ArticleJournal of biological engineering2017
Re-using biological devices: a model-aided analysis of interconnected transcriptional cascades designed from the bottom-up.
Article in Journal of biological engineering, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Structural properties and asymptotic behavior of bacterial two-component systems.Frontiers in systems biology · 2025Article
- A synthetic biology toolkit for rationally designing genetic circuits inFrontiers in systems biology · 2025Article
- dCas9 regulator to neutralize competition in CRISPRi circuits.Nature communications · 2021Article
- CRISPR Interference Modules as Low-Burden Logic Inverters in Synthetic Circuits.Frontiers in bioengineering and biotechnology · 2021Article
- A quasi-integral controller for adaptation of genetic modules to variable ribosome demand.Nature communications · 2018Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe study of simplified, ad-hoc constructed model systems can help to elucidate if quantitatively characterized biological parts can be effectively re-used in composite circuits to yield predictable functions. Synthetic systems designed from the bottom-up can enable the building of complex interconnected devices via rational approach, supported by mathematical modelling. However, such process is affected by different, usually non-modelled, unpredictability sources, like cell burden.
methodsHere, we analyzed a set of synthetic transcriptional cascades in
resultsAmong the constructed configurations, two test set circuits showed unexpected logic behaviour. Both NBM and BM were able to predict the quantitative output of interconnected devices with expected behaviour, but only the BM was also able to predict the output of one circuit with unexpected behaviour. Moreover, considering training and test set data together, the BM captures circuits output with higher accuracy than the NBM, which is unable to capture the experimental output exhibited by some of the circuits even qualitatively. Finally, resource usage parameters, estimated via BM, guided the successful construction of new corrected variants of the two circuits showing unexpected behaviour.
conclusionsSuperior descriptive and predictive capabilities were achieved considering resource limitation modelling, but further efforts are needed to improve the accuracy of models for biological engineering.
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