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

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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

An expanded role for the transcription factor WRINKLED1 in the biosynthesis of triacylglycerols during seed development

The transcription factor WRINKLED1 ( WRI1 ) is known as a master regulator of fatty acid synthesis in developing oilseeds of Arabidopsis thaliana and other species. WRI1 is known to directly stimulate the expression of many fatty acid biosynthetic enzymes and a few targets in the lower part of the glycolytic pathway. However, it remains unclear to what extent and how the conversion of sugars into fatty acid biosynthetic precursors is controlled by WRI 1. To shortlist possible gene targets for future in-planta experimental validation, here we present a strategy that combines phylogenetic foot printing of cis-regulatory elements with additional layers of evidence. Upstream regions of protein-encoding genes in A. thaliana were searched for the previously described DNA-binding consensus for WRI1, the ASML1/WRI1 (AW)-box. For about 900 genes, AW-box sites were found to be conserved across orthologous upstream regions in 11 related species of the crucifer family. For 145 select potential target genes identified this way, affinity of upstream AW-box sequences to WRI1 was assayed by Microscale Thermophoresis. This allowed definition of a refined WRI1 DNA-binding consensus. We find that known WRI1 gene targets are predictable with good confidence when upstream AW-sites are phylogenetically conserved, specifically binding WRI1 in the in vitro assay, positioned in proximity to the transcriptional start site, and if the gene is co-expressed with WRI1 during seed development. When targets predicted in this way are mapped to central metabolism, a conserved regulatory blueprint emerges that infers concerted control of contiguous pathway sections in glycolysis and fatty acid biosynthesis by WRI1. Several of the newly predicted targets are in the upper glycolysis pathway and the pentose phosphate pathway. Of these, plastidic isoforms of fructokinase ( FRK 3) and of phosphoglucose isomerase ( PGI 1) are particularly corroborated by previously reported seed phenotypes of respective null mutations.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1998

Archaeal translation initiation revisited: the initiation factor 2 and eukaryotic initiation factor 2B alpha-beta-delta subunit families

As the amount of available sequence data increases, it becomes apparent that our understanding of translation initiation is far from comprehensive and that prior conclusions concerning the origin of the process are wrong. Contrary to earlier conclusions, key elements of translation initiation originated at the Universal Ancestor stage, for homologous counterparts exist in all three primary taxa. Herein, we explore the evolutionary relationships among the components of bacterial initiation factor 2 (IF-2) and eukaryotic IF-2 (eIF-2)/eIF-2B, i.e., the initiation factors involved in introducing the initiator tRNA into the translation mechanism and performing the first step in the peptide chain elongation cycle. All Archaea appear to posses a fully functional eIF-2 molecule, but they lack the associated GTP recycling function, eIF-2B (a five-subunit molecule). Yet, the Archaea do posses members of the gene family defined by the (related) eIF-2B subunits alpha, beta, and delta, although these are not specifically related to any of the three eukaryotic subunits. Additional members of this family also occur in some (but by no means all) Bacteria and even in some eukaryotes. The functional significance of the other members of this family is unclear and requires experimental resolution. Similarly, the occurrence of bacterial IF-2-like molecules in all Archaea and in some eukaryotes further complicates the picture of translation initiation. Overall, these data lend further support to the suggestion that the rudiments of translation initiation were present at the Universal Ancestor stage.

NASA Discipline Exobiology↗
DOE OSTI2016

A microbial sensor for organophosphate hydrolysis exploiting an engineered specificity switch in a transcription factor

A whole-cell biosensor utilizing a transcription factor (TF) is an effective tool for sensitive and selective detection of specialty chemicals or anthropogenic molecules, but requires access to an expanded repertoire of TFs. Using homology modeling and ligand docking for binding pocket identification, assisted by conservative mutations in the pocket, we engineered a novel specificity in an Acinetobacter TF, PobR, to ‘sense’ a chemical p-nitrophenol (pNP) and measured the response via a fluorescent protein reporter expressed from a PobR promoter. Out of 107 variants of PobR, four were active when dosed with pNP, with two mutants showing a specificity switch from the native effector 4-hydroxybenzoate (4HB). One of the mutants, pNPmut1 was then used to create a smart microbial cell responding to pNP production from hydrolysis of an insecticide, paraoxon, in a coupled assay involving phosphotriesterase (PTE) enzyme expressed from a separate promoter. We show the fluorescence of the cells correlated with the catalytic efficiency of the PTE variant expressed in each cell. High selectivity between similar molecules (4HB versus pNP), high sensitivity for pNP detection (~2 μM) and agreement of apo- and holo-structures of PobR scaffold with predetermined computational models are other significant results presented in this work.

Jha, Ramesh K.↗
DOE OSTI2023

A fast two-stage algorithm for non-negative matrix factorization in smoothly varying data

This article reports the study of algorithms for non-negative matrix factorization (NMF) in various applications involving smoothly varying data such as time or temperature series diffraction data on a dense grid of points. Utilizing the continual nature of the data, a fast two-stage algorithm is developed for highly efficient and accurate NMF. In the first stage, an alternating non-negative least-squares framework is used in combination with the active set method with a warm-start strategy for the solution of subproblems. In the second stage, an interior point method is adopted to accelerate the local convergence. The convergence of the proposed algorithm is proved. The new algorithm is compared with some existing algorithms in benchmark tests using both real-world data and synthetic data. Furthermore, the results demonstrate the advantage of the algorithm in finding high-precision solutions.

interior point method↗
DOE OSTI2024

Factor VIII moiety of recombinant Factor VIII Fc fusion protein impacts Fc effector function and CD16 + NK cell activation

Recombinant Factor VIII-Fc fusion protein (rFVIIIFc) is an enhanced half-life therapeutic protein product used for the management of hemophilia A. Recent studies have demonstrated that rFVIIIFc interacts with Fc gamma receptors (FcγR) resulting in the activation or inhibition of various FcγR-expressing immune cells. We previously demonstrated that rFVIIIFc, unlike recombinant Factor IX-Fc (rFIXFc), activates natural killer (NK) cells via Fc-mediated interactions with FcγRIIIA (CD16). Additionally, we showed that rFVIIIFc activated CD16 + NK cells to lyse a FVIII-specific B cell clone. Here, we used human NK cell lines and primary NK cells enriched from peripheral blood leukocytes to study the role of the FVIII moiety in rFVIIIFc-mediated NK cell activation. Following overnight incubation of NK cells with rFVIIIFc, cellular activation was assessed by measuring secretion of the inflammatory cytokine IFNγ by ELISA or by cellular degranulation. We show that anti-FVIII, anti-Fc, and anti-CD16 all inhibited indicating that these molecules were involved in rFVIIIFc-mediated NK cell activation. To define which domains of FVIII were involved, we used antibodies that are FVIII domain-specific and demonstrated that blocking FVIII C1 or C2 domain-mediated membrane binding potently inhibited rFVIIIFc-mediated CD16 + NK cell activation, while targeting the FVIII heavy chain domains did not. We also show that rFVIIIFc binds CD16 with about five-fold higher affinity than rFIXFc. Based on our results we propose that FVIII light chain-mediated membrane binding results in tethering of the fusion protein to the cell surface, and this, together with increased binding affinity for CD16, allows for Fc-CD16 interactions to proceed, resulting in NK cellular activation. Our working model may explain our previous results where we observed that rFVIIIFc activated NK cells via CD16, whereas rFIXFc did not despite having identical IgG1 Fc domains.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Effective Pressure Law for the Intrinsic Formation Factor in Low Permeability Sandstones: EPL law for the formation factor

The effective pressure law for the intrinsic formation factor of low permeability sandstones from the Ordos Basin (northwest of China) was studied experimentally by measuring the electrical resistivity of brine saturated rock samples while cycling the pore and confining pressures, p p and p c . We used a 100,000 ppm NaCl solution so that the results could be directly interpreted in terms of the intrinsic formation factor F. The Response Surface method was used to construct a quadratic function of pp and pc fitting the experimental data, from which the coefficient α of the effective pressure law, p eff = p c – αp p , was determined. We found that the coefficient α generally had low values, mainly from 0.2 to 0.4, thus contradicting the theoretical prediction that α should be equal to 1 for scale-invariant properties, such as F, in linear elastic materials having a homogeneous solid matrix. Since the two underlying assumptions, linear elasticity and homogeneity of the solid matrix, are likely violated in reservoir rocks, we tried to assess their effects on α using simple analytical models, based on idealized geometries of the pore and solid phases. Analysis of these models suggests that non-linear elasticity associated with the formation of solid–solid contacts in the compressed rocks (e.g., during closure of rough cracks or crack-like pores along the grain boundaries), may be more effective in producing the low α values observed than inhomogeneity of the solid matrix.

58 GEOSCIENCES↗
DOE OSTI2016

The role of nuclear factor E2-Related factor 2 and uncoupling protein 2 in glutathione metabolism: Evidence from an in vivo gene knockout study

Nuclear factor E2-related factor 2 (NRF2) and uncoupling protein 2 (UCP2) are indicated to protect from oxidative stress. They also play roles in the homeostasis of glutathione. However, the detailed mechanisms are not well understood. In the present study, we found Nrf2-knockout (Nrf2-KO) mice exhibited altered glutathione homeostasis and reduced expression of various genes involved in GSH biosynthesis, regeneration, utilization and transport in the liver. Ucp2-knockout (Ucp2-KO) mice exhibited altered glutathione homeostasis in the liver, spleen and blood, as well as increased transcript of cystic fibrosis transmembrane conductance regulator in the liver, a protein capable of mediating glutathione efflux. Nrf2-Ucp2-double knockout (DKO) mice showed characteristics of both Nrf2-KO and Ucp2-KO mice. But no significant difference was observed in DKO mice when compared with Nrf2-KO or Ucp2-KO mice, except in blood glutathione levels. These data suggest that ablation of Nrf2 and Ucp2 leads to disrupted GSH balance, which could result from altered expression of genes involved in GSH metabolism. DKO may not evoke more severe oxidative stress than the single gene knockout. - Highlights: • Nrf2/Ucp2 deficiency leads to alteration of glutathione homeostasis. • Nrf2 regulates expression of genes in glutathione generation and utilization. • Ucp2 affects glutathione metabolism by regulating hepatic efflux of glutathione. • Nrf2 deficiency may not aggravate oxidative stress in Ucp2-deficient mice.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Monte Carlo calculation and verification of the geometrical factors for the NPDGamma experiment

The NPDGamma experiment measures the parity-violating asymmetry in gamma-ray emission in the capture of polarized neutrons on liquid parahydrogen. The sensitivity to the asymmetry for each detector in the array is used as a parameter in the extraction of the physics asymmetry from the measured data. The detector array is approximately cylindrically symmetric around the target and a step-wise sinusoidal function has been used for the sensitivity in the previous iteration of the NPDGamma experiment, but deviations from cylindrical symmetry necessitate the use of a Monte Carlo model to determine corrections to the geometrical factors. For the calculations, source code modifications to MCNPX were done in order to calculate the sensitivity of each cesium iodide detector to the physics asymmetry. We describe the MCNPX model and results from calculations and how the results are validated through measurement of the parity violating asymmetry of gamma-rays from neutron capture on chlorine.

Grammer, K. B.↗
DOE OSTI2024

Supramolecular Motion Enables Chondrogenic Bioactivity of a Cyclic Peptide Mimetic of Transforming Growth Factor-β1

Transforming growth factor (TGF)-β1 is a multifunctional protein that is essential in many cellular processes that include fibrosis, inflammation, chondrogenesis, and cartilage repair. In particular, cartilage repair is important to avoid physical disability since this tissue does not have the inherent capacity to regenerate beyond full development. We report here on supramolecular coassemblies of two peptide amphiphile molecules, one containing a TGF-β1 mimetic peptide, and another which is one of two constitutional isomers lacking bioactivity. Using human articular chondrocytes, we investigated the bioactivity of the supramolecular copolymers of each isomer displaying either the previously reported linear form of the mimetic peptide or a novel cyclic analogue. Based on fluorescence depolarization and 1 H NMR spin–lattice relaxation times, we found that coassemblies containing the cyclic compound and the most dynamic isomer exhibited the highest intracellular TGF-β1 signaling and gene expression of cartilage extracellular matrix components. Here, we conclude that control of supramolecular motion is emerging as an important factor in the binding of synthetic molecules to receptors that can be tuned through chemical structure.

Antigens↗
DOE OSTI2021

Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins

Tailocins are bactericidal protein complexes produced by a wide variety of bacteria that kill closely related strains and may play a role in microbial community structure. Thanks to their high specificity, tailocins have been proposed as precision antibacterial agents for therapeutic applications. Compared to tailed phages, with whom they share an evolutionary and morphological relationship, bacterially produced tailocins kill their host upon production but producing strains display resistance to self-intoxication. Though lipopolysaccharide (LPS) has been shown to act as a receptor for tailocins, the breadth of factors involved in tailocin sensitivity, and the mechanisms behind resistance to self-intoxication, remain unclear. Here, we employed genome-wide screens in four non-model pseudomonads to identify mutants with altered fitness in the presence of tailocins produced by closely related pseudomonads. Our mutant screens identified O-antigen composition and display as most important in defining sensitivity to our tailocins. In addition, the screens suggest LPS thinning as a mechanism by which resistant strains can become more sensitive to tailocins. Furthermore, we validate many of these novel findings, and extend these observations of tailocin sensitivity to 130 genome-sequenced pseudomonads. This work offers insights into tailocin–bacteria interactions, informing the potential use of tailocins in microbiome manipulation and antibacterial therapy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Important Factors for the Reliable and Reproducible Preparation of Non-aqueous Electrolyte Solutions for Lithium Batteries

Electrolyte solutions play a crucial role in rechargeable lithium batteries. Driven by an ever-increasing demand for better batteries, more and more stringent performance requirements are being asked of electrolytes. This demand to achieve electrolytes beyond the state-of-the-art has driven an increasing number of publications over the past decade. Nevertheless, a detailed description of electrolyte preparation is frequently missing when reporting new electrolytes for batteries, creating a barrier for others to reproduce important findings. In addition, false or misleading information in a paper may result from unintentional inaccuracies during the electrolyte preparation process. This article highlights important factors for the reliable and reproducible preparation of non-aqueous electrolyte solutions for lithium batteries, with the aim of encouraging researchers to follow more rigorous reporting standards.

Cao, Xia↗
DOE OSTI2018

Ni and Se co-doping increases the power factor and thermoelectric performance of CoSbS

In this paper, we present a new investigation on paracostibite (CoSbS), a potential thermoelectric material for power generation in the intermediate temperature range (700–900 K) consisting of earth abundant elements. We report an improved synthesis of single phase materials of Co 1–x Ni x SbS 1–y Se y (x = 0–0.07, y = 0–0.09) using vacuum melting and annealing followed by SPS processing. The effects of Ni and Se co-doping on the electronic and thermal transport properties of CoSbS were investigated. Doping with Ni on the Co site increases the carrier concentration and moves the Fermi level deep into the conduction band, producing an enhanced power factor. First-principles electronic band structure calculations indicate a multi valley nature of the conduction band where Ni doping leads to n-type behaviour and a sharp increase of the density of states effective mass, enhancing the Seebeck coefficient. Unlike the Ni doping which has little effect on thermal transport, alloying Se on the S site intensifies the alloying scattering resulting in a lower lattice thermal conductivity of 2.4 W m –1 K –1 at 900 K for Co 0.93 Ni 0.07 SbS 0.93 Se 0.07 . Alloying Se on the S site of the structure further boosts the power factor to 22 μW cm –1 K –2 and leads to a maximum ZT of 0.58 at 900 K, which is the best ZT value achieved in the system.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Neutrino-Nucleus Cross Section within the Extended Factorization Scheme

The factorization scheme, based on the impulse approximation and the spectral function formalism, has been recently generalized to allow the description of electromagnetic nuclear interactions driven by two-nucleon currents. We have extended this framework to the case of weakly charged and neutral currents, and carried out calculations of the double-differential neutrino-carbon and neutrino-oxygen cross sections using two different models of the target spectral functions. The results, showing a moderate dependence on the input spectral function, confirm that our approach provides a consistent treatment of all reaction mechanisms contributing to the signals detected by accelerator-based neutrino experiments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

Effective J -factor of the Galactic Center for velocity-dependent dark matter annihilation

Here, we introduce the effective J -factors for the Milky Way for scenarios in which dark matter annihilation is p -wave or d -wave suppressed. We find that the velocity suppression of dark matter annihilation can have a sizable effect on the morphology of a potential dark matter annihilation signal in the Galactic Center. The gamma-ray flux from the innermost region of the Galactic Center is in particular suppressed. We discover that for dark matter density profiles with steep inner slopes, the morphology of the inner Galaxy gamma-ray emission in p -wave models can be made similar to the morphology in standard s -wave models. This similarity may suggest that model discrimination between s wave and p wave is challenging, e.g., when fitting the Galactic Center excess. However, we show that it is difficult to simultaneously match s - and p -wave morphologies at both large and small angular scales. The J -factors we calculate may be implemented with astrophysical foreground models to self-consistently determine the morphology of the excess with velocity-suppressed dark matter annihilation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗