Draft:ATM-Wip1 (Cancer) Oscillator Model

Submission declined on 7 July 2024 by DoubleGrazing (talk).

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Declined by DoubleGrazing 3 months ago. Last edited by DoubleGrazing 3 months ago. Reviewer: Inform author.

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Comment: Also noting that the 'Repertoire of Dynamical Behaviors' is empty. If this is intended to be populated, please do so before resubmitting; otherwise remove it. DoubleGrazing (talk) 08:17, 7 July 2024 (UTC)

Comment: This is clearly written by subject-matter experts for subject-matter experts. Bear in mind that Wikipedia is a general encyclopaedia, and many of our readers are looking for information on topics which they are not experts in. This would benefit from more elaboration on the context, significance of the subject, and also explanations and/or explanatory wikilinks for some of the terminology used.
I'm also adding notability as a decline reason. I note that two of the four sources cited appear to be co-authored by the author of this draft. While citing one's own works is allowed, this shouldn't be done to an excessive degree, to avoid bias and ensure balance of views. Moreover, due to the way the offline sources are cited, it isn't clear whether, and to what extent, they discuss the subject of this draft specifically. It would help if online versions of those sources could be cited instead, if available, or else further details including page numbers, possible quotes, etc. included in the citations (see WP:OFFLINE for advice on citing offline sources). DoubleGrazing (talk) 08:17, 7 July 2024 (UTC)

The ATM-(p53)-Wip1 oscillator is a parametric relaxation type of oscillator model with polynomial and biologically-interpretable terms introduced to model the topological structure constructed by bistable dynamics of ATM protein and a long negative feedback loop mediated by Wip1 (the product of PPM1D gene) protein.^[1]. The ATM-Wip1 topological structure resembles the frustrated bistable unit that is known to produce oscillations as well as other modes of dynamics^[2]

Model Equations

$dx/dt=-x(rx^{2}-r(a+b)x+ab+cy-rd)/\tau _{1}$

$dy/dt=(z+mx-ny)/\tau _{2}$

where

$x$ represents ATM protein concentration levels in arbitrary units.
$y$ represents Wip1 protein concentration levels in arbitrary units.

p53 protein (concentration) levels are not introduced as a dynamical variable; instead, it is assumed to follow ATM dynamics proportionally and algebraically under the quasy-steady state assumption for p53-Mdm2 interaction.

The constant parameters of the model are $a,b,c,d,n,z,\tau _{1},\tau _{2}$ and they take only positive values. The control parameters are $r$ and $m$ . $r$ represents the damage severity and is restricted to $0<r<1$ , with 0 representing no damage and 1 representing the most severe situation. $m$ represents inversely the duration of the DNA repair and is controlled by proapoptotic genes via mechanisms similar to the "death by integration.^[3]". Normally, $m$ stays at a high value indicated as $m_{0}$ and decreased towards 0 as the repair continues ^[4]

Repertoire of Dynamical Behaviors

References

^ Demirkıran, Gökhan, Güleser Kalaycı Demir, and Cüneyt Güzeliş. "Two‐dimensional polynomial type canonical relaxation oscillator model for p53 dynamics." IET Systems Biology 12, no. 4 (2018): 138-147.
^ Krishna, S., Semsey, S., & Jensen, M. H. (2009). Frustrated bistability as a means to engineer oscillations in biological systems. Physical biology, 6(3), 036009.
^ Li, Zhiyuan, Ming Ni, Jikun Li, Yuping Zhang, Qi Ouyang, and Chao Tang. "Decision making of the p53 network: Death by integration." Journal of theoretical biology 271, no. 1 (2011): 205-211.
^ DEMİRKIRAN, Gökhan, Güleser KALAYCI DEMİR, and Cüneyt Güzeliş. "A canonical 3-D P53 network model that determines cell fate by counting pulses." Electrica 18, no. 2 (2018): 284-291.

[Demirkıran1-1] Demirkıran, Gökhan, Güleser Kalaycı Demir, and Cüneyt Güzeliş. "Two‐dimensional polynomial type canonical relaxation oscillator model for p53 dynamics." IET Systems Biology 12, no. 4 (2018): 138-147.

[2] Krishna, S., Semsey, S., & Jensen, M. H. (2009). Frustrated bistability as a means to engineer oscillations in biological systems. Physical biology, 6(3), 036009.

[3] Li, Zhiyuan, Ming Ni, Jikun Li, Yuping Zhang, Qi Ouyang, and Chao Tang. "Decision making of the p53 network: Death by integration." Journal of theoretical biology 271, no. 1 (2011): 205-211.

[4] DEMİRKIRAN, Gökhan, Güleser KALAYCI DEMİR, and Cüneyt Güzeliş. "A canonical 3-D P53 network model that determines cell fate by counting pulses." Electrica 18, no. 2 (2018): 284-291.

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