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Tradeoffs in gene regulatory networks: the plasmid replication control problem

I. Lestas, G. Vinnicombe, T. Bishop
Proceedings of the 44th IEEE Conference on Decision and Control  
The control of plasmid copy numbers in bacteria is discussed.  ...  By interpreting the fluctuation dissipation theorem in a noise filtering setting, we illustrate in the paper ways of exploiting conventional tools from robust control theory to reveal tradeoffs in gene  ...  INTRODUCTION The importance of intrinsic noise in gene regulatory networks has recently been emphasized with systematic analysis methods being proposed (see [1] and references therein).  ... 
doi:10.1109/cdc.2005.1582615 fatcat:vuh3cx35c5gutbuai2wcmea3fy

Expression optimization and synthetic gene networks in cell-free systems

David K. Karig, Sukanya Iyer, Michael L. Simpson, Mitchel J. Doktycz
2011 Nucleic Acids Research  
Using the resulting constructs, we then explore different approaches for composing regulatory systems, leading to the implementation of inducible negative feedback in Escherichia coli extracts and in the  ...  to fast track the development of live cell systems in synthetic biology.  ...  ORNL is managed by UT-Battelle, LLC, for the U.S. Department of Energy under contract DE-AC05-00OR22725.  ... 
doi:10.1093/nar/gkr1191 pmid:22180537 pmcid:PMC3333853 fatcat:acblhrkwcbf7xitqjbpcqmmhia

Evolutionary constraints in regulatory networks defined by partial order between phenotypes [article]

Manjunatha Kogenaru, Philippe Nghe, Frank J Poelwijk, Sander J Tans
2019 bioRxiv   pre-print
We find that populations: 1) expand in fitness space along the Pareto-optimal front predicted by conflicts in regulatory demands, by fine-tuning binding affinities within the network, 2) expand beyond  ...  Gene regulation networks allow organisms to adapt to diverse environmental niches.  ...  Work in the S. J. T. group is part by the Netherlands Organization for Scientific  ... 
doi:10.1101/722520 fatcat:3bbtubfjvjh3lncbwjtlbgvzam

Negative Feedback and Transcriptional Overshooting in a Regulatory Network for Horizontal Gene Transfer

Raul Fernandez-Lopez, Irene del Campo, Carlos Revilla, Ana Cuevas, Fernando de la Cruz, Ivan Matic
2014 PLoS Genetics  
We analyzed the transcriptional network of plasmid R388, one of the most promiscuous plasmids in Proteobacteria.  ...  The regulatory network relied on strong promoters, which were tightly repressed in negative feedback loops.  ...  However this problem is restricted mainly to replication, and does not explain why the same regulatory strategy is widespread in the entire plasmid backbone.  ... 
doi:10.1371/journal.pgen.1004171 pmid:24586200 pmcid:PMC3937220 fatcat:qae7tqyx4jdqdkuui57qs4pvum

Increasing Signal Specificity of the TOL Network of Pseudomonas putida mt-2 by Rewiring the Connectivity of the Master Regulator XylR

Aitor de las Heras, Sofia Fraile, Victor de Lorenzo, Josep Casadesús
2012 PLoS Genetics  
The non-natural connectivity engineered in the network resulted both in a higher promoter activity and also in a much-increased signal-to-background ratio.  ...  In the first case (xylR under the strong promoter of the upper TOL operon, Pu), the reporter system displayed an increased transcriptional capacity in the resulting network for both the optimal and the  ...  Rocha for critical reading of the manuscript. Author Contributions Conceived and designed the experiments: AdlH VdL. Performed the experiments: AdlH SF. Analyzed the data: AdlH VdL.  ... 
doi:10.1371/journal.pgen.1002963 pmid:23071444 pmcid:PMC3469447 fatcat:lg2bugmbg5hsjnjpwpr7ekl4ku

Inferring stable genetic networks from steady-state data

Michael M. Zavlanos, A. Agung Julius, Stephen P. Boyd, George J. Pappas
2011 Automatica  
In some applications, the topology of the regulatory network is not known, and has to be inferred from experimental data.  ...  Gene regulatory networks capture the interactions between genes and other cell substances, resulting from the fundamental biological process of transcription and translation.  ...  Then U can be quantified using a second strain with a reporter gene in place of the over-expressed gene on the plasmid.  ... 
doi:10.1016/j.automatica.2011.02.006 fatcat:jpoajumeqjahlcv3fs6yfvrwmi

On the Origin of Biomolecular Networks

Heeralal Janwa, Steven E. Massey, Julian Velev, Bud Mishra
2019 Frontiers in Genetics  
Among many possible variations, we emphasize particularly the essential role of gene duplication in terms of signaling game theory, whereby sender and receiver gene players accrue benefit from gene duplication  ...  encoded in such networks from among all types of variations they induce.  ...  This is so, because they are cellularized, chromosome replication is synchronized and so the genes replicate in concert.  ... 
doi:10.3389/fgene.2019.00240 pmid:31024611 pmcid:PMC6467946 fatcat:auvvb24ugvcm3g7xs362xlyneu

Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks [article]

Jacob W Freimer, Oren Shaked, Sahin Naqvi, Nasa Sinnott-Armstrong, Arwa Kathiria, Amy F Chen, Jessica Cortez, William J Greenleaf, Jonathan K Pritchard, Alexander Marson
2021 bioRxiv   pre-print
These results provide insight into how immune-associated disease genes are regulated in T cells and broader principles about the structure of human gene regulatory networks.  ...  Complex gene regulatory networks ensure that important genes are expressed at precise levels. When gene expression is sufficiently perturbed it can lead to disease.  ...  , the American Endowment Foundation, the Cancer Research Institute (CRI), the Lloyd J.  ... 
doi:10.1101/2021.04.18.440363 fatcat:qzlvxbozqjgirolrvyjstjsiym

Computational design of small transcription activating RNAs for versatile and dynamic gene regulation

James Chappell, Alexandra Westbrook, Matthew Verosloff, Julius B. Lucks
2017 Nature Communications  
Central to this is the creation of versatile regulatory toolsets that allow for programmable control of gene expression.  ...  Of the many regulatory molecules available, RNA regulators offer the intriguing possibility of de novo design-allowing for the bottom-up molecular-level design of genetic control systems.  ...  Acknowledgements The authors gratefully acknowledge the gift of TX-TL extract and buffers used in this work from Vincent Noireaux's laboratory (University of Minnesota).  ... 
doi:10.1038/s41467-017-01082-6 pmid:29051490 pmcid:PMC5648800 fatcat:k557c42xsfgr3jnhph2swlm7ey

Optimal parameter identification of synthetic gene networks using harmony search algorithm

Wei Zhang, Wenchao Li, Jianming Zhang, Ning Wang, Pratyoosh Shukla
2019 PLoS ONE  
The proposed optimal identification methodology involves estimation errors and the sample size to pursue a trade-off between estimation accuracy and measurement cost in modeling gene networks.  ...  Computational modeling of engineered gene circuits is an important while challenged task in systems biology.  ...  Acknowledgments We thank Prof Guang Li and Wuming Zhang for the instructive discussions and suggestions. Author Contributions Conceptualization: Wei Zhang.  ... 
doi:10.1371/journal.pone.0213977 pmid:30925150 pmcid:PMC6440652 fatcat:nfnm7ufnvbad3k72pzyhocdrke

Computational design of Small Transcription Activating RNAs (STARs) for versatile and dynamic gene regulation [article]

James Chappell, Alexandra Westbrook, Matthew Verosloff, Julius Lucks
2017 bioRxiv   pre-print
Central to this goal is the creation of versatile regulatory toolsets that allow for programmable control of gene expression.  ...  Of the many regulatory molecules available, RNA regulators offer the intriguing possibility of de novo design, allowing for the bottom-up molecular-level design of genetic control systems.  ...  regulatory networks 45 .  ... 
doi:10.1101/169391 fatcat:tyo75lqrkrfthbt42qzc62jrzu

The predictability of molecular evolution during functional innovation

D. Blank, L. Wolf, M. Ackermann, O. K. Silander
2014 Proceedings of the National Academy of Sciences of the United States of America  
In addition, we find that regulatory mutations affect genes that act in pathways relevant to the novel function, whereas structural mutations affect genes that act in unrelated pathways.  ...  the specific characteristics of the pathway or interaction networks in which the function acts (12).  ...  Bollenbach for sharing the pNDL1 plasmid. D.B. and O.K.S. were supported by grants from the Swiss National Foundation (PZ00P3_126617 and PZ00P3_144605).  ... 
doi:10.1073/pnas.1318797111 pmid:24516157 pmcid:PMC3939917 fatcat:33obze6oprfljivglocl6ohn4y

Discovery of Dynamical Network Models for Genetic Circuits from Time-Series Data with Incomplete Measurements [article]

Enoch Yeung, Jongmin Kim, Ye Yuan, Jorge Goncalves, Richard M Murray
2021 bioRxiv   pre-print
We introduce the theory of dynamical structure functions as a tool for understanding network dynamics in synthetic gene networks.  ...  Synthetic biological gene networks are typically conceptualized and visualized as static graphs with nodal and edge dynamics that are time invariant.  ...  14 National Science Foundation, Grant 1317291, and the John and Ursula Kanel Charitable Foundation.  ... 
doi:10.1101/2021.03.10.434835 fatcat:c5dyo37lurhjjfepzxssys5yzq

Independent component analysis of E. coli's transcriptome reveals the cellular processes that respond to heterologous gene expression

Justin Tan, Anand V. Sastry, Karoline S. Fremming, Sara P. Bjørn, Alexandra Hoffmeyer, Sangwoo Seo, Bjørn G. Voldborg, Bernhard O. Palsson
2020 Metabolic Engineering  
If these responses can be controlled, then the success rate with predicting heterologous gene expression should increase.  ...  Achieving the predictable expression of heterologous genes in a production host has proven difficult.  ...  We would like to thank Rebecca Lennen for her contribution of the gene templates and help in designing the plasmid backbone.  ... 
doi:10.1016/j.ymben.2020.07.002 pmid:32710928 fatcat:ejkcpso4rjdd3jjjy2vrkieeh4

The Plasmidome of Firmicutes: Impact on the Emergence and the Spread of Resistance to Antimicrobials

Val Fernández Lanza, Ana P. Tedim, José Luís Martínez, Fernando Baquero, Teresa M. Coque
2015 Microbiology spectrum  
This work analyzes the dynamics of antimicrobial resistance genes using gene exchange networks; the role of plasmids in the emergence, dissemination, and maintenance of genes encoding resistance to antimicrobials  ...  the understanding of gene and plasmid dynamics and their role in the evolution of bacterial communities.  ...  ACKNOWLEDGMENTS Research in the authors' laboratories is funded by the European Val F. Lanza and Ana P. Tedim contributed equally to the elaboration of this article.  ... 
doi:10.1128/microbiolspec.plas-0039-2014 pmid:26104702 fatcat:4tue5i44cncaji66bye5cmzpuq
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