH. p53-independent upregulation of miR-34a during oncogene-induced senescence represses MYC. Cell Death Differ. 2010;17(2):236–45.
Article
CAS
PubMed
Google Scholar
Li N, Muthusamy S, Liang R, Sarojini H, Wang E. Increased expression of miR-34a and miR-93 in rat liver during aging, and their impact on the expression of Mgst1 and Sirt1. Mech Ageing Dev. 2011;132(3):75–85.
Article
CAS
PubMed
Google Scholar
Hu H, Wang B, Borde M, Nardone J, Maika S, Allred L, Tucker PW, Rao A. Foxp1 is an essential transcriptional regulator of B cell development. Nat Immunol. 2006;7(8):819–26.
Article
CAS
PubMed
Google Scholar
Shi C, Zhang X, Chen Z, Sulaiman K, Feinberg MW, Ballantyne CM, Jain MK, Simon DI. Integrin engagement regulates monocyte differentiation through the forkhead transcription factor Foxp1. J Clin Invest. 2004;114(3):408–18.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shi C, Sakuma M, Mooroka T, Liscoe A, Gao H, Croce KJ, Sharma A, Kaplan D, Greaves DR, Wang Y, et al. Down-regulation of the forkhead transcription factor Foxp1 is required for monocyte differentiation and macrophage function. Blood. 2008;112(12):4699–711.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bommer GT, Gerin I, Feng Y, Kaczorowski AJ, Kuick R, Love RE, Zhai Y, Giordano TJ, Qin ZS, Moore BB, et al. p53-mediated activation of miRNA34 candidate tumor-suppressor genes. Curr Biol. 2007;17(15):1298–307.
Article
CAS
PubMed
Google Scholar
Rao DS, O’Connell RM, Chaudhuri AA, Garcia-Flores Y, Geiger TL, Baltimore D. MicroRNA-34a perturbs B lymphocyte development by repressing the forkhead box transcription factor Foxp1. Immun. 2010;33(1):48–59.
Article
CAS
Google Scholar
Ciraci C, Tuggle CK, Wannemuehler MJ, Nettleton D, Lamont SJ. Unique genome-wide transcriptome profiles of chicken macrophages exposed to Salmonella-derived endotoxin. BMC Genomics. 2010;11:545.
Article
PubMed
PubMed Central
Google Scholar
Ma L, Cantley LC, Janmey PA, Kirschner MW. Corequirement of specific phosphoinositides and small GTP-binding protein Cdc42 in inducing actin assembly in Xenopus egg extracts. J Cell Biol. 1998;140(5):1125–36.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ma L, Rohatgi R, Kirschner MW. The Arp2/3 complex mediates actin polymerization induced by the small GTP-binding protein Cdc42. Proc Natl Acad Sci U S A. 1998;95(26):15362–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rohatgi R, Ma L, Miki H, Lopez M, Kirchhausen T, Takenawa T, Kirschner MW. The interaction between N-WASP and the Arp2/3 complex links Cdc42-dependent signals to actin assembly. Cell. 1999;97(2):221–31.
Article
CAS
PubMed
Google Scholar
Stender S, Friebel A, Linder S, Rohde M, Mirold S, Hardt WD. Identification of SopE2 from Salmonella typhimurium, a conserved guanine nucleotide exchange factor for Cdc42 of the host cell. Mol Microbiol. 2000;36(6):1206–21.
Article
CAS
PubMed
Google Scholar
Bhattacharyya S, Borthakur A, Pant N, Dudeja PK, Tobacman JK. Bcl10 mediates LPS-induced activation of NF-kappaB and IL-8 in human intestinal epithelial cells. Am J Physiol Gastrointest Liver Physiol. 2007;293(2):G429–37.
Article
CAS
PubMed
Google Scholar
Ruan WK, Wu YH, An J, Zheng SJ. Polymorphisms of chicken Toll-like receptors 4, 15, and 21 in different breeds. Poult Sci. 2012;91(10):2512–6.
Article
CAS
PubMed
Google Scholar
MacKinnon KM, He H, Nerren JR, Swaggerty CL, Genovese KJ, Kogut MH. Expression profile of toll-like receptors within the gastrointestinal tract of 2-day-old Salmonella enteriditis-infected broiler chickens. Vet Microbiol. 2009;137(3-4):313–9.
Article
CAS
PubMed
Google Scholar
Takeda K, Akira S. Toll-like receptors. Curr Protoc Immunol. 2015;109:12–4.
PubMed
Google Scholar
Manicassamy S, Pulendran B. Modulation of adaptive immunity with Toll-like receptors. Semin Immunol. 2009;21(4):185–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Higuchi M, Matsuo A, Shingai M, Shida K, Ishii A, Funami K, Suzuki Y, Oshiumi H, Matsumoto M, Seya T. Combinational recognition of bacterial lipoproteins and peptidoglycan by chicken Toll-like receptor 2 subfamily. Dev Comp Immunol. 2008;32(2):147–55.
Article
CAS
PubMed
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
An J, Lai J, Lehman ML, Nelson CC. miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res. 2013;41(2):727–37.
Article
CAS
PubMed
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139–40.
Article
CAS
PubMed
Google Scholar
John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. Human MicroRNA targets. PLoS Biol. 2004;2(11):e363.
Article
PubMed
PubMed Central
Google Scholar
Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS. MicroRNA targets in Drosophila. Genome Biol. 2003;5(1):R1.
Article
PubMed
PubMed Central
Google Scholar
Dennis GJ, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 2003;4(5):3.
Article
Google Scholar
Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44–57.
Article
CAS
Google Scholar
Huang DW, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009;37(1):1–13.
Article
Google Scholar
Al-Shahrour F, Diaz-Uriarte R, Dopazo J. FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics. 2004;20(4):578–80.
Article
CAS
PubMed
Google Scholar
Joslyn CA, Mniszewski SM, Fulmer A, Heaton G. The gene ontology categorizer. Bioinformatics. 2004;20 (Suppl 1):i169–77.
Article
CAS
PubMed
Google Scholar
Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011;27(3):431–2.
Article
CAS
PubMed
Google Scholar