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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 811 records · Page 45
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Characterization of a novel aromatic substrate-processing microcompartment in Actinobacteria

ABSTRACT We have discovered a new cluster of genes that is found exclusively in the Actinobacteria phylum. This locus includes genes for the 2-aminophenol meta -cleavage pathway and the shell proteins of a bacterial microcompartment (BMC) and has been named aromatics (ARO) for its putative role in the breakdown of aromatic compounds. In this study, we provide details about the distribution and composition of the ARO BMC locus and conduct phylogenetic, structural, and functional analyses of the first two enzymes in the catabolic pathway: a unique 2-aminophenol dioxygenase, which is exclusively found alongside BMC shell genes in Actinobacteria, and a semialdehyde dehydrogenase, which works downstream of the dioxygenase. Genomic analysis reveals variations in the complexity of the ARO loci across different orders. Some loci are simple, containing shell proteins and enzymes for the initial steps of the catabolic pathway, while others are extensive, encompassing all the necessary genes for the complete breakdown of 2-aminophenol into pyruvate and acetyl-CoA. Furthermore, our analysis uncovers two subtypes of ARO BMC that likely degrade either 2-aminophenol or catechol, depending on the presence of a pathway-specific gene within the ARO locus. The precise precursor of 2-aminophenol, which serves as the initial substrate and/or inducer for the ARO pathway, remains unknown, as our model organism Micromonospora rosaria cannot utilize 2-aminophenol as its sole energy source. However, using enzymatic assays, we demonstrate the dioxygenase’s ability to cleave both 2-aminophenol and catechol in vitro , in collaboration with the aldehyde dehydrogenase, to facilitate the rapid conversion of these unstable and toxic intermediates. IMPORTANCE Bacterial microcompartments (BMCs) are proteinaceous organelles that are widespread among bacteria and provide a competitive advantage in specific environmental niches. Studies have shown that the genetic information necessary to form functional BMCs is encoded in loci that contain genes encoding shell proteins and the enzymatic core. This allows the bioinformatic discovery of BMCs with novel functions and expands our understanding of the metabolic diversity of BMCs. ARO loci, found only in Actinobacteria, contain genes encoding for phylogenetically remote shell proteins and homologs of the meta -cleavage degradation pathway enzymes that were shown to convert central aromatic intermediates into pyruvate and acetyl-CoA in gamma Proteobacteria. By analyzing the gene composition of ARO BMC loci and characterizing two core enzymes phylogenetically, structurally, and functionally, we provide an initial functional characterization of the ARO BMC, the most unusual BMC identified to date, distinctive among the repertoire of studied BMCs.

2-AP 1,6-dioxygenase↗
DOE OSTI2022

Metagenomes and Metagenome-Assembled Genomes from Substrate-Amended Hot Spring Sediment Incubations from Yellowstone National Park

Here, we report on eight sediment metagenomes obtained from an alkaline hot spring, with their corresponding metagenome-assembled genomes. Samples had been incubated for 48 h with various substrate amendments in conjunction with the amino acid analog l-homopropargylglycine in a study targeted at identifying anabolicly active uncultured thermophilic archaea and bacteria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

RNAseq analysis of Cellvibrio japonicus during starch utilization differentiates between genes encoding carbohydrate active enzymes controlled by substrate detection or growth rate

ABSTRACT Bacterial utilization of starch is increasingly of interest as the importance and contributions of animal gut microbiomes become more defined. Consequently, identifying and characterizing the bacterial enzymes responsible for the degradation, transport, and metabolism of starch will enable developments in pharmaceutical, biotechnological, and culinary industries searching for novel prebiotics, carrier molecules, and low glycemic index sweeteners. The current challenge is that bacteria proficient at starch utilization often have hundreds of carbohydrate active enzymes, and it is unclear which are essential for starch utilization using only homology-based bioinformatics or computational methods. Complementary experimental data are also needed, especially to understand the regulation of bacterial starch utilization. We have completed an RNAseq analysis of the Gram-negative bacterium Cellvibrio japonicus and found that it has sophisticated regulation that includes substrate sensing and growth rate components for genes that encode starch-degrading enzymes. Among the 22 genes predicted to encode starch-active enzymes, C. japonicus has 10 alpha-amylases, 4 alpha-glucosidases, 2 pullulnases, and 2 cyclomaltodextrin glucanotransferases, 15 of which were up-regulated during exponential growth on starch and 8 up-regulated in stationary phase. Growth analyses with an enzyme secretion deficient mutant of C. japonicus suggested that secreted amylases are essential for this bacterium to degrade starch. Our approach of coupling a physiological growth assay with transcriptomic data provides a platform to identify targets for further genetic or biochemical analysis that can be broadly applied to other starch-utilizing bacteria. IMPORTANCE Understanding the bacterial metabolism of starch is important as this polysaccharide is a ubiquitous ingredient in foods, supplements, and medicines, all of which influence gut microbiome composition and health. Our RNAseq and growth data set provides a valuable resource to those who want to better understand the regulation of starch utilization in Gram-negative bacteria. These data are also useful as they provide an example of how to approach studying a starch-utilizing bacterium that has many putative amylases by coupling transcriptomic data with growth assays to overcome the potential challenges of functional redundancy. The RNAseq data can also be used as a part of larger meta-analyses to compare how C. japonicus regulates carbohydrate active enzymes, or how this bacterium compares to gut microbiome constituents in terms of starch utilization potential.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Perspective—Lithium Metal Nucleation and Growth on Conductive Substrates: A Multi-Scale Understanding from Atomistic, Nano-, Meso-, to Micro-Scales

Reversible lithium (Li) deposition and stripping on conductive substrates like copper is vital for long-life high-energy rechargeable Li batteries. The reversibility is believed hindered by solid electrolyte interphase (SEI) formation and Li dendritic growth. Via in situ, operando cryo-microscopy and molecular dynamics simulation, we discovered amorphous Li before a disorder-order phase transition to bcc phase. The kinetics plays a significant role in Li nucleation and morphology evolution. This perspective on Li nucleation and growth from atomistic to nano- (<20 nm), meso- (20–100 nm), and micro-scales (>100 nm) provides a practical guidance on regulating dense Li deposits reversibly for long life performance.

25 ENERGY STORAGE↗
DOE OSTI2020

Electrically conductive carbon fiber layers as lightning strike protection for non-conductive epoxy-based CFRP substrate

A large amount of electrically conductive fillers is needed to enhance a Carbon Fiber Reinforced Plastics (CFRP) electrical conductivity enough to withstand lightning strikes of peak currents. However, such large alien constituents hamper the inherent good mechanical properties of CFRP structures. In this work, a solution has been proposed to retain both desired properties in a CFRP laminate. Layer-wise hybrid laminate has been demonstrated as a solution for lightning strike protection of Carbon Fiber Reinforced Plastics (CFRP). Top few layers of a hybrid laminate are prepared using electrically conductive polymer-based resin (CF/C-POLY) to provide effective dissipation of lightning current while epoxy-based CFRP substrate (CF/Epoxy) provides the main structural strength. An insulating adhesive layer is used to bond CF/C-POLY and CF/Epoxy to prepare the laminate. The hybrid laminates were tested for their effectiveness against lightning strikes. Laminates were struck by modified lightning waveform of component A with peak current of -14 kA and -40 kA. The performance of the laminates against lightning strike were evaluated using high speed camera, high-speed and thermal camera. It is found that CF/C-POLY layer successfully defended the main structural component i.e. CF/Epoxy from lightning direct damage.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Pattern formation and transport for externally driven active matter on periodic substrates (a)

Abstract We investigate the transport of interacting active run-and-tumble particles moving under an external drift force through a periodic array of obstacles for increasing drive amplitudes. For high activity where the system forms a motility-induced phase-separated state, there are several distinct dynamic phases including a low drive pinned cluster phase, an intermediate uniform fluid, and a higher drive stripe crystal state. The transitions between the phases are correlated with signatures in the transport curves, differential mobility, and power spectra of the velocity fluctuations. In contrast, in the low activity regime the transport curves and power spectra undergo little change as a function of drive. We argue that in the high activity limit, the behavior is similar to that of driven solids on periodic substrates, while in the low activity limit the system behaves like a driven fluid.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Skyrmion soliton motion on periodic substrates by atomistic and particle-based simulations

Abstract We compare the dynamical behavior of magnetic skyrmions interacting with square and triangular defect arrays just above commensuration using both atomistic and particle-based models. Under applied drives, the initial motion is a kink traveling through the pinned skyrmion lattice. For the square defect array, both models agree well and show a regime in which the soliton motion is locked along 45°. The atomistic model also produces locking of a soliton along 30°, which is absent in the particle-based model. For the triangular defect array, the atomistic model exhibits 30° soliton motion over a wide region of external current values. In contrast, the particle-based model gives 45° soliton motion over a small range of external driving force values. The difference arises because the nondeforming particle model facilitates meandering skyrmion orbits while the deformable atomistic model enables stronger skyrmion-skyrmion interactions that reduce the meandering. Our results indicate that soliton motion through pinned skyrmion lattices on a periodic substrate is a robust effect.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Data from Enhanced 2′-Fucosyllactose Production by Engineered Saccharomyces cerevisiae using Xylose as a Co-Substrate

2′-Fucosyllactose (2′-FL), a human milk oligosaccharide with confirmed benefits for infant health, is a promising infant formula ingredient. Although Escherichia coli , Saccharomyces cerevisiae , Corynebacterium glutamicum , and Bacillus subtilis have been engineered to produce 2′-FL, their titers and productivities need be improved for economic production. Glucose along with lactose have been used as substrates for producing 2′-FL, but accumulation of by-products due to overflow metabolism of glucose hampered efficient production of 2′-FL regardless of a host strain. To circumvent this problem, we used xylose, which is the second most abundant sugar in plant cell wall hydrolysates and is metabolized through oxidative metabolism, for the production of 2′-FL by engineered yeast. Specifically, we modified an engineered S. cerevisiae strain capable of assimilating xylose to produce 2′-FL from a mixture of xylose and lactose. First, a lactose transporter (Lac12) from Kluyveromyces lactis was introduced. Second, a heterologous 2′-FL biosynthetic pathway consisting of enzymes Gmd, WcaG, and WbgL from E. coli was introduced. Third, we adjusted expression levels of the heterologous genes to maximize 2′-FL production. The resulting engineered yeast produced 25.5 g/L of 2′-FL with a volumetric productivity of 0.35 g/L∙h in a fed-batch fermentation with lactose and xylose feeding to mitigate the glucose repression. Interestingly, the major location of produced 2′-FL by the engineered yeast can be changed using different culture media. While 72% of the produced 2′-FL was secreted when a complex medium was used, 82% of the produced 2′-FL remained inside the cells when a minimal medium was used. As yeast extract is already used as food and animal feed ingredients, 2′-FL enriched yeast extract can be produced cost-effectively using the 2′-FL-accumulating yeast cells.

Conversion↗
DOE OSTI2023

High external quantum efficiency (6.5%) InGaN V-defect LEDs at 600 nm on patterned sapphire substrates

Highly efficient long-wavelength InGaN LEDs have been a research focus in nitride LEDs for their potential applications in displays and solid-state lighting. A key breakthrough has been the use of laterally injected quantum wells via naturally occurring V-defects which promote hole injection through semipolar sidewalls and help to overcome the barriers to carrier injection that plague long wavelength nitride LEDs. In this article, we study V-defect engineered LEDs on (0001) patterned sapphire substrates (PSS) and GaN on (111) Si. V-defects were formed using a 40-period InGaN/GaN superlattice and we report a packaged external quantum efficiency (EQE) of 6.5% for standard 0.1 mm 2 . LEDs on PSS at 600 nm. We attribute the high EQE in these LEDs to lateral injection via V-defects.

Ewing, Jacob J.↗
DOE OSTI2020

X-ray verification of sol-gel resist shrinkage in substrate-conformal imprint lithography for a replicated blazed reflection grating

Surface-relief gratings fabricated through nanoimprint lithography (NIL) are prone to topographic distortion induced by resist shrinkage. Characterizing the impact of this effect on blazed diffraction efficiency is particularly important for applications in astrophysical spectroscopy at soft x-ray wavelengths ( λ ≈ 0.5 − 5 nm) that call for the mass-production of large-area grating replicas with sub-micron, sawtooth surface-relief profiles. A variant of NIL that lends itself well for this task is substrate-conformal imprint lithography (SCIL), which uses a flexible, composite stamp formed from a rigid master template to imprint nanoscale features in an inorganic resist that cures thermodynamically through a silica sol-gel process. While SCIL enables the production of several hundred imprints before stamp degradation and avoids many of the detriments associated with large-area imprinting in NIL, the sol-gel resist suffers shrinkage dependent on the post-imprint cure temperature. Through atomic force microscopy and diffraction-efficiency testing at beamline 6.3.2 of the Advanced Light Source, the impact of this effect on blaze response is constrained for a ∼160-nm-period grating replica cured at 90 ° C. Results demonstrate a ∼2 ° reduction in blaze angle relative to the master grating, which was fabricated by anisotropic wet etching in 〈311〉-oriented silicon to yield a facet angle close to 30 ° .

McCoy, Jake A. (ORCID:0000000216057517)↗
DOE OSTI2021

Data from Raczka et al., Interactions between microbial diversity and substrate chemistry determine the fate of carbon in soil, from Elizabeth Woods in Morgantown, West Virginia, USA

File types include: Soil respiration as 13C cumulative respiration from soil incubation experiment, qSIP (quantitative stable isotope probing) data that is "18S apes wide" which is the fungal atom percent excess or how much the fungi took up of the labeled litter and "16S apes wide" which is the bacterial atom percent excess or how much the bacteria took up of the labeled litter, metabolomic data from the incubated soil samples called "Metab Soil Unique Filtered", which is the metabolomic data that had an initial filter from the raw data, and lipidomic data from the incubated soil samples called "All lipids soil". These files were used according to methods in Raczka et al. 2021 Scientific Reports. Headers show soil type (Oak, Poplar) and litter type (also called substrate here, which is labeled as no litter (control), poplar, and oak). This research was done to understand interactions between ecosystem-level processes and microbial diversity that impacts the composition of decomposition products that can form stable soil organic matter.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Substrate Effects When Using Photons to Make Perovskite Solar Cells

To shorten annealing time and minimize substrate heating, flash lamps that deliver short, intense light pulses, commonly called photonic curing, are used to replace thermal annealing using hot plates or ovens. This method is different from equilibrium heating in that the radiant energy is selectively absorbed by the film. The high-intensity light pulses produce a high peak temperature in the film. Because most processes follow Arrhenius behavior, reaching high temperatures allow chemical reactions/phase transformations to occur in a short time, significantly reducing the processing time. Often the results are non-intuitive. We will present fabricating flexible halide perovskite solar cells (PSCs) on indium tin oxide (ITO) coated Willow glass. The effect of ITO transmittance on the photonic curing of nickel nitrate sol-gel precursors into nickel oxide to fabricate hole transport layer and consequently the performance of PSCs. Unexpectedly, ITO samples processed by photonic curing show improved optical and electrical properties.

14 SOLAR ENERGY↗
DOE OSTI2025

Nanopore Activity Assays for Detection of Biomarker Protease Activity: Design and Testing of Substrates for Both Nanopore Sequencing and PCR-Based Detection Methods

The work performed in this project has demonstrated the ability to construct proteolytic enzyme substrates that are PCR and sequencing-readable reporter molecules. Specifically, the goal was to detect those reporter molecules via PCR and Oxford Nanopore Technologies MinION sequencing methods following exposure to the biomarker protease thrombin. The assay development focused on binding the constructed peptide-oligonucleotide chimera to immobilized streptavidin. The action of thrombin on the peptide portion of the molecule released the oligonucleotide for detection. Detection of protease activity was demonstrated in a concentration-dependent manner using MALDI-MS, RT-PCR and DNA sequencing. Additional steps to remove background release of reporter molecules during the assay was used to improve the difference in detected oligonucleotide reporter following protease activity. Additional steps in assay development will be to (1) test the assay in an appropriate matrix, (2) investigate detection using additional DNA sequencing platforms and (3) demonstrate multiplexed detection of multiple protease markers in a single reaction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Broadband mm-Wave Substrate Integrated Waveguides [Poster]

At mm-wave frequencies, signals need to be supported by specialized, low-loss transmission lines such as waveguides. Substrate-integrated waveguides (SIWs) combine the good electrical properties of rectangular waveguides with the compactness of planar transmission lines. Additionally, SIWs can be fabricated using standard PCB manufacturing techniques and can be easily integrated with other mm-wave components. This study explores SIWs in the 50-75 GHz range, with designs optimized for simple fabrication.

42 ENGINEERING↗
DOE OSTI2026

TCF Base Technology-Specific Final Report: Engineering Enzymes for Crystalline PET Substrate

The primary objective of this project was to develop a new polyethylene terephthalate (PET) hydrolase enzyme to depolymerize relevant PET substrates for Birch Biosciences, using high-throughput protein expression, purification, and assaying systems and machine learning-guided enzyme design. As a secondary project objective, we also aimed to develop a more energy-efficient ethylene glycol (EG) recovery strategy relative to distillation.

09 BIOMASS FUELS↗
DOE OSTI2026

Gold Catalyzed Polymerization Reactions of Unsaturated Substrates: Towards New Functional, Recyclable, and Upcycled Aromatic Polymers (Final Report)

The overarching goal of this project lied in the translation of gold (Au) catalyzed small molecule synthetic transformations to the field of polymer science, the generation of new macromolecular structures, and the application of the materials and methodologies produced toward sustainable polymer development and chemical upcycling. Specifically, this project aimed to polymerize monomers based on unsaturated precursors and access novel polymeric materials through the extension of Au catalyzed intermolecular processes. The specific objectives of this project comprised: (1) the extension of Au-catalyzed intermolecular reactions to bifunctional monomers and the polycondensation of diverse nucleophiles; (2) to gain fundamental mechanistic insight into Au-catalyzed polymerizations; (3) the application of these reactions to the synthesis of new classes of aromatic polymers that can be readily and/or selectively deconstructed; and (4) to apply these chemistries to post-polymerization modification (PPM) of commercially relevant polyaromatic substrates, including post-industrial plastics and post-consumer waste.

36 MATERIALS SCIENCE↗
DOE OSTI2021

A Swollenin From Talaromyces leycettanus JCM12802 Enhances Cellulase Hydrolysis Toward Various Substrates

Swollenins exist within some fungal species and are candidate accessory proteins for the biodegradation of cellulosic substrates. Here, we describe the identification of a swollenin gene, Tlswo , in Talaromyces leycettanus JCM12802. Tlswo was successfully expressed in both Trichoderma reesei and Pichia pastoris . Assay results indicate that Tl SWO is capable of releasing reducing sugars from lichenan, barley β-glucan, carboxymethyl cellulose sodium (CMC-Na) and laminarin. The specific activity of Tl SWO toward lichenan, barley β-glucan, carboxymethyl cellulose sodium (CMC-Na) and laminarin is 9.0 ± 0.100, 8.9 ± 0.100, 2.3 ± 0.002 and 0.79 ± 0.002 U/mg, respectively. Additionally, Tl SWO had disruptive activity on Avicel and a synergistic effect with cellobiohydrolases, increasing the activity on pretreated corn stover by up to 72.2%. The functional diversity of Tl SWO broadens its applicability in experimental settings, and indicating that it may be a promising candidate for future industrial applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Substrate-independent expression of key functional genes in Cycloclasticus pugetii strain PS-1 limits their use as markers for PAH biodegradation

Microbial degradation of petroleum hydrocarbons is a crucial process for the clean-up of oil-contaminated environments. Cycloclasticus spp. are well-known polycyclic aromatic hydrocarbon (PAH) degraders that possess PAH-degradation marker genes including rhd3α, rhd2α, and pahE. However, it remains unknown if the expression of these genes can serve as an indicator for active PAH degradation. Here, we determined transcript-to-gene (TtG) ratios with (reverse transcription) qPCR in cultures of Cycloclasticus pugetii strain PS-1 grown with naphthalene, phenanthrene, a mixture of these PAHs, or alternate substrates (i.e., no PAHs). Mean TtG ratios of 1.99 × 10 −2 , 1.80 × 10 −3 , and 3.20 × 10 −3 for rhd3α, rhd2α, and pahE, respectively, were measured in the presence or absence of PAHs. The TtG values suggested that marker-gene expression is independent of PAH degradation. Measurement of TtG ratios in Arctic seawater microcosms amended with water-accommodated crude oil fractions, and incubated under in situ temperature conditions (i.e., 1.5°C), only detected Cycloclasticus spp. rhd2α genes and transcripts (mean TtG ratio of 4.15 × 10 −1 ). The other marker genes—rhd3α and pahE—were not detected, suggesting that not all Cycloclasticus spp. carry these genes and a broader yet-to-be-identified repertoire of PAH-degradation genes exists. The results indicate that the expression of PAH marker genes may not correlate with PAH-degradation activity, and transcription data should be interpreted cautiously.

59 BASIC BIOLOGICAL SCIENCES↗