ArticleBMC biology2015
Layering genetic circuits to build a single cell, bacterial half adder.
Article in BMC biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed, 54 citations in OpenAlex.
- Bacterial gene regulatory neural network as a biocomputing library of mathematical solvers.NPJ systems biology and applications · 2026Article
- Engineered bacteria: Strategies and applications in cancer immunotherapy.Fundamental research · 2025Review
- Engineering intercellular communication using M13 phagemid and CRISPR-based gene regulation for multicellular computing in Escherichia coli.Nature communications · 2025Article
- Translating weighted probabilistic bits to synthetic genetic circuits.The plant genome · 2025Article
- Multicellular artificial neural network-type architectures demonstrate computational problem solving.Nature chemical biology · 2024Article
- Research and application of intelligent diagnosis and treatment engineering bacteria.Frontiers in bioengineering and biotechnology · 2024Review
- The naringenin-dependent regulator FdeR can be applied as a NIMPLY gate controlled by naringenin and arabinose.Synthetic biology (Oxford, England) · 2024Article
- Expanding the genetic programmability of Lactiplantibacillus plantarum.Microbial biotechnology · 2024Review
- Living electronics: A catalogue of engineered living electronic components.Microbial biotechnology · 2023Review
- A Network Approach to Genetic Circuit Designs.ACS synthetic biology · 2022Article
- Cellular Computational Logic Using Toehold Switches.International journal of molecular sciences · 2022Article
- Implementation of novel boolean logic gates for IMPLICATION and XOR functions using riboregulators.Bioengineered · 2022Article
- A single layer artificial neural network type architecture with molecular engineered bacteria for reversible and irreversible computing.Chemical science · 2021Article
- Modelling co-translational dimerization for programmable nonlinearity in synthetic biology.Journal of the Royal Society, Interface · 2020Article
- Novel Tunable Spatio-Temporal Patterns From a Simple Genetic Oscillator Circuit.Frontiers in bioengineering and biotechnology · 2020Article
- Label-Free Colorimetric Detection of Mercury (II) Ions Based on Gold Nanocatalysis.Sensors (Basel, Switzerland) · 2018Article
- Designing cell function: assembly of synthetic gene circuits for cell biology applications.Nature reviews. Molecular cell biology · 2018Review
- Binary addition in a living cell based on riboregulation.PLoS genetics · 2018Article
- Controlled communication between physically separated bacterial populations in a microfluidic device.Communications biology · 2018Article
- Synthesis of control unit for future biocomputer.Journal of biological engineering · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGene regulation in biological systems is impacted by the cellular and genetic context-dependent effects of the biological parts which comprise the circuit. Here, we have sought to elucidate the limitations of engineering biology from an architectural point of view, with the aim of compiling a set of engineering solutions for overcoming failure modes during the development of complex, synthetic genetic circuits.
resultsUsing a synthetic biology approach that is supported by computational modelling and rigorous characterisation, AND, OR and NOT biological logic gates were layered in both parallel and serial arrangements to generate a repertoire of Boolean operations that include NIMPLY, XOR, half adder and half subtractor logics in a single cell. Subsequent evaluation of these near-digital biological systems revealed critical design pitfalls that triggered genetic context-dependent effects, including 5' UTR interferences and uncontrolled switch-on behaviour of the supercoiled σ54 promoter. In particular, the presence of seven consecutive hairpins immediately downstream of the promoter transcription start site severely impeded gene expression.
conclusionsAs synthetic biology moves forward with greater focus on scaling the complexity of engineered genetic circuits, studies which thoroughly evaluate failure modes and engineering solutions will serve as important references for future design and development of synthetic biological systems. This work describes a representative case study for the debugging of genetic context-dependent effects through principles elucidated herein, thereby providing a rational design framework to integrate multiple genetic circuits in a single prokaryotic cell.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.