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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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26 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Diverse array of neutralizing antibodies elicited upon Spike Ferritin Nanoparticle vaccination in rhesus macaques

The repeat emergence of SARS-CoV-2 variants of concern (VoC) with decreased susceptibility to vaccine-elicited antibodies highlights the need to develop next-generation vaccine candidates that confer broad protection. Here we describe the antibody response induced by the SARS-CoV-2 Spike Ferritin Nanoparticle (SpFN) vaccine candidate adjuvanted with the Army Liposomal Formulation including QS21 (ALFQ) in non-human primates. By isolating and characterizing several monoclonal antibodies directed against the Spike Receptor Binding Domain (RBD), N-Terminal Domain (NTD), or the S2 Domain, we define the molecular recognition of vaccine-elicited cross-reactive monoclonal antibodies (mAbs) elicited by SpFN. We identify six neutralizing antibodies with broad sarbecovirus cross-reactivity that recapitulate serum polyclonal antibody responses. In particular, RBD mAb WRAIR-5001 binds to the conserved cryptic region with high affinity to sarbecovirus clades 1 and 2, including Omicron variants, while mAb WRAIR-5021 offers complete protection from B.1.617.2 (Delta) in a murine challenge study. Our data further highlight the ability of SpFN vaccination to stimulate cross-reactive B cells targeting conserved regions of the Spike with activity against SARS CoV-1 and SARS-CoV-2 variants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

tRNA shape is an identity element for an archaeal pyrrolysyl-tRNA synthetase from the human gut

Protein translation is orchestrated through tRNA aminoacylation and ribosomal elongation. Among the highly conserved structure of tRNAs, they have distinguishing features which promote interaction with their cognate aminoacyl tRNA synthetase (aaRS). These key features are referred to as identity elements. In our study, we investigated the tRNA:aaRS pair that installs the 22nd amino acid, pyrrolysine (tRNAPyl:PylRS). Pyrrolysyl-tRNA synthetases (PylRSs) are naturally encoded in some archaeal and bacterial genomes to acylate tRNAPyl with pyrrolysine. Their large amino acid binding pocket and poor recognition of the tRNA anticodon have been instrumental in incorporating > 200 noncanonical amino acids. PylRS enzymes can be divided into three classes based on their genomic structure. Two classes contain both an N-terminal and C-terminal domain, however the third class (ΔpylSn) lacks the N-terminal domain. In this study we explored the tRNA identity elements for a ΔpylSn tRNAPyl from Candidatus Methanomethylophilus alvus which drives the orthogonality seen with its cognate PylRS (MaPylRS). From aminoacylation and translation assays we identified five key elements in ΔpylSn tRNAPyl necessary for MaPylRS activity. The absence of a base (position 8) and a G–U wobble pair (G28:U42) were found to affect the high-resolution structure of the tRNA, while molecular dynamic simulations led us to acknowledge the rigidity imparted from the G–C base pairs (G3:C70 and G5:C68).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Water narratives in local newspapers within the United States

Sustainable use of water resources continues to be a challenge across the globe. This is in part due to the complex set of physical and social behaviors that interact to influence water management from local to global scales. Analyses of water resources have been conducted using a variety of techniques, including qualitative evaluations of media narratives. This study aims to augment these methods by leveraging computational and quantitative techniques from the social sciences focused on text analyses. Specifically, we use natural language processing methods to investigate a large corpus (approx. 1.8M) of newspaper articles spanning approximately 35 years (1982–2017) for insights into human-nature interactions with water. Focusing on local and regional United States publications, our analysis demonstrates important dynamics in water-related dialogue about drinking water and pollution to other critical infrastructures, such as energy, across different parts of the country. Our assessment, which looks at water as a system, also highlights key actors and sentiments surrounding water. Extending these analytical methods could help us further improve our understanding of the complex roles of water in current society that should be considered in emerging activities to mitigate and respond to resource conflicts and climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Direct writing of PVBVA/Ti 3 C 2 T x (MXene) triboelectric nanogenerators for energy harvesting and sensing applications

Triboelectric nanogenerators (TENGs) have gained recognition for their potential to convert mechanical energy into electrical energy, making them attractive for applications in healthcare, robotics, and human-device interfaces. However, many TENG devices rely on fluorinated polymers for high charge generation and involve complex fabrication processes, which limit their practicality and environmental sustainability. Here, we developed an eco-friendly composite of poly (vinyl butyral-co-vinyl alcohol-co-vinyl acetate) (PVBVA) and Ti 3 C 2 T x MXene for extrusion printing onto aluminum foil substrates, enabling the additive manufacturing of TENGs. Experimental results indicate that integrating 5.5 mg mL -1 of MXene (P-MX 5.5) into PVBVA resulted in a power density of 760 mW·m -2 , with simultaneous improvements in open-circuit voltage (129 %) and short-circuit current (250 %), demonstrating enhanced charge transfer efficiency. Beyond aluminum foil-based devices, we further explored the fully printed P-MX 5.5 TENG by utilizing silver ink electrodes, eliminating the need for aluminum foil. This fully printed, flexible TENG was successfully used for real-time human motion sensing, demonstrating its ability to detect activities such as walking, running, knee bending, and jumping. Collectively, our additively manufactured and sustainable PVBVA-MXene TENG composites, including both aluminum-based and fully printed versions, show promise for future energy harvesters, sensors, wearable electronics, healthcare, and robotic applications.

Additive manufacturing↗
DOE OSTI2024

A minimal complex of KHNYN and zinc-finger antiviral protein binds and degrades single-stranded RNA

Detecting viral infection is a key role of the innate immune system. The genomes of some RNA viruses have a high CpG dinucleotide content relative to most vertebrate cell RNAs, making CpGs a molecular marker of infection. The human zinc-finger antiviral protein (ZAP) recognizes CpG, mediates clearance of the foreign CpG-rich RNA, and causes attenuation of CpG-rich RNA viruses. While ZAP binds RNA, it lacks enzymatic activity that might be responsible for RNA degradation and thus requires interacting cofactors for its function. One of these cofactors, KHNYN, has a predicted nuclease domain. Using biochemical approaches, we found that the KHNYN NYN domain is a single-stranded RNA ribonuclease that does not have sequence specificity and digests RNA with or without CpG dinucleotides equivalently in vitro. We show that unlike most KH domains, the KHNYN KH domain does not bind RNA. Indeed, a crystal structure of the KH region revealed a double-KH domain with a negatively charged surface that accounts for the lack of RNA binding. Rather, the KHNYN C-terminal domain (CTD) interacts with the ZAP RNA-binding domain (RBD) to provide target RNA specificity. We define a minimal complex composed of the ZAP RBD and the KHNYN NYN-CTD and use a fluorescence polarization assay to propose a model for how this complex interacts with a CpG dinucleotide-containing RNA. In the context of the cell, this module would represent the minimum ZAP and KHNYN domains required for CpG-recognition and ribonuclease activity essential for attenuation of viruses with clusters of CpG dinucleotides.

Yeoh, Zoe C. (ORCID:0000000226949068)↗
DOE OSTI2025

Structural and functional analyses of SARS-CoV-2 Nsp3 and its specific interactions with the 5’ UTR of the viral genome

ABSTRACT Non-structural protein 3 (Nsp3) is the largest open reading frame encoded in the SARS-CoV-2 genome, essential for the formation of double-membrane vesicles (DMV) wherein viral RNA replication occurs. We conducted an extensive structure-function analysis of Nsp3 and determined the crystal structures of the ubiquitin-like 1 (Ubl1), nucleic acid binding (NAB), β-coronavirus-specific marker (βSM) domains, and a sub-region of the Y domain of this protein. We show that the Ubl1, ADP-ribose phosphatase (ADRP), human SARS Unique (HSUD), NAB, and Y domains of Nsp3 bind the 5’ UTR of the viral genome and that the Ubl1 and Y domains possess affinity for recognition of this region, suggesting high specificity. The Ubl1-Nucleocapsid (N) protein complex binds the 5’ UTR with greater affinity than the individual proteins alone. Our results suggest that multiple domains of Nsp3, particularly Ubl1 and Y, shepherd the 5’ UTR of the viral genome during translocation through the DMV membrane, priming the Ubl1 domain to load the genome onto N protein. IMPORTANCE The largest protein encoded by the SARS-CoV-2 genome is Nsp3. In infected cells, this multi-domain protein forms a pore structure in the virus-induced double-membrane vesicles (DMV). We have incomplete data on Nsp3 molecular structure, and here, we describe crystal structures for multiple domains of Nsp3. It is thought that newly replicated viral RNA transits through the DMV pore; however, we possess incomplete data on which regions of Nsp3 actually interact with RNA. Here, we present data showing that five domains of Nsp3 interact with the 5’ UTR of the SARS-CoV-2 RNA, including the Y domain for which no function has ever been discovered. These data suggest that the pore structure plays an active role in recognizing the terminal end of the genome, transiting and loading the viral RNA onto the cytoplasmic nucleocapsid protein. These data help expand our knowledge of Nsp3 structure and function and the SARS-CoV-2 replication cycle.

Microbiology↗
DOE OSTI2024

Bactericidal effectors of the Stenotrophomonas maltophilia type IV secretion system: functional definition of the nuclease TfdA and structural determination of TfcB

ABSTRACT Stenotrophomonas maltophilia expresses a type IV protein secretion system (T4SS) that promotes contact-dependent killing of other bacteria and does so partly by secreting the effector TfcB. Here, we report the structure of TfcB, comprising an N-terminal domain similar to the catalytic domain of glycosyl hydrolase (GH-19) chitinases and a C-terminal domain for recognition and translocation by the T4SS. Utilizing a two-hybrid assay to measure effector interactions with the T4SS coupling protein VirD4, we documented the existence of five more T4SS substrates. One of these was protein 20845, an annotated nuclease. A S. maltophilia mutant lacking the gene for 20845 was impaired for killing Escherichia coli , Klebsiella pneumoniae , and Pseudomonas aeruginosa . Moreover, the cloned 20845 gene conferred robust toxicity, with the recombinant E. coli being rescued when 20845 was co-expressed with its cognate immunity protein. The 20845 effector was an 899 amino-acid protein, comprised of a GHH-nuclease domain in its N-terminus, a large central region of indeterminant function, and a C-terminus for secretion. Engineered variants of the 20845 gene that had mutations in the predicted catalytic site did not impede E. coli , indicating that the antibacterial effect of 20845 involves its nuclease activity. Using flow cytometry with DNA staining, we determined that 20845, but not its mutant variants, confers a loss in DNA content of target bacteria. Database searches revealed that uncharacterized homologs of 20845 occur within a range of bacteria. These data indicate that the S. maltophilia T4SS promotes interbacterial competition through the action of multiple toxic effectors, including a potent, novel DNase. IMPORTANCE Stenotrophomonas maltophilia is a multi-drug-resistant, Gram-negative bacterium that is an emerging pathogen of humans. Patients with cystic fibrosis are particularly susceptible to S. maltophilia infection. In hospital water systems and various types of infections, S. maltophilia co-exists with other bacteria, including other pathogens such as Pseudomonas aeruginosa . We previously demonstrated that S. maltophilia has a functional VirB/D4 type VI protein secretion system (T4SS) that promotes contact-dependent killing of other bacteria. Since most work on antibacterial systems involves the type VI secretion system, this observation remains noteworthy. Moreover, S. maltophilia currently stands alone as a model for a human pathogen expressing an antibacterial T4SS. Using biochemical, genetic, and cell biological approaches, we now report both the discovery of a novel antibacterial nuclease (TfdA) and the first structural determination of a bactericidal T4SS effector (TfcB).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Pantex Plant Ogallala Aquifer and Perched Groundwater Contingency Plan

The Pantex Plant Ogallala Aquifer and Perched Groundwater Contingency Plan has been developed in accordance with the requirements identified in the: • Interagency Agreement for the Pantex Superfund Site, Article 8.5 Work to be Performed, • Compliance Plan Provision of Hazardous Waste Permit No. 50284, and • Record of Decision for Groundwater, Soil, and Associated Media, Pantex Plant. A Long‐Term Monitoring System Design has been designed to monitor conditions in the perched groundwater including changes in the perched aquifer as a result of implementing the response actions. Monitoring is required for verifying the effectiveness of perched groundwater response actions (i.e., conditions in the perched aquifer are being affected as intended) and for confirming that the perched aquifer and Ogallala Aquifer characterization as defined in the Resource Conservation and Recovery Act Facility Investigation Report and the Corrective Measure Studies/Feasibility Study remains accurate. If monitoring results obtained through the monitoring network identify an unexpected condition or deviation, contingent actions will be considered and implemented as necessary to ensure continued protection of the Ogallala Aquifer and human health and the environment. Potential deviations to expected technology performance may be encountered for each of the four primary response actions that compose the selected remedy for perched groundwater; Playa 1 Pump and Treat System, Southeast Area Pump and Treat System, Southeast Area In‐Situ Bioremediation System (comprised of the Southeast In‐Situ Bioremediation System Original System, Southeast Area In‐Situ Bioremediation System Extension System, Offsite In‐Situ Bioremediation System, Perchlorate/Chromium ISB, Northeast ISB and County Road 8 ISB), and Zone 11 In‐Situ Bioremediation System. Monitoring will also be conducted to determine if there are deviations to the expected characterization, e.g., contaminants not expected as a result of the RCRA Facility Investigation characterization. Deviations to expected conditions in the Ogallala Aquifer could also be encountered if the response actions in the perched groundwater are not performing as expected, i.e., preventing contaminants from migrating to the Ogallala Aquifer. Currently, Pantex has begun investigation of detections of high explosives above groundwater protection standards in wells on the Texas Tech University property and a plume that is moving to the northeast from that area. Due to those detections, this Plan recognizes the fact that future detections in the Ogallala will be focused on first‐ time detections of analytes. After a remedy is determined, this Plan will require modification to address-deviations and contingent actions. This Plan was developed to identify the contingent actions necessary to mitigate impacts resulting from deviations to site conditions or response action performance. The Plan defines the environmental problem being addressed by the response actions, clarifies the expected conditions and objectives of the response actions, and identifies the potential deviations to the response actions (due to site conditions or technology performance) that could be encountered. The deviations were evaluated to determine the likelihood of occurrence, potential impact, and time to respond to avoid impact. The Plan also identifies the monitoring outlined in the Long‐Term Monitoring System Design Report (Consolidated Nuclear Security, 2024) and Sampling Analysis Plan (PanTeXas Deterrence, 2024) that will be used to detect the deviations. Lastly, the Plan specifies the contingent actions that could be implemented in response to the deviations. Because each response focuses on a discrete portion of the perched aquifer and contaminant plume, each response action has a different set of expected conditions, and therefore differing impacts from deviations to the site and technology expectations. As a result, the contingent actions are identified for each response action and potential deviation including specific constituents, location, and conditions. If deviations are encountered that impact the ability of the response action to meet performance objectives, the contingent actions will be focused on ensuring the response action can meet the performance objective. Contingent actions may be implemented as interim actions (ISMs/removal actions) in accordance with the Record of Decision, Interagency Agreement, and Hazardous Waste Permit‐50284, if warranted by the specific circumstances. For deviations to site characterization expected conditions, the contingent action will focus on determination of the source of the deviation, determination of the appropriate response, and evaluation of additional work to be completed. However, if the deviation to characterization impacts the performance of the response action, the contingent action will again focus on ensuring performance objectives can be met. Early source term removals and cleanup actions have been implemented to protect the Ogallala Aquifer. Because of these actions and based on modeling results, the expected conditions in the Ogallala Aquifer are that constituents of concern will not be detected above the Groundwater Protection Standards (GWPSs) nor will they reach potential points of exposure above the GWPS. The primary deviation of concern for the Ogallala is if constituents are detected in the Ogallala Aquifer near or above GWPSs. If it occurs, this change in expected conditions would require further evaluation of site and contaminant characteristics to determine an appropriate course of action. The evaluation would include additional monitoring, source identification, implementation of interim protective measures (if necessary), and delineation of extent. These evaluations are necessary to determine an appropriate response action for the Ogallala. The primary goal of the Plan is to provide for the continued protection of the Ogallala Aquifer and the health of its consumers. In recognition, this Plan presents a flexible and rational approach for making future decisions associated with confirming the change in perched and Ogallala aquifer conditions and identifying a response (technical activities, changes to response actions, regulatory oversight, and public involvement).

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗