This FOA invites R01 applications for mechanistic studies in clinical trials of: (1) immunomodulatory interventions for immune system mediated diseases, including, but not limited to: asthma and allergic diseases; graft rejection in solid organ, cell, and tissue transplantation; graft versus host disease in hematopoietic stem cell transplantation; and chronic inflammatory, autoimmune, and immunodeficiency diseases; and (2) preventative and therapeutic, vaccines for non-HIV/AIDS infectious diseases, including NIAID Category A, B, and C agents of bioterrorism and emerging/re-emerging infectious diseases. This FOA is a renewal with modifications of RFA AI-05-028 (http://grants.nih.gov/grants/guide/rfa-files/RFA-AI-05-028.html). In order to review and confer awards to grant applications received in response to this FOA in a timely fashion, without delay of the parent clinical trial, applications submitted in response to the FOA will be subject to an accelerated review/award process. Highly meritorious applications selected for funding under this FOA may receive their awards as early as thirteen weeks after the application receipt date. Holidays and other circumstances may alter this schedule slightly.