Journal: Nature Communications

Article Title: Engineering wetware and software for the predictive design of compressed genetic circuits for higher-state decision-making

doi: 10.1038/s41467-025-64457-0

Figure Lengend Snippet: a – c A representative single-input BUFFER gate responding to cellobiose is shown in four distinct contexts defined by host strain ( E. coli 3.32 or BL21) and growth media (minimal medium or LB). Logic operation ( a ), genetic circuit schematic ( b ), and corresponding reporter expression levels in Expression Units (EU; see Methods for definition) ( c ) are shown. d – f A second single-input BUFFER gate responding to ribose is similarly characterized across contexts with the logic operation ( d ), genetic circuit schematic ( e ), and experimental data ( f ) shown. g – i A two-input AND gate responsive to cellobiose and ribose shows that quantitative performance varies across chassis and media. Logic operation ( g ), genetic circuit schematic ( h ), and predicted vs. measured outputs ( i ) highlight that accurate prediction is possible after context re-characterization. j Ribosome binding-site (RBS) scaling factors measured using constitutive expression of 25ADR-GFP fusion protein under the P ttg promoter across different contexts reveal differing expression levels, necessitating re-characterization. LacI stands for the lactose repressor, and GFP is green fluorescent protein. k – l Compressed T-Pro logic gates outperform inversion-based designs in NOT ( k ) and NOR ( l ) configurations, with improved dynamic performance. Circuit schematics (left) and time-course outputs (right) are shown. Ligand(s) were added 180 min after cells were passaged into fresh media. Source data are provided as a Source Data file. Data represent the mean of n = 3 biological replicates, each measured on a separate day. Error bars indicate the standard error of the mean (SEM).

Article Snippet: E. coli strains used were NEB® 10-beta (for cloning), chemically competent BL21 (NEB) (for assays), and 3.320 ( lacZ13(Oc) lacI22 λ − el4- relA1 spoT1 thiE1 ; Yale CGSC #5237) (for assays).

Techniques: Expressing, Binding Assay