Biology subjects

Chory, E. J.

Publications and source records attributed to Chory, E. J..

11 recordsLinked to original sources

bioRxiv2026

Hydrogel microneedle patch for low-cost, colorimetric, continuous glucose monitoring

Diabetes is a chronic condition characterized by dysregulated blood glucose levels. Continuous glucose monitors (CGMs) enable minimally invasive, real-time monitoring of glucose levels, but broader access requires devices that are both effective and affordable. Popular CGMs such as Dexcom and FreeStyle Libre have high accuracy and are integrated with mobile applications to display real-time data and alerts but are limited by high cost. We developed a low-cost, electronic-free, microneedle hydrogel patch CGM that utilizes colorimetric detection to continuously monitor glucose levels. The proposed patch penetrates the skin and absorbs interstitial fluid (ISF) containing glucose. This glucose reacts with glucose oxidase (GOx) enzyme embedded in the hydrogel, producing gluconic acid and decreasing the pH of the hydrogel. As glucose levels increase, decreasing pH levels are reported by the loaded pH indicator bromocresol purple (BCP) via a color change from purple to yellow. This system was validated through a combination of in vitro experiments and COMSOL computational modeling to assess performance at physiologically relevant glucose concentrations. The resulting hydrogels demonstrated reversible and dynamic color changes in response to glucose levels ranging from 3.5-10 mmol/L (63-180 mg/dL), supporting their potential for continuous monitoring applications. A quantitative, image-based analysis method enabled estimation of glucose concentration from photographs, demonstrating strong predictive performance (RMSE=8.59 mg/dL, R2=0.94). Although optimization of mechanical strength and diffusion kinetics remain necessary, these findings highlight the promise of integrating colorimetric sensing with microneedle-based sampling for affordable, user-friendly glucose monitoring.

bioengineering↗

bioRxiv2026

Gene circuit-driven amplified selection enables evolution of fast-growing Escherichia coli

The laboratory Escherichia coli K-12 strain has doubled no faster than [~]20 minutes for decades. This plateau could reflect a biophysical limit or simply the way batch culture selects on growth rate. Here we show it can be broken through amplified selection with a Red Queen gene circuit, which takes advantage of growth rate heterogeneity in monoclonal populations to selectively suppress slow-growing cells and creates a tunable mapping from intrinsic growth rate to survival. After 70 days ([~]1,000 generations) of amplified selection in MG1655+FHr and subsequent removal of the circuit, a top evolved clone (RQ70) reached a maximum specific growth rate of 2.61 h-{superscript 1} in shake-flask culture. This corresponds to a doubling time of 15.9 minutes, to our knowledge the shortest reported for E. coli K-12, against 18.1 minutes for evolved controls and 20.3 minutes for the ancestor. The gain came at the cost of a [~]3-fold increase in lag time, indicating that the 20-minute plateau is a multi-trait optimum under conventional batch selection rather than an absolute constraint. We argue that synthetic gene circuits can therefore reshape the evolutionary process itself, pushing performance beyond apparent physiological limits.

synthetic biology↗

bioRxiv2026

A Purpose-Built Open Source Liquid Handler for Industry-Class Automated Experiments

The expanding scope of laboratory automation increasingly demands systems that can be tailored to specific experimental constraints, including footprint, timing, cost, and control. While open-source software has improved protocol flexibility, liquid-handling hardware itself remains largely closed, limiting the ability of academic and startup laboratories to build instruments around biological requirements rather than vendor defaults. Here, we present a fully open-source, purpose-built liquid-handling robot assembled from commercially available components and developed entirely in a research setting. The platform integrates open hardware, electronics, and a Python-based control stack compatible with PyLabRobot, exposing low-level motion dynamics and liquid-handling behaviors directly to experiment code. We validate the system using a high-throughput turbidostat workflow that requires rapid, closed-loop measurement and actuation to maintain microbial cultures at defined density setpoints. The robot sustains stable steady-state growth across approximately 200 cultures with heterogeneous growth dynamics. A replica build completed by two lab members in approximately one week confirms that the platform can be reproduced from its bill of materials and assembly guide. Its compact footprint and use of off-the-shelf components make it suitable for rapid, parallel deployment in settings such as public health emergencies or by distributed laboratories. Together, these results demonstrate that industry-class liquid handlers can be custom-built for specific experimental goals, establishing a blueprint for open, purpose-driven hardware development across research and industrial automation contexts. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC="FIGDIR/small/709168v1_ufig1.gif" ALT="Figure 1"> View larger version (63K): org.highwire.dtl.DTLVardef@1b2cb4eorg.highwire.dtl.DTLVardef@1418e8dorg.highwire.dtl.DTLVardef@f60618org.highwire.dtl.DTLVardef@a3d3b_HPS_FORMAT_FIGEXP M_FIG Open Liquid Handler (OLH) Design Goals. Left: Design goals for a purpose-built platform for time-sensitive, closed-loop biological workflows, emphasizing high-accuracy dosing (low variability liquid handling), rapid integrated measurement (plate deck and isolated workspace), customizable deck and peripheral options, compact footprint with high throughput, containment via an enclosed wet workspace for biosafety and sterility, and a replicable build using off-the-shelf OEM components with open design files. Right: Open Liquid Handler design and physical implementation, with aerial and front views highlighting the enclosed cabinet and the working envelope over a compact deck. C_FIG

bioengineering↗

bioRxiv2026

An autonomous system for multi-objective continuous evolution at scale

Natural evolution is high-dimensional; organisms adapt to many pressures at once, across substrates, environments, and genetic backgrounds. Yet most directed evolution methods flatten this landscape to a single selection axis, hiding tradeoffs, and limiting what can be learned. Phage-assisted continuous evolution (PACE) is uniquely suited for multivariate selection because horizontal gene transfer couples genotype to propagation and allows the same phage lineage to traverse different selection environments. In practice, implementing this at scale has been prohibitive because each selection demands its own host culture, and every culture must be held for days to weeks within a narrow, infectable density window using continuously responsive bioreactors. In this work, TurboPRANCE is presented as an open-source, queueable robotic platform that integrates [~]200 independently controlled turbidostats with 96 parallel PACE lagoons under closed-loop control. Each turbidostat operates as a fully separate unit that can be equilibrated and initiated on its own schedule, enabling asynchronous starts and sustained operation without intervention. Automated media formulation, programmable dosing, on-deck sterilization, and adaptive scheduling coordinate growth control with the changing needs of the robotic workflow, dynamically adjusting dilution and transfer timing around formulation, sampling, and handling steps to keep each culture at consistent infectable densities despite unpredictable method demands. Cultures can be multiplexed and titrated into lagoons at defined ratios, swapped in and out on a schedule, or kept fully separate across experiments, creating a combinatorial space of selection pressures and programs that is effectively unbounded. Additionally, to enable high-throughput evolutionary tracking that scales with TurboPRANCE, Nanopore long-read sequencing was combined with DeepVariant, a deep learning-based variant caller, enabling population-level tracking of evolving variants. The result is a system that generates high-resolution time-resolvable evolutionary trajectories and large parallel datasets spanning diverse selection regimes, yielding dense, multivariate training data to map and engineer complex fitness landscapes at scale. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/709196v2_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@b0f8daorg.highwire.dtl.DTLVardef@a1d57eorg.highwire.dtl.DTLVardef@c771aeorg.highwire.dtl.DTLVardef@1f8729a_HPS_FORMAT_FIGEXP M_FIG Turbidostat, Phage, and Robotics-Assisted Near Continuous Evolution (TurboPRANCE) In phage-assisted continuous evolution (PACE), biomolecular activity is coupled to pIII expression, linking function to phage propagation. By altering the host strain, distinct selection pressures can be imposed on the same evolving phage population. In TurboPRANCE, [~]200 selection programs can vary over time, including periodic "drift" (mutagenesis), alternation between pressures, or rotational reassignment of host sources, enabling a combinatorial space of selection pressures. C_FIG

bioengineering↗

bioRxiv2024

Heritable Immunization Establishes a New Model for Pathogen Control

Heritable immunization represents a promising approach for controlling infectious diseases by embedding immunity directly into the genomes of wild species that spread human pathogens. Here, we report the genetic engineering of Mus musculus to produce a neutralizing, protective single-chain antibody against Borrelia burgdorferi, the causative agent of Lyme disease. Engineered mice stably produced a LA-2 scFv-albumin fusion protein across multiple generations, demonstrating robust heritability and stability of gene expression. Following sequential challenges with infected and uninfected ticks, heterozygous mice exhibited strong resistance to infection, effectively interrupting the Borrelia burgdorferi disease transmission cycle. Having recently established novel protocols to genetically engineer the white-footed mouse, Peromyscus leucopus, a key reservoir of Lyme disease, these findings demonstrate the feasibility of heritable immunization as a potential strategy for mitigating Lyme disease transmission in the environment. More broadly, engineered reservoir immunity may offer a generalizable approach to controlling vector-borne and zoonotic disease with profound potential to improve human health.

bioengineering↗

bioRxiv2023

Low-cost camera-based estrous tracking enables transgenesis in Peromyscus leucopus, the primary reservoir for Lyme disease

CRISPR/Cas9 technology has revolutionized the production of animal models by reducing experimental timelines, slashing costs and streamlining gene editing, leading to a rapid expansion in the number of unique models for the study of human disease and gene function. However, most non-model animals, many of which are important in cancer and aging research, remain recalcitrant to genome engineering due to our limited understanding of their reproductive biology. Many wild rodents that transmit human diseases remain particularly challenging to engineer due to low pregnancy rates, the lack of external copulatory plugs, and susceptibility to premature termination of pregnancy. Here, we present low-cost activity-based estrous tracking for the efficient generation of timed pregnant and pseudopregnant white-footed mice and extend this tracking method to both lab mice and hamsters. Leveraging this technology, we demonstrate the generation of engineered Peromyscus leucopus, the primary reservoir for Lyme disease-causing bacteria and a putative model organism for studies of aging. These tools have broad implications for biomedical research and ecological engineering. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/563285v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@19a3fb2org.highwire.dtl.DTLVardef@1cbce4corg.highwire.dtl.DTLVardef@1551e0corg.highwire.dtl.DTLVardef@127c028_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2022

High-throughput Approaches to Uncover Synergistic Drug Combinations in Leukemia

We report a comprehensive drug synergy study in acute myeloid leukemia (AML). In this work, we investigate 11 cell lines spanning both MLL-rearranged and non-rearranged subtypes. The work comprises a resource for the community, with many synergistic drug combinations that could not have been predicted a priori, and open source code for automation and analyses. We base our definitions of drug synergy on the Chou-Talalay method, which is useful for visualizations of synergy experiments in isobolograms, and median-effects plots, among other representations. Our key findings include drug synergies affecting the chromatin state, specifically in the context of regulation of the modification state of histone H3 lysine-27. We report open source high throughput methodology such that multidimensional drug screening can be accomplished with equipment that is accessible to most laboratories. This study will enable preclinical investigation of new drug combinations in a lethal blood cancer, with data analysis and automation workflows freely available to the community. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/518409v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1e85ef9org.highwire.dtl.DTLVardef@b3369eorg.highwire.dtl.DTLVardef@1c6d705org.highwire.dtl.DTLVardef@14ec6b2_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2020

Flexible open-source automation for robotic bioengineering

INTRODUCTIONLiquid handling robots have become a biotechnology staple1,2, allowing laborious or repetitive protocols to be executed in high-throughput. However, software narrowly designed to automate traditional hand-pipetting protocols often struggles to harness the full capabilities of robotic manipulation. Here we present Pyhamilton, an open-source Python package that eliminates these constraints, enabling experiments that could never be done by hand. We used Pyhamilton to double the speed of automated bacterial assays over current software and execute complex pipetting patterns to simulate population dynamics. Next, we incorporated feedback-control to maintain hundreds of remotely monitored bacterial cultures in log-phase growth without user intervention. Finally, we applied these capabilities to comprehensively optimize bioreactor protein production by maintaining and monitoring fluorescent protein expression of nearly 500 different continuous cultures to explore the carbon, nitrogen, and phosphorus fitness landscape. Our results demonstrate Pyhamiltons empowerment of existing hardware to new applications ranging from biomanufacturing to fundamental biology.

bioengineering↗

bioRxiv2020

A high-throughput platform for feedback-controlled directed evolution.

Continuous directed evolution rapidly implements cycles of mutagenesis, selection, and replication to accelerate protein engineering. However, individual experiments are typically cumbersome, reagent-intensive, and require manual readjustment, limiting the number of evolutionary trajectories that can be explored. We report the design and validation of Phage-and-Robotics-Assisted Near-Continuous Evolution (PRANCE), an automation platform for the continuous directed evolution of biomolecules that enables real-time activitydependent reporter and absorbance monitoring of up to 96 parallel evolution experiments. We use this platform to characterize the evolutionary stochasticity of T7 RNA polymerase evolution, conserve precious reagents with miniaturized evolution volumes during evolution of aminoacyl-tRNA synthetases, and perform a massively parallel evolution of diverse candidate quadruplet tRNAs. Finally, we implement a feedback control system that autonomously modifies the selection strength in response to real-time fitness measurements. By addressing many of the limitations of previous methods within a single platform, PRANCE simultaneously enables multiplexed, miniaturized, and feedback-controlled continuous directed evolution.

bioengineering↗

bioRxiv2019

Inhibition of a Selective SWI/SNF Function Synergizes with ATR Inhibitors in Cancer Cell Killing

SWI/SNF (BAF) complexes are a diverse family of ATP-dependent chromatin remodelers produced by combinatorial assembly that are mutated in and thought to contribute to 20% of human cancers and a large number of neurologic diseases. The gene-activating functions of BAF complexes are essential for viability of many cell types, limiting the development of small molecule inhibitors. To circumvent the potential toxicity of SWI/SNF inhibition, we identified small molecules that inhibit the specific repressive function of these complexes but are relatively non-toxic and importantly synergize with ATR inhibitors in killing cancer cells. Our studies suggest an avenue for therapeutic enhancement of ATR/ATM inhibition and provide evidence for chemical synthetic lethality of BAF complexes as a therapeutic strategy in cancer.

cancer biology↗

bioRxiv2018

Nucleosome turnover is sufficient to establish varied histone methylation states

Transcription-dependent methylation of histone H3 at lysine 79 (H3K79) is evolutionarily conserved from yeast to mammals, critical for normal development and frequently deregulated by genetic recombination in Mixed Lineage Leukemia. Although this histone modification is associated with gene activity, little is known about the cellular mechanisms of H3K79 methylation regulation. Because no H3K79 demethylase has been discovered, the mechanism of its removal remains unclear. Utilizing chemical-induced-proximity to control histone methylation in vivo we show that the dynamics of methylation state (mono, di, tri-methylation) is genome-context specific. Further, Monte Carlo simulations coupling systems of kinetic reactions with histone turnover rates, suggest that nucleo-some turnover is sufficient to establish varied genome-wide methylation states without active demethylation.

molecular biology↗