Search NASA⌕ Search

SEARCH · Search NASA

Results for “sequencing experiments”

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 829 records · Page 46

Minimizing magnetic fields for precision experiments

An increasing number of measurements in fundamental and applied physics rely on magnetically shielded environments with sub nano-Tesla residual magnetic fields. State of the art magnetically shielded rooms (MSRs) consist of up to seven layers of high permeability materials in combination with highly conductive shields. Proper magnetic equilibration is crucial to obtain such low magnetic fields with small gradients in any MSR. Here, we report on a scheme to magnetically equilibrate MSRs with a 10 times reduced duration of the magnetic equilibration sequence and a significantly lower magnetic field with improved homogeneity. For the search of the neutron's electric dipole moment, our finding corresponds to a 40% improvement of the statistical reach of the measurement. However, this versatile procedure can improve the performance of any MSR for any application.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Overview of IMPACT Data Acquisition System and Data Reduction Process

This report documents the development of the data acquisition system (DAS) and data reduction methodologies for the Irradiated Material Property Accelerated Characterization Test (IMPACT) experiment at the Advanced Test Reactor (ATR). The IMPACT experiment is designed to enable in-pile measurement of thermal conductivity in metallic nuclear fuels, specifically U-10Zr, using an instrumented thermal conductivity probe. The DAS supports both passive temperature monitoring and active thermal interrogation of the probe through controlled AC and DC excitation. Significant modifications to laboratory-scale systems were required to accommodate the higher resistance paths associated with the in-pile application. Custom electronics and relay-controlled measurement sequencing were developed to enable the measurement and sufficient power delivery to the sensing region. A reduced-order, axisymmetric thermal model based on the thermal quadrupoles method is presented to support data interpretation. This model enables efficient evaluation of transient heat transfer behavior and facilitates solution of the inverse problem required to extract thermal properties from measured signals. Multiple boundary condition formulations are discussed to address varying experimental time scales and geometries. Additionally, machine learning techniques are introduced to support data reduction and improve confidence in inverse solutions. Convolutional neural networks are applied to identify the presence of gas gaps and other evolving geometric features that significantly impact thermal response during irradiation. These efforts contribute to the broader integration of digital twin frameworks and real-time modeling capabilities within the Advanced Fuels Campaign.

46 - INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AN↗

Comparison of PsbQ and Psb27 in photosystem II provides insight into their roles

Photosystem II (PSII) catalyzes the oxidation of water at its active site that harbors a high-valent inorganic Mn 4 CaO x cluster called the oxygen-evolving complex (OEC). Extrinsic subunits generally serve to protect the OEC from reductants and stabilize the structure, but diversity in the extrinsic subunits exists between phototrophs. Recent cryo-electron microscopy experiments have provided new molecular structures of PSII with varied extrinsic subunits. We focus on the extrinsic subunit PsbQ, that binds to the mature PSII complex, and on Psb27, an extrinsic subunit involved in PSII biogenesis. PsbQ and Psb27 share a similar binding site and have a four-helix bundle tertiary structure, suggesting they are related. Here, we use sequence alignments, structural analyses, and binding simulations to compare PsbQ and Psb27 from different organisms. We find no evidence that PsbQ and Psb27 are related despite their similar structures and binding sites. Evolutionary divergence within PsbQ homologs from different lineages is high, probably due to their interactions with other extrinsic subunits that themselves exhibit vast diversity between lineages. This may result in functional variation as exemplified by large differences in their calculated binding energies. Psb27 homologs generally exhibit less divergence, which may be due to stronger evolutionary selection for certain residues that maintain its function during PSII biogenesis which is consistent with their more similar calculated binding energies between organisms. Previous experimental inconsistencies, low confidence binding simulations, and recent structural data suggest that Psb27 is likely to exhibit flexibility that may be an important characteristic of its activity. Furthermore, the analysis provides insight into the functions and evolution of PsbQ and Psb27, and an unusual example of proteins with similar tertiary structures and binding sites that probably serve different roles.

59 BASIC BIOLOGICAL SCIENCES↗

Lichen ketosynthase domains are not responsible for inoperative polyketide synthases in Ascomycota hosts

Highlights: • Lichen ketosynthase domains evolved from Ascomycota fungi. • Structure and mechanism appear identical to non-lichen species. • Heterologous translation of lichen ketosynthase proteins achieved. Efforts by lichenologists to characterize lichen polyketide synthases (PKS) through heterologous expression experiments have so far proved unfruitful. A determination of systematic causes of failure is therefore required. Three hypotheses involving the ketosynthase (KS) domain of lichen polyketide synthases (PKS) from Cladonia uncialis are tested: (1) Horizontal versus vertical gene transfer; (2) Typical versus atypical active site residues; (3) Typical versus atypical tertiary protein structure and active site architecture. Phylogenetics, amino acid sequence alignment, and protein modelling indicate that C. uncialis PKS evolved through vertical transfer from Ascomycota fungi, possess Cys-His-His catalytic triads typical of KS from most organisms, and possess protein and catalytic site architecture identical to well-characterized KS from non-lichen organisms. Though the reason for lack of functional activity in heterologous hosts remains unknown, complications involving the KS are ruled out as a likely explanation. Heterologous translation of lichen PKS (or parts thereof) have not been reported. We demonstrate heterologous translation of two lichen KS domains in E. coli.

60 APPLIED LIFE SCIENCES↗

Enhanced 1 H-X D-HMQC performance through improved 1 H homonuclear decoupling

The sensitivity of solid-state NMR experiments that utilize 1 H zero-quantum heteronuclear dipolar recoupling, such as D-HMQC, is compromised by poor homonuclear decoupling. This leads to a rapid decay of recoupled magnetization and an inefficient recoupling of long-range dipolar interactions, especially for nuclides with low gyromagnetic ratios. We investigated the use, in symmetry-based 1 H heteronuclear recoupling sequences, of a basic R element that was principally designed for efficient homonuclear decoupling. By shortening the time required to suppress the effects of homonuclear dipolar interactions to the duration of a single inversion pulse, spin diffusion was effectively quenched and long-lived recoupled coherence lifetimes could be obtained. Furthermore we show, both theoretically and experimentally, that these modified sequences can yield considerable sensitivity improvements over the current state-of-the-art methods and applied them to the indirect detection of 89Y in a metal-organic framework.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Control of the spin to charge conversion using the inverse Rashba-Edelstein effect

We show here that using spin orbit coupling interactions at a metallic interface it is possible to control the sign of the spin to charge conversion in a spin pumping experiment. Using the intrinsic symmetry of the “Inverse Rashba Edelstein Effect” (IREE) in a Bi/Ag interface, the charge current changes sign when reversing the order of the Ag and Bi stacking. This confirms the IREE nature of the conversion of spin into charge in these interfaces and opens the way to tailoring the spin sensing voltage by an appropriate trilayer sequence.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Unbiased millimeter-wave line surveys of TW Hya and V4046 Sgr: The enhanced C{sub 2}H and CN abundances of evolved protoplanetary disks

We have conducted the first comprehensive millimeter-wave molecular emission line surveys of the evolved circumstellar disks orbiting the nearby, roughly solar-mass, pre-main-sequence (T Tauri) stars, TW Hya (D = 54 pc) and V4046 Sgr AB (D = 73 pc). Both disks are known to retain significant residual gaseous components despite the advanced ages of their host stars (∼8 Myr and ∼21 Myr, respectively). Our unbiased broadband radio spectral surveys of the TW Hya and V4046 Sgr disks were performed with the Atacama Pathfinder Experiment 12 m telescope, and are intended to yield a complete census of the bright molecular emission lines in the range 275-357 GHz (1.1-0.85 mm). We find that lines of {sup 12}CO, {sup 13}CO, HCN, CN, and C{sub 2}H, all of which lie in the higher frequency (>330 GHz) range, constitute the strongest molecular emission from both disks in the spectral region surveyed. The molecule C{sub 2}H is detected here for the first time in both disks, as is CS in the TW Hya disk. The survey results also include the first measurements of the full suite of the hyperfine transitions of CN N = 3 → 2 and C{sub 2}H N = 4 → 3 in both disks. Modeling of these CN and C{sub 2}H hyperfine complexes in the spectrum of TW Hya indicates that the emission from both species is optically thick and may originate from very cold (≲10 K) disk regions. The latter result, if confirmed, would suggest the efficient production of CN and C{sub 2}H in the outer disk and/or near the disk midplane. It furthermore appears that the fractional abundances of CN and C{sub 2}H are significantly enhanced in these evolved protoplanetary disks, relative to the fractional abundances of the same molecules in the environments of deeply embedded protostars. These results, combined with previous determinations of the enhanced abundances of other species (such as HCO{sup +}) in T Tauri star disks, underscore the importance of properly accounting for high-energy (FUV and X-ray) radiation from the central T Tauri star when modeling protoplanetary disk gas chemistry and physical conditions.

79 ASTRONOMY AND ASTROPHYSICS↗

Validation in the Absence of Observed Events

Here our paper addresses the problem of validating models in the absence of observed events, in the area of Weapons of Mass Destruction terrorism risk assessment. We address that problem with a broadened definition of “Validation,” based on “backing up” to the reason why modelers and decision makers seek validation, and from that basis re-define validation as testing how well the model can advise decision makers in terrorism risk management decisions. We develop that into two conditions: Validation must be based on cues available in the observable world; and it must focus on what can be done to affect that observable world, i.e. risk management. That in turn leads to two foci: 1.) the risk generating process, 2.) best use of available data. Based on our experience with nine WMD terrorism risk assessment models, we then describe three best use of available data pitfalls: SME confidence bias, lack of SME cross-referencing, and problematic initiation rates. Those two foci and three pitfalls provide a basis from which we define validation in this context in terms of four tests -- Does the model: … capture initiation? … capture the sequence of events by which attack scenarios unfold? … consider unanticipated scenarios? … consider alternative causal chains? Finally, we corroborate our approach against three key validation tests from the DOD literature: Is the model a correct representation of the simuland? To what degree are the model results comparable to the real world? Over what range of inputs are the model results useful?

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Dynamic tumor tracking using the Elekta Agility MLC

Purpose: To evaluate the performance of the Elekta Agility multileaf collimator (MLC) for dynamic real-time tumor tracking. Methods: The authors have developed a new control software which interfaces to the Agility MLC to dynamically program the movement of individual leaves, the dynamic leaf guides (DLGs), and the Y collimators (“jaws”) based on the actual target trajectory. A motion platform was used to perform dynamic tracking experiments with sinusoidal trajectories. The actual target positions reported by the motion platform at 20, 30, or 40 Hz were used as shift vectors for the MLC in beams-eye-view. The system latency of the MLC (i.e., the average latency comprising target device reporting latencies and MLC adjustment latency) and the geometric tracking accuracy were extracted from a sequence of MV portal images acquired during irradiation for the following treatment scenarios: leaf-only motion, jaw + leaf motion, and DLG + leaf motion. Results: The portal imager measurements indicated a clear dependence of the system latency on the target position reporting frequency. Deducting the effect of the target frequency, the leaf adjustment latency was measured to be 38 ± 3 ms for a maximum target speed v of 13 mm/s. The jaw + leaf adjustment latency was 53 ± 3 at a similar speed. The system latency at a target position frequency of 30 Hz was in the range of 56–61 ms for the leaves (v ≤ 31 mm/s), 71–78 ms for the jaw + leaf motion (v ≤ 25 mm/s), and 58–72 ms for the DLG + leaf motion (v ≤ 59 mm/s). The tracking accuracy showed a similar dependency on the target position frequency and the maximum target speed. For the leaves, the root-mean-squared error (RMSE) was between 0.6–1.5 mm depending on the maximum target speed. For the jaw + leaf (DLG + leaf) motion, the RMSE was between 0.7–1.5 mm (1.9–3.4 mm). Conclusions: The authors have measured the latency and geometric accuracy of the Agility MLC, facilitating its future use for clinical tracking applications.

60 APPLIED LIFE SCIENCES↗

Physiological and genomic evidence of cysteine degradation and aerobic hydrogen sulfide production in freshwater bacteria

The sulfur-containing amino acid cysteine is abundant in the environment, including in freshwater lakes. Biological cysteine degradation can result in hydrogen sulfide (H 2 S), a toxic and ecologically relevant compound that is a central player in biogeochemical cycling in aquatic environments. Here, we investigated the ecological significance of cysteine in oxic freshwater, using isolated cultures, controlled experiments, and multiomics. We screened bacterial isolates enriched from natural lake water for their ability to produce H 2 S when provided cysteine. We identified 29 isolates (Bacteroidota, Proteobacteria, and Actinobacteria) that produced H 2 S. To understand the genomic and genetic basis for cysteine degradation and H 2 S production, we further characterized three isolates using whole-genome sequencing (using a combination of short-read and long-read sequencing) and tracked cysteine and H 2 S levels over their growth ranges: Stenotrophomonas maltophilia (Gammaproteobacteria), S. bentonitica (Gammaproteobacteria), and Chryseobacterium piscium (Bacteroidota). Cysteine decreased and H 2 S increased, and all three genomes had genes involved in cysteine degradation. Finally, to assess the presence of these organisms and genes in the environment, we surveyed a 5-year time series of metagenomic data from the same isolation source (Lake Mendota, Madison, WI, USA) and identified their presence throughout the time series. Overall, our study shows that diverse isolated bacterial strains can use cysteine and produce H 2 S under oxic conditions, and we show evidence using metagenomic data that this process may occur more broadly in natural freshwater lakes. Future considerations of sulfur cycling and biogeochemistry in oxic environments should account for H 2 S production from the degradation of organosulfur compounds.

59 BASIC BIOLOGICAL SCIENCES↗

Early immune response to Coccidioides is characterized by robust neutrophil and fibrotic macrophage recruitment and differentiation

Coccidioidomycosis, or Valley fever, is an emerging respiratory disease caused by soil-dwelling fungi of the Coccidioides genus that is expected to spread from the southwest into the central U.S. by 2050. While 60% of infections are asymptomatic, the other 40% of patients experience a range of symptoms, from self-limiting pneumonia to life-threatening disseminated disease. The immunological events that underlie the progression to severe disease remain underdefined. Here, we probed the early immune response to Coccidioides using a high dose of an attenuated strain of Coccidioides posadasii in a mouse model of infection coupled with single-cell RNA sequencing. At 24 h post-infection, robust immune infiltration is detected in the lung, marked by high levels of inflammatory PD-L1 + neutrophils and fungal-contact-dependent pro-fibrotic Spp1 + macrophages. These findings elucidate the early dynamics of the host response to Coccidioides and provide a deeper understanding of host-pathogen interactions in the lung.

Coccidioides↗

The Toxoplasma gondii cyst wall protein CST1 is critical for cyst wall integrity and promotes bradyzoite persistence

Toxoplasma gondii infects up to one third of the world’s population. A key to the success of T.gondii is its ability to persist for the life of its host as bradyzoites within tissue cysts. The glycosylated cyst wall is the key structural feature that facilitates persistence and oral transmission of this parasite. We have identified CST1 (TGME49_064660) as a 250 kDa SRS (SAG1 related sequence) domain protein with a large mucin-like domain. CST1 is responsible for the Dolichos biflorus Agglutinin (DBA) lectin binding characteristic of T. gondii cysts. Deletion of CST1 results in a fragile brain cyst phenotype revealed by a thinning and disruption of the underlying region of the cyst wall. These defects are reversed by complementation of CST1. Additional complementation experiments demonstrate that the CST1-mucin domain is necessary for the formation of a normal cyst wall structure, the ability of the cyst to resist mechanical stress and binding of DBA to the cyst wall. RNA-seq transcriptome analysis demonstrated dysregulation of bradyzoite genes within the various cst1 mutants. These results indicate that CST1 functions as a key structural component that reinforces the cyst wall structure and confers essential sturdiness to the T. gondii tissue cyst.

bradyzoite↗

Quantification and Controls of Wetland Greenhouse Gas Emissions

Wetlands cover only a small fraction of the Earth’s land surface, but have a disproportionately large influence on global climate. Low oxygen conditions in wetland soils slows down decomposition, leading to net carbon dioxide sequestration over long timescales, while also favoring the production of redox sensitive gases such as nitrous oxide and methane. Freshwater marshes in particular sustain large exchanges of greenhouse gases under temperate or tropical climates and favorable nutrient regimes, yet have rarely been studied, leading to poor constraints on the magnitude of marsh gas sources, and the biogeochemical drivers of flux variability. The Sacramento-San Joaquin Delta in California was once a great expanse of tidal and freshwater marshes but underwent drainage for agriculture during the last two centuries. The resulting landscape is unsustainable with extreme rates of land subsidence and oxidation of peat soils lowering the surface elevation of much of the Delta below sea level. Wetland restoration has been proposed as a means to slow further subsidence and rebuild peat however the balance of greenhouse gas exchange in these novel ecosystems is still poorly described. In this dissertation I first explore oxygen availability as a control on the composition and magnitude of greenhouse gas emissions from drained wetland soils. In two separate experiments I quantify both the temporal dynamics of greenhouse gas emission and the kinetic sensitivity of gas production to a wide range of oxygen concentrations. This work demonstrated the very high sensitivity of carbon dioxide, methane, and nitrous oxide production to oxygen availability, in carbon rich wetland soils. I also found the temporal dynamics of gas production to follow a sequence predicted by thermodynamics and observed spatially in other soil or sediment systems. In the latter part of my dissertation I conduct two field studies to quantify greenhouse gas exchange and understand the carbon sources for decomposition in a 1 km2 restored wetland in the Sacramento Delta. By coupling flux measurements at multiple-scales with remote sensing imagery I showed that large methane emissions produce an overall climate warming effect from the wetland for the next several centuries, despite relatively high productivity. I also used radiocarbon analyses of wetland sediment carbon dioxide and methane to show that both bulk peat and recently fixed carbon contribute to decomposition in the wetland, and that their relative importance is regulated by proximity to, and the phenological cycles of, emergent vegetation.

07 ISOTOPE AND RADIATION SOURCES↗

Evaluating the Impact of gRNA SNPs in CasRx Activity for Reducing Viral RNA in HCoV-OC43

Viruses within a given family often share common essential genes that are highly conserved due to their critical role for the virus’s replication and survival. In this work, we developed a proof-of-concept for a pan-coronavirus CRISPR effector system by designing CRISPR targets that are cross-reactive among essential genes of different human coronaviruses (HCoV). We designed CRISPR targets for both the RNA-dependent RNA polymerase (RdRp) gene as well as the nucleocapsid (N) gene in coronaviruses. Using sequencing alignment, we determined the most highly conserved regions of these genes to design guide RNA (gRNA) sequences. In regions that were not completely homologous among HCoV species, we introduced mismatches into the gRNA sequence and tested the efficacy of CasRx, a Cas13d type CRISPR effector, using reverse transcription quantitative polymerase chain reaction (RT-qPCR) in HCoV-OC43. We evaluated the effect that mismatches in gRNA sequences has on the cleavage activity of CasRx and found that this CRISPR effector can tolerate up to three mismatches while still maintaining its nuclease activity in HCoV-OC43 viral RNA. This work highlights the need to evaluate off-target effects of CasRx with gRNAs containing up to three mismatches in order to design safe and effective CRISPR experiments.

59 BASIC BIOLOGICAL SCIENCES↗

Light-driven quinone reduction in heliobacterial membranes

We report that photosynthetic reaction centers (RCs) evolved > 3 billion years ago and have diverged into Type II RCs reducing quinones and Type I RCs reducing soluble acceptors via iron–sulfur clusters. Photosystem I (PSI), the exemplar Type I RC, uses modi- fied menaquinones as intermediate electron transfer cofactors, but it has been controversial if the Type I RC of heliobacteria (HbRC) uses its two bound menaquinones in the same way. The sequence of the quinone-binding site in PSI is not conserved in the HbRC, and the recently solved crystal structure of the HbRC does not reveal a quinone in the analogous site. We found that illumination of heliobacterial membranes resulted in reduction of menaquinone to menaquinol, suggesting that the HbRC can perform a function thought restricted to Type II RCs. Experiments on membranes and live cells are consistent with the hypothesis that the HbRC preferentially reduces soluble electron acceptors (e.g., ferredoxins) in low light, but switches to reducing lipophilic quinones in high light, when the soluble acceptor pool becomes full. Therefore, the HbRC may represent a functional evolutionary intermediate between PSI and the Type II RCs.

59 BASIC BIOLOGICAL SCIENCES↗

Systematic Comparison of High-throughput Single-Cell and Single-Nucleus Transcriptomes during Cardiomyocyte Differentiation

A comprehensive reference map of all cell types in the human body is necessary for improving our understanding of fundamental biological processes and in diagnosing and treating disease. High-throughput single-cell RNA sequencing techniques have emerged as powerful tools to identify and characterize cell types in complex and heterogeneous tissues. However, extracting intact cells from tissues and organs is often technically challenging or impossible, for example in heart or brain tissue. Single-nucleus RNA sequencing provides an alternative way to obtain transcriptome profiles of such tissues. To systematically assess the differences between high-throughput single-cell and single-nuclei RNA-seq approaches, we compared Drop-seq and DroNc-seq, two microfluidic-based 3' RNA capture technologies that profile total cellular and nuclear RNA, respectively, during a time course experiment of human induced pluripotent stem cells (iPSCs) differentiating into cardiomyocytes. Clustering of timeseries transcriptomes from Drop-seq and DroNc-seq revealed six distinct cell types, five of which were found in both techniques. Furthermore, single-cell trajectories reconstructed from both techniques reproduced expected differentiation dynamics. We then applied DroNc-seq to postmortem heart tissue to test its performance on heterogeneous human tissue samples. Our data confirm that DroNcseq yields similar results to Drop-seq on matched samples and can be successfully used to generate reference maps for the human cell atlas.

59 BASIC BIOLOGICAL SCIENCES↗

Spatially dependent modeling and simulation of runaway electron mitigation in DIII-D

New simulations with the Kinetic Orbit Runaway electron (RE) Code (KORC) show RE deconfinement losses to the wall during plasma scrape off are the primary current dissipation mechanism in DIII-D experiments with high-Z impurity injection, and not collisional slowing down. The majority of simulations also exhibit an increase in the RE beam energy due to acceleration by the induced toroidal electric field, even while the RE beam current is decreasing. In this study, KORC integrates RE orbits using the relativistic guiding center equations of motion and incorporates time-sequenced, experimental reconstructions of the magnetic and electric fields and line integrated electron density to construct spatiotemporal models of electron and partially ionized impurity transport in the companion plasma. Comparisons of experimental current evolution and KORC results demonstrate the importance of including Coulomb collisions with partially ionized impurity physics, initial RE energy, pitch angle, and spatial distributions, and spatiotemporal electron and partially ionized impurity transport. The research presented here provides an initial quantification of the efficacy of RE mitigation via injected impurities and identification of the critical role played by loss of confinement due to plasma scrape off on the inner wall as compared to the relatively slow collisional damping.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Design, modeling and experimental validation of a micro cantilever beam with an electro-controllable twisting ability

The structure design of micro cantilever beams (MCBs), which has a significant effect on MCBs' controllable actuation range, is usually restricted by the establishment of the inner electric circuit. This paper proposes the design of a micro electro-controllable twisting cantilever beam (METCB). The architecture and the fabrication diagram of the proposed METCB are presented before its features are theoretically and experimentally validated. In detail, the analytical validation includes a sequence of two models: electro-thermal and thermo-mechanical. Through these two models, the thermal distribution along the METCB and the deformation brought by the thermal distribution are investigated, respectively. On the basis of the design and equations, the METCB samples have been manufactured using a planar deposition technique with an e-beam evaporator. Two in-site experiments are then conducted to sequentially figure out the upper voltage limit of the inner electric circuit and the maximum temperature limit of the METCB. Finally, another experiment is carried out to explore the relation between the applied voltage and the relative twisting angle of the METCB sample. Here, the theoretical prediction and the observed experiment result both prove the feasibility of the proposed METCB and its electro-controllable twisting ability.

36 MATERIALS SCIENCE↗