Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Function analysis”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 775 records · Page 43
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

miR-217 suppresses proliferation and promotes apoptosis in cardiac myxoma by targeting Interleukin-6

Cardiac myxoma (CM) is a prevalent primary cardiac tumor. miR-217 plays a vital role in tumorigenesis of various cancers, however, its role and underlying molecular mechanism in human CM remain poorly understood. Here, we reported that the expression of miR-217 was downregulated in CM tissues and inversely correlated with the expression of Interleukin-6 (IL-6) mRNA. Gain-of-function analysis indicated that overexpression of miR-217 inhibited the proliferation and promoted the apoptosis of the primary CM cells. Bioinformatics analysis showed that IL-6 was a direct target gene of miR-217, which is confirmed by the dual luciferase assays. Moreover, downregulation of IL-6 by small interference RNA (siRNA) mimicked the tumor-suppressive effects of miR-217 in CM. Furthermore, rescue experiments pointed out that restoration of IL-6 expression abrogated the anti-proliferative and pro-apoptotic effect induced by miR-217 overexpression in CM cells. Taken together, we validated that miR-217 could act as a tumor suppressor in CM by directly targeting 3′UTR of IL-6 gene, indicating that manipulation of miR-217 may be a potential therapeutic strategy for CM patients. - Highlights: • Lower expression of miR-217 and higher expression of IL-6 mRNA was observed in CM tissues. • miR-217 overexpression suppressed proliferation and promoted apoptosis of primary CM cells. • miR-217 targeted IL-6 3′-UTR to inhibit its expression. • Reintroduction of IL-6 reversed the effect of miR-217 overexpression on CM cell proliferation and apoptosis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Roles of surface Mn(III) and MgOH + /CaOH + complexation in photochemically assisted Mn 2+ oxidation and Todorokite formation

Todorokite, a Mn oxide phase commonly found in seafloor Mn nodules, is one of the most abundant Mn oxides in nature and has wide applications in environmental engineering, including heavy metal remediation, contaminant adsorption for water purification, and catalysis for organic pollutant degradation. However, traditional abiotic formation of todorokite reported to date typically requires high temperature, pressure, and pH outside circumneutral conditions, or involves several days of phase transformations from precursor phases. In this study, we demonstrate rapid todorokite formation within 6 h via photochemically assisted oxidation of Mn 2+ (aq) in the presence of Mg 2+ or Ca 2+ , notably at ambient temperature and pressure. The concentrations of aqueous MgOH + and CaOH + , as well as the pH (initial 9 or 6), had significant collective influences on the crystalline phases of the formed Mn oxide solids. The proportions of the Mn oxidation states (IV, III, and II) and the extent of Mn(III) surface complexation with MgOH + or CaOH + controlled the crystalline phases (todorokite, feitknechtite, and birnessite) and the extent of cation incorporation into the resulting Mn oxide solids. Specifically, the oxidation state of Mn influenced the crystallization of different Mn oxide phases, and the formed Mn(III) complexed with MgOH + or CaOH + facilitated the formation of todorokite, along with cation incorporation. X-ray pair distribution function analysis revealed that incorporated Mg species were located at the inside corner sites of the 5 × 3 MnO 6 octahedral tunnel structure of todorokite, suggesting complexation between MgOH + and Mn(III) at the corners of the tunnel. Furthermore, this study provides novel insights into the elusive formation of todorokite and its potential for applications in advanced water treatment and environmental remediation.

Abiotic Mn2+ oxidation↗
DOE OSTI2024

Structural basis of selective TRPM7 inhibition by the anticancer agent CCT128930

TRP channels are implicated in various diseases, but high structural similarity between them makes selective pharmacological modulation challenging. Here, we study the molecular mechanism underlying specific inhibition of the TRPM7 channel, which is essential for cancer cell proliferation, by the anticancer agent CCT128930 (CCT). Using cryo-EM, functional analysis, and MD simulations, we show that CCT binds to a vanilloid-like (VL) site, stabilizing TRPM7 in the closed non-conducting state. Similar to other allosteric inhibitors of TRPM7, NS8593 and VER155008, binding of CCT is accompanied by displacement of a lipid that resides in the VL site in the apo condition. Moreover, we demonstrate the principal role of several residues in the VL site enabling CCT to inhibit TRPM7 without impacting the homologous TRPM6 channel. Hence, our results uncover the central role of the VL site for the selective interaction of TRPM7 with small molecules that can be explored in future drug design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

The storage performance of automotive cryo-compressed hydrogen vessels

Cryo-compressed hydrogen storage promises to deliver the highest system storage density leading to practical vehicles with range comparable to today's gasoline vehicles and fundamental cost and safety advantages. Yet, cryogenic vessels are complex systems, continuously drifting in thermodynamic space depending on use patterns, insulation performance, vessel characteristics, liquid hydrogen pump performance, and para-H 2 to ortho-H 2 conversion. In this paper, cryogenic vessel fill density results from a previous publication are extended to calculate system storage performance, including volumetric (gH 2 /L), gravimetric (H 2 weight fraction), and vent losses over a broad range of conditions. The results validate previous experiments and models indicating that cryogenic pressure vessels have maximum system density of all available storage technologies while avoiding vent losses in all but the most extreme situations. Design pressures in the range 250–350 bar seem most advantageous due to high system density and low weight and cost, although determining an optimum pressure demands a complete economic and functional analysis. Future insulation, vessel, and liquid hydrogen pump improvements are finally analyzed that, while not experimentally exhibited to date, show promise of being feasible in the future as their level of technical maturity increases, leading to maximum H 2 storage performance for cryo-compressed storage. If proven feasible and incorporated into future cryogenic vessels, these improvements will enable 50 + gH 2 /L system density at 10+% H 2 weight fraction.

08 HYDROGEN↗
DOE OSTI2022

Hot-melt extrudability of amorphous solid dispersions of flubendazole-copovidone: An exploratory study of the effect of drug loading and the balance of adjuvants on extrudability and dissolution

The FDA-approved anthelmintic flubendazole has shown potential to be repositioned to treat cancer and dry macular degeneration; however, its poor water solubility limits its use. Amorphous solid dispersions may overcome this challenge, but the balance of excipients may impact the preparation method and drug release. Here, we evaluate the influence of adjuvants and drug loading on the development of an amorphous solid dispersion of flubendazole-copovidone by hot-melt extrusion. The drug, copovidone, and adjuvants (magnesium stearate and hydroxypropyl cellulose) mixtures were statistically designed, and the process was performed in a twin-screw extruder. The study showed that flubendazole and copovidone mixtures were highly extrudable, except when drug loading was high (>40%). Furthermore, magnesium stearate positively impacted the extrusion and was more effective than hydroxypropyl cellulose. The extruded materials were evaluated by modulated differential scanning calorimetry and X-ray powder diffraction, obtaining positive amorphization and physical stability results. Pair distribution function analysis indicated the presence of drug rich domains with medium-range order structure and no evidence of polymer-drug interaction. All extrudates presented faster dissolution (HCl, pH 1.2) than pure flubendazole, and both adjuvants had a notable influence on the dissolution rate. In conclusion, hot-melt extrusion may be a viable option to obtain stable flubendazole: copovidone amorphous dispersions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Sas20 is a highly flexible starch-binding protein in the Ruminococcus bromii cell-surface amylosome

Ruminococcus bromii is a keystone species in the human gut that has the rare ability to degrade dietary resistant starch (RS). This bacterium secretes a suite of starch-active proteins that work together within larger complexes called amylosomes that allow R. bromii to bind and degrade RS. Starch adherence system protein 20 (Sas20) is one of the more abundant proteins assembled within amylosomes, but little could be predicted about its molecular features based on amino acid sequence. Here, we performed a structure–function analysis of Sas20 and determined that it features two discrete starch-binding domains separated by a flexible linker. We show that Sas20 domain 1 contains an N-terminal β-sandwich followed by a cluster of α-helices, and the nonreducing end of maltooligosaccharides can be captured between these structural features. Furthermore, the crystal structure of a close homolog of Sas20 domain 2 revealed a unique bilobed starch-binding groove that targets the helical α1,4-linked glycan chains found in amorphous regions of amylopectin and crystalline regions of amylose. Affinity PAGE and isothermal titration calorimetry demonstrated that both domains bind maltoheptaose and soluble starch with relatively high affinity (K d ≤ 20 μM) but exhibit limited or no binding to cyclodextrins. Finally, small-angle X-ray scattering analysis of the individual and combined domains support that these structures are highly flexible, which may allow the protein to adopt conformations that enhance its starch-targeting efficiency. Taken together, we conclude that Sas20 binds distinct features within the starch granule, facilitating the ability of R. bromii to hydrolyze dietary RS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Theory meets experiment: Insights into structure and magnetic properties of Fe 1-x Ni x B alloy

Here, we studied the structural and magnetic properties of the solid solution Fe 1-x Ni x B through theoretical and experimental approaches. Powder X-ray diffraction, X-ray Pair Distribution Function analysis, and energy dispersive X-ray spectroscopy reveal that the Fe 1-x Ni x B solid solution crystallizes in the β-FeB structure type up to x = 0.6–0.7 and exhibits anisotropic unit cell volume contraction with increasing Ni concentration. Magnetic measurements showed a transition from ferromagnetism to paramagnetism around x = 0.7. For x = 0.5, the low (< 0.3 μ B ) magnetic moments suggest itinerant magnetism despite the relatively high Curie temperature (up to 225 K). Theoretical calculations indicated different types of magnetic orderings depending on the Fe/Ni atomic order, with the antiferromagnetic state being stable for ordered FeNiB 2 , whereas the ground state is ferromagnetic for the disordered alloy. Calculations also predicted the coexistence of low- and high-spin states in Fe atoms around the composition with x = 0.5, in line with the experimental evidence from 57 Fe Mössbauer spectroscopy. The two magnetically distinct Fe sites for x = 0.3, 0.4, and 0.5 observed by 57 Fe Mössbauer spectroscopy can also be interpreted as two magnetically different regions or clusters. The formation of these clusters could affect the critical behavior near a quantum magnetic transition based on a potential ferromagnetic quantum critical point identified computationally and experimentally near x = 0.64. This work highlights the complex interplay between structure and magnetism in Fe 1-x Ni x B alloys, suggesting areas for future research on quantum critical behavior.

Bhaskar, Gourab [Iowa State Univ., Ames, IA (Unite↗
DOE OSTI2016

Structural Basis for Noncanonical Substrate Recognition of Cofilin/ADF Proteins by LIM Kinases

Cofilin/actin-depolymerizing factor (ADF) proteins are critical nodes that relay signals from protein kinase cascades to the actin cytoskeleton, in particular through site-specific phosphorylation at residue Ser3. This is important for regulation of the roles of cofilin in severing and stabilizing actin filaments. Consequently, cofilin/ADF Ser3 phosphorylation is tightly controlled as an almost exclusive substrate for LIM kinases. Here we determine the LIMK1:cofilin-1 co-crystal structure. We find an interface that is distinct from canonical kinase-substrate interactions. We validate this previously unobserved mechanism for high-fidelity kinase-substrate recognition by in vitro kinase assays, examination of cofilin phosphorylation in mammalian cells, and functional analysis in S. cerevisiae. The interface is conserved across all LIM kinases. Remarkably, we also observe both pre- and postphosphotransfer states in the same crystal lattice. Furthermore, this study therefore provides a molecular understanding of how kinase-substrate recognition acts as a gatekeeper to regulate actin cytoskeletal dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Unraveling local structures of Salt-in-Water and Water-in-Salt electrolytes via ab initio molecular dynamics

Water-in-salt electrolytes (WiSE) are attractive for electrochemical energy storage applications owing to their wide electrochemical stability windows and inherent safety. The high concentration of salts is widely known to suppress the decomposition of water, which otherwise limits the stability of conventional aqueous salt-in-water electrolytes (SiWE). Nevertheless, the microstructural features of WiSE that lead to this enhanced stability have not yet been fully elucidated. In this work, ab initio molecular dynamics simulations were performed to study the energetic, structural, and spectroscopic properties of LiTFSI SiWE and WiSE solutions. A detailed mapping of water-water and water-anion hydrogen bonding and cation–anion electrostatic interactions is reported for both electrolytes. Structural features are presented in terms of both radial and spatial distribution functions. Analysis of IR and vibrational power spectra reveal key differences in the intermolecular interactions in SiWE and WiSE that arise from modified solvation shell structures. Finally, the results obtained herein reveal the most important structural and spectroscopic differences between the electrolytes in normal and superconcentrated concentrations.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Probing lead acetate in solution using X-ray diffraction

Here, for the purpose of water purification involving toxic metal sensing and removal, high energy X-ray diffraction experiments have been performed on lead acetate Pb(Ac) 2 solutions, liquid and amorphous glutathione disulfide (GSSG), and their mixtures. The data have been interpreted using Empirical Potential Structure Refinement and pair distribution function analysis. At the highest concentration of 1 M Pb(Ac) 2 in water, the lead molecules are found to cluster and the second shell in the water structure becomes slightly more ordered as the water molecules become compressed. Liquid and amorphous GSSG are found to hydrogen bond primarily via OH-O interactions, while NH-O bonds are much more distorted. Aqueous solutions of Pb(Ac) 2 + GSSG show the closest Pb-O (carboxyl) and Pb-N (amine) bonds both at a distance of 2.5 ± 0.1 Å at a concentration of 1 M Pb(Ac) 2 in water. At 0.75 M Pb(Ac) 2 in water, strong Pb-S bonds are found at a distance of 2.8 ± 0.1 Å. The implications for lead removal using capacitive deionization are discussed.

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

Uranium measurements in the field using high-resolution cadmium zinc telluride detectors

A new generation of cadmium zinc telluride (CZT) detectors has become available and is being evaluated by the International Atomic Energy Agency (IAEA) for safeguards verifications in the field. The new CZT detector, model M400, is a room temperature spectrometer manufactured by H3D, Inc. The M400 demonstrates superior energy resolution, effective isotope identification capabilities, and convenient usability features when tested in a controlled laboratory environment. These characteristics define the M400 as a potential platform for IAEA field detection applications, which could become suitable for nuclear material characterization (e.g., enrichment verification) and nuclear safeguards missions. The capabilities of gamma spectrometry codes including Fixed energy, Response function Analysis with Multiple efficiencies (FRAM) from Los Alamos National Laboratory, CZT for Uranium (CZTU) from Lawrence Livermore National Laboratory, and Gamma Detector Response and Analysis Software (GADRAS) from Sandia National Laboratories were adapted for M400 spectra, and the performance of the codes has been validated. This was reported in a prior work. To further validate the performance of the high-energy resolution CZT detector and the isotopic analysis codes, a field measurement campaign consisting of uranium hexafluoride (UF 6 ) cylinder measurements was conducted at a fuel fabrication facility. A total of 34 Type 30B cylinders containing UF6 were measured using three different M400 CZT detectors. Each detector was outfitted with a custom rectangular collimator and shield made out T-Flex®, a tungsten-impregnated polymer. Measurements were performed at three different locations of the cylinder, ensuring that the measurement geometry satisfied the infinite thickness criterion. The spectra from the M400 CZT were analyzed using the code General Enrichment Meter (GEM). For analyzing the gamma-ray spectra from UF 6 cylinder, the GEM code is the appropriate tool since it relies only on the gamma-ray emissions from 235 U and not from other isotopes. Results from the spectral analysis were compared with the known abundance of 235 U in the cylinders, as well as with the International Target Values 2020 (ITV2020). The suitability of the different underlying techniques used by the various codes for UF 6 analysis is discussed. The challenges of measuring UF 6 contained in cylinders and mitigation strategies are highlighted.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2016

Advances and perspectives on the use of CRISPR/Cas9 systems in plant genomics research

Genome editing with site-specific nucleases has become a powerful tool for functional characterization of plant genes and genetic improvement of agricultural crops. Among the various site-specific nuclease-based technologies available for genome editing, the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems have shown the greatest potential for rapid and efficient editing of genomes in plant species. Here, this article reviews the current status of application of CRISPR/Cas9 to plant genomics research, with a focus on loss-of-function and gain-of-function analysis of individual genes in the context of perennial plants and the potential application of CRISPR/Cas9 to perturbation of gene expression, as well as identification and analysis of gene modules as part of an accelerated domestication and synthetic biology effort.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Screening a phage display library for a novel FGF8b-binding peptide with anti-tumor effect on prostate cancer

Fibroblast growth factor 8b (FGF8b) is the major isoform of FGF8 expressed in prostate cancer and it correlates with the stage and grade of the disease. FGF8b has been considered as a potential target for prostate cancer therapy. Here we isolated 12 specific FGF8b-binding phage clones by screening a phage display heptapeptide library with FGF8b. The peptide (HSQAAVP, named as P12) corresponding to one of these clones showed high homology to the immunoglobulin-like (Ig-like) domain II(D2) of high-affinity FGF8b receptor (FGFR3c), contained 3 identical amino acids (AVP) to the authentic FGFR3 D2 sequence aa 163–169 (LLAVPAA) directly participating in ligand binding, carried the same charges as its corresponding motif (aa163–169) in FGFR3c, suggesting that P12 may have a greater potential to interrupt FGF8b binding to its receptors than other identified heptapeptides do. Functional analysis indicated that synthetic P12 peptides mediate significant inhibition of FGF8b-induced cell proliferation, arrest cell cycle at the G0/G1 phase via suppression of Cyclin D1 and PCNA, and blockade of the activations of Erk1/2 and Akt cascades in both prostate cancer cells and vascular endothelial cells. The results demonstrated that the P12 peptide acting as an FGF8b antagonist may have therapeutic potential in prostate cancer. - Highlights: ► A novel FGF8b-binding peptide P12 was isolated from a phage display library. ► The mechanisms for P12 peptide inhibiting cell proliferation were proposed. ► P12 caused cell cycle arrest at G0/G1 phase via suppression of Cyclin D1 and PCNA. ► P12 suppressed FGF8b-induced activations of Akt and MAP kinases. ► P12 acting as an FGF8b antagonist may have therapeutic potential in prostate cancer.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Synthesis of cerium oxide (CeO 2 ) by co-precipitation for application as a reference material for X-ray powder diffraction peak widths

Several methods can be used to obtain, from powder diffraction patterns, crystallite size and lattice strain of polycrystalline samples. Some examples are the Scherrer equation, Williamson–Hall plots, Warren/Averbach Fourier decomposition, Whole Powder Pattern Modeling, and Debye function analysis. To apply some of these methods, it is necessary to remove the contribution of the instrument to the widths of the diffraction peaks. Nowadays, one of the main samples used for this purpose is the LaB6 SRM660b commercialized by the National Institute of Standard Technology; the width of the diffraction peak of this sample is caused only by the instrumental apparatus. However, this sample can be expensive for researchers in developing countries. In this work, the authors present a simple route to obtain micron-sized polycrystalline CeO 2 that have a full width at half maximum comparable with the SRM660b and therefore it can be used to remove instrumental broadening.

de Lima Batista, Anderson Márcio↗
DOE OSTI2022

Chemical and Structural Alterations in the Amorphous Structure of Obsidian due to Nanolites

Obsidian is volcanic glass that results from the rapid cooling of silica-rich melt. Nanoscale crystallites precipitate out of the melt prior to solidification and remain embedded in the amorphous matrix. These crystallites provide information on the flow kinetics and composition of the melt. Due to the sparsity and size of nanolites, studies often focus on supramicron crystallites. This research takes advantage of the conchoidal fracture of obsidian by knapping samples with nanometer-thin edges for transmission electron microscopy characterization. Nanolites in the amorphous matrix are studied using energy-dispersive spectroscopy (EDS) and electron diffraction. Certain alkali and alkaline-earth cations exhibit patterns of depletion near Fe-oxide nanolites. EDS is used to identify nanolites and variations in the composition of the matrix. Parallel beam diffraction and radial distribution function analysis of nearest-neighbor distances determine average bond lengths in the matrix near nanolites, showing that nanolites influence the nearby short-range ordering and atomic character of the matrix. Analysis reveals decreased mean nearest-neighbor distances in the matrix adjacent to nanolites compared to the bulk. Our methods exhibit the required sensitivity to detect variations in the composition and structure near nanolites, and our findings indicate that obsidian nanolites contribute to quantifiable localized changes in the amorphous structure.

36 MATERIALS SCIENCE↗
DOE OSTI2021

High Throughput Mapping of Single Molecules’ Redox Potentials on Electrode

By synchronizing electrochemical potential scanning with a single-molecule localization super-resolution fluorescence microscope, kinetic fluorescence changes of hundreds of single molecular redox events were tracked simultaneously with high throughput, and subsequent cross-correlation function analysis mapped single molecules’ redox potentials (times) out on the imaging area from site to site in unprecedented detail by extracting electrochemically induced fluorescence change from apparently random fluorescence on/off blinking. This work paves the way toward mapping redox states at single-molecule levels in high throughput in chemical and biological systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Crystal Structure of Aspirin-Acetylated Human Cyclooxygenase-2: Insight into the Formation of Products with Reversed Stereochemistry

Aspirin and other nonsteroidal anti-inflammatory drugs target the cyclooxygenase enzymes (COX-1 and COX-2) to block the formation of prostaglandins. Aspirin is unique in that it covalently modifies each enzyme by acetylating Ser-530 within the cyclooxygenase active site. Acetylation of COX-1 leads to complete loss of activity, while acetylation of COX-2 results in the generation of the monooxygenated product 15(R)-hydroxyeicosatetraenoic acid (15R-HETE). Ser-530 has also been shown to influence the stereochemistry for the addition of oxygen to the prostaglandin product. In this work, we determined the crystal structures of S530T murine (mu) COX-2, aspirin-acetylated human (hu) COX-2, and huCOX-2 in complex with salicylate to 1.9, 2.0, and 2.4 Å, respectively. The structures reveal that (1) the acetylated Ser-530 completely blocks access to the hydrophobic groove, (2) the observed binding pose of salicylate is reflective of the enzyme–inhibitor complex prior to acetylation, and (3) the observed Thr-530 rotamer in the S530T muCOX-2 crystal structure does not impede access to the hydrophobic groove. On the basis of these structural observations, along with functional analysis of the S530T/G533V double mutant, we propose a working hypothesis for the generation of 15R-HETE by aspirin-acetylated COX-2. We also observe differential acetylation of COX-2 purified in various detergent systems and nanodiscs, indicating that detergent and lipid binding within the membrane-binding domain of the enzyme alters the rate of the acetylation reaction in vitro.

60 APPLIED LIFE SCIENCES↗