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Results for “substrate selection”

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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Dynamic Conformational States Dictate Selectivity toward the Native Substrate in a Substrate-Permissive Acyltransferase

Hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyltransferase (HCT) is an essential acyltransferase that mediates flux through plant phenylpropanoid metabolism by catalyzing a reaction between p-coumaroyl-CoA and shikimate, yet it also exhibits broad substrate permissiveness in vitro. How do enzymes like HCT avoid functional derailment by cellular metabolites that qualify as non-native substrates? Here, we combine X-ray crystallography and molecular dynamics to reveal distinct dynamic modes of HCT under native and non-native catalysis. We find that essential electrostatic and hydrogen-bonding interactions between the ligand and active site residues, permitted by active site plasticity, are elicited more effectively by shikimate than by other non-native substrates. This work provides a structural basis for how dynamic conformational states of HCT favor native over non-native catalysis by reducing the number of futile encounters between the enzyme and shikimate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Phase selective growth and characterization of vanadium dioxide films on silicon substrates

We report on selective growth of VO{sub 2} films with M1, M2, and intermediate T phases on silicon (Si) substrates by using inductively coupled plasma (ICP)-assisted sputtering (ICPS) under particular conditions. The film composed of M2 phase was proved to be under strong in-plane compressive stress, which is consistent with stress-induced M2 phase. Crystalline structural phase transition (SPT) properties of these films were demonstrated together with infrared light transmittance as a measure of insulator-metal transition (IMT) against temperature. Characteristic correlations between SPT and IMT for films with M2 and intermediate-T phases were reported. Ultraviolet photoelectron spectroscopy measurements probed an energy gap of the film in the M2 phase at around 0.4 eV from the Fermi level indicating the presence of a Mott gap.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Optically transparent frequency selective surfaces on flexible thin plastic substrates

A novel 2D simple low cost frequency selective surface was screen printed on thin (0.21 mm), flexible transparent plastic substrate (relative permittivity 3.2). It was designed, fabricated and tested in the frequency range 10-20 GHz. The plane wave transmission and reflection coefficients agreed with numerical modelling. The effective permittivity and thickness of the backing sheet has a significant effect on the frequency characteristics. The stop band frequency reduced from 15GHz (no backing) to 12.5GHz with polycarbonate. The plastic substrate thickness beyond 1.8mm has minimal effect on the resonant frequency. While the inner element spacing controls the stop-band frequency, the substrate thickness controls the bandwidth. The screen printing technique provided a simple, low cost FSS fabrication method to produce flexible, conformal, optically transparent and bio-degradable FSS structures which can find their use in electromagnetic shielding and filtering applications in radomes, reflector antennas, beam splitters and polarizers.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Mechanisms of mTORC1 activation by RHEB and inhibition by PRAS40

The mechanistic target of rapamycin complex 1 (mTORC1) controls cell growth and metabolism in response to nutrients, energy levels, and growth factors. It contains the atypical kinase mTOR and the RAPTOR subunit that binds to the Tor signalling sequence (TOS) motif of substrates and regulators. mTORC1 is activated by the small GTPase RHEB (Ras homologue enriched in brain) and inhibited by PRAS40. Here we present the 3.0 ångström cryo-electron microscopy structure of mTORC1 and the 3.4 ångström structure of activated RHEB–mTORC1. RHEB binds to mTOR distally from the kinase active site, yet causes a global conformational change that allosterically realigns active-site residues, accelerating catalysis. Here, cancer-associated hyperactivating mutations map to structural elements that maintain the inactive state, and we provide biochemical evidence that they mimic RHEB relieving auto-inhibition. We also present crystal structures of RAPTOR–TOS motif complexes that define the determinants of TOS recognition, of an mTOR FKBP12–rapamycin-binding (FRB) domain–substrate complex that establishes a second substrate-recruitment mechanism, and of a truncated mTOR–PRAS40 complex that reveals PRAS40 inhibits both substrate-recruitment sites. These findings help explain how mTORC1 selects its substrates, how its kinase activity is controlled, and how it is activated by cancer-associated mutations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Single-molecule imaging at high fluorophore concentrations by local activation of dye

Single-molecule fluorescence microscopy is a powerful approach to observe biomolecular interactions with high spatial and temporal resolution. Detecting fluorescent signals from individual, labeled proteins above high levels of background fluorescence remains challenging, however. For this reason, the concentrations of labeled proteins in in vitro assays are often kept low compared to their in vivo concentrations. Here, we present a new fluorescence imaging technique by which single fluorescent molecules can be observed in real time at high, physiologically relevant concentrations. The technique requires a protein and its macromolecular substrate to be labeled each with a different fluorophore. Then, making use of short-distance energy-transfer mechanisms, the fluorescence from only those proteins bound to their substrate are selectively activated. This approach is demonstrated by labeling a DNA substrate with an intercalating stain, exciting the stain, and using energy transfer from the stain to activate the fluorescence of only those labeled DNA-binding proteins bound to the DNA. Such an experimental design allowed us to observe the sequence-independent interaction of Cy5-labeled interferon-inducible protein 16 (IFI16) with DNA and the sliding via one-dimensional diffusion of Cy5-labeled adenovirus protease (pVIc-AVP) on DNA in the presence of a background of hundreds of nM Cy5 fluorophore.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Dynamic Phaeodactylum tricornutum exometabolites shape surrounding bacterial communities

Summary Roles of different ecological classes of algal exometabolites in regulating microbial community composition are not well understood. Here, we identify exometabolites from the model diatom Phaeodactylum tricornutum and demonstrate their potential to influence bacterial abundances. We profiled exometabolites across a time course of axenic algal growth using liquid chromatography–tandem mass spectrometry. We then investigated growth of 12 bacterial isolates on individual‐identified exometabolites. Lastly, we compared responses of a P. tricornutum ‐adapted enrichment community to additions of two contrasting metabolites: selective growth substrate 4‐hydroxybenzoic acid and putative signaling/facilitator molecule lumichrome. We identified 50 P. tricornutum metabolites and found distinct temporal accumulation patterns. Two exometabolites (of 12 tested) supported growth of distinct subsets of bacterial isolates. While algal exudates and algal presence drove similar changes in community composition compared with controls, exogenous 4‐hydroxybenzoic acid addition promoted increased abundances of taxa that utilized it in isolation, and also revealed the importance of factors relating to algal presence in regulating community composition. This work demonstrates that secretion of selective bacterial growth substrates represents one mechanism by which algal exometabolites can influence bacterial community composition and illustrates how the algal exometabolome has the potential to modulate bacterial communities as a function of algal growth.

4-hydroxybenzoic acid↗
DOE OSTI2014

Effect of interwire separation on growth kinetics and properties of site-selective GaAs nanowires

We report tuning of the growth kinetics, geometry, and properties of autocatalytic GaAs nanowires (NW) by precisely controlling their density on SiO{sub 2}-mask patterned Si (111) substrates using selective area molecular beam epitaxy. Using patterned substrates with different mask opening size (40–120 nm) and pitch (0.25–3 μm), we find that the NW geometry (length, diameter) is independent of the opening size, in contrast to non-catalytic GaAs NWs, whereas the NW geometry strongly depends on pitch, i.e., interwire separation and NW density. In particular, two distinct growth regimes are identified: a diffusion-limited regime for large pitches (low NW density) and a competitive growth regime for smaller pitches (high NW density), where axial and radial NW growth rates are reduced. The transition between these two regimes is significantly influenced by the growth conditions and shifts to smaller pitches with increasing As/Ga flux ratio. Ultimately, the pitch-dependent changes in growth kinetics lead to distinctly different photoluminescence properties, highlighting that mask template design is a very critical parameter for tuning intrinsic NW properties.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2024

Identification of carbohydrate gene clusters obtained from in vitro fermentations as predictive biomarkers of prebiotic responses

Prebiotic fibers are non-digestible substrates that modulate the gut microbiome by promoting expansion of microbes having the genetic and physiological potential to utilize those molecules. Although several prebiotic substrates have been consistently shown to provide health benefits in human clinical trials, responder and non-responder phenotypes are often reported. These observations had led to interest in identifying, a priori, prebiotic responders and non-responders as a basis for personalized nutrition. In this study, we conducted in vitro fecal enrichments and applied shotgun metagenomics and machine learning tools to identify microbial gene signatures from adult subjects that could be used to predict prebiotic responders and non-responders. Using short chain fatty acids as a targeted response, we identified genetic features, consisting of carbohydrate active enzymes, transcription factors and sugar transporters, from metagenomic sequencing of in vitro fermentations for three prebiotic substrates: xylooligosacharides, fructooligosacharides, and inulin. A machine learning approach was then used to select substrate-specific gene signatures as predictive features. These features were found to be predictive for XOS responders with respect to SCFA production in an in vivo trial. Our results confirm the bifidogenic effect of commonly used prebiotic substrates along with inter-individual microbial responses towards these substrates. We successfully trained classifiers for the prediction of prebiotic responders towards XOS and inulin with robust accuracy (≥ AUC 0.9) and demonstrated its utility in a human feeding trial. Overall, the findings from this study highlight the practical implementation of pre-intervention targeted profiling of individual microbiomes to stratify responders and non-responders.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Selective area growth of semiconductors using patterned sol-gel materials

Systems and methods for growing semiconductor materials on substrates by using patterned sol-gel materials are provided. According to a first aspect of the invention, a method includes forming a pattern of a sol-gel material on a first region of substrate, and depositing a semiconductor material on a second region of the substrate by selective area growth. The second region is adjacent to the first region.

Warren, Emily L.↗
DOE OSTI2018

Effect of bacterial inoculants on phytomining of metals from waste incineration bottom ash

Highlights: • Plants inoculated with PGP-bacteria were grown on waste incineration bottom ash. • Rhizobacteria Rhodococcus erythropolis P30 enhanced biomass of Nicotiana tabacum. • Selected PGP-strains enhanced biomass and nutritional status of Salix smithiana. • Strains enhancing growth on contaminated soil had a similar effect on bottom ash. • Bacterial inoculants did not enhance trace element accumulation in plants. - Abstract: Waste incineration bottom ash is considered a secondary resource for valuable trace elements (TE), which is currently neglected in most European countries. Phytomining could potentially recover valuable TE from such waste materials but is still at an exploratory stage with many challenges. The use of bioaugmentation to improve plant growth and TE accumulation of metal-tolerant high biomass plants growing on waste incineration bottom ash was evaluated. Bacterial strains that were previously isolated from rhizosphere, roots and contaminated soil were selected according to their plant growth promoting characteristics and tolerance to the bottom ash substrate. Those selected bacterial strains were tested for their beneficial effects on Nicotiana tabacum and Salix smithiana with regards to phytomining. The rhizobacterial strain Rhodococcus erythropolis P30 enhanced the shoot dry weight of N. tabacum by on average 57% compared to the control plants. Several bacterial inoculants enhanced biomass production and the nutritional status of S. smithiana. Moreover, those bacterial strains previously described to enhance biomass production of N. tabacum and members of the Salicaceae on TE-contaminated soils, also enhanced biomass production of these species on bottom ash. However, bacterial inoculants could not enhance trace element accumulation in plants.

09 BIOMASS FUELS↗
DOE OSTI2024

Bench-Scale Development of a Novel Direct Air Capture Technology Using High-Capacity Structured Sorbents

The work performed under this project has resulted into development of a DAC technology utilizing a structured sorbent to capture CO 2 from ambient air with a key innovation of direct Joule heating of the sorbent for CO 2 desorption. A working SMA, fully integrated with an electrically resistive heating layer, high surface area support, and high CO 2 capacity sorbent coated onto a commercial ceramic monolithic substrate, was successfully developed and demonstrated over >200 adsorption-desorption cycles in a high-fidelity bench test unit directly using ambient air. A cordierite-based monolith was selected as a substrate owing to its high surface area, low bulk density, low heat capacity, and commercial availability. Reaction kinetics study conducted during this project led to development of a promoter for the base Na 2 CO 3 sorbent that could be incorporated into the sorbent to enhance to achieve higher CO 2 adsorption/desorption rates, greater working capacity, and reduced regeneration temperature. An accelerated aging study was conducted in a TGA to determine sorbent stability and no degradation in the sorbent performance was observed even after 250 adsorption-desorption cycles. An electrically resistive heating layer was developed with tunable electrical properties. The heating layer was coated onto the selected cordierite substrate. Aging studies performed showed the electrical properties and heating performance was stable after 500 heating and cooling cycles. The collective findings on the selected cordierite substrate, robust heating layer, promoter and sorbent selection were used to synthesize a full, 6”x6” SMA for bench-scale testing. The bench-scale DAC system was constructed to test full size SMAs using real ambient air for adsorption and joule heating for regeneration. After completing shakedown and commissioning of the 1 kg/day of CO 2 capacity DAC bench unit, an extended operation was performed to complete over 230 cycles with the full size SMA. This testing showed no observable degradation in sorbent performance. A detailed process model, TEA and LCA were developed for a conceptual 100,000 TPY CO 2 removal DAC facility. The LCA results show the net CO 2 e emissions from the DAC system are highly dependent on the electricity source. All other factors, including SMA manufacturing, materials for facility enclosure, etc., are minor cost contributors compared to the energy consumption required for CO 2 removal. With the successful development and validation of the SMA for the sustained performance for CO 2 removal from ambient air with joule heated regeneration in this project, a fully integrated 1 TPY bench-scale DAC system is currently in development with the support of DOE/FECM (DE-FE0032243). The project objective is to demonstrate the engineering design of the DAC system to produce a continuous, high purity CO 2 stream from ambient air. This project will address and validate key engineering features of the DAC system including the gas sealing mechanism and panels, enclosure and air contactor design, and automation sequence to achieve continuous CO 2 production.

42 ENGINEERING↗
DOE OSTI2018

Control of Polar Orientation and Lattice Strain in Epitaxial BaTiO 3 Films on Silicon

Conventional strain engineering of epitaxial ferroelectric oxide thin films is based on the selection of substrates with a suitable lattice parameter. In this work, we show that the variation of oxygen pressure during pulsed laser deposition is a flexible strain engineering method for epitaxial ferroelectric BaTiO 3 films either on perovskite substrates or on Si(001) wafers. This unconventional growth strategy permits continuous tuning of strain up to high levels (ε > 0.8%) in films greater than one hundred nanometers thick, as well as selecting the polar axis orientation to be either parallel or perpendicular to the substrate surface plane.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

J-domain proteins interaction with neurodegenerative disease-related proteins

HSP70 chaperones, J-domain proteins (JDPs) and nucleotide exchange factors (NEF) form functional networks that have the ability to prevent and reverse the aggregation of proteins associated with neurodegenerative diseases. JDPs can interact with specific substrate proteins, hold them in a refolding-competent conformation and target them to specific HSP70 chaperones for remodeling. Thereby, JDPs select specific substrates and constitute an attractive target for pharmacological intervention of neurodegenerative diseases. This, under the condition that the exact mechanism of JDPs interaction with specific substrates is unveiled. In this review, we provide an overview of the structural and functional variety of JDPs that interact with neurodegenerative disease-associated proteins and we highlight those studies that identified specific residues, domains or regions of JDPs that are crucial for substrate binding.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Complete replacement of Arabidopsis oil-producing enzymes with heterologous diacylglycerol acyltransferases

Acyl-CoA:diacylglycerol acyltransferase 1 (DGAT1) and phospholipid:diacylglycerol acyltransferase 1 (PDAT1) share responsibility for triacylglycerol (TAG) biosynthesis, and their selectivities control TAG fatty acid (FA) compositions. For rational metabolic engineering of seed oils, replacing endogenous TAG biosynthesis with exogenous enzymes containing different substrate FA selectivities is desirable; however, the dgat1-1/pdat1-2 double mutant is pollen lethal. Here, we evaluated the ability of 3 DGAT1s, from phylogenetically diverse plants with distinct TAG assembly processes, to completely replace endogenous TAG biosynthesis in Arabidopsis ( Arabidopsis thaliana ). We transformed dgat1-1 mutant plants with expression constructs for DGAT1 s from Camelina sativa , Physaria fendleri , and castor ( Ricinus communis ). Transgene expression was properly “contextualized” by using a previously determined minimum necessary expression unit containing the promoter/5′ UTR and first intron of native AtDGAT1 ; both of these DNA elements are essential for pollen expression. Next, we crossed homozygous lines with a DGAT1/DGAT1/PDAT1/pdat1-2 parent. C. sativa and P. fendleri DGAT1s restored the FA compositions and transcriptional differences of dgat1-1 to near wild-type and rescued the dgat1-1/pdat1-2 pollen lethality. R. communis DGAT1 was active in dgat1-1 seeds but produced unique oil profiles and alterations in the expression of lipid metabolic genes; it also failed to rescue dgat1-1/pdat1-2 lethality. This study confirms that the promoter and first intron of AtDGAT1 can modulate the expression of foreign DGAT1 genes to fit the correct spatiotemporal profile necessary for completely replacing endogenous TAG biosynthesis. Furthermore, it demonstrates an additional layer of unexpected enzyme incompatibility between oilseed lineages, which may complicate bioengineering approaches that seek to replace essential genes with orthologs.

McGuire, Sean T. [Washington State Univ., Pullman,↗
DOE OSTI2016

Molecular basis for allosteric specificity regulation in class Ia ribonucleotide reductase from Escherichia coli

Ribonucleotide reductase (RNR) converts ribonucleotides to deoxyribonucleotides, a reaction that is essential for DNA biosynthesis and repair. This enzyme is responsible for reducing all four ribonucleotide substrates, with specificity regulated by the binding of an effector to a distal allosteric site. In all characterized RNRs, the binding of effector dATP alters the active site to select for pyrimidines over purines, whereas effectors dGTP and TTP select for substrates ADP and GDP, respectively. Here, we have determined structures of Escherichia coli class Ia RNR with all four substrate/specificity effector-pairs bound (CDP/dATP, UDP/dATP, ADP/dGTP, GDP/TTP) that reveal the conformational rearrangements responsible for this remarkable allostery. These structures delineate how RNR ‘reads’ the base of each effector and communicates substrate preference to the active site by forming differential hydrogen bonds, thereby maintaining the proper balance of deoxynucleotides in the cell.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Selective area doping for Mott neuromorphic electronics

The cointegration of artificial neuronal and synaptic devices with homotypic materials and structures can greatly simplify the fabrication of neuromorphic hardware. We demonstrate experimental realization of vanadium dioxide (VO 2 ) artificial neurons and synapses on the same substrate through selective area carrier doping. By locally configuring pairs of catalytic and inert electrodes that enable nanoscale control over carrier density, volatility or nonvolatility can be appropriately assigned to each two-terminal Mott memory device per lithographic design, and both neuron- and synapse-like devices are successfully integrated on a single chip. Feedforward excitation and inhibition neural motifs are demonstrated at hardware level, followed by simulation of network-level handwritten digit and fashion product recognition tasks with experimental characteristics. Spatially selective electron doping opens up previously unidentified avenues for integration of emerging correlated semiconductors in electronic device technologies.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Selective heteroepitaxy on deeply grooved substrate: A route to low cost semipolar GaN platforms of bulk quality

Semipolar GaN crystal stripes larger than 100 μm with dislocation densities below 5 × 10{sup 6} cm{sup −2} are achieved using a low cost fabrication process. An original sapphire patterning procedure is proposed, enabling selective growth of semipolar oriented GaN stripes while confining the defects to specific areas. Radiative and non-radiative crystalline defects are investigated by cathodoluminescence and can be correlated to the development of crystal microstructure during the growth process. A dislocation reduction mechanism, supported by transmission electron microscopy, is proposed. This method represents a step forward toward low-cost quasi-bulk semipolar GaN epitaxial platforms with an excellent structural quality which will allow for even more efficient III-nitride based devices.

36 MATERIALS SCIENCE↗