Two major health-related research challenges are: i) ending the human immunodeficiency virus type-1 (HIV-1) pandemic by developing a protective vaccine, and ii) combatting the rising prevalence of allergy and autoimmunity. We are attempting to tackle these two areas by studying the effects on the immune system of post-translational modifications of proteins and sugars. HIV-1 antibody-based vaccine design attempts to elicit neutralizing antibodies by active vaccination, and we are using chemical cross-linking and post-translational glycan modification to stabilise, enhance and focus the immunogenicity of experimental vaccine antigens. The environmental triggers of allergy and autoimmunity have not been well defined, and our working hypothesis is that post-translational modification of proteins may be responsible for triggering unwanted immune activation under oxidative conditions. We are attempting to define molecular mechanisms underlying the modulating effect of these oxidative modifications on the immune system.