{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Taketani M"],"funding":["NIBIB NIH HHS","U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences","United States Department of Defense | Defense Advanced Research Projects Agency","U.S. Department of Defense","United States Department of Defense | United States Navy | ONR | Office of Naval Research Global","NIGMS NIH HHS","National Science Foundation","U.S. Department of Health &amp; Human Services | NIH | National Institute of Biomedical Imaging and Bioengineering"],"pagination":["962-969"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC8922546"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["38(8)"],"pubmed_abstract":["Bacteroides thetaiotaomicron is a human-associated bacterium that holds promise for delivery of therapies in the gut microbiome<sup>1</sup>. Therapeutic bacteria would benefit from the ability to turn on different programs of gene expression in response to conditions inside and outside of the gut; however, the availability of regulatory parts, and methods to combine them, have been limited in B. thetaiotaomicron<sup>2-5</sup>. We report implementation of Cello circuit design automation software<sup>6</sup> for this species. First, we characterize a set of genome-integrated NOT/NOR gates based on single guide RNAs (CRISPR-dCas9) to inform a Bt user constraint file (UCF) for Cello. Then, logic circuits are designed to integrate sensors that respond to bile acid and anhydrotetracycline (aTc),"],"journal":["Nature biotechnology"],"pubmed_title":["Genetic circuit design automation for the gut resident species Bacteroides thetaiotaomicron."],"pmcid":["PMC8922546"],"funding_grant_id":["CCF-1807575","P50 GM098792","N00014-13-1-0074","P50-GM098792","R01 EB021908","FA8750-17-C-0229","R01EB021908"],"pubmed_authors":["Zhang J","Huang YJ","Voigt CA","Taketani M","Triassi AJ","Griffith LG","Zhang S"],"additional_accession":[]},"is_claimable":false,"name":"Genetic circuit design automation for the gut resident species Bacteroides thetaiotaomicron.","description":"Bacteroides thetaiotaomicron is a human-associated bacterium that holds promise for delivery of therapies in the gut microbiome<sup>1</sup>. Therapeutic bacteria would benefit from the ability to turn on different programs of gene expression in response to conditions inside and outside of the gut; however, the availability of regulatory parts, and methods to combine them, have been limited in B. thetaiotaomicron<sup>2-5</sup>. We report implementation of Cello circuit design automation software<sup>6</sup> for this species. First, we characterize a set of genome-integrated NOT/NOR gates based on single guide RNAs (CRISPR-dCas9) to inform a Bt user constraint file (UCF) for Cello. Then, logic circuits are designed to integrate sensors that respond to bile acid and anhydrotetracycline (aTc),","dates":{"release":"2020-01-01T00:00:00Z","publication":"2020 Aug","modification":"2025-05-29T21:04:25.224Z","creation":"2025-05-29T21:04:25.224Z"},"accession":"S-EPMC8922546","cross_references":{"pubmed":["32231334"],"doi":["10.1038/s41587-020-0468-5"]}}