Daniel C. Ducat
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Uncovering the Design Rules for Sustainable Growth of Mineralized Mycomaterials Open
Mycomaterials, materials made from filamentous fungi, have several advantages over traditional materials, such as their genetic programmability and self-healing properties. However, their lack of mechanical strength and cost of production …
Plastoquinone redox status influences carboxysome integrity via a <span>RpaA</span>‐ and reactive oxygen species‐dependent regulatory network Open
SUMMARY Carboxysomes are bacterial microcompartments that encapsulate Rubisco and are a core component of the cyanobacterial carbon concentration mechanism (CCM). While carboxysome number, size, and spatial organization vary in different e…
Engineering quorum-sensing circuits in Synechococcus elongatus PCC 7942 towards self-inducible systems Open
Despite significant potential for cyanobacteria as sustainable bioproduction chases, there are limited examples of scaled cyanobacterial bioproduction. In part, this is because most cyanobacterial species are poorly adapted to bioreactor c…
HIGH CO <sub>2</sub> LEVELS OVERCOME THE NIGHTTIME LETHALITY OF CIRCADIAN MUTANTS IN CYANOBACTERIA Open
Cyanobacteria have adapted to daily fluctuations in light intensity through a circadian clock that aligns their physiology and metabolism to the external daytime. In the model cyanobacterium Synechococcus elongatus PCC 7942, the rhythm gen…
Autoinduction expression systems via engineered quorum-sensing circuits in <i>Synechococcus elongatus PCC 7942</i> Open
Despite significant potential for cyanobacteria as sustainable bioproduction chases, there are limited examples of scaled cyanobacterial bioproduction. In part, this is because most cyanobacterial species are poorly adapted to bioreactor c…
Plastoquinone redox status influences carboxysome integrity via a RpaA- and ROS-dependent regulatory network Open
Carboxysomes are bacterial microcompartments that encapsulate Rubisco and are a core component of the cyanobacterial carbon concentration mechanism (CCM). While carboxysome number, size and spatial organization are observed to vary in diff…
Plastic-binding peptides as anchors for protein scaffolds on synthetic plastics: opportunities and challenges Open
Plastic-binding peptides integrated into programmable multienzyme scaffolds validate binding capacity but reveal off-target binding challenges for rational scaffold design.
Nature-Inspired Strategies for Sustainable Degradation of Synthetic Plastics Open
Synthetic plastics have become integral to our daily lives, yet their escalating production, limited biodegradability, and inadequate waste management contribute to environmental contamination. Biological plastic degradation is one promisi…
Impact of irradiance and inorganic carbon availability on heterologous sucrose production in Synechococcus elongatus PCC 7942 Open
Cyanobacteria have been proposed as a potential alternative carbohydrate feedstock and multiple species have been successfully engineered to secrete fermentable sugars. To date, the most productive cyanobacterial strains are those designed…
Orthogonality of shell proteins across BMC subclasses in cyanobacteria Open
Bacterial microcompartments (BMC) are protein-based organelles broadly distributed across all bacterial phyla and subclassified into ≥60 functional variants. Despite their evolutionary and metabolic diversity, shell proteins that structura…
A new era of synthetic biology—microbial community design Open
Synthetic biology conceptualizes biological complexity as a network of biological parts, devices, and systems with predetermined functionalities and has had a revolutionary impact on fundamental and applied research. With the unprecedented…
Population-level heterogeneity complicates utilization of Synechococcus elongatus PCC 7942 surface display platforms Open
Surface display technologies have been primarily developed for heterotrophic microbes, leaving photosynthetic counterparts like cyanobacteria with limited molecular tools. Here, we expanded upon surface display systems in Synechococcus elo…
View article: Predicting partner fitness based on spatial structuring in a light-driven microbial community
Predicting partner fitness based on spatial structuring in a light-driven microbial community Open
Microbial communities have vital roles in systems essential to human health and agriculture, such as gut and soil microbiomes, and there is growing interest in engineering designer consortia for applications in biotechnology ( e . g ., per…
Cyanobacteria as cell factories for the photosynthetic production of sucrose Open
Biofuels and other biologically manufactured sustainable goods are growing in popularity and demand. Carbohydrate feedstocks required for industrial fermentation processes have traditionally been supplied by plant biomass, but the large qu…
Developing Cyanobacterial Quorum Sensing Toolkits: Toward Interspecies Coordination in Mixed Autotroph/Heterotroph Communities Open
There has been substantial recent interest in the promise of sustainable, light-driven bioproduction using cyanobacteria, including developing efforts for microbial bioproduction using mixed autotroph/heterotroph communities, which could p…
View article: Predicting partner fitness based on spatial structuring in a light-driven microbial community
Predicting partner fitness based on spatial structuring in a light-driven microbial community Open
Microbial communities have vital roles in systems essential to human health and agriculture, such as gut and soil microbiomes, and there is growing interest in engineering designer consortia for applications in biotechnology ( e.g ., perso…
View article: Investigating Carboxysome Morphology Dynamics with a Rotationally Invariant Variational Autoencoder
Investigating Carboxysome Morphology Dynamics with a Rotationally Invariant Variational Autoencoder Open
Carboxysomes are a class of bacterial microcompartments that form proteinaceous organelles within the cytoplasm of cyanobacteria and play a central role in photosynthetic metabolism by defining a cellular microenvironment permissive to CO2…
Developing cyanobacterial quorum sensing toolkits: towards interspecies coordination in mixed autotroph/heterotroph communities Open
1. Abstract There has been substantial recent interest in the promise of sustainable, light-driven bioproduction using cyanobacteria, including developing efforts for microbial bioproduction using mixed autotroph/heterotroph communities, w…
Designing synthetic communities with organism-free modular computational models Open
Synthetic biology designs and constructs new biological parts, devices and systems with predetermined functionalities. With the unlimited ability to synthesise any DNA and RNA and transfer it to almost any organism, we are at the dawn of a…
Rubisco regulation in response to altered carbon status in the cyanobacterium<i>Synechococcus elongatus</i>PCC 7942 Open
Photosynthetic organisms possess a variety of mechanisms to achieve balance between absorbed light (source) and the capacity to metabolically utilize or dissipate this energy (sink). While regulatory processes that detect changes in metabo…
View article: Investigating Carboxysome Morphology Dynamics with a Rotationally Invariant Variational Autoencoder
Investigating Carboxysome Morphology Dynamics with a Rotationally Invariant Variational Autoencoder Open
Carboxysomes are a class of bacterial microcompartments that form proteinaceous organelles within the cytoplasm of cyanobacteria and play a central role in photosynthetic metabolism by defining a cellular microenvironment permissive to CO …
Decision letter: Pyruvate:ferredoxin oxidoreductase and low abundant ferredoxins support aerobic photomixotrophic growth in cyanobacteria Open
Article Figures and data Abstract Editor's evaluation Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract The decarboxylation of…
View article: Investigating the growth of an engineered strain of Cyanobacteria with an Agent-Based Model and a Recurrent Neural Network
Investigating the growth of an engineered strain of Cyanobacteria with an Agent-Based Model and a Recurrent Neural Network Open
A computational framework combining Agent-Based Models (ABMs) and Deep Learning techniques was developed to help design microbial communities that convert light and CO 2 into useful bioproducts. An ABM that accounts for CO 2 , light, sucro…
Multi-layer Regulation of Rubisco in Response to Altered Carbon Status in <i>Synechococcus elongatus</i> PCC 7942 Open
Photosynthetic organisms possess a variety of mechanisms to achieve balance between absorbed light (source) and the capacity to metabolically utilize or dissipate this energy (sink). While regulatory processes that detect changes in metabo…
Editorial: Exploring the Growing Role of Cyanobacteria in Industrial Biotechnology and Sustainability Open
EDITORIAL article Front. Microbiol., 13 July 2021Sec.Microbiotechnology https://doi.org/10.3389/fmicb.2021.725128
Orthogonal Degron System for Controlled Protein Degradation in Cyanobacteria Open
Synechococcus elongatus PCC 7942 is a model cyanobacterium for study of the circadian clock, photosynthesis, and bioproduction of chemicals, yet nearly 40% of its gene identities and functions remain unknown, in part due to limitations of …
Sink Engineering in Photosynthetic Microbes Open
Photosynthetic organisms must balance harvested light energy (source) with a corresponding capacity to utilize the energy via downstream metabolic processes (sink). Insufficient source energy leads to starvation conditions, while insuffici…
Improved photosynthetic capacity and photosystem I oxidation via heterologous metabolism engineering in cyanobacteria Open
Significance Cyanobacteria have been increasingly explored as a biotechnological platform, although their economic feasibility relies in part on the capacity to maximize their photosynthetic, solar-to-biomass energy conversion efficiency. …