scholarly journals On the principles of cell decision-making: intracellular coupling improves cell responses fidelity of noisy signals

2017 ◽  
Author(s):  
Andreas I. Reppas ◽  
Eduard A. Jorswieck ◽  
Haralampos Hatzikirou
Keyword(s):  
Decision Making ◽  
Cell Fate ◽  
Cell Responses ◽  
Intracellular Signalling Pathway ◽  
Noisy Signals ◽  
Coupling Principle ◽  
Fate Decision ◽  
Influence Of Noise ◽  
Pathway Networks ◽  
Phenotypic Responses

Reliability of cell fate decision-making is crucial to biological development. Until today it has not been clear what are biology’s design principles that allow for reliable cell decision making under the influence of noise. Here, we attempt to answer this question by drawing an analogy between cell decision-making and information theory. We show that coupling of intracellular signalling pathway networks makes cell phenotypic responses reliable for noisy signals. As a proof of concept, we show how cis-interaction of the Notch-Delta pathway allows for increased performance under the influence of noise. Interestingly, in this case, the coupling principle leads to an efficient energy management. Finally, our postulated principle offers a compelling argument why cellular encoding is organized in a non-linear and non-hierarchical manner.

scholarly journals A hydraulic instability drives the cell death decision in the nematode germline

2020 ◽  
Author(s):  
N. T. Chartier ◽  
A. Mukherjee ◽  
J. Pfanzelter ◽  
S. Fürthauer ◽  
B. T. Larson ◽  
...  
Keyword(s):  
Decision Making ◽  
Cell Death ◽  
Cell Fate ◽  
Germ Cells ◽  
Cell Fate Decision ◽  
Homogeneous Population ◽  
C Elegans ◽  
The Common ◽  
Fate Decision ◽  
Cell Volumes

AbstractOocytes are large and resourceful. During oogenesis some germ cells grow, typically at the expense of others that undergo apoptosis. How germ cells are selected to live or die out of a homogeneous population remains unclear. Here we show that this cell fate decision in C. elegans is mechanical and related to tissue hydraulics. Germ cells become inflated when the pressure inside them is lower than in the common cytoplasmic pool. This condition triggers a hydraulic instability which amplifies volume differences and causes some germ cells to grow and others to shrink. Shrinking germ cells are extruded and die, as we demonstrate by reducing germ cell volumes via thermoviscous pumping. Together, this reveals a robust mechanism of mechanochemical cell fate decision making in the germline.

scholarly journals Wnt/B-catenin signalling facilitates cell fate decision making in the early mouse embryo

2017 ◽  
Vol 145 ◽  
pp. S159 ◽  
Author(s):  
Elena Corujo-Simon ◽  
Joaquin Lilao-Garzon ◽  
Silvia Muñoz-Descalzo
Keyword(s):  
Decision Making ◽  
Cell Fate ◽  
Mouse Embryo ◽  
Cell Fate Decision ◽  
Early Mouse Embryo ◽  
Fate Decision ◽  
Early Mouse

scholarly journals Uncertainty in cell fate decision making: Lessons from potential landscapes of bifurcation systems

2021 ◽  
Author(s):  
Anissa Guillemin ◽  
Elisabeth Roesch ◽  
Michael P.H. Stumpf
Keyword(s):  
Decision Making ◽  
Cell Fate ◽  
Qualitative Change ◽  
Pictorial Representation ◽  
Cell Fate Decision ◽  
Ample Evidence ◽  
Molecular Noise ◽  
Intrinsic Complexity ◽  
Fate Decision ◽  
The Stability

AbstractCell fate decision making is known to be a complex process and is still far from being understood. The intrinsic complexity, but also features such as molecular noise represent challenges for modelling these systems. Waddington’s epigenetic landscape has become the overriding metaphor for developmental processes: it both serves as pictorial representation, and can be related to mathematical models. In this work we investigate how the landscape is affected by noise in the underlying system. Specifically, we focus on those systems where minor changes in the parameters cause major changes in the stability properties of the system, especially bifurcations. We analyse and quantify the changes in the landscape’s shape as the effects of noise increase. We find ample evidence for intricate interplay between noise and dynamics which can lead to qualitative change in a system’s dynamics and hence the corresponding landscape. In particular, we find that the effects can be most pronounced in the vicinity of the bifurcation point of the underlying deterministic dynamical systems, which would correspond to the cell fate decision event in cellular differentiation processes.

scholarly journals Quantifying Waddington landscapes and paths of non-adiabatic cell fate decisions for differentiation, reprogramming and transdifferentiation

2013 ◽  
Vol 10 (89) ◽  
pp. 20130787 ◽  
Author(s):  
Chunhe Li ◽  
Jin Wang
Keyword(s):  
Decision Making ◽  
Stem Cell ◽  
Cell Fate ◽  
Intermediate State ◽  
Regulatory Networks ◽  
Experimental Studies ◽  
Cell Fate Decision ◽  
Cell Fate Decisions ◽  
Decision Making Processes ◽  
Fate Decision

Cellular differentiation, reprogramming and transdifferentiation are determined by underlying gene regulatory networks. Non-adiabatic regulation via slow binding/unbinding to the gene can be important in these cell fate decision-making processes. Based on a stem cell core gene network, we uncovered the stem cell developmental landscape. As the binding/unbinding speed decreases, the landscape topography changes from bistable attractors of stem and differentiated states to more attractors of stem and other different cell states as well as substates. Non-adiabaticity leads to more differentiated cell types and provides a natural explanation for the heterogeneity observed in the experiments. We quantified Waddington landscapes with two possible cell fate decision mechanisms by changing the regulation strength or regulation timescale (non-adiabaticity). Transition rates correlate with landscape topography through barrier heights between different states and quantitatively determine global stability. We found the optimal speeds of these cell fate decision-making processes. We quantified biological paths and predict that differentiation and reprogramming go through an intermediate state (IM1), whereas transdifferentiation goes through another intermediate state (IM2). Some predictions are confirmed by recent experimental studies.

scholarly journals Cell Fate Decision Making through Oriented Cell Division

2015 ◽  
Vol 3 (4) ◽  
pp. 129-157 ◽  
Author(s):  
Evan Dewey ◽  
Danielle Taylor ◽  
Christopher Johnston
Keyword(s):  
Decision Making ◽  
Cell Division ◽  
Cell Fate ◽  
Cell Fate Decision ◽  
Oriented Cell Division ◽  
Fate Decision

scholarly journals Decoding the mechanisms underlying cell-fate decision-making during stem cell differentiation by random circuit perturbation

2020 ◽  
Vol 17 (169) ◽  
pp. 20200500
Author(s):  
Bin Huang ◽  
Mingyang Lu ◽  
Madeline Galbraith ◽  
Herbert Levine ◽  
Jose N. Onuchic ◽  
...  
Keyword(s):  
Decision Making ◽  
Stem Cells ◽  
Stem Cell ◽  
Cell Fate ◽  
Expression Patterns ◽  
Stem Cell Differentiation ◽  
Computational Method ◽  
Embryonic Cells ◽  
Fate Decision ◽  
Stem Cell Populations

Stem cells can precisely and robustly undergo cellular differentiation and lineage commitment, referred to as stemness. However, how the gene network underlying stemness regulation reliably specifies cell fates is not well understood. To address this question, we applied a recently developed computational method, ra ndom ci rcuit pe rturbation (RACIPE), to a nine-component gene regulatory network (GRN) governing stemness, from which we identified robust gene states. Among them, four out of the five most probable gene states exhibit gene expression patterns observed in single mouse embryonic cells at 32-cell and 64-cell stages. These gene states can be robustly predicted by the stemness GRN but not by randomized versions of the stemness GRN. Strikingly, we found a hierarchical structure of the GRN with the Oct4/Cdx2 motif functioning as the first decision-making module followed by Gata6/Nanog. We propose that stem cell populations, instead of being viewed as all having a specific cellular state, can be regarded as a heterogeneous mixture including cells in various states. Upon perturbations by external signals, stem cells lose the capacity to access certain cellular states, thereby becoming differentiated. The new gene states and key parameters regulating transitions among gene states proposed by RACIPE can be used to guide experimental strategies to better understand differentiation and design reprogramming. The findings demonstrate that the functions of the stemness GRN is mainly determined by its well-evolved network topology rather than by detailed kinetic parameters.

Noise and the molecular processes underlying cell fate decision-making

2021 ◽  
Vol 18 (1) ◽  
pp. 011002
Author(s):  
Anissa Guillemin ◽  
Michael P H Stumpf
Keyword(s):  
Decision Making ◽  
Cell Fate ◽  
Molecular Processes ◽  
Cell Fate Decision ◽  
Fate Decision
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