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At least 811 records · Page 45
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Biostimulation of Salicornia europaea L. crops with plant growth-promoting bacteria in laboratory and field conditions: effects on growth and metabolite profile

Abstract Aim The objective of the work was to assess the effect of biostimulation with selected plant growth-promoting bacteria on growth and metabolite profile of Salicornia europaea. Methods and results Salicornia europaea seeds were inoculated with different combinations of plant growth-promoting bacteria Brevibacterium casei EB3, Pseudomonas oryzihabitans RL18, and Bacillus aryabhattai SP20. Plants germinated from inoculated seeds were grown either in laboratory conditions or in a saline crop field. Fresh and dry weight were determined at the end of the experiment, for biomass quantification. The microbiological quality of fresh shoots for human consumption as salad greens was assessed, and the persistence of the inoculated strains in the plant rhizosphere was confirmed by next-generation sequencing (Illumina) of the 16S rDNA gene. The primary metabolite profile of biostimulated plants was characterized by GC–TOF-MS. In laboratory conditions, inoculation with the two strains Br. casei EB3 and Ps. oryzihabitans RL18 caused the most significant increase in biomass production (fresh and dry weight), and caused a shift in the central metabolic pathways of inoculated plants toward amino acid biosynthesis. In the field experiment, no significant biostimulation effect was detected with any of the tested inoculants. Seed inoculation had no significant effect on the microbiological quality of the edible parts. The persistence of inoculants was confirmed in both experiments. Conclusions Manipulation of the plant microbiome can trigger primary metabolic reconfiguration and modulate the plant metabolism while promoting plant growth.

Ferreira, Maria J.↗
DOE OSTI2023

Critical magnetic Reynolds number of the turbulent dynamo in collisionless plasmas

The intracluster medium of galaxy clusters is an extremely hot and diffuse, nearly collisionless plasma, which hosts dynamically important magnetic fields of ~μG strength. Seed magnetic fields of much weaker strength of astrophysical or primordial origin can be present in the intracluster medium. In collisional plasmas, which can be approximated in the magnetohydrodynamical (MHD) limit, the turbulent dynamo mechanism can amplify weak seed fields to strong dynamical levels efficiently by converting turbulent kinetic energy into magnetic energy. However, the viability of this mechanism in weakly collisional or completely collisionless plasma is much less understood. In this study, we explore the properties of the collisionless turbulent dynamo using three-dimensional hybrid-kinetic particle-in-cell simulations. We explore the properties of the collisionless turbulent dynamo in the kinematic regime for different values of the magnetic Reynolds number, Rm, initial magnetic-to-kinetic energy ratio, (E mag /E kin ) i , and initial Larmor ratio, (r Larmor /L box ) i , i.e. the ratio of the Larmor radius to the size of the turbulent system. We find that in the ‘un-magnetized’ regime, (r Larmor /L box ) i > 1, the critical magnetic Reynolds number for the dynamo action Rm crit ≈ 107 ± 3. In the ‘magnetized’ regime, (r Larmor /L box ) i ≲ 1, we find a marginally higher Rm crit = 124 ± 8. We find that the growth rate of the magnetic energy does not depend on the strength of the seed magnetic field when the initial magnetization is fixed. We also study the distribution and evolution of the pressure anisotropy in the collisionless plasma and compare our results with the MHD turbulent dynamo.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Transcriptome and DNA methylome divergence of inflorescence development between 2 ecotypes in Panicum hallii

The morphological diversity of the inflorescence determines flower and seed production, which is critical for plant adaptation. Hall's panicgrass (Panicum hallii, P. hallii) is a wild perennial grass that has been developed as a model to study perennial grass biology and adaptive evolution. Highly divergent inflorescences have evolved between the 2 major ecotypes in P. hallii, the upland ecotype (P. hallii var hallii, HAL2 genotype) with compact inflorescence and large seed and the lowland ecotype (P. hallii var filipes, FIL2 genotype) with an open inflorescence and small seed. Here we conducted a comparative analysis of the transcriptome and DNA methylome, an epigenetic mark that influences gene expression regulation, across different stages of inflorescence development using genomic references for each ecotype. Global transcriptome analysis of differentially expressed genes (DEGs) and co-expression modules underlying the inflorescence divergence revealed the potential role of cytokinin signaling in heterochronic changes. Comparing DNA methylome profiles revealed a remarkable level of differential DNA methylation associated with the evolution of P. hallii inflorescence. We found that a large proportion of differentially methylated regions (DMRs) were located in the flanking regulatory regions of genes. Intriguingly, we observed a substantial bias of CHH hypermethylation in the promoters of FIL2 genes. The integration of DEGs, DMRs, and $K_a$/$K_s$ ratio results characterized the evolutionary features of DMR-associated DEGs that contribute to the divergence of the P. hallii inflorescence. This study provides insights into the transcriptome and epigenetic landscape of inflorescence divergence in P. hallii and a genomic resource for perennial grass biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Propelling sustainable energy: Multi-omics analysis of pennycress FATTY ACID ELONGATION1 knockout for biofuel production

Abstract The aviation industry’s growing interest in renewable jet fuel has encouraged the exploration of alternative oilseed crops. Replacing traditional fossil fuels with a sustainable, domestically sourced crop can substantially reduce carbon emissions, thus mitigating global climate instability. Pennycress (Thlaspi arvense L.) is an emerging oilseed intermediate crop that can be grown during the offseason between maize (Zea mays) and soybean (Glycine max) to produce renewable biofuel. Pennycress is being domesticated through breeding and mutagenesis, providing opportunities for trait enhancement. Here, we employed metabolic engineering strategies to improve seed oil composition and bolster the plant's economic competitiveness. FATTY ACID ELONGATION1 (FAE1) was targeted using CRISPR-Cas 9 gene editing to eliminate very long chain fatty acids (VLCFAs) from pennycress seed oil, thereby enhancing its cold flow properties. Through an integrated multiomics approach, we investigated the impact of eliminating VLCFAs in developing and mature plant embryos. Our findings revealed improved cold-germination efficiency in fae1, with seedling emergence occurring up to 3 d earlier at 10 °C. However, these alterations led to a tradeoff between storage oil content and composition. Additionally, these shifts in lipid biosynthesis were accompanied by broad metabolic changes, such as the accumulation of glucose and ADP-glucose quantities consistent with increased starch production. Furthermore, shifts to shorter FA chains triggered the upregulation of heat shock proteins, underscoring the importance of VLCFAs in stress signaling pathways. Overall, this research provides crucial insights for optimizing pennycress seed oil while preserving essential traits for biofuel applications.

Rasoul, Amira (ORCID:0009000714290175)↗
DOE OSTI2025

PII interactions with the acetyl-CoA carboxylase subunits BADC and BCCP co-regulate lipid and nitrogen metabolism in Arabidopsis

In plants, the initiation of fatty acid synthesis is catalyzed by acetyl-CoA carboxylase (ACCase), which produces malonyl-CoA. The heteromeric form of ACCase (htACCase) is a holoenzyme consisting of biotin carboxylase and carboxyltransferase sub-complexes, both of which are subject to extensive regulation. Biotin carboxylase activity is controlled in part by the presence of the catalytic biotin carboxyl carrier proteins (BCCP1/2) and/or the non-catalytic, non-biotinylated, biotin/lipoyl attachment domain-containing proteins (BADC1/2/3) that associate with backbone biotin carboxylase (BC) protein. However, the mechanisms regulating BADC and BCCP interactions with BC and, consequently, ACCase activity in planta , remain unclear. Here, we demonstrate that the Arabidopsis ( Arabidopsis thaliana ) regulatory protein PII modulates htACCase activity through independent interactions with BADC and BCCP proteins in a selective manner. Analysis of badc1 badc2 and badc1 badc3 mutant lines and the respective pii triple mutants revealed that changes in seed oil and protein accumulation of badc double mutants are PII/nitrogen dependent. Absolute quantification of htACCase subunits and PII in developing seeds suggests that Arabidopsis exerts tight regulation over individual protein stoichiometry to balance oil and protein accumulation. The effects on vegetative and seed development indicate that PII and BADC proteins have distinct yet overlapping roles in regulating plant metabolism.

Garneau, Matthew G. [Washington State Univ., Pullm↗
DOE OSTI2021

Nucleosynthetic signatures of primordial origin around supermassive black holes

We report that if primordial black holes (PBHs) seeded the supermassive black holes (SMBHs) at the centers of high-redshift quasars, then the gas surrounding these black holes may reveal nucleosynthetic clues to their primordial origins. We present predictions of altered primordial abundances around PBHs massive enough to seed SMBHs at z ≈ 6 – 7.5. We find that if PBHs with initial masses of ~10 5 M ⊙ are responsible for such SMBHs, they may produce primordial deuterium and Helium fractions enhanced by ≥ 10%, and lithium abundance depleted by ≥ 10%, at distances of up to ≈ a comoving kiloparsec away from the black hole after decoupling. We estimate that ~ 10 8 M ⊙ of gas is enhanced (or depleted) by at least one percent. Evidence of these modified primordial deuterium, helium, and lithium abundances could still be present if this circum-PBH gas remains unaccreted by the SMBH and in or near the host galaxies of high-redshift quasars. Measuring the abundance anomalies will be challenging, but could offer a novel way to reveal the primordial origin of such SMBH seeds.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Spectrotemporal Shaping of Attosecond X-Ray Pulses with a Fresh-Slice Free-Electron Laser

We propose a scheme allowing coherent shaping, i.e., controlling both the amplitude and phase, of attosecond x-ray pulses at free-electron lasers. Here, we show that by seeding an FEL with a short coherent seed that overfills the amplification bandwidth, one can shape the Wigner function of the pulse by controlling the undulator taper profile. The examples of controllable pulse pairs and trains, as well as isolated spectrotemporally shaped pulses with very broad bandwidths are examined in detail. Existing attosecond XFELs can achieve these experimental conditions in a two-stage cascade, in which the seed is generated by a short current spike in an electron bunch and shaped in an unspoiled region within the same bunch. We experimentally demonstrate the production and control of phase-stable pulse trains using this method at the Linac Coherent Light Source II.

47 OTHER INSTRUMENTATION↗
DOE OSTI2026

Measurement of the Alfvén Wave Parametric Decay Instability Growth Rate

Alfvén waves, a fundamental mode of magnetized plasmas, are ubiquitous in space and laboratory plasmas. The nonlinear behavior of these modes is thought to play a key role in important problems in space plasma, such as the heating of the solar corona and solar wind turbulence. In particular, theoretical predictions show that these Alfvén waves may be unstable to various parametric instabilities, but space observations of these processes are limited. We demonstrate the first measurement of the Alfvén wave parametric decay instability (PDI) growth rate. Experiments are conducted on the Large Plasma Device at UCLA in which a high amplitude 𝛿⁢𝐵/𝐵 0 ∼ 0.7% pump Alfvén wave is launched from one end of the device and a smaller seed Alfvén wave is launched from the other side. When the frequency of the seed wave is chosen to match the backward wave expected from PDI, damping of the seed wave is reduced. We compare this reduction in damping to the theoretically expected PDI growth rate while accounting for acoustic mode damping. Results show agreement between measurements and theoretical predictions. As a result, this not only provides critical validation for PDI theories and simulations that could help interpret future space observations but also suggests a new way of studying similar nonlinear wave phenomena.

Alfvén waves↗
DOE OSTI2020

The functional roles of species in metacommunities, as revealed by metanetwork analyses of bird–plant frugivory networks

Abstract Understanding how biodiversity and interaction networks change across environmental gradients is a major challenge in ecology. We integrated metacommunity and metanetwork perspectives to test species’ functional roles in bird–plant frugivory interactions in a fragmented forest landscape in Southwest China, with consequences for seed dispersal. Availability of fruit resources both on and under trees created vertical feeding stratification for frugivorous birds. Bird–plant interactions involving birds feeding only on‐the‐tree or both on and under‐the‐tree (shared) had a higher centrality and contributed more to metanetwork organisation than interactions involving birds feeding only under‐the‐tree. Moreover, bird–plant interactions associated with large‐seeded plants disproportionately contributed to metanetwork organisation and centrality. Consequently, on‐the‐tree and shared birds contributed more to metanetwork organisation whereas under‐the‐tree birds were more involved in local processes. We would expect that species’ roles in the metanetwork will translate into different conservation values for maintaining functioning of seed‐dispersal networks.

Li, Hai‐Dong↗
DOE OSTI2022

Disturbance: a double-edged sword for restoration in a changing climate

Ecological restoration often relies on disturbance as a tool for establishing target plant communities, but disturbance can be a double-edged sword, at times initiating invasion and unintended outcomes. Here, in this study, we test how fire disturbance, designed to enhance restoration seeding success, combines with climate and initial vegetation conditions to shift perennial versus annual grass dominance and overall community diversity in Pacific Northwest grasslands. We seeded both native and introduced perennial grasses and native forbs in paired, replicated burned-unburned plots in three sites along a latitudinal climate gradient from southern Oregon to central-western Washington. Past restoration and climate manipulations at each site had increased the variation of starting conditions between plots. Burning promoted the expansion of extant forbs and perennial grasses across all sites. Burning also enhanced the seeding success of native perennial grass and native forbs at the northern and central site, and the success of introduced perennial grasses across all three sites. Annual grass dominance was driven more by latitude than burning, with annuals maintaining their dominance in the south and perennials in the north. At the same time, unrestored grasslands surrounding all sites remained dominated by perennial grasses, suggesting that initial plot clearing may have allowed for annual grass invasion in the southern site. When paired with disturbance, further warming may increase the risk of annual grass dominance, a potentially persistent state.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Exploring Camelina sativa lipid metabolism regulation by combining gene co-expression and DNA affinity purification analyses

Camelina (Camelina sativa) is an annual oilseed plant that is gaining momentum as a biofuel cover crop. Understanding gene regulatory networks is essential to deciphering plant metabolic pathways, including lipid metabolism. Furthermore, we take advantage of a growing collection of gene expression datasets to predict transcription factors (TFs) associated with the control of Camelina lipid metabolism. We identified approximately 350 TFs highly co-expressed with lipid-related genes (LRGs). These TFs are highly represented in the MYB, AP2/ERF, bZIP, and bHLH families, including a significant number of homologs of well-known Arabidopsis lipid and seed developmental regulators. After prioritizing the top 22 TFs for further validation, we identified DNA-binding sites and predicted target genes for 16 out of the 22 TFs tested using DNA affinity purification followed by sequencing (DAP-seq). Enrichment analyses of targets supported the co-expression prediction for most TF candidates, and the comparison to Arabidopsis revealed some common themes, but also aspects unique to Camelina. Within the top potential lipid regulators, we identified CsaMYB1, CsaABI3AVP1-2, CsaHB1, CsaNAC2, CsaMYB3, and CsaNAC1 as likely involved in the control of seed fatty acid elongation and CsaABI3AVP1-2 and CsabZIP1 as potential regulators of the synthesis and degradation of triacylglycerols (TAGs), respectively. Altogether, the integration of co-expression data and DNA-binding assays permitted us to generate a high-confidence and short list of Camelina TFs involved in the control of lipid metabolism during seed development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

SEEDling [SWR-20-99]

SEEDling is intended to simplify the merging of multiple data sources prior to importing into the SEED platform. Geographic information about buildings and taxlots is often obtained from various data sources, and the process of synthesizing this information for many buildings across a city can be burdensome for city data managers. SEEDling uses GIS tools to automate and simplify this process, as well as apply criteria for SEED inclusion (ex: sqft > 50k) and assign UBIDs, to create records that can be easily imported into the SEED platform.

Long, Nicholas↗
DOE OSTI2024

Ergot alkaloid consumption alters serotonin receptor-induced vasoactivity in ovine umbilical vasculature

Consumption of ergot alkaloids during the second half of gestation has been shown to decrease umbilical artery vasoactivity resulting in decreased birth weights. Negative vascular effects of ergot alkaloids are mediated predominantly through serotonergic and adrenergic receptors in other tissues. Vasoactivity of serotonin (5-HT) receptors 5-HT 2A and 5-HT 1B/1D in umbilical artery and vein from ewes receiving endophyte-infected seed (E + 1.77 mg ergovaline/hd/d) or a control total mixed ration (CON; 0 mg ergovaline/hd/d) tall fescue seed at d-110 and d-133 of gestation was evaluated. Gravid reproduction tracts were collected from ewes. Two-mm sections of umbilical artery and vein were exposed to increasing concentrations of a 5-HT 1B/1D agonist and 5-HT 2A agonist. The 5-HT 1B/1D agonist did not stimulate a contractile response in artery or vein or either gestation time point. 5-HT 2A agonist caused large responses in artery with greatest occurring at d-110 and decreasing in magnitude as days of gestation increased ( p < 0.05). On d-110 and 133 of gestation, arteries from CON ewes had greater contractile response than arteries collected from E+ ewes ( p < 0.05). Veins responded to increasing concentrations of the 5-HT 2A agonist. Maximal d-110 vein response was greater than d-133 when exposed to 5-HT 2A agonist ( p < 0.05). Unlike the artery, veins from E+ ewes had greater d-133 contractile response than CON ( p < 0.05). Vascular contractions of umbilical artery and vein are induced by 5-HT 2A receptor activity and not 5-HT 1B/1D . Umbilical artery 5-HT 2A receptor activity was more sensitive to seed treatment and could be responsible for ergot alkaloid-induced intra-uterine growth restriction.

Toxicology↗
DOE OSTI2024

Chromosome-level assembly and analysis of Camelina neglecta : a novel diploid model for Camelina biotechnology research

Camelina neglecta is a new diploid Brassicaceae species, which has great research value because of its close relationship with the hexaploid oilseed crop Camelina sativa. Here, we report a chromosome-level assembly of C. neglecta with a total length of 210 Mb. By adopting PacBio sequencing and Hi-C technology, the C. neglecta genome was assembled into 6 chromosomes with scaffold N50 of 29.62 Mb. C. neglecta has undergone the whole-genome triplication (γ) shared among eudicots and two whole-genome duplications (α and β) shared by crucifers, but it has not undergone a specific whole-genome duplication event. By synteny analysis between C. neglecta and C. sativa, we successfully used the method of calculating Ks to distinguish the three subgenomes of C. sativa and determined that C. neglecta was closest to the first subgenome (SG1) of C. sativa. Further, transcriptomic analysis revealed the key genes associated with seed oil biosynthesis and its transcriptional regulation, including SAD, FAD2, FAD3, FAE1, ABI3, WRI1 and FUS3 displaying high expression levels in C. neglecta seeds. The high representability of C. neglecta as a model species for Camelina-based biotechnology research has been demonstrated for the first time. In particular, floral Agrobacterium tumefaciens infiltration-based transformation of C. neglecta, leading to overexpression of CvLPAT2, CpDGAT1 and CvFatB1 transgenes, was demonstrated for medium-chain fatty acid accumulation in C. neglecta seed oil. This study provides an important genomic resource and establishes C. neglecta as a new model for oilseed biotechnology research.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Analysis of pump-to-signal noise transfer in two-stage ultra-broadband optical parametric chirped-pulse amplification

In optical parametric chirped-pulse amplification (OPCPA), pump temporal intensity modulation is transferred to the chirped-signal spectrum via instantaneous parametric gain and results in contrast degradation of the recompressed signal. We investigate, for the first time to our knowledge, the pump-to-signal noise transfer in a two-stage ultra-broadband OPCPA pumped by a single laser and show the dependence of pump-induced signal noise, characterized both before and after pulse compression, on the difference in pump-seed delay in the two stages. We demonstrate an up-to-15-dB reduction of the pump-induced contrast degradation via pump-seed delay optimization. Experiments and simulations show that, even when parametric amplifiers are operated in saturation, the pump-seed delay can be used to minimize the pump-induced contrast degradation that is attributed largely to the noises from the unsaturated edges of the pulse and that of the beam.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Single-shot measurements of shaped XUV FEL pulses with frequency-resolved optical gating

The ability to control the amplitude and phase of extreme ultraviolet (XUV) and X-ray free-electron laser (FEL) pulses can allow for the extension of optical techniques, such as multidimensional spectroscopy or coherent control, to higher photon energies, for probing and controlling core electronic transitions. However, this requires the ability to make single-shot, and complete, electric field measurements of potentially complex FEL pulses, in order to develop, and verify, pulse shaping strategies. Here, we present direct, single-shot measurements of XUV pulses generated under special operating configurations for producing specific pulse shapes from a laser-seeded XUV FEL. To do this, we built upon our past work using transient grating (TG) cross correlation frequency-resolved optical gating (FROG), where an optical reference pulse is diffracted from an XUV TG produced by a pair of interfering FEL pulses. The resulting nonlinear signal versus frequency and delay, i.e., the FROG trace, contains the electric field of the FEL pulse. The FEL pulse electric field is reconstructed from the FROG trace using a phase retrieval algorithm. Here we confirmed three different pulse shaping strategies for generating chirped, double and multiple FEL pulses by tuning the seed laser and FEL parameters and measuring the resulting shaped FEL pulses with TG XFROG. This work paves the way for generating on-demand pulse shapes with a seeded FEL by improving the characterization of FEL pulses, for transform-limited to more complex shapes.

Elverson, Francesca↗
DOE OSTI2025

High-Spectral Resolution Lidar (HSRL) Instrument Handbook

High-spectral-resolution lidar (HSRL) systems provide vertical profiles of optical depth, backscatter cross-section, depolarization, and backscatter phase function. All HSRL measurements are calibrated by reference to molecular scattering, which is measured at each point in the lidar profile. Like the Raman lidar (RL), but unlike simple backscatter lidars such as the micropulse lidar (MPL), this enables the HSRL to measure backscatter cross-sections and optical depths without prior assumptions about the scattering properties of the atmosphere. The depolarization observations allow robust discrimination between ice and water clouds. Rigorous error estimates can be computed for all measurements. A very narrow angular field of view reduces multiple scattering contributions. The small field of view, coupled with a narrow optical bandwidth, nearly eliminates noise due to scattered sunlight. The laser transmitter is a diode-pumped, frequency-doubled Nd:YAG laser. Narrow-band, single-frequency operation is provided by injection seeding with a single-frequency, cw-diode-pumped diode laser. The main laser cavity is maintained in resonance with the seed laser by adjusting the cavity length to minimize the time between the Q-switch trigger and the emission of the laser pulse. The emission wavelength is tuned via temperature control of the seed laser crystal and is locked to line #1109 of the iodine absorption spectra. Locking is accomplished by minimizing the transmission through a 2-cm-long iodine absorption cell. Use of a high-repetition-rate laser and expansion of the transmitted beam through a 400-mm telescope reduces the transmitted energy density to eye-safe levels. It is possible to look directly into the output beam without hazard. The receiver and transmitter use the same afocal telescope, simplifying the maintenance of stable alignment of the transmitter and receiver although the angular FOV is only 100 μrad. The small FOV and the 4-kHz repetition rate also limit the near-field signal strength, making it possible to record continuous profiles that start at an altitude of ~100 m and extend to 30 km using photon counting detectors. The small FOV also suppresses multiple scattering contributions.

54 ENVIRONMENTAL SCIENCES↗