Implementation of integral feedback control in biological systems

Somvanshi, Pramod R.; Patel, Anilkumar K.; Bhartiya, Sharad; Venkatesh, K. V.

doi:10.1002/wsbm.1307

Cited by 28 publications

(32 citation statements)

References 81 publications

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“…Our observations suggest a rationale for why centriole biogenesis may be regulated by an oscillatory system: in the model we describe here, Asl functions as an integrator (Ferrell, 2016;Somvanshi et al, 2015) whose levels are kept constant so that the oscillator can monitor changes in the input (in this case, cytoplasmic Plk4 levels) and respond accordingly by adapting the oscillation to maintain a constant output (in this case, centriole size). If this is correct, the Plk4 oscillator should be able to adapt to changes in Plk4 levels to maintain a consistent centriole size, but not to changes in Asl levels.…”

Section: Resultsmentioning

confidence: 96%

A free-running oscillator times and executes centriole biogenesis

Aydogan

Steinacker

Mofatteh

et al. 2019

Preprint

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Section: Resultsmentioning

confidence: 96%

A free-running oscillator times and executes centriole biogenesis

Aydogan

Steinacker

Mofatteh

et al. 2019

Preprint

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“…Many examples of basic control loops arise in simple cellular controls (Alon, 2007a;Iglesias & Ingalls, 2009;Somvanshi, Patel, Bhartiya, & Venkatesh, 2015). Larger eukaryotic regulatory networks often seem densely connected and perhaps overwired.…”

Section: Speciesmentioning

confidence: 99%

“…The theory arose in engineering (Davison, Chen, Ploen, & Bernstein, 2007;Dorf & Bishop, 2016;Doyle, Francis, & Tannenbaum, 2009;Ogata, 2009). Many studies of cellular regulatory control have adopted the conceptual framework of engineering control (Alon, 2007a;Cosentino & Bates, 2011;Csete & Doyle, 2002;Iglesias & Ingalls, 2009;Somvanshi et al, 2015). Roughly speaking, one can think of control theory in systems biology as the theoretical and mechanistic study of cellular phenotypic plasticity.…”

Section: Appendixmentioning

confidence: 99%

Receptor uptake arrays for vitamin B₁₂, siderophores, and glycans shape bacterial communities

Frank

2017

Ecology and Evolution

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Molecular variants of vitamin B12, siderophores, and glycans occur. To take up variant forms, bacteria may express an array of receptors. The gut microbe Bacteroides thetaiotaomicron has three different receptors to take up variants of vitamin B12 and 88 receptors to take up various glycans. The design of receptor arrays reflects key processes that shape cellular evolution. Competition may focus each species on a subset of the available nutrient diversity. Some gut bacteria can take up only a narrow range of carbohydrates, whereas species such as B. thetaiotaomicron can digest many different complex glycans. Comparison of different nutrients, habitats, and genomes provides opportunity to test hypotheses about the breadth of receptor arrays. Another important process concerns fluctuations in nutrient availability. Such fluctuations enhance the value of cellular sensors, which gain information about environmental availability and adjust receptor deployment. Bacteria often adjust receptor expression in response to fluctuations of particular carbohydrate food sources. Some species may adjust expression of uptake receptors for specific siderophores. How do cells use sensor information to control the response to fluctuations? This question about regulatory wiring relates to problems that arise in control theory and artificial intelligence. Control theory clarifies how to analyze environmental fluctuations in relation to the design of sensors and response systems. Recent advances in deep learning studies of artificial intelligence focus on the architecture of regulatory wiring and the ways in which complex control networks represent and classify environmental states. I emphasize the similar design problems that arise in cellular evolution, control theory, and artificial intelligence. I connect those broad conceptual aspects to many testable hypotheses for bacterial uptake of vitamin B12, siderophores, and glycans.

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“…Many examples of basic control loops arise in simple cellular controls 88,89,91 . Larger eukaryotic regulatory networks often seem densely connected and perhaps overwired.…”

Section: Regulatory Overwiringmentioning

confidence: 99%

Receptor uptake arrays for vitamin B₁₂, siderophores and glycans shape bacterial communities

Frank

2017

Preprint

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Control theory clarifies how to analyze environmental fluctuations in relation to the design of sensors and response systems. Recent advances in deep learning studies of artificial intelligence focus on the architecture of regulatory wiring and the ways in which complex control networks represent and classify environmental states. I emphasize the similar design problems that arise in cellular evolution, control theory, and artificial intelligence. I connect those broad conceptual aspects to many testable hypotheses for bacterial uptake of vitamin B 12 , siderophores, and glycans. K E Y W O R D Scontrol theory, corrinoids, deep learning, microbiome, phenotypic plasticity, public goods, Plastic response requires sensor arrays to perceive availability.Environmental perception must then be transduced through a regulatory network that integrates information and alters deployment of the receptor array. How do aspects of environmental fluctuation shape the evolutionary design of sensory perception and the regulatory control to achieve a conditional response?I discuss how perception, classification, and response through a network relate to recent breakthroughs in artificial intelligence, neural networks, and deep learning. Bacterial systems provide great opportunity to link conceptual aspects of evolutionary design and deep learning to hypotheses that can be tested by comparative genomics and by experimental laboratory studies.I synthesize aspects of receptor arrays for vitamin B 12 analogs, for siderophores, and for glycans. By considering these different cases together, deeper principles of receptor variety and specificity emerge.Here, I use the word "receptor" to include the various binding and transport processes that influence specificity and rate of uptake. Degnan, Barry, et al. (2014), estimate that the human microbiome contains more than 30 receptor families for uptake of B 12 -like corrinoid variants. Genomic analyses predict that a significant fraction of all bacteria and archaea require a corrinoid variant for growth, yet only a minority can produce corrinoids (Rodionov, Vitreschak, Mironov, & Gelfand, 2003;Zhang, Rodionov, Gelfand, & Gladyshev, 2009). Competition over corrinoid variants shapes the receptor arrays of individual species and the dynamics of bacterial communities.Siderophores are secreted molecules that bind free iron. Bacteria use siderophore receptors to take up the siderophore-iron complexes.Iron often sets a limiting resource for microbial growth. Thus, competitive and cooperative processes over siderophore uptake shape bacterial community dynamics (Chakraborty, Braun, Hantke, & Cornelis, 2013;Niehus, Picot, Oliveira, Mitri, & Foster, 2017;West, Diggle, Buckling, Gardner, & Griffin, 2007). Individual bacteria may secrete more than one type of siderophore, or none at all. Bacteria typically have uptake receptors tuned for their own secreted types. In addition, bacteria often express an array of siderophore uptake receptors for types produced by other species (Loper & Henkels, 1999). Bacte...

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Implementation of integral feedback control in biological systems

Cited by 28 publications

References 81 publications

A free-running oscillator times and executes centriole biogenesis

A free-running oscillator times and executes centriole biogenesis

Receptor uptake arrays for vitamin B₁₂, siderophores, and glycans shape bacterial communities

Receptor uptake arrays for vitamin B₁₂, siderophores and glycans shape bacterial communities

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Implementation of integral feedback control in biological systems

Cited by 28 publications

References 81 publications

A free-running oscillator times and executes centriole biogenesis

A free-running oscillator times and executes centriole biogenesis

Receptor uptake arrays for vitamin B12, siderophores, and glycans shape bacterial communities

Receptor uptake arrays for vitamin B12, siderophores and glycans shape bacterial communities

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Product

Resources

About

Receptor uptake arrays for vitamin B₁₂, siderophores, and glycans shape bacterial communities

Receptor uptake arrays for vitamin B₁₂, siderophores and glycans shape bacterial communities