19 Mar 2025

Peptide Display for Rare Earth Element Binding

Abstract: Rare earth elements (REEs) are metals that are indispensable to the function of many advanced systems and materials. The supply chain of REEs is heavily dependent on foreign sources and supply shortages are a major concern to the US government. Biological recovery approaches could be an economically feasible approach to recover REEs from unconventional or secondary sources. The objective of this project was to express a lanthanide-binding tag, with an affinity for adsorption of REEs, on the surface of the biomining bacterium, Acidithiobacillus ferrooxidans. This was to be accomplished using synthetic biology tools. The initial cloning steps were performed in Escherichia coli, since techniques are well established in this strain. Using a peptide display approach, several DNA constructs with the binding tag were designed that were regulated by constitutive or inducible promoters and cloned into plasmids that replicate in E. coli and A. ferrooxidans. All plasmids were observed to be unstable or lethal in E. coli, exhibiting sequence rearrangements or deletion of the designed construct. Conjugation between E. coli and A. ferrooxidans and subsequent REE binding assays were thus not possible due to the absence of a structurally and functionally intact plasmid.

26 Sep 2023

Isolation and Characterization of Bacterial Isolates from Alaskan Permafrost for Synthetic Biology Applications

Abstract: Operations in the Artic and other cold regions require technologies that can perform reliably under extreme cold conditions. Permafrost and frozen soils harbor a wide range of microorganisms that have adapted to extremely low temperatures and have unique metabolic capabilities relevant to military operations and that could be exploited to develop biotechnologies optimized for cold environments. Cold-tolerant bacteria (psychrophiles and psychrotrophs) are critical to the development of synthetic biology technologies meant to work in cold environments like the Arctic. Using bacteria isolated from Alaskan permafrost, we applied an experimental pipeline to test the best candidates for use as biological platforms, or chassis, for low-temperature synthetic biology. Since synthetic biology constructs will perform only as well as their chassis, it is critical that circuits expected to perform under extreme cold conditions are housed in chassis that are adapted to those conditions. We identified one permafrost isolate, PTI8, related to Rhodococcus fascians, that is capable of growing from −1°C to at least 25°C and which we experimentally confirmed to uptake and express the broad host range plasmid pBTK519, suggesting PTI8 is a candidate for use as a novel cold-adapted chassis for synthetic biology.

30 Jul 2021

A Quantitative Risk Assessment Method for Synthetic Biology Products in the Environment

Abstract: The need to prevent possible adverse environmental health impacts resulting from synthetic biology (SynBio) products is widely acknowledged in both the SynBio risk literature and the global regulatory community. However, discussions of potential risks of SynBio products have been largely speculative, and the attempts to characterize the risks of SynBio products have been non-uniform and entirely qualitative. As the discipline continues to accelerate, a standardized risk assessment framework will become critical for ensuring that the environmental risks of these products are characterized in a consistent, reliable, and objective manner that incorporates all SynBio-unique risk factors. Current established risk assessment frameworks fall short of the features required of this standard framework. To address this, we propose the Quantitative Risk Assessment Method for Synthetic Biology Products (QRA-SynBio) – an incremental build on established risk assessment methodologies that supplements traditional paradigms with the SynBio risk factors that are currently absent and necessitates quantitative analysis for more transparent and objective risk characterizations. The proposed framework facilitates defensible quantification of the environmental risks of SynBio products in both foreseeable and hypothetical use scenarios. Additionally, we show how the proposed method can promote increased experimental investigation into the likelihood of hazard and exposure parameters and highlight the parameters where uncertainty should be reduced, leading to more targeted risk research and more precise characterizations of risk.