Variation in the limiting factor for phage production across host growth rates.

<p>Modeling results overlaid with experimental phage production measurements. The machinery-feasible region represents phage production values from T7 ODEs alone, with the growth rate supplied to correlations for availability of the host replication machinery; phage production values above the machinery-feasible boundary are considered machinery infeasible. The upper boundary of the metabolically feasible region was calculated using the integrated simulation, but with access to excess host replication factors, which we simulated by multiplying the host growth rate from FBA by a factor of 1.25 when it was passed to the T7 ODE host machinery correlations. Growth rate variation for calculating limitation boundaries and integrated simulation was evaluated with a set of modified flux bounds, with most growth rate sampling values simulated with both carbon and oxygen limitation, which produced essentially identical phage production predictions (resulting points lie within width of the line displayed). Error bars are standard deviation of n = 3.</p

Host population and phage population time courses.

<p>(A) Dynamic time courses of experimental host population data uninfected (line is mean of n = 2) and infected cultures (line is mean of n = 3); an immediate drop in population density occurs when the solution of phage is added at , due to dilution. Initial infection multiplicity was 0.1. (B) Measured and simulated phage production per infected host in tryptone broth media (circles are mean, error bars shown are the standard deviation, n = 3). Simulation presented for the integrated model and T7 ODEs alone simulated at . (C) Expanded comparison of the simulated concentrations of critical phage replication machinery and phage virion components compared to T7 ODEs alone. Gene Product 1 is the T7 RNA polymerase; Gene product 10A is the major capsid protein.</p

Measured and simulated phage production.

<p>Shown per infected host, across time, experiment compared to model predictions for integrated model system, and the T7 ODEs alone, on M9 minimal media with glucose, succinate, or acetate as carbon source (growth rates for T7 ODEs alone are , respectively). Error bars are standard deviation of n = 3. For glucose and succinate media the T7 ODEs time course is not visible because it falls directly beneath the integrated simulation line. The lower right panel quantifies the goodness of fit of the integrated simulation and the T7 ODEs alone to experimental observations using normalized mean squared error.</p

Blocking paracrine signaling by TNF across all concentrations and preparations.

<p>The average time course for N number of active cells is plotted for cells stimulated in the absence (blue trace, top value of n) and presence (orange trace, bottom value) of sTNFRII, which competes to bind TNF. Concentrations are indicated at left, and the preparation at top.</p

Comparison of single-cell NF-κB activation dynamics for three different LPS preparations.

<p>Intensity represents the relative nuclear localization of p65-dsRed fusion protein, calculated as mean nuclear intensity divided by initial mean cytoplasmic intensity. The concentration for all three preparations was 0.5 µg/mL. The black line shows the average time course for all cells; the light blue traces are ten randomly selected individual cells. The number of active cells (N), as well as the maximum peak amplitude (Peak Amp), and time elapsed until the maximum amplitude is reached (Time to Peak) are also shown. The maximum intensity is indicated by a dot and the two dashed lines indicate how Peak Amp and Time to Peak are determined. The duration of the first peak (Peak Width) is also shown. This value is determined by drawing a horizontal line at the intensity that is halfway between the minimum and maximum peak value. The region above the line and shaded in green denotes the time during which the p65-dsRed nuclear intensity is more than half of the maximum p65-dsRed nuclear intensity. Below each plot, corresponding representative microscope images are shown for the first 200 minutes after stimulation, as labeled.</p

The effect of blocking TNF on the NF-κB activation time courses as a function of concentration and preparation.

<p>The cosine vector distances between the average time courses in the presence and absence of sTNFRII are shown. Almost no cells were activated by UP LPS at low concentrations; hence the dashed light blue line is included for completeness but is not statistically defensible.</p