James Chappell

The paper demonstrates how to use orthogonal trans-splicing ribozymes to store and report on multiple plasmid-encoded traits in microbial communities using RNA barcoding.

The paper evaluates how toxin-based biocontainment systems affect horizontal gene transfer in a wastewater microbiome using orthogonal catalytic RNA to track plasmid host range and persistence.

This study engineers ligand-activated splicing ribozymes (LASRs) using domain insertion and high-throughput screening, showing their functionality across multiple kingdoms and applications in genetic regulation and information recording.

This paper introduces a droplet microfluidic platform that significantly improves DNA delivery efficiency in non-model organisms through enhanced conjugation.

The paper improves an RNA barcoding technology for tracking gene transfer in microbiomes by enhancing signal strength and modularity.

This paper introduces a signal amplifier platform integrated with RNA sensors to improve sensitivity and dynamic range for detecting low-abundance transcripts.

The paper designs synthetic origins of replication (SynORI) that allow customizable and modular plasmid copy numbers and environmental signal responses in E. coli.

The paper introduces Ribodesigner, a tool to design catalytic RNAs that selectively barcode specific taxonomic groups, demonstrating increased selectivity over broad host range designs.

The paper uses a synthetic ribozyme to detect phage-host interactions in microbial communities through 16S rRNA sequencing, identifying Aeromonadales as a novel host for phage P1.

The paper uses synthetic RNA to store and detect information in microbial communities through rRNA sequencing, revealing differences in information storage across variants.

This paper introduces a ribozyme-mediated gene-fragment complementation system to report DNA transfer in soil by detecting methyl halides produced through conjugation events.

This paper introduces a CRISPR-associated transposon system for targeted gene activation in E. coli and shows its ability to induce antibiotic resistance.

This paper designs a portable regulatory RNA array for tunable gene regulation across diverse bacteria, enabling complex circuitry without requiring large regulatory libraries.

This paper introduces RENDR, a system that uses RNA to control protein outputs by splicing split ribozymes, demonstrating detection of antibiotic resistance in bacteria.

This paper develops CRISPRi and CRISPRa systems in Streptomyces to activate silent biosynthetic gene clusters for antibiotic discovery.

This study develops a bacterial CRISPRa system using type I-E CRISPR-Cas, showing distinct activation range and periodicity compared to type II systems.

This paper introduces RNA compensation, a positive feedback strategy to mitigate RNA signal consumption in RNA-based circuits, improving composability and modularity.

This paper describes a synthetic genetic circuit in E. coli that enables asymmetric cell division through plasmid partitioning, leading to differentiated daughter cells.

This paper develops a portable, low-cost diagnostic system for detecting plant pathogens using synthetic biology and isothermal amplification with colorimetric output.

The paper characterizes two RNA regulators with distinct timescales and demonstrates their use in creating a genetic pulse generator through computational modeling and experimental validation.

The paper designs computational methods to create STARs, RNA regulators that activate genes up to 9000-fold, and demonstrates their use in genetic circuits.

This paper improves the fold activation of STAR regulators using rational RNA engineering strategies, increasing activation from 5.4-fold to 13.4-fold and demonstrating generalizability across unrelated STARs.

This paper demonstrates the use of cell-free TX-TL systems to rapidly characterize genetic networks, including an RNA transcriptional cascade and a protein-regulated incoherent feed-forward loop.

This study uses cell-free TX-TL systems to rapidly prototype and characterize RNA genetic circuits, showing response times of ~5 minutes per cascade step and demonstrating temporal gene expression staging.