Related papers: An equilibrium model for ribosome competition
We study the emergence of cell differentiation under the assumption of the existence of a given number of tradeoffs between genes encoding different functions. In the model the viability of colonies is determined by the capability of their…
Large-scale simultaneous mRNA translation and the resulting competition for the available ribosomes has important implications to the cell's functioning and evolution. Developing a better understanding of the intricate correlations between…
The resources in a cell are finite, which implies that the various components of the cell must compete for resources. One such resource is the ribosomes used during translation to create proteins. Motivated by this example, we explore this…
Genetic circuits need a cellular environment to operate in, which naturally couples the circuit function with the overall functionality of gene regulatory network. To execute their functions all gene circuits draw resources in the form of…
Models of transcriptional regulation that assume equilibrium binding of transcription factors have been very successful at predicting gene expression from sequence in bacteria. However, analogous equilibrium models do not perform as well in…
In this paper we motivate and develop a model of gene expression for the purpose of studying the interaction between synthetic gene circuits and the chassis cell within which they are in- serted. This model focuses on the translational…
The production processes of proteins in prokaryotic cells are investigated. Most of the mathematical models in the literature study the production of {\em one} fixed type of proteins. When several classes of proteins are considered, an…
Synthetic biology constructs often rely upon the introduction of "circuit" genes into host cells, in order to express novel proteins and thus endow the host with a desired behavior. The expression of these new genes "consumes" existing…
The problem of unicellular-multicellular transition is one of the main issues that is discussing in evolutionary biology. In [1] the fitness of a colony of cells is considered in terms of its two basic components, viability and fecundity.…
Translation of proteins is a fundamental part of gene expression that is mediated by ribosomes. As ribosomes significantly contribute to both cellular mass and energy consumption, achieving efficient management of the ribosome population is…
Translation is a key step in the synthesis of proteins. Accordingly, cells have evolved an intricate array of control mechanisms to regulate this process. By constructing a multi-component mathematical framework for translation we uncover…
Living cells deploy many resources to sense their environments, including receptors, downstream signaling molecules, time and fuel. However, it is not known which resources fundamentally limit the precision of sensing, like weak links in a…
In recent times whole-genome gene expression analysis has turned out to be a highly important tool to study the coordinated function of a very large number of genes within their corresponding cellular environment, especially in relation to…
Translation is one of the most fundamental processes in the biological cell. Because of the central role that translation plays across all domains of life, the enzyme that carries out this process, the ribosome, is required to process…
The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM),…
Proteins are polymers of amino acids. These macromolecules are synthesized by intracellular machines called ribosomes. Although the experimental investigation of protein synthesis has been a traditional area of research in molecular cell…
Protein expression levels optimize cell fitness: Too low an expression level of essential proteins will slow growth by compromising essential processes; whereas overexpression slows growth by increasing the metabolic load. This trade-off…
In this paper, we study the exploration / exploitation trade-off in cellular genetic algorithms. We define a new selection scheme, the centric selection, which is tunable and allows controlling the selective pressure with a single…
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…
In order to express specific genes at the right time, the transcription of genes is regulated by the presence and absence of transcription factor molecules. With transcription factor concentrations undergoing constant changes, gene…