Related papers: Differential gene expression in Bacillus subtilis
We introduce a particle-based model of self-replicating cells on a deformable substrate composed of the dermis and the basement membrane and investigate the relationship between dermal deformations and stem cell pattering on it. We show…
In unicellular organisms such as bacteria the same acquired mutations beneficial in one environment can be restrictive in another. However, evolving Escherichia coli populations demonstrate remarkable flexibility in adaptation. The…
Molecular communication is an expanding body of research. Recent advances in biology have encouraged using genetically engineered bacteria as the main component in the molecular communication. This has stimulated a new line of research that…
Through extensive studies of dynamical system modeling cellular growth and reproduction, we find evidence that complexity arises in multicellular organisms naturally through evolution. Without any elaborate control mechanism, these systems…
We analyse a model that describes the propagation of many pathogens within and between many species. A branching process approximation is used to compute the probability of disease outbreaks. Special cases of aquatic environments with two…
E. coli bacteria swim following a run and tumble pattern. In the run state all flagella join in a single helical bundle that propels the cell body along approximately straight paths. When one or more flagellar motors reverse direction the…
Gene expression is inherently noisy, posing a challenge to understanding how precise and reproducible patterns of gene expression emerge in mammals. We investigate this phenomenon using gastruloids, an in vitro model for early mammalian…
Drying of biologically-relevant sessile droplets, including passive systems (like DNA and proteins), as well as active microbial systems comprising bacteria and algae, have garnered considerable attention over the last decades. Distinct…
We investigate the use of an extension of rule-based modelling for cellular signalling to create a structured space of model variants. This enables the incremental development of rule sets that start from simple mechanisms and which, by a…
The immune response to a pathogen has two basic features. The first is the expansion of a few pathogen-specific cells to form a population large enough to control the pathogen. The second is the process of differentiation of cells from an…
We investigate the oscillatory dynamics and bifurcation structure of a reaction-diffusion system with bistable nonlinearity and mass conservation, which was proposed by [Otsuji et al, PLoS Comp. Biol. 3 (2007), e108]. The system is a useful…
It has been known for many years that small fractions of persister cells resist killing in many bacterial colony-antimicrobial confrontations. These persisters are not believed to be mutants. Rather it has been hypothesized that they are…
Successful biological development via spatial regulation of cell differentiation relies on action of multiple signaling molecules that are known as morphogens. It is now well established that signaling molecules create non-uniform…
The fundamental biological processes of development of tissues and organs in multicellular organisms is governed by various signaling molecules, which are called morphogens. It is known that spatial and temporal variations in concentration…
One of the many ways cells transmit information within their volume is through steady spatial gradients of different proteins. However, the mechanism through which proteins without any sources or sinks form such single-cell gradients is not…
Proteus mirabilis are bacteria that make strikingly regular spatial-temporal patterns on agar surfaces. In this paper we investigate a mathematical model that has been shown to display these structures when solved numerically. The model…
Heterogeneous systems of active matter exhibit a range of complex emergent dynamical patterns. In particular, it is difficult to predict the properties of the mixed system based on its constituents. These considerations are particularly…
The evolution of multicellular organisms from monocellular ancestors represents one of the greatest advances of the history of life. The assembly of such multicellular organisms requires signalling and response between cells: over millions…
We present a novel model that describes the within-host evolutionary dynamics of parasites undergoing antigenic variation. The approach uses a multi-type branching process with two types of entities defined according to their relationship…
In nature, bacterial collectives typically consist of multiple species, which are interacting both biochemically and physically. Nonetheless, past studies on the physical properties of swarming bacteria were focused on axenic (single…