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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 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

IsoMatchMS : Open-Source Software for Automated Annotation and Visualization of High Resolution MALDI-MS Spectra

Due to its speed, accuracy, and adaptability to various sample types, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has become a popular method to identify molecular isotope profiles from biological samples. Often MALDI-MS data do not include tandem MS fragmentation data, and thus the identification of compounds in samples requires external databases so that the accurate mass of detected signals can be matched to known molecular compounds. Most relevant MALDI-MS software tools developed to confirm compound identifications are focused on small molecules (e.g., metabolites, lipids) and cannot be easily adapted to protein data due to their more complex isotopic distributions. Here, we present an R package called IsoMatchMS for the automated annotation of MALDI-MS data for multiple datatypes: intact proteins, peptides, and glycans. This tool accepts already derived molecular formulas or, for proteomics applications, can derive molecular formulas from a list of input peptides or proteins including proteins with post-translational modifications. In conclusion, visualization of all matched isotopic profiles is provided in a highly accessible HTML format called a trelliscope display, which allows users to filter and sort by several parameters such as match scores and the number of peaks matched. IsoMatchMS simplifies the annotation and visualization of MALDI-MS data for downstream analyses.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Non-Contact Vapor Detection of Illicit Drugs via Atmospheric Flow Tube-Mass Spectrometry

Real-time, non-contact detection of illicit drugs is a desirable goal for the interdiction of these controlled substances, but the relatively low vapor pressures of such species present a challenge for trace vapor detection technologies. The introduction of atmospheric flow tube-mass spectrometry (AFT-MS), which has previously been demonstrated to detect gas-phase analytes at low parts-per-quadrillion levels for explosives and organophosphorus compounds, also enables the potential for non-contact drug detection. With AFT-MS, direct vapor detection of cocaine and methamphetamine from ~5 µg residues at room temperature is demonstrated herein. Furthermore, thermal desorption of low- to sub-picogram levels of cocaine, methamphetamine, fentanyl, and heroin is observed via AFT-MS using a carrier flow rate of several L/min of air. These low levels can permit non-contact sampling through collection of vapor, effectively preconcentrating the analyte before desorption and analysis. Quantitative evaluation of the thermal desorption approach has yielded limits of detection (LODs) on order of 10 fg for cocaine and fentanyl, 100 fg for methamphetamine, and 1.6 pg for heroin. The LOD for heroin was lowered to 200 fg by using tributyl phosphate as a dopant to form a proton-bound heterodimer with heroin. When used with AFT-MS, the intentional formation of specific drug-dopant adducts has the potential to enhance detection limits and selectivity of additional drug species. Species that are prone to form adducts present a challenge to analysis, but that difficulty can be overcome by the intentional addition of a dopant. Molecules unlikely to form adducts will remain essentially unimpacted, but the adduct-forming species will interact with the dopant to compress the analyte signal into a single peak. This approach would be valuable in the application of non-contact screening for illicit substances via vapor collection followed by thermal desorption for analysis.

methamphetamine, cocaine, heroin, fentanyl, atmosp↗
DOE OSTI2022

Δ133p53 coordinates ECM-driven morphogenesis and gene expression in 3-dimensional mammary epithelial acini

Growing evidence indicates that p53 has a crucial role in normal tissue development. The role of the canonical p53 (p53α) and its 12± isoforms in development and homeostasis of healthy tissue remains poorly understood. Here we demonstrate that Δ133p53, three short isoforms of p53 isoform, responds specifically to laminin-111 and plays an important regulatory role in formation of mammary organoids in concert with p53α. We demonstrate that down-modulation of Δ133p53 isoforms leads to changes in gene expression of extracellular matrix molecules: fibronectin (FN), EDA+-FN, laminin α5, and laminin α3 in human breast epithelial cells. These changes resulted in increased actin stress fibers and enhanced migratory behavior of cells in 2-dimensional culture. We found that α5β1-integrin coupled with the extracellularly deposited EDA+-FN activates Akt signaling pathway in 3-dimensional (3D) culture when Δ133p53 is dysregulated. Cells that do not express detectable Δ133p53 isoforms or express low levels of these isoforms failed to form polarized structures in 3D. These results uncover that Δ133p53 isoforms coordinate expression and deposition of organ-specific ECM molecules that are critical for maintenance of tissue architecture and function.

Lee, Sun-Young (ORCID:000000034970241X)↗
DOE OSTI2020

Modular protein-oligonucleotide signal exchange

Abstract While many methods are available to measure the concentrations of proteins in solution, the development of a method to quantitatively report both increases and decreases in different protein concentrations in real-time using changes in the concentrations of other molecules, such as DNA outputs, has remained a challenge. Here, we present a biomolecular reaction process that reports the concentration of an input protein in situ as the concentration of an output DNA oligonucleotide strand. This method uses DNA oligonucleotide aptamers that bind either to a specific protein selectively or to a complementary DNA oligonucleotide reversibly using toehold-mediated DNA strand-displacement. It is possible to choose the sequence of output strand almost independent of the sensing protein. Using this strategy, we implemented four different exchange processes to report the concentrations of clinically relevant human α-thrombin and vascular endothelial growth factor using changes in concentrations of DNA oligonucleotide outputs. These exchange processes can operate in tandem such that the same or different output signals can indicate changes in concentration of distinct or identical input proteins. The simplicity of our approach suggests a pathway to build devices that can direct diverse output responses in response to changes in concentrations of specific proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

An anti-PD-1–GITR-L bispecific agonist induces GITR clustering-mediated T cell activation for cancer immunotherapy

Costimulatory receptors such as glucocorticoid-induced tumor necrosis factor receptor–related protein (GITR) play key roles in regulating the effector functions of T cells. In human clinical trials, however, GITR agonist antibodies have shown limited therapeutic effect, which may be due to suboptimal receptor clustering-mediated signaling. To overcome this potential limitation, a rational protein engineering approach is needed to optimize GITR agonist-based immunotherapies. Here we show a bispecific molecule consisting of an anti-PD-1 antibody fused with a multimeric GITR ligand (GITR-L) that induces PD-1-dependent and FcγR-independent GITR clustering, resulting in enhanced activation, proliferation and memory differentiation of primed antigen-specific GITR + PD-1 + T cells. The anti-PD-1–GITR-L bispecific is a PD-1-directed GITR-L construct that demonstrated dose-dependent, immunologically driven tumor growth inhibition in syngeneic, genetically engineered and xenograft humanized mouse tumor models, with a dose-dependent correlation between target saturation and Ki67 and TIGIT upregulation on memory T cells. Anti-PD-1–GITR-L thus represents a bispecific approach to directing GITR agonism for cancer immunotherapy.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1987

Sensitivity analysis for airborne and spaceborne DIAL measurements of H2O profiles

Random and systematic error sourses are presently analyzed for atmospheric H2O detection in the vicinity of the 720 nm absorption bands with Differential Absorption Lidar (DIAL). Attention is given to the random errors due to undertainties in the measurement of the lidar signal and noise that are associated with the background and detector dark currents. Systematic errors are related to Doppler broadening due to backscattering from air molecules, the pressure shift of H2O lines, laser line distortions, spectral impurities, and laser tuning errors. Global measurements of H2O profiles from spaceborne DIAL systems are achievable with 200 m vertical x 10 km horizontal during nighttime, and 250 m vertical x 20 km horizontal during daytime.

Ismail, Syed↗
NASA NTRS1988

Electron attachment lineshapes, cross sections and rate constants at ultra-low energies in several halomethyl and haloethyl molecules

Electron attachment lineshapes, cross sections and rate constants are reported for the molecules CH2Br2, CF2Br2, CF3Br, CBrCl3, BrCN, C2H2Br4, CH3l, C2H5l and 1,1,1,-C2Cl3F3. Use is made of the krypton photoionization method. In addition, the signal intercomparison technique is used to obtain individual channel cross sections and rate constants for Br(-) and CN(-) formation from BrCN, and for Br(-) and Br2(-) formation from CF2Br2. Present results in 1,1,1,-C2Cl3F3 using a new ion extraction grid geometry are compared with earlier results, and differences discussed in terms of the electric field equipotentials of two extraction systems used in the present work. Approximate potential energy curves for BrCN are presented, and the temperature dependence of the Br(-) channel cross section discussed.

Alajajian, S. H.↗
DOE OSTI2020

A Search for FeH in Hot-Jupiter Atmospheres with High-dispersion Spectroscopy

Most of the molecules detected thus far in exoplanet atmospheres, such as water and CO, are present for a large range of pressures and temperatures. In contrast, metal hydrides exist in much more specific regimes of parameter space, and so can be used as probes of atmospheric conditions. Iron hydride (FeH) is a dominant source of opacity in low-mass stars and brown dwarfs, and evidence for its existence in exoplanets has recently been observed at low resolution. We performed a systematic search of archival CARMENES near-infrared data for signatures of FeH during transits of 12 exoplanets. These planets span a large range of equilibrium temperatures (600 ≲ T eq ≲ 4000 K) and surface gravities (2.5 ≲ logg ≲ 3.5). We did not find a statistically significant FeH signal in any of the atmospheres, but obtained potential low-confidence signals (signal-to-noise ratio ~ 3) in two planets, WASP-33b and MASCARA-2b. Previous modeling of exoplanet atmospheres indicate that the highest volume mixing ratios (VMRs) of 10 -7 to 10 -9 are expected for temperatures between 1800 and 3000 K and log g≳3. The two planets for which we find low-confidence signals are in the regime where strong FeH absorption is expected. We performed injection and recovery tests for each planet and determined that FeH would be detected in every planet for VMRs ≫10 -6 , and could be detected in some planets for VMRs as low as 10 -9.5 . Additional observations are necessary to conclusively detect FeH and assess its role in the temperature structures of hot-Jupiter atmospheres.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

A novel regulator of the fungal phosphate starvation response revealed by transcriptional profiling and DNA affinity purification sequencing

Cells must accurately sense and respond to nutrients to compete for resources and establish growth. Phosphate is a critical nutrient source necessary for signaling, energy metabolism, and synthesis of nucleic acids, phospholipids, and cellular metabolites. During phosphate limitation, fungi import phosphate from the environment and liberate phosphate from phosphate-containing molecules in the cell. In the model filamentous fungus Neurospora crassa, the phosphate starvation response is regulated by the conserved transcription factor NUC-1. The activity of NUC-1 is repressed by a complex of the cyclin-dependent kinase MDK-1 and the cyclin PREG when phosphate is plentiful. When phosphate is limiting, NUC-1 repression by MDK-1/PREG is relieved by the cyclin-dependent kinase inhibitor NUC-2. We investigated the global response of N. crassa to phosphate starvation. During phosphate starvation, NUC-1 directly activated the expression of genes encoding phosphatases, nucleases, and a phosphate transporter and directly repressed genes associated with the ribosome. Additionally, NUC-1 indirectly activated the expression of an uncharacterized transcription factor, which we named nuc-3. NUC-3 directly repressed the expression of genes involved in phosphate acquisition and liberation after an extended period of phosphate starvation. Additionally, NUC-3 directly repressed the expression of the cyclin-dependent kinase inhibitor nuc-2. Thus, through the combination of NUC-3 direct repression of genes in the phosphate starvation response and nuc-2, an activator of the phosphate starvation response, NUC-3 serves to act as a brake on the phosphate starvation response after an extended period of phosphate starvation. This braking mechanism could reduce transcription, a phosphate-intensive process, under conditions of extended phosphate limitation.IMPORTANCEFungi have evolved regulatory networks to respond to available nutrients. Phosphate is often a limiting nutrient for fungi that is critical for many cellular functions, including nucleic acid and phospholipid biosynthesis, cell signaling, and energy metabolism. The fungal response to phosphate limitation is important in interactions with plants and animals. We investigated the global transcriptional response to phosphate starvation and the role of a major transcriptional regulator, NUC-1, in the model filamentous fungus Neurospora crassa. Our data show that NUC-1 is a bifunctional transcription factor that directly activates phosphate acquisition genes, while directly repressing genes associated with phosphate-intensive processes. NUC-1 indirectly regulates an uncharacterized transcription factor, which we named nuc-3. NUC-3 directly represses phosphate acquisition genes and nuc-2, an activator of the phosphate starvation response, during extended periods of phosphate starvation. Thus, NUC-3 acts as a brake on the phosphate starvation response to reduce phosphate-intensive activities, like transcriptional activation, when phosphate starvation persists.

DNA affinity purification sequencing↗
NASA NTRS1995

On the uncertainty in single molecule fluorescent lifetime and energy emission measurements

Time-correlated single photon counting has recently been combined with mode-locked picosecond pulsed excitation to measure the fluorescent lifetimes and energy emissions of single molecules in a flow stream. Maximum likelihood (ML) and least square methods agree and are optimal when the number of detected photons is large however, in single molecule fluorescence experiments the number of detected photons can be less than 20, 67% of those can be noise and the detection time is restricted to 10 nanoseconds. Under the assumption that the photon signal and background noise are two independent inhomogeneous poisson processes, we derive the exact joint arrival time probably density of the photons collected in a single counting experiment performed in the presence of background noise. The model obviates the need to bin experimental data for analysis, and makes it possible to analyze formally the effect of background noise on the photon detection experiment using both ML or Bayesian methods. For both methods we derive the joint and marginal probability densities of the fluorescent lifetime and fluorescent emission. the ML and Bayesian methods are compared in an analysis of simulated single molecule fluorescence experiments of Rhodamine 110 using different combinations of expected background nose and expected fluorescence emission. While both the ML or Bayesian procedures perform well for analyzing fluorescence emissions, the Bayesian methods provide more realistic measures of uncertainty in the fluorescent lifetimes. The Bayesian methods would be especially useful for measuring uncertainty in fluorescent lifetime estimates in current single molecule flow stream experiments where the expected fluorescence emission is low. Both the ML and Bayesian algorithms can be automated for applications in molecular biology.

Brown, Emery N.↗
NASA NTRS1996

On the Uncertainty in Single Molecule Fluorescent Lifetime and Energy Emission Measurements

Time-correlated single photon counting has recently been combined with mode-locked picosecond pulsed excitation to measure the fluorescent lifetimes and energy emissions of single molecules in a flow stream. Maximum likelihood (ML) and least squares methods agree and are optimal when the number of detected photons is large, however, in single molecule fluorescence experiments the number of detected photons can be less than 20, 67 percent of those can be noise, and the detection time is restricted to 10 nanoseconds. Under the assumption that the photon signal and background noise are two independent inhomogeneous Poisson processes, we derive the exact joint arrival time probability density of the photons collected in a single counting experiment performed in the presence of background noise. The model obviates the need to bin experimental data for analysis, and makes it possible to analyze formally the effect of background noise on the photon detection experiment using both ML or Bayesian methods. For both methods we derive the joint and marginal probability densities of the fluorescent lifetime and fluorescent emission. The ML and Bayesian methods are compared in an analysis of simulated single molecule fluorescence experiments of Rhodamine 110 using different combinations of expected background noise and expected fluorescence emission. While both the ML or Bayesian procedures perform well for analyzing fluorescence emissions, the Bayesian methods provide more realistic measures of uncertainty in the fluorescent lifetimes. The Bayesian methods would be especially useful for measuring uncertainty in fluorescent lifetime estimates in current single molecule flow stream experiments where the expected fluorescence emission is low. Both the ML and Bayesian algorithms can be automated for applications in molecular biology.

Brown, Emery N.↗
DOE OSTI2023

A Suite of Constitutive Promoters for Tuning Gene Expression in Plants

The need for convenient tools to express transgenes over a large dynamic range is pervasive throughout plant synthetic biology; however, current efforts are largely limited by the heavy reliance on a small set of strong promoters, precluding more nuanced and refined engineering endeavors in planta . To address this technical gap, we characterize a suite of constitutive promoters that span a wide range of transcriptional levels and develop a GoldenGate-based plasmid toolkit named PCONS, optimized for versatile cloning and rapid testing of transgene expression at varying strengths. We demonstrate how easy access to a stepwise gradient of expression levels can be used for optimizing synthetic transcriptional systems and the production of small molecules in planta . We also systematically investigate the potential of using PCONS as an internal standard in plant biology experimental design, establishing the best practices for signal normalization in experiments. Although our library has primarily been developed for optimizing expression in N. benthamiana , we demonstrate the translatability of our promoters across distantly related species using a multiplexed reporter assay with barcoded transcripts. In conclusion, our findings showcase the advantages of the PCONS library as an invaluable toolkit for plant synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1965

A Laboratory Investigation of Turbulence Detection Using a Laser

Calculations and experiments have been undertaken to determine the property of the backscattered laser-return signal that undergoes the most significant change in a turbulent region as compared with a nonturbulent region. If the turbulent region is composed mainly of air molecules, the detection of a shift in the frequency property appears to be the most promising. Therefore at this time the main effort at the Ames Research Center is focused on the implementation and laboratory evaluation of a clear-air turbulence detector utilizing a laser source and observing the frequency change.

Bourquin, Kent↗
DOE OSTI2026

Heterogeneous Multilayer Nanopores via Chemically Tuned Dielectric Breakdown for Single‐Molecule Sensing

Solid-state nanopores are powerful platforms for single-molecule sensing, yet their performance is often constrained by fabrication complexity, noise, and limited control over surface properties. Here we report a direct method to fabricate heterogeneous multilayer nanopores using chemically tuned controlled dielectric breakdown (CT-CDB). We integrate hBN, MoS 2 , or graphene atop a silicon nitride membrane to form five distinct bilayer and tri-layer architectures, with bare SiN x nanopore as a control. CT-CDB achieves pore formation reproducibly through material-stacks with high efficiency, good pore size control, and strong yield, validated by various characterizations. Transferrin protein translocation experiments, supported by simulations, reveal that multilayer configurations modulate protein conformations, ionic current blockade and dwell time distributions, reflecting combined effects of membrane type, interfacial chemistry, and local electric field gradients. A supervised machine learning framework is implemented to assist identifying multilayer structure effects embedded in signal signatures, with over 96% accuracy. This work presents a modular and scalable framework for functional nanopore engineering with complex structural integration, thereby expanding the potential of 2D materials in single-molecule sensing applications.

2D materials↗
NASA NTRS1998

Mechanotransduction molecules in the plant gravisensory response: amyloplast/statolith membranes contain a beta 1 integrin-like protein

It has been hypothesized that the sedimentation of amyloplasts within root cap cells is the primary event in the plant gravisensory-signal transduction cascade. Statolith sedimentation, with its ability to generate weighty mechanical signals, is a legitimate means for organisms to discriminate the direction of the gravity vector. However, it has been demonstrated that starchless mutants with reduced statolith densities maintain some ability to sense gravity, calling into question the statolith sedimentation hypothesis. Here we report on the presence of a beta 1 integrin-like protein localized inside amyloplasts of tobacco NT-1 suspension culture, callus cells, and whole-root caps. Two different antibodies to the beta 1 integrin, one to the cytoplasmic domain and one to the extracellular domain, localize in the vicinity of the starch grains within amyloplasts of NT-1. Biochemical data reveals a 110-kDa protein immunoprecipitated from membrane fractions of NT-1 suspension culture indicating size homology to known beta 1 integrin in animals. This study provides the first direct evidence for the possibility of integrin-mediated signal transduction in the perception of gravity by higher plants. An integrin-mediated pathway, initiated by starch grain sedimentation within the amyloplast, may provide the signal amplification necessary to explain the gravitropic response in starch-depleted cultivars.

NASA Discipline Plant Biology↗
DOE OSTI2020

Ultra-Fast Electron Microscopic Imaging of Single Molecules With a Direct Electron Detection Camera and Noise Reduction

Time-resolved imaging of molecules and materials made of light elements is an emerging field of transmission electron microscopy (TEM), and the recent development of direct electron detection cameras, capable of taking as many as 1,600 fps, has potentially broadened the scope of the time-resolved TEM imaging in chemistry and nanotechnology. However, such a high frame rate reduces electron dose per frame, lowers the signal-to-noise ratio (SNR), and renders the molecular images practically invisible. Here, we examined image noise reduction to take the best advantage of fast cameras and concluded that the Chambolle total variation denoising algorithm is the method of choice, as illustrated for imaging of a molecule in the 1D hollow space of a carbon nanotube with ~1 ms time resolution. Through the systematic comparison of the performance of multiple denoising algorithms, we found that the Chambolle algorithm improves the SNR by more than an order of magnitude when applied to TEM images taken at a low electron dose as required for imaging at around 1,000 fps. Open-source code and a standalone application to apply Chambolle denoising to TEM images and video frames are available for download.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

The role of ambient gas confinement, plasma chemistry, and focusing conditions on emission features of femtosecond laser-produced plasmas

Ultrafast laser ablation coupled with optical emission spectroscopy is currently under development for standoff detection of elements and their isotopes for a wide range of application areas. In this work, we explore the role of ambient air pressure during the interaction of an ultrafast laser beam with two metallic targets (brass and uranium) with significantly different oxygen gas-phase reactivity. Plasma plumes were generated by focusing ~800 nm, ~35 fs pulses from an ultrafast laser system using a long focal length lens with f = 1 m. Two-dimensional spectral imaging was performed over the pressure range of 30 mTorr-700 Torr air to evaluate emission dynamics, plasma chemistry, signal-to-background ratio, and characteristic parameters (i.e. excitation temperature, electron density). An increase in ambient air pressure during ultrafast laser ablation leads to plume confinement and subsequent changes in the emission dynamics due to plasma chemistry as well as changes in plasma generation conditions (i.e. focused fs laser ablation versus filament ablation). Ablation crater morphologies were also investigated via scanning electron microscopy. Results indicate atomic emission intensity and signal-to-background ratios peak at moderate pressure levels (~50-100 Torr air) for both targets studied, although plasma chemistry influences uranium emission signatures. The emission features of the uranium plasma at pressures = 10 Torr showed the presence of atoms and oxide molecules which are co-located within the plume. We also find filament ablation leads to wider, more shallow craters compared to focused laser ablation. Our study provides unique insight into the interplay between plume dynamics, confinement, and oxygen chemistry of fs laser-produced plasmas and how these phenomena evolve with changing ambient air pressure.

Laser-produced plasma↗
DOE OSTI2021

Grazer-induced changes in molecular signatures of cyanobacteria

Algal biomass production is an emerging renewable source of fuels, nutrients, manufacturing materials, and pharmaceuticals. Industrial-scale production is predominantly performed in open raceway ponds that are inexpensive to build, operate, and maintain compared to closed bioreactors. However, these open pond systems suffer from increased opportunities for biological contamination from predators, pathogens, and competitors, which result in reduced biomass quality and yields and often the complete destruction of the crop over a short period of time. Early detection of contaminants is a necessary step of integrated pest management for triggering and informing interventions to prevent crop losses. To develop a sensitive method of detection utilizing mass spectrometry (MS), we used three methods – imaging mass spectrometry (imaging MS), liquid chromatography MS/MS (LC-MS/MS) combined with molecular networking, and gas chromatography MS/MS (GC–MS/MS) – to observe and identify molecular signatures from a model predator-prey system of the heterolobosean amoeba HGG1 preying on the filamentous cyanobacterium Anabaena sp. PCC 7120. Imaging MS enabled the association of molecules with the crop, the predator, or the activity of protozoan grazing, while LC-MS/MS-based molecular networking identified a subset of the grazing-specific signals as the chlorophyll breakdown products pyropheophytin, pheophorbide A, and pyropheophorbide. Application of MS techniques to other amoebacyanobacterial predator-prey pairs allowed categorization of grazing signatures as universal or specific to the species of prey, predator, or the prey-predator pairing, indicating that MS-based techniques can distinguish crops from competitors and potentially identify predators. Finally, GCMS/MS was shown to be capable of monitoring novel volatile organic compounds (VOCs), including those predicted to be released through chlorophyll breakdown, in the headspace over algal cultures under predation. Furthermore, these results demonstrate that the combination of multiple MS technologies creates a predictive framework to identify and catalog relevant molecular signatures for informing crop protection strategies.

09 BIOMASS FUELS↗