Quantifying the entropic cost of cellular growth control.

@article{DeMartino2017QuantifyingTE,
  title={Quantifying the entropic cost of cellular growth control.},
  author={Daniele De Martino and Fabrizio Capuani and Andrea De Martino},
  journal={Physical review. E},
  year={2017},
  volume={96 1-1},
  pages={
          010401
        }
}
Viewing the ways a living cell can organize its metabolism as the phase space of a physical system, regulation can be seen as the ability to reduce the entropy of that space by selecting specific cellular configurations that are, in some sense, optimal. Here we quantify the amount of regulation required to control a cell's growth rate by a maximum-entropy approach to the space of underlying metabolic phenotypes, where a configuration corresponds to a metabolic flux pattern as described by… 

Figures from this paper

Statistical mechanics for metabolic networks during steady state growth
TLDR
A generalization of flux balance analysis to single cells based on maximum entropy modeling is applied, and it is found that growth rate fluctuations of E. coli reflect metabolic flux variability and growth sub-optimality, in turn highlighting information costs for growth optimization.
Maximum entropy and population heterogeneity in continuous cell cultures
TLDR
The maximum entropy principle is used to model the phenotypic distribution of cells in a chemostat as a function of the dilution rate and discusses several consequences of heterogeneity, such as: qualitative changes in the dynamical landscape of the system, increasing concentrations of byproducts that vanish in the homogeneous case, and larger population sizes.
The Empirical Fluctuation Pattern of E. coli Division Control
TLDR
The linear-response framework correctly predicts consistency relations between a priori independent experimental measurements, which confirms its validity, and defines relevant constraints that any theoretical description should reproduce.
Initial cell density encodes proliferative potential in cancer cell populations
TLDR
By following the growth of hundreds of populations of cancer cells, it is found that the time they need to adapt to the environment decreases as the initial cell density increases, and the population growth rate shows a maximum at intermediate initial densities.
Inoculum-density dependent growth reveals inherent cooperative effects and stochasticity in cancer cell cultures
TLDR
The results support the idea that cell cultures can preserve a memory of the initial condition, possibly via contact interactions or through metabolic coupling.
Probing single cell fermentation flux and intercellular exchange networks via pH-microenvironment sensing and inverse modeling
TLDR
A method to quantify single cell fermentation fluxes over time by integrating high-resolution pH microenvironment sensing via ratiometric nanofibers with constraint-based inverse modeling is devised, which finds that the proton trafficking underlying bulk acidification is strongly heterogeneous, with maximal single cell fluxes exceeding typical values by up to 3 orders of magnitude.
Exploration-exploitation tradeoffs dictate the optimal distributions of phenotypes for populations subject to fitness fluctuations.
TLDR
Analytical insight is obtained into the limiting cases of very fast and very slow exploration rates by directly linking population growth to the features of the environment.
Genome heterogeneity drives the evolution of species
TLDR
Heterogeneity together with spatial correlations is responsible for spontaneous sympatric speciation, and it is proved that the relevance of each gene in the manifestation of the phenotype is a key feature for evolution.
Information costs in the control of protein synthesis.
TLDR
This analysis, using data from E. coli, indicates that reasonable synthesis rates are consistent only with rather low entropies, so that the cell's regulatory mechanisms must encode a large amount of information about the "correct" tRNA abundances.
Entropy evaluation sheds light on ecosystem complexity
TLDR
A minimal ecosystem on a lattice in which two species struggle for survival is studied, using the entropy definition from thermodynamics to assess ecosystem stability and sheds new light on three different phase transitions the system undergoes by tuning animal phenotypes.
...
...

References

SHOWING 1-10 OF 16 REFERENCES
Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli.
TLDR
This work shows that empirical growth rate distributions recently obtained in experiments at single-cell resolution can be explained in terms of a trade-off between the higher fitness of fast-growing phenotypes and the higher entropy of slow-growing ones.
Individuality and universality in the growth-division laws of single E. coli cells.
TLDR
It is found that scaling relations based on the means collapse both size and doubling-time distributions across different conditions and give a rationale for the universal body-size distributions observed in microbial ecosystems across many microbial species, presumably dividing with multiple mechanisms.
Quantitative constraint-based computational model of tumor-to-stroma coupling via lactate shuttle
TLDR
The characterization obtained by tuning the aberrant cell’s demand for ATP, amino-acids and fatty acids and/or the imbalance in nutrient partitioning provides quantitative support to the idea that synergistic multi-cell effects play a central role in cancer sustainment.
Information and fitness
TLDR
Estimates based on recent experiments suggest that the minimum information required for reasonable growth rates is close to the maximum information that can be conveyed through biologically realistic regulatory mechanisms.
Constrained Allocation Flux Balance Analysis
TLDR
Constrained Allocation Flux Balance Analysis, CAFBA, is introduced, in which the biosynthetic costs associated to growth are accounted for in an effective way through a single additional genome-wide constraint.
A dynamic approach to predicting bacterial growth in food.
Very slow growth of Escherichia coli
TLDR
In both phases 2 and 3, orcinol, diphenylamine, and Lowry reactive materials were secreted at near-constant rates such that over 50% as much biosynthetic mass was secreted as was retained by the cells.
Maximum entropy models for antibody diversity
TLDR
The results suggest that antibody diversity is not limited by the sequences encoded in the genome and may reflect rapid adaptation to antigenic challenges.
...
...