Biology subjects

Sheppard, T. J.

Publications and source records attributed to Sheppard, T. J..

4 recordsLinked to original sources

bioRxiv2023

Constraints on Lanthanide Separation by Selective Biosorption

Rare Earth Elements (REE) are essential ingredients of sustainable energy technologies1-5, but separation of lanthanides is considered one of the hardest problems in chemistry today6. Biosorption, where molecules adsorb to the surface of biological materials, offers a sustainable alternative to environmentally harmful solvent extractions currently used for REE separations. The REE-biosorption capabilities of some microorganisms already allow for REE separations that under specialized conditions are competitive with solvent extractions7. Our recent work has discovered the genetic basis for REE biosorption selectivity8. However, it is unclear if the small changes to selectivity produced by changes to single genetic loci could allow biosorption to leapfrog existing REE separation technologies. In this article we present three models of lanthanide separation by biosorption and desorption. The first model shows that if a biosorbing microbe behaves as it if has a single type of binding site with small preference for one lanthanide, then the small changes in selectivity produced by changes to a single genetic locus could reduce the length of a separation process by {approx} 25%. Large multi-locus gene edits could reduce a separation process length by almost 90%. On the other hand, if the microbe contains multiple sites each with a distinct preference for an individual lanthanide, then separations become challenging and larger genetic edits would be needed to enable high purity. However, even if these large genetic edits are not possible, high purity separations could still be possible by combining multiple microbes, each with small increases in selectivity, with the first designed to enrich for the target lanthanide, while subsequent microbes are designed to remove contaminants.

synthetic biology↗

bioRxiv2023

Efficient Natural Plasmid Transformation of Vibrio natriegens Enables Zero-capital Molecular Biology

The fast-growing microbe Vibrio natriegens is capable of natural transformation where it draws DNA in from media via an active process under physiological conditions. Using an engineered strain with a genomic copy of the master competence regulator tfoX from Vibrio cholera in combination with a new minimal competence media (MCM) that uses acetate as an energy source, we demonstrate naturally competent cells which are created, transformed, and recovered entirely in the same media, without exchange or addition of new media. Cells are naturally competent to plasmids, recombination with linear DNA, and co-transformation of both to select for scarless and markerless genomic edits. The entire process is simple and inexpensive, requiring no capital equipment for an entirely room temperature process (Zero Capital protocol, 104 cfu/{micro}g), or just an incubator (High Efficiency protocol, 105-6 cfu/{micro}g). These cells retain their naturally competent state when frozen and are transformable immediately upon thawing like a typical chemical or electrochemical competent cell. Since the optimized transformation protocol requires only 50 minutes of hands-on time, and V. natriegens grows quickly even on plates, a transformation started at 9 AM yields abundant culturable single colonies by 5 PM. Further, because all stages of transformation occur in the same media, and the process can be arbitrarily scaled in volume, this natural competence strain and media could be ideal for automated directed evolution applications. As a result, naturally competent V. natriegens could compete with E. coli as an excellent chassis for low-cost and highly scalable synthetic biology.

synthetic biology↗

bioRxiv2023

Efficiency Estimates for Electromicrobial Production of Branched-chain Hydrocarbons

Electromicrobial production is a process where microorganisms use electricity as a charge and energy source for the production of complex molecules, often from starting compounds as simple as CO2. The aviation industry is in need for sustainable fuel alternatives that can meet their requirements of high-altitude performance while also meeting 21st century carbon emissions standards. The electromicrobial production of jet fuel components with CO2-derived carbon provides a unique opportunity to generate jet fuel blends that are compatible with modern engines with net-neutral carbon emissions. In this study, we analyze the pathways necessary to generate single- and multi-branched-chain hydrocarbons in vivo utilizing both extracellular electron uptake (EEU) and H2-oxidation as methods for electron delivery, the Calvin cycle for CO2-fixation and the ADO decarboxylation pathway. We find the maximum electrical-to-fuel energy conversion efficiencies for single- and multi-branched chain hydrocarbons are [Formula] and [Formula]. Utilizing this information, as well as previously collected predictions on straight-chain alkane and terpenoid biosynthesis, we calculate the efficiency of electromicrobial production of jet fuel blends containing straight-chain, branched-chain, and terpenoid components. Increasing the fraction of branched-chain alkanes in the blend from zero to 47% only lowers the electrical energy conversion efficiency from [Formula] to [Formula].

synthetic biology↗

bioRxiv2022

Upper Limit Efficiency Estimates for Electromicrobial Production of Drop-In Jet Fuels

Microbes which participate in extracellular electron uptake or H2 oxidation have an extraordinary ability to manufacture organic compounds using electricity as the primary source of metabolic energy. So-called electromicrobial production could be of particular value in the efficient production of hydrocarbon blends for use in aviation. Because of exacting standards for fuel energy density and the costs of new aviation infrastructure, liquid hydrocarbon fuels will be necessary for the foreseeable future, precluding direct electrification. Production of hydrocarbons using electrically-powered microbes employing fatty acid synthesis-based production of alkanes could be an efficient means to produce drop-in replacement jet fuels using renewable energy. Here, we calculate the upper limit electrical-to-energy conversion efficiency for a model jet fuel blend containing 85% straight-chain alkanes and 15% terpenoids. When using the Calvin cycle for carbon-fixation, the energy conversion efficiency is [Formula] when using extracellular electron uptake for electron delivery and [Formula] when using H2-oxidation. The efficiency of production of the jet fuel blend can be raised to [Formula] when using the Formolase formate-assimilation pathway and H2-oxidation, and to [Formula] with the Wood-Ljungdahl pathway. The production efficiency can be further raised by swapping the well-known ADO pathway for alkane termination with for the recently discovered MCH pathway. If these systems were were supplied with electricity with a maximally-efficient silicon solar photovoltaic, even the least efficient would exceed the maximum efficiency of all known forms of photosynthesis.

synthetic biology↗