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The regulation of metabolic activity by tuning enzyme expression levels is crucial to sustain cellular growth in changing environments. Metabolic networks are often studied at steady state using constraint-based models and optimization…
Marine microorganisms often reach high swimming speeds, either to take advantage of evanescent nutrient patches or to beat Brownian forces. Since this implies that a sizable part of their energetic budget must be allocated to motion, it is…
Living systems continuously transform matter and energy through the chemical processes that constitute their metabolism. The overall metabolic rate of an organism correlates positively with its body mass, however both the exact scaling…
Metabolism and evolution are closely connected: if a mutation incurs extra energetic costs for an organism, there is a baseline selective disadvantage that may or may not be compensated for by other adaptive effects. A long-standing, but to…
We propose a new scheme to infer the metabolic fluxes of cell cultures in a chemostat. Our approach is based on the Maximum Entropy Principle and exploits the understanding of the chemostat dynamics and its connection with the actual…
Bacteria are highly adaptive microorganisms that thrive in a wide range of growth conditions via changes in cell morphologies and macromolecular composition. How bacterial morphologies are regulated in diverse environmental conditions is a…
We present significantly advanced studies of the previously introduced physical growth mechanism and unite it with biochemical growth factors. Obtained results allowed formulating the general growth law which governs growth and evolutional…
Production of chemicals from engineered organisms in a batch culture involves an inherent trade-off between productivity, yield, and titer. Existing strategies for strain design typically focus on designing mutations that achieve the…
During batch growth on mixtures of two growth-limiting substrates, microbes consume the substrates either sequentially or simultaneously. These growth patterns are manifested in all types of bacteria and yeasts. The ubiquity of these growth…
Most organisms grow according to simple laws, which in principle can be derived from energy conservation and scaling arguments, critically dependent on the relation between the metabolic rate B of energy flow and the organism mass m.…
One of the major research questions regarding human microbiome studies is the feasibility of designing interventions that modulate the composition of the microbiome to promote health and cure disease. This requires extensive understanding…
Nutrient limitation is one of the most common triggers of antibiotic tolerance and persistence. Here, we present two microfluidic setups to study how spatial and temporal variation in nutrient availability lead to increased survival of…
When bacteria are grown on a mixture of two growth-limiting substrates, they exhibit a rich spectrum of substrate consumption patterns including diauxic growth, simultaneous consumption, and bistable growth. In previous work, we showed that…
Natural selection has shaped the evolution of cells and multi-cellular organisms such that social cooperation can often be preferred over an individualistic approach to metabolic regulation. This paper extends a framework for dynamic…
During the last decades, medical observations and multiscale data concerning tumor growth are mounting. At the same time, contemporary imaging techniques well established in clinical practice, provide a variety of information on real-time,…
Dormancy is an essential strategy for microorganisms to cope with environmental stress. However, global ecosystem models typically ignore microbial dormancy, resulting in major model uncertainties. To facilitate the consideration of…
Optimization-based models have been used to predict cellular behavior for over 25 years. The constraints in these models are derived from genome annotations, measured macro-molecular composition of cells, and by measuring the cell's growth…
Growth patterns generated by filamentous organisms (e.g. actinomycetes and fungi) involve spatial and temporal dynamics at different length scales. Several mathematical models have been proposed in the last thirty years to address these…
Microbial populations exhibit a broad spectrum of nutrient utilization strategies, ranging from strategies utilizing diverse nutrients, called "generalists," to those being highly adapted to specific nutrients, called "specialists." The…
The growth rate of organisms depends both on external conditions and on internal states, such as the expression levels of various genes. We show that to achieve a criterion mean growth rate over an ensemble of conditions, the internal…