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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 829 records · Page 46
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoë fedtschenkoi, a plant with crassulacean acid metabolism

Abstract Background Crassulacean acid metabolism (CAM), a specialized mode of photosynthesis, enables plant adaptation to water-limited environments and improves photosynthetic efficiency via an inorganic carbon-concentrating mechanism. Kalanchoë fedtschenkoi is an obligate CAM model featuring a relatively small genome and easy stable transformation. However, the molecular responses to light quality and intensity in CAM plants remain understudied. Results Here we present a genome-wide expression atlas of K. fedtschenkoi plants grown under 12 h/12 h photoperiod with different light quality (blue, red, far-red, white light) and intensity (0, 150, 440, and 1,000 μmol m–2 s–1) based on RNA sequencing performed for mature leaf samples collected at dawn (2 h before the light period) and dusk (2 h before the dark period). An eFP web browser was created for easy access of the gene expression data. Based on the expression atlas, we constructed a light-responsive co-expression network to reveal the potential regulatory relationships in K. fedtschenkoi. Measurements of leaf titratable acidity, soluble sugar, and starch turnover provided metabolic indicators of the magnitude of CAM under the different light treatments and were used to provide biological context for the expression dataset. Furthermore, CAM-related subnetworks were highlighted to showcase genes relevant to CAM pathway, circadian clock, and stomatal movement. In comparison with white light, monochrome blue/red/far-red light treatments repressed the expression of several CAM-related genes at dusk, along with a major reduction in acid accumulation. Increasing light intensity from an intermediate level (440 μmol m-2 s-1) of white light to a high light treatment (1,000 μmol m–2 s–1) increased expression of several genes involved in dark CO2 fixation and malate transport at dawn, along with an increase in organic acid accumulation. Conclusions This study provides a useful genomics resource for investigating the molecular mechanism underlying the light regulation of physiology and metabolism in CAM plants. Our results support the hypothesis that both light intensity and light quality can modulate the CAM pathway through regulation of CAM-related genes in K. fedtschenkoi.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

CRISPR/Cas9-based gene activation and base editing in Populus

The genus Populus has long been used for environmental, agroforestry and industrial applications worldwide. Today Populus is also recognized as a desirable crop for biofuel production and a model tree for physiological and ecological research. As such, various modern biotechnologies, including CRISPR/Cas9-based techniques, have been actively applied to Populus for genetic and genomic improvements for traits such as increased growth rate and tailored lignin composition. However, CRISPR/Cas9 has been primarily used as the active Cas9 form to create knockouts in the hybrid poplar clone “717-1B4” (P. tremula x P. alba clone INRA 717-1B4). Alternative CRISPR/Cas9-based technologies, e.g. those involving modified Cas9 for gene activation and base editing, have not been evaluated in most Populus species for their efficacy. Here we employed a deactivated Cas9 (dCas9)-based CRISPR activation (CRISPRa) technique to fine-tune the expression of two target genes, TPX2 and LecRLK-G which play important roles in plant growth and defense response, in hybrid poplar clone “717-1B4” and poplar clone “WV94” (P. deltoides “WV94”), respectively. We observed that CRISPRa resulted in 1.2-fold to 7.0-fold increase in target gene expression through transient expression in protoplasts and Agrobacterium-mediated stable transformation, demonstrating the effectiveness of dCas9-based CRISPRa system in Populus. In addition, we applied Cas9 nickase (nCas9)-based cytosine base editor (CBE) to precisely introduce premature stop codons via C-to-T conversion, with an efficiency of 13%–14%, in the target gene PLATZ which encodes a transcription factor involved in plant fungal pathogen response in hybrid poplar clone “717-1B4”. Overall, we showcase the successful application of CRISPR/Cas-based technologies in gene expression regulation and precise gene engineering in two Populus species, facilitating the adoption of emerging genome editing tools in woody species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A small secreted protein serves as a plant-derived effector mediating symbiosis between Populus and Laccaria bicolor

Beneficial symbiotic fungi colonize plant tissues, delivering crucial ecosystem services such as carbon sequestration and plant fertilization. Specifically, trees that form a nutrient-acquiring symbiosis with mutualistic ectomycorrhizal (ECM) fungi gain advantages from these associations by experiencing enhanced growth rates and increased resilience to both biotic and abiotic stresses. Despite the vital role ECM fungi play in the nutrition and well-being of trees, identifying key regulators participating in the molecular communication between plant and fungal cells is still in its early stages. The mutualistic relationship between Laccaria bicolor and Populus spp. has been utilized as a model system for investigating ECM symbiosis at the molecular level. It has been demonstrated that the fungus L. bicolor secretes Mycorrhiza-induced Small Secreted Proteins (MiSSPs) required for ECM development. Meanwhile, we have previously shown that P. trichocarpa small, secreted proteins (PtSSPs) are highly induced during mutualistic symbiosis and some of them can enter, via in-vitro feeding, L. bicolor hyphae affecting their growth and morphology. However, the exact role and mode of action of PtSSPs in mutualistic symbiosis remain unknown. Because previous study showed that PtSSP1 is taking up by fungal cell and then localize in fungal cells, we decide to dig further on its putative role in fungal cells and also by overexpressing it in poplar because it is not technically possible yet to overexpress poplar protein in Laccaria bicolor hyphae. Here, we further characterized the function of PtSSP1(Potri.009G063200) in ectomycorrhization, which accumulates in the nucleus of L. bicolor in an in-vitro feeding experiment. Our results provide new knowledge for the genetic engineering of plants to control associated microbes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom

Abstract Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Agave REVEILLE1 regulates the onset and release of seasonal dormancy in Populus

Abstract Deciduous woody plants like poplar (Populus spp.) have seasonal bud dormancy. It has been challenging to simultaneously delay the onset of bud dormancy in the fall and advance bud break in the spring, as bud dormancy, and bud break were thought to be controlled by different genetic factors. Here, we demonstrate that heterologous expression of the REVEILLE1 gene (named AaRVE1) from Agave (Agave americana) not only delays the onset of bud dormancy but also accelerates bud break in poplar in field trials. AaRVE1 heterologous expression increases poplar biomass yield by 166% in the greenhouse. Furthermore, we reveal that heterologous expression of AaRVE1 increases cytokinin contents, represses multiple dormancy-related genes, and up-regulates bud break-related genes, and that AaRVE1 functions as a transcriptional repressor and regulates the activity of the DORMANCY-ASSOCIATED PROTEIN 1 (DRM1) promoter. Our findings demonstrate that AaRVE1 appears to function as a regulator of bud dormancy and bud break, which has important implications for extending the growing season of deciduous trees in frost-free temperate and subtropical regions to increase crop yield.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Overexpression of REDUCED WALL ACETYLATION C increases xylan acetylation and biomass recalcitrance in Populus

Abstract Plant lignocellulosic biomass, i.e. secondary cell walls of plants, is a vital alternative source for bioenergy. However, the acetylation of xylan in secondary cell walls impedes the conversion of biomass to biofuels. Previous studies have shown that REDUCED WALL ACETYLATION (RWA) proteins are directly involved in the acetylation of xylan but the regulatory mechanism of RWAs is not fully understood. In this study, we demonstrate that overexpression of a Populus trichocarpa PtRWA-C gene increases the level of xylan acetylation and increases the lignin content and S/G ratio, ultimately yielding poplar woody biomass with reduced saccharification efficiency. Furthermore, through gene coexpression network and expression quantitative trait loci (eQTL) analysis, we found that PtRWA-C was regulated not only by the secondary cell wall hierarchical regulatory network but also by an AP2 family transcription factor HARDY (HRD). Specifically, HRD activates PtRWA-C expression by directly binding to the PtRWA-C promoter, which is also the cis-eQTL for PtRWA-C. Taken together, our findings provide insights into the functional roles of PtRWA-C in xylan acetylation and consequently saccharification and shed light on synthetic biology approaches to manipulate this gene and alter cell wall properties. These findings have substantial implications for genetic engineering of woody species, which could be used as a sustainable source of biofuels, valuable biochemicals, and biomaterials.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Variation in Flooding Tolerance in Populus deltoides ‘D-124’ and P. trichocarpa x P. deltoides Hybrid ‘52–225’

Flooding poses a substantial challenge to plant survival and productivity, particularly in riparian genus like Populus. This study examines the physiological, morphological, metabolic, and molecular responses of Populus deltoides ‘D-124’ and P. trichocarpa x P. deltoides hybrid clone ‘52–225’ under control and inundated conditions to identify differences in flooding tolerance. Under flooding conditions, physiological and cellular stress was more pronounced in P. deltoides ‘D-124’ than in the hybrid clone ‘52–225,’ as evidenced by lower transpiration (E), photosynthesis (A), and chlorophyll content. In contrast, ‘52–225’ showed reduced ROS accumulation suggesting better cellular function under stress. Morphologically, ‘52–225’ produced more shoot-born roots, which likely enhance oxygen transport and metabolic activity during flooding. Metabolite profiling revealed both overlapping and distinct patterns of sugar and amino acid accumulation between genotypes. Gene expression analysis revealed that flooding-responsive genes, including ALCOHOL DEHYDROGENASE 1 and HYPOXIA RESPONSIVE ERF 2, were activated in both genotypes, with a more pronounced response noted in ‘52–225.’ These findings extend our understanding of flooding tolerance mechanisms in Populus by connecting physiological traits, stress responses, and genetic regulation. This research contributes to the development of more flooding-resilient poplar varieties, with potential applications in breeding and restoration programs for flooding-prone environments.

Flooding stress↗
DOE OSTI2021

Metabolic patterns in Septoria canker resistant and susceptible Populus trichocarpa genotypes 24 hours post-inoculation

Sphaerulina musiva is an economically and ecologically important fungal pathogen that causes Septoria stem canker and leaf spot disease of Populus species. Here, to bridge the gap between genetic markers and structural barriers previously found to be linked to Septoria (Sphaerulina musiva) canker disease resistance in poplar, we employed hydrophilic interaction liquid chromatography (HILIC) and tandem mass spectrometry (MS/MS) to identify and quantify metabolites involved with signaling and cell wall re-modelling. Fluctuations in signaling molecules, organic acids, amino acids, sterols, phenolics, and saccharides in resistant and susceptible Populus trichocarpa inoculated with Sphaerulina musiva, were observed. The patterns of 222 metabolites in the resistant host implicates systemic acquired resistance (SAR), cell wall apposition, and lignin deposition as modes of resistance to this hemibiotrophic pathogen. This pattern is consistent with the expected response to the biotrophic phase of S. musiva colonization during the first 24 hours post-inoculation. The fungal pathogen metabolized key regulatory signals of SAR, other phenolics, and precursors of lignin biosynthesis which were depleted in the susceptible host. This is the first study to characterize metabolites associated with the response to initial colonization by S. musiva between resistant and susceptible hosts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Large-scale Genetic Characterization of a Model Sulfate-Reducing Bacterium

ABSTRACTSulfate-reducing bacteria (SRB) are obligate anaerobes that can couple their growth to the reduction of sulfate. Despite the importance of SRB to global nutrient cycles and their damage to the petroleum industry, our molecular understanding of their physiology remains limited. To systematically provide new insights into SRB biology, we generated a randomly barcoded transposon mutant library in the model SRB Desulfovibrio vulgaris Hildenborough (DvH) and used this genome-wide resource to assay the importance of its genes under a range of metabolic and stress conditions. In addition to defining the essential gene set of DvH, we identified a conditional phenotype for 1,137 non-essential genes. Through examination of these conditional phenotypes, we were able to make a number of novel insights into our molecular understanding of DvH, including how this bacterium synthesizes vitamins. For example, we identified DVU0867 as an atypical L-aspartate decarboxylase required for the synthesis of pantothenic acid, provided the first experimental evidence that biotin synthesis in DvH occurs via a specialized acyl carrier protein and without methyl esters, and demonstrated that the uncharacterized dehydrogenase DVU0826:DVU0827 is necessary for the synthesis of pyridoxal phosphate. In addition, we used the mutant fitness data to identify genes involved in the assimilation of diverse nitrogen sources, and gained insights into the mechanism of inhibition of chlorate and molybdate. Our large-scale fitness dataset and RB-TnSeq mutant library are community-wide resources that can be used to generate further testable hypotheses into the gene functions of this environmentally and industrially important group of bacteria.

Trotter, Valentine V↗
DOE OSTI2015

Superfluid density and Berezinskii-Kosterlitz-Thouless transition of a spin-orbit-coupled Fulde-Ferrell superfluid

We theoretically investigate the superfluid density and Berezinskii-Kosterlitz-Thouless (BKT) transition of a two-dimensional Rashba spin-orbit-coupled atomic Fermi gas with both in-plane and out-of-plane Zeeman fields. It was recently predicted that, by tuning the two Zeeman fields, the system may exhibit different exotic Fulde-Ferrell (FF) superfluid phases, including the gapped FF, gapless FF, gapless topological FF, and gapped topological FF states. Due to the FF paring, we show that the superfluid density (tensor) of the system becomes anisotropic. When an in-plane Zeeman field is applied along the x direction, the tensor component along the y direction n s ,yy is generally larger than n s ,xx in most parameter space. At zero temperature, there is always a discontinuity jump in n s ,xx as the system evolves from a gapped FF into a gapless FF state. With increasing temperature, such a jump is gradually washed out. The critical BKT temperature has been calculated as functions of the spin-orbit-coupling strength, interatomic interaction strength, and in-plane and out-of-plane Zeeman fields. We predict that the novel FF superfluid phases have a significant critical BKT temperature, typically at the order of 0.1T F , where T F is the Fermi degenerate temperature. Furthermore, their observation is within the reach of current experimental techniques in cold-atom laboratories.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2017

Hybrid-Functional Calculations of the Copper Impurity in Silicon

We calculate formation energies and transition levels for copper-related defects in silicon using the screened hybrid functional of Heyd, Scuseria, and Ernzerhof HSE06. We consider Cu siting on interstitial sites ( Cu i ), a substitutional site ( Cu Si ), a Cu Si - Cu i pair, a complex formed from substitutional Cu and interstitial hydrogen ( Cu Si - H i ), and a complex formed from a substitutional Cu and three interstitial Cu atoms ( Cu Si - 3 Cu i ). We find that Cu i is a fast diffuser, with a migration barrier of only 0.19 eV, in good agreement with experimental values. Cu i is a shallow donor and its formation energy is lower than that of Cu Si for all Fermi-level positions in the band gap. Cu Si , on the other hand, induces levels in the gap which are related to the occupation of antibonding states originating from the coupling between the Cu 3 d states ( t 2 ( d ) ), resonant in the valence band, and the vacancy-induced gap states ( t 2 ( p ) ). The stable charge states of Cu Si in the gap are + 1 , 0, - 1 , and - 2 . The transition levels of Cu Si - Cu i and Cu Si - H i are closely related to the levels of isolated Cu Si : a donor level ( + / 0 ) near the valence band, an acceptor level near midgap, and a double-acceptor level in the upper part of the gap. Overall, the calculated transition levels are in good agreement with experimental results, and the formation energies explain the observed solubility.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Crystal growth and quantum oscillations in the topological chiral semimetal CoSi

Here, we survey the electrical transport properties of single-crystalline, topological chiral semimetal CoSi grown via different methods. High-quality CoSi single crystals were found in the growth from a tellurium solution. The sample's high carrier mobility enables us to observe quantum oscillations (QOs) in its thermoelectrical signals. Our analysis of QOs reveals two spherical Fermi surfaces around the R point in its Brillouin zone corner. The extracted Berry phases of these electron orbits are consistent with the -2 chiral charge as reported in density functional theory (DFT) calculations. A detailed analysis of the QOs reveals that the spin-orbit-coupling-induced band splitting is less than 2 meV near the Fermi level, one order of magnitude smaller than our DFT calculation. We also report a large phonon-drag-induced Nernst effect in CoSi at intermediate temperatures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Spin-orbit coupling induced robust spin-Seebeck effect and pure thermal spin currents in achiral molecule systems

Spin-Seebeck effect (SSE) is an effective route to realize pure spin current by using spin-polarized electrons or spin-wave transport in magnetic systems. In this work we propose a route, i.e., by using spin-orbit coupling (SOC), to achieve robust SSE characterized by pure thermal spin current. The material examples are constructed on achiral nanotubes, and the theoretical results reveal that (i) as temperature gradient is applied along the nanotubes, thermal spin-up and spin-down currents with opposite flow directions are produced without any accompanying charge current, (ii) the SSE is robust against decoherence and nonuniform interchain SOC, (iii) the thermal spin currents display a multioscillation feature with increasing device temperatures, supporting their potential device applications in thermal spin-current multiswitcher, and (vi) strain engineering in the radical direction of nanotubes is an effective way to improve SSE and to control pure thermal spin current. These inspiring spin transport behaviors in achiral molecular systems put forward a mechanism to realize the robust SSE characterized by pure spin current and develop the research field of spin-orbito-caloritronics, which focuses on the interplay of electrons’ spin and orbital degrees of freedom in the presence of temperature gradient.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Evidence from transport measurements for YRh 6 Ge 4 being a triply degenerate nodal semimetal

We have investigated magnetotransport properties of YRh 6 Ge 4 , which was recently predicted to be a triply degenerate nodal semimetal. We find it exhibits remarkable signatures of a chiral anomaly, manifested by large negative longitudinal magnetoresistance, the quadratic field dependence of magnetoconductance and the planar Hall effect. Furthermore, we have also observed Shubnikov-de Haas (SdH) quantum oscillations in the magnetoresistivity measurements on this material. The analyses of the SdH data reveal two pointlike Fermi surfaces and these pockets are found to host nearly massless fermions. The small size of these Fermi pockets is in a good agreement with the theoretical prediction that the triply degenerate point in YRh 6 Ge 4 is much closer to the Fermi level than previously demonstrated triply degenerate nodal semimetals such as MoP and WC. These results suggest YRh 6 Ge 4 may serve as a model system to probe exotic properties of three-component fermions and understand their underlying physics.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Canted Eu magnetic structure in EuMnSb 2

Magnetic ordering breaks the time-reversal symmetry, greatly impacting material topological properties. Here, we report the investigation of the magnetic properties of the layered EuMnSb 2 , which has two sets of magnetic sublattices. Both the magnetization and electrical resistivity reveal two phase transitions with one at T N,Eu ~21K and the other at T N,Mn ~346K. Single crystal neutron diffraction refinement indicates that both transitions are originated from magnetic ordering. Below T N,Mn , the Mn sublattice forms the C-type antiferromagnetic (AFM) structure with moments [(4.5±0.6)μB at 7 K] pointing along the a axis. Below T N,Eu , the Eu sublattice forms the canted A-type AFM structure with moments [(5.9±0.8)μB at 7 K] lying in the ac plane but pointing (41 ± 1)° away from the a axis. Quantitative analysis indicates that the spin-spin correlation length, while anisotropic, has long-range characteristic in all directions for both the Eu and Mn sublattices.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Electrical detection of magnon-photon interactions via an auxiliary spin-wave mode

We report on the electrical detection of a hybrid magnon-photon system which comprises a magnetic sample coupled to a planar cavity. While the uniform Kittel mode has the largest coupling strength among all the magnon modes, it generates only a modest voltage signal by means of the inverse spin-Hall effect. We have found that the generated voltage can be significantly enhanced by introducing a higher-order magnon mode, which possesses a much higher spin pumping efficiency, and furthermore, it is nearly degenerated with the Kittel mode. In this work, the experimental results can be explained by our theoretical model and suggest that the use of an auxiliary magnon mode can realize the configuration of a magnon-photon system with both strong coupling and large spin current.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Topological Hall effect and magnetic states in the Nowotny chimney ladder compound Cr 11 Ge 19

In this report, we have investigated the magnetic and charge transport properties of single crystals of the Nowotny chimney ladder compound Cr 11 Ge 19 and mapped out a comprehensive phase diagram reflecting the complicated interplay between the Dzyaloshinskii-Moriya (DM) interaction, the dipolar interaction, and the magnetic anisotropy. We have identified a set of interesting magnetic phases and attributed a finite topological Hall effect to the recently discovered biskyrmion phase. These data also suggest the existence of an antiskyrmion state at finite fields for temperatures just below the magnetic ordering temperature T c as indicated by a distinct change in sign of the topological Hall effect. Above T c , we discovered a region of enhanced magnetic response corresponding to a disordered phase likely existing near the ferromagnetic critical point under small magnetic fields. Strong spin chirality fluctuations are demonstrated by the large value of the topological Hall resistivity persisting up to 1 T, which is most likely due to the existence of the DM interaction. We argue that changes to the topological Hall effect correspond to different topological spin textures that are controlled by magnetic dipolar and DM interactions that vary in importance with temperature

36 MATERIALS SCIENCE↗