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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Unifying themes and distinct features of carbon and nitrogen assimilation by polysaccharide-degrading bacteria: a summary of four model systems

Our current understanding of enzymatic polysaccharide degradation has come from a huge number of in vitro studies with purified enzymes. While this vast body of work has been invaluable in identifying and characterizing novel mechanisms of action and engineering desirable traits into these enzymes, a comprehensive picture of how these enzymes work as part of a native in vivo system is less clear. Recently, several model bacteria have emerged with genetic systems that allow for a more nuanced study of carbohydrate active enzymes (CAZymes) and how their activity affects bacterial carbon metabolism. With these bacterial model systems it is now possible to not only study a single nutrient system in isolation (i.e. carbohydrate degradation and carbon metabolism), but also how multiple systems are integrated. Given that most environmental polysaccharides are carbon rich but nitrogen poor (e.g. lignocellulose), the interplay between carbon and nitrogen metabolism in polysaccharide-degrading bacteria can now be studied in a physiologically relevant manner. Therefore, in this review we have summarized what has been experimentally determined for CAZyme regulation, production, and export in relation to nitrogen metabolism for two Gram-positive (Caldicellulosiruptor bescii and Clostridium thermocellum) and two Gram-negative (Bacteroides thetaiotaomicron and Cellvibrio japonicus) polysaccharide-degrading bacteria. By comparing and contrasting these four bacteria we have highlighted the shared and unique features of each, with a focus on in vivo studies, in regard to carbon and nitrogen assimilation. Finally, we conclude with what we believe are two important questions that can act as guideposts for future work to better understand the integration of carbon and nitrogen metabolism in polysaccharide-degrading bacteria.

Cellvibrio japonicus↗
DOE OSTI2022

Post-closure Nuclear Criticality Safety Evaluations for Disposition of Criticality Control Overpacks at the Waste Isolation Pilot Plant

The Waste Isolation Pilot Plant (WIPP) is a geological repository in southern New Mexico that provides for disposal of transuranic (TRU) wastes from atomic energy defense activities. The Sandia National Laboratories (Sandia) Report, Consideration of Nuclear Criticality When Disposing of Transuranic Waste at the Waste Isolation Pilot Plant, addresses nuclear criticality safety based on the projected inventory characteristics for the initial compliance certification application of WIPP in 1996. As the inventory, waste forms, and disposal package designs change, revised or new analyses are necessary to demonstrate acceptability for these configurations within the WIPP safety basis and compliance with 10,000-year post-closure standards of the US Environmental Protection Agency (EPA). Saylor and Scaglione evaluated criticality control overpacks (CCOs) in 2017 based on conservative assumptions for post-closure repository structural conditions with resulting effects on containers and container spacing, The Saylor and Scaglione evaluation of CCOs addressed a single waste configuration that represents the Surplus Plutonium Disposition Program’s dilute and dispose waste form and composition. This initial CCO study demonstrated that 50 grams of boron carbide (B 4 C) per CCO is sufficient to ensure post-closure criticality safety based on a well-mixed waste composition, and Oak Ridge National Laboratory (ORNL) subsequently determined that this amount of B 4 C does not require constraints on moisture or plastic present as moderator. The Saylor and Scaglione analysis conservatively assumes repository room closure that eliminates all space between fissile gram equivalent (FGE) 239 Pu masses. The close-packed array was selected based on limited availability of repository salt creep modeling results at that time. In 2019, Brickner provided additional evaluations for pipe overpack containers (POCs), building on the conservative basis provided by Saylor and Scaglione. Brickner’s 2019 analysis made use of new geomechanical data for post-closure spacing that rely on advances in repository modeling as documented in the work by Reedlunn and Bean. This current CCO evaluation for generic waste materials expands on earlier work performed at ORNL and includes evaluation of CCOs across a much broader range of possible waste compositions and geometries. This evaluation is intended to provide input for the required feature, event and process (FEP) screening to determine if post-closure criticality must be included as an event in the 10,000-year regulatory evaluation. As such, the approach to modeling post-closure criticality presented in this report has been coordinated with the Sandia team responsible for FEP screening. The resulting analysis supports disposition of fissile materials in the CCO containing up to 380 FGE 239 Pu and expands conditions acceptable for disposal of fissile material in CCOs. This evaluation builds on the methodology of Saylor and Scaglione and Brickner, using the most recently available geomechanical data for CCO spacing under salt creep compaction scenarios provided by Reedlunn and Bean. The broad range of fissile material configurations analyzed in this report are intended to account for configurations that may occur during the post-closure disposal time period, and it also includes waste configurations that are not physically possible to support analysis of conditions that influence neutron fluence.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

Metabolic Synergy between Human Symbionts Bacteroides and Methanobrevibacter

Trophic interactions between microbes are postulated to determine whether a host microbiome is healthy or causes predisposition to disease. Two abundant taxa, the Gram-negative heterotrophic bacterium Bacteroides thetaiotaomicron and the methanogenic archaeon Methanobrevibacter smithii, are proposed to have a synergistic metabolic relationship. Both organisms play vital roles in human gut health; B. thetaiotaomicron assists the host by fermenting dietary polysaccharides, whereas M. smithii consumes end-stage fermentation products and is hypothesized to relieve feedback inhibition of upstream microbes such as B. thetaiotaomicron. To study their metabolic interactions, we defined and optimized a coculture system and used software testing techniques to analyze growth under a range of conditions representing the nutrient environment of the host. Here we verify that B. thetaiotaomicron fermentation products are sufficient for M. smithii growth and that accumulation of fermentation products alters secretion of metabolites by B. thetaiotaomicron to benefit M. smithii. Studies suggest that B. thetaiotaomicron metabolic efficiency is greater in the absence of fermentation products or in the presence of M. smithii. Under certain conditions, B. thetaiotaomicron and M. smithii form interspecies granules consistent with behavior observed for syntrophic partnerships between microbes in soil or sediment enrichments and anaerobic digesters. Furthermore, when vitamin B 12 , hematin, and hydrogen gas are abundant, coculture growth is greater than the sum of growth observed for monocultures, suggesting that both organisms benefit from a synergistic mutual metabolic relationship.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Cryo-EM structures of engineered active bc 1- cbb 3 type CIII 2 CIV super-complexes and electronic communication between the complexes

Respiratory electron transport complexes are organized as individual entities or combined as large supercomplexes (SC). Gram-negative bacteria deploy a mitochondrial-like cytochrome (cyt) bc 1 (Complex III, CIII 2 ), and may have specific cbb 3 -type cyt c oxidases (Complex IV, CIV) instead of the canonical aa 3 -type CIV. Electron transfer between these complexes is mediated by soluble ( c 2 ) and membrane-anchored ( c y ) cyts. Here, we report the structure of an engineered bc 1 - cbb 3 type SC (CIII 2 CIV, 5.2Å resolution) and three conformers of native CIII 2 (3.3 Å resolution). The SC is active in vivo and in vitro, contains all catalytic subunits and cofactors, and two extra transmembrane helices attributed to cyt c y and the assembly factor CcoH. The cyt c y is integral to SC, its cyt domain is mobile and it conveys electrons to CIV differently than cyt c 2 . The successful production of a native-like functional SC and determination of its structure illustrate the characteristics of membrane-confined and membrane-external respiratory electron transport pathways in Gram-negative bacteria.

42 ENGINEERING↗
DOE OSTI2021

Predictive Rules of Efflux Inhibition and Avoidance in Pseudomonas aeruginosa

Antibiotic-resistant bacteria rapidly spread in clinical and natural environments and challenge our modern lifestyle. A major component of defense against antibiotics in Gram-negative bacteria is a drug permeation barrier created by active efflux across the outer membrane. We identified molecular determinants defining the propensity of small peptidomimetic molecules to avoid and inhibit efflux pumps in Pseudomonas aeruginosa, a human pathogen notorious for its antibiotic resistance. Combining experimental and computational protocols, we mapped the fate of the compounds from structure-activity relationships through their dynamic behavior in solution, permeation across both the inner and outer membranes, and interaction with MexB, the major efflux transporter of P. aeruginosa. We identified predictors of efflux avoidance and inhibition and demonstrated their power by using a library of traditional antibiotics and compound series and by generating new inhibitors of MexB. The identified predictors will enable the discovery and optimization of antibacterial agents suitable for treatment of P. aeruginosa infections.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The multifaceted role of c-di-AMP signaling in the regulation of Porphyromonas gingivalis lipopolysaccharide structure and function

This study unveils the intricate functional association between cyclic di-3’,5’-adenylic acid (c-di-AMP) signaling, cellular bioenergetics, and the regulation of lipopolysaccharide (LPS) profile in Porphyromonas gingivalis, a Gram-negative obligate anaerobe considered as a keystone pathogen involved in the pathogenesis of chronic periodontitis. Previous research has identified variations in P. gingivalis LPS profile as a major virulence factor, yet the underlying mechanism of its modulation has remained elusive. We employed a comprehensive methodological approach, combining two mutants exhibiting varying levels of c-di-AMP compared to the wild type, alongside an optimized analytical methodology that combines conventional mass spectrometry techniques with a novel approach known as FLAT n . We demonstrate that c-di-AMP acts as a metabolic nexus, connecting bioenergetic status to nuanced shifts in fatty acid and glycosyl profiles within P. gingivalis LPS. Notably, the predicted regulator gene cdaR, serving as a potent regulator of c-di-AMP synthesis, was found essential for producing N-acetylgalactosamine and an unidentified glycolipid class associated with the LPS profile. The multifaceted roles of c-di-AMP in bacterial physiology are underscored, emphasizing its significance in orchestrating adaptive responses to stimuli. Furthermore, our findings illuminate the significance of LPS variations and c-di-AMP signaling in determining the biological activities and immunostimulatory potential of P. gingivalis LPS, promoting a pathoadaptive strategy. The study expands the understanding of c-di-AMP pathways in Gram-negative species, laying a foundation for future investigations into the mechanisms governing variations in LPS structure at the molecular level and their implications for host-pathogen interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Single-Use Destructive Assay for Uranium Hexafluoride Sampling

Sampling uranium hexafluoride (UF6) for the determination of enrichments by destructive analysis (DA) is a critical component in the International Atomic Energy Agency’s layered safeguards approach for uranium processing facilities. Typically, gram-quantity UF6 samples are collected during inspections and stored under tag-and-seal until transportation to an off-site analytical laboratory. The shipping times can be long, and evolving restrictions on radioactive/corrosive materials shipments may increasingly limit the IAEA’s ability to transport UF6 samples easily. Pacific Northwest National Laboratory has developed a low-cost UF6 sampling technology called Single-Use Destructive Assay (SUDA) that addresses these challenges, as well as provides DA sample geometries that can be tailored for different analytical methods, including potential on-site analyses. The SUDA samplers, along with a unique holder, are designed for direct attachment to existing taps at uranium processing facilities, allowing gaseous UF6 to come into direct contact with a zeolite film. The SUDA technology features the ability to capture uranium in a more easily shipped and handled form as the solid, more stable, and relatively less hazardous hydrated uranyl fluoride (UO2F2•nH2O), which is formed through the controlled hydrolysis of UF6. We have recently simulated uranium collection under enrichment plant sampling conditions to further improve our understanding of SUDA sampling. Presented here is our recent work on measuring the relationship between sampling conditions and uranium collection, which includes control of the uranium-mass-to-zeolite ratio and assessing variable UF6 gas and sampling parameters that can affect collection using the SUDA sampler.

Pope, Timothy R.↗
DOE OSTI2020

Designing Flexibility into the Authorized Radioactive Contents of the 9982 Shipping Package

The 9982 radioactive material shipping package, or the 9982, differs from the others by allowing a multitude of radionuclides instead of a single defined set. While allowing flexibility, this requires more justification on why these contents would be worthwhile and why they would not cause various safety hazards when shipped together. The latter was covered through mass limit calculations, and the potential uses for the package are shown through comparison with historical shipments. Here, the mass limits were already calculated[1] and used to show three example shipments are suitable for the 9982 as well. Plutonium stored in 3013 containers[2], training sources shipped in 9977 packages[3], and americium standards shipped in 9978 packages[4] were all analyzed. The mass of each radionuclide and the corresponding mass limit were used to first determine if the listed content could be shipped. If so, the maximum allowed mass of such contents is also calculated in order to see if the 200-gram fissile limit for the 9982 would be violated if additional material was packed. The sum-of-the-fractions method produces contents that do not violate the mass limits or exceed the 200-gram fissile limit. These sets also serve as realistic examples of what may be shipped in the 9982. Well-founded example contents will help the approval of the package by showing its compatibility with previously shipped material. Unfounded hypothetical contents would not show the usefulness of having a wide variety of allowed radionuclides. More contents may be developed in order to incorporate other radionuclides that were not present in these three examples. The light elements will also need to be evaluated due to their exclusion currently preventing some materials from being allowed in the 9982.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2020

Directed energy system technology for the control of soilborne fungal pathogens and plant‐parasitic nematodes

Abstract BACKGROUND It is challenging to manage soilborne pathogens and plant‐parasitic nematodes using sustainable practices. Here, we evaluated a novel energy application system, Directed Energy System (DES). This system generates pulses of energy capable of impacting selected biological organisms. The oomycete Phytophthora cinnamomi , the fungus Verticillium dahliae , and the plant‐parasitic nematodes Meloidogyne hapla and Globodera ellingtonae were added to soil. Then DES‐generated energy was applied to soil and impacts on target organisms were determined. RESULTS DES applied at 20, 40 and 70 J cm −3 to P. cinnamomi and V. dahliae resulted in ≥50% and 92% reductions (respectively) of propagules per gram of soil in comparison to the untreated control. There was a significant reduction of M. hapla eggs per gram of host tomato root between the untreated control, and 2.2, 13 and 25 J cm −3 DES dosages applied pre‐ or post‐planting. Additionally, an 84% reduction in hatch from G. ellingtonae encysted eggs after treatment with 70 J cm −3 DES was observed. The dosages ranged from 40 or 80V mm −1 for nematodes to 200 V mm −1 for fungi. CONCLUSION DES‐generated energy reduced survival of the soilborne pathogens P. cinnamomi and V. dahlia, and the plant‐parasitic nematodes M. hapla and G. ellingtonae . The application of this technology to a field setting remains to be considered. Published 2020. This article is a U.S. Government work and is in the public domain in the USA. Pest Management Science published by Wiley Periodicals, Inc. on behalf of © 2020 Society of Chemical Industry.

Riga, Ekaterini↗
DOE OSTI2022

Structural and biochemical analyses of selectivity determinants in chimeric Streptococcus Class A sortase enzymes

Abstract Sequence variation in related proteins is an important characteristic that modulates activity and selectivity. An example of a protein family with a large degree of sequence variation is that of bacterial sortases, which are cysteine transpeptidases on the surface of gram‐positive bacteria. Class A sortases are responsible for attachment of diverse proteins to the cell wall to facilitate environmental adaption and interaction. These enzymes are also used in protein engineering applications for sortase‐mediated ligations (SML) or sortagging of protein targets. We previously investigated SrtA from Streptococcus pneumoniae , identifying a number of putative β7–β8 loop‐mediated interactions that affected in vitro enzyme function. We identified residues that contributed to the ability of S. pneumoniae SrtA to recognize several amino acids at the P1′ position of the substrate motif, underlined in LPXT G , in contrast to the strict P1′ Gly recognition of SrtA from Staphylococcus aureus . However, motivated by the lack of a structural model for the active, monomeric form of S. pneumoniae SrtA, here, we expanded our studies to other Streptococcus SrtA proteins. We solved the first monomeric structure of S. agalactiae SrtA which includes the C‐terminus, and three others of β7–β8 loop chimeras from S. pyogenes and S. agalactiae SrtA. These structures and accompanying biochemical data support our previously identified β7–β8 loop‐mediated interactions and provide additional insight into their role in Class A sortase substrate selectivity. A greater understanding of individual SrtA sequence and structural determinants of target selectivity may also facilitate the design or discovery of improved sortagging tools.

Gao, Melody↗
DOE OSTI2020

Calculating Potential Radiological Emissions for Waste Management Activities at INL - 20068

At Idaho National Laboratory (INL), work involving radionuclides is evaluated for potential emissions from a project in order to comply with the National Emission Standards for Hazardous Air Pollutants (NESHAP) regulations, 40 CFR 61 Subpart H. Emission calculations are documented in an Air Permitting Applicability Determination (APAD) to analyze unmitigated and mitigated emissions and determine if an Application to Construct (ATC) or continuous monitoring is required. To calculate the unmitigated and mitigated emissions, a spreadsheet was developed to provide ease in determining potential emissions by providing the maximum operating temperature and the material being used. The spreadsheet aids in determining the potential emissions for research projects and waste management activities at Materials and Fuels Complex (MFC) and other locations across the INL site. Furthermore, it can also be used for periodic confirmatory measurements (PCM) to justify low emissions. Elements that factor into the unmitigated and mitigated calculations include the amount of each radionuclide used (in curies or grams), specific activity (if amount is given in grams), the temperature the material is heated to in Celsius, the dose conversion factor which is derived from Clean Air Act Assessment Package - 1988 (CAP-88) modeling, and the number of HEPA filters used for mitigated measures. The main drivers for calculating the unmitigated emissions for a project are the amount used per radionuclide, the maximum operating temperature, and the location of the work. The maximum operating temperature determines the airborne release factor which is dependent on the physical state of the radionuclide. Prior to October 2017, if the radionuclide was heated to greater than 100 deg. C, the radionuclide was assumed to be a gas, which has the highest airborne release factor. This assumption would be overly conservative for radionuclides with high melting and boiling points, which provided a challenge to demonstrate low emissions. In October 2017, the Environmental Protection Agency (EPA) approved an alternative method for INL. This method allows the airborne release factor to be determined by using the melting point and 90% of the boiling point of the radionuclide. This methodology was included in the spreadsheet to allow unmitigated emission calculations for APADs to be completed more efficiently and effectively. Results show a reduction in time completing air emission calculations as well as lower total emissions across all facilities at INL. MFC annual emissions were reduced by 62% from the previous year and Research and Education Campus (REC) facilities were reduced by 38% due to implementation of the approved alternative method. Time spent on APADs, PCMs, and documentation for the annual NESHAP report was also reduced significantly. The spreadsheet provided in Table I provides the potential emission calculations for the 'Advanced Retrieval and Disposition Techniques for Remote Handled Mixed Low Level Waste (RH MLLW) at the Radioactive Scrap and Waste Facility (RSWF)' project. Calculations show the Potential Effective Dose Equivalent (PEDE) at RSWF to be 7.27 E-04 mrem/yr (7.27 E-09 Sv/yr) which is well below the 0.1 mrem/yr threshold. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Correlating transcription and protein expression profiles of immune biomarkers following lipopolysaccharide exposure in lung epithelial cells

Universal and early recognition of pathogens occurs through recognition of evolutionarily conserved pathogen associated molecular patterns (PAMPs) by innate immune receptors and the consequent secretion of cytokines and chemokines. The intrinsic complexity of innate immune signaling and associated signal transduction challenges our ability to obtain physiologically relevant, reproducible and accurate data from experimental systems. One of the reasons for the discrepancy in observed data is the choice of measurement strategy. Immune signaling is regulated by the interplay between pathogen-derived molecules with host cells resulting in cellular expression changes. However, these cellular processes are often studied by the independent assessment of either the transcriptome or the proteome. Correlation between transcription and protein analysis is lacking in a variety of studies. In order to methodically evaluate the correlation between transcription and protein expression profiles associated with innate immune signaling, we measured cytokine and chemokine levels following exposure of human cells to the PAMP lipopolysaccharide (LPS) from the Gram-negative pathogen Pseudomonas aeruginosa . Expression of 84 messenger RNA (mRNA) transcripts and 69 proteins, including 35 overlapping targets, were measured in human lung epithelial cells. We evaluated 50 biological replicates to determine reproducibility of outcomes. Following pairwise normalization, 16 mRNA transcripts and 6 proteins were significantly upregulated following LPS exposure, while only five (CCL2, CSF3, CXCL5, CXCL8/IL8, and IL6) were upregulated in both transcriptomic and proteomic analysis. This lack of correlation between transcription and protein expression data may contribute to the discrepancy in the immune profiles reported in various studies. The use of multiomic assessments to achieve a systems-level understanding of immune signaling processes can result in the identification of host biomarker profiles for a variety of infectious diseases and facilitate countermeasure design and development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

NEAr Transporter (NEAT) Domains: Unique Surface Displayed Heme Chaperones That Enable Gram-Positive Bacteria to Capture Heme-Iron From Hemoglobin

Iron is an important micronutrient that is required by bacteria to proliferate and to cause disease. Many bacterial pathogens forage iron from human hemoglobin (Hb) during infections, which contains this metal within heme (iron–protoporphyrin IX). Several clinically important pathogenic species within the Firmicutes phylum scavenge heme using surface-displayed or secreted NEAr Transporter (NEAT) domains. In this review, we discuss how these versatile proteins function in the Staphylococcus aureus Iron-regulated surface determinant system that scavenges heme-iron from Hb. S. aureus NEAT domains function as either Hb receptors or as heme-binding chaperones. In vitro studies have shown that heme-binding NEAT domains can rapidly exchange heme amongst one another via transiently forming transfer complexes, leading to the interesting hypothesis that they may form a protein-wire within the peptidoglycan layer through which heme flows from the microbial surface to the membrane. In Hb receptors, recent studies have revealed how dedicated heme- and Hb-binding NEAT domains function synergistically to extract Hb’s heme molecules, and how receptor binding to the Hb-haptoglobin complex may block its clearance by macrophages, prolonging microbial access to Hb’s iron. The functions of NEAT domains in other Gram-positive bacteria are also reviewed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Qualification of Processing Batches for Tank Closure Cesium Removal Through In-Tank Batch Contact Testing - 20470

The Tank Closure Cesium Removal (TCCR) process at the Savannah River Site (SRS) is currently processing waste from Tank 10H, generating decontaminated salt solution that is sent to Tank 11H. Transfers out of Tank 11H are then disposed of on site as a grout wasteform in the SRS Saltstone Processing Facility. This is a full-scale demonstration of the use of Crystalline Silicotitanate (CST) for the decontamination of aqueous nuclear waste supernate. CST primarily removes cesium from the high sodium alkaline feed, but also adsorbs strontium, actinides, and some other trace metals. The TCCR unit is an at-tank set of four ion exchange columns, with two typically being operated in series during waste processing. Tank 10H is serving a dual function as both the salt dissolution tank as well as the feed tank for the TCCR system. Prior to operation of TCCR, Tank 10H must undergo dissolution campaigns, dissolving the salt cake to form an aqueous salt solution (supernate). After each dissolution campaign, the supernate created must be qualified prior to processing through the TCCR system. Qualification includes detailed characterization of the supernate as well as in-tank batch contact tests to determine the equilibrium loading of Cs-137 on the CST ion exchange media (IONSIV{sup TM} R9120-Ba). In support of the in-tank batch contact testing, Savannah River National Laboratory (SRNL) developed a CST sample holder, also referred to as a 'tea-bag', to hold a measured amount (∼0.1 grams) of pretreated CST between stainless steel screens. The tea-bag fits within a standard stainless steel sample vial that has been modified to allow the flow of supernate to the CST. This sample holder is then immersed in the waste tank allowing free contact between the CST beads and the surrounding liquid, at an effectively infinite liquid-to-solid phase ratio. A pair of tea-bags are deployed in the tank for a period of 10 days for each batch, after which the CST is recovered, digested, and analyzed to determine the loading of cesium isotopes on the CST. This result then supports the TCCR column thermal loading limits for processing as part of the TCCR safety basis. This paper will discuss the design and testing of the CST sample holder, as well as results from the first few batches of waste qualified and subsequently processed through the TCCR system. In addition, results from analyses of Tank 11H samples, showing decontamination of the product will be included. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2020

Universal Approach to Fabricating Graphene-Supported Single-Atom Catalysts from Doped ZnO Solid Solutions

Single-atom catalysts (SACs) have attracted widespread interest for many catalytic applications because of their distinguishing properties. However, general and scalable synthesis of efficient SACs remains significantly challenging, which limits their applications. Here we report an efficient and universal approach to fabricating a series of high-content metal atoms anchored into hollow nitrogen-doped graphene frameworks (M-N-Grs; M represents Fe, Co, Ni, Cu, etc.) at gram-scale. The highly compatible doped ZnO templates, acting as the dispersants of targeted metal heteroatoms, can react with the incoming gaseous organic ligands to form doped metal-organic framework thin shells, whose composition determines the heteroatom species and contents in M-N-Grs. We achieved over 1.2 atom % (5.85 wt %) metal loading content, superior oxygen reduction activity over commercial Pt/C catalyst, and a very high diffusion-limiting current (6.82 mA cm -2 ). Both experimental analyses and theoretical calculations reveal the oxygen reduction activity sequence of M-N-Grs. Additionally, the superior performance in Fe-N-Gr is mainly attributed to its unique electron structure, rich exposed active sites, and robust hollow framework: This synthesis strategy will stimulate the rapid development of SACs for diverse energy-related fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Fitness factors impacting survival of a subsurface bacterium in contaminated groundwater

Many factors contribute to the ability of a microbial species to persist when encountering complexly contaminated environments, including time of exposure, the nature and concentration of contaminants, availability of nutritional resources, and possession of a combination of appropriate molecular mechanisms needed for survival. Herein we sought to identify genes that are most important for survival of Gram-negative Enterobacteriaceae in contaminated groundwater environments containing high concentrations of nitrate and metals using the metal-tolerant Oak Ridge Reservation isolate, Pantoea sp. MT58 (MT58). Survival fitness experiments in which a randomly barcoded transposon insertion (RB-TnSeq) library of MT58 was exposed directly to contaminated Oak Ridge Reservation groundwater samples from across a nitrate and mixed metal contamination plume were used to identify genes important for survival with increasing exposure times and concentrations of contaminants, and availability of a carbon source. Genes involved in controlling and using carbon, encoding transcriptional regulators, and related to Gram-negative outer membrane processes were among those found to be important for survival in contaminated Oak Ridge Reservation groundwater. A comparative genomics analysis of 75 Pantoea genus strains allowed us to further separate the survival determinants into core and non-core genes in the Pantoea pangenome, revealing insights into the survival of subsurface microorganisms during contaminant plume intrusion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Characterization of Interactions between CTX-M-15 and Clavulanic Acid, Desfuroylceftiofur, Ceftiofur, Ampicillin, and Nitrocefin

Cefotaximase-Munich (CTX-M) extended-spectrum beta-lactamases (ESBLs) are commonly associated with Gram-negative, hospital-acquired infections worldwide. Several beta-lactamase inhibitors, such as clavulanate, are used to inhibit the activity of these enzymes. To understand the mechanism of CTX-M-15 activity, we have determined the crystal structures of CTX-M-15 in complex with two specific classes of beta-lactam compounds, desfuroylceftiofur (DFC) and ampicillin, and an inhibitor, clavulanic acid. The crystal structures revealed that Ser70 and five other residues (Lys73, Tyr105, Glu166, Ser130, and Ser237) participate in catalysis and binding of those compounds. Based on analysis of steady-state kinetics, thermodynamic data, and molecular docking to both wild-type and S70A mutant structures, we determined that CTX-M-15 has a similar affinity for all beta-lactam compounds (ceftiofur, nitrocefin, DFC, and ampicillin), but with lower affinity for clavulanic acid. A catalytic mechanism for tested β-lactams and two-step inhibition mechanism of clavulanic acid were proposed. CTX-M-15 showed a higher activity toward DFC and nitrocefin, but significantly lower activity toward ampicillin and ceftiofur. The interaction between CTX-M-15 and both ampicillin and ceftiofur displayed a higher entropic but lower enthalpic effect, compared with DFC and nitrocefin. DFC, a metabolite of ceftiofur, displayed lower entropy and higher enthalpy than ceftiofur. This finding suggests that compounds containing amine moiety (e.g., ampicillin) and the furfural moiety (e.g., ceftiofur) could hinder the hydrolytic activity of CTX-M-15.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Molecular simulation of lignin-related aromatic compound permeation through gram-negative bacterial outer membranes

Lignin, an abundant aromatic heteropolymer in secondary plant cell walls, is the single largest source of renewable aromatics in the biosphere. Leveraging this resource for renewable bioproducts through targeted microbial action depends on lignin fragment uptake by microbial hosts and subsequent enzymatic action to obtain the desired product. Recent computational work has emphasized that bacterial inner membranes are permeable to many aromatic compounds expected from lignin depolymerization processes. In this study, we expand on these findings through simulations for 42 lignin-related compounds across a gram-negative bacterial outer membrane model. Unbiased simulation trajectories indicate that spontaneous crossing for the full outer membrane is relatively rare at molecular simulation timescales, primarily due to preferential membrane partitioning and slow diffusion within the lipopolysaccharide layer within the outer membrane. Membrane partitioning and permeability coefficients were determined through replica exchange umbrella sampling simulations to overcome sampling limitations. We find that the glycosylated lipopolysaccharides found in the outer membrane increase the permeation barrier to many lignin-related compounds, particularly the most hydrophobic compounds. However, the effect is relatively modest; at industrially relevant concentrations, uncharged lignin-related compounds will readily diffuse across the outer membrane without the need for specific porins. Together, our results provide insight into the permeability of the bacterial outer membrane for assessing lignin fragment uptake and the future production of renewable bioproducts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗