We present models of dormancy in a planktonic culture and in biofilm, and examine the relative advantage of short dormancy versus long dormancy times in each case. Simulations and analyses indicate that in planktonic batch cultures and in chemostats, live biomass is maximized by the fastest possible exit from dormancy. The lower limit of time to reawakening is thus perhaps governed by physiolog...

Experimental evolution of microbes is a powerful tool to study adaptation to strong selection, the mechanism of evolution and the development of new traits. The development of high-throughput sequencing methods has given researchers a new ability to cheaply and easily identify mutations genome wide that are selected during the course of experimental evolution. Here we provide a protocol for con...

Studying evolution in the laboratory provides a means of understanding the processes, dynamics and outcomes of adaptive evolution in precisely controlled and readily replicated conditions. The advantages of experimental evolution are maximized when the selection is well defined, which enables linking genotype, phenotype and fitness. One means of maintaining a defined selection is continuous cul...

The stabilization of equilibria in chemostats with measurement delays is a complex and challenging problem, and is of significant ongoing interest in bioengineering and population dynamics. In this paper, we solve an output feedback stabilization problem for chemostat models having two species, one limiting substrate, and either Haldane or Monod growth functions. Our feedback stabilizers depend...

The physiological and nutritional factors that regulate protease synthesis in Clostridium sporogenes C25 were studied in batch and continuous cultures. Formation of extracellular proteases occurred at the end of active growth and during the stationary phase in batch cultures. Protease production was inversely related to growth rate in glucose-excess and glucose-limited chemostats over the range...

Oscillations in patterns of expression of a large fraction of yeast genes are associated with the "metabolic cycle," usually seen only in prestarved, continuous cultures of yeast. We used FISH of mRNA in individual cells to test the hypothesis that these oscillations happen in single cells drawn from unsynchronized cultures growing exponentially in chemostats. Gene-expression data from synchron...

The gradostat consists of multiple chemostats interconnected by mass flows and diffusion. It has been used to model biochemical systems such as wastewater treatment networks microbial activity in soil. In this paper we maximize the production biogas a at steady state. physical decision variables are water, substrate, biomass entering each tank through interconnecting pipes. Our main technical f...