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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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

CRISPRa-mediated NEAT1 lncRNA upregulation induces formation of intact paraspeckles

Long noncoding RNAs (lncRNAs) are fundamental genomic regulatory factors under various physiological and pathological conditions. A class of lncRNAs termed architectural RNAs (arcRNAs) plays an essential scaffolding role in building nuclear bodies. NEAT1 arcRNA is an abundant, nuclear-retained lncRNA that constructs paraspeckle nuclear bodies. NEAT1 is upregulated in various developmental and disease conditions including cancer and virus infection. However, it remains unclear how elevated expression of NEAT1 influences such conditions. Here, we set up an experimental method to selectively increase NEAT1 expression. We applied the synergistic activation mediator (SAM) system using catalytically dead Cas9 (dCas9) proteins to activate transcription of the NEAT1 gene. We examined 10 pre-designed and 15 originally designed single-guide RNAs (sgRNAs) in the NEAT1 promoter region for CRISPR activation (CRISPRa). We validated several sgRNAs that we designed for the SAM system to strongly activate NEAT1 expression in two human cell lines and induced formation of paraspeckles with intact core-shell structures. Thus, this selective NEAT1 upregulation method using the SAM system would be useful for further functional analyses of NEAT1 lncRNA in both basic and applied research.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Effects of diisononyl phthalate on osteopenia in intact mice

Osteopenia is characterized by bone loss and deterioration of trabecular bone, which leads to osteoporotic fractures. This disease is highly prevalent in industrialized areas and is associated with exposure to endocrine disrupting chemicals (EDCs). Diisononyl phthalate (DINP) is one of these EDCs and is mainly used as a plasticizer in flexible polyvinyl chloride (PVC) products. Although it is well known that exposure to DINP is harmful to humans, no studies have been reported concerning its contribution to osteopenia. Therefore, in this study, we injected DINP (2, 20, and 200 mg/kg) into C3H/HeN mice for 6 weeks and found that the uterus weight, bone (femur and tibia) weight, and bone length of the DINP-exposed mice were reduced compared to those of the SHAM group. On the other hand, body weight, the serum alkaline phosphatase (ALP) and inorganic phosphorus (IP) levels in the DINP treated mice were increased compared with those of the SHAM group. The tartrate-resistant acid phosphatase (TRAP) activity (bone resorption marker) was increased and the bone alkaline phosphatase (BALP) activity was lowered by the treatment with DINP as compared with the SHAM group. Furthermore, the microarchitecture of the femur and tibia in the intact mice was destroyed by the DINP injection. The tissue volume (TV), bone volume (BV), BV/TV, bone surface (BS), BS/TV, trabecular thickness (Tb.Th), and trabecular number (Tb.N) were reduced and the trabecular pattern factor (Tb.Pf), structure model index (SMI), and trabecular separation (Tb.Sp) were increased by the DINP injection. The bone mineral density (BMD) of the femur and tibia was lower in the DINP group than in the SHAM group. These results indicate that DINP contributes to an increased risk of osteopenia via destruction of the microarchitecture and enhancement of osteoclast activity. - Highlights: • DINP induces reduction of the uterus weight, bone weight, bone length. • DINP induces enhancement of TRAP activity and suppression of BALP activity. • DINP induces cancellous bone loss in the tibia and femur. • DINP induces reduction of BMD in femur and tibia.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Diffusion in intact secondary cell wall models of plants at different equilibrium moisture content

Secondary plant cell walls are composed of carbohydrate and lignin polymers, and collectively represent a significant renewable resource. Leveraging these resources depends in part on a mechanistic understanding for diffusive processes within plant cell walls. Common wood protection treatments and biomass conversion processes to create biorefinery feedstocks feature ion or solvent diffusion within the cell wall. X-ray fluorescence microscopy experiments have determined that ionic diffusion rates are dependent on cell wall hydration as well as the ionic species through non-linear relationships. In this work, we use classical molecular dynamics simulations to map the diffusion behavior of different plant cell wall components (cellulose, hemicellulose, lignin), ions (Na + , K + , Cu2 + , Cl - ) and water within a model for an intact plant cell wall at various hydration states (3-30 wt% water). From these simulations, we analyze the contacts between different plant cell wall components with each other and their interaction with the ions. Generally, diffusion increases with increasing hydration, with lignin and hemicellulose components increasing diffusion by an order of magnitude over the tested hydration range. Ion diffusion depends on charge. Positively charged cations preferentially interact with hemicellulose components, which include negatively charged carboxylates. As a result, positive ions diffuse more slowly than negatively charged ions. Measured diffusion coefficients are largely observed to best fit piecewise linear trends, with an inflection point between 10 and 15% hydration. These observations shed light onto the molecular mechanisms for diffusive processes within secondary plant cell walls at atomic resolution.

09 BIOMASS FUELS↗
DOE OSTI2024

Overexpression of human ACE2 protein in mouse fibroblasts stably transfected with the intact ACE2 gene

Infection by SARS-CoV-2 is dependent on binding of the viral spike protein to angiotensin converting enzyme 2 (ACE2), a membrane glycoprotein expressed on epithelial cells in the human upper respiratory tract. Recombinant ACE2 protein has potential application for anti-viral therapy. Here we co-transfected mouse fibroblasts (A9 cells) with a cloned fragment of human genomic DNA containing the intact ACE2 gene and an unlinked neomycin phosphotransferase gene, and then selected stable neomycin-resistant transfectants. Transfectant clones expressed ACE2 protein at levels that were generally proportional to the number of ACE2 gene copies integrated in the cell genome, ranging up to approximately 50 times the level of ACE2 present of Vero-E6 cells. Cells overexpressing ACE2 were hypersensitive to infection by spike-pseudotyped vesicular stomatitis virus (VSV-S), and adsorption of VSV-S to these cells occurred at an accelerated rate compared to Vero-E6 cells. In conclusion, the transfectant cell clones described here therefore have favorable attributes as feedstocks for large-scale production of recombinant human ACE2 protein.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Molecular Modeling and Molecular Dynamics Simulation of a Packed and Intact Bacterial Microcompartment

Bacterial microcompartments (BMCs) are protein-bound organelles found in some bacteria which encapsulate enzymes for enhanced catalytic activity. These compartments spatially sequester enzymes within semipermeable shell proteins and are packed full of enzyme cargoes and metabolites as they fulfill their function. Coupling together recent SAXS and proteomics work, it is possible to develop molecular models for these microcompartments and interrogate enzyme and metabolite dynamics within. Our primary goal of this study is to quantify the permeability of metabolite glyceraldehyde-3-phosphate (G3P) and dihydroxyacetone phosphate (DHAP) across the BMC shell through classical molecular dynamics simulation. The Haliangium ochraceum model of BMC shell (PDB: 6MZX) was used to model an intact BMC of approximately 10 million atoms. Working at this scale presented its own challenges in managing large data sets, with multiple challenges and hardware advances discussed that facilitated this work. Over approximately 750 ns of aggregate simulation, we see multiple permeation events for these metabolites that were added at high concentration through the pores present within BMC shell tiles. When compared to independent permeability estimates for the same metabolites determined through replica exchange umbrella sampling simulations, the permeabilities varied by approximately 3 orders of magnitude. Regardless, the permeability coefficients for both G3P and DHAP are highly similar and very high, such that only very small concentration gradients can be maintained across the BMC shell between the cytosol and BMC interior. The large simulation systems also facilitated comparisons for molecular diffusivity in the crowded environment within the BMC shell. By our estimates, the viscosity within a packed BMC shell is at least 10-fold higher than it would be in neat solution and is the real driver for varying permeability estimates we obtained through simulation. These findings will be used as design inputs for future bioengineering efforts to make products from BMCs, highlighting how permeable BMC shells can be.

Diffusion↗
DOE OSTI2018

Increasing the Separation Capacity of Intact Histone Proteoforms Chromatography Coupling Online Weak Cation Exchange-HILIC to Reversed Phase LC UVPD-HRMS

Top-down proteomics is an emerging analytical strategy to characterize combinatorial protein post-translational modifications (PTMs). However, sample complexity and small mass differences between chemically closely related proteoforms often limit the resolution attainable by separations employing a single liquid chromatographic (LC) principle. In particular, for ultra-modified proteins like histones, extensive and time-consuming fractionation is needed to achieve deep proteoform coverage. Herein, we present the first online nano-flow comprehensive two-dimensional liquid chromatography (nLC×LC) platform top-down mass spectrometry analysis of histone proteoforms. The described two-dimensional LC system combines weak cation exchange chromatography under hydrophilic interaction LC conditions (i.e. charge- and hydrophilicity-based separation) with reversed phase liquid chromatography (i.e. hydrophobicity-based separation). The two independent chemical selectivities were run at nanoflows (300 nL/min) and coupled online with high-resolution mass spectrometry employing ultraviolet photodissociation (UVPD-HRMS). The nLC×LC workflow increased the number of intact protein masses observable relative to one-dimensional approaches and allowed characterization of hundreds of proteforms starting from limited sample quantities (~1.5 µg).

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

Surface Energy Dynamics and Canopy Structural Properties in Intact and Disturbed Forests in the Southern Amazon

The Brazilian Amazon has been a focus of land development with large swaths of forests converted to agriculture. Forest degradation by selective logging and fires has accompanied the agricultural frontier and has resulted in significant impacts on Amazonian ecosystems. Changes in forest structure resulting from forest disturbances have large impacts on the surface energy balance, including on land surface temperature (LST) and evapotranspiration (ET). This study's objective is to assess the effects of forest disturbances on water fluxes and forest structure in a transitional forest site in the Southern Amazon. We used ET and LST products from MODIS and Landsat 8 and GEDI-derived forest structure data to address our research questions. We found that disturbances induced seasonal water stress, more pronounced in croplands/pastures than in forests (differences up to 20% in the dry season), and more pronounced in second-growth and recently burned areas than in logged and intact forests (differences up to 12% in the dry season). Moreover, ET and LST were negatively related, with more consistent relationships across disturbance classes in the dry season (R 2 : 0.41–0.87) than in the wet season (R 2 : 0.18–0.49). Forest and cropland or pasture classes showed contrasting relationships in the dry season. Finally, we found that forest structure exhibited stronger relationships with ET and LST in the most disturbed forests (R 2 : 0.01–0.43) than in the least disturbed forests (R 2 < 0.05). Our findings help to elucidate degraded forests functioning under a changing climate and to improve estimates of water and energy fluxes in Amazonian degraded forests.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Dynamics of Intact MexAB-OprM Efflux Pump: Focusing on the MexA-OprM Interface

Antibiotic efflux is one of the most critical mechanisms leading to bacterial multidrug resistance. Antibiotics are effluxed out of the bacterial cell by a tripartite efflux pump, a complex machinery comprised of outer membrane, periplasmic adaptor, and inner membrane protein components. Understanding the mechanism of efflux pump assembly and its dynamics could facilitate discovery of novel approaches to counteract antibiotic resistance in bacteria. We built here an intact atomistic model of the Pseudomonas aeruginosa MexAB-OprM pump in a Gram-negative membrane model that contained both inner and outer membranes separated by a periplasmic space. All-atom molecular dynamics (MD) simulations confirm that the fully assembled pump is stable in the microsecond timescale. Using a combination of all-atom and coarse-grained MD simulations and sequence covariation analysis, we characterized the interface between MexA and OprM in the context of the entire efflux pump. These analyses suggest a plausible mechanism by which OprM is activated via opening of its periplasmic aperture through a concerted interaction with MexA.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Stochastic Optical Reconstruction Microscopy Imaging of Microtubule Arrays in Intact Arabidopsis thaliana Seedling Roots

Super-resolution fluorescence microscopy has generated tremendous success in revealing detailed subcellular structures in animal cells. However, its application to plant cell biology remains extremely limited due to numerous technical challenges, including the generally high fluorescence background of plant cells and the presence of the cell wall. In the current study, stochastic optical reconstruction microscopy (STORM) imaging of intact Arabidopsis thaliana seedling roots with a spatial resolution of 20–40nm was demonstrated. Using the super-resolution images, the spatial organization of cortical microtubules in different parts of a whole Arabidopsis root tip was analyzed quantitatively, and the results show the dramatic differences in the density and spatial organization of cortical microtubules in cells of different differentiation stages or types. The method developed can be applied to plant cell biological processes, including imaging of additional elements of the cytoskeleton, organelle substructure, and membrane domains.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Spectroscopic evidence for intact carbonic acid stabilized by halide anions in the gas phase

Here we show elusive carbonic acid being effectively stabilized in the gas phase by interacting with halide anions X – (X = F, Cl, Br, and I). The formed H 2 CO 3 ·X – complexes, characterized by negative ion photoelectron spectroscopy and ab initio calculations, all contain intact trans – trans carbonic acid binding onto the respective halide via two identical strong ionic O–H...X – hydrogen bonds. For X = Cl, Br, and I, the complex spectra exhibit the corresponding X – signature by simply shifting to the higher binding energy side, while an extremely 2 eV wide broader band is observed for X = F. This spectroscopic evidence indicates that an excess electron is removed from each halide in the former case, while a proton is transferred from carbonic acid to fluoride upon electron detachment for the latter. The above H 2 CO 3 ·X – structures as well as those of the previously studied H 2 SO 4 ·X – along the homologous halogen series cannot be explained using the proton affinity (PA) argument. Instead, a qualitative correlation is found between these structural motifs and the constituent acid p K a values, strongly suggesting that p K a is a more suitable factor to predict correct acid–base chemistry between these diprotic oxyacids and halides.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Fast imaging of intact and shattered cryogenic neon pellets

Compact condensed-matter injection technologies are increasingly used in magnetic fusion. One recent application is in disruption mitigation. An imaging system with less-than-100-µm- and sub-µs-resolution is described and used to characterize intact and shattered cryogenic neon pellets. Shattered pellets contain fine particles ranging from tens of µm to about 7 mm. Time-of-flight analyses indicate that pellets could slow down if hitting the wall of the guide tube. Fast high-resolution imaging systems are thus useful to neon and other condensed-matter injector development.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2014

A setup for simultaneous measurement of infrared spectra and light scattering signals: Watching amyloid fibrils grow from intact proteins

A setup for the simultaneous measurement of mid-infrared spectra and static light scattering is described that can be used for the analysis of the formation of nanoscale and microscopic aggregates from smaller molecules to biopolymers. It can be easily integrated into sample chambers of infrared spectrometers or combined with laser beams from tunable infrared lasers. Here, its use for the analysis of the formation of amyloid fibrils from intact proteins is demonstrated. The formation of amyloid fibrils or plaques from proteins is a widespread and pathogenetic relevant process, and a number of diseases are caused and correlated with the deposition of amyloid fibrils in cells and tissues. The molecular mechanisms of these transformations, however, are still unclear. We report here the simultaneous measurement of infrared spectra and static light scattering for the analysis of fibril formation from egg-white lysozyme. The transformation of the native form into non-native forms rich in β-sheet structure is measured by analysis of the amide I spectral region in the infrared spectra, which is sensitive for local structures. At the same time, light scattering signals at forward direction as well as the forward/backward ratio, which are sensitive for the number of scattering centers and their approximate sizes, respectively, are collected for the analysis of fibril growth. Thermodynamic and kinetic parameters as well as mechanistic information are deduced from the combination of the two complementary techniques.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Isotopomer-selective spectra of a single intact H 2 O molecule in the Cs + (D 2 O) 5 H 2 O isotopologue: Going beyond pattern recognition to harvest the structural information encoded in vibrational spectra

We report the vibrational signatures of a single H 2 O water molecule occupying distinct sites of the hydration network in the Cs + (H 2 O) 6 cluster. This is accomplished using isotopomer selective IR-IR hole-burning on the Cs + (D 2 O) 5 (H 2 O) clusters formed by gas-phase exchange of a single, intact H 2 O molecule for D 2 O in the Cs + (D 2 O) 6 ion. The OH stretching pattern of the Cs + (H 2 O) 6 isotopologue is accurately recovered by superposition of the isotopomer spectra, thus establishing that the H 2 O incorporation is random and that the OH stretching manifold is largely due to contributions from decoupled water molecules. This behavior enables a powerful new way to extract structural information from vibrational spectra of size-selected clusters by explicitly identifying the local environments responsible for specific infrared features. The Cs + (H 2 O) 6 structure was unambiguously assigned to the 4.1.1 isomer (a homodromic water tetramer with two additional flanking water molecules) from the fact that its computed IR spectrum matches the observed overall pattern and recovers the embedded correlations in the two OH stretching bands of the water molecule in the Cs + (D 2 O) 5 (H 2 O) isotopomers. The 4.1.1 isomer is the lowest in energy among other candidate networks at advanced (e.g., CCSD(T)) levels of theoretical treatment after corrections for (anharmonic) zero-point energy (ZPE). With the structure in hand, we then explore the mechanical origin of the various band locations using a local electric field formalism. Furthermore, this approach promises to provide a transferrable scheme for the prediction of the OH stretching fundamentals displayed by water networks in close proximity to solute ions.

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

Seedling Chloroplast Responses Induced by N-Linolenoylethanolamine Require Intact G-Protein Complexes

In animals, several long-chain N-acylethanolamines (NAEs) have been identified as endocannabinoids and are autocrine signals that operate through cell surface G-protein coupled, cannabinoid receptors. Despite the occurrence of N-acylethanolamines in land plants, including non-vascular plants, their precise signaling properties and molecular targets are not well defined. Here we show that the activity of N-linolenoylethanolamine (NAE 18:3) requires an intact G-protein complex. Specifically, genetic ablation of the Gβγ dimer or loss of the full set of atypical Gα subunits strongly attenuates an NAE 18:3-induced de-greening of cotyledons in Arabidopsis seedlings. This effect involves, at least in part, transcriptional regulation of chlorophyll biosynthesis and catabolism genes. In addition, there is feedforward transcriptional control of G-protein signaling components and G-protein interactors. These results are consistent with NAE 18:3 being a lipid signaling molecule in plants with a requirement for G-proteins to mediate signal transduction, a situation similar, but not identical, to the action of NAE endocannabinoids in animal systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Dielectric Spectroscopy on Thermally Aged, Intact Poly-vinyl Chloride/Ethylene Propylene Rubber (PVC/EPR) Multipolar Cables

As a contribution to condition monitoring diagnostics on low voltage cables used in nuclear power plants, this work shows that broadband dielectric spectroscopy can be an effective technique to assess aging state of these cables. Broadband dielectric spectroscopy has been performed on three-conductor (tri-core) cables, insulated by EPR with PVC jacket. The main challenge has been to perform the measurement on the intact cables, by means of a custom-built connector, conceiving a non-destructive and non-intrusive technique. Results show that capacitance and dissipation factor can provide information about the aging state of the cable, without the need to destroy the sample in the measurement process.

dielectric spectroscopy, nondestructive evaluation↗
DOE OSTI2020

Visualizing subcellular rearrangements in intact β cells using soft x-ray tomography

Characterizing relationships between cell structures and functions requires mesoscale mapping of intact cells showing subcellular rearrangements following stimulation; however, current approaches are limited in this regard. Here, we report a unique application of soft x-ray tomography to generate three-dimensional reconstructions of whole pancreatic β cells at different time points following glucose-stimulated insulin secretion. Reconstructions following stimulation showed distinct insulin vesicle distribution patterns reflective of altered vesicle pool sizes as they travel through the secretory pathway. Our results show that glucose stimulation caused rapid changes in biochemical composition and/or density of insulin packing, increased mitochondrial volume, and closer proximity of insulin vesicles to mitochondria. Costimulation with exendin-4 (a glucagon-like peptide-1 receptor agonist) prolonged these effects and increased insulin packaging efficiency and vesicle maturation. This study provides unique perspectives on the coordinated structural reorganization and interactions of organelles that dictate cell responses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Utah FORGE: Pump and Probe Test on an Intact Westerly Granite Sample

This dataset contains results from a pump and probe experiment conducted on an intact Westerly Granite sample with a diameter of 1 inch and a height of 1 3/8 inches. The experiment was performed within an aluminum triaxial pressure vessel (TEMCO) to investigate the non-linear acoustic parameters of the sample under varying axial pressures. The confining pressure was maintained at 4 MPa, while the axial pressure was incrementally increased from 1 MPa to 17 MPa before being reduced back to 1 MPa. 5 dynamic pressure oscillations of 0.5 MPa were applied over a 10 minute interval. The dataset includes pump controller data, linear variable differential transformer (LVDT) measurements, and acoustic data. The pump controller data tracks the confining and axial pressures, flow rates, and pump volumes. LVDT measurements provide detailed records of the axial displacement of the cell piston. Additionally, acoustic data captured by s-wave transducers is archived in a compressed file.

15 GEOTHERMAL ENERGY↗
DOE OSTI2015

Experimental Investigation of Two-Phase Flow in Consolidating and Intact Salt: Analysis of Capillary Pressure Measurements from Core Labs

Two-phase flow of brine and air through very low permeability porous media is the dominant fluid flow state in and around geologic repositories for nuclear waste disposal. Constitutive models developed for other subsurface media (shale, sandstone, limestone, etc.) have been adopted but never experimentally parameterized for geologic salt. This report summarizes results of scoping capillary pressure and brine saturation measurements on reconsolidated run-of-mine salt and intact geologic salt samples. These measurements were obtained using mercury injection tests and yielded values of threshold pressure, pore-size distribution, and mercury saturation. The brine capillary pressure curve was then inferred from the raw mercury capillary pressure data. This report also summarizes estimates of the constitutive model parameters from the brine saturation and capillary pressure data (Brooks and Corey, 1964; van Genuchten, 1980). The results suggests that the model of van Genuchten (1980) is better suited for brine-air-salt systems. Additional testing is needed for the low brine saturation range of the capillary pressure curve where the present suite of tests did not yield sufficient data.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗