CHAPTER 14 Innate ImmunityINTRODUCTION M any different cell types of the innate immune system can recognize pathogens and tumor cells, and it is their quick response that constitutes the first line of defense against infectious agents and malignant transformation. Innate immunity against microbes and tumors can be initiated and/or executed by macrophages, dendritic cells, NK cells, NKT cells and others. The biological consequences of pathogen recognition by these cell types is elimination of the pathogen and the induction of expression of costimulatory molecules, cytokines, and chemokines that facilitate development of the adaptive immune response. In addition, macrophages and dendritic cells can internalize apoptotic cells and cellular debris, as well as pathogenic organisms, and in this fashion, eliminate cellular waste and noxious agents.At this time, Chapter 14 remains a chapter in transition, in which new protocols for the analysis of the innate immune response will be combined with updated protocols currently presented at other locations in earlier versions of Current Protocols in Immunology. Complement will continue to keep its own place in this series (see Chapter 13), but NK cells will gradually be introduced into Chapter 14. UNITS 14.1-14.9 contain protocols for studying macrophages (detailed below). A commentary unit on the receptors and ligands involved in NK cell recognition is now included in this chapter (UNIT 14.10). A commentary section on signaling through NK receptors (UNIT 11.9B) can be found in Chapter 11. Protocols on isolating mouse (UNIT 3.22) and human (UNIT 7.7) NK cells are provided elsewhere, and assays for measuring cytotoxic NK cell function can be found in UNIT 7.18. UNIT 14.11 provides protocols for isolating and functional analysis of human NKT cells. UNIT 14.13 describes basic methods for the characterization, quantification, and functional analysis of murine invariant NKT (iNKT) cells in vivo or in vitro. These cells recognize CD1d-restricted lipid antigens and have immunoregulatory properties. Human and mouse CD1d restricted glycolipid antigen(s) and the iNKT cell functions they elicit are highly conserved and, hence, mouse is an excellent animal model for understanding iNKT cell biology in vivo. Protocols on other cell types that form integral parts of the innate immune system, such as neutrophils (UNIT 7.23) and dendritic cells (UNITS 3.7 & 7.32) are also presented elsewhere. A primary means of pathogen recognition by cells of the innate immune response is via Toll-like receptors (TLR). TLRs recognize biochemical molecular patterns that are characteristic of microbial structural components, e.g., Tolllike receptor 9 (TLR9) recognizes CpG DNA that is characteristic of bacterial DNA. A commentary unit (UNIT 14.12) describes the known TLRs. Eventually, after updating, many of the outlying units will be brought together in this chapter.Macrophages originate in the bone marrow from stem cells that are thought to give rise to a bipotent granulocyte/macrophage progenitor popu...