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At least 739 records · Page 41
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Influence of Carbon-Nitride Dot-Emitting Species and Evolution on Fluorescence-Based Sensing and Differentiation

Carbon dots have attracted widespread interest for sensing applications based on their low cost, ease of synthesis, and robust optical properties. We investigate structure–function evolution on multiemitter fluorescence patterns for model carbon-nitride dots (CNDs) and their implications on trace-level sensing. Hydrothermally synthesized CNDs with different reaction times were used to determine how specific functionalities and their corresponding fluorescence signatures respond upon the addition of trace-level analytes. Archetype explosives molecules were chosen as a testbed due to similarities in substituent groups or inductive properties (i.e., electron withdrawing), and solution-based assays were performed using ratiometric fluorescence excitation–emission mapping (EEM). Analyte-specific quenching and enhancement responses were observed in EEM landscapes that varied with the CND reaction time. We then used self-organizing map models to examine EEM feature clustering with specific analytes. Finally, the results reveal that interactions between carbon-nitride frameworks and molecular-like species dictate response characteristics that may be harnessed to tailor sensor development for specific applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Bridging the Flux Gap: Sap Flow Measurements Reveal Species-Specific Patterns of Water Use in a Tallgrass Prairie

Woody encroachment, the process through which woody plants (trees and shrubs) replace grasses and wildflowers in grassland ecosystems, is occurring globally. Because woody plants use water differently (e.g., rates, soil depths of uptake, and time periods of activity) than grasses, woody encroachment could potentially change the water cycle in grasslands. In order to understand how grassland water use might change with ongoing woody encroachment, we measured continuous rates of water loss in common plant species in a North American grassland. Furthermore, we found that the main encroaching shrub in this grassland used more water over time than grasses or wildflowers. Additionally, this shrub and grasses used a large amount of water at night compared to wildflowers. Finally, we found that different weather conditions had different impacts on how water was used by woody plants, grasses, and wildflowers. We suggest that woody encroachment might reduce the amount of water stored in grasslands, which could alter the composition of grassland plants in the future.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Cave Thiovulum ( Candidatus Thiovulum stygium) differs metabolically and genomically from marine species

Thiovulum spp. (Campylobacterota) are large sulfur bacteria that form veil-like structures in aquatic environments. The sulfidic Movile Cave (Romania), sealed from the atmosphere for ~5 million years, has several aqueous chambers, some with low atmospheric O 2 (~7%). The cave’s surface-water microbial community is dominated by bacteria we identified as Thiovulum. We show that this strain, and others from subsurface environments, are phylogenetically distinct from marine Thiovulum. We assembled a closed genome of the Movile strain and confirmed its metabolism using RNAseq. We compared the genome of this strain and one we assembled from public data from the sulfidic Frasassi caves to four marine genomes, including Candidatus Thiovulum karukerense and Ca. T. imperiosus, whose genomes we sequenced. Despite great spatial and temporal separation, the genomes of the Movile and Frasassi Thiovulum were highly similar, differing greatly from the very diverse marine strains. We concluded that cave Thiovulum represent a new species, named here Candidatus Thiovulum stygium. Based on their genomes, cave Thiovulum can switch between aerobic and anaerobic sulfide oxidation using O 2 and NO 3 - as electron acceptors, the latter likely via dissimilatory nitrate reduction to ammonia. Thus, Thiovulum is likely important to both S and N cycles in sulfidic caves. Electron microscopy analysis suggests that at least some of the short peritrichous structures typical of Thiovulum are type IV pili, for which genes were found in all strains. These pili may play a role in veil formation, by connecting adjacent cells, and in the motility of these exceptionally fast swimmers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Operando Raman spectroscopy uncovers hydroxide and CO species enhance ethanol selectivity during pulsed CO 2 electroreduction

Pulsed CO 2 electroreduction (CO 2 RR) has recently emerged as a facile way to in situ tune the product selectivity, in particular toward ethanol, without re-designing the catalytic system. However, in-depth mechanistic understanding requires comprehensive operando time-resolved studies to identify the kinetics and dynamics of the electrocatalytic interface. Here, we track the adsorbates and the catalyst state of pre-reduced Cu 2 O nanocubes (~30 nm) during pulsed CO 2 RR using sub-second time-resolved operando Raman spectroscopy. By screening a variety of product-steering pulse length conditions, we unravel the critical role of co-adsorbed OH and CO on the Cu surface next to the oxidative formation of Cu-O ad or CuO x /(OH) y species, impacting the kinetics of CO adsorption and boosting the ethanol selectivity. However, a too low OH ad coverage following the formation of bulk-like Cu 2 O induces a significant increase in the C 1 selectivity, while a too high OH ad coverage poisons the surface for C-C coupling. Thus, we unveil the importance of co-adsorbed OH on the alcohol formation under CO 2 RR conditions and thereby, pave the way for improved catalyst design and operating conditions.

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

Active species in chloroaluminate ionic liquids catalyzing low-temperature polyolefin deconstruction

Abstract Chloroaluminate ionic liquids selectively transform (waste) polyolefins into gasoline-range alkanes through tandem cracking-alkylation at temperatures below 100 °C. Further improvement of this process necessitates a deep understanding of the nature of the catalytically active species and the correlated performance in the catalyzing critical reactions for the tandem polyolefin deconstruction with isoalkanes at low temperatures. Here, we address this requirement by determining the nuclearity of the chloroaluminate ions and their interactions with reaction intermediates, combining in situ 27 Al magic-angle spinning nuclear magnetic resonance spectroscopy, in situ Raman spectroscopy, Al K-edge X-ray absorption near edge structure spectroscopy, and catalytic activity measurement. Cracking and alkylation are facilitated by carbenium ions initiated by AlCl 3 - tert -butyl chloride (TBC) adducts, which are formed by the dissociation of Al 2 Cl 7 − in the presence of TBC. The carbenium ions activate the alkane polymer strands and advance the alkylation cycle through multiple hydride transfer reactions. In situ 1 H NMR and operando infrared spectroscopy demonstrate that the cracking and alkylation processes occur synchronously; alkenes formed during cracking are rapidly incorporated into the carbenium ion-mediated alkylation cycle. The conclusions are further supported by ab initio molecular dynamics simulations coupled with an enhanced sampling method, and model experiments using n-hexadecane as a feed.

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

Adsorption space for microporous polymers with diverse adsorbate species

Abstract The enormous number of combinations of adsorbing molecules and porous materials that exist is known as adsorption space. The adsorption space for microporous polymers has not yet been systematically explored, especially when compared with efforts for crystalline adsorbents. We report molecular simulation data for the adsorptive and structural properties of polymers of intrinsic microporosity with a diverse set of adsorbate species with 345 distinct adsorption isotherms and over 240,000 fresh and swollen structures. These structures and isotherms were obtained using a sorption-relaxation technique that accounts for the critical role of flexibility of the polymeric adsorbents. This enables us to introduce a set of correlations that can estimate adsorbent swelling and fractional free volume dilation as a function of adsorbate uptake based on readily characterized properties. The separation selectivity of the 276 distinct binary molecular pairs in our data is reported and high-performing adsorbent systems are identified.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Towards single-species selectivity of membranes with subnanometre pores

Synthetic membranes with pores at the subnanometre scale are at the core of processes for separating solutes from water, such as water purification and desalination. While these membrane processes have achieved substantial industrial success, the capability of state-of-the-art membranes to selectively separate a single solute from a mixture of solutes is limited. Such high-precision separation would enable fit-for-purpose treatment, improving the sustainability of current water-treatment processes and opening doors for new applications of membrane technologies. In this paper, we introduce the challenges of state-of-the-art membranes with subnanometre pores to achieve high selectivity between solutes. Here, we then analyse experimental and theoretical literature to discuss the molecular-level mechanisms that contribute to energy barriers for solute transport through subnanometre pores. We conclude by providing principles and guidelines for designing next-generation single-species selective membranes that are inspired by ion-selective biological channels.

42 ENGINEERING↗
DOE OSTI2020

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

Abstract Polyploidy is an evolutionary innovation for many animals and all flowering plants, but its impact on selection and domestication remains elusive. Here we analyze genome evolution and diversification for all five allopolyploid cotton species, including economically important Upland and Pima cottons. Although these polyploid genomes are conserved in gene content and synteny, they have diversified by subgenomic transposon exchanges that equilibrate genome size, evolutionary rate heterogeneities and positive selection between homoeologs within and among lineages. These differential evolutionary trajectories are accompanied by gene-family diversification and homoeolog expression divergence among polyploid lineages. Selection and domestication drive parallel gene expression similarities in fibers of two cultivated cottons, involving coexpression networks and N 6 -methyladenosine RNA modifications. Furthermore, polyploidy induces recombination suppression, which correlates with altered epigenetic landscapes and can be overcome by wild introgression. These genomic insights will empower efforts to manipulate genetic recombination and modify epigenetic landscapes and target genes for crop improvement.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Phylogenomics and genetic analysis of solvent-producing Clostridium species

Abstract The genus Clostridium is a large and diverse group within the Bacillota (formerly Firmicutes), whose members can encode useful complex traits such as solvent production, gas-fermentation, and lignocellulose breakdown. We describe 270 genome sequences of solventogenic clostridia from a comprehensive industrial strain collection assembled by Professor David Jones that includes 194 C. beijerinckii , 57 C. saccharobutylicum , 4 C. saccharoperbutylacetonicum , 5 C. butyricum , 7 C. acetobutylicum , and 3 C. tetanomorphum genomes. We report methods, analyses and characterization for phylogeny, key attributes, core biosynthetic genes, secondary metabolites, plasmids, prophage/CRISPR diversity, cellulosomes and quorum sensing for the 6 species. The expanded genomic data described here will facilitate engineering of solvent-producing clostridia as well as non-model microorganisms with innately desirable traits. Sequences could be applied in conventional platform biocatalysts such as yeast or Escherichia coli for enhanced chemical production. Recently, gene sequences from this collection were used to engineer Clostridium autoethanogenum , a gas-fermenting autotrophic acetogen, for continuous acetone or isopropanol production, as well as butanol, butanoic acid, hexanol and hexanoic acid production.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Radiation exposure induces cross-species temporal metabolic changes that are mitigated in mice by amifostine

Exposure to acute, damaging radiation may occur through a variety of events from cancer therapy and industrial accidents to terrorist attacks and military actions. Our understanding of how to protect individuals and mitigate the effects of radiation injury or Acute Radiation Syndrome (ARS) is still limited. There are only a few Food and Drug Administration-approved therapies for ARS; whereas, amifostine is limited to treating low dose (0.7–6 Gy) radiation poisoning arising from cancer radiotherapy. An early intervention is critical to treat ARS, which necessitates identifying diagnostic biomarkers to quickly characterize radiation exposure. Towards this end, a multiplatform metabolomics study was performed to comprehensively characterize the temporal changes in metabolite levels from mice and non-human primate serum samples following γ-irradiation. The metabolomic signature of amifostine was also evaluated in mice as a model for radioprotection. The NMR and mass spectrometry metabolomics analysis identified 23 dysregulated pathways resulting from the radiation exposure. These metabolomic alterations exhibited distinct trajectories within glucose metabolism, phospholipid biosynthesis, and nucleotide metabolism. A return to baseline levels with amifostine treatment occurred for these pathways within a week of radiation exposure. Together, our data suggests a unique physiological change that is independent of radiation dose or species. Furthermore, a metabolic signature of radioprotection was observed through the use of amifostine prophylaxis of ARS.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Assessing rodents as carriers of pathogenic Leptospira species in the U.S. Virgin Islands and their risk to animal and public health

Leptospirosis is a global zoonotic disease caused by pathogenic bacteria of the genus Leptospira. We sought to determine if rodents in U.S. Virgin Islands (USVI) are carriers of Leptospira. In total, 140 rodents were sampled, including 112 Mus musculus and 28 Rattus rattus. A positive carrier status was identified for 64/140 (45.7%); 49 (35.0%) were positive by dark-field microscopy, 60 (42.9%) by culture, 63 (45.0%) by fluorescent antibody testing, and 61 (43.6%) by real-time polymerase chain reaction (rtPCR). Molecular typing indicated that 48 isolates were L. borgpetersenii and 3 were L. kirschneri; the remaining nine comprised mixed species. In the single culture-negative sample that was rtPCR positive, genotyping directly from the kidney identified L. interrogans. Serotyping of L. borgpetersenii isolates identified serogroup Ballum and L. kirschneri isolates as serogroup Icterohaemorrhagiae. These results demonstrate that rodents are significant Leptospira carriers and adds to understanding the ecoepidemiology of leptospirosis in USVI.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Unique trajectory of gene family evolution from genomic analysis of nearly all known species in an ancient yeast lineage

Gene gains and losses are a major driver of genome evolution; their precise characterization can provide insights into the origin and diversification of major lineages. Here, we examined gene family evolution of 1154 genomes from nearly all known species in the medically and technologically important yeast subphylum Saccharomycotina. We found that yeast gene family evolution differs from that of plants, animals, and filamentous ascomycetes, and is characterized by smaller overall gene numbers yet larger gene family sizes for a given gene number. Faster-evolving lineages (FELs) in yeasts experienced significantly higher rates of gene losses—commensurate with a narrowing of metabolic niche breadth—but higher speciation rates than their slower-evolving sister lineages (SELs). Gene families most often lost are those involved in mRNA splicing, carbohydrate metabolism, and cell division and are likely associated with intron loss, metabolic breadth, and non-canonical cell cycle processes. Our results highlight the significant role of gene family contractions in the evolution of yeast metabolism, genome function, and speciation, and suggest that gene family evolutionary trajectories have differed markedly across major eukaryotic lineages.

Comparative Genomics↗
DOE OSTI2022

Spatial arrangement of dynamic surface species from solid-state NMR and machine learning-accelerated MD simulations

Here, the surface arrangement of motional organic functionalities is explored by experimental dipolar coupling measurements and the prediction of motionally-averaged coupling constant from molecular dynamics simulations. The use of machine learning potentials was key to reaching the timescale required. The distance between dynamic surface species are important in cooperative heterogeneous catalysis.

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

Nanoscale heterogeneity of arsenic and selenium species in coal fly ash particles: analysis using enhanced spectroscopic imaging and speciation techniques

Coal combustion byproducts are known to be enriched in arsenic (As) and selenium (Se). This enrichment is a concern during the handling, disposal, and reuse of the ash as both elements can be harmful to wildlife and humans if mobilized into water and soils. The leaching potential and bioaccessibility of As and Se in coal fly ash depends on the chemical forms of these elements and their association with the large variety of particles that comprise coal fly ash. The overall goal of this research was to determine nanoscale and microscale solid phase mineral associations and oxidation states of As and Se in fly ash. We utilized nanoscale 2D imaging (30–50 nm spot size) with the Hard X-ray Nanoprobe (HXN) in combination with microprobe X-ray capabilities (~5 μm resolution) to determine the As and Se elemental associations. Speciation of As and Se was also measured at the nano- to microscale with X-ray absorption spectroscopy. The enhanced resolution of HXN showed As and Se as either diffusely located around or comingled with Ca- and Fe-rich particles. The results also showed nanoparticles of Se attached to the surface of fly ash grains. Overall, a comparison of As and Se species across scales highlights the heterogeneity and complexity of chemical associations for these trace elements of concern in coal fly ash.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2020

Nonlinear coupling of electromagnetic and electron acoustic waves in multi-species degenerate astrophysical plasma

Nonlinear wave-coupling is studied in a multispecies degenerate astrophysical plasma consisting of two electron species (at different temperatures): a highly degenerate main component plus a smaller classical relativistic flow immersed in a static neutralizing ion background. It is shown that the high frequency electromagnetic waves through their strong nonlinear interactions with the electron-acoustic waves [sustained by a multielectron component (degenerate) plasma surrounding a compact astrophysical object] can scatter to lower frequencies so that the radiation observed faraway will be spectrally shifted downward. It is also shown that, under definite conditions, the electromagnetic waves could settle into stationary solitonic states. It is expected that the effects of such structures may persist as detectable signatures in forms of modulated micropulses in the radiation observed far away from the accreting compact object. Both these effects will advance our abilities to interpret the radiation coming out of the compact objects.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗