Related papers: Differential gene expression in Bacillus subtilis
A diffusion-reaction model for the growth of bacterial colonies is presented. The often observed cooperative behavior developed by bacteria which increases their motility in adverse growth conditions is here introduced as a nonlinear…
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…
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…
A model of pattern formation in living systems is presented. The pattern is achieved by the sequential interaction of two signaling pathways. The coupling of the pattern to the (thick) epithelial sheet changes is given, when the Gauss…
The growth, form, and division of prebiotic vesicles, membraneous bags of fluid of varying components and shapes is hypothesized to have served as the substrate for the origin of life. The dynamics of these out-of-equilibrium structures is…
Phenotype switching can be triggered by external stimuli and by intrinsic stochasticity. Here, we focus on the motility-matrix production switch in Bacillus subtilis. We use modeling to describe the SinR-SlrR bistable switch its regulation…
The conditions under which biological cells switch from a static to a motile state are fundamental to the understanding of many healthy and pathological processes. In this paper, we show that even in the presence of a fully symmetric…
Biological systems are promising substrates for computation because they naturally process environmental information through complex internal dynamics. In this study, we investigate whether bacterial metabolic models can act as physical…
Information processing in the mammalian brain relies on a careful regulation of the membrane potential dynamics of its constituent neurons, which propagates across the neuronal tissue via electrical signalling. We recently reported the…
The data we analyze derives from the observation of numerous cells of the bacterium Escherichia coli (E. coli) growing and dividing. Single cells grow and divide to give birth to two daughter cells, that in turn grow and divide. Thus, a…
In multicellular organisms, several cell states coexist. For determining each cell type, cell-cell interactions are often essential, in addition to intracellular gene expression dynamics. Based on dynamical systems theory, we propose a…
The enteric bacterium Proteus mirabilis, which is a pathogen that forms biofilms in vivo, can swarm over hard surfaces and form concentric ring patterns in colonies. Colony formation involves two distinct cell types: swarmer cells that…
Stem cells are characterized by their ability to self-renew, as well as to differentiate and give rise to new populations of cells. Stem cell divisions are crucial for generative processes that occur during early development, and later in…
A computational theory and model of the ontogeny and development of bilateral symmetry in multicellular organisms is presented. Understanding the origin and evolution of bilateral organisms requires an understanding of how bilateral…
A probabilistic discrete model for 2D protein crystal growth is presented. This model takes into account the available space and can describe growing processes of different nature due to the versatility of its parameters which gives the…
The revival mechanism in dormant bacteria is a puzzling and open issue. We propose a model of information diffusion on a regular grid where agents represent bacteria and their mutual interactions implement quorum sensing. Agents may have…
In multicellular organisms, epithelial cells form layers separating compartments responsible for different physiological functions. At the early stage of epithelial layer formation, each cell of an aggregate defines an inner and an outer…
Isologous diversification theory for cell differentiation is proposed, based on simulations of interacting cells with biochemical networks and cell division process following consumption of some chemicals. According to the simulations of…
Multicellular tissues are the building blocks of many biological systems and organs. These tissues are not static, but dynamically change over time. Even if the overall structure remains the same there is a turnover of cells within the…
A splicing system is a formal model of a recombinant behaviour of sets of double stranded DNA molecules when acted on by restriction enzymes and ligase. In this survey we will concentrate on a specific behaviour of a type of splicing…