Systems infection biology: A compartmentalized immune network of pig spleen challenged with Haemophilus parasuis

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Zhao, Ming ^a   Liu, Xiang dong ^a   Li, Xin yun ^a   Chen, Hong bo ^a,b   Jin, Hui ^a   Zhou, Rui ^a   Zhu, Meng jin ^a   Zhao, Shu hong ^a  

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^b WUHAN POLYTECHNIC UNIVERSITY   (China)

Author keywords

Haemophilus parasuis; Immunogenome; Network; Pig model; Quantitative topology; Scale free, C1R; Spleen

Indexed keywords

ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; EXPERIMENTAL PIG; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC ASSOCIATION; HAEMOPHILUS INFECTION; HAEMOPHILUS PARASUIS; IMMUNE RESPONSE; IMMUNOGENETICS; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; SIGNAL TRANSDUCTION; SPLEEN; SYSTEMS BIOLOGY;

ANIMALS; HAEMOPHILUS INFECTIONS; HAEMOPHILUS PARASUIS; HUMANS; IMMUNITY, INNATE; SPLEEN; SWINE; SWINE DISEASES; SYSTEMS BIOLOGY;

BACILLI (CLASS); HAEMOPHILUS PARASUIS; MAMMALIA; NEGIBACTERIA; SUIDAE; SUS;

EID: 84872447784     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-46     Document Type: Article

References (53)

1. Olvera A, Pina S, Pérez-Simó M, Aragón V, Segalés J, Bensaid A. Immunogenicity and protection against Haemophilus parasuis infection after vaccination with recombinant virulence associated trimeric autotransporters (VtaA). Vaccine 2011, 29:2797-2802.
2. Frandoloso R, Martínez S, Rodríguez-Ferri EF, García-Iglesias MJ, Pérez-Martínez C, Martínez-Fernández B, Gutiérrez-Martín CB. Development and characterization of protective Haemophilus parasuis subunit vaccines based on native proteins with affinity to porcine transferrin and comparison with other subunit and commercial vaccines. Clin Vaccine Immunol 2011, 18:50-58.
3. Cerdà-Cuéllar M, Naranjo JF, Verge A, Nofrarías M, Cortey M, Olvera A, Segalés J, Aragon V. Sow vaccination modulates the colonization of piglets by Haemophilus parasuis. Vet Microbiol 2010, 145:315-320.
4. Olvera A, Pina S, Pérez-Simó M, Oliveira S, Bensaid A. Virulence-associated trimeric autotransporters of Haemophilus parasuis are antigenic proteins expressed in vivo. Vet Res 2010, 41:26.
5. Zhou M, Zhang A, Guo Y, Liao Y, Chen H, Jin M. A comprehensive proteome map of the Haemophilus parasuis serovar 5. Proteomics 2009, 9:2722-2739.
6. Olvera A, Segalés J, Aragón V. Update on the diagnosis of Haemophilus parasuis infection in pigs and novel genotyping methods. Vet J 2007, 174:522-529.
7. Wang Y, Liu C, Fang Y, Liu X, Li W, Liu S, Liu Y, Liu Y, Charreyre C, Audonnet JC, Chen P, He Q. Transcription analysis on response of porcine alveolar macrophages to Haemophilus parasuis. BMC Genomics 2012, 13:68.
8. Liu XD, Chen HB, Tong Q, Li XY, Zhu MJ, Wu ZF, Zhou R, Zhao SH. Molecular characterization of caveolin-1 in pigs infected with Haemophilus parasuis. J Immunol 2011, 186:3031-3046.
9. Wilkinson JM, Sargent CA, Galina-Pantoja L, Tucker AW. Gene expression profiling in the lungs of pigs with different susceptibilities to Glässer's disease. BMC Genomics 2010, 11:455.
10. Chen HB, Li CC, Fang MD, Zhu MJ, Li XY, Zhou R, Li K, Zhao SH. Understanding Haemophilus parasuis infection in porcine spleen through a transcriptomics approach. BMC Genomics 2009, 10:64.
11. de la Fuente AJ, Gutiérrez-Martín CB, Rodríguez-Barbosa JI, Martínez-Martínez S, Frandoloso R, Tejerina F, Rodríguez-Ferri EF. Blood cellular immune response in pigs immunized and challenged with Haemophilus parasuis. Res Vet Sci 2009, 86:230-234.
12. Lunney JK. Advances in Swine Biomedical Model Genomics. Int J Biol Sci 2007, 3:179-184.
13. Aderem A, Adkins JN, Ansong C, Galagan J, Kaiser S, Korth MJ, Law GL, McDermott JG, Proll SC, Rosenberger C, Schoolnik G, Katze MG. A systems biology approach to infectious disease research: innovating the pathogen-host research paradigm. MBio 2011, 2:pii: e00325-10.
14. Kellam P, Weiss RA. Infectogenomics: Insights from the Host Genome into Infectious Diseases. Cell 2006, 124:695-697.
15. Nibali L, Donos N, Henderson B. Periodontal infectogenomics. J Med Microbiol 2009, 58(Pt 10):1269-1274.
16. Lebet T, Chiles R, Hsu AP, Mansfield ES, Warrington JA, Puck JM. Mutations causing severe combined immunodeficiency: detection with a custom resequencing microarray. Genet Med 2008, 10:575-585.
17. Anisimov SV, Christophersen NS, Correia AS, Li JY, Brundin P. "NeuroStem Chip": a novel highly specialized tool to study neural differentiation pathways in human stem cells. BMC Genomics 2007, 8:46.
18. Braga-Neto UM, Marques ET. From functional genomics to functional immunomics: new challenges, old problems, big rewards. PLoS Comput Biol 2006, 2:e81.
19. Nikula T, West A, Katajamaa M, Lönnberg T, Sara R, Aittokallio T, Nevalainen OS, Lahesmaa R. A human ImmunoChip cDNA microarray provides a comprehensive tool to study immune responses. J Immunol Methods 2005, 303:122-134.
20. Newton SS, Bennett A, Duman RS. Production of custom microarrays for neuroscience research. Methods 2005, 37:238-246.
21. Walder K, Segal D, Chehab S, Augert G, Cameron-Smith D, Hargreaves M, Collier GR. A custom-built insulin resistance gene chip. Ann N Y Acad Sci 2002, 967:274-282.
22. Bourgon R, Gentleman R, Huber W. Independent filtering increases detection power for high-throughput experiments. Proc Natl Acad Sci USA 2010, 107:9546-9551.
23. Hackstadt A, Hess A. Filtering for increased power for microarray data analysis. BMC Bioinformatics 2009, 10:11.
24. Calza S, Raffelsberger W, Ploner A, Sahel J, Leveillard T, Pawitan Y. Filtering genes to improve sensitivity in oligonucleotide microarray data analysis. Nucleic Acids Res 2007, 35:e102.
25. Roitt I, Brostoff J, Male D. Immunology 1989, London: J.B. Lippincott Co, second edition.
26. Engwerda CR, Kaye PM. Organ-specific immune responses associated with infectious disease. Immunol Today 2000, 21:73-78.
27. Mukherjee P, Ghosh AK, Ghose AC. Infection pattern and immune response in the spleen and liver of BALB/c mice intracardially infected with Leishmania donovani amastigotes. Immunol Lett 2003, 86:131-138.
28. Kang SJ, Liang HE, Reizis B, Locksley RM. Regulation of hierarchical clustering and activation of innate immune cells by dendritic cells. Immunity 2008, 29:819-833.
29. Maroof A, Beattie L, Zubairi S, Svensson M, Stager S, Kaye PM. Posttranscriptional regulation of II10 gene expression allows natural killer cells to express immunoregulatory function. Immunity 2008, 29:295-305.
30. Bhattacharyya S, Deb J, Patra AK, Thuy Pham DA, Chen W, Vaeth M, Berberich-Siebelt F, Klein-Hessling S, Lamperti ED, Reifenberg K, Jellusova J, Schweizer A, Nitschke L, Leich E, Rosenwald A, Brunner C, Engelmann S, Bommhardt U, Avots A, Müller MR, Kondo E, Serfling E. NFATc1 affects mouse splenic B cell function by controlling the calcineurin-NFAT signaling network. J Exp Med 2011, 208:823-839.
31. Bonnefoy F, Perruche S, Couturier M, Sedrati A, Sun Y, Tiberghien P, Gaugler B, Saas P. Plasmacytoid dendritic cells play a major role in apoptotic leukocyte-induced immune modulation. J Immunol 2011, 186:5696-5705.
32. McGaha TL, Chen Y, Ravishankar B, van Rooijen N, Karlsson MC. Marginal zone macrophages suppress innate and adaptive immunity to apoptotic cells in the spleen. Blood 2011, 117:5403-5412.
33. Osmond DG. The ontogeny and organization of the lymphoid system. J Invest Dermatol 1985, 85(Suppl):2s-9s.
34. Brown AR. Immunological functions of splenic B-lymphocytes. Crit Rev Immunol 1992, 11:395-417.
35. Mitchell LM, Brzoza-Lewis KL, Henry CJ, Grayson JM, Westcott MM, Hiltbold EM. Distinct responses of splenic dendritic cell subsets to infection with Listeria monocytogenes: Maturation phenotype, level of infection, and T cell priming capacity ex vivo. Cell Immunol 2011, 268:79-86.
36. Favila-Castillo L, Monroy-Ostria A, Kobayashi E, Hirunpetcharat C, Kamada N, Good MF. Protection of rats against malaria by a transplanted immune spleen. Parasite Immunol 1996, 18:325-331.
37. Husson F, Lê S, Pagès J. Exploratory multivariate analysis by example using R 2011, Boca Raton, FL: Chapman & Hall/CRC Press.
38. Smyth GK. Limma: linear models for microarray data. Bioinformatics and Computational Biology Solutions using R and Bioconductor 2005, New York: Springer, Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W.
39. Altay G, Emmert-Streib F. Inferring the conservative causal core of gene regulatory networks. BMC Syst Biol 2010, 4:132.
40. Chen H, Lunney JK, Cheng L, Li X, Cao J, Zhu M, Zhao S. Porcine S100A8 and S100A9: molecular characterizations and crucial functions in response to Haemophilus parasuis infection. Dev Comp Immunol 2011, 35:490-500.
41. Barabasi AL, Albert R. Emergence of scaling in random networks. Science 1999, 286:509-512.
42. Erdos P, Rényi A. On the evolution of random graphs. Publications of the Mathematical Institute of the Hungarian Academy of Sciences 1960, 5:17-61.
43. Bansal K, Narayana Y, Patil SA, Balaji KN. M. bovis BCG induced expression of COX-2 involves nitric oxide-dependent and -independent signaling pathways. J Leukoc Biol 2009, 5:804-816.
44. Greene LH, Higman VA. Uncovering Network Systems Within Protein Structures. J Mol Biol 2003, 334:781-791.
45. Arita M. The metabolic world of Escherichia coli is not small. Proc Natl Acad Sci USA 2004, 101:1543-1547.
46. Dong YA. Statistical analysis of protein interaction network topology. PhD thesis 2005, Massachusetts Institute of Technology: Department of Mathematics.
47. Small M, Xu X, Zhou J, Zhang J, Sun J, Lu JA. Scale-free networks which are highly assortative but not small world. Phys Rev E Stat Nonlin Soft Matter Phys 2008, 77(6 Pt 2):066112.
48. Hert J, Keiser MJ, Irwin JJ, Oprea TI, Shoichet BK. Quantifying the Relationships among Drug Classes. J Chem Inf Model 2008, 48:755-765.
49. Rodriguez A, Infante D. Characterization in silico of flavonoids biosynthesis in Theobroma cacao L. Network Biology 2011, 1:34-45.
50. Newman M. Networks: An Introduction 2010, Oxford University Press: Oxford University Press.
51. Kitsak M, Gallos LK, Havlin S, Liljeros F, Muchnik L, Stanley HE, Makse HA. Identification of influential spreaders in complex networks. Nat Phys 2010, 6:888-893.
52. Duncan DT, Prodduturi N, Zhang B. WebGestalt2: an updated and expanded version of the Web-based Gene Set Analysis Toolkit. BMC Bioinformatics 2010, 11(Suppl 4):P10.
53. Zhang B, Kirov SA, Snoddy JR. WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res 2005, 33(Web Server issue):W741-W748.