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Systematic characterization of maturation time of fluorescent proteins in living cells
Slow maturation time of fluorescent proteins limits accurate measurement of rapid gene expression dynamics and effectively reduces fluorescence signal in growing cells. We used high-precision time-lapse microscopy to characterize, at two different temperatures in E. coli, the maturation kinetics of 50 FPs that span the visible spectrum. We identified fast-maturing FPs that yield the highest signal-to-noise ratio and temporal resolution in individual growing cells
Critical Dynamics in Genetic Regulatory Networks: Examples from Four Kingdoms
The coordinated expression of the different genes in an organism is essential to sustain functionality under the random external perturbations to which the organism might be subjected. To cope with such external variability, the global dynamics of the genetic network must possess two central properties. (a) It must be robust enough as to guarantee stability under a broad range of external conditions, and (b) it must be flexible enough to recognize and integrate specific external signals that may help the organism to change and adapt to different environments. This compromise between robustness and adaptability has been observed in dynamical systems operating at the brink of a phase transition between order and chaos. Such systems are termed critical. Thus, criticality, a precise, measurable, and well characterized property of dynamical systems, makes it possible for robustness and adaptability to coexist in living organisms. In this work we investigate the dynamical properties of the gene transcription networks reported for S. cerevisiae, E. coli, and B. subtilis, as well as the network of segment polarity genes of D. melanogaster, and the network of flower development of A. thaliana. We use hundreds of microarray experiments to infer the nature of the regulatory interactions among genes, and implement these data into the Boolean models of the genetic networks. Our results show that, to the best of the current experimental data available, the five networks under study indeed operate close to criticality. The generality of this result suggests that criticality at the genetic level might constitute a fundamental evolutionary mechanism that generates the great diversity of dynamically robust living forms that we observe around us
Fig. 2 Data
Fig. 2 Data from "Systematic characterization of maturation time of fluorescent proteins in living cells
SFig.16 Data
SFig.16 Data from "Systematic characterization of maturation time of fluorescent proteins in living cells
Flow Cytometry Data
Flow Cytometry data from "Systematic characterization of maturation time of fluorescent proteins in living cells
Software to reproduce Fig.2 and SFig.16
Software to reproduce Fig.2 and SFig.16 from "Systematic characterization of maturation time of fluorescent proteins in living cells".
This repository contains (i) Matlab functions to generate the panels in Fig.2 and SFig. 16 that contain data, (ii)a ReadMe file that describes how to run the programs
Maturation Time Experiments Single-Cell Data
Maturation Time Experiments Single-Cell Data from "Systematic characterization of maturation time of fluorescent proteins in living cells
Maturation Time Experiments Single-Cell Data, Codon Optimized and 2nd Valine variants
Single cell data of codon optimized and 2nd valine variants from "Systematic characterization of maturation time of fluorescent proteins in living cells