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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 OSTI2026

Nanopore Readable Activity Probes for Ribosomal Inactivating Protein (RIP) Toxins

Ribosome inactivating proteins (RIPs) such as ricin and abrin depurinate an adenine base in the sarcin/ricin loop in the large ribosomal subunit, leading to inhibtion of protein synthesis and cell death. Here, we demonstrate that RIP toxin activity can be detected via nanopore-based DNA sequencing using synthetic oligonucleotide substrates. This is achieved by monitoring the mismatch proportion at the canonical target sequences incorporated into the synthetic substrate and determining the sequence length distribution throughout the entire substrate sequence. The mismatch proportion increases and sequence length distribution decreases with increasing toxin concentration for both ricin and abrin in buffer as well as in more complex backgrounds such as saliva and nasal secretions.

Turner, Matthew W [Pacific Northwest National Labo↗
DOE OSTI2022

Genome sequence, phylogenetic analysis, and structure-based annotation reveal metabolic potential of Chlorella sp. SLA-04

Algae are a broad class of photosynthetic eukaryotes that are phylogenetically and physiologically diverse. Most of the phylogenetic diversity has been inferred from 18S rDNA sequencing since there are only a few complete genomes available in public databases. Here we use ultra-long-read Nanopore sequencing to determine a gapless, telomere-to-telomere complete genome sequence of Chlorella sp. SLA-04, previously described as Chlorella sorokiniana SLA-04. Chlorella sp. SLA-04 is a green alga that grows to high cell density in a wide variety of environments - high and neutral pH, high and low alkalinity, and high and low salinity. SLA-04's ability to grow in high pH and high alkalinity media without external CO 2 supply is favorable for large-scale algal biomass production. Phylogenetic analysis performed using ribosomal DNA and conserved protein sequences consistently reveal that Chlorella sp. SLA-04 forms a distinct lineage from other strains of Chlorella sorokiniana. We complement traditional genome annotation methods with high throughput structural predictions and demonstrate that this approach expands functional prediction of the SLA-04 proteome. Genomic analysis of the SLA-04 genome identifies the genes capable of utilizing TCA cycle intermediates to replenish cytosolic acetyl-CoA pools for lipid production. We also identify a complete metabolic pathway for sphingolipid anabolism that may allow SLA-04 to readily adapt to changing environmental conditions and facilitate robust cultivation in mass production systems. Altogether, this work clarifies the phylogeny of Chlorella sp. SLA-04 within Trebouxiophyceae and demonstrates how structural predictions can be used to improve annotation beyond sequencebased methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Single-nuclei transcriptome analysis of the shoot apex vascular system differentiation in Populus

ABSTRACT Differentiation of stem cells in the plant apex gives rise to aerial tissues and organs. Presently, we lack a lineage map of the shoot apex cells in woody perennials – a crucial gap considering their role in determining primary and secondary growth. Here, we used single-nuclei RNA-sequencing to determine cell type-specific transcriptomes of the Populus vegetative shoot apex. We identified highly heterogeneous cell populations clustered into seven broad groups represented by 18 transcriptionally distinct cell clusters. Next, we established the developmental trajectories of the epidermis, leaf mesophyll and vascular tissue. Motivated by the high similarities between Populus and Arabidopsis cell population in the vegetative apex, we applied a pipeline for interspecific single-cell gene expression data integration. We contrasted the developmental trajectories of primary phloem and xylem formation in both species, establishing the first comparison of vascular development between a model annual herbaceous and a woody perennial plant species. Our results offer a valuable resource for investigating the principles underlying cell division and differentiation conserved between herbaceous and perennial species while also allowing us to examine species-specific differences at single-cell resolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Machine learning reveals sequence-function relationships in family 7 glycoside hydrolases

Family 7 glycoside hydrolases (GH7) are among the principal enzymes for cellulose degradation in nature and industrially. These important enzymes are often bimodular, including a catalytic domain and carbohydrate binding module (CBM) attached via a flexible linker, and exhibit an active site that binds cello-oligomers of up to ten glucosyl moieties. GH7 cellulases consist of two major subtypes: cellobiohydrolases (CBH) and endoglucanases (EG). Despite the critical importance of GH7 enzymes, there remain gaps in our understanding of how GH7 sequence and structure relate to function. Here, we employed machine learning to gain data-driven insights into relationships between sequence, structure, and function across the GH7 family. Machine-learning models, trained only on the number of residues in the active-site loops as features, were able discriminate GH7 CBHs and EGs with up to 99% accuracy, demonstrating that the lengths of loops A4, B2, B3, and B4 strongly correlate with functional subtype across the GH7 family. Classification rules were derived such that specific residues at 42 different sequence positions each predicted the functional subtype with accuracies surpassing 87%. A random forest model trained on residues at 19 positions in the catalytic domain predicted the presence of a CBM with 89.5% accuracy. Our ML results recapitulate, as top-performing features, a substantial number of the sequence positions determined by previous experimental studies to play vital roles in GH7 activity. We surmise that the yet-to-be-explored sequence positions among the top-performing features also contribute to GH7 functional variation and may be exploited to understand and manipulate function.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Structural basis of divergent substrate recognition and inhibition of human neurolysin

A zinc metallopeptidase neurolysin (Nln) processes diverse bioactive peptides to regulate signaling in the mammalian nervous system. To understand how Nln interacts with various peptides with dissimilar sequences, we determined crystal structures of Nln in complex with diverse peptides including dynorphins, angiotensin, neurotensin, and bradykinin. The structures show that Nln binds these peptides in a large dumbbell-shaped interior cavity constricted at the active site, making minimal structural changes to accommodate different peptide sequences. The structures also show that Nln readily binds similar peptides with distinct registers, which can determine whether the peptide serves as a substrate or a competitive inhibitor. We analyzed the activities and binding of Nln toward various forms of dynorphin A peptides, which highlights the promiscuous nature of peptide binding and shows how dynorphin A (1–13) potently inhibits the Nln activity while dynorphin A (1–8) is efficiently cleaved. Our work provides insights into the broad substrate specificity of Nln and may aid in the future design of small molecule modulators for Nln.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Mapping the determinants of catalysis and substrate specificity of the antibiotic resistance enzyme CTX-M β-lactamase

Abstract CTX-M β-lactamases are prevalent antibiotic resistance enzymes and are notable for their ability to rapidly hydrolyze the extended-spectrum cephalosporin, cefotaxime. We hypothesized that the active site sequence requirements of CTX-M-mediated hydrolysis differ between classes of β-lactam antibiotics. Accordingly, we use codon randomization, antibiotic selection, and deep sequencing to determine the CTX-M active-site residues required for hydrolysis of cefotaxime and the penicillin, ampicillin. The study reveals positions required for hydrolysis of all β-lactams, as well as residues controlling substrate specificity. Further, CTX-M enzymes poorly hydrolyze the extended-spectrum cephalosporin, ceftazidime. We further show that the sequence requirements for ceftazidime hydrolysis follow those of cefotaxime, with the exception that key active-site omega loop residues are not required, and may be detrimental, for ceftazidime hydrolysis. These results provide insights into cephalosporin hydrolysis and demonstrate that changes to the active-site omega loop are likely required for the evolution of CTX-M-mediated ceftazidime resistance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Transcriptome analysis and immune gene expression of channel catfish ( Ictalurus punctatus ) fed diets with inclusion of frass from black soldier fly larvae

The larval waste, exoskeleton shedding, and leftover feed components of the black soldier fly and its larvae make up the by-product known as frass. In this study, we subjected channel catfish (Ictalurus punctatus) to a 10-week feeding trial to assess how different dietary amounts of frass inclusion would affect both systemic and mucosal tissue gene expression, especially in regard to growth and immune-related genes. Fish were divided in quadruplicate aquaria, and five experimental diets comprising 0, 50, 100, 200, and 300 g of frass per kilogram of feed were fed twice daily. At the end of the trial, liver, head kidney, gill, and intestine samples were collected for gene expression analyses. First, liver and intestine samples from fish fed with a no frass inclusion diet (control), low-frass (50 g/kg) inclusion diet, or a high-frass (300 g/kg) inclusion diet were subjected to Illumina RNA sequencing to determine global differential gene expression among diet groups. Differentially expressed genes (DEGs) included the upregulation of growth-related genes such as glucose-6-phosphatase and myostatin, as well as innate immune receptors and effector molecules such as toll-like receptor 5, apolipoprotein A1, C-type lectin, and lysozyme. Based on the initial screenings of low/high frass using RNA sequencing, a more thorough evaluation of immune gene expression of all tissues sampled, and all levels of frass inclusion, was further conducted. Using targeted quantitative PCR panels for both innate and adaptive immune genes from channel catfish, differential expression of genes was identified, which included innate receptors (TLR1, TLR5, TLR9, and TLR20A), proinflammatory cytokines (IL-1β type a, IL-1β type b, IL-17, IFN-γ, and TNFα), chemokines (CFC3 and CFD), and hepcidin in both systemic (liver and head kidney) and mucosal (gill and intestine) tissues. Overall, frass from black soldier fly larvae inclusion in formulated diets was found to alter global gene expression and activate innate and adaptive immunity in channel catfish, which has the potential to support disease resistance in this species in addition to demonstrated growth benefits.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural insights into plasmalemma vesicle-associated protein (PLVAP): Implications for vascular endothelial diaphragms and fenestrae

In many organs, small openings across capillary endothelial cells (ECs) allow the diffusion of low–molecular weight compounds and small proteins between the blood and tissue spaces. These openings contain a diaphragm composed of radially arranged fibers, and current evidence suggests that a single-span type II transmembrane protein, plasmalemma vesicle-associated protein-1 (PLVAP), constitutes these fibers. Here, we present the three-dimensional crystal structure of an 89-amino acid segment of the PLVAP extracellular domain (ECD) and show that it adopts a parallel dimeric alpha-helical coiled-coil configuration with five interchain disulfide bonds. The structure was solved using single-wavelength anomalous diffraction from sulfur-containing residues (sulfur SAD) to generate phase information. Biochemical and circular dichroism (CD) experiments show that a second PLVAP ECD segment also has a parallel dimeric alpha-helical configuration—presumably a coiled coil—held together with interchain disulfide bonds. Overall, ~2/3 of the ~390 amino acids within the PLVAP ECD adopt a helical configuration, as determined by CD. We also determined the sequence and epitope of MECA-32, an anti-PLVAP antibody. Taken together, these data lend strong support to the model of capillary diaphragms formulated by Tse and Stan in which approximately ten PLVAP dimers are arranged within each 60- to 80-nm-diameter opening like the spokes of a bicycle wheel. Passage of molecules through the wedge-shaped pores is presumably determined both by the length of PLVAP—i.e., the long dimension of the pore—and by the chemical properties of amino acid side chains and N-linked glycans on the solvent-accessible faces of PLVAP.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Systems and methods for single-axis tracking via sky imaging and machine leanring comprising a neural network to determine an angular position of a photovoltaic power system

A system and method is disclosed for solar tracking and controlling an angular position of a photovoltaic power system. The solar tracking system includes an imaging device for capturing images of the sky; a solar position data generating module; and a control system comprising a neural network. The neural network has multiple convolutional layers to generate a first output associated with the images, and a solar position data module. A first dense layer module receives the solar position data and generates a second output. A second dense layer module receives the first output and the second output and generates a concatenated data sequence. A processor is programmed to generate a multi-planar irradiance signal (MPIS) in response to the concatenated data sequence, and determine an angular position of the PV power system and adjust the angular position in response to an angle of maximum irradiance.

Stein, Joshua↗
DOE OSTI2025

Hybridization capture sequencing for Vibrio spp. and associated virulence factors

ABSTRACT Proliferation ofVibriospp. in aquatic ecosystems is associated with climate change and, concomitantly, increased incidence of vibriosis. They are autochthonous to aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenicVibriospp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing (HCS) was employed to profile low-abundanceVibriospp. in environmental samples. The HCS panel targeted a family of molecular chaperones (CPN60) specific to 69Vibriospp. and 162Vibrio-specific virulence factors. This approach was evaluated in parallel with traditional whole-community shotgun sequencing in a metagenomic analysis of water and oyster samples collected from the Chesapeake Bay. In addition,Vibrio parahaemolyticusandVibrio vulnificusstrains isolated from the samples were subjected to whole-genome sequencing to determine the genetic characteristics of pathogenicVibriospp. circulating in an aquatic environment. HCS, employed to determine the incidence and characterization of specificVibriospp., yielded significantly greater metagenomic insight, notably a variety of otherVibriospp., including detection ofVibrio cholerae,Vibrio fluvialis, andVibrio aestuarianus, in addition toVibrio parahaemolyticusandVibrio vulnificus, and also important virulence factors not detectable using traditional molecular methods. Thus, pathogenicVibriospp. in aquatic ecosystems may be far more common than currently understood. It is concluded that environmental surveillance should include HCS, a valuable tool for the detection and characterization of pathogenic agents in aquatic ecosystems, notably vibrios. IMPORTANCE The increasing prevalence of pathogenicVibriospp. in aquatic ecosystems, driven by climate change, is closely linked to a rise in cholera and vibriosis cases, emphasizing the need for improved environmental surveillance. Vibrios are naturally occurring in aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenicVibriospp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing was employed to profile low-abundanceVibriospp. in metagenomic samples, namely water and oysters collected from the Chesapeake Bay. This approach was evaluated in parallel with traditional whole-community shotgun sequencing and whole-genome sequencing ofVibrio parahaemolyticusandVibrio vulnificusstrains isolated from the samples. Results suggest pathogenicVibriospp. in aquatic ecosystems may be far more common than currently understood, when multiple methods are considered for environmental surveillance.

Microbiology↗
DOE OSTI2026

Surface Reordering During Layer‐by‐Layer Growth on SrTiO 3

With the development of layer‐by‐layer growth techniques such as molecular beam epitaxy (MBE), it is now possible to construct materials with atomic‐level precision, with the layer sequence primarily determined by the growth recipe. However, materials can still restructure in the high‐temperature growth environment with surface thermodynamics strongly influencing growth behavior. Here, we demonstrate that growth on ${\rm SrTiO}_{3}$ (001), the principal platform for oxide electronics, does not occur in a layer‐by‐layer fashion but follows a more complex process in which a ${\rm TiO}_{2}$ plane continually diffuses toward the growth surface. Employing in situ synchrotron X‐ray scattering combined with ab initio thermodynamic calculations, we discover the existence of a stable ${\rm TiO}_{2}$ double‐layer structure on the pristine substrate and the occurrence of dynamic layer rearrangement during homoepitaxial growth by oxide MBE. Our findings suggest that the current methods used to precisely control ${\rm SrTiO}_{3}$ surfaces are limited, as well as our ability to dictate the composition of ultrathin films, resulting in important ramifications regarding the surface reactivity of perovskite materials grown on ${\rm SrTiO}_{3}$.

Coherent Bragg Rod Analysis↗
DOE OSTI2023

Exploring novel HIV ‐1 reverse transcriptase inhibitors with drug‐resistant mutants: A double mutant surprise

Abstract HIV‐1 reverse transcriptase (RT) remains a key target for HIV drug development. As successful management of the disease requires lifelong treatment, the emergence of resistance mutations is inevitable, making development of new RT inhibitors, which remain effective against resistant variants crucial. To this end, previous computationally guided drug design efforts have resulted in catechol diether compounds, which inhibit wildtype RT with picomolar affinities and appear to be promising preclinical candidates. To confirm that these compounds remain potent against Y181C, a widespread mutation conferring resistance to first generation inhibitors, they were screened against the HIV‐1 N119 clinical isolate, reported as a Y181C single mutant. In comparison to a molecular clone with the same mutation, N119 appears less susceptible to inhibition by our preclinical candidate compounds. A more detailed sequencing effort determined that N119 was misidentified and carries V106A in combination with Y181C. While both indolizine and naphthalene substituted catechol diethers are potent against the classical Y181C single mutant, the addition of V106A confers more resistance against the indolizine derivatives than the naphthalene derivatives. Crystal structures presented in this study highlight key features of the naphthyl group, which allow these compounds to remain potent in the double mutant, including stronger interactions with F227 and less reliance on V106 for stabilization of the ethoxy‐uracil ring, which makes critical hydrogen bonds with other residues in the binding pocket.

Biochemistry & Molecular Biology↗
DOE OSTI2025

Physics-Informed Neural Networks for PDE-Constrained Optimization and Control

The goal of optimal control is to determine a sequence of inputs for maximizing or minimizing a given performance criterion subject to the dynamics and constraints of the system under observation. This work introduces Control Physics-Informed Neural Networks (PINNs), which simultaneously learn both the system states and the optimal control signal in a single-stage framework that leverages the system’s underlying physical laws. While prior approaches often follow a two-stage process-modeling, the system first and then devising its control—the presented novel framework embeds the necessary optimality conditions directly into the network architecture and loss function. We demonstrate the effectiveness of the novel methodology by solving various open-loop optimal control problems governed by analytical, one-dimensional, and two-dimensional partial differential equations (PDEs).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Geometry-independent microstructure optimization for electron beam powder bed fusion additive manufacturing

The ability to manipulate the formation of microstructure is one of the potential advantages of additive manufacturing. Yet, the additive manufacturing process is riddled with complex interactions between processing parameters, geometry, and spot melting sequence which makes the task of controlling microstructure challenging. This paper proposes a method to solve the microstructure texture optimization problem by leveraging established optimization techniques and increasingly fast and accurate analytical heat transfer models. Respectively, we apply two different optimization algorithms, genetic algorithm and concurrent greedy line search, in order to induce arbitrarily shaped microstructure regions and we use a heat transfer model to evaluate the fitness of solutions in an iterative approach that is far more efficient than pure trial and error. The objective of the optimization algorithm is to control local thermal conditions – hence microstructure formation – during the melting process by manipulating the order and the dwell time of all the points of the infill pattern sequence. We then analyze the optimized sequence to determine important path characteristics that affect the microstructure formation. Through examples, we show that relative order and frequency, as measured by weighted average and variance of spot order, are important factors that influence the final characteristics.

36 MATERIALS SCIENCE↗
DOE OSTI2021

A comprehensive analysis of transient pressure and rate data from CO 2 storage projects in a depleted pinnacle reef oil field complex, Michigan, USA

Pressure and rate data are commonly recorded as part of a basic monitoring program in CCS projects. This paper discusses the application of multiple analytical techniques to interpret pressure and rate transient data from CO 2 injection and storage operations. The techniques of interest, i.e., injection-falloff analysis, injectivity/productivity index analysis and pressure pulse arrival time analysis, are commonly used in the oil and gas industry to assess reservoir properties, but not well known in the CCS literature (especially the last two). Injection-falloff analysis involves log-log pressure derivative plotting for the falloff data and history-matching of the entire injection-falloff sequence to determine permeability. In the injectivity/productivity index analysis, rate-normalized pressure buildup is plotted against material balance time or ratio of cumulative injection to injection rate to determine the injectivity index (ratio of injection rate to stabilized pressure buildup) which can be related to the permeability-thickness product. The arrival time analysis identifies the arrival of a pressure disturbance (~0.1 psi change from ambient) to determine the hydraulic diffusivity from which permeability can be estimated. The applicability of these techniques is demonstrated via illustrative examples from multiple wells in different pinnacle carbonate reefs undergoing CO 2 -EOR in Northern Michigan. The paper ends with a discussion of the relative merits of each interpretive technique, as well as recommendations that could be useful for other field projects.

42 ENGINEERING↗
DOE OSTI2026

Selectivity mechanisms of ion intercalation in Prussian blue analogs

Prussian blue analogs (PBAs) are a family of materials with facile, reversible, and selective ion transport capability for various ions via electrochemical intercalation, owing to their vacancy structure. The large tunable compositional space of PBAs allows for manipulation of intercalation behavior and selectivity by controlling structural vacancy level through choice of transition metal centers and modifications to the synthesis process. However, a lack of understanding of the mechanisms of ion selectivity hinders the material’s design process. Here, for this work, we investigated the origins of ion selectivity using a model PBA, copper hexacyanoferrate, and focused on eight technologically and biologically prominent ions, for which we determined a sequence of selectivity: Rb + > K + > Na + > Ba 2+ > Sr 2+ ≈ Ca 2+ > Mg 2+ > Li + . We provide electrochemical, structural, and redox evidence of strong correlation between the ion identity, the dominant charge-compensating redox, and preferred occupancy site. Specifically, using synchrotron anomalous X-ray diffraction (AXRD), we reveal that monovalent ions exhibit significant association with the corner sites of the unit cell and iron redox, whereas divalent ions display affinity toward the center site with higher ratios of copper redox. Informed by selectivity results, we applied CuHCFe to Li purification and achieved 99.9% purity. Our findings demonstrate an approach to elucidating ion intercalation behavior in order to distinguish and manipulate material properties to optimize separation performance.

Prussian blue analog↗
DOE OSTI2023

Layer-engineered interlayer charge transfer in WSe 2 /WS 2 heterostructures

The layer thickness determines the electronic structure of two-dimensional (2D) materials, leading to different band alignments, which are crucial for the transition metal dichalcogenides heterostructures. Here, we investigated the heterostructure of WSe 2 /WS 2 with different layer thicknesses by steady-state and transient absorption spectroscopy. We observed different ultrafast charge transfer behaviors in 1L-WSe 2 /2L-WS 2 and 2L-WSe 2 /2L-WS 2 few-layer heterostructures. We demonstrate that the layer thickness determines the sequence of intralayer exciton relaxation and interlayer charge transfer. The valley transfer of the band edge induced by the layer thickness can effectively mediate the hot carrier transfer time and interlayer exciton lifetime. Furthermore, these provide us a deeper understanding of carrier dynamics in 2D indirect bandgap semiconductor heterostructures.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

Taxonomic and functional restoration of tallgrass prairie soil microbial communities in comparison to remnant and agricultural soils

Abstract Restoring ecosystems requires the re-establishment of diverse soil microbial communities that drive critical ecosystem functions. In grasslands, restoration and management require the application of disturbances like fire and grazing. Disturbances can shape microbial taxonomic composition and potentially functional composition as well. We characterized taxonomic and functional gene composition of soil communities using whole genome shotgun metagenomic sequencing to determine how restored soil communities differed from pre-restoration agricultural soils and original remnant soils, how management affects soil microbes, and whether restoration and management affect the number of microbial genes associated with carbohydrate degradation. We found distinct differences in both taxonomic and functional diversity and composition among restored, remnant, and agricultural soils. Remnant soils had low taxonomic and functional richness and diversity, as well as distinct composition, indicating that restoration of agricultural soils does not re-create soil microbial communities that match remnants. Prescribed fire management increased functional diversity, which also was higher in more recently planted restorations. Finally, restored and post-fire soils included high abundances of genes encoding cellulose-degrading enzymes, so restorations and their ongoing management can potentially support functions important in carbon cycling.

Mason, Cayla N. (ORCID:0000000345983824)↗