Biology subjects

Dundas, C. M.

Publications and source records attributed to Dundas, C. M..

8 recordsLinked to original sources

bioRxiv2026

Rhizobacterial Biosensors Spatially Map Natural and Engineered Sucrose Exudation

Root exudation mediates the delivery of plant primary and secondary metabolites into soil, where they regulate plant-microbe interactions and terrestrial carbon cycling. Conventional exudate analyses quantify total root-released carbon yet obscure the spatial origin and rhizosphere influence of individual compounds. Here, we develop a rhizobacterial biosensor platform, named Suc-MAPP, to map local exudate profiles along the surface of colonized root tissues. Focusing on sucrose, we engineered sfGFP-based, sucrose-responsive gene circuits in Pseudomonas putida KT2440 for live imaging of exudate concentrations in the micromolar range. These biosensors reveal spatially structured sucrose exudation patterns across eudicots and monocots and implicate photoassimilated source-sink dynamics as a major determinant. We further apply this platform to phenotype exudation modulated by synthetic gene circuitry in Arabidopsis thaliana, identifying genetic design rules for graded sucrose release and quantifying how engineered export sculpts rhizosphere assembly of a defined bacterial community. Together, these results establish programmable rhizobacterial biosensors as tools to spatially resolve plant-environment carbon exchange in situ and provide a framework for extending this approach to diverse exudate targets.

synthetic biology↗

bioRxiv2023

A Hybrid Transistor with Transcriptionally Controlled Computation and Plasticity

Organic electrochemical transistors (OECTs) are ideal devices for translating biological signals into electrical readouts and have applications in bioelectronics, biosensing, and neuromorphic computing. Despite their potential, developing programmable and modular methods for living systems to interface with OECTs has proven challenging. Here we describe hybrid OECTs containing the model electroactive bacterium Shewanella oneidensis that enable the transduction of biological computations to electrical responses. Specifically, we fabricated planar p-type OECTs and demonstrated that channel de-doping is driven by extracellular electron transfer (EET) from S. oneidensis. Leveraging this mechanistic understanding and our ability to control EET flux via transcriptional regulation, we used plasmid-based Boolean logic gates to translate biological computation into current changes within the OECT. Finally, we demonstrated EET-driven changes to OECT synaptic plasticity. This work enables fundamental EET studies and OECT- based biosensing and biocomputing systems with genetically controllable and modular design elements.

bioengineering↗

bioRxiv2021

Transcriptional Regulation of Synthetic Polymer Networks

Individual cells direct non-equilibrium processes through coordinated signal transduction and gene expression, allowing for dynamic control over multicellular, system-wide behavior. This behavior extends to remodeling the extracellular polymer matrix that encases biofilms and tissues, where constituent cells dictate spatiotemporal network properties including stiffness, pattern formation, and transport properties. The majority of synthetic polymer networks cannot recreate these phenomena due to their lack of autonomous centralized actuators (i.e., cells). In addition, non-living polymer networks that perform computation are generally restricted to a few inputs (e.g., light, pH, enzymes), limiting the logical complexity available to a single network chemistry. Toward synergizing the advantages of living and synthetic systems, engineered living materials leverage genetic and metabolic programming to establish control over material-wide properties. Here we demonstrate that a bacterial metal respiration mechanism, extracellular electron transfer (EET), can control metal-catalyzed radical cross-linking of polymer networks. Linking metabolic electron flux to a synthetic redox catalyst allows dynamic, tunable, and predictable control over material formation and bulk polymer network mechanics using genetic circuits. By programming key EET genes with transcriptional Boolean logic, we rationally design computational networks that sense-and-respond to multiple inputs in biological contexts. Finally, we capitalize on the wide reactivity of EET and redox catalyses to predictably control another class of living synthetic materials using copper(I) alkyne-azide cycloaddition click chemistry. Our results demonstrate the utility of EET as a bridge for controlling abiotic materials and how the design rules of synthetic biology can be applied to emulate physiological behavior in polymer networks.

synthetic biology↗

bioRxiv2019

Tuning Extracellular Electron Transfer by Shewanella oneidensis Using Transcriptional Logic Gates

Extracellular electron transfer pathways, such as those in the bacterium Shewanella oneidensis, interface cellular metabolism with a variety of redox-driven applications. However, designer control over EET flux in S. oneidensis has proven challenging since a functional understanding of its EET pathway proteins and their effect on engineering parameterizations (e.g., response curves, dynamic range) is generally lacking. To address this, we systematically altered transcription and translation of single genes encoding parts of the primary EET pathway of S. oneidensis, CymA/MtrCAB, and examined how expression differences affected model-fitted parameters for Fe(III) reduction kinetics. Using a suite of plasmid-based inducible circuits maintained by appropriate S. oneidensis knockout strains, we pinpointed construct/strain pairings that expressed cymA, mtrA, and mtrC with maximal dynamic range of Fe(III) reduction rate. These optimized EET gene constructs were employed to create Buffer and NOT gate architectures, that predictably turn on and turn off EET flux, respectively, in response to IPTG. Furthermore, we found that response functions generated by these logic gates (i.e., EET activity vs. inducer concentration) were comparable to those generated by conventional synthetic biology circuits, where fluorescent reporters are the output. Our results provide insight on programming EET activity with transcriptional logic gates and suggest that previously developed transcriptional circuitry can be adapted to predictably control EET flux.

synthetic biology↗

bioRxiv2019

Genetic Control of Radical Crosslinking in a Semi-Synthetic Hydrogel

Enhancing materials with the qualities of living systems, including sensing, computation, and adaptation, is an important challenge in designing next-generation technologies. Living materials seek to address this challenge by incorporating live cells as actuating components that control material function. For abiotic materials, this requires new methods that couple genetic and metabolic processes to material properties. Toward this goal, we demonstrate that extracellular electron transfer (EET) from Shewanella oneidensis can be leveraged to control radical crosslinking of a methacrylate-functionalized hyaluronic acid hydrogel. Crosslinking rates and hydrogel mechanics, specifically storage modulus, were dependent on a variety of chemical and biological factors, including S. oneidensis genotype. Bacteria remained viable and metabolically active in the crosslinked network for a least one week, while cell tracking revealed that EET genes also encode control over hydrogel microstructure. Moreover, construction of an inducible gene circuit allowed transcriptional control of storage modulus and crosslinking rate via the tailored expression of a key electron transfer protein, MtrC. Finally, we quantitatively modeled dependence of hydrogel stiffness on steady-state gene expression, and generalized this result by demonstrating the strong relationship between relative gene expression and material properties. This general mechanism for radical crosslinking provides a foundation for programming the form and function of synthetic materials through genetic control over extracellular electron transfer.\n\nSignificance StatementNext-generation materials will require coupling the advantages of engineered and natural systems to solve complex challenges in energy, health, and the environment. Living cells, such as bacteria, naturally possess many of the qualities essential to addressing these challenges, including sensing, computation, and actuation, using their genetic and metabolic machinery. In addition, bacteria are attractive for incorporation into materials due to their durability, ease-of-use, and programmability. Here, we develop a platform for controlling hydrogel properties (e.g., stiffness, crosslinking rate) using extracellular electron transfer from the bacterium Shewanella oneidensis. In our system, metabolic electron flux from S. oneidensis to a metal catalyst generates radical species that crosslink an acrylate-based macromer to form the gel. This synthetic reaction is under direct control of bacterial genetics and metabolism, which we demonstrate through inducible circuits and quantitative modeling of gene expression and resultant hydrogel properties. Developing methods that capitalize on the programmability of biological systems to control synthetic material properties will enable hybrid material designs with unprecedented functions.

synthetic biology↗

bioRxiv2018

Extracellular Electron Transfer by Shewanella oneidensis Controls Pd Nanoparticle Phenotype

AbstarctBiological production of inorganic materials is impeded by relatively few organisms possessing genetic and metabolic linkage to material properties. The physiology of electroactive bacteria is intimately tied to inorganic transformations, which makes genetically tractable and well-studied electrogens, such as Shewanella oneidensis, attractive hosts for material synthesis. Notably, this species is capable of reducing a variety of transition-metal ions into functional nanoparticles, but exact mechanisms of nanoparticle biosynthesis remain ill-defined. We report two key factors of extracellular electron transfer by S. oneidensis, the outer membrane cytochrome, MtrC, and soluble redox shuttles (flavins), that affect Pd nanoparticle formation. Changes in the expression and availability of these electron transfer components drastically modulated particle phenotype, including particle synthesis rate, structure, and cellular localization. These relationships may serve as the basis for biologically tailoring Pd nanoparticle catalysts and could potentially be used to direct the biogenesis of other metal nanomaterials.

synthetic biology↗

bioRxiv2018

Microbial Reduction of Metal-Organic Frameworks Enables Synergistic Chromium Removal

Microbe-material redox interactions underpin many emerging technologies, including bioelectrochemical cells and bioremediation. However, commonly utilized material substrates, such as metal oxides, suffer from a lack of tunability and can be challenging to characterize. In contrast, metal-organic frameworks, a class of porous materials, exhibit well-defined structures, high crystallinity, large surface areas, and extensive chemical tunability. Here, we report that metal-organic frameworks can support the growth of the electroactive bacterium Shewanella oneidensis. Specifically, we demonstrate that Fe(III)-containing frameworks, MIL-100 and Fe-BTC, can be reduced by the bacterium via its extracellular electron transfer pathways and that reduction rate/extent is tied to framework structure, surface area, and particle morphology. In a practical application, we show that cultures containing S. oneidensis and reduced frameworks can remediate lethal concentrations of Cr(VI), and that pollutant removal exceeds the performance of either component in isolation or bioreduced iron oxides. Repeated cycles of Cr(VI) dosing had little effect on bacterial viability or Cr(VI) adsorption capacity, demonstrating that the framework confers protection to the bacteria and that no regenerative step is needed for continued bioremediation. In sum, our results show that metal-organic frameworks can serve as microbial respiratory substrates and suggest that they may offer a promising alternative to metal oxides in applications seeking to combine the advantages of bacterial metabolism and synthetic materials.

microbiology↗

bioRxiv2016

Super-resolution Imaging of Synaptic and Extra-synaptic Pools of AMPA Receptors with Different-sized Fluorescent Probes

Whether AMPA receptors (AMPARs) enter into neuronal synapses, by exocytosis from an internal pool, or by diffusion from an external membrane-bound pool, is hotly contested. 3D super-resolution fluorescent nanoscopy to measure the dynamics and placement of AMPAR is a powerful method for addressing this issue. However, probe size and accessibility to tightly packed spaces can be limiting. We have therefore labeled AMPARs with differently sized fluorophores: small organic fluorescent dyes (~ 4 nm), small quantum dots (sQD, ~10 nm in diameter), or big (commercial) quantum dots (bQD, ~ 20 nm in diameter). We then compared their diffusion rate, trajectories, and placement with respect to a postsynaptic density (PSD) protein, Homer 1c. Labeled with the small probes of sQDs or organic fluorophores, we find that AMPARs are located largely within PSDs (~73-93%), and generally reside in \"nanodomains\" with constrained diffusion. In contrast, when labeled with bQDs, only 5-10% of AMPARs are within PSDs. The results can be explained by relatively free access, or lack thereof, to synaptic clefts of the AMPARs when labeled with small or big probes, respectively. This implies that AMPARs primarily enter PSDs soon after their exocytosis and not from a large diffusive pool of extrasynaptic AMPARs.

neuroscience↗