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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Automating methods for estimating metabolite volatility

The volatility of metabolites can influence their biological roles and inform optimal methods for their detection. Yet, volatility information is not readily available for the large number of described metabolites, limiting the exploration of volatility as a fundamental trait of metabolites. Here, we adapted methods to estimate vapor pressure from the functional group composition of individual molecules (SIMPOL.1) to predict the gas-phase partitioning of compounds in different environments. We implemented these methods in a new open pipeline called volcalc that uses chemoinformatic tools to automate these volatility estimates for all metabolites in an extensive and continuously updated pathway database: the Kyoto Encyclopedia of Genes and Genomes (KEGG) that connects metabolites, organisms, and reactions. We first benchmark the automated pipeline against a manually curated data set and show that the same category of volatility (e.g., nonvolatile, low, moderate, high) is predicted for 93% of compounds. We then demonstrate how volcalc might be used to generate and test hypotheses about the role of volatility in biological systems and organisms. Specifically, we estimate that 3.4 and 26.6% of compounds in KEGG have high volatility depending on the environment (soil vs. clean atmosphere, respectively) and that a core set of volatiles is shared among all domains of life (30%) with the largest proportion of kingdom-specific volatiles identified in bacteria. With volcalc , we lay a foundation for uncovering the role of the volatilome using an approach that is easily integrated with other bioinformatic pipelines and can be continually refined to consider additional dimensions to volatility. The volcalc package is an accessible tool to help design and test hypotheses on volatile metabolites and their unique roles in biological systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Chemical and Biological Catalysis for Plastics Recycling and Upcycling

Plastics pollution is causing an environmental crisis, prompting the development of new approaches for recycling, and upcycling. Here, we review challenges and opportunities in chemical and biological catalysis for plastics deconstruction, recycling, and upcycling. We stress the need for rigorous characterization and use of widely available substrates, such that catalyst performance can be compared across studies. Where appropriate, we draw parallels between catalysis on biomass and plastics, as both substrates are low-value, solid, recalcitrant polymers. Innovations in catalyst design and reaction engineering are needed to overcome kinetic and thermodynamic limitations of plastics deconstruction. Either chemical and biological catalysts will need to act interfacially, where catalysts function at a solid surface, or polymers will need to be solubilized or processed to smaller intermediates to facilitate improved catalyst–substrate interaction. Overall, developing catalyst-driven technologies for plastics deconstruction and upcycling is critical to incentivize improved plastics reclamation and reduce the severe global burden of plastic waste.

28 EE - Advanced Manufacturing Office (EE-5A)↗
DOE OSTI2019

Electrocatalytic cleavage of lignin model dimers using ruthenium supported on activated carbon cloth

Biomass lignin is the largest natural source of renewable aromatic compounds, creating an opportunity for its use as a feedstock provided that deconstruction and upgrading methods become available. Valorization of lignin is challenging because its complex structure is naturally recalcitrant to biological degradation. Deconstruction of this amorphous cross-linked polymer requires cleavage of aryl ether bonds, which account for more than half of the linkages between lignin's phenylpropanoid building blocks. High temperature cracking of lignin is possible via pyrolysis, but linkages such as 4-O-5 bonds are resistant to thermal degradation. Electrocatalytic hydrogenation offers a mild alternative; operated at low temperature and atmospheric pressure, it cleaves ether bonds while saturating aromatic rings with in situ generated hydrogen. To investigate the use of catalytic ruthenium supported on activated carbon cloth to cleave 4-O-5 bonds, model compounds that exhibit this linkage were selected, including 3-phenoxyphenol, 4-phenoxyphenol, 3-phenoxyanisole, and 3-phenoxytoluene. The two phenols, 3-phenoxyphenol and 4-phenoxyphenol, were cleaved and hydrogenated to form cyclohexanol. 3-Phenoxyanisole and 3-phenoxytoluene were also cleaved but with lower conversion rates and cyclohexanol yields. Alkaline electrolyte solutions showed the highest cyclohexanol yields for both substrates. Increasing substrate concentrations from 10 mM to 40 mM increased faradaic efficiency to 25%, while decreasing current density from 100 mA (33.33 mA cm -2 ) to 20 mA (6.67 mA cm -2 ) greatly improved the faradaic efficiency to 96%.

09 BIOMASS FUELS↗
DOE OSTI2026

Multi-strain analysis of Pseudomonas putida reveals the metabolic and genetic diversity of the species

Pseudomonas putida is a gram-negative bacterial species increasingly utilized in biotechnology due to its robust growth, ability to degrade aromatic compounds, solvent tolerance, and genetic tractability. In this study, we report a comprehensive multi-strain analysis of 164 P. putida strains based on the reconstruction of a pan-putida metabolic network and the formulation of strain-specific genome-scale metabolic models (GEMs). We performed whole-genome sequencing and hybrid assembly for 40 strains, contributing a ~8% increase to the available genomic data for P. putida . Furthermore, high-throughput phenotypic profiling using the Biolog phenotype microarray system for 24 strains on 190 unique carbon sources, along with 15 aromatic compounds not present on Biolog plates, yielded 4,920 unique strain-phenotype measurements. These data were leveraged to curate GEMs for 24 representative strains, including a refined model for strain KT2440, which comprised 1,480 genes and 2,191 metabolites, achieving a prediction accuracy of 91.2% in carbon utilization. Systematic comparison of genomes and GEMs revealed both conserved core pathways and significant allelic and functional divergence across strains, highlighting strain-specific variation in aromatic degradation. While pathways for protocatechuate and phenylacetate degradation were widely conserved, metabolic capabilities for compounds such as ferulate, phenol, and cresols varied markedly, suggesting adaptation to distinct ecological niches. Alleleome analysis of enzymes, such as PcaI and PcaJ, revealed distinct, functionally similar clades, indicating possible convergent evolution or horizontal gene transfer. These results provide computable resources and informative models for selecting P. putida strains with desired traits for biomanufacturing and bioremediation and offer insights into the evolution and phylogeny of the P. putida species.

aromatics utilization↗
DOE OSTI2025

New technology for an ancient fish: A lamprey life cycle modeling tool with an R Shiny application

Lampreys (Petromyzontiformes) are an ancient group of fishes with complex life histories. We created a life cycle model that includes an R Shiny interactive web application interface to simulate abundance by life stage. This will allow scientists and managers to connect available demographic information in a framework that can be applied to questions regarding lamprey biology and conservation. We used Pacific lamprey ( Entosphenus tridentatus ) as a case study to highlight the utility of this model. We applied a global sensitivity analysis to explore the importance of individual life stage parameters to overall population size, and to better understand the implications of existing gaps in knowledge. We also provided example analyses of selected management scenarios (dam passage, fish translocations, and hatchery additions) influencing Pacific lamprey in fresh water. These applications illustrate how the model can be applied to inform conservation efforts. This tool will provide new capabilities for users to explore their own questions about lamprey biology and conservation. Simulations can hone hypotheses and predictions, which can then be empirically tested in the real world.

Gomes, Dylan G. E. (ORCID:0000000226423728)↗
DOE OSTI2023

Development of Scalable Reactive Transport Framework for PFAS

Research on PFAS chemicals is extensive and covers all aspects, including analytical quantification, determination of properties, toxicology, ex situ treatment, and in situ remediation. PFAS chemicals are very stable and thus persistent/recalcitrant in the environment. Although there are many unknowns about PFAS chemicals, degradation pathways, reaction rates, etc., many different sorption, oxidation, reduction, biological, and innovative treatment approaches are being developed. Sorption with activated carbon is currently the only fully available in situ treatment technology for PFAS-impacted groundwater. Given the wide array of PFAS chemicals and transformation products, remediation may need multi-step treatment trains to fully address the PFAS contamination. The work here provides kinetic reaction modules that represent an initial cut at functionality representing PFAS migration and reaction in groundwater aquifer flow and transport models. One reaction kinetics module provides a method to model kinetically limited adsorption using a mass transfer model. The second reaction module represents biological transformation of 8:2 FTOH and daughter species, illustrating how a complex reaction pathway network can be represented. Both reaction modules allow for spatially variable parameter values so that a variety of remediation approaches (e.g., a PRB or volumetric treatment or variations in geochemical conditions) can be simulated. The intent with these PFAS reaction modules is to provide tools for practitioners to aid in the selection, design, and assessment of potential in situ PFAS remediation strategies. It is anticipated that, as PFAS remediation technologies and scientific understanding advances, these modules would be refined or replaced to match new knowledge.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Biological Consequences of Marine Energy Development on Marine Animals

Marine energy devices harness power from attributes of ocean water to form a sustainable energy source. Knowledge gaps remain about whether marine energy systems can affect the environment, adding another threat to animal populations and habitats already under pressure from climate change and anthropogenic activities. To date, potential environmental effects have been studied under the scope of stressor–receptor interactions, where moving parts of, or emissions from, a system could harm the animals, habitats, and natural processes. While crucial for understanding effects and identifying knowledge gaps, this approach misses a holistic view of what animals may experience in the presence of marine energy systems. We look at six biological consequences and forces that drive the health of an animal population and the effects expected from marine energy development: success of early life stages; changes in competitive capabilities; growth and survival based on food availability; susceptibility to predators; injury or death; and reproductive success. We use case studies to develop this approach, focusing on a variety of marine animals. An approximate level of risk is assigned for each interaction based on the biological consequences. This work highlights the need to examine the effects of marine energy development on animal populations within their natural habitats.

16 TIDAL AND WAVE POWER↗
DOE OSTI2025

Hydrogel-Immobilized Multienzyme Systems for Cell-Free Chemical Bioproduction

Cell-free gene expression systems derived from bacterial lysates enable the expression of biosynthetic pathways from inexpensive and easily prepared DNA templates. These systems hold great promise for modular and on-demand bioproduction of valuable small molecules in resource-limited settings but are constrained in their long-term stability, reusability, and deployability. In this work, we demonstrate that multiple cell-free expressed enzymes can be co-immobilized in biocompatible hydrogels made from poly(ethylene glycol) diacrylate (PEGDA) with added glycerol for enhanced gel integrity. Using small-angle X-ray scattering (SAXS), we show that the mesh size of PEGDA-glycerol hydrogels is comparable to the globular sizes of many proteins and enzymes, which could be used for protein entrapment. We found that the combination between entrapment and chemical ligation of the enzymes was effective to retain proteins. By employing a method for direct fluorescence measurement from hydrogels, we found that proteins can be retained in PEGDA-glycerol for at least a week. By separating the cell-free enzyme expression from the immobilization step, we successfully fabricated enzyme-laden hydrogels with three heterologous cell-free enzymes for the bioconversion of pyruvic acid to malic acid, an industrially valuable and versatile precursor chemical. Both heterologous and endogenous enzymes from the lysate remain functional in photo-cross-linked hydrogels and can be reused for multiple biocatalytic cycles. Moreover, we also found that the immobilized enzymes exhibit up to 1.6-fold higher activity and 2-fold longer lifetimes than free enzymes in liquid reactions. Furthermore, these results could advance the deployment of cell-free synthetic biology because they show that reusable, stable, and durable multienzyme systems can be created using readily available materials and fabrication techniques.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Resource availability governs polyhydroxyalkanoate (PHA) accumulation and diversity of methanotrophic enrichments from wetlands

Aquatic environments account for half of global CH 4 emissions, with freshwater wetlands being the most significant contributors. These CH 4 fluxes can be partially offset by aerobic CH 4 oxidation driven by methanotrophs. Additionally, some methanotrophs can convert CH 4 into polyhydroxyalkanoate (PHA), an energy storage molecule as well as a promising bioplastic polymer. In this study, we investigate how PHA-accumulating methanotrophic communities enriched from wetlands were shaped by varying resource availability (i.e., C and N concentrations) at a fixed C/N ratio. Cell yields, PHA accumulation, and community composition were evaluated in high (20% CH 4 and 10 mM NH 4 + ) and low resource (0.2% CH 4 and 0.1 mM NH 4 + ) conditions simulating engineered and environmental settings, respectively. High resource availability decreased C-based cell yields, while N-based cell yields remained stable, suggesting nutrient exchange patterns differed between methanotrophic communities at different resource concentrations. PHA accumulation was only observed in high resource enrichments, producing approximately 12.6% ± 2.4% (m/m) PHA, while PHA in low resource enrichments remained below detection. High resource enrichments were dominated by Methylocystis methanotrophs, while low resource enrichments remained significantly more diverse and contained only a minor population of methanotrophs. This study demonstrates that resource concentration shapes PHA-accumulating methanotrophic communities. Together, this provides useful information to leverage such communities in engineering settings as well as to begin understanding their role in the environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Multiomics Data Collection, Visualization, and Utilization for Guiding Metabolic Engineering

Biology has changed radically in the past two decades, growing from a purely descriptive science into also a design science. The availability of tools that enable the precise modification of cells, as well as the ability to collect large amounts of multimodal data, open the possibility of sophisticated bioengineering to produce fuels, specialty and commodity chemicals, materials, and other renewable bioproducts. However, despite new tools and exponentially increasing data volumes, synthetic biology cannot yet fulfill its true potential due to our inability to predict the behavior of biological systems. Here, we showcase a set of computational tools that, combined, provide the ability to store, visualize, and leverage multiomics data to predict the outcome of bioengineering efforts. We show how to upload, visualize, and output multiomics data, as well as strain information, into online repositories for several isoprenol-producing strain designs. We then use these data to train machine learning algorithms that recommend new strain designs that are correctly predicted to improve isoprenol production by 23%. This demonstration is done by using synthetic data, as provided by a novel library, that can produce credible multiomics data for testing algorithms and computational tools. In short, this paper provides a step-by-step tutorial to leverage these computational tools to improve production in bioengineered strains.

09 BIOMASS FUELS↗
DOE OSTI2022

Zng1 is a GTP-dependent zinc transferase needed for activation of methionine aminopeptidase

The evolution of zinc (Zn) as a protein cofactor altered the functional landscape of biology, but dependency on Zn also created an Achilles' heel, necessitating adaptive mechanisms to ensure Zn availability to proteins. A debated strategy is whether metallochaperones exist to prioritize essential Zn-dependent proteins. Here, we present evidence for a conserved family of putative metal transferases in human and fungi, which interact with Zn-dependent methionine aminopeptidase type I (MetAP1/Map1p/Fma1). Deletion of the putative metal transferase in Saccharomyces cerevisiae (ZNG1; formerly YNR029c) leads to defective Map1p function and a Zn-deficiency growth defect. In vitro, Zng1p can transfer Zn 2+ or Co 2+ to apo-Map1p, but unlike characterized copper chaperones, transfer is dependent on GTP hydrolysis. Proteomics reveal mis-regulation of the Zap1p transcription factor regulon due to loss of ZNG1 and Map1p activity, suggesting that Zng1p is required to avoid a compounding effect of Map1p dysfunction on survival during Zn limitation.

59 BASIC BIOLOGICAL SCIENCES↗