During primary HIV infection the viral load in plasma increases, reaches a peak, and then declines. Phillips has suggested that the decline is due to a limitation in the number of cells susceptible to HIV infection, while other authors have suggested that the decline in viremia is due to an...

During an immune response the affinity of antibodies that react with the antigen that triggered the response increases with time, a phenomenon known as affinity maturation. The molecular basis of affinity maturation has been partially elucidated. It involves the somatic mutation of immunoglobin...

The immune system is a complex system that learns, remembers what it has learned, and acts to protect us from a variety of pathogens. Here we address the question of how the immune system is able to recognize and learn about pathogens that can rapidly evolve and hence potentially change so as to...

Cross-reactive memory responses occur when the immune system is primed by one strain of a pathogen and challenged with a related, but different strain. Much of the nature of a cross-reactive response is determined by the quantity and distribution of the memory cells, raised to the primary...

We describe a method of implementing efficient computer simulations of immune systems that have a large number of unique B and/or T cell clones. The method uses an implementation technique called lazy evaluation to create the illusion that all clones are being simulated, while only actually...

We develop various mathematical models of the clinical latency stage of HIV-1 infection assuming that HIV-1 infection is limited either by the availability of cells that HIV can infect of by a specific anti-HIV cellular immune response. The former models we call "target-cell-limited." Comparing...

A quantitative technique was developed to determine HIV-1 viral burden in two important cellular compartments in lymphoid tissues (LT). Image analysis and in situ hybridization were combined to show that in the presymptomatic stages of infection there is a large pool of about 108 copies per gram...

Though most mutations are deleterious, an interplay between somatic mutation and selection within germinal centers (GC) results in rapid generation of high affinity memory B cells. How high affinity B cells with large numbers of mutations are generated and preserved, within GC containing at...

Using a new mathematical model to analyze a detailed set of viral load data collected from five infected patients after the administration of a potent inhibitor of HIV-1 protease, it was estimated that productively infected cells have, on average, a lifespan of 2.2 days (t[sub 1/2]=1.6 days) and...