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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Dose-efficient automatic differentiation for ptychographic reconstruction

Ptychography, as a powerful lensless imaging method, has become a popular member of the coherent diffractive imaging family over decades of development. The ability to utilize low-dose X-rays and/or fast scans offers a big advantage in a ptychographic measurement (for example, when measuring radiation-sensitive samples), but results in low-photon statistics, making the subsequent phase retrieval challenging. Here, we demonstrate a dose-efficient automatic differentiation framework for ptychographic reconstruction (DAP) at low-photon statistics and low overlap ratio. As no reciprocal space constraint is required in this DAP framework, the framework, based on various forward models, shows superior performance under these conditions. It effectively suppresses potential artifacts in the reconstructed images, especially for the inherent periodic artifact in a raster scan. We validate the effectiveness and robustness of this method using both simulated and measured datasets.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

AmeriFlux FLUXNET-1F US-xSL NEON North Sterling, CO (STER)

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-xSL NEON North Sterling, CO (STER). This is the FLUXNET version of the carbon flux data for the site US-xSL NEON North Sterling, CO (STER) produced by applying the standard ONEFlux (1F) software. Site Description - The North Sterling site, located outside of Sterling in Northeastern Colorado, is characterized by flat terrain and represents an agronomic site within urban and formerly urban areas. The site is at the edge of a non-tilled experimental field that is used for the long-term sustainable Dryland Agroecosystems Project (DAP), which was initiated in 1985 at three sites in eastern Colorado (Sterling, Stratton, and Walsh) to evaluate the effects of cropping intensity on production, water use efficiency and selected soil chemical and physical properties. The DAP site was established in 1985 and was chosen because of representative soils present in the catena.

Network), NEON (National Ecological Observatory↗
DOE OSTI2022

Validation and functional characterization of transcription factors in wheat using cell-free protein expression and high-throughput sequencing technologies

Transcription factors (TFs) are critical biomolecules that control and regulate gene expression in every organism. In wheat, there are 3,606 genes annotated as putative TFs which are primarily uncharacterized. In this work, using a DAP-seq approach, we have validated and characterized a select number of TFs (5bl and 5dl) belonging to GeBP family of proteins, responsible for plant cellular growth, development, and differentiation. We found that top DNA binding motifs for 5bl and 5dl are (G/T)N(T/G)GTGGT and (C/G)AA(C/G)AA respectively. These motifs/peaks are enriched in the promoter regions of the genes, which are associated with rRNA biogenesis and protein maturation pathways. This study is also a first demonstration that DAP-seq can be applied for such a complex and large genome such as wheat.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Genome-Wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum

Clostridium thermocellum is a thermophilic bacterium recognized for its natural ability to effectively deconstruct cellulosic biomass. While there is a large body of studies on the genetic engineering of this bacterium and its physiology to-date, there is limited knowledge in the transcriptional regulation in this organism and thermophilic bacteria in general. The study herein is the first report of a large-scale application of DNA-affinity purification sequencing (DAP-seq) to transcription factors (TFs) from a bacterium. We applied DAP-seq to > 90 TFs in C. thermocellum and detected genome-wide binding sites for 11 of them. We then compiled and aligned DNA binding sequences from these TFs to deduce the primary DNA-binding sequence motifs for each TF. These binding motifs are further validated with electrophoretic mobility shift assay (EMSA) and are used to identify individual TFs’ regulatory targets in C. thermocellum . Our results led to the discovery of novel, uncharacterized TFs as well as homologues of previously studied TFs including RexA-, LexA-, and LacI-type TFs. We then used these data to reconstruct gene regulatory networks for the 11 TFs individually, which resulted in a global network encompassing the TFs with some interconnections. As gene regulation governs and constrains how bacteria behave, our findings shed light on the roles of TFs delineated by their regulons, and potentially provides a means to enable rational, advanced genetic engineering of C. thermocellum and other organisms alike toward a desired phenotype.

59 BASIC BIOLOGICAL 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 OSTI2023

Functional analysis of Salix purpurea genes support roles for ARR17 and GATA15 as master regulators of sex determination

Abstract The Salicaceae family is of growing interest in the study of dioecy in plants because the sex determination region (SDR) has been shown to be highly dynamic, with differing locations and heterogametic systems between species. Without the ability to transform and regenerate Salix in tissue culture, previous studies investigating the mechanisms regulating sex in the genus Salix have been limited to genome resequencing and differential gene expression, which are mostly descriptive in nature, and functional validation of candidate sex determination genes has not yet been conducted. Here, we used Arabidopsis to functionally characterize a suite of previously identified candidate genes involved in sex determination and sex dimorphism in the bioenergy shrub willow Salix purpurea . Six candidate master regulator genes for sex determination were heterologously expressed in Arabidopsis, followed by floral proteome analysis. In addition, 11 transcription factors with predicted roles in mediating sex dimorphism downstream of the SDR were tested using DAP‐Seq in both male and female S. purpurea DNA. The results of this study provide further evidence to support models for the roles of ARR17 and GATA15 as master regulator genes of sex determination in S. purpurea , contributing to a regulatory system that is notably different from that of its sister genus Populus . Evidence was also obtained for the roles of two transcription factors, an AP2 / ERF family gene and a homeodomain‐like transcription factor, in downstream regulation of sex dimorphism.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Cyclometallated Co(III) Complexes with Lowest-Energy Charge Transfer Excited States Accessible with Visible Light

The Co(III) complexes, cis-[Co(ppy) 2 (L)]PF 6 , where ppy = 2-phenylpyridine and L = bpy (2,2′-bipyridine; 1), phen (1,10-phenanthroline; 2), and DAP (1,12-diazaperylene; 3), are reported and their photophysical properties were investigated to evaluate their potential as sensitizers for applications that include solar energy conversion schemes and photoredox catalysis. Calculations show that cyclometallation in the cis-[Co(ppy) 2 (L)]PF 6 series affords strong Co(dπ)/ppy(π) orbital interactions that result in a Co/ppy(π*) highest occupied molecular orbital (HOMO) and a lowest unoccupied molecular orbital (LUMO) localized on the diimine ligand, L(π*). Complexes 1–3 exhibit relatively invariant oxidation potentials, whereas the reduction event is dependent on the identity of the diimine ligand, L, consistent with the theoretical predictions. For 3 a broad Co/ppy(π*) → L(π*) metal/ligand-to-ligand charge transfer (ML-LCT) absorption band is observed in CH 3 CN with a maxima at 507 nm, extending beyond 600 nm. Upon excitation of the 1ML-LCT transition, transient absorption features consistent with the population of a 3 ML-LCT excited state with lifetimes, τ, of 3.0 ps, 4.6 and 42 ps for 1, 2 and 3 in CH 3 CN respectively are observed. Upon irradiation with 505 nm, 3 is able to reduce methyl viologen (MV 2+ ), an electron acceptor commonly in photocatalytic schemes. Here, to our knowledge, 3 represents the first heteroleptic molecular Co(III) complex that combines cyclometallation with a diimine ligand with lowest-lying metal-to-ligand charge transfer excited states able to undergo photoinduced charge transfer with low-energy green light. As such, the structural design of 3 represents an important step toward d6 photosensitizers based on earth abundant metals.

Energy↗
DOE OSTI2025

Unveiling a pervasive DNA adenine methylation regulatory network in the early-diverging fungus Rhizopus microsporus

Development of the DNA affinity purification and sequencing (DAP-seq) technique has allowed genome-scale studies of transcription factor (TF)-binding sites with high reproducibility. Here, we apply this technique to the human opportunistic pathogen Rhizopus microsporus, a mucoralean fungus belonging to the understudied group of early-diverging fungi. We characterize genome-wide binding sites of 58 TFs encoded by genes regulated through adenine methylation and representing major TF families. This analysis reveals their binding profiles and recognized sequences, expanding and diversifying the catalog of known fungal motifs. By integrating this data with DNA 6-methyladenine profiling, we uncover the extensive direct and indirect impact of this epigenetic modification on the regulation of gene expression. Furthermore, we use the generated data to identify TFs involved in biologically relevant processes such as zinc metabolism and light response. Our work enhances our understanding of regulatory mechanisms in R. microsporus and provides broader insights into gene regulation across the fungal kingdom.

Lax, Carlos [Universidad de Murcia (Spain)] (ORCID↗
DOE OSTI2024

Carbon-related donor–acceptor pair transition in the infrared in h-BN

Experimental studies of intentionally doped impurities for the understanding of conductivity control in hexagonal boron nitride (h-BN) ultrawide bandgap (UWBG) semiconductor are limited but are highly desired for emerging applications of h-BN. We report synthesis by hydride vapor phase epitaxy and comparison photoluminescence (PL) emission spectroscopy studies of intentionally carbon (C)-doped and undoped h-BN semi-bulk crystals. In addition to the well-known C-related emission lines observed previously, a C-impurity-related transition near 1.31 eV consisting of multiple phonon replicas has been observed in C-doped h-BN at room temperature. Phonon replicas involved in the 1.31 eV emission have been identified using polarization resolve PL spectroscopy as the transverse acoustic (TA)/longitudinal acoustic (LA) and out-of-plane optical phonon (ZO) modes at the middle point, T, between the Γ- and K-points in the first Brillouin zone. Based on the agreement between the spectral peak position of the observed dominant emission line at 1.31 eV and the calculated energy-level separation between CB donor (carbon replacing boron) and Ci acceptor (carbon interstitial), the observed IR emission line can be decisively assigned to the donor–acceptor pair (DAP) transition involving the CB donor and Ci acceptor assisted by the intervalley (Κ → Μ) scattering processes. The results reinforce the perception that C impurities form deep-level centers and provided an improved understanding of C impurities in h-BN.

Physics↗
DOE OSTI2024

Discovering Innovations in Stress Tolerance through Comparative Gene Regulatory Network Analysis and Cell-Type Specific Expression Maps (Final Technical Report with Cover Page)

Through this grant, we developed a comparative framework to elucidate the mechanisms behind variations in environmental stress responses among a diverse group of species within the Brassicaceae family. Our focus was on the differences in physiological and transcriptomic responses to abscisic acid (ABA), a hormone associated with water stress. We examined the differential growth responses of four Brassicaceae species, finding that most exhibited reduced root growth correlated with smaller meristem size. In contrast, Schrenkiella parvula showed accelerated growth due to increased root cell elongation. We employed RNA sequencing to analyze the transcriptional responses to ABA across these species, and innovative bioinformatics techniques were used to pinpoint biological pathways with significant divergence. Additionally, we utilized DAP-seq to map the gene regulatory networks associated with ABAresponsive transcription factors, revealing that variations in the regulation of growth hormone biosynthesis play a critical role in the distinct ABA effects on root growth among the species. This research sets a new standard for comparative physiology by integrating comparative genomics and transcriptomics to uncover pathway divergences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Impact of ultraviolet-B radiation on early-season morpho-physiological traits of indica and japonica rice genotypes

Ultraviolet (UV)-B radiation is considered one of the major detrimental rays coming from the Sun. UV-B radiation has a harmful impact on plant growth and development. The effect of UV-B radiation was studied on 64 rice (Oryza sativa L.) genotypes during the vegetative season. An equal number of genotypes from the japonica (50%) and indica (50%) subspecies were phenotyped using the Soil-Plant-Atmosphere-Research (SPAR) units. The 10 kJ UV-B was imposed 12 days after planting (DAP) and continued for three weeks (21 d). Based on the combined ultraviolet-B radiation response index (CUVBRI) for each genotype, the 64 rice genotypes were classified into sensitive, moderately sensitive, moderately tolerant, and tolerant. Various shoot traits, such as plant height, tiller, and leaf numbers, were measured. We also studied critical root phenological traits like root volume, diameter, tips, and forks. Out of all the studied shoot traits, leaf area showed maximum reduction for both indica (54%) and japonica (48%). Among the root traits, root length decreased by negligible (1%) for indica as compared to japonica (5%), while root crossing and forks showed a maximum decline for japonica (37 and 42%), respectively. This study is timely, meaningful, and required because it will help breeders select a tolerant or sensitive rice line for better yield and production under abiotic stresses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Estimation of Corn Latent Heat Flux from High Resolution Thermal Imagery

Crop evapotranspiration (ET), which is directly related to latent heat flux, is also a key indicator in determining the water status of crops. In order to estimate the latent heat flux, two-source energy balance (TSEB) models have been developed for thermal imagery from satellite platforms. However, because of the coarse resolution of thermal sensors on the satellite, distinguishing soil and vegetation is difficult which complicates the calculation process and introduces errors in latent heat estimates. In this research, high-resolution thermal datasets (0.05 m) and corresponding RGB datasets (0.03 m) were used for calculating crop latent heat flux using an adapted TSEB model. The RGB datasets were used for supervised classification of soil and vegetation, and the classification results were then used to filter the thermal mosaics to separate vegetation and soil temperatures. The vegetation temperature is used for calculating latent heat flux and the results are validated against the ground reference measurements of latent heat using a handheld porometer. The objective of this research is to introduce a workflow including an adapted TSEB model which is customized for high resolution thermal images from unmanned aircraft systems (UAS) to estimate the latent heat flux of row crops in agricultural fields. Nine dates of data collection in 2018 and 2020 have been evaluated and the root mean square error (RMSE) varies between 16 to 106 W/m2 depending on the days after planting (DAP) and the time of measurement for each day. The results indicate that the workflow introduced here is able to provide estimates of instantaneous latent heat flux (evapotranspiration) measurements for row crops in agricultural fields which will enable people to make reliable decisions related to irrigation scheduling.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Measurement of the Primary Beam of the Tianlai Cylindrical Antenna Using an Unmanned Aerial Vehicle

The Tianlai Cylinder Pathfinder Array consists of three adjacent cylindrical reflectors fixed on the ground, each 40 m long and 15 m wide, with the cylinder axis oriented along the North–South (N–S) direction. Dual linear polarization feeds are distributed along the focus line, parallel to the cylinder axis. Measurement of the primary beam profile of these cylindrical reflectors is difficult, as they are too large to be placed in an anechoic chamber. While the beam profile along the East–West (E–W) direction can be measured with the transit observations of bright astronomical radio sources, the beam profile along the N–S direction remains very uncertain. Here, we present a preliminary measurement of the beam profile of the Tianlai cylindrical antenna along both the N–S direction and E–W direction in the frequency range of 700–800 MHz, using a calibrator source carried by an unmanned aerial vehicle (UAV) flying in the far field. The beam profile of the Tianlai cylindrical antenna is determined from the analysis of the auto-correlation signals from the cylinder array correlator, taking into account the emitter antenna beam profile, itself measured with a dipole antenna on the ground. The accuracy of the UAV-based determination of the cylinder beam profiles is validated by comparing the results with the one derived from bright astronomical source transits, and with simulated beams.

Li, Jixia [Chinese Academy of Sciences (CAS), Beij↗
DOE OSTI2025

Through the lens of bioenergy crops: advances, bottlenecks, and promises of plant engineering

Advances in engineering of bioenergy crops were driven over the past years by adapting technological breakthroughs and accelerating conventional applications but also exposed intriguing challenges. New tools revealed rich interconnectivity in the exponentially growing and dynamic 'big' omics data' of metabolomes, transcriptomes, and genomes at previously inaccessible magnitude (global, cross-species, meta-) and resolution (single cell). Insights enabled fresh hypotheses and stimulated disciplines such as functional genomics with discovery of broad regulatory networks and their determinants, that is, DNA parts, including promoters, regulatory elements, and transcription factors. Their rational design, assembly into increasingly complex blueprints, and installation into diverse chassis is an existing frontier that may benefit from emerging technologies to address bottlenecks. Interweaving nature-inspired to fully synthetic parts has already allowed building of fine-tuned regulatory circuits, or new-to-nature metabolic routes insulated from the biological context of the chassis species. Similarly, developments and the evolving need for unifying principles in plant transformation and species-agnostic technologies highlight future opportunities for engineering the next generation of bioenergy plants.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Novosphingobium aromaticivorans LigR coordinates transcription of genes involved in metabolism of multiple types of aromatics

Aromatic compounds are a ubiquitous and diverse family of chemicals with functions as biomolecules, natural products, industrial chemicals, and pollutants. Novosphingobium aromaticivorans DSM 12444 uses multiple inducible pathways to catabolize H-, G-, and S-type aromatics that contain zero, one, or two methoxy groups, respectively. Here, we obtain a systems-level view of the transcriptional control of its aromatic metabolic pathways. Several in vitro analyses found that a N. aromaticivorans homolog of the Sphingobium lignivorans SYK-6 transcription factor LigR bound genomic DNA upstream of genes involved in metabolism of multiple aromatic types. We found that a ΔLigR mutant had growth defects on all three types of aromatics as sole carbon sources. Transcriptomic analysis revealed that LigR was required to increase expression of gene products that function in metabolism of all three aromatic types. We also found that, in media containing both glucose and an aromatic carbon source, the ΔLigR mutant directed intermediates through alternative aromatic metabolic pathways. Protein-DNA binding assays showed that N. aromaticivorans LigR binds immediately upstream of promoters of genes involved in aromatic metabolism. We found that N. aromaticivorans LigR coordinates the expression of enzymes that function in the catabolism of H-, G-, and S-type aromatics, and that there are differences in the role of LigR in N. aromaticivorans and S. lignivorans. A comparative genomic analysis predicted that LigR homologs and the aromatic-metabolizing genes that it directly regulates are often co-localized in the genomes of Sphingomonadales, but often not found in this arrangement in many other known aromatic metabolizing bacteria.

Aromatic Compound Degradation↗
DOE OSTI2021

Digital Infrastructure Migration Framework Report

This document presents a full-scope Digital Infrastructure implementation and associated lifecycle support recommendations that enable a plant life of 80+ years. Specific technologies and software applications are researched, developed, selected, implemented, and then integrated by utilities to enhance safety, reliability, and economic performance such that the result provides much more than the sum of its parts. Specific selection of these technologies is driven by business case analyses which are utility, station, and unit specific.

42 ENGINEERING↗