1. De Silva, N. S. & Klein, U. Dynamics of B cells in germinal centres. Nat. Rev. Immunol. 15, 137–148 (2015).

2. Kurosaki, T., Kometani, K. & Ise, W. Memory B cells. Nat. Rev. Immunol. 15, 149–159 (2015).

3. Mesin, L., Ersching, J. & Victora, G. D. Germinal center B cell dynamics. Immunity 45, 471–482 (2016).

4. Bannard, O. & Cyster, J. G. Germinal centers: programmed for affinity maturation and antibody diversification. Curr. Opin. Immunol. 45, 21–30 (2017).

5. DeFranco, A. L., Rookhuizen, D. C. & Hou, B. Contribution of Toll-like receptor signaling to germinal center antibody responses. Immunol. Rev. 247, 64–72 (2012).

6. Rawlings, D. J., Schwartz, M. A., Jackson, S. W. & Meyer-Bahlburg, A. Integration of B cell responses through Toll-like receptors and antigen receptors. Nat. Rev. Immunol. 12, 282–294 (2012).

7. Akkaya, M. et al. B cells produce type 1 IFNs in response to the TLR9 agonist CpG-A conjugated to cationic lipids. J. Immunol. 199, 931–940 (2017).

8. Roche, P. A. & Furuta, K. The ins and outs of MHC class II-mediated antigen processing and presentation. Nat. Rev. Immunol. 15, 203–216 (2015).

9. Rookhuizen, D. C. & DeFranco, A. L. Toll-like receptor 9 signaling acts on multiple elements of the germinal center to enhance antibody responses. Proc. Natl Acad. Sci. USA 111, E3224–E3233 (2014).

10. Akkaya, M. et al. T cell-dependent antigen adjuvanted with DOTAP-CpG-B but not DOTAP-CpG-A induces robust germinal center responses and high affinity antibodies in mice. Eur. J. Immunol. 47, 1890–1899 (2017).

11. Gavin, A. L. et al. Adjuvant-enhanced antibody responses in the absence of toll-like receptor signaling. Science 314, 1936–1938 (2006).

12. Coffman, R. L., Sher, A. & Seder, R. A. Vaccine adjuvants: putting innate immunity to work. Immunity 33, 492–503 (2010).

13. Francica, J. R. et al. Analysis of immunoglobulin transcripts and hypermutation following SHIV(AD8) infection and protein-plus-adjuvant immunization. Nat. Commun. 6, 6565 (2015).

14. Basso, K. & Dalla-Favera, R. Roles of BCL6 in normal and transformed germinal center B cells. Immunol. Rev. 247, 172–183 (2012).

15. Fleire, S. J. et al. B cell ligand discrimination through a spreading and contraction response. Science 312, 738–741 (2006).

16. Weber, M. et al. Phospholipase C-γ2 and Vav cooperate within signaling microclusters to propagate B cell spreading in response to membrane-bound antigen. J. Exp. Med. 205, 853–868 (2008).

17. Tolar, P., Sohn, H. W., Liu, W. & Pierce, S. K. The molecular assembly and organization of signaling active B-cell receptor oligomers. Immunol. Rev. 232, 34–41 (2009).

18. Liu, W., Meckel, T., Tolar, P., Sohn, H. W. & Pierce, S. K. Intrinsic properties of immunoglobulin IgG1 isotype-switched B cell receptors promote microclustering and the initiation of signaling. Immunity 32, 778–789 (2010).

19. Akkaya, B. et al. A simple, versatile antibody-based barcoding method for flow cytometry. J. Immunol. 197, 2027–2038 (2016).

20. Crompton, P. D. et al. The TLR9 ligand CpG promotes the acquisition of Plasmodium falciparum-specific memory B cells in malaria-naive individuals. J. Immunol. 182, 3318–3326 (2009).

21. Lanzavecchia, A. Antigen presentation by B lymphocytes: a critical step in T-B collaboration. Curr. Top. Microbiol. Immunol. 130, 65–78 (1986).

22. Eckl-Dorna, J. & Batista, F. D. BCR-mediated uptake of antigen linked to TLR9 ligand stimulates B-cell proliferation and antigen-specific plasma cell formation. Blood 113, 3969–3977 (2009).

23. Genestier, L. et al. TLR agonists selectively promote terminal plasma cell differentiation of B cell subsets specialized in thymus-independent responses. J. Immunol. 178, 7779–7786 (2007).

24. Hoogeboom, R. & Tolar, P. Molecular mechanisms of B cell antigen gathering and endocytosis. Curr. Top. Microbiol. Immunol. 393, 45–63 (2016).

25. Mason, D. Y., Jones, M. & Goodnow, C. C. Development and follicular localization of tolerant B lymphocytes in lysozyme/anti-lysozyme IgM/IgD transgenic mice. Int. Immunol. 4, 163–175 (1992).

26. Ho, W. Y., Cooke, M. P., Goodnow, C. C. & Davis, M. M. Resting and anergic B cells are defective in CD28-dependent costimulation of naive CD4+ T cells. J. Exp. Med. 179, 1539–1549 (1994).

27. Akkaya, M., Kwong, L. S., Akkaya, E., Hatherley, D. & Barclay, A. N. Rabbit CD200R binds host CD200 but not CD200-like proteins from poxviruses. Virology 488, 1–8 (2016).

28. Dadaglio, G., Nelson, C. A., Deck, M. B., Petzold, S. J. & Unanue, E. R. Characterization and quantitation of peptide-MHC complexes produced from hen egg lysozyme using a monoclonal antibody. Immunity 6, 727–738 (1997).

29. Cauerhff, A., Goldbaum, F. A. & Braden, B. C. Structural mechanism for affinity maturation of an anti-lysozyme antibody. Proc. Natl. Acad. Sci. USA 101, 3539–3544 (2004).

30. Traba, J., Miozzo, P., Akkaya, B., Pierce, S. K. & Akkaya, M. An optimized protocol to analyze glycolysis and mitochondrial respiration in lymphocytes. J. Vis. Exp. 117, e54918 (2016).

31. Akkaya, B. et al. Ex-vivo iTreg differentiation revisited: Convenient alternatives to existing strategies. J. Immunol. Meth. 441, 67–71 (2017).

32. Mullen, G. E. et al. Phase 1 trial of AMA1-C1/Alhydrogel plus CPG 7909: an asexual blood-stage vaccine for Plasmodium falciparum malaria. PLoS ONE 3, e2940 (2008).

33. Tomlinson, D. C., L’Hôte, C. G., Kennedy, W., Pitt, E. & Knowles, M. A. Alternative splicing of fibroblast growth factor receptor 3 produces a secreted isoform that inhibits fibroblast growth factor-induced proliferation and is repressed in urothelial carcinoma cell lines. Cancer. Res. 65, 10441–10449 (2005).

34. Akkaya, M., Aknin, M. L., Akkaya, B. & Barclay, A. N. Dissection of agonistic and blocking effects of CD200 receptor antibodies. PLoS ONE 8, e63325 (2013).

35. Sohn, H. W., Tolar, P., Brzostowski, J. & Pierce, S. K. A method for analyzing protein-protein interactions in the plasma membrane of live B cells by fluorescence resonance energy transfer imaging as acquired by total internal reflection fluorescence microscopy. Methods. Mol. Biol. 591, 159–183 (2010).

36. Natkanski, E. et al. B cells use mechanical energy to discriminate antigen affinities. Science 340, 1587–1590 (2013).

37. Liu, W., Meckel, T., Tolar, P., Sohn, H. W. & Pierce, S. K. Antigen affinity discrimination is an intrinsic function of the B cell receptor. J. Exp. Med. 207, 1095–1111 (2010).

38. Davey, A. M. & Pierce, S. K. Intrinsic differences in the initiation of B cell receptor signaling favor responses of human IgG+ memory B cells over IgM+ naive B cells. J. Immunol. 188, 3332–3341 (2012).

39. Wang, J., Sohn, H., Sun, G., Milner, J. D. & Pierce, S. K. The autoinhibitory C-terminal SH2 domain of phospholipase C-γ2 stabilizes B cell receptor signalosome assembly. Sci. Signal. 7, ra89 (2014).

40. Offerdahl, D. K., Dorward, D. W., Hansen, B. T. & Bloom, M. E. A three-dimensional comparison of tick-borne flavivirus infection in mammalian and tick cell lines. PLoS ONE 7, e47912 (2012).

41. Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36–51 (2005).

42. Kremer, J. R., Mastronarde, D. N. & McIntosh, J. R. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116, 71–76 (1996).

43. Gordon, E. B. et al. Targeting glutamine metabolism rescues mice from late-stage cerebral malaria. Proc. Natl Acad. Sci. USA 112, 13075–13080 (2015).

44. Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10–12 (2011).