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At least 1,621 records · Page 90

Improving precision and accuracy of genetic mapping with genotyping‐by‐sequencing data in outcrossing species

Abstract Genotyping‐by‐sequencing (GBS) is a widely used strategy for obtaining large numbers of genetic markers in model and non‐model organisms. In crop plants, GBS‐derived marker datasets are frequently used to perform quantitative trait locus (QTL) mapping. In some plant species, however, high heterozygosity and complex genome structure mean that researchers must use care in handling GBS data to conduct QTL mapping most effectively. Such outbred crops include most of the perennial grass and tree species used for bioenergy. To identify strategies for increasing accuracy and precision of QTL mapping using GBS data in outbred crops, we conducted an empirical study of SNP‐calling and genetic map‐building pipeline parameters in a Miscanthus sinensis population, and a complementary simulation study to estimate the relationship between genome‐wide error rate, read depth, and marker number. The bioenergy grass Miscanthus is an obligate outcrossing species with a recent (diploidized) whole‐genome duplication. For the study of empirical M. sinensis data, we compared two SNP‐calling methods (one non‐reference‐based and one reference‐based), a series of depth filters (12×, 20×, 30×, and 40×) and two map‐construction methods (i.e., marker ordering: linkage‐only and order‐corrected based on a reference genome). We found that correcting the order of markers on a linkage map by using a high‐quality reference genome improved QTL precision (shorter confidence intervals). For typical GBS datasets of between 1000 and 5000 markers to build a genetic map for biparental populations, a depth filter set at 30× to 40× applied to outbred populations provided a genome‐wide genotype‐calling error rate of less than 1%, improved accuracy of QTL point estimates and minimized type I errors for identifying QTL. Based on these results, we recommend using a reference genome to correct the marker order of genetic maps and a robust genotype depth filter to improve QTL mapping for outbred crops.

59 BASIC BIOLOGICAL SCIENCES↗

Statistical generic design of glass and optimization: Selective review on oxide glasses

Designing a single glass composition for a multidimensional property space is challenging, and the difficulty increases with the number of design criteria. Traditionally, the task is accomplished using multiple statistical models that describe the relationships between composition (C) and property (P) values, i.e., C-P models. Recently, the structure (S)-property (P) statistical modeling has emerged as a complementary approach. The S-P modeling approach has also been shown to be a preferred method for modeling glass properties, particularly when a small data set is available, such as in single-component studies, or when strong nonlinearities exist between composition and properties. The combined model package, C-S-P, implements the concept of generic glass design, i.e., designing glass for performance by first selecting a specific or optimized set of glass network structural groups using S-P models and then transferring the designed structures (genes) to a particular composition using C-S models. This article reviews a set of supporting cases from the previous C-S-P modeling studies of phosphate, silicate, and borosilicate glasses, which are relevant for many critical commercial applications. The methodology for developing the statistical C-S-P database is presented, enabling the application of P?S?C to achieve a generic glass design and optimization, targeting multiple design criteria for both performance and processing properties simultaneously.

Network structure↗

Cracking during pyrolysis of preceramic polymers within glass microtubes

Abstract Cracking of preceramic polymers during pyrolysis under highly‐constrained conditions is examined by X‐ray computed tomography of fine glass microtubes containing the pyrolyzing material. The microtubes represent model geometries that mimic the long channels between fibers during production of ceramic composites by precursor impregnation and pyrolysis. Complementary fracture mechanics analyses of interface cracking and crack kinking are used to glean insights into the conditions under which periodic alternating cracks form. A key finding is that alternating cracks are an inherent feature of constrained pyrolysis . This feature is attributable in large part to the high energy release rates for interface cracks to kink into the pyrolyzing material under the hydrostatic tension developed during pyrolysis. It also requires interfaces with toughness comparable to that of the pyrolyzing material, to prevent large‐scale interface separation. The results further indicate the need for small uniform spaces for pyrolysis within fiber preforms in order to produce networks of fine periodic pyrolysis cracks; these networks in turn facilitate impregnation and pyrolysis in subsequent processing cycles.

Larson, Natalie M.↗

Material efficiency and climate change mitigation of passenger vehicles

A transition to electric vehicles and renewable energy is currently underway but may not be rapid enough in order to reach ambitious climate change mitigation targets. Therefore, additional, preferably instantaneous, measures are needed for quick emissions reductions, which is where material efficiency (ME) could constitute a promising solution. ME strategies include but are not limited to vehicle lightweighting through material substitution, increased recycling of materials, reuse and remanufacturing of vehicle components, vehicle downsizing (switching to a smaller vehicle) and more intensive use by means of increased vehicle occupancy through sharing practices. While recent analyses have focused on a narrow subset of these, we find striking differences in the overall potential of different strategies to decrease vehicular carbon footprints. Downsizing and more intensive use offer the largest mitigation potential but strongly depend on consumer behavior and are highly sensitive to modeling assumptions. Combined, the analyzed strategies can achieve emission reductions of up to 57% over the life cycle of a single vehicle, which is comparable to up to 83% achieved through a shift to low-carbon energy supply. ME can cut carbon footprints of already efficient vehicles charging renewable electricity by half again. This makes ME both an excellent short-term solution for climate change mitigation targeting the light vehicle sector but also an important complementary strategy to the long-term transition towards electric vehicles and renewable energy supply.

54 ENVIRONMENTAL SCIENCES↗

Mycorrhizal effects on crop yield and soil ecosystem functions in a long‐term tillage and fertilization experiment

Summary It is well understood that agricultural management influences arbuscular mycorrhizal (AM) fungi, but there is controversy about whether farmers should manage for AM symbiosis. We assessed AM fungal communities colonizing wheat roots for three consecutive years in a long‐term (> 14 yr) tillage and fertilization experiment. Relationships among mycorrhizas, crop performance, and soil ecosystem functions were quantified. Tillage, fertilizers and continuous monoculture all reduced AM fungal richness and shifted community composition toward dominance of a few ruderal taxa. Rhizophagus and Dominikia were depressed by tillage and/or fertilization, and their abundances as well as AM fungal richness correlated positively with soil aggregate stability and nutrient cycling functions across all or no‐tilled samples. In the field, wheat yield was unrelated to AM fungal abundance and correlated negatively with AM fungal richness. In a complementary glasshouse study, wheat biomass was enhanced by soil inoculum from unfertilized, no‐till plots while neutral to depressed growth was observed in wheat inoculated with soils from fertilized and conventionally tilled plots. This study demonstrates contrasting impacts of low‐input and conventional agricultural practices on AM symbiosis and highlights the importance of considering both crop yield and soil ecosystem functions when managing mycorrhizas for more sustainable agroecosystems.

Peng, Zhenling↗

Signatures of local nitrogen adaptation in the Brachypodium distachyon root microbiome

Plants associate with diverse microbiomes that impact their fitness, yet the contribution of the microbiome to plant adaptation is uncertain. As plant recruitment of its microbiome can be both highly variable and genetically determined, we hypothesized this recruitment process may be the result of adaptive evolution, and contributing to plant local adaptation. We investigated the evolution and adaptive benefit of plant–microbiome recruitment by characterizing the rhizosphere communities across a genotypic panel of Brachypodium distachyon in a common garden experiment. By linking microbial communities to their host genotype's historic environment, we identified signatures of selection on plant–microbiome recruitment. Plant–microbiome composition was significantly correlated with the host genotype's historic environment, with enrichment of microbial traits aligned to local resource conditions. For example, genotypes from low-nitrogen environments recruited communities enriched in nitrogen acquisition traits. In a complementary experiment evaluating plant nitrogen response, these same genotypes were well-adapted to low-nitrogen environments, contingent on the presence of key nitrogen-cycling microbes. These results suggest that local adaptation in plants may partially be mediated by recruitment of beneficial microbiomes. This perspective suggests that plant adaptation may be an emergent property of host–microbe interactions, where evolutionary responses favor traits that promote recruitment of locally beneficial microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗

PPT1-mediated plastidic phospho enol pyruvate import enhances fatty acid biosynthesis in sugar-rich tissues

Metabolic engineering of vegetative tissues for lipid production holds transformative potential for sustainable biofuels, yet achieving sufficient yields remains challenging. Here, we present a strategy to enhance fatty acid synthesis by redirecting cytosolic phospho enol pyruvate (PEP) into plastids through overexpression of the plastidial phospho enol pyruvate/phosphate translocator ( PPT1 ) in vegetative tissues of Arabidopsis thaliana . Integrated metabolomic and transcriptomic analyses revealed that AtPPT1 overexpression alleviated metabolite overaccumulation in high-sugar tissues, consistent with enhanced carbon flux coordination between the cytosol and chloroplast. Notably, phosphofructokinase activity, a key step in glycolysis, was elevated, linking plastidic PEP import to increased glycolytic throughput. In Arabidopsis, overexpression of AtPPT1 increased fatty acid content and lipid droplet accumulation in the sugar-accumulating sweet11;12;13 mutant, but not in wild-type Col-0. Together, these findings establish PEP redirection as an effective strategy to boost fatty acid and lipid production in sugar-rich vegetative tissues and provide a complementary metabolic module for future lipid-engineering efforts.

Arabidopsis thaliana↗

Metabolic and transcriptomic study of pennycress natural variation identifies targets for oil improvement

Pennycress (Thlaspi arvense L.), a member of the Brassicaceae family, produces seed oil high in erucic acid, suitable for biodiesel and aviation fuel. Although pennycress, a winter annual, could be grown as a dedicated bioenergy crop, an increase in its seed oil content is required to improve its economic competitiveness. The success of crop improvement relies upon finding the right combination of biomarkers and targets, and the best genetic engineering and/or breeding strategies. In this work, we combined biomass composition with metabolomic and transcriptomic studies of developing embryos from 22 pennycress natural variants to identify targets for oil improvement. The selected accession collection presented diverse levels of fatty acids at maturity ranging from 29% to 41%. Pearson correlation analyses, weighted gene co‐expression network analysis and biomarker identifications were used as complementary approaches to detect associations between metabolite level or gene expression and oil content at maturity. The results indicated that improving seed oil content can lead to a concomitant increase in the proportion of erucic acid without affecting the weight of embryos. Processes, such as carbon partitioning towards the chloroplast, lipid metabolism, photosynthesis, and a tight control of nitrogen availability, were found to be key for oil improvement in pennycress. Besides identifying specific targets, our results also provide guidance regarding the best timing for their modification, early or middle maturation. Thus, this work lays out promising strategies, specific for pennycress, to accelerate the successful development of lines with increased seed oil content for biofuel applications.

59 BASIC BIOLOGICAL SCIENCES↗

Adaptive management of large-scale ecosystem restoration: increasing certainty of habitat outcomes in the Columbia River Estuary, U.S.A.

Ecological restoration programs in dynamic coastal environments can benefit from adaptive management, including an iterative process for identifying and addressing critical uncertainties. We highlight key developments under the three pillars that have increased the rate of restoration by the Columbia Estuary Ecosystem Restoration Program (CEERP) over 20 years: science, coordination, and management. We show how such programs can be institutionalized to ensure that estuary ecosystems are better understood, conserved, and restored. The principal conservation effort under CEERP is to reconnect historical floodplain wetlands to the mainstem. The program also supports other restoration actions that demonstrate a high potential to benefit ecosystem function and endangered salmon populations, however, there is greater uncertainty regarding these less-utilized techniques. Through adaptive management, we address both technical uncertainty regarding benefits to the environmental resource and programmatic uncertainty pertaining to decision-making. Here, we examine three periods of CEERP growth to establish how complementary research and restoration actions have improved program outcomes over time. We highlight the tools and processes that were developed and integrated into the program to refine program strategy, improve project design, and maximize ecological benefits. CEERP supported 77 restoration projects and reconnected over 7,000 acres of floodplain habitat to the lower Columbia River between 2004 and 2021. Building on these successes, we outline current plans to better engage landowners and local communities, solicit new project types, and maintain enough flexibility within the program to adapt to new priorities.

54 ENVIRONMENTAL SCIENCES↗

Actinide in Air (Rn-Progeny Rejected) Alpha Spectroscopy With Tensioned Metastable Fluid Detectors

Here, this article discusses outcome of research for deriving a methodology and apparatus for ascertaining for the presence of ultratrace-level actinides in air from their alpha emission signatures, while remaining blind to the relatively large (1000× higher activity) alpha emissions from Rn-progeny. Apparatus and techniques were developed to collect and characterize alpha-emitting nuclides of Rn-progeny and actinides in air on a polycarbonate 3 μm pore size continuous air monitor (CAM) filter. A wet-chemistry approach was developed and validated for successfully separating the Rn-progeny alpha emitting isotopes of Po-214 and Po-218, while extracting the actinides (U, Pu, Am) in a fluid mixture that is suitable for conduct of alpha spectroscopy with a centrifugally tensioned metastable fluid detector (CTMFD). The resulting α-TMFD technology was compared against the state-of-art “Alpha-Sentry™” Continuous Air Monitor (CAM) system commonly utilized world-wide. Results indicate that the α-TMFD technology can potentially offer complementary and superior performance in multiple performance categories, and ∼18× improvement in the time to detect (e.g., at 0.02 derived air concentration (DAC) within ∼3 h, versus ∼70 h for Alpha-Sentry) for actinides of interest while also remaining ∼100% blind to ∼10 3 × higher Rn-progeny background—with the added potential for offering few keV scale energy resolution without resorting to peak shape fitting, versus ∼300–400 keV for existing CAM systems.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Code Verification of Multiple Physics-Fidelity Models in Hypersonic Aerodynamics

Hypersonic aerodynamics models exist across a range of physics fidelities with associated computational expenses. These models may be run independently or in a multifidelity framework that leverages their complementary strengths of speed for lower-fidelity and accuracy for higher-fidelity models. This work presents applied code verification of two lower-fidelity models contained within the Sandia hypersonic aerodynamics code. Each model has a different form that requires individualized verification approaches, including comparison to analytical solutions as well as manufactured solutions with order-of-accuracy testing. In conclusion, results of this effort include the identification and resolution of code errors and shortcomings, as well as the demonstration of code correctness and consistency for both models.

Aerodynamics↗

Aluminum hydroxide, bayerite, boehmite, and gibbsite ToF-SIMS spectra in the negative ion mode. I

We report time-of-flight secondary ion mass spectrometry (ToF-SIMS) was performed for boehmite (AOH-60) and its potential products of oxidation including pseudo-boehmite (AOH-180), α- and γ-Al 2 O 3 , and α- and γ-Al(OH) 3 . Since boehmite is often incorporated on cladding materials to prevent corrosion, surface analysis techniques are performed to determine the amount of oxidation present. This ToF-SIMS spectral library is of significance because it includes boehmite and its potential oxidation products (i.e., aluminum oxide and hydroxide), which can be used to compare to spectra obtained for real-world samples containing boehmite. Furthermore, ToF-SIMS is often used as a complementary technique to x-ray photoelectron spectroscopy due to its surface sensitivity and ability to compare spectra via a multivariate analysis, therefore establishing that the molecular signatures of boehmite and relevant compounds are essential for peak identification. The SIMS spectra shown are acquired from commercially available powders, which were deposited onto a silicon wafer substrate via liquid slurry drop casting. This library of SIMS mass spectra will serve as a comparison of boehmite [γ-AlO(OH)], pseudo-boehmite [AlOOH∙nH 2 O], α- and γ-Al 2 O 3 aluminum oxide, and α- and γ-Al 2 O 3 aluminum hydroxide in the negative ion mode, which compliments those reported in the positive ion mode.

36 MATERIALS SCIENCE↗

Aluminum hydroxide, bayerite, boehmite, and gibbsite ToF-SIMS spectra in the positive ion mode. II

We report time-of-flight secondary ion mass spectrometry (ToF-SIMS) was performed for boehmite (AOH-60) and its potential products of oxidation including pseudo-boehmite (AOH-180), α- and γ-Al 2 O 3 , and α- and γ-Al(OH) 3 . Since boehmite often forms on the cladding materials to prevent corrosion, surface analysis techniques are performed to determine the amount of oxidation present. This ToF-SIMS spectral library is of significance because it includes boehmite and its potential oxidation products (i.e., aluminum oxide and hydroxide), which can be used to compare to spectra obtained for real-world samples containing boehmite. Furthermore, ToF-SIMS is often used as a complementary technique to x-ray photoelectron spectroscopy (XPS) due to its surface sensitivity and ability to compare spectra via multivariate analysis, therefore establishing the molecular signatures of boehmite and relevant compounds are essential for peak identification. The SIMS spectra shown are acquired from commercially available powders, which were deposited onto a Si wafer substrate via liquid slurry drop casting. This library of SIMS mass spectra will serve as a comparison of boehmite [γ-AlO(OH)], pseudo-boehmite [AlOOH∙nH 2 O], α- and γ-Al 2 O 3 aluminum oxide, and α- and γ-Al 2 O 3 aluminum hydroxide in the positive ion mode, which compliments those reported in the negative ion mode (Part 1).

36 MATERIALS SCIENCE↗

Soft X-ray quantum efficiency of a commercial CMOS imaging sensor

The demonstrated performance and cost-effectiveness of complementary metal-oxide-semiconductor (CMOS) sensors make them a potentially attractive option for low-cost space-based X-ray observatories. We have previously reported on the performance of a commercially available backside-illuminated Sony IMX290LLR-C CMOS sensor and found it to offer X-ray spectral resolutions comparable to the charged coupled devices (CCDs) aboard Suzaku and Chandra and to have a sufficient radiation hardness for use in low Earth orbit. Here, in this work, we report on the quantum efficiency (QE) of this sensor, an essential metric for modeling the sensitivity of an instrument as an X-ray detector. Using the Advanced Photon Source at Argonne National Laboratory, we measure the soft X-ray QE of this CMOS sensor to be 0.28 ± 0.02 at a photon energy of 490.5 eV. This energy was chosen for its proximity to the astrophysically important O VII triplet emission lines (~574 eV) studied by the HaloSat mission. Although not surpassing that of the back-illuminated CCDs aboard Suzaku and Chandra, this QE compares favorably to that of the front-illuminated CCDs aboard the same observatories and is competitive with that of the silicon drift detectors used aboard HaloSat, making it a strong candidate for use on future X-ray small satellite (SmallSat) missions.

47 OTHER INSTRUMENTATION↗

Soft x-ray detection for small satellites with a commercial CMOS sensor at room temperature

Recently CMOS (complementary metal-oxide-semiconductor) sensors have progressed to a point where they may offer improved performance in imaging x-ray detection compared to the CCDs often used in x-ray satellites. We demonstrate x-ray detection in the soft x-ray band (250-1700 eV) by a commercially available back-illuminated Sony IMX290LLR CMOS sensor using the Advanced Photon Source at the Argonne National Laboratory. Additionally, while operating the device at room temperature, we measure energy resolutions (FWHM) of 47 eV at 250 eV and and 77 eV 1700 eV which are comparable to the performance of the Chandra ACIS and the Suzaku XIS. Furthermore, we demonstrate that the IMX290LLR can withstand radiation up to 17.1 krad, making it suitable for use on spacecraft in low earth orbit.

47 OTHER INSTRUMENTATION↗

NACHOS, a CubeSat-based high-resolution UV-Visible hyperspectral imager for remote sensing of trace gases: system overview and science objectives

Here, the Nano-satellite Atmospheric Chemistry Hyperspectral Observation System (NACHOS) is a high-throughput (f/2.9), high spectral resolution (~1.3 nm optical resolution, 0.6 nm sampling) Offner-design hyperspectral imager operating in the 300-500 nm spectral region. The 1.5U instrument payload (1U optical system, 0.5U electronics module) is hosted by a 1.5U LANL-designed CubeSat bus to comprise a 3U complete satellite. Spectroscopically similar to NASA’s Ozone Monitoring Instrument (OMI), which provides wide-field global mapping of ozone and other gases at coarse spatial resolution, NACHOS fills the complementary niche of targeted measurements at much higher spatial resolution. With 350 across-track spatial pixels and a 15-degree across-track field of view, NACHOS will provide spectral imaging at roughly 0.4 km per pixel from 500 km altitude. NACHOS incorporates highly streamlined gas-retrieval algorithms for rapid onboard processing, alleviating the need to routinely downlink massive hyperspectral data cubes. We will discuss the instrument design, challenges in achieving mechanical robustness to launch vibration in such a compact instrument, the onboard calibration system, and gas-retrieval data downlink strategy. We will also discuss potential science missions, including monitoring of NO 2 as an easily detected proxy for anthropogenic fossil-fuel greenhouse gases, monitoring lowlevel SO 2 degassing at pre-eruptive volcanoes, H 2 CO from wildfires, and characterization of aerosols. The long-term vision is for a many-satellite constellation that could provide both high spatial resolution and frequent revisits for selected targets of interest. As an initial technology demonstration of this vision, the NACHOS project is currently slated to launch two CubeSats in early 2022.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Investigation of the relationship between classical and nonclassical ultrasound nonlinearity parameters and microstructural mechanisms in metals

This research studies two nonlinear ultrasound techniques: second harmonic generation and nonlinear resonant ultrasound spectroscopy, and the relationship to microstructural mechanisms in metals. The results show that there is a large change in both the classical, β, and nonclassical, α, ultrasound nonlinearity parameters in response to three specific microstructural mechanisms: precipitate growth in and along the grain boundaries, dislocations, and precipitate pinned dislocations. For example, both β and α increase with the growth of the precipitate radii (precipitate-pinned-dislocations). Additionally, both β and α increase when there is a growth of precipitates in and along the grain boundaries. As expected, β and α decrease when there is a removal of dislocations in the material. The relationship between β and α, and the microstructural mechanisms studied provide a quantitative understanding of the relationship between measured nonlinearity parameters and microstructural changes in metals, helping to demonstrate the possibility of using these two independent, but complementary, nonlinear ultrasound procedures to monitor microstructural damage.

Levy, Katherine Marie Scott↗

Picoscale structural insight into superconductivity of monolayer FeSe/SrTiO 3

Remarkable enhancement of the superconducting transition temperature ( c ) has been observed for monolayer (ML) FeSe films grown on SrTiO 3 substrates. The atomic-scale structure of the FeSe/SrTiO 3 interface is an important determinant of both the magnetic and interfacial electron-phonon interactions and is a key ingredient to understanding its high- T c superconductivity. We resolve the atomic-scale structure of the FeSe/SrTiO 3 interface through a complementary analysis of scanning transmission electron microscopy and in situ surface x-ray diffraction. We find that the interface is more strongly bonded for a particular registration, which leads to a coherently strained ML. We also determine structural parameters, such as the distance between ML FeSe and the oxide, Se-Fe-Se bond angles, layer-resolved distances between Fe-Se, and registry of the FeSe lattice relative to the oxide. This picoscale structure determination provides an explicit structural framework and constraint for theoretical approaches addressing the high- T c mechanism in FeSe/SrTiO 3 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗