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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 613 records · Page 34
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Incomplete cell disruption of resistant microbes

Abstract Biomolecules for OMIC analysis of microbial communities are commonly extracted by bead-beating or ultra-sonication, but both showed varying yields. In addition to that, different disruption pressures are necessary to lyse bacteria and fungi. However, the disruption efficiency and yields comparing bead-beating and ultra-sonication of different biological material have not yet been demonstrated. Here, we show that ultra-sonication in a bath transfers three times more energy than bead-beating over 10 min. TEM imaging revealed intact gram-positive bacterial and fungal cells whereas the gram-negative bacterial cells were destroyed beyond recognition after 10 min of ultra-sonication. DNA extraction using 10 min of bead-beating revealed higher yields for fungi but the extraction efficiency was at least three-fold lower considering its larger genome. By our critical viewpoint, we encourage the review of the commonly used extraction techniques as we provide evidence for a potential underrepresentation of resistant microbes, particularly fungi, in ecological studies.

Starke, Robert↗
DOE OSTI2019

Hair Proteome Variation at Different Body Locations on Genetically Variant Peptide Detection for Protein-Based Human Identification

Abstract Human hair contains minimal intact nuclear DNA for human identification in forensic and archaeological applications. In contrast, proteins offer a pathway to exploit hair evidence for human identification owing to their persistence, abundance, and derivation from DNA. Individualizing single nucleotide polymorphisms (SNPs) are often conserved as single amino acid polymorphisms in genetically variant peptides (GVPs). Detection of GVP markers in the hair proteome via high-resolution tandem mass spectrometry permits inference of SNPs with known statistical probabilities. To adopt this approach for forensic investigations, hair proteomic variation and its effects on GVP identification must first be characterized. This research aimed to assess variation in single-inch head, arm, and pubic hair, and discover body location-invariant GVP markers to distinguish individuals. Comparison of protein profiles revealed greater body location-specific variation in keratin-associated proteins and intracellular proteins, allowing body location differentiation. However, robust GVP markers derive primarily from keratins that do not exhibit body location-specific differential expression, supporting GVP identification independence from hair proteomic variation at the various body locations. Further, pairwise comparisons of GVP profiles with 8 SNPs demonstrated greatest interindividual variation and high intraindividual consistency, enabling similar differentiative potential of individuals using single hairs irrespective of body location origin.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Systematic Comparison of High-throughput Single-Cell and Single-Nucleus Transcriptomes during Cardiomyocyte Differentiation

A comprehensive reference map of all cell types in the human body is necessary for improving our understanding of fundamental biological processes and in diagnosing and treating disease. High-throughput single-cell RNA sequencing techniques have emerged as powerful tools to identify and characterize cell types in complex and heterogeneous tissues. However, extracting intact cells from tissues and organs is often technically challenging or impossible, for example in heart or brain tissue. Single-nucleus RNA sequencing provides an alternative way to obtain transcriptome profiles of such tissues. To systematically assess the differences between high-throughput single-cell and single-nuclei RNA-seq approaches, we compared Drop-seq and DroNc-seq, two microfluidic-based 3' RNA capture technologies that profile total cellular and nuclear RNA, respectively, during a time course experiment of human induced pluripotent stem cells (iPSCs) differentiating into cardiomyocytes. Clustering of timeseries transcriptomes from Drop-seq and DroNc-seq revealed six distinct cell types, five of which were found in both techniques. Furthermore, single-cell trajectories reconstructed from both techniques reproduced expected differentiation dynamics. We then applied DroNc-seq to postmortem heart tissue to test its performance on heterogeneous human tissue samples. Our data confirm that DroNcseq yields similar results to Drop-seq on matched samples and can be successfully used to generate reference maps for the human cell atlas.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structure and function of bacteriophage CBA120 ORF211 (TSP2), the determinant of phage specificity towards E. coli O157:H7

The genome of Escherichia coli O157:H7 bacteriophage vB_EcoM_CBA120 encodes four distinct tailspike proteins (TSPs). The four TSPs, TSP1-4, attach to the phage baseplate forming a branched structure. We report the 1.9 Å resolution crystal structure of TSP2 (ORF211), the TSP that confers phage specificity towards E. coli O157:H7. The structure shows that the N-terminal 168 residues involved in TSPs complex assembly are disordered in the absence of partner proteins. The ensuing head domain contains only the first of two fold modules seen in other phage vB_EcoM_CBA120 TSPs. The catalytic site resides in a cleft at the interface between adjacent trimer subunits, where Asp506, Glu568, and Asp571 are located in close proximity. Replacement of Asp506 and Asp571 for alanine residues abolishes enzyme activity, thus identifying the acid/base catalytic machinery. However, activity remains intact when Asp506 and Asp571 are mutated into asparagine residues. Analysis of additional site-directed mutants in the background of the D506N:D571N mutant suggests engagement of an alternative catalytic apparatus comprising Glu568 and Tyr623. Finally, we demonstrate the catalytic role of two interacting glutamate residues of TSP1, located in a cleft between two trimer subunits, Glu456 and Glu483, underscoring the diversity of the catalytic apparatus employed by phage vB_EcoM_CBA120 TSPs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Mapping O 2 concentration in ex-vivo tissue samples on a fast PLIM macro-imager

O 2 PLIM microscopy was employed in various studies, however current platforms have limitations in sensitivity, image acquisition speed, accuracy and general usability. We describe a new PLIM imager based on the Timepix3 camera (Tpx3cam) and its application for imaging of O 2 concentration in various tissue samples stained with a nanoparticle based probe, NanO 2 -IR. Upon passive staining of mouse brain, lung or intestinal tissue surface with minute quantities of NanO 2 -IR or by microinjecting the probe into the lumen of small or large intestine fragments, robust phosphorescence intensity and lifetime signals were produced, which allow mapping of O 2 in the tissue within 20 s. Inhibition of tissue respiration or limitation of O 2 diffusion to tissue produced the anticipated increases or decreases in O 2 levels, respectively. The difference in O 2 concentration between the colonic lumen and air-exposed serosal surface was around 140 µM. Furthermore, subcutaneous injection of 5 µg of the probe in intact organs (a paw or tail of sacrificed mice) enabled efficient O 2 imaging at tissue depths of up to 0.5 mm. Overall, the PLIM imager holds promise for metabolic imaging studies with various ex vivo models of animal tissue, and also for use in live animals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Pore architecture and particulate organic matter in soils under monoculture switchgrass and restored prairie in contrasting topography

Bioenergy cropping systems can substantially contribute to climate change mitigation. However, limited information is available on how they affect soil characteristics, including pores and particulate organic matter (POM), both essential components of the soil C cycle. The objective of this study was to determine effects of bioenergy systems and field topography on soil pore characteristics, POM, and POM decomposition under new plant growth. We collected intact soil cores from two systems: monoculture switchgrass (Panicum virgatum L.) and native prairie, at two contrasting topographical positions (depressions and slopes), planting half of the cores with switchgrass. Pore and POM characteristics were obtained using X-ray computed micro-tomography (μCT) (18.2 µm resolution) before and after new switchgrass growth. Diverse prairie vegetation led to higher soil C than switchgrass, with concomitantly higher volumes of 30–90 μm radius pores and greater solid-pore interface. Yet, that effect was present only in the coarse-textured soils on slopes and coincided with higher root biomass of prairie vegetation. Surprisingly, new switchgrass growth did not intensify decomposition of POM, but even somewhat decreased it in monoculture switchgrass as compared to non-planted controls. Our results suggest that topography can play a substantial role in regulating factors driving C sequestration in bioenergy systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Low-temperature (< 200 °C) degradation of electronic nicotine delivery system liquids generates toxic aldehydes

Electronic cigarette usage has spiked in popularity over recent years. The enhanced prevalence has consequently resulted in new health concerns associated with the use of these devices. Degradation of the liquids used in vaping have been identified as a concern due to the presence of toxic compounds such as aldehydes in the aerosols. Typically, such thermochemical conversions are reported to occur between 300 and 400 °C. Herein, the low-temperature thermal degradation of propylene glycol and glycerol constituents of e-cigarette vapors are explored for the first time by natural abundance 13 C NMR and 1 H NMR, enabling in situ detection of intact molecules from decomposition. The results demonstrate that the degradation of electronic nicotine delivery system (ENDS) liquids is strongly reliant upon the oxygen availability, both in the presence and absence of a material surface. When oxygen is available, propylene glycol and glycerol readily decompose at temperatures between 133 and 175 °C over an extended time period. Among the generated chemical species, formic and acrylic acids are observed which can negatively affect the kidneys and lungs of those who inhale the toxin during ENDS vapor inhalation. Further, the formation of hemi- and formal acetals is noted from both glycerol and propylene glycol, signifying the generation of both formaldehyde and acetaldehyde, highly toxic compounds, which, as a biocide, can lead to numerous health ailments. The results also reveal a retardation in decomposition rate when material surfaces are prevalent with no directly observed unique surface spectator or intermediate species as well as potentially slower conversions in mixtures of the two components. The generation of toxic species in ENDS liquids at low temperatures highlights the dangers of low-temperature ENDS use.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Dynamic compression of Ce and Pr with millisecond time-resolved X-ray diffraction

Abstract Both cerium (Ce) and praseodymium (Pr) undergo a volume collapse transition under compression that originate from similar electronic mechanisms. Yet the outcome could not be more different. In the case of Ce with one affected 4f electron the volume collapse leaves the crystal symmetry intact, whereas for Pr with two 4f electrons the crystal symmetry changes from a distorted face centered cubic structure to a lower symmetry orthorhombic structure. In this paper, we present a study of the effect of strain/compression rate spanning nearly 4 orders of magnitude on the volume collapse phase transitions in Ce and Pr. These dynamic compression experiments in a diamond anvil cell also reveal kinetic differences between the phase transformations observed in these two materials. The transition cannot be overdriven in pressure in Ce, which indicates a fast kinetic process, whereas fast compression rates in Pr lead to a shift of the phase boundary to higher pressures, pointing to slower kinetics possibly due to the realization of a new crystal structure.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Soil pore characteristics and the fate of new switchgrass-derived carbon in switchgrass and prairie bioenergy cropping systems

Abstract Monoculture switchgrass and restored prairie are promising perennial feedstock sources for bioenergy production on the lands unsuitable for conventional agriculture. Such lands often display contrasting topography that influences soil characteristics and interactions between plant growth and soil C gains. This study aimed at elucidating the influences of topography and plant systems on the fate of C originated from switchgrass plants and on its relationships with soil pore characteristics. For that, switchgrass plants were grown in intact soil cores collected from two contrasting topographies, namely steep slopes and topographical depressions, in the fields in multi-year monoculture switchgrass and restored prairie vegetation. The 13 C pulse labeling allowed tracing the C of switchgrass origin, which X-ray computed micro-tomography enabled in-detail characterization of soil pore structure. In eroded slopes, the differences between the monoculture switchgrass and prairie in terms of total and microbial biomass C were greater than those in topographical depressions. While new switchgrass increased the CO 2 emission in depressions, it did not significantly affect the CO 2 emission in slopes. Pores of 18–90 µm Ø facilitated the accumulation of new C in soil, while > 150 µm Ø pores enhanced the mineralization of the new C. These findings suggest that polyculture prairie located in slopes can be particularly beneficial in facilitating soil C accrual and reduce C losses as CO 2 .

09 BIOMASS FUELS↗
DOE OSTI2023

Delivered complementation in planta (DCIP) enables measurement of peptide-mediated protein delivery efficiency in plants

Abstract Using a fluorescence complementation assay, Delivered Complementation in Planta (DCIP), we demonstrate cell-penetrating peptide-mediated cytosolic delivery of peptides and recombinant proteins in Nicotiana benthamiana. We show that DCIP enables quantitative measurement of protein delivery efficiency and enables functional screening of cell-penetrating peptides for in-planta protein delivery. Finally, we demonstrate that DCIP detects cell-penetrating peptide-mediated delivery of recombinantly expressed proteins such as mCherry and Lifeact into intact leaves. We also demonstrate delivery of a recombinant plant transcription factor, WUSCHEL (AtWUS), into N. benthamiana. RT-qPCR analysis of AtWUS delivery in Arabidopsis seedlings also suggests delivered WUS can recapitulate transcriptional changes induced by overexpression of AtWUS. Taken together, our findings demonstrate that DCIP offers a new and powerful tool for interrogating cytosolic delivery of proteins in plants and highlights future avenues for engineering plant physiology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Anti-fungal bioactive terpenoids in the bioenergy crop switchgrass (Panicum virgatum) may contribute to ecotype-specific microbiome composition

Abstract Plant derived bioactive small molecules have attracted attention of scientists across fundamental and applied scientific disciplines. We seek to understand the influence of these phytochemicals on rhizosphere and root-associated fungi. We hypothesize that – consistent with accumulating evidence that switchgrass genotype impacts microbiome assembly – differential terpenoid accumulation contributes to switchgrass ecotype-specific microbiome composition. An initial in vitro Petri plate-based disc diffusion screen of 18 switchgrass root derived fungal isolates revealed differential responses to upland- and lowland-isolated metabolites. To identify specific fungal growth-modulating metabolites, we tested fractions from root extracts on three ecologically important fungal isolates – Linnemania elongata, Trichoderma sp. and Fusarium sp. Saponins and diterpenoids were identified as the most prominent antifungal metabolites. Finally, analysis of liquid chromatography-purified terpenoids revealed fungal inhibition structure – activity relationships (SAR). Saponin antifungal activity was primarily determined by the number of sugar moieties – saponins glycosylated at a single core position were inhibitory whereas saponins glycosylated at two core positions were inactive. Saponin core hydroxylation and acetylation were also associated with reduced activity. Diterpenoid activity required the presence of an intact furan ring for strong fungal growth inhibition. These results inform future breeding and biotechnology strategies for crop protection with reduced pesticide application.

09 BIOMASS FUELS↗
DOE OSTI2024

Coherence mapping to identify the intermediates of multi-channel dissociative ionization

Identifying the short-lived intermediates and reaction mechanisms of multi-channel radical cation fragmentation processes remains a current and important challenge to understanding and predicting mass spectra. We find that coherent oscillations in the femtosecond time-dependent yields of several product ions following ultrafast strong-field ionization represent spectroscopic signatures that elucidate their mechanism of formation and identify the intermediate(s) they originate from. Experiments on endo-dicyclopentadiene show that vibrational frequencies from various intermediates are mapped onto their resulting products. Aided by ab initio methods, we identify the vibrational modes of both the cleaved and intact molecular ion intermediates. These results confirm stepwise and concerted fragmentation pathways of the dicyclopentadiene ion. This study highlights the power of tracking the femtosecond dynamics of all product ions simultaneously and sheds further light onto one of the fundamental reaction mechanisms in mass spectrometry, the retro-Diels Alder reaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Hole doping in a negative charge transfer insulator

RE NiO 3 is a negative charge transfer energy system and exhibits a temperature-driven metal-insulator transition (MIT), which is also accompanied by a bond disproportionation (BD) transition. In order to explore how hole doping affects the BD transition, we have investigated the electronic structure of single-crystalline thin films of Nd 1-x Ca x NiO 3 by synchrotron based experiments and ab-initio calculations. Here we show that for a small value of x, the doped holes are localized on one or more Ni sites around the dopant Ca 2+ ions, while the BD state for the rest of the lattice remains intact. The effective charge transfer energy (Δ) increases with Ca concentration and the formation of BD phase is not favored above a critical x, suppressing the insulating phase. Our present study firmly demonstrates that the appearance of BD mode is essential for the MIT of the RE NiO 3 series.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

Correlating the electrocatalytic stability of platinum monolayer catalysts with their structural evolution in the oxygen reduction reaction

Platinum monolayer (Pt ML ) core–shell electrocatalysts for the oxygen reduction reaction (ORR) have attracted great attention because of their exceptional activity and stability for promising practical applications in fuel cells. In this paper, we describe our in-depth investigation of the relationship between the ORR activity and structure of the Pt ML /Pd/C catalyst during the stability test. By virtue of the rotating disk electrode technique, an accelerated degradation test with the potential window of 0.65 to 1.05 V was applied to the Pt ML /Pd/C to interrogate its long-term reliability in the ORR, the change of its electrochemical surface area, and its surface composition and components. The Pt ML /Pd/C catalyst displayed a volcano-like mass/dollar activity profile in the stability test up to 100k cycles. The overall loss of the activity was recorded to be as low as 17% of the initial value. The ORR activity increased in the initial 20k cycles because the freshly prepared Pt ML did not entirely encompass the whole Pd core, but it was integrated to a full coverage with a more stable configuration during the potential cycling owing to its self-healing property. Then, the activity decreased at a much slower rate than the standard Pt/C because the Pd–Pt core–shell structure due to its structural self-retaining property remained intact and impeded the electrochemical Ostwald ripening of the entire particles. Changes in the morphology and configuration of Pt ML were mapped by combining our experimental investigation with model analyses. Finally, the proposed self-healing and self-retaining mechanisms account for the structure-dependent stability in the ORR and play cornerstone roles in formulating ORR core–shell electrocatalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Site dependent reactivity of Pt single atoms on anatase TiO 2 (101) in an aqueous environment

The TiO 2 –Pt–water interface is of great relevance in photocatalysis where Pt is widely used as a co-catalyst for The TiO 2 –Pt–water interface is of great relevance in photocatalysis where Pt is widely used as a co-catalyst for enhancing hydrogen evolution in aqueous TiO 2 . Using ab initio molecular dynamics, we investigated this interface focusing on Pt single atoms supported on anatase TiO 2 (101) in a water environment. Based on recent experiments showing a broad distribution of Pt coordination sites in TiO 2 , we examined six distinct single-Pt supported species with different nominal Pt oxidation states, namely: Pt, PtOH, and PtO 2 species adsorbed on the stoichiometric surface; Pt adsorbed at a surface oxygen vacancy (O v ); and Pt substituting a surface Ti cation (PtTi), both without and with an accompanying O v (Pt Ti + O v ). As found for the pristine anatase surface, interfacial water remained intact in the presence of a nearly neutral Pt adatom within the time duration of our simulations (~15 ps). Similarly, no (or only temporary) water dissociation was observed at the Pt Ti + O v and PtO 2 interfaces, due to the formation of very stable planar Pt coordination structures that interact only weakly with water. In contrast, water dissociated with OH – (H + ) on the Pt atom when this substituted a surface Ti (oxygen) ion as well as on PtOH. Lastly, the significant proton affinity of Pt atoms at surface oxygen vacancies suggests that negatively charged Pt species are particularly efficient at catalyzing hydrogen evolution in aqueous TiO 2 .hydrogen evolution in aqueous TiO 2 .

36 MATERIALS SCIENCE↗
DOE OSTI2019

Cellulolytic enzyme-aided extraction of hemicellulose from switchgrass and its characteristics

The isolation of biomass components with their intact structure is integral for understanding the characteristics of biomass. Compared to other major biomass components such as cellulose and lignin, hemicellulose remains a challenging component to be isolated from the plant cell wall without significant depolymerization and modification. Here, a novel cellulolytic enzyme-aided hemicellulose (CEH) isolation method was developed to isolate hemicellulose with a near-native branched structure from switchgrass. The structural characteristics of CEH were investigated and compared with hemicelluloses isolated by conventional alkaline extracted hemicellulose (AEH) and DMSO extracted hemicellulose (DMSOH) methods. Gel permeation chromatography (GPC) analysis indicated that CEH had a weight-average molecular weight of 44 kDa, which was comparable to that of AEH (43 kDa) but higher than that of DMSOH (37 kDa). The chemical composition analysis revealed that CEH retained a higher proportion of glucuronic acid compared to AEH and DMSOH. The 2D 13 C– 1 H heteronuclear single quantum coherence (HSQC) NMR spectra containing the β-(1,4)-linked-D-xylan backbone, non-reducing-end peaks and both α- and β-reducing-end peaks in CEH were comparable to the spectra of the commercial beechwood xylan. CEH showed a highly branched hemicellulose structure, which retained methoxyl groups, O -acetyl groups, and 4- O -methyl-glucuronic acid attached to the xylan backbone.

59 BASIC BIOLOGICAL SCIENCES↗