Results for “Analysis preservation” — Page 17

DOE OSTI2020

Genomic and Transcriptomic Evidence Supports Methane Metabolism in Archaeoglobi

Euryarchaeal lineages have been believed to have a methanogenic last common ancestor. However, members of euryarchaeal Archaeoglobi have long been considered nonmethanogenic and their evolutionary history remains elusive. Here, three high-quality metagenomic-assembled genomes (MAGs) retrieved from high-temperature oil reservoir and hot springs, together with three newly assembled Archaeoglobi MAGs from previously reported hot spring metagenomes, are demonstrated to represent a novel genus of Archaeoglobaceae, “Candidatus Methanomixophus.” All “Ca. Methanomixophus” MAGs encode an M methyltransferase (MTR) complex and a traditional type of methyl-coenzyme M reductase (MCR) complex, which is different from the divergent MCR complexes found in “Ca. Polytropus marinifundus.” In addition, “Ca. Methanomixophus dualitatem” MAGs preserve the genomic capacity for dissimilatory sulfate reduction. Comparative phylogenetic analysis supports a laterally transferred origin for an MCR complex and vertical heritage of the MTR complex in this lineage. Metatranscriptomic analysis revealed concomitant in situ activity of hydrogen-dependent methylotrophic methanogenesis and heterotrophic fermentation within populations of “Ca. Methanomixophus hydrogenotrophicum” in a high-temperature oil reservoir.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1977

Airborne particle monitoring by electrostatic precipitation

For qualitative analysis of atmospheric particulates by microscopy, the sampling device should preserve the particles in the state existing at the moment of capture. A collector is described that uses electrostatic precipitation to capture and disperse specimens on various substrates for direct insertion into microscopes. Sampling runs in various atmospheres are described. Micrographs are presented to show particle morphology and distribution on the substrates. Chemical identification by X-ray energy probe and electron diffraction is illustrated.

Robinson, J. C.↗

NASA NTRS1982

A research in support of NASA's space science

Instrumentation, the interpretation of data from space-borne instruments and the development of theoretical studies of the Earth's environment are reported. New circuitry was introduced to the existing ion drift meter to enable the detection of light ion velocities that are different from the major ion species. Significant progress was made in the tailoring of magnetic mass analysis to stratospheric ions where care must be taken to preserve the original species and to obtain good mass resolution at high mass numbers. Also a rugged and durable zoom imaging spectrometer was successfully tested and important modifications are being undertaken to allow larger scanning ranges for observation of weak airglow emissions from the Earth's atmosphere. Data interpretation efforts led to the discovery of a new class of plasma irregularities on the bottomside of the F-region. Studies of all the available plasma properties from satellite measurements in the high latitude ionosphere revealed regions of field aligned currents where it is reasonable to expect thermal electrons to be the dominant current carriers.

Hanson, W. B.↗

NASA NTRS1985

Extraction of information from major element chemical analyses of lunar basalts

Major element chemical analyses often form the framework within which similarities and differences of analyzed specimens are noted and used to propose or devise models. When percentages are formed the ratios of pairs of components are preserved whereas many familiar statistical and geometrical descriptors are likely to exhibit major changes. This ratio preserving aspect forms the basis for a proposed framework. An analysis of compositional variability within the data set of 42 major element analyses of lunar reference samples was selected to investigate this proposal.

Butler, J. C.↗

NASA NTRS2018

Maximum Sample Temperature for Mars Sample Return: A Historical Perspective

Since the first Mars Sample Return (MSR) report published by the Jet Propulsion Laboratory (JPL) in 1974 [1], a series of panels, reports, and white papers have recognized the importance of sample temperature and offered an informed sample maximum temperature (henceforth SMT) limit for returning martian samples to Earth. The Mars Sample Handling and Requirements Panel (MSHARP, 1999) stated that "[t]he main issue in sample preservation is temperature" [2]. More recently, the Mars Exploration Program Analysis Group (MEPAG)'s "Science Priorities for Mars Sample Return" report (2008), declared that "[s]ignificant loss, particularly to biological studies, occurs if samples reach +50C for three hours", whereby "scientific objectives related to life goals could be seriously compromised" [3]. By contrast, the Mars 2020 mission has adopted a SMT of +60C as spelled out in Beaty et al., 2016 [4]. Samples will be collected and then deposited on the surface in sealed tubes for possible retrieval and return to Earth. Beaty et al. [4] calculates that the samples will experience maximum temperatures of ~+30 to +60C, depending on latitude. At present, there is no mission requirement for the measurement/data logging of sample temperature during this period. We will explore the history of martian SMTs, as they have been recorded since 1974 [1], effectively representing input across multiple generations of Mars scientists. Ten separate publications present SMTs for MSR samples [1-10]. One report [10] is for a mission concept specifically designed to exclude life detection investigations, and recommended an SMT of 50C. Another did not specify a temperature, recommending "Mars ambient temperature" [5]. Of the remaining eight, SMTs are given as: -30C [1], -20C [3], 60C [4], -73 to 41C depending on sample type [6], -40C [7], -43 to 13C depending on type [2,8], and -33C [9]. If we restrict the temperatures to samples highlighted in the Mars 2020 mission goals, i.e. organics-bearing and sedimentary rocks, then the average SMT is -28+/-39C (n=8). Applying a Dixon's Q Test at P=0.05 (two-tailed), the 60C SMT [4] fails with Q=0.602 versus Qcrit=0.526. Excluding the outlier produces an average SMT of -40+/-17C (n=7). Therefore, the average SMT expressed by the Mars science community over the past 44 years (two generations) is a sample temperature no greater than -40C. The difference in chemical reaction rates between this average SMT and Beaty et al [4] can be estimated using the Arrhenius equation. Assuming a generic chemical reaction with an activation energy of 50 kJ/mol and a pre-exponential factor invariant with temperature, this reaction will proceed 2300x faster at 60C than at -40C. To illustrate the effects of the increased reaction rate, consider 10 ppb of alanine in a Mars 2020 cache, and assume that it becomes unmeasurable if it degrades to 1 ppb, as per the Mars 2020 Organic Contamination Panel contamination limits [11]. If we illustrate the effect with an arbitrary degradation rate such that the alanine will become undetectable in ten years at -40C, then the same 10 ppb alanine degrades beyond detectability in only 38 days at 60C. Further research is required to quantify expected analyte losses in the cached samples due to thermal processing.

Fries, Marc↗

NASA NTRSDate not supplied

A Gene Expression and Histologic Approach to Study Production and Outflow of Cerebrospinal Fluid in Hindlimb Suspended Rats

INTRODUCTION: The Spaceflight Associated Neuro-ocular Syndrome (SANS) is thought to be associated with weightlessness-induced cephalad fluid shift, possibly associated with a chronic elevation of intracranial pressure (ICP) during long-duration ISS missions. Changes in cerebrospinal fluid (CSF) dynamics and cranial compliance might be involved in the ICP increase. It is not known whether CSF production and/or outflow are altered in microgravity, but changes at the molecular and cellular level in the structures that produce and regulate the transcellular and paracellular secretion and reabsorption of CSF may be relevant. In this study, we used the rat hindlimb suspension (HS) model to examine the relationship between intracranial pressure (ICP) and the cellular responses to the prolonged change in body posture elicited specifically in the choroid plexus (CP). This was evaluated by transcriptomics, histopathology and ultrastructure of the CP and arachnoid villi (AV). METHODS: ICP was measured by telemetry. The morphology, ultrastructure, and gene expression profile of the CP was examined using male 9-month-old Long Evans rats subjected to HS for 14 and 90 days. A subset of animals completing 90-day HS returned to normal posture for 14 and 90 additional days of recovery. All HS rats had age-matched cage controls maintained in normal posture. A group of animals was maintained in conditions of 1% CO2 throughout the entire protocol. The rat brains were carefully removed and preserved for various analyses, including transmission electron microscopy (TEM), immunohistochemical analysis of specific targets involved in CSF regulation, and RNA sequencing analysis of laser capture micro-dissected CP tissue from the lateral ventricles. SUMMARY OF RESULTS: The ICP record was limited, which impacted any conclusions derived from the results. However, the ICP of rats in the CO2-enriched atmosphere appeared increased compared to those in a normal air composition. HS of rats resulted in an altered transcriptomics profile in the choroid plexus compared to animals maintained at normal posture. This was observed during both the HS period and during normal posture recovery period following 90 days of suspension. The greatest number of differentially expressed genes was observed at 90 days HS. Elevated CO2 also led to a different transcriptomics profile in the CP. The histology and ultrastructure results should be considered preliminary due to the limited number of samples. Examination of the CP by TEM showed blood vessel congestion and microvilli swelling in the CP, as well as some subpial and periventricular gliosis, but no associations were observed with treatment. There was no evidence of a reduced clearance of b-amyloid in the periventricular, perivascular and subpial regions of the brain in HS animals versus those in normal posture. Immunohistochemical staining of aquaporin 4, showed the localization to the subpial region and ependyma with increased immunoreactivity in the brains of CO2 exposed rats. This work was supported by awards NNX15AW48G to S.Z. Animal tissue and live data was provided under a tissue/data sharing agreement with Dr. Charles Fuller, UC Davis.

S B Zanello↗

NASA NTRSDate not supplied

A Gene Expression and Histologic Approach to Study Production and Outflow of Cerebrospinal Fluid in Hindlimb Suspended RATS

INTRODUCTION: The Spaceflight Associated Neuro-ocular Syndrome (SANS) is thought to be associated with weightlessness-induced cephalad fluid shift, possibly associated with a chronic elevation of intracranial pressure (ICP) during long-duration ISS missions. Changes in cerebrospinal fluid (CSF) dynamics and cranial compliance might be involved in the ICP increase. It is not known whether CSF production and/or outflow are altered in microgravity, but changes at the molecular and cellular level in the structures that produce and regulate the transcellular and paracellular secretion and reabsorption of CSF may be relevant. In this study, we used the rat hindlimb suspension (HS) model to examine the relationship between intracranial pressure (ICP) and the cellular responses to the prolonged change in body posture elicited specifically in the choroid plexus (CP). This was evaluated by transcriptomics, histopathology and ultrastructure of the CP and arachnoid villi (AV). METHODS: ICP was measured by telemetry. The morphology, ultrastructure, and gene expression profile of the CP was examined using male 9-month-old Long Evans rats subjected to HS for 14 and 90 days. A subset of animals completing 90-day HS returned to normal posture for 14 and 90 additional days of recovery. All HS rats had age-matched cage controls maintained in normal posture. A group of animals was maintained in conditions of 1% CO2 throughout the entire protocol. The rat brains were carefully removed and preserved for various analyses, including transmission electron microscopy (TEM), immunohistochemical analysis of specific targets involved in CSF regulation, and RNA sequencing analysis of laser capture micro-dissected CP tissue from the lateral ventricles. SUMMARY OF RESULTS: The ICP record was limited, which impacted any conclusions derived from the results. However, the ICP of rats in the CO2-enriched atmosphere appeared increased compared to those in a normal air composition. HS of rats resulted in an altered transcriptomics profile in the choroid plexus compared to animals maintained at normal posture. This was observed during both the HS period and during normal posture recovery period following 90 days of suspension. The greatest number of differentially expressed genes was observed at 90 days HS. Elevated CO2 also led to a different transcriptomics profile in the CP. The histology and ultrastructure results should be considered preliminary due to the limited number of samples. Examination of the CP by TEM showed blood vessel congestion and microvilli swelling in the CP, as well as some subpial and periventricular gliosis, but no associations were observed with treatment. There was no evidence of a reduced clearance of b-amyloid in the periventricular, perivascular and subpial regions of the brain in HS animals versus those in normal posture. Immunohistochemical staining of aquaporin 4, showed the localization to the subpial region and ependyma with increased immunoreactivity in the brains of CO2 exposed rats. This work was supported by awards NNX15AW48G to S.Z. Animal tissue and live data was provided under a tissue/data sharing agreement with Dr. Charles Fuller, UC Davis.

S B Zanello↗

DOE OSTI2020

FPDetect: Efficient Reasoning About Stencil Programs Using Selective Direct Evaluation

We present FPDetect, a low-overhead approach for detecting logical errors and soft errors affecting stencil computations without generating false positives. We develop an offline analysis that tightly estimates the number of floating-point bits preserved across stencil applications. This estimate rigorously bounds the values expected in the data space of the computation. Violations of this bound can be attributed with certainty to errors. FPDetect helps synthesize error detectors customized for user-specified levels of accuracy and coverage. FPDetect also enables overhead reduction techniques based on deploying these detectors coarsely in space and time. Experimental evaluations demonstrate the practicality of our approach.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Developing Data-Driven Synthetic Infrastructure Models for Resilience Analysis

Research on infrastructure resilience has produced promising methods to simulate and optimize complex networks to improve performance. However, restrictions on sharing infrastructure models and the steep cost of developing and maintaining infrastructure models presents a roadblock to adoption. To overcome this limitation, this research focuses on methods to create data-driven infrastructure models that will help improve infrastructure resilience and security. The analysis couples incomplete utility data, geospatial data, machine learning, and synthetic network generation methods to rapidly develop and update infrastructure models. The methods are validated using realistic utility models and site-specific data, with a focus on Puerto Rico due to its unique infrastructure challenges and available data. This research highlights promising opportunities for the use of synthetic network generation and machine learning to create infrastructure models when very little data is available. Results demonstrate that hybrid methods, which combine sparse utility data with synthetic models, can enhance model accuracy, and machine learning can predict model attributes using training data from other models. However, the complexity of infrastructure systems means that even minor changes in network connectivity can significantly impact simulation results. Resilience analysis using synthetic infrastructure models shows that while some system behaviors are preserved, the magnitude of disruptions may not be accurately represented, indicating the need for more research and validation before using synthetic models for critical infrastructure investment decisions. The framework outlined in this report represents a significant advance to infrastructure model development and could be applied to additional domains and sites. Future research will continue to streamline and validate methods to help reduce roadblocks to resilience analysis.

24 POWER TRANSMISSION AND DISTRIBUTION↗

NASA NTRS2018

Organic Matter Preserved in 3-Billion-Year-Old Mudstones at Gale Crater, Mars

Establishing the presence and state of organic matter, including its possible biosignatures, in martian materials has been an elusive quest, despite limited reports of the existence of organic matter on Mars. We report the in situ detection of organic matter preserved in lacustrine mudstones at the base of the ~3.5-billion-year-old Murray formation at Pahrump Hills, Gale crater, by the Sample Analysis at Mars instrument suite onboard the Curiosity rover. Diverse pyrolysis products, including thiophenic, aromatic, and aliphatic compounds released at high temperatures (500Â° to 820Â°C), were directly detected by evolved gas analysis. Thiophenes were also observed by gas chromatographyâ€“mass spectrometry. Their presence suggests that sulfurization aided organic matter preservation. At least 50 nanomoles of organic carbon persists, probably as macromolecules containing 5% carbon as organic sulfur molecules.

Eigenbrode, Jennifer L.↗

DOE OSTI2021

ExoMars Mars Organic Molecule Analyzer (MOMA) Laser Desorption/Ionization Mass Spectrometry (LDI-MS) Analysis of Phototrophic Communities from a Silica-Depositing Hot Spring in Yellowstone National Park, USA

The Mars Organic Molecule Analyzer (MOMA) is a key scientific instrument on the ExoMars Rover mission. MOMA is designed to detect and characterize organic compounds, over a wide range of volatility and molecular weight, in samples obtained from up to two meters below the martian surface. Thorough analog sample studies are required to best prepare to interpret MOMA data collected on Mars. We present here the MOMA characterization of Mars analog samples collected from an alkaline silica depositing hot spring in Yellowstone National Park, WY, USA. These samples contain microbial streamer communities composed primarily of oxygenic and anoxygenic phototrophs. Additionally, in a study focused on detection of key classes of nonvolatile organics, samples of microbial streamers and their total lipid extract (TLE) have been measured on a MOMA Engineering Test Unit (ETU) instrument using its laser desorption/ionization mass spectrometry (LDI-MS) mode. MOMA LDI-MS detected a variety of lipids and pigments in the TLE sample. Species such as chlorophyll a were also detected from the streamer sample with the help of mass isolation. The results add to the LDI-MS sample characterization database, as well as demonstrate the benefit of using mass isolation on the MOMA instrument to reveal the presence of complex organics, and potential biomarkers, preserved in a natural sample, providing guidance to the in situ analysis of surface samples during Mars operations.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2018

The CAESAR New Frontiers Mission: Comet Surface Sample Acquisition and Preservation

NASA recently selected the Comet Astrobiology Exploration Sample Return (CAESAR) mission for Phase A study in the New Frontiers Program. This mission will acquire and return to Earth for laboratory analysis at least 80 g of surface material from the nucleus of comet 67P/Churyumov-Gerasimenko (hereafter 67P). CAESAR will characterize the surface region sampled, preserve the sample in a pristine state, and return evolved volatiles by capturing them in a separate gas reservoir. The system protects both volatile and non-volatile components from contamination or alteration thatwould hamper their scientific analysis. Laboratory analyses of comet samples provide unparalleled knowledge about the presolar history through the initial stages of planet formation to the origin of life.

CAESAR↗

DOE OSTI2025

Large CO 2 removal potential of woody debris preservation in managed forests

Limiting climate warming to 1.5 °C requires reductions in greenhouse gas emissions and CO 2 removal. While various CO 2 removal strategies have been explored to achieve global net-zero greenhouse gas emissions and account for legacy emissions, additional exploration is warranted to examine more durable, scalable and sustainable approaches to achieve climate targets. Here, in this study, we show that preserving woody debris in managed forests can remove gigatonnes of CO 2 from the atmosphere sustainably based on a carbon cycle analysis using three Earth system models. Woody debris is produced from logging, sawmill wastes and abandoned woody products, and can be preserved in deep soil to lengthen its residence time (a measure of durability) by thousands of years. Preserving annual woody debris production in managed forests has the capacity to remove 769–937 GtCO 2 from the atmosphere cumulatively (10.1–12.4 GtCO 2 yr −1 on average) from 2025 to 2100, if its residence time is lengthened for 100–2,000 years and after 5% CO 2 removal is discounted to account for CO 2 emission due to machine operation for wood debris preservation. This translates to a reduction in global temperatures of 0.35–0.42 °C. Given the large potential, relatively low cost and long durability, future efforts should be focused on establishing large-scale demonstration projects for this technology in a variety of contexts, with rigorous monitoring of CO 2 removal, its co-benefits and side-effects.

Luo, Yiqi [Cornell Univ., Ithaca, NY (United State↗

DOE OSTI2021

ALPINE Overview

Data-driven sampling enables probabilistic identification of interesting regions in the data automatically, prioritizing important regions. Applied in situ to Nyx, important halo regions are preserved.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1996

Fossil preservation and the stratigraphic ranges of taxa

The incompleteness of the fossil record hinders the inference of evolutionary rates and patterns. Here, we derive relationships among true taxonomic durations, preservation probability, and observed taxonomic ranges. We use these relationships to estimate original distributions of taxonomic durations, preservation probability, and completeness (proportion of taxa preserved), given only the observed ranges. No data on occurrences within the ranges of taxa are required. When preservation is random and the original distribution of durations is exponential, the inference of durations, preservability, and completeness is exact. However, reasonable approximations are possible given non-exponential duration distributions and temporal and taxonomic variation in preservability. Thus, the approaches we describe have great potential in studies of taphonomy, evolutionary rates and patterns, and genealogy. Analyses of Upper Cambrian-Lower Ordovician trilobite species, Paleozoic crinoid genera, Jurassic bivalve species, and Cenozoic mammal species yield the following results: (1) The preservation probability inferred from stratigraphic ranges alone agrees with that inferred from the analysis of stratigraphic gaps when data on the latter are available. (2) Whereas median durations based on simple tabulations of observed ranges are biased by stratigraphic resolution, our estimates of median duration, extinction rate, and completeness are not biased.(3) The shorter geologic ranges of mammalian species relative to those of bivalves cannot be attributed to a difference in preservation potential. However, we cannot rule out the contribution of taxonomic practice to this difference. (4) In the groups studied, completeness (proportion of species [trilobites, bivalves, mammals] or genera [crinoids] preserved) ranges from 60% to 90%. The higher estimates of completeness at smaller geographic scales support previous suggestions that the incompleteness of the fossil record reflects loss of fossiliferous rock more than failure of species to enter the fossil record in the first place.

NASA Program Exobiology↗

DOE OSTI2022

Describing the Influence of Ball-milling on the Amorphization of Flubendazole Using the PDF and RMC Methods with X-ray Powder Diffraction Data

Flubendazole (FBZ) is a poorly water-soluble drug, and different methodologies have been proposed to improve its oral bioavailability. Obtaining the amorphous drug phase is an alternative to improve its water solubility. Several techniques for drug amorphization, such as spray drying, lyophilization, melt quenching, solvent-evaporation, and ball milling, can yield various types of structural disorder and possibly render variations in physicochemical properties. Herein, we focus on evaluating the influence of the ball-milling process on the amorphization of FBZ. The characterization of the average global and local structures before, during, and after the milling process is described by sequential Rietveld refinements, pair distribution function analysis, and the Reverse Monte Carlo method. In conclusion, we show that preserving the local structure (nearest molecules) can be responsible for avoiding the fast structure recrystallization commonly observed when using the solvent-evaporation process for the studied drug.

60 APPLIED LIFE SCIENCES↗

NASA NTRS1981

Preserved signatures of ion flux modulations observed by ATS 6

The considered investigation is concerned with a detailed analysis of the event of August 13, 1974. The considered day was a geomagnetically quiet day, and ATS 6 was stationed at 94 deg W longitude. On the basis of the conducted analysis it is found that the observed flux oscillations may be a fossil signature of flux modulations which have occurred in ions at an earlier time and at a region away from the spot of observation. In conclusion, it is pointed out that the August 13, 1974, and the January 23, 1975, events of proton flux oscillations observed by ATS 6 are of great importance. They reveal another unique capability of the drifting particles for preserving small modulation signatures imposed upon them during earlier wave-particle interactions. At the present, no conclusions are drawn as to what kind of the wave-particle interaction process was responsible for the observation.

Su, S.-Y.↗

NASA NTRS2004

Analysis of Organic Compounds in Mars Analog Samples

The detailed characterization of organic compounds that might be preserved in rocks, ices, or sedimentary layers on Mars would be a significant step toward resolving the question of the habitability and potential for life on that planet. The fact that the Viking gas chromatograph mass spectrometer (GCMS) did not detect organic compounds should not discourage further investigations since (a) an oxidizing environment in the near surface fines analyzed by Viking is likely to have destroyed many reduced carbon species; (b) there are classes of refractory or partially oxidized species such as carboxylic acids that would not have been detected by the Viking GCMS; and (c) the Viking landing sites are not representative of Mars overall. These factors motivate the development of advanced in situ analytical protocols to carry out a comprehensive survey of organic compounds in martian regolith, ices, and rocks. We combine pyrolysis GCMS for analysis of volatile species, chemical derivatization for transformation of less volatile organics, and laser desorption mass spectrometry (LDMS) for analysis of elements and more refractory, higher-mass organics. To evaluate this approach and enable a comparison with other measurement techniques we analyze organics in Mars simulant samples.

Mahaffy, P. R.↗