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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Natural variation in the consequences of gene overexpression during osmotic stress [RNA-Seq]

RNA-seq and transcriptome analysis of 4 strains (BY4743, BC187, NCYC3290, and YPS128) that were grown in YPD+ 0.7M NaCl. For each strain, 3 samples were collected: T0 (unstressed cells), T30 (30 mins after cells placed in 0.7M NaCl), and T3h (3 hours after cells placed in NaCl). These strains were collected in 3 biological replicates. The library for sample YPS128 Rep 3 T30 failed so this sample is missing and there are a total of 35 samples in the dataset.

copy-number variation↗
DOE OSTI2020

Thermal dissipation sensors enter a new age: Navigating frontiers in transpiration and hydrologic function

Thermal dissipation (TD) sensors have been used extensively for a wide array of sap flow applications, and yet recently several limitations of this approach have been identified, including a tendency to underestimate absolute flows, especially in small stems with very high flows. However, when used properly, the TD method remains the most cost effective and reliable approach for determining relative flows in comparison studies. Major advantages of this method include the ability to replicate maximally within trees, across trees of different sizes, and across multiple species to capture the full range of natural variation in the study system. From early studies, such variation has been deemed a major challenge for representing stand-level dynamics. In a series of recent comparison studies, we determined mean sap flux density dynamics within and among groups of trees. These studies were conducted within temperate coniferous forest (n=46), temperate oak savanna (n=36), temperate pine forest (n=49), temperate bottomland hardwood forest (n=23), tropical premontane rainforest (n=43), semiarid subtropical shrubland (n=25), and tropical dry forest (n=15), with a total of 237 sensors. Two study sites were also equipped with eddy covariance systems for determination of stand-level evapotranspiration. Sites subject to high background thermal gradients used the transient thermal dissipation method. Comparisons varied between studies but tended to focus on relative flow differences between species, between wetter and drier microsites, between understory and overstory components, or between wetter and drier periods of the growing season. Except for the shrubland sites, study trees tended to be at least 15-cm diameter and frequently exceeded 50-cm diameter. Results of this cross-site comparison highlight the inherent variation in natural stands and the importance of using large sample sizes. The TD approach remains a valuable and preferred method for the future determination of water use in trees. However, sensor replication can fundamentally impact a study's outcomes and should be more carefully considered in study design. Customized error mitigation strategies are best to address the sources of variation most problematic for a particular study. In conclusion, the development of “smart” calibration approaches that correct for fundamental effects of radial variation inherent in thermal dissipation studies is discussed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Evolution of homologous recombination rates across bacteria

Bacteria are nonsexual organisms but are capable of exchanging DNA at diverse degrees through homologous recombination. Intriguingly, the rates of recombination vary immensely across lineages where some species have been described as purely clonal and others as “quasi-sexual.” However, estimating recombination rates has proven a difficult endeavor and estimates often vary substantially across studies. It is unclear whether these variations reflect natural variations across populations or are due to differences in methodologies. Consequently, the impact of recombination on bacterial evolution has not been extensively evaluated and the evolution of recombination rate—as a trait—remains to be accurately described. Here, we developed an approach based on Approximate Bayesian Computation that integrates multiple signals of recombination to estimate recombination rates. We inferred the rate of recombination of 162 bacterial species and one archaeon and tested the robustness of our approach. Our results confirm that recombination rates vary drastically across bacteria; however, we found that recombination rate—as a trait—is conserved in several lineages but evolves rapidly in others. Although some traits are thought to be associated with recombination rate (e.g., GC-content), we found no clear association between genomic or phenotypic traits and recombination rate. Overall, our results provide an overview of recombination rate, its evolution, and its impact on bacterial evolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Characterizing the gene–environment interaction underlying natural morphological variation in Neurospora crassa conidiophores using high-throughput phenomics and transcriptomics

Abstract Neurospora crassa propagates through dissemination of conidia, which develop through specialized structures called conidiophores. Recent work has identified striking variation in conidiophore morphology, using a wild population collection from Louisiana, United States of America to classify 3 distinct phenotypes: Wild-Type, Wrap, and Bulky. Little is known about the impact of these phenotypes on sporulation or germination later in the N. crassa life cycle, or about the genetic variation that underlies them. In this study, we show that conidiophore morphology likely affects colonization capacity of wild N. crassa isolates through both sporulation distance and germination on different carbon sources. We generated and crossed homokaryotic strains belonging to each phenotypic group to more robustly fit a model for and estimate heritability of the complex trait, conidiophore architecture. Our fitted model suggests at least 3 genes and 2 epistatic interactions contribute to conidiophore phenotype, which has an estimated heritability of 0.47. To uncover genes contributing to these phenotypes, we performed RNA-sequencing on mycelia and conidiophores of strains representing each of the 3 phenotypes. Our results show that the Bulky strain had a distinct transcriptional profile from that of Wild-Type and Wrap, exhibiting differential expression patterns in clock-controlled genes (ccgs), the conidiation-specific gene con-6, and genes implicated in metabolism and communication. Combined, these results present novel ecological impacts of and differential gene expression underlying natural conidiophore morphological variation, a complex trait that has not yet been thoroughly explored.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Entanglement rearrangement in self-consistent nuclear structure calculations

Background: Entanglement plays a central role in a diverse array of increasingly important research areas, including quantum computation, simulation, measurement, sensing, and communication. Extensive suites of investigations have been performed to better understand entanglement in atomic and molecular quantum many-body systems, while the exploration of entanglement in the structure of nuclei and their reactions is presently in its infancy. Purpose: The goal of this work is to begin investigating the entanglement properties of nuclei from first-principles nuclear many-body calculations. We attempt to identify common features and emergent structures of entanglement that could ultimately lead to new and natural many-body schemes. With an eye toward quantum accelerators in future hybrid-supercomputers, criteria for partitioning nuclear many-body calculations into quantum and classical components may provide advantages in future large-scale computations. Along the way we look for explanations of the relative success of phenomenological models such as the nuclear shell model, and for better ways to match to low-energy nuclear effective field theories and lattice QCD calculations to nuclear many-body techniques that are based upon entanglement. Method: We explore the entanglement between single-particle states in 4 He and 6 He. The patterns of entanglement emerging from different single-particle bases are compared, and possible links with the convergence of observables are explored, in particular, ground-state energies. The nuclear wave functions are obtained by performing active-space no-core configuration-interaction calculations using a two-body nucleon-nucleon interaction derived from chiral effective field theory. Entanglement measures within single-particle bases exhibiting different degrees of complexity are determined, in particular, harmonic oscillator (HO), Hartree-Fock (HF), natural (NAT) and variational natural (VNAT) bases. Specifically, single-orbital entanglement entropy, two-orbital mutual information, and negativity are studied. Results: The entanglement structures in 4 He and 6 He are found to be more localized within NAT and VNAT bases than within a HO basis for the optimal HO parameters we have worked with. In particular a core-valence structure clearly emerges from the full no-core calculation of 6 He. Here, the two-nucleon mutual information shows that the VNAT basis, which typically exhibits good convergence properties, effectively decouples the active and inactive spaces. Conclusions: Measures of one- and two-nucleon entanglement are found to be useful in analyzing the structure of nuclear wave functions, in particular the efficacy of basis states, and may provide useful metrics toward developing more efficient schemes for ab initio computations of the structure and reactions of nuclei, and quantum many-body systems more generally.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Mexico and U.S. Power Systems Under Variations in Natural Gas Prices

This study examines the impact of natural gas prices on the power systems of Mexico and the United States. For this, we develop an integrated modeling framework by soft linking three different techno-economic bottom-up models of the power and energy systems, one partial equilibrium model of the natural gas sector, and a partial equilibrium model of the Mexican energy sector. Our results show several interesting results: high natural gas prices raise the use of carbon-intensive technologies in the short-term and boost renewable investments at longer time intervals, increasing emissions in earlier periods and reducing them thereafter. Regarding system costs, because of more capital-intensive green power and lower expenditures in raw energy carriers, capital costs rise and operating costs decrease in the long haul. Furthermore, we see an increase in natural gas demand when its price is low, reducing long-term capital and operating costs through cheaper energy inputs in natural gas facilities and a lower share of capital-intensive renewable facilities in the power system. Concerning emissions, low natural-gas prices decrease coal use in the United States, reducing anthropogenic emissions until the last stages of the optimization period. For Mexico, they show heterogeneous results across models. Policymakers can use this study's results to understand the influence of natural gas prices in the Mexican and United States energy sectors.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
DOE OSTI2020

Impacts of Soil Microbiome Variations on Root Colonization by Fungi and Bacteria and on the Metabolome of Populus tremula × alba

Trees depend on beneficial interactions between roots and soil microbes for their nutrition and protection against stresses. The soil microbiome provides the main reservoir of microbes for root colonization and is subject to natural variations that can affect its composition. It is not clear whether the tree’s root system is able to buffer the natural variations occurring in the soil microbiome to capture a stable and effective microbiome or whether these variations affect its microbiome to impact its physiology. To address this question, we planted cuttings of Gray Poplar (Populus tremula × alba clone 717-1B4) in natural soil taken from a poplar stand under the same tree over two consecutive years and grew them in a greenhouse. We analyzed the soil and root microbiomes by high throughput Illumina MiSeq sequencing of fungal rDNA internal transcribed spacer and bacterial 16S rRNA amplicons and we characterized the root metabolome by gas chromatography-mass spectrometry. Soil and root microbial communities significantly shifted over the 2 years. A modification of the balance between endophytes, saprophytes, and mycorrhizal fungi occurred in the roots as well as a replacement of some dominant operational taxonomic units by others. These modifications were correlated with a significant alteration of the levels of about 10% of primary and secondary metabolites, suggesting that natural fluctuations in soil microbial communities can have a profound impact on tree root metabolism and physiology. Tree roots functioning may thus be indirectly strongly affected by the effects of future extreme climatic variations on the soil microbiome.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2004

Optimal Aerosol Parameterization for Remote Sensing Retrievals

We have developed a new algorithm for the retrieval of aerosol and gases from SAGE It1 solar transmission measurements. This algorithm improves upon the NASA operational algorithm in several key aspects, including solving the problem non-linearly and incorporating a new methodology for separating the contribution of aerosols and gases. In order to extract aerosol information we have built a huge database of aerosol models for both stratospheric and tropospheric aerosols, and polar stratospheric cloud particles. This set of models allows us to calculate a vast range of possible extinction spectra for aerosols. and from these, derive a set of eigenvectors which then provide the basis set used in our inversion algorithm. Our aerosol algorithm and retrievals are described in several articles (listed in References Section) published under this grant. In particular they allow us to analyze the spectral properties of aerosols and PSCs and ultimately derive their microphysical properties. We have found some considerable differences between our spectra and the ones derived from the SAGE III operational algorithm. These are interesting as they provide an independent check on the validity of published aerosol data and, in particular, on their associated uncertainties. In order to understand these differences, we are assembling independent aerosol data from other sources with which to make comparisons. We have carried out extensive comparisons of our ozone retrievals with both SAGE III and independent lidar, ozonesonde, and satellite measurements (Polyakov et al., 2004). These show very good agreement throughout the stratosphere and help to quantify differences which can be attributed to natural variation in ozone versus that produced by algorithmic differences. In the mid - upper stratosphere, agreement with independent data was generally within 5 - 20%. but in the lower stratosphere the differences were considerably larger. We believe that a large proportion of this discrepancy in the lower stratosphere is attributable to natural variation, and is also seen in comparisons between lidar and ozonesonde measurements. NO2 profiles obtained with our algorithm were compared to those obtained through the SAGE III operational algorithm and exhibited differences of 20 - 40%. Our retrieved profiles agree with the HALOE NO2 measurements significantly better than those of the operational retrieval. In other work (described below), we are extending our aerosol retrievals into the infrared regime and plan to perform retrievals from combined uv-visible-infrared spectra. This work will allow us to use the spectra to derive the size and composition of aerosols, and we plan to employ our algorithms in the analysis of PSC spectra. We are presently also developing a limb-scattering algorithm to retrieve aerosol data from limb measurements of solar scattered radiation.

Newchurch, Michael J.↗
DOE OSTI2021

Calculated Roughness Changes due to Clear-Cutting At Savannah River Site

At the Savannah River Site (SRS), multiple facilities are routinely producing and working with radiological constituents which require safety basis modeling by the National Nuclear Safety Administration. The models used to determine the safety basis employ roughness length as an input parameter which describes the roughness of the ground surface which influences momentum exchange near the surface and the subsequent generation of mechanical turbulence. Because roughness length is dependent on surface characteristics, including vegetation, any changes to the surface would have a subsequent impact on the roughness length and require a new safety basis analysis to be performed. An analysis of measurements prior to and after the dear-cuts and thinning was performed and roughness lengths were calculated for each of sixteen wind sectors. Not all sectors contained dear-cuts, so this provides comparison of natural variations in roughness. Based on the results of the estimated changes, consideration will be given to how these changes may affect atmospheric dispersion modeling. It was found that clear-cutting activities generally led to a reduction in roughness. Reductions in roughness length also occurred in some of the wind sectors containing only undisturbed forest, but those in sectors with dear-cuts were found to be slightly greater in magnitude than natural variation. Only in one instance was the change in roughness length found to exceed a decrease of 10%, indicating that there is no significant safety basis to the site as a whole based on previous clear-cutting activities.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Multiple highly expressed phospho enol pyruvate carboxylase genes have divergent enzyme kinetic properties in two C4 grasses

Abstract Background and Aims Phosphoenolpyruvate (PEP) carboxylase (PEPC) catalyses the irreversible carboxylation of PEP with bicarbonate to produce oxaloacetate. This reaction powers the carbon-concentrating mechanism (CCM) in plants that perform C4 photosynthesis. This CCM is generally driven by a single PEPC gene product that is highly expressed in the cytosol of mesophyll cells. We found two C4 grasses, Panicum miliaceum and Echinochloa colona, that each have two highly expressed PEPC genes. We characterized the kinetic properties of the two most abundant PEPCs in E. colona and P. miliaceum to better understand how the enzyme’s amino acid structure influences its function. Methods Coding sequences of the two most abundant PEPC proteins in E. colona and P. miliaceum were synthesized by GenScript and were inserted into bacteria expression plasmids. Point mutations resulting in substitutions at conserved amino acid residues (e.g. N-terminal serine and residue 890) were created via site-directed PCR mutagenesis. The kinetic properties of semi-purified plant PEPCs from Escherichia coli were analysed using membrane-inlet mass spectrometry and a spectrophotometric enzyme-coupled reaction. Key Results The two most abundant P. miliaceum PEPCs (PmPPC1 and PmPPC2) have similar sequence identities (>95 %), and as a result had similar kinetic properties. The two most abundant E. colona PEPCs (EcPPC1 and EcPPC2) had identities of ~78 % and had significantly different kinetic properties. The PmPPCs and EcPPCs had different responses to allosteric inhibitors and activators, and substitutions at the conserved N-terminal serine and residue 890 resulted in significantly altered responses to allosteric regulators. Conclusions The two, significantly expressed C4Ppc genes in P. miliaceum were probably the result of genomes combining from two closely related C4Panicum species. We found natural variation in PEPC’s sensitivity to allosteric inhibition that seems to bypass the conserved 890 residue, suggesting alternative evolutionary pathways for increased malate tolerance and other kinetic properties.

DiMario, Robert J. (ORCID:0000000250566868)↗
DOE OSTI2022

Variation in natural attenuation rates of polychlorinated biphenyls (PCBs) in fish from streams and reservoirs in East Tennessee observed over a 35-year period

Environmental contamination due to human activities is a major concern, particularly for persistent chemicals. Within catchments, persistent chemicals linked to negative health outcomes such as polychlorinated biphenyls (PCBs) have great potential to be transported, through adsorption or biological uptake, with downstream locations acting as sinks for accumulation. Here we present long-term trends in PCB bioaccumulation in fish found in lower-order tributaries on the Oak Ridge Reservation, an impacted US Department of Energy property in East Tennessee, USA, and a large reservoir system adjacent to it composed of parts of the Clinch and Tennessee Rivers. Given that the reservoir system has experienced no direct PCB mitigation activities, this record offers an opportunity to explore potential natural attenuation of PCBs within a large lotic ecosystem. Additionally, attenuation rates ranged from 0% to 8% yr -1 in minnows and sunfish at stream sites and 5.4–11.3% yr -1 in catfish at reservoir sites. These rates are comparable to findings from similar studies in other regions, suggesting a consistency in responses since the banning of PCB production in 1979. Further, results suggest that PCB sources from discharge outfalls are important locally but are not primarily responsible for sustaining PCB contamination in downstream reservoirs.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Programmed cell death regulator BAP2 is required for IRE1-mediated unfolded protein response in Arabidopsis

Environmental and physiological situations can challenge the balance between protein synthesis and folding capacity of the endoplasmic reticulum (ER) and cause ER stress, a potentially lethal condition. The unfolded protein response (UPR) restores ER homeostasis or actuates programmed cell death (PCD) when ER stress is unresolved. The cell fate determination mechanisms of the UPR are not well understood, especially in plants. Here, we integrate genetics and ER stress profiling with natural variation and quantitative trait locus analysis of 350 natural accessions of the model species Arabidopsis thaliana . Our analyses implicate a single nucleotide polymorphism to the loss of function of the general PCD regulator BON-ASSOCIATED PROTEIN2 (BAP2) in UPR outcomes. We establish that ER stress-induced BAP2 expression is antagonistically regulated by the UPR master regulator, inositol-requiring enzyme 1 (IRE1), and that BAP2 controls adaptive UPR amplitude in ER stress and ignites pro-death mechanisms in conditions of UPR insufficiency.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1991

Space Shuttle Redesigned Solid Rocket Motor nozzle natural frequency variations with burn time

The effects of erosion and thermal degradation on the Space Shuttle Redesigned Solid Rocket Motor (RSRM) nozzle's structural dynamic characteristics were analytically evaluated. Also considered was stiffening of the structure due to internal pressurization. A detailed NASTRAN finite element model of the nozzle was developed and used to evaluate the influence of these effects at several discrete times during motor burn. Methods were developed for treating erosion and thermal degradation, and a procedure was developed to account for internal pressure stiffening using differential stiffness matrix techniques. Results were verified using static firing test accelerometer data. Fast Fourier Transform and Maximum Entropy Method techniques were applied to the data to generate waterfall plots which track modal frequencies with burn time. Results indicate that the lower frequency nozzle 'vectoring' modes are only slightly affected by erosion, thermal effects and internal pressurization. The higher frequency shell modes of the nozzle are, however, significantly reduced.

Lui, C. Y.↗
NASA NTRS1985

The cryptoendolithic microbial environment in the Antarctic cold desert: temperature variations in nature

In the Antarctic cold desert, cryptoendolithic microorganisms live under the surface of porous sandstone rocks. During the austral summer, the environment of the near-surface rock layers colonized by organisms is characterized by two kinds of temperature oscillations, both occurring across the freezing point. Low-frequency (diurnal) and large-amplitude (up to about 20 degrees C) oscillations on the sunlit surface of rocks result in a daily freeze-thaw cycle. This is a result of the diurnal changes in the sun altitude and angle with respect to the rock surface. The biological effect of this oscillation is the regulation of the onset and cessation of metabolic activity. The high-frequency (few minutes) oscillations occur only under certain weather conditions (sunny days with light winds) and are superimposed on the low-frequency oscillations. They are caused by the cooling effect of wind gusts on rock surfaces that are much warmer than ambient air temperatures. High-frequency oscillations result in a rapid freeze-thaw cycle on the surface, which, however, does not reach the microbial zone. These high-frequency freeze-thaw oscillations are probably the cause of the abiotic nature of the rock surface. Both oscillations seem to have an effect on rock weathering.

Cold Climate↗
NASA NTRS2019

Seasonal- and Beta-Angle-Dependent Latitude Bias Variations in Natural Decays

Prior work has demonstrated pronounced statistical clustering of natural decays of medium-to-high-inclination orbital objects peaking approximately 30 degrees in Argument of Latitude ahead of nodal crossings. This effect is caused by the physical bulge in the Earth and the overlying atmosphere, that cyclically modifies effective altitude (and therefore density) faster than the trajectory's decay itself. While prior work has averaged seasonal and RAAN effects over all non-uniform atmosphere possibilities to support long-term characterization of the clustering of final entries in generating a pre-mission Expectation of Casualty, the current study characterizes seasonal and beta angle effects as potential influences on the near-term statistical risks of specific tactical decay scenarios, relative to the average. Such effects on the density profile along an orbit may be important considerations in any scenario where small orbital adjustments are used to optimize the timing and location of final entry trajectories. I.E., two identical spacecraft entering in different seasons and/or beta angles may have different minimum-risk scenarios for identical control capabilities and space weather conditions. Further, the early heating history of shallow trajectories is explored, examining the influence of dramatically different density profiles over the final orbit as the spacecraft either skims over or dives into the atmosphere.

Bacon, John B.↗