Simplified Computational Design of Digital Synthetic Gene Circuits

2014 ◽  
pp. 257-271 ◽  
Author(s):  
Mario Andrea Marchisio ◽  
Jörg Stelling
Keyword(s):  
Computational Design ◽  
Synthetic Gene ◽  
Gene Circuits ◽  
Synthetic Gene Circuits

scholarly journals Computational design of synthetic gene circuits with composable parts

2008 ◽  
Vol 24 (17) ◽  
pp. 1903-1910 ◽  
Author(s):  
M.A. Marchisio ◽  
J. Stelling
Keyword(s):  
Computational Design ◽  
Synthetic Gene ◽  
Gene Circuits ◽  
Synthetic Gene Circuits

Computational design of biological circuits: putting parts into context

2017 ◽  
Vol 2 (4) ◽  
pp. 410-421 ◽  
Author(s):  
Eleni Karamasioti ◽  
Claude Lormeau ◽  
Jörg Stelling
Keyword(s):  
Computational Design ◽  
Context Dependence ◽  
Synthetic Gene ◽  
Gene Circuits ◽  
Computational Approaches ◽  
Synthetic Gene Circuits ◽  
Biological Circuits

We review computational approaches to deal with uncertainty and context-dependence in the design of synthetic gene circuits.

Synthetic Gene Circuits: Design, Implement, and Apply

2021 ◽  
pp. 1-18
Author(s):  
Andrew Lezia ◽  
Arianna Miano ◽  
Jeff Hasty
Keyword(s):  
Synthetic Gene ◽  
Gene Circuits ◽  
Synthetic Gene Circuits

Synthetic Gene Circuits

2014 ◽  
pp. 1-56 ◽  
Author(s):  
Barbara Jusiak ◽  
Ramiz Daniel ◽  
Fahim Farzadfard ◽  
Lior Nissim ◽  
Oliver Purcell ◽  
...  
Keyword(s):  
Synthetic Gene ◽  
Gene Circuits ◽  
Synthetic Gene Circuits

scholarly journals Cooperating on synthetic gene circuits

2019 ◽  
Vol 37 (7) ◽  
pp. 729-729
Author(s):  
Ross Cloney
Keyword(s):  
Synthetic Gene ◽  
Gene Circuits ◽  
Synthetic Gene Circuits

scholarly journals Two cellular resource‐based models linking growth and parts characteristics aids the study and optimisation of synthetic gene circuits

2017 ◽  
Vol 1 (1) ◽  
pp. 30-39 ◽  
Author(s):  
Huijuan Wang ◽  
Maurice H.T. Ling ◽  
Tze Kwang Chua ◽  
Chueh Loo Poh
Keyword(s):  
Synthetic Gene ◽  
Gene Circuits ◽  
Synthetic Gene Circuits

scholarly journals Multistable and dynamic CRISPRi-based synthetic circuits

2019 ◽  
Author(s):  
Javier Santos-Moreno ◽  
Eve Tasiudi ◽  
Joerg Stelling ◽  
Yolanda Schaerli
Keyword(s):  
Context Dependency ◽  
Synthetic Gene ◽  
Toggle Switch ◽  
Stripe Pattern ◽  
Gene Circuits ◽  
Synthetic Gene Circuits ◽  
Gene Expression Control ◽  
Unspecific Binding ◽  
High Predictability ◽  
Pattern Forming

AbstractGene expression control based on CRISPRi (clustered regularly interspaced short palindromic repeats interference) has emerged as a powerful tool for creating synthetic gene circuits, both in prokaryotes and in eukaryotes; yet, its lack of cooperativity has been pointed out as a potential obstacle for dynamic or multistable circuit construction. Here we use CRISPRi to build prominent synthetic gene circuits in Escherichia coli. We report the first-ever CRISPRi oscillator (“CRISPRlator”), bistable network (toggle switch) and stripe pattern-forming incoherent feed-forward loop (IFFL). Our circuit designs, conceived to feature high predictability and orthogonality, as well as low metabolic burden and context-dependency, allowed us to achieve robust circuit behaviors. Mathematical modeling suggests that unspecific binding in CRISPRi is essential to establish multistability. Our work demonstrates the wide applicability of CRISPRi in synthetic circuits and paves the way for future efforts towards engineering more complex synthetic networks, boosted by the advantages of CRISPR technology.

scholarly journals Synthetic Gene Circuits for Antimicrobial Resistance and Cancer Research

2021 ◽  
Author(s):  
Kevin S. Farquhar ◽  
Michael Tyler Guinn ◽  
Gábor Balázsi ◽  
Daniel A. Charlebois
Keyword(s):  
Mammalian Cells ◽  
Rational Design ◽  
Study Drug ◽  
Quantitative Model ◽  
Synthetic Gene ◽  
Modeling Tools ◽  
Gene Circuits ◽  
Novel Treatments ◽  
Synthetic Gene Circuits ◽  
Temporal Dimensions

Mathematical models and synthetic gene circuits are powerful tools to develop novel treatments for patients with drug-resistant infections and cancers. Mathematical modeling guides the rational design of synthetic gene circuits. These systems are then assembled into unified constructs from existing and/or modified genetic components from a range of organisms. In this chapter, we describe modeling tools for the design and characterization of chemical- and light-inducible synthetic gene circuits in different organisms and highlight how synthetic gene circuits are advancing biomedical research. Specifically, we demonstrate how these quantitative model systems are being used to study drug resistance in microbes and to probe the spatial–temporal dimensions of cancer in mammalian cells.

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