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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Spatially confined protein assembly in hierarchical mesoporous metal-organic framework

Immobilization of biomolecules into porous materials could lead to significantly enhanced performance in terms of stability towards harsh reaction conditions and easier separation for their reuse. Metal-Organic Frameworks (MOFs), offering unique structural features, have emerged as a promising platform for immobilizing large biomolecules. Although many indirect methods have been used to investigate the immobilized biomolecules for diverse applications, understanding their spatial arrangement in the pores of MOFs is still preliminary due to the difficulties in directly monitoring their conformations. To gain insights into the spatial arrangement of biomolecules within the nanopores. We used in situ small-angle neutron scattering (SANS) to probe deuterated green fluorescent protein (d-GFP) entrapped in a mesoporous MOF. Our work revealed that GFP molecules are spatially arranged in adjacent nanosized cavities of MOF-919 to form “assembly” through adsorbate-adsorbate interactions across pore apertures. Our findings, therefore, lay a crucial foundation for the identification of proteins structural basics under confinement environment of MOFs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Plastic recognition and electrogenic uniport translocation of 1 st -, 2 nd -, and 3 rd -row transition and post-transition metals by primary-active transmembrane P 1B-2 -type ATPase pumps

Transmembrane P 1B -type ATPase pumps catalyze the extrusion of transition metal ions across cellular lipid membranes to maintain essential cellular metal homeostasis and detoxify toxic metals. Zn(II)-pumps of the P 1B-2 -type subclass, in addition to Zn 2+ , select diverse metals (Pb 2+ , Cd 2+ and Hg 2+ ) at their transmembrane binding site and feature promiscuous metal-dependent ATP hydrolysis in the presence of these metals. Yet, a comprehensive understanding of the transport of these metals, their relative translocation rates, and transport mechanism remain elusive. We developed a platform for the characterization of primary-active Zn(II)-pumps in proteoliposomes to study metal selectivity, translocation events and transport mechanism in real-time, employing a “multi-probe” approach with fluorescent sensors responsive to diverse stimuli (metals, pH and membrane potential). Together with atomic-resolution investigation of cargo selection by X-ray absorption spectroscopy (XAS), we demonstrate that Zn(II)-pumps are electrogenic uniporters that preserve the transport mechanism with 1 st -, 2 nd - and 3 rd -row transition metal substrates. Promiscuous coordination plasticity, guarantees diverse, yet defined, cargo selectivity coupled to their translocation.

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

CRISPR-Cas12a bends DNA to destabilize base pairs during target interrogation

RNA-guided endonucleases are involved in processes ranging from adaptive immunity to site-specific transposition and have revolutionized genome editing. CRISPR-Cas9, -Cas12 and related proteins use guide RNAs to recognize ~20-nucleotide target sites within genomic DNA by mechanisms that are not yet fully understood. We used structural and biochemical methods to assess early steps in DNA recognition by Cas12a protein-guide RNA complexes. We show here that Cas12a initiates DNA target recognition by bending DNA to induce transient nucleotide flipping that exposes nucleobases for DNA-RNA hybridization. Cryo-EM structural analysis of a trapped Cas12a–RNA–DNA surveillance complex and fluorescence-based conformational probing show that Cas12a-induced DNA helix destabilization enables target discovery and engagement. This mechanism of initial DNA interrogation resembles that of CRISPR-Cas9 despite distinct evolutionary origins and different RNA-DNA hybridization directionality of these enzyme families. Our findings support a model in which RNA-mediated DNA interference begins with local helix distortion by transient CRISPR-Cas protein binding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Rhodol fluorophores for near-infrared imaging

The present disclosure encompasses embodiments of a novel near-infrared-emitting molecular fluorophore and probes incorporating said fluorophore advantageous for in vitro and in vivo research studies. The fluorophore is robust, photostable, and possesses functionalities for easy bioorthogonal conjugation (e.g., click chemistry, hydrazone formation, Diels Alder, Staudinger ligation, etc.). It is biocompatible and emits at 711 nm in aqueous conditions. These fluorophores may be used to fluorescently tag biological molecules or structures of interest, or used as optical reporters (i.e., activatable molecular probes, fluorescent dyes) for specific biomarkers/analytes as they can be switched from “off” to “on.” This fluorophore is useful for cellular assays and preclinical small animal imaging as the near-infrared emission is highly penetrating, and the photophysical properties are outstanding. As such, the properties of this class of fluorophores could easily be translated for use in clinical applications.

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

Demonstration of Selective Single-Barium Ion Detection with Dry Diazacrown Ether Naphthalimide Turn-on Chemosensors

Single-molecule fluorescence imaging (SMFI) of gas-phase ions has been proposed for “barium tagging,” a burgeoning area of research in particle physics to detect individual barium daughter ions. This has potential to significantly enhance the sensitivity of searches for neutrinoless double-beta decay (0νββ) that is obscured by background radiation events. The chemistry required to make such sensitive detection of Ba 2+ by SMFI in dry Xe gas at solid interfaces has implications for solid-phase detection methods but has not been demonstrated. Here, we synthesized simple, robust, and effective Ba 2+ -selective chemosensors capable of function within ultrapure high-pressure 136 Xe gas. Turn-on fluorescent naphthalimide-(di)azacrown ether chemosensors were Ba 2+ -selective and achieved SMFI in a polyacrylamide matrix. Here, fluorescence and NMR experiments supported a photoinduced electron transfer mechanism for turn-on sensing. Ba 2+ selectivity was achieved with computational calculations correctly predicting the fluorescence responses of sensors to barium, mercury, and potassium ions. With these molecules, dry-phase single-Ba 2+ ion imaging with turn-on fluorescence was realized using an oil-free microscopy technique for the first time—a significant advance toward single-Ba 2+ ion detection within large volumes of 136 Xe, plausibly enabling a background-independent technique to search for the hypothetical process of 0νββ.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

New Instrument for Time-Resolved OH and HO 2 Quantification in High-Pressure Laboratory Kinetics Studies

Here, we have constructed a new time-resolved high-pressure fluorescence assay by gas expansion (HP-FAGE) apparatus, optimized for the detection of OH and HO 2 radicals in complex gas-phase reactions. The new instrument fills a gap in the existing experimental toolkit for chemical kinetics by enabling the quantification of two key reactive species with microsecond time resolution from high-pressure sources, which was previously not attainable. The HP-FAGE is interfaced with a flow reactor, designed for pressures up to 100 bar and temperatures up to 1000 K, in which reactions are initiated by laser photolysis of radical precursors at repetition rates of 1–10 Hz. The HP-FAGE samples gas out of the reactor into a miniature FAGE chamber, where OH is detected by resonant laser-induced fluorescence using a time-delayed probe laser pulse. HO 2 is converted to OH via reaction with NO and then detected by OH fluorescence. The novel FAGE design places the probe region very close to the gas expansion, minimizing the transport time of sampled molecules and resulting in time resolution better than 20 μs for both OH and HO 2 . We calibrate the sensitivity of HP-FAGE, validate its performance with measurements of well-known reaction kinetics (OH + CH 4 , OH + OH, OH + HO 2 , and HO 2 + HO 2 ), and discuss prospects for its future use.

calibration↗
DOE OSTI2021

Visualizing Interfacial Jamming Using an Aggregation-Induced-Emission Molecular Reporter

With the interfacial jamming of nanoparticles (NPs), a load-bearing network of NPs forms as the areal density of NPs increases, converting the assembly from a liquid-like into a solid-like assembly. Unlike vitrification, the lineal packing of the NPs in the network is denser, while the remaining NPs can remain in a liquid-like state. It is a challenge to determine the point at which the assemblies jam, since both jamming and vitrification lead to a solid-like behavior of the assemblies. Herein, we show a real-time fluorescence imaging method to probe the evolution of the interfacial dynamics of NP surfactants at the water/oil interface using aggregation-induced emission (AIE) as a reporter for the transition of the assemblies into the jammed state. The AIEgens show typical fluorescence behavior at densities at which they can move and rotate. However, when aggregation of these fluorophores occurs, the smaller intermolecular separation distance arrests rotation, and a significant enhancement in the fluorescence intensity occurs.

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

Structure of V-defects in long wavelength GaN-based light emitting diodes

The V-defect is a naturally occurring inverted hexagonal pyramid structure that has been studied in GaN and InGaN growth since the 1990s. Strategic use of V-defects in pre-quantum well superlattices or equivalent preparation layers has enabled record breaking efficiencies for green, yellow, and red InGaN light emitting diodes (LEDs) utilizing lateral injection of holes through the semi-polar sidewalls of the V-defects. In this article, we use advanced characterization techniques such as scattering contrast transmission electron microscopy, high angle annular dark field scanning transmission electron microscopy, x-ray fluorescence maps, and atom probe tomography to study the active region compositions, V-defect formation, and V-defect structure in green and red LEDs grown on (0001) patterned sapphire and (111) Si substrates. We identify two distinct types of V-defects. The “large” V-defects are those that form in the pre-well superlattice and promote hole injection, usually nucleating on mixed (Burgers vector b = ±a±c⁠) character threading dislocations. In addition, “small” V-defects often form in the multi-quantum well region and are believed to be deleterious to high-efficiency LEDs by providing non-radiative pathways. The small V-defects are often associated with basal plane stacking faults or stacking fault boxes. Furthermore, we show through scattering contrast transmission electron microscopy that during V-defect filling, the threading dislocation, which runs up the center of the V-defect, will “bend” onto one of the six {10$\overline{1}$1} semi-polar planes. In conclusion, this result is essential to understanding non-radiative recombination in V-defect engineered LEDs.

42 ENGINEERING↗
DOE OSTI2022

Pectin-associated mannans and xylans play distinct roles in cell-cell adhesion in pine and poplar wood

Wood particles of pine required longer treatments of acidic chlorite and dilute alkali to achieve similar proportions of cell separation as of poplar. Chemical extraction and enzymatic digestion studies indicated that rhamnogalacturonan-I (RG-I), mannan and xylan contribute to cell-cell adhesion in pine wood. Mannan associated with lignin in an acidic chlorite fraction and with xylan in a dilute alkali fraction. RG-I and xylan were extracted in both chlorite and dilute alkali in poplar. Scanning electron microscopy and a probe diffusion study using Fluorescence Recovery After Photobleaching showed that lignin, RG-I and mannan initiated cell separation at cell corners and dilute alkali extraction of xylan was required for complete cell separation in pine. Cell-cell separation increased enzymatic saccharification within 24 h by 2-fold in poplar and 3.4-fold in pine. Finally, our results inform a strategy to reduce particle size in woody biomass and provide insights into different molecular bases of cell-cell adhesion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Enzyme-Directed Functionalization of Designed, Two-Dimensional Protein Lattices

The design and construction of crystalline protein arrays to selectively assemble ordered nanoscale materials has potential applications in sensing, catalysis and medicine. Whereas numerous designs have been implemented for the bottom-up construction of novel protein assemblies, the generation of artificial functional materials has been relatively unexplored. Enzyme-directed post-translational modifications are responsible for the functional diversity of the proteome and thus, could be harnessed to selectively modify artificial protein assemblies. In this study, we describe the use of phosphopantetheinyl transferases (PPTases), a class of enzymes that covalently modify proteins using coenzyme A (CoA), to site-selectively tailor the surface of designed, two-dimensional (2D) protein crystals. We demonstrate that a short peptide (ybbR) or a molecular tag (CoA) can be covalently tethered to 2D arrays to enable enzymatic functionalization using Sfp PPTase. Here, the site-specific modification of two different protein array platforms is facilitated by PPTases to afford both small-molecule- and protein-functionalized surfaces with no loss in crystalline order. This work highlights the potential for chemoenzymatic modification of large protein surfaces towards the generation of sophisticated protein platforms reminiscent of the complex landscape of cell surfaces.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Precise Linker Length and Dynamic Bond Exchange Control Penetrant Diffusion in Dense Vitrimers

Polymer networks with dynamic covalent bonds have been investigated for their self-healing ability, recyclability, and potential as more sustainable materials. Recent results have indicated that in some cases, bond exchange can enhance the transport of penetrants in dense networks, pointing to their potential for separations of membranes. Here, imine dynamic bonds in ethylene oxide (EO) networks with precise linker lengths were synthesized to investigate the transport of N,N′-bis(2,5-di-tert-butylphenyl)-3,4,9,10-perylenedicarboximide (BTBP), a large, anisotropic dye molecule. Networks with mesh sizes smaller than, comparable to, and greater than the size of the penetrant axes were investigated to probe the effects of bond exchange and network confinement on transport. Mesh sizes, which ranged from 0.5 to 1.62 nm, were determined from shear rheology, glass transitions by calorimetry, and probe diffusion coefficients by fluorescence recovery after photobleaching. Permanent networks with identical EO chain lengths were prepared as control samples, and up to a 3 orders of magnitude increase in diffusion coefficient is observed in the dynamic systems for short linkers containing 13 backbone atoms. The longest linkers with 71 backbone atoms show no difference between the permanent and dynamic networks. Linkers shorter than 11 backbone atoms, corresponding to a mesh size smaller than the penetrant small axis, diffusion is no longer observable on the experimental time scale, indicating a sharp cutoff attributed to the precise linkers and narrow mesh size distribution. The dynamic imine exchange time scales were compared to the diffusive hopping times of penetrants and indicate that exchange can occur during a diffusive displacement. Furthermore, these findings provide insights into the factors affecting penetrant transport in dense polymers and inspire the development of next-generation selective polymer membranes.

Diffusion↗
DOE OSTI2021

Synthase-Selective Exploration of a Tunicate Microbiome by Activity-Guided Single-Cell Genomics

While thousands of environmental metagenomes have been mined for the presence of novel biosynthetic gene clusters, such computational predictions do not provide evidence of their in vivo biosynthetic functionality. Using fluorescent in situ enzyme assay targeting carrier proteins common to polyketide (PKS) and nonribosomal peptide synthetases (NRPS), we applied fluorescence-activated cell sorting to tunicate microbiome to enrich for microbes with active secondary metabolic capabilities. Single-cell genomics uncovered the genetic basis for a wide biosynthetic diversity in the enzyme-active cells and revealed a member of marine Oceanospirillales harboring a novel NRPS gene cluster with high similarity to phylogenetically distant marine and terrestrial bacteria. Interestingly, this synthase belongs to a larger class of siderophore biosynthetic gene clusters commonly associated with pestilence and disease. Furthermore, this demonstrates activity-guided single-cell genomics as a tool to guide novel biosynthetic discovery.

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

Action at a distance: The remarkable coupling of CO 2 uptake to electron transfer in specialized cyanobacterial NDH-1 complexes

Cyanobacteria achieve highly efficient photosynthesis using a CO 2 -concentrating mechanism relying on specialized Type I (NDH-1) complexes. Among these, NDH-1 3 and NDH-1 4 catalyze redox-coupled hydration of CO 2 to bicarbonate, supporting carbon fixation in carboxysomes. The mechanism of coupling electron transfer to CO 2 -hydration by these variant NDH-1 complexes remains unknown. We engineered a Synechococcus PCC7942 strain that expresses exclusively the high flux/low affinity NDH-14 complex, enabling the observation of the coupling of CO 2 hydration to cyclic electron flow in isolation from the other NDH-1 isoforms normally present in cells. We found that inhibition of the CupB protein by the carbonic anhydrase inhibitor ethoxzolamide (EZ) suppressed CO 2 uptake, slowed photosystem I rereduction, and abolished proton pumping as probed by acridine orange fluorescence. These effects were absent in strains lacking Cup proteins, confirming specificity. The results demonstrate that CO 2 hydration and electron transfer through NDH-14 are tightly coupled via proton translocation across the thylakoid membrane. These findings provide direct evidence for the bidirectional interaction in bioenergetic coupling between the plastoquinone reduction and the CO 2 uptake at the distal Zn-site over a span of ~150 Å and support a proton-removal hypothesis involving the proton transfer pathways from the Zn-site of CO2 hydration to an energetically coupled proton loading site evolutionarily repurposed from the ancestral proton pumping mechanism to enable energetic CO 2 uptake.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Impact of PrsA on membrane lipid composition during daptomycin-resistance-mediated β-lactam sensitization in clinical MRSA strains

Abstract Background The cyclic anionic lipopeptide daptomycin is used in the treatment of severe infections caused by Gram-positive pathogens, including MRSA. Daptomycin resistance, although rare, often results in treatment failure. Paradoxically, in MRSA, daptomycin resistance is usually accompanied by a concomitant decrease in β-lactam resistance in what is known as the ‘see-saw effect’. This resensitization is extensively used for the treatment of MRSA infections, by combining daptomycin and a β-lactam antibiotic, such as oxacillin. Objectives We aimed: (i) to investigate the combined effects of daptomycin and oxacillin on the lipid composition of the cellular membrane of both daptomycin-resistant and -susceptible MRSA strains; and (ii) to assess the involvement of the post-translocational protein PrsA, which plays an important role in oxacillin resistance in MRSA, in membrane lipid composition and remodelling during daptomycin resistance/β-lactam sensitization. Results The combination of microbiological and biochemical studies, with fluorescence microscopy using lipid probes, showed that the lipid composition and surface charge of the daptomycin-resistant cells exposed to daptomycin/oxacillin were dependent on antibiotic concentration and directly associated with PrsA, which influenced cardiolipin remodelling/relocation. Conclusions Our findings show that PrsA, in addition to its post-transcriptional role in the maturation of PBP 2a, is a key mediator of cell membrane remodelling connected to the see-saw effect and may have a key role in the resensitization of daptomycin-resistant strains to β-lactams, such as oxacillin.

de Carvalho, Carla C. C. R.↗
DOE OSTI2023

Analysis of human invasive cytotrophoblasts demonstrates mosaic aneuploidy

A total of 24 chromosome-specific fluorescence in situ hybridization probes for interphase nucleus analysis were developed to determine the chromosomal content of individual human invasive cytotrophoblasts derived from in vitro cultured assays. At least 75% of invasive cytotrophoblasts were hyperdiploid and the total number of chromosomes ranged from 47 to 61. The results also demonstrated that these hyperdiploid invasive cytotrophoblasts showed significant heterogeneity. The most copy number gains were observed for chromosomes 13, 14, 15, 19, 21, and 22 with average copy number greater than 2.3. A parallel study using primary invasive cytotrophoblasts also showed a similar trend of copy number changes. Conclusively, 24-chromosome analysis of human non-proliferating cytotrophoblasts (interphase nuclei) was achieved. Hyperdiploidy and chromosomal heterogeneity without endoduplication in invasive cytotrophoblasts may suggest a selective advantage for invasion and short lifespan during normal placental development.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

DEVELOPMENT OF A QUANTUM ELECTRON BEAM DIAGNOSTIC APPARATUS

Spatial properties of electron beams are the essential parameters needed in particle physics and accelerator research. Beam characterization using optical detection methods through the interaction between photons and electrons such as Compton scattering, or electro-optic sampling of the electric field of electrons have been extensively explored and successfully implemented as non-invasive diagnostics at various accelerator facilities. However, such methods often suffer from inherently low sensitivity. Here we present the study of a new type of electron beam diagnostic device for direct optical imaging of electron beams at various energy levels. The concept is based on the extremely high sensitivity of atoms, prepared in a specific "dark superposition" quantum state, to the external electric or magnetic perturbations induced by the passing charged particle, which allows atoms to change polarization of the probe light or absorb probe light and to fluoresce, enabling direct 3D imaging of the charged particles with high resolution. We report our recent experiment results and the design effort on a compact apparatus intended to be tested with the relativistic electron beams at Jefferson Laboratory.

Zhang, S.↗
DOE OSTI2021

Quantum Enhanced Tracker

We report the study and development of a novel new charged particle detector, a "Quantum Enhanced Tracker" for 3D imaging of charged particle tracks. The proposed detector relies on, and benefits from, the extremely high sensitivity of atoms, prepared in a specific quantum superposition, to external perturbations. Atoms are prepared in a so-called "dark superposition" state, a passing charged particle will disturb this quantum state, allowing atoms to change polarization of the probe light or absorb probe light and to fluoresce, enabling direct imaging of the particle trajectory with high resolution. This method has similarities with Cherenkov detectors where a charged particle produces light along its track, but with the major advantages of enhanced sensitivity due to the low energy required to perturb the engineered quantum state, the ability to amplify the signal using a drive laser passing through the medium, and the ability to provide a 3D track.

Zhang, Shukui↗
DOE OSTI2023

Understanding Plant Signaling Via Innovations in Probe Delivery and Imaging

The goal of this project was to develop tools for studying plant processes in living tissues. We wanted a method for introducing probes for studying plant processes such that plants could remain intact and imaged iteratively. Towards this end, we successfully optimized carbon nanofibers that we showed could deliver non-permeable signaling probes/biomolecules to plant cells. These were created on a rigid backing and also successfully transferred to a flexible backing to use with curved plant structures. We also built fiber optic microscopes that permit iterative non-destructive fluorescence or light micrographs and created protocols and devices to stabilize plant organs during imaging. These tools were developed in conjunction with research aimed understanding receptor-mediated peptide trafficking and responses relevant to plant cell growth and defense tradeoff. During this project, we designed and built two fiberoptic fluorescence microscopes; (b) designed, fabricated and validated different nanospike designs for delivering probes to plants, including the feasibility of delivering DNA constructs for expression studies; (c) developed fluorescent peptide probes (active and inactive versions of a secreted receptor ligand called phytosulfokine or PSK) and performed mobility tests after application to plants using microscopy; (d) used appropriate genetic plant backgrounds to facilitate PSK trafficking and response mechanisms; (e) determined the transcriptional changes due to PSK-induced signaling related to growth/defense tradeoff; (f) performed experiments showing the growth/defense tradeoff involves repression of specific defense components in response to PSK. This project also involved the training of two PhD students and five Masters students.

47 OTHER INSTRUMENTATION↗