The minimization routine uses the function fminsearch from the Matlab Optimization toolbox, which is a derivative-free method to search for minima of unconstrained multivariable functions. The time-shifts (τ) of the different curves were then used to recreate a time series of L-rhamnose quantifications. Results Mathematical model supporting the growth curve synchronization method The range of inoculum densities that may be used for

growth curve synchronization has both an upper and a lower limit. While one can determine these limits experimentally by testing whether the experiment works over a large range of values, the factors behind these constraints have the following straightforward theoretical explanation. The lower limit for initial cell density is set by small number statistics. MEK inhibitor clinical trial If the inoculum is too dilute then there is a significant probability that some wells will not receive any cells. The probability of having empty wells can be calculated since the number of cells in the inoculum follows a Poisson distribution. For example, in the extreme case where an inoculum has an average

of 1 cell per replicate, the probability see more of having at least one replicate among eight with zero cells is 97%. The upper limit for inoculum density, on the other hand, is determined by the carrying capacity of the growth media. In order to guarantee reproducibility between growth curves started from inocula at different densities, the differences between the initial cell densities must be negligible compared to the carrying capacity yet they must not suffer from the small number statistics. Typical growth curves are subdivided into three phases [1]: a lag phase, an exponential phase and a stationary phase. The exponential phase starts when cells begin dividing at a constant rate, such that density increase follows (μ max is called the maximum specific growth rate.) Non-specific serine/threonine protein kinase The stationary phase starts when growth

slows down as the system approaches carrying capacity. Decreasing growth rate can attributed to nutrient depletion, accumulation of metabolic waste or density-dependent growth regulation, among other things [1, 30–35]. Here, we formulate a mathematical model assuming that growth limitation is due to nutrient depletion, but the same analysis can be applied to any other limiting factor. Without loss of generality we use Monod’s equation [1] to model bacterial growth based on nutrient concentration (N) where K N is the half-saturation constant. The nutrient concentration, initially N 0, decreases as a function of cell growth and the yield (Y) such that at a time t it has the value The maximum cell density reached (i.e.