James Chappell
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View article: Establishing an RNA sensor with high sensitivity and dynamic range utilizing a signal amplifier platform
Establishing an RNA sensor with high sensitivity and dynamic range utilizing a signal amplifier platform Open
Precise control of gene expression in a cell-state-specific manner is essential for effective therapeutic interventions in complex and dynamic disease microenvironments. Traditional targeting strategies that rely on surface markers or cell…
View article: Cross-order detection of bacteriophage transduction in communities using ribosomal RNA barcoding
Cross-order detection of bacteriophage transduction in communities using ribosomal RNA barcoding Open
Bacteriophages (phages) facilitate gene transfer and microbial evolution in all ecosystems and have applications as tools for engineering microbiomes and as antimicrobials. Historic efforts to map phage hosts, such as plaque assays, are li…
View article: Controlling the taxonomic composition of biological information storage in 16S ribosomal RNA
Controlling the taxonomic composition of biological information storage in 16S ribosomal RNA Open
Microbes can be programmed to record participation in gene transfer by coding biological-recording devices into mobile DNA. Upon DNA uptake, these devices transcribe a catalytic RNA (cat-RNA) that binds to conserved sequences within riboso…
View article: Engineering Plasmids with Synthetic Origins of Replication
Engineering Plasmids with Synthetic Origins of Replication Open
Plasmids remain by far the most common medium for delivering engineered DNA to microorganisms. However, the reliance on natural plasmid replication mechanisms limits their tunability, compatibility, and modularity. Here we refactor the nat…
View article: Ten Years of the Synthetic Biology Summer Course at Cold Spring Harbor Laboratory
Ten Years of the Synthetic Biology Summer Course at Cold Spring Harbor Laboratory Open
The Cold Spring Harbor Laboratory (CSHL) Summer Course on Synthetic Biology, established in 2013, has emerged as a premier platform for immersive education and research in this dynamic field. Rooted in CSHL's rich legacy of biological disc…
View article: Ribozyme-mediated gene-fragment complementation for non-destructive reporting of DNA transfer within soil
Ribozyme-mediated gene-fragment complementation for non-destructive reporting of DNA transfer within soil Open
Enzymes that produce volatile metabolites can be coded into genetic circuits to report non-disruptively on microbial behaviors in hard-to-image soils. However, these enzyme reporters remain challenging to apply in gene transfer studies due…
View article: Targeted Transcriptional Activation using a CRISPR-Associated Transposon System
Targeted Transcriptional Activation using a CRISPR-Associated Transposon System Open
Synthetic perturbation of gene expression is central to our ability to reliably uncover genotype-phenotype relationships in microbes. Here, we present a novel gene transcription activation strategy that uses the Vibrio cholerae CRISPR-Asso…
View article: Information storage across a microbial community using universal RNA memory
Information storage across a microbial community using universal RNA memory Open
Biological recorders can code information in DNA, but they remain challenging to apply in complex microbial communities. To program microbiome information storage, a synthetic catalytic RNA (cat-RNA) was used to write information in riboso…
View article: A portable regulatory RNA array design enables tunable and complex regulation across diverse bacteria
A portable regulatory RNA array design enables tunable and complex regulation across diverse bacteria Open
A lack of composable and tunable gene regulators has hindered efforts to engineer non-model bacteria and consortia. To address this, we explore the broad-host potential of small transcription activating RNA (STAR) and propose a novel desig…
View article: Activating natural product synthesis using CRISPR interference and activation systems in <i>Streptomyces</i>
Activating natural product synthesis using CRISPR interference and activation systems in <i>Streptomyces</i> Open
The rise of antibiotic-resistant bacteria represents a major threat to global health, creating an urgent need to discover new antibiotics. Natural products derived from the genus Streptomyces represent a rich and diverse repertoire of chem…
View article: A split ribozyme that links detection of a native RNA to orthogonal protein outputs
A split ribozyme that links detection of a native RNA to orthogonal protein outputs Open
Individual RNA remains a challenging signal to synthetically transduce into different types of cellular information. Here, we describe Ribozyme-ENabled Detection of RNA (RENDR), a plug-and-play strategy that uses cellular transcripts to te…
View article: Activating natural product synthesis using CRISPR interference and activation systems in<i>Streptomyces</i>
Activating natural product synthesis using CRISPR interference and activation systems in<i>Streptomyces</i> Open
The rise of antibiotic-resistant bacteria represents a major threat to global health, creating an urgent need to discover new antibiotics. Natural products derived from the genus Streptomyces represent a rich and diverse repertoire of chem…
View article: RNA compensation: A positive feedback insulation strategy for RNA-based networks
RNA compensation: A positive feedback insulation strategy for RNA-based networks Open
The lack of signalling modularity of biomolecular systems poses major challenges toward engineering complex networks. An important problem is posed by the consumption of signaling molecules upon circuit interconnection, which makes it poss…
View article: Uncovering the distinct properties of a bacterial type I-E CRISPR activation system
Uncovering the distinct properties of a bacterial type I-E CRISPR activation system Open
Synthetic gene regulators based upon CRISPR-Cas systems offer highly programmable technologies to control gene expression in bacteria. Bacterial CRISPR activators (CRISPRa) have been developed that use engineered type II CRISPR-dCas9 to lo…
View article: Rational engineering of a modular bacterial CRISPR–Cas activation platform with expanded target range
Rational engineering of a modular bacterial CRISPR–Cas activation platform with expanded target range Open
CRISPR–Cas activator (CRISPRa) systems that selectively turn on transcription of a target gene are a potentially transformative technology for programming cellular function. While in eukaryotes versatile CRISPRa systems exist, in bacteria …
View article: Biotechnology and Bioengineering: Volume 116, Number 5, May 2019
Biotechnology and Bioengineering: Volume 116, Number 5, May 2019 Open
US$18141 (US and Rest of World), € 11707 (Europe), £ 9260 (UK
View article: PLANT-Dx: A Molecular Diagnostic for Point-of-Use Detection of Plant Pathogens
PLANT-Dx: A Molecular Diagnostic for Point-of-Use Detection of Plant Pathogens Open
Synthetic biology based diagnostic technologies have improved upon gold standard diagnostic methodologies by decreasing cost, increasing accuracy, and enhancing portability. However, there has been little effort in adapting these technolog…
View article: Distinct timescales of RNA regulators enable the construction of a genetic pulse generator
Distinct timescales of RNA regulators enable the construction of a genetic pulse generator Open
To build complex genetic networks with predictable behaviors, synthetic biologists use libraries of modular parts that can be characterized in isolation and assembled together to create programmable higher‐order functions. Characterization…
View article: PLANT-Dx: A Molecular Diagnostic for Point of Use Detection of Plant Pathogens
PLANT-Dx: A Molecular Diagnostic for Point of Use Detection of Plant Pathogens Open
Synthetic biology based diagnostic technologies have improved upon gold standard diagnostic methodologies by decreasing cost, increasing accuracy, and enhancing portability. However there has been little effort in adapting these technologi…
View article: Synthetic pluripotent bacterial stem cells
Synthetic pluripotent bacterial stem cells Open
A defining property of stem cells is their ability to differentiate via asymmetric cell division, in which a stem cell creates a differentiated daughter cell but retains its own phenotype. Here, we describe a synthetic genetic circuit for …
View article: Distinct timescales of RNA regulators enable the construction of a genetic pulse generator
Distinct timescales of RNA regulators enable the construction of a genetic pulse generator Open
To build complex genetic networks with predictable behaviours, synthetic biologists use libraries of modular parts that can be characterized in isolation and assembled together to create programmable higher-order functions. Characterizatio…
View article: A Cell-Free Biosensor for Detecting Quorum Sensing Molecules in <i>P. aeruginosa</i>-Infected Respiratory Samples
A Cell-Free Biosensor for Detecting Quorum Sensing Molecules in <i>P. aeruginosa</i>-Infected Respiratory Samples Open
Synthetic biology designed cell-free biosensors are a promising new tool for the detection of clinically relevant biomarkers in infectious diseases. Here, we report that a modular DNA-encoded biosensor in cell-free protein expression syste…
View article: Computational design of Small Transcription Activating RNAs (STARs) for versatile and dynamic gene regulation
Computational design of Small Transcription Activating RNAs (STARs) for versatile and dynamic gene regulation Open
A longstanding goal of synthetic biology has been the programmable control of cellular functions. Central to this goal is the creation of versatile regulatory toolsets that allow for programmable control of gene expression. Of the many reg…