Browsing by Author "Fulk, Emily M."

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    Parallelizing Interproscan with SLURM
    (Rice University, 6/27/2023) Fulk, Emily M.; Goldman, Annelise L.; Momper, Lily; Heider, Clinton; Mulligan, John; Osburn, Magdalena; Masiello, Caroline A.; Silberg, Jonathan J.; Systems, Synthetic, and Physical Biology
    This repository contains code to facilitate analysis of large numbers of proteins by Interproscan with minimum user oversight and efficient use of computational resources. It provides templates for parallelizing Interproscan with SLURM on the Rice NOTS computing cluster, following a high-throughput computing model.
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    Translating New Synthetic Biology Advances for Biosensing Into the Earth and Environmental Sciences
    (Frontiers, 2021) Del Valle, Ilenne; Fulk, Emily M.; Kalvapalle, Prashant; Silberg, Jonathan J.; Masiello, Caroline A.; Stadler, Lauren B.; Bioengineering; Biosciences; Chemical and Biomolecular Engineering; Chemistry; Civil and Environmental Engineering
    The rapid diversification of synthetic biology tools holds promise in making some classically hard-to-solve environmental problems tractable. Here we review longstanding problems in the Earth and environmental sciences that could be addressed using engineered microbes as micron-scale sensors (biosensors). Biosensors can offer new perspectives on open questions, including understanding microbial behaviors in heterogeneous matrices like soils, sediments, and wastewater systems, tracking cryptic element cycling in the Earth system and establishing the dynamics of microbe-microbe, microbe-plant, and microbe-material interactions. Before these new tools can reach their potential, however, a suite of biological parts and microbial chassis appropriate for environmental conditions must be developed by the synthetic biology community. This includes diversifying sensing modules to obtain information relevant to environmental questions, creating output signals that allow dynamic reporting from hard-to-image environmental materials, and tuning these sensors so that they reliably function long enough to be useful for environmental studies. Finally, ethical questions related to the use of synthetic biosensors in environmental applications are discussed.
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    Understanding how gas-producing biosensors can be used in living soils to study biological processes in situ
    (2022-04-13) Fulk, Emily M.; Silberg, Jonathan J.; Masiello, Caroline A.
    Soil microbes regulate critical Earth system processes, including mediating the transformation of biogeochemical cycle intermediates, regulating the production and consumption of greenhouse gases, and forming essential plant symbioses. However, little is known about how macroscale conditions, including soil properties like or- ganic matter content or climactic properties like hydration, influence the microscale environment and microbial behavior in soils. Engineered microbes that function as biosensors present an opportunity to understand how microbial consortia members re- spond to dynamic conditions within a spatially and temporally heterogeneous matrix environment. In this thesis, I review opportunities to engineer microbial biosensors that can sense the microscale environment and produce a detectable signal to report on their experiences. Then, I describe my work to enable ultrasensitive detection of a volatile gas signal produced by biosensing cells, enabling non-invasive monitoring of microbial behavior within a living soil. I show that these tools enable non-destructive detection of a sugar in bulk soil at biosensor cell titers that are orders of magnitude below the abundance of native microbial consortia in soils. I also describe my efforts to expand the use of gas-producing enzymes to report on post-translational protein interactions, and show my progress towards developing a nitrate biosensor for in situ applications in soil. Finally, I discuss opportunities to further advance applications of synthetic biology to address Earth and environmental science questions.