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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Modification and analysis of context-specific genome-scale metabolic models: methane-utilizing microbial chassis as a case study

ABSTRACT Context-specific genome-scale model (CS-GSM) reconstruction is becoming an efficient strategy for integrating and cross-comparing experimental multi-scale data to explore the relationship between cellular genotypes, facilitating fundamental or applied research discoveries. However, the application of CS modeling for non-conventional microbes is still challenging. Here, we present a graphical user interface that integrates COBRApy, EscherPy, and RIPTiDe, Python-based tools within the BioUML platform, and streamlines the reconstruction and interrogation of the CS genome-scale metabolic frameworks via Jupyter Notebook. The approach was tested using -omics data collected for Methylotuvimicrobium alcaliphilum 20Z R , a prominent microbial chassis for methane capturing and valorization. We optimized the previously reconstructed whole genome-scale metabolic network by adjusting the flux distribution using gene expression data. The outputs of the automatically reconstructed CS metabolic network were comparable to manually optimized i IA409 models for Ca-growth conditions. However, the CS model questions the reversibility of the phosphoketolase pathway and suggests higher flux via primary oxidation pathways. The model also highlighted unresolved carbon partitioning between assimilatory and catabolic pathways at the formaldehyde-formate node. Only a very few genes and only one enzyme with a predicted function in C1 metabolism, a homolog of the formaldehyde oxidation enzyme ( fae1-2 ), showed a significant change in expression in La-growth conditions. The CS-GSM predictions agreed with the experimental measurements under the assumption that the Fae1-2 is a part of the tetrahydrofolate-linked pathway. The cellular roles of the tungsten (W)-dependent formate dehydrogenase ( fdhAB ) and fae homologs ( fae1-2 and fae3 ) were investigated via mutagenesis. The phenotype of the f dhAB mutant followed the model prediction. Furthermore, a more significant reduction of the biomass yield was observed during growth in La-supplemented media, confirming a higher flux through formate. M. alcaliphilum 20Z R mutants lacking fae1-2 did not display any significant defects in methane or methanol-dependent growth. However, contrary to fae1, the fae1-2 homolog failed to restore the formaldehyde-activating enzyme function in complementation tests. Overall, the presented data suggest that the developed computational workflow supports the reconstruction and validation of CS-GSM networks of non-model microbes. IMPORTANCE The interrogation of various types of data is a routine strategy to explore the relationship between genotype and phenotype. An efficient approach for integrating and cross-comparing experimental multi-scale data in the context of whole-genome-based metabolic network reconstruction becomes a powerful tool that facilitates fundamental and applied research discoveries. The present study describes the reconstruction of a context-specific (CS) model for the methane-utilizing bacterium, Methylotuvimicrobium alcaliphilum 20Z R . M. alcaliphilum 20Z R is becoming an attractive microbial platform for the production of biofuels, chemicals, pharmaceuticals, and bio-sorbents for capturing atmospheric methane. We demonstrate that this pipeline can help reconstruct metabolic models that are similar to manually curated networks. Furthermore, the model is able to highlight previously overlooked pathways, thus advancing fundamental knowledge of non-model microbial systems or promoting their development toward biotechnological or environmental implementations.

Kulyashov, M. A.↗
NASA NTRS1981

Cross section for Ly-alpha emission by electron impact on methane

Utilizing Lyman-alpha emission cross sections for H2 as secondary standards, absolute values of Lyman-alpha emission cross sections for CH4 have been obtained for electron impact energies varying from threshold to 100 eV. A crossed electron beam-molecular beam geometry was employed and the Lyman-alpha radiation was detected at 90 deg and 45 deg with respect to the incident electron beam by a solar blind photomultiplier in tandem with an oxygen filter. The results are compared with previous measurements. Appreciable differences among the various experimental data are found.

Orient, O. J.↗
NASA NTRS2018

GES DISC Long-Term Data Analysis Services Using AIRS and CMS Methane Data as an Example

NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) archives and distributes rich collections of data on atmospheric greenhouse gases from multiple satellite missions and model results. Among those greenhouse gases, atmospheric methane is a powerful greenhouse gas contributing ~0.5 (W/m^2) to total radiative forcing, and its concentration has increased by about 150% since 1750. Observations or estimates of methane emissions typically have sparse spatial and temporal coverage. The lack of comprehensive spatial and temporal coverage of methane source and sink observations has made analyzing atmospheric methane trends challenging. In this study the GES DISC aims to provide the community with the resources to better understand changes in atmospheric methane concentrations and the underlying causes. We will utilize methane datasets from Atmospheric Infrared Sounder (AIRS) retrieved methane concentration and three Carbon Monitoring System (CMS) methane emission datasets (in regions of North America, Canada, and Mexico) to compare AIRS methane growth with corresponding CMS regional methane emissions. Comparisons of AIRS methane growth rates and CMS methane emissions suggests wetland emissions may impact methane growth rate trends over North America. As the record for CMS methane data is extended, both datasets can be used in conjunction to better understand impacts on atmospheric methane trends. GES DISCs new anomaly tool can also be used on select datasets to further quantify trends in atmospheric greenhouse gases.

long-term data analysis↗
DOE OSTI2024

Quantitative assessment of methane bioconversion based on kinetics and bioenergetics

The biological conversion of methane under ambient conditions can be performed by methanotrophs that utilize methane as both a sole source of energy and a carbon source. However, compared to the established microbial chassis used for general fermentation with sugar as a feedstock, the productivity of methanotrophs is low. The fundamental knowledge of their metabolic or cellular bottlenecks is limited. In this review, the industrial-scale potential of methane bioconversion was evaluated. In particular, the enzyme kinetics associated with the oxidation and assimilation of methane were investigated to evaluate the potential of methane fermentation. Furthermore, the kinetics of enzymes involved in methane metabolism were compared with those used in the metabolic processes of traditional fermentation (glycolysis). Through this analysis, the current limitations of methane metabolism were identified. Methods for increasing the efficiency of methane bioconversion and directions for the industrial application of methane-based fermentation were discussed.

09 BIOMASS FUELS↗
NASA NTRS2017

Engineering of Methane Metabolism in Pichia Pastoris Through Methane Monooxygenase Expression

Exploration of the solar system is constrained by the cost of moving mass off Earth. Producing materials in situ will reduce the mass that must be delivered from earth. CO2 is abundant on Mars and manned spacecraft. On the ISS, NASA reacts excess CO2 with H2 to generate CH4 and H2O using the Sabatier System. The resulting water is recovered into the ISS, but the methane is vented to space. Thus, there is a capability need for systems that convert methane into valuable materials. Methanotrophic bacteria consume methane but these are poor synthetic biology platforms. Thus, there is a knowledge gap in utilizing methane in a robust and flexible synthetic biology platform. The yeast Pichia pastoris is a refined microbial factory that is used widely by industry because it efficiently secretes products. Pichia could produce a variety of useful products in space. Pichia does not consume methane but robustly consumes methanol, which is one enzymatic step removed from methane. Our goal is to engineer Pichia to consume methane thereby creating a powerful methane-consuming microbial factory.

Pichia↗
NASA NTRS2017

New Frontiers in Synthetic Biology for Spaceflight

Exploration of the solar system is constrained by the cost of moving mass off Earth. Producing materials in situ will reduce the mass that must be delivered from earth. CO2 is abundant on Mars and manned spacecraft. On the ISS, NASA reacts excess CO2 with H2 to generate CH4 and H2O using the Sabatier System. The resulting water is recovered into the ISS, but the methane is vented to space. Thus, there is a capability need for systems that convert methane into valuable materials. Methanotrophic bacteria consume methane but these are poor synthetic biology platforms. Thus, there is a knowledge gap in utilizing methane in a robust and flexible synthetic biology platform. The yeast Pichia pastoris is a refined microbial factory that is used widely by industry because it efficiently secretes products. Pichia could produce a variety of useful products in space. Pichia does not consume methane but robustly consumes methanol, which is one enzymatic step removed from methane. Our goal is to engineer Pichia to consume methane thereby creating a powerful methane-consuming microbial factory.

Galazka, Jonathan M.↗
NASA NTRS2017

Methane Metabolism by Yeast for Solar System Exploration

Exploration of the solar system is constrained by the cost of moving mass off Earth. Producing materials in situ will reduce the mass that must be delivered from earth. CO2 is abundant on Mars and manned spacecraft. On the ISS, NASA reacts excess CO2 with H2 to generate CH4 and H2O using the Sabatier System. The resulting water is recovered into the ISS, but the methane is vented to space. Thus, there is a capability need for systems that convert methane into valuable materials. Methanotrophic bacteria consume methane but these are poor synthetic biology platforms. Thus, there is a knowledge gap in utilizing methane in a robust and flexible synthetic biology platform. The yeast Pichia pastoris is a refined microbial factory that is used widely by industry because it efficiently secretes products. Pichia could produce a variety of useful products in space. Pichia does not consume methane but robustly consumes methanol, which is one enzymatic step removed from methane. Our goal is to engineer Pichia to consume methane thereby creating a powerful methane-consuming microbial factory.

Galazka, Jonathan M.↗
NASA NTRS2017

Engineering of Methane Metabolism in Pichia Pastoris Through Methane Monooxygenase Expression

Exploration of the solar system is constrained by the cost of moving mass off Earth. Producing materials in situ will reduce the mass that must be delivered from earth. CO2 is abundant on Mars and manned spacecraft. On the ISS, NASA reacts excess CO2 with H2 to generate CH4 and H2O using the Sabatier System. The resulting water is recovered into the ISS, but the methane is vented to space. Thus, there is a capability need for systems that convert methane into valuable materials. Methanotrophic bacteria consume methane but these are poor synthetic biology platforms. Thus, there is a knowledge gap in utilizing methane in a robust and flexible synthetic biology platform. The yeast Pichia pastoris is a refined microbial factory that is used widely by industry because it efficiently secretes products. Pichia could produce a variety of useful products in space. Pichia does not consume methane but robustly consumes methanol, which is one enzymatic step removed from methane. Our goal is to engineer Pichia to consume methane thereby creating a powerful methane-consuming microbial factory.

Methane↗
NASA NTRSDate not supplied

New Frontiers in Synthetic Biology for Spaceflight

Exploration of the solar system is constrained by the cost of moving mass off Earth. Producing materials in situ will reduce the mass that must be delivered from earth. CO2 is abundant on Mars and manned spacecraft. On the ISS, NASA reacts excess CO2 with H2 to generate CH4 and H2O using the Sabatier System. The resulting water is recovered into the ISS, but the methane is vented to space. Thus, there is a capability need for systems that convert methane into valuable materials. Methanotrophic bacteria consume methane but these are poor synthetic biology platforms. Thus, there is a knowledge gap in utilizing methane in a robust and flexible synthetic biology platform. The yeast Pichia pastoris is a refined microbial factory that is used widely by industry because it efficiently secretes products. Pichia could produce a variety of useful products in space. Pichia does not consume methane but robustly consumes methanol, which is one enzymatic step removed from methane. Our goal is to engineer Pichia to consume methane thereby creating a powerful methane-consuming microbial factory.

methane↗
DOE OSTI2025

Theoretical and Experimental Insights into CO 2 Capture and Methanation over Amine-Grafted Ru-Based Catalysts

Carbon capture and storage (CCS) technologies, along with CO 2 capture and conversion methods, have emerged as crucial research areas to address rising CO 2 emissions. In this study, we seek to understand the mechanistic role of amines in enabling lower-energy pathways for CO 2 conversion. Our research focuses on the development and analysis of dual-functional materials (DFMs) engineered for the reactive capture and conversion (RCC) of CO 2 into methane, utilizing Ru catalysts grafted with amine groups. We employ Density Functional Theory (DFT) calculations using methylamine as a model amine to investigate the impact of amine groups on CO 2 methanation on a Ru(0001) surface, both in the presence and absence of amine groups. The amine ligand alters the carbon coordination environment, promoting direct C–O dissociation and potentially destabilizing the CO* adsorbate, thereby reducing the risk of CO poisoning. Additionally, we observe a preference for hydrogenation, although it becomes more energetically uphill in the amine-bound scenario. Our experiments, however, report similar CO 2 conversion and CH 4 production rates over the synthesized catalysts “Ru/TiO 2 ” and the amine (N-(2-aminoethyl)-3-aminoproplytrimethoxysilane (“diaminosilane”)) deposited catalyst “Diamine−Ru/TiO 2 ”. By constructing comparative reaction-free energy diagrams and performing microkinetic modeling (MKM) simulations, we link our theoretical findings with experimentally observed CO 2 uptake, conversion, and methane production rates. A microkinetic model was employed to investigate the anomaly, showing reduced amine–carbon complex coverage and increased CO 2 coverage at all temperatures. The MKM simulations consistently confirmed these trends. In conclusion, this comprehensive approach offers key insights into the role of the amine-CO 2 bond in methanation, highlighting a pathway toward lower-energy, more efficient CO 2 capture and conversion processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1993

Temperature Affects Fatty Acids In Methylococcus Capsulatus

According to report, temperature of growth of thermotolerant, methane-oxidizing bacterium Methylococcus capsulatus (Bath) affects both proportion of monounsaturated fatty acids and cis/trans ratio of these acids in cell membrane. Because suboptimum growth temperature is potential stress factor, it may be possible to use such cis/trans ratios as indices of stresses upon methane-oxidizing microbial communities. Research in microbiology of methanotrophs increasing because of possible commercial exploitation of these organisms as biocatalysts or as sources of useful polymers; knowledge of effect of temperature on ability of methanotrophs to utilize methane useful in optimization of conditions of growth.

Jahnke, Linda L.↗
NASA NTRS1973

Hydrogen-methane fuel control systems for turbojet engines

Design, development, and test of a fuel conditioning and control system utilizing liquid methane (natural gas) and liquid hydrogen fuels for operation of a J85 jet engine were performed. The experimental program evaluated the stability and response of an engine fuel control employing liquid pumping of cryogenic fuels, gasification of the fuels at supercritical pressure, and gaseous metering and control. Acceptably stable and responsive control of the engine was demonstrated throughout the sea level power range for liquid gas fuel and up to 88 percent engine speed using liquid hydrogen fuel.

Goldsmith, J. S.↗
DOE OSTI2025

Noble-Metal-Free, Nickel-Based Dual Functional Materials for Improved Methane Production from In Situ Carbon Dioxide Capture and Conversion

Promoters for dual functional materials have not been well explored, but promoters could improve the efficiency of the process by improving the selectivity of the CO 2 methanation process. Utilizing integrated capture and conversion, where CO 2 is captured and converted to useful products, would allow for a useful avenue to control CO 2 emissions. One such way to accomplish this would be to utilize materials that can both capture and convert CO 2 to useful products. However, these materials are often based on costly noble metals, like ruthenium and platinum, decreasing their viability on an industrial scale. Less expensive metals, for example, nickel, would allow for dual functional materials to be more readily utilized in industrial settings. Nickel-based dual functional materials often do not react with the captured CO 2 and merely desorb the CO 2 rather than form a useful product. However, promoters have not been well explored for these types of materials to improve the catalytic properties, which would be beneficial to improve nickel-based materials. Herein, we report the addition of ytterbium on a nickel-based dual functional material and the improvements to the production of methane from captured CO 2 with the incorporated ytterbium promoter. The ytterbium promoter improves the selectivity of the catalysts for the hydrogenation of captured CO 2 to methane and increases the ability for the material to capture CO 2 due to additional basic sites being formed on the surface of alumina. As a result, the 12%Ni/4%Yb/6%Na 2 O/Al 2 O 3 catalyst was utilized to capture carbon dioxide and then convert the captured CO 2 to methane over five cycles, where both the amount captured and the amount converted remained stable, indicating the stability of the material over long-term use.

Catalysts↗
DOE OSTI2025

Methane pyrolysis by Joule heating for graphitic carbon and hydrogen production

The global energy transition toward sustainability requires technologies that can decarbonize energy carriers and fuels while producing valuable materials. Methane, a primary component of natural gas, is both a high-energy-density fuel and a significant greenhouse gas. This study reports an approach for methane pyrolysis utilizing Joule heating within the deposition substrate to drive the endothermic reaction. With electric current passing through a resistive porous carbon cloth, heat is generated to break C-H bonds of methane molecules. Here, the decomposition of methane as it flows through the cloth results in hydrogen production and the formation of conformally layered graphite around the carbon fibers. The effects of input power, chamber pressure, feedstock flow rate, and process duration on hydrogen and graphite production are characterized via in situ mass spectrometry and laser absorption spectroscopy, resulting in methane conversion rates up to 88%, with hydrogen and carbon yields of 82% and 72%, respectively. Material characterization verifies uniform high-quality graphite deposition, with a Raman I D /I G ratio of 0.1 and 3.38 Å d-spacing. This Joule heating method for catalyst-free methane pyrolysis offers the potential for advancing hydrogen production technology by simultaneously producing valuable materials such as solid graphite, thus enhancing the economic viability of the fuel decarbonization process.

Energy Resources↗
NASA NTRS2016

Liquid Oxygen/Liquid Methane Integrated Power and Propulsion

The proposed paper will cover ongoing work at the National Aeronautics and Space Administration (NASA) Johnson Space Center (JSC) on integrated power and propulsion for advanced human exploration. Specifically, it will present findings of the integrated design, testing, and operational challenges of a liquid oxygen / liquid methane (LOx/LCH4) propulsion brassboard and Solid Oxide Fuel Cell (SOFC) system. Human-Mars architectures point to an oxygen-methane economy utilizing common commodities, scavenged from the planetary atmosphere and soil via In-Situ Resource Utilization (ISRU), and common commodities across sub-systems. Due to the enormous mass gear-ratio required for human exploration beyond low-earth orbit, (for every 1 kg of payload landed on Mars, 226 kg will be required on Earth) increasing commonality between spacecraft subsystems such as power and propulsion can result in tremendous launch mass and volume savings. Historically, propulsion and fuel cell power subsystems have had little interaction outside of the generation (fuel cell) and consumption (propulsion) of electrical power. This was largely due to a mismatch in preferred commodities (hypergolics for propulsion; oxygen & hydrogen for fuel cells). Although this stove-piped approach benefits from simplicity in the design process, it means each subsystem has its own tanks, pressurization system, fluid feed system, etc. increasing overall spacecraft mass and volume. A liquid oxygen / liquid methane commodities architecture across propulsion and power subsystems would enable the use of common tankage and associated pressurization and commodity delivery hardware for both. Furthermore, a spacecraft utilizing integrated power and propulsion could use propellant residuals - propellant which could not be expelled from the tank near depletion due to hydrodynamic considerations caused by large flow demands of a rocket engine - to generate power after all propulsive maneuvers are complete thus utilizing previously wasted mass. Such is the case for human and robotic planetary landers. Although many potential benefits through integrated power & propulsion exist, integrated operations have yet to be successfully demonstrated and many challenges have already been identified the most obvious of which is the large temperature gradient. SOFC chemistry is exothermic with operating temperatures in excess of 1,000 K; however, any shared commodities will be undoubtedly stored at cryogenic temperatures (90-112 K) for mass efficiency reasons. Spacecraft packaging will drive these two subsystems in close proximity thus heat leak into the commodity tankage must be minimized and/or mitigated. Furthermore, commodities must be gasified prior to consumption by the SOFC. Excess heat generated by the SOFC could be used to perform this phase change; however, this has yet to be demonstrated. A further identified challenge is the ability of the SOFC to handle the sudden power spikes created by the propulsion system. A power accumulator (battery) will likely be necessary to handle these sudden demands while the SOFC thermally adjusts. JSC's current SOFC test system consists of a 1 kW fuel cell designed by Delphi. The fuel cell is currently undergoing characterization testing at the NASA JSC Energy Systems Test Area (ESTA) after which a Steam Methane Reformer (SMR) will be integrated and the combined system tested in closed-loop. The propulsion brassboard is approximately the size of what could be flown on a sounding rocket. It consists of one 100 lbf thrust "main" engine developed for NASA by Aerojet and two 10 lbf thrusters to simulate a reaction control system developed at NASA JSC. This system is also under development and initial testing at ESTA. After initial testing, combined testing will occur which will provide data on the fuel cell's ability to sufficiently handle the power spikes created by the propulsion system. These two systems will also be modeled using General-Use Nodal Network Solver (GUNNS) software. Once anchored with test data, this model will be used to extrapolate onto other firing profiles and used to size the power accumulator.

Banker, Brian↗