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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 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Salmonella Typhoid Toxin PltB Subunit and Its Non-typhoidal Salmonella Ortholog Confer Differential Host Adaptation and Virulence

Typhoidal and non-typhoidal Salmonelleae (NTS) cause typhoid fever and gastroenteritis, respectively, in humans. Salmonella typhoid toxin contributes to typhoid disease progression and chronic infection, but little is known about the role of its NTS ortholog. We found that typhoid toxin and its NTS ortholog induce different clinical presentations. The PltB subunit of each toxin exhibits different glycan-binding preferences that correlate with glycan expression profiles of host cells targeted by each bacterium at the primary infection or intoxication sites. Through co-crystal structures of PltB subunits bound to specific glycan receptor moieties, we show that they induce markedly different glycan-binding preferences and virulence outcomes. Furthermore, immunization with the NTS S. Javiana or its toxin offers cross-reactive protection against lethal-dose typhoid toxin challenge. Cumulatively, these results offer insights into the evolution of host adaptations in Salmonella AB toxins, their cell and tissue tropisms, and the design for improved typhoid vaccines and therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The protist Aurantiochytrium has universal subtelomeric rDNAs and is a host for mirusviruses

Viruses are the most abundant biological entities in the world's oceans, where they play important ecological and biogeochemical roles. Metagenomics is revealing new groups of eukaryotic viruses, although disconnected from known hosts. Among these are the recently described mirusviruses, which share some similarities with herpesviruses.50 years ago, "herpes-type" viral particles were found in a thraustochytrid member of the labyrinthulomycetes, a diverse group of abundant and ecologically important marine eukaryotes, but could not be further characterized by methods then available. Long-read sequencing has allowed us to connect the biology of mirusviruses and thraustochytrids. We sequenced the genome of the genetically tractable model thraustochytrid Aurantiochytrium limacinum ATCC MYA-1381 and found that its 26 linear chromosomes have an extraordinary configuration. Subtelomeric ribosomal DNAs (rDNAs) found at all chromosome ends are interspersed with long repeated sequence elements denoted as long repeated-telomere and rDNA spacers (LORE-TEARS). We identified two genomic elements that are related to mirusvirus genomes. The first is a ~300-kbp episome (circular element 1 [CE1]) present at a high copy number. Strikingly, the second, distinct, mirusvirus-like element is integrated between two sets of rDNAs and LORE-TEARS at the left end of chromosome 15 (LE-Chr15). Similar to metagenomically derived mirusviruses, these putative A. limacinum mirusviruses have a virion module related to that of herpesviruses along with an informational module related to nucleocytoplasmic large DNA viruses (NCLDVs). CE1 and LE-Chr15 bear striking similarities to episomal and endogenous latent forms of herpesviruses, respectively, and open new avenues of research into marine virus-host interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Giant virus diversity and host interactions through global metagenomics

Our current knowledge about nucleocytoplasmic large DNA viruses (NCLDVs) is largely derived from viral isolates that are co-cultivated with protists and algae. Here we reconstructed 2,074 NCLDV genomes from sampling sites across the globe by building on the rapidly increasing amount of publicly available metagenome data. This led to an 11-fold increase in phylogenetic diversity and a parallel 10-fold expansion in functional diversity. Analysis of 58,023 major capsid proteins from large and giant viruses using metagenomic data revealed the global distribution patterns and cosmopolitan nature of these viruses. The discovered viral genomes encoded a wide range of proteins with putative roles in photosynthesis and diverse substrate transport processes, indicating that host reprogramming is probably a common strategy in the NCLDVs. Furthermore, inferences of horizontal gene transfer connected viral lineages to diverse eukaryotic hosts. We anticipate that the global diversity of NCLDVs that we describe here will establish giant viruses-which are associated with most major eukaryotic lineages-as important players in ecosystems across Earth's biomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Identification of hidden N4-like viruses and their interactions with hosts

The N4-like viruses, which were recently assigned to the novel viral family Schitoviridae in 2021, belong to a podoviral-like viral lineage and possess conserved genomic characteristics and a unique replication mechanism. Despite their significance, our understanding of N4-like viruses is primarily based on viral isolates. To address this knowledge gap, this study has established a comprehensive N4-like viral data sets comprising 342 high-quality N4-like viruses/proviruses (144 viral isolates, 158 uncultured viruses, and 40 integrated N4-like proviruses). These viruses were classified into 97 subfamilies (89 of which are newly identified), 148 genera (100 of which are newly identified), and 253 species (177 of which are newly identified). The study reveals that N4-like viruses inhibit the polar region, oligotrophic open oceans, and the human gut, where they infect various bacterial lineages, such as Alpha/Beta/Gamma/Epsilon-proteobacteria in the Proteobacteria phylum. Although N4-like viral endogenization appears to be prevalent in Proteobacteria, it has also been observed in Firmicutes. Additionally, the phylogenetic analysis has identified evolutionary divergence within the hallmark genes of N4-like viruses, indicating a complex origin of the different conserved parts of viral genomes. Moreover, 1,101 putative auxiliary metabolic genes (AMGs) were identified in the N4-like viral pan-proteome, which mainly participate in nucleotide and cofactor/vitamin metabolisms. Of these AMGs, 27 were found to be associated with virulence, suggesting their potential involvement in the spread of bacterial pathogenicity. The findings of this study are significant, as N4-like viruses represent a unique viral lineage with a distinct replication mechanism and a conserved core genome. This work has resulted in a comprehensive global map of the entire N4-like viral lineage, including information on their distribution in different biomes, evolutionary divergence, genomic diversity, and the potential for viral-mediated host metabolic reprogramming. As such, this work significantly contributes to our understanding of the ecological function and viral-host interactions of bacteriophages.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Challenges in Firmware Re-Hosting, Emulation, and Analysis

System emulation and firmware re-hosting have become popular techniques to answer various security and performance related questions, such as determining whether a firmware contain security vulnerabilities or meet timing requirements when run on a specific hardware platform. While this motivation for emulation and binary analysis has previously been explored and reported, starting to either work or research in the field is difficult. To this end, we provide a comprehensive guide for the practitioner or system emulation researcher. Here, we layout common challenges faced during firmware re-hosting, explaining successive steps and surveying common tools used to overcome these challenges. We provide classification techniques on five different axes, including emulator methods, system type, fidelity, emulator purpose, and control. These classifications and comparison criteria enable the practitioner to determine the appropriate tool for emulation. We use our classifications to categorize popular works in the field and present 28 common challenges faced when creating, emulating, and analyzing a system from obtaining firmwares to post emulation analysis.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

No evidence of Bartonella infections in host-seeking Ixodes scapularis and Ixodes pacificus ticks in the United States

Background. Bartonella spp. infect a variety of vertebrates throughout the world, with generally high prevalence. Several Bartonella spp. are known to cause diverse clinical manifestations in humans and have been recognized as emerging pathogens. These bacteria are mainly transmitted by blood-sucking arthropods, such as fleas and lice. The role of ticks in the transmission of Bartonella spp. is unclear. Methods. A recently developed quadruplex polymerase chain reaction (PCR) amplicon next-generation sequencing approach that targets Bartonella-specific fragments on gltA, ssrA, rpoB, and groEL was applied to test host-seeking Ixodes scapularis ticks (n=1641; consisting of 886 nymphs and 755 adults) collected in 23 states of the eastern half of the United States and Ixodes pacificus ticks (n=966; all nymphs) collected in California in the western United States for the presence of Bartonella DNA. These species were selected because they are common human biters and serve as vectors of pathogens causing the greatest number of vector-borne diseases in the United States. Results. No Bartonella DNA was detected in any of the ticks tested by any target. Conclusions. Owing to the lack of Bartonella detection in a large number of host-seeking Ixodes spp. ticks tested across a broad geographical region, our results strongly suggest that I. scapularis and I. pacificus are unlikely to contribute more than minimally, if at all, to the transmission of Bartonella spp.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Five key aspects of metaproteomics as a tool to understand functional interactions in host-associated microbiomes

Host-associated microbial communities (microbiomes) play critical roles in human, animal, and plant health and development. However, interactions between the host, members of the microbiome, and invading pathogens are in most cases still poorly understood. Such interactions are multidimensional and can alter the taxonomic composition and/or the functional metabolic activities of the microbiome in response to disease or treatment conditions. For example, after 2 days of antibiotic treatment, the mouse gut microbiome is altered and more susceptible to invasion by the pathogen Clostridioides difficile. Studies of these multidimensional interactions have been fueled by the ability to use high-throughput sequencing of phylogenetic marker genes to profile microbial community composition and shotgun metagenomics to profile functional potential. However, many protein-coding genes predicted from metagenomes are not necessarily expressed under a given condition, and thus, it is difficult to assess the activities and functional interactions in microbial communities based on DNA sequencing data alone. The physiological and pathological processes expressed in these communities under specific conditions are better reflected by the abundances of transcripts or proteins. In this Pearl, we provide a brief introduction to metaproteomics, which is a tool for the large-scale analysis of proteins in microbiomes that allows researchers to address a diversity of questions related to functions and interactions in microbiomes. The term “metaproteomics” was first used in 2004 for “the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time”, and since then, a large array of metaproteomics approaches have been developed. Our objective in this Pearl is to highlight what we feel are 5 essential elements to be considered for a metaproteomics research campaign and to introduce nonexpert readers to the topic without going into too much technical detail.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Electric Vehicle Charging Management in Smart Energy Communities to Increase Renewable Energy Hosting Capacity

Abnormal climates due to global warming have emerged as a big concern in the global community. To mitigate climate change and achieve sustainability, distributed energy resources (DERs), including solar and wind, have been recently deployed in power systems. As the penetration level of DERs has increased, however, it caused a multitude of issues in the power systems, such as voltage fluctuation in the distribution network limiting renewable hosting capacity. On the other hand, the electric vehicle (EV) industry is rapidly growing to facilitate the transition to a carbon-neutral community, illuminating the potential of EVs as a flexible grid asset to mitigate some of the issues and improve grid operation, if properly exploited. To explore the potential of EVs, this paper proposes an EV scheduling strategy. By using an optimal EV charging scheduling proposed, distribution system operators (DSOs) can minimize their operating costs and stably operate the system with a high level of DERs. To validate the method, a modified IEEE 33-bus system with DERs is developed. The case study shows the proposed scheduling strategizes EV charging to reduce the cost of PV curtailment. In the study, the method outperforms the renewable-only case with curtailment by 4.97% in DSO cost. It also demonstrates its potential to increase the renewable hosting capacity by harmonizing EV charging with renewables.

ADVANCED PROPULSION SYSTEMS,POWER TRANSMISSION AND↗
DOE OSTI2022

Evidence of Asexual Overwintering of Melampsora paradoxa and Mapping of Stem Rust Host Resistance in Salix

Melampsora rust is a devastating disease of shrub willow in North America. Previous work has identified Melampsora paradoxa as one of two identified rust species in New York State that infect Salix purpurea and other important Salix host species, however little is known about the population of this rust species in this region. Genotyping-by-sequencing was used to identify single nucleotide polymorphisms (SNPs) and assess population diversity of M. paradoxa isolates collected from three Salix breeding populations in Geneva, NY between 2015 and 2020. Statistical analyses of SNP revealed that all isolates collected were clonally derived even though they were collected across years. In 2020, isolates were collected from stem infections where uredospore pustules were observed, and these isolates were also identical to M. paradoxa collected in previous seasons. These data suggest that M. paradoxa sampled across multiple years overwintered and reproduced asexually and that stem infection is a possible mechanism for overwintering, both of which are novel findings for this rust species. Additionally, field disease ratings were conducted on a S. purpurea × S. suchowensis F 1 breeding population with high disease severity, enabling the discovery of QTL for resistance on chromosomes 1 and 19. Lastly, Colletotrichum salicis was frequently associated with stem rust and may play a role in M. paradoxa stem infection. Together, this work is the first substantial exploration into M. paradoxa population biology, stem infection, and host resistance in Salix.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Modeling Within-Host Dynamics of SARS-CoV-2 Infection: A Case Study in Ferrets

The pre-clinical development of antiviral agents involves experimental trials in animals and ferrets as an animal model for the study of SARS-CoV-2. Here, we used mathematical models and experimental data to characterize the within-host infection dynamics of SARS-CoV-2 in ferrets. We also performed a global sensitivity analysis of model parameters impacting the characteristics of the viral infection. We provide estimates of the viral dynamic parameters in ferrets, such as the infection rate, the virus production rate, the infectious virus proportion, the infected cell death rate, the virus clearance rate, as well as other related characteristics, including the basic reproduction number, pre-peak infectious viral growth rate, post-peak infectious viral decay rate, pre-peak infectious viral doubling time, post-peak infectious virus half-life, and the target cell loss in the respiratory tract. These parameters and indices are not significantly different between animals infected with viral strains isolated from the environment and isolated from human hosts, indicating a potential for transmission from fomites. While the infection period in ferrets is relatively short, the similarity observed between our results and previous results in humans supports that ferrets can be an appropriate animal model for SARS-CoV-2 dynamics-related studies, and our estimates provide helpful information for such studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A Van der Waals Interface Hosting Two Groups of Magnetic Skyrmions

Multiple magnetic skyrmion phases add an additional degree of freedom for skyrmion-based ultrahigh-density spin memory devices. Extending the field to 2D van der Waals magnets is a rewarding challenge, where the realizable degree of freedoms (e.g., thickness, twist angle, and electrical gating) and high skyrmion density result in intriguing new properties and enhanced functionality. In this work, a van der Waals interface, formed by two 2D ferromagnets Cr 2 Ge 2 Te 6 and Fe 3 GeTe 2 with a Curie temperature of ≈65 and ≈205 K, respectively, hosting two groups of magnetic skyrmions, is reported. Two sets of topological Hall effect signals are observed below 6s0 K when Cr 2 Ge 2 Te 6 is magnetically ordered. These two groups of skyrmions are directly imaged using magnetic force microscopy, and supported by micromagnetic simulations. Interestingly, the magnetic skyrmions persist in the heterostructure with zero applied magnetic field. The results are promising for the realization of skyrmionic devices based on van der Waals heterostructures hosting multiple skyrmion phases.

2D magnetism↗
DOE OSTI2023

Polarity‐Driven Atomic Displacements at the 2D Mg 2 TiO 4 ‐MgO (001) Oxide Interface for Hosting Potential Interlayer Excitons

Abstract Interlayer excitons in solid‐state systems have emerged as candidates for realizing novel platforms ranging from excitonic transistors and optical qubits to exciton condensates. Interlayer excitons have been discovered in 2D transition metal dichalcogenides, with large exciton binding energies and the ability to form various van der Waals heterostructures. Here, an oxide system consisting of a single unit cell of Mg 2 TiO 4 on MgO (001) is proposed as a platform for hosting interlayer excitons. Using a combination of density functional theory (DFT) calculations, molecular beam epitaxy growth, and in situ crystal truncation rod measurements, it is shown that the Mg 2 TiO 4 ‐MgO interface can be precisely controlled to yield an internal electric field suitable for hosting interlayer excitons. The atoms in the polar Mg 2 TiO 4 layers are observed to be displaced to reduce polarity at the interface with the non‐polar MgO (001) surface. Such polarity‐driven atomic displacements strongly affect electrostatics of the film and the interface, resulting in localization of filled and empty band‐edge states in different layers of the Mg 2 TiO 4 film. The DFT calculations suggest that the electronic structure is favorable for localization of photoexcited electrons in the bottom layer and holes in the top layer, which may bind to form interlayer exciton states.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Dual-mycorrhizal colonization is determined by plant age and host identity in two species of Populus

Plants have evolved symbioses with mycorrhizal and endophytic fungi that are essential for their growth and survival. While most plants associate with a single guild of mycorrhizal fungi, a select group termed “dual-mycorrhizal plants” associate with both arbuscular mycorrhizal and ectomycorrhizal fungi. Although a shift from predominance of arbuscular mycorrhizal to ectomycorrhizal colonization with plant development has been demonstrated on other dual-mycorrhizal hosts, it is not known how mycorrhizal colonization shifts with plant age in Populus species. We performed a controlled growth experiment with natural field-sourced inocula to test for age-dependent shifts in fungal colonization rates and for host-specific patterns of colonization in two species of Populus (P. tremuloides and P. trichocarpa). We found that only P. trichocarpa displayed dual-mycorrhizal colonization, while P. tremuloides associated with ectomycorrhizal fungi, but not arbuscular mycorrhizal fungi. Both guilds of mycorrhizal fungi increased in abundance with plant age, while root endophytic fungal colonization decreased. Many of the early-colonizing endophytic fungi that we documented have strong saprotrophic capabilities, which may be an important trait for fast colonization. Dark septate endophytes were more abundant than either guild of mycorrhizal fungi, and are likely to be functionally important members of the Populus root fungal community. Our findings represent a novel pattern in the development of dual-mycorrhizal colonization and illustrate that Populus species vary in their association with arbuscular mycorrhizal fungi. In conclusion, our results also highlight the importance of dark septate endophyte colonization dynamics on dual-mycorrhizal plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Quartz-hosted inclusions and embayments reveal storage, fluxing, and ascent of the Mesa Falls Tuff, Yellowstone

Quartz-hosted glasses from the Mesa Falls Tuff provide a geochemical window into the pre-eruptive magmatic system from one of Yellowstone's largest-volume caldera-forming eruptions. H 2 O and CO 2 concentrations, along with major and trace elements, were measured in both fully enclosed glass inclusions and partially enclosed embayments in the same quartz crystals. Major elements are largely consistent between the inclusions and embayments, except for K 2 O and Na 2 O. Of note, K 2 O is enriched by ~1 wt.% in embayment interiors relative to inclusions. Most trace elements are also enriched in the embayment interiors compared to inclusions from the same crystals. Fractionation trends of trace elements are consistent with ~30-60% crystallization. Quartz-hosted glass inclusions preserve 3.1±0.9 wt.% H 2 O and 493±227 ppm CO 2 whereas embayment interiors have 0.9±0.1 wt.% H 2 O and 399±229 ppm CO 2 . The CO 2 is roughly similar, but the distinct ~2 wt.% discrepancy between inclusion and embayment interior H 2 O contents may have been produced by CO 2 fluxing sourced from underplated Yellowstone basalts. H 2 O gradients within embayments are flat in their interiors and modified by sharp positive gradients near embayment exteriors which were produced by post-eruptive rehydration. CO 2 gradients occur as gently sloping concentration gradients that extend inward 150 to 250 μm from the embayment exterior. Finally, finite-difference 1D and 2D diffusion modeling indicates the distribution of H 2 O and CO 2 in embayments was produced by slow, fluid-saturated decompression that preceded rapid ascent during the caldera-forming eruption.

2D diffusion modeling↗
DOE OSTI2023

Protecting groups in insertion chemistry: Site-selective positioning of lithium ions in intercalation hosts

The expanding toolbox of functionalization chemistries for selectively installing moieties on specific sites of a substrate underpins almost all modern organic and biochemical syntheses. Likewise, the installation of mobile guest ions in specific interstitial sites and their transport along specific diffusion pathways forms the basis of modern lithium (Li)-ion battery electrodes. Many insertion hosts afford a diverse range of accessible interstitial sites. However, site-selective positioning of cations with atomic precision remains almost entirely unexplored. Here, we show that by deciphering site preferences of co/pre-intercalated cations, we can position Li ions in four distinct sites within a 1D ζ-V 2 O 5 insertion host. The use of topochemistry to effect single-crystal-to-single-crystal transformations enables atomic-resolution mapping of the selective positioning of Li ions through single-crystal X-ray diffraction. Here we image interstitial sites that are occupied at high depths of discharge, thereby obtaining unprecedented structural insight into “fully stuffed” frameworks critical for the realization of high-energy-density intercalation electrodes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Dynamic Control of Photocatalytic Proton Reduction through the Mechanical Actuation of a Hydrogel Host Matrix

This paper describes a photocatalytic hydrogen evolution system that is dynamically and reversibly responsive to the pH of the surrounding solution through actuation of a micro-hydrogel (microgel) matrix that hosts the photocatalysts (CdSe/CdS nanorods). Here, the reversible actuation occurs within 0.7 s (swelling) and 1.7 s (contraction). A ΔpH of 0.01 relative to the pK a of the tertiary amine on the microgel polymer (7.27) results in a reversible change in the average diameter of the microgel hosts by a factor of 2.5 and a change in the photocatalytic turnover frequency (TOF) by a factor of five. Kinetic isotope effect and photoluminescence quenching experiments reveal that the scavenging of the photoexcited hole by sulfite ions is the rate-limiting step and leads to the observed response of the TOF to pH through actuation of the microgel. Molecular dynamics simulations quantify a greater local concentration of sulfite hole scavengers for pH < pK a .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Beyond Duality: Rationalizing Repulsive Coulomb Barriers in Host–Guest Cyclodextrin–Dodecaborate Complexes

The repulsive Coulomb barrier (RCB), an intrinsic potential energy barrier along electron detachment or charge-separation coordinates in multiply charged anions (MCAs), provides dynamic stability to MCAs whose electronic and thermodynamic stabilities are largely dictated by strong internal Coulomb repulsions. Spectroscopic and theoretical characterizations of the RCB have been focused on isolated MCAs. In this work, we extend the RCB investigation beyond the previous scope by including noncovalent host–guest cyclodextrin-closo-dodecaborate dianionic complexes χCD·B 12 X 12 2– (χ = α, β, γ; X = H, F–I). Here, photodechment photoelectron spectroscopy reveals the existence of two distinctly different RCBs, derived from detaching electrons from the guest dianions (RCB 1 ) or ionizing the host neutrals (RCB 2 ), respectively, with the latter being substantially smaller than the former. In conclusion, theoretical calculations support the duality of RCBs in these complexes and further exhibit highly anisotropic nature of the RCBs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

SARS-CoV-2 M pro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals

The main protease of SARS-CoV-2 (M pro ) is the most promising drug target against coronaviruses due to its essential role in virus replication. With newly emerging variants there is a concern that mutations in M pro may alter the structural and functional properties of protease and subsequently the potency of existing and potential antivirals. We explored the effect of 31 mutations belonging to 5 variants of concern (VOCs) on catalytic parameters and substrate specificity, which revealed changes in substrate binding and the rate of cleavage of a viral peptide. Crystal structures of 11 M pro mutants provided structural insight into their altered functionality. Additionally, we show M pro mutations influence proteolysis of an immunomodulatory host protein Galectin-8 (Gal-8) and a subsequent significant decrease in cytokine secretion, providing evidence for alterations in the escape of host-antiviral mechanisms. Accordingly, mutations associated with the Gamma VOC and highly virulent Delta VOC resulted in a significant increase in Gal-8 cleavage. Importantly, IC50s of nirmatrelvir (Pfizer) and our irreversible inhibitor AVI-8053 demonstrated no changes in potency for both drugs for all mutants, suggesting M pro will remain a high-priority antiviral drug candidate as SARS-CoV-2 evolves.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗