Related papers: Bacterial cartels at steady supply
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…
The solution space of genome-scale models of cellular metabolism provides a map between physically viable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the corresponding growth rates. By…
Bacteria regulate their motility through a variety of mechanisms, including quorum sensing (QS) and other density-dependent responses mediated by diffusible signals. While nonlinear density-dependent motility is well known in active-matter…
Bacteria populations rely on mechanisms such as quorum sensing to coordinate complex tasks that cannot be achieved by a single bacterium. Quorum sensing is used to measure the local bacteria population density, and it controls cooperation…
We model an enclosed system of bacteria, whose motility-induced phase separation is coupled to slow population dynamics. Without noise, the system shows both static phase separation and a limit cycle, in which a rising global population…
Bacteria commonly live in structured communities that affect human health and influence ecological systems. Heterogeneous populations, such as motile and non-motile populations, often coexist in bacteria communities. Motile subpopulations…
Phenotypic heterogeneity is a strategy commonly used by bacteria to rapidly adapt to changing environmental conditions. Here, we study the interplay between phenotypic heterogeneity and genetic diversity in spatially extended populations.…
Cell cultures exhibit rich and complex behaviors driven by dynamic metabolic interactions among cells. In this work, we present a model that captures these interactions through a framework inspired by statistical mechanics. Using Monte…
In apparent contradiction to competition theory, the number of known, co-existing plankton species far exceeds their explicable biodiversity - a discrepancy termed the Paradox of the Plankton. We introduce a new game-theoretic model for…
Why, contrary to theoretical predictions, do marine microbe communities harbor tremendous phenotypic heterogeneity? How can so many marine microbe species competing in the same niche coexist? We discovered a unifying explanation for both…
As cells grow and divide under a given environment, they become crowded and resources are limited, as seen in bacterial biofilms and multicellular aggregates. These cells often show strong interactions through exchanging chemicals, as in…
Bacterial swarming is a rapid mass-migration, in which thousands of cells spread collectively to colonize a surface. Physically, swarming is a natural example of active particles that use energy to generate motion. Accordingly,…
Standard models of population dynamics focus on the the interaction, survival, and extinction of the competing species individually. Real ecological systems, however, are characterized by an abundance of species (or strategies, in the…
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…
The metabolic state of a cell, comprising fluxes, metabolite concentrations and enzyme levels, is shaped by a compromise between metabolic benefit and enzyme cost. This hypothesis and its consequences can be studied by computational models…
Experimental studies of microbial communities routinely reveal that they have multiple stable states. While each of these states is generally resilient, certain perturbations such as antibiotics, probiotics and diet shifts, result in…
Metabolic fluxes in cells are governed by physical, physiological, and economic principles. Here I assume an optimal allocation of enzyme resources and postulate a general principle for metabolism: each enzyme must convert less valuable…
Adaptive control in biological systems, such as intestinal immunity, remains poorly understood despite detailed knowledge of underlying regulatory networks. We propose an alternative framework based on stochastic martingale turnover, in…
The tolerance of bacterial populations to biocidal or antibiotic treatment has been well documented in both biofilm and planktonic settings. However, there is still very little known about the mechanisms that produce this tolerance.…
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…