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Classification of infinitesimal homeostasis in four-node input-output networks. (English) Zbl 1496.92025

The paper presents some new conclusions based on recent work from Y. Wang et al. [J. Math. Biol. 82, No. 7, Paper No. 62, 43 p. (2021; Zbl 1467.92083)], describing in detail the twenty types of 4-node core networks and 17 types of infinitesimal homeostasis in 4 node core networks. The paper starts with an introduction that recapitulates the core concepts on input-output functions and infinitesimal homeostasis, on the definition of the homeostasis matrix, and on core networks and core equivalence classes, the latter described in detail with numerous examples. The introduction concludes with an overview of infinitesimal homeostasis types. Next, the authors present biochemical examples that support the subsequent enumeration of four-node core equivalent classes. The paper closes on the classification of infinitesimal homeostasis in four-node input-output networks on degree 1 (no cycle appendage homeostasis, null degradation and structural homeostasis, Haldane) and degree 2 (structural homeostasis, feed-forward loop and no cycle appendage homeostasis). All examples are thoroughly presented and discussed; the results are backed up with full proofs and richly decorated with references.

MSC:

92C42 Systems biology, networks

Citations:

Zbl 1467.92083
Full Text: DOI

References:

[1] Antoneli, F.; Golubitsky, M.; Stewart, I., Homeostasis in a feed forward loop gene regulatory network motif, J Theor Biol, 445, 103-109 (2018) · Zbl 1397.92179 · doi:10.1016/j.jtbi.2018.02.026
[2] Andrade PPA, Madeira JLO, Antoneli F Infinitesimal homeostasis of intracellular copper regulation. In preparation
[3] Best, J.; Nijhout, HF; Reed, M., Homeostatic mechanisms in dopamine synthesis and release: a mathematical model, Theor Biol Med Model, 6, 21 (2009) · doi:10.1186/1742-4682-6-21
[4] Golubitsky, M.; Stewart, I., Nonlinear dynamics of networks: the groupoid formalism, Bull Am Math Soc, 43, 305-364 (2006) · Zbl 1119.37036 · doi:10.1090/S0273-0979-06-01108-6
[5] Golubitsky, M.; Stewart, I., Homeostasis, singularities and networks, J Math Biol, 74, 387-407 (2017) · Zbl 1369.92040 · doi:10.1007/s00285-016-1024-2
[6] Golubitsky, M.; Stewart, I., Homeostasis with multiple inputs, SIAM J Appl Dyn Syst, 17, 2, 1816-1832 (2018) · Zbl 1395.92067 · doi:10.1137/17M115147X
[7] Golubitsky, M.; Wang, Y., Infinitesimal homeostasis in three-node input-output networks, J Math Biol, 80, 1163-1185 (2020) · Zbl 1436.92009 · doi:10.1007/s00285-019-01457-x
[8] Harary, F.; Palmer, EM, Graphical enumeration, 241 (1973), New York: Academic Press, New York · Zbl 0266.05108
[9] Huang Z (2021) A classification of homeostasis types in four-node input-output networks. The Ohio State University. Department of Mathematics Undergraduate Research Theses
[10] Ma, W.; Trusina, A.; El-Samad, H.; Lim, WA; Tang, C., Defining network topologies that can achieve biochemical adaptation, Cell, 138, 760-773 (2009) · doi:10.1016/j.cell.2009.06.013
[11] Mulukutla, BC; Yongky, A.; Daoutidis, P.; Hu, W-S, Bistability in glycolysis pathway as a physiological switch in energy metabolism, PLoS ONE, 9, 6 (2014) · doi:10.1371/journal.pone.0098756
[12] Reed, M.; Best, J.; Golubitsky, M.; Stewart, I.; Nijhout, HF, Analysis of homeostatic mechanisms in biochemical networks, Bull Math Biol, 79, 9, 1-24 (2017) · Zbl 1382.92131
[13] Wang Y, Huang Z, Antoneli F, Golubitsky M (2021) The structure of infinitesimal homeostasis in input-output networks. J Math Biol 82:62. doi:10.1007/s00285-021-01614-1 · Zbl 1467.92083
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