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Feedback Control Architecture and the Bacterial Chemotaxis Network

Abdullah Hamadeh, Mark A. J. Roberts, Elias August, Patrick E. McSharry, Philip K. Maini, Judith P. Armitage, Antonis Papachristodoulou, Jason M. Haugh
2011 PLoS Computational Biology  
This response is regulated by the chemotaxis signalling pathway, which has an important feature: it uses feedback to 'reset' (adapt) the bacterial sensing ability, which allows the bacteria to sense a  ...  Moreover, it has a 'cascade control' feedback architecture which is used extensively in engineering to improve system performance, including robustness.  ...  The chemotaxis signalling pathway in the bacterium Escherichia coli is a simple network with one feedback loop [3] which has been extensively studied and used as a paradigm for the mechanism of chemotaxis  ... 
doi:10.1371/journal.pcbi.1001130 pmid:21573199 pmcid:PMC3088647 fatcat:bipekcocrnguvglqdd4knpia5q

Adaptive molecular networks controlling chemotactic migration: dynamic inputs and selection of the network architecture

H. Chang, A. Levchenko
2013 Philosophical Transactions of the Royal Society of London. Biological Sciences  
The authors thank Adriel Bergmann for valuable discussions. Funding statement. The work was funded by NIH grant nos. GM072024 and GM084332.  ...  It is of interest, and as suggested below, of possible importance, that the current biochemically informed models of bacterial chemotaxis postulate a type of negative feedback that carries information  ...  However, when applied to the high osmolarity response pathway in yeast or in bacterial chemotaxis, the lack of adaptation to ramp stimulation strongly supported NFB architecture [24] .  ... 
doi:10.1098/rstb.2013.0117 pmid:24062588 pmcid:PMC3785968 fatcat:aaogpbzrxvgvxdjh3idk6zq32m

Feedback control architecture of the R. sphaeroides chemotaxis network

Abdullah Hamadeh, Elias August, Mark Roberts, Philip K. Maini, Judith P. Armitage, Brian Ingalls, Antonis Papachristodoulou
2011 IEEE Conference on Decision and Control and European Control Conference  
From a control theoretic perspective, we show that, compared to the other models posed, this model exhibits better and more robust chemotactic performance.  ...  This decision mechanism parallels a feedback architecture that has been used extensively to improve performance in engineered systems.  ...  One such pathway is bacterial chemotaxis, which controls bacterial motion in response to environmental stimuli, towards favorable concentrations of chemoeffectors.  ... 
doi:10.1109/cdc.2011.6161020 dblp:conf/cdc/HamadehARMAIP11 fatcat:bbmxoccskvcbjabprivxwckidy

How to Understand and Outwit Adaptation

Oliver Hoeller, Delquin Gong, Orion D. Weiner
2014 Developmental Cell  
ACKNOWLEDGMENTS We would like to thank the members of the Weiner laboratory for helpful discussion.  ...  Inspired by bacterial chemotaxis, we take a look at the less understood signaling network of eukaryotic chemotaxis and suggest that adaptation, as in bacteria, might happen at several places in the signaling  ...  inputs can help to distinguish the underlying network architecture.  ... 
doi:10.1016/j.devcel.2014.03.009 pmid:24697896 pmcid:PMC4012857 fatcat:k3dtrnkpkfhajhke6g2dogk7hy

Molecular Information Processing: Lessons from Bacterial Chemotaxis

Robert B. Bourret, Ann M. Stock
2002 Journal of Biological Chemistry  
The overall layout of the information processing network that controls E. coli chemotaxis is displayed in Fig.  ...  Genetic investigations in many bacterial species have identified the elements from which logic circuits controlling chemotaxis are constructed.  ...  Acknowledgments-We thank Dennis Bray, Sandy Parkinson, and Ruth Silversmith for useful discussions.  ... 
doi:10.1074/jbc.r100066200 pmid:11779877 fatcat:fb3qjitijzbhzoawhtdta6ibmy

Internal Feedback in Biological Control: Architectures and Examples [article]

Anish A. Sarma, Jing Shuang Li, Josefin Stenberg, Gwyneth Card, Elizabeth S. Heckscher, Narayanan Kasthuri, Terrence Sejnowski, John C. Doyle
2021 arXiv   pre-print
Feedback is ubiquitous in both biological and engineered control systems.  ...  In biology, in addition to typical feedback between plant and controller, we observe feedback pathways within control systems, which we call internal feedback pathways (IFPs), that are often very complex  ...  Bacterial Chemotaxis Bacterial chemotaxis, a behavior in which bacteria swim up nutrient gradients, is a canonical case study in robust biomolecular signal transduction and control (typically studied in  ... 
arXiv:2110.05029v3 fatcat:lr4rhfe5frhdderadnrepkhgoi

Adaptation in Living Systems

Yuhai Tu, Wouter-Jan Rappel
2018 Annual Review of Condensed Matter Physics  
We focus on understanding the basic biochemical interaction networks in living matter that are responsible for adaptation dynamics.  ...  We take the minimalist (or the physicist) approach and study the simplest systems that exhibit generic adaptive behaviors.  ...  We apologize to authors in the field whose work are not cited due to space limitations. LITERATURE CITED  ... 
doi:10.1146/annurev-conmatphys-033117-054046 pmid:30057689 pmcid:PMC6060625 fatcat:wo43rx27fbaeda6hxzzjfqj45y

Hydrogen Exchange Reveals Differences between Bacterial Chemoreceptor Signaling States

Seena S. Koshy, Xuni Li, Stephen J. Eyles, Robert M. Weis, Lynmarie K. Thompson
2015 Biophysical Journal  
Multidomain scaffold proteins serve as hubs in the signal transduction network. By physically colocalizing sequential steps in a transduction pathway, scaffolds catalyze and direct incoming signals.  ...  Here we will review these unique surfaces built on cross-b structures of amyloid, and extend that pattern to mixing of positively-and negatively-charged surfaces to give even higher order architectures  ...  Platform: Member Organized Session: Protein Nanoassemblies and Networks in Bacterial Chemotaxis and other Two-component Signaling Systems 201-Plat Insights from Phosphorylation Profiling of an Autoregulated  ... 
doi:10.1016/j.bpj.2014.11.255 fatcat:y5nfjvdy6bdqfgc4jruk3vxsfm

Relationship between cellular response and behavioral variability in bacterial chemotaxis

T. Emonet, P. Cluzel
2008 Proceedings of the National Academy of Sciences of the United States of America  
Bacterial chemotaxis in Escherichia coli is a canonical system for the study of signal transduction.  ...  Finally, Large-scale simulations of digital bacteria suggest that the chemotaxis network is tuned to simultaneously optimize the random spread of cells in absence of nutrients and the cellular response  ...  Bacterial chemotaxis is a system that controls the locomotion of cells and has arisen as a model system for signal transduction.  ... 
doi:10.1073/pnas.0705463105 pmid:18299569 pmcid:PMC2265172 fatcat:udoexw4gsnfhjnrohx6zg53564

Control Motifs for Intracellular Regulatory Networks

Christopher V. Rao, Adam P. Arkin
2001 Annual Review of Biomedical Engineering  
These motifs, recurring elements of control, may help to deduce the structure and function of partially known networks and form the basis for fulfilling the goals described above.  ...  A number of approaches to identifying and analyzing control motifs in intracellular networks are reviewed.  ...  Rather, the network is characterized by both the stoichiometry and the regulatory architecture.  ... 
doi:10.1146/annurev.bioeng.3.1.391 pmid:11447069 fatcat:day7ilkuwrcznpapvragyjzgdu

Robustness of Cellular Functions

Jörg Stelling, Uwe Sauer, Zoltan Szallasi, Francis J. Doyle, John Doyle
2004 Cell  
Apparently, mathematical models in biology as well as "network cartoons" are 1 Max Planck Institute for Dynamics of Complex Technical Systems idealizations and not perfect representations of reality.  ...  Once biological knowledge is formalized, the rules of CH-8093 Zü rich Switzerland mathematics take over; this may often provide a fresh insight into biology (Endy and Brent, 2001; May, 2004).  ...  Hence, chemotaxis is an excellent example for nested feedback as a means to achieve robustness, and it underlines individual roles and significances that Bacterial Chemotaxis different instances of feedback  ... 
doi:10.1016/j.cell.2004.09.008 pmid:15369668 fatcat:ocrpvw32azcszgcf2224h6x26q

A novel IMC controller based on bacterial foraging optimization algorithm applied to a high speed range PMSM drive

Aymen Flah, Lassaâd Sbita
2012 Applied intelligence (Boston)  
Neural network controller and estimator are respectively added to replace the conventional speed regulator and the speed encoder in the global drive scheme.  ...  Therefore, a method based on the bacterial foraging optimization (BFO) algorithm is performed to optimize and adjust the IMC low pass filter parameters.  ...  and the source are credited.  ... 
doi:10.1007/s10489-012-0361-0 fatcat:2roid6wtmvhzdgf32bbk3nrpzm

Multi-bit Boolean model for chemotactic drift of Escherichia coli

Anuj Deshpande, Sibendu Samanta, Sutharsan Govindarajan, Ritwik Kumar Layek
2020 IET Systems Biology  
The chemotaxis network of the bacterium Escherichia coli (E. coli) is one of the most investigated biological systems.  ...  Dynamic biological systems can be modelled to an equivalent modular structure using Boolean networks (BNs) due to their simple construction and relative ease of integration.  ...  Symbols → and ⊢ represent the activation and inhibition of a process, respectively Fig. 2 Control block diagram of the chemotaxis network.  ... 
doi:10.1049/iet-syb.2020.0060 pmid:33399098 pmcid:PMC8687284 fatcat:on3arsomfrci7kzdc3oqia6eae

HOMEOSTATIC CONTROL OF NEURAL ACTIVITY: From Phenomenology to Molecular Design

Graeme W. Davis
2006 Annual Review of Neuroscience • Principles of Neural Homeostasis INTEGRATIVE FEEDBACK CONTROL AND PRECISION IN BACTERIAL CHEMOTAXIS Feedback control systems that achieve perfect homeostatic compensation are  ...  The question that remains is whether there is evidence of integral feedback control in biological systems ← −−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−− − Figure 3 Integrative feedback and bacterial chemotaxis.  ...  Ranum and Thomas A.  ... 
doi:10.1146/annurev.neuro.28.061604.135751 pmid:16776588 fatcat:42jxk3k7ffd6vfotvleg6asi6m

Simulating the evolution of signal transduction pathways

Orkun S. Soyer, Thomas Pfeiffer, Sebastian Bonhoeffer
2006 Journal of Theoretical Biology  
Furthermore, we find that the dynamics and topology of such networks show many similarities to the natural chemotaxis pathway, that the response magnitude can increase with increasing network size and  ...  We use a generic model of a network of proteins that can activate or deactivate each other to explore the emergence and evolution of signal transduction networks and to gain a basic understanding of their  ...  Neubig, Dennis Bray, Matthew Levin, Karen Lipkow and two anonymous reviewers for very useful comments on the manuscript.  ... 
doi:10.1016/j.jtbi.2005.11.024 pmid:16403533 fatcat:dj4jcx4uivcdlh57nde453hxam
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