New strategies to control cholera are urgently needed. This study develops an in vitro proof-of-concept sense-and-kill system a wild-type Escherichia coli strain target the causative pathogen Vibrio cholerae using synthetic biology approach. Our engineered E. specifically detects V. via its quorum-sensing molecule CAI-1 and responds by expressing lysis protein YebF-Art-085, thereby self-lysing release killing Art-085 kill cholerae. For this report, we individually characterized YebF-Art-085...

Temperature is a physical cue that easy to apply, allowing cellular behaviors be controlled in contactless and dynamic manner via heat-inducible/repressible systems. However, existing heat-repressible systems are limited number, rely on thermal sensitive mRNA or transcription factors function at low temperatures, lack tunability, suffer delays, overly complex. To provide an alternative mode of regulation, we developed library compact, reversible, tunable thermal-repressible split-T7 RNA...

Abstract The increasing integration between biological and digital interfaces has led to heightened interest in utilizing materials store data, with the most promising one involving storage of data within defined sequences DNA that are created by de novo synthesis. However, there is a lack methods can obviate need for synthesis, which tends be costly inefficient. Here, this work, we detail method capturing 2-dimensional light patterns into DNA, optogenetic circuits record exposure encoding...

Detecting alterations in plasmid structures is often performed using conventional molecular biology. However, these methods are laborious and time-consuming for studying the conditions inducing mutations, which prevent real-time access to cell heterogeneity during bioproduction. In this work, we propose combining both flow cytometry fluorescence-activated sorting, integrated with mechanistic modelling study that lead recombination a limonene-producing microbial system as case study. A gene...

Machine learning (ML) shows great promise in protein engineering but has yet to be integrated with ultra-high throughput sorting (ultra-HTS) and NGS for large-scale sequence-function data generation harness its capability explore wider search space more complex mutation events. Here, we introduce PUSDA, a framework that rapidly sorts mutant libraries into multiple performance groups good accuracy generates power ML-driven design. As demonstration, PUSDA generated over five million of an...

Optogenetic tools provide a new and efficient way to dynamically program gene expression with unmatched spatiotemporal precision. To date, their vast potential remains untapped in the field of cell-free synthetic biology, largely due lack simple light-switchable systems. Here, bridge gap between systems optogenetics, we studied our previously engineered one component-based blue light-inducible Escherichia coli promoter environment through experimental characterization mathematical modeling....

Constructing a complex functional gene circuit composed of different modular biological parts to achieve the desired performance remains challenging without proper understanding how individual module behaves. To address this, mathematical models serve as an important tool toward better interpretation by quantifying overall circuit, providing insights, and guiding experimental designs. As circuits might require exclusively representations in form ordinary differential equations capture their...

Due to sustainability concerns, bio-based production capitalizing on microbes as cell factories is in demand synthesize valuable products. Nevertheless, the nonhomogenous variations of extracellular environment bioprocesses often challenge biomass growth and bioproduction yield. To enable a more rational bioprocess optimization, we have established model-driven approach that systematically integrates experiments with modeling, executed from flask bioreactor scale, using ferulic acid vanillin...

To program cells in a dynamic manner, synthetic biologists require precise control over the threshold levels and timing of gene expression. However, practice, modulating expression is widely carried out using prototypical ligand-inducible promoters, which have limited tunability spatiotemporal resolution. Here, we built two dual-input hybrid each retaining function promoter while being enhanced with blue-light-switchable tuning knob. Using new show that both ligand light inputs can be...

Abstract Advances in hardware automation synthetic biology laboratories are not yet fully matched by those of their software counterparts. Such automated laboratories, now commonly called biofoundries, require solutions that would help with many specialized tasks such as batch DNA design, sample and data tracking, analysis, among others. Typically, the challenges facing biofoundries shared, there is frequent wheel-reinvention where labs develop similar parallel. In this article, we present...

Abstract Summary Modelling in Synthetic Biology constitutes a powerful tool our continuous search for improved performance with rational Design-Build-Test-Learn approach. In particular, kinetic models unravel system dynamics, enabling analysis guiding experimental designs. However, systematic yet modular pipeline that allows one to identify the “right” model and guide designs while tracing entire development is still lacking. Here, we introduce unified python package, BMSS2, which offers...

Overexpression of a single enzyme in multigene heterologous pathway may be out balance with the other enzymes pathway, leading to accumulated toxic intermediates, imbalanced carbon flux, reduced productivity or an inhibited growth phenotype. Therefore, optimal, balanced, and synchronized expression levels particular metabolic is critical maximize production desired compounds while maintaining cell fitness growing culture. Furthermore, optimal intracellular concentration determined by...

Modeling in synthetic biology constitutes a powerful means our continuous search for improved performance with rational Design–Build–Test–Learn approach. Particularly, kinetic models unravel system dynamics and enable analysis guiding experimental design. However, systematic yet modular pipeline that allows one to identify the appropriate model guide designs while tracing entire development is still lacking. Here, we develop BMSS2, unified tool streamlines automates selection by combining...

SUMMARY Temperature is a physical cue that easy to apply, allowing cellular behaviors be controlled in contactless and dynamic manner via heat-inducible/repressible systems. However, existing heat-repressible systems are limited rely on thermal sensitive mRNA or transcription factors which function at low temperatures, lack tunability, suffer delays overly-complex. To provide an alternative mode of regulation, we developed library compact, reversible tunable thermal-repressible split-T7 RNA...

ABSTRACT Colony screening in single and multi-species environments is an essential step for microbiome studies. However, it possesses a high possibility of inaccurately classifying the species interest demands degree manpower time. Thus, automating classification microbes beneficial to minimize time inaccuracy colony screening/picking step. Here, we developed automated microbial system five target species, based on deep Convolutional Neural Networks (CNN) using images captured by robotic...