Thesis advisor: Kenneth C. Williams / HIV infection elicits dysregulation of the immune system and is associated with a number of comorbidities. A common link among HIV-associated comorbidities is monocyte and macrophage activation, accumulation, and high turnover. Anti-retroviral therapy (ART), while useful in preventing HIV infection from progressing to immune dysfunction characterized by AIDS, does not eliminate infection. Even with ART, individuals retain a low level of virus that is able to reseed infection and a higher rate of comorbidities than uninfected people. Prior research has revealed an inflammatory monocyte/macrophage cell population that is uniquely in tissues with infection in an HIV model that uses simian immunodeficiency viral (SIV) infection of rhesus macaques. This cell type is characterized by expression of the inflammatory marker calprotectin. Through measurements of soluble calprotectin present in the plasma of SIV-infected rhesus macaques, I found that calprotectin levels remained low within the first two weeks of infection, sharply increased around three weeks post-infection, typically increased to a maximum during late stage chronic disease, and positively correlated with plasma viral load. Initial calprotectin levels suggests a trend that high pre-infection levels are associated with not progressing to AIDS or SIV encephalitis. Through immunostaining monocytes and flow cytometry, I found that calprotectin expression on classical, intermediate, and non-classical monocytes initially decreases with SIV infection, rebounds for most of infection, and sharply decreases again with late-stage chronic disease. Flow cytometry further showed that the calprotectin-expressing monocyte expresses CD163, CD169, and CCR2, but lacks expression for CX3CR1 and CCR5. Analysis of RNAseq data illustrates trends that suggest an increase in gene expression of genes involved in antiviral/antibacterial and chemotactic functions during conditions when calprotectin gene expression is also increasing. In summary, the data presented in this thesis suggest that the calprotectin-expressing monocyte/macrophage may come from an intermediate monocyte and play a role in inflammation through calprotectin secretion, activation, and increased chemotactic function. / Thesis (MS) — Boston College, 2020. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.