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At least 505 records · Page 28
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Robust surfactant-assisted one-pot sample preparation for label-free single-cell and nanoscale proteomics

With advanced mass spectrometry (MS)-based proteomics, genome-scale proteome coverage can be achieved from bulk cells. However, such bulk measurement obscures cell to cell heterogeneity, precluding proteome profiling of single cells and small numbers of cells of interest. To address this issue, in recent 5 years there are a surge of small sample preparation methods developed for robust effective collection and processing of single cells and small numbers of cells for in-depth MS-based proteome profiling. Based on their broad accessibility, they can be categorized into two types: specific device- and standard PCR tube- or multi-well plate-based methods. Herein we describe the detailed protocol of our recently developed, easily adoptable, Surfactant-assisted One-Pot (SOP) sample preparation coupled with MS method termed SOP-MS for label-free single-cell and nanoscale proteomics. SOP-MS capitalizes on the combination of a MS-compatible surfactant, DDM (n-Dodecyl-ß-D-maltoside), and standard low-bind PCR tube or multi-well plate for ‘all-in-one’ one-pot sample preparation without sample transfer. With its robust and convenient features, SOP-MS can be readily implemented in any MS laboratory for single-cell and nanoscale proteomics. With further improvements in MS detection sensitivity and sample throughput, we believe that SOP-MS could open an avenue for single-cell proteomics with broad applicability in the biological and biomedical research.

Single-cell proteomics, nanoscale proteomics, SOP-↗
DOE OSTI2021

Efficient verification of anticoncentrated quantum states

I present a method for estimating the fidelity F(μ, τ) between a preparable quantum state μ and a classically specified pure target state τ=|τ> <τ|, using simple quantum circuits and on-the-fly classical calculation (or lookup) of selected amplitudes of |τ>. The method is sample efficient for anticoncentrated states (including many states that are hard to simulate classically), with approximate cost 4ϵ –2 (1 – F)dpcoll where ϵ is the desired precision of the estimate, d is the dimension of the Hilbert space, and pcoll is the collision probability of the target distribution. Furthermore, this scaling is exponentially better than that of any method based on classical sampling. I also present a more sophisticated version of the method that uses any efficiently preparable and well-characterized quantum state as an importance sampler to further reduce the number of copies of μ needed. Though some challenges remain, this work takes a significant step toward scalable verification of complex states produced by quantum processors.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Method for determining a histogram of variable sample rate waveforms

A computer-implemented method comprises receiving a plurality of sampled data points, each data point including a y value and a t value; defining an array of bins, each bin identified by a unique number and including histogram data for a range of y values; for each consecutive pair of data points including a current data point and a next data point, determining a corresponding one of a plurality of linear equations, each linear equation defining a line between the current data point and the next data point; for each line, determining an amount of time that the y value of the line is within the range of values for each bin from the current data point to the next data point; and adding the time to the histogram data for each bin.

Tohlen, Michael Aaron↗
DOE OSTI2022

Method for determining a histogram of variable sample rate waveforms

A computer-implemented method comprises receiving a plurality of sampled data points, each data point including a y value and a t value; defining a plurality of bins; defining an array of elements; dividing the sampled data points into a plurality of sections; assigning a plurality of polynomial equations, one polynomial equation to each section, each polynomial equation having a waveform that fits the data points of the associated section; determining a plurality of section bin times, one section bin time for each bin in each section, each section bin time determined using the polynomial equation and indicating an amount of time that the waveform has values in the range of one of the bins; and adding the section bin time for each bin in each section to the histogram data in the array element pointed to by the number of the bin.

Tohlen, Michael Aaron↗
NASA NTRS1998

Mars Molecular and Isotopic Analysis Research Study

Recently, the Martian atmosphere and surface constituents have become of great interest. The Viking in situ gas chromatograph mass spectrometer experiment contributed greatly to our knowledge of the composition of the Martian atmosphere. However, important questions remain such as the abundance of water on Mars. The Viking experiment employed solid reagents to enhance their carbon measurements. Techniques of chemical conversion using simple solid reagents have advanced considerably in the past 20 years. In this investigation we researched the advancements in techniques to reversibly adsorb and desorb water and focused on the techniques potentially useful for the temperatures and pressures on the Martian surface. During the granting period from June 15, 1998 to August 14, 1998, a literature study of the material appropriate for use in a chemical conversion device and the availability of these materials were undertaken. The focus of this investigation was searching for methods and materials potentially useful in enhancing the measurements of water. Three different methods were considered for the means to extract water from a given gas sample. These methods included adsorption in a desiccant, adsorption on a clean metal surface, and adsorption in a carbon molecular sieve or zeolite. Each method was evaluated with feasibility and reversibility in mind. By far the simplest and perhaps cheapest way to remove water from a gaseous sample is by means of a bulk desiccant. Desiccants are commercially available from many companies including those that supply chemicals. The main feature of a desiccant is its ability to rapidly bind or absorb water from the atmosphere. Calcium chloride, for example, is frequently incorporated into drying tubes by organic chemists when reactions require the absence of water. Other desiccants include sodium hydroxide, calcium hydride, and commercial products such as Drierite, available from Aldrich Chemical. The disadvantage to most desiccants is a direct consequence of what makes them so advantageous. Desiccants rapidly and strongly bind water, often reacting chemically with it. This strong binding makes reversibly desorbing the water from the desiccant very difficult. The third method by which to absorb water from a gas sample involves the use of molecular sieves of other ziolites.

Manning, Heidi L. K.↗
DOE OSTI2022

X-ray fluorescence microscopy methods for biological tissues

Abstract Synchrotron-based X-ray fluorescence microscopy is a flexible tool for identifying the distribution of trace elements in biological specimens across a broad range of sample sizes. The technique is not particularly limited by sample type and can be performed on ancient fossils, fixed or fresh tissue specimens, and in some cases even live tissue and live cells can be studied. The technique can also be expanded to provide chemical specificity to elemental maps, either at individual points of interest in a map or across a large field of view. While virtually any sample type can be characterized with X-ray fluorescence microscopy, common biological sample preparation methods (often borrowed from other fields, such as histology) can lead to unforeseen pitfalls, resulting in altered element distributions and concentrations. A general overview of sample preparation and data-acquisition methods for X-ray fluorescence microscopy is presented, along with outlining the general approach for applying this technique to a new field of investigation for prospective new users. Considerations for improving data acquisition and quality are reviewed as well as the effects of sample preparation, with a particular focus on soft tissues. The effects of common sample pretreatment steps as well as the underlying factors that govern which, and to what extent, specific elements are likely to be altered are reviewed along with common artifacts observed in X-ray fluorescence microscopy data.

Pushie, M. Jake (ORCID:0000000174945427)↗
NASA NTRSDate not supplied

Method Development for In-situ Detection of Latent Herpesvirus DNA from Saliva using Nanopore Sequencing

Research toward latent herpesvirus reactivation has been intensively addressed through Space Shuttle and International Space Station (ISS) investigations. This work has provided the understanding that persistent reactivation of herpesviruses from asymptomatic crew can be detected through viral shedding in saliva, urine, and blood. Occasionally, viral reactivation from the latency stage can pose a threat to crew health (clinical manifestation) before, during, and after flight missions. Furthermore, previous work detailing correlations with immunity indicate that monitoring viral reactivation could be implemented to assess potential immune dysfunction. While in-flight monitoring is desirable, there is no well-established procedure or method for real-time evaluations, and research to date has relied on postflight, ground-based analysis. The development of portable molecular technologies like the miniPCR™ (miniPCR Bio) thermal cycler and the MinION™ sequencer (Oxford Nanopore Technologies) have confirmed that real-time monitoring is possible in extreme and low resource environments. These devices, combined with simple sample preparation methods, have been used to demonstrate bacterial identification onboard the ISS, as well as rapid viral detection in remote locations on Earth. The work here builds upon previous molecular advancements onboard the ISS toward the development and validation of a spaceflight-compatible method for viral detection from crew samples. Several herpesviruses can be detected in saliva, which provides a non-invasive means to collect samples for monitoring. While the basis for this method lies in previous spaceflight investigations, key points for method optimization include DNA extraction from saliva, viral primer selection, and bioinformatic processes for data analysis. To increase viral yield, numerous DNA extraction methods have been evaluated and will be discussed in detail. For initial development and testing, varicella-zoster virus (VZV) is being targeted though open reading frame 51 and 63 (ORF51, ORF63), as the replication origin-binding protein is highly expressed during latency. Optimization of the thermal cycling parameters has resulted in the ability to test the entire process. The full method has been tested with both viral VZV DNA standards and saliva spiked with varying concentrations of VZV. Viral sequence data were mapped to the reference sequence using minimap2. Prior to mapping, DNA sequencing reads were filtered for length and quality, barcodes were removed, and alignment identity calculated. Following further assessments, statistics were compared across multiple sequencing experiments and are being used to determine the success of the protocols. Forward work will include the incorporation of herpes simplex virus 1 (HSV-1) and Epstein-Barr virus (EBV) primers as well as the validation of results to the terrestrial qPCR standard assay. Upon full validation of the developed method, saliva will be collected from 20 healthy subjects and spiked with viral DNA. These samples will be split and assayed with the MinION and standard qPCR assay.

Hang N Nguyen↗
DOE OSTI2022

Evaluation of a parasite-density based pooled targeted amplicon deep sequencing (TADS) method for molecular surveillance of Plasmodium falciparum drug resistance genes in Haiti

Sequencing large numbers of individual samples is often needed for countrywide antimalarial drug resistance surveillance. Pooling DNA from several individual samples is an alternative cost and time saving approach for providing allele frequency (AF) estimates at a population level. Using 100 individual patient DNA samples of dried blood spots from a 2017 nationwide drug resistance surveillance study in Haiti, we compared codon coverage of drug resistance-conferring mutations in four Plasmodium falciparum genes ( crt , dhps , dhfr , and mdr1 ), for the same deep sequenced samples run individually and pooled. Samples with similar real-time PCR cycle threshold (Ct) values (+/- 1.0 Ct value) were combined with ten samples per pool. The sequencing success for samples in pools were higher at a lower parasite density than the individual samples sequence method. The median codon coverage for drug resistance-associated mutations in all four genes were greater than 3-fold higher in the pooled samples than in individual samples. The overall codon coverage distribution for pooled samples was wider than the individual samples. The sample pools with < 40 parasites/μL blood showed more discordance in AF calls for dhfr and mdr1 between the individual and pooled samples. This discordance in AF estimation may be due to low amounts of parasite DNA, which could lead to variable PCR amplification efficiencies. Grouping samples with an estimated ≥ 40 parasites/μL blood prior to pooling and deep sequencing yielded the expected population level AF. Pooling DNA samples based on estimates of > 40 parasites/μL prior to deep sequencing can be used for rapid genotyping of a large number of samples for these four genes and possibly other drug resistant markers in population-based studies. As Haiti is a low malaria transmission country with very few mixed infections and continued chloroquine sensitivity, the pooled sequencing approach can be used for routine national molecular surveillance of resistant parasites.

Louha, Swarnali (ORCID:0000000207778507)↗
NASA NTRS1982

Analyzing Multirate-Sampled Systems

New method available for monitoring stability of system on basis of data sampled at multiple rates--in particular, at two rates, one of which is twice frequency of other. Method is called Multirate Matrix Frequency Response (MMFR) analysis. MMFR was used in Space Shuttle to evaluate effect of decreasing sample rate of error loop in ascent-phase digital autopilot. Should also be useful to designers of other control systems and to structural, civil, and mechanical engineers for structure and vibration analysis.

Hendrix, N.↗
DOE OSTI2022

Differentiating supported platinum single atoms, clusters and nanoparticles by styrene hydrogenation

Supported metal catalysts often consist of metal sites ranging from nanoparticles to subnanometer clusters and single atoms. It remains a necessity to differentiate these sites to guide design of optimal catalysts. Here we report a simple method to assess the distribution of metal active sites in catalyst samples. The method takes the advantage of the structure sensitivity of styrene hydrogenation over titania supported platinum (Pt) catalysts with Pt aggregates varied from single atom to ~1.40 nm nanoparticles. The physicochemical properties were characterized by STEM, XPS, XANES, H2-TPR and CO-chemisorption measurements. The reactivity of Pt sites was quantified by styrene hydrogenation at ambient conditions. The nanometer-sized Pt clusters have significantly higher activity than Pt nanoparticles, sub-nanometer clusters or isolated single atoms. Additionally, the relationship between activity and structural/electronic properties of Pt sites influenced by particle sizes was discussed. Similar relationship was found in the carbon supported Pt catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1990

Spatial conductivity measurements on high T(sub c) superconducting films

High T(sub c) superconducting thin and thick films have potential applications in future NASA flight projects. In anticipation of film use, the Materials Branch is developing a nondestructive, non-contact method of measuring the spatial variation of conductivity across a film sample. This method uses a computer-controlled, X-Y positioning table to scan a conventional eddy current probe across the surface of a film. The induced changes in impedance caused by variations in film conductivity are recorded during the scanning process. Ultimately the two-dimensional data set is displayed using imaging equipment on a personal computer.

Vansant, J. Timothy↗
DOE OSTI2021

Sampling probe

A system for sampling a surface includes a sampling probe including a housing with a probe end having a sampling fluid opening, a sampling fluid supply conduit and a sampling fluid exhaust conduit. The sampling fluid supply conduit supplies sampling fluid to the sampling fluid opening. The sampling fluid exhaust conduit includes a wall, a sampling fluid exhaust conduit inlet opening for removing sampling fluid from the sampling fluid opening, and a sampling fluid exhaust conduit outlet opening for removing fluid from the sampling fluid exhaust conduit. A sampling fluid analytic conduit is also provided in the sampling probe and has a sampling fluid analytic conduit inlet opening spaced upstream from the sampling fluid exhaust conduit outlet opening, downstream from the sampling fluid exhaust conduit inlet opening, and from the wall of the sampling fluid exhaust conduit. A wash conduit can also be provided. Methods for sampling are also disclosed.

Van Berkel, Gary↗
DOE OSTI2025

Development of a high-throughput method for processing sponge-stick samples to detect viable Bacillus anthracis spores

Since the national validation of the sponge-stick based method for detection of Bacillus anthracis spores in environmental samples, there have not been focused efforts to address the low throughput nature of the method, which processes only one sample at one time. Sample processing remains a serious bottleneck for rapidly analyzing large numbers of samples expected from a biological warfare attack. Therefore, we developed a high-throughput method to simultaneously process multiple sponge-stick samples to be better prepared for rapid response and recovery after wide area anthrax incidents. In this method, sponges are placed in 50 mL tubes containing 25 mL extraction buffer and shaken to release spores, after which the suspension is recovered for analysis. Here, we determined that an additional extraction step, conducted in the same tubes with 10 mL buffer, further increased spore recovery from sponge-stick by approximately 10 %. We determined that orbital shaking and multi-tube vortexing were both more effective than reciprocating shaking for recovering spores. We conducted simultaneous processing of up to 12 sponge-stick samples and demonstrated comparable spore recovery efficiencies to the traditional low-throughput stomacher-based method (approximately 60 % recovery at 10 2 -spore level and 75 % recovery at 10 4 -spore level for both methods in three replicate experiments, P > 0.05 for two-tailed t-tests for each experiment and spore level). We also demonstrated that our high-throughput method could be integrated with Rapid Viability-Polymerase Chain Reaction (RV-PCR) analysis and could detect levels as low as 40 spores per sponge even when challenged by a PCR particulate contaminant.

Anthrax↗
DOE OSTI2020

Improved sampling technique to collect natural gas from hydrate-bearing pressure cores

High quality gas compositional data are an important factor in interpreting the genetic source of natural gas hosted in hydrate-bearing sediments and other subsurface systems. In order to accurately characterize the composition of gas samples degassed from hydrate-bearing pressure cores, one must use a reproducible sampling technique that minimizes artifacts of the sampling process. Herein, we review sediment core degassing techniques and compare data obtained from a commonly used degassing approach, which we term the standard quantitative degassing (SQD) technique, to our newly developed modified quantitative degassing (MQD) method designed to minimize atmospheric contamination and gas-water interactions. The SQD method allows sample gas to interact with water in a bubbling chamber, which we hypothesize could alter the gas composition following mixing with water or dissolved gases in the bubbling chamber. Whereas, the MQD method allows for the collection of sample gas prior to the bubbling chamber. To compare the SQD and MQD methods, we performed a side-by-side comparison of noble (He, Ne, Ar, Kr, and Xe), major (H 2 , N 2 , O 2 , and CO 2 ), and hydrocarbon (CH 4 , C 2 H 6 , C 3 H 8 , i-C 4 H 10 , C 4 H 10 , i-C 5 H 12 , C 5 H 12 ) gas concentrations and select isotopic compositions obtained using both sample collection techniques. Gas samples were collected from hydrate-bearing pressure cores recovered and maintained under hydrate stable conditions from the northern Gulf of Mexico during the UT-GOM 2 -1 Expedition. The MQD method displayed significantly lower concentrations of atmospheric gases, higher proportions of hydrocarbon gases, lower ratios of C 1 /C 2 + , and heavier stable carbon and hydrogen isotopes of methane than the SQD method. These results demonstrate that the MQD method reduced air contamination and minimized alteration of the hydrocarbon gases. Finally, we conclude this method may be important for future work that seeks to determine the composition of natural gas from pressure cores using quantitative degassing experiments, especially those seeking to measure major (e.g., N 2 ) and noble gases.

58 GEOSCIENCES↗
DOE OSTI2020

More chemical detection through less sampling: amplifying chemical signals in hyperspectral data cubes through compressive sensing

Compressive sensing (CS) is a method of sampling which permits some classes of signals to be reconstructed with high accuracy even when they were sampled at sub-Nyquist rates. In this paper we explore a phenomenon in which bandwise CS sampling of a hyperspectral data cube followed by reconstruction can actually result in amplification of chemical signals contained in the cube. Perhaps most surprisingly, chemical signal amplification generally seems to increase as the level of sampling decreases. In some examples, the chemical signal is significantly stronger in a data cube reconstructed from 10% CS sampling than it is in the raw, 100% sampled data cube. We explore this phenomenon in two real-world datasets including the Physical Sciences Inc. Fabry-Perot interferometer sensor multispectral dataset and the Johns Hopkins Applied Physics Lab FTIR-based longwave infrared sensor hyperspectral dataset. Each of these datasets contains the release of a chemical simulant, such as glacial acetic acid, triethyl phospate, and sulfur hexafluoride, and in all cases we use the adaptive coherence estimator (ACE) to detect a target signal in the hyperspectral data cube. We end the paper by suggesting some theoretical justifications for why chemical signals would be amplified in CS sampled and reconstructed hyperspectral data cubes and discuss some practical implications.

Hyperspectral imagery, Compressive Sensing, single↗
NASA NTRS2006

Thermal Imaging Applied to Cryocrystallography: Cryocooling and Beam Heating (Part I)

Thermal imaging provides a non-invasive method to study both the cryocooling process and the heating due to the X-ray beam interaction with a sample. The method has been used successfully to image cryocooling in a number of experimental situations, i.e. cooling as a function of sample volume and as a function of cryostream orientation. Although there are experimental limitations to the method, it has proved a powerful technique to aid cryocrystallography development. Due to the rapid spatial temperature information provided about the sample it is also a powerful tool in the testing of mathematical models. Recently thermal imaging has been used to measure the temperature distribution on both a model and typical crystal samples illuminated with an X-ray beam produced by an undulator. A brief overview of thermal imaging and previous results will be presented. In addition, a detailed description of the calibration and experimental aspects of the beam heating measurements will be described. This will complement the following talk on the mathematical modeling and analysis of the results.

Snell, Edward↗
DOE OSTI2024

Ice Nucleation Spectrometer (INS) Instrument Handbook

The Ice Nucleation Spectrometer (INS) is an offline analytical measurement system used to process filter samples for freezing temperature spectra of immersion-mode ice nucleating particle (INP) number concentrations. It is almost identical to the CSU Ice Spectrometer (IS) design. While basic immersion freezing methods have been applied for decades, recent intercomparison studies (DeMott et al. 2017, 2018b) with other methods for sampling ambient INPs support the method’s utility. Use of the INS with filters produces spectra spanning wide dynamic ranges of temperature and, hence, INP concentration (e.g., six orders of magnitude). The INS is supported with well-established experimental protocols and has been applied in many diverse scenarios.

54 ENVIRONMENTAL SCIENCES↗