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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Long noncoding RNA AK023096 interacts with hnRNP-K and contributes to the maintenance of self-renewal in bladder cancer stem-like cells

Highlights: • BCSLCs play a critical role for the high risk of recurrence and we identified that lncRNA-AK023096 was required for controls stemness of BCSLCs. • LncRNA-AK023096 recruits hnRNP-K and epigenetically upregulated SOX2 expression by modulating H3K4 trimethylation of SOX2 promoter. • Overexpression of lncRNA-AK023096 expression in the tumor tissue was significantly associated with high risk of recurrence following TUR-Bt. LncRNA contribution to self-renewal of bladder cancer stem-like cells (CSLCs) remains largely unknown. We investigated the expression profile and biological function of lncRNAs in urothelial CSLCs by microarray analysis. Among these, lncRNA-AK023096 was identified as potentially playing a role in maintaining self-renewal of CSLCs. Knockdown of this transcript inhibited spheroid formation and tumor formation. We found that AK023096 mediates recruitment of hnRNP-K to SOX2 promoter and increases H3K4 trimethylation status on SOX2 promoter, leading to a robust change in SOX2 mRNA and protein levels. Moreover, AK023096 expression in primary tumors was found to be a powerful predictor of recurrence following transurethral resection in patients with nonmuscle-invasive bladder cancer, highlighting the critical role of lncRNA in the bladder cancer regulatory network.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Deconvoluting Structures of Component Plant Biopolymers Using Deuterium Labeled Brassica oleracea Stems

Several Brassica species are cultivated globally for the production of seed oils as food, lubricants, and increasingly biofuels. The stem and leaf residues of these herbaceous dicotyledonous crops constitute another feedstock for biofuels and other products. Plant cell walls are complex, multipolymeric structures that consist primarily of polysaccharides and lignin. Cellulose chains coalesce to form crystalline microfibrils while the amorphous biopolymers, hemicellulose, and lignin form a network structure and fill the interstitial space. Neutron scattering has been used for the structural study of the assembly and deconstruction of the plant cell walls. However, similar neutron sensitivity of the different amorphous biopolymers has made structural association to individual component biopolymers nontrivial and ambiguous. To improve the association of structural features to specific biopolymer components, partial deuteration of the plant cell wall can be employed to increase the difference in the neutron scattering length density between amorphous carbohydrate and lignin plant polymers. Vegetative stems from partially deuterated Brassica oleracea acephala (kale) plants were obtained commercially, and the plant cell wall structures were studied by contrast-variation small-angle neutron scattering (CV-SANS) and Fourier-transform infrared spectroscopy (FTIR). FTIR results indicated that deuterium substitution for hydrogen in the carbohydrates was higher than that in lignin. By combining CV-SANS and FTIR results, the neutron scattering length density (nSLD) of the polysaccharides and lignin was determined to match nSLD of 65%:35% and 48%:52% D 2 O/H 2 O solvent mixtures, respectively. These nSLD values were higher than the nSLD values of polysaccharides and lignin for H 2 O grown biopolymers. The nSLD increase correlates to replacing about 42.5% of hydrogens present as both C–H and O–H groups in cellulose with deuterium atoms, while only 21% for lignin. In conclusion, this study lays the foundation to use partially deuterated plants to deconvolute structural features of the different component biopolymers, especially cellulose, hemicellulose, and lignin, of the plant cell wall without introducing unintended structural modifications due to the pretreatment extraction processes.

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

Dynamic Evolution of Copper Nanowires during CO 2 Reduction Probed by Operando Electrochemical 4D-STEM and X-ray Spectroscopy

Nanowires have emerged as an important family of one-dimensional (1D) nanomaterials owing to their exceptional optical, electrical, and chemical properties. In particular, Cu nanowires (NWs) show promising applications in catalyzing the challenging electrochemical CO 2 reduction reaction (CO 2 RR) to valuable chemical fuels. Despite early reports showing morphological changes of Cu NWs after CO 2 RR processes, their structural evolution and the resulting exact nature of active Cu sites remain largely elusive, which calls for the development of multimodal operando time-resolved nm-scale methods. Here, in this study, we report that well-defined 1D copper nanowires, with a diameter of around 30 nm, have a metallic 5-fold twinned Cu core and around 4 nm Cu 2 O shell. Operando electrochemical liquid-cell scanning transmission electron microscopy (EC-STEM) showed that as-synthesized Cu@Cu 2 O NWs experienced electroreduction of surface Cu 2 O to disordered (spongy) metallic Cu shell (Cu@Cu S NWs) under CO 2 RR relevant conditions. Cu@Cu S NWs further underwent a CO-driven Cu migration leading to a complete evolution to polycrystalline metallic Cu nanograins. Operando electrochemical four-dimensional (4D) STEM in liquid, assisted by machine learning, interrogates the complex structures of Cu nanograin boundaries. Correlative operando synchrotron-based high-energy-resolution X-ray absorption spectroscopy unambiguously probes the electroreduction of Cu@Cu 2 O to fully metallic Cu nanograins followed by partial reoxidation of surface Cu during postelectrolysis air exposure. This study shows that Cu nanowires evolve into completely different metallic Cu nanograin structures supporting the operando (operating) active sites for the CO 2 RR.

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

Robust design of semi-automated clustering models for 4D-STEM datasets

Materials discovery and design require characterizing material structures at the nanometer and sub-nanometer scale. Four-Dimensional Scanning Transmission Electron Microscopy (4D-STEM) resolves the crystal structure of materials, but many 4D-STEM data analysis pipelines are not suited for the identification of anomalous and unexpected structures. This work introduces improvements to the iterative Non-Negative Matrix Factorization (NMF) method by implementing consensus clustering for ensemble learning. We evaluate the performance of models during parameter tuning and find that consensus clustering improves performance in all cases and is able to recover specific grains missed by the best performing model in the ensemble. The methods introduced in this work can be applied broadly to materials characterization datasets to aid in the design of new materials.

Bruefach, Alexandra (ORCID:0000000209323477)↗
DOE OSTI2021

Equity for women and underrepresented minorities in STEM: Graduate experiences and career plans in chemistry

Significance On June 10, 2020, as part of the Black Lives Matter movement, scientists in the United States and throughout the world paused to consider how systematic racism affects the scientific enterprise. As a result, many academic departments are now assessing policies and practices that may contribute to this situation. This paper provides evidence of the nature of inequities related to race–ethnicity and gender in graduate school experiences and career plans of PhD students in one science, technology, engineering, and math (STEM) discipline, chemistry. The results can help promote understanding of the problems and guide efforts toward equity within STEM and, potentially, other academic areas. In turn, these changes can strengthen the scientific enterprise and the well-being of society.

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

Multidimensional images and aberrations in STEM

Recent advances in scanning transmission electron microscopy (STEM) have led to increased development of multi-dimensional STEM imaging modalities and novel image reconstruction methods. This interest arises because the main electron lens in a modern transmission electron microscope usually has a diffraction-space information limit that is significantly better than the real-space resolution of the same lens. This state-of-affairs is sometimes shared by other scattering methods in modern physics and contributes to a broader excitement surrounding multidimensional techniques that scan a probe while recording diffraction-space images, such as ptychography and scanning nano-beam diffraction. However, the contrasting resolution in the two spaces raises the question as to what is limiting their effective performance. Here, we examine this paradox by considering the effects of aberrations in both image and diffraction planes, and likewise separate the contributions of pre- and post-sample aberrations. In conclusion, this consideration provides insight into aberration-measurement techniques and might also indicate improvements for super-resolution techniques.

Hoglund, Eric R.↗
DOE OSTI2023

Starch depletion in the xylem and phloem ray parenchyma of grapevine stems under drought

Abstract While nonstructural carbohydrate (NSC) storage can support long-lived woody plants during abiotic stress, the timing and extent of their use are less understood, as are the thresholds for cell mortality as NSCs and water supplies are consumed. Here, we combine physiological and imaging tools to study the response of Vitis riparia to a 6-week experimental drought. We focused on the spatial and temporal dynamics of starch consumption and cell viability in the xylem and phloem of the stem. Starch dynamics were further corroborated with enzymatic starch digestion and X-ray microcomputed tomography imaging. Starch depletion in the stems of droughted plants was detected after 2 weeks and continued over time. We observed distinct differences in starch content and cell viability in the xylem and phloem. By the end of the drought, nearly all the starch was consumed in the phloem ray parenchyma (98 % decrease), and there were almost no metabolically active cells in the phloem. In contrast, less starch was consumed in the xylem ray parenchyma (30 % decrease), and metabolically active cells remained in the ray and vessel-associated parenchyma in the xylem. Our data suggest that the higher proportion of living cells in the phloem and cambium, combined with smaller potential NSC storage area, rapidly depleted starch, which led to cell death. In contrast, the larger cross-sectional area of the xylem ray parenchyma with higher NSC storage and lower metabolically active cell populations depleted starch at a slower pace. Why NSC source-sink relationships between xylem and phloem do not allow for a more uniform depletion of starch in ray parenchyma over time is unclear. Our data help to pinpoint the proximate and ultimate causes of plant death during prolonged drought exposure and highlight the need to consider the influence of within-organ starch dynamics and cell mortality on abiotic stress response.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Enabling the Acquisition of Electron Beam-Induced Current (EBIC) Images in Conventional SEM and STEM Instruments

Electron beam-induced current (EBIC) imaging is a well-established scanning electron microscope (SEM) technique used to analyze the behavior of microelectronic devices including solar cells. Recently, the application of EBIC imaging in an aberration-corrected scanning transmission electron microscope (STEM) has been demonstrated and offers great potential for the in situ study of electronic materials, correlating charge transport properties to atomic structural and elemental information. Here, this work presents two ways to implement EBIC imaging in conventional SEM and STEM systems: one relying on the instrument's inherent scanning and imaging electronics and the other involving third-party systems usually available in electron microscopes. The implementation of lock-in EBIC in systems equipped with a fast beam blanker is also described. In addition, this work shows and discusses the different mechanisms at play in EBIC imaging and their dependence on beam energy, sample impedance, and electrical measurement configuration, providing researchers with the basic information needed to apply the technique to their research.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Secreted Effector Proteins of Poplar Leaf Spot and Stem Canker Pathogen Sphaerulina musiva Manipulate Plant Immunity and Contribute to Virulence in Diverse Ways

We report fungal effectors play critical roles in manipulating plant immune responses and promoting colonization. Sphaerulina musiva is a heterothallic ascomycete fungus that causes Septoria leaf spot and stem canker disease in poplar (Populus spp.) plantations. This disease can result in premature defoliation, branch and stem breakage, increased mortality, and plantation failure. However, little is known about the interaction between S. musiva and poplar. Previous work predicted 142 candidate secreted effector proteins in S. musiva (SmCSEPs), 19 of which were selected for further functional characterization in this study. SmCSEP3 induced plant cell death in Nicotiana benthamiana, while 8 out of 19 tested SmCSEPs suppressed cell death. The signal peptides of these eight SmCSEPs exhibited secretory activity in a yeast signal sequence trap assay. Confocal microscopy revealed that four of these eight SmCSEPs target both the cytoplasm and the nucleus, whereas four predominantly localize to discrete punctate structures. Pathogen challenge assays in N. benthamiana demonstrated that the transient expression of six SmCSEPs promoted Fusarium proliferatum infection. The expression of these six SmCSEP genes were induced during infection. SmCSEP2, SmCSEP13, and SmCSEP25 suppressed chitin-triggered reactive oxygen species burst and callose deposition in N. benthamiana. The candidate secreted effector proteins of S. musiva target multiple compartments in the plant cell and modulate different pattern-triggered immunity pathways.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Infrared plasmonics: STEM-EELS characterization of Fabry-Pérot resonance damping in gold nanowires

Materials possessing strong midinfrared responses are of current interest because of their potential application to long-wavelength metamaterials, photonic devices, molecular detection, and catalysis. In this work, we utilize high-energy resolution (80 cm -1 , 10 meV) electron-energy-loss spectroscopy (EELS) in a monochromated and aberration-corrected scanning transmission electron microscope (STEM) to resolve multipolar surface plasmon resonances (SPRs), sometimes called Fabry-Pérot (FP) resonances, in gold nanowires with mode energies spanning from ~1000 to 8000 cm -1 . STEM-EELS provides access to these mid- to near-IR responses in a single acquisition, avoiding the difficulties inherent in obtaining the same data using near-field optical techniques. The experimentally measured FP resonance energies and linewidths, together with analytical modeling and full-wave numerical electrodynamics simulations, provide a comprehensive picture of the radiative and intrinsic contributions to the total damping rates. We find some FP modes with dephasing times >60fs, which is almost twice the longest previously reported plasmon dephasing time for individual Au nanoparticles in the infrared. The long dephasing times and the broad tunability of the FP resonance energies throughout the infrared region suggest additional opportunities for harnessing infrared plasmonic energy before dephasing occurs.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Seeing the forest for all the trees: Mycorrhizal‐associated nutrient economies are modulated by stem density and the synchrony between overstorey and understorey communities

1. Identifying relationships between plant communities and soil characteristics is a critical step in understanding the consequences of species gains and losses in ecosystems. The mycorrhizal associated nutrient economy (MANE) hypothesis predicts that the degree to which tree species and their mycorrhizal associates affect soil properties is driven by the relative dominance of different mycorrhizal types (often measured by relative basal area). While this approach emphasizes the importance of canopy trees, it does not account for how other factors (e.g. the density and composition of understorey trees) may alter tree–soil relationships. 2. We analysed tree–soil data from an eastern deciduous forest in southern Indiana, USA that contains >29,000 georeferenced stems, including 21 species that associate with arbuscular mycorrhizal (AM) fungi and 14 that associate with ectomycorrhizal (ECM) fungi. We sampled soils (upper 5 cm) from across the plot and modelled soil characteristics to tree communities. Given differences in soil characteristics among AM-dominated and ECM-dominated neighbourhoods, we hypothesized that relationships between tree-mycorrhizal dominance and soils would be affected by both the density of stems in the plot (owing to ‘Zinke’ individual plant effects) and composition of the understorey trees (owing to ‘trait divergence effects’) 3. In support of our Zinke hypothesis, we found that the relationships between tree-mycorrhizal dominance and soil variables (soil pH, nitrification rates and carbon to nitrogen ratio) were strengthened as stand density increased. In support of the trait divergence hypothesis, we found that as the mismatch between overstorey and understorey composition increased (e.g. AM-dominated understories beneath ECM-dominated overstories and vice versa), the relationship between tree dominance and soil variables weakened. We were able to use these insights to create mycorrhizal metrics to predict soil variables that were sensitive to the structural composition of neighbourhoods. 4. Synthesis. Our results indicate that relationships between plants and soils in forests are not only shaped by dominant overstorey trees but also the density and composition of understorey trees. Thus, efforts to predict the ecosystem consequences of species gains and losses may benefit from considering these elements of forest structure and not only the basal area of the dominant trees.

MANE framework↗
DOE OSTI2024

Dynamic STEM-EELS for single-atom and defect measurement during electron beam transformations

This study introduces the integration of dynamic computer vision–enabled imaging with electron energy loss spectroscopy (EELS) in scanning transmission electron microscopy (STEM). This approach involves real-time discovery and analysis of atomic structures as they form, allowing us to observe the evolution of material properties at the atomic level, capturing transient states traditional techniques often miss. Rapid object detection and action system enhances the efficiency and accuracy of STEM-EELS by autonomously identifying and targeting only areas of interest. This machine learning (ML)–based approach differs from classical ML in that it must be executed on the fly, not using static data. We apply this technology to V-doped MoS 2 , uncovering insights into defect formation and evolution under electron beam exposure. This approach opens uncharted avenues for exploring and characterizing materials in dynamic states, offering a pathway to increase our understanding of dynamic phenomena in materials under thermal, chemical, and beam stimuli.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Advancing stem cell technologies for conservation of wildlife biodiversity

ABSTRACT Wildlife biodiversity is essential for healthy, resilient and sustainable ecosystems. For biologists, this diversity also represents a treasure trove of genetic, molecular and developmental mechanisms that deepen our understanding of the origins and rules of life. However, the rapid decline in biodiversity reported recently foreshadows a potentially catastrophic collapse of many important ecosystems and the associated irreversible loss of many forms of life on our planet. Immediate action by conservationists of all stripes is required to avert this disaster. In this Spotlight, we draw together insights and proposals discussed at a recent workshop hosted by Revive & Restore, which gathered experts to discuss how stem cell technologies can support traditional conservation techniques and help protect animal biodiversity. We discuss reprogramming, in vitro gametogenesis, disease modelling and embryo modelling, and we highlight the prospects for leveraging stem cell technologies beyond mammalian species.

Developmental Biology↗
NASA NTRS1974

Brain stem auditory evoked responses in human infants and adults

Brain stem evoked potentials were recorded by conventional scalp electrodes in infants (3 weeks to 3 years of age) and adults. The latency of one of the major response components (wave V) is shown to be a function both of click intensity and the age of the subject; this latency at a given signal strength shortens postnatally to reach the adult value (about 6 msec) by 12 to 18 months of age. The demonstrated reliability and limited variability of these brain stem electrophysiological responses provide the basis for an optimistic estimate of their usefulness as an objective method for assessing hearing in infants and adults.

Hecox, K.↗
NASA NTRS1983

Short-term and long-term clinostat and vibration-induced biochemical changes in dwarf marigold stems

Stems of 21-day dwarf marigold plants cultivated on the clinostat were compared with plants cultivated on vertical axis rotators ('vibrational controls') and stationary controls for long-term changes in cell wall composition. Stems of 21-day plants grown under stationary conditions and subsequently exposed to the clinostat for 24 hours were also analyzed. Among the long-term markers, calcium, lignin, and protein-bound hemicellulose (possibly cell wall glycoprotein) clearly differentiated the effects of vibration from those of the clinostat. Short-term differential responses included rate of ethylene production, nastic movement and peroxidase activity of the cell wall, but not of the protoplast.

Siegel, S. M.↗
NASA NTRS1984

Small gravitationally elicited voltage transients in pea stems

Decapitated veritcal stem segments were observed for 45 min, noting the number of transients mu V for each 5-min interval. Results for two sets of stem segments are plotted. The average frequencies were 0.72 + or -0.05 and 0.66 + or - 0.04 per 5 min. One set of segments was swiveled gently to the horizontal position; then, recording continued for another 90 min. Transients continued in the vertical controls at a closely similar average rate 0.78 + or - 0.04 per 5 min. However, after the first 5-min interval the horizontally placed plants exhibited transients at an increased average rate of 1.08 + or - 0.04 per 5 min. The frequency of transients also increased following horizontal placement of intact shoots. However, it appears that this increase had two components: one due to gravity reception, and one due to the redistribution of indolacetic acid (IAA) believed to mediate gravitropic curvature (or, more specifically, to the increase of IAA in the lower tissue.

Pickard, B. G.↗
NASA NTRS1985

Ohio River main stem study - The role of geographic information systems and remote sensing in flood damage assessments

The Pittsburgh District, Corps of Engineers, has conducted feasibility analyses of various procedures for performing flood damage assessments along the main stem of the Ohio River. Procedures using traditional, although highly automated, techniques and those based on geographic information systems have been evaluated at a test site, the City of New Martinsville, Wetzel County, WV. The flood damage assessments of the test site developed from an automated, conventional structure-by-structure appraisal served as the ground truth data set. A geographic information system was developed for the test site which includes data on hydraulic reach, ground and reference flood elevations, and land use/cover. Damage assessments were made using land use mapping developed from an exhaustive field inspection of each tax parcel. This ground truth condition was considered to provide the best comparison of flood damages to the conventional approach. Also, four land use/cover data sets were developed from Thematic Mapper Simulator (TMS) and Landsat-4 Thematic Mapper (TM) data. One of these was also used to develop a damage assessment of the test site. This paper presents the comparative absolute and relative accuracies of land use/cover mapping and flood damage assessments, and the recommended role of geographic information systems aided by remote sensing for conducting flood damage assessments and updates along the main stem of the Ohio River.

Edwardo, H. A.↗
NASA NTRS1987

Possible role of brain stem respiratory neurons in mediating vomiting during space motion sickness

The object of this study was to determine if brain stem expiratory neurons control abdominal muscle activity during vomiting. The activity of 27 ventral respiratory group expiratory neurons, which are known to be of primary importance for control of abdominal muscle activity during respiration, was recorded. It is concluded that abdominal muscle activity during vomiting must be controlled not only by some brain stem expiratory neurons but also by other input(s).

Miller, A. D.↗