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DOE OSTI2018

Architecture of the U6 snRNP reveals specific recognition of 3'-end processed U6 snRNA

The spliceosome removes introns from precursor messenger RNA (pre-mRNA) to produce mature mRNA. Prior to catalysis, spliceosomes are assembled de novo onto pre-mRNA substrates. During this assembly process, U6 small nuclear RNA (snRNA) undergoes extensive structural remodeling. The early stages of this remodeling process are chaperoned by U6 snRNP proteins Prp24 and the Lsm2–8 heteroheptameric ring. We now report a structure of the U6 snRNP from Saccharomyces cerevisiae. The structure reveals protein–protein contacts that position Lsm2–8 in close proximity to the chaperone “active site” of Prp24. The structure also shows how the Lsm2–8 ring specifically recognizes U6 snRNA that has been post-transcriptionally modified at its 3' end, thereby elucidating the mechanism by which U6 snRNPs selectively recruit 3' end-processed U6 snRNA into spliceosomes. Additionally, the structure reveals unanticipated homology between the C-terminal regions of Lsm8 and the cytoplasmic Lsm1 protein involved in mRNA decay.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Plasmonic Landau damping in active environments

Optical manipulation of charge on the nanoscale is of fundamental importance to an array of proposed technologies from selective photocatalysis to nanophotonics. Open plasmonic systems where collective electron oscillations release energy and charge to their environments offer a potential means to this end as plasmons can rapidly decay into energetic electron-hole pairs; however, isolating this decay from other plasmon-environment interactions remains a challenge. Here we introduce an analytic theory of noble-metal nanoparticles that quantitatively models plasmon decay into electron-hole pairs, demonstrates that this decay depends significantly on the nanoparticle's dielectric environment, and disentangles this effect from competing decay pathways. Using our method to incorporate embedding material and substrate effects on plasmon-electron interaction, we show that predictions from the model agree with four separate experiments. Finally, examination of coupled nanoparticle-emitter systems further shows that the hybridized in-phase mode more efficiently decays to photons whereas the out-of-phase mode more efficiently decays to electron-hole pairs, offering a strategy to tailor open plasmonic systems for charge manipulation.

36 MATERIALS SCIENCE↗

DOE OSTI2018

A New Method of Selective Laser Cladding

A new approach to selective laser cladding using conical laser beams has been elaborated. The initial round laser beam is divided into two or more circular beams with regulated distribution of the laser power between them. The circular beams are converted into conical beams that are focused separately on the surface and on different areas of the deposited material for their efficient heating. The delivery of laser energy into the powder stream is very effective because it provides a complete uniform absorption of laser energy in a dense powder stream (10{sup 4}–10{sup 6} cm{sup –3}). Under wire deposition, substrate heating reduces residual stresses due to temperature gradients and compensates for heat loss from the deposition zone by thermal conduction. The required power density for melt contact formation is significantly reduced.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS2005

Development of Solid State Thermal Sensors for Aeroshell TPS Flight Applications

In-situ Thermal Protection System (TPS) sensors are required to provide verification by traceability of TPS performance and sizing tools. Traceability will lead to higher fidelity design tools, which in turn will lead to lower design safety margins, and decreased heatshield mass. Decreasing TPS mass will enable certain missions that are not otherwise feasible, and directly increase science payload. NASA Ames is currently developing two flight measurements as essential to advancing the state of TPS traceability for material modeling and aerothermal simulation: heat flux and surface recession (for ablators). The heat flux gage is applicable to both ablators and non-ablators and is therefore the more generalized sensor concept of the two with wider applicability to mission scenarios. This paper describes the continuing development of a thermal microsensor capable of surface and in-depth temperature and heat flux measurements for TPS materials appropriate to Titan, Neptune, and Mars aerocapture, and direct entry. The thermal sensor is a monolithic solid state device composed of thick film platinum RTD on an alumina substrate. Choice of materials and critical dimensions are used to tailor gage response, determined during calibration activities, to specific (forebody vs. aftbody) heating environments. Current design has maximum operating temperature of 1500K, and allowable constant heat flux of q=28.7 W/cm(sup 2), and time constants between 0.05 and 0.2 seconds. The catalytic and radiative response of these heat flux gages can also be changed through the use of appropriate coatings. By using several co-located gages with various surface coatings, data can be obtained to isolate surface heat flux components due to radiation, catalycity and convection. Selectivity to radiative heat flux is a useful feature even for an in-depth gage, as radiative transport may be a significant heat transport mechanism for porous TPS materials in Titan aerocapture.

Martinez, Ed↗

DOE OSTI2016

Characterization of oxide scales grown on alloy 310S stainless steel after long term exposure to supercritical water at 500 °C

The oxide scale grown of static capsules made of alloy 310S stainless steel was investigated by exposure to the supercritical water at 500 °C 25 MPa for various exposure times up to 20,000 h. Characterization techniques such as X-ray diffraction, scanning/transmission electron microscopy, energy dispersive spectroscopy, and fast Fourier transformation were employed on the oxide scales. The elemental and phase analyses indicated that long term exposure to the SCW resulted in the formation of scales identified as Fe{sub 3}O{sub 4} (outer layer), Fe-Cr spinel (inner layer), Cr{sub 2}O{sub 3} (transition layer) on the substrate, and Ni-enrichment (chrome depleted region) in the alloy 310S. It was found that the layer thickness and weight gain vs. exposure time followed parabolic law. The oxidation mechanism and scales grown on the alloy 310S stainless steel exposed to SCW are discussed. - Highlights: •Oxidation of alloy 310S stainless steel exposed to SCW (500 °C/25 MPa) •The layer thickness and weight gain vs. exposure time followed parabolic law. •Oxide layers including Fe{sub 3}O{sub 4} (outer), Fe-Cr spinel (inner) and Cr{sub 2}O{sub 3} (transition) •Ni element is segregated by the selective oxidation of Cr.

36 MATERIALS SCIENCE↗

DOE OSTI2015

Sample-morphology effects on x-ray photoelectron peak intensities. III. Simulated spectra of model core–shell nanoparticles

The National Institute of Standards and Technology database for the simulation of electron spectra for surface analysis has been used to simulate Cu 2p photoelectron spectra for four types of spherical copper–gold nanoparticles (NPs). These simulations were made to extend the work of Tougaard [J. Vac. Sci. Technol. A 14, 1415 (1996)] and of Powell et al. [J. Vac. Sci. Technol. A 31, 021402 (2013)] who performed similar simulations for four types of planar copper–gold films. The Cu 2p spectra for the NPs were compared and contrasted with analogous results for the planar films and the effects of elastic scattering were investigated. The new simulations were made for a monolayer of three types of Cu/Au core–shell NPs on a Si substrate: (1) an Au shell of variable thickness on a Cu core with diameters of 0.5, 1.0, 2.0, 5.0, and 10.0 nm; (2) a Cu shell of variable thickness on an Au core with diameters of 0.5, 1.0, 2.0, 5.0, and 10.0 nm; and (3) an Au shell of variable thickness on a 1 nm Cu shell on an Au core with diameters of 0.5, 1.0, 2.0, 5.0, and 10.0 nm. For these three morphologies, the outer-shell thickness was varied until the Cu 2p{sub 3/2} peak intensity was the same (within 2%) as that found in our previous work with planar Cu/Au morphologies. The authors also performed similar simulations for a monolayer of spherical NPs consisting of a CuAu{sub x} alloy (also on a Si substrate) with diameters of 0.5, 1.0, 2.0, 5.0, and 10.0 nm. In the latter simulations, the relative Au concentration (x) was varied to give the same Cu 2p{sub 3/2} peak intensity (within 2%) as that found previously. For each morphology, the authors performed simulations with elastic scattering switched on and off. The authors found that elastic-scattering effects were generally strong for the Cu-core/Au-shell and weak for the Au-core/Cu-shell NPs; intermediate elastic-scattering effects were found for the Au-core/Cu-shell/Au-shell NPs. The shell thicknesses required to give the selected Cu 2p{sub 3/2} peak intensity for the three types of core–shell NPs were less than the corresponding film thicknesses of planar samples since Cu 2p photoelectrons can be detected from the sides and, for the smaller NPs, bottoms of the NPs. Elastic-scattering effects were also observed on the Au atomic fractions found for the CuAu{sub x} NP alloys with different diameters.

36 MATERIALS SCIENCE↗

DOE OSTI2015

Nanodevices for generating power from molecules and batteryless sensing

A nanoconverter or nanosensor is disclosed capable of directly generating electricity through physisorption interactions with molecules that are dipole containing organic species in a molecule interaction zone. High surface-to-volume ratio semiconductor nanowires or nanotubes (such as ZnO, silicon, carbon, etc.) are grown either aligned or randomly-aligned on a substrate. Epoxy or other nonconductive polymers are used to seal portions of the nanowires or nanotubes to create molecule noninteraction zones. By correlating certain molecule species to voltages generated, a nanosensor may quickly identify which species is detected. Nanoconverters in a series parallel arrangement may be constructed in planar, stacked, or rolled arrays to supply power to nano- and micro-devices without use of external batteries. In some cases breath, from human or other life forms, contain sufficient molecules to power a nanoconverter. A membrane permeable to certain molecules around the molecule interaction zone increases specific molecule nanosensor selectivity response.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2017

Nanodevices for generating power from molecules and batteryless sensing

36 MATERIALS SCIENCE↗

DOE OSTI2022

Newly developed sugarbeet lines with altered postharvest respiration rates differ in transcription factor and glycolytic enzyme expression

Respiration is the principal cause for postharvest sucrose loss in sugarbeet (Beta vulgaris L.) roots. Although reductions in respiration rate could mitigate these losses, developing sugarbeet cultivars and storage procedures that reduce respiration are hindered by a lack of knowledge of the genetic and metabolic factors that control storage respiration rate. Research was conducted to identify genes and gene products that affect storage respiration rate by creating two sugarbeet lines that differ in respiration rate and characterizing gene expression differences between these lines. Sugarbeet lines F1056 and F1057, which differ by up to 42% in respiration rate, were created by divergent selection of a sugarbeet population using root respiration rate after 30 d in storage as the principal selection criterion. RNA sequencing identified 287 differentially expressed genes (DEGs) between these lines on the day of harvest and after 28-d storage. Of these DEGs, nine encoded transcription factors and five encoded enzymes involved in the respiratory pathway. Other DEGs contributed to a variety of biological and molecular functions based on gene ontology classifications. Of respiratory pathway DEGS, genes for NAD+- and NADP+-dependent forms of glyceraldehyde-3-phosphate dehydrogenase were of note due to their high upregulation in the high respiring line and for their established role in glycolysis, a pathway identified as a likely bottleneck in respiratory substrate production. Overall, lines F1056 and F1057 provide new tools for investigating genetic and physiological differences in storage respiration rate, and their DEGs identify candidates for genes affecting sugarbeet root respiration rate.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2003

Current Developments in Future Planetary Probe Sensors for TPS

In-situ Thermal Protection System (TPS) sensors are required to provide traceability of TPS performance and sizing tools. Traceability will lead to higher fidelity design tools, which in turn will lead to lower design safety margins, and decreased heatshield mass. Decreasing TPS mass will enable certain missions that are not otherwise feasible, and directly increase science payload. NASA Ames is currently developing two flight measurements as essential to advancing the state of TPS traceability for material modeling and aerothermal simulation: heat flux and surface recession (for ablators). The heat flux gage is applicable to both ablators and non-ablators and is therefore the more generalized sensor concept of the two with wider applicability to mission scenarios. This paper describes the development of a microsensor capable of surface and in-depth temperature and heat flux measurements for TPS materials appropriate to Titan, Neptune, and Mars aerocapture, and direct entry. The thermal sensor will be monolithic solid state devices composed of thick film platinum RTD on an alumina substrate. Choice of materials and critical dimensions are used to tailor gage response, determined during calibration activities, to specific (forebody vs. aftbody) heating environments. Current design has maximum operating temperature of 1500 K, and allowable constant heat flux of q=28.7 watts per square centimeter, and time constants between 0.05 and 0.2 seconds. The catalytic and radiative response of these heat flux gages can also be changed through the use of appropriate coatings. By using several co-located gages with various surface coatings, data can be obtained to isolate surface heat flux components due to radiation, catalycity and convection. Selectivity to radiative heat flux is a useful feature even for an in-depth gage, as radiative transport may be a significant heat transport mechanism for porous TPS materials in Titan aerocapture. This paper also reports on progress to adapt a previously flown surface recession sensor, based on the Jupiter probe Galileo Analog Resistance Ablation Detector (ARAD), to appropriate aerocapture conditions.

Martinez, Ed↗

NASA NTRS2002

Semicarbazide-sensitive amine oxidase and extracellular matrix deposition by smooth-muscle cells

We have recently reported in vivo disruption of collagen and elastin architecture within blood vessel walls resulting from the selective inhibition of the enzyme semicarbazide-sensitive amine oxidase (SSAO). This study further investigates the effects of SSAO inhibition on extracellular matrix deposition by smooth-muscle cells (SMCs) cultured from neonatal rat hearts. SMCs were characterized, SSAO activity was measured, and soluble and insoluble collagen and elastin in the extracellular matrix (ECM) were quantified. Cultured neonatal rat heart SMC exhibited a monotypic synthetic phenotype that likely represents a myofibroblast. Detectable levels of SSAO activity present throughout 30-d culture peaked at 7-14 d, coinciding with the production of ECM. The addition of enzyme inhibitors and alternate SSAO substrates (benzylamine) produced varied and, in some cases, marked changes in SSAO activity as well as in the composition of mature and soluble matrix components. Similar to our previous in vivo findings, in vitro SSAO inhibition produced aberrations in collagen and elastin deposition by heart SMC. Because changes in SSAO activity are associated with cardiovascular pathologic states, this enzyme may play a protective or modulating role by regulating ECM production during pathologic insult.

Allylamine/administration & dosage/analogs & deriv↗

NASA NTRS1998

Rates of ubiquitin conjugation increase when muscles atrophy, largely through activation of the N-end rule pathway

The rapid loss of muscle mass that accompanies many disease states, such as cancer or sepsis, is primarily a result of increased protein breakdown in muscle, and several observations have suggested an activation of the ubiquitin-proteasome system. Accordingly, in extracts of atrophying muscles from tumor-bearing or septic rats, rates of 125I-ubiquitin conjugation to endogenous proteins were found to be higher than in control extracts. On the other hand, in extracts of muscles from hypothyroid rats, where overall proteolysis is reduced below normal, the conjugation of 125I-ubiquitin to soluble proteins decreased by 50%, and treatment with triiodothyronine (T3) restored ubiquitination to control levels. Surprisingly, the N-end rule pathway, which selectively degrades proteins with basic or large hydrophobic N-terminal residues, was found to be responsible for most of these changes in ubiquitin conjugation. Competitive inhibitors of this pathway that specifically block the ubiquitin ligase, E3alpha, suppressed most of the increased ubiquitin conjugation in the muscle extracts from tumor-bearing and septic rats. These inhibitors also suppressed ubiquitination in normal extracts toward levels in hypothyroid extracts, which showed little E3alpha-dependent ubiquitination. Thus, the inhibitors eliminated most of the differences in ubiquitination under these different pathological conditions. Moreover, 125I-lysozyme, a model N-end rule substrate, was ubiquitinated more rapidly in extracts from tumor-bearing and septic rats, and more slowly in those from hypothyroid rats, than in controls. Thus, the rate of ubiquitin conjugation increases in atrophying muscles, and these hormone- and cytokine-dependent responses are in large part due to activation of the N-end rule pathway.

Non-NASA Center↗

DOE OSTI2015

A Priori Estimation of Organic Reaction Yields

Abstract A thermodynamically guided calculation of free energies of substrate and product molecules allows for the estimation of the yields of organic reactions. The non‐ideality of the system and the solvent effects are taken into account through the activity coefficients calculated at the molecular level by perturbed‐chain statistical associating fluid theory (PC‐SAFT). The model is iteratively trained using a diverse set of reactions with yields that have been reported previously. This trained model can then estimate a priori the yields of reactions not included in the training set with an accuracy of ca. ±15 %. This ability has the potential to translate into significant economic savings through the selection and then execution of only those reactions that can proceed in good yields.

Emami, Fateme S.↗

DOE OSTI2022

Development of optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for treatment of COVID-19

The SARS-CoV-2 3CL protease is a critical drug target for small molecule COVID-19 therapy, given its likely druggability and essentiality in the viral maturation and replication cycle. Based on the conservation of 3CL protease substrate binding pockets across coronaviruses and using screening, we identified four structurally distinct lead compounds that inhibit SARS-CoV-2 3CL protease. After evaluation of their binding specificity, cellular antiviral potency, metabolic stability, and water solubility, we prioritized the GC376 scaffold as being optimal for optimization. We identified multiple drug-like compounds with <10nM potency for inhibiting SARS-CoV-2 3CL and the ability to block SARS-CoV-2 replication in human cells, obtained co-crystal structures of the 3CL protease in complex with these compounds, and determined that they have pan-coronavirus activity. We selected one compound, termed coronastat, as an optimized lead and characterized it in pharmacokinetic and safety studies in vivo. Coronastat represents a new candidate for a small molecule protease inhibitor for the treatment of SARS-CoV-2 infection for eliminating pandemics involving coronaviruses.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

Eelgrass (Zostera marina L.) Restoration in Puget Sound: Development of a Site Suitability Assessment Process

The restoration of eelgrass (Zostera marina L.), a critical ecosystem component and ‘vital sign’ indicator of ecosystem health, is a high priority in Puget Sound, Washington, United States. In 2011, the state set a restoration target to increase eelgrass area by 4,200 ha, a 20%) increase over the present 21,500 ha by 2020. In a region as large and complex as Puget Sound, locating areas to restore eelgrass effectively and efficiently is challenging. We developed a modeling and screening process to identify and test potential restoration sites. The spatially explicit analysis of habitat suitability incorporated information from predictive models of hydrodynamics and eelgrass biomass, shoreline manager input, historical and current eelgrass area, substrate, stressors, test plantings, and monitoring of light, temperature, and survival. We evaluated 2,630 sites from which we identified 6,292 ha of highly to very highly suitable conditions for potential eelgrass habitat, which provides ample area for restoring eelgrass to meet the 20% target. Test plantings were successful at four of nine areas, and indicated significant site-specific data needs to improve predictive capability. We summarized the results of our analysis on maps of habitat suitability for the majority of the ~3,220 km of shoreline in Puget Sound, which serve as a starting point for restoration site selection and planning. Overall, our approach provides a foundation for identifying and testing potential restoration sites, and highlights information needs and potential management actions to reduce stressors and increase eelgrass cover to meet the challenging restoration goal.

eelgrass model, Puget Sound, restoration sites, Zo↗

DOE OSTI2019

Seeded Lateral Solid-Phase Crystallization of the Perovskite Oxide SrTiO 3

Crystallization from an amorphous precursor presents a new route to control the properties of complex oxides by selecting their nanoscale morphology. A key challenge in crystal growth from the amorphous form is to select the locations of nucleation and the crystallographic orientation of the resulting crystals. Nucleation sites for crystallization of the prototypical perovskite complex oxide SrTiO 3 (STO) from its amorphous form can be reproducibly introduced using nanoscale seed crystals. The results of two seeding strategies are reported here: (i) SrRuO 3 (SRO) (001)-oriented nanomembranes and (ii) STO nanocrystalline seeds. Amorphous STO crystallizes laterally over distances of several microns from the seeds before encountering separately nucleated crystals. The lateral crystallization rates for both types of seeding methods are close to the values measured in solidphase epitaxy (SPE) of STO on single-crystal substrates. The lateral crystallization distances along different crystallographic orientations are equal, indicating that the lateral crystallization rate is isotropic. The isotropic crystallization suggests that the rate-limiting steps for crystallization occur within the amorphous STO away from the amorphous/crystalline interface. In addition to the lateral crystallization, STO crystallizes on top of the planar SRO nanomembrane seeds via SPE, forming partially relaxed [001]-oriented heteroepitaxial STO layers. The in-plane orientation of laterally crystallized STO near the SRO nanomembrane seeds exhibits overall polycrystallinity with regions in which micron-scale grains of laterally crystallized STO share the same in-plane orientation as the SRO nanomembrane seeds. Crystallization from seed crystals provides opportunities to create a wide range of other perovskite oxides in nanoscale geometries.

36 MATERIALS SCIENCE↗

NASA NTRS1973

Property investigation and sputter deposition of dispersion-hardened copper for fatigue specimen fabrication

Sputter-deposited alloys of dispersion-hardenable Cu-0.25 vol% SiC and Cu-0.50 vol% SiC and precipitation-hardenable Cu-0.15 wt% Zr and Cu-0.05 wt% Mg-0.15 wt% Zr-0.40 wt% Cr were investigated for selection to evaluate fatigue specimen performance with potential application in fabricating regeneratively cooled rocket thrust chambers. Yield strengths in the 700 to 1000-MN/sq m range were observed with uniform elongation ranging from 0.5 to 1.5% and necking indicative of greater ductility. Electrical conductivity measured as an analog to thermal conductivity gave values 90% IACS for Cu-0.15 wt% Zr and Cu-0.05 wt% Mg-0.15 wt% Zr-0.40 wt% Cr. A 5500-g sputtered deposit of Cu-0.15 wt% Zr alloy, 12.29 mm (0.484 in.) average thickness in the fatigue specimen gage length, was provided to NASA on one of their substrates.

Mcclanahan, E. D.↗

NASA NTRS1997

Biodiversity within hot spring microbial mat communities: molecular monitoring of enrichment cultures

We have begun to examine the basis for incongruence between hot spring microbial mat populations detected by cultivation or by 16S rRNA methods. We used denaturing gradient gel electrophoresis (DGGE) to monitor enrichments and isolates plated therefrom. At near extincting inoculum dilutions we observed Chloroflexus-like and cyanobacterial populations whose 16S rRNA sequences have been detected in the 'New Pit' Spring Chloroflexus mat and the Octopus Spring cyanobacterial mat. Cyanobacterial populations enriched from 44 to 54 degrees C and 56 to 63 degrees C samples at near habitat temperatures were similar to those previously detected in mat samples of comparable temperatures. However, a lower temperature enrichment from the higher temperature sample selected for the populations found in the lower temperature sample. Three Thermus populations detected by both DGGE and isolation exemplify even more how enrichment may bias our view of community structure. The most abundant population was adapted to the habitat temperature (50 degrees C), while populations adapted to 65 degrees C and 70 degrees C were 10(2)- and 10(4)-fold less abundant, respectively. However, enrichment at 70 degrees C favored the least abundant strain. Inoculum dilution and incubation at the habitat temperature favored the more numerically relevant populations. We enriched many other aerobic chemoorganotrophic populations at various inoculum dilutions and substrate concentrations, most of whose 16S rRNA sequences have not been detected in mats. A common feature of numerically relevant cyanobacterial, Chloroflexus-like and aerobic chemorganotrophic populations, is that they grow poorly and resist cultivation on solidified medium, suggesting plating bias, and that the medium composition and incubation conditions may not reflect the natural microenvironments these populations inhabit.

Non-NASA Center↗

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