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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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Human DNA polymerase η promotes RNA-templated error-free repair of DNA double-strand breaks

A growing body of evidence indicates that RNA plays a critical role in orchestrating DNA double-strand break repair (DSBR). Recently, we showed that homologous nascent RNA can be used as a template for error-free repair of double-strand breaks (DSBs) in the transcribed genome and to restore the missing sequence at the break site via the transcription-coupled classical nonhomologous end-joining (TC-NHEJ) pathway. TC-NHEJ is a complex multistep process in which a reverse transcriptase (RT) is essential for synthesizing the DNA strand from template RNA. However, the identity of the RT involved in the TC-NHEJ pathway remained unknown. Here, we report that DNA polymerase eta (Pol η), known to possess RT activity, plays a critical role in TC-NHEJ. We found that Pol η forms a multiprotein complex with RNAP II and other TC-NHEJ factors, while also associating with nascent RNA. Moreover, purified Pol η, along with DSBR proteins PNKP, XRCC4, and Ligase IV can fully repair RNA templated 3'-phosphate-containing gapped DNA substrate. In addition, we demonstrate here that Pol η deficiency leads to accumulation of R-loops and persistent strand breaks in the transcribed genes. Finally, we determined that, in Pol η depleted but not in control cells, TC-NHEJ-mediated repair was severely abrogated when a reporter plasmid containing a DSB with several nucleotide deletion within the E. coli lacZ gene was introduced for repair in lacZ-expressing mammalian cells. Thus, our data strongly suggest that RT activity of Pol η is required in error-free DSBR.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2023

Optimizing Surfactant Templating of Yttria-Stabilized Zirconia Aerogels for High-Temperature Applications: Effect of Anionic and Nonionic Surfactant

Aerogels, mesoporous materials with extreme material properties including high specific surface area, low density, and low thermal conductivity, can be useful for applications including catalysis, sorption media, and drug delivery. The low thermal conductivity and high surface area of aerogels makes them advantageous as thermal management systems, specifically for aerospace or aeronautics applications. However, the pore collapse and subsequent surface area decrease of aerogels following exposure to high temperatures must be mitigated to allow aerogels to be effectively used in thermal management applications. This work investigates the anionic surfactant sodium dodecyl sulfate (SDS) and the nonionic surfactant Pluronic® P-123 as surfactant templates in yttria-stabilized zirconia (YSZ) aerogels. By utilizing surfactant templates, known to influence pore structure, it is anticipated that sintering and densification of the aerogels following high-temperature exposure will be mitigated. It was determined that the addition of SDS and P-123 increased the surface area and pore volume of as-dried aerogels and suppressed crystallite growth at high temperatures. However, the impact of surfactant templates on the surface area and pore volume of heat-treated aerogels was negligible, potentially due to low concentrations of surfactant and the removal of the surfactant following high-temperature exposure.

Yttria-stabilized zirconia aerogels↗
DOE OSTI2024

CRISPR-GRIT: Guide RNAs with Integrated Repair Templates Enable Precise Multiplexed Genome Editing in the Diploid Fungal Pathogen Candida albicans

Candida albicans, an opportunistic fungal pathogen, causes severe infections in immunocompromised individuals. Limited classes and overuse of current antifungals have led to the rapid emergence of antifungal resistance. Thus, there is an urgent need to understand fungal pathogen genetics to develop new antifungal strategies. Genetic manipulation of C. albicans is encumbered by its diploid chromosomes requiring editing both alleles to elucidate gene function. Although the recent development of CRISPR-Cas systems has facilitated genome editing in C. albicans, large-scale and multiplexed functional genomic studies are still hindered by the necessity of cotransforming repair templates for homozygous knockouts. Here, we present CRISPR-GRIT (Guide RNAs with Integrated Repair Templates), a repair template-integrated guide RNA design for expedited gene knockouts and multiplexed gene editing in C. albicans. Here, we envision that this method can be used for high-throughput library screens and identification of synthetic lethal pairs in both C. albicans and other diploid organisms with strong homologous recombination machinery.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Application of templated vapor-liquid-solid growth to heteroepitaxy of InP on Si

Direct growth of III–V semiconductors on Si promises to combine the superior optoelectronic properties of III–Vs with the existing large-scale fabrication capabilities for Si. Vapor-liquid-solid-based growth techniques have previously been used to grow optoelectronic-quality III–Vs in polycrystalline films and various photolithography-defined features. We show that templated vapor-liquid-solid growth can produce epitaxial material when performed on crystalline substrates. In templated vapor-liquid-solid growth, the metal group-III precursor is evaporated along with a capping SiO 2 layer on the crystalline substrate, then melted and converted with exposure to a vapor-phase group-V precursor. We demonstrate homoepitaxial growth of InP on InP wafers using two forms of the SiO x capping layer to confine the liquid metal: evaporated SiO 2 and solgel SiO x , the latter of which is necessary for growth on Si. We then demonstrate heteroepitaxial growth of InP islands on Si substrates from both evaporated and electroplated In metals. The templated vapor-liquid-solid process provides better material utilization and growth rates than common vapor-phase techniques, with similar control and convenience, providing a path toward the large-scale fabrication of integrated optoelectronic components.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NASA NTRS1999

Nonenzymatic synthesis of RNA and DNA oligomers on hexitol nucleic acid templates: the importance of the A structure

Hexitol nucleic acid (HNA) is an analogue of DNA containing the standard nucleoside bases, but with a phosphorylated 1,5-anhydrohexitol backbone. HNA oligomers form duplexes having the nucleic acid A structure with complementary DNA or RNA oligomers. The HNA decacytidylate oligomer is an efficient template for the oligomerization of the 5'-phosphoroimidazolides of guanosine or deoxyguanosine. Comparison of the oligomerization efficiencies on HNA, RNA, and DNA decacytidylate templates under various conditions suggests strongly that only nucleic acid double helices with the A structure support efficient template-directed synthesis when 5'-phosphoroimidazolides of nucleosides are used as substrates.

Non-NASA Center↗
NASA NTRS2000

A comparison of RNA with DNA in template-directed synthesis

Nonenzymatic template-directed copying of RNA sequences rich in cytidylic acid using nucleoside 5'-(2-methylimidazol-1-yl phosphates) as substrates is substantially more efficient than the copying of corresponding DNA sequences. However, many sequences cannot be copied, and the prospect of replication in this system is remote, even for RNA. Surprisingly, wobble-pairing leads to much more efficient incorporation of G opposite U on RNA templates than of G opposite T on DNA templates.

Non-NASA Center↗
NASA NTRS1992

Nonenzymatic template-directed synthesis on oligodeoxycytidylate sequences in hairpin oligonucleotides

We have developed a novel method for studying template-directed synthesis in hairpin oligonucleotides. An unpaired segment at the 5'-terminus of the hairpin acts as an intramolecular template for the extension of the paired 3'-terminus. Products are analyzed by denaturing gel electrophoresis of [32P]-labeled hairpins. Using this system, we have studied the synthesis of oligoguanylates on an oligodeoxycytidylate template. We find that guanosine 5'-phosphoro(2-methyl)imidazolide adds efficiently to a terminal riboguanylate residue at temperatures in the range 0-37 degrees C but not at 50 degrees C. At 0 degree C, the half-time for addition of the first G residue is about 3 h, and the reaction rate is independent of pH in the range 6.5-8.0. The first addition reaction results in the formation of a predominantly 3'-5'-internucleotide bond. When the 3'-terminal riboguanylate residue is placed by a deoxyguanylate residue, the half-time for the first addition increases from about 3 to about 30 h.

NASA Discipline Exobiology↗
NASA NTRS1995

Faster rates with less catalyst in template-directed reactions

We have recently shown that the polycytidylic acid-directed polymerization of guanosine 5'-monophosphate 2-methylimidazolide (2-MeImpG) is amenable to kinetic study and that rate determinations as a function of 2-MeImpG concentration can reveal much mechanistic detail (Kanavarioti et al. 1993). Here we report kinetic data which show that, once the reaction has been initiated by the formation of dimers, the elongation of dimers to form longer oligomers is accelerated by decreasing polycytidylate (poly(C)) concentration from 0.05 to 0.002 M. This result is consistent with the previously proposed mechanism. The increase in the observed pseudo-first order rate constant for formation of the trimer, k3', and the corresponding constant for formation of oligomers longer than the trimer, ki' (ki' is independent of oligomer length for i > or = 4), with decreasing template concentration for a given monomer concentration is attributed to an increase in template occupancy as template concentration is reduced.

NASA Discipline Exobiology↗
NASA NTRS1997

Information transfer from peptide nucleic acids to RNA by template-directed syntheses

Peptide nucleic acids (PNAs) are uncharged analogs of DNA and RNA in which the ribose-phosphate backbone is substituted by a backbone held together by amide bonds. PNAs are interesting as models of alternative genetic systems because they form potentially informational base paired helical structures. A PNA C10 oligomer has been shown to act as template for efficient formation of oligoguanylates from activated guanosine ribonucleotides. In a previous paper we used heterosequences of DNA as templates in sequence-dependent polymerization of PNA dimers. In this paper we show that information can be transferred from PNA to RNA. We describe the reactions of activated mononucleotides on heterosequences of PNA. Adenylic, cytidylic and guanylic acids were incorporated into the products opposite their complement on PNA, although less efficiently than on DNA templates.

NASA Discipline Exobiology↗
DOE OSTI2023

Effect of Silica and Mixing Time on Microstructures of Porous Polymer Composite by Emulsion Templating

Porous polymer composite with tailored porosity is applied in the myriads of areas such as energy storage, oil/water absorption, bioengineering, and advanced areas of material science. The emulsion templating technology is one of the most popular methods for synthesizing porous polymer composite. It involves solidifying a two-phase mixture of porogen and polymer, then removing porogen to create pores within the continuous emulsion phase by polymerization or curing. The surfactant plays a pivotal role in accomplishing a stable emulsion, a key factor in designing the internal porous structure. This study highlights the effect of silica filler and mixing time on pore morphology, i.e., shape, size, and distribution. on polydimethylsiloxane (PDMS) porous structure utilizing the water-in-oil emulsion templating method. Span® 80 is used as a surfactant to reduce the surface tension between water, silica, and PDMS and simultaneously create a strong foaming effect. Different weight concentrations of silica (1-10 wt%) were chosen while keeping the internal phase, i.e., water (50 wt%) constant. The designed porous structures were further characterized through scanning electron microscopy (SEM). Porous composite specimens fabricated with higher silica content and mixing time consistently exhibit smaller pore sizes than specimens fabricated with lower mixing time and silica content. A breakthrough of pore morphology is seen at silica content higher than 5wt% at 1 min mixing, however, pore morphology drastically changes when mixing time increases from 1 min to 6 min. Variation of finer mixing time beyond 1 min shows stepwise changes in pore morphology from a large single-phase porous structure to a bi-modal porous structure which eventually become a smaller single-mode porous structure. Thus, the emulsion templating technique, in combination with different filler content and mixing time, will effectively aid in designing engineered porous polymer composite with varying stiffness and pore morphology.

Porous polymer, Emulsion templating, Surfactant, P↗
DOE OSTI2023

Thermoresponsive antifouling ultrafiltration membranes from mesophase templating

Nanostructured polymers synthesized by lyotropic liquid crystal (LLC) templates with normal hexagonal (H 1 ) structure exhibit a 3D-continuous transport path, which makes them ideal for membrane separation application. Incorporating additional functionality, especially stimuli-responsiveness, in such an ordered structure provides even more application opportunities. Here, in this work, we present the first successful synthesis of H 1 -structured thermoresponsive ultrafiltration (UF) membranes via LLC templating. The membrane contains thermoresponsive Pluronic P84 diacrylate (P84DA) which not only acts as the monomer and structure-directing amphiphile, but also enables the pore size change with temperature. Experimental studies reveal that the swelling capacity of H 1 -templated polymer as well as permeability and selectivity of the obtained membrane can be altered by changing the temperature. Increasing the temperature from 25 to 45 °C increases the normalized flux from 28 to 68 L m -2 h -1 μm and molecular weight cut-off (MWCO) from 2200 to 3900 Da. Furthermore, the membrane shows an outstanding fouling resistance against different solutes.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Kinetic Pathways Templated by Low-Temperature Intermediates during Solid-State Synthesis of Layered Oxides

Layered oxides have been the dominant cathodes in lithium-ion batteries, and among them, high-nickel (Ni) systems are attractive because of their high capacity. For practical use, synthetic control of stoichiometry and structural ordering is crucial but has been nontrivial due to the complexity inherent to synthesis reactions, which often proceed via nonequilibrium pathways. In this paper, we report here a combined in situ synchrotron X-ray diffraction and ab initio study of solid-state synthesis of layered oxides starting from acetate precursors for LiCoO 2 and LiNiO 2 and their solid solution LiNi 0.8 Co 0.2 O 2 . While all three systems ultimately evolve into the same thermodynamically stable layered phase ($R\overline{3}m$), each chemistry involves distinct metastable intermediates. We explain the phase progressions using a structural template model, demonstrating that during the synthesis of LiCoO 2 , the formed metastable spinel polymorph (Li 2 Co 2 O 4 ; $Fd\overline{3}m$) is a kinetically facile lithiation product of spinel Co 3 O 4 —the low-temperature (LT) intermediate from the decomposed Co-acetate. Similarly, in the Ni-based systems, the acetate decomposition products, rocksalts (Ni,Co)O, topotactically template the kinetic pathways of forming disordered rocksalts (Li x (Ni,Co) 2–x O 2 ; $Fm\overline{3}m$), consequently leading to off-stoichiometric Li x (Ni,Co)O 2 with undesired high Li/Ni mixing. These findings highlight new opportunities for engineering precursors to form LT intermediates that template the synthesis of target phases and structural properties.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Diastereoselective Template Synthesis on Iron and Uranium

The addition of 2 equiv of t Bu 2 PSiMe 3 to 2,6-pyridinedicarboxaldehyde ((CHO) 2 Py) results in a rac / meso diastereomeric mixture of the PNP-chelating ligand 2,6-bis((trimethylsiloxy)(di- tert -butylphosphino)-methyl)-pyridine ( (OTMS) PNP t Bu ) ( 1 - r / m ) via addition of the P–Si bond across both of the aldehyde C–O bonds. Chelation of (OTMS) PNP t Bu to FeCl 2 results in the same diastereotopic ratio of ( (OTMS) PNP t Bu )FeCl 2 ( 2- r / m ) as the free ligand. Fractional crystallization allows for the isolation of the C 2 isomer, 2- r , and a template synthesis protocol allows for the synthesis and isolation of the C s isomer, 2- m , in good yield. Furthermore, the template synthesis protocol was also expanded to the f -block with the use of UCl 4 in order to assess the specificity of the template synthesis on a larger metal cation. This reaction performed on UCl 4 forms the meso diastereospecific uranium complex ( ( t Bu2P) ONO)UCl 2 (dtbpy), 3 - m , with observation of the rational intermediate ( (OTMS) PNO t Bu )UCl 3 (dtbpy), 4 - m , which arose from the respective formation of two- or one-equivalents of TMS–Cl and formation of the corresponding U–O bond.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Templating Bicarbonate in the Second Coordination Sphere Enhances Electrochemical CO 2 Reduction Catalyzed by Iron Porphyrins

Bicarbonate-based electrolytes are ubiquitous in aqueous electrochemical CO 2 reduction, particularly in heterogenous catalysis, where they demonstrate improved catalytic performance relative to other buffers. In contrast, the presence of bicarbonate in organic electrolytes and its roles in homogeneous electrocatalysis remain underexplored. Here, we investigate the influence of bicarbonate on iron porphyrin-catalyzed electrochemical CO 2 reduction. In this work, we show that bicarbonate is a viable proton donor in organic electrolyte (p K a = 20.8 in dimethyl sulfoxide) and that urea pendants in the second coordination sphere can be used to template bicarbonate in the vicinity of a molecular iron porphyrin catalyst. The templated binding of bicarbonate increases its acidity, resulting in a 1500-fold enhancement in catalytic rates relative to unmodified parent iron porphyrin. This work emphasizes the importance of bicarbonate speciation in wet organic electrolytes and establishes second-sphere bicarbonate templating as a design strategy to harness this adventitious acid and enhance CO 2 reduction catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase

Recognition of promoters in bacterial RNA polymerases (RNAPs) is controlled by sigma subunits. The key sequence motif recognized by the sigma, the -10 promoter element, is located in the non-template strand of the double-stranded DNA molecule ~10 nucleotides upstream of the transcription start site. Here, we explain the mechanism by which the phage AR9 non-virion RNAP (nvRNAP), a bacterial RNAP homolog, recognizes the -10 element of its deoxyuridine-containing promoter in the template strand. The AR9 sigma-like subunit, the nvRNAP enzyme core, and the template strand together form two nucleotide base-accepting pockets whose shapes dictate the requirement for the conserved deoxyuridines. A single amino acid substitution in the AR9 sigma-like subunit allows one of these pockets to accept a thymine thus expanding the promoter consensus. Our work demonstrates the extent to which viruses can evolve host-derived multisubunit enzymes to make transcription of their own genes independent of the host.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structured sequences emerge from random pool when replicated by templated ligation

The central question in the origin of life is to understand how structure can emerge from randomness. The Eigen theory of replication states, for sequences that are copied one base at a time, that the replication fidelity has to surpass an error threshold to avoid that replicated specific sequences become random because of the incorporated replication errors [M. Eigen, Naturwissenschaften 58 (10), 465–523 (1971)]. Here, we showed that linking short oligomers from a random sequence pool in a templated ligation reaction reduced the sequence space of product strands. We started from 12-mer oligonucleotides with two bases in all possible combinations and triggered enzymatic ligation under temperature cycles. Surprisingly, we found the robust creation of long, highly structured sequences with low entropy. At the ligation site, complementary and alternating sequence patterns developed. However, between the ligation sites, we found either an A-rich or a T-rich sequence within a single oligonucleotide. Our modeling suggests that avoidance of hairpins was the likely cause for these two complementary sequence pools. What emerged was a network of complementary sequences that acted both as templates and substrates of the reaction. This self-selecting ligation reaction could be restarted by only a few majority sequences. The findings showed that replication by random templated ligation from a random sequence input will lead to a highly structured, long, and nonrandom sequence pool. This is a favorable starting point for a subsequent Darwinian evolution searching for higher catalytic functions in an RNA world scenario.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

FLIT: A Generic Fortran Library based on Interfaces and Templates

This Fortran code consists of multiple modules with a focus on simplifying array operations, image processing, and numerical computation especially for computational geophysics applications. We intend to use this code to demonstrate the application and usefulness of Fortran interface and templates for generic programming, especially for computational geophysics and seismology applications. The code has several notable features. Firstly, it is based on a modularized structure, where each module contains multiple functions but with a focus of functionality. Secondly, it heavily uses interfaces and templates for improving the genericness and convenience of the resulting code, where a same function interface can enclose a group of functions that perform the same functionality but with inputs/output variables of different data types. Thirdly, it includes a variety of generic functions with an emphasis on array operations, such as rotation, flipping, cropping, padding, fast Fourier transform, Gaussian blurring, interpolation, and so on. We name this package FLIP – a generic Fortran Library based on Interfaces and Templates.

Gao, Kai↗
DOE OSTI2026

Genesis Data Card Schema, Template and Supporting Tools

Genesis Data Cards provide a standardized template and schema for documenting scientific datasets in support of discovery, access, interoperability, reusability, governed use, and AI usability. This release of the Genesis Data Card repository includes a versioned Markdown template, a LinkML schema with generated Pydantic and JSON artifacts, schema documentation, and example completed data cards. Validation tooling is provided to ensure that completed data cards conform to the schema prior to submission. Accompanying documentation for the structured metadata is provided as a Field Reference Guide. The schema and accompanying template provided in this repository address the call for actionable context that enables humans and AI systems to find, access, interpret, cite, and reuse data, and, when appropriate, integrate it into AI and machine learning workflows. The data card is intended to serve as a common metadata artifact intended to support standardized, cross-program dataset documentation across Department of Energy (DOE)-aligned efforts, including but not limited to Genesis Mission-related implementations, the Office of Science, National Nuclear Security Administration (NNSA), and Advanced Simulation and Computing (ASC) data governance and stewardship initiatives.

data card↗