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DOE OSTI2020

Single-Cell Metabolic Profiling: Metabolite Formulas from Isotopic Fine Structures in Heterogeneous Plant Cell Populations

Characterization of the metabolic heterogeneity in cell populations requires the analysis of single cells. Most current methods in single-cell analysis rely on cell manipulation, potentially altering the abundance of metabolites in individual cells. Small sample volume and the chemical diversity of metabolites are additional challenges in single-cell metabolomics. Here, we describe the combination of fiber-based laser ablation electrospray ionization (f-LAESI) with 21 tesla Fourier transform ion cyclotron resonance mass spectrometry (21TFTICR-MS) for in situ single-cell metabolic profiling in plant tissue. Single plant cells infected by bacteria were selected and sampled directly from the tissue without cell manipulation through mid-infrared ablation with a fine optical fiber tip for ionization by f-LAESI. Finally, ultrahigh performance 21T-FTICR-MS enabled the simultaneous capture of isotopic fine structures (IFSs) for 47 known and 11 unknown compounds, thus elucidating their elemental compositions from single cells, and providing information on metabolic heterogeneity in the cell population.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Local-scale panmixia in the lichenized fungus Xanthoria parietina contrasts with substantial genetic structure in its Trebouxia photobionts

Microsatellite markers can provide valuable information about gene flow and population history. We developed and tested new microsatellites for the nitrophilic lichenized fungus Xanthoria parietina and studied its genetic diversity and structure within the urban area of Munich, Bavaria. We compared its local genetic pattern with that of its photobiont partner Trebouxia decolorans, for which existing microsatellites were applied. For comparison, a reference site with clean air was included in the sampling. We found support for three genetic clusters in the fungus X. parietina, which occurred intermingled in collecting sites. There was a high degree of admixture within fungal populations and individuals, and analysis of molecular variance revealed a lack of population structure in the mycobiont. The Trebouxia photobiont, in contrast, exhibited structured populations which grouped into two to five genetic clusters, and individuals showed less admixture than in the mycobiont. This indicates that the two lichen partners differ in their ability to move around in the landscape. The microsatellite markers we report are polymorphic and are suitable for population genetic studies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Illuminating otoliths: New insights for life history of Balistes triggerfishes

Our understanding of fish life-history strategies is informed by key biological processes, such as growth, survival/mortality, recruitment and sexual maturation, used to characterize fish stocks (populations). Characterizing the life-history traits of fish populations requires the application of accurate age estimation for managed species. Grey triggerfish Balistes capriscus and queen triggerfish Balistes vetula are important reef-associated species for commercial and recreational fisheries in the Atlantic Ocean. Both species exhibit a unique reproductive strategy for large-bodied fisheries-targeted reef fishes in that they are nesting benthic spawners and invest substantial energy in defence and care of their benthic nests and fertilized eggs. Until recently, our understanding of the life-history strategies of triggerfishes assumed the main method used to obtain age estimates, increments counted from thin sections of the first dorsal spine, provided an accurate characterization of population age-based parameters. However, results from bomb radiocarbon validation studies on the two Balistes species demonstrated that spines do not provide accurate ages, but sagittal otoliths do. The main goal of the current study was to provide an updated understanding for triggerfish life-history strategies by using otolith-based age estimates to characterize population age structure and growth for grey triggerfish and queen triggerfish from waters of the south-eastern U.S. Atlantic. The current study is the first to report on sex-specific age and growth information for grey triggerfish using the Δ 14 C-validated otolith-based age estimation method and the results indicate that the previous characterization of Balistes species as exhibiting moderately rapid growth and as relatively short-lived, based on spine-derived age estimates, are flawed. Otolith-based ages indicated that grey triggerfish and queen triggerfish are moderately slow-growing and long-lived species, attaining maximum ages of 21 and 40 years, respectively. Management efforts for triggerfishes should evaluate these new insights and incorporate the results of otolith-based age estimation into future population monitoring efforts.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Genomic variation across Chinook salmon populations reveals effects of a duplication on migration alleles and supports fine scale structure

Abstract The distribution of ecotypic variation in natural populations is influenced by neutral and adaptive evolutionary forces that are challenging to disentangle. This study provides a high‐resolution portrait of genomic variation in Chinook salmon ( Oncorhynchus tshawytscha ) with emphasis on a region of major effect for ecotypic variation in migration timing. With a filtered data set of ~13 million single nucleotide polymorphisms (SNPs) from low‐coverage whole genome resequencing of 53 populations (3566 barcoded individuals), we contrasted patterns of genomic structure within and among major lineages and examined the extent of a selective sweep at a major effect region underlying migration timing (GREB1L/ROCK1). Neutral variation provided support for fine‐scale structure of populations, while allele frequency variation in GREB1L/ROCK1 was highly correlated with mean return timing for early and late migrating populations within each of the lineages ( r 2 = .58–.95; p < .001). However, the extent of selection within the genomic region controlling migration timing was much narrower in one lineage (interior stream‐type) compared to the other two major lineages, which corresponded to the breadth of phenotypic variation in migration timing observed among lineages. Evidence of a duplicated block within GREB1L/ROCK1 may be responsible for reduced recombination in this portion of the genome and contributes to phenotypic variation within and across lineages. Lastly, SNP positions across GREB1L/ROCK1 were assessed for their utility in discriminating migration timing among lineages, and we recommend multiple markers nearest the duplication to provide highest accuracy in conservation applications such as those that aim to protect early migrating Chinook salmon. These results highlight the need to investigate variation throughout the genome and the effects of structural variants on ecologically relevant phenotypic variation in natural species.

Horn, Rebekah L.↗

DOE OSTI2020

Genome resequencing reveals demographic history and genetic architecture of seed salinity tolerance in Populus euphratica

Populus euphratica is a dominant tree species in desert riparian forests and possesses extraordinary adaptation to salinity stress. Exploration of its genomic variation and molecular underpinning of salinity tolerance is important for elucidating population evolution and identifying stress-related genes. Here, we identify approximately 3.15 million single nucleotide polymorphisms using whole-genome resequencing. The natural populations of P. euphratica in northwest China are divided into four distinct clades that exhibit strong geographical distribution patterns. Pleistocene climatic fluctuations and tectonic deformation jointly shaped the extant genetic patterns. A seed germination rate-based salinity tolerance index was used to evaluate seed salinity tolerance of P. euphratica and a genome-wide association study was implemented. A total of 38 single nucleotide polymorphisms were associated with seed salinity tolerance and were located within or near 82 genes. Expression profiles showed that most of these genes were regulated under salt stress, revealing the genetic complexity of seed salinity tolerance. Furthermore, DEAD-box ATP-dependent RNA helicase 57 and one undescribed gene (CCG029559) were demonstrated to improve the seed salinity tolerance in transgenic Arabidopsis. These results provide new insights into the demographic history and genetic architecture of seed salinity tolerance in desert poplar.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Integration of ultra-low coverage whole-genome sequences for reconstructing the evolutionary history of Galapagos giant tortoises

Genomic data from contemporary and historical samples often need to be coupled for evolutionary reconstructions of multitaxon complexes. However, the genetic data recovered from historical samples may result only in ultra-low coverage whole-genome sequences (ulcWGS; <0.15× depth), leading to inaccurate evolutionary inferences given a preponderance of missing data. Using the Galapagos giant tortoise radiation as a study system (Chelonoidis spp., composed of 13 extant and four extinct lineages), we assembled a novel methodological pipeline that removes potential noise introduced by the missing data and enhances the evolutionary signal from ulcWGS samples. We leveraged existing tools for phylogenomic placement (EPA-ng), population genomic structure (smartsnp) and admixture (Admixfrog, NGSadmix) to demonstrate that the evolutionary history of samples can be uncovered with sequencing depths as low as 0.008–0.139×. Importantly, these approaches do not use genotype imputation of the ulcWGS samples, which would require extensive reference datasets. Our application to two cases of extinct lineages of Galapagos giant tortoises, with and without references from the same lineage, demonstrates the general value of the approach. We confirm where the extinct lineages from San Cristóbal and Santa Fe islands fit into the Galapagos giant tortoise radiation, and that these lineages were evolutionarily distinct entities.

ancient DNA↗

DOE OSTI2024

Theory of strong-field sequential double ionization of polyatomic molecules

Understanding of strong-field sequential double ionization (SDI) of molecules by a highly intense infrared laser pulse could be the key to observing electron motion in molecules in the attosecond to femtosecond timescale. Based on a novel density matrix approach for SDI (DM-SDI), a recent theoretical study has shown that SDI can be used as a probe to monitor the changes in vibronic coherence in homonuclear diatomic molecules. In this article, we extend the DM-SDI model to general molecules that could possess permanent dipole moments and arbitrary symmetry. We apply the model to SDI of a water molecule and identify the formation pathway of individual dication states. We further deduce that kinetic energy release spectra from two- and three-body fragments could carry the signature of vibronic coherence between the lowest two states of the water cation. Furthermore, our results suggest that observables from the SDI probe can be interpreted intuitively with only the knowledge of electronic structures of populated ionic states, making the SDI probe to be a highly desirable probing scheme for vibronic coherence in generic molecules.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2021

Optical coherence and energy-level properties of a Tm 3+ -doped LiNbO 3 waveguide at subKelvin temperatures

We characterize the optical coherence and energy-level properties of the 795-nm 3 H 6 to 3 H 4 transition of Tm 3+ in a Ti 4+ :LiNbO 3 waveguide at temperatures as low as 0.65 K. Coherence properties are measured with varied temperature, magnetic field, optical excitation power and wavelength, and measurement timescale. We also investigate nuclear spin-induced hyperfine structure and population dynamics with varying magnetic field and laser excitation power. Except for accountable differences due to different Ti 4+ - and Tm 3+ -doping concentrations, we find that the properties of Tm 3+ :Ti 4+ :LiNbO 3 produced by indiffusion doping are consistent with those of a bulk-doped Tm 3+ :LiNbO 3 crystal measured under similar conditions. Furthermore, our results, which complement previous work in a narrower parameter space, support using rare-earth ions for integrated optical and quantum signal processing.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2020

Quantifying redox heterogeneity in single-crystalline LiCoO 2 cathode particles

Active cathode particles are fundamental architectural units for the composite electrode of Li-ion batteries. The microstructure of the particles has a profound impact on their behavior and, consequently, on the cell-level electrochemical performance. LiCoO 2 (LCO, a dominant cathode material) is often in the form of well-shaped particles, a few micrometres in size, with good crystallinity. In contrast to secondary particles (an agglomeration of many fine primary grains), which are the other common form of battery particles populated with structural and chemical defects, it is often anticipated that good particle crystallinity leads to superior mechanical robustness and suppressed charge heterogeneity. Yet, sub-particle level charge inhomogeneity in LCO particles has been widely reported in the literature, posing a frontier challenge in this field. Herein, this topic is revisited and it is demonstrated that X-ray absorption spectra on single-crystalline particles with highly anisotropic lattice structures are sensitive to the polarization configuration of the incident X-rays, causing some degree of ambiguity in analyzing the local spectroscopic fingerprint. To tackle this issue, a methodology is developed that extracts the white-line peak energy in the X-ray absorption near-edge structure spectra as a key data attribute for representing the local state of charge in the LCO crystal. This method demonstrates significantly improved accuracy and reveals the mesoscale chemical complexity in LCO particles with better fidelity. In addition to the implications on the importance of particle engineering for LCO cathodes, the method developed herein also has significant impact on spectro-microscopic studies of single-crystalline materials at synchrotron facilities, which is broadly applicable to a wide range of scientific disciplines well beyond battery research.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Towards a more general understanding of the algorithmic utility of recurrent connections

Lateral and recurrent connections are ubiquitous in biological neural circuits. Yet while the strong computational abilities of feedforward networks have been extensively studied, our understanding of the role and advantages of recurrent computations that might explain their prevalence remains an important open challenge. Foundational studies by Minsky and Roelfsema argued that computations that require propagation of global information for local computation to take place would particularly benefit from the sequential, parallel nature of processing in recurrent networks. Such “tag propagation” algorithms perform repeated, local propagation of information and were originally introduced in the context of detecting connectedness, a task that is challenging for feedforward networks. Here, we advance the understanding of the utility of lateral and recurrent computation by first performing a large-scale empirical study of neural architectures for the computation of connectedness to explore feedforward solutions more fully and establish robustly the importance of recurrent architectures. In addition, we highlight a tradeoff between computation time and performance and construct hybrid feedforward/recurrent models that perform well even in the presence of varying computational time limitations. We then generalize tag propagation architectures to propagating multiple interacting tags and demonstrate that these are efficient computational substrates for more general computations of connectedness by introducing and solving an abstracted biologically inspired decision-making task. Our work thus clarifies and expands the set of computational tasks that can be solved efficiently by recurrent computation, yielding hypotheses for structure in population activity that may be present in such tasks.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1972

New horizons in astronomy.

Besides the study of astronomy itself, other topics included cover the geological and biological developments on earth and basic physics of matter, heat, and light. Optical and radio telescopes are discussed, as well as photographic and photoelectric means of detection. The immediate solar system is described by topics on the properties and atmospheres of the inner and outer planets, the sun's energy, sunspots, and the solar spectrum. Stars both on and off the main sequence are discussed in terms of distances, intrinsic properties, lifetimes and evolution. The Milky Way is compared to other galaxies in size, star population and structure, and the different galaxy shapes are pictured. Topics of most recent interest are covered by results of the lunar explorations, new concepts of Mars, and problems of space travel. Problems of modern astronomy include pulsars, neutron stars, and quasars.

Brandt, J. C.↗

NASA NTRS1988

Large molecules in diffuse interstellar clouds

The effects of the presence of a substantial component of large molecules on the chemistry of diffuse molecular clouds are explored, and detailed models of the zeta Persei and zeta Ophiuchi clouds are constructed. The major consequence is a reduction in the abundances of singly charged atomic species. The long-standing discrepancy between cloud densities inferred from rotational and fine-structure level populations and from the ionization balance can be resolved by postulating a fractional abundance of large molecules of 1 x 10 to the -7th for zeta Persei and 6 x 10 to the -7th for zeta Ophiuchi. If the large molecules are polycyclic aromatic hydrocarbons (PAH) containing about 50 carbon atoms, they contain 1 percent of the carbon in zeta Persei and 7 percent in zeta Ophiuchi. Other consequences of the possible presence of PAH molecules are discussed.

Lepp, S.↗

NASA NTRS1994

Abundances, planetary nebulae, and stellar evolution

Among Henry Norris Russell's many achievements were his contributions to solar and stellar spectroscopy, in particular, to an analysis of the chemical composition of the solar atmosphere. The question of composition differences between stars was hotly debated; some distinguished astronomers argued that all stars had the solar composition. Some early challenges to this doctrine are described. Determinations of chemical compositions of gaseous nebulae were much more difficult. If we observe the lines of a given chemical element in one ionization stage in a stellar spectrum, we can deduce readily the abundance of that element. No such luxury is available for a planetary or diffuse gaseous nebula. We must measure lines of as many ionization stages as we can. Furthermore, a nebula is an extended object. Often detailed spectroscopy is at hand only for narrow pencil columns taken through the image. Different observers use a variety of apertures. Fortunately it is possible to calculate theoretical spectra for any arbitrary cross section taken through a symmetrical model, so UV, optical, and IR observations all can be compared properly with a prediction. The value of high-resolution spectra obtained with instruments such as the Hamilton Echelle Spectrograph at Lick Observatory is emphasized. Improved fluxes for weak but important transitions are found. Close blends of lines of different ions can be resolved, and checks can be made on predictions of atomic parameters such as Einstein A-values and collision strengths. High spectral resolution data have been obtained and reduced for 22 planetary nebulae of varying size, structure, stellar population membership, dustiness, level of excitation, evolutionary status, and chemical compositions. The promise seems justified that with such extensive, high quality data, additional insights on nebular genesis and late states of stellar evolution can be found. The present survey is confined to nebulae of high surface brightness, but among these are found some engaging objects such as NGC 7027, IC 4997, and NGC 6572.

Aller, Lawrence H.↗

NASA NTRS1997

Improving Search Properties in Genetic Programming

With the advancing computer processing capabilities, practical computer applications are mostly limited by the amount of human programming required to accomplish a specific task. This necessary human participation creates many problems, such as dramatically increased cost. To alleviate the problem, computers must become more autonomous. In other words, computers must be capable to program/reprogram themselves to adapt to changing environments/tasks/demands/domains. Evolutionary computation offers potential means, but it must be advanced beyond its current practical limitations. Evolutionary algorithms model nature. They maintain a population of structures representing potential solutions to the problem at hand. These structures undergo a simulated evolution by means of mutation, crossover, and a Darwinian selective pressure. Genetic programming (GP) is the most promising example of an evolutionary algorithm. In GP, the structures that evolve are trees, which is a dramatic departure from previously used representations such as strings in genetic algorithms. The space of potential trees is defined by means of their elements: functions, which label internal nodes, and terminals, which label leaves. By attaching semantic interpretation to those elements, trees can be interpreted as computer programs (given an interpreter), evolved architectures, etc. JSC has begun exploring GP as a potential tool for its long-term project on evolving dextrous robotic capabilities. Last year we identified representation redundancies as the primary source of inefficiency in GP. Subsequently, we proposed a method to use problem constraints to reduce those redundancies, effectively reducing GP complexity. This method was implemented afterwards at the University of Missouri. This summer, we have evaluated the payoff from using problem constraints to reduce search complexity on two classes of problems: learning boolean functions and solving the forward kinematics problem. We have also developed and implemented methods to use additional problem heuristics to fine-tune the searchable space, and to use typing information to further reduce the search space. Additional improvements have been proposed, but they are yet to be explored and implemented.

Janikow, Cezary Z.↗

NASA NTRS2003

Modeling of Iron K Lines: Radiative and Auger Decay Data for Fe II-Fe IX

A detailed analysis of the radiative and Auger de-excitation channels of K-shell vacancy states in Fe II-Fe IX has been carried out. Level energies, wavelengths, A-values, Auger rates and fluorescence yields have been calculated for the lowest fine-structure levels populated by photoionization of the ground state of the parent ion. Different branching ratios, namely K alpha 2/K alpha 1, K beta/K alpha, KLM/KLL, KMM/KLL, and the total K-shell fluorescence yields, omega(sub k), obtained in the present work have been compared with other theoretical data and solid-state measurements, finding good general agreement with the latter. The Kalpha 2/K alpha l ratio is found to be sensitive to the excitation mechanism. From these comparisons it has been possible to estimate an accuracy of approx.10% for the present transition probabilities.

Palmeri, P.↗

NASA NTRS2002

Understanding and responding to earthquake hazards

Advances in understanding of the earthquake cycle and in assessing earthquake hazards is a topic of great importance. Dynamic earthquake hazard assessments resolved for a range of spatial scales and time scales will allow a more systematic approach to prioritizing the retrofitting of vulnerable structures, relocating populations at risk, protecting lifelines, preparing for disasters, and educating the public.

earth science vision distributed spacecraft virtua↗

NASA NTRSDate not supplied

Multiscale Modeling of Fracture Strength in Fibrous Thermal Protection System Materials

This work presents a multiscale modeling approach to predict the fracture strength of fibrous Thermal Protection System (TPS) materials. The model assumes that system failure is initiated at the joints between individual fibers. We investigated three distinct TPS compositions: amorphous silica, alumina and aluminosilicate fibers. Molecular dynamics (MD) simulations were employed to determine the fracture strength values of these fiber joints for both material systems. These fracture strength values were then integrated into simulations of 3D randomly populated fiber structures, where tensile load transfer occurs through the fiber joints. These microscale properties are upscaled through a renormalization approach [1] to predict macroscale tensile strength of 3D random fiber networks, accounting for joint-dominated failure and effective load-bearing area. The study concludes by demonstrating the resulting strength variation as a function of material composition, fiber density, and morphology. We also show validation of results by comparing them against explicit fiber finite element (FE) modeling [2] where fiber joint fracture is represented by cohesive elements.

Jaehyun Cho↗

DOE OSTI2020

Characterization of multi-regime reaction zones in a piloted inhomogeneous jet flame with local extinction

In this study, gradient free regime identification (GFRI) is applied to 1D Raman/Rayleigh/LIF measurements of temperature and major species from the intermediate velocity case of the Sydney piloted inhomogeneous jet flame series to better understand the structure of reaction zones and the downstream evolution of multi-regime characteristics. The GFRI approach allows local reaction zones to be detected and characterized as premixed, dominantly premixed, multi-regime, dominantly non-premixed, or non-premixed flame structures, based on flame markers (mixture fraction, chemical mode, and heat release rate) derived from the experimental data. The statistics of chemical mode zero-crossings, which mark premixed reaction zones, and the relative populations of flame structures are shown to be sensitive to the state of mixing in the near field of the flame and to the level of local extinction farther downstream. Multi-regime structures, where premixed and non-premixed reaction zones occur in close proximity and both contribute to overall heat release, account for nearly half the total population at streamwise locations within the first several jet diameters. There is a rapid transition within the near field whereby the relative population of non-premixed and dominantly non-premixed structures grows from 0.05 to nearly 0.5, and the population of premixed and dominantly premixed structures decreases correspondingly as fluid entering the reaction zone becomes progressively fuel-rich. Local extinction and re-ignition bring a resurgence in premixed-type structures, many of which occur at fuel-lean conditions. There are also modest populations of multi-regime structures, having chemical mode zero-crossings at lean conditions, which would not exist in a fully burning jet flame.

42 ENGINEERING↗