SEARCH · Engineering Papers
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.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
DNA affinity purification sequencing (DAP-seq) to identify putative transcriptional regulators of aromatic metabolism in Novosphingobium aromaticivorans
DNA affinity purification sequencing (DAP-seq) to identify putative transcriptional regulators of aromatic metabolism in Novosphingobium aromaticivorans
The genome-wide binding sites of 44 transcription factors from the aromatic metabolizing Alphaproteobacterium Novosphingobium aromaticivorans were identified using DNA Affinity Purification sequencing (DAP-seq). We report 32 of these transcription factors have at least one area of enrichment. These data will be valuable for better understanding of aromatic metabolism.
Genome-wide binding sites of 44 putative transcription factors (TFs) from Novosphingobium aromaticivorans DSM12444 were analyzed using DNA affinity purification sequencing. We report that 32 of these TFs have at least one area of enrichment. These data will help better understand aromatic metabolism and other features of N. aromaticivorans biology.
As photoredox catalysis continues to yield promising chemical transformations, there is an increased need to understand how specific photocatalysts function to improve reaction efficiencies while expanding their scope. Copper-phenanthroline-based photocatalysts such as Cu II (dap)Cl 2 (dap = 2,9-di(p-anisyl)-1,10-phenanthroline) and [Cu I (dap) 2 ]Cl were both found to be equally capable of olefin activation through electrophilic atom transfer radical addition (ATRA) reactions. Although these molecular catalysts have proven successful, many intermediates suggested in the proposed catalytic cycles have never been detected. One undetermined aspect in this chemistry is related to how one equivalent of Cu II (dap)Cl 2 generates half of an equivalent of [Cu I (dap) 2 ] + during the photocatalytic sequence. To this end, we initially used more synthetically accessible model systems, namely, [Cu I (dpp) 2 ]Cl and Cu II (dpp)Cl 2 (dpp = 2,9-diphenyl-1,10-phenanthroline), to glean detailed mechanistic insights into this unusual symbiotic relationship. We directly detected several intermediates involved in the ATRA photocatalytic cycle using these model chromophores in conjunction with electronic spectroscopy, infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) mass spectrometry, electronic structure calculations, EPR spin-trap experiments, and 1 H NMR spectroscopy. We found that the unique ligand lability and coordinating properties of acetonitrile enable both the in situ oxidation of [Cu I (dpp) 2 ] + by tosyl chloride into Cu II (dpp)Cl 2 and the visible-light-induced homolysis of the Cu II –Cl bond, which initiates the conversion to the Cu I species [Cu I (dpp) 2 ][Cu I Cl 2 ]. Here, the combined findings from the present study of the catalytic cycle demonstrate that the symbiotic relationship between Cu II (dpp)Cl 2 and [Cu I (dpp) 2 ] + , as well as between Cu II (dap)Cl 2 and [Cu I (dap) 2 ] + , is the critical factor enabling the ATRA photoreaction by departing from either photocatalyst.
Radiative recombination processes can occur in solid-state systems through the pairing of donor and acceptor defects of the lattice. Recently, donor-acceptor pairs (DAP) have been proposed as promising candidates for quantum applications, and their signature has been observed in emerging low-dimensional materials. Therefore, the identification of such processes is gaining interest and requires methods to efficiently and reliably characterize them. Here, we introduce a general algorithm to identify DAP processes starting from the experimental photoluminescence (PL) emission spectrum and basic material parameters, including the lattice structure and dielectric constant. The algorithm recognizes possible DAP transitions from the emission pattern in the spectrum and returns the characteristic energy of the DAP transition and the separation between the donor and acceptor sites. By testing the algorithm on the photoluminescence spectrum of hexagonal boron nitride (hBN), we show that our method is robust against experimental errors and adds new capabilities to the investigation toolbox of semiconductors and their optical properties.
Phosphorus (P) is an essential macronutrient for agriculture, yet global reliance on finite phosphorite reserves raises concerns about long-term food and nutrient security. Struvite (MgNH 4 PO 4 ·6H 2 O), a mineral recovered from municipal wastewater, represents a sustainable and circular source of P, but uncertainty remains regarding its nutrient availability relative to conventional fertilizers. This study evaluated the fertilizer value and environmental safety of electrochemically recovered struvite (RecoP) in comparison with diammonium phosphate (DAP), triple superphosphate (TSP), and rock phosphate (RockP). Nutrient availability, potential contaminant concentrations, and soil P and nitrogen (N) dynamics were assessed using standardized chemical analyses and an 8-week incubation experiment across three soils with contrasting soil types. RecoP contained 14.7% citrate-soluble P, significantly greater than RockP and comparable to DAP and TSP. Across all soils, RecoP increased both readily available and moderately labile P pools (p < 0.01), matching the performance of conventional fast-release fertilizers. Despite containing approximately half the total of DAP, RecoP stimulated nitrification rates that were 2.2 times greater than the control and exceeded those of TSP, suggesting that fertilizer-derived N bioavailability, rather than total N loading, governed microbial N transformation responses. Concentrations of potentially toxic elements in RecoP were consistently well below US Environmental Protection Agency regulatory limits thresholds. Collectively, these results indicate that RecoP functions as a readily available source of both P and N, comparable to widely used conventional fertilizers, while meeting environmental safety standards. RecoP therefore represents a viable component of sustainable nutrient management strategies that support P recycling and agricultural productivity.
The use of a liquid sorbent in a traditional Haber-Bosch process enables significant improvements in energy efficiency and potential cost savings for arguably the most important chemical process on the planet. The approach presented in this report employs an incompressible liquid sorbent that absorbs and releases ammonia (NH 3 ) under specific conditions. To achieve this, we investigate reactions of ammonia and pure phosphoric acid (H 3 PO 4 , PA), which rapidly neutralize to form an equilibrated solution of monoammonium phosphate (MAP) and diammonium phosphate (DAP) that functions as a reversible and regenerable sorbent. Through intimate contact of the gas-phase Haber-Bosch reaction mixture with this liquid absorbent, complete equilibrium uptake may be achieved in an appropriately sized separator, and facile separation occurs through the use of independent liquid and gas phases. Following depressurization and release of the ammonia product, only the incompressible fluid needs to be repressurized and returned to the reactor. This study documents proof-of-concept absorption and desorption experiments carried out in 75 mL batch reactors, predominantly charged with precise MAP and DAP mixtures that equilibrate at process-relevant temperatures and pressures. We then assemble the first thermodynamic relationships that underlie this advantaged separation strategy, validated by reactive force field (ReaxFF) interatomic potential simulations, and benchmarked with traditional separation routes via process modeling and technoeconomic analysis. The scale of energy consumption in the century-old Haber-Bosch process is massive, and the elegant liquid sorption approach reported here offers opportunities to enhance its energy efficiency for the next frontier of ammonia synthesis.
Scenedesmus obliquus UTEX393 is a promising microalgal candidate for sustainable biomanufacturing but its limited halotolerance hinders large-scale cultivation in saline environments. To investigate the molecular basis of salt stress responses, we conducted a comprehensive multi-omic analysis integrating genomics, transcriptomics, proteomics, lipidomics, metabolomics, and DNA affinity purification sequencing (DAP-seq). An improved nuclear genome assembly and annotation yielded 19,017 gene models and a 97% BUSCO completeness score, enabling construction of a genome-scale metabolic model. Comparing 15 ppt salinity stress to 5 ppt control, growth and productivity were significantly reduced, accompanied by widespread transcriptomic and proteomic changes. Transcriptomic analysis revealed downregulation of photosynthetic machinery and energy conservation genes, and upregulation of stress-responsive elements such as expansins, flavodoxins, and osmoprotectants. Lipidomic profiling showed accumulation of triacylglycerols (TAGs) and degradation of galactosyl lipids, consistent with a shift toward lipid biosynthesis to mitigate redox imbalance. Depletion of key polar metabolites and branched-chain amino acids suggested a rerouting of central carbon metabolism under stress. DAP-seq identified key transcription factors, including LHY1 and SPL12, that target central metabolic enzymes involved in redox balancing, such as glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and malate dehydrogenase (MDH). These findings establish a regulatory-metabolic framework linking redox stress to lipid accumulation and reveal potential engineering targets to enhance salt tolerance. Overall, the multi-omic analysis supports the “overflow” hypothesis, where impaired photosynthesis results in excess reducing equivalents being diverted into TAG synthesis and highlights transcriptional regulators as candidates for improving algal robustness in brackish environments.
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.
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.
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.
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.
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.
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.
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.