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Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology

Stefano Ciliberti, Olivier C. Martin, Andreas Wagner
2007 PLoS Computational Biology  
Citation: Ciliberti S, Martin OC, Wagner A (2007) Robustness can evolve gradually in complex regulatory gene networks with varying topology. PLoS Comput Biol 3(2): e15.  ...  Remarkably, this graph is connected and can be easily traversed by gradual changes of network topologies. Thus, robustness is an evolvable property.  ...  This means that nearly all viable networks can evolve toward greater robustness through gradual changes in topology.  ... 
doi:10.1371/journal.pcbi.0030015 pmid:17274682 pmcid:PMC1794322 fatcat:cobelscafbhhlihtq2knsllhqy

Evolving Robust Gene Regulatory Networks

Nasimul Noman, Taku Monjo, Pablo Moscato, Hitoshi Iba, Alberto de la Fuente
2015 PLoS ONE  
The robustness of gene regulatory networks (GRNs) is ascribed chiefly to the underlying topology.  ...  A recent study shows that Darwinian evolution can gradually develop higher topological robustness.  ...  Yoshihiko Hasegawa for providing us with the code for phase response analysis as well as for commenting on the manuscript. Author Contributions  ... 
doi:10.1371/journal.pone.0116258 pmid:25616055 pmcid:PMC4304830 fatcat:nzzzbfj5p5ctfmkdotjjf5w64a

Circuit topology and the evolution of robustness in two-gene circadian oscillators

A. Wagner
2005 Proceedings of the National Academy of Sciences of the United States of America  
The regulatory interlocking of several oscillating gene products in biological circadian oscillators may exist because it provides robustness. complexity ͉ gene networks This paper was submitted directly  ...  If so, can a process of gradual molecular evolution find highly robust topologies when starting from less robust topologies?  ...  Variation in the number of parameters alone can thus not explain variation in robustness. Robust Topologies Are Connected in a Topology Network.  ... 
doi:10.1073/pnas.0501094102 pmid:16087882 pmcid:PMC1183445 fatcat:5zogj3tuo5flfd5v5odl4jlfte

Evolvable network architectures

Constantine Dovrolis, J. Todd Streelman
2010 Computer communication review  
In this paper, we review some relevant ideas about evolvability from the biological literature. We examine the role of robustness and modularity in evolution, and their relation with evolvability.  ...  A key question then is: what makes a network architecture evolvable? What determines the ability of a network architecture to evolve as its environment changes?  ...  It has been observed in Gene Regulatory Networks, metabolic networks, protein-protein interactions networks, and networks of species in ecosystems.  ... 
doi:10.1145/1764873.1764886 fatcat:lxnnrei2dvhifdpu35rv7pnndu

Generation of oscillating gene regulatory network motifs

M. van Dorp, B. Lannoo, E. Carlon
2013 Physical Review E  
USA 101, 580 (2004)], we generated small gene regulatory networks in which the concentration of a target protein oscillates in time.  ...  Furthermore, we show that the set of evolved networks can serve as a database of models whose behavior can be compared to experimentally observed oscillations.  ...  This corresponds to the network shown in Fig. 5(g) , which is a two gene oscillator with no regulatory interactions.  ... 
doi:10.1103/physreve.88.012722 pmid:23944505 fatcat:z45ut5wigjf5xksvbnb3lka4da

Weather and Seasons Together Demand Complex Biological Clocks

Carl Troein, James C.W. Locke, Matthew S. Turner, Andrew J. Millar
2009 Current Biology  
To answer this, we have evolved gene regulatory networks in silico, selecting for networks that correctly predict particular phases of the day under light/dark cycles.  ...  gradually and the light intensity fluctuates with the weather.  ...  By evolving systems in silico, we have explored the interactions between functional requirements on the timing of gene expression and robustness to noise in order to identify factors that can explain the  ... 
doi:10.1016/j.cub.2009.09.024 pmid:19818616 fatcat:2c3zyvou3vfh7gaf6yrpb5psru

Generating Synthetic Gene Regulatory Networks [chapter]

Ramesh Ram, Madhu Chetty
2008 Lecture Notes in Computer Science  
The synthetic networks can have varying topologies such as small world, random, scale free, or hierarchical topologies based on the well-defined GRN properties.  ...  In this paper, we present an approach for synthetically generating gene networks using causal relationships.  ...  With a clear understanding gene regulation problem, it would be possible to simulate the process of complex gene regulatory networks.  ... 
doi:10.1007/978-3-540-88436-1_21 fatcat:attlzm6hdfahrfc7udgrhlltvy

Functionality and metagraph disintegration in boolean networks

Jamie X. Luo, Matthew S. Turner
2011 Journal of Theoretical Biology  
We find that the number of networks which generate a function decreases approximately exponentially with its complexity T and show there is a corresponding weakening of the robustness of those networks  ...  Finally we extend our analysis to functions with more exotic topologies in expression space, including "stars" and "trees".  ...  This lead to the suggestions (i) that through gradual topological changes (point mutations) any viable network could evolve towards greater robustness (Ciliberti et al., 2007a) and (ii) that gene circuits  ... 
doi:10.1016/j.jtbi.2011.05.006 pmid:21600222 fatcat:xopmeojopvchlgeig3xd6nuk5m

Mechanisms and constraints shaping the evolution of body plan segmentation

K. H. W. J. ten Tusscher
2013 The European Physical Journal E : Soft matter  
The model contains an evolving population of individuals, with each individual having a gene regulatory network as its genotype (A).  ...  In contrast, few animals such as Drosophila use a complex gene regulatory hierarchy to simultaneously subdivide their entire body axis into segments.  ...  By subsequently varying for example developmental and gene expression noise, or fitness criterium we can also determine how these outcomes differ in robustness or future evolutionary potential.  ... 
doi:10.1140/epje/i2013-13054-7 pmid:23708840 fatcat:vcu4zsdjnzejncdnnkv42can5a

Emergent biases in compensatory mutation can drive gene regulatory network evolution [article]

Yifei Wang, Marios Richards, Steve Dorus, Nicholas K. Priest, Joanna J. Bryson
2019 bioRxiv   pre-print
Using a well-established in silico model of gene regulatory networks, we show that compensatory mutation can drive the evolution of regulatory pathways because it biases the response to natural selection  ...  In our simulations, we find that compensatory mutation is common during periods of relaxed selection, with 8-15% of degraded networks having regulatory function restored by a single randomly-generated  ...  [2006] , which indicates that larger networks with complex topology tend to be unstable.  ... 
doi:10.1101/2019.12.18.881276 fatcat:ipva4w65tnfazpgjrhk2bsfj64

Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks

K.-K. Yan, G. Fang, N. Bhardwaj, R. P. Alexander, M. Gerstein
2010 Proceedings of the National Academy of Sciences of the United States of America  
The transcriptional regulatory network coordinates gene expression in response to environmental and intracellular signals, resulting in the execution of cellular processes such as cell divisions and metabolism  ...  A computer OS is described by a regulatory control network termed the call graph, which is analogous to the transcriptional regulatory network in a cell.  ...  As shown in Fig. 4A (Left) , the distribution of dN∕dS among persistent genes in E. coli has a gradual decreasing trend.  ... 
doi:10.1073/pnas.0914771107 pmid:20439753 pmcid:PMC2889091 fatcat:cl7l3ij2ffberkblhqw2wkcbgu

The effect of scale-free topology on the robustness and evolvability of genetic regulatory networks

Sam F. Greenbury, Iain G. Johnston, Matthew A. Smith, Jonathan P.K. Doye, Ard A. Louis
2010 Journal of Theoretical Biology  
We investigate how scale-free (SF) and Erdos-Renyi (ER) topologies affect the interplay between evolvability and robustness of model gene regulatory networks with Boolean threshold dynamics.  ...  In spite of their greater evolvability, we find that networks with SFout topologies are also more robust to mutations than ER networks.  ...  In this paper we focus on gene regulatory networks (GRNs), another set of biological systems that can be analyzed computationally.  ... 
doi:10.1016/j.jtbi.2010.08.006 pmid:20696172 fatcat:gnpzgpop6jambbfiz4wf6ualyi

Adaptation of cells to new environments

Aaron N. Brooks, Serdar Turkarslan, Karlyn D. Beer, Fang Yin Lo, Nitin S. Baliga
2010 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
Such studies provide spectacular insight into the mechanisms of adaptation, including rewiring of regulatory networks via natural selection of horizontal gene transfers, gene duplication, deletion, readjustment  ...  Here, we will discuss advances in prokaryotic systems biology from the perspective of evolutionary principles that have shaped regulatory networks for dynamic adaptation to environmental change.  ...  Gene regulatory networks evolve through a number of molecular mechanisms that vary in frequency and magnitude of effect.  ... 
doi:10.1002/wsbm.136 pmid:21197660 pmcid:PMC3081528 fatcat:l7khouleyrctxnicuahxshk67a

Robustness and evolvability in genetic regulatory networks

Maximino Aldana, Enrique Balleza, Stuart Kauffman, Osbaldo Resendiz
2007 Journal of Theoretical Biology  
The above is true in a variety of network topologies and even for the case of extreme divergence in which the duplicate gene bears almost no relation with its parent.  ...  Here we address this problem by studying the robustness and evolvability of the attractor landscape of genetic regulatory network models under the process of gene duplication followed by divergence.  ...  In this work, as a test-bed for the study of robustness and evolvability in GRN, we choose to model gene activities by random Boolean networks (RBN) with different topologies.  ... 
doi:10.1016/j.jtbi.2006.10.027 pmid:17188715 fatcat:32rftv5s7nc47mu7hlzcnkfjue

In SilicoEvolution of Gene Cooption in Pattern-Forming Gene Networks

Alexander V. Spirov, Marat A. Sabirov, David M. Holloway
2012 The Scientific World Journal  
We compare two mechanisms of gene cooption: a simpler one with gene Introduction and Withdrawal operators; and one in which GRN elements can be altered by transposon infection.  ...  Gene recruitment or cooption occurs when a gene, which may be part of an existing gene regulatory network (GRN), comes under the control of a new regulatory system.  ...  We can also study how the 4-gene network may have evolved; for example, by starting with 2gene models, we can study how these might have recruited genes into the current network.  ... 
doi:10.1100/2012/560101 pmid:23365523 pmcid:PMC3540831 fatcat:ebc677suwjh6zfvlive6euf6du
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