A data-driven method for quantifying the impact of a genetic circuit on its host

Aqib Hasnain, Diveena Becker, Atsede Siba, Narendra Maheshri, Ben Gordon, Chris Voigt, Enoch Yeung, Subhrajit Sinha, Yuval Dorfan, Amin Espah Borujeni, Yongjin Park, Paul Maschhoff, Uma Saxena, Joshua Urrutia, Niall Gaffney

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

3 Scopus citations

Abstract

Genetic circuits aredesigned to implement certain logic in living cells, keeping burden on the host cell minimal. However, manipulating the genome often will have a significant impact for various reasons (usage of the cell machinery to express new genes, toxicity of genes, interactions with native genes, etc.). In this work we utilize Koopman operator theory to construct data-driven models of transcriptomic-level dynamics from noisy and temporally sparse RNAseq measurements. We show how Koopman models can be used to quantify impact on genetic circuits. We consider an experimental example, using high-Throughput RNAseq measurements collected from wild-Type E. coli, single gate components transformed in E. coli, and a NAND circuit composed from individual gates in E. coli, to explore how Koopman subspace functions encode increasing circuit interference on E. coli chassis dynamics. The algorithm provides a novel method for quantifying the impact of synthetic biological circuits on host-chassis dynamics.

Original languageEnglish
Title of host publicationBioCAS 2019 - Biomedical Circuits and Systems Conference, Proceedings
PublisherInstitute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)9781509006175
DOIs
StatePublished - Oct 2019
Externally publishedYes
Event2019 IEEE Biomedical Circuits and Systems Conference, BioCAS 2019 - Nara, Japan
Duration: 17 Oct 201919 Oct 2019

Publication series

NameBioCAS 2019 - Biomedical Circuits and Systems Conference, Proceedings

Conference

Conference2019 IEEE Biomedical Circuits and Systems Conference, BioCAS 2019
Country/TerritoryJapan
CityNara
Period17/10/1919/10/19

Bibliographical note

Publisher Copyright:
© 2019 IEEE.

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