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Limit cycles in models of circular gene networks regulated by negative feedback loops

Vitaly A. Likhoshvai, Vladimir P. Golubyatnikov, Tamara M. Khlebodarova
2020 BMC Bioinformatics  
Results We study dynamical properties of models of simplest circular gene networks regulated by negative feedback mechanisms.  ...  Conclusions The modeling results demonstrate that non-stationary dynamics in the models of circular gene networks with negative feedback loops is achieved by a high degree of non-linearity of the mechanism  ...  About this supplement This article has been published as part of BMC Bioinformatics Volume 21 Supplement 11, 2020: Selected Topics in "Systems Biology and Bioinformatics"-2019: bioinformatics.  ... 
doi:10.1186/s12859-020-03598-z pmid:32921311 fatcat:2h2m4mydwbdlhdktyo5ipis3xe

Boolean Dynamics of Biological Networks with Multiple Coupled Feedback Loops

Yung-Keun Kwon, Kwang-Hyun Cho
2007 Biophysical Journal  
We show that networks have a larger proportion of basins corresponding to fixed-point attractors as they have more coupled positive feedback loops, and a larger proportion of basins for limit-cycle attractors  ...  as they have more coupled negative feedback loops.  ...  Then, a circular chain of relationships (a feedback loop) appears in the network. The sign of a feedback loop is easily determined by the parity of the number of negative relationships involved.  ... 
doi:10.1529/biophysj.106.097097 pmid:17259267 pmcid:PMC1831709 fatcat:gifqfip6kjgotchko2b5bwdwi4

The Network of Time: Understanding the Molecular Circadian System

Till Roenneberg, Martha Merrow
2003 Current Biology  
These new results are moving the model paradigm away from a simple negative feedback loop to a molecular network.  ...  conditions and in different tissues; and from the discovery and analysis of a growing number of additional clock genes.  ...  Our work is supported by the Eppendorf Company, Hamburg, by the Deutsche Forschungsgemeinschaft, the Dr.-Meyer-Struckmann-Stiftung, and by BrainTime from the European Commission of the European Union.  ... 
doi:10.1016/s0960-9822(03)00124-6 pmid:12620213 fatcat:6v7f5lyhdjgdda6draprwehgpa

Analytic theory of stochastic oscillations in single-cell gene expression [article]

Chen Jia, Michael Q. Zhang, Hong Qian
2019 arXiv   pre-print
Single-cell stochastic gene expression, with gene state switching, transcription, translation, and negative feedback, can exhibit oscillatory kinetics that is statistically characterized in terms of a  ...  Using a solvable model, we illustrate the oscillation as a stochastic circulation along a hysteresis loop.  ...  Zhang was supported by NIH Grants MH102616 and MH109665 and also by NSFC Grants 31671384 and 91329000.  ... 
arXiv:1909.09769v1 fatcat:z3k4f367ebfefmif4avcl4qotu

Co-existing feedback loops generate tissue-specific circadian rhythms [article]

Jan Patrick Pett, Matthew Kondoff, Grigory Bordyugov, Achim Kramer, Hanspeter Herzel
2018 bioRxiv   pre-print
Gene regulatory feedback loops generate autonomous circadian rhythms in mammalian tissues. The well-studied core clock network contains many negative and positive regulations.  ...  Self-inhibitions of Per and Cry genes are characteristic for models of SCN clocks, while in liver models many loops act in synergy and are connected by a repressilator motif.  ...  Conflict of Interest The authors declare that they have no conflict of interest. References  ... 
doi:10.1101/304451 fatcat:6eohuzlbanheplclrr52lyjh6m

Mean-field versus stochastic models for transcriptional regulation

R. Blossey, C. V. Giuraniuc
2008 Physical Review E  
We introduce a minimal model description for the dynamics of transcriptional regulatory networks.  ...  Two examples are addressed in detail: the repressilator, a transcriptional clock based on a three-gene network realized experimentally in E. coli, and a bistable two-gene circuit under external driving  ...  Circuits in (2): a linear array and a linear array with a head feedback: hence a mixture of a circular and a linear circuit.The autoinhibitory loop neg(a; a) is shown inFig 2.1.  ... 
doi:10.1103/physreve.78.031909 pmid:18851067 fatcat:j6kkgj3pofdvlj7ko3gh4qhlrq

Enriching for direct regulatory targets in perturbed gene-expression profiles

Susannah G Tringe, Andreas Wagner, Stephanie W Ruby
2004 Genome Biology  
The updated algorithm can process networks containing feedback loops, incorporate positive and negative regulatory relationships during network reconstruction, and utilize data from double mutants to resolve  ...  Here we build on a previously proposed algorithm to infer direct regulatory relationships using gene-expression profiles from cells in which individual genes are deleted or overexpressed.  ...  Gilchrist for critical reading of the manuscript, and P. Renaud for hosting S.L.G. in his lab during part of this project. This work was supported by the W. M. Keck Foundation.  ... 
doi:10.1186/gb-2004-5-4-r29 pmid:15059262 pmcid:PMC395788 fatcat:jj2by66qpjbkbmwfkx55gtp6hu

From Endogenous to Synthetic microRNA-Mediated Regulatory Circuits: An Overview

Elsi Ferro, Chiara Enrico Bena, Silvia Grigolon, Carla Bosia
2019 Cells  
MicroRNAs are short non-coding RNAs that are evolutionarily conserved and are pivotal post-transcriptional mediators of gene regulation.  ...  Together with transcription factors and epigenetic regulators, they form a highly interconnected network whose building blocks can be classified depending on the number of molecular species involved and  ...  PPARG positively regulates adipogenesis, while SCAMP3 is an endogenous limiter of adipogenesis driven by PPARG. In other words, SCAMP3 negatively regulates the process.  ... 
doi:10.3390/cells8121540 pmid:31795372 pmcid:PMC6952906 fatcat:7inhpxhqt5cpzb5t5g4dkvlvni

Mathematical Modelling of p53 Signalling during DNA Damage Response: A Survey

Ján Eliaš, Cicely K. Macnamara
2021 International Journal of Molecular Sciences  
We review the standard modelling approaches used in the field categorising them into three types: time delay models, spatial models and coupled negative-positive feedback models, providing sample model  ...  In this review we survey and distill the extensive literature of mathematical models of p53.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms221910590 pmid:34638930 pmcid:PMC8508851 fatcat:kslggk2grzdvfptpm2lclierii

Stochastic models of cellular circadian rhythms in plants help to understand the impact of noise on robustness and clock structure

Maria L. Guerriero, Ozgur E. Akman, Gerben van Ooijen
2014 Frontiers in Plant Science  
that coordinates the expression of specific clock genes in a circadian rhythm reflecting the 24-h day/night cycle.  ...  Circadian clocks exhibit stochastic noise due to the low copy numbers of clock genes and the consequent cell-to-cell variation: this intrinsic noise plays a major role in circadian clocks by inducing more  ...  For example, the circadian clock network of the model fungal species Neurospora crassa is built around a central negative feedback loop augmented by an interlocking positive loop (Baker et al., 2012)  ... 
doi:10.3389/fpls.2014.00564 pmid:25374576 pmcid:PMC4204444 fatcat:ie4i5wbz6badfpqjsmjr2u4t4q

Analysis of feedback loops and robustness in network evolution based on Boolean models

Yung-Keun Kwon, Kwang-Hyun Cho
2007 BMC Bioinformatics  
Through simulations using Boolean network models, we found that preferential attachment increases the number of coupled feedback loops in the course of network evolution.  ...  Conclusion: The presented analysis demonstrates that coupled feedback loops may play an important role in network evolution to acquire robustness.  ...  However, the transcriptional network of mRNAs for Notch signaling molecules shows an oscillation with a 2-h cycle by Hes1 transcription [30] and this corresponds to a limit-cycle attractor.  ... 
doi:10.1186/1471-2105-8-430 pmid:17988389 pmcid:PMC2249609 fatcat:yknr27c45vgztfacx4phaenmti

Switching between oscillations and homeostasis in competing negative and positive feedback motifs

Weihan Li, Sandeep Krishna, Simone Pigolotti, Namiko Mitarai, Mogens H. Jensen
2012 Journal of Theoretical Biology  
We analyze a class of network motifs in which a short, two-node positive feed- back motif is inserted in a three-node negative feedback loop.  ...  We find that this switching also occurs in previous models of circadian clocks that use this combination of positive and negative feedback.  ...  This work is supported by the Danish National Research Foundation.  ... 
doi:10.1016/j.jtbi.2012.04.011 pmid:22762992 fatcat:vgvoby3kjnf7xid3v5enf7pc7y

Are There Biomimetic Lessons from Genetic Regulatory Networks for Developing a Lunar Industrial Ecology?

Alex Ellery
2021 Biomimetics  
captured by traditional electrical engineering design with emphasis on feedforward and feedback loops to implement robustness.  ...  We then examine genetic regulatory networks and their application in the biological cell cycle.  ...  Conflicts of Interest: The author declares no conflict of interest.  ... 
doi:10.3390/biomimetics6030050 fatcat:yglsxb2mzzc75bbiqlx2rlzkha

Quantitative analysis of robustness and fragility in biological networks based on feedback dynamics

Yung-Keun Kwon, Kwang-Hyun Cho
2008 Computer applications in the biosciences : CABIOS  
Results: Through extensive computational experiments, we found that networks with a larger number of positive feedback loops and a smaller number of negative feedback loops are likely to be more robust  ...  It is still, however, not clear how a number of coupled feedback loops actually affect the robustness of large complex biological networks.  ...  Feedback loops in robust networks We examine the distributions of the NuFBL, the number of positive feedback loops (NuFBL þ ) and the number of negative feedback loops (NuFBL À ) in random networks and  ... 
doi:10.1093/bioinformatics/btn060 pmid:18285369 fatcat:ncldrvfng5cwnl7zhp7n7uztta

The Complex Interaction between P53 and miRNAs Joins New Awareness in Physiological Stress Responses

Camilla Capaccia, Silvana Diverio, Danilo Zampini, Gabriella Guelfi
2022 Cells  
In physiological stress generated by any external or internal condition that challenges cell homeostasis, P53 exerts its function as a transcription factor for target genes or by regulating the expression  ...  In turn, P53 controls the expression level of miRNAs targeted by P53 through the regulation of their transcription or biogenesis.  ...  in this review.  ... 
doi:10.3390/cells11101631 pmid:35626668 pmcid:PMC9139524 fatcat:afqzz3yekbebxmorxcivf7lhuy
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