Adaptive circuits in synthetic biology

Frei, Timothy; Khammash, Mustafa

doi:10.1016/j.coisb.2021.100399

Cited by 20 publications

(13 citation statements)

References 54 publications

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“…They regulate natural and engineered cellular systems, as well as phase transitions and adaptation to resource changes of bacteriophages (Pitsili, Phukan and Coll 2020 , Brady et al . 2021 , Frei and Khammash 2021 , Yao et al . 2021 ).…”

Section: Immune Evasion Through Leader and Non-core Modules Of Potyvi...mentioning

confidence: 99%

Proteome expansion in thePotyviridaeevolutionary radiation

Pasin

Daròs

Tzanetakis

2022

FEMS Microbiology Reviews

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Potyviridae, the largest family of known RNA viruses (realm Riboviria), belongs to the picorna-like supergroup and has important agricultural and ecological impacts. Potyvirid genomes are translated into polyproteins, which are in turn hydrolyzed to release mature products. Recent sequencing efforts revealed an unprecedented number of potyvirids with a rich variability in gene content and genomic layouts. Here we review the heterogeneity of non-core modules that expand the structural and functional diversity of the potyvirid proteomes. We provide a family-wide classification of P1 proteinases into the functional Types A and B, and discuss pretty interesting sweet potato potyviral ORF (PISPO), putative zinc fingers, and alkylation B (AlkB) – non-core modules found within P1 cistrons. The atypical modules inosine triphosphate pyrophosphatase (ITPase/HAM1), as well as the pseudo tobacco mosaic virus-like coat protein (TMV-like CP) are discussed alongside homologs of unrelated virus taxa. Family-wide abundance of the multitasking helper component proteinase (HC-pro) is revised. Functional connections between non-core modules are highlighted to support host niche adaptation and immune evasion as main drivers of the Potyviridae evolutionary radiation. Potential biotechnological and synthetic biology applications of potyvirid leader proteinases and non-core modules are finally explored.

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Section: Immune Evasion Through Leader and Non-core Modules Of Potyvi...mentioning

confidence: 99%

Proteome expansion in thePotyviridaeevolutionary radiation

Pasin

Daròs

Tzanetakis

2022

FEMS Microbiology Reviews

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“…One control motif that has been discovered repeatedly in natural systems is the so-called feedforward motif [48], [67]. There are several types of feedforward motifs, but they can generally be divided into two classes: coherent and incoherent.…”

Section: B Engineering Robust Controllers With Feedforward Controlmentioning

confidence: 99%

Cybergenetics: Theory and Applications of Genetic Control Systems

Khammash

2022

Proc. IEEE

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“…Arguably, one of the main challenges of building synthetic bio-devices operating in the uncertain cellular environment is achieving a reliable and predictable behaviour. Feedback control theory provides a large variety of tools that have proven to be of fundamental importance in regulating such devices, optimizing their function and rendering them robust to disturbances [5], [6], [7], [8], [9].…”

Section: Introductionmentioning

confidence: 99%

On the Design of a PID Bio-controller with Set Point Weighting and Filtered Derivative Action

Alexis

Cardelli²,

Papachristodoulou³

2022

Preprint

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Effective and robust regulation of biomolecular processes is crucial for designing reliable synthetic bio-devices functioning in uncertain and constantly changing biological environments. Proportional-Integral-Derivative (PID) controllers are undeniably the most common way of implementing feedback control in modern technological applications. Here, we introduce a highly tunable PID bio-controller with set point weighting and filtered derivative action presented as a chemical reaction network with mass action kinetics. To demonstrate its effectiveness, we apply our PID scheme on a simple biological process of two mutually activated species, one of which is assumed to be the output of interest. To highlight its performance advantages we compare it to PI regulation using numerical simulations in both the deterministic and stochastic setting.

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Adaptive circuits in synthetic biology

Cited by 20 publications

References 54 publications

Proteome expansion in thePotyviridaeevolutionary radiation

Proteome expansion in thePotyviridaeevolutionary radiation

Cybergenetics: Theory and Applications of Genetic Control Systems

On the Design of a PID Bio-controller with Set Point Weighting and Filtered Derivative Action

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