Advertisement

Defining the Elusive Molecular Self

  • Matthew N. Davies
  • Darren R. FlowerEmail author
Chapter
Part of the Immunomics Reviews: book series (IMMUN, volume 3)

Abstract

Within this chapter, and within the concept of immunology, we review the key idea of “self,” and thus the idea of “non-self,” as it manifests itself at the molecular level. Operationally, and at a high level, the immune system can rightly be seen as a community of agents that discriminates between self and non-self and attempts to suppress or eliminate the latter. Much discussion of self within immunology has been abstract and quasi-philosophical. Indeed, self and non-self are important and inspiring metaphors for both theoretical immunology and computer science. In this review, we look instead at the molecular components of self and non-self, and thus actualise reified abstractions into the concrete and corporeal entities that can form the basis of molecular therapeutics.

Keywords

Endoplasmic Reticulum Monozygotic Twin Cell Epitope iNKT Cell Dizygotic Twin 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. Joseph J (2002) Twin studies in psychiatry and psychology: Science or pseudoscience? Psychiatr Q 73:71–82CrossRefPubMedGoogle Scholar
  2. Lykken DT (2006) The mechanism of emergenesis. Genes Brain Behav 5:306–310CrossRefPubMedGoogle Scholar
  3. Flower DR (2008) Bioinformatics for vaccinology. Wiley BlackwellGoogle Scholar
  4. Matzinger P (2002) An innate sense of danger. Ann NY Acad Sci 961:341–342CrossRefPubMedGoogle Scholar
  5. Ada G (2008) The enunciation and impact of Macfarlane Burnet’s clonal selection theory of acquired immunity. Immunol Cell Biol 86:116–118CrossRefPubMedGoogle Scholar
  6. Ferdinand de S (1983) Course in General Linguistics. In: Bally C, Sechehaye A (eds) Trans. Roy Harris, La Salle, IL: Open CourtGoogle Scholar
  7. Jerne NK (1971) The somatic generation of immune recognition. Eur J Immunol 1:1–9CrossRefPubMedGoogle Scholar
  8. Cohen IR (2007) Biomarkers, self-antigens and the immunological homunculus. J Autoimmun 29:246–249CrossRefPubMedGoogle Scholar
  9. Janeway CA Jr, Medzhitov R (2002) Innate immune recognition. Annu Rev Immunol 20:197–216CrossRefPubMedGoogle Scholar
  10. Southan C (2004) Has the yo-yo stopped? An assessment of human protein-coding gene number. Proteomics 4:1712–1726CrossRefPubMedGoogle Scholar
  11. Nordström KJ, Mirza MA, Larsson TP, Gloriam DE, Fredriksson R, Schiöth HB (2006) Comprehensive comparisons of the current human, mouse, and rat RefSeq, Ensembl, EST, and FANTOM3 datasets: Identification of new human genes with specific tissue expression profile. Biochem Biophys Res Commun 348:1063–1074CrossRefPubMedGoogle Scholar
  12. Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K, Lander ES (2007) Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci USA 104:19428–19433CrossRefPubMedGoogle Scholar
  13. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, Lin Y, MacDonald JR, Pang AW, Shago M, Stockwell TB, Tsiamouri A, Bafna V, Bansal V, Kravitz SA, Busam DA, Beeson KY, McIntosh TC, Remington KA, Abril JF, Gill J, Borman J, Rogers YH, Frazier ME, Scherer SW, Strausberg RL, Venter JC (2007) The diploid genome sequence of an individual human. PLoS Biol 5:e254CrossRefPubMedGoogle Scholar
  14. Doerfler W (2008) In pursuit of the first recognized epigenetic signal – DNA methylation: A 1976 to 2008 synopsis. Epigenetics 3:125–133CrossRefPubMedGoogle Scholar
  15. Sims RJ III, Reinberg D (2008) Is there a code embedded in proteins that is based on post-translational modifications? Nat Rev Mol Cell Biol 9:815–820CrossRefPubMedGoogle Scholar
  16. de Diego JL, Gerold G, Zychlinsky A (2007) Sensing, presenting, and regulating PAMPs. Ernst Schering Found Symp Proc 3:83–95CrossRefPubMedGoogle Scholar
  17. Areschoug T, Gordon S (2008) Pattern recognition receptors and their role in innate immunity: Focus on microbial protein ligands. Contrib Microbiol 15:45–60CrossRefPubMedGoogle Scholar
  18. Kornbluth RS, Stone GW (2006) Immunostimulatory combinations: Designing the next generation of vaccine adjuvants. J Leukoc Biol 80:1084–1102CrossRefPubMedGoogle Scholar
  19. Aguilar JC, Rodriguez EG (2007) Vaccine adjuvants revisited. Vaccine 25:3752–3762CrossRefPubMedGoogle Scholar
  20. Bayry J, Tchilian EZ, Davies MN, Forbes EK, Draper SJ, Kaveri SV, Hill AVS, Kazatchkine MD, Beverley PCL, Flower DR, Tough DF (2008) Targeting regulatory T cells in vaccination: In silico-identified CCR4 antagonists possess adjuvant activity. Proc Natl Acad Sci 105:10221–10226CrossRefPubMedGoogle Scholar
  21. Flower DR (2003) Towards in silico prediction of immunogenic epitopes. Trends Immunol 24:667–674CrossRefPubMedGoogle Scholar
  22. Flower DR, Doytchinova IA (2002) Immunoinformatics and the prediction of immunogenicity. Appl Bioinform 1:167–176Google Scholar
  23. Vivona S, Gardy JL, Ramachandran S, Brinkman FS, Raghava GP, Flower DR, Filippini F (2008) Computer-aided biotechnology: From immuno-informatics to reverse vaccinology. Trends Biotechnol 26:190–200CrossRefPubMedGoogle Scholar
  24. Davies MN, Flower DR (2007) Harnessing bioinformatics to discover new vaccines. Drug Discov Today 12:389–395CrossRefPubMedGoogle Scholar
  25. Vyas JM, Van der Veen AG, Ploegh HL (2008) The known unknowns of antigen processing and presentation. Nat Rev Immunol 8:607–618CrossRefPubMedGoogle Scholar
  26. Lin ML, Zhan Y, Villadangos JA, Lew AM (2008) The cell biology of cross-presentation and the role of dendritic cell subsets. Immunol Cell Biol 86:353–362CrossRefPubMedGoogle Scholar
  27. Loureiro J, Ploegh HL (2006) Antigen presentation and the ubiquitin-proteasome system in host-pathogen interactions. Adv Immunol 92:225–305CrossRefPubMedGoogle Scholar
  28. Menéndez-Benito V, Neefjes J (2007) Autophagy in MHC class II presentation: Sampling from within. Immunity 26:1–3CrossRefPubMedGoogle Scholar
  29. Strawbridge AB, Blum JS (2007) Autophagy in MHC class II antigen processing. Curr Opin Immunol 19:87–92CrossRefPubMedGoogle Scholar
  30. Florence WC, Bhat RK, Joyce S (2008) CD1d-restricted glycolipid antigens: Presentation principles, recognition logic and functional consequences. Expert Rev Mol Med 10:e20CrossRefPubMedGoogle Scholar
  31. Mori L, De Libero G (2008) Presentation of lipid antigens to T cells. Immunol Lett 117:1–8CrossRefPubMedGoogle Scholar
  32. Zajonc DM, Kronenberg M (2007) CD1 mediated T cell recognition of glycolipids. Curr Opin Struct Biol 17:521–529CrossRefPubMedGoogle Scholar
  33. Barral DC, Brenner MB (2007) CD1 antigen presentation: How it works. Nat Rev Immunol 7:929–941CrossRefPubMedGoogle Scholar
  34. Blythe MJ, Flower DR (2005) Benchmarking B cell epitope prediction: Underperformance of existing methods. Protein Sci 14(1):246–248CrossRefPubMedGoogle Scholar
  35. Mapara MY, Sykes M (2004) Tolerance and cancer: Mechanisms of tumor evasion and strategies for breaking tolerance. J Clin Oncol 22:1136–1151CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  1. 1.The Jenner InstituteUniversity of OxfordBerkshireUK

Personalised recommendations