Search NASA⌕ Search

SEARCH · Search NASA

Results for “ENCODE”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 847 records · Page 47
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

COnfirmation using Gamma-ray Non-Imaging Zero-knowledge ANti-mask Time-encoding (COGNIZANT) Final Summary Report

In potential future arms reduction treaties in which the numbers of nuclear warheads may approach small numbers, using delivery systems as a proxy for the warheads themselves may be insufficient. Therefore, a technical means of verifying the presence of a nuclear warhead may become necessary. Verifying that a declared item actually is a warhead is technically challenging within a verification regime: providing assurance to the monitoring party that a presented item is a warhead while protecting sensitive information about that warhead may be required. It is generally believed that strong assurance will require the confirmation of key attributes that may reveal closely-guarded critical design information. This provides high confidence to the monitoring party, but presents a risk of information loss to the host. A verification system must overcome this hurdle. Over the last several decades, systems have been developed that balance host and monitoring partner needs by using sensitive information to confirm treaty accountable items (TAI) as warheads while sequestering that information behind an information barrier (1). These are designed to meet the needs of the host but places the onus on the monitor to authenticate the hardware, firmware, and software. Authentication requires that the monitor confirm that all components of the system have not been modified and work as intended. In 2014, Glaser et al. proposed applying the concept of “zero knowledge protocols” (ZKP) from the field of cryptography to the problem of warhead verification (2). In mathematical cryptography, ZKP is accomplished by challenging one party to solve a problem that is only possible if that party possesses the information being authenticated. After repeated challenges, the party provides confidence that it possesses this information without revealing any details about the information itself. Systems have been in development based on this idea at both Princeton and MIT (2) (3) (4). The final measurement results produced by these systems can be viewed by both the host and the monitoring party without the worry of revealing sensitive information. However, in both of these physical implementations, there remains an information barrier within the system. The need for a digital information barrier to protect a measurement result is eliminated, but it has been replaced with the need to sequester physical components of the system, potentially obfuscating the measurement process itself. Both implementations physically insert information into the system that requires protection to prevent undesired disclosure of sensitive information: in the Princeton method, one must physically load the complement of the expected image of a true warhead into the system, and in the MIT technique, one loads a collection of spectator foils whose thicknesses physically encrypt a measured spectrum. This complicates authentication of the hardware and measurement process. The CONFIDANTE/COGNIZANT concept developed in this project do not load sensitive information into the system at any time, and could therefore open the possibility of allowing the inspector to not only view the final data but also the measurement as it is being performed and all associated equipment.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2020

MassIVE MSV000085948 - Utilization of syringyl lignin-derived compounds and production of 2-pyrone-4,6-dicarboxylic acid by Pseudomonas putida KT2440: Lignin is an abundant aromatic polymer formed in plants by coupling reactions of p-coumaryl, coniferyl, and sinapyl alcohols. Pseudomonas putida KT2440 (P. putida KT2440), a robust soil bacterium, naturally catabolizes many aromatic compounds derived from lignin as carbon and energy sources and has been extensively engineered to valorize guaiacyl (G) and p-hydroxyphenyl (H) lignin-derived aromatic species to valuable chemicals. However, only a few studies report the capacity of Pseudomonads to grow on syringyl (S) lignin-derived compounds. In this work, we demonstrate that P. putida KT2440 catabolizes syringate in the presence of an auxiliary energy source. Overexpression of vanAB, encoding a native Rieske non-heme iron monooxygenase, enabled catabolism of syringate and syringaldehyde without an additional carbon and energy source. In vitro biochemical characterization of VanAB confirmed that this enzyme O-demethylates syringate to 3-O-methylgallate and, subsequently, 3-O-methylgallate to gallate, albeit 4- and 55-fold less efficiently than vanillate, respectively. Transcriptomics and proteomics experiments demonstrate that the galADBC transcripts and enzymes required for gallate catabolism are induced when vanAB is overexpressed during cultivation in syringate. Further, we show that that the endogenous protocatechuate-3,4-dioxygenase PcaHG ring-opens gallate to produce 2-pyrone-4,6-dicarboxylic acid (PDC), a promising bio-based chemical. Constitutive overexpression of vanAB and pcaHG along with galA deletion enabled PDC production from SA at a 70% (mol/mol) yield. Furthermore, leveraging the LigAB dioxygenase from Sphingobium sp. SYK-6 and VanAB O-demethylase from Pseudomonas sp. HR199 enabled simultaneous conversion of monomers with S-, G-, and H-type functionality to PDC at 82% (mol/mol) yield. Overall, this study elucidates a native pathway for catabolism of syringyl lignin-derived compounds in P. putida KT2440 and demonstrates the potential of this robust host for biological funneling of substrates derived from all three canonical monolignols.

Explore the source record for details and available documents.

Beckham, Gregg↗
DOE OSTI2026

An mRNA vaccine encoding the Ebola virus glycoprotein induces high neutralizing antibody titers and provides strong protection against lethal infections in mouse models

Ebola virus (EBOV) is the causative agent of Ebola disease (EBOD), a viral hemorrhagic fever with a notably high case fatality rate. Current treatments for EBOD are limited to monoclonal antibodies or two licensed viral vector vaccines, a recombinant vesicular stomatitis virus (rVSV)-vectored vaccine or an adenovirus and modified vaccinia Ankara regimen. However, comparisons of protection, efficacy, and durability with alternative nucleotide platforms remain understudied. Here, we evaluated the immunogenicity of an mRNA vaccine expressing the EBOV glycoprotein (GP) in parallel with rVSV- and DNA-based vaccine platforms. The mRNA EBOV-GP vaccine, formulated in lipid nanoparticles, elicited significantly higher levels of total IgG and neutralizing antibody titers compared to the rVSV-EBOV-GP vaccine. Linear antibody epitope analysis indicated a preference for targeting the mucin-like domain in EBOV-GP1 following rVSV-based vaccination, while the mRNA platform distinctly targeted the internal fusion loop of EBOV-GP2. After characterizing the immunogenicity of the mRNA vaccine, two models of EBOD were used to demonstrate its protective efficacy: a surrogate rVSV-based challenge model of EBOD using type-I interferon deficient C57BL/6 mice and infection of BALB/c mice with authentic mouse-adapted EBOV. In both studies, the EBOV mRNA vaccine fully protected the mouse cohorts against morbidity and mortality. Additionally, the EBOV mRNA vaccine produced greater neutralizing antibody titers compared to the DNA EBOV-GP vaccine. These results suggest that an mRNA vaccine expressing EBOV-GP can induce robust, functional humoral responses that are protective against EBOD, warranting further development as an alternative to, or as part of a vaccine strategy including, viral vectored vaccines.

DNA vaccines↗
DOE OSTI2022

Iodate Reduction by Shewanella oneidensis Requires Genes Encoding an Extracellular Dimethylsulfoxide Reductase

Microbial iodate (IO 3 – ) reduction is a major component of the iodine biogeochemical reaction network in anaerobic marine basins and radioactive iodine-contaminated subsurface environments. Alternative iodine remediation technologies include microbial reduction of IO 3 – to iodide (I – ) and microbial methylation of I – to volatile gases. The metal reduction pathway is required for anaerobic IO 3 – respiration by the gammaproteobacterium Shewanella oneidensis . However, the terminal IO 3 – reductase and additional enzymes involved in the S. oneidensis IO 3 – electron transport chain have not yet been identified. In this study, gene deletion mutants deficient in four extracellular electron conduits (EECs; Δ mtrA , Δ mtrA -Δ mtrDEF , Δ mtrA -Δ dmsEF , Δ mtr A-ΔSO4360) and DMSO reductase (Δ dmsB ) of S. oneidensis were constructed and examined for anaerobic IO 3 – reduction activity with either 20 mM lactate or formate as an electron donor. IO 3 – reduction rate experiments were conducted under anaerobic conditions in defined minimal medium amended with 250 μM IO 3 – as anaerobic electron acceptor. Only the Δ mtrA mutant displayed a severe deficiency in IO 3 – reduction activity with lactate as the electron donor, which suggested that the EEC-associated decaheme cytochrome was required for lactate-dependent IO 3 – reduction. The Δ mtrA -Δ dmsEF triple mutant displayed a severe deficiency in IO 3 – reduction activity with formate as the electron donor, whereas Δ mtrA -Δ mtrDEF and Δ mtr A-ΔSO4360 retained moderate IO 3 – reduction activity, which suggested that the EEC-associated dimethylsulfoxide (DMSO) reductase membrane-spanning protein DmsE, but not MtrA, was required for formate-dependent IO 3 – reduction. Furthermore, gene deletion mutant Δ dmsB (deficient in the extracellular terminal DMSO reductase protein DmsB) and wild-type cells grown with tungsten replacing molybdenum (a required co-factor for DmsA catalytic activity) in defined growth medium were unable to reduce IO 3 – with either lactate or formate as the electron donor, which indicated that the DmsAB complex functions as an extracellular IO 3 – terminal reductase for both electron donors. Results of this study provide complementary genetic and phenotypic evidence that the extracellular DMSO reductase complex DmsAB of S. oneidensis displays broad substrate specificity and reduces IO 3 – as an alternate terminal electron acceptor.

, Shewanella oneidensis↗
DOE OSTI2024

Pseudomonas aeruginosa gene PA4880 encodes a Dps-like protein with a Dps fold, bacterioferritin-type ferroxidase centers, and endonuclease activity

We report the biochemical, structural, and functional characterization of the protein coded by gene PA4880 in the P. aeruginosa PAO1 genome. The PA4880 gene had been annotated as coding a probable bacterioferritin. Our structural work shows that the product of gene PA4880 is a protein that adopts the Dps subunit fold, which oligomerizes into a 12-mer quaternary structure. Unlike Dps, however, the ferroxidase di-iron centers and iron coordinating ligands are buried within each subunit, in a manner identical to that observed in the ferroxidase center of P. aeruginosa bacterioferritin. Since these structural characteristics correspond to Dps-like proteins, we term the protein as P. aeruginosa Dps-like, or Pa DpsL. The ferroxidase centers in Pa DpsL catalyze the oxidation of Fe 2+ utilizing O 2 or H 2 O 2 as oxidant, and the resultant Fe 3+ is compartmentalized in the interior cavity. Interestingly, incubating Pa DpsL with plasmid DNA results in efficient nicking of the DNA and at higher concentrations of Pa DpsL the DNA is linearized and eventually degraded. The nickase and endonuclease activities suggest that Pa DpsL, in addition to participating in the defense of P. aeruginosa cells against iron-induced toxicity, may also participate in the innate immune mechanisms consisting of restriction endonucleases and cognate methyl transferases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Solution NMR Structure of Hypothetical Protein CV_2116 Encoded by a Viral Prophage Element in Chromobacterium violaceum

CV{_}2116 from Chromobacterium violaceum is a small hypothetical protein of 82 amino acids. A PSI-BLAST search using the CV{_}2116 protein sequence as a query identified only two hits, both with amino acid sequence identities of less than 40%. After the CV{_}2116 gene was cloned into the p15TvLic expression plasmid and transformed into E. coli, the desired CV{_}2116 protein was expressed and purified. A high quality solution structure of CV{_}2116 was determined by NMR spectroscopy. The tertiary structure of CV{_}2116 adopts a novel alpha + beta fold containing two anti-parallel beta sheets and one alpha helix in the C-terminal end. CV{_}2116 does not belong to any known protein sequence families and no similar structures exist in the protein data bank. To date, no function of CV{_}2116 can be derived from either sequence or structural similarity searches.

59 BASIC BIOLOGICAL SCIENCES↗