Related papers: Detecting the Escherichia coli metabolic backbone
Metabolic networks are complex systems that comprise hundreds of chemical reactions which synthesize biomass molecules from chemicals in an organism's environment. The metabolic network of any one organism is encoded by a metabolic…
We study the transport of bacteria in a porous media modeled by a square channel containing one cylindrical obstacle via molecular dynamics simulations coupled to a lattice Boltzmann fluid. Our bacteria model is a rod-shaped rigid body…
We propose a discrete model to determine the metabolic scaling exponent based on Fibonacci growth patterns and discrete biological development phases. In contrast to continuous fractal models such as the West-Brown-Enquist (WBE) theory, the…
Cells generally convert nutrient resources to useful products via energy transduction. Accordingly, the thermodynamic efficiency of this conversion process is one of the most essential characteristics of living organisms. However, although…
Background: The rational identification of essential genes is a cornerstone of drug discovery, yet standard computational methods like Flux Balance Analysis (FBA) often struggle to produce accurate predictions in complex, redundant…
In this paper mathematical models for the evolutionary conserved Notch-Delta pathway are developed and analyzed in order to better understand how two neighboring biological cells can become different. We pursue a structure-based…
We provide evidence that the energy landscapes of folded proteins do not shift with temperature, but the onset of functional dynamics is associated with its effective sampling. The motion of the backbone is described by three distinct…
Plants rarely occur in isolated systems. Bacteria can inhabit either the endosphere, the region inside the plant root, or the rhizosphere, the soil region just outside the plant root. Our goal is to understand if using genomic data and…
Metabolic networks play a crucial role in biology since they capture all chemical reactions in an organism. While there are networks of high quality for many model organisms, networks for less studied organisms are often of poor quality and…
Metabolomics complements investigation of the genome, transcriptome, and proteome of an organism. Today, the vast majority of metabolites remain unknown, in particular for non-model organisms. Mass spectrometry is one of the predominant…
Organisms use specialized sensors to measure their environments, but the fundamental principles that determine their accuracy remain largely unknown. In Escherichia coli chemotaxis, we previously found that gradient-climbing speed is…
Evolution has provided many organisms with sophisticated sensory systems that enable them to respond to signals in their environment. The response frequently involves alteration in the pattern of movement, such as the chemokinesis of the…
C4 plants, such as maize, concentrate carbon dioxide in a specialized compartment surrounding the veins of their leaves to improve the efficiency of carbon dioxide assimilation. Nonlinear relationships between carbon dioxide and oxygen…
The chemotaxis pathway of the bacterium Rhodobacter sphaeroides has many similarities to the well-studied pathway in Escherichia coli. It exhibits robust adaptation and has several homologues of the latter's chemotaxis proteins. Recent…
Many methods have been developed for finding the commonalities between different organisms to study their phylogeny. The structure of metabolic networks also reveal valuable insights into metabolic capacity of species as well as into the…
The rise in the availability of bacterial genomes defines a need for synthesis: abstracting from individual taxa, to see larger patterns of bacterial lifestyles across systems. A key concept for such synthesis in ecology is the niche, the…
Phenotypic variation is a hallmark of cellular physiology. Metabolic heterogeneity, in particular, underpins single-cell phenomena such as microbial drug tolerance and growth variability. Much research has focussed on transcriptomic and…
The rapidly expanding market for regenerative medicines and cell therapies highlights the need to advance the understanding of cellular metabolisms and improve the prediction of cultivation production process for human induced pluripotent…
The chemotactic network of Escherichia coli has been studied extensively both biophysically and information-theoretically. Nevertheless, the connection between these two aspects is still elusive. In this work, we report such a connection by…
Intercellular exchange networks are essential for the adaptive capabilities of populations of cells. While diffusional exchanges have traditionally been difficult to map, recent advances in nanotechnology enable precise probing of exchange…