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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Proteomics Analysis of Human Contaminant Proteins

Complete characterization of unknowns via proteomics remains challenging. There exist regions of mass spectrometry-based proteomics data where empirical measurements are not attributed to peptides, and/or sequenced peptides from mass spectra are not attributed to any source. These uncharacterized regions are known as the “dark” proteome. Many proteomics tools rely on some a priori knowledge of sample composition; few tools allow for investigation of unknowns without relying on composition assumptions. Further, the potential low abundance of minor traces in these uncharacterized regions can make elucidation of the “dark” proteome challenging. Herein, we describe the development and evaluation of approaches to study the “dark” proteome and move towards an untargeted approach for more complete characterization, namely by studying minor human protein traces in non-human samples and combining that approach with non-human source organism identification without relying on assumptions. Human protein markers, in the form of genetically variant peptides, have been extensively examined in a variety of human matrices, including blood, plasma, and hair, but have yet to be investigated in non-human samples, such as cell cultures, as human contaminant traces. Genetically variant peptides are those that are found in proteins carrying single nucleotide polymorphisms. In this work, we aimed to (1) investigate the feasibility of detecting human contaminant genetically variant peptides (GVPs) in a diverse set of non-human organisms using public proteomics data and a computational pipeline, as well as to (2) develop a combined capability for untargeted source organism characterization and GVP detection. To our knowledge, this is the first report of applying these approaches towards a more complete proteomic characterization of unknowns. We successfully demonstrate the feasibility of broad human contaminant GVP detection in proteomics data, develop a better understanding of GVP detectability, characterize the sample-to-sample variability in GVP detection, and identify a core set of GVPs that can potentially be used as markers indicative of the human contaminant traces portion of the “dark” proteome. Further, we developed and evaluated a combined pipeline, MARLOWE-GVP, that enables both untargeted source organism characterization and GVP detection. We show high accuracy of correct source organism characterization and high degree of similarity of human contaminant GVP detection compared to the conventional approach. Success on both these efforts have allowed us to advance our understanding and characterization of the “dark” proteome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Single Amino Acid Mutations Affect Zika Virus Replication In Vitro and Virulence In Vivo

The 2014–2016 Zika virus (ZIKV) epidemic in the Americas resulted in large deposits of next-generation sequencing data from clinical samples. This resource was mined to identify emerging mutations and trends in mutations as the outbreak progressed over time. Information on transmission dynamics, prevalence, and persistence of intra-host mutants, and the position of a mutation on a protein were then used to prioritize 544 reported mutations based on their ability to impact ZIKV phenotype. Using this criteria, six mutants (representing naturally occurring mutations) were generated as synthetic infectious clones using a 2015 Puerto Rican epidemic strain PRVABC59 as the parental backbone. The phenotypes of these naturally occurring variants were examined using both cell culture and murine model systems. Mutants had distinct phenotypes, including changes in replication rate, embryo death, and decreased head size. In particular, a NS2B mutant previously detected during in vivo studies in rhesus macaques was found to cause lethal infections in adult mice, abortions in pregnant females, and increased viral genome copies in both brain tissue and blood of female mice. Additionally, mutants with changes in the region of NS3 that interfaces with NS5 during replication displayed reduced replication in the blood of adult mice. This analytical pathway, integrating both bioinformatic and wet lab experiments, provides a foundation for understanding how naturally occurring single mutations affect disease outcome and can be used to predict the of severity of future ZIKV outbreaks. To determine if naturally occurring individual mutations in the Zika virus epidemic genotype affect viral virulence or replication rate in vitro or in vivo, we generated an infectious clone representing the epidemic genotype of stain Puerto Rico, 2015. Using this clone, six mutants were created by changing nucleotides in the genome to cause one to two amino acid substitutions in the encoded proteins. The six mutants we generated represent mutations that differentiated the early epidemic genotype from genotypes that were either ancestral or that occurred later in the epidemic. We assayed each mutant for changes in growth rate, and for virulence in adult mice and pregnant mice. Three of the mutants caused catastrophic embryo effects including increased embryonic death or significant decrease in head diameter. Three other mutants that had mutations in a genome region associated with replication resulted in changes in in vitro and in vivo replication rates. These results illustrate the potential impact of individual mutations in viral phenotype.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

AGNs on the Move: A Search for Off-nuclear AGNs from Recoiling Supermassive Black Holes and Ongoing Galaxy Mergers with the Zwicky Transient Facility

A supermassive black hole (SMBH) ejected from the potential well of its host galaxy via gravitational wave recoil carries important information about the mass ratio and spin alignment of the pre-merger SMBH binary. Such a recoiling SMBH may be detectable as an active galactic nucleus (AGN) broad-line region offset by up to 10 kpc from a disturbed host galaxy. We describe a novel methodology using forward modeling with The Tractor to search for such offset AGNs in a sample of 5493 optically variable AGNs detected with the Zwicky Transient Facility (ZTF). We present the discovery of nine AGNs that may be spatially offset from their host galaxies and are candidates for recoiling SMBHs. Five of these offset AGNs exhibit double-peaked broad Balmer lines, which may have arisen from unobscured accretion disk emission, and four show radio emission indicative of a relativistic jet. The fraction of double-peaked emitters in our spatially offset AGN sample is significantly larger than the 16% double-peaked emitter fraction observed for ZTF AGNs overall. In our sample of variable AGNs we also identified 52 merging galaxies, including a new spectroscopically confirmed dual AGN. Finally, we detected the dramatic rebrightening of SDSS 1133, a previously discovered variable object and recoiling SMBH candidate, in ZTF. The flare was accompanied by the reemergence of strong P Cygni line features, indicating that SDSS 1133 may be an outbursting luminous blue variable star.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Checking It Twice: Using [C/N] Masses and Asteroseismic Masses as a Diagnostic of Mass Loss and Transfer on the Red Giant Branch

Red giants experience significant mass loss, but the mechanism is poorly understood. The surface [C/N] of red giants is correlated with birth mass but not directly impacted by mass loss. Exploiting this, we compare asteroseismic masses of red giants with the same [C/N] but different evolutionary states. We find bulk differences between stars at the beginning of the red giant branch (RGB) and in the subsequent evolutionary phase, the red clump, providing a direct constraint on the strength of net RGB mass loss in field stars. We find that net mass loss decreases with metallicity and mass, matching recent studies for field giants but contradicting expectations from the widely used Reimers’s mass-loss formula. We propose a mass- and metallicity-dependent Reimers’s η calibration that reproduces the empirical trends that we see. In addition, we identify 200 stars (3.12% of our sample) that are clear outliers from their population in these birth mass bins, which we believe are likely candidates for mass transfer events. These stars do not show any obvious discrepancies in abundances or binary properties from their counterparts. This population should be accounted for in Galactic archeological studies. Further follow-up is required to quantify their occurrence rate and origin.

Roberts, John D. [The Ohio State Univ., Columbus, ↗
DOE OSTI2024

Technical note: Optimizing the in situ cosmogenic 36 Cl extraction and measurement workflow for geologic applications

Abstract. In situ cosmogenic 36Cl analysis by accelerator mass spectrometry (AMS) is routinely employed to date Quaternary surfaces and assess rates of landscape evolution. However, standard laboratory preparation procedures for 36Cl dating require the addition of large amounts of isotopically enriched chlorine spike solution; these solutions are expensive and increasingly difficult to acquire from commercial sources. In addition, the typical workflow for 36Cl dating involves measuring both 35Cl/37Cl and 36Cl/Cl concurrently on the high-energy (post-accelerator) end of the AMS system, but 35Cl/37Cl determinations using this technique can be complicated by isotope fractionation and system memory during measurement. The traditional workflow also does not provide 36Cl extraction laboratories with the data needed to calculate native Cl concentrations in advance of 36Cl/Cl measurements. In light of these concerns, we present an improved workflow for extracting and measuring chlorine in geologic materials. Our initial step is to characterize 35Cl/37Cl on sample aliquots of up to ∼1 g prepared in Ag(Cl, Br) matrices, which greatly reduces the amount of isotopically enriched spike solution required to measure native Cl content in each sample. To avoid potential issues with isotope fractionation through the accelerator, 35Cl/37Cl is measured on the low-energy, pre-accelerator end of the AMS line. Then, for 36Cl/Cl measurements, we extract Cl as AgCl or Ag(Cl, Br) in analytical batches with a consistent total Cl load across all samples; this step is intended to minimize source memory effects during 36Cl/Cl measurements and allows the preparation of AMS standards that are customized to match known Cl contents in the samples. To assess the efficacy of this extraction and measurement workflow, we compare chlorine isotope ratio measurements on seven geologic samples prepared using standard procedures and the updated workflow. Measurements of 35Cl/37Cl and 36Cl/Cl are consistent between the two workflows, and 35Cl/37Cl values measured using our methods have considerably higher precision than those measured following standard protocols. The chemical preparation and measurement workflow presented here (1) reduces the amount of isotopically enriched chlorine spike used per rock sample by up to 95 %; (2) identifies rocks with high native Cl concentrations, which may be lower priority for 36Cl surface exposure dating, at an early stage of analysis; and (3) allows laboratory users to maintain control over the total chlorine content within and across analytical batches. These methods can be incorporated into existing laboratory and AMS protocols for 36Cl analyses and will increase the accessibility of 36Cl dating for geologic applications.

58 GEOSCIENCES↗
DOE OSTI2020

NGEE Arctic Plant Traits: Plant Community Composition, Kougarok Road Mile Marker 64, Seward Peninsula, Alaska, 2016

This dataset reports the characteristics of the dominant vegetation communities at the NGEE Arctic Kougarok field site, Kougarok Road Mile Marker 64 on the Seward Peninsula. Selected plots were surveyed from 18-23 July 2016. Environmental data (e.g., elevation, slope, soil moisture regime, disturbance type and degree, mean canopy height, etc.) were also recorded for each plot. Elevation measurements were updated 2020-08-18. All plant species (vascular plants, bryophytes and lichens) were recorded along with their percent cover in the plots as determined visually by the lead author. Plots were chosen subjectively in areas of homogeneous and representative vegetation and varied in size from 1-25 m2 depending on canopy structure and height. The site is an east-facing hillslope with vegetation that varies from the summit to the toeslope. The 30 total plots were selected as five replicate plots sampled from each of the six identified habitat types: 1) non-acidic mountain complex at the hillcrest, 2) dwarf-shrub lichen tundra on the shoulder, 3) alder shrublands predominantly on an elevational band across the backslope, 4) willow-birch tundra on the upper backslope, 5) tussock tundra on the footslope in inter-water tracks, and 6) tussock tundra mixed with willow-birch tundra or alder savanna in poor developed water tracks on the footslope. This dataset is comprised of two comma-separated (*.csv) files containing species and environmental data for the plant community composition plots. It also contains seven zipped folders of plot photographs, one map showing plot locations (*.pdf), one blank datasheet with the key to codes used in the field (*.pdf), select photos organized in a (*.pdf), and one User file (*.pdf). The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1972

Coastal applications of the ERTS-1 satellite imagery

There are no author-identified significant results in this report. Samples are given of the possible applications of ERTS-1 imagery to coastal and nearshore studies. Briefly discussed are: (1) obtaining regional views of extended coastal areas; (2) distribution of sediments; (3) coastal configurations and changes; (4) barrier islands; (5) underwater penetration, and (6) coastal waves.

Magoon, O. T.↗
NASA NTRS1973

Use of ERTS-1 to utlitize and apply marine station data to study productivity along eastern shelf expanded waters of the United States

The author has identified the following significant results. Water samples taken in offshore waters between Cap Cod, Massachusetts, and Charleston, South Carolina have been used with other sea truth information as a basis to correlate productivity values with ERTS-1 sensory data. Positive correlations were established on January 26, 1973 regarding chlorophyll concentrations and optical density values.

Marshall, H. G.↗
NASA NTRS1974

X-ray diffraction identification of minerals in lunar regolith returned by Luna 16 automatic station

The methods of powder and monocrystal X-ray diffraction served in identifying the mineral composition of gross samples of regolith from different levels of the drill core and about 80 individual regolith particles returned by the Luna 16 station. It was established that the Sea of Fertility regolith includes pyroxenes of the augite-pigeonite series, anorthites, ilmenite, olivines, spinels, alpha cristobalite, iron particles, glass, and several as yet unidentified particles. Crystallographic and roentgenometric data are given for all the lunar minerals found.

Makarov, Y. S.↗
NASA NTRS1975

Investigation to develop a multistage forest sampling inventory system using ERTS-1 imagery

The author has identified the following significant results. The annotation system produced a RMSE of about 200 m ground distance in the MSS data system with the control data used. All the analytical MSS interpretation models tried were highly significant. However, the gains in forest sampling efficiency that can be achieved by using the models vary from zero to over 50 percent depending on the area to which they are applied and the sampling method used. Among the sampling methods tried, regression sampling yielded substantial and the most consistent gains. The single most significant variable in the interpretation model was the difference between bands 5 and 7. The contrast variable, computed by the Hadamard transform was significant but did not contribute much to the interpretation model. Forest areas containing very large timber volumes because of large tree sizes were not separable from areas of similar crown cover but containing smaller trees using ERTS image interpretation only. All correlations between space derived timber volume predictions and estimates obtained from aerial and ground sampling were relatively low but significant and stable. There was a much stronger relationship between variables derived from MSS and U2 data than between U2 and ground data.

Langley, P. G.↗
NASA NTRS1975

Air pollution source identification

Techniques for air pollution source identification are reviewed, and some results obtained with them are evaluated. Described techniques include remote sensing from satellites and aircraft, on-site monitoring, and the use of injected tracers and pollutants themselves as tracers. The use of a large number of trace elements in ambient airborne particulate matter as a practical means of identifying sources is discussed in detail. Sampling and analysis techniques are described, and it is shown that elemental constituents can be related to specific source types such as those found in the earth's crust and those associated with specific industries. Source identification sytems are noted which utilize charged particle X-ray fluorescence analysis of original field data.

Fordyce, J. S.↗
NASA NTRS1977

Diterpenoid compounds and other lipids in deep-sea sediments and their geochemical significance

Cyclic diterpenoid compounds have been found by various investigators in the geosphere (e.g., fossil resins, coals, soil, shale, and deep-sea sediments). These compounds occur in significant amounts only in higher plants and are therefore potential markers of terrigenous plant lipids. Diterpenoids with the abietane skeleton (mainly dehydroabietic acid) have been identified in the lipids of sediment samples from the northeast Pacific Ocean, Black Sea, and North Atlantic Ocean. The presence of these resin-derived compounds was correlated with the terrigenous clay components and with the presence of pollen. The presence of polycyclic diterpenoids was also correlated with the distribution patterns and inferred sources of other sediment lipid constituents. Potamic transport, followed by turbidite redistribution, is the probable input mechanism of these resin-derived compounds to the deep-sea sediments. These diterpenoids appear to be excellent biological markers of resinous higher plants.

Simoneit, B. R. T.↗
NASA NTRS1985

Analysis of Nonvolatile Residue (NVR) from Spacecraft Systems

Organic contamination on critical spacecraft surfaces can cause electronic problems, serious attenuation of various optical signals, thermal control changes, and adhesion problems. Such contaminants can be detected early by the controlled use of witness mirrors, witness plates, wipe sampling, or direct solvent extraction. Each method requires careful control of variables of technique and materials to attain the ultimate sensitivities inherent to that procedure. Subsequent chemical analysis of the contaminant sample by infrared and mass spectrometry identifies the components, gives semiquantitative estimates of contaminant thickness, indicates possible sources of the nonvolatile residue (NVR), and provides guidance for effective cleanup procedures.

Colony, J. A.↗
NASA NTRS1986

Aerial detection of leaf senescence for a geobotanical study

A geobotanical investigation based on the detection of premature leaf senescence was conducted in an area of predominantly chalcocite mineralization of the Keweenaw Peninsula in Michigan's Upper Peninsula. Spectrophotometric measurements indicated that the region from 600 to 700 nm captures the rise in red reflectance characteristic of senescent leaves. Observations at other wavelengths do not distinguish between senescent and green leaves as clearly and unequivocably as observations at these wavelengths. Small format black and white aerial photographs filtered for the red band (600 to 700 nm) and Thematic Mapper Simulator imagery were collected during the period of fall senescence in the study area. Soil samples were collected from two areas identified by leaf senescence and from two additional sites where the leaf canopy was still green. Geochemical analysis revealed that the sites characterized by premature leaf senescence had a significantly higher median soil copper concentration than the other two areas.

Schwaller, M.↗
NASA NTRS1991

Airborne sulfur trace species intercomparison campaign: Sulfur dioxide, dimethylsulfide, hydrogen sulfide, carbon disulfide, and carbonyl sulfide

Results from an airborne intercomparison of techniques to measure tropospheric levels of sulfur trace gases are presented. The intercomparison was part of the NASA Global Tropospheric Experiment (GTE) and was conducted during the summer of 1989. The intercomparisons were conducted on the Wallops Electra aircraft during flights from Wallops Island, Virginia, and Natal, Brazil. Sulfur measurements intercompared included sulfur dioxide (SO2), dimethylsulfide (DMS), hydrogen sulfide (H2S), carbon disulfide (CS2), and carbonyl sulfide (OCS). Measurement techniques ranged from filter collection systems with post-flight analyses to mass spectrometer and gas chromatograph systems employing various methods for measuring and identifying the sulfur gases during flight. Sampling schedules for the techniques ranged from integrated collections over periods as long as 50 minutes to one- to three-minute samples every ten or fifteen minutes. Several of the techniques provided measurements of more than one sulfur gas. Instruments employing different detection principles were involved in each of the sulfur intercomparisons. Also included in the intercomparison measurement scenario were a host of supporting measurements (i.e., ozone, nitrogen oxides, carbon monoxide, total sulfur, aerosols, etc.) for purposes of: (1) interpreting results (i.e., correlation of any noted instrument disagreement with the chemical composition of the measurement environment); and (2) providing supporting chemical data to meet CITE-3 science objectives of studying ozone/sulfur photochemistry, diurnal cycles, etc. The results of the intercomparison study are briefly discussed.

Gregory, Gerald L.↗
NASA NTRS1992

The study of the thermal behavior of a new semicrystalline polyimide

Thermal properties of a new semicrystalline polyimide synthesized from 3,3',4,4' benzophenone tetracarboxylic dianhydride (BTDA) and 2,2 dimethyl 1,2-(4 aminophenoxy) propane (DMDA) were studied. Heat capacities in the solid and liquid states of BTDA-DMDA were measured. The heat capacity increase at the glass transition temperature (T sub g = 230 C) is 145 J/(C mol) for amorphous BTDA-DMDA. The equilibrium heat of fusion of the BTDA-DMDA crystals was obtained using wide angle X ray diffraction and differential scanning calorimetry measurements, and it is 75.8 kJ/mol. Based on the information of crystallinity and the heat capacity increase at T sub g, a rigid amorphous fraction is identified in semicrystalline BTDA-DMDA samples. The rigid amorphous fraction represents an interfacial region between the crystalline and amorphous states. In particular, this fraction increases with the crystallinity of the sample which should be associated with crystal sizes, and therefore, with crystal morphology. It was also found that this polymer has a high temperature crystal phase upon annealing above its original melting temperature. The thermal degradation activation energies are determined to be 154 and 150 kJ/mol in nitrogen and air, respectively.

Cheng, Stephen Z. D.↗
NASA NTRS1991

Elevated temperature cracking of RSP aluminum alloy 8009 - Characterization of the environmental influence

Degradation of the material properties of the Al alloy is examined to determine the effects of moist air and predissolved hydrogen on elevated-temperature fatigue and fracture resistance. Experiments are conducted at 175 C in both moist air and high vacuum with as-processed specimens and specimens that are vacuum-heat-treated. Fracture mechanics characterizations are made for initiation and propagation fracture toughnesses during rising load, fatigue-crack propagation kinetics, and sustained-load crack-growth rates. Time-dependent embrittlement at intermediate temperatures is identified in both plate and extrusion samples of the Al-Fe-Si-V alloy 8009. Intermediate temperature cracking is found to be the same for each case in both vacuum and moist air, and the vacuum heat treatment does not significantly affect the results.

Porr, William C., Jr.↗
NASA NTRS1992

Volatile species in halide-activated-diffusion coating packs

An atmospheric pressure sampling mass spectrometer was used to identify the vapor species generated in a halide-activated cementation pack. Pack powder mixtures containing a Cr-Al binary masteralloy powder, an NH4Cl activator salt, and either ZrO2 or Y2O3 (or neither) were analyzed at 1000 C. Both the equilibrium calculations for the pack and mass spectrometer results indicated that volatile AlCl(x) and CrCl(y) species were generated by the pack powder mixture; in packs containing the reactive element oxide, volatile ZrCl(z) and YCl(w) species were formed by the conversion of their oxide sources.

Bianco, Robert↗