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At least 685 records · Page 38
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Multigeneration Pedigrees to Monitor Hatchery Broodstock Composition and Genetic Variation of Spring/Summer Chinook Salmon in the Columbia River Basin

Abstract Hatchery production of Chinook Salmon Oncorhynchus tshawytscha in the Columbia River basin comprises most of the anadromous salmonid production in this region. Hatchery facilities and programs serve to mitigate for impacts to salmonids due to the construction and operation of hydropower dams and habitat impacts from development in addition to the conservation and restoration of natural populations. A genetic method referred to as parentage-based tagging (PBT) enables highly reliable detection of hatchery-origin fish and inference of multigeneration pedigrees. This study compiles 11 years of PBT data from nearly 125,000 interior stream-type Chinook Salmon from 24 spawning hatcheries located on tributaries of the mid- and upper Columbia River and in the Salmon, Clearwater, and Grande Ronde River subbasins. Multigenerational pedigrees allowed for investigation of the proportions of natural- and hatchery-origin broodstock (pNOB and pHOB, respectively) for each hatchery and enumeration of the scale of production between segregated and integrated programs. We then compared how pHOB and the scale of production influenced the number of stray fish observed, genetic diversity, relatedness, and age-class compositions within broodstocks. Over 91.0% of hatchery broodstock could be assigned back to their parents, and overall less than 1.0% of broodstock consisted of fish that were unintentionally incorporated into nonnatal hatchery programs. We evaluated 11 segregated programs with 0.0–10.0% pNOB, 9 intermediate programs (10.1–50.0% pNOB), and 3 integrated programs (>50.0% pNOB). There was no correlation between the scale of production or pNOB with the level of genetic diversity, but as production size increased, so did the effective number of breeders. This study demonstrates the utility of PBT as a monitoring tool for hatchery broodstocks, and results suggest that segregated and integrated programs have tradeoffs that generally align with their intended broodstock management purpose of providing fish for harvest and/or fish for supplementation or reintroduction.

Horn, Rebekah L.↗
DOE OSTI2022

Smoothed aggregation for difficult stretched mesh and coefficient variation problems

Abstract Four adaptations of the smoothed aggregation algebraic multigrid (SA‐AMG) method are proposed with an eye toward improving the convergence and robustness of the solver in situations when the discretization matrix contains many weak connections. These weak connections can cause higher than expected levels of fill‐in within the coarse discretization matrices and can also give rise to suboptimal smoothing within the prolongator smoothing phase. These smoothing drawbacks are due to the relatively small size of some diagonal entries within the filtered matrix that one obtains after dropping the weak connections. The new algorithms consider modifications to the Jacobi‐like step that defines the prolongator smoother, modifications to the filtered matrix, and also direct modifications to the resulting grid transfer operators. Numerical results are given illustrating the potential benefits of the proposed adaptations.

Hu, Jonathan J.↗
DOE OSTI2023

Effect of recycled fibers and shredded intermediates variation on the mechanical properties and energy absorption of fiber‐reinforced composite panels

Abstract The global composite industry generates large quantities of waste which mostly ends up in landfills due to a lack of established end‐use applications for multiple waste streams. The scrap from end‐of‐life (EoL) includes manufacturing waste such as dry chopped fiber tows, loose fibers, shredded fibers from fabric textile operations, cured/semi‐cured prepregs, and fully cured composite structure waste from aircraft, automobiles, wind blades, boats, and pressure vessels. In this work, different composite waste streams were reduced to shredded intermediates, followed by simple blending, and subjected to wet compression molding to produce composite panels. The panels/plaques were tested for mechanical properties (flexure and impact), fiber‐matrix wet‐out, and property bounds. It was found that wet‐compression molding was a viable and scale‐able approach to produce recycled panels from EoL composites shredded scrap. Furthermore, full‐scale size panels for use in truck bodies and intermodal shipping container flooring were manufactured and their impact resistance was tested using a drop weight impact test. They were tested both for high‐ and low‐velocity load. In the case of high‐velocity load, the average impact load was 14,673 N; the average absorbed energy was 101.6 J; the average elastic energy was 11.7 J and the impact resistance was 1065 J/m. In the case of the low‐velocity drop weight impact test, it was found that the average impact load was 7877.358 N; the average absorbed energy was 9.718 J; the average elastic energy was 9.14 J, and the impact resistance was 184.1 J/m. The shredded composite was shown to be a candidate material for the manufacture of truck bodies and intermodal containers’ flooring panels. Highlights By using shredded intermediates from different composite waste streams, it is possible to manufacture composite panels. Wet–compression process is an appropriate technique for manufacturing recycled fiber composite panels. Regardless of the source of scrap, the mechanical properties of the produced composite panels were improved. The recycling process technology can be transformed to commercial scale to produce full‐size transportation flooring panels. A product pathway is established in consideration of lower cost and improved recyclability.

Vaidya, Uday↗
DOE OSTI2020

Observation of Variations in Condensed Carbon Morphology Dependent on Composition B Detonation Conditions

Carbon particulates generated during detonation depend upon high explosive type, composition, and detonation conditions. Although explosive composition greatly affects particulates, the focus of this work is on how detonation geometries that induce much higher temperatures and pressures in the high explosive lead to differing particulate morphologies. In this study, two geometries were used: Detonations were initiated in Composition B cylinders at one end in conventional detonations and initiated at both ends to produce colliding detonations. Each of these detonations was observed on the sub-μs timescale using fast radiography capturing images of the front moving through the cylinder, and colliding detonation fronts in real-time. These imaging experiments were complemented with time-resolved small-angle x-ray scattering (SAXS) experiments that were able to observe and determine the varying condensed carbon morphologies at different locations and times in each detonation. The detonations could be timed in such a way that the spatial and temporal dependence of the carbon morphology could be superimposed onto radiography images collected at the same point in time. The complementary approach is able to show that the carbon condensates are much larger when formed in the elevated temperature and pressure conditions near the location of colliding detonation fronts. Thermochemical modeling suggests that these larger particulates form either in the diamond phase or on the liquidus line of the carbon phase diagram. The increase in size observed by SAXS may correlate well with the increased residence time deeply in the diamond phase. Finally, these particulates can be described as nano-sized phases with some surface texture or otherwise near-surface intra-particle heterogeneity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Molecular structures reveal the origin of spectral variation in cryptophyte light harvesting antenna proteins

In addition to their membrane-bound chlorophyll a/c light-harvesting antenna, the cryptophyte algae have evolved a unique phycobiliprotein antenna system located in the thylakoid lumen. The basic unit of this antenna consists of two copies of an αβ protomer where the α and β subunits scaffold different combinations of a limited number of linear tetrapyrrole chromophores. While the β subunit is highly conserved, encoded by a single plastid gene, the nuclear-encoded α subunits have evolved diversified multigene families. It is still unclear how this sequence diversity results in the spectral diversity of the mature proteins. By careful examination of three newly determined crystal structures in comparison with three previously obtained, we show how the α subunit amino acid sequences control chromophore conformations and hence spectral properties even when the chromophores are identical. Previously we have shown that α subunits control the quaternary structure of the mature αβ.αβ complex (either open or closed), however, each species appeared to only harbor a single quaternary form. Here we show that species of the Hemiselmis genus contain expressed α subunit genes that encode both distinct quaternary structures. Finally, we have discovered a common single-copy gene (expressed into protein) consisting of tandem copies of a small α subunit that could potentially scaffold pairs of light harvesting units. Together, our results show how the diversity of the multigene α subunit family produces a range of mature cryptophyte antenna proteins with differing spectral properties, and the potential for minor forms that could contribute to acclimation to varying light regimes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Understanding Synthesis and Structural Variation of Nanomaterials Through In Situ/Operando XAS and SAXS

Nanostructured materials with high surface area and low coordinated atoms present distinct intrinsic properties from their bulk counterparts. However, nanomaterials' nucleation/growth mechanism during the synthesis process and the changes of the nanomaterials in the working state are still not thoroughly studied. As two indispensable methods, X-ray absorption spectroscopy (XAS) provides nanomaterials' electronic structure and coordination environment, while small-angle X-ray scattering (SAXS) offers structural properties and morphology information. Here, a combination of in situ/operando XAS and SAXS provides high temporal and spatial resolution to monitor the evolution of nanomaterials. This review gives a brief introduction to in situ/operando SAXS/XAS cells. In addition, the application of in situ/operando XAS and SAXS in preparing nanomaterials and studying changes of working nanomaterials are summarized.

25 ENERGY STORAGE↗
DOE OSTI2023

Assembly and comparative genome analysis of a Patagonian Aureobasidium pullulans isolate reveals unexpected intraspecific variation

Aureobasidium pullulans is a yeast-like fungus with remarkable phenotypic plasticity widely studied for its importance for the pharmaceutical and food industries. So far, genomic studies with strains from all over the world suggest they constitute a genetically unstructured population, with no association by habitat. However, the mechanisms by which this genome supports so many phenotypic permutations are still poorly understood. Recent works have shown the importance of sequencing yeast genomes from extreme environments to increase the repertoire of phenotypic diversity of unconventional yeasts. In this study, we present the genomic draft of A. pullulans strain from a Patagonian yeast diversity hotspot, re-evaluate its taxonomic classification based on taxogenomic approaches, and annotate its genome with high-depth transcriptomic data. Here, our analysis suggests this isolate could be considered a novel variant at an early stage of the speciation process. The discovery of divergent strains in a genomically homogeneous group, such as A. pullulans, can be valuable in understanding the evolution of the species. The identification and characterization of new variants will not only allow finding unique traits of biotechnological importance, but also optimize the choice of strains whose phenotypes will be characterized, providing new elements to explore questions about plasticity and adaptation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Veneziano variations: how unique are string amplitudes?

String theory offers an elegant and concrete realization of how to consistently couple states of arbitrarily high spin. But how unique is this construction? In this paper we derive a novel, multi-parameter family of four-point scattering amplitudes exhibiting i) polynomially bounded high-energy behavior and ii) exchange of an infinite tower of high-spin modes, albeit with a finite number of states at each resonance. These amplitudes take an infinite-product form and, depending on parameters, exhibit mass spectra that are either unbounded or bounded, thus corresponding to generalizations of the Veneziano and Coon amplitudes, respectively. For the bounded case, masses converge to an accumulation point, a peculiar feature seen in the Coon amplitude but more recently understood to arise naturally in string theory [1]. Importantly, our amplitudes contain free parameters allowing for the customization of the slope and offset of the spin-dependence in the Regge trajectory. We compute all partial waves for this multi-parameter class of amplitudes and identify unitary regions of parameter space. For the unbounded case, we apply similar methods to derive new deformations of the Veneziano and Virasoro-Shapiro amplitudes.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Quantitative trait locus mapping combined with variant and transcriptome analyses identifies a cluster of gene candidates underlying the variation in leaf wax between upland and lowland switchgrass ecotypes

Switchgrass (Panicum virgatum L.) is a promising warm-season candidate energy crop. It occurs in two ecotypes, upland and lowland, which vary in a number of phenotypic traits, including leaf glaucousness. To initiate trait mapping, two F 2 mapping populations were developed by crossing two different F 1 sibs derived from a cross between the tetraploid lowland genotype AP13 and the tetraploid upland genotype VS16, and high-density linkage maps were generated. Quantitative trait locus (QTL) analyses of visually scored leaf glaucousness and of hydrophobicity of the abaxial leaf surface measured using a drop shape analyzer identified highly significant colocalizing QTL on chromosome 7K (Chr07K). Using a multipronged approach, we identified a cluster of genes including Pavir.7KG077009, which encodes a Type III polyketide synthase-like protein, and Pavir.7KG013754 and Pavir.7KG030500, two highly similar genes that encode putative acyl-acyl carrier protein (ACP) thioesterases, as strong candidates underlying the QTL. The lack of homoeologs for any of the three genes on Chr07N, the relatively low level of identity with other switchgrass KCS proteins and thioesterases, as well as the organization of the surrounding region suggest that Pavir.7KG077009 and Pavir.7KG013754/Pavir.7KG030500 were duplicated into a fast-evolving chromosome region, which led to their neofunctionalization. Furthermore, sequence analyses showed all three genes to be absent in the two upland compared to the two lowland accessions analyzed. This study provides an example of and practical guide for trait mapping and candidate gene identification in a complex genetic system by combining QTL mapping, transcriptomics and variant analysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The genetic basis for panicle trait variation in switchgrass ( Panicum virgatum )

Grass species exhibit large diversity in panicle architecture influenced by genes, the environment, and their interaction. The genetic study of panicle architecture in perennial grasses is limited. In this study, we evaluate the genetic basis of panicle architecture including panicle length, primary branching number, and secondary branching number in an outcrossed switchgrass QTL population grown across ten field sites in the central USA through multi-environment mixed QTL analysis. We also evaluate genetic effects in a diversity panel of switchgrass grown at three of the ten field sites using genome-wide association (GWAS) and multivariate adaptive shrinkage. Furthermore, we search for candidate genes underlying panicle traits in both of these independent mapping populations. Overall, 18 QTL were detected in the QTL mapping population for the three panicle traits, and 146 unlinked genomic regions in the diversity panel affected one or more panicle trait. Twelve of the QTL exhibited consistent effects (i.e., no QTL by environment interactions or no QTL × E), and most (four of six) of the effects with QTL × E exhibited site-specific effects. Most (59.3%) significant partially linked diversity panel SNPs had significant effects in all panicle traits and all field sites and showed pervasive pleiotropy and limited environment interactions. Panicle QTL co-localized with significant SNPs found using GWAS, providing additional power to distinguish between true and false associations in the diversity panel.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Sediment transport and morphodynamic changes due to upstream variation and sea level rise on the Western Mekong Delta, Vietnam

The hydrological and morphological dynamics across the Vietnam Mekong Delta (VMD) coastline are increasingly shaped by human interventions and climate change, affecting the sustainability of socio-economic environments. This study employs the TELEMAC-MASCARET modeling system (TELEMAC-2D, TOMAWAC, and SISYPHE modules) to simulate hydrodynamics, sediment transport, and morphological changes for a 10-year period under baseline (SC1) and future climate (SC2) scenarios, considering wave climatology of Northeast (NEM) and Southwest monsoons (SWM). The results of sedimentation and erosion were analyzed across five key coastal zones from Ca Mau Cape (KV1) to Ha Tien (KV5). Model results highlight distinct seasonal patterns of sediment redistribution shaped by monsoonal flows, wave action, and seabed morphology. During the NEM, sediment deposition is concentrated near estuarine zones, while the SWM favors offshore sediment accumulation due to perpendicular wave actions, and shallow, gently sloping bathymetry that dissipates wave energy. Coastal erosion predominantly occurs at convex shoreline features subjected to stronger coastal currents, particularly in fine-grained sediment areas. Under future sea level rise and land subsidence scenarios, reduced flow velocities lead to lower bottom shear stress, promoting deposition and mitigating erosion problems despite increased wave energy. Besides that, sediment transport analyses across 14 cross-sections (C-S) reveal a southward trend during the NEM and a northward reversal during the SWM, with upstream sediment reductions primarily influencing near-estuarine zones and exerting minimal impact beyond the mid-coastal regions. Furthermore, these findings advance the understanding of sediment redistribution processes under climate change and seasonal change, and provide a scientific basis for adaptive coastal management and sustainable development.

Climate change↗
DOE OSTI2022

Interspecific variation in the timing and magnitude of hydraulic redistribution in a forest with distinct water sources

Trees regulate water availability among their rooting strata through a nocturnal, passive transference of water known as hydraulic redistribution (HR). This study investigates differences in HR and groundwater use among common canopy species in longleaf pine (Pinus palustris Mill., Pinaceae) woodlands and explores environmental factors influencing HR. HR was estimated by sap flux of lateral roots and main stems of three mature canopy species (P. palustris, Quercus laevis Walter., Fagaceae and Quercus margarettae Ashe., Fagaceae). We used δ18O and δD of xylem water, soil water, and groundwater to determine water source. Finally, we related HR to environmental factors (Temperature, VWC, VPD) to better understand controls of HR dynamics. Pinus palustris had higher water use than either Quercus species, and also redistributed significantly more water as a nocturnal subsidy. HR fluxes were inversely related with mean nightly temperature and independent of shallow soil moisture. Stable isotope mixing models, based on δ 18 O and δD, indicated that all species have access to groundwater, but utilized shallow soil water in differing amounts when available. In systems with strong water potential gradients among soil strata, any species with access to a groundwater source is likely capable of HR; however, the magnitude of HR varies significantly by species, even among closely related taxa.

54 ENVIRONMENTAL SCIENCES↗